From 34ea81b14810bf3b9d14a9072b4e4d640b39a33f Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sat, 27 Apr 2019 13:42:21 -0600
Subject: [PATCH 01/68] Removed matrix files

---
 src/libcatnip/matrix.cpp | 946 ---------------------------------------
 src/libcatnip/matrix.hpp | 100 -----
 2 files changed, 1046 deletions(-)
 delete mode 100644 src/libcatnip/matrix.cpp
 delete mode 100644 src/libcatnip/matrix.hpp

diff --git a/src/libcatnip/matrix.cpp b/src/libcatnip/matrix.cpp
deleted file mode 100644
index b206b70..0000000
--- a/src/libcatnip/matrix.cpp
+++ /dev/null
@@ -1,946 +0,0 @@
-#include <cmath>
-#include <cstdlib>
-#include <exception>
-#include <iostream>
-#include <sstream>
-#include <stdexcept>
-#include <stdio.h>
-#include <string>
-#include <vector>
-
-#include "matrix.hpp"
-
-using namespace std;
-
-namespace catnip {
-
-Matrix Matrix_diag(const Matrix &mat) {
-
-  if (mat.get_cols() > 1 && mat.get_rows() > 1) {
-    throw invalid_argument(
-        "ERROR Matrix_diag can only create a diagonal "
-        "matrix from a vector.\n");
-  }
-
-  if (mat.get_shel() > 1) {
-    throw invalid_argument(
-        "ERROR Matrix_diag cannot create diagonal matrix "
-        "from a 3d matrix, it must be passed a vector.\n");
-  }
-
-  if (mat.get_cols() > mat.get_rows()) {
-    int len = mat.get_cols();
-    Matrix mat2(len, len);
-    for (int i = 1; i <= len; i++) {
-      double val = mat.get_elem(1, i);
-      mat2.set_elem(val, i, i);
-    }
-    return mat2;
-  } else {
-    int len = mat.get_rows();
-    Matrix mat2(len, len);
-    for (int i = 1; i <= len; i++) {
-      double val = mat.get_elem(i, 1);
-      mat2.set_elem(val, i, i);
-    }
-    return mat2;
-  }
-}
-
-Matrix Matrix_copy(const Matrix &mat) {
-
-  Matrix mat2(mat.get_rows(), mat.get_cols(), mat.get_shel());
-
-  int i;
-  int j;
-  int k;
-  double val;
-
-  for (i = 1; i <= mat.get_rows(); i++) {
-    for (j = 1; j <= mat.get_cols(); j++) {
-      for (k = 1; k <= mat.get_shel(); k++) {
-        val = mat.get_elem(i, j, k);
-        mat2.set_elem(val, i, j, k);
-      }
-    }
-  }
-
-  return mat2;
-}
-
-Matrix Matrix_concatenate_rows(Matrix mat1,const Matrix & mat2) {
-
-  // For this function to work both mat1 and mat2 must have
-  // the same number of columns and shelves
-
-  if (mat1.get_cols() != mat2.get_cols()) {
-    std::cerr << "ERROR to concatenate the rows mat1 and mat2 must\n";
-    std::cerr << " 			have the same number of cols!\n";
-    Matrix m;
-    return m;
-  }
-
-  if (mat1.get_shel() != mat2.get_shel()) {
-    std::cerr << "ERROR to concatenate the rows mat1 and mat2 must\n";
-    std::cerr << " 			have the same number of shelves!\n";
-    Matrix m;
-    return m;
-  }
-
-  int totalrows;
-  int rowsMat1 = mat1.get_rows();
-  totalrows = rowsMat1 + mat2.get_rows();
-  Matrix mat3(totalrows, mat1.get_cols(), mat1.get_shel());
-
-  int i;
-  int j;
-  int k;
-  double val;
-
-  for (i = 1; i <= mat1.get_rows(); i++) {
-    for (j = 1; j <= mat1.get_cols(); j++) {
-      for (k = 1; k <= mat1.get_shel(); k++) {
-        val = mat1.get_elem(i, j, k);
-        mat3.set_elem(val, i, j, k);
-      }
-    }
-  }
-
-  for (i = 1; i <= mat2.get_rows(); i++) {
-    for (j = 1; j <= mat2.get_cols(); j++) {
-      for (k = 1; k <= mat2.get_shel(); k++) {
-        val = mat2.get_elem(i, j, k);
-        mat3.set_elem(val, i + rowsMat1, j, k);
-      }
-    }
-  }
-
-  return mat3;
-}
-
-Matrix Matrix_concatenate_cols(const Matrix &mat1, const Matrix &mat2) {
-
-  // For this function to work both mat1 and mat2 must have
-  // the same number of columns and shelves
-
-  if (mat1.get_rows() != mat2.get_rows()) {
-    std::cerr << "ERROR to concatenate the cols mat1 and mat2 must\n";
-    std::cerr << " 			have the same number of rows!\n";
-    Matrix m;
-    return m;
-  }
-
-  if (mat1.get_shel() != mat2.get_shel()) {
-    std::cerr << "ERROR to concatenate the rows mat1 and mat2 must\n";
-    std::cerr << " 			have the same number of shelves!\n";
-    Matrix m;
-    return m;
-  }
-
-  int totalcols;
-  int colsMat1 = mat1.get_cols();
-  totalcols = colsMat1 + mat2.get_cols();
-  Matrix mat3(mat1.get_rows(), totalcols, mat1.get_shel());
-
-  int i;
-  int j;
-  int k;
-  double val;
-
-  for (i = 1; i <= mat1.get_rows(); i++) {
-    for (j = 1; j <= mat1.get_cols(); j++) {
-      for (k = 1; k <= mat1.get_shel(); k++) {
-        val = mat1.get_elem(i, j, k);
-        mat3.set_elem(val, i, j, k);
-      }
-    }
-  }
-
-  for (i = 1; i <= mat2.get_rows(); i++) {
-    for (j = 1; j <= mat2.get_cols(); j++) {
-      for (k = 1; k <= mat2.get_shel(); k++) {
-        val = mat2.get_elem(i, j, k);
-        mat3.set_elem(val, i, j + colsMat1, k);
-      }
-    }
-  }
-
-  return mat3;
-}
-
-string double_tos(double f, int nd) {
-  ostringstream ostr;
-  int tens = stod("1" + string(nd, '0'));
-  ostr << round(f * tens) / tens;
-  return ostr.str();
-}
-
-std::ostream &operator<<(std::ostream &out, Matrix &mat) {
-  out << "Matrix Attributes\n";
-  out << "rows " << mat.get_rows();
-  out << "\ncols " << mat.get_cols();
-  out << "\nshel " << mat.get_shel();
-  int i;
-  int j;
-  int k;
-  for (k = 1; k <= mat.get_shel(); k++) {
-    out << "\nShelf " << k << "\n\t";
-
-    for (j = 1; j <= mat.get_cols(); j++) {
-      out << "Col " << j << "\t";
-    }
-    out << "\n";
-    for (i = 1; i <= mat.get_rows(); i++) {
-      out << "Row " << i << "\t";
-      for (j = 1; j <= mat.get_cols(); j++) {
-        out << mat.get_elem(i, j) << "\t";
-      }
-      out << "\n";
-    }
-  }
-  return out;
-}
-
-Matrix &operator*(const Matrix &mat1, const Matrix &mat2) {
-
-  if (mat1.get_shel() != 1 || mat2.get_shel() != 1) {
-    printf(
-        "ERROR Matrix_Multiply only allowed for 2d nxm matrix not 3d nxmxl\n");
-    exit(1);
-  }
-  if (mat1.get_cols() != mat2.get_rows()) {
-    printf("ERROR Matrix_Multiply only allowed for nxm by lxn matrices\n");
-    printf("      second matrix must have same number of colums as first\n");
-    printf("      matrix has number of rows\n");
-    exit(1);
-  }
-
-  Matrix *mat3 = new Matrix(mat1.get_rows(), mat2.get_cols());
-
-  int i;
-  int j;
-  int k;
-  double sum;
-
-  for (i = 1; i <= mat1.get_rows(); i++) {
-    for (j = 1; j <= mat2.get_cols(); j++) {
-      sum = 0;
-      for (k = 1; k <= mat1.get_cols(); k++) {
-        sum += (mat1.get_elem(i, k)) * (mat2.get_elem(k, j));
-      }
-      (*mat3).set_elem(sum, i, j);
-    }
-  }
-  return *mat3;
-}
-
-}  // namespace catnip
-
-using namespace catnip;
-
-Matrix::Matrix() {
-  rows = 1;
-  cols = 1;
-  shel = 1;
-  elem = new double[rows * cols];
-  elem[0] = 0;
-}
-
-Matrix::Matrix(vector<double> v_data) {
-  rows = v_data.size();
-  cols = 1;
-  shel = 1;
-  elem = new double[rows * cols];
-
-  int r = 1;
-  int c = 1;
-  for (auto val : v_data) {
-    elem[(r - 1) * cols + c - 1] = val;
-    ++r;
-  }
-}
-
-Matrix::Matrix(vector<int> v_data) {
-  rows = v_data.size();
-  cols = 1;
-  shel = 1;
-  elem = new double[rows * cols];
-
-  int r = 1;
-  int c = 1;
-  for (auto val : v_data) {
-    elem[(r - 1) * cols + c - 1] = static_cast<double>(val);
-    ++r;
-  }
-}
-
-Matrix::Matrix(vector<vector<double>> vv_data) {
-  rows = vv_data.size();
-  cols = vv_data.at(0).size();
-  shel = 1;
-  elem = new double[rows * cols];
-  elem = new double[rows * cols];
-
-  int r = 1;
-  for (auto v : vv_data) {
-    int c = 1;
-    if (static_cast<int>(v.size()) != cols) {
-      throw invalid_argument(
-          "vector<vector<double>> not consistent "
-          "in matrix constructor ");
-    }
-    for (auto val : v) {
-      elem[(r - 1) * cols + c - 1] = val;
-      ++c;
-    }
-    ++r;
-  }
-}
-
-Matrix::Matrix(const int r) {
-  if (r < 0) {
-    cerr << "ERROR rows of matrix must be greater than or equal to 0" << endl;
-    cerr << " you have r " << r << endl;
-    exit(1);
-  }
-  if (r == 0) {
-    rows = 0;
-    cols = 0;
-    shel = 0;
-    elem = nullptr;
-  } else {
-    rows = r;
-    cols = 1;
-    shel = 1;
-
-    elem = new double[rows];
-    for (int i = 1; i <= rows; i++) {
-      elem[i - 1] = 0;
-    }
-  }
-}
-
-Matrix::Matrix(const int r, const int c) {
-  if (r < 1) {
-    printf("ERROR negative number of rows submitted to Matrix\n");
-    exit(1);
-  } else if (c < 1) {
-    printf("ERROR negative number of cols submitted to Matrix\n");
-    exit(1);
-  }
-  rows = r;
-  cols = c;
-  shel = 1;
-  elem = new double[rows * cols];
-  for (int i = 1; i <= rows; i++) {
-    for (int j = 1; j <= cols; j++) {
-      elem[(i - 1) * cols + j - 1] = 0;
-    }
-  }
-}
-
-Matrix::Matrix(const int r, const int c, const int s) {
-  if (r < 1) {
-    printf("ERROR negative number of rows submitted to Matrix\n");
-    exit(1);
-  } else if (c < 1) {
-    printf("ERROR negative number of cols submitted to Matrix\n");
-    exit(1);
-  } else if (s < 1) {
-    printf("ERROR negative number of shelves submitted to Matrix\n");
-    exit(1);
-  }
-  rows = r;
-  cols = c;
-  shel = s;
-  elem = new double[rows * cols * shel];
-  for (int i = 1; i <= rows; i++) {
-    for (int j = 1; j <= cols; j++) {
-      for (int k = 1; k <= shel; k++) {
-        elem[(i - 1) * cols * shel + (j - 1) * shel + k - 1] = 0;
-      }
-    }
-  }
-}
-
-int Matrix::resize(int r, int c) {
-
-  if (r < 1) {
-    printf("ERROR must resize row to a value of 1 or greater\n");
-    exit(1);
-  }
-  if (c < 1) {
-    printf("ERROR must resize column to a value of 1 or greater\n");
-    exit(1);
-  }
-
-  double *temp;
-  temp = new double[r * c];
-
-  // adding values from old matrix to new
-  if (r <= rows) {
-    for (int i = 1; i <= r; i++) {
-      if (c <= cols) {
-        for (int j = 1; j <= c; j++) {
-          temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = elem[index(i, j, 1)];
-        }
-      } else {
-        for (int j = 1; j <= c; j++) {
-          if (j <= cols) {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = elem[index(i, j, 1)];
-          } else {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = 0;
-          }
-        }
-      }
-    }
-  } else {
-    for (int i = 1; i <= r; i++) {
-      if (c <= cols) {
-        for (int j = 1; j <= c; j++) {
-          if (i <= rows) {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = elem[index(i, j, 1)];
-          } else {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = 0;
-          }
-        }
-      } else {
-        for (int j = 1; j <= c; j++) {
-          if (i <= rows && j <= cols) {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = elem[index(i, j, 1)];
-          } else {
-            temp[(i - 1) * c * 1 + (j - 1) * 1 + 1 - 1] = 0;
-          }
-        }
-      }
-    }
-  }
-
-  delete elem;
-  rows = r;
-  cols = c;
-  shel = 1;
-  elem = temp;
-
-  return 0;
-}
-
-Matrix &Matrix::operator=(const Matrix &m) {
-  this->resize(m.get_rows(), m.get_cols());
-
-  for (int i = 1; i <= m.get_rows(); ++i) {
-    for (int j = 1; j <= m.get_cols(); ++j) {
-      this->set_elem(m.get_elem(i, j), i, j);
-    }
-  }
-  return *this;
-}
-
-int Matrix::index(const int r, const int c, const int s) const {
-  return (r - 1) * cols * shel + (c - 1) * shel + s - 1;
-}
-
-void Matrix::set_row(vector<double> row, int r) {
-
-  if (get_cols() != static_cast<int>(row.size())) {
-    throw invalid_argument("vector is not the same size as matrix");
-  }
-
-  for (int j = 1; j <= get_cols(); j++) {
-    if (r <= rows) {
-      elem[index(r, j, 1)] = row.at(j - 1);
-    } else {
-      elem[index(r, j, 1)] = 0;
-    }
-  }
-}
-
-void Matrix::set_col(vector<double> col, int c) {
-
-  if (get_cols() != static_cast<int>(col.size())) {
-    throw invalid_argument("vector is not the same size as matrix");
-  }
-  for (int i = 1; i <= get_rows(); ++i) {
-    if (c <= cols) {
-      elem[index(i, c, 1)] = col.at(i - 1);
-    } else {
-      elem[index(i, c, 1)] = 0;
-    }
-  }
-}
-
-void Matrix::set_rows(int r) {
-  if (r < 0) {
-    printf("ERROR negative number submitted to set_rows\n");
-    exit(1);
-  }
-  if (r > rows) {
-
-    double *temp = new double[r * cols * shel];
-    for (int i = 1; i <= r; i++) {
-      for (int j = 1; j <= cols; j++) {
-        for (int k = 1; k <= shel; k++) {
-          if (r <= rows) {
-            temp[index(i, j, k)] = elem[index(i, j, k)];
-          } else {
-            temp[index(i, j, k)] = 0;
-          }
-        }
-      }
-    }
-    delete elem;
-    rows = r;
-    elem = temp;
-  } else if (r < rows) {
-
-    double *temp = new double[r * cols * shel];
-    printf("WARNING reducing matrix rows below previous value\n");
-    printf("could lose data in the process\n");
-    for (int i = 1; i <= r; i++) {
-      for (int j = 1; j <= cols; j++) {
-        for (int k = 1; k <= shel; k++) {
-          temp[index(i, j, k)] = elem[index(i, j, k)];
-        }
-      }
-    }
-    delete elem;
-    rows = r;
-    elem = temp;
-  }
-}
-
-vector<double> Matrix::get_col(int c) const{
-  vector<double> col_data;
-  for (int i = 1; i <= rows; i++) {
-    col_data.push_back(elem[index(i, c, 1)]);
-  }
-  return col_data;
-}
-
-vector<double> Matrix::get_row(int r) const {
-  vector<double> row_data;
-  for (int i = 1; i <= cols; i++) {
-    row_data.push_back(elem[index(r, i, 1)]);
-  }
-  return row_data;
-}
-
-void Matrix::set_cols(int c) {
-  if (c < 0) {
-    printf("ERROR negative number submitted to set_cols\n");
-    exit(1);
-  }
-
-  if (c > cols) {
-
-    double *temp = new double[rows * c * shel];
-    for (int i = 1; i <= rows; i++) {
-      for (int j = 1; j <= c; j++) {
-        for (int k = 1; k <= shel; k++) {
-          if (c <= cols) {
-            temp[index(i, j, k)] = elem[index(i, j, k)];
-          } else {
-            temp[index(i, j, k)] = 0;
-          }
-        }
-      }
-    }
-    delete elem;
-    cols = c;
-    elem = temp;
-  } else if (c < cols) {
-
-    double *temp = new double[rows * c * shel];
-    printf("WARNING reducing matrix cols below previous value\n");
-    printf("could lose data in the process\n");
-    for (int i = 1; i <= rows; i++) {
-      for (int j = 1; j <= c; j++) {
-        for (int k = 1; k <= shel; k++) {
-          temp[index(i, j, k)] = elem[index(i, j, k)];
-        }
-      }
-    }
-    delete elem;
-    cols = c;
-    elem = temp;
-  }
-}
-
-void Matrix::set_shel(int s) {
-  if (s < 0) {
-    printf("ERROR negative number submitted to set_shel\n");
-    exit(1);
-  }
-  if (s > shel) {
-
-    double *temp = new double[rows * cols * s];
-    for (int i = 1; i <= rows; i++) {
-      for (int j = 1; j <= cols; j++) {
-        for (int k = 1; k <= s; k++) {
-          if (s <= shel) {
-            temp[index(i, j, k)] = elem[index(i, j, k)];
-          } else {
-            temp[index(i, j, k)] = 0;
-          }
-        }
-      }
-    }
-    delete elem;
-    shel = s;
-    elem = temp;
-  } else if (s < shel) {
-
-    double *temp = new double[rows * cols * s];
-    printf("WARNING reducing matrix shel below previous value\n");
-    printf("could lose data in the process\n");
-    for (int i = 1; i <= rows; i++) {
-      for (int j = 1; j <= cols; j++) {
-        for (int k = 1; k <= s; k++) {
-          temp[index(i, j, k)] = elem[index(i, j, k)];
-        }
-      }
-    }
-    delete elem;
-    shel = s;
-    elem = temp;
-  }
-}
-
-void Matrix::set_elem(double val) { elem[0] = val; }
-
-void Matrix::set_elem(double val, int r) {
-  if (r > rows) {
-    printf(
-        "ERROR r value is greater than rows in set_elem(double val, int r)\n");
-    exit(1);
-  } else if (r < 1) {
-    printf(
-        "ERROR r value is less than or equal to 0 in set_elem(double val, int "
-        "r)\n");
-    exit(1);
-  };
-
-  elem[index(r, 1, 1)] = val;
-}
-
-void Matrix::set_elem(double val, int r, int c) {
-  if (r > rows) {
-    printf(
-        "ERROR r value is greater than rows in set_elem(double val, int r, int "
-        "c)\n");
-    exit(1);
-  } else if (r < 1) {
-    printf(
-        "ERROR r value is less than or equal to 0 in set_elem(double val, int "
-        "r, int c)\n");
-    exit(1);
-  };
-  if (c > cols) {
-    printf(
-        "ERROR c value is greater than rows in set_elem(double val, int r, int "
-        "c)\n");
-    exit(1);
-  } else if (c < 1) {
-    printf(
-        "ERROR c value is less than or equal to 0 in set_elem(double val, int "
-        "r, int c)\n");
-    exit(1);
-  };
-
-  elem[index(r, c, 1)] = val;
-}
-
-void Matrix::set_elem(double val, int r, int c, int s) {
-  if (r > rows) {
-    printf(
-        "ERROR r value is greater than rows in set_elem(double val, int r, int "
-        "c, int s)\n");
-    exit(1);
-  } else if (r < 1) {
-    printf(
-        "ERROR r value is less than or equal to 0 in set_elem(double val, int "
-        "r, int c, int s)\n");
-    exit(1);
-  };
-  if (c > cols) {
-    printf(
-        "ERROR c value is greater than rows in set_elem(double val, int r, int "
-        "c, int s)\n");
-    exit(1);
-  } else if (c < 1) {
-    printf(
-        "ERROR c value is less than or equal to 0 in set_elem(double val, int "
-        "r, int c, int s)\n");
-    exit(1);
-  };
-  if (s > shel) {
-    printf(
-        "ERROR s value is greater than rows in set_elem(double val, int r, int "
-        "c, int s)\n");
-    exit(1);
-  } else if (s < 1) {
-    printf(
-        "ERROR s value is less than or equal to 0 in set_elem(double val, int "
-        "r, int c, int s)\n");
-    exit(1);
-  };
-
-  elem[index(r, c, s)] = val;
-}
-
-int Matrix::get_rows() const { return rows; }
-
-int Matrix::get_cols() const { return cols; }
-
-int Matrix::get_shel() const { return shel; }
-
-int Matrix::total_elem() { return rows * cols * shel; }
-
-double Matrix::get_elem() const { return elem[0]; }
-
-double Matrix::get_elem(const int r) const {
-  if (r < 1) {
-    printf("ERROR get_elem(int r): 0 or negative row submitted\n");
-    exit(1);
-  } else if (r > rows) {
-    printf(
-        "ERROR get_elem(int r): row value larger than the scope of the "
-        "Matrix\n");
-    exit(1);
-  }
-  return elem[index(r, 1, 1)];
-}
-
-double Matrix::get_elem(const int r, const int c) const {
-  if (r < 1) {
-    printf("ERROR get_elem(int r, int c): 0 or negative row submitted\n");
-    exit(1);
-  } else if (r > rows) {
-    printf(
-        "ERROR get_elem(int r, int c): row value larger than the scope of the "
-        "Matrix\n");
-    exit(1);
-  } else if (c < 1) {
-    printf("ERROR get_elem(int r, int c): 0 or negative col submitted\n");
-    exit(1);
-  } else if (c > cols) {
-    printf(
-        "ERROR get_elem(int r, int c): col value larger than the scope of the "
-        "Matrix\n");
-    exit(1);
-  }
-  return elem[index(r, c, 1)];
-}
-
-double *Matrix::get_elem_ptr(const int r, const int c) const {
-  return &elem[index(r, c, 1)];
-}
-
-double Matrix::get_elem(const int r, const int c, const int s) const {
-  if (r < 1) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): 0 or negative row submitted\n");
-    exit(1);
-  } else if (r > rows) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): row value larger than the scope "
-        "of the Matrix\n");
-    exit(1);
-  } else if (c < 1) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): 0 or negative col submitted\n");
-    exit(1);
-  } else if (c > cols) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): col value larger than the scope "
-        "of the Matrix\n");
-    exit(1);
-  } else if (s < 1) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): 0 or negative shelf submitted\n");
-    exit(1);
-  } else if (s > shel) {
-    printf(
-        "ERROR get_elem(int r, int c, int s): shelf value larger than the "
-        "scope of the Matrix\n");
-    exit(1);
-  }
-  return elem[index(r, c, s)];
-}
-
-void Matrix::swap_row(int r_from, int r_to) {
-  if (r_from == r_to) return;
-
-  vector<double> row_f = get_row(r_from);
-  vector<double> row_t = get_row(r_to);
-  set_row(row_f, r_to);
-  set_row(row_t, r_from);
-}
-
-void Matrix::swap_col(int c_from, int c_to) {
-  if (c_from == c_to) return;
-
-  vector<double> col_f = get_col(c_from);
-  vector<double> col_t = get_col(c_to);
-  set_col(col_f, c_to);
-  set_col(col_t, c_from);
-}
-
-void Matrix::move_row(int r_from, int r_to) {
-
-  if (r_from == r_to) return;
-
-  // Shift all rows down
-  vector<double> row = get_row(r_from);
-  // Shift all values down
-  if (r_from < r_to) {
-    for (int r = r_from; r < r_to; r++) {
-      for (int c = 1; c <= get_cols(); c++) {
-        set_elem(get_elem(r + 1, c), r, c);
-      }
-    }
-  } else {
-    for (int r = r_from; r >= (r_to + 1); r--) {
-      for (int c = 1; c <= get_cols(); c++) {
-        set_elem(get_elem(r - 1, c), r, c);
-      }
-    }
-  }
-  // Insert the row we took out
-  this->set_row(row, r_to);
-}
-
-void Matrix::move_col(int c_from, int c_to) {
-
-  if (c_from == c_to) return;
-
-  // Shift all rows down
-  vector<double> col = get_col(c_from);
-  // Shift all values down
-  if (c_from < c_to) {
-    for (int c = c_from; c < c_to; c++) {
-      for (int r = 1; r <= get_rows(); r++) {
-        set_elem(get_elem(r, c + 1), r, c);
-      }
-    }
-  } else {
-    for (int c = c_from; c >= (c_to + 1); c--) {
-      for (int r = 1; r <= get_rows(); r++) {
-        set_elem(get_elem(r, c - 1), r, c);
-      }
-    }
-  }
-  // Insert the row we took out
-  set_col(col, c_to);
-}
-
-vector<int> Matrix::matchRow(const Matrix & mat, int sf) {
-  if (mat.get_shel() != 1 || this->get_shel() != 1) {
-    cerr << "ERROR shel should be 1" << endl;
-    exit(1);
-  }
-  if (mat.get_cols() != this->get_cols()) {
-    throw invalid_argument(
-        "match function only works when matrices have same number of columns");
-  }
-  vector<int> m_vec(this->get_rows(), -1);
-
-  for (int i = 1; i <= get_rows(); ++i) {
-    for (int ii = 1; ii <= mat.get_rows(); ++ii) {
-      bool match = true;
-      for (int j = 1; j <= get_cols(); ++j) {
-        string val1 = double_tos(get_elem(i, j), sf);
-        string val2 = double_tos(mat.get_elem(ii, j), sf);
-        if (val1.compare(val2) != 0) {
-          match = false;
-          break;
-        }
-      }
-      if (match) m_vec.at(i - 1) = ii;
-    }
-  }
-  return m_vec;
-}
-
-vector<int> Matrix::matchCol(const Matrix &mat, const int sf) const {
-  if (mat.get_shel() != 1 || this->get_shel() != 1) {
-    cerr << "ERROR shel should be 1" << endl;
-    exit(1);
-  }
-  if (mat.get_rows() != this->get_rows()) {
-    throw invalid_argument(
-        "match function only works when matrices have same number of rows");
-  }
-  vector<int> m_vec(this->get_cols(), -1);
-
-  for (int i = 1; i <= get_cols(); ++i) {
-    for (int ii = 1; ii <= mat.get_cols(); ++ii) {
-      bool match = true;
-      for (int j = 1; j <= get_rows(); ++j) {
-        string val1 = double_tos(get_elem(j, i), sf);
-        string val2 = double_tos(mat.get_elem(j, ii), sf);
-        if (val1.compare(val2) != 0) {
-          match = false;
-          break;
-        }
-      }
-      if (match) m_vec.at(i - 1) = ii;
-    }
-  }
-  return m_vec;
-}
-
-Matrix Matrix::invert() const{
-
-  if (this->get_shel() != 1) {
-    printf("ERROR Matrix_Invert only allowed for 1d and 2d arrays not 3d\n");
-    exit(1);
-  }
-
-  Matrix *mat2 = new Matrix(this->get_cols(), this->get_rows());
-
-  for (int i = 1; i <= this->get_rows(); i++) {
-    for (int j = 1; j <= this->get_cols(); j++) {
-      double val = this->get_elem(i, j);
-      (*mat2).set_elem(val, j, i);
-    }
-  }
-  return *mat2;
-}
-
-Matrix Matrix::getRow(int R) const{
-
-  if (this->get_rows() < R) {
-    printf("ERROR Matrix_getRow cannot return R %d", R);
-    printf(" because mat has only %d rows\n.", this->get_rows());
-    exit(1);
-  }
-
-  Matrix mat2(1, this->get_cols(), this->get_shel());
-
-  for (int j = 1; j <= this->get_cols(); j++) {
-    for (int k = 1; k <= this->get_shel(); k++) {
-      double val = this->get_elem(R, j, k);
-      mat2.set_elem(val, 1, j, k);
-    }
-  }
-  return mat2;
-}
-
-Matrix Matrix::getCol(int C) const {
-
-  if (this->get_cols() < C) {
-    printf("ERROR Matrix_getCol cannot return C %d", C);
-    printf(" because mat has only %d cols\n.", this->get_cols());
-    exit(1);
-  }
-  Matrix mat2(this->get_cols(), 1, this->get_shel());
-
-  for (int i = 1; i <= this->get_rows(); i++) {
-    for (int k = 1; k <= this->get_shel(); k++) {
-      double val = this->get_elem(i, C, k);
-      mat2.set_elem(val, i, 1, k);
-    }
-  }
-  return mat2;
-}
diff --git a/src/libcatnip/matrix.hpp b/src/libcatnip/matrix.hpp
deleted file mode 100644
index cce1c3e..0000000
--- a/src/libcatnip/matrix.hpp
+++ /dev/null
@@ -1,100 +0,0 @@
-#ifndef _CATNIP_Matrix_HPP
-#define _CATNIP_Matrix_HPP
-#include <iostream>
-#include <stdlib.h>
-#include <vector>
-
-namespace catnip {
-
-class Matrix {
- private:
-  int rows;
-  int cols;
-  int shel;
-  double *elem;
-
- public:
-  // constructors
-  explicit Matrix(void);
-  explicit Matrix(std::vector<double>);
-  explicit Matrix(std::vector<int>);
-  explicit Matrix(std::vector<std::vector<double>>);
-  explicit Matrix(const int r);
-  Matrix(const int r, const int c);
-  Matrix(const int r, const int c, const int s);
-
-  Matrix &operator=(const Matrix &m);
-  // manipulators
-  void set_rows(int r);
-  void set_cols(int c);
-  void set_shel(int s);
-  void set_row(std::vector<double> row, int r);
-  void set_col(std::vector<double> col, int c);
-  int resize(int r, int c);
-  void set_elem(double val);
-  void set_elem(double val, int r);
-  void set_elem(double val, int r, int c);
-  void set_elem(double val, int r, int c, int s);
-  // accessors
-  int index(const int r, const int c, const int s) const;
-  int get_rows() const;
-  int get_cols() const;
-  int get_shel() const;
-  int total_elem();
-  double get_elem() const;
-  double get_elem(const int r) const;
-  double get_elem(const int r, const int c) const;
-  double get_elem(const int r, const int c, const int s) const;
-  double *get_elem_ptr(const int r, const int c) const;
-  std::vector<double> get_col(int c) const;
-  std::vector<double> get_row(int r) const;
-
-  // WARNING This is not a swap row operation
-  // All rows are shifted to make way
-  // for the new row/col. 'r_from' is moved to 'r_to' while
-  // all rows are appropriately shifted to make this happen.
-  void move_row(int r_from, int r_to);
-  void move_col(int c_from, int c_to);
-
-  // The intial and final row/col simply change places
-  // none of the rows and cols other than the ones swapped
-  // are affected
-  void swap_row(int r_from, int r_to);
-  void swap_col(int c_from, int c_to);
-
-  Matrix getCol(int c) const;
-  Matrix getRow(int r) const;
-  // Basically switches the rows and columns
-  Matrix invert(void) const;
-  // Responsible for matching the rows between two matrices they do not need
-  // Returns which row in the current matrix matches which row in the one
-  // passed in, -1 means there is no match
-  // sf is the number of significant figures that will be checked to ensure
-  // the same value
-  std::vector<int> matchRow(const Matrix & mat, int sf);
-  std::vector<int> matchCol(const Matrix &mat, const int sf) const;
-};
-
-std::ostream &operator<<(std::ostream &out, Matrix &mat);
-
-Matrix &operator*(const Matrix &mat1, const Matrix &mat2);
-
-// Takes a vector and diagonalized the
-// vector in a 2 dimensional matrix where
-// everything but the diagonal is assigned
-// a 0
-Matrix Matrix_diag(const Matrix &mat);
-
-// Copies a matrix and returns the new
-// matrix
-Matrix Matrix_copy(const Matrix &mat);
-
-// Add two matrices together to create a third
-// mat1 will always appear above mat2 in the rows
-// of the matrix that is returned.
-Matrix Matrix_concatenate_rows(Matrix mat1,const Matrix & mat2);
-Matrix Matrix_concatenate_cols(const Matrix &mat1, const Matrix &mat2);
-
-}  // namespace catnip
-
-#endif  // _CATNIP_Matrix_HPP

From e7f15641ab8473ebd5ac0dc8a7e258e95b3b46a6 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sat, 27 Apr 2019 13:42:47 -0600
Subject: [PATCH 02/68] Switched file readers to using eigen matrices as
 opposed to local matrix type

---
 src/libcatnip/io/file_readers/logreader.cpp | 46 +++++++++++++--------
 src/libcatnip/io/file_readers/logreader.hpp |  9 ++--
 src/libcatnip/io/file_readers/punreader.cpp | 17 ++++++--
 src/libcatnip/io/file_readers/punreader.hpp |  8 ++--
 4 files changed, 53 insertions(+), 27 deletions(-)

diff --git a/src/libcatnip/io/file_readers/logreader.cpp b/src/libcatnip/io/file_readers/logreader.cpp
index f55ffdf..b3624be 100644
--- a/src/libcatnip/io/file_readers/logreader.cpp
+++ b/src/libcatnip/io/file_readers/logreader.cpp
@@ -7,6 +7,7 @@
 #include <sstream>
 #include <string>
 
+#include <Eigen/Dense>
 #include "../../log.hpp"
 #include "../../string_support.hpp"
 #include "logreader.hpp"
@@ -164,18 +165,25 @@ void LogReader::OverlapSectionReader(void *ptr) {
   }
 
   // Create a matrix and place all the current values in there
-  Matrix *mat_S = new Matrix(countCoef, countCoef);
+  
+  //Matrix *mat_S = new Matrix(countCoef, countCoef);
+  Eigen::MatrixXd matrix_S(countCoef,countCoef);
   for (size_t row_ind = 0; row_ind < first_coefs.size(); ++row_ind) {
-    vector<double> row = first_coefs.at(row_ind);
-    size_t col_ind = 1;
-    for (auto val : row) {
-      mat_S->set_elem(val, row_ind + 1, col_ind);
+//    vector<double> row = first_coefs.at(row_ind);
+    matrix_S.row(row_ind) << first_coefs.at(row_ind);
+ //   size_t col_ind = 1;
+//    size_t col_ind = 0;
+ //   for (double & val : row) {
+ //     mat_S->set_elem(val, row_ind + 1, col_ind);
+  //    matrix_S(row_ind,col_ind) = val;
       // Because diagonally symetric
-      if (row_ind + 1 != col_ind) {
-        mat_S->set_elem(val, col_ind, row_ind + 1);
-      }
-      ++col_ind;
-    }
+//      if (row_ind + 1 != col_ind) {
+   //   if (row_ind != col_ind) {
+        //mat_S->set_elem(val, col_ind, row_ind + 1);
+   //     matrix_S(col_ind,row_ind) = val;
+    //  }
+    //  ++col_ind;
+    //}
   }
 
   int sectionReads = countCoef / 5;
@@ -193,19 +201,23 @@ void LogReader::OverlapSectionReader(void *ptr) {
       istringstream iss(line);
       string dummy;
       iss >> dummy;
-      int localCoefCount = 1;
+      //int localCoefCount = 1;
+      int localCoefCount = 0;
       while (!iss.eof()) {
         string s_coef;
         iss >> s_coef;
         string val = grabStrBeforeFirstOccurance(s_coef, "D");
         string expon = grabStrAfterFirstOccurance(s_coef, "D");
         double value = stod(val) * pow(10.0, stod(expon));
-        mat_S->set_elem(value, sectionCoef + 1,
-                        currentSectionStart + localCoefCount);
-        if ((sectionCoef + 1) != (currentSectionStart + localCoefCount)) {
-
-          mat_S->set_elem(value, currentSectionStart + localCoefCount,
-                          sectionCoef + 1);
+       
+        //mat_S->set_elem(value, sectionCoef + 1,
+        //                currentSectionStart + localCoefCount);
+        matrix_S(sectionCoef,currentSectionStart + localCoefCount) = value;
+        //if ((sectionCoef + 1) != (currentSectionStart + localCoefCount)) {
+        if ((sectionCoef) != (currentSectionStart + localCoefCount)) {
+          matrix_S(currentSectionStart + localCoefCount,sectionCoef) = value;
+          //mat_S->set_elem(value, currentSectionStart + localCoefCount,
+          //               sectionCoef + 1);
         }
         ++localCoefCount;
       }
diff --git a/src/libcatnip/io/file_readers/logreader.hpp b/src/libcatnip/io/file_readers/logreader.hpp
index 46cde5d..4583ed3 100644
--- a/src/libcatnip/io/file_readers/logreader.hpp
+++ b/src/libcatnip/io/file_readers/logreader.hpp
@@ -4,8 +4,10 @@
 
 #include <vector>
 
-#include "../../matrix.hpp"
+//#include "../../matrix.hpp"
 #include "filereader.hpp"
+
+#include <Eigen/Dense>
 // Gaussian log file reader
 
 namespace catnip {
@@ -18,7 +20,7 @@ class LogReader : public FileReader {
  public:
   explicit LogReader(const std::string &str);
   orb_cont getOrbitalInfo() const { return orb_; }
-  Matrix *getOverlapMatrix() const { return S_; }
+  Eigen::MatrixXd getOverlapMatrix() const { return S_; }
   std::vector<double> getOE(const std::string &orb_type) const {
     return OREnergies.at(orb_type);
   }
@@ -48,7 +50,8 @@ class LogReader : public FileReader {
   std::map<std::string, int> homoLevel;
   orb_cont orb_;
   // Overlap matrix
-  Matrix *S_;
+  //Matrix *S_;
+  Eigen::MatrixXd S_;
   std::map<std::string, std::vector<double>> OREnergies;
 
   std::vector<std::vector<double>> xyz;
diff --git a/src/libcatnip/io/file_readers/punreader.cpp b/src/libcatnip/io/file_readers/punreader.cpp
index 0b5a92c..669693b 100644
--- a/src/libcatnip/io/file_readers/punreader.cpp
+++ b/src/libcatnip/io/file_readers/punreader.cpp
@@ -11,6 +11,8 @@
 #include "../../string_support.hpp"
 #include "punreader.hpp"
 
+#include <Eigen/Dense>
+
 using namespace catnip;
 using namespace std;
 
@@ -29,12 +31,12 @@ void PunReader::registerSections_() {
   FileReader::registerSections_();
 }
 
-Matrix *PunReader::getCoefsMatrix(const string &orb_type) {
+MatrixXd PunReader::getCoefsMatrix(const string &orb_type) {
   if (coefs.count(orb_type) != 1) {
     throw invalid_argument("Coefficients for spin " + orb_type +
                            " were not found");
   }
-  return coefs[orb_type];
+  return *(coefs[orb_type]);
 }
 
 void PunReader::validFileName_() {
@@ -93,8 +95,15 @@ void PunReader::ReadCoef(const string &orb_type) {
     allCoefsRead = !(foundSubStrInStr(line, orb_type));
   }
 
-  Matrix *Coefs = new Matrix(v_vec);
-  coefs[orb_type] = Coefs;
+  //Matrix *Coefs = new Matrix(v_vec);
+  coefs[orb_type] = unique_ptr<Eigen:::MatrixXd>(Eigen::MatrixXd Coefs(v_vec.size(),v_vec.at(0).size()));
+
+  size_t row_count = 0;
+  for( vector<double> & row : v_vec) {
+    coefs[orb_type]->row(row_count) = row;
+    ++row_count;
+  }
+  //coefs[orb_type] = Coefs;
   LOG("Success reading atomic orbital coefficients from .pun file.", 2);
 }
 
diff --git a/src/libcatnip/io/file_readers/punreader.hpp b/src/libcatnip/io/file_readers/punreader.hpp
index 73f8846..2bc4b0b 100644
--- a/src/libcatnip/io/file_readers/punreader.hpp
+++ b/src/libcatnip/io/file_readers/punreader.hpp
@@ -2,17 +2,19 @@
 #ifndef _CATNIP_PUNREADER_HPP_
 #define _CATNIP_PUNREADER_HPP_
 
+#include <memory>
 #include <vector>
 
-#include "../../matrix.hpp"
+//#include "../../matrix.hpp"
 #include "filereader.hpp"
+#include <Eigen/Dense>
 // Gaussian fort.7/.pun file reader
 namespace catnip {
 
 class PunReader : public FileReader {
  public:
   explicit PunReader(const std::string &str);
-  Matrix *getCoefsMatrix(const std::string &orb_type);
+  Eigen::MatrixXd getCoefsMatrix(const std::string &orb_type);
   bool restrictedShell() { return coefs.size() == 1; }
 
  private:
@@ -25,7 +27,7 @@ class PunReader : public FileReader {
   void ReadCoef(const std::string &orb_type);
   std::vector<double> readGausCoefLine(const std::string &line);
 
-  std::map<std::string, Matrix *> coefs;
+  std::map<std::string, std::unique_ptr<Eigen::MatrixXd>> coefs;
 };
 
 }  // namespace catnip

From 094177e9c27ce07cce8604f57437d36d801e9d07 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sat, 27 Apr 2019 13:54:31 -0600
Subject: [PATCH 03/68] Switched to eigen matrices in main

---
 src/tools/main.cpp | 50 +++++++++++++++++++++++++++-------------------
 1 file changed, 30 insertions(+), 20 deletions(-)

diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index be9d395..0455c80 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -17,12 +17,14 @@
 #include "../libcatnip/io/file_readers/punreader.hpp"
 #include "../libcatnip/io/io.hpp"
 #include "../libcatnip/log.hpp"
-#include "../libcatnip/matrix.hpp"
+//#include "../libcatnip/matrix.hpp"
 #include "../libcatnip/parameters.hpp"
 #include "../libcatnip/qc_functions.hpp"
 
 #include "../libcatnip/calcJconfig.hpp"
 
+#include <Eigen/Dense>
+
 using namespace catnip;
 using namespace std;
 
@@ -77,23 +79,31 @@ int main(int argc, const char *argv[]) {
   // No need to worry about beta orbitals
 
   {
-    Matrix *mat_S = lr_P.getOverlapMatrix();
+    //Matrix *mat_S = lr_P.getOverlapMatrix();
+    Eigen::MatrixXd mat_S = lr_P.getOverlapMatrix();
 
-    Matrix *mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
-    auto vec_P_OE = lr_P.getOE(par->getSpinP());
-    Matrix *mat_P_OE = new Matrix(vec_P_OE);
+    //Matrix *mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
+    Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
+    
+    //auto vec_P_OE = lr_P.getOE(par->getSpinP());
+    Eigen::MatrixXd mat_P_OE = Eigen::MatrixXd(lr_P.getOE(par->getSpinP()));
+    //Matrix *mat_P_OE = new Matrix(vec_P_OE);
 
     int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
     LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
-    Matrix *mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
-    auto vec_1_OE = lr_1.getOE(par->getSpin1());
-    Matrix *mat_1_OE = new Matrix(vec_1_OE);
+    Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
+    //Matrix *mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
+    //auto vec_1_OE = lr_1.getOE(par->getSpin1());
+    //Matrix *mat_1_OE = new Matrix(vec_1_OE);
+    Eigen::MatrixXd mat_1_OE = Eigen::MatrixXd(vec_1_OE);
 
     int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
     LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
-    Matrix *mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
-    auto vec_2_OE = lr_2.getOE(par->getSpin2());
-    Matrix *mat_2_OE = new Matrix(vec_2_OE);
+    //Matrix *mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
+    Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
+    //auto vec_2_OE = lr_2.getOE(par->getSpin2());
+    //Matrix *mat_2_OE = new Matrix(vec_2_OE);
+    Eigen::MatrixXd mat_2_OE = Eigen::MatrixXd(vec_2_OE);
 
     // Unscramble dimer coef and energies first need to see how the dimer
     // and monomer coefficients line up. To determine how the ceofficients
@@ -103,18 +113,18 @@ int main(int argc, const char *argv[]) {
     // the position of the atoms in the monomer unit and the positions of
     // the atoms in the dimer we can determine how the coefficients need
     // to be rearranged.
-    auto coord_P = lr_P.getCoords();
-    auto coord_1 = lr_1.getCoords();
-    auto coord_2 = lr_2.getCoords();
+    vector<vector<double>> coord_P = lr_P.getCoords();
+    vector<vector<double>> coord_1 = lr_1.getCoords();
+    vector<vector<double>> coord_2 = lr_2.getCoords();
 
     // Convert coords to matrices
-    Matrix coord_P_mat(coord_P);
-    Matrix coord_1_mat(coord_1);
-    Matrix coord_2_mat(coord_2);
+    MatrixXd coord_P_mat(coord_P);
+    MatrixXd coord_1_mat(coord_1);
+    MatrixXd coord_2_mat(coord_2);
 
-    auto basis_P = lr_P.getBasisFuncCount();
-    auto basis_1 = lr_1.getBasisFuncCount();
-    auto basis_2 = lr_2.getBasisFuncCount();
+    int basis_P = lr_P.getBasisFuncCount();
+    int basis_1 = lr_1.getBasisFuncCount();
+    int basis_2 = lr_2.getBasisFuncCount();
 
     int MO1 = mat_1_OE->get_rows();
     int MO2 = mat_2_OE->get_rows();

From 47257b00c4f12363b7a763cbecc165099fc7b8d8 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sat, 27 Apr 2019 18:21:18 -0600
Subject: [PATCH 04/68] Removed matrix tests

---
 src/tests/CMakeLists.txt  |   1 -
 src/tests/test_matrix.cpp | 298 --------------------------------------
 2 files changed, 299 deletions(-)
 delete mode 100644 src/tests/test_matrix.cpp

diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 0b88df6..bf8fc4b 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -6,7 +6,6 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_argumentstring
   test_argumentswitch
   test_log
-  test_matrix
   test_parameters
   test_propertydouble
   test_propertyfileexist
diff --git a/src/tests/test_matrix.cpp b/src/tests/test_matrix.cpp
deleted file mode 100644
index db78067..0000000
--- a/src/tests/test_matrix.cpp
+++ /dev/null
@@ -1,298 +0,0 @@
-#include "../libcatnip/matrix.hpp"
-#include <cassert>
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-int main() {
-
-  cout << "Testing Constructors\n" << endl;
-
-  cout << "Testing: Matrix::Matrix()\n" << endl;
-  {
-    Matrix mat0;
-    cout << mat0 << endl;
-  }
-
-  cout << "Testing: Matrix::Matrix(int r)\n" << endl;
-  {
-    Matrix mat1(3);
-    cout << mat1 << endl;
-  }
-
-  cout << "Testing: Matrix::Matrix(int r, int c)\n" << endl;
-  {
-    Matrix mat2(2, 3);
-    cout << mat2 << endl;
-  }
-
-  cout << "Testing: Matrix::Matrix(int r, int c, int s)\n" << endl;
-  {
-    Matrix mat3(3, 1, 2);
-    cout << mat3 << endl;
-  }
-
-  cout << "Testing: Matrix::Matrix(vector<double> v_data)\n" << endl;
-  {
-    vector<double> v = {1.2, 324.4, 23};
-    Matrix mat3(v);
-  }
-
-  cout << "Testing: Matrix::Matrix(vector<vector<double>> vv_data)\n" << endl;
-  {
-    vector<vector<double>> vv_data;
-    vector<double> v = {1.2, 324.4, 23};
-    vv_data.push_back(v);
-    v.at(1) = -12.5;
-    vv_data.push_back(v);
-    Matrix mat3(vv_data);
-  }
-
-  cout << "\nTesting: Matrix::set_rows(int r)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_rows(3);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::set_cols(int c)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_cols(4);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::set_shel(int s)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_shel(2);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::operator=(const Matrix mat)\n" << endl;
-  {
-    vector<vector<double>> vv_data;
-    vector<double> v = {1.2, 324.4, 23};
-    vv_data.push_back(v);
-    v.at(1) = -12.5;
-    vv_data.push_back(v);
-    Matrix mat3(vv_data);
-    Matrix mat1;
-    mat1 = mat3;
-    assert(static_cast<int>(mat1.get_elem(1, 1) * 10) == 12);
-    assert(static_cast<int>(mat1.get_elem(1, 2) * 10) == 3244);
-    assert(static_cast<int>(mat1.get_elem(1, 3)) == 23);
-    assert(static_cast<int>(mat1.get_elem(2, 1) * 10) == 12);
-    assert(static_cast<int>(mat1.get_elem(2, 2) * 10) == -125);
-    assert(static_cast<int>(mat1.get_elem(2, 3)) == 23);
-  }
-  cout << "\nTesting: Matrix::set_elem(double val)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_elem(5.4);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::set_elem(double val, int r)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_rows(3);
-    mat0.set_elem(4.4, 3);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::set_elem(double val, int r, int c)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_rows(3);
-    mat0.set_cols(4);
-    mat0.set_elem(4.2, 3, 4);
-    cout << mat0 << endl;
-  }
-
-  cout << "\nTesting: Matrix::set_elem(double val, int r, int c)\n" << endl;
-  {
-    Matrix mat0;
-    mat0.set_rows(3);
-    mat0.set_cols(4);
-    mat0.set_shel(2);
-    mat0.set_elem(0.3, 3, 4, 2);
-    cout << mat0 << endl;
-  }
-
-  {
-    Matrix mat4(2, 3);
-    Matrix mat5(3, 2);
-
-    mat4.set_elem(5, 1, 1);
-    mat4.set_elem(3, 1, 2);
-    mat4.set_elem(1, 1, 3);
-    mat4.set_elem(2, 2, 2);
-    mat4.set_elem(1, 2, 3);
-
-    mat5.set_elem(2, 1, 1);
-    mat5.set_elem(1, 1, 2);
-    mat5.set_elem(1, 2, 1);
-    mat5.set_elem(3, 3, 1);
-    mat5.set_elem(4, 3, 2);
-
-    cout << mat4 << endl;
-    cout << mat5 << endl;
-
-    Matrix mat6 = mat4 * mat5;
-    cout << mat6 << endl;
-
-    cout << "\nResizing matrix 6" << endl;
-    mat6.resize(3, 3);
-    cout << mat6 << endl;
-  }
-
-  cerr << "Testing: matchRow" << endl;
-  {
-    Matrix mat4(2, 3);
-    Matrix mat5(3, 3);
-
-    // mat4
-    // 5 3 1
-    // 0 2 1
-
-    mat4.set_elem(5, 1, 1);
-    mat4.set_elem(3, 1, 2);
-    mat4.set_elem(1, 1, 3);
-    mat4.set_elem(2, 2, 2);
-    mat4.set_elem(1, 2, 3);
-
-    // mat5
-    // 2 1 0
-    // 1 0 0
-    // 5 3 1
-    mat5.set_elem(2, 1, 1);
-    mat5.set_elem(1, 1, 2);
-    mat5.set_elem(1, 2, 1);
-    mat5.set_elem(5, 3, 1);
-    mat5.set_elem(3, 3, 2);
-    mat5.set_elem(1, 3, 3);
-
-    auto m_vec = mat4.matchRow(mat5, 4);
-    assert(m_vec.at(0) == 3);
-  }
-
-  cerr << "Testing: set_row & set_col" << endl;
-  {
-    // mat5
-    // 2 1 0
-    // 1 0 0
-    // 5 3 1
-    Matrix mat5(3, 3);
-    mat5.set_elem(2, 1, 1);
-    mat5.set_elem(1, 1, 2);
-    mat5.set_elem(0, 1, 3);
-    mat5.set_elem(1, 2, 1);
-    mat5.set_elem(0, 2, 2);
-    mat5.set_elem(0, 2, 3);
-    mat5.set_elem(5, 3, 1);
-    mat5.set_elem(3, 3, 2);
-    mat5.set_elem(1, 3, 3);
-
-    vector<double> values{9, 12, 13};
-    mat5.set_row(values, 1);
-    assert(mat5.get_elem(1, 1) == 9);
-    assert(mat5.get_elem(1, 2) == 12);
-    assert(mat5.get_elem(1, 3) == 13);
-    assert(mat5.get_elem(2, 1) == 1);
-    assert(mat5.get_elem(2, 2) == 0);
-    assert(mat5.get_elem(2, 3) == 0);
-    assert(mat5.get_elem(3, 1) == 5);
-    assert(mat5.get_elem(3, 2) == 3);
-    assert(mat5.get_elem(3, 3) == 1);
-
-    vector<double> values2{-12, 23, 101};
-    mat5.set_col(values2, 2);
-    assert(mat5.get_elem(1, 1) == 9);
-    assert(mat5.get_elem(1, 2) == -12);
-    assert(mat5.get_elem(1, 3) == 13);
-    assert(mat5.get_elem(2, 1) == 1);
-    assert(mat5.get_elem(2, 2) == 23);
-    assert(mat5.get_elem(2, 3) == 0);
-    assert(mat5.get_elem(3, 1) == 5);
-    assert(mat5.get_elem(3, 2) == 101);
-    assert(mat5.get_elem(3, 3) == 1);
-  }
-
-  cerr << "Testing: move_row & move_col" << endl;
-  {
-    // mat5
-    // 2 1 0
-    // 1 0 0
-    // 5 3 1
-    Matrix mat5(3, 3);
-    mat5.set_elem(2, 1, 1);
-    mat5.set_elem(1, 1, 2);
-    mat5.set_elem(0, 1, 3);
-    mat5.set_elem(1, 2, 1);
-    mat5.set_elem(0, 2, 2);
-    mat5.set_elem(0, 2, 3);
-    mat5.set_elem(5, 3, 1);
-    mat5.set_elem(3, 3, 2);
-    mat5.set_elem(1, 3, 3);
-
-    // 5 3 1
-    // 2 1 0
-    // 1 0 0
-    mat5.move_row(3, 1);
-    assert(mat5.get_elem(1, 1) == 5);
-    assert(mat5.get_elem(1, 2) == 3);
-    assert(mat5.get_elem(1, 3) == 1);
-    assert(mat5.get_elem(2, 1) == 2);
-    assert(mat5.get_elem(2, 2) == 1);
-    assert(mat5.get_elem(2, 3) == 0);
-    assert(mat5.get_elem(3, 1) == 1);
-    assert(mat5.get_elem(3, 2) == 0);
-    assert(mat5.get_elem(3, 3) == 0);
-
-    // 1 5 3
-    // 0 2 1
-    // 0 1 0
-    mat5.move_col(3, 1);
-    cerr << mat5 << endl;
-    assert(mat5.get_elem(1, 1) == 1);
-    assert(mat5.get_elem(1, 2) == 5);
-    assert(mat5.get_elem(1, 3) == 3);
-    assert(mat5.get_elem(2, 1) == 0);
-    assert(mat5.get_elem(2, 2) == 2);
-    assert(mat5.get_elem(2, 3) == 1);
-    assert(mat5.get_elem(3, 1) == 0);
-    assert(mat5.get_elem(3, 2) == 1);
-    assert(mat5.get_elem(3, 3) == 0);
-
-    // 0 2 1
-    // 0 1 0
-    // 1 5 3
-    mat5.move_row(1, 3);
-    assert(mat5.get_elem(1, 1) == 0);
-    assert(mat5.get_elem(1, 2) == 2);
-    assert(mat5.get_elem(1, 3) == 1);
-    assert(mat5.get_elem(2, 1) == 0);
-    assert(mat5.get_elem(2, 2) == 1);
-    assert(mat5.get_elem(2, 3) == 0);
-    assert(mat5.get_elem(3, 1) == 1);
-    assert(mat5.get_elem(3, 2) == 5);
-    assert(mat5.get_elem(3, 3) == 3);
-
-    // 2 1 0
-    // 1 0 0
-    // 5 3 1
-    mat5.move_col(1, 3);
-    assert(mat5.get_elem(1, 1) == 2);
-    assert(mat5.get_elem(1, 2) == 1);
-    assert(mat5.get_elem(1, 3) == 0);
-    assert(mat5.get_elem(2, 1) == 1);
-    assert(mat5.get_elem(2, 2) == 0);
-    assert(mat5.get_elem(2, 3) == 0);
-    assert(mat5.get_elem(3, 1) == 5);
-    assert(mat5.get_elem(3, 2) == 3);
-    assert(mat5.get_elem(3, 3) == 1);
-  }
-  return 0;
-}

From 0ad1283890453be82eb6b4ffd982280c2fb39468 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sat, 27 Apr 2019 19:34:23 -0600
Subject: [PATCH 05/68] Updated main and qc_functions to use Eigen matrix and
 vector classes

---
 src/libcatnip/qc_functions.cpp | 428 +++++++++++++++++++++------------
 src/libcatnip/qc_functions.hpp | 157 ++++++++----
 src/tools/main.cpp             |  10 +-
 3 files changed, 384 insertions(+), 211 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index 963c6fd..3cb76b8 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -18,28 +18,33 @@ using namespace std;
 
 namespace catnip {
 
-unordered_map<int, pair<double, string>> findRank(Matrix &Orb_E_Alpha,
-                                                  Matrix &Orb_E_Beta) {
+unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
+                                                  Eigen::VectorXd &Orb_E_Beta) {
 
   vector<pair<double, string>> all;
 
-  auto m_a = Orb_E_Alpha.getCol(1);
+  //auto m_a = Orb_E_Alpha.getCol(1);
 
-  for (int ind = 1; ind <= m_a.get_rows(); ind++) {
+  /*for (int ind = 1; ind <= m_a.get_rows(); ind++) {
     auto val = m_a.get_elem(ind);
     pair<double, string> pr(val, "Alpha");
     all.push_back(pr);
+  }*/
+  for( double & val : Orb_E_Alpha){
+    all.push_back(pair<double, string>(val,"Alpha"));
   }
 
-  if (Orb_E_Beta.get_cols() > 0) {
-    auto m_b = Orb_E_Beta.getCol(1);
-
-    for (int ind = 1; ind <= m_b.get_rows(); ind++) {
-      auto val = m_b.get_elem(ind);
-      pair<double, string> pr(val, "Beta");
-      all.push_back(pr);
+  //if (Orb_E_Beta.get_cols() > 0) {
+  //  auto m_b = Orb_E_Beta.getCol(1);
+  
+  //  for (int ind = 1; ind <= m_b.get_rows(); ind++) {
+    for( double & val : Orb_E_Beta ){ 
+      //auto val = m_b.get_elem(ind);
+      //pair<double, string> pr(val, "Beta");
+      //all.push_back(pr);
+      all.push_back(pair<double, string>(val, "Beta"));
     }
-  }
+ // }
   // Sort the vectors
   sort(all.begin(), all.end(),
        [](const pair<double, string> &P1, const pair<double, string> &P2)
@@ -57,45 +62,61 @@ unordered_map<int, pair<double, string>> findRank(Matrix &Orb_E_Alpha,
 }
 
 // Essentially calculates the transfer integral
-double calculate_transfer_integral(const Matrix & mat_1_Coef, const Matrix & mat_2_Coef,
-                                   Matrix mat_P_Coef,const Matrix & mat_S,
-                                   const Matrix &mat_P_OE, bool counterPoise_) {
+void TransferComplex::calculate_transfer_integral_() {
 
-  Matrix mat_1_Coefinv = mat_1_Coef.invert();
-  Matrix mat_2_Coefinv = mat_2_Coef.invert();
-  Matrix mat_P_Coefinv = mat_P_Coef.invert();
+  //Matrix mat_1_Coefinv = mat_1_Coef.invert();
+  //Matrix mat_2_Coefinv = mat_2_Coef.invert();
+  //Matrix mat_P_Coefinv = mat_P_Coef.invert();
 
-  Matrix zetaA;
-  Matrix zetaB;
+  auto dimension = mat_1_Coef.rows()+mat_2_Coef.rows();
+  Eigen::MatrixXd zetaA(dimension,dimension);
+  Eigen::MatrixXd zetaB(dimension,dimension);
   if (counterPoise_) {
     LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
-    zetaA = (mat_1_Coefinv);
-    zetaB = (mat_2_Coefinv);
+    //zetaA = (mat_1_Coefinv);
+    //zetaB = (mat_2_Coefinv);
+    zetaA = mat_1_Coef();
+    zetaB = mat_2_Coef();
   } else {
     LOG("Creating zeta matrices from coefficients", 2);
-    Matrix zerosA(mat_1_Coefinv.get_rows(), 1, mat_1_Coefinv.get_shel());
-    Matrix zerosB(mat_2_Coefinv.get_rows(), 1, mat_2_Coefinv.get_shel());
-    zetaA = Matrix_concatenate_rows(mat_1_Coefinv, zerosB);
-    zetaB = Matrix_concatenate_rows(zerosA, mat_2_Coefinv);
+   // Matrix zerosA(mat_1_Coefinv.get_rows(), 1, mat_1_Coefinv.get_shel());
+    //Matrix zerosB(mat_2_Coefinv.get_rows(), 1, mat_2_Coefinv.get_shel());
+    //zetaA = Matrix_concatenate_rows(mat_1_Coefinv, zerosB);
+    //zetaB = Matrix_concatenate_rows(zerosA, mat_2_Coefinv);
+    //zetaA.resize(mat_1_Coef.rows()+mat_2_Coef.rows(),1);
+    //zetaB.resize(mat_1_Coef.rows()+mat_2_Coef.rows(),1);
+    zetaA << mat_1_Coef(), Eigen::MatrixXd.Zeros(mat_1_Coef.rows(),mat_2_Coef.cols()); 
+    zetaA << Eigen::MatrixXd.Zeros(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef(); 
   }
-  Matrix zetaAinv = zetaA.invert();
-  Matrix zetaBinv = zetaB.invert();
+  //Matrix zetaAinv = zetaA.invert();
+  //Matrix zetaBinv = zetaB.invert();
 
-  LOG("Creating intermediate matrix", 3);
-  Matrix Inter = mat_S * mat_P_Coefinv;
+  //LOG("Creating intermediate matrix", 3);
+  //Matrix Inter = mat_S * mat_P_Coefinv;
+  //MatrixXd Inter = mat_S * mat_P_Coefinv;
 
   LOG("Creating gamma and beta matrices", 2);
-  Matrix gammaA = zetaAinv * Inter;
-  Matrix gammaB = zetaBinv * Inter;
+  //Matrix gammaA = zetaAinv * Inter;
+  //Matrix gammaB = zetaBinv * Inter;
+  Eigen::MatrixXd gammaA = zetaA * mat_S * mat_P_Coef.transpose(); 
+  Eigen::MatrixXd gammaB = zetaB * mat_S * mat_P_Coef.transpose(); 
 
-  Matrix gammaA_inv = gammaA.invert();
-  Matrix gammaB_inv = gammaB.invert();
+  //Matrix gammaA_inv = gammaA.invert();
+  //Matrix gammaB_inv = gammaB.invert();
 
   LOG("Calculating S_AB", 2);
-  Matrix S_AB = gammaB * gammaA_inv;
+  //Matrix S_AB = gammaB * gammaA_inv;
+  Eigen::MatrixXd S_AB = gammaB * gammaA.transpose();
+  Eigen::MatrixXd S_AB_inv_sqrt = S_AB.operatorInverseSqrt();
 
-  Matrix Energy = Matrix_diag(mat_P_OE);
-  Matrix J_AB = gammaB * (Energy * gammaA_inv);
+  //Matrix Energy = Matrix_diag(mat_P_OE);
+  Eigen::MatrixXd Energy = vec_P_OE.asDiagona();
+
+  Eigen::MatrixXd Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
+ 
+  Eigen::MatrixXd Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt.transpose();  
+  
+/*  Matrix J_AB = gammaB * (Energy * gammaA_inv);
 
   Matrix e_B = gammaB * (Energy * gammaB_inv);
   Matrix e_A = gammaA * (Energy * gammaA_inv);
@@ -113,11 +134,184 @@ double calculate_transfer_integral(const Matrix & mat_1_Coef, const Matrix & mat
   cout << "e_b   " << e_b * hartreeToeV << " eV\n";
   cout << "S_ab  " << S_ab << "\n";
   cout << "J_eff " << J_eff * hartreeToeV << " eV\n";
-
   return J_eff;
+*/
+}
+
+void TransferComplex::printTransferIntegral(
+    const map<string, string> &orbitaltype,
+    const map<string, int> &orbnum) const {
+
+  //Matrix mat1coef;
+  //Matrix mat2coef;
+
+  string HOMO_OR_LUMO_A = orbitaltype.at("mon1");
+  int MO_A = orbnum.at("mon1");
+  if (HOMO_OR_LUMO_A.compare("HOMO") == 0) {
+    if (MO_A > 0) {
+      throw invalid_argument(
+          "Having specified HOMO the MO_A"
+          " value is in reference to the HOMO and must be a negative number");
+    }
+    // Number of orbitals that are choices
+    if (MO_A <= (-1 * Orbs1.second)) {
+      string err = "You are trying to access HOMO" + to_string(MO_A) +
+                   " but there "
+                   "are only " +
+                   to_string(Orbs1.second) + " HOMO orbitals";
+      throw invalid_argument(err);
+    }
+    //mat1coef = mat_1_Coef->getRow(Orbs1.second + MO_A);
+  } else if (HOMO_OR_LUMO_A.compare("LUMO") == 0) {
+    if (MO_A < 0) {
+      throw invalid_argument(
+          "Having specified LUMO the MO_A"
+          " value is in reference to the LUMO and must be a positive number");
+    }
+    int allowed_LUMO = Orbs1.first - Orbs1.second;
+    if (MO_A >= allowed_LUMO) {
+      string err = "You are trying to access LUMO+" + to_string(MO_A) +
+                   " but there "
+                   "are only " +
+                   to_string(allowed_LUMO) + " LUMO orbitals";
+      throw invalid_argument(err);
+    }
+    //mat1coef = mat_1_Coef->getRow(Orbs1.second + MO + 1);
+  } else {
+    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
+  }
+
+  string HOMO_OR_LUMO_B = orbitaltype.at("mon2");
+  int MO_B = orbnum.at("mon2");
+  if (HOMO_OR_LUMO_B.compare("HOMO") == 0) {
+    if (MO_B > 0) {
+      throw invalid_argument(
+          "Having specified HOMO the MO_B"
+          " value is in reference to the HOMO and must be a negative number");
+    }
+    if (MO_B <= (-1 * Orbs2.second)) {
+      string err = "You are trying to access HOMO" + to_string(MO_B) +
+                   " but there "
+                   "are only " +
+                   to_string(Orbs2.second) + " HOMO orbitals";
+      throw invalid_argument(err);
+    }
+    //mat2coef = mat_2_Coef->getRow(Orbs2.second + MO_B);
+  } else if (HOMO_OR_LUMO_B.compare("LUMO") == 0) {
+    if (MO_B < 0) {
+      throw invalid_argument(
+          "Having specified LUMO the MO_B"
+          " value is in reference to the LUMO and must be a positive number");
+    }
+    int allowed_LUMO = Orbs2.first - Orbs2.second;
+    if (MO_B >= allowed_LUMO) {
+      string err = "You are trying to access LUMO+" + to_string(MO_B) +
+                   " but there "
+                   "are only " +
+                   to_string(allowed_LUMO) + " LUMO orbitals";
+      throw invalid_argument(err);
+    }
+    //mat2coef = mat_2_Coef->getRow(Orbs2.second + MO_B + 1);
+  } else {
+    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
+  }
+
+  printTransferIntegral_(
+      pair<string,int>(HOMO_OR_LUMO_A,MO_A),
+      pair<string,int>(HOMO_OR_LUMO_B,MO_B));
+}
+// Find the transfer integral between two orbitals. 
+// pair<string,int> string - Either HOMO or LUMO
+//                  int    - is the orbital number HOMO-3 LUMO+5
+void TransferComplex::printTransferIntegral_(pair<string,int> Orbital1, pair<string,int> Orbital2) const {
+
+  int obrital1_num = 0;
+  int obrital2_num = 0;
+  if(orbital1.first.compare("HOMO")==0){
+    assert(orbitalValid_(Orbital1)==true); 
+    orbital1_num = Orbital1.second;
+  }else if(orbital2.first.compare("LUMO")==0){
+    assert(orbitalValid_(Orbital2)==true); 
+    orbital2_num = Orbital2.second;
+  }
+  double J_ab = Hamiltonian(orbital1_num,orbital2_num);
+  double e_a = Hamiltonaian(orbital1_num,orbital1_num);
+  double e_b = Hamiltonaian(orbital2_num,orbital2_num);
+  double S_ab = S_AB(orbital1_num,orbital2_num); 
+  double J_eff = Hamiltonaian_eff(orbital1_num,orbital2_num);
+  cout << "J_ab  " << J_ab * hartreeToeV << " eV\n";
+  cout << "e_a   " << e_a * hartreeToeV << " eV\n";
+  cout << "e_b   " << e_b * hartreeToeV << " eV\n";
+  cout << "S_ab  " << S_ab << "\n";
+  cout << "J_eff " << J_eff * hartreeToeV << " eV\n";
+}
+
+void TransferComplex::printAll() const {
+
+  int column_width = 8;
+  cout << "Effective Hamiltonian" << endl;
+  cout << setw(column_width+2) << ""; 
+  for(int orbital_num = 0;orbital_num<Hamiltonian.cols();++orbital_num){
+    string column_label = "";
+    if(orbital_num<HOMO_Orb_){
+      column_label+=string("HOMO");
+      if(orbital_num!=(HOMO_Orb_-1)){
+        column_label+=string("-")+to_string(HOMO_Orb-orbital_num-1);
+      }
+    }else {
+      column_label+=string("LUMO");
+      if(orbital_num!=LUMO_Orb_){
+        column_label+=string("+")+to_string(orbital_num-LUMO_Orb_);
+      }
+    } 
+    cout << "| " << setw(column_width) << column_label << " ";
+  }
+  cout << "|" << endl; 
+ 
+  for(int orbital_num = 0;orbital_num<Hamiltonian.rows();++orbital_num){
+    string column_label = "";
+    if(orbital_num<HOMO_Orb_){
+      column_label+=string("HOMO");
+      if(orbital_num!=(HOMO_Orb_-1)){
+        column_label+=string("-")+to_string(HOMO_Orb-orbital_num-1);
+      }
+    }else {
+      column_label+=string("LUMO");
+      if(orbital_num!=LUMO_Orb_){
+        column_label+=string("+")+to_string(orbital_num-LUMO_Orb_);
+      }
+    } 
+    cout << setw(column_width+2) << column_label;
+    for(int orbital_num2 = 0;orbital_num2<Hamiltonian.cols();++orbital2_num){
+      cout << "| " << setw(column_width) << Hamiltonian_eff(orbital_num2,orbital_num2) << " ";
+    }
+    cout << "|" << endl; 
+  }
+ 
 }
 
-// Split a matrix up into a list of smaller matrices. The marix can be split
+bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital) const{
+  if(orbital.first.compare("HOMO")==0){
+    if(orbital.second>0){
+      cerr << "HOMO orbital number is not negative or 0" << endl;
+      return false;  
+    }
+    if(orbital.second<=(-1*HOMO_Orb_)){
+      cerr << "HOMO orbital does not exst " << orbital.second << endl;
+      return false;
+    }
+  }else if(orbital.first.compare("LUMO")==0){
+    if(orbital.second<0){
+      cerr << "LUMO orbital number is not positive or 0" << endl; return false;  
+    }
+    if(orbital.second>(Hamiltonian_eff.rows()-LUMO_Orb_)){
+      cerr << "LUMO orbital does not exst " << orbital.second << endl;
+      return false;
+    }
+  }
+  return true;
+} 
+// Split a matrix up into a list of smaller matrices. The matrix can be split
 // in columns or in rows. The number of rows/cols in each smaller matrix is
 // held in the vector<int> subMatrixDimension
 //
@@ -136,36 +330,34 @@ double calculate_transfer_integral(const Matrix & mat_1_Coef, const Matrix & mat
 //   1 2         3
 //   3 4         5
 //
-list<Matrix *> splitMatrixIntoList(const vector<int> &subMatrixDimension,
-                                   const Matrix *const mat,
+list<MatrixXd> splitMatrixIntoList(const vector<int> &subMatrixDimension,
+                                   const MatrixXd const mat,
                                    const string &ColRowSplit) {
 
-  list<Matrix *> list_matrix;
+  list<MatrixXd> list_matrix;
   int num_sub_matrices = subMatrixDimension.size();
   if (ColRowSplit.compare("Columns") == 0) {
     int col = 0;
-    for (auto i = 1; i <= num_sub_matrices; ++i) {
-      Matrix *mat_new =
-          new Matrix(mat->get_rows(), subMatrixDimension.at(i - 1));
-      for (auto k = 1; k <= mat->get_rows(); ++k) {
-        for (auto j = 1; j <= subMatrixDimension.at(i - 1); ++j) {
-          mat_new->set_elem(mat->get_elem(k, col + j), k, j);
+    for (int i = 0; i < num_sub_matrices; ++i) {
+      MatrixXd mat_new(mat.rows(), subMatrixDimension.at(i));
+      for (auto k = 0; k < mat.rows(); ++k) {
+        for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
+          mat_new(k,j) = mat(k, col + j);
         }
       }
-      col += subMatrixDimension.at(i - 1);
+      col += subMatrixDimension.at(i);
       list_matrix.push_back(mat_new);
     }
   } else if (ColRowSplit.compare("Rows") == 0) {
     int row = 0;
-    for (auto i = 1; i <= num_sub_matrices; ++i) {
-      Matrix *mat_new =
-          new Matrix(subMatrixDimension.at(i - 1), mat->get_cols());
-      for (auto k = 1; k <= mat->get_cols(); ++k) {
-        for (auto j = 1; j <= subMatrixDimension.at(i - 1); ++j) {
-          mat_new->set_elem(mat->get_elem(row + j, k), j, k);
+    for (auto i = 0; i < num_sub_matrices; ++i) {
+      MatrixXd mat_new(subMatrixDimension.at(i), mat.cols());
+      for (auto k = 0; k < mat->get_cols(); ++k) {
+        for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
+          mat_new(j,k) = mat(row + j, k);
         }
       }
-      row += subMatrixDimension.at(i - 1);
+      row += subMatrixDimension.at(i);
       list_matrix.push_back(mat_new);
     }
   } else {
@@ -174,7 +366,7 @@ list<Matrix *> splitMatrixIntoList(const vector<int> &subMatrixDimension,
   return list_matrix;
 }
 
-list<Matrix *> splitCoefsUpByAtoms(const vector<int> & basisFuncP, Matrix *Coefs,
+list<MatrixXd> splitCoefsUpByAtoms(const vector<int> & basisFuncP, MatrixXd Coefs,
                                    const string & ColRow) {
   return splitMatrixIntoList(basisFuncP, Coefs, ColRow);
 }
@@ -483,13 +675,13 @@ Matrix *unscramble_Coef(const std::vector<int> &matchDimerB,
 
 // Similar to the above function but we will be moving both the rows
 // and columns
-Matrix *unscramble_S(const std::vector<int> &matchDimerA,
+Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
                      const std::vector<int> &matchDimerB,
-                     const std::vector<int> &basisFuncP, Matrix *S) {
+                     const std::vector<int> &basisFuncP, const MatrixXd & S) {
 
-  Matrix *S_new;
+  Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
-    list<Matrix *> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
 
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
@@ -511,7 +703,7 @@ Matrix *unscramble_S(const std::vector<int> &matchDimerA,
   S = S_new;
 
   {
-    list<Matrix *> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
 
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
@@ -541,7 +733,7 @@ Matrix *unscramble_S(const std::vector<int> &matchDimerA,
 
   Matrix *S_new;
   {
-    list<Matrix *> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
 
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
@@ -557,7 +749,7 @@ Matrix *unscramble_S(const std::vector<int> &matchDimerA,
   S = S_new;
 
   {
-    list<Matrix *> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
 
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
@@ -574,16 +766,12 @@ Matrix *unscramble_S(const std::vector<int> &matchDimerA,
   return S_new;
 }
 
-}  // namespace catnip
-
-using namespace catnip;
-
-TransferComplex::TransferComplex(Matrix *mat1Coef, Matrix *mat2Coef,
-                                 Matrix *matPCoef, std::pair<int, int> MOs1,
-                                 std::pair<int, int> MOs2, Matrix *matS,
-                                 Matrix *matPOE, bool cp) {
+TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2Coef,
+                                 Eigen::MatrixXd matPCoef, std::pair<int, int> MOs1,
+                                 std::pair<int, int> MOs2, Eigen::MatrixXd matS,
+                                 Eigen::VectorXd vecPOE, bool cp) {
 
-  unscrambled = false;
+  unscrambled_ = false;
   counterPoise_ = cp;
   // Consistency check
   if (matS->get_cols() != matPCoef->get_cols()) {
@@ -620,16 +808,16 @@ TransferComplex::TransferComplex(Matrix *mat1Coef, Matrix *mat2Coef,
   Orbs1 = MOs1;
   Orbs2 = MOs2;
   mat_S = matS;
-  mat_P_OE = matPOE;
+  vec_P_OE = vecPOE;
 }
 
-void TransferComplex::unscramble(const Matrix &coord_1_mat,
-                                 const Matrix &coord_2_mat,
-                                 const Matrix &coord_P_mat,
+void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
+                                 const Eigen::MatrixXd &coord_2_mat,
+                                 const Eigen::MatrixXd &coord_P_mat,
                                  const std::vector<int> &basisP,
                                  const std::vector<int> &basis2) {
 
-  unscrambled = true;
+  unscrambled_ = true;
 
   const int sig_fig = 4;
 
@@ -673,10 +861,9 @@ void TransferComplex::unscramble(const Matrix &coord_1_mat,
   }
 }
 
-double TransferComplex::calcJ(const map<string, string> &orbitaltype,
-                              const map<string, int> &orbnum) {
+double TransferComplex::calcJ() {
 
-  if (unscrambled == false) {
+  if (unscrambled_ == false) {
     cerr << "WARNING unable to automatically line up basis functions of"
             " monomers with dimers, you better make sure they correctly"
             " line up or run the calculations again with the correct "
@@ -684,80 +871,7 @@ double TransferComplex::calcJ(const map<string, string> &orbitaltype,
          << endl;
   }
 
-  Matrix mat1coef;
-  Matrix mat2coef;
-
-  string HOMO_OR_LUMO = orbitaltype.at("mon1");
-  int MO = orbnum.at("mon1");
-  if (HOMO_OR_LUMO.compare("HOMO") == 0) {
-    if (MO > 0) {
-      throw invalid_argument(
-          "Having specified HOMO the MO"
-          " value is in reference to the HOMO and must be a negative number");
-    }
-    // Number of orbitals that are choices
-    if (MO <= (-1 * Orbs1.second)) {
-      string err = "You are trying to access HOMO" + to_string(MO) +
-                   " but there "
-                   "are only " +
-                   to_string(Orbs1.second) + " HOMO orbitals";
-      throw invalid_argument(err);
-    }
-    mat1coef = mat_1_Coef->getRow(Orbs1.second + MO);
-  } else if (HOMO_OR_LUMO.compare("LUMO") == 0) {
-    if (MO < 0) {
-      throw invalid_argument(
-          "Having specified LUMO the MO"
-          " value is in reference to the LUMO and must be a positive number");
-    }
-    int allowed_LUMO = Orbs1.first - Orbs1.second;
-    if (MO >= allowed_LUMO) {
-      string err = "You are trying to access LUMO+" + to_string(MO) +
-                   " but there "
-                   "are only " +
-                   to_string(allowed_LUMO) + " LUMO orbitals";
-      throw invalid_argument(err);
-    }
-    mat1coef = mat_1_Coef->getRow(Orbs1.second + MO + 1);
-  } else {
-    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
-  }
-
-  HOMO_OR_LUMO = orbitaltype.at("mon2");
-  MO = orbnum.at("mon2");
-  if (HOMO_OR_LUMO.compare("HOMO") == 0) {
-    if (MO > 0) {
-      throw invalid_argument(
-          "Having specified HOMO the MO"
-          " value is in reference to the HOMO and must be a negative number");
-    }
-    if (MO <= (-1 * Orbs2.second)) {
-      string err = "You are trying to access HOMO" + to_string(MO) +
-                   " but there "
-                   "are only " +
-                   to_string(Orbs2.second) + " HOMO orbitals";
-      throw invalid_argument(err);
-    }
-    mat2coef = mat_2_Coef->getRow(Orbs2.second + MO);
-  } else if (HOMO_OR_LUMO.compare("LUMO") == 0) {
-    if (MO < 0) {
-      throw invalid_argument(
-          "Having specified LUMO the MO"
-          " value is in reference to the LUMO and must be a positive number");
-    }
-    int allowed_LUMO = Orbs2.first - Orbs2.second;
-    if (MO >= allowed_LUMO) {
-      string err = "You are trying to access LUMO+" + to_string(MO) +
-                   " but there "
-                   "are only " +
-                   to_string(allowed_LUMO) + " LUMO orbitals";
-      throw invalid_argument(err);
-    }
-    mat2coef = mat_2_Coef->getRow(Orbs2.second + MO + 1);
-  } else {
-    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
-  }
-
-  return calculate_transfer_integral(mat1coef, mat2coef, *mat_P_Coef, *mat_S,
-                                     *mat_P_OE, counterPoise_);
+  return calculate_transfer_integral_();
 }
+
+}  // namespace catnip
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index e8bc1a6..11bc0b8 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -7,82 +7,139 @@
 #include <unordered_map>
 #include <vector>
 
-#include "matrix.hpp"
+//#include "matrix.hpp"
+#include <Eigen/Dense>
 
 namespace catnip {
 
 class TransferComplex {
- private:
-  Matrix* mat_1_Coef;
-  Matrix* mat_2_Coef;
-  Matrix* mat_P_Coef;
-  // Stores the number of Molecular orbitals
-  // and the HOMO for both monomer 1 and 2
-  std::pair<int, int> Orbs1;
-  std::pair<int, int> Orbs2;
-  Matrix* mat_S;
-  Matrix* mat_P_OE;
-  // If unscrambaling is required
-  bool unscrambled;
-  bool counterPoise_;
-
- public:
-  TransferComplex(Matrix* mat1Coef, Matrix* mat2Coef, Matrix* matPCoef,
-                  std::pair<int, int> MOs1, std::pair<int, int> MOs2,
-                  Matrix* matS, Matrix* matPOE, bool cp);
-
-  void unscramble(const Matrix& coord_1_mat, const Matrix& coord_2_mat,
-                  const Matrix& coord_P_mat, const std::vector<int>& basisP,
-                  const std::vector<int>& basis2);
-
-  // Orbital type and a map of the corresponding number
-  // E.g.
-  // orbital type    orbital number
-  // "mon1" "LUMO"    "mon1" -3
-  // "mon2" "HOMO"    "mon2"  0
-  //
-  //    monomer1 LUMO-3
-  //    monomer2 HOMO
-  double calcJ(const std::map<std::string, std::string>& orbitaltype,
-               const std::map<std::string, int>& orbitalnum);
+  private:
+    Eigen::MatrixXd mat_1_Coef;
+    Eigen::MatrixXd mat_2_Coef;
+    Eigen::MatrixXd mat_P_Coef;
+    // Stores the number of Molecular orbitals
+    // and the HOMO for both monomer 1 and 2
+    std::pair<int, int> Orbs1;
+    std::pair<int, int> Orbs2;
+
+    /**
+     * \brief basis function overlap matrix
+     **/
+    Eigen::MatrixXd mat_S;
+    /**
+     * \brief Molecular orbital overlap matrix
+     **/
+    Eigen::MatrixXd S_AB;
+
+    /**
+     * \brief Non orthonormalized Hamiltonian matrix
+     **/
+    Eigen::MatrixXd Hamiltonian;
+
+    /**
+     * \brief Orthonormalized Hamiltonian Matrix
+     **/
+    Eigen::MatrixXd Hamiltonian_eff;
+
+    int HOMO_Orb_;
+    int LUMO_Orb_;
+    Eigen::VectorXd vec_P_OE;
+    // If unscrambaling is required
+    bool unscrambled_;
+    bool counterPoise_;
+
+    /*
+     * \brief Determine if the provided orbital is valid
+     **/
+    bool orbitalValid_(const std::pair<std::string,int> & orbital) const;
+
+    void calculate_transfer_integral_(
+        const Eigen::MatrixXd & mat_1_Coef, 
+        const Eigen::MatrixXd & mat_2_Coef,
+        Eigen::MatrixXd mat_P_Coef,
+        const Eigen::MatrixXd & mat_S,
+        const Eigen::VectorXd& vec_P_OE, 
+        bool counterPoise_);
+
+    void printTransferIntegral_(std::pair<std::string,int> Orbital1,
+                               std::pair<std::string,int> Orbital2) const;
+  public:
+    TransferComplex(
+        Eigen::MatrixXd mat1Coef, 
+        Eigen::MatrixXd mat2Coef, 
+        Eigen::MatrixXd matPCoef,
+        std::pair<int, int> MOs1, 
+        std::pair<int, int> MOs2,
+        Eigen::MatrixXd matS, 
+        Eigen::VectorXd vecPOE, 
+        bool cp);
+
+    void unscramble(
+        const Eigen::MatrixXd& coord_1_mat, 
+        const Eigen::MatrixXd& coord_2_mat,
+        const Eigen::MatrixXd& coord_P_mat, 
+        const std::vector<int>& basisP,
+        const std::vector<int>& basis2);
+
+    // Orbital type and a map of the corresponding number
+    // E.g.
+    // orbital type    orbital number
+    // "mon1" "LUMO"    "mon1" -3
+    // "mon2" "HOMO"    "mon2"  0
+    //
+    //    monomer1 LUMO-3
+    //    monomer2 HOMO
+    double calcJ(const std::map<std::string, std::string>& orbitaltype,
+        const std::map<std::string, int>& orbitalnum);
+
+    /**
+     * \brief Print the transfer integral specified
+     **/
+    void printTransferIntegral(std::pair<std::string,int> Orbital1,
+                               std::pair<std::string,int> Orbital2) const;
+
+    /**
+     * \brief Print All info in matrix form
+     **/
+    void printAll() const;
 };
 
 std::unordered_map<int, std::pair<double, std::string>> findRank(
-    Matrix& Orb_E_Alpha, Matrix& Orb_E_Beta);
+    Eigen::VectorXd& Orb_E_Alpha, Eigen::VectorXd& Orb_E_Beta);
 
-double calculate_transfer_integral(const Matrix & mat_1_Coef, const Matrix & mat_2_Coef,
-                                   Matrix mat_P_Coef,const Matrix & mat_S,
-                                   const Matrix& mat_P_OE, bool counterPoise_);
+/*double calculate_transfer_integral(const Eigen::MatrixXd & mat_1_Coef, const Eigen::MatrixXd & mat_2_Coef,
+                                   Eigen::MatrixXd mat_P_Coef,const Eigen::MatrixXd & mat_S,
+                                   const Eigen::VectorXd& vec_P_OE, bool counterPoise_);*/
 
 // Reorganize the dimer coefficients to match up with the monomers
-Matrix organize_P_Coef(std::vector<int> matchDimerA,
+Eigen::MatrixXd organize_P_Coef(std::vector<int> matchDimerA,
                        std::vector<int> matchDimerB,
                        std::vector<int> basisFuncA, std::vector<int> basisFuncB,
-                       std::vector<int> basisFuncDimer, Matrix dimerCoef);
+                       std::vector<int> basisFuncDimer, Eigen::MatrixXd dimerCoef);
 
 // Unscramble the coefficients of the dimer matrix
 // Assumes that the match vectors describe swaps looking at a single
 // instance of the dimerCoef matrix
-Matrix* unscramble_Coef(const std::vector<int>& matchDimerA,
+Eigen::MatrixXd unscramble_Coef(const std::vector<int>& matchDimerA,
                         const std::vector<int>& matchDimerB,
                         const std::vector<int>& basisFuncDimer,
-                        Matrix* dimerCoef);
+                        Eigen::MatrixXd dimerCoef);
 
-Matrix* unscramble_Coef(const std::vector<int>& matchDimerA,
-                        const std::vector<int>& basisFuncDimer, Matrix* dimerCoef);
+Eigen::MatrixXd unscramble_Coef(const std::vector<int>& matchDimerA,
+                        const std::vector<int>& basisFuncDimer, Eigen::MatrixXd dimerCoef);
 
 // Reorganize the dimer overlap matrix to line up with the monomer
 // coefficients.
-Matrix* unscramble_S(const std::vector<int>& matchDimerA,
+Eigen::MatrixXd unscramble_S(const std::vector<int>& matchDimerA,
                      const std::vector<int>& matchDimerB,
-                     const std::vector<int>& basisFuncDimer, Matrix* S);
+                     const std::vector<int>& basisFuncDimer, Eigen::MatrixXd S);
 
-Matrix* unscramble_S(const std::vector<int>& matchDimerA,
-                     const std::vector<int>& basisFuncDimer, Matrix* S);
+Eigen::MatrixXd unscramble_S(const std::vector<int>& matchDimerA,
+                     const std::vector<int>& basisFuncDimer, Eigen::MatrixXd S);
 
-Matrix* unscramble_OE(std::vector<int> matchDimerA,
+Eigen::MatrixXd unscramble_OE(std::vector<int> matchDimerA,
                       std::vector<int> matchDimerB,
-                      std::vector<int> basisFuncDimer, Matrix* OE);
+                      std::vector<int> basisFuncDimer, Eigen::VectorXd OE);
 
 }  // namespace catnip
 #endif  // _CATNIP_QC_FUNCTIONS_HPP
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 0455c80..580c84e 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -86,8 +86,8 @@ int main(int argc, const char *argv[]) {
     Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
     
     //auto vec_P_OE = lr_P.getOE(par->getSpinP());
-    Eigen::MatrixXd mat_P_OE = Eigen::MatrixXd(lr_P.getOE(par->getSpinP()));
-    //Matrix *mat_P_OE = new Matrix(vec_P_OE);
+    Eigen::VectorXd vec_P_OE = Eigen::VectorXd(lr_P.getOE(par->getSpinP()));
+    //Matrix *vec_P_OE = new Matrix(vec_P_OE);
 
     int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
     LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
@@ -134,7 +134,7 @@ int main(int argc, const char *argv[]) {
 
     LOG("Creating transfercomplex", 1);
     TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, Orbs1, Orbs2, mat_S,
-                       mat_P_OE, par->getCounterPoise());
+                       vec_P_OE, par->getCounterPoise());
 
     // Set the transfer complex to counterpoise if it is the case.
 
@@ -178,7 +178,9 @@ int main(int argc, const char *argv[]) {
     orbitalnums["mon2"] = par->getOrbNum2();
 
     LOG("Calculating transfer integral", 1);
-    TC.calcJ(orbitaltypes, orbitalnums);
+    TC.calcJ();
+    TC.printTransferIntegral(orbitaltypes, orbitalnums);
+
   }
 
   return 0;

From f99db21aaa596b69ec2a08065547f78ed20a4ef8 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sun, 28 Apr 2019 16:37:32 -0600
Subject: [PATCH 06/68] Added matrix helper functions

---
 src/libcatnip/matrix.cpp | 80 ++++++++++++++++++++++++++++++++++++++++
 src/libcatnip/matrix.hpp | 49 ++++++++++++++++++++++++
 2 files changed, 129 insertions(+)
 create mode 100644 src/libcatnip/matrix.cpp
 create mode 100644 src/libcatnip/matrix.hpp

diff --git a/src/libcatnip/matrix.cpp b/src/libcatnip/matrix.cpp
new file mode 100644
index 0000000..14f2af0
--- /dev/null
+++ b/src/libcatnip/matrix.cpp
@@ -0,0 +1,80 @@
+
+#include <sstream>
+#include <stdexcept>
+#include <string>
+#include <vector>
+#include <Eigen/Dense>
+
+#include "matrix.hpp"
+
+using namespace std;
+
+namespace catnip {
+
+string double_tos(double f, int nd) {
+  ostringstream ostr;
+  int tens = stod("1" + string(nd, '0'));
+  ostr << round(f * tens) / tens;
+  return ostr.str();
+}
+
+vector<int> matchRow(const Matrix & mat1, const Matrix & mat2, const int sf) {
+
+  if (mat1.cols() != mat2.cols()) {
+    throw invalid_argument(
+        "match function only works when matrices have same number of columns");
+  }
+  vector<int> m_vec(mat1.rows(), -1);
+
+  for (int i = 0; i < mat1.rows(); ++i) {
+    for (int ii = 0; ii < mat2.rows(); ++ii) {
+      bool match = true;
+      for (int j = 0; j < mat1.cols(); ++j) {
+        string val1 = double_tos(mat1(i, j), sf);
+        string val2 = double_tos(mat2(ii, j), sf);
+        if (val1.compare(val2) != 0) {
+          match = false;
+          break;
+        }
+      }
+      if (match) m_vec.at(i) = ii;
+    }
+  }
+  return m_vec;
+}
+
+vector<int> matchCol(const Eigen::MatrixXd & mat1,
+    const Eigen::MatrixXd &mat2, 
+    const int sf) {
+
+  if (mat1.rows() != mat2.rows()) {
+    throw invalid_argument(
+        "match function only works when matrices have same number of rows");
+  }
+  vector<int> m_vec(mat1.cols(), -1);
+
+  for (int i = 0; i < mat1.cols(); ++i) {
+    for (int ii = 0; ii < mat2.cols(); ++ii) {
+      bool match = true;
+      for (int j = 0; j < mat1.rows(); ++j) {
+        string val1 = double_tos(mat1(j, i), sf);
+        string val2 = double_tos(mat2(j, ii), sf);
+        if (val1.compare(val2) != 0) {
+          match = false;
+          break;
+        }
+      }
+      if (match) m_vec.at(i) = ii;
+    }
+  }
+  return m_vec;
+}
+
+
+
+
+
+
+
+
+}
diff --git a/src/libcatnip/matrix.hpp b/src/libcatnip/matrix.hpp
new file mode 100644
index 0000000..903327a
--- /dev/null
+++ b/src/libcatnip/matrix.hpp
@@ -0,0 +1,49 @@
+
+#ifndef MATRIX_HELPER_HPP
+#define MATRIX_HELPER_HPP
+
+namespace catnip {
+#include <vector>
+#include <Eigen/Dense>
+
+  /** 
+   * Responsible for matching the rows between two matrices Returns which row
+   * in matrix 1 matches which row in matrix 2, -1 means there is no match sf
+   * is the number of significant figures that will be checked to ensure the
+   * same value.
+   * 
+   * E.g. 
+   *
+   * Matrix 1
+   *
+   * 1.0 0.0 0.0
+   * 0.0 3.0 0.0
+   * 0.0 2.5 1.0
+   * 0.0 0.0 5.0
+   * 6.0 0.0 0.0
+   *
+   * Matrix 2 
+   *
+   * 1.0 0.0 0.0
+   * 8.0 8.0 8.0
+   * 0.0 0.0 5.0
+   *
+   * The vector returned would return 
+   *
+   * vector matched rows
+   *  0
+   * -1 // indicates no match
+   *  3 
+   **/ 
+  std::vector<int> matchRow(
+      const Eigen::MatrixXd &mat1, 
+      const Eigen::MatrixXd &mat2, 
+      const int sig_fig);
+
+  std::vector<int> matchCol(
+      const Eigen::MatrixXd &mat1, 
+      const Eigen::MatrixXd &mat2, 
+      const int sig_fig);
+
+} // namespace catnip
+#endif // MATRIX_HELPER_HPP

From e77984a944b0ec9a209f768ec3e254cb75941c91 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sun, 28 Apr 2019 16:37:57 -0600
Subject: [PATCH 07/68] Updated tests and qc_functions.cpp

---
 src/libcatnip/qc_functions.cpp  | 248 ++++++++++++--------------------
 src/tests/test_logreader.cpp    |   2 +-
 src/tests/test_qc_functions.cpp | 228 +++++++++++++++--------------
 3 files changed, 208 insertions(+), 270 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index 3cb76b8..be8bbdb 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -23,32 +23,16 @@ unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
 
   vector<pair<double, string>> all;
 
-  //auto m_a = Orb_E_Alpha.getCol(1);
-
-  /*for (int ind = 1; ind <= m_a.get_rows(); ind++) {
-    auto val = m_a.get_elem(ind);
-    pair<double, string> pr(val, "Alpha");
-    all.push_back(pr);
-  }*/
   for( double & val : Orb_E_Alpha){
     all.push_back(pair<double, string>(val,"Alpha"));
   }
 
-  //if (Orb_E_Beta.get_cols() > 0) {
-  //  auto m_b = Orb_E_Beta.getCol(1);
-  
-  //  for (int ind = 1; ind <= m_b.get_rows(); ind++) {
-    for( double & val : Orb_E_Beta ){ 
-      //auto val = m_b.get_elem(ind);
-      //pair<double, string> pr(val, "Beta");
-      //all.push_back(pr);
-      all.push_back(pair<double, string>(val, "Beta"));
-    }
- // }
-  // Sort the vectors
+  for( double & val : Orb_E_Beta ){ 
+    all.push_back(pair<double, string>(val, "Beta"));
+  }
   sort(all.begin(), all.end(),
-       [](const pair<double, string> &P1, const pair<double, string> &P2)
-           -> bool { return P1.first < P2.first; });
+      [](const pair<double, string> &P1, const pair<double, string> &P2)
+      -> bool { return P1.first < P2.first; });
   // Now that they are sorted we are going to update the ranks
   int rank = 1;
 
@@ -64,87 +48,40 @@ unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
 // Essentially calculates the transfer integral
 void TransferComplex::calculate_transfer_integral_() {
 
-  //Matrix mat_1_Coefinv = mat_1_Coef.invert();
-  //Matrix mat_2_Coefinv = mat_2_Coef.invert();
-  //Matrix mat_P_Coefinv = mat_P_Coef.invert();
-
   auto dimension = mat_1_Coef.rows()+mat_2_Coef.rows();
   Eigen::MatrixXd zetaA(dimension,dimension);
   Eigen::MatrixXd zetaB(dimension,dimension);
   if (counterPoise_) {
     LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
-    //zetaA = (mat_1_Coefinv);
-    //zetaB = (mat_2_Coefinv);
     zetaA = mat_1_Coef();
     zetaB = mat_2_Coef();
   } else {
     LOG("Creating zeta matrices from coefficients", 2);
-   // Matrix zerosA(mat_1_Coefinv.get_rows(), 1, mat_1_Coefinv.get_shel());
-    //Matrix zerosB(mat_2_Coefinv.get_rows(), 1, mat_2_Coefinv.get_shel());
-    //zetaA = Matrix_concatenate_rows(mat_1_Coefinv, zerosB);
-    //zetaB = Matrix_concatenate_rows(zerosA, mat_2_Coefinv);
-    //zetaA.resize(mat_1_Coef.rows()+mat_2_Coef.rows(),1);
-    //zetaB.resize(mat_1_Coef.rows()+mat_2_Coef.rows(),1);
-    zetaA << mat_1_Coef(), Eigen::MatrixXd.Zeros(mat_1_Coef.rows(),mat_2_Coef.cols()); 
-    zetaA << Eigen::MatrixXd.Zeros(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef(); 
+    zetaA << mat_1_Coef(), Eigen::MatrixXd::Zeros(mat_1_Coef.rows(),mat_2_Coef.cols()); 
+    zetaA << Eigen::MatrixXd::Zeros(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef(); 
   }
-  //Matrix zetaAinv = zetaA.invert();
-  //Matrix zetaBinv = zetaB.invert();
-
-  //LOG("Creating intermediate matrix", 3);
-  //Matrix Inter = mat_S * mat_P_Coefinv;
-  //MatrixXd Inter = mat_S * mat_P_Coefinv;
 
   LOG("Creating gamma and beta matrices", 2);
-  //Matrix gammaA = zetaAinv * Inter;
-  //Matrix gammaB = zetaBinv * Inter;
   Eigen::MatrixXd gammaA = zetaA * mat_S * mat_P_Coef.transpose(); 
   Eigen::MatrixXd gammaB = zetaB * mat_S * mat_P_Coef.transpose(); 
 
-  //Matrix gammaA_inv = gammaA.invert();
-  //Matrix gammaB_inv = gammaB.invert();
 
   LOG("Calculating S_AB", 2);
-  //Matrix S_AB = gammaB * gammaA_inv;
   Eigen::MatrixXd S_AB = gammaB * gammaA.transpose();
   Eigen::MatrixXd S_AB_inv_sqrt = S_AB.operatorInverseSqrt();
 
-  //Matrix Energy = Matrix_diag(mat_P_OE);
   Eigen::MatrixXd Energy = vec_P_OE.asDiagona();
 
   Eigen::MatrixXd Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
  
   Eigen::MatrixXd Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt.transpose();  
   
-/*  Matrix J_AB = gammaB * (Energy * gammaA_inv);
-
-  Matrix e_B = gammaB * (Energy * gammaB_inv);
-  Matrix e_A = gammaA * (Energy * gammaA_inv);
-
-  double J_ab = J_AB.get_elem(1, 1);
-  double e_b = e_B.get_elem(1, 1);
-  double e_a = e_A.get_elem(1, 1);
-  double S_ab = S_AB.get_elem(1, 1);
-
-  double J_eff = (J_ab - 1 / ((double)2) * (e_b + e_a) * S_ab);
-  J_eff = J_eff / ((double)(1 - pow(S_ab, 2)));
-
-  cout << "J_ab  " << J_ab * hartreeToeV << " eV\n";
-  cout << "e_a   " << e_a * hartreeToeV << " eV\n";
-  cout << "e_b   " << e_b * hartreeToeV << " eV\n";
-  cout << "S_ab  " << S_ab << "\n";
-  cout << "J_eff " << J_eff * hartreeToeV << " eV\n";
-  return J_eff;
-*/
 }
 
 void TransferComplex::printTransferIntegral(
     const map<string, string> &orbitaltype,
     const map<string, int> &orbnum) const {
 
-  //Matrix mat1coef;
-  //Matrix mat2coef;
-
   string HOMO_OR_LUMO_A = orbitaltype.at("mon1");
   int MO_A = orbnum.at("mon1");
   if (HOMO_OR_LUMO_A.compare("HOMO") == 0) {
@@ -161,7 +98,6 @@ void TransferComplex::printTransferIntegral(
                    to_string(Orbs1.second) + " HOMO orbitals";
       throw invalid_argument(err);
     }
-    //mat1coef = mat_1_Coef->getRow(Orbs1.second + MO_A);
   } else if (HOMO_OR_LUMO_A.compare("LUMO") == 0) {
     if (MO_A < 0) {
       throw invalid_argument(
@@ -176,7 +112,6 @@ void TransferComplex::printTransferIntegral(
                    to_string(allowed_LUMO) + " LUMO orbitals";
       throw invalid_argument(err);
     }
-    //mat1coef = mat_1_Coef->getRow(Orbs1.second + MO + 1);
   } else {
     throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
   }
@@ -196,7 +131,6 @@ void TransferComplex::printTransferIntegral(
                    to_string(Orbs2.second) + " HOMO orbitals";
       throw invalid_argument(err);
     }
-    //mat2coef = mat_2_Coef->getRow(Orbs2.second + MO_B);
   } else if (HOMO_OR_LUMO_B.compare("LUMO") == 0) {
     if (MO_B < 0) {
       throw invalid_argument(
@@ -211,7 +145,6 @@ void TransferComplex::printTransferIntegral(
                    to_string(allowed_LUMO) + " LUMO orbitals";
       throw invalid_argument(err);
     }
-    //mat2coef = mat_2_Coef->getRow(Orbs2.second + MO_B + 1);
   } else {
     throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
   }
@@ -330,16 +263,17 @@ bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital)
 //   1 2         3
 //   3 4         5
 //
-list<MatrixXd> splitMatrixIntoList(const vector<int> &subMatrixDimension,
-                                   const MatrixXd const mat,
-                                   const string &ColRowSplit) {
+list<Eigen::MatrixXd> splitMatrixIntoList(
+    const vector<int> &subMatrixDimension,
+    const Eigen::MatrixXd const mat,
+    const string &ColRowSplit) {
 
-  list<MatrixXd> list_matrix;
+  list<Eigen::MatrixXd> list_matrix;
   int num_sub_matrices = subMatrixDimension.size();
   if (ColRowSplit.compare("Columns") == 0) {
     int col = 0;
     for (int i = 0; i < num_sub_matrices; ++i) {
-      MatrixXd mat_new(mat.rows(), subMatrixDimension.at(i));
+      Eigen::MatrixXd mat_new(mat.rows(), subMatrixDimension.at(i));
       for (auto k = 0; k < mat.rows(); ++k) {
         for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
           mat_new(k,j) = mat(k, col + j);
@@ -351,8 +285,8 @@ list<MatrixXd> splitMatrixIntoList(const vector<int> &subMatrixDimension,
   } else if (ColRowSplit.compare("Rows") == 0) {
     int row = 0;
     for (auto i = 0; i < num_sub_matrices; ++i) {
-      MatrixXd mat_new(subMatrixDimension.at(i), mat.cols());
-      for (auto k = 0; k < mat->get_cols(); ++k) {
+      Eigen::MatrixXd mat_new(subMatrixDimension.at(i), mat.cols());
+      for (auto k = 0; k < mat.cols(); ++k) {
         for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
           mat_new(j,k) = mat(row + j, k);
         }
@@ -366,7 +300,7 @@ list<MatrixXd> splitMatrixIntoList(const vector<int> &subMatrixDimension,
   return list_matrix;
 }
 
-list<MatrixXd> splitCoefsUpByAtoms(const vector<int> & basisFuncP, MatrixXd Coefs,
+list<Eigen::MatrixXd> splitCoefsUpByAtoms(const vector<int> & basisFuncP, Eigen::MatrixXd Coefs,
                                    const string & ColRow) {
   return splitMatrixIntoList(basisFuncP, Coefs, ColRow);
 }
@@ -521,77 +455,77 @@ void refreshSwapOrder(vector<pair<int, int>> &monAmatch) {
 // then actually implements the swaps by exchanging the matrices in the list.
 void updateSwapLists(vector<pair<int, int>> &monBmatch,
                      vector<pair<int, int>> &monAmatch,
-                     list<Matrix *> &p_atom_mat_coef) {
+                     list<Eigen::MatrixXd> &p_atom_mat_coef) {
 
   for (auto p : monBmatch) {
     if (p.first != p.second) {
       auto it = p_atom_mat_coef.begin();
-      Matrix *temp = *(next(it, p.first - 1));
-      *(next(it, p.first - 1)) = *(next(it, p.second - 1));
-      *(next(it, p.second - 1)) = temp;
+      Eigen::MatrixXd & temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
     }
   }
   for (auto p : monAmatch) {
     if (p.first != p.second) {
       auto it = p_atom_mat_coef.begin();
-      Matrix *temp = *(next(it, p.first - 1));
-      *(next(it, p.first - 1)) = *(next(it, p.second - 1));
-      *(next(it, p.second - 1)) = temp;
+      Eigen::MatrixXd & temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
     }
   }
   return;
 }
 void updateSwapLists(vector<pair<int, int>> &monAmatch,
-                     list<Matrix *> &atom_mat_coef) {
+                     list<Eigen::MatrixXd> &atom_mat_coef) {
 
   for (auto p : monAmatch) {
     if (p.first != p.second) {
       auto it = atom_mat_coef.begin();
-      Matrix *temp = *(next(it, p.first - 1));
-      *(next(it, p.first - 1)) = *(next(it, p.second - 1));
-      *(next(it, p.second - 1)) = temp;
+      Eigen::MatrixXd & temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
     }
   }
   return;
 }
 
-Matrix *mergeListOfMatrices(list<Matrix *> &matrix_list, const int rows,
+Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const int rows,
                             const int cols, const string &ColRowMerge) {
 
-  Matrix *full_matrix = new Matrix(rows, cols);
+  Eigen::MatrixXd full_matrix(rows, cols);
   if (ColRowMerge.compare("Columns") == 0) {
     int col = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
-      Matrix *mat_ptr = *it;
-      int row = 1;
+      Eigen::MatrixXd & mat = *it;
+      int row = 0;
       if (col > cols)
         throw runtime_error("Your new matrix is not large enough");
-      for (auto i = 1; i <= mat_ptr->get_rows(); ++i) {
+      for (auto i = 0; i < mat.rows(); ++i) {
         if (row > rows)
           throw runtime_error("Your new matrix is not large enough");
-        for (auto j = 1; j <= mat_ptr->get_cols(); ++j) {
-          full_matrix->set_elem(mat_ptr->get_elem(i, j), row, j + col);
+        for (auto j = 0; j < mat.cols(); ++j) {
+          full_matrix(row,j+col) = mat(i, j);
         }
         ++row;
       }
-      col += mat_ptr->get_cols();
+      col += mat.cols();
     }
   } else if (ColRowMerge.compare("Rows") == 0) {
     int row = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
-      Matrix *mat_ptr = *it;
-      int col = 1;
+      Matrix *mat = *it;
+      int col = 0;
       if (row > rows)
         throw runtime_error("Your new matrix is not large enough");
-      for (auto j = 1; j <= mat_ptr->get_cols(); ++j) {
+      for (auto j = 0; j < mat.cols(); ++j) {
         if (col > cols)
           throw runtime_error("Your new matrix is not large enough");
-        for (auto i = 1; i <= mat_ptr->get_rows(); ++i) {
-          full_matrix->set_elem(mat_ptr->get_elem(i, j), row + i, col);
+        for (auto i = 0; i < mat.rows(); ++i) {
+          full_matrix(row + i, col) = mat(i, j);
         }
         ++col;
       }
-      row += mat_ptr->get_rows();
+      row += mat.rows();
     }
   } else {
     throw invalid_argument("Unrecognized merge type for list of matrices");
@@ -600,22 +534,24 @@ Matrix *mergeListOfMatrices(list<Matrix *> &matrix_list, const int rows,
 }
 
 // This function
-Matrix *createNewMatrix(list<Matrix *> &p_atom_mat_coef, int rows, int cols,
+Eigen::MatrixXd createNewMatrix(list<Eigen::MatrixXd> &p_atom_mat_coef, int rows, int cols,
                         const string &ColRow) {
   return mergeListOfMatrices(p_atom_mat_coef, rows, cols, ColRow);
 }
 
 // unscramble the coefficients
-Matrix *unscramble_Coef(const std::vector<int> &matchDimerA,
-                        const std::vector<int> &matchDimerB,
-                        const std::vector<int> &basisFuncP, Matrix *dimerCoef) {
+Eigen::MatrixXd unscramble_Coef(
+    const std::vector<int> &matchDimerA,
+    const std::vector<int> &matchDimerB,
+    const std::vector<int> &basisFuncP, 
+    const Eigen::MatrixXd & dimerCoef) {
 
   // Let's reduce the complexity of the problem by instead of working
   // with the basis functions lets just work with the atoms. We can do
   // this by treating all the basis functions associated with a single
   // atom as a block.
 
-  list<Matrix *> p_atom_mat_coef =
+  list<Eigen::MatrixXd> p_atom_mat_coef =
       splitCoefsUpByAtoms(basisFuncP, dimerCoef, "Columns");
 
   // Place all of monomer A atom basis functions on the left side of the
@@ -625,33 +561,36 @@ Matrix *unscramble_Coef(const std::vector<int> &matchDimerA,
   // Second int is the col in the dimer the atom is presently at
 
   vector<pair<int, int>> monAmatch;
-  for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
-    pair<int, int> pr(i, matchDimerA.at(i - 1));
+  for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+    pair<int, int> pr(i, matchDimerA.at(i));
     monAmatch.push_back(pr);
   }
   vector<pair<int, int>> monBmatch;
-  for (unsigned i = 1; i <= matchDimerB.size(); ++i) {
-    pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i - 1));
+  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+    pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
     monBmatch.push_back(pr);
   }
 
   refreshSwapOrder(monBmatch, monAmatch);
   updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
-  Matrix *dimerCoef_new = createNewMatrix(
-      p_atom_mat_coef, dimerCoef->get_rows(), dimerCoef->get_cols(), "Columns");
+  Eigen::MatrixXd dimerCoef_new = createNewMatrix(
+      p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
+
   return dimerCoef_new;
 }
 
 // unscramble the coefficients
-Matrix *unscramble_Coef(const std::vector<int> &matchDimerB,
-                        const std::vector<int> &basisFuncB, Matrix *Coef) {
+Eigen::MatrixXd unscramble_Coef(
+    const std::vector<int> &matchDimerB,
+    const std::vector<int> &basisFuncB,
+    const Eigen::MatrixXd & Coef) {
 
   // Let's reduce the complexity of the problem by instead of working
   // with the basis functions lets just work with the atoms. We can do
   // this by treating all the basis functions associated with a single
   // atom as a block.
 
-  list<Matrix *> atom_mat_coef =
+  list<MatrixXd> atom_mat_coef =
       splitCoefsUpByAtoms(basisFuncB, Coef, "Columns");
 
   // Place all of monomer A atom basis functions on the left side of the
@@ -661,15 +600,15 @@ Matrix *unscramble_Coef(const std::vector<int> &matchDimerB,
   // Second int is the col in the dimer the atom is presently at
 
   vector<pair<int, int>> monBmatch;
-  for (unsigned i = 1; i <= matchDimerB.size(); ++i) {
-    pair<int, int> pr(i, matchDimerB.at(i - 1));
+  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+    pair<int, int> pr(i, matchDimerB.at(i));
     monBmatch.push_back(pr);
   }
 
   refreshSwapOrder(monBmatch);
   updateSwapLists(monBmatch, atom_mat_coef);
-  Matrix *Coef_new = createNewMatrix(atom_mat_coef, Coef->get_rows(),
-                                     Coef->get_cols(), "Columns");
+  Eigen::MatrixXd Coef_new = createNewMatrix(atom_mat_coef, Coef.rows(),
+                                     Coef.cols(), "Columns");
   return Coef_new;
 }
 
@@ -677,48 +616,49 @@ Matrix *unscramble_Coef(const std::vector<int> &matchDimerB,
 // and columns
 Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
                      const std::vector<int> &matchDimerB,
-                     const std::vector<int> &basisFuncP, const MatrixXd & S) {
+                     const std::vector<int> &basisFuncP, 
+                     const Eigen::MatrixXd & S) {
 
   Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
-    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
 
     vector<pair<int, int>> monAmatch;
-    for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
-      pair<int, int> pr(i, matchDimerA.at(i - 1));
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
       monAmatch.push_back(pr);
     }
     vector<pair<int, int>> monBmatch;
-    for (unsigned i = 1; i <= matchDimerB.size(); ++i) {
-      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i - 1));
+    for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
       monBmatch.push_back(pr);
     }
 
     refreshSwapOrder(monBmatch, monAmatch);
     updateSwapLists(monBmatch, monAmatch, p_atom_mat_S);
     S_new =
-        createNewMatrix(p_atom_mat_S, S->get_rows(), S->get_cols(), "Columns");
+        createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Columns");
   }
 
   S = S_new;
 
   {
-    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
 
     vector<pair<int, int>> monAmatch;
-    for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
-      pair<int, int> pr(i, matchDimerA.at(i - 1));
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
       monAmatch.push_back(pr);
     }
     vector<pair<int, int>> monBmatch;
-    for (unsigned i = 1; i <= matchDimerB.size(); ++i) {
-      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i - 1));
+    for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
       monBmatch.push_back(pr);
     }
 
     refreshSwapOrder(monBmatch, monAmatch);
     updateSwapLists(monBmatch, monAmatch, p_atom_mat_S);
-    S_new = createNewMatrix(p_atom_mat_S, S->get_rows(), S->get_cols(), "Rows");
+    S_new = createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Rows");
   }
 
   // Return the correctly swapped dimerCoef
@@ -728,38 +668,38 @@ Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
 // Same as the above function but here we are assuming counterpoise correction
 // is being used and thus we do not need to match with both monomer A and
 // monomer B but only need to match with A.
-Matrix *unscramble_S(const std::vector<int> &matchDimerA,
-                     const std::vector<int> &basisFuncP, Matrix *S) {
+Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
+                     const std::vector<int> &basisFuncP, Eigen::MatrixXd & S) {
 
-  Matrix *S_new;
+  MatrixXd & S_new(S.rows(),S.cols());
   {
-    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
 
     vector<pair<int, int>> monAmatch;
-    for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
-      pair<int, int> pr(i, matchDimerA.at(i - 1));
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
       monAmatch.push_back(pr);
     }
     refreshSwapOrder(monAmatch);
     updateSwapLists(monAmatch, p_atom_mat_S);
     S_new =
-        createNewMatrix(p_atom_mat_S, S->get_rows(), S->get_cols(), "Columns");
+        createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Columns");
   }
 
   S = S_new;
 
   {
-    list<MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
 
     vector<pair<int, int>> monAmatch;
-    for (unsigned i = 1; i <= matchDimerA.size(); ++i) {
-      pair<int, int> pr(i, matchDimerA.at(i - 1));
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
       monAmatch.push_back(pr);
     }
 
     refreshSwapOrder(monAmatch);
     updateSwapLists(monAmatch, p_atom_mat_S);
-    S_new = createNewMatrix(p_atom_mat_S, S->get_rows(), S->get_cols(), "Rows");
+    S_new = createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Rows");
   }
 
   // Return the correctly swapped dimerCoef
@@ -774,28 +714,28 @@ TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2C
   unscrambled_ = false;
   counterPoise_ = cp;
   // Consistency check
-  if (matS->get_cols() != matPCoef->get_cols()) {
+  if (matS.cols() != matPCoef.cols()) {
     throw invalid_argument(
         "The overlap matrix must have the same number "
         "of basis functions as the dimer");
   }
   if (cp) {
-    if (mat1Coef->get_cols() != matPCoef->get_cols()) {
+    if (mat1Coef.cols() != matPCoef.cols()) {
       throw invalid_argument(
           "Counter poise correction requires that the"
           " monomers have the same number of coefficients as the dimer. "
           "Your monomer 1 does not");
     }
-    if (mat2Coef->get_cols() != matPCoef->get_cols()) {
+    if (mat2Coef.cols() != matPCoef.cols()) {
       throw invalid_argument(
           "Counter poise correction requires that the"
           " monomers have the same number of coefficients as the dimer. "
           "Your monomer 2 does not");
     }
   } else {
-    int total_cols = mat1Coef->get_cols() + mat2Coef->get_cols();
+    int total_cols = mat1Coef.cols() + mat2Coef.cols();
 
-    if (total_cols > matPCoef->get_cols()) {
+    if (total_cols > matPCoef.cols()) {
       throw invalid_argument(
           "Counter poise has not been specified and your "
           "monomers have more basis function cols than your dimer");
diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index dfca2cc..be908eb 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -25,7 +25,7 @@ int main(void) {
     auto orb_info = lr.getOrbitalInfo();
 
     auto Soverlap = lr.getOverlapMatrix();
-    cout << Soverlap->get_rows() << endl;
+    cout << Soverlap.rows() << endl;
     auto Alpha = lr.getOE("Alpha");
 
     auto basisFuncCount = lr.getBasisFuncCount();
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index 0f94b9a..237901e 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -1,9 +1,9 @@
-#include "../libcatnip/matrix.hpp"
+//#include "../libcatnip/matrix.hpp"
 #include "../libcatnip/qc_functions.hpp"
 #include <cassert>
 #include <iostream>
 #include <vector>
-
+#include <Eigen/Dense>
 using namespace catnip;
 using namespace std;
 
@@ -11,20 +11,21 @@ int main(void) {
 
   cout << "Testing: unscramble_Coef" << endl;
   {
-    Matrix* dimerCoef = new Matrix(8, 8);
-    for (int i = 1; i <= 8; ++i) {
-      dimerCoef->set_elem(1.3, i, 1);
-      dimerCoef->set_elem(0.2, i, 3);
-      dimerCoef->set_elem(82.4, i, 4);
-      dimerCoef->set_elem(9.4, i, 5);
-      dimerCoef->set_elem(3.4, i, 6);
-      dimerCoef->set_elem(-3.0, i, 8);
+    Eigen::MatrixXd dimerCoef = Eigen::MatrixXd::Zero(8, 8);
+    for (int i = 0; i < 8; ++i) {
+      dimerCoef(i, 0) = 1.3;
+      dimerCoef(i, 2) = 0.2;
+      dimerCoef(i, 3) = 82.4;
+      dimerCoef(i, 4) = 9.4;
+      dimerCoef(i, 5) = 3.4;
+      dimerCoef(i, 7) = -3.0;
     }
 
     // Our coefficient matrix should look like this
     //
-    //         col 1  col 2  col 3  col 4  col 5  col 6  col 7  col 8
+    //         col 0  col 1  col 2  col 3  col 4  col 5  col 6  col 7
     //        _______________________________________________________
+    // row 0 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     // row 1 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     // row 2 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     // row 3 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
@@ -32,51 +33,49 @@ int main(void) {
     // row 5 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     // row 6 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     // row 7 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
-    // row 8 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
     //         atm3   atm1   atm1   atm5   atm4   atm4   atm2   atm2
 
     // Contains the x y and z position of atoms in monomer A
-    Matrix* coordA = new Matrix(2, 3);
+    Eigen::MatrixXd coordA(2, 3);
     // Atom 1 at (1.0,1.0,1.0)
     // Atom 2 at (0.0,0.0,0.0)
-    coordA->set_elem(1.0, 1, 1);
-    coordA->set_elem(1.0, 1, 2);
-    coordA->set_elem(1.0, 1, 3);
+    coordA << 1.0, 1.0, 1.0,
+              0.0, 0.0, 0.0;
 
     // Contains the x y and z position of atoms in monomer B
-    Matrix* coordB = new Matrix(3, 3);
+    Eigen::MatrixXd coordB(3, 3);
     // Atom 3 at (1.0,0.0,0.0)
     // Atom 4 at (2.0,0.0,0.0)
     // Atom 5 at (3.0,0.0,0.0)
-    coordB->set_elem(1.0, 1, 1);
-    coordB->set_elem(2.0, 2, 1);
-    coordB->set_elem(3.0, 3, 1);
+    coordB << 1.0, 0.0, 0.0,
+              2.0, 0.0, 0.0,
+              3.0, 0.0, 0.0;
 
-    Matrix* coordDimer = new Matrix(5, 3);
+    Eigen::MatrixXd coordDimer(5, 3);
     // Arrange atoms in the dimer so they do not appear in the
     // same order as the monomers
 
-    // row1 Atom 3
-    coordDimer->set_elem(1.0, 1, 1);
-    // row2 Atom 1
-    coordDimer->set_elem(1.0, 2, 1);
-    coordDimer->set_elem(1.0, 2, 2);
-    coordDimer->set_elem(1.0, 2, 3);
-    // row3 Atom 5
-    coordDimer->set_elem(3.0, 3, 1);
-    // row4 Atom 4
-    coordDimer->set_elem(2.0, 4, 1);
-    // row5 Atom 2 (0.0,0.0,0.0)
+    // Atom 3   1.0, 0.0, 0.0
+    // Atom 1   1.0, 1.0, 1.0
+    // Atom 5   3.0, 0.0, 0.0
+    // Atom 4   2.0, 0.0, 0.0
+    // Atom 2   0.0, 0.0, 0.0
 
-    vector<int> matchA = coordA->matchRow(*coordDimer, 2);
-    vector<int> matchB = coordB->matchRow(*coordDimer, 2);
+    coordDimer << 1.0, 0.0, 0.0,
+                  1.0, 1.0, 1.0,
+                  3.0, 0.0, 0.0,
+                  2.0, 0.0, 0.0,
+                  0.0, 0.0, 0.0;
 
-    assert(matchA.at(0) == 2);
-    assert(matchA.at(1) == 5);
+    vector<int> matchA = matchRow(coordA,coordDimer, 2);
+    vector<int> matchB = matchRow(coordB,coordDimer, 2);
 
-    assert(matchB.at(0) == 1);
+    assert(matchA.at(0) == 1);
+    assert(matchA.at(1) == 4);
+
+    assert(matchB.at(0) == 0);
     assert(matchB.at(1) == 4);
-    assert(matchB.at(2) == 3);
+    assert(matchB.at(2) == 2);
 
     vector<int> basisFuncDimer;
     // Basis functions per atom
@@ -103,8 +102,9 @@ int main(void) {
 
     // According to the basis functions and the atom positions the current
     // coef table for monomer A should look like this
-    //         col 1  col 2  col 3  col 4
+    //         col 0  col 1  col 2  col 3
     //        ____________________________
+    // row 0 |  0.0    0.2    0.0   -3.0
     // row 1 |  0.0    0.2    0.0   -3.0
     // row 2 |  0.0    0.2    0.0   -3.0
     // row 3 |  0.0    0.2    0.0   -3.0
@@ -112,7 +112,6 @@ int main(void) {
     // row 5 |  0.0    0.2    0.0   -3.0
     // row 6 |  0.0    0.2    0.0   -3.0
     // row 7 |  0.0    0.2    0.0   -3.0
-    // row 8 |  0.0    0.2    0.0   -3.0
     //         atm1   atm1   atm2   atm2
 
     cerr << "Before passing in" << endl;
@@ -122,7 +121,8 @@ int main(void) {
     // If we correct the dimer coefficient matrix to line up with the
     // coefficients of the monomers it should look like this
     //
-    //        Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7   Col 8
+    //        Col 0   Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7
+    // Row 0   1.3     9.4     3.4     82.4    0       0.2     0       -3
     // Row 1   1.3     9.4     3.4     82.4    0       0.2     0       -3
     // Row 2   1.3     9.4     3.4     82.4    0       0.2     0       -3
     // Row 3   1.3     9.4     3.4     82.4    0       0.2     0       -3
@@ -130,101 +130,99 @@ int main(void) {
     // Row 5   1.3     9.4     3.4     82.4    0       0.2     0       -3
     // Row 6   1.3     9.4     3.4     82.4    0       0.2     0       -3
     // Row 7   1.3     9.4     3.4     82.4    0       0.2     0       -3
-    // Row 8   1.3     9.4     3.4     82.4    0       0.2     0       -3
 
     cerr << "Calling unscramble" << endl;
-    auto NewCoef = unscramble_Coef(matchB, matchA, basisFuncDimer, dimerCoef);
-
-    cerr << *NewCoef << endl;
-
-    for (int i = 1; i <= 8; ++i) {
-      assert(static_cast<int>(NewCoef->get_elem(i, 1) * 10) == 13);
-      assert(static_cast<int>(NewCoef->get_elem(i, 2) * 10) == 94);
-      assert(static_cast<int>(NewCoef->get_elem(i, 3) * 10) == 34);
-      assert(static_cast<int>(NewCoef->get_elem(i, 4) * 10) == 824);
-      assert(static_cast<int>(NewCoef->get_elem(i, 5)) == 0);
-      assert(static_cast<int>(NewCoef->get_elem(i, 6) * 10) == 2);
-      assert(static_cast<int>(NewCoef->get_elem(i, 7)) == 0);
-      assert(static_cast<int>(NewCoef->get_elem(i, 8)) == -3);
+    Eigen::MatrixXd NewCoef = unscramble_Coef(matchB, matchA, basisFuncDimer, dimerCoef);
+
+    cerr << NewCoef << endl;
+
+    for (int i = 0; i < 8; ++i) {
+      assert(static_cast<int>(NewCoef(i, 0) * 10) == 13);
+      assert(static_cast<int>(NewCoef(i, 1) * 10) == 94);
+      assert(static_cast<int>(NewCoef(i, 2) * 10) == 34);
+      assert(static_cast<int>(NewCoef(i, 3) * 10) == 824);
+      assert(static_cast<int>(NewCoef(i, 4)) == 0);
+      assert(static_cast<int>(NewCoef(i, 5) * 10) == 2);
+      assert(static_cast<int>(NewCoef(i, 6)) == 0);
+      assert(static_cast<int>(NewCoef(i, 7)) == -3);
     }
   }
 
   cout << "Testing: unscramble_S_Coef" << endl;
   {
-    Matrix* SCoef = new Matrix(8, 8);
-    for (int i = 1; i <= 8; ++i) {
-      SCoef->set_elem(1.3, i, 2);
-      SCoef->set_elem(1.3, i, 3);
-      SCoef->set_elem(4.0, i, 4);
+    Eigen::MatrixXd SCoef = Eigen::MatrixXd::Zero(8, 8);
+    for (int i = 0; i < 8; ++i) {
+      SCoef(i, 1) = 1.3;
+      SCoef(i, 2) = 1.3;
+      SCoef(i, 3) = 4.0;
     }
 
-    for (int i = 1; i <= 8; ++i) {
-      SCoef->set_elem(1.3, 2, i);
-      SCoef->set_elem(1.3, 3, i);
-      SCoef->set_elem(4.0, 4, i);
+    for (int i = 0; i < 8; ++i) {
+      SCoef(1, i) = 1.3;
+      SCoef(2, i) = 1.3;
+      SCoef(3, i) = 4.0;
     }
 
-    SCoef->set_elem(6.0, 2, 4);
-    SCoef->set_elem(6.0, 3, 4);
-    SCoef->set_elem(6.0, 4, 2);
-    SCoef->set_elem(6.0, 4, 3);
+    SCoef(1, 3) = 6.0;
+    SCoef(2, 3) = 6.0;
+    SCoef(3, 1) = 6.0;
+    SCoef(3, 2) = 6.0;
 
     // Our coefficient matrix should look like this
     //
-    //               col 1  col 2  col 3  col 4  col 5  col 6  col 7  col 8
+    //               col 0  col 1  col 2  col 3  col 4  col 5  col 6  col 7
     //              _______________________________________________________
-    // atm 3 row 1 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 3 row 0 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 1 row 1 |  1.3    1.3    1.3    6.0    1.3    1.3    1.3    1.3
     // atm 1 row 2 |  1.3    1.3    1.3    6.0    1.3    1.3    1.3    1.3
-    // atm 1 row 3 |  1.3    1.3    1.3    6.0    1.3    1.3    1.3    1.3
-    // atm 5 row 4 |  4.0    6.0    6.0    4.0    4.0    4.0    4.0    4.0
+    // atm 5 row 3 |  4.0    6.0    6.0    4.0    4.0    4.0    4.0    4.0
+    // atm 4 row 4 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
     // atm 4 row 5 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
-    // atm 4 row 6 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 2 row 6 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
     // atm 2 row 7 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
-    // atm 2 row 8 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
     //                atm3   atm1   atm1   atm5   atm4   atm4   atm2   atm2
 
     // Contains the x y and z position of atoms in monomer A
-    Matrix* coordA = new Matrix(2, 3);
+    Eigen::MatrixXd coordA(2, 3);
     // Atom 1 at (1.0,1.0,1.0)
     // Atom 2 at (0.0,0.0,0.0)
-    coordA->set_elem(1.0, 1, 1);
-    coordA->set_elem(1.0, 1, 2);
-    coordA->set_elem(1.0, 1, 3);
+    coordA << 1.0, 1.0, 1.0,
+              0.0, 0.0, 0.0;
 
     // Contains the x y and z position of atoms in monomer B
-    Matrix* coordB = new Matrix(3, 3);
+    Eigen::MatrixXd coordB(3, 3);
     // Atom 3 at (1.0,0.0,0.0)
     // Atom 4 at (2.0,0.0,0.0)
     // Atom 5 at (3.0,0.0,0.0)
-    coordB->set_elem(1.0, 1, 1);
-    coordB->set_elem(2.0, 2, 1);
-    coordB->set_elem(3.0, 3, 1);
+    coordB << 1.0, 0.0, 0.0,
+              2.0, 0.0, 0.0,
+              3.0, 0.0, 0.0;
 
-    Matrix* coordDimer = new Matrix(5, 3);
+    Eigen::MatrixXd coordDimer = Eigen::MatrixXd::Zero(5, 3);
     // Arrange atoms in the dimer so they do not appear in the
     // same order as the monomers
 
     // row1 Atom 3
-    coordDimer->set_elem(1.0, 1, 1);
+    coordDimer(0, 0) = 1.0;
     // row2 Atom 1
-    coordDimer->set_elem(1.0, 2, 1);
-    coordDimer->set_elem(1.0, 2, 2);
-    coordDimer->set_elem(1.0, 2, 3);
+    coordDimer(1, 0) = 1.0;
+    coordDimer(1, 1) = 1.0;
+    coordDimer(1, 2) = 1.0;
     // row3 Atom 5
-    coordDimer->set_elem(3.0, 3, 1);
+    coordDimer(2, 0) = 3.0;
     // row4 Atom 4
-    coordDimer->set_elem(2.0, 4, 1);
+    coordDimer(3, 0) = 2.0;
     // row5 Atom 2 (0.0,0.0,0.0)
 
-    vector<int> matchA = coordA->matchRow(*coordDimer, 2);
-    vector<int> matchB = coordB->matchRow(*coordDimer, 2);
+    vector<int> matchA = matchRow(coordA,coordDimer, 2);
+    vector<int> matchB = matchRow(coordB,coordDimer, 2);
 
-    assert(matchA.at(0) == 2);
-    assert(matchA.at(1) == 5);
+    assert(matchA.at(0) == 1);
+    assert(matchA.at(1) == 4);
 
-    assert(matchB.at(0) == 1);
-    assert(matchB.at(1) == 4);
-    assert(matchB.at(2) == 3);
+    assert(matchB.at(0) == 0);
+    assert(matchB.at(1) == 3);
+    assert(matchB.at(2) == 2);
 
     vector<int> basisFuncDimer;
     // Basis functions per atom
@@ -256,37 +254,37 @@ int main(void) {
     // If we correct the dimer coefficient matrix to line up with the
     // coefficients of the monomers it should look like this
     //
-    //        Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7   Col 8
+    //        Col 0   Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7
+    // Row 0   0       0       0       4       1.3     1.3     0       0
     // Row 1   0       0       0       4       1.3     1.3     0       0
     // Row 2   0       0       0       4       1.3     1.3     0       0
-    // Row 3   0       0       0       4       1.3     1.3     0       0
-    // Row 4   4       4       4       4       6       6       4       4
+    // Row 3   4       4       4       4       6       6       4       4
+    // Row 4   1.3     1.3     1.3     6       1.3     1.3     1.3     1.3
     // Row 5   1.3     1.3     1.3     6       1.3     1.3     1.3     1.3
-    // Row 6   1.3     1.3     1.3     6       1.3     1.3     1.3     1.3
+    // Row 6   0       0       0       4       1.3     1.3     0       0
     // Row 7   0       0       0       4       1.3     1.3     0       0
-    // Row 8   0       0       0       4       1.3     1.3     0       0
     cerr << "Calling unscramble" << endl;
-    auto NewCoef = unscramble_S(matchB, matchA, basisFuncDimer, SCoef);
+    Eigen::MatrixXd NewCoef = unscramble_S(matchB, matchA, basisFuncDimer, SCoef);
 
-    cerr << *NewCoef << endl;
+    cerr << NewCoef << endl;
 
-    for (int i = 1; i <= 8; ++i) {
-      if (i != 4) {
-        assert(static_cast<int>(NewCoef->get_elem(i, 5) * 10) == 13);
-        assert(static_cast<int>(NewCoef->get_elem(i, 6) * 10) == 13);
+    for (int i = 0; i < 8; ++i) {
+      if (i != 3) {
+        assert(static_cast<int>(NewCoef(i, 4) * 10) == 13);
+        assert(static_cast<int>(NewCoef(i, 5) * 10) == 13);
 
-        assert(static_cast<int>(NewCoef->get_elem(5, i) * 10) == 13);
-        assert(static_cast<int>(NewCoef->get_elem(6, i) * 10) == 13);
+        assert(static_cast<int>(NewCoef(4, i) * 10) == 13);
+        assert(static_cast<int>(NewCoef(5, i) * 10) == 13);
       }
     }
 
-    for (int i = 1; i <= 8; ++i) {
-      if (i == 5 || i == 6) {
-        assert(static_cast<int>(NewCoef->get_elem(i, 4)) == 6);
-        assert(static_cast<int>(NewCoef->get_elem(4, i)) == 6);
+    for (int i = 0; i < 8; ++i) {
+      if (i == 4 || i == 5) {
+        assert(static_cast<int>(NewCoef(i, 3)) == 6);
+        assert(static_cast<int>(NewCoef(3, i)) == 6);
       } else {
-        assert(static_cast<int>(NewCoef->get_elem(4, i)) == 4);
-        assert(static_cast<int>(NewCoef->get_elem(i, 4)) == 4);
+        assert(static_cast<int>(NewCoef(3, i)) == 4);
+        assert(static_cast<int>(NewCoef(i, 3)) == 4);
       }
     }
   }

From 8239b144a2bc48a00f7bc410c9477ae13dfd712d Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Sun, 28 Apr 2019 19:51:10 -0600
Subject: [PATCH 08/68] Fixing compiler errors

---
 CMakeLists.txt                 |  6 +++-
 src/libcatnip/io/io.hpp        |  1 -
 src/libcatnip/matrix.cpp       |  4 +--
 src/libcatnip/matrix.hpp       |  5 +--
 src/libcatnip/qc_functions.cpp | 56 +++++++++++++++++++++-------------
 src/libcatnip/qc_functions.hpp | 20 +++++-------
 src/tests/CMakeLists.txt       |  6 ++--
 src/tools/main.cpp             |  3 +-
 8 files changed, 56 insertions(+), 45 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 858a1bd..bfdae7d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,6 +42,10 @@ configure_file(
 # Find bash it is important for testing using scripts
 find_program (BASH_PROGRAM bash)
 find_library (GCOV gcov)
+find_package (Eigen3 3.3 REQUIRED NO_MODULE)
+if (TARGET Eigen3::Eigen)
+  message("-- Eigen found")
+endif(TARGET Eigen3::Eigen)
 add_definitions(-DLOG_LEVEL=${LOG_LEVEL})
 
 ##############################################################################
@@ -116,5 +120,5 @@ if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
   target_link_libraries(calc_J gcov)
   set_source_files_properties( src/tools/main.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
 endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
-target_link_libraries(calc_J libcatnip ${COMMON_LIBRARIES})
+target_link_libraries(calc_J libcatnip ${COMMON_LIBRARIES} Eigen3::Eigen)
 install( TARGETS calc_J DESTINATION bin)
diff --git a/src/libcatnip/io/io.hpp b/src/libcatnip/io/io.hpp
index ce57b8e..f38cf5d 100644
--- a/src/libcatnip/io/io.hpp
+++ b/src/libcatnip/io/io.hpp
@@ -1,6 +1,5 @@
 #ifndef _CATNIP_IO_HPP
 #define _CATNIP_IO_HPP
-#include "../matrix.hpp"
 #include "../parameters.hpp"
 #include "argumentparser.hpp"
 #include <map>
diff --git a/src/libcatnip/matrix.cpp b/src/libcatnip/matrix.cpp
index 14f2af0..d84c54d 100644
--- a/src/libcatnip/matrix.cpp
+++ b/src/libcatnip/matrix.cpp
@@ -3,7 +3,7 @@
 #include <stdexcept>
 #include <string>
 #include <vector>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 #include "matrix.hpp"
 
@@ -18,7 +18,7 @@ string double_tos(double f, int nd) {
   return ostr.str();
 }
 
-vector<int> matchRow(const Matrix & mat1, const Matrix & mat2, const int sf) {
+vector<int> matchRow(const Eigen::MatrixXd & mat1, const Eigen::MatrixXd & mat2, const int sf) {
 
   if (mat1.cols() != mat2.cols()) {
     throw invalid_argument(
diff --git a/src/libcatnip/matrix.hpp b/src/libcatnip/matrix.hpp
index 903327a..36529f6 100644
--- a/src/libcatnip/matrix.hpp
+++ b/src/libcatnip/matrix.hpp
@@ -2,9 +2,10 @@
 #ifndef MATRIX_HELPER_HPP
 #define MATRIX_HELPER_HPP
 
-namespace catnip {
 #include <vector>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
 
   /** 
    * Responsible for matching the rows between two matrices Returns which row
diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index be8bbdb..eb681a2 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -14,21 +14,23 @@
 #include "matrix.hpp"
 #include "qc_functions.hpp"
 
-using namespace std;
-
+#include <eigen3/Eigen/Dense>
+#include <eigen3/Eigen/Eigenvalues>
 namespace catnip {
 
+  using namespace std;
+
 unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
                                                   Eigen::VectorXd &Orb_E_Beta) {
 
   vector<pair<double, string>> all;
 
-  for( double & val : Orb_E_Alpha){
-    all.push_back(pair<double, string>(val,"Alpha"));
+  for( int i = 0; i<Orb_E_Alpha.size();++i){
+    all.push_back(pair<double, string>(Orb_E_Alpha(i),"Alpha"));
   }
 
-  for( double & val : Orb_E_Beta ){ 
-    all.push_back(pair<double, string>(val, "Beta"));
+  for( int i = 0; i<Orb_E_Beta.size();++i){
+    all.push_back(pair<double, string>(Orb_E_Beta(i), "Beta"));
   }
   sort(all.begin(), all.end(),
       [](const pair<double, string> &P1, const pair<double, string> &P2)
@@ -53,12 +55,12 @@ void TransferComplex::calculate_transfer_integral_() {
   Eigen::MatrixXd zetaB(dimension,dimension);
   if (counterPoise_) {
     LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
-    zetaA = mat_1_Coef();
-    zetaB = mat_2_Coef();
+    zetaA = mat_1_Coef;
+    zetaB = mat_2_Coef;
   } else {
     LOG("Creating zeta matrices from coefficients", 2);
-    zetaA << mat_1_Coef(), Eigen::MatrixXd::Zeros(mat_1_Coef.rows(),mat_2_Coef.cols()); 
-    zetaA << Eigen::MatrixXd::Zeros(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef(); 
+    zetaA << mat_1_Coef, Eigen::MatrixXd::Zero(mat_1_Coef.rows(),mat_2_Coef.cols()); 
+    zetaA << Eigen::MatrixXd::Zero(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef; 
   }
 
   LOG("Creating gamma and beta matrices", 2);
@@ -67,14 +69,19 @@ void TransferComplex::calculate_transfer_integral_() {
 
 
   LOG("Calculating S_AB", 2);
-  Eigen::MatrixXd S_AB = gammaB * gammaA.transpose();
-  Eigen::MatrixXd S_AB_inv_sqrt = S_AB.operatorInverseSqrt();
+  S_AB.resize(gammaB.rows(),gammaA.cols());
+  S_AB = gammaB * gammaA.transpose();
+  Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
+  Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
-  Eigen::MatrixXd Energy = vec_P_OE.asDiagona();
+  auto Energy = Eigen::MatrixXd::Identity(vec_P_OE.size(),vec_P_OE.size());
+  Energy *= vec_P_OE.transpose(); 
 
-  Eigen::MatrixXd Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
- 
-  Eigen::MatrixXd Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt.transpose();  
+  Hamiltonian.resize(mat_S.rows(),mat_S.cols());
+  Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
+
+  Hamiltonian_eff.resize(Hamiltonian.rows(),Hamiltonian.cols());
+  Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt.transpose();  
   
 }
 
@@ -156,7 +163,9 @@ void TransferComplex::printTransferIntegral(
 // Find the transfer integral between two orbitals. 
 // pair<string,int> string - Either HOMO or LUMO
 //                  int    - is the orbital number HOMO-3 LUMO+5
-void TransferComplex::printTransferIntegral_(pair<string,int> Orbital1, pair<string,int> Orbital2) const {
+void TransferComplex::printTransferIntegral_(
+    const pair<string,int> Orbital1,
+    const pair<string,int> Orbital2) const {
 
   int obrital1_num = 0;
   int obrital2_num = 0;
@@ -168,8 +177,8 @@ void TransferComplex::printTransferIntegral_(pair<string,int> Orbital1, pair<str
     orbital2_num = Orbital2.second;
   }
   double J_ab = Hamiltonian(orbital1_num,orbital2_num);
-  double e_a = Hamiltonaian(orbital1_num,orbital1_num);
-  double e_b = Hamiltonaian(orbital2_num,orbital2_num);
+  double e_a = Hamiltonian(orbital1_num,orbital1_num);
+  double e_b = Hamiltonian(orbital2_num,orbital2_num);
   double S_ab = S_AB(orbital1_num,orbital2_num); 
   double J_eff = Hamiltonaian_eff(orbital1_num,orbital2_num);
   cout << "J_ab  " << J_ab * hartreeToeV << " eV\n";
@@ -742,12 +751,17 @@ TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2C
     }
   }
 
+  mat_1_Coef.resize(mat1Coef.rows(),mat1Coef.cols());
   mat_1_Coef = mat1Coef;
+  mat_2_Coef.resize(mat2Coef.rows(),mat2Coef.cols());
   mat_2_Coef = mat2Coef;
+  mat_P_Coef.resize(matPCoef.rows(),matPCoef.cols());
   mat_P_Coef = matPCoef;
   Orbs1 = MOs1;
   Orbs2 = MOs2;
+  mat_S.resize(matS.rows(),matS.cols());
   mat_S = matS;
+  vec_P_OE.resize(vecPOE.size());
   vec_P_OE = vecPOE;
 }
 
@@ -801,7 +815,7 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
   }
 }
 
-double TransferComplex::calcJ() {
+void TransferComplex::calcJ() {
 
   if (unscrambled_ == false) {
     cerr << "WARNING unable to automatically line up basis functions of"
@@ -811,7 +825,7 @@ double TransferComplex::calcJ() {
          << endl;
   }
 
-  return calculate_transfer_integral_();
+  calculate_transfer_integral_();
 }
 
 }  // namespace catnip
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index 11bc0b8..b78deeb 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -8,7 +8,7 @@
 #include <vector>
 
 //#include "matrix.hpp"
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 namespace catnip {
 
@@ -53,16 +53,10 @@ class TransferComplex {
      **/
     bool orbitalValid_(const std::pair<std::string,int> & orbital) const;
 
-    void calculate_transfer_integral_(
-        const Eigen::MatrixXd & mat_1_Coef, 
-        const Eigen::MatrixXd & mat_2_Coef,
-        Eigen::MatrixXd mat_P_Coef,
-        const Eigen::MatrixXd & mat_S,
-        const Eigen::VectorXd& vec_P_OE, 
-        bool counterPoise_);
+    void calculate_transfer_integral_();
 
-    void printTransferIntegral_(std::pair<std::string,int> Orbital1,
-                               std::pair<std::string,int> Orbital2) const;
+    void printTransferIntegral_(const std::pair<std::string,int> & Orbital1,
+                                const std::pair<std::string,int> & Orbital2) const;
   public:
     TransferComplex(
         Eigen::MatrixXd mat1Coef, 
@@ -89,14 +83,14 @@ class TransferComplex {
     //
     //    monomer1 LUMO-3
     //    monomer2 HOMO
-    double calcJ(const std::map<std::string, std::string>& orbitaltype,
+    void calcJ(const std::map<std::string, std::string>& orbitaltype,
         const std::map<std::string, int>& orbitalnum);
 
     /**
      * \brief Print the transfer integral specified
      **/
-    void printTransferIntegral(std::pair<std::string,int> Orbital1,
-                               std::pair<std::string,int> Orbital2) const;
+    void printTransferIntegral(const std::pair<std::string,int> & Orbital1,
+                               const std::pair<std::string,int> & Orbital2) const;
 
     /**
      * \brief Print All info in matrix form
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index bf8fc4b..134ca4b 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -28,7 +28,7 @@ if(ENABLE_TESTS)
     if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS} )
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-    target_link_libraries(unit_${PROG} libcatnip)
+    target_link_libraries(unit_${PROG} libcatnip Eigen3::Eigen)
     add_test(unit_${PROG} unit_${PROG})
   endforeach(PROG)
 endif(ENABLE_TESTS)
@@ -44,7 +44,7 @@ if(ENABLE_INTEGRATION_TESTS)
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
-    target_link_libraries(integration${PROG} libcatnip)
+    target_link_libraries(integration${PROG} libcatnip Eigen3::Eigen)
     add_test(integration${PROG} integration${PROG})
 
   endforeach(PROG)
@@ -53,7 +53,7 @@ if(ENABLE_INTEGRATION_TESTS)
   if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
     set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
   endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-  target_link_libraries(test_io libcatnip)
+  target_link_libraries(test_io libcatnip Eigen3::Eigen)
   add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
 
   add_custom_command(TARGET test_io
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 580c84e..890797e 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -17,13 +17,12 @@
 #include "../libcatnip/io/file_readers/punreader.hpp"
 #include "../libcatnip/io/io.hpp"
 #include "../libcatnip/log.hpp"
-//#include "../libcatnip/matrix.hpp"
 #include "../libcatnip/parameters.hpp"
 #include "../libcatnip/qc_functions.hpp"
 
 #include "../libcatnip/calcJconfig.hpp"
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 
 using namespace catnip;
 using namespace std;

From 23f393fd21a37acd47d9fc5e210e8962ea64445b Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Mon, 29 Apr 2019 13:25:26 -0600
Subject: [PATCH 09/68] First successful compile

---
 src/libcatnip/io/file_readers/filereader.hpp |  2 +-
 src/libcatnip/io/file_readers/logreader.cpp  | 29 ++-------
 src/libcatnip/io/file_readers/logreader.hpp  | 11 ++--
 src/libcatnip/io/file_readers/punreader.cpp  | 18 +++---
 src/libcatnip/io/file_readers/punreader.hpp  |  5 +-
 src/libcatnip/matrix.cpp                     | 18 +++---
 src/libcatnip/matrix.hpp                     |  1 +
 src/libcatnip/qc_functions.cpp               | 67 ++++++++++----------
 src/libcatnip/qc_functions.hpp               | 52 +++++++++------
 src/tests/test_qc_functions.cpp              |  2 +-
 src/tools/main.cpp                           | 28 ++++----
 11 files changed, 115 insertions(+), 118 deletions(-)

diff --git a/src/libcatnip/io/file_readers/filereader.hpp b/src/libcatnip/io/file_readers/filereader.hpp
index 91d374d..55d2f1d 100644
--- a/src/libcatnip/io/file_readers/filereader.hpp
+++ b/src/libcatnip/io/file_readers/filereader.hpp
@@ -1,4 +1,4 @@
-
+#pragma once
 #ifndef _CATNIP_FILEREADER_HPP_
 #define _CATNIP_FILEREADER_HPP_
 
diff --git a/src/libcatnip/io/file_readers/logreader.cpp b/src/libcatnip/io/file_readers/logreader.cpp
index b3624be..1657492 100644
--- a/src/libcatnip/io/file_readers/logreader.cpp
+++ b/src/libcatnip/io/file_readers/logreader.cpp
@@ -7,7 +7,7 @@
 #include <sstream>
 #include <string>
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Core>
 #include "../../log.hpp"
 #include "../../string_support.hpp"
 #include "logreader.hpp"
@@ -168,22 +168,10 @@ void LogReader::OverlapSectionReader(void *ptr) {
   
   //Matrix *mat_S = new Matrix(countCoef, countCoef);
   Eigen::MatrixXd matrix_S(countCoef,countCoef);
+  
   for (size_t row_ind = 0; row_ind < first_coefs.size(); ++row_ind) {
-//    vector<double> row = first_coefs.at(row_ind);
-    matrix_S.row(row_ind) << first_coefs.at(row_ind);
- //   size_t col_ind = 1;
-//    size_t col_ind = 0;
- //   for (double & val : row) {
- //     mat_S->set_elem(val, row_ind + 1, col_ind);
-  //    matrix_S(row_ind,col_ind) = val;
-      // Because diagonally symetric
-//      if (row_ind + 1 != col_ind) {
-   //   if (row_ind != col_ind) {
-        //mat_S->set_elem(val, col_ind, row_ind + 1);
-   //     matrix_S(col_ind,row_ind) = val;
-    //  }
-    //  ++col_ind;
-    //}
+    Eigen::Map<Eigen::VectorXd> eigen_vec((first_coefs.at(row_ind).data()),first_coefs.at(row_ind).size());
+    matrix_S.row(row_ind) = eigen_vec;
   }
 
   int sectionReads = countCoef / 5;
@@ -210,14 +198,9 @@ void LogReader::OverlapSectionReader(void *ptr) {
         string expon = grabStrAfterFirstOccurance(s_coef, "D");
         double value = stod(val) * pow(10.0, stod(expon));
        
-        //mat_S->set_elem(value, sectionCoef + 1,
-        //                currentSectionStart + localCoefCount);
         matrix_S(sectionCoef,currentSectionStart + localCoefCount) = value;
-        //if ((sectionCoef + 1) != (currentSectionStart + localCoefCount)) {
         if ((sectionCoef) != (currentSectionStart + localCoefCount)) {
           matrix_S(currentSectionStart + localCoefCount,sectionCoef) = value;
-          //mat_S->set_elem(value, currentSectionStart + localCoefCount,
-          //               sectionCoef + 1);
         }
         ++localCoefCount;
       }
@@ -227,7 +210,7 @@ void LogReader::OverlapSectionReader(void *ptr) {
     currentSectionStart += 5;
     getline(LR_ptr->fid_, line);
   }
-  LR_ptr->S_ = mat_S;
+  LR_ptr->S_ = matrix_S;
   LOG("Success reading Overlap coefficients from .log file", 2);
   return;
 }
@@ -253,7 +236,7 @@ void LogReader::ReadOrbEnergies(const string &orb_type) {
 
       auto vec_str = splitSt(line);
       for (size_t inc = 4; inc < vec_str.size(); inc++) {
-        OREnergies[orb_type].push_back((double)atof(vec_str.at(inc).c_str()));
+        OREnergies[orb_type].push_back(stod(vec_str.at(inc)));
         if (occFound) homoLevel[orb_type]++;
       }
     } else {
diff --git a/src/libcatnip/io/file_readers/logreader.hpp b/src/libcatnip/io/file_readers/logreader.hpp
index 4583ed3..4ec11a4 100644
--- a/src/libcatnip/io/file_readers/logreader.hpp
+++ b/src/libcatnip/io/file_readers/logreader.hpp
@@ -1,13 +1,14 @@
-
+#pragma once
 #ifndef _CATNIP_LOGREADER_HPP_
 #define _CATNIP_LOGREADER_HPP_
 
+#include <map>
+#include <string>
 #include <vector>
 
-//#include "../../matrix.hpp"
 #include "filereader.hpp"
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Core>
 // Gaussian log file reader
 
 namespace catnip {
@@ -21,8 +22,8 @@ class LogReader : public FileReader {
   explicit LogReader(const std::string &str);
   orb_cont getOrbitalInfo() const { return orb_; }
   Eigen::MatrixXd getOverlapMatrix() const { return S_; }
-  std::vector<double> getOE(const std::string &orb_type) const {
-    return OREnergies.at(orb_type);
+  Eigen::VectorXd getOE(const std::string &orb_type) {
+    return Eigen::Map<Eigen::VectorXd>(OREnergies.at(orb_type).data(),OREnergies.at(orb_type).size());
   }
   int getHOMOLevel(const std::string &orb_type) const {
     return homoLevel.at(orb_type);
diff --git a/src/libcatnip/io/file_readers/punreader.cpp b/src/libcatnip/io/file_readers/punreader.cpp
index 669693b..0dee70d 100644
--- a/src/libcatnip/io/file_readers/punreader.cpp
+++ b/src/libcatnip/io/file_readers/punreader.cpp
@@ -4,6 +4,7 @@
 #include <fstream>
 #include <iostream>
 #include <map>
+#include <memory>
 #include <sstream>
 #include <string>
 
@@ -11,7 +12,7 @@
 #include "../../string_support.hpp"
 #include "punreader.hpp"
 
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Core>
 
 using namespace catnip;
 using namespace std;
@@ -31,7 +32,7 @@ void PunReader::registerSections_() {
   FileReader::registerSections_();
 }
 
-MatrixXd PunReader::getCoefsMatrix(const string &orb_type) {
+Eigen::MatrixXd PunReader::getCoefsMatrix(const string &orb_type) {
   if (coefs.count(orb_type) != 1) {
     throw invalid_argument("Coefficients for spin " + orb_type +
                            " were not found");
@@ -95,15 +96,12 @@ void PunReader::ReadCoef(const string &orb_type) {
     allCoefsRead = !(foundSubStrInStr(line, orb_type));
   }
 
-  //Matrix *Coefs = new Matrix(v_vec);
-  coefs[orb_type] = unique_ptr<Eigen:::MatrixXd>(Eigen::MatrixXd Coefs(v_vec.size(),v_vec.at(0).size()));
-
-  size_t row_count = 0;
-  for( vector<double> & row : v_vec) {
-    coefs[orb_type]->row(row_count) = row;
-    ++row_count;
+  coefs[orb_type] = unique_ptr<Eigen::MatrixXd>(new Eigen::MatrixXd(v_vec.size(),v_vec.at(0).size()));
+  for( size_t row_ind=0; row_ind<v_vec.size();++row_ind){
+    Eigen::Map<Eigen::VectorXd> eigen_vec(v_vec.at(row_ind).data(),v_vec.at(row_ind).size());
+    coefs[orb_type]->row(row_ind) = eigen_vec;
   }
-  //coefs[orb_type] = Coefs;
+
   LOG("Success reading atomic orbital coefficients from .pun file.", 2);
 }
 
diff --git a/src/libcatnip/io/file_readers/punreader.hpp b/src/libcatnip/io/file_readers/punreader.hpp
index 2bc4b0b..af9128d 100644
--- a/src/libcatnip/io/file_readers/punreader.hpp
+++ b/src/libcatnip/io/file_readers/punreader.hpp
@@ -1,13 +1,12 @@
-
+#pragma once
 #ifndef _CATNIP_PUNREADER_HPP_
 #define _CATNIP_PUNREADER_HPP_
 
 #include <memory>
 #include <vector>
 
-//#include "../../matrix.hpp"
 #include "filereader.hpp"
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 // Gaussian fort.7/.pun file reader
 namespace catnip {
 
diff --git a/src/libcatnip/matrix.cpp b/src/libcatnip/matrix.cpp
index d84c54d..cd000db 100644
--- a/src/libcatnip/matrix.cpp
+++ b/src/libcatnip/matrix.cpp
@@ -3,14 +3,12 @@
 #include <stdexcept>
 #include <string>
 #include <vector>
-#include <eigen3/Eigen/Dense>
+#include <eigen3/Eigen/Core>
 
 #include "matrix.hpp"
 
 using namespace std;
-
-namespace catnip {
-
+namespace catnip { 
 string double_tos(double f, int nd) {
   ostringstream ostr;
   int tens = stod("1" + string(nd, '0'));
@@ -70,11 +68,13 @@ vector<int> matchCol(const Eigen::MatrixXd & mat1,
   return m_vec;
 }
 
+Eigen::MatrixXd convert(vector<vector<double>> coords){
 
-
-
-
-
-
+  Eigen::MatrixXd coord_mat(coords.size(),coords.at(0).size());
+  for ( size_t row_ind = 0; row_ind < coords.size();++row_ind){
+    coord_mat.row(row_ind) = Eigen::Map<Eigen::VectorXd>(coords.at(row_ind).data(),coords.at(row_ind).size()); 
+  }
+  return coord_mat;
+}
 
 }
diff --git a/src/libcatnip/matrix.hpp b/src/libcatnip/matrix.hpp
index 36529f6..c236385 100644
--- a/src/libcatnip/matrix.hpp
+++ b/src/libcatnip/matrix.hpp
@@ -46,5 +46,6 @@ namespace catnip {
       const Eigen::MatrixXd &mat2, 
       const int sig_fig);
 
+  Eigen::MatrixXd convert(std::vector<std::vector<double>> coords);
 } // namespace catnip
 #endif // MATRIX_HELPER_HPP
diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index eb681a2..d40d2f7 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -1,6 +1,7 @@
 #include <algorithm>
 #include <cmath>
 #include <fstream>
+#include <iomanip>
 #include <iostream>
 #include <list>
 #include <sstream>
@@ -74,8 +75,7 @@ void TransferComplex::calculate_transfer_integral_() {
   Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
   Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
-  auto Energy = Eigen::MatrixXd::Identity(vec_P_OE.size(),vec_P_OE.size());
-  Energy *= vec_P_OE.transpose(); 
+  Eigen::MatrixXd Energy = Eigen::MatrixXd::Identity(vec_P_OE.size(),vec_P_OE.size());
 
   Hamiltonian.resize(mat_S.rows(),mat_S.cols());
   Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
@@ -164,23 +164,23 @@ void TransferComplex::printTransferIntegral(
 // pair<string,int> string - Either HOMO or LUMO
 //                  int    - is the orbital number HOMO-3 LUMO+5
 void TransferComplex::printTransferIntegral_(
-    const pair<string,int> Orbital1,
-    const pair<string,int> Orbital2) const {
+    const pair<string,int>& orbital1,
+    const pair<string,int>& orbital2) const {
 
-  int obrital1_num = 0;
-  int obrital2_num = 0;
+  int orbital1_num = 0;
+  int orbital2_num = 0;
   if(orbital1.first.compare("HOMO")==0){
-    assert(orbitalValid_(Orbital1)==true); 
-    orbital1_num = Orbital1.second;
+    assert(orbitalValid_(orbital1)==true); 
+    orbital1_num = orbital1.second;
   }else if(orbital2.first.compare("LUMO")==0){
-    assert(orbitalValid_(Orbital2)==true); 
-    orbital2_num = Orbital2.second;
+    assert(orbitalValid_(orbital2)==true); 
+    orbital2_num = orbital2.second;
   }
   double J_ab = Hamiltonian(orbital1_num,orbital2_num);
   double e_a = Hamiltonian(orbital1_num,orbital1_num);
   double e_b = Hamiltonian(orbital2_num,orbital2_num);
   double S_ab = S_AB(orbital1_num,orbital2_num); 
-  double J_eff = Hamiltonaian_eff(orbital1_num,orbital2_num);
+  double J_eff = Hamiltonian_eff(orbital1_num,orbital2_num);
   cout << "J_ab  " << J_ab * hartreeToeV << " eV\n";
   cout << "e_a   " << e_a * hartreeToeV << " eV\n";
   cout << "e_b   " << e_b * hartreeToeV << " eV\n";
@@ -198,7 +198,7 @@ void TransferComplex::printAll() const {
     if(orbital_num<HOMO_Orb_){
       column_label+=string("HOMO");
       if(orbital_num!=(HOMO_Orb_-1)){
-        column_label+=string("-")+to_string(HOMO_Orb-orbital_num-1);
+        column_label+=string("-")+to_string(HOMO_Orb_-orbital_num-1);
       }
     }else {
       column_label+=string("LUMO");
@@ -215,7 +215,7 @@ void TransferComplex::printAll() const {
     if(orbital_num<HOMO_Orb_){
       column_label+=string("HOMO");
       if(orbital_num!=(HOMO_Orb_-1)){
-        column_label+=string("-")+to_string(HOMO_Orb-orbital_num-1);
+        column_label+=string("-")+to_string(HOMO_Orb_-orbital_num-1);
       }
     }else {
       column_label+=string("LUMO");
@@ -224,7 +224,7 @@ void TransferComplex::printAll() const {
       }
     } 
     cout << setw(column_width+2) << column_label;
-    for(int orbital_num2 = 0;orbital_num2<Hamiltonian.cols();++orbital2_num){
+    for(int orbital_num2 = 0;orbital_num2<Hamiltonian.cols();++orbital_num2){
       cout << "| " << setw(column_width) << Hamiltonian_eff(orbital_num2,orbital_num2) << " ";
     }
     cout << "|" << endl; 
@@ -274,7 +274,7 @@ bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital)
 //
 list<Eigen::MatrixXd> splitMatrixIntoList(
     const vector<int> &subMatrixDimension,
-    const Eigen::MatrixXd const mat,
+    const Eigen::MatrixXd mat,
     const string &ColRowSplit) {
 
   list<Eigen::MatrixXd> list_matrix;
@@ -522,7 +522,7 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
   } else if (ColRowMerge.compare("Rows") == 0) {
     int row = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
-      Matrix *mat = *it;
+      Eigen::MatrixXd mat = *it;
       int col = 0;
       if (row > rows)
         throw runtime_error("Your new matrix is not large enough");
@@ -592,14 +592,14 @@ Eigen::MatrixXd unscramble_Coef(
 Eigen::MatrixXd unscramble_Coef(
     const std::vector<int> &matchDimerB,
     const std::vector<int> &basisFuncB,
-    const Eigen::MatrixXd & Coef) {
+    const Eigen::MatrixXd &Coef) {
 
   // Let's reduce the complexity of the problem by instead of working
   // with the basis functions lets just work with the atoms. We can do
   // this by treating all the basis functions associated with a single
   // atom as a block.
 
-  list<MatrixXd> atom_mat_coef =
+  list<Eigen::MatrixXd> atom_mat_coef =
       splitCoefsUpByAtoms(basisFuncB, Coef, "Columns");
 
   // Place all of monomer A atom basis functions on the left side of the
@@ -623,10 +623,11 @@ Eigen::MatrixXd unscramble_Coef(
 
 // Similar to the above function but we will be moving both the rows
 // and columns
-Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
-                     const std::vector<int> &matchDimerB,
-                     const std::vector<int> &basisFuncP, 
-                     const Eigen::MatrixXd & S) {
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int> &matchDimerA,
+    const std::vector<int> &matchDimerB,
+    const std::vector<int> &basisFuncP, 
+    Eigen::MatrixXd S) {
 
   Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
@@ -677,10 +678,12 @@ Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
 // Same as the above function but here we are assuming counterpoise correction
 // is being used and thus we do not need to match with both monomer A and
 // monomer B but only need to match with A.
-Eigen::MatrixXd unscramble_S(const std::vector<int> &matchDimerA,
-                     const std::vector<int> &basisFuncP, Eigen::MatrixXd & S) {
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int> &matchDimerA,
+    const std::vector<int> &basisFuncP,
+    Eigen::MatrixXd S) {
 
-  MatrixXd & S_new(S.rows(),S.cols());
+  Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
     list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
 
@@ -778,16 +781,16 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
   // If dealing with counter poise correction may also need to unscramble
   // the basis functions of the monomers
   if (counterPoise_) {
-    vector<int> match_1_2 = coord_1_mat.matchCol(coord_2_mat, sig_fig);
+    vector<int> match_1_2 = matchCol(coord_1_mat,coord_2_mat, sig_fig);
 
     LOG("Counter Poise unscrambling matrix 2 with respect to matrix 1", 2);
-    auto unscrambled_2_Coef = unscramble_Coef(match_1_2, basis2, mat_2_Coef);
+    Eigen::MatrixXd unscrambled_2_Coef = unscramble_Coef(match_1_2, basis2, mat_2_Coef);
 
     this->mat_2_Coef = unscrambled_2_Coef;
 
-    vector<int> match_1_P = coord_1_mat.matchCol(coord_P_mat, sig_fig);
+    vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
 
-    auto unscrambled_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
+    Eigen::MatrixXd unscrambled_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
 
     this->mat_P_Coef = unscrambled_P_Coef;
 
@@ -798,13 +801,13 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
   } else {
 
     // Stores the rows in P that match 1
-    vector<int> match_1_P = coord_1_mat.matchCol(coord_P_mat, sig_fig);
+    vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
 
     // Stores the rows in P that match 2
-    vector<int> match_2_P = coord_2_mat.matchCol(coord_P_mat, sig_fig);
+    vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
 
     LOG("Unscrambling dimer matrix with respect to matrix 1 and 2", 2);
-    auto unscrambled_P_Coef =
+    Eigen::MatrixXd unscrambled_P_Coef =
         unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
 
     this->mat_P_Coef = unscrambled_P_Coef;
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index b78deeb..a84bfb1 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -1,3 +1,4 @@
+#pragma once
 #ifndef _CATNIP_QC_FUNCTIONS_HPP
 #define _CATNIP_QC_FUNCTIONS_HPP
 
@@ -83,14 +84,14 @@ class TransferComplex {
     //
     //    monomer1 LUMO-3
     //    monomer2 HOMO
-    void calcJ(const std::map<std::string, std::string>& orbitaltype,
-        const std::map<std::string, int>& orbitalnum);
+    void calcJ();
 
     /**
      * \brief Print the transfer integral specified
      **/
-    void printTransferIntegral(const std::pair<std::string,int> & Orbital1,
-                               const std::pair<std::string,int> & Orbital2) const;
+    void printTransferIntegral(
+        const std::map<std::string,std::string> & orbital_type,
+        const std::map<std::string,int> & orbnum) const;
 
     /**
      * \brief Print All info in matrix form
@@ -101,10 +102,6 @@ class TransferComplex {
 std::unordered_map<int, std::pair<double, std::string>> findRank(
     Eigen::VectorXd& Orb_E_Alpha, Eigen::VectorXd& Orb_E_Beta);
 
-/*double calculate_transfer_integral(const Eigen::MatrixXd & mat_1_Coef, const Eigen::MatrixXd & mat_2_Coef,
-                                   Eigen::MatrixXd mat_P_Coef,const Eigen::MatrixXd & mat_S,
-                                   const Eigen::VectorXd& vec_P_OE, bool counterPoise_);*/
-
 // Reorganize the dimer coefficients to match up with the monomers
 Eigen::MatrixXd organize_P_Coef(std::vector<int> matchDimerA,
                        std::vector<int> matchDimerB,
@@ -114,22 +111,37 @@ Eigen::MatrixXd organize_P_Coef(std::vector<int> matchDimerA,
 // Unscramble the coefficients of the dimer matrix
 // Assumes that the match vectors describe swaps looking at a single
 // instance of the dimerCoef matrix
-Eigen::MatrixXd unscramble_Coef(const std::vector<int>& matchDimerA,
-                        const std::vector<int>& matchDimerB,
-                        const std::vector<int>& basisFuncDimer,
-                        Eigen::MatrixXd dimerCoef);
+Eigen::MatrixXd unscramble_Coef(
+    const std::vector<int>& matchDimerA,
+    const std::vector<int>& matchDimerB,
+    const std::vector<int>& basisFuncDimer,
+    const Eigen::MatrixXd & dimerCoef);
 
-Eigen::MatrixXd unscramble_Coef(const std::vector<int>& matchDimerA,
-                        const std::vector<int>& basisFuncDimer, Eigen::MatrixXd dimerCoef);
+Eigen::MatrixXd unscramble_Coef(
+    const std::vector<int>& matchDimerA,
+    const std::vector<int>& basisFuncDimer,
+    const Eigen::MatrixXd & dimerCoef);
 
 // Reorganize the dimer overlap matrix to line up with the monomer
 // coefficients.
-Eigen::MatrixXd unscramble_S(const std::vector<int>& matchDimerA,
-                     const std::vector<int>& matchDimerB,
-                     const std::vector<int>& basisFuncDimer, Eigen::MatrixXd S);
-
-Eigen::MatrixXd unscramble_S(const std::vector<int>& matchDimerA,
-                     const std::vector<int>& basisFuncDimer, Eigen::MatrixXd S);
+/**
+ *
+ * Note S must not be a reference because it is altered during the unscrambling
+ **/
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int>& matchDimerA,
+    const std::vector<int>& matchDimerB,
+    const std::vector<int>& basisFuncDimer,
+    Eigen::MatrixXd S);
+
+/**
+ *
+ * Note S must not be a reference because it is altered during the unscrambling
+ **/
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int>& matchDimerA,
+    const std::vector<int>& basisFuncDimer,
+    Eigen::MatrixXd S);
 
 Eigen::MatrixXd unscramble_OE(std::vector<int> matchDimerA,
                       std::vector<int> matchDimerB,
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index 237901e..452e850 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -1,5 +1,5 @@
-//#include "../libcatnip/matrix.hpp"
 #include "../libcatnip/qc_functions.hpp"
+#include "../libcatnip/matrix.hpp"
 #include <cassert>
 #include <iostream>
 #include <vector>
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 890797e..2e4db86 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -19,10 +19,10 @@
 #include "../libcatnip/log.hpp"
 #include "../libcatnip/parameters.hpp"
 #include "../libcatnip/qc_functions.hpp"
-
+#include "../libcatnip/matrix.hpp"
 #include "../libcatnip/calcJconfig.hpp"
 
-#include <eigen3/Eigen/Dense>
+#include <eigen3/Eigen/Core>
 
 using namespace catnip;
 using namespace std;
@@ -92,17 +92,17 @@ int main(int argc, const char *argv[]) {
     LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
     Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
     //Matrix *mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
-    //auto vec_1_OE = lr_1.getOE(par->getSpin1());
+    Eigen::VectorXd vec_1_OE = lr_1.getOE(par->getSpin1());
     //Matrix *mat_1_OE = new Matrix(vec_1_OE);
-    Eigen::MatrixXd mat_1_OE = Eigen::MatrixXd(vec_1_OE);
+    //Eigen::MatrixXd mat_1_OE = vec_1_OE.asDiagonal();
 
     int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
     LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
     //Matrix *mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
     Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
-    //auto vec_2_OE = lr_2.getOE(par->getSpin2());
+    Eigen::VectorXd vec_2_OE = lr_2.getOE(par->getSpin2());
     //Matrix *mat_2_OE = new Matrix(vec_2_OE);
-    Eigen::MatrixXd mat_2_OE = Eigen::MatrixXd(vec_2_OE);
+    //Eigen::MatrixXd mat_2_OE = vec_2_OE.asDiagonal();
 
     // Unscramble dimer coef and energies first need to see how the dimer
     // and monomer coefficients line up. To determine how the ceofficients
@@ -117,16 +117,16 @@ int main(int argc, const char *argv[]) {
     vector<vector<double>> coord_2 = lr_2.getCoords();
 
     // Convert coords to matrices
-    MatrixXd coord_P_mat(coord_P);
-    MatrixXd coord_1_mat(coord_1);
-    MatrixXd coord_2_mat(coord_2);
+    Eigen::MatrixXd coord_P_mat = convert(coord_P);
+    Eigen::MatrixXd coord_1_mat = convert(coord_1);
+    Eigen::MatrixXd coord_2_mat = convert(coord_2);
 
-    int basis_P = lr_P.getBasisFuncCount();
-    int basis_1 = lr_1.getBasisFuncCount();
-    int basis_2 = lr_2.getBasisFuncCount();
+    vector<int> basis_P = lr_P.getBasisFuncCount();
+    vector<int> basis_1 = lr_1.getBasisFuncCount();
+    vector<int> basis_2 = lr_2.getBasisFuncCount();
 
-    int MO1 = mat_1_OE->get_rows();
-    int MO2 = mat_2_OE->get_rows();
+    int MO1 = static_cast<int>(vec_1_OE.size());
+    int MO2 = static_cast<int>(vec_2_OE.size());
 
     pair<int, int> Orbs1 = {MO1, HOMO1};
     pair<int, int> Orbs2 = {MO2, HOMO2};

From 47e30780ead5812ea16cf5f7788da7722a050b9a Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Mon, 29 Apr 2019 22:14:36 -0600
Subject: [PATCH 10/68] Add testing to log reader

---
 src/tests/test_logreader.cpp | 120 ++++++++++++++++++++++++++++++++++-
 1 file changed, 118 insertions(+), 2 deletions(-)

diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index be908eb..83702f3 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -2,6 +2,7 @@
 
 #include <cassert>
 #include <iostream>
+#include <set>
 #include <sstream>
 #include <string>
 #include <vector>
@@ -14,10 +15,125 @@ using namespace std;
 
 int main(void) {
 
-  cerr << "Testing: LogReader Constructor" << endl;
+  cout << "Testing: LogReader Constructor" << endl;
   { LogReader lr("file.log"); }
 
-  cerr << "Testing: LogReader read" << endl;
+  cout << "Testing: LogReader read energies" << endl;
+  {
+
+    string test_file = "testfile_energies.log";
+    {
+      ofstream fid;
+      fid.open(test_file);
+      fid << "Test log file contains sections that the log reader";
+      fid << " will search and read from." << endl;
+      fid << " Alpha  occ. eigenvalues --  -10.19871 -10.19791  -0.76206  -0.58448  -0.47269" << endl; 
+      fid << " Alpha  occ. eigenvalues --   -0.42268  -0.36322  -0.27597" << endl; 
+      fid << " Alpha virt. eigenvalues --   -0.00988   0.02500   0.03257   0.04671   0.06946" << endl;
+      fid << " Alpha virt. eigenvalues --    0.08668   0.08746   0.12753   0.15670   0.17639" << endl; 
+      fid.close();
+    }
+
+    LogReader lr(test_file);
+    lr.read();
+
+    Eigen::VectorXd orbital_energies = lr.getOE("Alpha");
+    
+    set<double> correct_orbital_energies = { 
+    -10.19871, -10.19791,  -0.76206, -0.58448, -0.47269, 
+     -0.42268,  -0.36322,  -0.27597, 
+     -0.00988,   0.02500,   0.03257,   0.04671,  0.06946,
+      0.08668,   0.08746,   0.12753,   0.15670,  0.17639};
+
+    vector<bool> found_energy(correct_orbital_energies.size(),false); 
+    for( int index = 0; index < orbital_energies.size();++index){
+      if( correct_orbital_energies.count(orbital_energies(index))){
+        found_energy.at(index) = true;
+      }
+      cout << "Found Energy " << orbital_energies(index);
+      cout << " " << found_energy.at(index) << endl;
+    }
+
+    for ( const bool & found : found_energy){
+      assert(found);
+    }
+  }
+
+  cout << "Testing: LogReader read coordinates" << endl;
+  {
+    string test_file = "testfile_coords.log";
+    {
+      ofstream fid;
+      fid.open(test_file);
+      fid << "Center     Atomic      Atomic" << endl;
+      fid << " Number     Number      Type              X           Y           Z" << endl;
+      fid << " ---------------------------------------------------------------------" << endl;
+      fid << "    1          6             0        0.672749    0.000000    5.000000" << endl;
+      fid << "    2          6             0       -0.672749    0.000000    5.000000" << endl;
+      fid << "    3          1             0        1.242623    0.162327    5.920604" << endl;
+      fid << "    4          1             0        1.242623   -0.162327    4.079396" << endl;
+      fid << "    5          1             0       -1.242623    0.162327    5.920604" << endl;
+      fid << "    6          1             0       -1.242623   -0.162327    4.079396" << endl;
+      fid << "-----------------------------------";
+      fid << "----------------------------------" << endl;
+      fid.close();
+    }
+
+    LogReader lr(test_file);
+    lr.read();
+
+    vector<vector<double>> atomic_coords = lr.getCoords();
+ 
+    cout << atomic_coords.at(0).at(0) << " ";
+    cout << atomic_coords.at(1).at(0) << " ";
+    cout << atomic_coords.at(2).at(0) << " ";
+    assert(atomic_coords.at(0).at(0) == 0.672749); 
+    assert(atomic_coords.at(1).at(0) == 0.000000); 
+    assert(atomic_coords.at(2).at(0) == 5.000000);
+    cout << "Atom 1 coordinates correct" << endl; 
+
+    cout << atomic_coords.at(0).at(1) << " ";
+    cout << atomic_coords.at(1).at(1) << " ";
+    cout << atomic_coords.at(2).at(1) << " ";
+    assert(atomic_coords.at(0).at(1) == -0.672749); 
+    assert(atomic_coords.at(1).at(1) == 0.0000000); 
+    assert(atomic_coords.at(2).at(1) == 5.0000000); 
+    cout << "Atom 2 coordinates correct" << endl; 
+
+    cout << atomic_coords.at(0).at(2) << " ";
+    cout << atomic_coords.at(1).at(2) << " ";
+    cout << atomic_coords.at(2).at(2) << " ";
+    assert(atomic_coords.at(0).at(2) == 1.242623); 
+    assert(atomic_coords.at(1).at(2) == 0.162327); 
+    assert(atomic_coords.at(2).at(2) == 5.920604); 
+    cout << "Atom 3 coordinates correct" << endl; 
+
+    cout << atomic_coords.at(0).at(3) << " ";
+    cout << atomic_coords.at(1).at(3) << " ";
+    cout << atomic_coords.at(2).at(3) << " ";
+    assert(atomic_coords.at(0).at(3) == 1.242623); 
+    assert(atomic_coords.at(1).at(3) == -0.162327); 
+    assert(atomic_coords.at(2).at(3) == 4.079396); 
+    cout << "Atom 4 coordinates correct" << endl; 
+
+    cout << atomic_coords.at(0).at(4) << " ";
+    cout << atomic_coords.at(1).at(4) << " ";
+    cout << atomic_coords.at(2).at(4) << " ";
+    assert(atomic_coords.at(0).at(4) == -1.242623); 
+    assert(atomic_coords.at(1).at(4) == 0.162327); 
+    assert(atomic_coords.at(2).at(4) == 5.920604); 
+    cout << "Atom 5 coordinates correct" << endl; 
+
+    cout << atomic_coords.at(0).at(5) << " ";
+    cout << atomic_coords.at(1).at(5) << " ";
+    cout << atomic_coords.at(2).at(5) << " ";
+    assert(atomic_coords.at(0).at(5) == -1.242623); 
+    assert(atomic_coords.at(1).at(5) == -0.162327); 
+    assert(atomic_coords.at(2).at(5) == 4.079396); 
+    cout << "Atom 6 coordinates correct" << endl; 
+ 
+  }
+  cout << "Testing: LogReader read" << endl;
   {
 
     LogReader lr("../../../GAUSSIANFILES/90_unordered/90_pair.log");

From 3bcf3296486fc7857dcb507c9e2ca6ed0a7d22fc Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Mon, 29 Apr 2019 22:32:16 -0600
Subject: [PATCH 11/68] Added test for overlap

---
 src/tests/test_logreader.cpp | 279 +++++++++++++++++++++++++++++++++++
 1 file changed, 279 insertions(+)

diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index 83702f3..a663a2a 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -133,6 +133,285 @@ int main(void) {
     cout << "Atom 6 coordinates correct" << endl; 
  
   }
+
+  cout << "Testing: LogReader read overlap" << endl;
+  {
+
+    string test_file = "testfile_overlap.log";
+    {
+      ofstream fid;
+      fid.open(test_file);
+      fid << "*** Overlap ***                                                             " << endl;
+      fid << "                1             2             3             4             5    " << endl;
+      fid << "      1  0.100000D+01                                                        " << endl;
+      fid << "      2  0.219059D+00  0.100000D+01                                          " << endl;
+      fid << "      3  0.000000D+00  0.000000D+00  0.100000D+01                            " << endl;
+      fid << "      4  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01              " << endl;
+      fid << "      5  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "      6  0.184261D+00  0.812273D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "      7  0.000000D+00  0.000000D+00  0.569754D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "      8  0.000000D+00  0.000000D+00  0.000000D+00  0.569754D+00  0.000000D+00" << endl;
+      fid << "      9  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.569754D+00" << endl;
+      fid << "     10  0.697718D-01  0.402091D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     11  0.000000D+00  0.000000D+00  0.164679D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     12  0.000000D+00  0.000000D+00  0.000000D+00  0.164679D+00  0.000000D+00" << endl;
+      fid << "     13  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.164679D+00" << endl;
+      fid << "     14  0.791027D-01  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     15  0.791027D-01  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     16  0.791027D-01  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     17  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     18  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     19  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     20  0.481399D-05  0.194904D-01 -0.426713D-01  0.000000D+00  0.000000D+00" << endl;
+      fid << "     21  0.194904D-01  0.203366D+00 -0.282219D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     22  0.426713D-01  0.282219D+00 -0.333594D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     23  0.000000D+00  0.000000D+00  0.000000D+00  0.115814D+00  0.000000D+00" << endl;
+      fid << "     24  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.115814D+00" << endl;
+      fid << "     25  0.643636D-01  0.359351D+00 -0.253511D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     26  0.129620D+00  0.562375D+00 -0.170740D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     27  0.000000D+00  0.000000D+00  0.000000D+00  0.242739D+00  0.000000D+00" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.242739D+00" << endl;
+      fid << "     29  0.527094D-01  0.309785D+00 -0.673317D-01  0.000000D+00  0.000000D+00" << endl;
+      fid << "     30  0.555561D-01  0.303665D+00  0.598522D-01  0.000000D+00  0.000000D+00" << endl;
+      fid << "     31  0.000000D+00  0.000000D+00  0.000000D+00  0.126532D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.126532D+00" << endl;
+      fid << "     33  0.526767D-01  0.334402D+00 -0.413876D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     34  0.113280D-02  0.928256D-01 -0.142160D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     35  0.113280D-02  0.928256D-01 -0.142160D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     36  0.000000D+00  0.000000D+00  0.000000D+00  0.183392D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.183392D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.320525D-01  0.270664D+00  0.190666D+00  0.543105D-01  0.308011D+00" << endl;
+      fid << "     40  0.916644D-01  0.473962D+00  0.138280D+00  0.393885D-01  0.223384D+00" << endl;
+      fid << "     41  0.320525D-01  0.270664D+00  0.190666D+00 -0.543105D-01 -0.308011D+00" << endl;
+      fid << "     42  0.916644D-01  0.473962D+00  0.138280D+00 -0.393885D-01 -0.223384D+00" << endl;
+      fid << "     43  0.430533D-04  0.789567D-02 -0.152645D-01  0.129366D-02  0.733675D-02" << endl;
+      fid << "     44  0.142782D-01  0.109874D+00 -0.102097D+00  0.865264D-02  0.490716D-01" << endl;
+      fid << "     45  0.430533D-04  0.789567D-02 -0.152645D-01 -0.129366D-02 -0.733675D-02" << endl;
+      fid << "     46  0.142782D-01  0.109874D+00 -0.102097D+00 -0.865264D-02 -0.490716D-01" << endl;
+      fid << "                6             7             8             9            10" << endl;
+      fid << "      6  0.100000D+01" << endl;
+      fid << "      7  0.000000D+00  0.100000D+01" << endl;
+      fid << "      8  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "      9  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     10  0.727666D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     11  0.000000D+00  0.588690D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     12  0.000000D+00  0.000000D+00  0.588690D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     13  0.000000D+00  0.000000D+00  0.000000D+00  0.588690D+00  0.000000D+00" << endl;
+      fid << "     14  0.629936D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00" << endl;
+      fid << "     15  0.629936D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00" << endl;
+      fid << "     16  0.629936D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00" << endl;
+      fid << "     17  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     18  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     19  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     20  0.643636D-01 -0.129620D+00  0.000000D+00  0.000000D+00  0.527094D-01" << endl;
+      fid << "     21  0.359351D+00 -0.562375D+00  0.000000D+00  0.000000D+00  0.309785D+00" << endl;
+      fid << "     22  0.253511D+00 -0.170740D+00  0.000000D+00  0.000000D+00  0.673317D-01" << endl;
+      fid << "     23  0.000000D+00  0.000000D+00  0.242739D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     24  0.000000D+00  0.000000D+00  0.000000D+00  0.242739D+00  0.000000D+00" << endl;
+      fid << "     25  0.579631D+00 -0.605354D+00  0.000000D+00  0.000000D+00  0.581168D+00" << endl;
+      fid << "     26  0.605354D+00 -0.525884D-01  0.000000D+00  0.000000D+00  0.250193D+00" << endl;
+      fid << "     27  0.000000D+00  0.000000D+00  0.579631D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00  0.000000D+00  0.579631D+00  0.000000D+00" << endl;
+      fid << "     29  0.581168D+00 -0.250193D+00  0.000000D+00  0.000000D+00  0.867984D+00" << endl;
+      fid << "     30  0.491037D+00  0.258780D+00  0.000000D+00  0.000000D+00  0.461882D+00" << endl;
+      fid << "     31  0.000000D+00  0.000000D+00  0.470171D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00  0.000000D+00  0.470171D+00  0.000000D+00" << endl;
+      fid << "     33  0.353148D+00 -0.422973D+00  0.000000D+00  0.000000D+00  0.254635D+00" << endl;
+      fid << "     34  0.255918D+00 -0.441451D+00  0.000000D+00  0.000000D+00  0.247363D+00" << endl;
+      fid << "     35  0.255918D+00 -0.441451D+00  0.000000D+00  0.000000D+00  0.247363D+00" << endl;
+      fid << "     36  0.000000D+00  0.000000D+00  0.161252D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.000000D+00  0.161252D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.375116D+00  0.267879D+00  0.763046D-01  0.432746D+00  0.258482D+00" << endl;
+      fid << "     40  0.702351D+00  0.303675D+00  0.865010D-01  0.490572D+00  0.640357D+00" << endl;
+      fid << "     41  0.375116D+00  0.267879D+00 -0.763046D-01 -0.432746D+00  0.258482D+00" << endl;
+      fid << "     42  0.702351D+00  0.303675D+00 -0.865010D-01 -0.490572D+00  0.640357D+00" << endl;
+      fid << "     43  0.740737D-01 -0.176934D+00  0.149950D-01  0.850413D-01  0.158045D+00" << endl;
+      fid << "     44  0.262382D+00 -0.381297D+00  0.323148D-01  0.183267D+00  0.424412D+00" << endl;
+      fid << "     45  0.740737D-01 -0.176934D+00 -0.149950D-01 -0.850413D-01  0.158045D+00" << endl;
+      fid << "     46  0.262382D+00 -0.381297D+00 -0.323148D-01 -0.183267D+00  0.424412D+00" << endl;
+      fid << "               11            12            13            14            15" << endl;
+      fid << "     11  0.100000D+01" << endl;
+      fid << "     12  0.000000D+00  0.100000D+01" << endl;
+      fid << "     13  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     14  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     15  0.000000D+00  0.000000D+00  0.000000D+00  0.333333D+00  0.100000D+01" << endl;
+      fid << "     16  0.000000D+00  0.000000D+00  0.000000D+00  0.333333D+00  0.333333D+00" << endl;
+      fid << "     17  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     18  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     19  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     20 -0.555561D-01  0.000000D+00  0.000000D+00  0.526767D-01  0.113280D-02" << endl;
+      fid << "     21 -0.303665D+00  0.000000D+00  0.000000D+00  0.334402D+00  0.928256D-01" << endl;
+      fid << "     22  0.598522D-01  0.000000D+00  0.000000D+00  0.413876D+00  0.142160D+00" << endl;
+      fid << "     23  0.000000D+00  0.126532D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     24  0.000000D+00  0.000000D+00  0.126532D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     25 -0.491037D+00  0.000000D+00  0.000000D+00  0.353148D+00  0.255918D+00" << endl;
+      fid << "     26  0.258780D+00  0.000000D+00  0.000000D+00  0.422973D+00  0.441451D+00" << endl;
+      fid << "     27  0.000000D+00  0.470171D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00  0.470171D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     29 -0.461882D+00  0.000000D+00  0.000000D+00  0.254635D+00  0.247363D+00" << endl;
+      fid << "     30  0.622202D+00  0.000000D+00  0.000000D+00  0.229601D+00  0.249594D+00" << endl;
+      fid << "     31  0.000000D+00  0.867984D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00  0.867984D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     33 -0.229601D+00  0.000000D+00  0.000000D+00  0.487216D+00  0.154963D+00" << endl;
+      fid << "     34 -0.249594D+00  0.000000D+00  0.000000D+00  0.154963D+00  0.753228D-01" << endl;
+      fid << "     35 -0.249594D+00  0.000000D+00  0.000000D+00  0.154963D+00  0.251076D-01" << endl;
+      fid << "     36  0.000000D+00  0.236690D-01  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.236690D-01  0.000000D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.109596D+00  0.312180D-01  0.177046D+00  0.207130D+00  0.123414D+00" << endl;
+      fid << "     40  0.226998D+00  0.646599D-01  0.366705D+00  0.371459D+00  0.351303D+00" << endl;
+      fid << "     41  0.109596D+00 -0.312180D-01 -0.177046D+00  0.207130D+00  0.123414D+00" << endl;
+      fid << "     42  0.226998D+00 -0.646599D-01 -0.366705D+00  0.371459D+00  0.351303D+00" << endl;
+      fid << "     43 -0.225200D+00  0.190856D-01  0.108240D+00  0.137730D-01  0.170528D-02" << endl;
+      fid << "     44 -0.505665D+00  0.428549D-01  0.243043D+00  0.120267D+00  0.707321D-01" << endl;
+      fid << "     45 -0.225200D+00 -0.190856D-01 -0.108240D+00  0.137730D-01  0.170528D-02" << endl;
+      fid << "     46 -0.505665D+00 -0.428549D-01 -0.243043D+00  0.120267D+00  0.707321D-01" << endl;
+      fid << "               16            17            18            19            20" << endl;
+      fid << "     16  0.100000D+01" << endl;
+      fid << "     17  0.000000D+00  0.100000D+01" << endl;
+      fid << "     18  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     19  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     20  0.113280D-02  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     21  0.928256D-01  0.000000D+00  0.000000D+00  0.000000D+00  0.219059D+00" << endl;
+      fid << "     22  0.142160D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     23  0.000000D+00 -0.183392D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     24  0.000000D+00  0.000000D+00 -0.183392D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     25  0.255918D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.184261D+00" << endl;
+      fid << "     26  0.441451D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     27  0.000000D+00 -0.161252D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00 -0.161252D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     29  0.247363D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.697718D-01" << endl;
+      fid << "     30  0.249594D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     31  0.000000D+00 -0.236690D-01  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00 -0.236690D-01  0.000000D+00  0.000000D+00" << endl;
+      fid << "     33  0.154963D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.791027D-01" << endl;
+      fid << "     34  0.251076D-01  0.000000D+00  0.000000D+00  0.000000D+00  0.791027D-01" << endl;
+      fid << "     35  0.753228D-01  0.000000D+00  0.000000D+00  0.000000D+00  0.791027D-01" << endl;
+      fid << "     36  0.000000D+00 -0.314243D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00 -0.314243D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.753228D-01  0.000000D+00" << endl;
+      fid << "     39  0.353785D+00  0.449500D-01  0.254925D+00  0.726146D-01  0.430533D-04" << endl;
+      fid << "     40  0.406770D+00  0.108227D-01  0.613785D-01  0.174835D-01  0.142782D-01" << endl;
+      fid << "     41  0.353785D+00 -0.449500D-01 -0.254925D+00  0.726146D-01  0.430533D-04" << endl;
+      fid << "     42  0.406770D+00 -0.108227D-01 -0.613785D-01  0.174835D-01  0.142782D-01" << endl;
+      fid << "     43  0.442596D-02 -0.178424D-02 -0.101190D-01  0.857578D-03  0.320525D-01" << endl;
+      fid << "     44  0.818999D-01 -0.732391D-02 -0.415360D-01  0.352016D-02  0.916644D-01" << endl;
+      fid << "     45  0.442596D-02  0.178424D-02  0.101190D-01  0.857578D-03  0.320525D-01" << endl;
+      fid << "     46  0.818999D-01  0.732391D-02  0.415360D-01  0.352016D-02  0.916644D-01" << endl;
+      fid << "               21            22            23            24            25" << endl;
+      fid << "     21  0.100000D+01" << endl;
+      fid << "     22  0.000000D+00  0.100000D+01" << endl;
+      fid << "     23  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     24  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     25  0.812273D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     26  0.000000D+00  0.569754D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     27  0.000000D+00  0.000000D+00  0.569754D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00  0.000000D+00  0.569754D+00  0.000000D+00" << endl;
+      fid << "     29  0.402091D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.727666D+00" << endl;
+      fid << "     30  0.000000D+00  0.164679D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     31  0.000000D+00  0.000000D+00  0.164679D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00  0.000000D+00  0.164679D+00  0.000000D+00" << endl;
+      fid << "     33  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.629936D+00" << endl;
+      fid << "     34  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.629936D+00" << endl;
+      fid << "     35  0.710235D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.629936D+00" << endl;
+      fid << "     36  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.789567D-02  0.152645D-01  0.129366D-02  0.733675D-02  0.740737D-01" << endl;
+      fid << "     40  0.109874D+00  0.102097D+00  0.865264D-02  0.490716D-01  0.262382D+00" << endl;
+      fid << "     41  0.789567D-02  0.152645D-01 -0.129366D-02 -0.733675D-02  0.740737D-01" << endl;
+      fid << "     42  0.109874D+00  0.102097D+00 -0.865264D-02 -0.490716D-01  0.262382D+00" << endl;
+      fid << "     43  0.270664D+00 -0.190666D+00  0.543105D-01  0.308011D+00  0.375116D+00" << endl;
+      fid << "     44  0.473962D+00 -0.138280D+00  0.393885D-01  0.223384D+00  0.702351D+00" << endl;
+      fid << "     45  0.270664D+00 -0.190666D+00 -0.543105D-01 -0.308011D+00  0.375116D+00" << endl;
+      fid << "     46  0.473962D+00 -0.138280D+00 -0.393885D-01 -0.223384D+00  0.702351D+00" << endl;
+      fid << "               26            27            28            29            30" << endl;
+      fid << "     26  0.100000D+01" << endl;
+      fid << "     27  0.000000D+00  0.100000D+01" << endl;
+      fid << "     28  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     29  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     30  0.588690D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     31  0.000000D+00  0.588690D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     32  0.000000D+00  0.000000D+00  0.588690D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     33  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00  0.000000D+00" << endl;
+      fid << "     34  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00  0.000000D+00" << endl;
+      fid << "     35  0.000000D+00  0.000000D+00  0.000000D+00  0.323540D+00  0.000000D+00" << endl;
+      fid << "     36  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.176934D+00  0.149950D-01  0.850413D-01  0.158045D+00  0.225200D+00" << endl;
+      fid << "     40  0.381297D+00  0.323148D-01  0.183267D+00  0.424412D+00  0.505665D+00" << endl;
+      fid << "     41  0.176934D+00 -0.149950D-01 -0.850413D-01  0.158045D+00  0.225200D+00" << endl;
+      fid << "     42  0.381297D+00 -0.323148D-01 -0.183267D+00  0.424412D+00  0.505665D+00" << endl;
+      fid << "     43 -0.267879D+00  0.763046D-01  0.432746D+00  0.258482D+00 -0.109596D+00" << endl;
+      fid << "     44 -0.303675D+00  0.865010D-01  0.490572D+00  0.640357D+00 -0.226998D+00" << endl;
+      fid << "     45 -0.267879D+00 -0.763046D-01 -0.432746D+00  0.258482D+00 -0.109596D+00" << endl;
+      fid << "     46 -0.303675D+00 -0.865010D-01 -0.490572D+00  0.640357D+00 -0.226998D+00" << endl;
+      fid << "               31            32            33            34            35" << endl;
+      fid << "     31  0.100000D+01" << endl;
+      fid << "     32  0.000000D+00  0.100000D+01" << endl;
+      fid << "     33  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     34  0.000000D+00  0.000000D+00  0.333333D+00  0.100000D+01" << endl;
+      fid << "     35  0.000000D+00  0.000000D+00  0.333333D+00  0.333333D+00  0.100000D+01" << endl;
+      fid << "     36  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     37  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
+      fid << "     39  0.190856D-01  0.108240D+00  0.137730D-01  0.170528D-02  0.442596D-02" << endl;
+      fid << "     40  0.428549D-01  0.243043D+00  0.120267D+00  0.707321D-01  0.818999D-01" << endl;
+      fid << "     41 -0.190856D-01 -0.108240D+00  0.137730D-01  0.170528D-02  0.442596D-02" << endl;
+      fid << "     42 -0.428549D-01 -0.243043D+00  0.120267D+00  0.707321D-01  0.818999D-01" << endl;
+      fid << "     43  0.312180D-01  0.177046D+00  0.207130D+00  0.123414D+00  0.353785D+00" << endl;
+      fid << "     44  0.646599D-01  0.366705D+00  0.371459D+00  0.351303D+00  0.406770D+00" << endl;
+      fid << "     45 -0.312180D-01 -0.177046D+00  0.207130D+00  0.123414D+00  0.353785D+00" << endl;
+      fid << "     46 -0.646599D-01 -0.366705D+00  0.371459D+00  0.351303D+00  0.406770D+00" << endl;
+      fid << "               36            37            38            39            40" << endl;
+      fid << "     36  0.100000D+01" << endl;
+      fid << "     37  0.000000D+00  0.100000D+01" << endl;
+      fid << "     38  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "     39  0.178424D-02  0.101190D-01  0.857578D-03  0.100000D+01" << endl;
+      fid << "     40  0.732391D-02  0.415360D-01  0.352016D-02  0.658292D+00  0.100000D+01" << endl;
+      fid << "     41 -0.178424D-02 -0.101190D-01  0.857578D-03  0.125798D-01  0.128011D+00" << endl;
+      fid << "     42 -0.732391D-02 -0.415360D-01  0.352016D-02  0.128011D+00  0.365470D+00" << endl;
+      fid << "     43 -0.449500D-01 -0.254925D+00  0.726146D-01  0.571644D-03  0.366357D-01" << endl;
+      fid << "     44 -0.108227D-01 -0.613785D-01  0.174835D-01  0.366357D-01  0.168873D+00" << endl;
+      fid << "     45  0.449500D-01  0.254925D+00  0.726146D-01  0.104764D-04  0.720595D-02" << endl;
+      fid << "     46  0.108227D-01  0.613785D-01  0.174835D-01  0.720595D-02  0.617178D-01" << endl;
+      fid << "               41            42            43            44            45" << endl;
+      fid << "     41  0.100000D+01" << endl;
+      fid << "     42  0.658292D+00  0.100000D+01" << endl;
+      fid << "     43  0.104764D-04  0.720595D-02  0.100000D+01" << endl;
+      fid << "     44  0.720595D-02  0.617178D-01  0.658292D+00  0.100000D+01" << endl;
+      fid << "     45  0.571644D-03  0.366357D-01  0.125798D-01  0.128011D+00  0.100000D+01" << endl;
+      fid << "     46  0.366357D-01  0.168873D+00  0.128011D+00  0.365470D+00  0.658292D+00" << endl;
+      fid << "               46" << endl;
+      fid << "     46  0.100000D+01" << endl;
+      fid.close();
+    }
+
+    LogReader lr(test_file);
+    lr.read();
+
+    Eigen::MatrixXd overlap = lr.getOverlapMatrix(); 
+
+    // We will test the corners of the overlap matrix and a few elements 
+    // at random
+    assert(overlap(0,0)==1);
+    assert(overlap(0,45)==0.01427);
+    assert(overlap(45,0)==0.01427);
+    assert(overlap(45,45)==1);
+
+    assert(overlap(10,6)==0.588690);
+    assert(overlap(6,10)==0.588690);
+
+    assert(overlap(38,27)==0.0850413);
+    assert(overlap(27,38)==0.0850413);
+
+    assert(overlap(26,22)==0.569754);
+    assert(overlap(26,22)==0.569754);
+  }
+
   cout << "Testing: LogReader read" << endl;
   {
 

From 9d704766d885724c576630b1235f98c1d1ebcc8c Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Mon, 29 Apr 2019 23:47:19 -0600
Subject: [PATCH 12/68] Added overlap test

---
 src/tests/test_logreader.cpp | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index a663a2a..7e570d0 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -141,12 +141,12 @@ int main(void) {
     {
       ofstream fid;
       fid.open(test_file);
-      fid << "*** Overlap ***                                                             " << endl;
-      fid << "                1             2             3             4             5    " << endl;
-      fid << "      1  0.100000D+01                                                        " << endl;
-      fid << "      2  0.219059D+00  0.100000D+01                                          " << endl;
-      fid << "      3  0.000000D+00  0.000000D+00  0.100000D+01                            " << endl;
-      fid << "      4  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01              " << endl;
+      fid << " *** Overlap ***                                                             " << endl;
+      fid << "                1             2             3             4             5" << endl;
+      fid << "      1  0.100000D+01" << endl;
+      fid << "      2  0.219059D+00  0.100000D+01" << endl;
+      fid << "      3  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
+      fid << "      4  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
       fid << "      5  0.000000D+00  0.000000D+00  0.000000D+00  0.000000D+00  0.100000D+01" << endl;
       fid << "      6  0.184261D+00  0.812273D+00  0.000000D+00  0.000000D+00  0.000000D+00" << endl;
       fid << "      7  0.000000D+00  0.000000D+00  0.569754D+00  0.000000D+00  0.000000D+00" << endl;
@@ -395,11 +395,18 @@ int main(void) {
 
     Eigen::MatrixXd overlap = lr.getOverlapMatrix(); 
 
+    cout << "Overlap Matrix rows " << overlap.rows() << " cols " << overlap.cols() << endl;
+    assert(overlap.rows()==46);
+    assert(overlap.cols()==46);
     // We will test the corners of the overlap matrix and a few elements 
     // at random
+    cout << "row  1  1 1.000 " << overlap(0,0) << endl;
     assert(overlap(0,0)==1);
-    assert(overlap(0,45)==0.01427);
-    assert(overlap(45,0)==0.01427);
+    cout << "row  1 46 0.01427 " << overlap(0,45) << endl;
+    assert(overlap(0,45)==0.0142782);
+    cout << "row 46  1 0.01427 " << overlap(45,0) << endl;
+    assert(overlap(45,0)==0.0142782);
+    cout << "row 46 46 1.000 " << overlap(45,45) << endl;
     assert(overlap(45,45)==1);
 
     assert(overlap(10,6)==0.588690);
@@ -427,7 +434,8 @@ int main(void) {
     for (auto c : basisFuncCount) {
       cout << c << endl;
     }
-    auto xyz = lr.getCoords();
+
+    vector<vector<double>> xyz = lr.getCoords();
     auto x = xyz.at(0);
     auto y = xyz.at(1);
     auto z = xyz.at(2);

From c84823dbff05ea86968d678392e22d2fbe55ec15 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Mon, 29 Apr 2019 23:48:49 -0600
Subject: [PATCH 13/68] checkpoint

---
 src/libcatnip/io/file_readers/logreader.cpp | 14 ++++++--------
 src/tests/test_logreader.cpp                |  4 ++--
 src/tests/test_punreader.cpp                |  5 +++--
 src/tests/test_qc_functions.cpp             |  2 +-
 4 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/libcatnip/io/file_readers/logreader.cpp b/src/libcatnip/io/file_readers/logreader.cpp
index 1657492..700339c 100644
--- a/src/libcatnip/io/file_readers/logreader.cpp
+++ b/src/libcatnip/io/file_readers/logreader.cpp
@@ -77,6 +77,7 @@ void LogReader::AOFunctionSectionReader(void *ptr) {
     while (!iss.eof()) {
       string Tot_Alpha_Beta_Spin;
       iss >> Tot_Alpha_Beta_Spin;
+      trim(Tot_Alpha_Beta_Spin);
       orbVals.push_back(stod(Tot_Alpha_Beta_Spin));
     }
     LR_ptr->orb_[make_pair(atom_num, elemType)][orbType] = orbVals;
@@ -116,7 +117,6 @@ void LogReader::AOFunctionSectionReader(void *ptr) {
     }
 
     ++atom_num;
-    // getline(LR_ptr->fid_,line);
     if (foundSubStrInStr(line, end_pattern)) {
       sectionEnd = true;
     }
@@ -166,14 +166,13 @@ void LogReader::OverlapSectionReader(void *ptr) {
 
   // Create a matrix and place all the current values in there
   
-  //Matrix *mat_S = new Matrix(countCoef, countCoef);
   Eigen::MatrixXd matrix_S(countCoef,countCoef);
-  
+
   for (size_t row_ind = 0; row_ind < first_coefs.size(); ++row_ind) {
-    Eigen::Map<Eigen::VectorXd> eigen_vec((first_coefs.at(row_ind).data()),first_coefs.at(row_ind).size());
-    matrix_S.row(row_ind) = eigen_vec;
+    Eigen::Map<Eigen::RowVectorXd> eigen_row((first_coefs.at(row_ind).data()),first_coefs.at(row_ind).size());
+    matrix_S.block(row_ind,0,1,eigen_row.size()) = eigen_row;
+    matrix_S.block(0,row_ind,eigen_row.size(),1) = eigen_row.transpose();
   }
-
   int sectionReads = countCoef / 5;
   if (countCoef % 5 > 0) {
     ++sectionReads;
@@ -189,7 +188,6 @@ void LogReader::OverlapSectionReader(void *ptr) {
       istringstream iss(line);
       string dummy;
       iss >> dummy;
-      //int localCoefCount = 1;
       int localCoefCount = 0;
       while (!iss.eof()) {
         string s_coef;
@@ -197,7 +195,6 @@ void LogReader::OverlapSectionReader(void *ptr) {
         string val = grabStrBeforeFirstOccurance(s_coef, "D");
         string expon = grabStrAfterFirstOccurance(s_coef, "D");
         double value = stod(val) * pow(10.0, stod(expon));
-       
         matrix_S(sectionCoef,currentSectionStart + localCoefCount) = value;
         if ((sectionCoef) != (currentSectionStart + localCoefCount)) {
           matrix_S(currentSectionStart + localCoefCount,sectionCoef) = value;
@@ -210,6 +207,7 @@ void LogReader::OverlapSectionReader(void *ptr) {
     currentSectionStart += 5;
     getline(LR_ptr->fid_, line);
   }
+  
   LR_ptr->S_ = matrix_S;
   LOG("Success reading Overlap coefficients from .log file", 2);
   return;
diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index 7e570d0..784d1a3 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -402,9 +402,9 @@ int main(void) {
     // at random
     cout << "row  1  1 1.000 " << overlap(0,0) << endl;
     assert(overlap(0,0)==1);
-    cout << "row  1 46 0.01427 " << overlap(0,45) << endl;
+    cout << "row  1 46 0.0142782 " << overlap(0,45) << endl;
     assert(overlap(0,45)==0.0142782);
-    cout << "row 46  1 0.01427 " << overlap(45,0) << endl;
+    cout << "row 46  1 0.0142782 " << overlap(45,0) << endl;
     assert(overlap(45,0)==0.0142782);
     cout << "row 46 46 1.000 " << overlap(45,45) << endl;
     assert(overlap(45,45)==1);
diff --git a/src/tests/test_punreader.cpp b/src/tests/test_punreader.cpp
index 87136cd..0893860 100644
--- a/src/tests/test_punreader.cpp
+++ b/src/tests/test_punreader.cpp
@@ -4,6 +4,7 @@
 #include <iostream>
 #include <string>
 #include <vector>
+#include <eigen3/Eigen/Dense>
 
 using namespace catnip;
 using namespace std;
@@ -18,8 +19,8 @@ int main(void) {
     PunReader pr("../../../GAUSSIANFILES/90_unordered/90_pair.pun");
     pr.read();
 
-    auto m = pr.getCoefsMatrix("Alpha");
-    assert(m->get_rows() == 92);
+    Eigen::MatrixXd m = pr.getCoefsMatrix("Alpha");
+    assert(m.rows() == 92);
     assert(pr.restrictedShell());
   }
   return 0;
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index 452e850..b377280 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -74,7 +74,7 @@ int main(void) {
     assert(matchA.at(1) == 4);
 
     assert(matchB.at(0) == 0);
-    assert(matchB.at(1) == 4);
+    assert(matchB.at(1) == 3);
     assert(matchB.at(2) == 2);
 
     vector<int> basisFuncDimer;

From 54b55e516a6507e0a25439c557a654516dd60e79 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 30 Apr 2019 00:05:09 -0600
Subject: [PATCH 14/68] Fixed error that was introduced

---
 src/libcatnip/qc_functions.cpp | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index d40d2f7..d978876 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -469,7 +469,7 @@ void updateSwapLists(vector<pair<int, int>> &monBmatch,
   for (auto p : monBmatch) {
     if (p.first != p.second) {
       auto it = p_atom_mat_coef.begin();
-      Eigen::MatrixXd & temp = *(next(it, p.first));
+      Eigen::MatrixXd temp = *(next(it, p.first));
       *(next(it, p.first)) = *(next(it, p.second));
       *(next(it, p.second)) = temp;
     }
@@ -477,7 +477,7 @@ void updateSwapLists(vector<pair<int, int>> &monBmatch,
   for (auto p : monAmatch) {
     if (p.first != p.second) {
       auto it = p_atom_mat_coef.begin();
-      Eigen::MatrixXd & temp = *(next(it, p.first));
+      Eigen::MatrixXd temp = *(next(it, p.first));
       *(next(it, p.first)) = *(next(it, p.second));
       *(next(it, p.second)) = temp;
     }
@@ -505,7 +505,9 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
   if (ColRowMerge.compare("Columns") == 0) {
     int col = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
-      Eigen::MatrixXd & mat = *it;
+      Eigen::MatrixXd mat = *it;
+      cout << "Cycling columns to merge" << endl;
+      cout << mat << endl;
       int row = 0;
       if (col > cols)
         throw runtime_error("Your new matrix is not large enough");
@@ -523,6 +525,7 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
     int row = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
       Eigen::MatrixXd mat = *it;
+      cout << "Cycling rows " << endl;
       int col = 0;
       if (row > rows)
         throw runtime_error("Your new matrix is not large enough");
@@ -539,6 +542,7 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
   } else {
     throw invalid_argument("Unrecognized merge type for list of matrices");
   }
+  cout << full_matrix << endl;
   return full_matrix;
 }
 
@@ -579,9 +583,23 @@ Eigen::MatrixXd unscramble_Coef(
     pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
     monBmatch.push_back(pr);
   }
+  cout << "Contents of list before swap" << endl;
+  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
+    cout << mat << "\n" << endl;
+  }
 
   refreshSwapOrder(monBmatch, monAmatch);
+  cout << "Contents of list before update" << endl;
+  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
+    cout << mat << "\n" << endl;
+  }
+
   updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
+  cout << "Contents of list" << endl;
+  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
+    cout << mat << "\n" << endl;
+  }
+
   Eigen::MatrixXd dimerCoef_new = createNewMatrix(
       p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
 
@@ -632,7 +650,10 @@ Eigen::MatrixXd unscramble_S(
   Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
     list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
-
+    cout << "List of split matrices" << endl;
+    for( Eigen::MatrixXd & mat : p_atom_mat_S ){
+      cout << mat << "\n" << endl;
+    }
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 0; i < matchDimerA.size(); ++i) {
       pair<int, int> pr(i, matchDimerA.at(i));

From e13daaa71cf601b3b2308d19ccbb5592d0e15d1e Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 30 Apr 2019 21:44:41 -0600
Subject: [PATCH 15/68] Updated print statment and fixed error

---
 src/libcatnip/qc_functions.cpp | 134 +++++++++++++++++----------------
 src/libcatnip/qc_functions.hpp |  16 ++--
 src/tools/main.cpp             |   9 +--
 3 files changed, 81 insertions(+), 78 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index d978876..3346699 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -52,37 +52,38 @@ unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
 void TransferComplex::calculate_transfer_integral_() {
 
   auto dimension = mat_1_Coef.rows()+mat_2_Coef.rows();
-  Eigen::MatrixXd zetaA(dimension,dimension);
-  Eigen::MatrixXd zetaB(dimension,dimension);
+  Eigen::MatrixXd zetaA(mat_1_Coef.cols(),dimension);
+  Eigen::MatrixXd zetaB(mat_2_Coef.cols(),dimension);
   if (counterPoise_) {
+
     LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
     zetaA = mat_1_Coef;
     zetaB = mat_2_Coef;
   } else {
     LOG("Creating zeta matrices from coefficients", 2);
     zetaA << mat_1_Coef, Eigen::MatrixXd::Zero(mat_1_Coef.rows(),mat_2_Coef.cols()); 
-    zetaA << Eigen::MatrixXd::Zero(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef; 
+    zetaB << Eigen::MatrixXd::Zero(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef; 
   }
 
+  Eigen::MatrixXd zeta(dimension,dimension);
   LOG("Creating gamma and beta matrices", 2);
   Eigen::MatrixXd gammaA = zetaA * mat_S * mat_P_Coef.transpose(); 
   Eigen::MatrixXd gammaB = zetaB * mat_S * mat_P_Coef.transpose(); 
 
+  Eigen::MatrixXd gamma(dimension,dimension);
+  gamma << gammaB, gammaA;
 
   LOG("Calculating S_AB", 2);
-  S_AB.resize(gammaB.rows(),gammaA.cols());
-  S_AB = gammaB * gammaA.transpose();
+  S_AB.resize(dimension,dimension);
+  S_AB = gamma * gamma.transpose();
+  
   Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
   Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
-  Eigen::MatrixXd Energy = Eigen::MatrixXd::Identity(vec_P_OE.size(),vec_P_OE.size());
-
   Hamiltonian.resize(mat_S.rows(),mat_S.cols());
-  Hamiltonian = mat_P_Coef * mat_S * mat_P_Coef.transpose();
-
-  Hamiltonian_eff.resize(Hamiltonian.rows(),Hamiltonian.cols());
-  Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt.transpose();  
+  Hamiltonian = gamma * vec_P_OE.asDiagonal() * gamma.transpose();
   
+  Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt;  
 }
 
 void TransferComplex::printTransferIntegral(
@@ -98,11 +99,11 @@ void TransferComplex::printTransferIntegral(
           " value is in reference to the HOMO and must be a negative number");
     }
     // Number of orbitals that are choices
-    if (MO_A <= (-1 * Orbs1.second)) {
+    if (MO_A <= (-1 * HOMO_A_)) {
       string err = "You are trying to access HOMO" + to_string(MO_A) +
                    " but there "
                    "are only " +
-                   to_string(Orbs1.second) + " HOMO orbitals";
+                   to_string(HOMO_A_) + " HOMO orbitals";
       throw invalid_argument(err);
     }
   } else if (HOMO_OR_LUMO_A.compare("LUMO") == 0) {
@@ -111,7 +112,7 @@ void TransferComplex::printTransferIntegral(
           "Having specified LUMO the MO_A"
           " value is in reference to the LUMO and must be a positive number");
     }
-    int allowed_LUMO = Orbs1.first - Orbs1.second;
+    int allowed_LUMO = mat_1_Coef.rows() - HOMO_A_;
     if (MO_A >= allowed_LUMO) {
       string err = "You are trying to access LUMO+" + to_string(MO_A) +
                    " but there "
@@ -131,11 +132,11 @@ void TransferComplex::printTransferIntegral(
           "Having specified HOMO the MO_B"
           " value is in reference to the HOMO and must be a negative number");
     }
-    if (MO_B <= (-1 * Orbs2.second)) {
+    if (MO_B <= (-1 * HOMO_B_)) {
       string err = "You are trying to access HOMO" + to_string(MO_B) +
                    " but there "
                    "are only " +
-                   to_string(Orbs2.second) + " HOMO orbitals";
+                   to_string(HOMO_B_) + " HOMO orbitals";
       throw invalid_argument(err);
     }
   } else if (HOMO_OR_LUMO_B.compare("LUMO") == 0) {
@@ -144,7 +145,7 @@ void TransferComplex::printTransferIntegral(
           "Having specified LUMO the MO_B"
           " value is in reference to the LUMO and must be a positive number");
     }
-    int allowed_LUMO = Orbs2.first - Orbs2.second;
+    int allowed_LUMO = mat_2_Coef.rows() - HOMO_B_;
     if (MO_B >= allowed_LUMO) {
       string err = "You are trying to access LUMO+" + to_string(MO_B) +
                    " but there "
@@ -167,43 +168,69 @@ void TransferComplex::printTransferIntegral_(
     const pair<string,int>& orbital1,
     const pair<string,int>& orbital2) const {
 
+  int offset = mat_1_Coef.rows();
   int orbital1_num = 0;
   int orbital2_num = 0;
   if(orbital1.first.compare("HOMO")==0){
     assert(orbitalValid_(orbital1)==true); 
-    orbital1_num = orbital1.second;
+    orbital1_num = orbital1.second + HOMO_A_-1;
+  }else if(orbital1.first.compare("LUMO")==0){
+    assert(orbitalValid_(orbital1)==true); 
+    orbital1_num = orbital1.second + HOMO_A_;
+  }
+  if(orbital2.first.compare("HOMO")==0){
+    assert(orbitalValid_(orbital2)==true); 
+    orbital2_num = offset+orbital2.second + HOMO_B_-1;
   }else if(orbital2.first.compare("LUMO")==0){
     assert(orbitalValid_(orbital2)==true); 
-    orbital2_num = orbital2.second;
+    orbital2_num = offset+orbital2.second + HOMO_B_;
   }
   double J_ab = Hamiltonian(orbital1_num,orbital2_num);
   double e_a = Hamiltonian(orbital1_num,orbital1_num);
   double e_b = Hamiltonian(orbital2_num,orbital2_num);
   double S_ab = S_AB(orbital1_num,orbital2_num); 
+  
+  cout << "\nPre-Orthonormalization" << endl;
+  cout << "J_ab             " << J_ab * hartreeToeV << " eV\n";
+  cout << "e_a              " << e_a * hartreeToeV << " eV\n";
+  cout << "e_b              " << e_b * hartreeToeV << " eV\n";
+  cout << "S_ab              " << S_ab << "\n" << endl;
+
+  cout << "Single Orbital DIPRO" << endl;
+  double J_ab_single = (J_ab - 0.5*(e_a+e_b)*S_ab)/(1-pow(S_ab,2.0));
+  double e_a_single = 0.5*((e_a+e_b)-2*J_ab*S_ab+(e_a-e_b)*pow(1-pow(S_ab,2.0),0.5))/(1-pow(S_ab,2.0));
+  double e_b_single = 0.5*((e_a+e_b)-2*J_ab*S_ab-(e_a-e_b)*pow(1-pow(S_ab,2.0),0.5))/(1-pow(S_ab,2.0));
+  cout << "J_ab_eff_single  " << J_ab_single * hartreeToeV << " eV\n";
+  cout << "e_a_eff_single   " << e_a_single * hartreeToeV << " eV\n";
+  cout << "e_b_eff_single   " << e_b_single * hartreeToeV << " eV\n" << endl;
+  
+  cout << "All Orbital DIPRO" << endl;
   double J_eff = Hamiltonian_eff(orbital1_num,orbital2_num);
-  cout << "J_ab  " << J_ab * hartreeToeV << " eV\n";
-  cout << "e_a   " << e_a * hartreeToeV << " eV\n";
-  cout << "e_b   " << e_b * hartreeToeV << " eV\n";
-  cout << "S_ab  " << S_ab << "\n";
-  cout << "J_eff " << J_eff * hartreeToeV << " eV\n";
+  double e_a_eff = Hamiltonian_eff(orbital1_num,orbital1_num);
+  double e_b_eff = Hamiltonian_eff(orbital2_num,orbital2_num);
+  cout << "J_ab_eff_all    " << J_eff * hartreeToeV << " eV\n";
+  cout << "e_a_eff_all     " << e_a_eff * hartreeToeV << " eV\n";
+  cout << "e_b_eff_all     " << e_b_eff * hartreeToeV << " eV\n" << endl;
 }
 
 void TransferComplex::printAll() const {
 
+  int HOMO_AB = HOMO_A_+HOMO_B_;
+  int LUMO_AB = HOMO_AB+1;
   int column_width = 8;
   cout << "Effective Hamiltonian" << endl;
   cout << setw(column_width+2) << ""; 
   for(int orbital_num = 0;orbital_num<Hamiltonian.cols();++orbital_num){
     string column_label = "";
-    if(orbital_num<HOMO_Orb_){
+    if(orbital_num<HOMO_AB){
       column_label+=string("HOMO");
-      if(orbital_num!=(HOMO_Orb_-1)){
-        column_label+=string("-")+to_string(HOMO_Orb_-orbital_num-1);
+      if(orbital_num!=(HOMO_AB-1)){
+        column_label+=string("-")+to_string(HOMO_AB-orbital_num-1);
       }
     }else {
       column_label+=string("LUMO");
-      if(orbital_num!=LUMO_Orb_){
-        column_label+=string("+")+to_string(orbital_num-LUMO_Orb_);
+      if(orbital_num!=LUMO_AB){
+        column_label+=string("+")+to_string(orbital_num-LUMO_AB);
       }
     } 
     cout << "| " << setw(column_width) << column_label << " ";
@@ -212,15 +239,15 @@ void TransferComplex::printAll() const {
  
   for(int orbital_num = 0;orbital_num<Hamiltonian.rows();++orbital_num){
     string column_label = "";
-    if(orbital_num<HOMO_Orb_){
+    if(orbital_num<HOMO_AB){
       column_label+=string("HOMO");
-      if(orbital_num!=(HOMO_Orb_-1)){
-        column_label+=string("-")+to_string(HOMO_Orb_-orbital_num-1);
+      if(orbital_num!=(HOMO_AB-1)){
+        column_label+=string("-")+to_string(HOMO_AB-orbital_num-1);
       }
     }else {
       column_label+=string("LUMO");
-      if(orbital_num!=LUMO_Orb_){
-        column_label+=string("+")+to_string(orbital_num-LUMO_Orb_);
+      if(orbital_num!=LUMO_AB){
+        column_label+=string("+")+to_string(orbital_num-LUMO_AB);
       }
     } 
     cout << setw(column_width+2) << column_label;
@@ -233,20 +260,22 @@ void TransferComplex::printAll() const {
 }
 
 bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital) const{
+  int HOMO_AB = HOMO_A_+HOMO_B_;
+  int LUMO_AB = HOMO_AB+1;
   if(orbital.first.compare("HOMO")==0){
     if(orbital.second>0){
       cerr << "HOMO orbital number is not negative or 0" << endl;
       return false;  
     }
-    if(orbital.second<=(-1*HOMO_Orb_)){
-      cerr << "HOMO orbital does not exst " << orbital.second << endl;
+    if(orbital.second>HOMO_AB){
+      cerr << "HOMO orbital does not exst " << orbital.second << " "<< HOMO_AB << endl;
       return false;
     }
   }else if(orbital.first.compare("LUMO")==0){
     if(orbital.second<0){
       cerr << "LUMO orbital number is not positive or 0" << endl; return false;  
     }
-    if(orbital.second>(Hamiltonian_eff.rows()-LUMO_Orb_)){
+    if(orbital.second>(Hamiltonian_eff.rows()-LUMO_AB)){
       cerr << "LUMO orbital does not exst " << orbital.second << endl;
       return false;
     }
@@ -506,8 +535,6 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
     int col = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
       Eigen::MatrixXd mat = *it;
-      cout << "Cycling columns to merge" << endl;
-      cout << mat << endl;
       int row = 0;
       if (col > cols)
         throw runtime_error("Your new matrix is not large enough");
@@ -525,7 +552,6 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
     int row = 0;
     for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
       Eigen::MatrixXd mat = *it;
-      cout << "Cycling rows " << endl;
       int col = 0;
       if (row > rows)
         throw runtime_error("Your new matrix is not large enough");
@@ -542,7 +568,6 @@ Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const in
   } else {
     throw invalid_argument("Unrecognized merge type for list of matrices");
   }
-  cout << full_matrix << endl;
   return full_matrix;
 }
 
@@ -583,22 +608,9 @@ Eigen::MatrixXd unscramble_Coef(
     pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
     monBmatch.push_back(pr);
   }
-  cout << "Contents of list before swap" << endl;
-  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
-    cout << mat << "\n" << endl;
-  }
 
   refreshSwapOrder(monBmatch, monAmatch);
-  cout << "Contents of list before update" << endl;
-  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
-    cout << mat << "\n" << endl;
-  }
-
   updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
-  cout << "Contents of list" << endl;
-  for( Eigen::MatrixXd & mat : p_atom_mat_coef ){
-    cout << mat << "\n" << endl;
-  }
 
   Eigen::MatrixXd dimerCoef_new = createNewMatrix(
       p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
@@ -650,10 +662,6 @@ Eigen::MatrixXd unscramble_S(
   Eigen::MatrixXd S_new(S.rows(),S.cols());
   {
     list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
-    cout << "List of split matrices" << endl;
-    for( Eigen::MatrixXd & mat : p_atom_mat_S ){
-      cout << mat << "\n" << endl;
-    }
     vector<pair<int, int>> monAmatch;
     for (unsigned i = 0; i < matchDimerA.size(); ++i) {
       pair<int, int> pr(i, matchDimerA.at(i));
@@ -740,8 +748,8 @@ Eigen::MatrixXd unscramble_S(
 }
 
 TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2Coef,
-                                 Eigen::MatrixXd matPCoef, std::pair<int, int> MOs1,
-                                 std::pair<int, int> MOs2, Eigen::MatrixXd matS,
+                                 Eigen::MatrixXd matPCoef, const int HOMO_A,
+                                 const int HOMO_B, Eigen::MatrixXd matS,
                                  Eigen::VectorXd vecPOE, bool cp) {
 
   unscrambled_ = false;
@@ -781,8 +789,8 @@ TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2C
   mat_2_Coef = mat2Coef;
   mat_P_Coef.resize(matPCoef.rows(),matPCoef.cols());
   mat_P_Coef = matPCoef;
-  Orbs1 = MOs1;
-  Orbs2 = MOs2;
+  HOMO_A_ = HOMO_A;
+  HOMO_B_ = HOMO_B;
   mat_S.resize(matS.rows(),matS.cols());
   mat_S = matS;
   vec_P_OE.resize(vecPOE.size());
@@ -842,7 +850,7 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
 void TransferComplex::calcJ() {
 
   if (unscrambled_ == false) {
-    cerr << "WARNING unable to automatically line up basis functions of"
+    cerr << "\nWARNING unable to automatically line up basis functions of"
             " monomers with dimers, you better make sure they correctly"
             " line up or run the calculations again with the correct "
             "flag pop=full"
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index a84bfb1..086af14 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -20,8 +20,8 @@ class TransferComplex {
     Eigen::MatrixXd mat_P_Coef;
     // Stores the number of Molecular orbitals
     // and the HOMO for both monomer 1 and 2
-    std::pair<int, int> Orbs1;
-    std::pair<int, int> Orbs2;
+    //std::pair<int, int> Orbs1;
+    //std::pair<int, int> Orbs2;
 
     /**
      * \brief basis function overlap matrix
@@ -42,9 +42,11 @@ class TransferComplex {
      **/
     Eigen::MatrixXd Hamiltonian_eff;
 
-    int HOMO_Orb_;
-    int LUMO_Orb_;
-    Eigen::VectorXd vec_P_OE;
+    int HOMO_A_;
+    int HOMO_B_;
+    //int HOMO_Orb_;
+    //int LUMO_Orb_;
+    Eigen::RowVectorXd vec_P_OE;
     // If unscrambaling is required
     bool unscrambled_;
     bool counterPoise_;
@@ -63,8 +65,8 @@ class TransferComplex {
         Eigen::MatrixXd mat1Coef, 
         Eigen::MatrixXd mat2Coef, 
         Eigen::MatrixXd matPCoef,
-        std::pair<int, int> MOs1, 
-        std::pair<int, int> MOs2,
+        const int HOMO_A, 
+        const int HOMO_B,
         Eigen::MatrixXd matS, 
         Eigen::VectorXd vecPOE, 
         bool cp);
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 2e4db86..57648b7 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -125,14 +125,8 @@ int main(int argc, const char *argv[]) {
     vector<int> basis_1 = lr_1.getBasisFuncCount();
     vector<int> basis_2 = lr_2.getBasisFuncCount();
 
-    int MO1 = static_cast<int>(vec_1_OE.size());
-    int MO2 = static_cast<int>(vec_2_OE.size());
-
-    pair<int, int> Orbs1 = {MO1, HOMO1};
-    pair<int, int> Orbs2 = {MO2, HOMO2};
-
     LOG("Creating transfercomplex", 1);
-    TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, Orbs1, Orbs2, mat_S,
+    TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, HOMO1, HOMO2, mat_S,
                        vec_P_OE, par->getCounterPoise());
 
     // Set the transfer complex to counterpoise if it is the case.
@@ -179,7 +173,6 @@ int main(int argc, const char *argv[]) {
     LOG("Calculating transfer integral", 1);
     TC.calcJ();
     TC.printTransferIntegral(orbitaltypes, orbitalnums);
-
   }
 
   return 0;

From eae3804efd7c0a3826370fd5d05f17790201b465 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 30 Apr 2019 21:46:20 -0600
Subject: [PATCH 16/68] Updated version

---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index bfdae7d..8ff81e4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,8 +12,8 @@ option(CODE_COVERAGE "Enable coverage reporting" OFF)
 ##############################################################################
 # Defining settings 
 ##############################################################################
-set(calcJ_VERSION_MAJOR 1 )
-set(calcJ_VERSION_MINOR 8 )
+set(calcJ_VERSION_MAJOR 2 )
+set(calcJ_VERSION_MINOR 0 )
 set(calcJ_YEAR_PUBLISHED 2018 )
 set(calcJ_AUTHOR_SURNAME "\"Brown\"" )
 set(calcJ_AUTHOR_INITIALS "\"J. S.\"" )

From c9ba31724aec6e255b5b9b99f4fc06fa01997b83 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 30 Apr 2019 21:58:12 -0600
Subject: [PATCH 17/68] Added switch for printing all transfer integrals

---
 src/libcatnip/io/io.cpp      | 17 +++++++++++++++++
 src/libcatnip/parameters.hpp |  7 +++++--
 src/tools/main.cpp           |  6 +++++-
 3 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/src/libcatnip/io/io.cpp b/src/libcatnip/io/io.cpp
index 28756bc..68e802c 100644
--- a/src/libcatnip/io/io.cpp
+++ b/src/libcatnip/io/io.cpp
@@ -167,6 +167,12 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   desc = "Print the version";
   flag18.push_back(desc);
 
+  vector<string> flag19;
+  flag19.push_back("--all");
+  flag19.push_back("-a");
+  desc = "Print all transfer integrals, in matrix form";
+  flag19.push_back(desc);
+
   set<vector<string>> flags;
   flags.insert(flag1);
   flags.insert(flag2);
@@ -184,6 +190,7 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   flags.insert(flag16);
   flags.insert(flag17);
   flags.insert(flag18);
+  flags.insert(flag19);
 
   unique_ptr<ArgumentParser> ArgPars(new ArgumentParser(flags));
 
@@ -303,6 +310,15 @@ unique_ptr<ArgumentParser> prepareParser(void) {
     ArgPars->setFlagDefaultValue("--counter_poise", "OFF");
   }
 
+  // Set argument for allowing printing of all transfer integrals
+  {
+    ArgPars->setFlagArgOpt("--all", "ARGUMENT_SWITCH",
+        "PROPERTY_SWITCH", "DEFAULT", "OFF");
+
+    // By default the flag counter poise is turned off
+    ArgPars->setFlagDefaultValue("--all", "OFF");
+  }
+
   {
     ArgPars->setFlagArgOpt("--citation", "ARGUMENT_SWITCH", "PROPERTY_SWITCH",
                            "DEFAULT", "OFF");
@@ -424,6 +440,7 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
 
   // Determine if we are doing a counterpoise calculation
   Par->setCounterPoise(ArgParse->getInt("--counter_poise"));
+  Par->setPrintSwitch(ArgParse->getInt("--all"));
   Par->setCitation(ArgParse->getInt("--citation"));
   // Read Orbital related flags
   {
diff --git a/src/libcatnip/parameters.hpp b/src/libcatnip/parameters.hpp
index 1664717..59590b4 100644
--- a/src/libcatnip/parameters.hpp
+++ b/src/libcatnip/parameters.hpp
@@ -29,7 +29,7 @@ class Parameters {
 
   bool citation;
   bool counterPoise;
-
+  bool all;
  public:
   Parameters()
       : log1_(""),
@@ -47,7 +47,8 @@ class Parameters {
         orb_numP(0),
         orb_num1(0),
         orb_num2(0),
-        counterPoise(false){};
+        counterPoise(false),
+        all(false) {};
 
   std::string getLog1() const { return log1_; }
   std::string getLog2() const { return log2_; }
@@ -68,6 +69,7 @@ class Parameters {
   int getOrbNum1() const { return orb_num1; }
   int getOrbNum2() const { return orb_num2; }
   bool getCounterPoise() const { return counterPoise; }
+  bool getPrintSwitch() const { return all; }
   bool getCitation() const { return citation; }
 
   void setLog1(const std::string& log1);
@@ -89,6 +91,7 @@ class Parameters {
   void setOrbNum1(const int& num) { orb_num1 = num; }
   void setOrbNum2(const int& num) { orb_num2 = num; }
   void setCounterPoise(bool cp) { counterPoise = cp; }
+  void setPrintSwitch(bool print_all) { all = print_all; }
   void setCitation(bool cite) { citation = cite; }
 };
 
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 57648b7..28742e8 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -172,7 +172,11 @@ int main(int argc, const char *argv[]) {
 
     LOG("Calculating transfer integral", 1);
     TC.calcJ();
-    TC.printTransferIntegral(orbitaltypes, orbitalnums);
+    if(par->getPrintSwitch()){
+      TC.printAll();
+    }else{
+      TC.printTransferIntegral(orbitaltypes, orbitalnums);
+    }
   }
 
   return 0;

From 7797dae999ef3c0b397b40025e49479ec2f40cde Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 30 Apr 2019 22:05:46 -0600
Subject: [PATCH 18/68] Add eigen as a package to ci

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 7b97a17..d5f8369 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,6 +17,7 @@ jobs:
       compiler: gcc
       script: ./scripts/deploy.bash
       apt:
+        packages: eigen
         packages: gcov
         packages: lcov
 

From 9cbfb04627a1956d8cafad005cbaea0950347ab8 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Wed, 1 May 2019 11:23:46 -0600
Subject: [PATCH 19/68] Added eigen to ci development stage

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index d5f8369..cbcd0fd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,7 @@ dist: xenial
 addons:
   apt:
     update: true
+    packages: eigen
 
 language: cpp
 

From ab1c42b8389d9276845259ffe7a2bd804342e360 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Wed, 1 May 2019 13:05:54 -0600
Subject: [PATCH 20/68] Corrected formatting of print all

---
 src/libcatnip/qc_functions.cpp | 123 ++++++++++++++++++++++-----------
 1 file changed, 84 insertions(+), 39 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index 3346699..d27f23a 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -215,48 +215,93 @@ void TransferComplex::printTransferIntegral_(
 
 void TransferComplex::printAll() const {
 
-  int HOMO_AB = HOMO_A_+HOMO_B_;
-  int LUMO_AB = HOMO_AB+1;
-  int column_width = 8;
+  int column_width = 14;
   cout << "Effective Hamiltonian" << endl;
-  cout << setw(column_width+2) << ""; 
-  for(int orbital_num = 0;orbital_num<Hamiltonian.cols();++orbital_num){
-    string column_label = "";
-    if(orbital_num<HOMO_AB){
-      column_label+=string("HOMO");
-      if(orbital_num!=(HOMO_AB-1)){
-        column_label+=string("-")+to_string(HOMO_AB-orbital_num-1);
-      }
-    }else {
-      column_label+=string("LUMO");
-      if(orbital_num!=LUMO_AB){
-        column_label+=string("+")+to_string(orbital_num-LUMO_AB);
-      }
-    } 
-    cout << "| " << setw(column_width) << column_label << " ";
-  }
-  cout << "|" << endl; 
- 
-  for(int orbital_num = 0;orbital_num<Hamiltonian.rows();++orbital_num){
-    string column_label = "";
-    if(orbital_num<HOMO_AB){
-      column_label+=string("HOMO");
-      if(orbital_num!=(HOMO_AB-1)){
-        column_label+=string("-")+to_string(HOMO_AB-orbital_num-1);
-      }
-    }else {
-      column_label+=string("LUMO");
-      if(orbital_num!=LUMO_AB){
-        column_label+=string("+")+to_string(orbital_num-LUMO_AB);
+
+  int col_offset = mat_1_Coef.cols();
+  int start_col = 0;
+  int end_col = 5;
+  while(start_col<Hamiltonian.cols()){
+  
+    cout << setw(column_width-2) << left << ""; 
+    if(end_col>Hamiltonian.cols()){
+      end_col = Hamiltonian.cols();
+    }
+    for(int orbital_num = start_col;orbital_num<end_col;++orbital_num){
+      string column_label = "";
+      if(orbital_num<HOMO_A_ || (orbital_num>=col_offset && orbital_num<(HOMO_B_+col_offset))){
+        if(orbital_num<col_offset){
+          column_label=string("A HOMO");
+        }else{
+          column_label=string("B HOMO");
+        }
+        if(orbital_num!=(HOMO_A_-1) && orbital_num!=(col_offset+HOMO_B_-1)){
+          if(orbital_num<col_offset){
+            column_label+=to_string(orbital_num+1-HOMO_A_);
+          }else {
+            column_label+=to_string(orbital_num+1-col_offset-HOMO_B_);
+          }
+        }
+      }else {
+        if((orbital_num>=HOMO_A_ && orbital_num<col_offset) || orbital_num>(col_offset+HOMO_B_)){
+          if(orbital_num<col_offset){
+            column_label=string("A LUMO");
+          }else{
+            column_label=string("B LUMO");
+          }
+          if(orbital_num!=(HOMO_A_) && orbital_num!=(col_offset+HOMO_B_)){
+            if(orbital_num<col_offset){
+              column_label+=string("+")+to_string(orbital_num-HOMO_A_);
+            }else{
+              column_label+=string("+")+to_string(orbital_num-col_offset-HOMO_B_);
+            }
+          }
+        }
+      } 
+      cout << " | " << setw(column_width) << right << column_label;
+    }
+    cout << " |" << endl; 
+
+    for(int orbital_num = 0;orbital_num<Hamiltonian.rows();++orbital_num){
+      string column_label = "";
+      if(orbital_num<HOMO_A_ || (orbital_num>=col_offset && orbital_num<(HOMO_B_+col_offset))){
+        if(orbital_num<col_offset){
+          column_label=string("A HOMO");
+        }else{
+          column_label=string("B HOMO");
+        }
+        if(orbital_num!=(HOMO_A_-1) && orbital_num!=(col_offset+HOMO_B_-1)){
+          if(orbital_num<col_offset){
+            column_label+=to_string(orbital_num+1-HOMO_A_);
+          }else {
+            column_label+=to_string(orbital_num+1-col_offset-HOMO_B_);
+          }
+        }
+      }else {
+        if(orbital_num < col_offset){
+          column_label=string("A LUMO");
+        }else{
+          column_label=string("B LUMO");
+        }
+        if(orbital_num!=(HOMO_A_) && orbital_num!=(col_offset+HOMO_B_)){
+          if(orbital_num<col_offset){
+            column_label+=string("+")+to_string(orbital_num-HOMO_A_);
+          }else{
+            column_label+=string("+")+to_string(orbital_num-col_offset-HOMO_B_);
+          }
+        }
+      } 
+      cout << " " << setw(column_width-3) << left << column_label << " ";
+      for(int orbital_num2 = start_col;orbital_num2<end_col;++orbital_num2){
+        cout << "| "<< right  << scientific << std::setprecision(6)  << setw(column_width) << Hamiltonian_eff(orbital_num,orbital_num2) << " ";
       }
-    } 
-    cout << setw(column_width+2) << column_label;
-    for(int orbital_num2 = 0;orbital_num2<Hamiltonian.cols();++orbital_num2){
-      cout << "| " << setw(column_width) << Hamiltonian_eff(orbital_num2,orbital_num2) << " ";
+      cout << "|" << endl; 
     }
-    cout << "|" << endl; 
-  }
- 
+
+    start_col+=5;
+    end_col+=5;
+    cout << endl;
+  } 
 }
 
 bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital) const{

From c71c9ae4a227199c9fb8cc49228414f42f8b47f1 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 2 May 2019 12:02:59 -0600
Subject: [PATCH 21/68] UPdate eigen install in travis

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cbcd0fd..fddda62 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,7 +4,7 @@ dist: xenial
 addons:
   apt:
     update: true
-    packages: eigen
+    packages: libeigen3-dev
 
 language: cpp
 
@@ -18,7 +18,7 @@ jobs:
       compiler: gcc
       script: ./scripts/deploy.bash
       apt:
-        packages: eigen
+        packages: libeigen3-dev
         packages: gcov
         packages: lcov
 

From 43745c9da7cf484f71e6fb60aa0819b0ead87e71 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 2 May 2019 18:07:38 -0600
Subject: [PATCH 22/68] fixing eigen includes

---
 src/tests/CMakeLists.txt        | 6 +++---
 src/tests/test_qc_functions.cpp | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 134ca4b..bf8fc4b 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -28,7 +28,7 @@ if(ENABLE_TESTS)
     if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS} )
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-    target_link_libraries(unit_${PROG} libcatnip Eigen3::Eigen)
+    target_link_libraries(unit_${PROG} libcatnip)
     add_test(unit_${PROG} unit_${PROG})
   endforeach(PROG)
 endif(ENABLE_TESTS)
@@ -44,7 +44,7 @@ if(ENABLE_INTEGRATION_TESTS)
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
-    target_link_libraries(integration${PROG} libcatnip Eigen3::Eigen)
+    target_link_libraries(integration${PROG} libcatnip)
     add_test(integration${PROG} integration${PROG})
 
   endforeach(PROG)
@@ -53,7 +53,7 @@ if(ENABLE_INTEGRATION_TESTS)
   if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
     set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
   endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-  target_link_libraries(test_io libcatnip Eigen3::Eigen)
+  target_link_libraries(test_io libcatnip)
   add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
 
   add_custom_command(TARGET test_io
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index b377280..a5d6759 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -3,7 +3,7 @@
 #include <cassert>
 #include <iostream>
 #include <vector>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
 using namespace catnip;
 using namespace std;
 

From 71238ece4d21b0662c9d1f467e3b72cecbe8fc4b Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 2 May 2019 18:12:30 -0600
Subject: [PATCH 23/68] Fix cmake eigen call

---
 CMakeLists.txt | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8ff81e4..1d8f065 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,10 +42,10 @@ configure_file(
 # Find bash it is important for testing using scripts
 find_program (BASH_PROGRAM bash)
 find_library (GCOV gcov)
-find_package (Eigen3 3.3 REQUIRED NO_MODULE)
-if (TARGET Eigen3::Eigen)
-  message("-- Eigen found")
-endif(TARGET Eigen3::Eigen)
+#find_package (Eigen3 3.3 REQUIRED NO_MODULE)
+#if (TARGET Eigen3::Eigen)
+#  message("-- Eigen found")
+#endif(TARGET Eigen3::Eigen)
 add_definitions(-DLOG_LEVEL=${LOG_LEVEL})
 
 ##############################################################################
@@ -120,5 +120,5 @@ if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
   target_link_libraries(calc_J gcov)
   set_source_files_properties( src/tools/main.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
 endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
-target_link_libraries(calc_J libcatnip ${COMMON_LIBRARIES} Eigen3::Eigen)
+target_link_libraries(calc_J libcatnip ${COMMON_LIBRARIES})
 install( TARGETS calc_J DESTINATION bin)

From 4188483e05d185c1756d25d396165f12d86f31d8 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Tue, 14 May 2019 00:26:31 -0600
Subject: [PATCH 24/68] Fixed problem when reading overlap matrix with only a
 few coefficients

---
 src/libcatnip/io/file_readers/logreader.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/libcatnip/io/file_readers/logreader.cpp b/src/libcatnip/io/file_readers/logreader.cpp
index 700339c..3c0a0c3 100644
--- a/src/libcatnip/io/file_readers/logreader.cpp
+++ b/src/libcatnip/io/file_readers/logreader.cpp
@@ -145,9 +145,12 @@ void LogReader::OverlapSectionReader(void *ptr) {
     getline(LR_ptr->fid_, line);
     istringstream iss(line);
     iss >> countC;
+    if( line.find("Kinetic")!=string::npos){
+      break;
+    }
     int countCint = stoi(countC);
     if (countCint != (countCoef + 1)) {
-      endFirstSection = true;
+      break;
     } else {
       ++countCoef;
       vector<double> row;
@@ -165,7 +168,7 @@ void LogReader::OverlapSectionReader(void *ptr) {
   }
 
   // Create a matrix and place all the current values in there
-  
+ 
   Eigen::MatrixXd matrix_S(countCoef,countCoef);
 
   for (size_t row_ind = 0; row_ind < first_coefs.size(); ++row_ind) {

From e97a27d67f3ca41425a341173dafd732b6d0508e Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Wed, 22 May 2019 01:31:14 -0600
Subject: [PATCH 25/68] Fixed error in script with J and, dimensions of
 matrices

---
 src/libcatnip/qc_functions.cpp  | 10 +++++-----
 src/tests/test_script_calc_J.sh |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index d27f23a..0b49126 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -51,9 +51,9 @@ unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
 // Essentially calculates the transfer integral
 void TransferComplex::calculate_transfer_integral_() {
 
-  auto dimension = mat_1_Coef.rows()+mat_2_Coef.rows();
-  Eigen::MatrixXd zetaA(mat_1_Coef.cols(),dimension);
-  Eigen::MatrixXd zetaB(mat_2_Coef.cols(),dimension);
+  auto dimension = mat_1_Coef.cols()+mat_2_Coef.cols();
+  Eigen::MatrixXd zetaA(mat_1_Coef.rows(),dimension);
+  Eigen::MatrixXd zetaB(mat_2_Coef.rows(),dimension);
   if (counterPoise_) {
 
     LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
@@ -65,12 +65,12 @@ void TransferComplex::calculate_transfer_integral_() {
     zetaB << Eigen::MatrixXd::Zero(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef; 
   }
 
-  Eigen::MatrixXd zeta(dimension,dimension);
   LOG("Creating gamma and beta matrices", 2);
   Eigen::MatrixXd gammaA = zetaA * mat_S * mat_P_Coef.transpose(); 
   Eigen::MatrixXd gammaB = zetaB * mat_S * mat_P_Coef.transpose(); 
 
-  Eigen::MatrixXd gamma(dimension,dimension);
+  assert(gammaA.cols() == gammaB.cols() && "Column count between gamma A and B must be consistent");
+  Eigen::MatrixXd gamma(gammaA.rows()+gammaB.rows(),gammaA.cols());
   gamma << gammaB, gammaA;
 
   LOG("Calculating S_AB", 2);
diff --git a/src/tests/test_script_calc_J.sh b/src/tests/test_script_calc_J.sh
index a84363e..27bcc4f 100644
--- a/src/tests/test_script_calc_J.sh
+++ b/src/tests/test_script_calc_J.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# -eq 0 ]; then
-    path="./../"
+    path="./.."
 else
     path=$1
 fi
@@ -29,7 +29,7 @@ findJeff() {
   echo "Num array "${#values[@]}
   for (( i=0; i < ${#values[@]}; i++ ))
   do
-    if [ "${values[$i]}" == "J_eff" ]
+    if [ "${values[$i]}" == "J_ab_eff_single" ]
     then
       J_val=${values[$i+1]}
       break

From 95fd3bd954f358428c0abdc8d8cd46e5a0521df6 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Wed, 22 May 2019 01:44:46 -0600
Subject: [PATCH 26/68] fixed script

---
 src/tests/test_script_calc_J.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 src/tests/test_script_calc_J.sh

diff --git a/src/tests/test_script_calc_J.sh b/src/tests/test_script_calc_J.sh
old mode 100644
new mode 100755

From c458d905b5af1ab4d26f6c3f5731ab8146ccbc86 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Wed, 22 May 2019 23:22:45 -0600
Subject: [PATCH 27/68] Temporary changes

---
 src/libcatnip/qc_functions.cpp | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index 0b49126..bdd4153 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -73,16 +73,29 @@ void TransferComplex::calculate_transfer_integral_() {
   Eigen::MatrixXd gamma(gammaA.rows()+gammaB.rows(),gammaA.cols());
   gamma << gammaB, gammaA;
 
+  std::cout << "Gamma Matrix" << std::endl;
+  std::cout << gamma << std::endl;
   LOG("Calculating S_AB", 2);
   S_AB.resize(dimension,dimension);
   S_AB = gamma * gamma.transpose();
   
+  std::cout << "Overlap Matrix" << std::endl; 
+  std::cout << S_AB << std::endl;
+  /// Find out if S_AB is invertible
+  if(S_AB.determinant()==0){
+    throw invalid_argument("Error the determinant of the Molecular Orbital Overlap matrix is 0, this means it is not invertible and thus Symmetric orthogonalization cannot be applied.");
+  }
   Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
   Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
   Hamiltonian.resize(mat_S.rows(),mat_S.cols());
   Hamiltonian = gamma * vec_P_OE.asDiagonal() * gamma.transpose();
-  
+
+  std::cout << "Inverse overlap Matrix" << std::endl;
+  std::cout << S_AB_inv_sqrt << std::endl; 
+
+  std::cout << "Hamiltonian Matrix" << std::endl;
+  std::cout << Hamiltonian << std::endl; 
   Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt;  
 }
 

From fcc12f27420922cbd69c5f67b6b919720162ab32 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 23 May 2019 11:06:53 -0600
Subject: [PATCH 28/68] Removed unused function

---
 src/libcatnip/qc_functions.cpp | 55 +++++++++++-----------------------
 src/libcatnip/qc_functions.hpp |  3 --
 src/tools/main.cpp             |  4 +++
 3 files changed, 22 insertions(+), 40 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index bdd4153..1f6588f 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -21,33 +21,6 @@ namespace catnip {
 
   using namespace std;
 
-unordered_map<int, pair<double, string>> findRank(Eigen::VectorXd &Orb_E_Alpha,
-                                                  Eigen::VectorXd &Orb_E_Beta) {
-
-  vector<pair<double, string>> all;
-
-  for( int i = 0; i<Orb_E_Alpha.size();++i){
-    all.push_back(pair<double, string>(Orb_E_Alpha(i),"Alpha"));
-  }
-
-  for( int i = 0; i<Orb_E_Beta.size();++i){
-    all.push_back(pair<double, string>(Orb_E_Beta(i), "Beta"));
-  }
-  sort(all.begin(), all.end(),
-      [](const pair<double, string> &P1, const pair<double, string> &P2)
-      -> bool { return P1.first < P2.first; });
-  // Now that they are sorted we are going to update the ranks
-  int rank = 1;
-
-  unordered_map<int, pair<double, string>> rank_map;
-
-  for (auto pr : all) {
-    rank_map[rank] = pr;
-    rank++;
-  }
-  return rank_map;
-}
-
 // Essentially calculates the transfer integral
 void TransferComplex::calculate_transfer_integral_() {
 
@@ -876,32 +849,40 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
     this->mat_2_Coef = unscrambled_2_Coef;
 
     vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
+    cout << "Matching coord1 with pair" << endl;
+    for( const int & val : match_1_P ) {
+      cout << val << endl;
+    }
 
-    Eigen::MatrixXd unscrambled_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
-
-    this->mat_P_Coef = unscrambled_P_Coef;
-
-    auto unscrambled_S = unscramble_S(match_1_P, basisP, mat_S);
+    this->mat_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
 
-    this->mat_S = unscrambled_S;
+    this->mat_S = unscramble_S(match_1_P, basisP, mat_S);
 
   } else {
 
     // Stores the rows in P that match 1
     vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
 
+    cout << "Matching coord1 with pair" << endl;
+    for( const int & val : match_1_P ) {
+      cout << val << endl;
+    }
     // Stores the rows in P that match 2
     vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
+    cout << "Matching coord2 with pair" << endl;
+    for( const int & val : match_2_P ) {
+      cout << val << endl;
+    }
 
     LOG("Unscrambling dimer matrix with respect to matrix 1 and 2", 2);
-    Eigen::MatrixXd unscrambled_P_Coef =
+    this->mat_P_Coef =
         unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
 
-    this->mat_P_Coef = unscrambled_P_Coef;
+    cout << "Unscrambled P Coef" << endl;
+    cout << mat_P_Coef << endl;
 
-    auto unscrambled_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
+    this->mat_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
 
-    this->mat_S = unscrambled_S;
   }
 }
 
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index 086af14..9bd7849 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -101,9 +101,6 @@ class TransferComplex {
     void printAll() const;
 };
 
-std::unordered_map<int, std::pair<double, std::string>> findRank(
-    Eigen::VectorXd& Orb_E_Alpha, Eigen::VectorXd& Orb_E_Beta);
-
 // Reorganize the dimer coefficients to match up with the monomers
 Eigen::MatrixXd organize_P_Coef(std::vector<int> matchDimerA,
                        std::vector<int> matchDimerB,
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 28742e8..3ea694c 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -131,6 +131,10 @@ int main(int argc, const char *argv[]) {
 
     // Set the transfer complex to counterpoise if it is the case.
 
+    cout << "Printing number of basis funct per atom in pair " << endl;
+    for ( const int & val : basis_P ){
+      cout << val << endl;
+    }
     // If the basis function search returns 0 for any of the components then
     // we cannot automatically determine what the transfer integral is
     if (basis_1.size() != 0 && basis_2.size() != 0 && basis_P.size() != 0) {

From 6a801be76d956e7f610940ef5a59d9c40d102970 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 23 May 2019 12:22:16 -0600
Subject: [PATCH 29/68] Fixed error, removed cout lines unneeded, added extra
 test

---
 src/libcatnip/qc_functions.cpp  | 45 ++++++++-------------------------
 src/libcatnip/qc_functions.hpp  | 16 ++++++------
 src/tests/test_script_calc_J.sh | 20 +++++++++++++++
 src/tools/main.cpp              |  7 +----
 4 files changed, 40 insertions(+), 48 deletions(-)

diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index 1f6588f..cff108b 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -44,31 +44,18 @@ void TransferComplex::calculate_transfer_integral_() {
 
   assert(gammaA.cols() == gammaB.cols() && "Column count between gamma A and B must be consistent");
   Eigen::MatrixXd gamma(gammaA.rows()+gammaB.rows(),gammaA.cols());
-  gamma << gammaB, gammaA;
+  gamma << gammaA, gammaB;
 
-  std::cout << "Gamma Matrix" << std::endl;
-  std::cout << gamma << std::endl;
   LOG("Calculating S_AB", 2);
   S_AB.resize(dimension,dimension);
   S_AB = gamma * gamma.transpose();
   
-  std::cout << "Overlap Matrix" << std::endl; 
-  std::cout << S_AB << std::endl;
-  /// Find out if S_AB is invertible
-  if(S_AB.determinant()==0){
-    throw invalid_argument("Error the determinant of the Molecular Orbital Overlap matrix is 0, this means it is not invertible and thus Symmetric orthogonalization cannot be applied.");
-  }
   Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
   Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
   Hamiltonian.resize(mat_S.rows(),mat_S.cols());
   Hamiltonian = gamma * vec_P_OE.asDiagonal() * gamma.transpose();
 
-  std::cout << "Inverse overlap Matrix" << std::endl;
-  std::cout << S_AB_inv_sqrt << std::endl; 
-
-  std::cout << "Hamiltonian Matrix" << std::endl;
-  std::cout << Hamiltonian << std::endl; 
   Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt;  
 }
 
@@ -175,7 +162,7 @@ void TransferComplex::printTransferIntegral_(
   double e_a = Hamiltonian(orbital1_num,orbital1_num);
   double e_b = Hamiltonian(orbital2_num,orbital2_num);
   double S_ab = S_AB(orbital1_num,orbital2_num); 
-  
+ 
   cout << "\nPre-Orthonormalization" << endl;
   cout << "J_ab             " << J_ab * hartreeToeV << " eV\n";
   cout << "e_a              " << e_a * hartreeToeV << " eV\n";
@@ -197,6 +184,7 @@ void TransferComplex::printTransferIntegral_(
   cout << "J_ab_eff_all    " << J_eff * hartreeToeV << " eV\n";
   cout << "e_a_eff_all     " << e_a_eff * hartreeToeV << " eV\n";
   cout << "e_b_eff_all     " << e_b_eff * hartreeToeV << " eV\n" << endl;
+
 }
 
 void TransferComplex::printAll() const {
@@ -778,10 +766,14 @@ Eigen::MatrixXd unscramble_S(
   return S_new;
 }
 
-TransferComplex::TransferComplex(Eigen::MatrixXd mat1Coef, Eigen::MatrixXd mat2Coef,
-                                 Eigen::MatrixXd matPCoef, const int HOMO_A,
-                                 const int HOMO_B, Eigen::MatrixXd matS,
-                                 Eigen::VectorXd vecPOE, bool cp) {
+TransferComplex::TransferComplex(
+    const Eigen::MatrixXd & mat1Coef, 
+    const Eigen::MatrixXd & mat2Coef,
+    const Eigen::MatrixXd & matPCoef, 
+    const int HOMO_A, 
+    const int HOMO_B, 
+    const Eigen::MatrixXd & matS,
+    const Eigen::VectorXd & vecPOE, bool cp) {
 
   unscrambled_ = false;
   counterPoise_ = cp;
@@ -849,10 +841,6 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
     this->mat_2_Coef = unscrambled_2_Coef;
 
     vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
-    cout << "Matching coord1 with pair" << endl;
-    for( const int & val : match_1_P ) {
-      cout << val << endl;
-    }
 
     this->mat_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
 
@@ -863,24 +851,13 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
     // Stores the rows in P that match 1
     vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
 
-    cout << "Matching coord1 with pair" << endl;
-    for( const int & val : match_1_P ) {
-      cout << val << endl;
-    }
     // Stores the rows in P that match 2
     vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
-    cout << "Matching coord2 with pair" << endl;
-    for( const int & val : match_2_P ) {
-      cout << val << endl;
-    }
 
     LOG("Unscrambling dimer matrix with respect to matrix 1 and 2", 2);
     this->mat_P_Coef =
         unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
 
-    cout << "Unscrambled P Coef" << endl;
-    cout << mat_P_Coef << endl;
-
     this->mat_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
 
   }
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index 9bd7849..6eef70b 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -62,13 +62,13 @@ class TransferComplex {
                                 const std::pair<std::string,int> & Orbital2) const;
   public:
     TransferComplex(
-        Eigen::MatrixXd mat1Coef, 
-        Eigen::MatrixXd mat2Coef, 
-        Eigen::MatrixXd matPCoef,
-        const int HOMO_A, 
+        const Eigen::MatrixXd & mat1Coef, 
+        const Eigen::MatrixXd & mat2Coef, 
+        const Eigen::MatrixXd & matPCoef,
+        const int HOMO_A,
         const int HOMO_B,
-        Eigen::MatrixXd matS, 
-        Eigen::VectorXd vecPOE, 
+        const Eigen::MatrixXd & matS, 
+        const Eigen::VectorXd & vecPOE, 
         bool cp);
 
     void unscramble(
@@ -141,10 +141,10 @@ Eigen::MatrixXd unscramble_S(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& basisFuncDimer,
     Eigen::MatrixXd S);
-
+/*
 Eigen::MatrixXd unscramble_OE(std::vector<int> matchDimerA,
                       std::vector<int> matchDimerB,
-                      std::vector<int> basisFuncDimer, Eigen::VectorXd OE);
+                      std::vector<int> basisFuncDimer, Eigen::VectorXd OE);*/
 
 }  // namespace catnip
 #endif  // _CATNIP_QC_FUNCTIONS_HPP
diff --git a/src/tests/test_script_calc_J.sh b/src/tests/test_script_calc_J.sh
index 27bcc4f..be21925 100755
--- a/src/tests/test_script_calc_J.sh
+++ b/src/tests/test_script_calc_J.sh
@@ -222,6 +222,26 @@ else
 fi
 echo $data >> $fileOut
 
+# Note the only difference in this test is that we have switched p_1 and p_2 
+# because the program auto matches the right basis function coordinates with 
+# the right atoms you should end up with the same numbers. 
+exec_command="${path}/build/calc_J -p_P ${path}/GAUSSIANFILES/CuBr2_Py/CuBr2-Py.pun -p_2 ${path}/GAUSSIANFILES/CuBr2_Py/CuBr2.pun -p_1 ${path}/GAUSSIANFILES/CuBr2_Py/Py.pun"
+data=$(${exec_command})
+if [ $? -eq 0 ]; then
+  findJeff 
+  if (( $(bc <<< "$J_val > -0.0055" ) )) && (( $(bc <<< "$J_val < -0.0053" ) ))
+  then
+    echo "${green}[SUCCESS]${reset} ${exec_command}" 
+  else
+    echo "${red}[FAILURE]${reset} ${exec_command} expected output -0.00542741"
+    echo "actual output $J_val"
+    count_fails=$(($count_fails+1))
+  fi
+else
+  echo "${red}[FAILURE]${reset} ${exec_command}"
+  count_fails=$((count_fails+1))
+fi
+echo $data >> $fileOut
 
 # The following commands should not work 
 
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 3ea694c..3809987 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -130,17 +130,12 @@ int main(int argc, const char *argv[]) {
                        vec_P_OE, par->getCounterPoise());
 
     // Set the transfer complex to counterpoise if it is the case.
-
-    cout << "Printing number of basis funct per atom in pair " << endl;
-    for ( const int & val : basis_P ){
-      cout << val << endl;
-    }
     // If the basis function search returns 0 for any of the components then
     // we cannot automatically determine what the transfer integral is
     if (basis_1.size() != 0 && basis_2.size() != 0 && basis_P.size() != 0) {
       LOG("Unscrambling matrices", 1);
       TC.unscramble(coord_1_mat, coord_2_mat, coord_P_mat, basis_P, basis_2);
-    }
+    } 
 
     cout << endl;
     cout << "Dimer     Spin " << par->getSpinP() << endl;

From 1d8fcc5b4bba12b468402df0bc570cea23c6ace4 Mon Sep 17 00:00:00 2001
From: Joshua Scott Brown <joshbro42867@yahoo.com>
Date: Thu, 30 May 2019 15:17:30 -0600
Subject: [PATCH 30/68] Cleanup comments

---
 src/libcatnip/io/file_readers/filereader.cpp |  3 +--
 src/libcatnip/qc_functions.hpp               | 11 +----------
 2 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/src/libcatnip/io/file_readers/filereader.cpp b/src/libcatnip/io/file_readers/filereader.cpp
index 1fd77ea..ffdd5f2 100644
--- a/src/libcatnip/io/file_readers/filereader.cpp
+++ b/src/libcatnip/io/file_readers/filereader.cpp
@@ -24,8 +24,6 @@ void FileReader::read() {
   close();
 }
 
-// Private member functions
-
 void FileReader::open() {
   if (!fileExist_()) {
     throw invalid_argument("File " + fileName_ + " does not exist.");
@@ -39,6 +37,7 @@ void FileReader::close() {
   fileOpen_ = false;
 }
 
+// Private member functions
 void FileReader::registerSections_() { checkSections_(); }
 
 // Basically check that for a given tag both a section reader
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index 6eef70b..72843e6 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -18,10 +18,6 @@ class TransferComplex {
     Eigen::MatrixXd mat_1_Coef;
     Eigen::MatrixXd mat_2_Coef;
     Eigen::MatrixXd mat_P_Coef;
-    // Stores the number of Molecular orbitals
-    // and the HOMO for both monomer 1 and 2
-    //std::pair<int, int> Orbs1;
-    //std::pair<int, int> Orbs2;
 
     /**
      * \brief basis function overlap matrix
@@ -44,8 +40,7 @@ class TransferComplex {
 
     int HOMO_A_;
     int HOMO_B_;
-    //int HOMO_Orb_;
-    //int LUMO_Orb_;
+
     Eigen::RowVectorXd vec_P_OE;
     // If unscrambaling is required
     bool unscrambled_;
@@ -141,10 +136,6 @@ Eigen::MatrixXd unscramble_S(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& basisFuncDimer,
     Eigen::MatrixXd S);
-/*
-Eigen::MatrixXd unscramble_OE(std::vector<int> matchDimerA,
-                      std::vector<int> matchDimerB,
-                      std::vector<int> basisFuncDimer, Eigen::VectorXd OE);*/
 
 }  // namespace catnip
 #endif  // _CATNIP_QC_FUNCTIONS_HPP

From 61e115a644bcabc17e286e715bd2c5d9a20239d4 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Tue, 11 Feb 2020 09:54:19 -0700
Subject: [PATCH 31/68] Added profiling options, for gprof

---
 CMakeLists.txt | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1d8f065..a36ae19 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -7,6 +7,7 @@ project (calc_J)
 option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" OFF)
 option(ENABLE_INTEGRATION_TESTS "Enable integration tests" OFF)
 option(ENABLE_TESTS "Enable tests" OFF)
+option(ENABLE_PROFILING "Enable profiling" OFF)
 option(CODE_COVERAGE "Enable coverage reporting" OFF)
 
 ##############################################################################
@@ -26,7 +27,6 @@ set(LOG_LEVEL 0 CACHE INT "Choose the log level" )
 # important for using gcov .o.gcno or .cpp.gcno now will be .gcno
 set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE 1)
 set(CMAKE_CXX_FLAGS "-Wall -Wextra -std=c++11 -pedantic -Werror")
-
 ##############################################################################
 # Configuring header file with cmake variables 
 ##############################################################################
@@ -48,6 +48,14 @@ find_library (GCOV gcov)
 #endif(TARGET Eigen3::Eigen)
 add_definitions(-DLOG_LEVEL=${LOG_LEVEL})
 
+##############################################################################
+# Setting up profiling 
+##############################################################################
+if(ENABLE_PROFILING)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pg")
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -pg")
+endif()
 ##############################################################################
 # Setting up testing 
 ##############################################################################

From e5d915baa45547065ab2865a6536134285857538 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Tue, 11 Feb 2020 09:54:37 -0700
Subject: [PATCH 32/68] Deleted comments

---
 src/tools/main.cpp | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/tools/main.cpp b/src/tools/main.cpp
index 3809987..51098f2 100644
--- a/src/tools/main.cpp
+++ b/src/tools/main.cpp
@@ -78,31 +78,21 @@ int main(int argc, const char *argv[]) {
   // No need to worry about beta orbitals
 
   {
-    //Matrix *mat_S = lr_P.getOverlapMatrix();
     Eigen::MatrixXd mat_S = lr_P.getOverlapMatrix();
 
-    //Matrix *mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
     Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
     
-    //auto vec_P_OE = lr_P.getOE(par->getSpinP());
     Eigen::VectorXd vec_P_OE = Eigen::VectorXd(lr_P.getOE(par->getSpinP()));
-    //Matrix *vec_P_OE = new Matrix(vec_P_OE);
 
     int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
     LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
     Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
-    //Matrix *mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
     Eigen::VectorXd vec_1_OE = lr_1.getOE(par->getSpin1());
-    //Matrix *mat_1_OE = new Matrix(vec_1_OE);
-    //Eigen::MatrixXd mat_1_OE = vec_1_OE.asDiagonal();
 
     int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
     LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
-    //Matrix *mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
     Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
     Eigen::VectorXd vec_2_OE = lr_2.getOE(par->getSpin2());
-    //Matrix *mat_2_OE = new Matrix(vec_2_OE);
-    //Eigen::MatrixXd mat_2_OE = vec_2_OE.asDiagonal();
 
     // Unscramble dimer coef and energies first need to see how the dimer
     // and monomer coefficients line up. To determine how the ceofficients

From 4195c019d6450817242bd4f11035621bc6e6b849 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Wed, 24 Jun 2020 06:38:11 -0600
Subject: [PATCH 33/68] Success compiling

---
 CMakeLists.txt                 |  51 ++--
 src/libcatnip/CMakeLists.txt   |   1 +
 src/libcatnip/qc_functions.cpp | 426 +++++++++++++++++++++------------
 src/libcatnip/qc_functions.hpp | 124 ++++++----
 src/tests/CMakeLists.txt       |   8 +-
 src/tools/main.cpp             | 172 -------------
 6 files changed, 378 insertions(+), 404 deletions(-)
 delete mode 100644 src/tools/main.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a36ae19..45ed8a6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,8 +5,8 @@ project (calc_J)
 # Defining options 
 ##############################################################################
 option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" OFF)
-option(ENABLE_INTEGRATION_TESTS "Enable integration tests" OFF)
-option(ENABLE_TESTS "Enable tests" OFF)
+option(ENABLE_INTEGRATION_TESTING "Enable integration tests" OFF)
+option(ENABLE_UNIT_TESTING "Enable tests" OFF)
 option(ENABLE_PROFILING "Enable profiling" OFF)
 option(CODE_COVERAGE "Enable coverage reporting" OFF)
 
@@ -26,7 +26,7 @@ set(LOG_LEVEL 0 CACHE INT "Choose the log level" )
 # Prevents multiple file extensions from being appended one after the other
 # important for using gcov .o.gcno or .cpp.gcno now will be .gcno
 set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE 1)
-set(CMAKE_CXX_FLAGS "-Wall -Wextra -std=c++11 -pedantic -Werror")
+set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -Werror")
 ##############################################################################
 # Configuring header file with cmake variables 
 ##############################################################################
@@ -59,7 +59,7 @@ endif()
 ##############################################################################
 # Setting up testing 
 ##############################################################################
-if(ENABLE_INTEGRATION_TESTS)
+if(ENABLE_INTEGRATION_TESTING)
   if(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
     message("GAUSSIANFILES found will not download")
     set(DOWNLOAD_TUTORIAL_FILES OFF)
@@ -74,12 +74,12 @@ if(DOWNLOAD_TUTORIAL_FILES)
   execute_process(COMMAND ${PROJECT_SOURCE_DIR}/scripts/test_suite_install.bash "${PROJECT_SOURCE_DIR}" )
 endif()
 
-if(ENABLE_TESTS OR ENABLE_INTEGRATION_TESTS)
-  enable_testing()
-  add_subdirectory("${PROJECT_SOURCE_DIR}/src/tests")
-endif()
+#if(ENABLE_TESTS OR ENABLE_INTEGRATION_TESTS)
+#  enable_testing()
+#  add_subdirectory("${PROJECT_SOURCE_DIR}/src/tests")
+#endif()
 
-if (ENABLE_INTEGRATION_TESTS)
+if (ENABLE_INTEGRATION_TESTING)
   file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 
     DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
   file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.pun" 
@@ -93,7 +93,7 @@ if (ENABLE_INTEGRATION_TESTS)
     DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
 endif()
 
-if (ENABLE_TESTS)
+if (ENABLE_UNIT_TESTING)
   file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.pun" 
     DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
   file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.log" 
@@ -105,28 +105,15 @@ endif()
 ##############################################################################
 # Add the binary tree to the search path for include files
 # so that we will find calcJconfig.hpp
-include_directories("${PROJECT_BINARY_DIR}/src")
-include_directories("${PROJECT_SOURCE_DIR}/src/libcatnip")
-include_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments/properties")
-include_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments")
-include_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/file_readers")
-include_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io")
+#target_include_directories(calc_J "${PROJECT_BINARY_DIR}/src")
+#target_link_directories(calc_J "${PROJECT_BINARY_DIR}/src")
 
-link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments/properties")
-link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments")
-link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/file_readers")
-link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io")
-link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip")
+#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments/properties")
+#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments")
+#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/file_readers")
+#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io")
+#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip")
+
+add_subdirectory("${PROJECT_SOURCE_DIR}/src")
 
-add_subdirectory("${PROJECT_SOURCE_DIR}/src/libcatnip")
 
-##############################################################################
-# Creating calc_J and setting up code coverage if on  
-##############################################################################
-add_executable(calc_J src/tools/main.cpp)
-if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
-  target_link_libraries(calc_J gcov)
-  set_source_files_properties( src/tools/main.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
-endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
-target_link_libraries(calc_J libcatnip ${COMMON_LIBRARIES})
-install( TARGETS calc_J DESTINATION bin)
diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index 9e7f650..a8f855a 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -7,3 +7,4 @@ file(GLOB CATNIP_SOURCE_FILES
   io/file_readers/*.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
+target_include_directories(libcatnip PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
diff --git a/src/libcatnip/qc_functions.cpp b/src/libcatnip/qc_functions.cpp
index cff108b..4132711 100644
--- a/src/libcatnip/qc_functions.cpp
+++ b/src/libcatnip/qc_functions.cpp
@@ -4,6 +4,7 @@
 #include <iomanip>
 #include <iostream>
 #include <list>
+#include <numeric> // For accumulate
 #include <sstream>
 #include <stdlib.h>
 #include <string>
@@ -20,7 +21,7 @@
 namespace catnip {
 
   using namespace std;
-
+/*
 // Essentially calculates the transfer integral
 void TransferComplex::calculate_transfer_integral_() {
 
@@ -46,17 +47,17 @@ void TransferComplex::calculate_transfer_integral_() {
   Eigen::MatrixXd gamma(gammaA.rows()+gammaB.rows(),gammaA.cols());
   gamma << gammaA, gammaB;
 
-  LOG("Calculating S_AB", 2);
-  S_AB.resize(dimension,dimension);
-  S_AB = gamma * gamma.transpose();
+  LOG("Calculating S_MO", 2);
+  S_MO.resize(dimension,dimension);
+  S_MO = gamma * gamma.transpose();
   
-  Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_AB);
-  Eigen::MatrixXd S_AB_inv_sqrt = eigen_solver.operatorInverseSqrt();
+  Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_MO);
+  Eigen::MatrixXd S_MO_inv_sqrt = eigen_solver.operatorInverseSqrt();
 
   Hamiltonian.resize(mat_S.rows(),mat_S.cols());
   Hamiltonian = gamma * vec_P_OE.asDiagonal() * gamma.transpose();
 
-  Hamiltonian_eff = S_AB_inv_sqrt * Hamiltonian * S_AB_inv_sqrt;  
+  Hamiltonian_eff = S_MO_inv_sqrt * Hamiltonian * S_MO_inv_sqrt;  
 }
 
 void TransferComplex::printTransferIntegral(
@@ -161,7 +162,7 @@ void TransferComplex::printTransferIntegral_(
   double J_ab = Hamiltonian(orbital1_num,orbital2_num);
   double e_a = Hamiltonian(orbital1_num,orbital1_num);
   double e_b = Hamiltonian(orbital2_num,orbital2_num);
-  double S_ab = S_AB(orbital1_num,orbital2_num); 
+  double S_ab = S_MO(orbital1_num,orbital2_num); 
  
   cout << "\nPre-Orthonormalization" << endl;
   cout << "J_ab             " << J_ab * hartreeToeV << " eV\n";
@@ -372,55 +373,56 @@ list<Eigen::MatrixXd> splitCoefsUpByAtoms(const vector<int> & basisFuncP, Eigen:
 // the wrong result.
 //
 // For instance say we have a matrix
-// 1 row1
-// 2 row2
-// 3 row3
-// 4 row4
+// index 1 | row 1
+// index 2 | row 2
+// index 3 | row 3
+// index 4 | row 4
 //
 // where:
-// Row 1 needs to be at row 3
-// Row 4 needs to be at row 1
-// Row 2 needs to be at row 2
-// Row 3 needs to be at row 4
+// Row 1 needs to be at index 3
+// Row 4 needs to be at index 1
+// Row 2 needs to be at index 2
+// Row 3 needs to be at index 4
 //
 // If we simply looked at our first instance of the matrix shown above
 // and came up with the following swaps
-// Swap row 1 with row 3
-// Swap row 4 with row 1
-// Swap row 2 with row 2
-// Swap row 3 with row 4
+// Swap row 1 with index 3
+// Swap row 4 with index 1
+// Swap row 2 with index 2
+// Swap row 3 with index 4
 //
 // First swap
-// 1 row3
-// 2 row2
-// 3 row1
-// 4 row4
+// index 1 row3
+// index 2 row2
+// index 3 row1
+// index 4 row4
 //
 // Second swap
-// 1 row4
-// 2 row2
-// 3 row1
-// 4 row3
+// index 1 row4
+// index 2 row2
+// index 3 row1
+// index 4 row3
 //
 // Third swap does nothing
 // Fourth swap
-// 1 row4
-// 2 row2
-// 3 row3
-// 4 row1
+// index 1 row4
+// index 2 row2
+// index 3 row3
+// index 4 row1
 //
 // When what we really wanted was
-// 1 row4
-// 2 row2
-// 3 row1
-// 4 row3
+// index 1 row4
+// index 2 row2
+// index 3 row1
+// index 4 row3
 //
 // Notice the row3 and row1 are in the wrong place
 // The instructions should be rewritten
-// Swap row 1 with row 3
-// Swap row 4 with row 3
-// Swap row 2 with row 2 - no swap
-// Swap row 3 with row 3 - no swap
+// Swap row 1 with index 3
+// Swap row 4 with index 3
+// Swap row 2 with index 2 - no swap
+// Swap row 3 with index 3 - no swap
+//
 void refreshSwapOrder(vector<pair<int, int>> &monBmatch,
                       vector<pair<int, int>> &monAmatch) {
 
@@ -508,6 +510,53 @@ void refreshSwapOrder(vector<pair<int, int>> &monAmatch) {
   return;
 }
 
+// To replace both refreshSwapOrder and updateSwapLists
+// instead of figuring out a proper order for swapping we will simply start
+// with a new link list of the same size and place the coefficents in that
+// new list
+Eigen::MatrixXd createSortedCoefMatrix(vector<pair<int,int>> & mon_match_ind, list<Eigen::MatrixXd> & atom_mat_coefs){
+
+  // Actually lets use a vector of pointers to the matrices that are in the list
+  vector<Eigen::MatrixXd *> mat_ptrs;
+  // Error checking
+  if(atom_mat_coefs.size()==0){
+    throw std::runtime_error("ERROR cannot create sorted coef matrix, there are atomically partitioned matrices to build the full sorted coef matrix from.");
+  } 
+
+  int cols = atom_mat_coefs.front().cols();
+  for ( list<Eigen::MatrixXd>::iterator coef_ptr = atom_mat_coefs.begin();
+        coef_ptr != atom_mat_coefs.end();
+        ++coef_ptr ){
+      if(coef_ptr->cols()!=cols){
+        throw std::runtime_error("ERROR cannot created sorted coef matrix from atomically partitioned matrices with varying number of columns.");
+      }
+  } 
+  // End of error checking
+ 
+  // Count the total number of rows in each atomically partitioned coef matrix 
+  vector<int> rows_per_mat; 
+  for ( list<Eigen::MatrixXd>::iterator coef_ptr = atom_mat_coefs.begin();
+      coef_ptr != atom_mat_coefs.end();
+      ++coef_ptr ){
+    rows_per_mat.push_back(coef_ptr->rows());
+  } 
+ 
+  int initial_value = 0;
+  int total_rows = std::accumulate(rows_per_mat.begin(),rows_per_mat.end(), initial_value);
+
+  // Determine the offset of each row to each index
+  std::map<int,int> row_to_index_offset; 
+  int offset = 0;
+  for ( std::pair<int,int> & row_ind : mon_match_ind ){
+    row_to_index_offset.at(row_ind.first) = offset; 
+    offset+= rows_per_mat.at(row_ind.second);
+  }
+
+  Eigen::MatrixXd sorted_atom_mat_coefs
+   
+   
+
+}
 // The above function determines the appropriate sequence of swaps this function
 // then actually implements the swaps by exchanging the matrices in the list.
 void updateSwapLists(vector<pair<int, int>> &monBmatch,
@@ -597,19 +646,91 @@ Eigen::MatrixXd createNewMatrix(list<Eigen::MatrixXd> &p_atom_mat_coef, int rows
 }
 
 // unscramble the coefficients
-Eigen::MatrixXd unscramble_Coef(
-    const std::vector<int> &matchDimerA,
-    const std::vector<int> &matchDimerB,
-    const std::vector<int> &basisFuncP, 
-    const Eigen::MatrixXd & dimerCoef) {
+//Eigen::MatrixXd unscramble_Coef(
+//    const std::vector<int> &matchDimerA,
+//    const std::vector<int> &matchDimerB,
+//    const std::vector<int> &basisFuncP, 
+//    const Eigen::MatrixXd & dimerCoef) {
+//
+//  // Let's reduce the complexity of the problem by instead of working
+//  // with the basis functions lets just work with the atoms. We can do
+//  // this by treating all the basis functions associated with a single
+//  // atom as a block.
+//
+//  list<Eigen::MatrixXd> p_atom_mat_coef =
+//      splitCoefsUpByAtoms(basisFuncP, dimerCoef, "Columns");
+//
+//  // Place all of monomer A atom basis functions on the left side of the
+//  // matrix and all of B monomer atom basis functions on the right side
+//  // of the dimer matrix
+//  // First int is the col in the dimer the atom should be at
+//  // Second int is the col in the dimer the atom is presently at
+//
+//  vector<pair<int, int>> monAmatch;
+//  for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerA.at(i));
+//    monAmatch.push_back(pr);
+//  }
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+//
+//  refreshSwapOrder(monBmatch, monAmatch);
+//  updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
+//
+//  Eigen::MatrixXd dimerCoef_new = createNewMatrix(
+//      p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
+//
+//  return dimerCoef_new;
+//}
+//
+//// unscramble the coefficients
+//Eigen::MatrixXd unscramble_Coef(
+//    const std::vector<int> &matchDimerB,
+//    const std::vector<int> &basisFuncB,
+//    const Eigen::MatrixXd &Coef) {
+//
+//  // Let's reduce the complexity of the problem by instead of working
+//  // with the basis functions lets just work with the atoms. We can do
+//  // this by treating all the basis functions associated with a single
+//  // atom as a block.
+//
+//  list<Eigen::MatrixXd> atom_mat_coef =
+//      splitCoefsUpByAtoms(basisFuncB, Coef, "Columns");
+//
+//  // Place all of monomer A atom basis functions on the left side of the
+//  // matrix and all of B monomer atom basis functions on the right side
+//  // of the  matrix
+//  // First int is the col in the dimer the atom should be at
+//  // Second int is the col in the dimer the atom is presently at
+//
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+//
+//  refreshSwapOrder(monBmatch);
+//  updateSwapLists(monBmatch, atom_mat_coef);
+//  Eigen::MatrixXd Coef_new = createNewMatrix(atom_mat_coef, Coef.rows(),
+//                                     Coef.cols(), "Columns");
+//  return Coef_new;
+//}
+
+Eigen::MatrixXd unscrambleCoef(
+    const std::vector<std::vector<int>> &match_mon_complex,
+    const std::vector<int> &basis_functions_complex, 
+    const Eigen::MatrixXd & complex_coefs) {
 
   // Let's reduce the complexity of the problem by instead of working
   // with the basis functions lets just work with the atoms. We can do
   // this by treating all the basis functions associated with a single
   // atom as a block.
 
-  list<Eigen::MatrixXd> p_atom_mat_coef =
-      splitCoefsUpByAtoms(basisFuncP, dimerCoef, "Columns");
+  list<Eigen::MatrixXd> complex_coef_block =
+      splitCoefsUpByAtoms(basis_functions_complex, complex_coefs, "Columns");
 
   // Place all of monomer A atom basis functions on the left side of the
   // matrix and all of B monomer atom basis functions on the right side
@@ -617,59 +738,32 @@ Eigen::MatrixXd unscramble_Coef(
   // First int is the col in the dimer the atom should be at
   // Second int is the col in the dimer the atom is presently at
 
-  vector<pair<int, int>> monAmatch;
-  for (unsigned i = 0; i < matchDimerA.size(); ++i) {
-    pair<int, int> pr(i, matchDimerA.at(i));
-    monAmatch.push_back(pr);
-  }
-  vector<pair<int, int>> monBmatch;
-  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
-    pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
-    monBmatch.push_back(pr);
-  }
-
-  refreshSwapOrder(monBmatch, monAmatch);
-  updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
-
-  Eigen::MatrixXd dimerCoef_new = createNewMatrix(
-      p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
-
-  return dimerCoef_new;
-}
-
-// unscramble the coefficients
-Eigen::MatrixXd unscramble_Coef(
-    const std::vector<int> &matchDimerB,
-    const std::vector<int> &basisFuncB,
-    const Eigen::MatrixXd &Coef) {
-
-  // Let's reduce the complexity of the problem by instead of working
-  // with the basis functions lets just work with the atoms. We can do
-  // this by treating all the basis functions associated with a single
-  // atom as a block.
-
-  list<Eigen::MatrixXd> atom_mat_coef =
-      splitCoefsUpByAtoms(basisFuncB, Coef, "Columns");
-
-  // Place all of monomer A atom basis functions on the left side of the
-  // matrix and all of B monomer atom basis functions on the right side
-  // of the  matrix
-  // First int is the col in the dimer the atom should be at
-  // Second int is the col in the dimer the atom is presently at
-
-  vector<pair<int, int>> monBmatch;
-  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
-    pair<int, int> pr(i, matchDimerB.at(i));
-    monBmatch.push_back(pr);
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+
+  vector<vector<pair<int,int>>> mon_match_index;
+  unsigned new_index = 0;
+  for ( const vector<int> & monomer_rows : match_mon_complex){
+    vector<pair<int,int>> mon_matching_index_row;
+    for( const int & row_index : monomer_rows ){
+      pair<int,int> pr(new_index,row_index);
+      mon_matching_index_row.push_back(pr); 
+    } 
+    mon_match_index.push_back(mon_matching_index_row);
   }
 
-  refreshSwapOrder(monBmatch);
-  updateSwapLists(monBmatch, atom_mat_coef);
+  //refreshSwapOrder(monBmatch);
+//  refreshSwapOrder(mon_match_index);
+ // updateSwapLists(monBmatch, atom_mat_coef);
   Eigen::MatrixXd Coef_new = createNewMatrix(atom_mat_coef, Coef.rows(),
                                      Coef.cols(), "Columns");
   return Coef_new;
-}
 
+
+}
 // Similar to the above function but we will be moving both the rows
 // and columns
 Eigen::MatrixXd unscramble_S(
@@ -766,66 +860,96 @@ Eigen::MatrixXd unscramble_S(
   return S_new;
 }
 
-TransferComplex::TransferComplex(
-    const Eigen::MatrixXd & mat1Coef, 
-    const Eigen::MatrixXd & mat2Coef,
-    const Eigen::MatrixXd & matPCoef, 
-    const int HOMO_A, 
-    const int HOMO_B, 
-    const Eigen::MatrixXd & matS,
-    const Eigen::VectorXd & vecPOE, bool cp) {
+
+//TransferComplex::TransferComplex(
+//    const Eigen::MatrixXd & mat1Coef, 
+//    const Eigen::MatrixXd & mat2Coef,
+//    const Eigen::MatrixXd & matPCoef, 
+//    const int HOMO_A, 
+//    const int HOMO_B, 
+//    const Eigen::MatrixXd & matS,
+//    const Eigen::VectorXd & vecPOE, bool cp) {
+//
+TransferComplex::TransferComplex(const Parameters params) : params_(params) { 
 
   unscrambled_ = false;
-  counterPoise_ = cp;
+//  counterPoise_ = cp;
   // Consistency check
-  if (matS.cols() != matPCoef.cols()) {
+  if (params_.S_AO.cols() != params_.mat_complex.cols()) {
     throw invalid_argument(
         "The overlap matrix must have the same number "
         "of basis functions as the dimer");
   }
-  if (cp) {
-    if (mat1Coef.cols() != matPCoef.cols()) {
-      throw invalid_argument(
-          "Counter poise correction requires that the"
-          " monomers have the same number of coefficients as the dimer. "
-          "Your monomer 1 does not");
-    }
-    if (mat2Coef.cols() != matPCoef.cols()) {
-      throw invalid_argument(
-          "Counter poise correction requires that the"
-          " monomers have the same number of coefficients as the dimer. "
-          "Your monomer 2 does not");
-    }
+  //if (cp) {
+  if (params_.counter_poise) {
+    int monomer_number = 1;
+    for ( const Eigen::MatrixXd & mat : params_.mat_monomers){
+      if(params_.mat_complex.cols() != mat.cols()){
+        throw invalid_argument(
+            "Counter poise correction requires that the"
+            " monomers have the same number of coefficients as the complex. "
+            "Your monomer " + std::to_string(monomer_number) +" does not");
+      }
+      ++monomer_number;
+    }
+//    if (mat1Coef.cols() != matPCoef.cols()) {
+//      throw invalid_argument(
+//          "Counter poise correction requires that the"
+//          " monomers have the same number of coefficients as the dimer. "
+//          "Your monomer 1 does not");
+//    }
+//    if (mat2Coef.cols() != matPCoef.cols()) {
+//      throw invalid_argument(
+//          "Counter poise correction requires that the"
+//          " monomers have the same number of coefficients as the dimer. "
+//          "Your monomer 2 does not");
+//    }
   } else {
-    int total_cols = mat1Coef.cols() + mat2Coef.cols();
-
-    if (total_cols > matPCoef.cols()) {
+    /// If not counter poise the sum of the cols should equal the same number as is in the complex
+//    int total_cols = mat1Coef.cols() + mat2Coef.cols();
+    int total_cols = 0; 
+    for ( const Eigen::MatrixXd & mat : params_.mat_monomers){
+      total_cols+=mat.cols();
+    }
+    
+    //if (total_cols > matPCoef.cols()) {
+    if (total_cols > params_.mat_complex.cols()) {
       throw invalid_argument(
-          "Counter poise has not been specified and your "
-          "monomers have more basis function cols than your dimer");
+          "Counter poise has not been specified and the total number of "
+          "basis functions in your monomers is more than the number of basis "
+          "functions in your complex.");
+    }else if(total_cols < params_.complex_coefs.cols()){
+      throw invalid_argument( 
+          "Counter poise has not been specified and the total number of "
+          "basis functions in your monomers is less than the number of basis "
+          "functions in your complex.");
     }
   }
-
-  mat_1_Coef.resize(mat1Coef.rows(),mat1Coef.cols());
-  mat_1_Coef = mat1Coef;
-  mat_2_Coef.resize(mat2Coef.rows(),mat2Coef.cols());
-  mat_2_Coef = mat2Coef;
-  mat_P_Coef.resize(matPCoef.rows(),matPCoef.cols());
-  mat_P_Coef = matPCoef;
-  HOMO_A_ = HOMO_A;
-  HOMO_B_ = HOMO_B;
-  mat_S.resize(matS.rows(),matS.cols());
-  mat_S = matS;
-  vec_P_OE.resize(vecPOE.size());
-  vec_P_OE = vecPOE;
+//
+//  mat_1_Coef.resize(mat1Coef.rows(),mat1Coef.cols());
+//  mat_1_Coef = mat1Coef;
+//  mat_2_Coef.resize(mat2Coef.rows(),mat2Coef.cols());
+//  mat_2_Coef = mat2Coef;
+//  mat_P_Coef.resize(matPCoef.rows(),matPCoef.cols());
+//  mat_P_Coef = matPCoef;
+//  HOMO_A_ = HOMO_A;
+//  HOMO_B_ = HOMO_B;
+//  mat_S.resize(matS.rows(),matS.cols());
+//  mat_S = matS;
+//  vec_P_OE.resize(vecPOE.size());
+//  vec_P_OE = vecPOE;
 }
 
-void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
-                                 const Eigen::MatrixXd &coord_2_mat,
-                                 const Eigen::MatrixXd &coord_P_mat,
-                                 const std::vector<int> &basisP,
+//void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
+//                                 const Eigen::MatrixXd &coord_2_mat,
+//                                 const Eigen::MatrixXd &coord_P_mat,
+//                                 const std::vector<int> &basisP,
+//                                 const std::vector<int> &basis2) {
+//
+void TransferComplex::unscramble(const vector<Eigen::MatrixXd> &coord_monomers,
+                                 const Eigen::MatrixXd &coord_complex,
+                                 const std::vector<int> &basis_complex,
                                  const std::vector<int> &basis2) {
-
   unscrambled_ = true;
 
   const int sig_fig = 4;
@@ -848,18 +972,20 @@ void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
 
   } else {
 
-    // Stores the rows in P that match 1
-    vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
-
+    vector<vector<int>> match_mon_complex;
+    for ( const Eigen::MatrixXd & coord_mon : coord_monomers){
+      // Returns each of the rows in complex that match each of the monomers
+      match_mon_complex.push_back(matchCol(coord_mon,coord_complex, sig_fig));
+    }
     // Stores the rows in P that match 2
-    vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
+    //vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
 
     LOG("Unscrambling dimer matrix with respect to matrix 1 and 2", 2);
-    this->mat_P_Coef =
-        unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
-
-    this->mat_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
-
+    //this->mat_P_Coef =
+    //    unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
+    this->params_.complex_coefs = unscrambleCoef(match_mon_complex,basis_complex,complex_coefs);
+//    this->mat_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
+    }
   }
 }
 
@@ -875,5 +1001,5 @@ void TransferComplex::calcJ() {
 
   calculate_transfer_integral_();
 }
-
+*/
 }  // namespace catnip
diff --git a/src/libcatnip/qc_functions.hpp b/src/libcatnip/qc_functions.hpp
index 72843e6..ba25bcc 100644
--- a/src/libcatnip/qc_functions.hpp
+++ b/src/libcatnip/qc_functions.hpp
@@ -14,57 +14,35 @@
 namespace catnip {
 
 class TransferComplex {
-  private:
-    Eigen::MatrixXd mat_1_Coef;
-    Eigen::MatrixXd mat_2_Coef;
-    Eigen::MatrixXd mat_P_Coef;
-
-    /**
-     * \brief basis function overlap matrix
-     **/
-    Eigen::MatrixXd mat_S;
-    /**
-     * \brief Molecular orbital overlap matrix
-     **/
-    Eigen::MatrixXd S_AB;
-
-    /**
-     * \brief Non orthonormalized Hamiltonian matrix
-     **/
-    Eigen::MatrixXd Hamiltonian;
-
-    /**
-     * \brief Orthonormalized Hamiltonian Matrix
-     **/
-    Eigen::MatrixXd Hamiltonian_eff;
 
-    int HOMO_A_;
-    int HOMO_B_;
-
-    Eigen::RowVectorXd vec_P_OE;
-    // If unscrambaling is required
-    bool unscrambled_;
-    bool counterPoise_;
-
-    /*
-     * \brief Determine if the provided orbital is valid
-     **/
-    bool orbitalValid_(const std::pair<std::string,int> & orbital) const;
+  public:
 
-    void calculate_transfer_integral_();
+    struct Parameters {
+      const std::vector<Eigen::MatrixXd> monomers_coefs;
+      const Eigen::MatrixXd complex_coefs;
+      /// Location of each of the homo_orbitals in each of the monomers
+      const std::vector<int> homo_orbitals;
+      //HOMO_A;
+      //const int HOMO_B;
+      /// Atomic Orbital overlap matrix
+      const Eigen::MatrixXd S_AO;
+      const Eigen::VectorXd complex_orbital_energies;
+      /// Counter poise flag
+      bool counter_poise = false;
+      /// Calculate all couplings
+      bool calculate_all = false;
+    };
 
-    void printTransferIntegral_(const std::pair<std::string,int> & Orbital1,
-                                const std::pair<std::string,int> & Orbital2) const;
-  public:
     TransferComplex(
-        const Eigen::MatrixXd & mat1Coef, 
+        const Parameters params
+        /*const Eigen::MatrixXd & mat1Coef, 
         const Eigen::MatrixXd & mat2Coef, 
         const Eigen::MatrixXd & matPCoef,
         const int HOMO_A,
         const int HOMO_B,
         const Eigen::MatrixXd & matS, 
         const Eigen::VectorXd & vecPOE, 
-        bool cp);
+        bool cp*/);
 
     void unscramble(
         const Eigen::MatrixXd& coord_1_mat, 
@@ -94,6 +72,49 @@ class TransferComplex {
      * \brief Print All info in matrix form
      **/
     void printAll() const;
+
+  private:
+
+    Parameters params_;
+//    Eigen::MatrixXd mat_1_Coef;
+//    Eigen::MatrixXd mat_2_Coef;
+//    Eigen::MatrixXd mat_P_Coef;
+
+    /**
+     * \brief basis function overlap matrix
+     **/
+    //Eigen::MatrixXd mat_S;
+    /**
+     * \brief Molecular orbital overlap matrix
+     **/
+    Eigen::MatrixXd S_MO_;
+
+    /**
+     * \brief Non orthonormalized Hamiltonian matrix
+     **/
+    Eigen::MatrixXd Hamiltonian_;
+
+    /**
+     * \brief Orthonormalized Hamiltonian Matrix
+     **/
+    Eigen::MatrixXd Hamiltonian_eff_;
+
+    //int HOMO_A_;
+    //int HOMO_B_;
+
+    //Eigen::RowVectorXd vec_P_OE;
+    // If unscrambaling is required
+    bool unscrambled_;
+    //bool counterPoise_;
+    /*
+     * \brief Determine if the provided orbital is valid
+     **/
+    bool orbitalValid_(const std::pair<std::string,int> & orbital) const;
+
+    void calculate_transfer_integral_();
+
+    void printTransferIntegral_(const std::pair<std::string,int> & Orbital1,
+                                const std::pair<std::string,int> & Orbital2) const;
 };
 
 // Reorganize the dimer coefficients to match up with the monomers
@@ -109,12 +130,18 @@ Eigen::MatrixXd unscramble_Coef(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& matchDimerB,
     const std::vector<int>& basisFuncDimer,
-    const Eigen::MatrixXd & dimerCoef);
+    const Eigen::MatrixXd & dimerCoef) {
+  Eigen::MatrixXd m;
+  return m;
+}
 
 Eigen::MatrixXd unscramble_Coef(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& basisFuncDimer,
-    const Eigen::MatrixXd & dimerCoef);
+    const Eigen::MatrixXd & dimerCoef){
+  Eigen::MatrixXd m;
+  return m;
+}
 
 // Reorganize the dimer overlap matrix to line up with the monomer
 // coefficients.
@@ -126,7 +153,10 @@ Eigen::MatrixXd unscramble_S(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& matchDimerB,
     const std::vector<int>& basisFuncDimer,
-    Eigen::MatrixXd S);
+    Eigen::MatrixXd S) {
+  Eigen::MatrixXd m;
+  return m;
+}
 
 /**
  *
@@ -135,7 +165,9 @@ Eigen::MatrixXd unscramble_S(
 Eigen::MatrixXd unscramble_S(
     const std::vector<int>& matchDimerA,
     const std::vector<int>& basisFuncDimer,
-    Eigen::MatrixXd S);
-
+    Eigen::MatrixXd S){
+  Eigen::MatrixXd m;
+  return m;
+}
 }  // namespace catnip
 #endif  // _CATNIP_QC_FUNCTIONS_HPP
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index bf8fc4b..ab1c7c6 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -22,7 +22,7 @@ if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
   link_libraries(gcov)
 endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
-if(ENABLE_TESTS)
+if(ENABLE_UNIT_TESTING)
   foreach(PROG IN LISTS UNIT_TEST_SOURCE_FILES)
     add_executable(unit_${PROG} ${PROG}.cpp)
     if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
@@ -31,9 +31,9 @@ if(ENABLE_TESTS)
     target_link_libraries(unit_${PROG} libcatnip)
     add_test(unit_${PROG} unit_${PROG})
   endforeach(PROG)
-endif(ENABLE_TESTS)
+endif(ENABLE_UNIT_TESTING)
 
-if(ENABLE_INTEGRATION_TESTS)
+if(ENABLE_INTEGRATION_TESTING)
 
   foreach(PROG 
       test_logreader
@@ -67,7 +67,7 @@ if(ENABLE_INTEGRATION_TESTS)
 
   endif(BASH_PROGRAM)
 
-endif(ENABLE_INTEGRATION_TESTS)
+endif(ENABLE_INTEGRATION_TESTING)
 
 
 
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
deleted file mode 100644
index 51098f2..0000000
--- a/src/tools/main.cpp
+++ /dev/null
@@ -1,172 +0,0 @@
-#include <algorithm>
-#include <cctype>
-#include <cstdlib>
-#include <cstring>
-#include <fstream>
-#include <functional>
-#include <iostream>
-#include <locale>
-#include <math.h>
-#include <sstream>
-#include <string>
-#include <sys/stat.h>
-#include <vector>
-
-#include "../libcatnip/io/argumentparser.hpp"
-#include "../libcatnip/io/file_readers/logreader.hpp"
-#include "../libcatnip/io/file_readers/punreader.hpp"
-#include "../libcatnip/io/io.hpp"
-#include "../libcatnip/log.hpp"
-#include "../libcatnip/parameters.hpp"
-#include "../libcatnip/qc_functions.hpp"
-#include "../libcatnip/matrix.hpp"
-#include "../libcatnip/calcJconfig.hpp"
-
-#include <eigen3/Eigen/Core>
-
-using namespace catnip;
-using namespace std;
-
-int main(int argc, const char *argv[]) {
-  cout << endl;
-  cout << "Running calc_J VERSION " << calcJ_VERSION_MAJOR << ".";
-  cout << calcJ_VERSION_MINOR << endl;
-
-  string line;
-  LOG("Preparing parser", 1);
-  auto ArgPars = prepareParser();
-  LOG("Parsing arguments", 1);
-  ArgPars->parse(argv, argc);
-  LOG("Preparing parameter object", 1);
-  auto par = prepareParameters(ArgPars);
-
-  cout << "log file for first monomer is:      " + par->getLog1() + '\n';
-  cout << "log file for second monomer is:     " + par->getLog2() + '\n';
-  cout << "log file for dimer is:              " + par->getLogP() + '\n';
-  cout << "pun file for the first monomer is:  " + par->getPun1() + '\n';
-  cout << "pun file for the second monomer is: " + par->getPun2() + '\n';
-  cout << "pun file for the dimer is:          " + par->getPunP() + '\n';
-
-  // Open the .pun file find the total number of molecular orbitals
-
-  LOG("Reading pun files", 1);
-  LOG("Reading pun file: " + par->getPunP(), 2);
-  PunReader pr_P(par->getPunP());
-  pr_P.read();
-  LOG("Reading pun file: " + par->getPun1(), 2);
-  PunReader pr_1(par->getPun1());
-  pr_1.read();
-  LOG("Reading pun file: " + par->getPun2(), 2);
-  PunReader pr_2(par->getPun2());
-  pr_2.read();
-
-  LOG("Reading log files", 1);
-  LOG("Reading log file: " + par->getLogP(), 2);
-  LogReader lr_P(par->getLogP());
-  lr_P.read();
-  LOG("Reading log file: " + par->getLog1(), 2);
-  LogReader lr_1(par->getLog1());
-  lr_1.read();
-  LOG("Reading log file: " + par->getLog2(), 2);
-  LogReader lr_2(par->getLog2());
-  lr_2.read();
-  // Load in general coefficients
-
-  // If there are only alpha orbitals then we can assume that restricted HF
-  // was used
-
-  // No need to worry about beta orbitals
-
-  {
-    Eigen::MatrixXd mat_S = lr_P.getOverlapMatrix();
-
-    Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
-    
-    Eigen::VectorXd vec_P_OE = Eigen::VectorXd(lr_P.getOE(par->getSpinP()));
-
-    int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
-    LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
-    Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
-    Eigen::VectorXd vec_1_OE = lr_1.getOE(par->getSpin1());
-
-    int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
-    LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
-    Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
-    Eigen::VectorXd vec_2_OE = lr_2.getOE(par->getSpin2());
-
-    // Unscramble dimer coef and energies first need to see how the dimer
-    // and monomer coefficients line up. To determine how the ceofficients
-    // line up we will first look at how the atoms appear in each of the
-    // .gjf files. We will also check to see how many coefficients are
-    // assocaited with each of the atoms by checking the .log files. Given
-    // the position of the atoms in the monomer unit and the positions of
-    // the atoms in the dimer we can determine how the coefficients need
-    // to be rearranged.
-    vector<vector<double>> coord_P = lr_P.getCoords();
-    vector<vector<double>> coord_1 = lr_1.getCoords();
-    vector<vector<double>> coord_2 = lr_2.getCoords();
-
-    // Convert coords to matrices
-    Eigen::MatrixXd coord_P_mat = convert(coord_P);
-    Eigen::MatrixXd coord_1_mat = convert(coord_1);
-    Eigen::MatrixXd coord_2_mat = convert(coord_2);
-
-    vector<int> basis_P = lr_P.getBasisFuncCount();
-    vector<int> basis_1 = lr_1.getBasisFuncCount();
-    vector<int> basis_2 = lr_2.getBasisFuncCount();
-
-    LOG("Creating transfercomplex", 1);
-    TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, HOMO1, HOMO2, mat_S,
-                       vec_P_OE, par->getCounterPoise());
-
-    // Set the transfer complex to counterpoise if it is the case.
-    // If the basis function search returns 0 for any of the components then
-    // we cannot automatically determine what the transfer integral is
-    if (basis_1.size() != 0 && basis_2.size() != 0 && basis_P.size() != 0) {
-      LOG("Unscrambling matrices", 1);
-      TC.unscramble(coord_1_mat, coord_2_mat, coord_P_mat, basis_P, basis_2);
-    } 
-
-    cout << endl;
-    cout << "Dimer     Spin " << par->getSpinP() << endl;
-
-    cout << "Monomer 1 Spin " << par->getSpin1() << " ";
-    if (par->getOrbNum1() == 0) {
-      cout << "Orbital " << par->getOrbType1() << endl;
-    } else if (par->getOrbNum1() > 0) {
-      cout << "Orbital " << par->getOrbType1();
-      cout << "+" << par->getOrbNum1() << endl;
-    } else {
-      cout << "Orbital " << par->getOrbType1();
-      cout << par->getOrbNum1() << endl;
-    }
-
-    cout << "Monomer 2 Spin " << par->getSpin2() << " ";
-    if (par->getOrbNum2() == 0) {
-      cout << "Orbital " << par->getOrbType2() << endl;
-    } else if (par->getOrbNum2() > 0) {
-      cout << "Orbital " << par->getOrbType2();
-      cout << "+" << par->getOrbNum2() << endl;
-    } else {
-      cout << "Orbital " << par->getOrbType2();
-      cout << par->getOrbNum2() << endl;
-    }
-
-    map<string, string> orbitaltypes;
-    map<string, int> orbitalnums;
-    orbitaltypes["mon1"] = par->getOrbType1();
-    orbitaltypes["mon2"] = par->getOrbType2();
-    orbitalnums["mon1"] = par->getOrbNum1();
-    orbitalnums["mon2"] = par->getOrbNum2();
-
-    LOG("Calculating transfer integral", 1);
-    TC.calcJ();
-    if(par->getPrintSwitch()){
-      TC.printAll();
-    }else{
-      TC.printTransferIntegral(orbitaltypes, orbitalnums);
-    }
-  }
-
-  return 0;
-}

From 3c14cae25b29eae0b3827e83fb187bee63e2420e Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Wed, 24 Jun 2020 06:57:55 -0600
Subject: [PATCH 34/68] Fixed make target tests

---
 CMakeLists.txt | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 45ed8a6..93d229e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -74,10 +74,9 @@ if(DOWNLOAD_TUTORIAL_FILES)
   execute_process(COMMAND ${PROJECT_SOURCE_DIR}/scripts/test_suite_install.bash "${PROJECT_SOURCE_DIR}" )
 endif()
 
-#if(ENABLE_TESTS OR ENABLE_INTEGRATION_TESTS)
-#  enable_testing()
-#  add_subdirectory("${PROJECT_SOURCE_DIR}/src/tests")
-#endif()
+if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+  enable_testing()
+endif()
 
 if (ENABLE_INTEGRATION_TESTING)
   file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 

From 0a142dd8eb28d5d162f9fc40eed358cc0325698c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 9 Jul 2020 07:33:01 -0600
Subject: [PATCH 35/68] checkpoint

---
 src/CMakeLists.txt                     |    7 +
 src/libcatnip/atom.hpp                 |   40 +
 src/libcatnip/atom_group.cpp           |   17 +
 src/libcatnip/atom_group.hpp           |   83 ++
 src/libcatnip/atom_group_container.cpp |  169 ++++
 src/libcatnip/atom_group_container.hpp |  107 +++
 src/libcatnip/calcJconfig.hpp          |   18 +
 src/libcatnip/elements.hpp             |  406 +++++++++
 src/libcatnip/index_map.cpp            |   43 +
 src/libcatnip/index_map.hpp            |   28 +
 src/libcatnip/organizer.hpp            |   29 +
 src/libcatnip/swap_engine.cpp          |   84 ++
 src/libcatnip/transfer_complex.cpp     | 1155 ++++++++++++++++++++++++
 src/libcatnip/transfer_complex.hpp     |   74 ++
 src/tests/test_qc_functions.cpp        |    3 +
 15 files changed, 2263 insertions(+)
 create mode 100644 src/CMakeLists.txt
 create mode 100644 src/libcatnip/atom.hpp
 create mode 100644 src/libcatnip/atom_group.cpp
 create mode 100644 src/libcatnip/atom_group.hpp
 create mode 100644 src/libcatnip/atom_group_container.cpp
 create mode 100644 src/libcatnip/atom_group_container.hpp
 create mode 100644 src/libcatnip/calcJconfig.hpp
 create mode 100644 src/libcatnip/elements.hpp
 create mode 100644 src/libcatnip/index_map.cpp
 create mode 100644 src/libcatnip/index_map.hpp
 create mode 100644 src/libcatnip/organizer.hpp
 create mode 100644 src/libcatnip/swap_engine.cpp
 create mode 100644 src/libcatnip/transfer_complex.cpp
 create mode 100644 src/libcatnip/transfer_complex.hpp

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..3637265
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,7 @@
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/libcatnip")
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tools")
+if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+  add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tests")
+endif()
+
+
diff --git a/src/libcatnip/atom.hpp b/src/libcatnip/atom.hpp
new file mode 100644
index 0000000..24c8b19
--- /dev/null
+++ b/src/libcatnip/atom.hpp
@@ -0,0 +1,40 @@
+
+#pragma once
+#ifndef _CATNIP_ATOM_HPP
+#define _CATNIP_ATOM_HPP
+
+
+#include "elements.hpp"
+
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
+
+  class Atom {
+    private:
+      Element element_;
+      Eigen::Vector3d xyz_;
+      int basis_func_count_ = -1;
+    public: 
+      Atom(Element element, double x, double y, double z) : element_(element), xyz_(x,y,z) {};
+
+      void setBasisFuncCount(int count) {
+        basis_func_count_ = count;
+      }
+
+      int getBasisFuncCount() const noexcept { return basis_func_count_; }
+
+      bool equal( Atom & atm2 ) const {
+        if ( element_ == atm2.element_ ){
+          if ( xyz_.isApprox(atm2.xyz_)) {
+            return true;
+          }
+        }
+        return false;
+      }
+  };
+
+
+}
+
+#endif // _CATNIP_ATOM_HPP
diff --git a/src/libcatnip/atom_group.cpp b/src/libcatnip/atom_group.cpp
new file mode 100644
index 0000000..cd5eb95
--- /dev/null
+++ b/src/libcatnip/atom_group.cpp
@@ -0,0 +1,17 @@
+
+#include "atom_group.hpp"
+#include "atom.hpp"
+
+namespace catnip {
+
+  int AtomGroup::findIndex(std::shared_ptr<Atom> atom) {
+    int index = 0;
+    for ( std::shared_ptr<Atom> & atom_ : atoms_){
+      if ( atom_->equal(*atom)){
+        return index;
+      }
+      ++index;
+    }
+    return -1;
+  }
+}
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
new file mode 100644
index 0000000..6647207
--- /dev/null
+++ b/src/libcatnip/atom_group.hpp
@@ -0,0 +1,83 @@
+#pragma once
+#ifndef _CATNIP_ATOM_GROUP_HPP
+#define _CATNIP_ATOM_GROUP_HPP
+
+#include <exception>
+#include <iterator>
+#include <memory>
+#include <numeric>
+#include <string>
+#include <vector>
+
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
+
+  class Atom;
+  
+  /**
+   * @brief Atom groups can either be a component or a complex
+   */
+  enum class GroupType {
+    PotentialComponent, // The atoms in all the components == the num atoms in the complex
+    Component, // All atoms in the components have a matching atom in the complex
+    Complex,
+    Unknown
+  };
+
+  /**
+   * @brief Stores the name of the atom group, the group type and the atoms in
+   * the group
+   *
+   */
+  class AtomGroup {
+    private: 
+      GroupType type_ = GroupType::Unknown;
+      std::string name_;
+      std::vector<std::shared_ptr<Atom>> atoms_;
+    public:
+      AtomGroup(std::string group_name) : name_(group_name) {};
+
+      size_t size() const noexcept { return atoms_.size(); }
+
+      std::vector<std::shared_ptr<Atom>>::iterator 
+        begin() { return atoms_.begin(); }
+
+      std::vector<std::shared_ptr<Atom>>::iterator 
+        end() { return atoms_.end(); }
+ 
+      std::shared_ptr<Atom> at(size_t ind) const {
+        return atoms_.at(ind);
+      }
+
+      void add(std::shared_ptr<Atom> atom){
+        atoms_.push_back(atom);
+      } 
+
+      void add(std::vector<std::shared_ptr<Atom>> atoms){
+        atoms_.insert(atoms_.end(),atoms.begin(),atoms.end());
+      } 
+
+      size_t numberOfAtoms() const noexcept {
+        return atoms_.size();
+      }
+
+      void setType(const GroupType & type) noexcept {
+        type_ = type;
+      }
+      GroupType getType() const noexcept { return type_; }
+
+      /**
+       * @brief Find the index of the atom in the group if it exists and return
+       * the index
+       *
+       * @param atom
+       *
+       * @return index if found -1 if not found 
+       */
+      int findIndex(std::shared_ptr<Atom> atom);
+  };
+
+
+}  // namespace catnip
+#endif  // _CATNIP_ATOM_GROUP_HPP
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
new file mode 100644
index 0000000..08874c3
--- /dev/null
+++ b/src/libcatnip/atom_group_container.cpp
@@ -0,0 +1,169 @@
+
+#include "atom_group_container.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+
+#include <exception>
+#include <iterator>
+#include <memory>
+#include <numeric>
+#include <string>
+#include <vector>
+
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
+
+  void AtomGroupContainer::assignBasisFuncCountToComplex_(const std::vector<int>& complex_basis_func_count) {
+    // Cycle through the atoms in the complex and assign the correct number of
+    // basis functions
+    int index = 0; 
+    for( std::shared_ptr<Atom> & atom_ptr : atom_groups_.at(index_of_complex_) ){
+      atom_ptr->setBasisFuncCount(complex_basis_func_count.at(index));
+      index++;
+    }
+  }
+
+  // Assumes the complex atoms already have been assigned the basis functioncount
+  void AtomGroupContainer::assignBasisFuncCountToComponents_() {
+    std::vector<AtomMatch> paired_atoms = matchComponentAtomsToComplex_();
+    for ( AtomMatch atom_match : paired_atoms ) {
+      int basis_func_count = atom_groups_.at(index_of_complex_).at(atom_match.index_complex_atom)->getBasisFuncCount();
+      atom_groups_.at(atom_match.index_component).at(atom_match.index_component_atom)->setBasisFuncCount(basis_func_count);
+    } 
+  }
+
+  std::vector<int> AtomGroupContainer::getGroups(const GroupType & type) const {
+    std::vector<int> groups;
+    int ind1 = 0;
+    for( const AtomGroup & group : atom_groups_ ){
+      if( group.getType() == type){
+        groups.push_back(ind1);
+      }
+      ++ind1;
+    }
+    return groups;
+  }
+  std::unordered_map<int,int> AtomGroupContainer::matchAtoms_( 
+      const AtomGroup & grp1, const AtomGroup & grp2) const {
+  
+    std::unordered_map<int,int> paired_atoms;  
+    for ( size_t ind1 = 0; ind1 < grp1.size(); ++ind1){
+      for (size_t ind2 = 0; ind2 < grp2.size(); ++ind2){
+        if ( grp1.at(ind1)->equal(*grp2.at(ind2)) ){
+          if ( paired_atoms.count(ind1) ) {
+            throw std::runtime_error("Atom in complex has already been paired with an atom in the component, you have two or more atoms in a component that are redundant with an atom in the complex");
+          }
+          paired_atoms[ind1] = ind2;
+          break;
+        } 
+      }
+    }
+    return paired_atoms;
+  }
+
+
+  void AtomGroupContainer::add( AtomGroup atom_group ) {
+    if( isUniqueGroup(atom_group) ){
+      atom_groups_.push_back(atom_group);
+    }
+    group_types_uptodate_ = false;
+    index_of_complex_ = -1;
+  }
+
+  void AtomGroupContainer::assignAtomGroupTypes(){
+    if (group_types_uptodate_ ) return;
+    std::vector<size_t> number_atoms;        
+    for( AtomGroup group : atom_groups_){
+      number_atoms.push_back(group.numberOfAtoms());
+    }
+    auto max_elem_it = max_element(number_atoms.begin(),number_atoms.end()); 
+    size_t max_elem = *max_elem_it; 
+    for( AtomGroup group : atom_groups_){
+      group.setType(GroupType::Component);
+    } 
+    size_t number_atoms_excluding_max = std::accumulate(number_atoms.begin(),number_atoms.end(),-1*max_elem);
+    if ( std::count(number_atoms.begin(),number_atoms.end(), max_elem) == 1 &&
+        number_atoms_excluding_max == max_elem ){
+      for( AtomGroup group : atom_groups_){
+        if( group.numberOfAtoms() == max_elem ){
+          group.setType(GroupType::Complex);
+          index_of_complex_ = std::distance(number_atoms.begin(),max_elem_it);
+        } 
+      }
+    }
+    group_types_uptodate_ = true;
+  }
+
+  int AtomGroupContainer::getTotalBasisFunctionCount(const GroupType & type) const {
+    int total_num_basis = 0;
+    std::vector<int> group_indices = getGroups(type);     
+    for ( int ind : group_indices ){
+      AtomGroup group = getGroup(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+        total_num_basis += atom_ptr->getBasisFuncCount();
+      }
+    } 
+    return total_num_basis;
+  }
+
+  int AtomGroupContainer::getMaxBasisFunctionCount(const GroupType & type) const {
+    int max_num_basis = 0;
+    std::vector<int> group_indices = getGroups(type);     
+    for ( int ind : group_indices ){
+      AtomGroup group = getGroup(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+        if( atom_ptr->getBasisFuncCount() > max_num_basis){
+          max_num_basis = atom_ptr->getBasisFuncCount();
+        }
+      }
+    } 
+    return max_num_basis;
+  }
+
+  bool AtomGroupContainer::complexExists() const {
+    // First check that all the group types have been assigned
+    if ( group_types_uptodate_ == false ){
+      throw std::runtime_error("Cannot determine if complex exists group types are not up to date");
+    }
+    return index_of_complex_ > -1;
+  }
+
+  std::vector<AtomGroupContainer::AtomMatch> AtomGroupContainer::matchComponentAtomsToComplex_(){
+
+    AtomGroup complex_group = atom_groups_.at(index_of_complex_);
+    std::vector<int> component_indices = getGroups(GroupType::Component);
+    std::vector<AtomMatch> all_paired_atoms;
+    for ( const int & component_index : component_indices ) {
+      std::unordered_map<int,int> paired_atoms = matchAtoms_(complex_group,atom_groups_.at(component_index));
+      // Pass to vector
+      for ( auto pr : paired_atoms ){
+        AtomMatch atom_match;
+        atom_match.index_component = component_index;
+        atom_match.index_component_atom = pr.second;
+        atom_match.index_complex_atom = pr.first;
+        all_paired_atoms.push_back(atom_match);
+      }
+    }
+  }
+
+  void AtomGroupContainer::assignBasisFunctionCount(
+      const std::vector<int>& complex_basis_func_count) {
+
+    // 1. Check that up to date
+    if ( group_types_uptodate_ == false ){
+      throw std::runtime_error("Cannot assign basis functions to atoms as group types are not up to date!");
+    }
+    // 2. Check that the number of atoms in the complex is consistent with the number of values provided
+    if ( complex_basis_func_count.size() != atom_groups_.at(index_of_complex_).numberOfAtoms() ){
+      throw std::runtime_error("Cannot assign basis function count to atoms as the basis function count vector is not equal to the number of atoms!");
+    }
+
+    assignBasisFuncCountToComplex_(complex_basis_func_count);
+    assignBasisFuncCountToComponents_();
+    
+  }
+
+   
+}  // namespace catnip
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
new file mode 100644
index 0000000..4203669
--- /dev/null
+++ b/src/libcatnip/atom_group_container.hpp
@@ -0,0 +1,107 @@
+#pragma once
+#ifndef _CATNIP_ATOM_GROUP_CONTAINER_HPP
+#define _CATNIP_ATOM_GROUP_CONTAINER_HPP
+
+#include "atom_group.hpp"
+
+#include <eigen3/Eigen/Dense>
+
+#include <exception>
+#include <iterator>
+#include <memory>
+#include <numeric>
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+namespace catnip {
+
+  class Atom;
+
+  class AtomGroupContainer {
+      std::vector<AtomGroup> atom_groups_;
+     
+      bool group_types_uptodate_ = false; 
+      /**
+       * @brief Checks to makes sure the group is unique
+       *
+       * @param atom_group
+       *
+       * @return 
+       */
+      bool isUniqueGroup_( AtomGroup atom_group );
+
+
+      /**
+       * @brief Match the indices of the first atom group with any that share 
+       * coordinates and the same element in atom group 2
+       *
+       * @param grp1
+       * @param grp2
+       *
+       * @return map returns indices in group two that match group 1 
+       */
+      std::unordered_map<int,int> matchAtoms_( const AtomGroup & grp1, const AtomGroup & grp2) const;
+
+      void assignBasisFuncCountToComplex_(const std::vector<int>& complex_basis_func_count);
+      void assignBasisFuncCountToComponents_();
+
+      struct AtomMatch {
+        int index_component;
+        int index_component_atom;
+        int index_complex_atom;
+      };
+
+      std::vector<AtomMatch> matchComponentAtomsToComplex_();
+      int index_of_complex_ = -1;
+    public: 
+      void add( AtomGroup atom_group );
+
+      /**
+       * @brief This algorithm determines if a complex exists
+       *
+       * This algorithm does not compare the atoms in the complex with the
+       * atoms in the components, so it is not a rigourous algorithm but should
+       * be sufficient for our purposes.
+       *
+       * Only a single atom group can be the complex
+       */
+      void assignAtomGroupTypes();
+
+      /**
+       * @brief Determine if a complex exists within the atom groups
+       *
+       * Only a single atom group can be a complex
+       *
+       * @return 
+       */
+      bool complexExists() const ;
+
+      /**
+       * @brief If a complex exists and we know the number of basis functions
+       * associated with each atom in the complex we can assign the basis function
+       * number to each of the atoms
+       *
+       * @param complex_basis_func_count
+       */
+      void assignBasisFunctionCount(const std::vector<int>& complex_basis_func_count);
+
+      int getTotalBasisFunctionCount(const GroupType & type) const;
+
+      int getMaxBasisFunctionCount(const GroupType & type) const;
+      /**
+       * @brief Get the indices of all the groups of the specified group type
+       *
+       * @param type
+       *
+       * @return 
+       */
+      std::vector<int> getGroups(const GroupType & type) const;     
+
+      AtomGroup getGroup(size_t ind) const { return  atom_groups_.at(ind);}
+
+      
+  };
+
+}  // namespace catnip
+#endif  // _CATNIP_ATOM_GROUP_CONTAINER_HPP
diff --git a/src/libcatnip/calcJconfig.hpp b/src/libcatnip/calcJconfig.hpp
new file mode 100644
index 0000000..e574fe9
--- /dev/null
+++ b/src/libcatnip/calcJconfig.hpp
@@ -0,0 +1,18 @@
+// Configured options and settings for calcJ
+
+#ifndef CATNIP_CONFIG_HPP
+#define CATNIP_CONFIG_HPP
+
+#include <string>
+
+namespace catnip {
+const int calcJ_VERSION_MAJOR = 2;
+const int calcJ_VERSION_MINOR = 0;
+const int calcJ_YEAR_PUBLISHED = 2018;
+const std::string calcJ_AUTHOR_SURNAME = "Brown";
+const std::string calcJ_AUTHOR_INITIALS = "J. S.";
+const std::string calcJ_TITLE = "CATNIP";
+const std::string calcJ_URL = "https://github.com/JoshuaSBrown/QC_Tools";
+}  // namespace catnip
+
+#endif  // CATNIP_CONFIG_HPP
diff --git a/src/libcatnip/elements.hpp b/src/libcatnip/elements.hpp
new file mode 100644
index 0000000..03fc1b5
--- /dev/null
+++ b/src/libcatnip/elements.hpp
@@ -0,0 +1,406 @@
+#include <algorithm>
+#include <cctype>
+#include <map>
+#include <string>
+
+namespace catnip {
+
+  enum class Element {
+    Ac,
+    Al,
+    Am,
+    Sb,
+    Ar,
+    As,
+    At,
+    Ba,
+    Bk,
+    Be,
+    Bi,
+    Bh,
+    B,
+    Br,
+    Cd,
+    Ca,
+    Cf,
+    C,
+    Ce,
+    Cs,
+    Cl,
+    Cr,
+    Co,
+    Cu,
+    Cm,
+    Ds,
+    Db,
+    Dy,
+    Es,
+    Er,
+    Eu,
+    Fm,
+    F,
+    Fr,
+    Gd,
+    Ga,
+    Ge,
+    Au,
+    Hf,
+    Hs,
+    He,
+    Ho,
+    H,
+    In,
+    I,
+    Ir,
+    Fe,
+    Kr,
+    La,
+    Lr,
+    Pb,
+    Li,
+    Lu,
+    Mg,
+    Mn,
+    Mt,
+    Md,
+    Hg,
+    Mo,
+    Nd,
+    Ne,
+    Np,
+    Ni,
+    Nb,
+    N,
+    No,
+    Uuo,
+    Os,
+    O,
+    Pd,
+    P,
+    Pt,
+    Pu,
+    Po,
+    K,
+    Pr,
+    Pm,
+    Pa,
+    Ra,
+    Rn,
+    Re,
+    Rh,
+    Rg,
+    Rb,
+    Ru,
+    Rf,
+    Sm,
+    Sc,
+    Sg,
+    Se,
+    Si,
+    Ag,
+    Na,
+    Sr,
+    S,
+    Ta,
+    Tc,
+    Te,
+    Tb,
+    Tl,
+    Th,
+    Tm,
+    Sn,
+    Ti,
+    W,
+    Uub,
+    Uuh,
+    Uup,
+    Uuq,
+    Uus,
+    Uut,
+    U,
+    V,
+    Xe,
+    Yb,
+    Y,
+    Zn,
+    Zr,
+    Unknown
+  };
+
+  /**
+   * @brief For manipulating Elements
+   *
+   * Converts string to enum class type
+   */
+  class Elements {
+
+    private:
+      void to_lower_(std::string & data) const noexcept {
+        std::transform(data.begin(), data.end(), data.begin(),
+          [](unsigned char c){ return std::tolower(c); });
+      }
+    public: 
+
+      /**
+       * @brief Case insensitive get Element enum
+       *
+       * @param element_name
+       *
+       * @return 
+       */
+      Element getElement(std::string element_name) const noexcept {
+        to_lower_(element_name);
+        if( elements_.count(element_name)) {
+          return elements_.at(element_name);
+        }
+        if( elementssym_.count(element_name)) {
+          return elementssym_.at(element_name);
+        }
+        return Element::Unknown;
+      }
+
+    private:
+      std::map<std::string, Element> elements_ = {
+        {"actinium",     Element::Ac},
+        {"aluminum",     Element::Al},
+        {"americium",    Element::Am},
+        {"antimony",     Element::Sb},
+        {"argon",        Element::Ar},
+        {"arsenic",      Element::As},
+        {"astatine",     Element::At},
+        {"barium",       Element::Ba},
+        {"berkelium",    Element::Bk},
+        {"beryllium",    Element::Be},
+        {"bismuth",      Element::Bi},
+        {"bohrium",      Element::Bh},
+        {"boron",        Element::B},
+        {"bromine",      Element::Br},
+        {"cadmium",      Element::Cd},
+        {"calcium",      Element::Ca},
+        {"californium",  Element::Cf},
+        {"carbon",       Element::C},
+        {"cerium",       Element::Ce},
+        {"cesium",       Element::Cs},
+        {"chlorine",     Element::Cl},
+        {"chromium",     Element::Cr},
+        {"cobalt",       Element::Co},
+        {"copper",       Element::Cu},
+        {"curium",       Element::Cm},
+        {"darmstadtium", Element::Ds},
+        {"dubnium",      Element::Db},
+        {"dysprosium",   Element::Dy},
+        {"einsteinium",  Element::Es},
+        {"erbium",       Element::Er},
+        {"europium",     Element::Eu},
+        {"fermium",      Element::Fm},
+        {"fluorine",     Element::F},
+        {"francium",     Element::Fr},
+        {"gadolinium",   Element::Gd},
+        {"gallium",      Element::Ga},
+        {"germanium",    Element::Ge},
+        {"gold",         Element::Au},
+        {"hafnium",      Element::Hf},
+        {"hassium",      Element::Hs},
+        {"helium",       Element::He},
+        {"holmium",      Element::Ho},
+        {"hydrogen",     Element::H},
+        {"indium",       Element::In},
+        {"iodine",       Element::I},
+        {"iridium",      Element::Ir},
+        {"iron",         Element::Fe},
+        {"krypton",      Element::Kr},
+        {"lanthanum",    Element::La},
+        {"lawrencium",   Element::Lr},
+        {"lead",         Element::Pb},
+        {"lithium",      Element::Li},
+        {"lutetium",     Element::Lu},
+        {"magnesium",    Element::Mg},
+        {"manganese",    Element::Mn},
+        {"meitnerium",   Element::Mt},
+        {"mendelevium",  Element::Md},
+        {"mercury",      Element::Hg},
+        {"molybdenum",   Element::Mo},
+        {"neodymium",    Element::Nd},
+        {"neon",         Element::Ne},
+        {"neptunium",    Element::Np},
+        {"nickel",       Element::Ni},
+        {"niobium",      Element::Nb},
+        {"nitrogen",     Element::N},
+        {"nobelium",     Element::No},
+        {"oganesson",    Element::Uuo},
+        {"osmium",       Element::Os},
+        {"oxygen",       Element::O},
+        {"palladium",    Element::Pd},
+        {"phosphorus",   Element::P},
+        {"platinum",     Element::Pt},
+        {"plutonium",    Element::Pu},
+        {"polonium",     Element::Po},
+        {"potassium",    Element::K},
+        {"praseodymium", Element::Pr},
+        {"promethium",   Element::Pm},
+        {"protactinium", Element::Pa},
+        {"radium",       Element::Ra},
+        {"radon",        Element::Rn},
+        {"rhenium",      Element::Re},
+        {"rhodium",      Element::Rh},
+        {"roentgenium",  Element::Rg},
+        {"rubidium",     Element::Rb},
+        {"ruthenium",    Element::Ru},
+        {"rutherfordium",Element::Rf},
+        {"samarium",     Element::Sm},
+        {"scandium",     Element::Sc},
+        {"seaborgium",   Element::Sg},
+        {"selenium",     Element::Se},
+        {"silicon",      Element::Si},
+        {"silver",       Element::Ag},
+        {"sodium",       Element::Na},
+        {"strontium",    Element::Sr},
+        {"sulfur",       Element::S},
+        {"tantalum",     Element::Ta},
+        {"technetium",   Element::Tc},
+        {"tellurium",    Element::Te},
+        {"terbium",      Element::Tb},
+        {"thallium",     Element::Tl},
+        {"thorium",      Element::Th},
+        {"thulium",      Element::Tm},
+        {"tin",          Element::Sn},
+        {"titanium",     Element::Ti},
+        {"tungsten",     Element::W},
+        {"ununbium",     Element::Uub},
+        {"ununhexium",   Element::Uuh},
+        {"ununpentium",  Element::Uup},
+        {"ununquadium",  Element::Uuq},
+        {"ununseptium",  Element::Uus},
+        {"ununtrium",    Element::Uut},
+        {"uranium",      Element::U},
+        {"vanadium",     Element::V},
+        {"xenon",        Element::Xe},
+        {"ytterbium",    Element::Yb},
+        {"yttrium",      Element::Y},
+        {"zinc",         Element::Zn},
+        {"zirconium",    Element::Zr}};
+
+      std::map<std::string, Element> elementssym_ = {
+        {"ac",    Element::Ac},
+        {"al",    Element::Al},
+        {"am",    Element::Am},
+        {"sb",    Element::Sb},
+        {"ar",    Element::Ar},
+        {"as",    Element::As},
+        {"at",    Element::At},
+        {"ba",    Element::Ba},
+        {"bk",    Element::Bk},
+        {"be",    Element::Be},
+        {"bi",    Element::Bi},
+        {"bh",    Element::Bh},
+        {"b",     Element::B},
+        {"br",    Element::Br},
+        {"cd",    Element::Cd},
+        {"ca",    Element::Ca},
+        {"cf",    Element::Cf},
+        {"c",     Element::C},
+        {"ce",    Element::Ce},
+        {"cs",    Element::Cs},
+        {"cl",    Element::Cl},
+        {"cr",    Element::Cr},
+        {"co",    Element::Co},
+        {"cu",    Element::Cu},
+        {"cm",    Element::Cm},
+        {"ds",    Element::Ds},
+        {"db",    Element::Db},
+        {"dy",    Element::Dy},
+        {"es",    Element::Es},
+        {"er",    Element::Er},
+        {"eu",    Element::Eu},
+        {"fm",    Element::Fm},
+        {"f",     Element::F},
+        {"fr",    Element::Fr},
+        {"gd",    Element::Gd},
+        {"ga",    Element::Ga},
+        {"ge",    Element::Ge},
+        {"au",    Element::Au},
+        {"hf",    Element::Hf},
+        {"hs",    Element::Hs},
+        {"he",    Element::He},
+        {"ho",    Element::Ho},
+        {"h",     Element::H},
+        {"in",    Element::In},
+        {"i",     Element::I},
+        {"ir",    Element::Ir},
+        {"fe",    Element::Fe},
+        {"kr",    Element::Kr},
+        {"la",    Element::La},
+        {"lr",    Element::Lr},
+        {"pb",    Element::Pb},
+        {"li",    Element::Li},
+        {"lu",    Element::Lu},
+        {"mg",    Element::Mg},
+        {"mn",    Element::Mn},
+        {"mt",    Element::Mt},
+        {"md",    Element::Md},
+        {"hg",    Element::Hg},
+        {"mo",    Element::Mo},
+        {"nd",    Element::Nd},
+        {"ne",    Element::Ne},
+        {"np",    Element::Np},
+        {"ni",    Element::Ni},
+        {"nb",    Element::Nb},
+        {"n",     Element::N},
+        {"no",    Element::No},
+        {"uuo",   Element::Uuo},
+        {"os",    Element::Os},
+        {"o",     Element::O},
+        {"pd",    Element::Pd},
+        {"p",     Element::P},
+        {"pt",    Element::Pt},
+        {"pu",    Element::Pu},
+        {"po",    Element::Po},
+        {"k",     Element::K},
+        {"pr",    Element::Pr},
+        {"pm",    Element::Pm},
+        {"pa",    Element::Pa},
+        {"ra",    Element::Ra},
+        {"rn",    Element::Rn},
+        {"re",    Element::Re},
+        {"rh",    Element::Rh},
+        {"rg",    Element::Rg},
+        {"rb",    Element::Rb},
+        {"ru",    Element::Ru},
+        {"rf",    Element::Rf},
+        {"sm",    Element::Sm},
+        {"sc",    Element::Sc},
+        {"sg",    Element::Sg},
+        {"se",    Element::Se},
+        {"si",    Element::Si},
+        {"ag",    Element::Ag},
+        {"na",    Element::Na},
+        {"sr",    Element::Sr},
+        {"s",     Element::S},
+        {"ta",    Element::Ta},
+        {"tc",    Element::Tc},
+        {"te",    Element::Te},
+        {"tb",    Element::Tb},
+        {"tl",    Element::Tl},
+        {"th",    Element::Th},
+        {"tm",    Element::Tm},
+        {"sn",    Element::Sn},
+        {"ti",    Element::Ti},
+        {"w",     Element::W},
+        {"uub",   Element::Uub},
+        {"uuh",   Element::Uuh},
+        {"uup",   Element::Uup},
+        {"uuq",   Element::Uuq},
+        {"uus",   Element::Uus},
+        {"uut",   Element::Uut},
+        {"u",     Element::U},
+        {"v",     Element::V},
+        {"xe",    Element::Xe},
+        {"yb",    Element::Yb},
+        {"y",     Element::Y},
+        {"zn",    Element::Zn},
+        {"zr",    Element::Zr}};
+
+  };
+
+}
+
diff --git a/src/libcatnip/index_map.cpp b/src/libcatnip/index_map.cpp
new file mode 100644
index 0000000..0497ca3
--- /dev/null
+++ b/src/libcatnip/index_map.cpp
@@ -0,0 +1,43 @@
+
+
+#include "index_map.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+
+namespace catnip {
+
+  IndexMap::IndexMap(AtomGroupContainer atom_groups){
+    std::vector<int> group_indices = atom_groups.getGroups(GroupType::Component);
+    int complex_ind = atom_groups.getGroups(GroupType::Complex).at(0);
+    AtomGroup complex_group = atom_groups.getGroup(complex_ind);
+    int sys_ind = 0;
+    for ( int & group_ind : group_indices) {
+      AtomGroup component_group = atom_groups.getGroup(group_ind);
+      for( std::shared_ptr<Atom> & atom : component_group){
+        int atom_ind = complex_group.findIndex(atom);
+        int num_basis = complex_group.at(atom_ind)->getBasisFuncCount();
+        for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
+          row_col_final[group_ind].push_back(sys_ind); 
+          row_col_init[group_ind].push_back(atom_ind);
+          sys_ind++;
+        }
+      }
+    }
+  }
+  // Searches the init row for the provided row and returns the group it is
+  // in as well as its current index
+  std::pair<int,int> IndexMap::findLocation(int row){
+    std::pair<int,int> group_row;
+    for( std::pair<int,std::vector<int>> group_rows : row_col_init){
+      int row_ind = 0;
+      for ( int row_ : group_rows.second ){
+        if (row_ == row){
+          return std::pair<int,int>(group_rows.first, row_ind);
+        }
+        ++row_ind;
+      } 
+    }
+  }
+
+}  // namespace catnip
diff --git a/src/libcatnip/index_map.hpp b/src/libcatnip/index_map.hpp
new file mode 100644
index 0000000..c1df94f
--- /dev/null
+++ b/src/libcatnip/index_map.hpp
@@ -0,0 +1,28 @@
+
+
+#include "transfer_complex.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+
+namespace catnip {
+
+  class IndexMap {
+    public:
+
+      IndexMap(AtomGroupContainer atom_groups);
+      // The component rows and colums in their current locations in  
+      // in the full system matrix of the complex
+      std::map<int,std::vector<int>> row_col_init;
+
+      // Map indicate where the rows and cols should go in the final state
+      // Each int in the vector represents the locatin in the full system matrix
+      std::map<int,std::vector<int>> row_col_final;
+
+      // Searches the init row for the provided row and returns the group it is
+      // in as well as its current index
+      std::pair<int,int> findLocation(int row);
+  };
+
+
+}  // namespace catnip
diff --git a/src/libcatnip/organizer.hpp b/src/libcatnip/organizer.hpp
new file mode 100644
index 0000000..fa992d5
--- /dev/null
+++ b/src/libcatnip/organizer.hpp
@@ -0,0 +1,29 @@
+#pragma once
+#ifndef _CATNIP_ORGANIZER_HPP
+#define _CATNIP_ORGANIZER_HPP
+
+
+#include <map>
+#include <memory>
+#include <sstream>
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+//#include "matrix.hpp"
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
+
+  /**
+   * @brief The purpose of this class is to be able to organize basis functions
+   * with the correct atoms in a molecule
+   */
+  class Organizer {
+
+
+    public:
+      void unscramble(AtomGroupContainer cont);
+  };
+}  // namespace catnip
+#endif  // _CATNIP_ORGANIZER_HPP
diff --git a/src/libcatnip/swap_engine.cpp b/src/libcatnip/swap_engine.cpp
new file mode 100644
index 0000000..a673b17
--- /dev/null
+++ b/src/libcatnip/swap_engine.cpp
@@ -0,0 +1,84 @@
+
+
+#include "swap_engine.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+
+namespace catnip {
+
+  // Swaps rows columns and keeps up with how future swaps should be updated
+  class SwapEngine {
+    private:
+      size_t size_;
+      IndexMap ind_map_;
+      Eigen::MatrixXd scratch_;
+
+    public:
+      SwapEngine(IndexMap ind_map, size_t size) : 
+        size_(size), ind_map_(ind_map) {
+          scratch_ = Eigen::MatrixXd::Zero(size, 1);
+
+
+        // Already have enough information to calculate the correct swap order
+        // Note the order of swaps is important.
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            std::pair<int,int> swap(row,final_row);
+            // Now we need to update index map, the row located at the final 
+            // position has now been moved     
+            auto group_and_row_ind = ind_map_.findLocation(final_row);
+            
+            // Final row location needs to be pointed to the starting row
+            ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
+          } 
+        }
+      };
+
+
+      // This method of swapping was chosen to keep the memory footprint
+      // reasonable.
+      // Will correctly sort the rows and columns of the matrix
+      void arrange(Eigen::MatrixXd & mat) {
+
+        // Check that matrix is square
+        if( mat.rows() != mat.cols() ) {
+          throw std::runtime_error("Can only arrange square matrices");
+        }
+        if( mat.rows() != size_ ) {
+          throw std::runtime_error("Index map has different number of basis functions to matrix");
+        }
+
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            if(final_row == row ) continue;
+            // Copy the data at the final row into the scratch space 
+            scratch_.col(0) = mat.row(final_row);
+            // Copy the data from the initial row into the final row
+            mat.row(final_row) = mat.row(row);
+            // Copy the data from the temporary row into the initial row
+            mat.row(row) = scratch_.col(0);
+          }
+        }
+
+        // Repeat for columns 
+        for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
+          int group_ind = group_col.first;
+          for ( int col : group_col.second ) {
+            int final_col = ind_map_.row_col_final[group_ind].at(col);
+            if(final_col == col ) continue;
+            // Copy the data at the final row into the scratch space
+            scratch_.col(0) = mat.col(final_col);
+            // Copy the data from the initial row into the final row
+            mat.col(final_col) = mat.col(col);
+            // Copy the data from the temporary row into the initial row
+            mat.col(col) = scratch_.col(0);
+          }
+        }
+      }
+  };
+}  // namespace catnip
diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
new file mode 100644
index 0000000..7575b7f
--- /dev/null
+++ b/src/libcatnip/transfer_complex.cpp
@@ -0,0 +1,1155 @@
+
+
+#include "transfer_complex.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+//#include "constants.hpp"
+//#include "io/io.hpp"
+//#include "log.hpp"
+//#include "matrix.hpp"
+//
+//#include <eigen3/Eigen/Dense>
+//#include <eigen3/Eigen/Eigenvalues>
+//
+//#include <algorithm>
+//#include <cmath>
+//#include <fstream>
+//#include <iomanip>
+//#include <iostream>
+//#include <list>
+//#include <numeric> // For accumulate
+//#include <sstream>
+//#include <stdlib.h>
+//#include <string>
+//#include <unordered_map>
+//
+
+namespace catnip {
+
+  class IndexMap {
+    public:
+
+      IndexMap(AtomGroupContainer atom_groups){
+        std::vector<int> group_indices = atom_groups.getGroups(GroupType::Component);
+        int complex_ind = atom_groups.getGroups(GroupType::Complex).at(0);
+        AtomGroup complex_group = atom_groups.getGroup(complex_ind);
+        int sys_ind = 0;
+        for ( int & group_ind : group_indices) {
+          AtomGroup component_group = atom_groups.getGroup(group_ind);
+          for( std::shared_ptr<Atom> & atom : component_group){
+            int atom_ind = complex_group.findIndex(atom);
+            int num_basis = complex_group.at(atom_ind)->getBasisFuncCount();
+            for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
+              row_col_final[group_ind].push_back(sys_ind); 
+              row_col_init[group_ind].push_back(atom_ind);
+              sys_ind++;
+            }
+          }
+        }
+      }
+
+      // The component rows and colums in their current locations in  
+      // in the full system matrix of the complex
+      std::map<int,std::vector<int>> row_col_init;
+
+      // Map indicate where the rows and cols should go in the final state
+      // Each int in the vector represents the locatin in the full system matrix
+      std::map<int,std::vector<int>> row_col_final;
+
+      // Searches the init row for the provided row and returns the group it is
+      // in as well as its current index
+      std::pair<int,int> findLocation(int row){
+        std::pair<int,int> group_row;
+        for( std::pair<int,std::vector<int>> group_rows : row_col_init){
+          int row_ind = 0;
+          for ( int row_ : group_rows.second ){
+            if (row_ == row){
+              return std::pair<int,int>(group_rows.first, row_ind);
+            }
+            ++row_ind;
+          } 
+        }
+      }
+  };
+
+  // Swaps rows columns and keeps up with how future swaps should be updated
+  class SwapEngine {
+    private:
+      size_t size_;
+      IndexMap ind_map_;
+      Eigen::MatrixXd scratch_;
+
+    public:
+      SwapEngine(IndexMap ind_map, size_t size) : 
+        size_(size), ind_map_(ind_map) {
+          scratch_ = Eigen::MatrixXd::Zero(size, 1);
+
+
+        // Already have enough information to calculate the correct swap order
+        // Note the order of swaps is important.
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            std::pair<int,int> swap(row,final_row);
+            // Now we need to update index map, the row located at the final 
+            // position has now been moved     
+            auto group_and_row_ind = ind_map_.findLocation(final_row);
+            
+            // Final row location needs to be pointed to the starting row
+            ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
+          } 
+        }
+      };
+
+
+      // This method of swapping was chosen to keep the memory footprint
+      // reasonable.
+      // Will correctly sort the rows and columns of the matrix
+      void arrange(Eigen::MatrixXd & mat) {
+
+        // Check that matrix is square
+        if( mat.rows() != mat.cols() ) {
+          throw std::runtime_error("Can only arrange square matrices");
+        }
+        if( mat.rows() != size_ ) {
+          throw std::runtime_error("Index map has different number of basis functions to matrix");
+        }
+
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            if(final_row == row ) continue;
+            // Copy the data at the final row into the scratch space 
+            scratch_.col(0) = mat.row(final_row);
+            // Copy the data from the initial row into the final row
+            mat.row(final_row) = mat.row(row);
+            // Copy the data from the temporary row into the initial row
+            mat.row(row) = scratch_.col(0);
+          }
+        }
+
+        // Repeat for columns 
+        for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
+          int group_ind = group_col.first;
+          for ( int col : group_col.second ) {
+            int final_col = ind_map_.row_col_final[group_ind].at(col);
+            if(final_col == col ) continue;
+            // Copy the data at the final row into the scratch space
+            scratch_.col(0) = mat.col(final_col);
+            // Copy the data from the initial row into the final row
+            mat.col(final_col) = mat.col(col);
+            // Copy the data from the temporary row into the initial row
+            mat.col(col) = scratch_.col(0);
+          }
+        }
+      }
+  };
+
+  void TransferComplex::unscramble(AtomGroupContainer atom_groups) {
+    // We should figure out how all the rows and columns should be
+    // rearranged before moving any of the coefficients in the matrix    
+    IndexMap ind_map = IndexMap(atom_groups);
+  
+    size_t total_basis = atom_groups.getTotalBasisFunctionCount(GroupType::Component); 
+    size_t total_basis_comp = atom_groups.getTotalBasisFunctionCount(GroupType::Complex); 
+
+    // If the total number of basis functions in the components is greater than
+    // the total number of basis functions in the complex, throw an error
+    if(total_basis != total_basis_comp) {
+      throw std::runtime_error("Sum of basis functions in components does not equal the number of basis functions in the complex");
+    }
+
+    auto swap_eng = SwapEngine(ind_map,total_basis);
+
+    swap_eng.arrange(*(params_->complex_coefs));
+    swap_eng.arrange(*(params_->S_AO));
+
+  }
+
+  void TransferComplex::calcJ() {};
+//  using namespace std;
+/*
+// Essentially calculates the transfer integral
+void TransferComplex::calculate_transfer_integral_() {
+
+  auto dimension = mat_1_Coef.cols()+mat_2_Coef.cols();
+  Eigen::MatrixXd zetaA(mat_1_Coef.rows(),dimension);
+  Eigen::MatrixXd zetaB(mat_2_Coef.rows(),dimension);
+  if (counterPoise_) {
+
+    LOG("Creating zeta matrices from coefficients assuming counterpoise", 2);
+    zetaA = mat_1_Coef;
+    zetaB = mat_2_Coef;
+  } else {
+    LOG("Creating zeta matrices from coefficients", 2);
+    zetaA << mat_1_Coef, Eigen::MatrixXd::Zero(mat_1_Coef.rows(),mat_2_Coef.cols()); 
+    zetaB << Eigen::MatrixXd::Zero(mat_2_Coef.rows(),mat_1_Coef.cols()), mat_2_Coef; 
+  }
+
+  LOG("Creating gamma and beta matrices", 2);
+  Eigen::MatrixXd gammaA = zetaA * mat_S * mat_P_Coef.transpose(); 
+  Eigen::MatrixXd gammaB = zetaB * mat_S * mat_P_Coef.transpose(); 
+
+  assert(gammaA.cols() == gammaB.cols() && "Column count between gamma A and B must be consistent");
+  Eigen::MatrixXd gamma(gammaA.rows()+gammaB.rows(),gammaA.cols());
+  gamma << gammaA, gammaB;
+
+  LOG("Calculating S_MO", 2);
+  S_MO.resize(dimension,dimension);
+  S_MO = gamma * gamma.transpose();
+  
+  Eigen::SelfAdjointEigenSolver<Eigen::MatrixXd> eigen_solver(S_MO);
+  Eigen::MatrixXd S_MO_inv_sqrt = eigen_solver.operatorInverseSqrt();
+
+  Hamiltonian.resize(mat_S.rows(),mat_S.cols());
+  Hamiltonian = gamma * vec_P_OE.asDiagonal() * gamma.transpose();
+
+  Hamiltonian_eff = S_MO_inv_sqrt * Hamiltonian * S_MO_inv_sqrt;  
+}
+
+void TransferComplex::printTransferIntegral(
+    const map<string, string> &orbitaltype,
+    const map<string, int> &orbnum) const {
+
+  string HOMO_OR_LUMO_A = orbitaltype.at("mon1");
+  int MO_A = orbnum.at("mon1");
+  if (HOMO_OR_LUMO_A.compare("HOMO") == 0) {
+    if (MO_A > 0) {
+      throw invalid_argument(
+          "Having specified HOMO the MO_A"
+          " value is in reference to the HOMO and must be a negative number");
+    }
+    // Number of orbitals that are choices
+    if (MO_A <= (-1 * HOMO_A_)) {
+      string err = "You are trying to access HOMO" + to_string(MO_A) +
+                   " but there "
+                   "are only " +
+                   to_string(HOMO_A_) + " HOMO orbitals";
+      throw invalid_argument(err);
+    }
+  } else if (HOMO_OR_LUMO_A.compare("LUMO") == 0) {
+    if (MO_A < 0) {
+      throw invalid_argument(
+          "Having specified LUMO the MO_A"
+          " value is in reference to the LUMO and must be a positive number");
+    }
+    int allowed_LUMO = mat_1_Coef.rows() - HOMO_A_;
+    if (MO_A >= allowed_LUMO) {
+      string err = "You are trying to access LUMO+" + to_string(MO_A) +
+                   " but there "
+                   "are only " +
+                   to_string(allowed_LUMO) + " LUMO orbitals";
+      throw invalid_argument(err);
+    }
+  } else {
+    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
+  }
+
+  string HOMO_OR_LUMO_B = orbitaltype.at("mon2");
+  int MO_B = orbnum.at("mon2");
+  if (HOMO_OR_LUMO_B.compare("HOMO") == 0) {
+    if (MO_B > 0) {
+      throw invalid_argument(
+          "Having specified HOMO the MO_B"
+          " value is in reference to the HOMO and must be a negative number");
+    }
+    if (MO_B <= (-1 * HOMO_B_)) {
+      string err = "You are trying to access HOMO" + to_string(MO_B) +
+                   " but there "
+                   "are only " +
+                   to_string(HOMO_B_) + " HOMO orbitals";
+      throw invalid_argument(err);
+    }
+  } else if (HOMO_OR_LUMO_B.compare("LUMO") == 0) {
+    if (MO_B < 0) {
+      throw invalid_argument(
+          "Having specified LUMO the MO_B"
+          " value is in reference to the LUMO and must be a positive number");
+    }
+    int allowed_LUMO = mat_2_Coef.rows() - HOMO_B_;
+    if (MO_B >= allowed_LUMO) {
+      string err = "You are trying to access LUMO+" + to_string(MO_B) +
+                   " but there "
+                   "are only " +
+                   to_string(allowed_LUMO) + " LUMO orbitals";
+      throw invalid_argument(err);
+    }
+  } else {
+    throw invalid_argument("orbitals must be referred to as HOMO or LUMO");
+  }
+
+  printTransferIntegral_(
+      pair<string,int>(HOMO_OR_LUMO_A,MO_A),
+      pair<string,int>(HOMO_OR_LUMO_B,MO_B));
+}
+// Find the transfer integral between two orbitals. 
+// pair<string,int> string - Either HOMO or LUMO
+//                  int    - is the orbital number HOMO-3 LUMO+5
+void TransferComplex::printTransferIntegral_(
+    const pair<string,int>& orbital1,
+    const pair<string,int>& orbital2) const {
+
+  int offset = mat_1_Coef.rows();
+  int orbital1_num = 0;
+  int orbital2_num = 0;
+  if(orbital1.first.compare("HOMO")==0){
+    assert(orbitalValid_(orbital1)==true); 
+    orbital1_num = orbital1.second + HOMO_A_-1;
+  }else if(orbital1.first.compare("LUMO")==0){
+    assert(orbitalValid_(orbital1)==true); 
+    orbital1_num = orbital1.second + HOMO_A_;
+  }
+  if(orbital2.first.compare("HOMO")==0){
+    assert(orbitalValid_(orbital2)==true); 
+    orbital2_num = offset+orbital2.second + HOMO_B_-1;
+  }else if(orbital2.first.compare("LUMO")==0){
+    assert(orbitalValid_(orbital2)==true); 
+    orbital2_num = offset+orbital2.second + HOMO_B_;
+  }
+  double J_ab = Hamiltonian(orbital1_num,orbital2_num);
+  double e_a = Hamiltonian(orbital1_num,orbital1_num);
+  double e_b = Hamiltonian(orbital2_num,orbital2_num);
+  double S_ab = S_MO(orbital1_num,orbital2_num); 
+ 
+  cout << "\nPre-Orthonormalization" << endl;
+  cout << "J_ab             " << J_ab * hartreeToeV << " eV\n";
+  cout << "e_a              " << e_a * hartreeToeV << " eV\n";
+  cout << "e_b              " << e_b * hartreeToeV << " eV\n";
+  cout << "S_ab              " << S_ab << "\n" << endl;
+
+  cout << "Single Orbital DIPRO" << endl;
+  double J_ab_single = (J_ab - 0.5*(e_a+e_b)*S_ab)/(1-pow(S_ab,2.0));
+  double e_a_single = 0.5*((e_a+e_b)-2*J_ab*S_ab+(e_a-e_b)*pow(1-pow(S_ab,2.0),0.5))/(1-pow(S_ab,2.0));
+  double e_b_single = 0.5*((e_a+e_b)-2*J_ab*S_ab-(e_a-e_b)*pow(1-pow(S_ab,2.0),0.5))/(1-pow(S_ab,2.0));
+  cout << "J_ab_eff_single  " << J_ab_single * hartreeToeV << " eV\n";
+  cout << "e_a_eff_single   " << e_a_single * hartreeToeV << " eV\n";
+  cout << "e_b_eff_single   " << e_b_single * hartreeToeV << " eV\n" << endl;
+  
+  cout << "All Orbital DIPRO" << endl;
+  double J_eff = Hamiltonian_eff(orbital1_num,orbital2_num);
+  double e_a_eff = Hamiltonian_eff(orbital1_num,orbital1_num);
+  double e_b_eff = Hamiltonian_eff(orbital2_num,orbital2_num);
+  cout << "J_ab_eff_all    " << J_eff * hartreeToeV << " eV\n";
+  cout << "e_a_eff_all     " << e_a_eff * hartreeToeV << " eV\n";
+  cout << "e_b_eff_all     " << e_b_eff * hartreeToeV << " eV\n" << endl;
+
+}
+
+void TransferComplex::printAll() const {
+
+  int column_width = 14;
+  cout << "Effective Hamiltonian" << endl;
+
+  int col_offset = mat_1_Coef.cols();
+  int start_col = 0;
+  int end_col = 5;
+  while(start_col<Hamiltonian.cols()){
+  
+    cout << setw(column_width-2) << left << ""; 
+    if(end_col>Hamiltonian.cols()){
+      end_col = Hamiltonian.cols();
+    }
+    for(int orbital_num = start_col;orbital_num<end_col;++orbital_num){
+      string column_label = "";
+      if(orbital_num<HOMO_A_ || (orbital_num>=col_offset && orbital_num<(HOMO_B_+col_offset))){
+        if(orbital_num<col_offset){
+          column_label=string("A HOMO");
+        }else{
+          column_label=string("B HOMO");
+        }
+        if(orbital_num!=(HOMO_A_-1) && orbital_num!=(col_offset+HOMO_B_-1)){
+          if(orbital_num<col_offset){
+            column_label+=to_string(orbital_num+1-HOMO_A_);
+          }else {
+            column_label+=to_string(orbital_num+1-col_offset-HOMO_B_);
+          }
+        }
+      }else {
+        if((orbital_num>=HOMO_A_ && orbital_num<col_offset) || orbital_num>(col_offset+HOMO_B_)){
+          if(orbital_num<col_offset){
+            column_label=string("A LUMO");
+          }else{
+            column_label=string("B LUMO");
+          }
+          if(orbital_num!=(HOMO_A_) && orbital_num!=(col_offset+HOMO_B_)){
+            if(orbital_num<col_offset){
+              column_label+=string("+")+to_string(orbital_num-HOMO_A_);
+            }else{
+              column_label+=string("+")+to_string(orbital_num-col_offset-HOMO_B_);
+            }
+          }
+        }
+      } 
+      cout << " | " << setw(column_width) << right << column_label;
+    }
+    cout << " |" << endl; 
+
+    for(int orbital_num = 0;orbital_num<Hamiltonian.rows();++orbital_num){
+      string column_label = "";
+      if(orbital_num<HOMO_A_ || (orbital_num>=col_offset && orbital_num<(HOMO_B_+col_offset))){
+        if(orbital_num<col_offset){
+          column_label=string("A HOMO");
+        }else{
+          column_label=string("B HOMO");
+        }
+        if(orbital_num!=(HOMO_A_-1) && orbital_num!=(col_offset+HOMO_B_-1)){
+          if(orbital_num<col_offset){
+            column_label+=to_string(orbital_num+1-HOMO_A_);
+          }else {
+            column_label+=to_string(orbital_num+1-col_offset-HOMO_B_);
+          }
+        }
+      }else {
+        if(orbital_num < col_offset){
+          column_label=string("A LUMO");
+        }else{
+          column_label=string("B LUMO");
+        }
+        if(orbital_num!=(HOMO_A_) && orbital_num!=(col_offset+HOMO_B_)){
+          if(orbital_num<col_offset){
+            column_label+=string("+")+to_string(orbital_num-HOMO_A_);
+          }else{
+            column_label+=string("+")+to_string(orbital_num-col_offset-HOMO_B_);
+          }
+        }
+      } 
+      cout << " " << setw(column_width-3) << left << column_label << " ";
+      for(int orbital_num2 = start_col;orbital_num2<end_col;++orbital_num2){
+        cout << "| "<< right  << scientific << std::setprecision(6)  << setw(column_width) << Hamiltonian_eff(orbital_num,orbital_num2) << " ";
+      }
+      cout << "|" << endl; 
+    }
+
+    start_col+=5;
+    end_col+=5;
+    cout << endl;
+  } 
+}
+
+bool TransferComplex::orbitalValid_(const std::pair<std::string, int> & orbital) const{
+  int HOMO_AB = HOMO_A_+HOMO_B_;
+  int LUMO_AB = HOMO_AB+1;
+  if(orbital.first.compare("HOMO")==0){
+    if(orbital.second>0){
+      cerr << "HOMO orbital number is not negative or 0" << endl;
+      return false;  
+    }
+    if(orbital.second>HOMO_AB){
+      cerr << "HOMO orbital does not exst " << orbital.second << " "<< HOMO_AB << endl;
+      return false;
+    }
+  }else if(orbital.first.compare("LUMO")==0){
+    if(orbital.second<0){
+      cerr << "LUMO orbital number is not positive or 0" << endl; return false;  
+    }
+    if(orbital.second>(Hamiltonian_eff.rows()-LUMO_AB)){
+      cerr << "LUMO orbital does not exst " << orbital.second << endl;
+      return false;
+    }
+  }
+  return true;
+} 
+// Split a matrix up into a list of smaller matrices. The matrix can be split
+// in columns or in rows. The number of rows/cols in each smaller matrix is
+// held in the vector<int> subMatrixDimension
+//
+// E.g. Given the matrix
+//
+// 1 2 3
+// 3 4 5
+//
+// subMatrixDimension = { 2 1 }
+//
+// And I split by cols
+//
+// list<Matrix *> contain
+//
+// matrix 1   matrix 2
+//   1 2         3
+//   3 4         5
+//
+list<Eigen::MatrixXd> splitMatrixIntoList(
+    const vector<int> &subMatrixDimension,
+    const Eigen::MatrixXd mat,
+    const string &ColRowSplit) {
+
+  list<Eigen::MatrixXd> list_matrix;
+  int num_sub_matrices = subMatrixDimension.size();
+  if (ColRowSplit.compare("Columns") == 0) {
+    int col = 0;
+    for (int i = 0; i < num_sub_matrices; ++i) {
+      Eigen::MatrixXd mat_new(mat.rows(), subMatrixDimension.at(i));
+      for (auto k = 0; k < mat.rows(); ++k) {
+        for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
+          mat_new(k,j) = mat(k, col + j);
+        }
+      }
+      col += subMatrixDimension.at(i);
+      list_matrix.push_back(mat_new);
+    }
+  } else if (ColRowSplit.compare("Rows") == 0) {
+    int row = 0;
+    for (auto i = 0; i < num_sub_matrices; ++i) {
+      Eigen::MatrixXd mat_new(subMatrixDimension.at(i), mat.cols());
+      for (auto k = 0; k < mat.cols(); ++k) {
+        for (auto j = 0; j < subMatrixDimension.at(i); ++j) {
+          mat_new(j,k) = mat(row + j, k);
+        }
+      }
+      row += subMatrixDimension.at(i);
+      list_matrix.push_back(mat_new);
+    }
+  } else {
+    throw invalid_argument("Unrecognized string tag provided");
+  }
+  return list_matrix;
+}
+
+list<Eigen::MatrixXd> splitCoefsUpByAtoms(const vector<int> & basisFuncP, Eigen::MatrixXd Coefs,
+                                   const string & ColRow) {
+  return splitMatrixIntoList(basisFuncP, Coefs, ColRow);
+}
+
+// The purpose of this function is to ensure that swapping occurs correctly
+// The following example explains in more detail what this is meant to do
+// Now if we have a matrix in a specific state and want to swap the rows
+// we can not simply list all the rows that need to be changed and then make
+// the changes.
+//
+// We have to figure out how to swap rows sequentially without ending up with
+// the wrong result.
+//
+// For instance say we have a matrix
+// index 1 | row 1
+// index 2 | row 2
+// index 3 | row 3
+// index 4 | row 4
+//
+// where:
+// Row 1 needs to be at index 3
+// Row 4 needs to be at index 1
+// Row 2 needs to be at index 2
+// Row 3 needs to be at index 4
+//
+// If we simply looked at our first instance of the matrix shown above
+// and came up with the following swaps
+// Swap row 1 with index 3
+// Swap row 4 with index 1
+// Swap row 2 with index 2
+// Swap row 3 with index 4
+//
+// First swap
+// index 1 row3
+// index 2 row2
+// index 3 row1
+// index 4 row4
+//
+// Second swap
+// index 1 row4
+// index 2 row2
+// index 3 row1
+// index 4 row3
+//
+// Third swap does nothing
+// Fourth swap
+// index 1 row4
+// index 2 row2
+// index 3 row3
+// index 4 row1
+//
+// When what we really wanted was
+// index 1 row4
+// index 2 row2
+// index 3 row1
+// index 4 row3
+//
+// Notice the row3 and row1 are in the wrong place
+// The instructions should be rewritten
+// Swap row 1 with index 3
+// Swap row 4 with index 3
+// Swap row 2 with index 2 - no swap
+// Swap row 3 with index 3 - no swap
+//
+void refreshSwapOrder(vector<pair<int, int>> &monBmatch,
+                      vector<pair<int, int>> &monAmatch) {
+
+  // Because matrix B appears at the top of our full matrix e.g.
+  //
+  // [ B ]
+  // [ A ]
+  //
+  // When sorting out the swap order we need to cycle through elements in B and
+  // see where they appear in both the B and A matrix
+  //
+  // B -> [ B ]
+  // B -> [ A ]
+  //
+  for (auto pr_ptr = monBmatch.begin(); pr_ptr != monBmatch.end(); ++pr_ptr) {
+    auto pr = *pr_ptr;
+
+    int row1was = pr.first;
+    int row1is = pr.second;
+    auto pr_ptr_temp = pr_ptr;
+    pr_ptr_temp++;
+    while (pr_ptr_temp != monBmatch.end()) {
+      pr_ptr_temp = find_if(
+          pr_ptr_temp, monBmatch.end(),
+          [row1was](const pair<int, int> &p) { return row1was == p.second; });
+      if (pr_ptr_temp != monBmatch.end()) {
+        pr_ptr_temp->second = row1is;
+      }
+    }
+    pr_ptr_temp = monAmatch.begin();
+    while (pr_ptr_temp != monAmatch.end()) {
+      pr_ptr_temp = find_if(
+          pr_ptr_temp, monAmatch.end(),
+          [row1was](const pair<int, int> &p) { return row1was == p.second; });
+      if (pr_ptr_temp != monAmatch.end()) {
+        pr_ptr_temp->second = row1is;
+      }
+    }
+  }
+  // Here we have already looked at the rows in B and they are up to date but
+  // we still need to make sure the rows in A are swapped in the appropriate
+  // order
+  //
+  //      [ B ]
+  // A -> [ A ]
+  //
+  for (auto pr_ptr = monAmatch.begin(); pr_ptr != monAmatch.end(); ++pr_ptr) {
+    auto pr = *pr_ptr;
+    int row1was = pr.first;
+    int row1is = pr.second;
+    if (row1was != row1is) {
+      auto pr_ptr_temp = pr_ptr;
+      pr_ptr_temp++;
+      while (pr_ptr_temp != monAmatch.end()) {
+        pr_ptr_temp = find_if(
+            pr_ptr_temp, monAmatch.end(),
+            [row1was](const pair<int, int> &p) { return row1was == p.second; });
+        if (pr_ptr_temp != monAmatch.end()) {
+          pr_ptr_temp->second = row1is;
+        }
+      }
+    }
+  }
+  return;
+}
+
+void refreshSwapOrder(vector<pair<int, int>> &monAmatch) {
+
+  for (auto pr_ptr = monAmatch.begin(); pr_ptr != monAmatch.end(); ++pr_ptr) {
+    auto pr = *pr_ptr;
+
+    int row1was = pr.first;
+    int row1is = pr.second;
+    auto pr_ptr_temp = pr_ptr;
+    pr_ptr_temp++;
+    while (pr_ptr_temp != monAmatch.end()) {
+      pr_ptr_temp = find_if(
+          pr_ptr_temp, monAmatch.end(),
+          [row1was](const pair<int, int> &p) { return row1was == p.second; });
+      if (pr_ptr_temp != monAmatch.end()) {
+        pr_ptr_temp->second = row1is;
+      }
+    }
+  }
+  return;
+}
+
+// To replace both refreshSwapOrder and updateSwapLists
+// instead of figuring out a proper order for swapping we will simply start
+// with a new link list of the same size and place the coefficents in that
+// new list
+Eigen::MatrixXd createSortedCoefMatrix(vector<pair<int,int>> & mon_match_ind, list<Eigen::MatrixXd> & atom_mat_coefs){
+
+  // Actually lets use a vector of pointers to the matrices that are in the list
+  vector<Eigen::MatrixXd *> mat_ptrs;
+  // Error checking
+  if(atom_mat_coefs.size()==0){
+    throw std::runtime_error("ERROR cannot create sorted coef matrix, there are atomically partitioned matrices to build the full sorted coef matrix from.");
+  } 
+
+  int cols = atom_mat_coefs.front().cols();
+  for ( list<Eigen::MatrixXd>::iterator coef_ptr = atom_mat_coefs.begin();
+        coef_ptr != atom_mat_coefs.end();
+        ++coef_ptr ){
+      if(coef_ptr->cols()!=cols){
+        throw std::runtime_error("ERROR cannot created sorted coef matrix from atomically partitioned matrices with varying number of columns.");
+      }
+  } 
+  // End of error checking
+ 
+  // Count the total number of rows in each atomically partitioned coef matrix 
+  vector<int> rows_per_mat; 
+  for ( list<Eigen::MatrixXd>::iterator coef_ptr = atom_mat_coefs.begin();
+      coef_ptr != atom_mat_coefs.end();
+      ++coef_ptr ){
+    rows_per_mat.push_back(coef_ptr->rows());
+  } 
+ 
+  int initial_value = 0;
+  int total_rows = std::accumulate(rows_per_mat.begin(),rows_per_mat.end(), initial_value);
+
+  // Determine the offset of each row to each index
+  std::map<int,int> row_to_index_offset; 
+  int offset = 0;
+  for ( std::pair<int,int> & row_ind : mon_match_ind ){
+    row_to_index_offset.at(row_ind.first) = offset; 
+    offset+= rows_per_mat.at(row_ind.second);
+  }
+
+  Eigen::MatrixXd sorted_atom_mat_coefs
+   
+   
+
+}
+// The above function determines the appropriate sequence of swaps this function
+// then actually implements the swaps by exchanging the matrices in the list.
+void updateSwapLists(vector<pair<int, int>> &monBmatch,
+                     vector<pair<int, int>> &monAmatch,
+                     list<Eigen::MatrixXd> &p_atom_mat_coef) {
+
+  for (auto p : monBmatch) {
+    if (p.first != p.second) {
+      auto it = p_atom_mat_coef.begin();
+      Eigen::MatrixXd temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
+    }
+  }
+  for (auto p : monAmatch) {
+    if (p.first != p.second) {
+      auto it = p_atom_mat_coef.begin();
+      Eigen::MatrixXd temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
+    }
+  }
+  return;
+}
+void updateSwapLists(vector<pair<int, int>> &monAmatch,
+                     list<Eigen::MatrixXd> &atom_mat_coef) {
+
+  for (auto p : monAmatch) {
+    if (p.first != p.second) {
+      auto it = atom_mat_coef.begin();
+      Eigen::MatrixXd & temp = *(next(it, p.first));
+      *(next(it, p.first)) = *(next(it, p.second));
+      *(next(it, p.second)) = temp;
+    }
+  }
+  return;
+}
+
+Eigen::MatrixXd mergeListOfMatrices(list<Eigen::MatrixXd> &matrix_list, const int rows,
+                            const int cols, const string &ColRowMerge) {
+
+  Eigen::MatrixXd full_matrix(rows, cols);
+  if (ColRowMerge.compare("Columns") == 0) {
+    int col = 0;
+    for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
+      Eigen::MatrixXd mat = *it;
+      int row = 0;
+      if (col > cols)
+        throw runtime_error("Your new matrix is not large enough");
+      for (auto i = 0; i < mat.rows(); ++i) {
+        if (row > rows)
+          throw runtime_error("Your new matrix is not large enough");
+        for (auto j = 0; j < mat.cols(); ++j) {
+          full_matrix(row,j+col) = mat(i, j);
+        }
+        ++row;
+      }
+      col += mat.cols();
+    }
+  } else if (ColRowMerge.compare("Rows") == 0) {
+    int row = 0;
+    for (auto it = matrix_list.begin(); it != matrix_list.end(); ++it) {
+      Eigen::MatrixXd mat = *it;
+      int col = 0;
+      if (row > rows)
+        throw runtime_error("Your new matrix is not large enough");
+      for (auto j = 0; j < mat.cols(); ++j) {
+        if (col > cols)
+          throw runtime_error("Your new matrix is not large enough");
+        for (auto i = 0; i < mat.rows(); ++i) {
+          full_matrix(row + i, col) = mat(i, j);
+        }
+        ++col;
+      }
+      row += mat.rows();
+    }
+  } else {
+    throw invalid_argument("Unrecognized merge type for list of matrices");
+  }
+  return full_matrix;
+}
+
+// This function
+Eigen::MatrixXd createNewMatrix(list<Eigen::MatrixXd> &p_atom_mat_coef, int rows, int cols,
+                        const string &ColRow) {
+  return mergeListOfMatrices(p_atom_mat_coef, rows, cols, ColRow);
+}
+
+// unscramble the coefficients
+//Eigen::MatrixXd unscramble_Coef(
+//    const std::vector<int> &matchDimerA,
+//    const std::vector<int> &matchDimerB,
+//    const std::vector<int> &basisFuncP, 
+//    const Eigen::MatrixXd & dimerCoef) {
+//
+//  // Let's reduce the complexity of the problem by instead of working
+//  // with the basis functions lets just work with the atoms. We can do
+//  // this by treating all the basis functions associated with a single
+//  // atom as a block.
+//
+//  list<Eigen::MatrixXd> p_atom_mat_coef =
+//      splitCoefsUpByAtoms(basisFuncP, dimerCoef, "Columns");
+//
+//  // Place all of monomer A atom basis functions on the left side of the
+//  // matrix and all of B monomer atom basis functions on the right side
+//  // of the dimer matrix
+//  // First int is the col in the dimer the atom should be at
+//  // Second int is the col in the dimer the atom is presently at
+//
+//  vector<pair<int, int>> monAmatch;
+//  for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerA.at(i));
+//    monAmatch.push_back(pr);
+//  }
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+//
+//  refreshSwapOrder(monBmatch, monAmatch);
+//  updateSwapLists(monBmatch, monAmatch, p_atom_mat_coef);
+//
+//  Eigen::MatrixXd dimerCoef_new = createNewMatrix(
+//      p_atom_mat_coef, dimerCoef.rows(), dimerCoef.cols(), "Columns");
+//
+//  return dimerCoef_new;
+//}
+//
+//// unscramble the coefficients
+//Eigen::MatrixXd unscramble_Coef(
+//    const std::vector<int> &matchDimerB,
+//    const std::vector<int> &basisFuncB,
+//    const Eigen::MatrixXd &Coef) {
+//
+//  // Let's reduce the complexity of the problem by instead of working
+//  // with the basis functions lets just work with the atoms. We can do
+//  // this by treating all the basis functions associated with a single
+//  // atom as a block.
+//
+//  list<Eigen::MatrixXd> atom_mat_coef =
+//      splitCoefsUpByAtoms(basisFuncB, Coef, "Columns");
+//
+//  // Place all of monomer A atom basis functions on the left side of the
+//  // matrix and all of B monomer atom basis functions on the right side
+//  // of the  matrix
+//  // First int is the col in the dimer the atom should be at
+//  // Second int is the col in the dimer the atom is presently at
+//
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+//
+//  refreshSwapOrder(monBmatch);
+//  updateSwapLists(monBmatch, atom_mat_coef);
+//  Eigen::MatrixXd Coef_new = createNewMatrix(atom_mat_coef, Coef.rows(),
+//                                     Coef.cols(), "Columns");
+//  return Coef_new;
+//}
+
+Eigen::MatrixXd unscrambleCoef(
+    const std::vector<std::vector<int>> &match_mon_complex,
+    const std::vector<int> &basis_functions_complex, 
+    const Eigen::MatrixXd & complex_coefs) {
+
+  // Let's reduce the complexity of the problem by instead of working
+  // with the basis functions lets just work with the atoms. We can do
+  // this by treating all the basis functions associated with a single
+  // atom as a block.
+
+  list<Eigen::MatrixXd> complex_coef_block =
+      splitCoefsUpByAtoms(basis_functions_complex, complex_coefs, "Columns");
+
+  // Place all of monomer A atom basis functions on the left side of the
+  // matrix and all of B monomer atom basis functions on the right side
+  // of the dimer matrix
+  // First int is the col in the dimer the atom should be at
+  // Second int is the col in the dimer the atom is presently at
+
+//  vector<pair<int, int>> monBmatch;
+//  for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+//    pair<int, int> pr(i, matchDimerB.at(i));
+//    monBmatch.push_back(pr);
+//  }
+
+  vector<vector<pair<int,int>>> mon_match_index;
+  unsigned new_index = 0;
+  for ( const vector<int> & monomer_rows : match_mon_complex){
+    vector<pair<int,int>> mon_matching_index_row;
+    for( const int & row_index : monomer_rows ){
+      pair<int,int> pr(new_index,row_index);
+      mon_matching_index_row.push_back(pr); 
+    } 
+    mon_match_index.push_back(mon_matching_index_row);
+  }
+
+  //refreshSwapOrder(monBmatch);
+//  refreshSwapOrder(mon_match_index);
+ // updateSwapLists(monBmatch, atom_mat_coef);
+  Eigen::MatrixXd Coef_new = createNewMatrix(atom_mat_coef, Coef.rows(),
+                                     Coef.cols(), "Columns");
+  return Coef_new;
+
+
+}
+// Similar to the above function but we will be moving both the rows
+// and columns
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int> &matchDimerA,
+    const std::vector<int> &matchDimerB,
+    const std::vector<int> &basisFuncP, 
+    Eigen::MatrixXd S) {
+
+  Eigen::MatrixXd S_new(S.rows(),S.cols());
+  {
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+    vector<pair<int, int>> monAmatch;
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
+      monAmatch.push_back(pr);
+    }
+    vector<pair<int, int>> monBmatch;
+    for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
+      monBmatch.push_back(pr);
+    }
+
+    refreshSwapOrder(monBmatch, monAmatch);
+    updateSwapLists(monBmatch, monAmatch, p_atom_mat_S);
+    S_new =
+        createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Columns");
+  }
+
+  S = S_new;
+
+  {
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+
+    vector<pair<int, int>> monAmatch;
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
+      monAmatch.push_back(pr);
+    }
+    vector<pair<int, int>> monBmatch;
+    for (unsigned i = 0; i < matchDimerB.size(); ++i) {
+      pair<int, int> pr(i + monAmatch.size(), matchDimerB.at(i));
+      monBmatch.push_back(pr);
+    }
+
+    refreshSwapOrder(monBmatch, monAmatch);
+    updateSwapLists(monBmatch, monAmatch, p_atom_mat_S);
+    S_new = createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Rows");
+  }
+
+  // Return the correctly swapped dimerCoef
+  return S_new;
+}
+
+// Same as the above function but here we are assuming counterpoise correction
+// is being used and thus we do not need to match with both monomer A and
+// monomer B but only need to match with A.
+Eigen::MatrixXd unscramble_S(
+    const std::vector<int> &matchDimerA,
+    const std::vector<int> &basisFuncP,
+    Eigen::MatrixXd S) {
+
+  Eigen::MatrixXd S_new(S.rows(),S.cols());
+  {
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Columns");
+
+    vector<pair<int, int>> monAmatch;
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
+      monAmatch.push_back(pr);
+    }
+    refreshSwapOrder(monAmatch);
+    updateSwapLists(monAmatch, p_atom_mat_S);
+    S_new =
+        createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Columns");
+  }
+
+  S = S_new;
+
+  {
+    list<Eigen::MatrixXd> p_atom_mat_S = splitCoefsUpByAtoms(basisFuncP, S, "Rows");
+
+    vector<pair<int, int>> monAmatch;
+    for (unsigned i = 0; i < matchDimerA.size(); ++i) {
+      pair<int, int> pr(i, matchDimerA.at(i));
+      monAmatch.push_back(pr);
+    }
+
+    refreshSwapOrder(monAmatch);
+    updateSwapLists(monAmatch, p_atom_mat_S);
+    S_new = createNewMatrix(p_atom_mat_S, S.rows(), S.cols(), "Rows");
+  }
+
+  // Return the correctly swapped dimerCoef
+  return S_new;
+}
+
+
+//TransferComplex::TransferComplex(
+//    const Eigen::MatrixXd & mat1Coef, 
+//    const Eigen::MatrixXd & mat2Coef,
+//    const Eigen::MatrixXd & matPCoef, 
+//    const int HOMO_A, 
+//    const int HOMO_B, 
+//    const Eigen::MatrixXd & matS,
+//    const Eigen::VectorXd & vecPOE, bool cp) {
+//
+TransferComplex::TransferComplex(const Parameters params) : params_(params) { 
+
+  unscrambled_ = false;
+//  counterPoise_ = cp;
+  // Consistency check
+  if (params_.S_AO.cols() != params_.mat_complex.cols()) {
+    throw invalid_argument(
+        "The overlap matrix must have the same number "
+        "of basis functions as the dimer");
+  }
+  //if (cp) {
+  if (params_.counter_poise) {
+    int monomer_number = 1;
+    for ( const Eigen::MatrixXd & mat : params_.mat_monomers){
+      if(params_.mat_complex.cols() != mat.cols()){
+        throw invalid_argument(
+            "Counter poise correction requires that the"
+            " monomers have the same number of coefficients as the complex. "
+            "Your monomer " + std::to_string(monomer_number) +" does not");
+      }
+      ++monomer_number;
+    }
+//    if (mat1Coef.cols() != matPCoef.cols()) {
+//      throw invalid_argument(
+//          "Counter poise correction requires that the"
+//          " monomers have the same number of coefficients as the dimer. "
+//          "Your monomer 1 does not");
+//    }
+//    if (mat2Coef.cols() != matPCoef.cols()) {
+//      throw invalid_argument(
+//          "Counter poise correction requires that the"
+//          " monomers have the same number of coefficients as the dimer. "
+//          "Your monomer 2 does not");
+//    }
+  } else {
+    /// If not counter poise the sum of the cols should equal the same number as is in the complex
+//    int total_cols = mat1Coef.cols() + mat2Coef.cols();
+    int total_cols = 0; 
+    for ( const Eigen::MatrixXd & mat : params_.mat_monomers){
+      total_cols+=mat.cols();
+    }
+    
+    //if (total_cols > matPCoef.cols()) {
+    if (total_cols > params_.mat_complex.cols()) {
+      throw invalid_argument(
+          "Counter poise has not been specified and the total number of "
+          "basis functions in your monomers is more than the number of basis "
+          "functions in your complex.");
+    }else if(total_cols < params_.complex_coefs.cols()){
+      throw invalid_argument( 
+          "Counter poise has not been specified and the total number of "
+          "basis functions in your monomers is less than the number of basis "
+          "functions in your complex.");
+    }
+  }
+//
+//  mat_1_Coef.resize(mat1Coef.rows(),mat1Coef.cols());
+//  mat_1_Coef = mat1Coef;
+//  mat_2_Coef.resize(mat2Coef.rows(),mat2Coef.cols());
+//  mat_2_Coef = mat2Coef;
+//  mat_P_Coef.resize(matPCoef.rows(),matPCoef.cols());
+//  mat_P_Coef = matPCoef;
+//  HOMO_A_ = HOMO_A;
+//  HOMO_B_ = HOMO_B;
+//  mat_S.resize(matS.rows(),matS.cols());
+//  mat_S = matS;
+//  vec_P_OE.resize(vecPOE.size());
+//  vec_P_OE = vecPOE;
+}
+
+//void TransferComplex::unscramble(const Eigen::MatrixXd &coord_1_mat,
+//                                 const Eigen::MatrixXd &coord_2_mat,
+//                                 const Eigen::MatrixXd &coord_P_mat,
+//                                 const std::vector<int> &basisP,
+//                                 const std::vector<int> &basis2) {
+//
+void TransferComplex::unscramble(const vector<Eigen::MatrixXd> &coord_monomers,
+                                 const Eigen::MatrixXd &coord_complex,
+                                 const std::vector<int> &basis_complex,
+                                 const std::vector<int> &basis2) {
+  unscrambled_ = true;
+
+  const int sig_fig = 4;
+
+  // If dealing with counter poise correction may also need to unscramble
+  // the basis functions of the monomers
+  if (counterPoise_) {
+    vector<int> match_1_2 = matchCol(coord_1_mat,coord_2_mat, sig_fig);
+
+    LOG("Counter Poise unscrambling matrix 2 with respect to matrix 1", 2);
+    Eigen::MatrixXd unscrambled_2_Coef = unscramble_Coef(match_1_2, basis2, mat_2_Coef);
+
+    this->mat_2_Coef = unscrambled_2_Coef;
+
+    vector<int> match_1_P = matchCol(coord_1_mat,coord_P_mat, sig_fig);
+
+    this->mat_P_Coef = unscramble_Coef(match_1_P, basisP, mat_P_Coef);
+
+    this->mat_S = unscramble_S(match_1_P, basisP, mat_S);
+
+  } else {
+
+    vector<vector<int>> match_mon_complex;
+    for ( const Eigen::MatrixXd & coord_mon : coord_monomers){
+      // Returns each of the rows in complex that match each of the monomers
+      match_mon_complex.push_back(matchCol(coord_mon,coord_complex, sig_fig));
+    }
+    // Stores the rows in P that match 2
+    //vector<int> match_2_P = matchCol(coord_2_mat,coord_P_mat, sig_fig);
+
+    LOG("Unscrambling dimer matrix with respect to matrix 1 and 2", 2);
+    //this->mat_P_Coef =
+    //    unscramble_Coef(match_1_P, match_2_P, basisP, mat_P_Coef);
+    this->params_.complex_coefs = unscrambleCoef(match_mon_complex,basis_complex,complex_coefs);
+//    this->mat_S = unscramble_S(match_1_P, match_2_P, basisP, mat_S);
+    }
+  }
+}
+
+void TransferComplex::calcJ() {
+
+  if (unscrambled_ == false) {
+    cerr << "\nWARNING unable to automatically line up basis functions of"
+            " monomers with dimers, you better make sure they correctly"
+            " line up or run the calculations again with the correct "
+            "flag pop=full"
+         << endl;
+  }
+
+  calculate_transfer_integral_();
+}
+*/
+}  // namespace catnip
diff --git a/src/libcatnip/transfer_complex.hpp b/src/libcatnip/transfer_complex.hpp
new file mode 100644
index 0000000..632725b
--- /dev/null
+++ b/src/libcatnip/transfer_complex.hpp
@@ -0,0 +1,74 @@
+#pragma once
+#ifndef _CATNIP_TRANSFER_COMPLEX_HPP
+#define _CATNIP_TRANSFER_COMPLEX_HPP
+
+#include "atom_group_container.hpp"
+
+#include <map>
+#include <sstream>
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+//#include "matrix.hpp"
+#include <eigen3/Eigen/Dense>
+
+namespace catnip {
+
+class TransferComplex {
+
+  public:
+
+    class Parameters {
+      public:
+        const std::vector<std::unique_ptr<Eigen::MatrixXd>> monomers_coefs;
+        const std::unique_ptr<Eigen::MatrixXd> complex_coefs;
+        /// Location of each of the homo_orbitals in each of the monomers
+        const std::vector<int> homo_orbitals;
+        //HOMO_A;
+        //const int HOMO_B;
+        /// Atomic Orbital overlap matrix
+        const std::unique_ptr<Eigen::MatrixXd> S_AO;
+        const std::unique_ptr<Eigen::VectorXd> complex_orbital_energies;
+        /// Counter poise flag
+        bool counter_poise = false;
+        /// Calculate all couplings
+        bool calculate_all = false;
+    };
+
+  private:
+
+    Parameters * params_;
+
+  public:
+
+    TransferComplex(Parameters * params) : params_(params) {};
+
+    void unscramble(AtomGroupContainer atom_groups);
+
+    // Orbital type and a map of the corresponding number
+    // E.g.
+    // orbital type    orbital number
+    // "mon1" "LUMO"    "mon1" -3
+    // "mon2" "HOMO"    "mon2"  0
+    //
+    //    monomer1 LUMO-3
+    //    monomer2 HOMO
+    void calcJ();
+
+    /**
+     * \brief Print the transfer integral specified
+     **/
+//    void printTransferIntegral(
+ //       const std::map<std::string,std::string> & orbital_type,
+  //      const std::map<std::string,int> & orbnum) const;
+
+    /**
+     * \brief Print All info in matrix form
+     **/
+   // void printAll() const;
+
+};
+
+}  // namespace catnip
+#endif  // _CATNIP_TRANSFER_COMPLEX_HPP
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index a5d6759..f4874d6 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -115,8 +115,11 @@ int main(void) {
     //         atm1   atm1   atm2   atm2
 
     cerr << "Before passing in" << endl;
+    cerr << "MatchA" << endl;
     for (auto it : matchA) cerr << it << endl;
+    cerr << "MatchB" << endl;
     for (auto it : matchB) cerr << it << endl;
+    cerr << "Basis Functions of Dimer" << endl;
     for (auto it : basisFuncDimer) cerr << it << endl;
     // If we correct the dimer coefficient matrix to line up with the
     // coefficients of the monomers it should look like this

From ecade9011c2a1e47c2f0055cd1149e2cb92bc27d Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 11 Jul 2020 22:06:32 -0600
Subject: [PATCH 36/68] update

---
 src/libcatnip/transfer_complex.cpp | 145 +----------------------------
 1 file changed, 3 insertions(+), 142 deletions(-)

diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
index 7575b7f..907e042 100644
--- a/src/libcatnip/transfer_complex.cpp
+++ b/src/libcatnip/transfer_complex.cpp
@@ -1,153 +1,14 @@
 
-
+// Local private includes
 #include "transfer_complex.hpp"
 
 #include "atom.hpp"
 #include "atom_group.hpp"
-//#include "constants.hpp"
-//#include "io/io.hpp"
-//#include "log.hpp"
-//#include "matrix.hpp"
-//
-//#include <eigen3/Eigen/Dense>
-//#include <eigen3/Eigen/Eigenvalues>
-//
-//#include <algorithm>
-//#include <cmath>
-//#include <fstream>
-//#include <iomanip>
-//#include <iostream>
-//#include <list>
-//#include <numeric> // For accumulate
-//#include <sstream>
-//#include <stdlib.h>
-//#include <string>
-//#include <unordered_map>
-//
+#include "index_map.hpp"
+#include "swap_engine.hpp"
 
 namespace catnip {
 
-  class IndexMap {
-    public:
-
-      IndexMap(AtomGroupContainer atom_groups){
-        std::vector<int> group_indices = atom_groups.getGroups(GroupType::Component);
-        int complex_ind = atom_groups.getGroups(GroupType::Complex).at(0);
-        AtomGroup complex_group = atom_groups.getGroup(complex_ind);
-        int sys_ind = 0;
-        for ( int & group_ind : group_indices) {
-          AtomGroup component_group = atom_groups.getGroup(group_ind);
-          for( std::shared_ptr<Atom> & atom : component_group){
-            int atom_ind = complex_group.findIndex(atom);
-            int num_basis = complex_group.at(atom_ind)->getBasisFuncCount();
-            for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
-              row_col_final[group_ind].push_back(sys_ind); 
-              row_col_init[group_ind].push_back(atom_ind);
-              sys_ind++;
-            }
-          }
-        }
-      }
-
-      // The component rows and colums in their current locations in  
-      // in the full system matrix of the complex
-      std::map<int,std::vector<int>> row_col_init;
-
-      // Map indicate where the rows and cols should go in the final state
-      // Each int in the vector represents the locatin in the full system matrix
-      std::map<int,std::vector<int>> row_col_final;
-
-      // Searches the init row for the provided row and returns the group it is
-      // in as well as its current index
-      std::pair<int,int> findLocation(int row){
-        std::pair<int,int> group_row;
-        for( std::pair<int,std::vector<int>> group_rows : row_col_init){
-          int row_ind = 0;
-          for ( int row_ : group_rows.second ){
-            if (row_ == row){
-              return std::pair<int,int>(group_rows.first, row_ind);
-            }
-            ++row_ind;
-          } 
-        }
-      }
-  };
-
-  // Swaps rows columns and keeps up with how future swaps should be updated
-  class SwapEngine {
-    private:
-      size_t size_;
-      IndexMap ind_map_;
-      Eigen::MatrixXd scratch_;
-
-    public:
-      SwapEngine(IndexMap ind_map, size_t size) : 
-        size_(size), ind_map_(ind_map) {
-          scratch_ = Eigen::MatrixXd::Zero(size, 1);
-
-
-        // Already have enough information to calculate the correct swap order
-        // Note the order of swaps is important.
-        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-          int group_ind = group_row.first;
-          for ( int row : group_row.second ) {
-            int final_row = ind_map_.row_col_final[group_ind].at(row);
-            std::pair<int,int> swap(row,final_row);
-            // Now we need to update index map, the row located at the final 
-            // position has now been moved     
-            auto group_and_row_ind = ind_map_.findLocation(final_row);
-            
-            // Final row location needs to be pointed to the starting row
-            ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
-          } 
-        }
-      };
-
-
-      // This method of swapping was chosen to keep the memory footprint
-      // reasonable.
-      // Will correctly sort the rows and columns of the matrix
-      void arrange(Eigen::MatrixXd & mat) {
-
-        // Check that matrix is square
-        if( mat.rows() != mat.cols() ) {
-          throw std::runtime_error("Can only arrange square matrices");
-        }
-        if( mat.rows() != size_ ) {
-          throw std::runtime_error("Index map has different number of basis functions to matrix");
-        }
-
-        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-          int group_ind = group_row.first;
-          for ( int row : group_row.second ) {
-            int final_row = ind_map_.row_col_final[group_ind].at(row);
-            if(final_row == row ) continue;
-            // Copy the data at the final row into the scratch space 
-            scratch_.col(0) = mat.row(final_row);
-            // Copy the data from the initial row into the final row
-            mat.row(final_row) = mat.row(row);
-            // Copy the data from the temporary row into the initial row
-            mat.row(row) = scratch_.col(0);
-          }
-        }
-
-        // Repeat for columns 
-        for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
-          int group_ind = group_col.first;
-          for ( int col : group_col.second ) {
-            int final_col = ind_map_.row_col_final[group_ind].at(col);
-            if(final_col == col ) continue;
-            // Copy the data at the final row into the scratch space
-            scratch_.col(0) = mat.col(final_col);
-            // Copy the data from the initial row into the final row
-            mat.col(final_col) = mat.col(col);
-            // Copy the data from the temporary row into the initial row
-            mat.col(col) = scratch_.col(0);
-          }
-        }
-      }
-  };
-
   void TransferComplex::unscramble(AtomGroupContainer atom_groups) {
     // We should figure out how all the rows and columns should be
     // rearranged before moving any of the coefficients in the matrix    

From 7eb2ff594c18fd98ee25510b15f6a2612ec25132 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 11 Jul 2020 23:57:58 -0600
Subject: [PATCH 37/68] Success compile

---
 CMakeLists.txt                         |  19 ++--
 cmake/InstallGdown.cmake               |  29 ++++++
 src/CMakeLists.txt                     |   2 +-
 src/libcatnip/atom.hpp                 |   3 +-
 src/libcatnip/atom_group_container.cpp |   3 +-
 src/libcatnip/elements.hpp             |   6 +-
 src/libcatnip/index_map.cpp            |   2 +-
 src/libcatnip/index_map.hpp            |   4 +
 src/libcatnip/size_type.hpp            |   9 ++
 src/libcatnip/swap_engine.cpp          | 123 ++++++++++++-------------
 src/libcatnip/swap_engine.hpp          |  29 ++++++
 11 files changed, 147 insertions(+), 82 deletions(-)
 create mode 100644 cmake/InstallGdown.cmake
 create mode 100644 src/libcatnip/size_type.hpp
 create mode 100644 src/libcatnip/swap_engine.hpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 93d229e..b987762 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,9 +4,10 @@ project (calc_J)
 ##############################################################################
 # Defining options 
 ##############################################################################
-option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" OFF)
-option(ENABLE_INTEGRATION_TESTING "Enable integration tests" OFF)
-option(ENABLE_UNIT_TESTING "Enable tests" OFF)
+option(ENABLE_TESTS "Enable testing" Off)
+option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" ${ENABLE_TESTS})
+option(ENABLE_INTEGRATION_TESTING "Enable integration tests" ${ENABLE_TESTS})
+option(ENABLE_UNIT_TESTING "Enable tests" ${ENABLE_TESTS})
 option(ENABLE_PROFILING "Enable profiling" OFF)
 option(CODE_COVERAGE "Enable coverage reporting" OFF)
 
@@ -22,7 +23,7 @@ set(calcJ_TITLE "\"CATNIP\"")
 set(calcJ_URL "\"https://github.com/JoshuaSBrown/QC_Tools\"" )
 set(COVERAGE_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 set(COMMON_LIBRARIES stdc++ m)
-set(LOG_LEVEL 0 CACHE INT "Choose the log level" )
+set(LOG_LEVEL 0 CACHE STRING "Choose the log level" )
 # Prevents multiple file extensions from being appended one after the other
 # important for using gcov .o.gcno or .cpp.gcno now will be .gcno
 set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE 1)
@@ -64,14 +65,10 @@ if(ENABLE_INTEGRATION_TESTING)
     message("GAUSSIANFILES found will not download")
     set(DOWNLOAD_TUTORIAL_FILES OFF)
   else(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-    message("GAUSSIANFILES not found will download")
-    set(DOWNLOAD_TUTORIAL_FILES ON)
-  endif(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-endif()
+    message("GAUSSIANFILES not found will attempt to download")
 
-if(DOWNLOAD_TUTORIAL_FILES)
-  message("Downloading gaussian tutorial files")
-  execute_process(COMMAND ${PROJECT_SOURCE_DIR}/scripts/test_suite_install.bash "${PROJECT_SOURCE_DIR}" )
+    include(${PROJECT_SOURCE_DIR}/cmake/InstallGdown.cmake)
+  endif(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
 endif()
 
 if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
diff --git a/cmake/InstallGdown.cmake b/cmake/InstallGdown.cmake
new file mode 100644
index 0000000..d1b5f7f
--- /dev/null
+++ b/cmake/InstallGdown.cmake
@@ -0,0 +1,29 @@
+
+if(NOT EXISTS "${CMAKE_SOURCE_DIR}/GAUSSIANFILES")
+  find_program(GDOWN gdown ~/.local/bin)
+
+  if( NOT GDOWN)
+    find_program(PIP NAMES pip pip3 PATHS ~/.local/bin)
+    if( NOT PIP)
+      message(FATAL_ERROR "Unable to download tutorial files with gdown, tutorial"
+      "files are needed to run both the tutorials and the integration tests," 
+      "unable to locate pip to install gdown, please install pip, or install gdown"
+      "through some other means.")
+    else()
+      message("Pip is ")
+      execute_process(COMMAND ${PIP} "install" "--user" "--upgrade" "pip")
+      execute_process(COMMAND ${PIP} "install" "--user" "gdown" )
+    endif()
+    find_program(GDOWN gdown ~/.local/bin)
+
+  endif()
+
+  if( GDOWN )
+    find_program(UNZIP unzip)
+    execute_process(COMMAND ${GDOWN} https://drive.google.com/uc?id=1rCsj_jpMyE0S0cokFJDyBSA0aPNiIHNb  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+    execute_process(COMMAND ${UNZIP} "GAUSSIANFILES.zip" WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} )
+    execute_process(COMMAND rm "GAUSSIANFILES.zip" WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+  else()
+    message(FATAL_ERROR "Found pip, but still unable to install or find gdown")
+  endif()
+endif()
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3637265..bc2fbfc 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,5 +1,5 @@
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/libcatnip")
-add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tools")
+#add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tools")
 if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
   add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tests")
 endif()
diff --git a/src/libcatnip/atom.hpp b/src/libcatnip/atom.hpp
index 24c8b19..434579a 100644
--- a/src/libcatnip/atom.hpp
+++ b/src/libcatnip/atom.hpp
@@ -3,9 +3,10 @@
 #ifndef _CATNIP_ATOM_HPP
 #define _CATNIP_ATOM_HPP
 
-
+// Private local includes
 #include "elements.hpp"
 
+// Third party includes
 #include <eigen3/Eigen/Dense>
 
 namespace catnip {
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 08874c3..6c4dca1 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -65,7 +65,7 @@ namespace catnip {
 
 
   void AtomGroupContainer::add( AtomGroup atom_group ) {
-    if( isUniqueGroup(atom_group) ){
+    if( isUniqueGroup_(atom_group) ){
       atom_groups_.push_back(atom_group);
     }
     group_types_uptodate_ = false;
@@ -146,6 +146,7 @@ namespace catnip {
         all_paired_atoms.push_back(atom_match);
       }
     }
+    return all_paired_atoms;
   }
 
   void AtomGroupContainer::assignBasisFunctionCount(
diff --git a/src/libcatnip/elements.hpp b/src/libcatnip/elements.hpp
index 03fc1b5..f5b7a14 100644
--- a/src/libcatnip/elements.hpp
+++ b/src/libcatnip/elements.hpp
@@ -1,3 +1,7 @@
+
+#pragma once
+#ifndef _CATNIP_ELEMENTS_HPP
+#define _CATNIP_ELEMENTS_HPP
 #include <algorithm>
 #include <cctype>
 #include <map>
@@ -403,4 +407,4 @@ namespace catnip {
   };
 
 }
-
+#endif // _CATNIP_ELEMENTS_HPP
diff --git a/src/libcatnip/index_map.cpp b/src/libcatnip/index_map.cpp
index 0497ca3..0f71bc4 100644
--- a/src/libcatnip/index_map.cpp
+++ b/src/libcatnip/index_map.cpp
@@ -28,7 +28,6 @@ namespace catnip {
   // Searches the init row for the provided row and returns the group it is
   // in as well as its current index
   std::pair<int,int> IndexMap::findLocation(int row){
-    std::pair<int,int> group_row;
     for( std::pair<int,std::vector<int>> group_rows : row_col_init){
       int row_ind = 0;
       for ( int row_ : group_rows.second ){
@@ -38,6 +37,7 @@ namespace catnip {
         ++row_ind;
       } 
     }
+    return std::pair<int,int>();
   }
 
 }  // namespace catnip
diff --git a/src/libcatnip/index_map.hpp b/src/libcatnip/index_map.hpp
index c1df94f..6029185 100644
--- a/src/libcatnip/index_map.hpp
+++ b/src/libcatnip/index_map.hpp
@@ -2,6 +2,9 @@
 
 #include "transfer_complex.hpp"
 
+#pragma once
+#ifndef _CATNIP_INDEX_MAP_HPP
+#define _CATNIP_INDEX_MAP_HPP
 #include "atom.hpp"
 #include "atom_group.hpp"
 
@@ -26,3 +29,4 @@ namespace catnip {
 
 
 }  // namespace catnip
+#endif // _CATNIP_INDEX_MAP_HPP
diff --git a/src/libcatnip/size_type.hpp b/src/libcatnip/size_type.hpp
new file mode 100644
index 0000000..7a4f4ce
--- /dev/null
+++ b/src/libcatnip/size_type.hpp
@@ -0,0 +1,9 @@
+#pragma once
+#ifndef _CATNIP_SIZE_TYPE_HPP
+#define _CATNIP_SIZE_TYPE_HPP
+
+namespace catnip {
+  using Size = long int;
+};
+#endif // _CATNIP_SIZE_TYPE_HPP
+
diff --git a/src/libcatnip/swap_engine.cpp b/src/libcatnip/swap_engine.cpp
index a673b17..0ce44e0 100644
--- a/src/libcatnip/swap_engine.cpp
+++ b/src/libcatnip/swap_engine.cpp
@@ -4,81 +4,72 @@
 
 #include "atom.hpp"
 #include "atom_group.hpp"
+#include "size_type.hpp"
 
 namespace catnip {
 
   // Swaps rows columns and keeps up with how future swaps should be updated
-  class SwapEngine {
-    private:
-      size_t size_;
-      IndexMap ind_map_;
-      Eigen::MatrixXd scratch_;
+  SwapEngine::SwapEngine(IndexMap ind_map, Size size) : 
+    size_(size), ind_map_(ind_map) {
+      scratch_ = Eigen::MatrixXd::Zero(size, 1);
 
-    public:
-      SwapEngine(IndexMap ind_map, size_t size) : 
-        size_(size), ind_map_(ind_map) {
-          scratch_ = Eigen::MatrixXd::Zero(size, 1);
 
+      // Already have enough information to calculate the correct swap order
+      // Note the order of swaps is important.
+      for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+        int group_ind = group_row.first;
+        for ( int row : group_row.second ) {
+          int final_row = ind_map_.row_col_final[group_ind].at(row);
+          std::pair<int,int> swap(row,final_row);
+          // Now we need to update index map, the row located at the final 
+          // position has now been moved     
+          auto group_and_row_ind = ind_map_.findLocation(final_row);
 
-        // Already have enough information to calculate the correct swap order
-        // Note the order of swaps is important.
-        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-          int group_ind = group_row.first;
-          for ( int row : group_row.second ) {
-            int final_row = ind_map_.row_col_final[group_ind].at(row);
-            std::pair<int,int> swap(row,final_row);
-            // Now we need to update index map, the row located at the final 
-            // position has now been moved     
-            auto group_and_row_ind = ind_map_.findLocation(final_row);
-            
-            // Final row location needs to be pointed to the starting row
-            ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
-          } 
-        }
-      };
-
-
-      // This method of swapping was chosen to keep the memory footprint
-      // reasonable.
-      // Will correctly sort the rows and columns of the matrix
-      void arrange(Eigen::MatrixXd & mat) {
+          // Final row location needs to be pointed to the starting row
+          ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
+        } 
+      }
+    }
+  // This method of swapping was chosen to keep the memory footprint
+  // reasonable.
+  // Will correctly sort the rows and columns of the matrix
+  void SwapEngine::arrange(Eigen::MatrixXd & mat) {
 
-        // Check that matrix is square
-        if( mat.rows() != mat.cols() ) {
-          throw std::runtime_error("Can only arrange square matrices");
-        }
-        if( mat.rows() != size_ ) {
-          throw std::runtime_error("Index map has different number of basis functions to matrix");
-        }
+    // Check that matrix is square
+    if( mat.rows() != mat.cols() ) {
+      throw std::runtime_error("Can only arrange square matrices");
+    }
+    if( mat.rows() != size_ ) {
+      throw std::runtime_error("Index map has different number of basis functions to matrix");
+    }
 
-        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-          int group_ind = group_row.first;
-          for ( int row : group_row.second ) {
-            int final_row = ind_map_.row_col_final[group_ind].at(row);
-            if(final_row == row ) continue;
-            // Copy the data at the final row into the scratch space 
-            scratch_.col(0) = mat.row(final_row);
-            // Copy the data from the initial row into the final row
-            mat.row(final_row) = mat.row(row);
-            // Copy the data from the temporary row into the initial row
-            mat.row(row) = scratch_.col(0);
-          }
-        }
+    for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+      int group_ind = group_row.first;
+      for ( int row : group_row.second ) {
+        int final_row = ind_map_.row_col_final[group_ind].at(row);
+        if(final_row == row ) continue;
+        // Copy the data at the final row into the scratch space 
+        scratch_.col(0) = mat.row(final_row);
+        // Copy the data from the initial row into the final row
+        mat.row(final_row) = mat.row(row);
+        // Copy the data from the temporary row into the initial row
+        mat.row(row) = scratch_.col(0);
+      }
+    }
 
-        // Repeat for columns 
-        for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
-          int group_ind = group_col.first;
-          for ( int col : group_col.second ) {
-            int final_col = ind_map_.row_col_final[group_ind].at(col);
-            if(final_col == col ) continue;
-            // Copy the data at the final row into the scratch space
-            scratch_.col(0) = mat.col(final_col);
-            // Copy the data from the initial row into the final row
-            mat.col(final_col) = mat.col(col);
-            // Copy the data from the temporary row into the initial row
-            mat.col(col) = scratch_.col(0);
-          }
-        }
+    // Repeat for columns 
+    for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
+      int group_ind = group_col.first;
+      for ( int col : group_col.second ) {
+        int final_col = ind_map_.row_col_final[group_ind].at(col);
+        if(final_col == col ) continue;
+        // Copy the data at the final row into the scratch space
+        scratch_.col(0) = mat.col(final_col);
+        // Copy the data from the initial row into the final row
+        mat.col(final_col) = mat.col(col);
+        // Copy the data from the temporary row into the initial row
+        mat.col(col) = scratch_.col(0);
       }
-  };
+    }
+  } 
 }  // namespace catnip
diff --git a/src/libcatnip/swap_engine.hpp b/src/libcatnip/swap_engine.hpp
new file mode 100644
index 0000000..e5d7d6e
--- /dev/null
+++ b/src/libcatnip/swap_engine.hpp
@@ -0,0 +1,29 @@
+
+#pragma once
+#ifndef _CATNIP_SWAP_ENGINE_HPP
+#define _CATNIP_SWAP_ENGINE_HPP
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+#include "index_map.hpp"
+#include "size_type.hpp"
+
+namespace catnip {
+
+  // Swaps rows columns and keeps up with how future swaps should be updated
+  class SwapEngine {
+    private:
+      Size size_;
+      IndexMap ind_map_;
+      Eigen::MatrixXd scratch_;
+
+    public:
+      SwapEngine(IndexMap ind_map, Size size);
+
+      void arrange(Eigen::MatrixXd & mat);
+  };
+
+
+}  // namespace catnip
+
+#endif // _CATNIP_SWAP_ENGINE_HPP

From c9ebdf6f281280cabd9fbec7db10b0686b36e41a Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Wed, 15 Jul 2020 06:59:02 -0600
Subject: [PATCH 38/68] Added Catch2 submodule

---
 .gitmodules     | 3 +++
 external/Catch2 | 1 +
 2 files changed, 4 insertions(+)
 create mode 100644 .gitmodules
 create mode 160000 external/Catch2

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..800345d
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "external/Catch2"]
+	path = external/Catch2
+	url = https://github.com/catchorg/Catch2.git
diff --git a/external/Catch2 b/external/Catch2
new file mode 160000
index 0000000..7f21cc6
--- /dev/null
+++ b/external/Catch2
@@ -0,0 +1 @@
+Subproject commit 7f21cc6c5599f59835f769debf13b4c3e6148a28

From ccfdb7023c9e8b850372d49e92241cb7201c4f0c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Wed, 15 Jul 2020 07:38:58 -0600
Subject: [PATCH 39/68] Added catch2 testing framework

---
 CMakeLists.txt                          | 72 ++++++++++++-------------
 cmake/InstallCatch2.cmake               | 25 +++++++++
 src/CMakeLists.txt                      |  1 +
 src/libcatnip/calcJconfig.hpp           |  2 +-
 src/libcatnip/calcJconfig.hpp.in        |  4 +-
 src/libcatnip/index_map.hpp             | 14 ++---
 src/tests/CMakeLists.txt                | 11 ++--
 src/tests/test_argumentdouble.cpp       |  6 ++-
 src/tests/test_argumentfile.cpp         |  5 +-
 src/tests/test_argumentint.cpp          |  5 +-
 src/tests/test_argumentparser.cpp       |  5 +-
 src/tests/test_argumentstring.cpp       |  6 ++-
 src/tests/test_argumentswitch.cpp       |  5 +-
 src/tests/test_log.cpp                  |  5 +-
 src/tests/test_logreader.cpp            |  5 +-
 src/tests/test_parameters.cpp           |  7 ++-
 src/tests/test_propertydouble.cpp       |  6 ++-
 src/tests/test_propertyfileexist.cpp    |  6 ++-
 src/tests/test_propertyfileext.cpp      |  6 ++-
 src/tests/test_propertyint.cpp          |  6 ++-
 src/tests/test_propertysisterfile.cpp   |  6 ++-
 src/tests/test_propertystring.cpp       |  6 ++-
 src/tests/test_propertystringchoice.cpp |  5 +-
 src/tests/test_propertyswitch.cpp       |  5 +-
 src/tests/test_punreader.cpp            |  5 +-
 src/tests/test_qc_functions.cpp         |  6 ++-
 src/tests/test_string_support.cpp       |  5 +-
 27 files changed, 148 insertions(+), 92 deletions(-)
 create mode 100644 cmake/InstallCatch2.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b987762..d7ba802 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
-cmake_minimum_required (VERSION 2.8)
-project (calc_J)
+cmake_minimum_required (VERSION 3.0)
+project (calc_J VERSION 2.0.0)
 
 ##############################################################################
 # Defining options 
@@ -14,9 +14,9 @@ option(CODE_COVERAGE "Enable coverage reporting" OFF)
 ##############################################################################
 # Defining settings 
 ##############################################################################
-set(calcJ_VERSION_MAJOR 2 )
-set(calcJ_VERSION_MINOR 0 )
-set(calcJ_YEAR_PUBLISHED 2018 )
+#set(calcJ_VERSION_MAJOR 2 )
+#set(calcJ_VERSION_MINOR 0 )
+set(calcJ_YEAR_PUBLISHED 2020 )
 set(calcJ_AUTHOR_SURNAME "\"Brown\"" )
 set(calcJ_AUTHOR_INITIALS "\"J. S.\"" )
 set(calcJ_TITLE "\"CATNIP\"")
@@ -41,7 +41,6 @@ configure_file(
 # Finding dependencies 
 ##############################################################################
 # Find bash it is important for testing using scripts
-find_program (BASH_PROGRAM bash)
 find_library (GCOV gcov)
 #find_package (Eigen3 3.3 REQUIRED NO_MODULE)
 #if (TARGET Eigen3::Eigen)
@@ -62,54 +61,49 @@ endif()
 ##############################################################################
 if(ENABLE_INTEGRATION_TESTING)
   if(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-    message("GAUSSIANFILES found will not download")
+    message(STATUS "GAUSSIANFILES found will not download")
     set(DOWNLOAD_TUTORIAL_FILES OFF)
   else(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-    message("GAUSSIANFILES not found will attempt to download")
-
+    message(STATUS "GAUSSIANFILES not found will attempt to download")
     include(${PROJECT_SOURCE_DIR}/cmake/InstallGdown.cmake)
   endif(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
 endif()
 
 if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+  find_package(Catch2 2.11.1)
+  if( NOT Catch2 )
+    include(${PROJECT_SOURCE_DIR}/cmake/InstallCatch2.cmake)
+  else()
+    message(STATUS "found system installed Catch2 will not download")
+  endif()
   enable_testing()
-endif()
+  include(ParseAndAddCatchTests)
 
-if (ENABLE_INTEGRATION_TESTING)
-  file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 
-    DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
-  file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.pun" 
-    DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
+  if (ENABLE_INTEGRATION_TESTING)
+    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 
+      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
+    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.pun" 
+      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
 
-  file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_pair.pun" 
-    DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
-  file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/ref.pun" 
-    DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
-  file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_2.pun" 
-    DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
-endif()
+    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_pair.pun" 
+      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/ref.pun" 
+      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_2.pun" 
+      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+  endif()
 
-if (ENABLE_UNIT_TESTING)
-  file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.pun" 
-    DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
-  file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.log" 
-    DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
-endif()
+  if (ENABLE_UNIT_TESTING)
+    file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.pun" 
+      DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
+    file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.log" 
+      DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
+  endif()
 
+endif()
 ##############################################################################
 # Compiling build tree/paths 
 ##############################################################################
-# Add the binary tree to the search path for include files
-# so that we will find calcJconfig.hpp
-#target_include_directories(calc_J "${PROJECT_BINARY_DIR}/src")
-#target_link_directories(calc_J "${PROJECT_BINARY_DIR}/src")
-
-#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments/properties")
-#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/arguments")
-#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io/file_readers")
-#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip/io")
-#link_directories("${PROJECT_SOURCE_DIR}/src/libcatnip")
-
 add_subdirectory("${PROJECT_SOURCE_DIR}/src")
 
 
diff --git a/cmake/InstallCatch2.cmake b/cmake/InstallCatch2.cmake
new file mode 100644
index 0000000..b645d23
--- /dev/null
+++ b/cmake/InstallCatch2.cmake
@@ -0,0 +1,25 @@
+
+#
+#if(NOT EXISTS "${CMAKE_SOURCE_DIR}/external/Catch2/includes")
+#  find_program(CURL curl)
+#  if( NOT CURL)
+#    message(FATAL_ERROR "Unable to download Catch2, unable to locate curl, please install curl")
+#  else()
+#    execute_process(COMMAND mkdir -p ${CMAKE_SOURCE_DIR}/external/Catch2/single_include/catch2)
+#    execute_process(COMMAND ${CURL} https://raw.githubusercontent.com/catchorg/Catch2/master/single_include/catch2/catch.hpp -o ${CMAKE_SOURCE_DIR}/external/Catch2/single_include/catch2/catch.hpp)
+#  endif()
+#  add_library(Catch2 INTERFACE) 
+#  target_include_directories(Catch2 INTERFACE ${CMAKE_SOURCE_DIR}/external/Catch2/single_include)
+#endif()
+
+# If Catch2 is not found, instead use the git submodule
+if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/external/Catch2/single_include)
+  # Unable to find the header files for Catch2 or they don't exist
+  message(STATUS "Downloading Catch2 submodule.")
+
+  # Clone the submodule
+  execute_process(COMMAND git submodule update --init --force -- external/Catch2 WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+endif()
+
+add_subdirectory(${CMAKE_SOURCE_DIR}/external/Catch2)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/external/Catch2/contrib")
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index bc2fbfc..6efb70d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,6 +1,7 @@
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/libcatnip")
 #add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tools")
 if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+  message(STATUS "adding test directory")
   add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tests")
 endif()
 
diff --git a/src/libcatnip/calcJconfig.hpp b/src/libcatnip/calcJconfig.hpp
index e574fe9..c8aaf0b 100644
--- a/src/libcatnip/calcJconfig.hpp
+++ b/src/libcatnip/calcJconfig.hpp
@@ -8,7 +8,7 @@
 namespace catnip {
 const int calcJ_VERSION_MAJOR = 2;
 const int calcJ_VERSION_MINOR = 0;
-const int calcJ_YEAR_PUBLISHED = 2018;
+const int calcJ_YEAR_PUBLISHED = 2020;
 const std::string calcJ_AUTHOR_SURNAME = "Brown";
 const std::string calcJ_AUTHOR_INITIALS = "J. S.";
 const std::string calcJ_TITLE = "CATNIP";
diff --git a/src/libcatnip/calcJconfig.hpp.in b/src/libcatnip/calcJconfig.hpp.in
index f7777ce..83ca160 100644
--- a/src/libcatnip/calcJconfig.hpp.in
+++ b/src/libcatnip/calcJconfig.hpp.in
@@ -6,8 +6,8 @@
 #include <string>
 
 namespace catnip {
-const int calcJ_VERSION_MAJOR = @calcJ_VERSION_MAJOR@;
-const int calcJ_VERSION_MINOR = @calcJ_VERSION_MINOR@;
+const int calcJ_VERSION_MAJOR = @PROJECT_VERSION_MAJOR@;
+const int calcJ_VERSION_MINOR = @PROJECT_VERSION_MINOR@;
 const int calcJ_YEAR_PUBLISHED = @calcJ_YEAR_PUBLISHED@;
 const std::string calcJ_AUTHOR_SURNAME = @calcJ_AUTHOR_SURNAME@;
 const std::string calcJ_AUTHOR_INITIALS = @calcJ_AUTHOR_INITIALS@;
diff --git a/src/libcatnip/index_map.hpp b/src/libcatnip/index_map.hpp
index 6029185..51b50b5 100644
--- a/src/libcatnip/index_map.hpp
+++ b/src/libcatnip/index_map.hpp
@@ -1,18 +1,20 @@
 
-
-#include "transfer_complex.hpp"
-
 #pragma once
 #ifndef _CATNIP_INDEX_MAP_HPP
 #define _CATNIP_INDEX_MAP_HPP
-#include "atom.hpp"
-#include "atom_group.hpp"
+
+// Local private includes
+#include "atom_group_container.hpp"
+
+// Standard includes
+#include <map>
+#include <vector>
 
 namespace catnip {
 
   class IndexMap {
     public:
-
+      IndexMap() = default;
       IndexMap(AtomGroupContainer atom_groups);
       // The component rows and colums in their current locations in  
       // in the full system matrix of the complex
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index ab1c7c6..2326895 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -19,7 +19,7 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_string_support)
 
 if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-  link_libraries(gcov)
+  find_library (GCOV gcov)
 endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
 if(ENABLE_UNIT_TESTING)
@@ -28,8 +28,8 @@ if(ENABLE_UNIT_TESTING)
     if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS} )
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-    target_link_libraries(unit_${PROG} libcatnip)
-    add_test(unit_${PROG} unit_${PROG})
+    target_link_libraries(unit_${PROG} libcatnip Catch2::Catch2)
+    ParseAndAddCatchTests(unit_${PROG})
   endforeach(PROG)
 endif(ENABLE_UNIT_TESTING)
 
@@ -44,7 +44,7 @@ if(ENABLE_INTEGRATION_TESTING)
       set_source_files_properties( ${PROG}.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
     endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
-    target_link_libraries(integration${PROG} libcatnip)
+    target_link_libraries(integration${PROG} libcatnip Catch2::Catch2)
     add_test(integration${PROG} integration${PROG})
 
   endforeach(PROG)
@@ -60,11 +60,14 @@ if(ENABLE_INTEGRATION_TESTING)
     POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:test_io> ${CMAKE_CURRENT_SOURCE_DIR})
 
+  find_program (BASH_PROGRAM bash)
   if(BASH_PROGRAM)
     add_test(regression_test_io_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_io.sh ${CMAKE_CURRENT_SOURCE_DIR})
 
     add_test(integration_test_calc_J_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_calc_J.sh ${CMAKE_SOURCE_DIR})
 
+  else()
+    message(STATUS "Unable to add integration tests, unable to find bash")
   endif(BASH_PROGRAM)
 
 endif(ENABLE_INTEGRATION_TESTING)
diff --git a/src/tests/test_argumentdouble.cpp b/src/tests/test_argumentdouble.cpp
index 51d64c2..781b3ef 100644
--- a/src/tests/test_argumentdouble.cpp
+++ b/src/tests/test_argumentdouble.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/argumentdouble.hpp"
 #include <cassert>
 #include <limits>
@@ -6,7 +9,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument Doubles","[unit]") {
 
   cerr << "Testing: argumentdouble" << endl;
   cerr << "Testing: constructor" << endl;
@@ -87,5 +90,4 @@ int main(void) {
     assert(opt_max_val);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_argumentfile.cpp b/src/tests/test_argumentfile.cpp
index 53e9484..00a7b3f 100644
--- a/src/tests/test_argumentfile.cpp
+++ b/src/tests/test_argumentfile.cpp
@@ -1,11 +1,13 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/arguments/argumentfile.hpp"
 #include <cassert>
 
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument File","[unit]") {
 
   cerr << "Testing: argumentfile" << endl;
   cerr << "Testing: constructor" << endl;
@@ -159,5 +161,4 @@ int main(void) {
     cerr << "extensions " << str_exts << endl;
   }
 
-  return 0;
 }
diff --git a/src/tests/test_argumentint.cpp b/src/tests/test_argumentint.cpp
index c059c3b..ab2746c 100644
--- a/src/tests/test_argumentint.cpp
+++ b/src/tests/test_argumentint.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/arguments/argumentint.hpp"
 #include <cassert>
 #include <limits>
@@ -6,7 +8,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument int","[unit]") {
 
   cerr << "Testing: argumentint" << endl;
   cerr << "Testing: constructor" << endl;
@@ -86,5 +88,4 @@ int main(void) {
     assert(opt_max_val);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_argumentparser.cpp b/src/tests/test_argumentparser.cpp
index 5cbac64..dbdb395 100644
--- a/src/tests/test_argumentparser.cpp
+++ b/src/tests/test_argumentparser.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 
 #include "../libcatnip/io/argumentparser.hpp"
 #include "../libcatnip/matrix.hpp"
@@ -11,7 +13,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument Parser","[unit]")  {
 
   cerr << "Testing: ArgumentParser" << endl;
   cerr << "Testing: constructor" << endl;
@@ -190,5 +192,4 @@ int main(void) {
     assert(sisFileNamePath.compare("testfile.log") == 0);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_argumentstring.cpp b/src/tests/test_argumentstring.cpp
index 66e93e3..b12619c 100644
--- a/src/tests/test_argumentstring.cpp
+++ b/src/tests/test_argumentstring.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/argumentstring.hpp"
 #include <cassert>
 #include <limits>
@@ -6,7 +9,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument String","[unit]") {
 
   cerr << "Testing: argumentstring" << endl;
   cerr << "Testing: constructor" << endl;
@@ -122,5 +125,4 @@ int main(void) {
     assert(opt_choices_val);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_argumentswitch.cpp b/src/tests/test_argumentswitch.cpp
index 943c16c..9db01ae 100644
--- a/src/tests/test_argumentswitch.cpp
+++ b/src/tests/test_argumentswitch.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/arguments/argumentswitch.hpp"
 #include <cassert>
 #include <limits>
@@ -6,7 +8,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Argument Switch","[unit]") {
 
   cerr << "Testing: argumentswitch" << endl;
   cerr << "Testing: constructor" << endl;
@@ -71,5 +73,4 @@ int main(void) {
     assert(opt_def_val);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_log.cpp b/src/tests/test_log.cpp
index 36446be..fdf3e54 100644
--- a/src/tests/test_log.cpp
+++ b/src/tests/test_log.cpp
@@ -1,9 +1,10 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/log.hpp"
 
 using namespace catnip;
 
-int main(void) {
+TEST_CASE("Log","[unit]") {
   LOG("Testing log message", 1);
-  return 0;
 }
diff --git a/src/tests/test_logreader.cpp b/src/tests/test_logreader.cpp
index 784d1a3..09e1286 100644
--- a/src/tests/test_logreader.cpp
+++ b/src/tests/test_logreader.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 
 #include <cassert>
 #include <iostream>
@@ -13,7 +15,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Log Reader","[unit]") {
 
   cout << "Testing: LogReader Constructor" << endl;
   { LogReader lr("file.log"); }
@@ -443,5 +445,4 @@ int main(void) {
       cout << x.at(ind) << " " << y.at(ind) << " " << z.at(ind) << endl;
     }
   }
-  return 0;
 }
diff --git a/src/tests/test_parameters.cpp b/src/tests/test_parameters.cpp
index 80847c4..50884bb 100644
--- a/src/tests/test_parameters.cpp
+++ b/src/tests/test_parameters.cpp
@@ -1,10 +1,13 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/parameters.hpp"
 
 using namespace catnip;
 
-int main(void) {
+TEST_CASE("Parameters","[unit]") {
 
   Parameters Par;
 
-  return 0;
 }
diff --git a/src/tests/test_propertydouble.cpp b/src/tests/test_propertydouble.cpp
index a70ec8e..c07a655 100644
--- a/src/tests/test_propertydouble.cpp
+++ b/src/tests/test_propertydouble.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertydouble.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property Double","[unit]") {
 
   cerr << "Testing: PropertyDouble" << endl;
   cerr << "Testing: constructor" << endl;
@@ -64,5 +67,4 @@ int main(void) {
     }
     assert(excep);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertyfileexist.cpp b/src/tests/test_propertyfileexist.cpp
index d405b16..dfb3429 100644
--- a/src/tests/test_propertyfileexist.cpp
+++ b/src/tests/test_propertyfileexist.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertyfileexist.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property File Exists","[unit]") {
 
   cerr << "Testing: PropertyFileExist" << endl;
   cerr << "Testing: constructor" << endl;
@@ -67,5 +70,4 @@ int main(void) {
     assert(fileExist == false);
   }
 
-  return 0;
 }
diff --git a/src/tests/test_propertyfileext.cpp b/src/tests/test_propertyfileext.cpp
index dc9fc2d..634be72 100644
--- a/src/tests/test_propertyfileext.cpp
+++ b/src/tests/test_propertyfileext.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertyfileext.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property File Extension","[unit]") {
 
   cerr << "Testing: PropertyFileExt" << endl;
   cerr << "Testing: constructor" << endl;
@@ -78,5 +81,4 @@ int main(void) {
     }
     assert(excep);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertyint.cpp b/src/tests/test_propertyint.cpp
index ecc50fb..54430ae 100644
--- a/src/tests/test_propertyint.cpp
+++ b/src/tests/test_propertyint.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertyint.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property Int","[unit]") {
 
   cerr << "Testing: PropertyInt" << endl;
   cerr << "Testing: constructor" << endl;
@@ -61,5 +64,4 @@ int main(void) {
     }
     assert(excep);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertysisterfile.cpp b/src/tests/test_propertysisterfile.cpp
index 60b947a..dc3af30 100644
--- a/src/tests/test_propertysisterfile.cpp
+++ b/src/tests/test_propertysisterfile.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertysisterfile.hpp"
 #include <cassert>
 #include <exception>
@@ -10,7 +13,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property Sister File","[unit]") {
   fstream fs;
   fs.open("testfile.pun", ios::out);
   fs.close();
@@ -110,5 +113,4 @@ int main(void) {
     assert(file_path_name.at(0).compare("testfile.pun") == 0);
     assert(fileExist.at(0).compare("true") == 0);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertystring.cpp b/src/tests/test_propertystring.cpp
index f0e0ce0..6050966 100644
--- a/src/tests/test_propertystring.cpp
+++ b/src/tests/test_propertystring.cpp
@@ -1,4 +1,7 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
 #include "../libcatnip/io/arguments/properties/propertystring.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property String","[unit]") {
 
   cerr << "Testing: PropertyString" << endl;
   cerr << "Testing: constructor" << endl;
@@ -63,5 +66,4 @@ int main(void) {
     }
     assert(excep);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertystringchoice.cpp b/src/tests/test_propertystringchoice.cpp
index 7c1cbcc..7e09874 100644
--- a/src/tests/test_propertystringchoice.cpp
+++ b/src/tests/test_propertystringchoice.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/arguments/properties/propertystringchoice.hpp"
 #include <cassert>
 #include <exception>
@@ -10,7 +12,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property String Choice","[unit]") {
   cerr << "Testing: PropertyStringChoice" << endl;
   cerr << "Testing: constructor" << endl;
   { PropertyStringChoice propStrChoice; }
@@ -95,5 +97,4 @@ int main(void) {
     string on = *(choice_on.begin());
     assert(on.compare("true") == 0);
   }
-  return 0;
 }
diff --git a/src/tests/test_propertyswitch.cpp b/src/tests/test_propertyswitch.cpp
index ec41006..18f40b0 100644
--- a/src/tests/test_propertyswitch.cpp
+++ b/src/tests/test_propertyswitch.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/arguments/properties/propertyswitch.hpp"
 #include <cassert>
 #include <exception>
@@ -9,7 +11,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Property Switch","[unit]") {
 
   cerr << "Testing: PropertySwitch" << endl;
   cerr << "Testing: constructor" << endl;
@@ -84,5 +86,4 @@ int main(void) {
     //    }
     //    assert(excep);
   }
-  return 0;
 }
diff --git a/src/tests/test_punreader.cpp b/src/tests/test_punreader.cpp
index 0893860..3d36a2b 100644
--- a/src/tests/test_punreader.cpp
+++ b/src/tests/test_punreader.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/io/file_readers/punreader.hpp"
 #include <cassert>
 #include <iostream>
@@ -9,7 +11,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("Pun Reader","[unit]") {
 
   cerr << "Testing: PunReader Constructor" << endl;
   { PunReader pr("file.pun"); }
@@ -23,5 +25,4 @@ int main(void) {
     assert(m.rows() == 92);
     assert(pr.restrictedShell());
   }
-  return 0;
 }
diff --git a/src/tests/test_qc_functions.cpp b/src/tests/test_qc_functions.cpp
index f4874d6..d0ef8a8 100644
--- a/src/tests/test_qc_functions.cpp
+++ b/src/tests/test_qc_functions.cpp
@@ -1,3 +1,6 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/qc_functions.hpp"
 #include "../libcatnip/matrix.hpp"
 #include <cassert>
@@ -7,7 +10,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("QC Functions","[unit]") {
 
   cout << "Testing: unscramble_Coef" << endl;
   {
@@ -291,5 +294,4 @@ int main(void) {
       }
     }
   }
-  return 0;
 }
diff --git a/src/tests/test_string_support.cpp b/src/tests/test_string_support.cpp
index b1f1204..dceedf6 100644
--- a/src/tests/test_string_support.cpp
+++ b/src/tests/test_string_support.cpp
@@ -1,4 +1,6 @@
 
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
 #include "../libcatnip/string_support.hpp"
 #include <cassert>
 #include <iostream>
@@ -8,7 +10,7 @@
 using namespace catnip;
 using namespace std;
 
-int main(void) {
+TEST_CASE("String Support","[unit]") {
 
   cerr << "Testing: splitSt" << endl;
   {
@@ -103,5 +105,4 @@ int main(void) {
     assert(str3.compare(str) == 0);
   }
 
-  return 0;
 }

From e63c815f10b0a219c854739a9bec4c1f792f18bf Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 16 Jul 2020 07:34:10 -0600
Subject: [PATCH 40/68] Added elements tests

---
 src/libcatnip/CMakeLists.txt           |   2 +-
 src/libcatnip/atom.hpp                 |   6 +-
 src/libcatnip/atom_group.cpp           |   2 +-
 src/libcatnip/atom_group_container.cpp |   2 +-
 src/libcatnip/elements.hpp             | 126 +++++++++++++++++++++++++
 src/tests/CMakeLists.txt               |   2 +
 6 files changed, 136 insertions(+), 4 deletions(-)

diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index a8f855a..2f4e8d8 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -7,4 +7,4 @@ file(GLOB CATNIP_SOURCE_FILES
   io/file_readers/*.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
-target_include_directories(libcatnip PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
+target_include_directories(libcatnip PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/src/libcatnip/atom.hpp b/src/libcatnip/atom.hpp
index 434579a..84eb703 100644
--- a/src/libcatnip/atom.hpp
+++ b/src/libcatnip/atom.hpp
@@ -25,7 +25,7 @@ namespace catnip {
 
       int getBasisFuncCount() const noexcept { return basis_func_count_; }
 
-      bool equal( Atom & atm2 ) const {
+      bool operator==( const Atom & atm2 ) const {
         if ( element_ == atm2.element_ ){
           if ( xyz_.isApprox(atm2.xyz_)) {
             return true;
@@ -33,6 +33,10 @@ namespace catnip {
         }
         return false;
       }
+
+      bool operator!=( const Atom & atm2 ) const {
+        return !(*this == atm2);
+      }
   };
 
 
diff --git a/src/libcatnip/atom_group.cpp b/src/libcatnip/atom_group.cpp
index cd5eb95..00524e2 100644
--- a/src/libcatnip/atom_group.cpp
+++ b/src/libcatnip/atom_group.cpp
@@ -7,7 +7,7 @@ namespace catnip {
   int AtomGroup::findIndex(std::shared_ptr<Atom> atom) {
     int index = 0;
     for ( std::shared_ptr<Atom> & atom_ : atoms_){
-      if ( atom_->equal(*atom)){
+      if ( *atom_ == (*atom)){
         return index;
       }
       ++index;
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 6c4dca1..7670c92 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -51,7 +51,7 @@ namespace catnip {
     std::unordered_map<int,int> paired_atoms;  
     for ( size_t ind1 = 0; ind1 < grp1.size(); ++ind1){
       for (size_t ind2 = 0; ind2 < grp2.size(); ++ind2){
-        if ( grp1.at(ind1)->equal(*grp2.at(ind2)) ){
+        if ( *(grp1.at(ind1)) == *(grp2.at(ind2)) ){
           if ( paired_atoms.count(ind1) ) {
             throw std::runtime_error("Atom in complex has already been paired with an atom in the component, you have two or more atoms in a component that are redundant with an atom in the complex");
           }
diff --git a/src/libcatnip/elements.hpp b/src/libcatnip/elements.hpp
index f5b7a14..6959d7d 100644
--- a/src/libcatnip/elements.hpp
+++ b/src/libcatnip/elements.hpp
@@ -6,6 +6,7 @@
 #include <cctype>
 #include <map>
 #include <string>
+#include <vector>
 
 namespace catnip {
 
@@ -163,7 +164,132 @@ namespace catnip {
         return Element::Unknown;
       }
 
+      std::string getString(Element element) const noexcept {
+        return elements_str_sym_.at(static_cast<int>(element));
+      }
     private:
+      
+      std::vector<std::string> elements_str_sym_ = {
+        "Ac", 
+        "Al", 
+        "Am", 
+        "Sb", 
+        "Ar", 
+        "As", 
+        "At", 
+        "Ba", 
+        "Bk", 
+        "Be", 
+        "Bi", 
+        "Bh", 
+        "B",  
+        "Br", 
+        "Cd", 
+        "Ca", 
+        "Cf", 
+        "C",  
+        "Ce", 
+        "Cs", 
+        "Cl", 
+        "Cr", 
+        "Co", 
+        "Cu", 
+        "Cm", 
+        "Ds", 
+        "Db", 
+        "Dy", 
+        "Es", 
+        "Er", 
+        "Eu", 
+        "Fm", 
+        "F",  
+        "Fr", 
+        "Gd", 
+        "Ga", 
+        "Ge", 
+        "Au", 
+        "Hf", 
+        "Hs", 
+        "He", 
+        "Ho", 
+        "H",  
+        "In", 
+        "I",  
+        "Ir", 
+        "Fe", 
+        "Kr", 
+        "La", 
+        "Lr", 
+        "Pb", 
+        "Li", 
+        "Lu", 
+        "Mg", 
+        "Mn", 
+        "Mt", 
+        "Md", 
+        "Hg", 
+        "Mo", 
+        "Nd", 
+        "Ne", 
+        "Np", 
+        "Ni", 
+        "Nb", 
+        "N",  
+        "No", 
+        "Uuo",
+        "Os", 
+        "O",  
+        "Pd", 
+        "P",  
+        "Pt", 
+        "Pu", 
+        "Po", 
+        "K",  
+        "Pr", 
+        "Pm", 
+        "Pa", 
+        "Ra", 
+        "Rn", 
+        "Re", 
+        "Rh", 
+        "Rg", 
+        "Rb", 
+        "Ru", 
+        "Rf", 
+        "Sm", 
+        "Sc", 
+        "Sg", 
+        "Se", 
+        "Si", 
+        "Ag", 
+        "Na", 
+        "Sr", 
+        "S",  
+        "Ta", 
+        "Tc", 
+        "Te", 
+        "Tb", 
+        "Tl", 
+        "Th", 
+        "Tm", 
+        "Sn", 
+        "Ti", 
+        "W",  
+        "Uub",
+        "Uuh",
+        "Uup",
+        "Uuq",
+        "Uus",
+        "Uut",
+        "U",  
+        "V",  
+        "Xe", 
+        "Yb", 
+        "Y",  
+        "Zn", 
+        "Zr", 
+        "Unknown"};
+
       std::map<std::string, Element> elements_ = {
         {"actinium",     Element::Ac},
         {"aluminum",     Element::Al},
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 2326895..7237b9d 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -5,6 +5,8 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_argumentparser
   test_argumentstring
   test_argumentswitch
+  test_atom
+  test_elements
   test_log
   test_parameters
   test_propertydouble

From adeaa09665717882a0a24110faa445ce3c0ec463 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 16 Jul 2020 07:34:24 -0600
Subject: [PATCH 41/68] Added elements test

---
 src/tests/test_elements.cpp | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 src/tests/test_elements.cpp

diff --git a/src/tests/test_elements.cpp b/src/tests/test_elements.cpp
new file mode 100644
index 0000000..164e8dc
--- /dev/null
+++ b/src/tests/test_elements.cpp
@@ -0,0 +1,20 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+#include "elements.hpp"
+
+using namespace catnip;
+
+TEST_CASE("Elements","[unit]") {
+
+  Elements elements;
+  Element elem = Element::H;
+  REQUIRE( elem == elements.getElement("H"));
+  REQUIRE( elements.getString(elem) == "H");
+  REQUIRE( elem == elements.getElement("h"));
+
+  Element unknown = Element::Unknown;
+  REQUIRE( unknown == elements.getElement("blah"));
+  REQUIRE( "Unknown" == elements.getString(unknown));
+}

From 430cd19f74e93beda2899c6bc6589d0461ee69bf Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 16 Jul 2020 23:45:03 -0600
Subject: [PATCH 42/68] GroupType assignment completed

---
 src/libcatnip/atom.hpp                  |  27 ++++-
 src/libcatnip/atom_group.cpp            |  22 +++-
 src/libcatnip/atom_group.hpp            |  60 ++++++++---
 src/libcatnip/atom_group_container.cpp  | 134 +++++++++++++++++++-----
 src/libcatnip/atom_group_container.hpp  |  31 ++++--
 src/libcatnip/index_map.cpp             |  11 +-
 src/libcatnip/transfer_complex.cpp      |   4 +-
 src/tests/CMakeLists.txt                |   2 +
 src/tests/test_atom.cpp                 |  23 ++++
 src/tests/test_atom_group.cpp           |  56 ++++++++++
 src/tests/test_atom_group_container.cpp |  52 +++++++++
 src/tests/test_index_map.cpp            |  16 +++
 12 files changed, 374 insertions(+), 64 deletions(-)
 create mode 100644 src/tests/test_atom.cpp
 create mode 100644 src/tests/test_atom_group.cpp
 create mode 100644 src/tests/test_atom_group_container.cpp
 create mode 100644 src/tests/test_index_map.cpp

diff --git a/src/libcatnip/atom.hpp b/src/libcatnip/atom.hpp
index 84eb703..7100708 100644
--- a/src/libcatnip/atom.hpp
+++ b/src/libcatnip/atom.hpp
@@ -9,16 +9,24 @@
 // Third party includes
 #include <eigen3/Eigen/Dense>
 
+// Standard includes
+#include <bits/stdc++.h> 
+
 namespace catnip {
 
   class Atom {
     private:
-      Element element_;
+      // Element should not be able to change
+      const Element element_;
       Eigen::Vector3d xyz_;
       int basis_func_count_ = -1;
     public: 
       Atom(Element element, double x, double y, double z) : element_(element), xyz_(x,y,z) {};
 
+      Element getElement() const noexcept { return element_; }
+
+      Eigen::Vector3d getPos() const noexcept { return xyz_; }
+
       void setBasisFuncCount(int count) {
         basis_func_count_ = count;
       }
@@ -39,7 +47,22 @@ namespace catnip {
       }
   };
 
-
+  double round(double N, double n);
 }
 
+namespace std {
+
+  template <>
+    struct hash<catnip::Atom>
+    {
+      std::size_t operator()(const catnip::Atom& atom) const
+      {
+        Eigen::Vector3d pos = atom.getPos();
+        return ((((std::hash<catnip::Element>()(atom.getElement())
+              ^ (hash<double>()(catnip::round(pos(0),4)) << 1)) >> 1)
+          ^ (hash<double>()(catnip::round(pos(1),4)) << 1)) >> 1)
+          ^ (hash<double>()(catnip::round(pos(2),4)) << 1);
+      }
+    };
+}
 #endif // _CATNIP_ATOM_HPP
diff --git a/src/libcatnip/atom_group.cpp b/src/libcatnip/atom_group.cpp
index 00524e2..618bff0 100644
--- a/src/libcatnip/atom_group.cpp
+++ b/src/libcatnip/atom_group.cpp
@@ -2,16 +2,32 @@
 #include "atom_group.hpp"
 #include "atom.hpp"
 
+// Standard includes
+#include <vector>
+
 namespace catnip {
 
-  int AtomGroup::findIndex(std::shared_ptr<Atom> atom) {
+  std::vector<int> AtomGroup::find(std::shared_ptr<Atom> atom) {
+    std::vector<int> indices;
     int index = 0;
     for ( std::shared_ptr<Atom> & atom_ : atoms_){
       if ( *atom_ == (*atom)){
-        return index;
+        indices.push_back(index);
+      }
+      ++index;
+    }
+    return indices;
+  }
+
+  std::vector<int> AtomGroup::findStrict(std::shared_ptr<Atom> atom) {
+    std::vector<int> indices;
+    int index = 0;
+    for ( std::shared_ptr<Atom> & atom_ : atoms_){
+      if ( atom_.get() == atom.get()){
+        indices.push_back(index);
       }
       ++index;
     }
-    return -1;
+    return indices;
   }
 }
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 6647207..4ca8eb7 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -1,7 +1,11 @@
 #pragma once
-#ifndef _CATNIP_ATOM_GROUP_HPP
-#define _CATNIP_ATOM_GROUP_HPP
+#ifndef CATNIP_ATOM_GROUP_HPP
+#define CATNIP_ATOM_GROUP_HPP
 
+// Third party libary includes
+#include <eigen3/Eigen/Dense>
+
+// Standard includes
 #include <exception>
 #include <iterator>
 #include <memory>
@@ -9,20 +13,30 @@
 #include <string>
 #include <vector>
 
-#include <eigen3/Eigen/Dense>
-
 namespace catnip {
 
   class Atom;
   
   /**
    * @brief Atom groups can either be a component or a complex
+   *
+   * Component - all atoms in the atom group have a matching atom in the 
+   * complex, but do not share atoms between other components
+   *
+   * Complex - all atoms in this atom group have a matching atom in a component
+   *
+   * Unit - non of the atoms appear in any of the other atom groups
+   *
+   * Unknown - some combination, may or may not have overlapping components
+   *
+   * Unassigned - has not yet been specified
    */
   enum class GroupType {
-    PotentialComponent, // The atoms in all the components == the num atoms in the complex
-    Component, // All atoms in the components have a matching atom in the complex
+    Component, 
     Complex,
-    Unknown
+    Unit,
+    Unknown,
+    Unassigned
   };
 
   /**
@@ -37,15 +51,23 @@ namespace catnip {
       std::vector<std::shared_ptr<Atom>> atoms_;
     public:
       AtomGroup(std::string group_name) : name_(group_name) {};
+    
+      std::string getName() const noexcept { return name_; }
 
       size_t size() const noexcept { return atoms_.size(); }
 
       std::vector<std::shared_ptr<Atom>>::iterator 
         begin() { return atoms_.begin(); }
 
+      std::vector<std::shared_ptr<Atom>>::const_iterator 
+        begin() const { return atoms_.begin(); }
+
       std::vector<std::shared_ptr<Atom>>::iterator 
         end() { return atoms_.end(); }
  
+      std::vector<std::shared_ptr<Atom>>::const_iterator 
+        end() const { return atoms_.end(); }
+
       std::shared_ptr<Atom> at(size_t ind) const {
         return atoms_.at(ind);
       }
@@ -58,26 +80,32 @@ namespace catnip {
         atoms_.insert(atoms_.end(),atoms.begin(),atoms.end());
       } 
 
-      size_t numberOfAtoms() const noexcept {
-        return atoms_.size();
-      }
-
       void setType(const GroupType & type) noexcept {
         type_ = type;
       }
-      GroupType getType() const noexcept { return type_; }
+      const GroupType & getType() const noexcept { return type_; }
 
       /**
        * @brief Find the index of the atom in the group if it exists and return
-       * the index
+       * the index, compares atoms 
+       *
+       * @param atom
+       *
+       * @return indeces of atoms that match
+       */
+      std::vector<int> find(std::shared_ptr<Atom> atom);
+     
+
+      /**
+       * @brief Finds the exact matching atom in memory by looking at the address
        *
        * @param atom
        *
-       * @return index if found -1 if not found 
+       * @return 
        */
-      int findIndex(std::shared_ptr<Atom> atom);
+      std::vector<int> findStrict(std::shared_ptr<Atom> atom);
   };
 
 
 }  // namespace catnip
-#endif  // _CATNIP_ATOM_GROUP_HPP
+#endif  // CATNIP_ATOM_GROUP_HPP
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 7670c92..058ec0a 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -1,17 +1,20 @@
-
+// Local private includes
 #include "atom_group_container.hpp"
 
 #include "atom.hpp"
 #include "atom_group.hpp"
 
+// Third party includes
+#include <eigen3/Eigen/Dense>
+
+// Standard includes
 #include <exception>
 #include <iterator>
 #include <memory>
 #include <numeric>
 #include <string>
 #include <vector>
-
-#include <eigen3/Eigen/Dense>
+#include <unordered_map>
 
 namespace catnip {
 
@@ -72,35 +75,112 @@ namespace catnip {
     index_of_complex_ = -1;
   }
 
-  void AtomGroupContainer::assignAtomGroupTypes(){
-    if (group_types_uptodate_ ) return;
-    std::vector<size_t> number_atoms;        
-    for( AtomGroup group : atom_groups_){
-      number_atoms.push_back(group.numberOfAtoms());
+  struct GroupAtomIndex {
+    int atm_ind;
+    int grp_ind; 
+  };
+
+  static std::unordered_map<Atom,std::vector<GroupAtomIndex>> mapAtomsToGroups(
+      const std::vector<AtomGroup> & atom_groups_ ){
+
+    std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map;
+    int grp_index = 0;
+    for ( const AtomGroup & grp : atom_groups_ ){
+      int atom_index = 0;
+      for ( auto & atom_ptr : grp ){
+        atm_map[*atom_ptr].push_back(GroupAtomIndex{atom_index,grp_index});
+        ++atom_index;
+      }
+      ++grp_index;
     }
-    auto max_elem_it = max_element(number_atoms.begin(),number_atoms.end()); 
-    size_t max_elem = *max_elem_it; 
-    for( AtomGroup group : atom_groups_){
-      group.setType(GroupType::Component);
-    } 
-    size_t number_atoms_excluding_max = std::accumulate(number_atoms.begin(),number_atoms.end(),-1*max_elem);
-    if ( std::count(number_atoms.begin(),number_atoms.end(), max_elem) == 1 &&
-        number_atoms_excluding_max == max_elem ){
-      for( AtomGroup group : atom_groups_){
-        if( group.numberOfAtoms() == max_elem ){
-          group.setType(GroupType::Complex);
-          index_of_complex_ = std::distance(number_atoms.begin(),max_elem_it);
+    return atm_map;
+  }
+
+  static const std::map<int,std::vector<int>> calculateConnectedGroups(
+      std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map,
+      const std::vector<AtomGroup> & atom_groups_ 
+      ){
+
+    std::map<int,std::vector<int>> grp_indices;
+    int grp_index = 0;
+    for ( const AtomGroup & grp : atom_groups_ ){
+      for ( const auto & atom_ptr : grp ){
+        for ( const GroupAtomIndex & grp_atm_ind : atm_map[*atom_ptr] ){
+          if (grp_atm_ind.grp_ind != grp_index ){
+            grp_indices[grp_index].push_back(grp_atm_ind.grp_ind);
+          }
+        } 
+      }
+      ++grp_index;
+    }
+    return grp_indices;
+  }
+
+  static void identifyAtomGroupsOfUnitType(
+      const std::map<int,std::vector<int>> & grp_indices,
+      std::vector<AtomGroup> & atom_groups_ 
+      ) {
+    for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
+      if(grp_groups.second.size() == 0) {
+        atom_groups_.at(grp_groups.first).setType(GroupType::Unit);
+      }
+    }
+  }
+
+  static void identifyAtomGroupsOfComponentComplexAndUnknownTypes(
+      const std::map<int,std::vector<int>> & grp_indices,
+      std::vector<AtomGroup> & atom_groups_ 
+      ){
+    std::vector<int> potential_complexes;
+    for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
+      if( grp_groups.second.size() > 1 ){
+        potential_complexes.push_back(grp_groups.first);
+      } 
+    }
+
+    for( const int & potential_complex : potential_complexes){
+      std::vector<int> candidate_components = grp_indices.at(potential_complex); 
+      bool candidate_components_valid = true;
+      for ( const int & candidate_component : candidate_components){
+        if ( grp_indices.at(candidate_component).size() != 1){
+          candidate_components_valid = false;
+          break; // these are not components, and potential complex is not a complex
         } 
       }
+      if ( candidate_components_valid){
+        atom_groups_.at(potential_complex).setType(GroupType::Complex);
+        for ( const int & candidate_component : candidate_components){
+          atom_groups_.at(candidate_component).setType(GroupType::Component);
+        }
+      }else{
+        atom_groups_.at(potential_complex).setType(GroupType::Unknown);
+        for ( const int & candidate_component : candidate_components){
+          atom_groups_.at(candidate_component).setType(GroupType::Unknown);
+        }
+      }
     }
-    group_types_uptodate_ = true;
+  }
+// Create a map with an atom as the key and a vector of indices to indicate 
+// where there is overlap, the group and index of where the overlap occurs 
+  void AtomGroupContainer::assignGroupTypes(){
+
+    std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map = mapAtomsToGroups( atom_groups_ );
+    // For each atom in a group find out how many other groups share the atoms
+    // First index is the group index the vector stores the other groups that
+    // share atoms
+    const std::map<int,std::vector<int>> grp_indices = calculateConnectedGroups(atm_map, atom_groups_ );
+
+    // Calculate which groups do not share atoms with other groups these are units
+    identifyAtomGroupsOfUnitType(grp_indices, atom_groups_);
+
+    identifyAtomGroupsOfComponentComplexAndUnknownTypes(grp_indices,atom_groups_ );
   }
 
-  int AtomGroupContainer::getTotalBasisFunctionCount(const GroupType & type) const {
+  int AtomGroupContainer::getTotalBasisFunctions(const GroupType & type) const {
     int total_num_basis = 0;
     std::vector<int> group_indices = getGroups(type);     
     for ( int ind : group_indices ){
-      AtomGroup group = getGroup(ind);
+      AtomGroup group = atom_groups_.at(ind);
       for( const std::shared_ptr<Atom> & atom_ptr : group ) {
         total_num_basis += atom_ptr->getBasisFuncCount();
       }
@@ -108,11 +188,11 @@ namespace catnip {
     return total_num_basis;
   }
 
-  int AtomGroupContainer::getMaxBasisFunctionCount(const GroupType & type) const {
+  int AtomGroupContainer::getMaxBasisFunctions(const GroupType & type) const {
     int max_num_basis = 0;
     std::vector<int> group_indices = getGroups(type);     
     for ( int ind : group_indices ){
-      AtomGroup group = getGroup(ind);
+      AtomGroup group = atom_groups_.at(ind);
       for( const std::shared_ptr<Atom> & atom_ptr : group ) {
         if( atom_ptr->getBasisFuncCount() > max_num_basis){
           max_num_basis = atom_ptr->getBasisFuncCount();
@@ -149,7 +229,7 @@ namespace catnip {
     return all_paired_atoms;
   }
 
-  void AtomGroupContainer::assignBasisFunctionCount(
+  void AtomGroupContainer::assignBasisFunctions(
       const std::vector<int>& complex_basis_func_count) {
 
     // 1. Check that up to date
@@ -157,7 +237,7 @@ namespace catnip {
       throw std::runtime_error("Cannot assign basis functions to atoms as group types are not up to date!");
     }
     // 2. Check that the number of atoms in the complex is consistent with the number of values provided
-    if ( complex_basis_func_count.size() != atom_groups_.at(index_of_complex_).numberOfAtoms() ){
+    if ( complex_basis_func_count.size() != atom_groups_.at(index_of_complex_).size() ){
       throw std::runtime_error("Cannot assign basis function count to atoms as the basis function count vector is not equal to the number of atoms!");
     }
 
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index 4203669..daa4f98 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -1,11 +1,14 @@
 #pragma once
-#ifndef _CATNIP_ATOM_GROUP_CONTAINER_HPP
-#define _CATNIP_ATOM_GROUP_CONTAINER_HPP
+#ifndef CATNIP_ATOM_GROUP_CONTAINER_HPP
+#define CATNIP_ATOM_GROUP_CONTAINER_HPP
 
+// Local private includes
 #include "atom_group.hpp"
 
+// Third party includes
 #include <eigen3/Eigen/Dense>
 
+// Standard includes
 #include <exception>
 #include <iterator>
 #include <memory>
@@ -18,10 +21,14 @@ namespace catnip {
 
   class Atom;
 
+  /// What we need is a function that will actually create the atom group
+  /// container so that the state is known, basically you need to pass in the
+  /// a vector of the atom groups
   class AtomGroupContainer {
       std::vector<AtomGroup> atom_groups_;
      
       bool group_types_uptodate_ = false; 
+
       /**
        * @brief Checks to makes sure the group is unique
        *
@@ -57,6 +64,8 @@ namespace catnip {
     public: 
       void add( AtomGroup atom_group );
 
+      size_t size() const noexcept { return  atom_groups_.size(); }
+
       /**
        * @brief This algorithm determines if a complex exists
        *
@@ -66,7 +75,7 @@ namespace catnip {
        *
        * Only a single atom group can be the complex
        */
-      void assignAtomGroupTypes();
+      void assignGroupTypes();
 
       /**
        * @brief Determine if a complex exists within the atom groups
@@ -75,7 +84,7 @@ namespace catnip {
        *
        * @return 
        */
-      bool complexExists() const ;
+      bool complexExists() const;
 
       /**
        * @brief If a complex exists and we know the number of basis functions
@@ -84,11 +93,11 @@ namespace catnip {
        *
        * @param complex_basis_func_count
        */
-      void assignBasisFunctionCount(const std::vector<int>& complex_basis_func_count);
+      void assignBasisFunctions(const std::vector<int>& complex_basis_func_count);
 
-      int getTotalBasisFunctionCount(const GroupType & type) const;
+      int getTotalBasisFunctions(const GroupType & type) const;
 
-      int getMaxBasisFunctionCount(const GroupType & type) const;
+      int getMaxBasisFunctions(const GroupType & type) const;
       /**
        * @brief Get the indices of all the groups of the specified group type
        *
@@ -98,10 +107,10 @@ namespace catnip {
        */
       std::vector<int> getGroups(const GroupType & type) const;     
 
-      AtomGroup getGroup(size_t ind) const { return  atom_groups_.at(ind);}
-
-      
+      AtomGroup & at(size_t ind) { return  atom_groups_.at(ind);}
   };
 
+  
+
 }  // namespace catnip
-#endif  // _CATNIP_ATOM_GROUP_CONTAINER_HPP
+#endif  // CATNIP_ATOM_GROUP_CONTAINER_HPP
diff --git a/src/libcatnip/index_map.cpp b/src/libcatnip/index_map.cpp
index 0f71bc4..3d4ad28 100644
--- a/src/libcatnip/index_map.cpp
+++ b/src/libcatnip/index_map.cpp
@@ -5,17 +5,22 @@
 #include "atom.hpp"
 #include "atom_group.hpp"
 
+// Standard includes
+#include <cassert>
+
 namespace catnip {
 
   IndexMap::IndexMap(AtomGroupContainer atom_groups){
     std::vector<int> group_indices = atom_groups.getGroups(GroupType::Component);
     int complex_ind = atom_groups.getGroups(GroupType::Complex).at(0);
-    AtomGroup complex_group = atom_groups.getGroup(complex_ind);
+    AtomGroup complex_group = atom_groups.at(complex_ind);
     int sys_ind = 0;
     for ( int & group_ind : group_indices) {
-      AtomGroup component_group = atom_groups.getGroup(group_ind);
+      AtomGroup component_group = atom_groups.at(group_ind);
       for( std::shared_ptr<Atom> & atom : component_group){
-        int atom_ind = complex_group.findIndex(atom);
+        std::vector<int> atom_indices = complex_group.find(atom);
+        assert(atom_indices.size() == 1);
+        int atom_ind = atom_indices.at(0);
         int num_basis = complex_group.at(atom_ind)->getBasisFuncCount();
         for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
           row_col_final[group_ind].push_back(sys_ind); 
diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
index 907e042..21134ad 100644
--- a/src/libcatnip/transfer_complex.cpp
+++ b/src/libcatnip/transfer_complex.cpp
@@ -14,8 +14,8 @@ namespace catnip {
     // rearranged before moving any of the coefficients in the matrix    
     IndexMap ind_map = IndexMap(atom_groups);
   
-    size_t total_basis = atom_groups.getTotalBasisFunctionCount(GroupType::Component); 
-    size_t total_basis_comp = atom_groups.getTotalBasisFunctionCount(GroupType::Complex); 
+    size_t total_basis = atom_groups.getTotalBasisFunctions(GroupType::Component); 
+    size_t total_basis_comp = atom_groups.getTotalBasisFunctions(GroupType::Complex); 
 
     // If the total number of basis functions in the components is greater than
     // the total number of basis functions in the complex, throw an error
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 7237b9d..c716fbd 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -6,7 +6,9 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_argumentstring
   test_argumentswitch
   test_atom
+  test_atom_group
   test_elements
+  test_index_map
   test_log
   test_parameters
   test_propertydouble
diff --git a/src/tests/test_atom.cpp b/src/tests/test_atom.cpp
new file mode 100644
index 0000000..7c4c88b
--- /dev/null
+++ b/src/tests/test_atom.cpp
@@ -0,0 +1,23 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "../libcatnip/atom.hpp"
+
+#include "../libcatnip/elements.hpp"
+
+using namespace catnip;
+
+TEST_CASE("Elements","[unit]") {
+
+  Elements elements;
+  Element H = elements.getElement("H");
+
+  Atom atom(H,0.0,0.0,0.0);
+  Atom atom2(H,1.0,0.0,0.0);
+  
+  REQUIRE( atom != atom2);
+  REQUIRE( atom == atom);
+  REQUIRE( atom2 == atom2);
+}
diff --git a/src/tests/test_atom_group.cpp b/src/tests/test_atom_group.cpp
new file mode 100644
index 0000000..2ed81ce
--- /dev/null
+++ b/src/tests/test_atom_group.cpp
@@ -0,0 +1,56 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "atom_group.hpp"
+
+#include "atom.hpp"
+#include "elements.hpp"
+
+// Standard includes
+#include <memory>
+
+using namespace catnip;
+
+TEST_CASE("Atom Group","[unit]") {
+
+  AtomGroup atom_grp("CH2");
+  
+  REQUIRE(atom_grp.getType() == GroupType::Unknown );
+  REQUIRE(atom_grp.getName() == "CH2");
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  // Same atom different memory location
+  Atom atom4(Element::H, 0.0, 0.0, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+
+  atom_grp.add(atom1_ptr);
+  atom_grp.add(atom2_ptr);
+  atom_grp.add(atom3_ptr);
+
+  REQUIRE(atom_grp.size() == 3); 
+ 
+  REQUIRE(atom_grp.find(atom1_ptr).size() == 1);  
+  REQUIRE(atom_grp.find(atom2_ptr).size() == 1);  
+  REQUIRE(atom_grp.find(atom3_ptr).size() == 1);  
+
+  REQUIRE(atom_grp.find(atom1_ptr).at(0) == 0);  
+  REQUIRE(atom_grp.find(atom2_ptr).at(0) == 1);  
+  REQUIRE(atom_grp.find(atom3_ptr).at(0) == 2);  
+
+  atom_grp.add(atom4_ptr);
+  REQUIRE(atom_grp.find(atom1_ptr).size() == 2);  
+  REQUIRE(atom_grp.find(atom1_ptr).at(0) == 0);  
+  REQUIRE(atom_grp.find(atom1_ptr).at(1) == 3);  
+
+  REQUIRE(atom_grp.findStrict(atom4_ptr).size() == 1);
+  REQUIRE(atom_grp.findStrict(atom4_ptr).at(0) == 3);  
+
+}
diff --git a/src/tests/test_atom_group_container.cpp b/src/tests/test_atom_group_container.cpp
new file mode 100644
index 0000000..b31a3eb
--- /dev/null
+++ b/src/tests/test_atom_group_container.cpp
@@ -0,0 +1,52 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "atom_group_container.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+#include "elements.hpp"
+
+// Standard includes
+#include <memory>
+
+using namespace catnip;
+
+TEST_CASE("Atom Group Container","[unit]") {
+
+  AtomGroup atom_grp("CH2");
+  
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+
+  atom_grp.add(atom1_ptr);
+  atom_grp.add(atom2_ptr);
+  atom_grp.add(atom3_ptr);
+
+  AtomGroup atom_grp2("O2");
+
+  Atom atom4(Element::O, 3.3, 4.3);
+  Atom atom5(Element::O, 3.0, 3.9);
+
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+  atom_grp2.add(atom4_ptr);  
+  atom_grp2.add(atom5_ptr);  
+
+  AtomGroupContainer atom_grp_cont;
+
+  atom_grp_cont.add(atom_grp1);
+  atom_grp_cont.add(atom_grp2);
+
+  REQUIRE(atom_grp_cont.size() == 2);
+
+  atom_grp_cont.assignGroupTypes();
+}
diff --git a/src/tests/test_index_map.cpp b/src/tests/test_index_map.cpp
new file mode 100644
index 0000000..504f421
--- /dev/null
+++ b/src/tests/test_index_map.cpp
@@ -0,0 +1,16 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+#include "index_map.hpp"
+
+#include "atom_group_container.hpp"
+
+using namespace catnip;
+
+TEST_CASE("Index Map","[unit]") {
+
+  AtomGroupContainer atom_cont;
+  IndexMap ind_map(atom_cont);
+
+}

From d08e466e89605ee5df6dfc1f6450a613696ffcba Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 17 Jul 2020 17:43:16 -0600
Subject: [PATCH 43/68] Group assignment test now working

---
 src/libcatnip/atom.cpp                  | 31 +++++++++
 src/libcatnip/atom_group.hpp            |  2 +-
 src/libcatnip/atom_group_container.cpp  | 84 +++++++++++++++++++++++--
 src/libcatnip/atom_group_container.hpp  | 20 +++---
 src/tests/CMakeLists.txt                |  1 +
 src/tests/test_atom_group.cpp           |  2 +-
 src/tests/test_atom_group_container.cpp | 49 ++++++++++++---
 7 files changed, 160 insertions(+), 29 deletions(-)
 create mode 100644 src/libcatnip/atom.cpp

diff --git a/src/libcatnip/atom.cpp b/src/libcatnip/atom.cpp
new file mode 100644
index 0000000..1c342e1
--- /dev/null
+++ b/src/libcatnip/atom.cpp
@@ -0,0 +1,31 @@
+#include "atom.hpp"
+
+namespace catnip {
+  double round(double N, double n) 
+  { 
+    int h; 
+    double  b, d, e, i, j, m, f; 
+    b = N; 
+
+    // Counting the no. of digits to the left of decimal point 
+    // in the given no. 
+    for (i = 0; b >= 1; ++i) 
+      b = b / 10; 
+
+    d = n - i; 
+    b = N; 
+    b = b * std::pow(10, d); 
+    e = b + 0.5; 
+    if ((float)e == (float)std::ceil(b)) { 
+      f = (std::ceil(b)); 
+      h = f - 2; 
+      if (h % 2 != 0) { 
+        e = e - 1; 
+      } 
+    } 
+    j = std::floor(e); 
+    m = std::pow(10, d); 
+    j = j / m; 
+    return j;
+  }
+}
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 4ca8eb7..db2a4d2 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -46,7 +46,7 @@ namespace catnip {
    */
   class AtomGroup {
     private: 
-      GroupType type_ = GroupType::Unknown;
+      GroupType type_ = GroupType::Unassigned;
       std::string name_;
       std::vector<std::shared_ptr<Atom>> atoms_;
     public:
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 058ec0a..8e29402 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -10,6 +10,7 @@
 // Standard includes
 #include <exception>
 #include <iterator>
+#include <iostream>
 #include <memory>
 #include <numeric>
 #include <string>
@@ -67,9 +68,54 @@ namespace catnip {
   }
 
 
+  bool AtomGroupContainer::isUniqueGroup_( const AtomGroup & atom_group ) const {
+    // Step 1 check the size of the atom group 
+    if(atom_groups_.size() == 0) return true;
+
+    for ( const AtomGroup & grp : atom_groups_ ){
+      if ( grp.size() == atom_group.size() ){
+        std::vector<bool> matchs(grp.size(),false);
+        // Determine if a match is found
+        for ( const auto & atm : atom_group ) {
+          size_t index = 0;
+          for ( bool matched : matchs ){
+            if ( not matched ){
+              // Compare atoms 
+              if ( *atm == *(grp.at(index)) ){
+                matchs.at(index) = true;
+                break;
+              }
+            } 
+            ++index;
+          }
+          // If an atom was not matched it means that there is at least one 
+          // difference, and so we do not need to cycle through the other
+          // atoms in this particular group 
+          if(index == grp.size()) break;
+        } 
+        // Count the number of matches in the vector if all of the elements match
+        // then the atom group is not unique
+        for ( bool match : matchs ) {
+          if ( match == false ) break;
+        } 
+        return false;
+      }
+    }
+    return true;
+  }
+  // As soon as we add a new atom group it should invalidate the labels on 
+  // all the other groups
   void AtomGroupContainer::add( AtomGroup atom_group ) {
+    std::cout << "Adding group " << atom_group.getName() << std::endl; 
     if( isUniqueGroup_(atom_group) ){
+      std::cout << "Is unique" << std::endl;
       atom_groups_.push_back(atom_group);
+    } else {
+      return;
+    }
+
+    for ( AtomGroup & grp : atom_groups_ ){
+      grp.setType(GroupType::Unassigned);
     }
     group_types_uptodate_ = false;
     index_of_complex_ = -1;
@@ -104,14 +150,24 @@ namespace catnip {
     std::map<int,std::vector<int>> grp_indices;
     int grp_index = 0;
     for ( const AtomGroup & grp : atom_groups_ ){
+      // Initialize
+      grp_indices[grp_index];
       for ( const auto & atom_ptr : grp ){
         for ( const GroupAtomIndex & grp_atm_ind : atm_map[*atom_ptr] ){
           if (grp_atm_ind.grp_ind != grp_index ){
-            grp_indices[grp_index].push_back(grp_atm_ind.grp_ind);
+            // Check that group has not already been added
+            if( grp_indices[grp_index].size() > 0 ){
+              if( grp_indices[grp_index].back() != grp_atm_ind.grp_ind ) {
+                grp_indices[grp_index].push_back(grp_atm_ind.grp_ind);
+              }
+            }else {
+              grp_indices[grp_index].push_back(grp_atm_ind.grp_ind);
+            }
           }
         } 
       }
       ++grp_index;
+
     }
     return grp_indices;
   }
@@ -122,6 +178,7 @@ namespace catnip {
       ) {
     for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
       if(grp_groups.second.size() == 0) {
+        std::cout << "Empty makeing unit, does not share atoms" << std::endl;
         atom_groups_.at(grp_groups.first).setType(GroupType::Unit);
       }
     }
@@ -142,6 +199,8 @@ namespace catnip {
       std::vector<int> candidate_components = grp_indices.at(potential_complex); 
       bool candidate_components_valid = true;
       for ( const int & candidate_component : candidate_components){
+        std::cout << "Candiate component " << candidate_component << std::endl;
+        std::cout << "number of other groups sharing atoms " << grp_indices.at(candidate_component).size() << std::endl;
         if ( grp_indices.at(candidate_component).size() != 1){
           candidate_components_valid = false;
           break; // these are not components, and potential complex is not a complex
@@ -164,15 +223,30 @@ namespace catnip {
 // where there is overlap, the group and index of where the overlap occurs 
   void AtomGroupContainer::assignGroupTypes(){
 
+    std::cout << "Assigning group types" << std::endl;
     std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map = mapAtomsToGroups( atom_groups_ );
+
+    std::cout << "Size of atom map " << atm_map.size() << std::endl;
     // For each atom in a group find out how many other groups share the atoms
     // First index is the group index the vector stores the other groups that
     // share atoms
     const std::map<int,std::vector<int>> grp_indices = calculateConnectedGroups(atm_map, atom_groups_ );
 
+    for ( const auto & pr : grp_indices ) {
+      std::cout << "group " << pr.first << std::endl;
+      for ( auto ind : pr.second ){
+        std::cout << "Atoms shared with group " << ind << std::endl;
+      }
+    }
     // Calculate which groups do not share atoms with other groups these are units
     identifyAtomGroupsOfUnitType(grp_indices, atom_groups_);
 
+    for ( const auto & pr : grp_indices ) {
+      std::cout << "group " << pr.first << std::endl;
+      for ( auto ind : pr.second ){
+        std::cout << "Atoms shared with group " << ind << std::endl;
+      }
+    }
     identifyAtomGroupsOfComponentComplexAndUnknownTypes(grp_indices,atom_groups_ );
   }
 
@@ -202,12 +276,12 @@ namespace catnip {
     return max_num_basis;
   }
 
-  bool AtomGroupContainer::complexExists() const {
+  bool AtomGroupContainer::exists(GroupType type) const {
     // First check that all the group types have been assigned
-    if ( group_types_uptodate_ == false ){
-      throw std::runtime_error("Cannot determine if complex exists group types are not up to date");
+    for ( const AtomGroup & grp : atom_groups_ ){
+      if( grp.getType() == type ) return true;
     }
-    return index_of_complex_ > -1;
+    return false; 
   }
 
   std::vector<AtomGroupContainer::AtomMatch> AtomGroupContainer::matchComponentAtomsToComplex_(){
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index daa4f98..d2b8b32 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -32,12 +32,13 @@ namespace catnip {
       /**
        * @brief Checks to makes sure the group is unique
        *
+       * Does not compare atom addresses just the atoms in the group the size
+       * Ignores the atom group name in the comparison
        * @param atom_group
        *
        * @return 
        */
-      bool isUniqueGroup_( AtomGroup atom_group );
-
+      bool isUniqueGroup_( const AtomGroup & atom_group ) const;
 
       /**
        * @brief Match the indices of the first atom group with any that share 
@@ -67,25 +68,18 @@ namespace catnip {
       size_t size() const noexcept { return  atom_groups_.size(); }
 
       /**
-       * @brief This algorithm determines if a complex exists
-       *
-       * This algorithm does not compare the atoms in the complex with the
-       * atoms in the components, so it is not a rigourous algorithm but should
-       * be sufficient for our purposes.
-       *
-       * Only a single atom group can be the complex
+       * @brief This algorithm assignes a group type to each each of the groups 
        */
       void assignGroupTypes();
 
       /**
-       * @brief Determine if a complex exists within the atom groups
-       *
-       * Only a single atom group can be a complex
+       * @brief Determine if a specified group type exists within the atom groups
        *
        * @return 
        */
-      bool complexExists() const;
+      bool exists(GroupType type) const;
 
+      GroupType getType(int index) const { return atom_groups_.at(index).getType(); }
       /**
        * @brief If a complex exists and we know the number of basis functions
        * associated with each atom in the complex we can assign the basis function
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index c716fbd..ee82c99 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -7,6 +7,7 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_argumentswitch
   test_atom
   test_atom_group
+  test_atom_group_container
   test_elements
   test_index_map
   test_log
diff --git a/src/tests/test_atom_group.cpp b/src/tests/test_atom_group.cpp
index 2ed81ce..34de2e4 100644
--- a/src/tests/test_atom_group.cpp
+++ b/src/tests/test_atom_group.cpp
@@ -17,7 +17,7 @@ TEST_CASE("Atom Group","[unit]") {
 
   AtomGroup atom_grp("CH2");
   
-  REQUIRE(atom_grp.getType() == GroupType::Unknown );
+  REQUIRE(atom_grp.getType() == GroupType::Unassigned );
   REQUIRE(atom_grp.getName() == "CH2");
 
   Atom atom1(Element::H, 0.0, 0.0, 0.0);
diff --git a/src/tests/test_atom_group_container.cpp b/src/tests/test_atom_group_container.cpp
index b31a3eb..d5b1dff 100644
--- a/src/tests/test_atom_group_container.cpp
+++ b/src/tests/test_atom_group_container.cpp
@@ -16,8 +16,6 @@ using namespace catnip;
 
 TEST_CASE("Atom Group Container","[unit]") {
 
-  AtomGroup atom_grp("CH2");
-  
   Atom atom1(Element::H, 0.0, 0.0, 0.0);
   Atom atom2(Element::H, 2.0, 0.0, 0.0);
   Atom atom3(Element::C, 1.0, 1.0, 0.0);
@@ -26,18 +24,18 @@ TEST_CASE("Atom Group Container","[unit]") {
   auto atom2_ptr = std::make_shared<Atom>(atom2);
   auto atom3_ptr = std::make_shared<Atom>(atom3);
 
-  atom_grp.add(atom1_ptr);
-  atom_grp.add(atom2_ptr);
-  atom_grp.add(atom3_ptr);
+  AtomGroup atom_grp1("CH2");
+  atom_grp1.add(atom1_ptr);
+  atom_grp1.add(atom2_ptr);
+  atom_grp1.add(atom3_ptr);
 
-  AtomGroup atom_grp2("O2");
-
-  Atom atom4(Element::O, 3.3, 4.3);
-  Atom atom5(Element::O, 3.0, 3.9);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
 
   auto atom4_ptr = std::make_shared<Atom>(atom4);
   auto atom5_ptr = std::make_shared<Atom>(atom5);
 
+  AtomGroup atom_grp2("O2");
   atom_grp2.add(atom4_ptr);  
   atom_grp2.add(atom5_ptr);  
 
@@ -49,4 +47,37 @@ TEST_CASE("Atom Group Container","[unit]") {
   REQUIRE(atom_grp_cont.size() == 2);
 
   atom_grp_cont.assignGroupTypes();
+
+  // Because it made a copy these should still be unassigned
+  REQUIRE(atom_grp1.getType() == GroupType::Unassigned);
+  REQUIRE(atom_grp2.getType() == GroupType::Unassigned);
+
+  // These should be changed
+  REQUIRE(atom_grp_cont.getType(0) == GroupType::Unit);
+  REQUIRE(atom_grp_cont.getType(1) == GroupType::Unit);
+  REQUIRE(atom_grp_cont.exists(GroupType::Unit));
+
+  // Now we make a third group that has all the atoms of the first two groups
+  AtomGroup atom_grp3("O2CH2");
+  atom_grp3.add(atom1_ptr);
+  atom_grp3.add(atom2_ptr);
+  atom_grp3.add(atom3_ptr);
+  atom_grp3.add(atom4_ptr);
+  atom_grp3.add(atom5_ptr);
+
+  atom_grp_cont.add(atom_grp3);
+
+  REQUIRE(atom_grp_cont.getType(0) == GroupType::Unassigned);
+  REQUIRE(atom_grp_cont.getType(1) == GroupType::Unassigned);
+  REQUIRE(atom_grp_cont.getType(2) == GroupType::Unassigned);
+  REQUIRE(atom_grp_cont.exists(GroupType::Unassigned));
+
+  atom_grp_cont.assignGroupTypes();
+  REQUIRE(atom_grp_cont.getType(0) == GroupType::Component);
+  REQUIRE(atom_grp_cont.getType(1) == GroupType::Component);
+  REQUIRE(atom_grp_cont.getType(2) == GroupType::Complex);
+
+  REQUIRE(atom_grp_cont.exists(GroupType::Complex));
+  REQUIRE(atom_grp_cont.exists(GroupType::Component));
+
 }

From 61b82171e5159f0d812f287d816a35989bac3fe0 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 18 Jul 2020 08:48:23 -0600
Subject: [PATCH 44/68] Added atom_system for handling basis functions and
 other improvements

---
 src/libcatnip/atom_group.cpp            |   4 +-
 src/libcatnip/atom_group.hpp            |  11 +-
 src/libcatnip/atom_group_container.cpp  | 275 ++++++++----------------
 src/libcatnip/atom_group_container.hpp  |  70 +++---
 src/libcatnip/atom_system.cpp           | 193 +++++++++++++++++
 src/libcatnip/atom_system.hpp           |  62 ++++++
 src/libcatnip/index_map.cpp             |  25 ++-
 src/libcatnip/index_map.hpp             |   6 +-
 src/tests/test_atom_group_container.cpp |  16 +-
 9 files changed, 408 insertions(+), 254 deletions(-)
 create mode 100644 src/libcatnip/atom_system.cpp
 create mode 100644 src/libcatnip/atom_system.hpp

diff --git a/src/libcatnip/atom_group.cpp b/src/libcatnip/atom_group.cpp
index 618bff0..dda5d71 100644
--- a/src/libcatnip/atom_group.cpp
+++ b/src/libcatnip/atom_group.cpp
@@ -7,10 +7,10 @@
 
 namespace catnip {
 
-  std::vector<int> AtomGroup::find(std::shared_ptr<Atom> atom) {
+  std::vector<int> AtomGroup::find(std::shared_ptr<Atom> atom) const {
     std::vector<int> indices;
     int index = 0;
-    for ( std::shared_ptr<Atom> & atom_ : atoms_){
+    for ( const std::shared_ptr<Atom> & atom_ : atoms_){
       if ( *atom_ == (*atom)){
         indices.push_back(index);
       }
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index db2a4d2..520b6a2 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -25,7 +25,7 @@ namespace catnip {
    *
    * Complex - all atoms in this atom group have a matching atom in a component
    *
-   * Unit - non of the atoms appear in any of the other atom groups
+   * Island - non of the atoms appear in any of the other atom groups
    *
    * Unknown - some combination, may or may not have overlapping components
    *
@@ -34,7 +34,7 @@ namespace catnip {
   enum class GroupType {
     Component, 
     Complex,
-    Unit,
+    Island,
     Unknown,
     Unassigned
   };
@@ -72,6 +72,10 @@ namespace catnip {
         return atoms_.at(ind);
       }
 
+      std::shared_ptr<Atom> & at(size_t ind) {
+        return atoms_.at(ind);
+      }
+
       void add(std::shared_ptr<Atom> atom){
         atoms_.push_back(atom);
       } 
@@ -93,8 +97,7 @@ namespace catnip {
        *
        * @return indeces of atoms that match
        */
-      std::vector<int> find(std::shared_ptr<Atom> atom);
-     
+      std::vector<int> find(std::shared_ptr<Atom> atom) const;
 
       /**
        * @brief Finds the exact matching atom in memory by looking at the address
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 8e29402..093d3ac 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -19,114 +19,18 @@
 
 namespace catnip {
 
-  void AtomGroupContainer::assignBasisFuncCountToComplex_(const std::vector<int>& complex_basis_func_count) {
-    // Cycle through the atoms in the complex and assign the correct number of
-    // basis functions
-    int index = 0; 
-    for( std::shared_ptr<Atom> & atom_ptr : atom_groups_.at(index_of_complex_) ){
-      atom_ptr->setBasisFuncCount(complex_basis_func_count.at(index));
-      index++;
-    }
-  }
-
-  // Assumes the complex atoms already have been assigned the basis functioncount
-  void AtomGroupContainer::assignBasisFuncCountToComponents_() {
-    std::vector<AtomMatch> paired_atoms = matchComponentAtomsToComplex_();
-    for ( AtomMatch atom_match : paired_atoms ) {
-      int basis_func_count = atom_groups_.at(index_of_complex_).at(atom_match.index_complex_atom)->getBasisFuncCount();
-      atom_groups_.at(atom_match.index_component).at(atom_match.index_component_atom)->setBasisFuncCount(basis_func_count);
-    } 
-  }
-
-  std::vector<int> AtomGroupContainer::getGroups(const GroupType & type) const {
-    std::vector<int> groups;
-    int ind1 = 0;
-    for( const AtomGroup & group : atom_groups_ ){
-      if( group.getType() == type){
-        groups.push_back(ind1);
-      }
-      ++ind1;
-    }
-    return groups;
-  }
-  std::unordered_map<int,int> AtomGroupContainer::matchAtoms_( 
-      const AtomGroup & grp1, const AtomGroup & grp2) const {
-  
-    std::unordered_map<int,int> paired_atoms;  
-    for ( size_t ind1 = 0; ind1 < grp1.size(); ++ind1){
-      for (size_t ind2 = 0; ind2 < grp2.size(); ++ind2){
-        if ( *(grp1.at(ind1)) == *(grp2.at(ind2)) ){
-          if ( paired_atoms.count(ind1) ) {
-            throw std::runtime_error("Atom in complex has already been paired with an atom in the component, you have two or more atoms in a component that are redundant with an atom in the complex");
-          }
-          paired_atoms[ind1] = ind2;
-          break;
-        } 
-      }
-    }
-    return paired_atoms;
-  }
-
-
-  bool AtomGroupContainer::isUniqueGroup_( const AtomGroup & atom_group ) const {
-    // Step 1 check the size of the atom group 
-    if(atom_groups_.size() == 0) return true;
-
-    for ( const AtomGroup & grp : atom_groups_ ){
-      if ( grp.size() == atom_group.size() ){
-        std::vector<bool> matchs(grp.size(),false);
-        // Determine if a match is found
-        for ( const auto & atm : atom_group ) {
-          size_t index = 0;
-          for ( bool matched : matchs ){
-            if ( not matched ){
-              // Compare atoms 
-              if ( *atm == *(grp.at(index)) ){
-                matchs.at(index) = true;
-                break;
-              }
-            } 
-            ++index;
-          }
-          // If an atom was not matched it means that there is at least one 
-          // difference, and so we do not need to cycle through the other
-          // atoms in this particular group 
-          if(index == grp.size()) break;
-        } 
-        // Count the number of matches in the vector if all of the elements match
-        // then the atom group is not unique
-        for ( bool match : matchs ) {
-          if ( match == false ) break;
-        } 
-        return false;
-      }
-    }
-    return true;
-  }
-  // As soon as we add a new atom group it should invalidate the labels on 
-  // all the other groups
-  void AtomGroupContainer::add( AtomGroup atom_group ) {
-    std::cout << "Adding group " << atom_group.getName() << std::endl; 
-    if( isUniqueGroup_(atom_group) ){
-      std::cout << "Is unique" << std::endl;
-      atom_groups_.push_back(atom_group);
-    } else {
-      return;
-    }
-
-    for ( AtomGroup & grp : atom_groups_ ){
-      grp.setType(GroupType::Unassigned);
-    }
-    group_types_uptodate_ = false;
-    index_of_complex_ = -1;
-  }
-
+  /****************************************************************************
+   * Local private structs
+   ****************************************************************************/
   struct GroupAtomIndex {
     int atm_ind;
     int grp_ind; 
   };
 
-  static std::unordered_map<Atom,std::vector<GroupAtomIndex>> mapAtomsToGroups(
+  /****************************************************************************
+   * Local private functions
+   ****************************************************************************/
+  static std::unordered_map<Atom,std::vector<GroupAtomIndex>> mapAtomsToGroups_(
       const std::vector<AtomGroup> & atom_groups_ ){
 
     std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map;
@@ -142,7 +46,7 @@ namespace catnip {
     return atm_map;
   }
 
-  static const std::map<int,std::vector<int>> calculateConnectedGroups(
+  static const std::map<int,std::vector<int>> calculateConnectedGroups_(
       std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map,
       const std::vector<AtomGroup> & atom_groups_ 
       ){
@@ -172,19 +76,19 @@ namespace catnip {
     return grp_indices;
   }
 
-  static void identifyAtomGroupsOfUnitType(
+  static void identifyAtomGroupsOfIslandType_(
       const std::map<int,std::vector<int>> & grp_indices,
       std::vector<AtomGroup> & atom_groups_ 
       ) {
     for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
       if(grp_groups.second.size() == 0) {
         std::cout << "Empty makeing unit, does not share atoms" << std::endl;
-        atom_groups_.at(grp_groups.first).setType(GroupType::Unit);
+        atom_groups_.at(grp_groups.first).setType(GroupType::Island);
       }
     }
   }
 
-  static void identifyAtomGroupsOfComponentComplexAndUnknownTypes(
+  static void identifyAtomGroupsOfComponentComplexAndUnknownTypes_(
       const std::map<int,std::vector<int>> & grp_indices,
       std::vector<AtomGroup> & atom_groups_ 
       ){
@@ -219,61 +123,93 @@ namespace catnip {
       }
     }
   }
-// Create a map with an atom as the key and a vector of indices to indicate 
-// where there is overlap, the group and index of where the overlap occurs 
-  void AtomGroupContainer::assignGroupTypes(){
 
-    std::cout << "Assigning group types" << std::endl;
-    std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map = mapAtomsToGroups( atom_groups_ );
-
-    std::cout << "Size of atom map " << atm_map.size() << std::endl;
-    // For each atom in a group find out how many other groups share the atoms
-    // First index is the group index the vector stores the other groups that
-    // share atoms
-    const std::map<int,std::vector<int>> grp_indices = calculateConnectedGroups(atm_map, atom_groups_ );
+  /****************************************************************************
+   * Private Methods
+   ****************************************************************************/
+  bool AtomGroupContainer::isUniqueGroup_( const AtomGroup & atom_group ) const {
+    // Step 1 check the size of the atom group 
+    if(atom_groups_.size() == 0) return true;
 
-    for ( const auto & pr : grp_indices ) {
-      std::cout << "group " << pr.first << std::endl;
-      for ( auto ind : pr.second ){
-        std::cout << "Atoms shared with group " << ind << std::endl;
+    for ( const AtomGroup & grp : atom_groups_ ){
+      if ( grp.size() == atom_group.size() ){
+        std::vector<bool> matchs(grp.size(),false);
+        // Determine if a match is found
+        for ( const auto & atm : atom_group ) {
+          size_t index = 0;
+          for ( bool matched : matchs ){
+            if ( not matched ){
+              // Compare atoms 
+              if ( *atm == *(grp.at(index)) ){
+                matchs.at(index) = true;
+                break;
+              }
+            } 
+            ++index;
+          }
+          // If an atom was not matched it means that there is at least one 
+          // difference, and so we do not need to cycle through the other
+          // atoms in this particular group 
+          if(index == grp.size()) break;
+        } 
+        // Count the number of matches in the vector if all of the elements match
+        // then the atom group is not unique
+        for ( bool match : matchs ) {
+          if ( match == false ) break;
+        } 
+        return false;
       }
     }
-    // Calculate which groups do not share atoms with other groups these are units
-    identifyAtomGroupsOfUnitType(grp_indices, atom_groups_);
+    return true;
+  }
 
-    for ( const auto & pr : grp_indices ) {
-      std::cout << "group " << pr.first << std::endl;
-      for ( auto ind : pr.second ){
-        std::cout << "Atoms shared with group " << ind << std::endl;
+  /****************************************************************************
+   * Public Methods
+   ****************************************************************************/
+
+  std::vector<int> AtomGroupContainer::getGroups(const GroupType & type) const noexcept{
+    std::vector<int> groups;
+    int ind1 = 0;
+    for( const AtomGroup & group : atom_groups_ ){
+      if( group.getType() == type){
+        groups.push_back(ind1);
       }
+      ++ind1;
     }
-    identifyAtomGroupsOfComponentComplexAndUnknownTypes(grp_indices,atom_groups_ );
+    return groups;
   }
 
-  int AtomGroupContainer::getTotalBasisFunctions(const GroupType & type) const {
-    int total_num_basis = 0;
-    std::vector<int> group_indices = getGroups(type);     
-    for ( int ind : group_indices ){
-      AtomGroup group = atom_groups_.at(ind);
-      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
-        total_num_basis += atom_ptr->getBasisFuncCount();
-      }
-    } 
-    return total_num_basis;
+  // As soon as we add a new atom group it should invalidate the labels on 
+  // all the other groups
+  void AtomGroupContainer::add( AtomGroup atom_group ) {
+    std::cout << "Adding group " << atom_group.getName() << std::endl; 
+    if( isUniqueGroup_(atom_group) ){
+      std::cout << "Is unique" << std::endl;
+      atom_groups_.push_back(atom_group);
+    } else {
+      return;
+    }
+
+    group_types_uptodate_ = false;
   }
 
-  int AtomGroupContainer::getMaxBasisFunctions(const GroupType & type) const {
-    int max_num_basis = 0;
-    std::vector<int> group_indices = getGroups(type);     
-    for ( int ind : group_indices ){
-      AtomGroup group = atom_groups_.at(ind);
-      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
-        if( atom_ptr->getBasisFuncCount() > max_num_basis){
-          max_num_basis = atom_ptr->getBasisFuncCount();
-        }
-      }
-    } 
-    return max_num_basis;
+// Create a map with an atom as the key and a vector of indices to indicate 
+// where there is overlap, the group and index of where the overlap occurs 
+  void AtomGroupContainer::assignGroupTypes(){
+
+    // If already uptodate do nothing
+    if( group_types_uptodate_ ) return;
+    std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map = mapAtomsToGroups_( atom_groups_ );
+
+    // For each atom in a group find out how many other groups share the atoms
+    // First index is the group index the vector stores the other groups that
+    // share atoms
+    const std::map<int,std::vector<int>> grp_indices = calculateConnectedGroups_(atm_map, atom_groups_ );
+
+    // Calculate which groups do not share atoms with other groups these are units
+    identifyAtomGroupsOfIslandType_(grp_indices, atom_groups_);
+
+    identifyAtomGroupsOfComponentComplexAndUnknownTypes_(grp_indices,atom_groups_ );
   }
 
   bool AtomGroupContainer::exists(GroupType type) const {
@@ -284,41 +220,4 @@ namespace catnip {
     return false; 
   }
 
-  std::vector<AtomGroupContainer::AtomMatch> AtomGroupContainer::matchComponentAtomsToComplex_(){
-
-    AtomGroup complex_group = atom_groups_.at(index_of_complex_);
-    std::vector<int> component_indices = getGroups(GroupType::Component);
-    std::vector<AtomMatch> all_paired_atoms;
-    for ( const int & component_index : component_indices ) {
-      std::unordered_map<int,int> paired_atoms = matchAtoms_(complex_group,atom_groups_.at(component_index));
-      // Pass to vector
-      for ( auto pr : paired_atoms ){
-        AtomMatch atom_match;
-        atom_match.index_component = component_index;
-        atom_match.index_component_atom = pr.second;
-        atom_match.index_complex_atom = pr.first;
-        all_paired_atoms.push_back(atom_match);
-      }
-    }
-    return all_paired_atoms;
-  }
-
-  void AtomGroupContainer::assignBasisFunctions(
-      const std::vector<int>& complex_basis_func_count) {
-
-    // 1. Check that up to date
-    if ( group_types_uptodate_ == false ){
-      throw std::runtime_error("Cannot assign basis functions to atoms as group types are not up to date!");
-    }
-    // 2. Check that the number of atoms in the complex is consistent with the number of values provided
-    if ( complex_basis_func_count.size() != atom_groups_.at(index_of_complex_).size() ){
-      throw std::runtime_error("Cannot assign basis function count to atoms as the basis function count vector is not equal to the number of atoms!");
-    }
-
-    assignBasisFuncCountToComplex_(complex_basis_func_count);
-    assignBasisFuncCountToComponents_();
-    
-  }
-
-   
 }  // namespace catnip
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index d2b8b32..c57fb0b 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -19,11 +19,13 @@
 
 namespace catnip {
 
-  class Atom;
-
-  /// What we need is a function that will actually create the atom group
-  /// container so that the state is known, basically you need to pass in the
-  /// a vector of the atom groups
+  /**
+   * @brief Allows auto detection of atom groups
+   *
+   * What this means is that if you pass in atom groups and thier state is not
+   * known, this class can automatically detect if they are related, if they
+   * are an island a complex or a component.
+   */
   class AtomGroupContainer {
       std::vector<AtomGroup> atom_groups_;
      
@@ -40,29 +42,25 @@ namespace catnip {
        */
       bool isUniqueGroup_( const AtomGroup & atom_group ) const;
 
-      /**
-       * @brief Match the indices of the first atom group with any that share 
-       * coordinates and the same element in atom group 2
-       *
-       * @param grp1
-       * @param grp2
-       *
-       * @return map returns indices in group two that match group 1 
-       */
-      std::unordered_map<int,int> matchAtoms_( const AtomGroup & grp1, const AtomGroup & grp2) const;
 
-      void assignBasisFuncCountToComplex_(const std::vector<int>& complex_basis_func_count);
-      void assignBasisFuncCountToComponents_();
+    public: 
+
+      // Invalidates groups if non const because cannot ensure that groups are
+      // not changed
+      std::vector<AtomGroup>::iterator 
+        begin() { group_types_uptodate_ = false; return atom_groups_.begin(); }
 
-      struct AtomMatch {
-        int index_component;
-        int index_component_atom;
-        int index_complex_atom;
-      };
+      std::vector<AtomGroup>::const_iterator 
+        begin() const { return atom_groups_.begin(); }
+
+      // Invalidates groups if non const because cannot ensure that groups are
+      // not changed
+      std::vector<AtomGroup>::iterator 
+        end() { group_types_uptodate_ = false; return atom_groups_.end(); }
+ 
+      std::vector<AtomGroup>::const_iterator 
+        end() const { return atom_groups_.end(); }
 
-      std::vector<AtomMatch> matchComponentAtomsToComplex_();
-      int index_of_complex_ = -1;
-    public: 
       void add( AtomGroup atom_group );
 
       size_t size() const noexcept { return  atom_groups_.size(); }
@@ -72,6 +70,8 @@ namespace catnip {
        */
       void assignGroupTypes();
 
+      bool isUpToDate() const noexcept { return group_types_uptodate_; }
+
       /**
        * @brief Determine if a specified group type exists within the atom groups
        *
@@ -80,18 +80,7 @@ namespace catnip {
       bool exists(GroupType type) const;
 
       GroupType getType(int index) const { return atom_groups_.at(index).getType(); }
-      /**
-       * @brief If a complex exists and we know the number of basis functions
-       * associated with each atom in the complex we can assign the basis function
-       * number to each of the atoms
-       *
-       * @param complex_basis_func_count
-       */
-      void assignBasisFunctions(const std::vector<int>& complex_basis_func_count);
-
-      int getTotalBasisFunctions(const GroupType & type) const;
 
-      int getMaxBasisFunctions(const GroupType & type) const;
       /**
        * @brief Get the indices of all the groups of the specified group type
        *
@@ -99,9 +88,14 @@ namespace catnip {
        *
        * @return 
        */
-      std::vector<int> getGroups(const GroupType & type) const;     
+      std::vector<int> getGroups(const GroupType & type) const noexcept;     
+
+      AtomGroup & at(size_t ind) { 
+        group_types_uptodate_ = false; 
+        return atom_groups_.at(ind);
+      }
 
-      AtomGroup & at(size_t ind) { return  atom_groups_.at(ind);}
+      const AtomGroup & at(size_t ind) const { return   atom_groups_.at(ind);}
   };
 
   
diff --git a/src/libcatnip/atom_system.cpp b/src/libcatnip/atom_system.cpp
new file mode 100644
index 0000000..66095d3
--- /dev/null
+++ b/src/libcatnip/atom_system.cpp
@@ -0,0 +1,193 @@
+
+// Local private includes 
+#include "atom_system.hpp"
+
+#include "atom.hpp"
+
+// Standard includes
+#include <memory>
+#include <vector>
+
+namespace catnip {
+
+  /****************************************************************************
+   * Local private structs
+   ****************************************************************************/
+/*  struct AtomMatch {
+    int index_component;
+    int index_component_atom;
+    int index_complex_atom;
+  };*/
+
+  /****************************************************************************
+   * Local private functions
+   ****************************************************************************/
+  
+  static void assignBasisFuncs_(
+      int grp_ind,
+      const std::vector<int>& basis_func_count,
+      AtomGroupContainer & atm_grp_cont) {
+    // Cycle through the atoms in the complex and assign the correct number of
+    // basis functions
+    int index = 0; 
+    for( std::shared_ptr<Atom> & atom_ptr : atm_grp_cont.at(grp_ind) ){
+      if( atom_ptr->getBasisFuncCount() == -1){
+        atom_ptr->setBasisFuncCount(basis_func_count.at(index));
+      } else if(atom_ptr->getBasisFuncCount() != basis_func_count.at(index) ){
+        // Make sure the new assignment is consistent with the old one
+        // if not throw an error, because you have a conflicting number of basis
+        // functions between groups
+        throw std::runtime_error("Inconsistency detected in the number of "
+            "basis functions detected between atom groups. Ensure that the "
+            "basis function count vector is in a consistent order with the "
+            "atoms in the atom group");
+      }
+      index++;
+    }
+  }
+/*
+  static std::vector<AtomMatch> matchComponentAtomsToComplex_(){
+
+    AtomGroup complex_group = atom_groups_.at(index_of_complex_);
+    std::vector<int> component_indices = getGroups(GroupType::Component);
+    std::vector<AtomMatch> all_paired_atoms;
+    for ( const int & component_index : component_indices ) {
+      std::unordered_map<int,int> paired_atoms = matchAtoms_(complex_group,atom_groups_.at(component_index));
+      // Pass to vector
+      for ( auto pr : paired_atoms ){
+        AtomMatch atom_match;
+        atom_match.index_component = component_index;
+        atom_match.index_component_atom = pr.second;
+        atom_match.index_complex_atom = pr.first;
+        all_paired_atoms.push_back(atom_match);
+      }
+    }
+    return all_paired_atoms;
+  }*/
+
+  static void checkValidSystemCriteria_(AtomGroupContainer & atm_grp_cont){
+    std::vector<int> complex_indices = 
+      atm_grp_cont.getGroups(GroupType::Complex);
+
+    if( complex_indices.size() == 0 ){
+      throw std::runtime_error("Cannot create atom system, no complexes were "
+          "found in the atom group container.");
+    } else if( complex_indices.size() > 1 ){
+      throw std::runtime_error("Cannot create atom system, several complexes "
+          "were found in the atom group. The atom system can only contain a "
+          "single complex.");
+    }
+
+    std::vector<int> component_indices = 
+      atm_grp_cont.getGroups(GroupType::Component);
+
+    if ( component_indices.size() < 2){
+      throw std::runtime_error("Cannot create atom system, must contain at "
+          "least two components"); 
+    }
+  }
+
+  static void synchroniseAtoms_(AtomGroupContainer & atm_grp_cont){
+
+    // Overwrite any of the pointers in the component that have the same atom
+    // with the complex, with the atom pointer from the complex
+    int complex_index = 
+      atm_grp_cont.getGroups(GroupType::Complex).at(0);
+
+    std::vector<int> component_indices = 
+      atm_grp_cont.getGroups(GroupType::Component);
+
+    AtomGroup & atm_complex = atm_grp_cont.at(complex_index);
+    for ( const int component_ind : component_indices){
+      AtomGroup & atm_grp = atm_grp_cont.at(component_ind);
+      // Cycle atoms in atm_grp 
+      for ( std::shared_ptr<Atom> & atm : atm_grp){
+        std::vector<int> complex_atm_ind = atm_complex.find(atm);
+        // This vector should be 0 or 1
+        if( complex_atm_ind.size() == 1){
+          // Change the pointer
+          atm = atm_complex.at(complex_atm_ind.at(0)); 
+        }
+      }
+    }
+  }
+  /****************************************************************************
+   * Public Methods
+   ****************************************************************************/
+
+  /**
+   * @brief Creates an atom system if possible
+   *
+   * The criteria to create an atom system is that the AtomGroupContainer must
+   * contain only a single complex and the components that belong to that
+   * complex
+   *
+   * @param atm_grp_cont
+   */
+  AtomSystem::AtomSystem(AtomGroupContainer atm_grp_cont) {
+    atm_grp_cont.assignGroupTypes();
+
+    checkValidSystemCriteria_(atm_grp_cont);
+
+    // Make atoms consistent between components and the complex, this is done
+    // by making atoms that share the same location point to the same place
+    // in memory
+    synchroniseAtoms_(atm_grp_cont);
+
+    atm_grp_cont_ = atm_grp_cont;
+  }
+
+  int AtomSystem::getTotalBasisFunctions(const GroupType & type) const {
+    int total_num_basis = 0;
+    std::vector<int> group_indices = atm_grp_cont_.getGroups(type);     
+    for ( int ind : group_indices ){
+      const AtomGroup & group = atm_grp_cont_.at(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+        total_num_basis += atom_ptr->getBasisFuncCount();
+      }
+    } 
+    return total_num_basis;
+  }
+
+  int AtomSystem::getMaxBasisFunctions(const GroupType & type) const {
+    int max_num_basis = 0;
+    std::vector<int> group_indices = atm_grp_cont_.getGroups(type);     
+    for ( int ind : group_indices ){
+      const AtomGroup & group = atm_grp_cont_.at(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+        if( atom_ptr->getBasisFuncCount() > max_num_basis){
+          max_num_basis = atom_ptr->getBasisFuncCount();
+        }
+      }
+    } 
+    return max_num_basis;
+  }
+
+
+  void AtomSystem::assignBasisFunctions(int index, 
+      const std::vector<int>& basis_func_count) {
+
+    // 2. Check that the number of atoms in the grp is consistent with 
+    // the number of values provided
+    if ( basis_func_count.size() != atm_grp_cont_.at(index).size() ){
+      throw std::runtime_error("Cannot assign basis function count to atoms "
+          "as the basis function count vector is not equal to the number of "
+          "atoms in the group!");
+    }
+
+    assignBasisFuncs_(index, basis_func_count, atm_grp_cont_);
+  }
+
+  bool AtomSystem::systemComplete() const noexcept {
+    for ( const AtomGroup & grp : atm_grp_cont_){
+      for( const std::shared_ptr<Atom> & atm : grp){
+        if(atm->getBasisFuncCount() == -1) return false;
+      }
+    }
+    return true;
+  }
+
+  const AtomGroup & AtomSystem::at(int ind) const {
+    return atm_grp_cont_.at(ind); 
+  }
+}
diff --git a/src/libcatnip/atom_system.hpp b/src/libcatnip/atom_system.hpp
new file mode 100644
index 0000000..65ae8f4
--- /dev/null
+++ b/src/libcatnip/atom_system.hpp
@@ -0,0 +1,62 @@
+
+#pragma once
+#ifndef CATNIP_ATOM_SYSTEM_HPP
+#define CATNIP_ATOM_SYSTEM_HPP
+#include "atom_group_container.hpp"
+
+namespace catnip {
+
+  /**
+   * @brief Unlike atom group container, this atom system does not allow to 
+   * change group types
+   *
+   * It can only be created if there are known group types and there is only
+   * a single complex, and it's components
+   */
+  class AtomSystem {
+
+      AtomGroupContainer atm_grp_cont_;    
+    public:
+
+      AtomSystem(AtomGroupContainer atm_cont);
+
+      /**
+       * @brief assign basis functions to atom group 
+       *
+       * @param complex_basis_func_count
+       */
+      void assignBasisFunctions(int index, const std::vector<int>& basis_funcs);
+
+      /**
+       * @brief Determine if there is a conflict between the basis functions
+       * you are attempting to assign and the currently assigned basis functions
+       *
+       * This is done by comparing the basis functions on atoms that shared
+       * between atom groups.
+       *
+       * @param index
+       * @param basis_funcs
+       *
+       * @return 
+       */
+      bool conflictBasisFunctions(int index, const std::vector<int> & basis_funcs) const; 
+
+      int getTotalBasisFunctions(const GroupType & type) const;
+
+      int getMaxBasisFunctions(const GroupType & type) const;
+
+      const AtomGroup & getComplex() const;       
+      std::vector<int> getComponentIndices() const noexcept { atm_grp_cont_.getGroups(GroupType::Component);}
+      const AtomGroup & at(int ind) const;       
+      /**
+       * @brief Check that every atom knows how many basis functions are
+       * assigned to it
+       *
+       * @return 
+       */
+      bool systemComplete() const noexcept;
+  }
+
+};
+
+#endif // CATNIP_ATOM_SYSTEM_HPP
diff --git a/src/libcatnip/index_map.cpp b/src/libcatnip/index_map.cpp
index 3d4ad28..c6a132d 100644
--- a/src/libcatnip/index_map.cpp
+++ b/src/libcatnip/index_map.cpp
@@ -10,21 +10,20 @@
 
 namespace catnip {
 
-  IndexMap::IndexMap(AtomGroupContainer atom_groups){
-    std::vector<int> group_indices = atom_groups.getGroups(GroupType::Component);
-    int complex_ind = atom_groups.getGroups(GroupType::Complex).at(0);
-    AtomGroup complex_group = atom_groups.at(complex_ind);
+  IndexMap::IndexMap(AtomSystem atm_sys){
+    std::vector<int> comp_indices = atm_sys.getComponentIndices();
+    const AtomGroup & complex_grp = atm_sys.getComplex();
     int sys_ind = 0;
-    for ( int & group_ind : group_indices) {
-      AtomGroup component_group = atom_groups.at(group_ind);
-      for( std::shared_ptr<Atom> & atom : component_group){
-        std::vector<int> atom_indices = complex_group.find(atom);
-        assert(atom_indices.size() == 1);
-        int atom_ind = atom_indices.at(0);
-        int num_basis = complex_group.at(atom_ind)->getBasisFuncCount();
+    for ( int & comp_ind : comp_indices) {
+      const AtomGroup & comp_grp = atm_sys.at(comp_ind);
+      for( const std::shared_ptr<Atom> & atm_ptr : comp_grp){
+        std::vector<int> atm_indices = complex_grp.find(atm_ptr);
+        assert(atm_indices.size() == 1);
+        int atm_ind = atm_indices.at(0);
+        int num_basis = comp_grp.at(atm_ind)->getBasisFuncCount();
         for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
-          row_col_final[group_ind].push_back(sys_ind); 
-          row_col_init[group_ind].push_back(atom_ind);
+          row_col_final[comp_ind].push_back(sys_ind); 
+          row_col_init[comp_ind].push_back(atm_ind);
           sys_ind++;
         }
       }
diff --git a/src/libcatnip/index_map.hpp b/src/libcatnip/index_map.hpp
index 51b50b5..6bdb530 100644
--- a/src/libcatnip/index_map.hpp
+++ b/src/libcatnip/index_map.hpp
@@ -4,7 +4,7 @@
 #define _CATNIP_INDEX_MAP_HPP
 
 // Local private includes
-#include "atom_group_container.hpp"
+#include "atom_system.hpp"
 
 // Standard includes
 #include <map>
@@ -15,13 +15,13 @@ namespace catnip {
   class IndexMap {
     public:
       IndexMap() = default;
-      IndexMap(AtomGroupContainer atom_groups);
+      IndexMap(AtomSystem atm_sys);
       // The component rows and colums in their current locations in  
       // in the full system matrix of the complex
       std::map<int,std::vector<int>> row_col_init;
 
       // Map indicate where the rows and cols should go in the final state
-      // Each int in the vector represents the locatin in the full system matrix
+      // Each int in the vector represents the location in the full system matrix
       std::map<int,std::vector<int>> row_col_final;
 
       // Searches the init row for the provided row and returns the group it is
diff --git a/src/tests/test_atom_group_container.cpp b/src/tests/test_atom_group_container.cpp
index d5b1dff..db95cea 100644
--- a/src/tests/test_atom_group_container.cpp
+++ b/src/tests/test_atom_group_container.cpp
@@ -46,16 +46,20 @@ TEST_CASE("Atom Group Container","[unit]") {
 
   REQUIRE(atom_grp_cont.size() == 2);
 
-  atom_grp_cont.assignGroupTypes();
+  REQUIRE(atom_grp_cont.getType(0) == GroupType::Unassigned);
+  REQUIRE(atom_grp_cont.getType(1) == GroupType::Unassigned);
+  REQUIRE(atom_grp_cont.isUpToDate() == false);
 
+  atom_grp_cont.assignGroupTypes();
+  REQUIRE(atom_grp_cont.isUpToDate() == true);
   // Because it made a copy these should still be unassigned
   REQUIRE(atom_grp1.getType() == GroupType::Unassigned);
   REQUIRE(atom_grp2.getType() == GroupType::Unassigned);
 
   // These should be changed
-  REQUIRE(atom_grp_cont.getType(0) == GroupType::Unit);
-  REQUIRE(atom_grp_cont.getType(1) == GroupType::Unit);
-  REQUIRE(atom_grp_cont.exists(GroupType::Unit));
+  REQUIRE(atom_grp_cont.getType(0) == GroupType::Island);
+  REQUIRE(atom_grp_cont.getType(1) == GroupType::Island);
+  REQUIRE(atom_grp_cont.exists(GroupType::Island));
 
   // Now we make a third group that has all the atoms of the first two groups
   AtomGroup atom_grp3("O2CH2");
@@ -66,13 +70,13 @@ TEST_CASE("Atom Group Container","[unit]") {
   atom_grp3.add(atom5_ptr);
 
   atom_grp_cont.add(atom_grp3);
+  REQUIRE(atom_grp_cont.isUpToDate() == false);
 
-  REQUIRE(atom_grp_cont.getType(0) == GroupType::Unassigned);
-  REQUIRE(atom_grp_cont.getType(1) == GroupType::Unassigned);
   REQUIRE(atom_grp_cont.getType(2) == GroupType::Unassigned);
   REQUIRE(atom_grp_cont.exists(GroupType::Unassigned));
 
   atom_grp_cont.assignGroupTypes();
+  REQUIRE(atom_grp_cont.isUpToDate() == true);
   REQUIRE(atom_grp_cont.getType(0) == GroupType::Component);
   REQUIRE(atom_grp_cont.getType(1) == GroupType::Component);
   REQUIRE(atom_grp_cont.getType(2) == GroupType::Complex);

From 7c4ac40a6c28e392f215e6afc9cdbb3cae5c2d8c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sun, 19 Jul 2020 18:17:35 -0600
Subject: [PATCH 45/68] Make handling of basis function assignment more
 refined, and add checks

---
 src/libcatnip/atom_group.cpp  |  12 +++
 src/libcatnip/atom_group.hpp  |  14 ++++
 src/libcatnip/atom_system.cpp | 152 ++++++++++++++++++++++++++++++++--
 src/libcatnip/atom_system.hpp |  25 ++++--
 4 files changed, 191 insertions(+), 12 deletions(-)

diff --git a/src/libcatnip/atom_group.cpp b/src/libcatnip/atom_group.cpp
index dda5d71..b910eab 100644
--- a/src/libcatnip/atom_group.cpp
+++ b/src/libcatnip/atom_group.cpp
@@ -7,6 +7,18 @@
 
 namespace catnip {
 
+  std::vector<int> AtomGroup::find(const Eigen::Vector3d pos) const {
+    std::vector<int> indices;
+    int index = 0;
+    for ( const std::shared_ptr<Atom> & atom_ : atoms_){
+      if ( atom_->getPos().isApprox( pos )){
+        indices.push_back(index);
+      }
+      ++index;
+    }
+    return indices;
+  }
+
   std::vector<int> AtomGroup::find(std::shared_ptr<Atom> atom) const {
     std::vector<int> indices;
     int index = 0;
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 520b6a2..badacf3 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -84,6 +84,10 @@ namespace catnip {
         atoms_.insert(atoms_.end(),atoms.begin(),atoms.end());
       } 
 
+      bool is(const GroupType & type) const noexcept {
+        return type == type_; 
+      }
+
       void setType(const GroupType & type) noexcept {
         type_ = type;
       }
@@ -99,6 +103,16 @@ namespace catnip {
        */
       std::vector<int> find(std::shared_ptr<Atom> atom) const;
 
+      /**
+       * @brief Find the index of the atom in the group if it shares the provided
+       * position  
+       *
+       * @param pos
+       *
+       * @return indeces of atoms that match the position
+       */
+      std::vector<int> find(const Eigen::Vector3d pos) const;
+
       /**
        * @brief Finds the exact matching atom in memory by looking at the address
        *
diff --git a/src/libcatnip/atom_system.cpp b/src/libcatnip/atom_system.cpp
index 66095d3..d2ed4e1 100644
--- a/src/libcatnip/atom_system.cpp
+++ b/src/libcatnip/atom_system.cpp
@@ -22,15 +22,15 @@ namespace catnip {
   /****************************************************************************
    * Local private functions
    ****************************************************************************/
-  
-  static void assignBasisFuncs_(
-      int grp_ind,
+
+  static AtomGroup & assignBasisFunctionsToSynchronisedAtoms_(
+      int grp_ind, 
       const std::vector<int>& basis_func_count,
-      AtomGroupContainer & atm_grp_cont) {
-    // Cycle through the atoms in the complex and assign the correct number of
-    // basis functions
+      AtomGroup & grp,
+      AtomGroupContainer & atm_grp_cont ){
+
     int index = 0; 
-    for( std::shared_ptr<Atom> & atom_ptr : atm_grp_cont.at(grp_ind) ){
+    for( std::shared_ptr<Atom> & atom_ptr : grp ){
       if( atom_ptr->getBasisFuncCount() == -1){
         atom_ptr->setBasisFuncCount(basis_func_count.at(index));
       } else if(atom_ptr->getBasisFuncCount() != basis_func_count.at(index) ){
@@ -44,6 +44,95 @@ namespace catnip {
       }
       index++;
     }
+
+  }
+
+  static void checkLinkedAtomsInComplexForConsistentBasisFunctionCounts(
+      int grp_ind, 
+      const AtomGroup & grp,
+      AtomGroupContainer & atm_grp_cont,
+      std::map<int,std::vector<std::pair<int,int>>> linked_atoms ){
+
+    for ( auto grp_linked_atms : linked_atoms ){ 
+      const AtomGroup & component = atm_grp_cont.at(grp_linked_atms.first);
+      for( std::pair<int,int> linked_atoms : grp_linked_atms.second ){
+        if ( component.at(linked_atoms.first)->getBasisFuncCount() != -1){
+          if ( component.at(linked_atoms.first)->getBasisFuncCount() != grp.at(linked_atoms.second)->getBasisFuncCount()){
+            throw std::runtime_error("There are inconsistencies between the "
+                "the number of basis functions used in a linked atom. Atoms "
+                "in a component must contain the same number of basis "
+                "functions as thier linked atoms in the complex");
+          }
+        }  
+      }
+    }
+  }
+
+  static void checkLinkedAtomsInComponentForConsistentBasisFunctionCounts(
+      int grp_ind, 
+      const AtomGroup & grp,
+      AtomGroupContainer & atm_grp_cont,
+      std::map<int,std::vector<std::pair<int,int>>> linked_atoms 
+      ) {
+
+    std::vector<int> complex_grps = atm_grp_cont.getGroups(GroupType::Complex);
+    assert(complex_grps.size() == 1 && "There must be at least one complex");
+    const AtomGroup & complex_grp = atm_grp_cont.at(complex_grps.at(0));
+    for( std::pair<int,int> linked_atoms : linked_atoms[grp_ind] ){
+      if ( complex_grp.at(linked_atoms.first)->getBasisFuncCount() != -1){
+        if ( complex_grp.at(linked_atoms.first)->getBasisFuncCount() != grp.at(linked_atoms.second)->getBasisFuncCount()){
+          throw std::runtime_error("There are inconsistencies between the "
+              "the number of basis functions used in a linked atom. Atoms "
+              "in a component must contain the same number of basis "
+              "functions as thier linked atoms in the complex");
+        }
+      }
+    }
+  }
+
+  /**
+   * @brief Assigns basis function to atoms in group
+   *
+   * This fucntions should only be called after the atoms have been syncrhonized
+   * between atom groups
+   *
+   * @param grp_ind
+   * @param basis_func_count
+   * @param atm_grp_cont
+   */
+  static void assignBasisFuncs_(
+      int grp_ind,
+      const std::vector<int>& basis_func_count,
+      AtomGroupContainer & atm_grp_cont,
+      std::map<int,std::vector<std::pair<int,int>>> linked_atoms 
+      ) {
+    // Cycle through the atoms in the complex and assign the correct number of
+    // basis functions
+  
+    AtomGroup & grp = atm_grp_cont.at(grp_ind);
+
+    assignBasisFunctionsToSynchronisedAtoms_(
+      grp_ind, 
+      basis_func_count,
+      grp,
+      atm_grp_cont);
+    // Make sure that there are no inconsistencies between the linked atoms
+    if ( atm_grp_cont.at(grp_ind).is(GroupType::Complex)){
+      // If it is a complex
+      checkLinkedAtomsInComplexForConsistentBasisFunctionCounts(
+          grp_ind, 
+          grp,
+          atm_grp_cont,
+          linked_atoms);
+
+    }else {
+      // If it is a component
+      checkLinkedAtomsInComponentForConsistentBasisFunctionCounts(
+          grp_ind, 
+          grp,
+          atm_grp_cont,
+          linked_atoms);
+    }
   }
 /*
   static std::vector<AtomMatch> matchComponentAtomsToComplex_(){
@@ -87,6 +176,51 @@ namespace catnip {
     }
   }
 
+  // Map 
+  // first int - index of the group
+  // first int of the pair - index of the atom in the component
+  // second int of the pair - index of the linked atom in the complex 
+  static std::map<int,std::vector<std::pair<int,int>>> findNonConsistentAtoms_(
+      AtomGroupContainer & atm_grp_cont) {
+
+    std::map<int,std::vector<std::pair<int,int>>> linked_atoms;
+    // Overwrite any of the pointers in the component that have the same atom
+    // with the complex, with the atom pointer from the complex
+    int complex_index = 
+      atm_grp_cont.getGroups(GroupType::Complex).at(0);
+
+    std::vector<int> component_indices = 
+      atm_grp_cont.getGroups(GroupType::Component);
+
+    AtomGroup & atm_complex = atm_grp_cont.at(complex_index);
+    for ( const int component_ind : component_indices){
+      AtomGroup & atm_grp = atm_grp_cont.at(component_ind);
+      // Cycle atoms in atm_grp 
+      int ind_atm = 0;
+      for ( std::shared_ptr<Atom> & atm : atm_grp){
+        std::vector<int> complex_atm_ind = atm_complex.find(atm->getPos());
+        // This vector must be of size 1
+        if( complex_atm_ind.size() == 1){
+          // If the elements dont' match it is non-consistent 
+          if( atm_complex.at(complex_atm_ind.at(0))->getElement() != atm_grp.at(ind_atm)->getElement() ){
+            linked_atoms[component_ind].push_back(std::pair<int,int>(ind_atm,complex_atm_ind.at(0)));
+          }
+        }else if (complex_atm_ind.size() == 0) {
+          throw std::runtime_error("A component atom did not have a matching "
+              "atom in the complex. The component atom does not have to have "
+              "the same element as the atom in the complex bust must share "
+              "the same position.");
+        } else {
+          throw std::runtime_error("A component atom matches more than a single"
+             " atom in the complex. There appears to be a problem with the "
+             "complex, as more than one atom occupies the same location.");
+        }
+        ++ind_atm;
+      }
+    }
+    return linked_atoms;
+  }
+
   static void synchroniseAtoms_(AtomGroupContainer & atm_grp_cont){
 
     // Overwrite any of the pointers in the component that have the same atom
@@ -129,6 +263,10 @@ namespace catnip {
 
     checkValidSystemCriteria_(atm_grp_cont);
 
+    // Searches for atoms that exist in the component that share a position with
+    // an atom in the complex, but are of a different element
+    linked_atoms_ = findNonConsistentAtoms_(atm_grp_cont);
+
     // Make atoms consistent between components and the complex, this is done
     // by making atoms that share the same location point to the same place
     // in memory
diff --git a/src/libcatnip/atom_system.hpp b/src/libcatnip/atom_system.hpp
index 65ae8f4..d3b37a5 100644
--- a/src/libcatnip/atom_system.hpp
+++ b/src/libcatnip/atom_system.hpp
@@ -2,8 +2,14 @@
 #pragma once
 #ifndef CATNIP_ATOM_SYSTEM_HPP
 #define CATNIP_ATOM_SYSTEM_HPP
+
+// Local private includes
 #include "atom_group_container.hpp"
 
+// Standard includes
+#include <map>
+#include <vector>
+
 namespace catnip {
 
   /**
@@ -11,17 +17,26 @@ namespace catnip {
    * change group types
    *
    * It can only be created if there are known group types and there is only
-   * a single complex, and it's components
+   * a single complex, and it's components, 
+   *
+   * Each atom in a component must only be shared with the complex, the atom of
+   * a component is allowed to be of a different element then what is in the 
+   * complex, but must have the same position
    */
   class AtomSystem {
-
+      // Atoms in each component that share the same location with atoms in
+      // the complex but do not share the same element
+      std::map<int,std::vector<std::pair<int,int>>> linked_atoms_;
       AtomGroupContainer atm_grp_cont_;    
     public:
 
       AtomSystem(AtomGroupContainer atm_cont);
 
       /**
-       * @brief assign basis functions to atom group 
+       * @brief assign basis functions to atom group
+       *
+       * Note that atoms that are linked between component and complex must 
+       * have the exact same number of basis functions.
        *
        * @param complex_basis_func_count
        */
@@ -31,7 +46,7 @@ namespace catnip {
        * @brief Determine if there is a conflict between the basis functions
        * you are attempting to assign and the currently assigned basis functions
        *
-       * This is done by comparing the basis functions on atoms that shared
+       * This is done by comparing the basis functions on atoms that are shared
        * between atom groups.
        *
        * @param index
@@ -55,7 +70,7 @@ namespace catnip {
        * @return 
        */
       bool systemComplete() const noexcept;
-  }
+  };
 
 };
 

From a4a3ed47704f4fab64ec04f0c67ade59f5200901 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 23 Jul 2020 13:02:42 -0600
Subject: [PATCH 46/68] Cleanup swap

---
 src/libcatnip/atom_group.hpp           |   4 +-
 src/libcatnip/atom_group_container.cpp |   2 +
 src/libcatnip/atom_group_container.hpp |   2 +-
 src/libcatnip/atom_system.cpp          |  49 +++++-
 src/libcatnip/atom_system.hpp          |  29 +++-
 src/libcatnip/index_map.cpp            |  47 ------
 src/libcatnip/index_map.hpp            |  34 ----
 src/libcatnip/swap_engine.cpp          | 218 ++++++++++++++++++++-----
 src/libcatnip/swap_engine.hpp          |  13 +-
 src/libcatnip/transfer_complex.cpp     |  12 +-
 src/libcatnip/transfer_complex.hpp     |  12 +-
 src/tests/CMakeLists.txt               |   6 +-
 src/tests/test_index_map.cpp           |  16 --
 13 files changed, 270 insertions(+), 174 deletions(-)
 delete mode 100644 src/libcatnip/index_map.cpp
 delete mode 100644 src/libcatnip/index_map.hpp
 delete mode 100644 src/tests/test_index_map.cpp

diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index badacf3..a47069e 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -68,11 +68,11 @@ namespace catnip {
       std::vector<std::shared_ptr<Atom>>::const_iterator 
         end() const { return atoms_.end(); }
 
-      std::shared_ptr<Atom> at(size_t ind) const {
+      std::shared_ptr<Atom> & at(size_t ind) {
         return atoms_.at(ind);
       }
 
-      std::shared_ptr<Atom> & at(size_t ind) {
+      const std::shared_ptr<Atom> & at(size_t ind) const {
         return atoms_.at(ind);
       }
 
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 093d3ac..4e88000 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -210,6 +210,8 @@ namespace catnip {
     identifyAtomGroupsOfIslandType_(grp_indices, atom_groups_);
 
     identifyAtomGroupsOfComponentComplexAndUnknownTypes_(grp_indices,atom_groups_ );
+
+    group_types_uptodate_ = true;
   }
 
   bool AtomGroupContainer::exists(GroupType type) const {
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index c57fb0b..5570655 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -79,7 +79,7 @@ namespace catnip {
        */
       bool exists(GroupType type) const;
 
-      GroupType getType(int index) const { return atom_groups_.at(index).getType(); }
+      const GroupType & getType(int index) const { return atom_groups_.at(index).getType(); }
 
       /**
        * @brief Get the indices of all the groups of the specified group type
diff --git a/src/libcatnip/atom_system.cpp b/src/libcatnip/atom_system.cpp
index d2ed4e1..3d802b8 100644
--- a/src/libcatnip/atom_system.cpp
+++ b/src/libcatnip/atom_system.cpp
@@ -5,6 +5,7 @@
 #include "atom.hpp"
 
 // Standard includes
+#include <iostream>
 #include <memory>
 #include <vector>
 
@@ -23,7 +24,7 @@ namespace catnip {
    * Local private functions
    ****************************************************************************/
 
-  static AtomGroup & assignBasisFunctionsToSynchronisedAtoms_(
+  static void assignBasisFunctionsToSynchronisedAtoms_(
       int grp_ind, 
       const std::vector<int>& basis_func_count,
       AtomGroup & grp,
@@ -31,6 +32,7 @@ namespace catnip {
 
     int index = 0; 
     for( std::shared_ptr<Atom> & atom_ptr : grp ){
+      std::cout << "Assigning basis function atom at index " << index << std::endl;
       if( atom_ptr->getBasisFuncCount() == -1){
         atom_ptr->setBasisFuncCount(basis_func_count.at(index));
       } else if(atom_ptr->getBasisFuncCount() != basis_func_count.at(index) ){
@@ -79,8 +81,8 @@ namespace catnip {
     assert(complex_grps.size() == 1 && "There must be at least one complex");
     const AtomGroup & complex_grp = atm_grp_cont.at(complex_grps.at(0));
     for( std::pair<int,int> linked_atoms : linked_atoms[grp_ind] ){
-      if ( complex_grp.at(linked_atoms.first)->getBasisFuncCount() != -1){
-        if ( complex_grp.at(linked_atoms.first)->getBasisFuncCount() != grp.at(linked_atoms.second)->getBasisFuncCount()){
+      if ( complex_grp.at(linked_atoms.second)->getBasisFuncCount() != -1){
+        if ( complex_grp.at(linked_atoms.second)->getBasisFuncCount() != grp.at(linked_atoms.first)->getBasisFuncCount()){
           throw std::runtime_error("There are inconsistencies between the "
               "the number of basis functions used in a linked atom. Atoms "
               "in a component must contain the same number of basis "
@@ -110,7 +112,7 @@ namespace catnip {
     // basis functions
   
     AtomGroup & grp = atm_grp_cont.at(grp_ind);
-
+    std::cout << "Assign to Synchronize atoms" << std::endl;
     assignBasisFunctionsToSynchronisedAtoms_(
       grp_ind, 
       basis_func_count,
@@ -119,6 +121,7 @@ namespace catnip {
     // Make sure that there are no inconsistencies between the linked atoms
     if ( atm_grp_cont.at(grp_ind).is(GroupType::Complex)){
       // If it is a complex
+      std::cout << "Assign to Linked atoms in complex" << std::endl;
       checkLinkedAtomsInComplexForConsistentBasisFunctionCounts(
           grp_ind, 
           grp,
@@ -127,6 +130,7 @@ namespace catnip {
 
     }else {
       // If it is a component
+      std::cout << "Assign to Linked atoms in component" << std::endl;
       checkLinkedAtomsInComponentForConsistentBasisFunctionCounts(
           grp_ind, 
           grp,
@@ -206,10 +210,12 @@ namespace catnip {
             linked_atoms[component_ind].push_back(std::pair<int,int>(ind_atm,complex_atm_ind.at(0)));
           }
         }else if (complex_atm_ind.size() == 0) {
-          throw std::runtime_error("A component atom did not have a matching "
-              "atom in the complex. The component atom does not have to have "
-              "the same element as the atom in the complex bust must share "
-              "the same position.");
+          std::string error_msg = "A component atom did not have a matching "
+              "atom in the complex (" + atm_complex.getName() + "). The "
+              "atom in the component (" + atm_grp.getName() + ") does not have "
+              "to have the same element as the atom in the complex but must "
+              "share the same position.";
+          throw std::runtime_error(error_msg);
         } else {
           throw std::runtime_error("A component atom matches more than a single"
              " atom in the complex. There appears to be a problem with the "
@@ -263,6 +269,9 @@ namespace catnip {
 
     checkValidSystemCriteria_(atm_grp_cont);
 
+    std::vector<int> complex_indices = 
+      atm_grp_cont.getGroups(GroupType::Complex);
+    index_complex_ = complex_indices.at(0);
     // Searches for atoms that exist in the component that share a position with
     // an atom in the complex, but are of a different element
     linked_atoms_ = findNonConsistentAtoms_(atm_grp_cont);
@@ -313,7 +322,7 @@ namespace catnip {
           "atoms in the group!");
     }
 
-    assignBasisFuncs_(index, basis_func_count, atm_grp_cont_);
+    assignBasisFuncs_(index, basis_func_count, atm_grp_cont_, linked_atoms_);
   }
 
   bool AtomSystem::systemComplete() const noexcept {
@@ -328,4 +337,26 @@ namespace catnip {
   const AtomGroup & AtomSystem::at(int ind) const {
     return atm_grp_cont_.at(ind); 
   }
+
+  std::vector<AtomSystem::Link> AtomSystem::getLinkedAtomsWithDifferentElements() const noexcept {
+
+    std::vector<Link> links;
+    std::string complex_name = atm_grp_cont_.at(index_complex_).getName();
+    for ( std::pair<int,std::vector<std::pair<int,int>>> grp_links : linked_atoms_){
+      int component_ind = grp_links.first;
+      std::string component_name = atm_grp_cont_.at(component_ind).getName(); 
+      for ( std::pair<int,int> atm1_atm2 : grp_links.second){
+        Link link{
+          component_name,     // Component name
+          component_ind,      // Component index
+          atm1_atm2.first,    // Component atom index
+          complex_name,       // Complex name
+          index_complex_,     // Complex index
+          atm1_atm2.second }; // Complex atom index
+
+        links.push_back(link);
+      }
+    }
+    return links;
+  }
 }
diff --git a/src/libcatnip/atom_system.hpp b/src/libcatnip/atom_system.hpp
index d3b37a5..2cfb1a7 100644
--- a/src/libcatnip/atom_system.hpp
+++ b/src/libcatnip/atom_system.hpp
@@ -28,8 +28,18 @@ namespace catnip {
       // the complex but do not share the same element
       std::map<int,std::vector<std::pair<int,int>>> linked_atoms_;
       AtomGroupContainer atm_grp_cont_;    
+      int index_complex_;
     public:
 
+      struct Link {
+        std::string component_name;
+        int component_ind;
+        int component_atm_ind;
+        std::string complex_name;
+        int complex_ind;
+        int complex_atm_ind;
+      };
+
       AtomSystem(AtomGroupContainer atm_cont);
 
       /**
@@ -60,8 +70,23 @@ namespace catnip {
 
       int getMaxBasisFunctions(const GroupType & type) const;
 
-      const AtomGroup & getComplex() const;       
-      std::vector<int> getComponentIndices() const noexcept { atm_grp_cont_.getGroups(GroupType::Component);}
+      const AtomGroup & getComplex() const {
+        return atm_grp_cont_.at(index_complex_); 
+      }       
+
+      std::vector<int> getComponentIndices() const noexcept { 
+        return atm_grp_cont_.getGroups(GroupType::Component);
+      }
+
+
+      /**
+       * @brief Gets atoms that are linked because they share the same position
+       * but don't share the same element 
+       *
+       * @return 
+       */
+      std::vector<Link> getLinkedAtomsWithDifferentElements() const noexcept;
+
       const AtomGroup & at(int ind) const;       
       /**
        * @brief Check that every atom knows how many basis functions are
diff --git a/src/libcatnip/index_map.cpp b/src/libcatnip/index_map.cpp
deleted file mode 100644
index c6a132d..0000000
--- a/src/libcatnip/index_map.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-
-
-#include "index_map.hpp"
-
-#include "atom.hpp"
-#include "atom_group.hpp"
-
-// Standard includes
-#include <cassert>
-
-namespace catnip {
-
-  IndexMap::IndexMap(AtomSystem atm_sys){
-    std::vector<int> comp_indices = atm_sys.getComponentIndices();
-    const AtomGroup & complex_grp = atm_sys.getComplex();
-    int sys_ind = 0;
-    for ( int & comp_ind : comp_indices) {
-      const AtomGroup & comp_grp = atm_sys.at(comp_ind);
-      for( const std::shared_ptr<Atom> & atm_ptr : comp_grp){
-        std::vector<int> atm_indices = complex_grp.find(atm_ptr);
-        assert(atm_indices.size() == 1);
-        int atm_ind = atm_indices.at(0);
-        int num_basis = comp_grp.at(atm_ind)->getBasisFuncCount();
-        for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
-          row_col_final[comp_ind].push_back(sys_ind); 
-          row_col_init[comp_ind].push_back(atm_ind);
-          sys_ind++;
-        }
-      }
-    }
-  }
-  // Searches the init row for the provided row and returns the group it is
-  // in as well as its current index
-  std::pair<int,int> IndexMap::findLocation(int row){
-    for( std::pair<int,std::vector<int>> group_rows : row_col_init){
-      int row_ind = 0;
-      for ( int row_ : group_rows.second ){
-        if (row_ == row){
-          return std::pair<int,int>(group_rows.first, row_ind);
-        }
-        ++row_ind;
-      } 
-    }
-    return std::pair<int,int>();
-  }
-
-}  // namespace catnip
diff --git a/src/libcatnip/index_map.hpp b/src/libcatnip/index_map.hpp
deleted file mode 100644
index 6bdb530..0000000
--- a/src/libcatnip/index_map.hpp
+++ /dev/null
@@ -1,34 +0,0 @@
-
-#pragma once
-#ifndef _CATNIP_INDEX_MAP_HPP
-#define _CATNIP_INDEX_MAP_HPP
-
-// Local private includes
-#include "atom_system.hpp"
-
-// Standard includes
-#include <map>
-#include <vector>
-
-namespace catnip {
-
-  class IndexMap {
-    public:
-      IndexMap() = default;
-      IndexMap(AtomSystem atm_sys);
-      // The component rows and colums in their current locations in  
-      // in the full system matrix of the complex
-      std::map<int,std::vector<int>> row_col_init;
-
-      // Map indicate where the rows and cols should go in the final state
-      // Each int in the vector represents the location in the full system matrix
-      std::map<int,std::vector<int>> row_col_final;
-
-      // Searches the init row for the provided row and returns the group it is
-      // in as well as its current index
-      std::pair<int,int> findLocation(int row);
-  };
-
-
-}  // namespace catnip
-#endif // _CATNIP_INDEX_MAP_HPP
diff --git a/src/libcatnip/swap_engine.cpp b/src/libcatnip/swap_engine.cpp
index 0ce44e0..1c6ef44 100644
--- a/src/libcatnip/swap_engine.cpp
+++ b/src/libcatnip/swap_engine.cpp
@@ -1,35 +1,119 @@
 
-
+// Local private includes
 #include "swap_engine.hpp"
 
 #include "atom.hpp"
 #include "atom_group.hpp"
+#include "basis_map.hpp"
 #include "size_type.hpp"
 
+// Standard includes
+#include <algorithm>
+
 namespace catnip {
 
-  // Swaps rows columns and keeps up with how future swaps should be updated
-  SwapEngine::SwapEngine(IndexMap ind_map, Size size) : 
-    size_(size), ind_map_(ind_map) {
-      scratch_ = Eigen::MatrixXd::Zero(size, 1);
-
-
-      // Already have enough information to calculate the correct swap order
-      // Note the order of swaps is important.
-      for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-        int group_ind = group_row.first;
-        for ( int row : group_row.second ) {
-          int final_row = ind_map_.row_col_final[group_ind].at(row);
-          std::pair<int,int> swap(row,final_row);
-          // Now we need to update index map, the row located at the final 
-          // position has now been moved     
-          auto group_and_row_ind = ind_map_.findLocation(final_row);
 
-          // Final row location needs to be pointed to the starting row
-          ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
+  /**
+   * @brief Serves as scracth space 
+   *
+   * Can store two rows at a time, the order they are loaded and unloaded is
+   * FIFO - first in first out
+   */
+  class Scratch {
+    private:
+      Eigen::MatrixXd scratch_;
+      int size_;
+      bool empty_ = true;
+    public:
+      Scratch(int size) : size_(size) {
+        scratch_ = Eigen::MatrixXd::Zero(1,size_);
+      }
+
+      bool empty() const noexcept { return empty_; }
+
+      void loadFromRow(const Eigen::MatrixXd & mat, int row){
+        for ( int i = 0; i < size_ ; ++i ){
+          scratch_(0, i) = mat(row,i);
+        }
+        empty_ = false;
+      }
+
+      void loadFromCol(const Eigen::MatrixXd & mat, int col){
+        for ( int i = 0; i < size_ ; ++i ){
+          scratch_(0, i) = mat(i,col);
+        }
+        empty_ = false;
+      }
+      void unloadToCol(Eigen::MatrixXd & mat, int col) {
+        for ( int i = 0; i < size_ ; ++i ){
+          mat(i,col) = scratch_(0, i);
+        } 
+        empty_ = true;
+      }
+      void unloadToRow(Eigen::MatrixXd & mat, int row) {
+        for ( int i = 0; i < size_ ; ++i ){
+          mat(row, i) = scratch_(0, i);
         } 
+        empty_ = true;
       }
+
+  };
+
+  // Swaps rows columns and keeps up with how future swaps should be updated
+  SwapEngine::SwapEngine(BasisMap basis_map) {
+
+    size_ = 0;
+    // The  with the largest index will tell us the size we need to allocate
+    for ( std::pair<int,std::vector<int>> grp_rows : basis_map.row_col_final ){
+      size_t max_value = *(std::max_element(grp_rows.second.begin(), grp_rows.second.end()));
+      size_ = std::max( max_value+1 , size_ ); 
+    }
+
+    // Want to order these 
+    // 4 
+    // 3
+    // 1
+    // 2
+
+    // How can we order
+    // 4 <-> 2   2 <-> 3   3 <-> 1
+    //
+    //  > 2       > 3       > 1
+    //    3         2         2
+    //    1         1         3
+    //    4         4         4
+    //
+
+    // Already have enough information to calculate the correct swap order
+    // Note the order of swaps is important.
+    for ( std::pair<const int, std::vector<int>> & group_row : basis_map.row_col_current ){
+      int group_ind = group_row.first;
+      size_t index = 0;
+
+      assert(group_row.second.size()>0 && "ERROR a component has no rows.");
+      do {
+        int current_row_in_complex = group_row.second.at(index);
+        int final_row_in_complex = basis_map.row_col_final[group_ind].at(index);
+
+
+        if ( current_row_in_complex != final_row_in_complex ){
+          // Row that currently occupies the location where the current row should
+          // go
+          auto group_and_row_ind = basis_map.findLocation(final_row_in_complex);
+          int replacement_row = basis_map.row_col_current[group_and_row_ind.first].at(group_and_row_ind.second);
+          std::pair<int,int> swap(replacement_row, current_row_in_complex);
+
+          // Final row location needs to be pointed to the starting row
+          basis_map.row_col_current[group_ind].at(index) = replacement_row;
+          basis_map.row_col_current[group_and_row_ind.first].at(group_and_row_ind.second) = current_row_in_complex;
+
+          swap_order_.push_back(swap);
+        } else {
+          ++index;
+        }
+      } while (index < group_row.second.size());
     }
+  }
   // This method of swapping was chosen to keep the memory footprint
   // reasonable.
   // Will correctly sort the rows and columns of the matrix
@@ -39,37 +123,81 @@ namespace catnip {
     if( mat.rows() != mat.cols() ) {
       throw std::runtime_error("Can only arrange square matrices");
     }
-    if( mat.rows() != size_ ) {
-      throw std::runtime_error("Index map has different number of basis functions to matrix");
+    if( mat.rows() != static_cast<Eigen::Index>(size_) ) {
+      throw std::runtime_error("Scratch space, swap procedure is not "
+          "consistent with the matrix.");
     }
+     
+    arrangeRows(mat);
+    // Repeat for columns 
+    arrangeCols(mat);
+  } 
 
-    for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
-      int group_ind = group_row.first;
-      for ( int row : group_row.second ) {
-        int final_row = ind_map_.row_col_final[group_ind].at(row);
-        if(final_row == row ) continue;
-        // Copy the data at the final row into the scratch space 
-        scratch_.col(0) = mat.row(final_row);
-        // Copy the data from the initial row into the final row
-        mat.row(final_row) = mat.row(row);
-        // Copy the data from the temporary row into the initial row
-        mat.row(row) = scratch_.col(0);
+  void SwapEngine::arrangeCols(Eigen::MatrixXd & mat) {
+    // Check that matrix is square
+    if( mat.rows() != mat.cols() ) {
+      throw std::runtime_error("Can only arrange square matrices");
+    }
+    if( mat.rows() != static_cast<Eigen::Index>(size_) ) {
+      throw std::runtime_error("Scratch space, swap procedure is not "
+          "consistent with the matrix.");
+    }
+    arrangeCols_(mat);
+  }
+
+  void SwapEngine::arrangeCols_(Eigen::MatrixXd & mat) {
+
+    Scratch scratch(size_);
+    for ( size_t swap_ind = 0; swap_ind < swap_order_.size(); ++swap_ind ){
+   
+      auto swap = swap_order_.at(swap_ind); 
+      if (scratch.empty() ) {
+        scratch.loadFromCol(mat, swap.first);
       }
+      // Write too the first instance
+      mat.col(swap.first) = mat.col(swap.second);
+      // If the next swap involves the row we just loaded don't bother writing
+      // it back into mat just keep it in scratch
+      if ( swap_ind + 1 < swap_order_.size() ){
+        if( swap_order_.at(swap_ind+1).first == swap.second ) continue;
+      }  
+      scratch.unloadToCol(mat, swap.second);
     }
+  }
 
-    // Repeat for columns 
-    for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
-      int group_ind = group_col.first;
-      for ( int col : group_col.second ) {
-        int final_col = ind_map_.row_col_final[group_ind].at(col);
-        if(final_col == col ) continue;
-        // Copy the data at the final row into the scratch space
-        scratch_.col(0) = mat.col(final_col);
-        // Copy the data from the initial row into the final row
-        mat.col(final_col) = mat.col(col);
-        // Copy the data from the temporary row into the initial row
-        mat.col(col) = scratch_.col(0);
+  void SwapEngine::arrangeRows(Eigen::MatrixXd & mat) {
+    // Check that matrix is square
+    if( mat.rows() != mat.cols() ) {
+      throw std::runtime_error("Can only arrange square matrices");
+    }
+    if( mat.rows() != static_cast<Eigen::Index>(size_) ) {
+      std::string error_msg = "Scratch space, swap procedure is not "
+          "consistent with the matrix. Rows in matrix "
+          + std::to_string(mat.rows()) + " size of scratch space "
+          + std::to_string(size_);
+      throw std::runtime_error(error_msg);
+    }
+    arrangeRows_(mat);
+  }
+
+  void SwapEngine::arrangeRows_(Eigen::MatrixXd & mat) {
+  
+    Scratch scratch(size_);
+    for ( size_t swap_ind = 0; swap_ind < swap_order_.size(); ++swap_ind ){
+   
+      auto swap = swap_order_.at(swap_ind); 
+      if (scratch.empty() ) {
+        scratch.loadFromRow(mat, swap.first);
       }
+      // Write too the first instance
+      mat.row(swap.first) = mat.row(swap.second);
+      // If the next swap involves the row we just loaded don't bother writing
+      // it back into mat just keep it in scratch
+      if ( swap_ind + 1 < swap_order_.size() ){
+        if( swap_order_.at(swap_ind+1).first == swap.second ) continue;
+      }  
+      scratch.unloadToRow(mat, swap.second);
     }
-  } 
+
+  }
 }  // namespace catnip
diff --git a/src/libcatnip/swap_engine.hpp b/src/libcatnip/swap_engine.hpp
index e5d7d6e..8f4c1eb 100644
--- a/src/libcatnip/swap_engine.hpp
+++ b/src/libcatnip/swap_engine.hpp
@@ -5,7 +5,7 @@
 
 #include "atom.hpp"
 #include "atom_group.hpp"
-#include "index_map.hpp"
+#include "basis_map.hpp"
 #include "size_type.hpp"
 
 namespace catnip {
@@ -13,14 +13,17 @@ namespace catnip {
   // Swaps rows columns and keeps up with how future swaps should be updated
   class SwapEngine {
     private:
-      Size size_;
-      IndexMap ind_map_;
-      Eigen::MatrixXd scratch_;
+      size_t size_;
+      std::vector<std::pair<int,int>> swap_order_;
 
+      void arrangeRows_(Eigen::MatrixXd & mat);
+      void arrangeCols_(Eigen::MatrixXd & mat);
     public:
-      SwapEngine(IndexMap ind_map, Size size);
+      SwapEngine(BasisMap basis_map);
 
       void arrange(Eigen::MatrixXd & mat);
+      void arrangeRows(Eigen::MatrixXd & mat);
+      void arrangeCols(Eigen::MatrixXd & mat);
   };
 
 
diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
index 21134ad..3638ac8 100644
--- a/src/libcatnip/transfer_complex.cpp
+++ b/src/libcatnip/transfer_complex.cpp
@@ -4,18 +4,18 @@
 
 #include "atom.hpp"
 #include "atom_group.hpp"
-#include "index_map.hpp"
+#include "basis_map.hpp"
 #include "swap_engine.hpp"
 
 namespace catnip {
 
-  void TransferComplex::unscramble(AtomGroupContainer atom_groups) {
+  void TransferComplex::unscramble(AtomSystem atom_sys) {
     // We should figure out how all the rows and columns should be
     // rearranged before moving any of the coefficients in the matrix    
-    IndexMap ind_map = IndexMap(atom_groups);
+    BasisMap basis_map = BasisMap(atom_sys);
   
-    size_t total_basis = atom_groups.getTotalBasisFunctions(GroupType::Component); 
-    size_t total_basis_comp = atom_groups.getTotalBasisFunctions(GroupType::Complex); 
+    size_t total_basis = atom_sys.getTotalBasisFunctions(GroupType::Component); 
+    size_t total_basis_comp = atom_sys.getTotalBasisFunctions(GroupType::Complex); 
 
     // If the total number of basis functions in the components is greater than
     // the total number of basis functions in the complex, throw an error
@@ -23,7 +23,7 @@ namespace catnip {
       throw std::runtime_error("Sum of basis functions in components does not equal the number of basis functions in the complex");
     }
 
-    auto swap_eng = SwapEngine(ind_map,total_basis);
+    auto swap_eng = SwapEngine(basis_map);
 
     swap_eng.arrange(*(params_->complex_coefs));
     swap_eng.arrange(*(params_->S_AO));
diff --git a/src/libcatnip/transfer_complex.hpp b/src/libcatnip/transfer_complex.hpp
index 632725b..e580efd 100644
--- a/src/libcatnip/transfer_complex.hpp
+++ b/src/libcatnip/transfer_complex.hpp
@@ -2,17 +2,19 @@
 #ifndef _CATNIP_TRANSFER_COMPLEX_HPP
 #define _CATNIP_TRANSFER_COMPLEX_HPP
 
-#include "atom_group_container.hpp"
+// Local private includes
+#include "atom_system.hpp"
 
+// Third party includes
+#include <eigen3/Eigen/Dense>
+
+// Standard includes
 #include <map>
 #include <sstream>
 #include <string>
 #include <unordered_map>
 #include <vector>
 
-//#include "matrix.hpp"
-#include <eigen3/Eigen/Dense>
-
 namespace catnip {
 
 class TransferComplex {
@@ -44,7 +46,7 @@ class TransferComplex {
 
     TransferComplex(Parameters * params) : params_(params) {};
 
-    void unscramble(AtomGroupContainer atom_groups);
+    void unscramble(AtomSystem atm_sys);
 
     // Orbital type and a map of the corresponding number
     // E.g.
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index ee82c99..63b41bf 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -8,8 +8,9 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_atom
   test_atom_group
   test_atom_group_container
+  test_atom_system
+  test_basis_map
   test_elements
-  test_index_map
   test_log
   test_parameters
   test_propertydouble
@@ -21,7 +22,8 @@ list( APPEND UNIT_TEST_SOURCE_FILES
   test_propertystring
   test_propertyswitch
   test_qc_functions
-  test_string_support)
+  test_string_support
+  test_swap_engine)
 
 if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
   find_library (GCOV gcov)
diff --git a/src/tests/test_index_map.cpp b/src/tests/test_index_map.cpp
deleted file mode 100644
index 504f421..0000000
--- a/src/tests/test_index_map.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "index_map.hpp"
-
-#include "atom_group_container.hpp"
-
-using namespace catnip;
-
-TEST_CASE("Index Map","[unit]") {
-
-  AtomGroupContainer atom_cont;
-  IndexMap ind_map(atom_cont);
-
-}

From b8119b84667f4cf5c58c4ce718e497e5151c3485 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 24 Jul 2020 08:17:30 -0600
Subject: [PATCH 47/68] Add test files

---
 src/tests/test_atom_system.cpp | 234 ++++++++++++++++++
 src/tests/test_basis_map.cpp   | 268 ++++++++++++++++++++
 src/tests/test_swap_engine.cpp | 437 +++++++++++++++++++++++++++++++++
 3 files changed, 939 insertions(+)
 create mode 100644 src/tests/test_atom_system.cpp
 create mode 100644 src/tests/test_basis_map.cpp
 create mode 100644 src/tests/test_swap_engine.cpp

diff --git a/src/tests/test_atom_system.cpp b/src/tests/test_atom_system.cpp
new file mode 100644
index 0000000..31602b1
--- /dev/null
+++ b/src/tests/test_atom_system.cpp
@@ -0,0 +1,234 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "atom_system.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+#include "atom_group_container.hpp"
+#include "elements.hpp"
+
+// Standard includes
+#include <memory>
+
+using namespace catnip;
+
+TEST_CASE("Atom System","[unit]") {
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
+  // Same position as atom5 but different element
+  Atom atom6(Element::C, 3.0, 3.9, 0.0); 
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+  auto atom6_ptr = std::make_shared<Atom>(atom6);
+
+  SECTION("Building component without atom 5") {
+    // Extra atoms are allowed in the complex but not in the componets
+    AtomGroup component1("CH2");
+    component1.add(atom1_ptr);
+    component1.add(atom2_ptr);
+    component1.add(atom3_ptr);
+
+    AtomGroup component2("O2");
+    component2.add(atom4_ptr);  
+
+    AtomGroup complex1("O2CH2");
+    complex1.add(atom1_ptr);
+    complex1.add(atom2_ptr);
+    complex1.add(atom3_ptr);
+    complex1.add(atom4_ptr);
+    complex1.add(atom5_ptr);
+
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(component1);
+    atom_grp_cont.add(component2);
+    atom_grp_cont.add(complex1);
+
+    REQUIRE_NOTHROW(AtomSystem(atom_grp_cont) );
+  }
+
+  SECTION("Building complex without atom 5") {
+    // Extra atoms are allowed in the complex but not in the componets
+    AtomGroup component1("CH2");
+    component1.add(atom1_ptr);
+    component1.add(atom2_ptr);
+    component1.add(atom3_ptr);
+
+    AtomGroup component2("O2");
+    component2.add(atom4_ptr);  
+    component2.add(atom5_ptr);  
+
+    AtomGroup complex1("O2CH2");
+    complex1.add(atom1_ptr);
+    complex1.add(atom2_ptr);
+    complex1.add(atom3_ptr);
+    complex1.add(atom4_ptr);
+
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(component1);
+    atom_grp_cont.add(component2);
+    atom_grp_cont.add(complex1);
+
+    REQUIRE_THROWS(AtomSystem(atom_grp_cont) );
+  }
+
+  SECTION("Building with atom 5") {
+    AtomGroup component1("CH2");
+    component1.add(atom1_ptr); // H
+    component1.add(atom2_ptr); // H 
+    component1.add(atom3_ptr); // C
+
+    AtomGroup component2("O2");
+    component2.add(atom4_ptr); // O
+    component2.add(atom5_ptr); // O 
+
+    AtomGroup complex1("O2CH2");
+    complex1.add(atom1_ptr); // H
+    complex1.add(atom2_ptr); // H
+    complex1.add(atom3_ptr); // C
+    complex1.add(atom4_ptr); // O
+    complex1.add(atom5_ptr); // O
+
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(component1);
+    atom_grp_cont.add(component2);
+    atom_grp_cont.add(complex1);
+
+    AtomSystem atm_sys(atom_grp_cont);
+    REQUIRE(atm_sys.getComplex().getType() == GroupType::Complex );
+    REQUIRE(atm_sys.getComplex().getName() == "O2CH2" );
+
+    std::vector<int> component_indices = atm_sys.getComponentIndices();
+    REQUIRE(component_indices.size() == 2);
+    REQUIRE(component_indices.at(0) == 0);
+    REQUIRE(component_indices.at(1) == 1);
+
+    std::vector<AtomSystem::Link> linked_atms = atm_sys.getLinkedAtomsWithDifferentElements();
+    REQUIRE(linked_atms.size() == 0); 
+
+    // Basis functions
+    std::vector<int> basis_comp1{ 1, 1, 4};
+    std::vector<int> basis_comp2{ 5, 5};
+    // should be 5, 5 at the end
+    std::vector<int> wrong_basis_complex{ 1, 1, 4, 3, 3}; 
+
+    atm_sys.assignBasisFunctions( 0, basis_comp1 );
+    atm_sys.assignBasisFunctions( 1, basis_comp2 );
+   
+    // Should be complete at this point
+    REQUIRE( atm_sys.systemComplete() );
+
+    // By using the basis functions for the complex we ensure that basis
+    // functions between the components and the complex are consistent
+    REQUIRE_THROWS( atm_sys.assignBasisFunctions( 2, wrong_basis_complex ));
+
+    std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
+    REQUIRE_NOTHROW( atm_sys.assignBasisFunctions( 2, basis_complex ));
+
+    REQUIRE( atm_sys.at(0).size() == 3);
+    REQUIRE( atm_sys.at(0).at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(0).at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(0).at(2)->getBasisFuncCount() == 4); // C
+    
+    REQUIRE( atm_sys.at(1).size() == 2);
+    REQUIRE( atm_sys.at(1).at(0)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(1).at(1)->getBasisFuncCount() == 5); // O
+
+    REQUIRE( atm_sys.at(2).size() == 5);
+    REQUIRE( atm_sys.at(2).at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(2).at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(2).at(2)->getBasisFuncCount() == 4); // C
+    REQUIRE( atm_sys.at(2).at(3)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(2).at(4)->getBasisFuncCount() == 5); // O
+  }
+
+  SECTION("Building complex with atom 6") {
+    AtomGroup component1("CH2");
+    component1.add(atom1_ptr);
+    component1.add(atom2_ptr);
+    component1.add(atom3_ptr);
+
+    AtomGroup component2("O2");
+    component2.add(atom4_ptr);  
+    component2.add(atom5_ptr);  
+
+    AtomGroup complex1("OC2H2");
+    complex1.add(atom1_ptr);
+    complex1.add(atom2_ptr);
+    complex1.add(atom3_ptr);
+    complex1.add(atom4_ptr);
+    complex1.add(atom6_ptr); // Carbon instead of Oxygen
+
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(component1);
+    atom_grp_cont.add(component2);
+    atom_grp_cont.add(complex1);
+
+    AtomSystem atm_sys(atom_grp_cont);
+    REQUIRE(atm_sys.getComplex().getType() == GroupType::Complex );
+    REQUIRE(atm_sys.getComplex().getName() == "OC2H2" );
+
+    std::vector<int> component_indices = atm_sys.getComponentIndices();
+    REQUIRE(component_indices.size() == 2);
+    REQUIRE(component_indices.at(0) == 0);
+    REQUIRE(component_indices.at(1) == 1);
+
+    std::vector<AtomSystem::Link> linked_atms = atm_sys.getLinkedAtomsWithDifferentElements();
+    REQUIRE(linked_atms.size() == 1);
+    AtomSystem::Link link = linked_atms.at(0);
+    // atm5 from component 2 should be linked with atom 5 of complex
+    REQUIRE(link.component_name == "O2");
+    REQUIRE(link.component_ind == 1);
+    REQUIRE(link.component_atm_ind == 1);
+    REQUIRE(link.complex_name == "OC2H2");
+    REQUIRE(link.complex_ind == 2);
+    REQUIRE(link.complex_atm_ind == 4);
+
+    // Basis functions
+    std::vector<int> basis_comp1{ 1, 1, 4};
+    std::vector<int> basis_comp2{ 5, 5};
+    // should be 5, 5 at the end
+    std::vector<int> wrong_basis_complex{ 1, 1, 4, 3, 3}; 
+
+    atm_sys.assignBasisFunctions( 0, basis_comp1 );
+    atm_sys.assignBasisFunctions( 1, basis_comp2 );
+   
+    // Should NOT be complete at this point, as atom 5 and 6 though positionally
+    // linked are not in the same memory space
+    REQUIRE( atm_sys.systemComplete() == false );
+
+    // By using the basis functions for the complex we ensure that basis
+    // functions between the components and the complex are consistent
+    REQUIRE_THROWS( atm_sys.assignBasisFunctions( 2, wrong_basis_complex ));
+ 
+    std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
+    REQUIRE_NOTHROW( atm_sys.assignBasisFunctions( 2, basis_complex ));
+    REQUIRE( atm_sys.systemComplete() );
+
+    REQUIRE( atm_sys.at(0).size() == 3);
+    REQUIRE( atm_sys.at(0).at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(0).at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(0).at(2)->getBasisFuncCount() == 4); // C
+
+    REQUIRE( atm_sys.at(1).size() == 2);
+    REQUIRE( atm_sys.at(1).at(0)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(1).at(1)->getBasisFuncCount() == 5); // O
+
+    REQUIRE( atm_sys.at(2).size() == 5);
+    REQUIRE( atm_sys.at(2).at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(2).at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(2).at(2)->getBasisFuncCount() == 4); // C
+    REQUIRE( atm_sys.at(2).at(3)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(2).at(4)->getBasisFuncCount() == 5); // O
+  }
+}
diff --git a/src/tests/test_basis_map.cpp b/src/tests/test_basis_map.cpp
new file mode 100644
index 0000000..4b1e248
--- /dev/null
+++ b/src/tests/test_basis_map.cpp
@@ -0,0 +1,268 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "basis_map.hpp"
+
+#include "atom.hpp"
+#include "atom_group_container.hpp"
+#include "atom_system.hpp"
+#include "elements.hpp"
+
+using namespace catnip;
+
+TEST_CASE("Basis Map Unscrambled","[integration]") {
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+  // Extra atoms are allowed in the complex but not in the componets
+  AtomGroup component1("CH2");
+  component1.add(atom1_ptr);
+  component1.add(atom2_ptr);
+  component1.add(atom3_ptr);
+
+  AtomGroup component2("O2");
+  component2.add(atom4_ptr);  
+  component2.add(atom5_ptr);  
+
+  AtomGroup complex1("O2CH2");
+  complex1.add(atom1_ptr);
+  complex1.add(atom2_ptr);
+  complex1.add(atom3_ptr);
+  complex1.add(atom4_ptr);
+  complex1.add(atom5_ptr);
+
+  AtomGroupContainer atom_grp_cont;
+  atom_grp_cont.add(component1);
+  atom_grp_cont.add(component2);
+  atom_grp_cont.add(complex1);
+
+  AtomSystem atm_sys(atom_grp_cont);
+
+  std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
+
+  int index_complex = 2;
+  atm_sys.assignBasisFunctions( index_complex, basis_complex);
+  BasisMap basis_map(atm_sys);
+
+  // Equal to the total number of basis in the group
+  REQUIRE( basis_map.row_col_current[0].size() == 6);
+  // comp1 atm 1 should map to location 0 in the complex at least currentially
+  REQUIRE( basis_map.row_col_current[0].at(0) == 0);
+  // comp1 atm 2 should map to location 1 in the complex at least currentially
+  REQUIRE( basis_map.row_col_current[0].at(1) == 1);
+  // comp1 atm 3 should map to location 2-5 in the complex at least currentially
+  REQUIRE( basis_map.row_col_current[0].at(2) == 2);
+  REQUIRE( basis_map.row_col_current[0].at(3) == 3);
+  REQUIRE( basis_map.row_col_current[0].at(4) == 4);
+  REQUIRE( basis_map.row_col_current[0].at(5) == 5);
+  
+  REQUIRE( basis_map.row_col_current[1].size() == 10);
+  // comp2 atm 1 should map to location 4 in the complex at least currentially
+  REQUIRE( basis_map.row_col_current[1].at(0) == 6);
+  // comp2 atm 2 should map to location 5 in the complex at least currentially
+  REQUIRE( basis_map.row_col_current[1].at(1) == 7);
+  REQUIRE( basis_map.row_col_current[1].at(2) == 8);
+  REQUIRE( basis_map.row_col_current[1].at(3) == 9);
+  REQUIRE( basis_map.row_col_current[1].at(4) == 10);
+  REQUIRE( basis_map.row_col_current[1].at(5) == 11);
+  REQUIRE( basis_map.row_col_current[1].at(6) == 12);
+  REQUIRE( basis_map.row_col_current[1].at(7) == 13);
+  REQUIRE( basis_map.row_col_current[1].at(8) == 14);
+  REQUIRE( basis_map.row_col_current[1].at(9) == 15);
+
+  // In this case the final and currential version should be the same
+  // Equal to the total number of basis in the group
+  REQUIRE( basis_map.row_col_final[0].size() == 6);
+  // comp1 atm 1 should map to location 0 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(0) == 0);
+  // comp1 atm 2 should map to location 1 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(1) == 1);
+  // comp1 atm 3 should map to location 2-5 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(2) == 2);
+  REQUIRE( basis_map.row_col_final[0].at(3) == 3);
+  REQUIRE( basis_map.row_col_final[0].at(4) == 4);
+  REQUIRE( basis_map.row_col_final[0].at(5) == 5);
+  
+  REQUIRE( basis_map.row_col_final[1].size() == 10);
+  // comp2 atm 1 should map to location 4 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[1].at(0) == 6);
+  // comp2 atm 2 should map to location 5 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[1].at(1) == 7);
+  REQUIRE( basis_map.row_col_final[1].at(2) == 8);
+  REQUIRE( basis_map.row_col_final[1].at(3) == 9);
+  REQUIRE( basis_map.row_col_final[1].at(4) == 10);
+  REQUIRE( basis_map.row_col_final[1].at(5) == 11);
+  REQUIRE( basis_map.row_col_final[1].at(6) == 12);
+  REQUIRE( basis_map.row_col_final[1].at(7) == 13);
+  REQUIRE( basis_map.row_col_final[1].at(8) == 14);
+  REQUIRE( basis_map.row_col_final[1].at(9) == 15);
+
+  std::pair<int,int> location = basis_map.findLocation(0);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 0 );
+  location = basis_map.findLocation(1);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 1 );
+  location = basis_map.findLocation(2);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 2 );
+
+  location = basis_map.findLocation(6);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 0 );
+  location = basis_map.findLocation(7);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 1 );
+  location = basis_map.findLocation(15);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 9 );
+}
+
+
+/**
+ * @brief In this test some of the atoms added to the complex will be added
+ * in a different order from how they were added to each of the components
+ *
+ * @param Scrambled"
+ * @param "[integration]"
+ */
+TEST_CASE("Basis Map Scrambled","[integration]") {
+
+  std::vector<int> basis_comp1{ 1, 1, 4};
+  std::vector<int> basis_comp2{ 5, 5}; 
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+  // Extra atoms are allowed in the complex but not in the componets
+  AtomGroup component1("CH2");
+  component1.add(atom1_ptr);
+  component1.add(atom2_ptr);
+  component1.add(atom3_ptr);
+
+  AtomGroup component2("O2");
+  component2.add(atom4_ptr);  
+  component2.add(atom5_ptr);  
+
+  // HERE: the order has been changed
+  AtomGroup complex1("O2CH2");
+  complex1.add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
+  complex1.add(atom1_ptr); // The basis functiosn of atom 1 : 5 - 5 
+  complex1.add(atom3_ptr); // The basis functiosn of atom 3 : 6 - 9
+  complex1.add(atom5_ptr); // The basis functiosn of atom 5 : 10 - 14
+  complex1.add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
+
+  AtomGroupContainer atom_grp_cont;
+  atom_grp_cont.add(component1);
+  atom_grp_cont.add(component2);
+  atom_grp_cont.add(complex1);
+
+  AtomSystem atm_sys(atom_grp_cont);
+
+
+  int index_component1 = 0;
+  int index_component2 = 1;
+  atm_sys.assignBasisFunctions( index_component1, basis_comp1);
+  atm_sys.assignBasisFunctions( index_component2, basis_comp2);
+
+  BasisMap basis_map(atm_sys);
+
+  // The row_col_current will now be different but the row_col_final should remail
+  // the same
+
+  // The basis functions of atom 4 : 0 - 4
+  // The basis functiosn of atom 1 : 5 - 5 
+  // The basis functiosn of atom 3 : 6 - 9
+  // The basis functiosn of atom 5 : 10 - 14
+  // The basis functions of atom 2 : 15 - 15
+  
+  // Equal to the total number of basis in the group
+  REQUIRE( basis_map.row_col_current[0].size() == 6);
+  REQUIRE( basis_map.row_col_current[0].at(0) == 5);  // atom 1
+  REQUIRE( basis_map.row_col_current[0].at(1) == 15); // atom 2
+  REQUIRE( basis_map.row_col_current[0].at(2) == 6);  // atom 3
+  REQUIRE( basis_map.row_col_current[0].at(3) == 7);
+  REQUIRE( basis_map.row_col_current[0].at(4) == 8);
+  REQUIRE( basis_map.row_col_current[0].at(5) == 9);
+  
+  REQUIRE( basis_map.row_col_current[1].size() == 10);
+  REQUIRE( basis_map.row_col_current[1].at(0) == 0); // atom 4
+  REQUIRE( basis_map.row_col_current[1].at(1) == 1);
+  REQUIRE( basis_map.row_col_current[1].at(2) == 2);
+  REQUIRE( basis_map.row_col_current[1].at(3) == 3);
+  REQUIRE( basis_map.row_col_current[1].at(4) == 4);
+  REQUIRE( basis_map.row_col_current[1].at(5) == 10); // atom 5
+  REQUIRE( basis_map.row_col_current[1].at(6) == 11);
+  REQUIRE( basis_map.row_col_current[1].at(7) == 12);
+  REQUIRE( basis_map.row_col_current[1].at(8) == 13);
+  REQUIRE( basis_map.row_col_current[1].at(9) == 14);
+
+  // In this case the final and currential version should be the same
+  // Equal to the total number of basis in the group
+  REQUIRE( basis_map.row_col_final[0].size() == 6);
+  // comp1 atm 1 should map to location 0 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(0) == 0);
+  // comp1 atm 2 should map to location 1 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(1) == 1);
+  // comp1 atm 3 should map to location 2-5 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[0].at(2) == 2);
+  REQUIRE( basis_map.row_col_final[0].at(3) == 3);
+  REQUIRE( basis_map.row_col_final[0].at(4) == 4);
+  REQUIRE( basis_map.row_col_final[0].at(5) == 5);
+  
+  REQUIRE( basis_map.row_col_final[1].size() == 10);
+  // comp2 atm 1 should map to location 4 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[1].at(0) == 6);
+  // comp2 atm 2 should map to location 5 in the complex at least finalially
+  REQUIRE( basis_map.row_col_final[1].at(1) == 7);
+  REQUIRE( basis_map.row_col_final[1].at(2) == 8);
+  REQUIRE( basis_map.row_col_final[1].at(3) == 9);
+  REQUIRE( basis_map.row_col_final[1].at(4) == 10);
+  REQUIRE( basis_map.row_col_final[1].at(5) == 11);
+  REQUIRE( basis_map.row_col_final[1].at(6) == 12);
+  REQUIRE( basis_map.row_col_final[1].at(7) == 13);
+  REQUIRE( basis_map.row_col_final[1].at(8) == 14);
+  REQUIRE( basis_map.row_col_final[1].at(9) == 15);
+
+  // Look for where in the currential rows the row of the complex can be found
+  std::pair<int,int> location = basis_map.findLocation(0);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 0 );
+  location = basis_map.findLocation(1);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 1 );
+  location = basis_map.findLocation(2);
+  REQUIRE( location.first == 1 );
+  REQUIRE( location.second == 2 );
+
+  location = basis_map.findLocation(6);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 2 );
+  location = basis_map.findLocation(7);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 3 );
+  location = basis_map.findLocation(15);
+  REQUIRE( location.first == 0 );
+  REQUIRE( location.second == 1 );
+}
diff --git a/src/tests/test_swap_engine.cpp b/src/tests/test_swap_engine.cpp
new file mode 100644
index 0000000..6fdd2de
--- /dev/null
+++ b/src/tests/test_swap_engine.cpp
@@ -0,0 +1,437 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+// Local private includes
+#include "swap_engine.hpp"
+
+#include "atom.hpp"
+#include "atom_group_container.hpp"
+#include "atom_system.hpp"
+#include "basis_map.hpp"
+#include "elements.hpp"
+
+// Third party includes
+#include <eigen3/Eigen/Dense>
+
+// Standard includes
+#include <iostream>
+#include <vector>
+
+using namespace catnip;
+/*
+TEST_CASE("Basis Map Unscrambled","[integration]") {
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+  // Extra atoms are allowed in the complex but not in the componets
+  AtomGroup component1("CH2");
+  component1.add(atom1_ptr);
+  component1.add(atom2_ptr);
+  component1.add(atom3_ptr);
+
+  AtomGroup component2("O2");
+  component2.add(atom4_ptr);  
+  component2.add(atom5_ptr);  
+
+  AtomGroup complex1("O2CH2");
+  complex1.add(atom1_ptr);
+  complex1.add(atom2_ptr);
+  complex1.add(atom3_ptr);
+  complex1.add(atom4_ptr);
+  complex1.add(atom5_ptr);
+
+  AtomGroupContainer atom_grp_cont;
+  atom_grp_cont.add(component1);
+  atom_grp_cont.add(component2);
+  atom_grp_cont.add(complex1);
+
+  AtomSystem atm_sys(atom_grp_cont);
+
+  std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
+
+  int index_complex = 2;
+  atm_sys.assignBasisFunctions( index_complex, basis_complex);
+  BasisMap basis_map(atm_sys);
+
+}
+*/
+
+/**
+ * @brief In this test some of the atoms added to the complex will be added
+ * in a different order from how they were added to each of the components
+ *
+ * @param Scrambled"
+ * @param "[integration]"
+ */
+TEST_CASE("Basis Map Scrambled","[integration]") {
+
+  std::vector<int> basis_comp1{ 1, 1, 4};
+  std::vector<int> basis_comp2{ 5, 5}; 
+
+  Atom atom1(Element::H, 0.0, 0.0, 0.0);
+  Atom atom2(Element::H, 2.0, 0.0, 0.0);
+  Atom atom3(Element::C, 1.0, 1.0, 0.0);
+  Atom atom4(Element::O, 3.3, 4.3, 0.0);
+  Atom atom5(Element::O, 3.0, 3.9, 0.0);
+
+  auto atom1_ptr = std::make_shared<Atom>(atom1);
+  auto atom2_ptr = std::make_shared<Atom>(atom2);
+  auto atom3_ptr = std::make_shared<Atom>(atom3);
+  auto atom4_ptr = std::make_shared<Atom>(atom4);
+  auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+  // Extra atoms are allowed in the complex but not in the componets
+  AtomGroup component1("CH2");
+  component1.add(atom1_ptr);
+  component1.add(atom2_ptr);
+  component1.add(atom3_ptr);
+
+  AtomGroup component2("O2");
+  component2.add(atom4_ptr);  
+  component2.add(atom5_ptr);  
+
+  // HERE: the order has been changed
+  AtomGroup complex1("O2CH2");
+  complex1.add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
+  complex1.add(atom1_ptr); // The basis functiosn of atom 1 : 5 - 5 
+  complex1.add(atom3_ptr); // The basis functiosn of atom 3 : 6 - 9
+  complex1.add(atom5_ptr); // The basis functiosn of atom 5 : 10 - 14
+  complex1.add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
+
+  AtomGroupContainer atom_grp_cont;
+  atom_grp_cont.add(component1);
+  atom_grp_cont.add(component2);
+  atom_grp_cont.add(complex1);
+
+  AtomSystem atm_sys(atom_grp_cont);
+
+
+  int index_component1 = 0;
+  int index_component2 = 1;
+  atm_sys.assignBasisFunctions( index_component1, basis_comp1);
+  atm_sys.assignBasisFunctions( index_component2, basis_comp2);
+
+  BasisMap basis_map(atm_sys);
+
+}
+
+TEST_CASE("QC Functions","[integration]") {
+
+  std::cout << "Testing: unscramble_Coef" << std::endl;
+  {
+    Eigen::MatrixXd dimerCoef = Eigen::MatrixXd::Zero(8, 8);
+    for (int i = 0; i < 8; ++i) {
+      dimerCoef(i, 0) = 1.3;
+      dimerCoef(i, 2) = 0.2;
+      dimerCoef(i, 3) = 82.4;
+      dimerCoef(i, 4) = 9.4;
+      dimerCoef(i, 5) = 3.4;
+      dimerCoef(i, 7) = -3.0;
+    }
+
+    // Our coefficient matrix should look like this
+    //
+    //         col 0  col 1  col 2  col 3  col 4  col 5  col 6  col 7
+    //        _______________________________________________________
+    // row 0 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 1 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 2 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 3 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 4 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 5 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 6 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    // row 7 |  1.3    0.0    0.2   82.4    9.4    3.4    0.0   -3.0
+    //         atm3   atm1   atm1   atm5   atm4   atm4   atm2   atm2
+
+    Atom atom1(Element::H, 1.0, 1.0, 1.0);
+    Atom atom2(Element::H, 0.0, 0.0, 0.0);
+
+    auto atom1_ptr = std::make_shared<Atom>(atom1);
+    auto atom2_ptr = std::make_shared<Atom>(atom2);
+
+    AtomGroup componentA("A");
+    componentA.add(atom1_ptr);
+    componentA.add(atom2_ptr);
+
+    Atom atom3(Element::C, 1.0, 0.0, 0.0);
+    Atom atom4(Element::O, 2.0, 0.0, 0.0);
+    Atom atom5(Element::O, 3.0, 0.0, 0.0);
+
+    auto atom3_ptr = std::make_shared<Atom>(atom3);
+    auto atom4_ptr = std::make_shared<Atom>(atom4);
+    auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+    AtomGroup componentB("B");
+    componentB.add(atom3_ptr);
+    componentB.add(atom4_ptr);
+    componentB.add(atom5_ptr);
+
+    // Arrange atoms in the dimer so they do not appear in the
+    // same order as the monomers
+
+    // Atom 3   1.0, 0.0, 0.0
+    // Atom 1   1.0, 1.0, 1.0
+    // Atom 5   3.0, 0.0, 0.0
+    // Atom 4   2.0, 0.0, 0.0
+    // Atom 2   0.0, 0.0, 0.0
+
+    AtomGroup complexAB("AB");
+    complexAB.add(atom3_ptr);
+    complexAB.add(atom1_ptr);
+    complexAB.add(atom5_ptr);
+    complexAB.add(atom4_ptr);
+    complexAB.add(atom2_ptr);
+
+    // Combine atom groups
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(componentA);
+    atom_grp_cont.add(componentB);
+    atom_grp_cont.add(complexAB);
+
+    // Basis functions per atom
+    //
+    // Atom 1 2
+    // Atom 2 2
+    // Atom 3 1
+    // Atom 4 2
+    // Atom 5 1
+
+    // According to the dimer coordinates they will appear in the following
+    // order
+    // Atom 3 1
+    // Atom 1 2
+    // Atom 5 1
+    // Atom 4 2
+    // Atom 2 2
+
+    std::vector<int> basisFuncDimer;
+    basisFuncDimer.push_back(1);
+    basisFuncDimer.push_back(2);
+    basisFuncDimer.push_back(1);
+    basisFuncDimer.push_back(2);
+    basisFuncDimer.push_back(2);
+
+    AtomSystem atm_sys(atom_grp_cont);
+
+    // Assign the basis functions to the atoms that are in the complex
+    int index_complex = 2;
+    atm_sys.assignBasisFunctions( index_complex, basisFuncDimer);
+    BasisMap basis_map(atm_sys);
+
+    // According to the basis functions and the atom positions the current
+    // coef table for monomer A should look like this
+    //         col 0  col 1  col 2  col 3
+    //        ____________________________
+    // row 0 |  0.0    0.2    0.0   -3.0
+    // row 1 |  0.0    0.2    0.0   -3.0
+    // row 2 |  0.0    0.2    0.0   -3.0
+    // row 3 |  0.0    0.2    0.0   -3.0
+    // row 4 |  0.0    0.2    0.0   -3.0
+    // row 5 |  0.0    0.2    0.0   -3.0
+    // row 6 |  0.0    0.2    0.0   -3.0
+    // row 7 |  0.0    0.2    0.0   -3.0
+    //         atm1   atm1   atm2   atm2
+
+    auto swap_eng = SwapEngine(basis_map);
+
+    std::cout << "Before arranging dimer coef" << std::endl;
+    std::cout << dimerCoef << std::endl;
+
+    swap_eng.arrangeCols(dimerCoef);
+
+    std::cout << "Expected output" << std::endl;
+    std::cout << "       Col 1   Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7 " << std::endl;
+    std::cout << "Row 0   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl; 
+    std::cout << "Row 1   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 2   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 3   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 4   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 5   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 6   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+    std::cout << "Row 7   0.0     0.2     0.0     -3.0    1.3     9.4     3.4     82.4" << std::endl;
+
+    std::cout << "After arranging dimer coef" << std::endl;
+    std::cout << dimerCoef << std::endl;
+
+    for (int i = 0; i < 8; ++i) {
+      REQUIRE(dimerCoef(i, 0) == Approx(0.0));
+      REQUIRE(dimerCoef(i, 1) == Approx(0.2));
+      REQUIRE(dimerCoef(i, 2) == Approx(0.0));
+      REQUIRE(dimerCoef(i, 3) == Approx(-3.0));
+      REQUIRE(dimerCoef(i, 4) == Approx(1.3));
+      REQUIRE(dimerCoef(i, 5) == Approx(9.4));
+      REQUIRE(dimerCoef(i, 6) == Approx(3.4));
+      REQUIRE(dimerCoef(i, 7) == Approx(82.4));
+    }
+  }
+
+  std::cout << "Testing: unscramble SCoef" << std::endl;
+  {
+    Eigen::MatrixXd SCoef = Eigen::MatrixXd::Zero(8, 8);
+    for (int i = 0; i < 8; ++i) {
+      SCoef(i, 1) = 1.3;
+      SCoef(i, 2) = 1.3;
+      SCoef(i, 3) = 4.0;
+    }
+
+    for (int i = 0; i < 8; ++i) {
+      SCoef(1, i) = 1.3;
+      SCoef(2, i) = 1.3;
+      SCoef(3, i) = 4.0;
+    }
+
+    SCoef(1, 3) = 6.0;
+    SCoef(2, 3) = 6.0;
+    SCoef(3, 1) = 6.0;
+    SCoef(3, 2) = 6.0;
+
+    // Our coefficient matrix should look like this
+    //
+    //               col 0  col 1  col 2  col 3  col 4  col 5  col 6  col 7
+    //              _______________________________________________________
+    // atm 3 row 0 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 1 row 1 |  1.3    1.3    1.3    6.0    1.3    1.3    1.3    1.3
+    // atm 1 row 2 |  1.3    1.3    1.3    6.0    1.3    1.3    1.3    1.3
+    // atm 5 row 3 |  4.0    6.0    6.0    4.0    4.0    4.0    4.0    4.0
+    // atm 4 row 4 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 4 row 5 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 2 row 6 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    // atm 2 row 7 |  0.0    1.3    1.3    4.0    0.0    0.0    0.0    0.0
+    //                atm3   atm1   atm1   atm5   atm4   atm4   atm2   atm2
+
+    // Contains the x y and z position of atoms in monomer A
+    Atom atom1(Element::H, 1.0, 1.0, 1.0);
+    Atom atom2(Element::H, 0.0, 0.0, 0.0);
+
+    auto atom1_ptr = std::make_shared<Atom>(atom1);
+    auto atom2_ptr = std::make_shared<Atom>(atom2);
+
+    AtomGroup componentB("B");
+    componentB.add(atom1_ptr);
+    componentB.add(atom2_ptr);
+
+    // Contains the x y and z position of atoms in monomer B
+    Atom atom3(Element::C, 1.0, 0.0, 0.0);
+    Atom atom4(Element::O, 2.0, 0.0, 0.0);
+    Atom atom5(Element::O, 3.0, 0.0, 0.0);
+
+    auto atom3_ptr = std::make_shared<Atom>(atom3);
+    auto atom4_ptr = std::make_shared<Atom>(atom4);
+    auto atom5_ptr = std::make_shared<Atom>(atom5);
+
+    AtomGroup componentA("A");
+    componentA.add(atom3_ptr);
+    componentA.add(atom4_ptr);
+    componentA.add(atom5_ptr);
+
+    // Positions of atoms in the complex
+    AtomGroup complexAB("AB");
+    complexAB.add(atom3_ptr);
+    complexAB.add(atom1_ptr);
+    complexAB.add(atom5_ptr);
+    complexAB.add(atom4_ptr);
+    complexAB.add(atom2_ptr);
+
+    // Combine atom groups
+    AtomGroupContainer atom_grp_cont;
+    atom_grp_cont.add(componentA);
+    atom_grp_cont.add(componentB);
+    atom_grp_cont.add(complexAB);
+
+    AtomSystem atm_sys(atom_grp_cont);
+    
+    // Basis functions per atom
+    //
+    // Atom 1 2
+    // Atom 2 2
+    // Atom 3 1
+    // Atom 4 2
+    // Atom 5 1
+
+    // According to the dimer coordinates they will appear in the following
+    // order
+    // Atom 3 1
+    // Atom 1 2
+    // Atom 5 1
+    // Atom 4 2
+    // Atom 2 2
+
+    std::vector<int> basisFuncDimer;
+    basisFuncDimer.push_back(1);
+    basisFuncDimer.push_back(2);
+    basisFuncDimer.push_back(1);
+    basisFuncDimer.push_back(2);
+    basisFuncDimer.push_back(2);
+
+    // Assign the basis functions to the atoms that are in the complex
+    int index_complex = 2;
+    atm_sys.assignBasisFunctions( index_complex, basisFuncDimer);
+    BasisMap basis_map(atm_sys);
+
+    // If we correct the dimer coefficient matrix to line up with the
+    // coefficients of the monomers it should look like this
+    //
+    //        Col 0   Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7
+    // Row 0   0       0       0       4       1.3     1.3     0       0
+    // Row 1   0       0       0       4       1.3     1.3     0       0
+    // Row 2   0       0       0       4       1.3     1.3     0       0
+    // Row 3   4       4       4       4       6       6       4       4
+    // Row 4   1.3     1.3     1.3     6       1.3     1.3     1.3     1.3
+    // Row 5   1.3     1.3     1.3     6       1.3     1.3     1.3     1.3
+    // Row 6   0       0       0       4       1.3     1.3     0       0
+    // Row 7   0       0       0       4       1.3     1.3     0       0
+    //        atm3    atm4    atm3    atm5    atm1    atm1    atm2    atm2
+
+    auto swap_eng = SwapEngine(basis_map);
+
+    std::cout << "Before arranging S" << std::endl;
+    std::cout << SCoef << std::endl;
+
+    swap_eng.arrange(SCoef);
+
+    std::cout << "Expected output" << std::endl;
+    std::cout << "       Col 1   Col 1   Col 2   Col 3   Col 4   Col 5   Col 6   Col 7 " << std::endl;
+    std::cout << "Row 0    0       0       0       4       1.3     1.3     0       0  " << std::endl; 
+    std::cout << "Row 1    0       0       0       4       1.3     1.3     0       0  " << std::endl;
+    std::cout << "Row 2    0       0       0       4       1.3     1.3     0       0  " << std::endl;
+    std::cout << "Row 3    4       4       4       4       6       6       4       4  " << std::endl;
+    std::cout << "Row 4    1.3     1.3     1.3     6       1.3     1.3     1.3     1.3" << std::endl;
+    std::cout << "Row 5    1.3     1.3     1.3     6       1.3     1.3     1.3     1.3" << std::endl;
+    std::cout << "Row 6    0       0       0       4       1.3     1.3     0       0  " << std::endl;
+    std::cout << "Row 7    0       0       0       4       1.3     1.3     0       0  " << std::endl;
+
+    std::cout << "After arranging dimer coef" << std::endl;
+    std::cout << SCoef << std::endl;
+
+    for (int i = 0; i < 8; ++i) {
+      if (i != 3) {
+        REQUIRE(SCoef(i, 4) == Approx(1.3));
+        REQUIRE(SCoef(i, 5) == Approx(1.3));
+
+        REQUIRE(SCoef(4, i) == Approx(1.3));
+        REQUIRE(SCoef(5, i) == Approx(1.3));
+      }
+    }
+
+    for (int i = 0; i < 8; ++i) {
+      if (i == 4 || i == 5) {
+        REQUIRE(SCoef(i, 3) == Approx(6));
+        REQUIRE(SCoef(3, i) == Approx(6));
+      } else {
+        REQUIRE(SCoef(3, i) == Approx(4));
+        REQUIRE(SCoef(i, 3) == Approx(4));
+      }
+    }
+  }
+}

From e9f9fd3dd432d300b19c1b503c014784ed6b8279 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 24 Jul 2020 21:47:01 -0600
Subject: [PATCH 48/68] Add missing header file

---
 src/libcatnip/swap_engine.hpp | 84 +++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 src/libcatnip/swap_engine.hpp

diff --git a/src/libcatnip/swap_engine.hpp b/src/libcatnip/swap_engine.hpp
new file mode 100644
index 0000000..a673b17
--- /dev/null
+++ b/src/libcatnip/swap_engine.hpp
@@ -0,0 +1,84 @@
+
+
+#include "swap_engine.hpp"
+
+#include "atom.hpp"
+#include "atom_group.hpp"
+
+namespace catnip {
+
+  // Swaps rows columns and keeps up with how future swaps should be updated
+  class SwapEngine {
+    private:
+      size_t size_;
+      IndexMap ind_map_;
+      Eigen::MatrixXd scratch_;
+
+    public:
+      SwapEngine(IndexMap ind_map, size_t size) : 
+        size_(size), ind_map_(ind_map) {
+          scratch_ = Eigen::MatrixXd::Zero(size, 1);
+
+
+        // Already have enough information to calculate the correct swap order
+        // Note the order of swaps is important.
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            std::pair<int,int> swap(row,final_row);
+            // Now we need to update index map, the row located at the final 
+            // position has now been moved     
+            auto group_and_row_ind = ind_map_.findLocation(final_row);
+            
+            // Final row location needs to be pointed to the starting row
+            ind_map_.row_col_init[group_and_row_ind.first].at(group_and_row_ind.second) = row;
+          } 
+        }
+      };
+
+
+      // This method of swapping was chosen to keep the memory footprint
+      // reasonable.
+      // Will correctly sort the rows and columns of the matrix
+      void arrange(Eigen::MatrixXd & mat) {
+
+        // Check that matrix is square
+        if( mat.rows() != mat.cols() ) {
+          throw std::runtime_error("Can only arrange square matrices");
+        }
+        if( mat.rows() != size_ ) {
+          throw std::runtime_error("Index map has different number of basis functions to matrix");
+        }
+
+        for ( std::pair<int, std::vector<int>> group_row : ind_map_.row_col_init ){
+          int group_ind = group_row.first;
+          for ( int row : group_row.second ) {
+            int final_row = ind_map_.row_col_final[group_ind].at(row);
+            if(final_row == row ) continue;
+            // Copy the data at the final row into the scratch space 
+            scratch_.col(0) = mat.row(final_row);
+            // Copy the data from the initial row into the final row
+            mat.row(final_row) = mat.row(row);
+            // Copy the data from the temporary row into the initial row
+            mat.row(row) = scratch_.col(0);
+          }
+        }
+
+        // Repeat for columns 
+        for ( std::pair<int, std::vector<int>> group_col : ind_map_.row_col_init ){
+          int group_ind = group_col.first;
+          for ( int col : group_col.second ) {
+            int final_col = ind_map_.row_col_final[group_ind].at(col);
+            if(final_col == col ) continue;
+            // Copy the data at the final row into the scratch space
+            scratch_.col(0) = mat.col(final_col);
+            // Copy the data from the initial row into the final row
+            mat.col(final_col) = mat.col(col);
+            // Copy the data from the temporary row into the initial row
+            mat.col(col) = scratch_.col(0);
+          }
+        }
+      }
+  };
+}  // namespace catnip

From 7d18f35f2356fe3cc83a7219105d307c02d0bb22 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 24 Jul 2020 21:47:23 -0600
Subject: [PATCH 49/68] Small fix to CMakeLists.txt

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 93d229e..0498611 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,7 +22,7 @@ set(calcJ_TITLE "\"CATNIP\"")
 set(calcJ_URL "\"https://github.com/JoshuaSBrown/QC_Tools\"" )
 set(COVERAGE_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 set(COMMON_LIBRARIES stdc++ m)
-set(LOG_LEVEL 0 CACHE INT "Choose the log level" )
+set(LOG_LEVEL 0 CACHE STRING "Choose the log level" )
 # Prevents multiple file extensions from being appended one after the other
 # important for using gcov .o.gcno or .cpp.gcno now will be .gcno
 set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE 1)

From 7c6d40e2950a08fcf0fceeba1624999c31e4c874 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 24 Jul 2020 21:58:43 -0600
Subject: [PATCH 50/68] Add back missing executable

---
 src/tools/calcJ.cpp | 172 ++++++++++++++++++++++++++++++++++++++++++++
 src/tools/main.cpp  | 172 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 344 insertions(+)
 create mode 100644 src/tools/calcJ.cpp
 create mode 100644 src/tools/main.cpp

diff --git a/src/tools/calcJ.cpp b/src/tools/calcJ.cpp
new file mode 100644
index 0000000..51098f2
--- /dev/null
+++ b/src/tools/calcJ.cpp
@@ -0,0 +1,172 @@
+#include <algorithm>
+#include <cctype>
+#include <cstdlib>
+#include <cstring>
+#include <fstream>
+#include <functional>
+#include <iostream>
+#include <locale>
+#include <math.h>
+#include <sstream>
+#include <string>
+#include <sys/stat.h>
+#include <vector>
+
+#include "../libcatnip/io/argumentparser.hpp"
+#include "../libcatnip/io/file_readers/logreader.hpp"
+#include "../libcatnip/io/file_readers/punreader.hpp"
+#include "../libcatnip/io/io.hpp"
+#include "../libcatnip/log.hpp"
+#include "../libcatnip/parameters.hpp"
+#include "../libcatnip/qc_functions.hpp"
+#include "../libcatnip/matrix.hpp"
+#include "../libcatnip/calcJconfig.hpp"
+
+#include <eigen3/Eigen/Core>
+
+using namespace catnip;
+using namespace std;
+
+int main(int argc, const char *argv[]) {
+  cout << endl;
+  cout << "Running calc_J VERSION " << calcJ_VERSION_MAJOR << ".";
+  cout << calcJ_VERSION_MINOR << endl;
+
+  string line;
+  LOG("Preparing parser", 1);
+  auto ArgPars = prepareParser();
+  LOG("Parsing arguments", 1);
+  ArgPars->parse(argv, argc);
+  LOG("Preparing parameter object", 1);
+  auto par = prepareParameters(ArgPars);
+
+  cout << "log file for first monomer is:      " + par->getLog1() + '\n';
+  cout << "log file for second monomer is:     " + par->getLog2() + '\n';
+  cout << "log file for dimer is:              " + par->getLogP() + '\n';
+  cout << "pun file for the first monomer is:  " + par->getPun1() + '\n';
+  cout << "pun file for the second monomer is: " + par->getPun2() + '\n';
+  cout << "pun file for the dimer is:          " + par->getPunP() + '\n';
+
+  // Open the .pun file find the total number of molecular orbitals
+
+  LOG("Reading pun files", 1);
+  LOG("Reading pun file: " + par->getPunP(), 2);
+  PunReader pr_P(par->getPunP());
+  pr_P.read();
+  LOG("Reading pun file: " + par->getPun1(), 2);
+  PunReader pr_1(par->getPun1());
+  pr_1.read();
+  LOG("Reading pun file: " + par->getPun2(), 2);
+  PunReader pr_2(par->getPun2());
+  pr_2.read();
+
+  LOG("Reading log files", 1);
+  LOG("Reading log file: " + par->getLogP(), 2);
+  LogReader lr_P(par->getLogP());
+  lr_P.read();
+  LOG("Reading log file: " + par->getLog1(), 2);
+  LogReader lr_1(par->getLog1());
+  lr_1.read();
+  LOG("Reading log file: " + par->getLog2(), 2);
+  LogReader lr_2(par->getLog2());
+  lr_2.read();
+  // Load in general coefficients
+
+  // If there are only alpha orbitals then we can assume that restricted HF
+  // was used
+
+  // No need to worry about beta orbitals
+
+  {
+    Eigen::MatrixXd mat_S = lr_P.getOverlapMatrix();
+
+    Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
+    
+    Eigen::VectorXd vec_P_OE = Eigen::VectorXd(lr_P.getOE(par->getSpinP()));
+
+    int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
+    LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
+    Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
+    Eigen::VectorXd vec_1_OE = lr_1.getOE(par->getSpin1());
+
+    int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
+    LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
+    Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
+    Eigen::VectorXd vec_2_OE = lr_2.getOE(par->getSpin2());
+
+    // Unscramble dimer coef and energies first need to see how the dimer
+    // and monomer coefficients line up. To determine how the ceofficients
+    // line up we will first look at how the atoms appear in each of the
+    // .gjf files. We will also check to see how many coefficients are
+    // assocaited with each of the atoms by checking the .log files. Given
+    // the position of the atoms in the monomer unit and the positions of
+    // the atoms in the dimer we can determine how the coefficients need
+    // to be rearranged.
+    vector<vector<double>> coord_P = lr_P.getCoords();
+    vector<vector<double>> coord_1 = lr_1.getCoords();
+    vector<vector<double>> coord_2 = lr_2.getCoords();
+
+    // Convert coords to matrices
+    Eigen::MatrixXd coord_P_mat = convert(coord_P);
+    Eigen::MatrixXd coord_1_mat = convert(coord_1);
+    Eigen::MatrixXd coord_2_mat = convert(coord_2);
+
+    vector<int> basis_P = lr_P.getBasisFuncCount();
+    vector<int> basis_1 = lr_1.getBasisFuncCount();
+    vector<int> basis_2 = lr_2.getBasisFuncCount();
+
+    LOG("Creating transfercomplex", 1);
+    TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, HOMO1, HOMO2, mat_S,
+                       vec_P_OE, par->getCounterPoise());
+
+    // Set the transfer complex to counterpoise if it is the case.
+    // If the basis function search returns 0 for any of the components then
+    // we cannot automatically determine what the transfer integral is
+    if (basis_1.size() != 0 && basis_2.size() != 0 && basis_P.size() != 0) {
+      LOG("Unscrambling matrices", 1);
+      TC.unscramble(coord_1_mat, coord_2_mat, coord_P_mat, basis_P, basis_2);
+    } 
+
+    cout << endl;
+    cout << "Dimer     Spin " << par->getSpinP() << endl;
+
+    cout << "Monomer 1 Spin " << par->getSpin1() << " ";
+    if (par->getOrbNum1() == 0) {
+      cout << "Orbital " << par->getOrbType1() << endl;
+    } else if (par->getOrbNum1() > 0) {
+      cout << "Orbital " << par->getOrbType1();
+      cout << "+" << par->getOrbNum1() << endl;
+    } else {
+      cout << "Orbital " << par->getOrbType1();
+      cout << par->getOrbNum1() << endl;
+    }
+
+    cout << "Monomer 2 Spin " << par->getSpin2() << " ";
+    if (par->getOrbNum2() == 0) {
+      cout << "Orbital " << par->getOrbType2() << endl;
+    } else if (par->getOrbNum2() > 0) {
+      cout << "Orbital " << par->getOrbType2();
+      cout << "+" << par->getOrbNum2() << endl;
+    } else {
+      cout << "Orbital " << par->getOrbType2();
+      cout << par->getOrbNum2() << endl;
+    }
+
+    map<string, string> orbitaltypes;
+    map<string, int> orbitalnums;
+    orbitaltypes["mon1"] = par->getOrbType1();
+    orbitaltypes["mon2"] = par->getOrbType2();
+    orbitalnums["mon1"] = par->getOrbNum1();
+    orbitalnums["mon2"] = par->getOrbNum2();
+
+    LOG("Calculating transfer integral", 1);
+    TC.calcJ();
+    if(par->getPrintSwitch()){
+      TC.printAll();
+    }else{
+      TC.printTransferIntegral(orbitaltypes, orbitalnums);
+    }
+  }
+
+  return 0;
+}
diff --git a/src/tools/main.cpp b/src/tools/main.cpp
new file mode 100644
index 0000000..51098f2
--- /dev/null
+++ b/src/tools/main.cpp
@@ -0,0 +1,172 @@
+#include <algorithm>
+#include <cctype>
+#include <cstdlib>
+#include <cstring>
+#include <fstream>
+#include <functional>
+#include <iostream>
+#include <locale>
+#include <math.h>
+#include <sstream>
+#include <string>
+#include <sys/stat.h>
+#include <vector>
+
+#include "../libcatnip/io/argumentparser.hpp"
+#include "../libcatnip/io/file_readers/logreader.hpp"
+#include "../libcatnip/io/file_readers/punreader.hpp"
+#include "../libcatnip/io/io.hpp"
+#include "../libcatnip/log.hpp"
+#include "../libcatnip/parameters.hpp"
+#include "../libcatnip/qc_functions.hpp"
+#include "../libcatnip/matrix.hpp"
+#include "../libcatnip/calcJconfig.hpp"
+
+#include <eigen3/Eigen/Core>
+
+using namespace catnip;
+using namespace std;
+
+int main(int argc, const char *argv[]) {
+  cout << endl;
+  cout << "Running calc_J VERSION " << calcJ_VERSION_MAJOR << ".";
+  cout << calcJ_VERSION_MINOR << endl;
+
+  string line;
+  LOG("Preparing parser", 1);
+  auto ArgPars = prepareParser();
+  LOG("Parsing arguments", 1);
+  ArgPars->parse(argv, argc);
+  LOG("Preparing parameter object", 1);
+  auto par = prepareParameters(ArgPars);
+
+  cout << "log file for first monomer is:      " + par->getLog1() + '\n';
+  cout << "log file for second monomer is:     " + par->getLog2() + '\n';
+  cout << "log file for dimer is:              " + par->getLogP() + '\n';
+  cout << "pun file for the first monomer is:  " + par->getPun1() + '\n';
+  cout << "pun file for the second monomer is: " + par->getPun2() + '\n';
+  cout << "pun file for the dimer is:          " + par->getPunP() + '\n';
+
+  // Open the .pun file find the total number of molecular orbitals
+
+  LOG("Reading pun files", 1);
+  LOG("Reading pun file: " + par->getPunP(), 2);
+  PunReader pr_P(par->getPunP());
+  pr_P.read();
+  LOG("Reading pun file: " + par->getPun1(), 2);
+  PunReader pr_1(par->getPun1());
+  pr_1.read();
+  LOG("Reading pun file: " + par->getPun2(), 2);
+  PunReader pr_2(par->getPun2());
+  pr_2.read();
+
+  LOG("Reading log files", 1);
+  LOG("Reading log file: " + par->getLogP(), 2);
+  LogReader lr_P(par->getLogP());
+  lr_P.read();
+  LOG("Reading log file: " + par->getLog1(), 2);
+  LogReader lr_1(par->getLog1());
+  lr_1.read();
+  LOG("Reading log file: " + par->getLog2(), 2);
+  LogReader lr_2(par->getLog2());
+  lr_2.read();
+  // Load in general coefficients
+
+  // If there are only alpha orbitals then we can assume that restricted HF
+  // was used
+
+  // No need to worry about beta orbitals
+
+  {
+    Eigen::MatrixXd mat_S = lr_P.getOverlapMatrix();
+
+    Eigen::MatrixXd mat_P_Coef = pr_P.getCoefsMatrix(par->getSpinP());
+    
+    Eigen::VectorXd vec_P_OE = Eigen::VectorXd(lr_P.getOE(par->getSpinP()));
+
+    int HOMO1 = lr_1.getHOMOLevel(par->getSpin1());
+    LOG("Getting " + par->getSpin1() + " of monomer 1", 2);
+    Eigen::MatrixXd mat_1_Coef = pr_1.getCoefsMatrix(par->getSpin1());
+    Eigen::VectorXd vec_1_OE = lr_1.getOE(par->getSpin1());
+
+    int HOMO2 = lr_2.getHOMOLevel(par->getSpin2());
+    LOG("Getting " + par->getSpin2() + " of monomer 2", 2);
+    Eigen::MatrixXd mat_2_Coef = pr_2.getCoefsMatrix(par->getSpin2());
+    Eigen::VectorXd vec_2_OE = lr_2.getOE(par->getSpin2());
+
+    // Unscramble dimer coef and energies first need to see how the dimer
+    // and monomer coefficients line up. To determine how the ceofficients
+    // line up we will first look at how the atoms appear in each of the
+    // .gjf files. We will also check to see how many coefficients are
+    // assocaited with each of the atoms by checking the .log files. Given
+    // the position of the atoms in the monomer unit and the positions of
+    // the atoms in the dimer we can determine how the coefficients need
+    // to be rearranged.
+    vector<vector<double>> coord_P = lr_P.getCoords();
+    vector<vector<double>> coord_1 = lr_1.getCoords();
+    vector<vector<double>> coord_2 = lr_2.getCoords();
+
+    // Convert coords to matrices
+    Eigen::MatrixXd coord_P_mat = convert(coord_P);
+    Eigen::MatrixXd coord_1_mat = convert(coord_1);
+    Eigen::MatrixXd coord_2_mat = convert(coord_2);
+
+    vector<int> basis_P = lr_P.getBasisFuncCount();
+    vector<int> basis_1 = lr_1.getBasisFuncCount();
+    vector<int> basis_2 = lr_2.getBasisFuncCount();
+
+    LOG("Creating transfercomplex", 1);
+    TransferComplex TC(mat_1_Coef, mat_2_Coef, mat_P_Coef, HOMO1, HOMO2, mat_S,
+                       vec_P_OE, par->getCounterPoise());
+
+    // Set the transfer complex to counterpoise if it is the case.
+    // If the basis function search returns 0 for any of the components then
+    // we cannot automatically determine what the transfer integral is
+    if (basis_1.size() != 0 && basis_2.size() != 0 && basis_P.size() != 0) {
+      LOG("Unscrambling matrices", 1);
+      TC.unscramble(coord_1_mat, coord_2_mat, coord_P_mat, basis_P, basis_2);
+    } 
+
+    cout << endl;
+    cout << "Dimer     Spin " << par->getSpinP() << endl;
+
+    cout << "Monomer 1 Spin " << par->getSpin1() << " ";
+    if (par->getOrbNum1() == 0) {
+      cout << "Orbital " << par->getOrbType1() << endl;
+    } else if (par->getOrbNum1() > 0) {
+      cout << "Orbital " << par->getOrbType1();
+      cout << "+" << par->getOrbNum1() << endl;
+    } else {
+      cout << "Orbital " << par->getOrbType1();
+      cout << par->getOrbNum1() << endl;
+    }
+
+    cout << "Monomer 2 Spin " << par->getSpin2() << " ";
+    if (par->getOrbNum2() == 0) {
+      cout << "Orbital " << par->getOrbType2() << endl;
+    } else if (par->getOrbNum2() > 0) {
+      cout << "Orbital " << par->getOrbType2();
+      cout << "+" << par->getOrbNum2() << endl;
+    } else {
+      cout << "Orbital " << par->getOrbType2();
+      cout << par->getOrbNum2() << endl;
+    }
+
+    map<string, string> orbitaltypes;
+    map<string, int> orbitalnums;
+    orbitaltypes["mon1"] = par->getOrbType1();
+    orbitaltypes["mon2"] = par->getOrbType2();
+    orbitalnums["mon1"] = par->getOrbNum1();
+    orbitalnums["mon2"] = par->getOrbNum2();
+
+    LOG("Calculating transfer integral", 1);
+    TC.calcJ();
+    if(par->getPrintSwitch()){
+      TC.printAll();
+    }else{
+      TC.printTransferIntegral(orbitaltypes, orbitalnums);
+    }
+  }
+
+  return 0;
+}

From 2dc07653ee8fa0734313bae4f877045fd325122b Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 18:52:38 -0600
Subject: [PATCH 51/68] Add CMakeLists.txt file for binary

---
 src/tools/CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 src/tools/CMakeLists.txt

diff --git a/src/tools/CMakeLists.txt b/src/tools/CMakeLists.txt
new file mode 100644
index 0000000..30e0830
--- /dev/null
+++ b/src/tools/CMakeLists.txt
@@ -0,0 +1,5 @@
+add_executable(calcJ calcJ.cpp)
+target_link_libraries(calcJ libcatnip)
+install(TARGETS calcJ EXPORT VOTCA_CSG_Targets RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+add_executable(CATNIP::calcJ ALIAS calcJ)
+set_property(TARGET catnip APPEND PROPERTY BINARIES "calcJ")

From 89d55e7d3f37b44fca88857e741b0b8814b0f3ba Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 18:53:53 -0600
Subject: [PATCH 52/68] Switch project name to catnip as opposed to calcJ

---
 CMakeLists.txt | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0498611..6cf6edb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,13 +13,13 @@ option(CODE_COVERAGE "Enable coverage reporting" OFF)
 ##############################################################################
 # Defining settings 
 ##############################################################################
-set(calcJ_VERSION_MAJOR 2 )
-set(calcJ_VERSION_MINOR 0 )
-set(calcJ_YEAR_PUBLISHED 2018 )
-set(calcJ_AUTHOR_SURNAME "\"Brown\"" )
-set(calcJ_AUTHOR_INITIALS "\"J. S.\"" )
-set(calcJ_TITLE "\"CATNIP\"")
-set(calcJ_URL "\"https://github.com/JoshuaSBrown/QC_Tools\"" )
+set(catnip_VERSION_MAJOR 2 )
+set(catnip_VERSION_MINOR 0 )
+set(catnip_YEAR_PUBLISHED 2018 )
+set(catnip_AUTHOR_SURNAME "\"Brown\"" )
+set(catnip_AUTHOR_INITIALS "\"J. S.\"" )
+set(catnip_TITLE "\"CATNIP\"")
+set(catnip_URL "\"https://github.com/JoshuaSBrown/QC_Tools\"" )
 set(COVERAGE_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 set(COMMON_LIBRARIES stdc++ m)
 set(LOG_LEVEL 0 CACHE STRING "Choose the log level" )
@@ -32,8 +32,8 @@ set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -Werror")
 ##############################################################################
 # Configure header file to pass some of the CMake settings to the source code
 configure_file(
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/calcJconfig.hpp.in"
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/calcJconfig.hpp"
+  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnipconfig.hpp.in"
+  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnipconfig.hpp"
   )
 
 ##############################################################################
@@ -103,7 +103,7 @@ endif()
 # Compiling build tree/paths 
 ##############################################################################
 # Add the binary tree to the search path for include files
-# so that we will find calcJconfig.hpp
+# so that we will find catnipconfig.hpp
 #target_include_directories(calc_J "${PROJECT_BINARY_DIR}/src")
 #target_link_directories(calc_J "${PROJECT_BINARY_DIR}/src")
 

From 2b084ae293acc01298d3b277ebe10a8274b20ac4 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 18:55:12 -0600
Subject: [PATCH 53/68] move calcJ config file to catnip config file

---
 src/libcatnip/catnip_config.hpp.in | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 src/libcatnip/catnip_config.hpp.in

diff --git a/src/libcatnip/catnip_config.hpp.in b/src/libcatnip/catnip_config.hpp.in
new file mode 100644
index 0000000..4632328
--- /dev/null
+++ b/src/libcatnip/catnip_config.hpp.in
@@ -0,0 +1,18 @@
+// Configured options and settings for catnip
+
+#ifndef CATNIP_CONFIG_HPP
+#define CATNIP_CONFIG_HPP
+
+#include <string>
+
+namespace catnip {
+  const int catnip_VERSION_MAJOR = @catnip_VERSION_MAJOR@;
+  const int catnip_VERSION_MINOR = @catnip_VERSION_MINOR@;
+  const int catnip_YEAR_PUBLISHED = @catnip_YEAR_PUBLISHED@;
+  const std::string catnip_AUTHOR_SURNAME = @catnip_AUTHOR_SURNAME@;
+  const std::string catnip_AUTHOR_INITIALS = @catnip_AUTHOR_INITIALS@;
+  const std::string catnip_TITLE = @catnip_TITLE@;
+  const std::string catnip_URL = @catnip_URL@;
+}  // namespace catnip
+
+#endif  // CATNIP_CONFIG_HPP

From f007e82f73c6759c79c76c13234553a9d3a4c15c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 19:06:31 -0600
Subject: [PATCH 54/68] bump cmake version

---
 CMakeLists.txt                |  8 ++++----
 src/libcatnip/calcJconfig.hpp | 18 ------------------
 2 files changed, 4 insertions(+), 22 deletions(-)
 delete mode 100644 src/libcatnip/calcJconfig.hpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6cf6edb..d987fa0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
-cmake_minimum_required (VERSION 2.8)
-project (calc_J)
+cmake_minimum_required (VERSION 3.14)
+project (catnip)
 
 ##############################################################################
 # Defining options 
@@ -32,8 +32,8 @@ set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -Werror")
 ##############################################################################
 # Configure header file to pass some of the CMake settings to the source code
 configure_file(
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnipconfig.hpp.in"
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnipconfig.hpp"
+  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnip_config.hpp.in"
+  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnip_config.hpp"
   )
 
 ##############################################################################
diff --git a/src/libcatnip/calcJconfig.hpp b/src/libcatnip/calcJconfig.hpp
deleted file mode 100644
index e574fe9..0000000
--- a/src/libcatnip/calcJconfig.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-// Configured options and settings for calcJ
-
-#ifndef CATNIP_CONFIG_HPP
-#define CATNIP_CONFIG_HPP
-
-#include <string>
-
-namespace catnip {
-const int calcJ_VERSION_MAJOR = 2;
-const int calcJ_VERSION_MINOR = 0;
-const int calcJ_YEAR_PUBLISHED = 2018;
-const std::string calcJ_AUTHOR_SURNAME = "Brown";
-const std::string calcJ_AUTHOR_INITIALS = "J. S.";
-const std::string calcJ_TITLE = "CATNIP";
-const std::string calcJ_URL = "https://github.com/JoshuaSBrown/QC_Tools";
-}  // namespace catnip
-
-#endif  // CATNIP_CONFIG_HPP

From 489e6256df9b978a039a99be29c91bb50ab79239 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 19:14:11 -0600
Subject: [PATCH 55/68] Fix small issues

---
 src/libcatnip/atom_group.hpp       | 20 +++++++++++++++++++-
 src/libcatnip/transfer_complex.cpp |  8 ++++++++
 src/libcatnip/transfer_complex.hpp | 10 +++++++---
 3 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index a47069e..e998fa9 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -11,6 +11,7 @@
 #include <memory>
 #include <numeric>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
 namespace catnip {
@@ -39,6 +40,11 @@ namespace catnip {
     Unassigned
   };
 
+  enum class MatrixType {
+    Overlap,
+    Coefficients,
+    MolecularOrbitalsEnergies
+  };
   /**
    * @brief Stores the name of the atom group, the group type and the atoms in
    * the group
@@ -48,10 +54,22 @@ namespace catnip {
     private: 
       GroupType type_ = GroupType::Unassigned;
       std::string name_;
+      // Files associated with this atom_group
+      std::vector<std::string> file_names_;
+      // Matries associated with the atom group
+      std::unordered_map<MatrixType,std::unique_ptr<Eigen::MatrixXd>> matrices_;
       std::vector<std::shared_ptr<Atom>> atoms_;
     public:
       AtomGroup(std::string group_name) : name_(group_name) {};
-    
+   
+      void addFile(const std::string file_name) { file_names_.push_back(file_name); }
+      
+      void addMatrix(const MatrixType type, std::unique_ptr<Eigen::MatrixXd> mat) { matrices_[type] = std::move(mat); }
+
+      // Attempt to load overlap matrix hopefully a log file exists which can do
+      // this
+      void loadOverlapMatrix() {};
+
       std::string getName() const noexcept { return name_; }
 
       size_t size() const noexcept { return atoms_.size(); }
diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
index 3638ac8..03e090c 100644
--- a/src/libcatnip/transfer_complex.cpp
+++ b/src/libcatnip/transfer_complex.cpp
@@ -28,6 +28,14 @@ namespace catnip {
     swap_eng.arrange(*(params_->complex_coefs));
     swap_eng.arrange(*(params_->S_AO));
 
+    auto dimension = mat_1_Coef.cols()+mat_2_Coef.cols();
+    Eigen::MatrixXd zetaA(mat_1_Coef.rows(),dimension);
+    Eigen::MatrixXd zetaB(mat_2_Coef.rows(),dimension);
+    if (params_->counter_poise) {
+
+    } else {
+
+    }
   }
 
   void TransferComplex::calcJ() {};
diff --git a/src/libcatnip/transfer_complex.hpp b/src/libcatnip/transfer_complex.hpp
index e580efd..2dbd63a 100644
--- a/src/libcatnip/transfer_complex.hpp
+++ b/src/libcatnip/transfer_complex.hpp
@@ -23,13 +23,17 @@ class TransferComplex {
 
     class Parameters {
       public:
-        const std::vector<std::unique_ptr<Eigen::MatrixXd>> monomers_coefs;
-        const std::unique_ptr<Eigen::MatrixXd> complex_coefs;
+
+        // It actually makes more sense to place these in the atom groups
+        //const std::vector<std::unique_ptr<Eigen::MatrixXd>> monomers_coefs;
+        //const std::unique_ptr<Eigen::MatrixXd> complex_coefs;
         /// Location of each of the homo_orbitals in each of the monomers
-        const std::vector<int> homo_orbitals;
+        //const std::vector<int> homo_orbitals;
         //HOMO_A;
         //const int HOMO_B;
         /// Atomic Orbital overlap matrix
+        
+        // The Overlap matrix can be added simply when it is needed  
         const std::unique_ptr<Eigen::MatrixXd> S_AO;
         const std::unique_ptr<Eigen::VectorXd> complex_orbital_energies;
         /// Counter poise flag

From 271ebee54988220e8b81eaad79edc27b10104ef9 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 19:14:33 -0600
Subject: [PATCH 56/68] Add missing files

---
 src/libcatnip/basis_map.cpp | 79 +++++++++++++++++++++++++++++++++++++
 src/libcatnip/basis_map.hpp | 45 +++++++++++++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 src/libcatnip/basis_map.cpp
 create mode 100644 src/libcatnip/basis_map.hpp

diff --git a/src/libcatnip/basis_map.cpp b/src/libcatnip/basis_map.cpp
new file mode 100644
index 0000000..67e639e
--- /dev/null
+++ b/src/libcatnip/basis_map.cpp
@@ -0,0 +1,79 @@
+
+
+#include "basis_map.hpp"
+
+#include "atom.hpp"
+#include "atom_system.hpp"
+
+// Standard includes
+#include <cassert>
+#include <iostream>
+
+namespace catnip {
+
+  BasisMap::BasisMap(AtomSystem atm_sys){
+    if ( not atm_sys.systemComplete() ) {
+      throw std::runtime_error("Cannot build an index map from an incomplete "
+          "atom system.");
+    }
+
+    // 1. map each of the atoms in complex to an offset based on the number 
+    // of basis functions up to that point, 
+    // E.g.
+    // atom1 2 basis functs
+    // atom2 3 basis functs
+    // atom3 1 basis functs
+    //
+    // offset_map[0] = 0; // atom1
+    // offset_map[1] = 2; // atom2
+    // offset_map[2] = 5; // atom3
+
+    std::unordered_map<int,int> offset_map;
+    const AtomGroup & complex_grp = atm_sys.getComplex();
+    int offset = 0;
+    int complex_atm_ind = 0;
+    for ( const std::shared_ptr<Atom> & atm_ptr : complex_grp){
+      offset_map[complex_atm_ind] = offset;
+      offset += atm_ptr->getBasisFuncCount();
+      ++complex_atm_ind;
+    } 
+
+    std::vector<int> component_indices = atm_sys.getComponentIndices();
+    int sys_ind = 0;
+    for ( int & component_ind : component_indices) {
+      const AtomGroup & component_grp = atm_sys.at(component_ind);
+      std::cout << "Component grp " << component_grp.getName() << " component ind " << component_ind << " size " << component_grp.size() << std::endl;
+      for( const std::shared_ptr<Atom> & atm_ptr : component_grp){
+        std::vector<int> atm_indices = complex_grp.find(atm_ptr->getPos());
+        assert(atm_indices.size() == 1);
+        int atm_ind = atm_indices.at(0);
+        int num_basis = complex_grp.at(atm_ind)->getBasisFuncCount();
+        int complex_offset = offset_map[atm_ind];
+
+        for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
+          // Where the row would ideally be located
+          row_col_final[component_ind].push_back(sys_ind); 
+          // Where the row of the component is currently located
+          row_col_current[component_ind].push_back(complex_offset+ind_temp);
+          sys_ind++;
+        }
+      }
+    }
+  }
+
+  // Searches the current row for the provided row and returns the group it is
+  // in as well as its current index
+  std::pair<int,int> BasisMap::findLocation(int row){
+    for( std::pair<int,std::vector<int>> group_rows : row_col_current){
+      int row_ind = 0;
+      for ( int row_ : group_rows.second ){
+        if (row_ == row){
+          return std::pair<int,int>(group_rows.first, row_ind);
+        }
+        ++row_ind;
+      } 
+    }
+    return std::pair<int,int>();
+  }
+
+}  // namespace catnip
diff --git a/src/libcatnip/basis_map.hpp b/src/libcatnip/basis_map.hpp
new file mode 100644
index 0000000..42517ab
--- /dev/null
+++ b/src/libcatnip/basis_map.hpp
@@ -0,0 +1,45 @@
+
+#pragma once
+#ifndef _CATNIP_INDEX_MAP_HPP
+#define _CATNIP_INDEX_MAP_HPP
+
+// Local private includes
+#include "atom_system.hpp"
+
+// Standard includes
+#include <map>
+#include <vector>
+
+namespace catnip {
+
+
+  /**
+   * @brief This class tracks how the basis functions map to the rows in the 
+   * complex
+   */
+  class BasisMap {
+    public:
+      BasisMap() = default;
+      BasisMap(AtomSystem atm_sys);
+      // The component rows and colums in their current locations in  
+      // in the full system matrix of the complex
+      std::map<int,std::vector<int>> row_col_current;
+
+      // Map indicate where the rows and cols should go in the final state
+      // Each int in the vector represents the location in the full system matrix
+      std::map<int,std::vector<int>> row_col_final;
+
+      /**
+       * @brief Given a row of the complex finds it's location in one of the 
+       * components
+       *
+       * @param row_complex
+       *
+       * @return 
+       */
+      std::pair<int,int> findLocation(int row_complex);
+  };
+
+
+}  // namespace catnip
+#endif // _CATNIP_INDEX_MAP_HPP

From 15bcb8fb63cb4f148875c779f077348aa3be9fb0 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 19:17:14 -0600
Subject: [PATCH 57/68] Small fix

---
 src/libcatnip/atom_group.hpp | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 6647207..1d8e6de 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -7,6 +7,7 @@
 #include <memory>
 #include <numeric>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
 #include <eigen3/Eigen/Dense>
@@ -25,6 +26,16 @@ namespace catnip {
     Unknown
   };
 
+  enum class FileType {
+    pun,
+    log
+  };
+
+  enum class MatrixType {
+    Overlap,
+    Coefficients,
+    MolecularOrbitalEnergies
+  };
   /**
    * @brief Stores the name of the atom group, the group type and the atoms in
    * the group
@@ -35,9 +46,15 @@ namespace catnip {
       GroupType type_ = GroupType::Unknown;
       std::string name_;
       std::vector<std::shared_ptr<Atom>> atoms_;
+      std::unordered_map<FileType,std::string> files_;
+      std::unordered_map<MatrixType,std::unique_ptr<Eigen::MatrixXd>> matrices_;
     public:
       AtomGroup(std::string group_name) : name_(group_name) {};
 
+      void addFile(FileType type, std::string file_name) {
+        files_[type] = file_name;
+      }
+
       size_t size() const noexcept { return atoms_.size(); }
 
       std::vector<std::shared_ptr<Atom>>::iterator 

From 781dc20405bd793aba9ff25e65dd7709b29c5b87 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 25 Jul 2020 19:45:21 -0600
Subject: [PATCH 58/68] Move to unique_ptrs to help with Memory issues because
 of large EIgen matrices

---
 src/libcatnip/atom_group.hpp           |   1 +
 src/libcatnip/atom_group_container.cpp |   2 +-
 src/libcatnip/atom_group_container.hpp |  14 ++--
 src/libcatnip/atom_system.cpp          | 110 ++++++++++++-------------
 src/libcatnip/atom_system.hpp          |  13 +--
 5 files changed, 71 insertions(+), 69 deletions(-)

diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 293503a..6f0ca80 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -67,6 +67,7 @@ namespace catnip {
       std::unordered_map<FileType,std::string> files_;
       std::unordered_map<MatrixType,std::unique_ptr<Eigen::MatrixXd>> matrices_;
     public:
+      AtomGroup() = default;
       AtomGroup(std::string group_name) : name_(group_name) {};
    
       void addFile(const std::string file_name) { file_names_.push_back(file_name); }
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 4e88000..1a61a4d 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -185,7 +185,7 @@ namespace catnip {
     std::cout << "Adding group " << atom_group.getName() << std::endl; 
     if( isUniqueGroup_(atom_group) ){
       std::cout << "Is unique" << std::endl;
-      atom_groups_.push_back(atom_group);
+      atom_groups_.push_back(std::move(atom_group));
     } else {
       return;
     }
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index 5570655..84697a1 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -27,7 +27,7 @@ namespace catnip {
    * are an island a complex or a component.
    */
   class AtomGroupContainer {
-      std::vector<AtomGroup> atom_groups_;
+      std::vector<std::unique_ptr<AtomGroup>> atom_groups_;
      
       bool group_types_uptodate_ = false; 
 
@@ -47,18 +47,18 @@ namespace catnip {
 
       // Invalidates groups if non const because cannot ensure that groups are
       // not changed
-      std::vector<AtomGroup>::iterator 
+      std::vector<std::unique_ptr<AtomGroup>>::iterator 
         begin() { group_types_uptodate_ = false; return atom_groups_.begin(); }
 
-      std::vector<AtomGroup>::const_iterator 
+      std::vector<std::unique_ptr<AtomGroup>>::const_iterator 
         begin() const { return atom_groups_.begin(); }
 
       // Invalidates groups if non const because cannot ensure that groups are
       // not changed
-      std::vector<AtomGroup>::iterator 
+      std::vector<std::unique_ptr<AtomGroup>>::iterator 
         end() { group_types_uptodate_ = false; return atom_groups_.end(); }
  
-      std::vector<AtomGroup>::const_iterator 
+      std::vector<std::unique_ptr<AtomGroup>>::const_iterator 
         end() const { return atom_groups_.end(); }
 
       void add( AtomGroup atom_group );
@@ -90,12 +90,12 @@ namespace catnip {
        */
       std::vector<int> getGroups(const GroupType & type) const noexcept;     
 
-      AtomGroup & at(size_t ind) { 
+      std::unique_ptr<AtomGroup> & at(size_t ind) { 
         group_types_uptodate_ = false; 
         return atom_groups_.at(ind);
       }
 
-      const AtomGroup & at(size_t ind) const { return   atom_groups_.at(ind);}
+      const std::unique_ptr<AtomGroup> & at(size_t ind) const { return   atom_groups_.at(ind);}
   };
 
   
diff --git a/src/libcatnip/atom_system.cpp b/src/libcatnip/atom_system.cpp
index 3d802b8..0043f74 100644
--- a/src/libcatnip/atom_system.cpp
+++ b/src/libcatnip/atom_system.cpp
@@ -27,11 +27,11 @@ namespace catnip {
   static void assignBasisFunctionsToSynchronisedAtoms_(
       int grp_ind, 
       const std::vector<int>& basis_func_count,
-      AtomGroup & grp,
-      AtomGroupContainer & atm_grp_cont ){
+      std::unique_ptr<AtomGroup> & grp,
+      std::unique_ptr<AtomGroupContainer> & atm_grp_cont ){
 
     int index = 0; 
-    for( std::shared_ptr<Atom> & atom_ptr : grp ){
+    for( std::shared_ptr<Atom> & atom_ptr : *grp ){
       std::cout << "Assigning basis function atom at index " << index << std::endl;
       if( atom_ptr->getBasisFuncCount() == -1){
         atom_ptr->setBasisFuncCount(basis_func_count.at(index));
@@ -51,15 +51,15 @@ namespace catnip {
 
   static void checkLinkedAtomsInComplexForConsistentBasisFunctionCounts(
       int grp_ind, 
-      const AtomGroup & grp,
-      AtomGroupContainer & atm_grp_cont,
+      const std::unique_ptr<AtomGroup> & grp,
+      std::unique_ptr<AtomGroupContainer> & atm_grp_cont,
       std::map<int,std::vector<std::pair<int,int>>> linked_atoms ){
 
     for ( auto grp_linked_atms : linked_atoms ){ 
-      const AtomGroup & component = atm_grp_cont.at(grp_linked_atms.first);
+      const std::unique_ptr<AtomGroup> & component = atm_grp_cont->at(grp_linked_atms.first);
       for( std::pair<int,int> linked_atoms : grp_linked_atms.second ){
-        if ( component.at(linked_atoms.first)->getBasisFuncCount() != -1){
-          if ( component.at(linked_atoms.first)->getBasisFuncCount() != grp.at(linked_atoms.second)->getBasisFuncCount()){
+        if ( component->at(linked_atoms.first)->getBasisFuncCount() != -1){
+          if ( component->at(linked_atoms.first)->getBasisFuncCount() != grp->at(linked_atoms.second)->getBasisFuncCount()){
             throw std::runtime_error("There are inconsistencies between the "
                 "the number of basis functions used in a linked atom. Atoms "
                 "in a component must contain the same number of basis "
@@ -72,17 +72,17 @@ namespace catnip {
 
   static void checkLinkedAtomsInComponentForConsistentBasisFunctionCounts(
       int grp_ind, 
-      const AtomGroup & grp,
-      AtomGroupContainer & atm_grp_cont,
+      const std::unique_ptr<AtomGroup> & grp,
+      std::unique_ptr<AtomGroupContainer> & atm_grp_cont,
       std::map<int,std::vector<std::pair<int,int>>> linked_atoms 
       ) {
 
-    std::vector<int> complex_grps = atm_grp_cont.getGroups(GroupType::Complex);
+    std::vector<int> complex_grps = atm_grp_cont->getGroups(GroupType::Complex);
     assert(complex_grps.size() == 1 && "There must be at least one complex");
-    const AtomGroup & complex_grp = atm_grp_cont.at(complex_grps.at(0));
+    const std::unique_ptr<AtomGroup> & complex_grp = atm_grp_cont->at(complex_grps.at(0));
     for( std::pair<int,int> linked_atoms : linked_atoms[grp_ind] ){
-      if ( complex_grp.at(linked_atoms.second)->getBasisFuncCount() != -1){
-        if ( complex_grp.at(linked_atoms.second)->getBasisFuncCount() != grp.at(linked_atoms.first)->getBasisFuncCount()){
+      if ( complex_grp->at(linked_atoms.second)->getBasisFuncCount() != -1){
+        if ( complex_grp->at(linked_atoms.second)->getBasisFuncCount() != grp->at(linked_atoms.first)->getBasisFuncCount()){
           throw std::runtime_error("There are inconsistencies between the "
               "the number of basis functions used in a linked atom. Atoms "
               "in a component must contain the same number of basis "
@@ -105,13 +105,13 @@ namespace catnip {
   static void assignBasisFuncs_(
       int grp_ind,
       const std::vector<int>& basis_func_count,
-      AtomGroupContainer & atm_grp_cont,
+      std::unique_ptr<AtomGroupContainer> & atm_grp_cont,
       std::map<int,std::vector<std::pair<int,int>>> linked_atoms 
       ) {
     // Cycle through the atoms in the complex and assign the correct number of
     // basis functions
   
-    AtomGroup & grp = atm_grp_cont.at(grp_ind);
+    std::unique_ptr<AtomGroup> & grp = atm_grp_cont->at(grp_ind);
     std::cout << "Assign to Synchronize atoms" << std::endl;
     assignBasisFunctionsToSynchronisedAtoms_(
       grp_ind, 
@@ -119,7 +119,7 @@ namespace catnip {
       grp,
       atm_grp_cont);
     // Make sure that there are no inconsistencies between the linked atoms
-    if ( atm_grp_cont.at(grp_ind).is(GroupType::Complex)){
+    if ( atm_grp_cont->at(grp_ind)->is(GroupType::Complex)){
       // If it is a complex
       std::cout << "Assign to Linked atoms in complex" << std::endl;
       checkLinkedAtomsInComplexForConsistentBasisFunctionCounts(
@@ -158,9 +158,9 @@ namespace catnip {
     return all_paired_atoms;
   }*/
 
-  static void checkValidSystemCriteria_(AtomGroupContainer & atm_grp_cont){
+  static void checkValidSystemCriteria_(std::unique_ptr<AtomGroupContainer> & atm_grp_cont){
     std::vector<int> complex_indices = 
-      atm_grp_cont.getGroups(GroupType::Complex);
+      atm_grp_cont->getGroups(GroupType::Complex);
 
     if( complex_indices.size() == 0 ){
       throw std::runtime_error("Cannot create atom system, no complexes were "
@@ -172,7 +172,7 @@ namespace catnip {
     }
 
     std::vector<int> component_indices = 
-      atm_grp_cont.getGroups(GroupType::Component);
+      atm_grp_cont->getGroups(GroupType::Component);
 
     if ( component_indices.size() < 2){
       throw std::runtime_error("Cannot create atom system, must contain at "
@@ -185,34 +185,34 @@ namespace catnip {
   // first int of the pair - index of the atom in the component
   // second int of the pair - index of the linked atom in the complex 
   static std::map<int,std::vector<std::pair<int,int>>> findNonConsistentAtoms_(
-      AtomGroupContainer & atm_grp_cont) {
+      std::unique_ptr<AtomGroupContainer> & atm_grp_cont) {
 
     std::map<int,std::vector<std::pair<int,int>>> linked_atoms;
     // Overwrite any of the pointers in the component that have the same atom
     // with the complex, with the atom pointer from the complex
     int complex_index = 
-      atm_grp_cont.getGroups(GroupType::Complex).at(0);
+      atm_grp_cont->getGroups(GroupType::Complex).at(0);
 
     std::vector<int> component_indices = 
-      atm_grp_cont.getGroups(GroupType::Component);
+      atm_grp_cont->getGroups(GroupType::Component);
 
-    AtomGroup & atm_complex = atm_grp_cont.at(complex_index);
+    std::unique_ptr<AtomGroup> & atm_complex = atm_grp_cont->at(complex_index);
     for ( const int component_ind : component_indices){
-      AtomGroup & atm_grp = atm_grp_cont.at(component_ind);
+      std::unique_ptr<AtomGroup> & atm_grp = atm_grp_cont->at(component_ind);
       // Cycle atoms in atm_grp 
       int ind_atm = 0;
-      for ( std::shared_ptr<Atom> & atm : atm_grp){
-        std::vector<int> complex_atm_ind = atm_complex.find(atm->getPos());
+      for ( std::shared_ptr<Atom> & atm : *atm_grp){
+        std::vector<int> complex_atm_ind = atm_complex->find(atm->getPos());
         // This vector must be of size 1
         if( complex_atm_ind.size() == 1){
           // If the elements dont' match it is non-consistent 
-          if( atm_complex.at(complex_atm_ind.at(0))->getElement() != atm_grp.at(ind_atm)->getElement() ){
+          if( atm_complex->at(complex_atm_ind.at(0))->getElement() != atm_grp->at(ind_atm)->getElement() ){
             linked_atoms[component_ind].push_back(std::pair<int,int>(ind_atm,complex_atm_ind.at(0)));
           }
         }else if (complex_atm_ind.size() == 0) {
           std::string error_msg = "A component atom did not have a matching "
-              "atom in the complex (" + atm_complex.getName() + "). The "
-              "atom in the component (" + atm_grp.getName() + ") does not have "
+              "atom in the complex (" + atm_complex->getName() + "). The "
+              "atom in the component (" + atm_grp->getName() + ") does not have "
               "to have the same element as the atom in the complex but must "
               "share the same position.";
           throw std::runtime_error(error_msg);
@@ -227,26 +227,26 @@ namespace catnip {
     return linked_atoms;
   }
 
-  static void synchroniseAtoms_(AtomGroupContainer & atm_grp_cont){
+  static void synchroniseAtoms_(std::unique_ptr<AtomGroupContainer> & atm_grp_cont){
 
     // Overwrite any of the pointers in the component that have the same atom
     // with the complex, with the atom pointer from the complex
     int complex_index = 
-      atm_grp_cont.getGroups(GroupType::Complex).at(0);
+      atm_grp_cont->getGroups(GroupType::Complex).at(0);
 
     std::vector<int> component_indices = 
-      atm_grp_cont.getGroups(GroupType::Component);
+      atm_grp_cont->getGroups(GroupType::Component);
 
-    AtomGroup & atm_complex = atm_grp_cont.at(complex_index);
+    std::unique_ptr<AtomGroup> & atm_complex = atm_grp_cont->at(complex_index);
     for ( const int component_ind : component_indices){
-      AtomGroup & atm_grp = atm_grp_cont.at(component_ind);
+      std::unique_ptr<AtomGroup> & atm_grp = atm_grp_cont->at(component_ind);
       // Cycle atoms in atm_grp 
-      for ( std::shared_ptr<Atom> & atm : atm_grp){
-        std::vector<int> complex_atm_ind = atm_complex.find(atm);
+      for ( std::shared_ptr<Atom> & atm : *atm_grp){
+        std::vector<int> complex_atm_ind = atm_complex->find(atm);
         // This vector should be 0 or 1
         if( complex_atm_ind.size() == 1){
           // Change the pointer
-          atm = atm_complex.at(complex_atm_ind.at(0)); 
+          atm = atm_complex->at(complex_atm_ind.at(0)); 
         }
       }
     }
@@ -264,13 +264,13 @@ namespace catnip {
    *
    * @param atm_grp_cont
    */
-  AtomSystem::AtomSystem(AtomGroupContainer atm_grp_cont) {
-    atm_grp_cont.assignGroupTypes();
+  AtomSystem::AtomSystem(std::unique_ptr<AtomGroupContainer> atm_grp_cont) {
+    atm_grp_cont->assignGroupTypes();
 
     checkValidSystemCriteria_(atm_grp_cont);
 
     std::vector<int> complex_indices = 
-      atm_grp_cont.getGroups(GroupType::Complex);
+      atm_grp_cont->getGroups(GroupType::Complex);
     index_complex_ = complex_indices.at(0);
     // Searches for atoms that exist in the component that share a position with
     // an atom in the complex, but are of a different element
@@ -281,15 +281,15 @@ namespace catnip {
     // in memory
     synchroniseAtoms_(atm_grp_cont);
 
-    atm_grp_cont_ = atm_grp_cont;
+    atm_grp_cont_ = std::move(atm_grp_cont);
   }
 
   int AtomSystem::getTotalBasisFunctions(const GroupType & type) const {
     int total_num_basis = 0;
-    std::vector<int> group_indices = atm_grp_cont_.getGroups(type);     
+    std::vector<int> group_indices = atm_grp_cont_->getGroups(type);     
     for ( int ind : group_indices ){
-      const AtomGroup & group = atm_grp_cont_.at(ind);
-      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+      const std::unique_ptr<AtomGroup> & group = atm_grp_cont_->at(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : *group ) {
         total_num_basis += atom_ptr->getBasisFuncCount();
       }
     } 
@@ -298,10 +298,10 @@ namespace catnip {
 
   int AtomSystem::getMaxBasisFunctions(const GroupType & type) const {
     int max_num_basis = 0;
-    std::vector<int> group_indices = atm_grp_cont_.getGroups(type);     
+    std::vector<int> group_indices = atm_grp_cont_->getGroups(type);     
     for ( int ind : group_indices ){
-      const AtomGroup & group = atm_grp_cont_.at(ind);
-      for( const std::shared_ptr<Atom> & atom_ptr : group ) {
+      const std::unique_ptr<AtomGroup> & group = atm_grp_cont_->at(ind);
+      for( const std::shared_ptr<Atom> & atom_ptr : *group ) {
         if( atom_ptr->getBasisFuncCount() > max_num_basis){
           max_num_basis = atom_ptr->getBasisFuncCount();
         }
@@ -316,7 +316,7 @@ namespace catnip {
 
     // 2. Check that the number of atoms in the grp is consistent with 
     // the number of values provided
-    if ( basis_func_count.size() != atm_grp_cont_.at(index).size() ){
+    if ( basis_func_count.size() != atm_grp_cont_->at(index)->size() ){
       throw std::runtime_error("Cannot assign basis function count to atoms "
           "as the basis function count vector is not equal to the number of "
           "atoms in the group!");
@@ -326,25 +326,25 @@ namespace catnip {
   }
 
   bool AtomSystem::systemComplete() const noexcept {
-    for ( const AtomGroup & grp : atm_grp_cont_){
-      for( const std::shared_ptr<Atom> & atm : grp){
+    for ( const std::unique_ptr<AtomGroup> & grp : *atm_grp_cont_){
+      for( const std::shared_ptr<Atom> & atm : *grp){
         if(atm->getBasisFuncCount() == -1) return false;
       }
     }
     return true;
   }
 
-  const AtomGroup & AtomSystem::at(int ind) const {
-    return atm_grp_cont_.at(ind); 
+  const std::unique_ptr<AtomGroup> & AtomSystem::at(int ind) const {
+    return atm_grp_cont_->at(ind); 
   }
 
   std::vector<AtomSystem::Link> AtomSystem::getLinkedAtomsWithDifferentElements() const noexcept {
 
     std::vector<Link> links;
-    std::string complex_name = atm_grp_cont_.at(index_complex_).getName();
+    std::string complex_name = atm_grp_cont_->at(index_complex_)->getName();
     for ( std::pair<int,std::vector<std::pair<int,int>>> grp_links : linked_atoms_){
       int component_ind = grp_links.first;
-      std::string component_name = atm_grp_cont_.at(component_ind).getName(); 
+      std::string component_name = atm_grp_cont_->at(component_ind)->getName(); 
       for ( std::pair<int,int> atm1_atm2 : grp_links.second){
         Link link{
           component_name,     // Component name
diff --git a/src/libcatnip/atom_system.hpp b/src/libcatnip/atom_system.hpp
index 2cfb1a7..ddc301c 100644
--- a/src/libcatnip/atom_system.hpp
+++ b/src/libcatnip/atom_system.hpp
@@ -8,6 +8,7 @@
 
 // Standard includes
 #include <map>
+#include <memory>
 #include <vector>
 
 namespace catnip {
@@ -27,7 +28,7 @@ namespace catnip {
       // Atoms in each component that share the same location with atoms in
       // the complex but do not share the same element
       std::map<int,std::vector<std::pair<int,int>>> linked_atoms_;
-      AtomGroupContainer atm_grp_cont_;    
+      std::unique_ptr<AtomGroupContainer> atm_grp_cont_;    
       int index_complex_;
     public:
 
@@ -40,7 +41,7 @@ namespace catnip {
         int complex_atm_ind;
       };
 
-      AtomSystem(AtomGroupContainer atm_cont);
+      AtomSystem(std::unique_ptr<AtomGroupContainer> atm_cont);
 
       /**
        * @brief assign basis functions to atom group
@@ -70,12 +71,12 @@ namespace catnip {
 
       int getMaxBasisFunctions(const GroupType & type) const;
 
-      const AtomGroup & getComplex() const {
-        return atm_grp_cont_.at(index_complex_); 
+      const std::unique_ptr<AtomGroup> & getComplex() const {
+        return atm_grp_cont_->at(index_complex_); 
       }       
 
       std::vector<int> getComponentIndices() const noexcept { 
-        return atm_grp_cont_.getGroups(GroupType::Component);
+        return atm_grp_cont_->getGroups(GroupType::Component);
       }
 
 
@@ -87,7 +88,7 @@ namespace catnip {
        */
       std::vector<Link> getLinkedAtomsWithDifferentElements() const noexcept;
 
-      const AtomGroup & at(int ind) const;       
+      const std::unique_ptr<AtomGroup> & at(int ind) const;       
       /**
        * @brief Check that every atom knows how many basis functions are
        * assigned to it

From a1855d1b0af93f0c68feef9b6732d6e3c23f982c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 30 Jul 2020 23:26:08 -0600
Subject: [PATCH 59/68] Move to c++17 standard

---
 src/libcatnip/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index 2f4e8d8..f5e395f 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -7,4 +7,5 @@ file(GLOB CATNIP_SOURCE_FILES
   io/file_readers/*.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
+set_property(TARGET libcatnip PROPERTY CXX_STANDARD 17)
 target_include_directories(libcatnip PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

From c5e08ee91ad14b1010ceb8a890fb2c18c1939a9b Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Thu, 30 Jul 2020 23:45:19 -0600
Subject: [PATCH 60/68] First step to refactor argumenent parsing

---
 .../arguments/properties/propertyobject.hpp   | 62 ++++++++-----------
 1 file changed, 27 insertions(+), 35 deletions(-)

diff --git a/src/libcatnip/io/arguments/properties/propertyobject.hpp b/src/libcatnip/io/arguments/properties/propertyobject.hpp
index 584c662..e28af14 100644
--- a/src/libcatnip/io/arguments/properties/propertyobject.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyobject.hpp
@@ -2,6 +2,7 @@
 #ifndef _CATNIP_PROPERTY_OBJECT_HPP
 #define _CATNIP_PROPERTY_OBJECT_HPP
 
+#include <any>
 #include <exception>
 #include <iostream>
 #include <map>
@@ -13,70 +14,61 @@
 
 namespace catnip {
 
-template <typename S, typename T>
+enum class PropertyType {
+  UNKNOWN
+};
+
+enum class Option {
+  NO_OPTIONS
+};
+
 class PropertyObject {
  protected:
   // Map key is the option name and the type "int, double etc"
   // void * points to the correct value for that type
-  std::map<std::string, void *> options_;
+  std::map<Option, std::any> options_;
 
-  bool propOptionValid_(const std::string &option) const {
-    for (const auto &opt : options_) {
-      if (opt.first.compare(option) == 0) return true;
-    }
-    return false;
+  bool propOptionValid_(const Option &option) const {
+    return options_.count(option);
   }
 
-  void setPropOption_(const std::string &option, const T &val) {
-
-    if (options_.count(option) == 0) {
-      T *opt = new T(val);
-      options_[option] = static_cast<void *>(opt);
-    } else {
-      T *opt = static_cast<T *>(options_[option]);
-      *opt = val;
-    }
+  void setPropOption_(const Option &option, const std::any &val) {
+      options_[option] = val;
   }
 
-  virtual std::string getName_(void) const { return "UNKNOWN"; }
+  virtual PropertyType getPropertyType_(void) const noexcept 
+  { return PropertyType::UNKNOWN; }
 
-  virtual std::vector<std::string> getOpts_(void) const {
-    std::vector<std::string> options{"NO_OPTIONS"};
+  virtual std::vector<Option> getOpts_(void) const noexcept {
+    std::vector<Option> options{Option::NO_OPTIONS};
     return options;
   }
 
  public:
   virtual ~PropertyObject(void) {
-    for (auto itr : options_) {
-      T *opt = static_cast<T *>(itr.second);
-      delete opt;
-    }
-    options_.clear();
   }
 
-  virtual bool propValid(const S &value) = 0;
+  virtual bool propValid(const std::any &value) = 0;
 
-  std::string getPropertyName(void) const { return getName_(); }
+  PropertyType getPropertyType(void) const noexcept { return getPropertyType_(); }
 
-  std::vector<std::string> getPropertyOptions(void) const { return getOpts_(); }
+  std::vector<Option> getPropertyOptions(void) const noexcept { return getOpts_(); }
 
   // Setup the valid options associated with the parameter
-  void setPropOption(std::string option, const T & val) {
+  void setPropOption(Option option, const std::any & val) {
     if (!propOptionValid_(option)) {
-      throw std::invalid_argument("Property option is unrecognized " + option);
+      throw std::invalid_argument("Property option is unrecognized.");
     }
     setPropOption_(option, val);
   }
 
-  T getPropOption(const std::string &option) const {
+  template<class T>
+  T getPropOption(const Option &option) const {
     if (!propOptionValid_(option)) {
-      std::string err = "" + option +
-                        " is an unrecognized property option for "
-                        "property " +
-                        getName_();
+      std::string err = " An unrecognized property option was detected.";
       throw std::invalid_argument(err);
     }
-    return *(static_cast<T *>(options_.at(option)));
+    return std::any_cast<T>(options_.at(option));
   }
 
   virtual void postCheck(void) const { return; }

From e7b99c5987acd3d6c4ce1e137c91a6a807c6984f Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 31 Jul 2020 00:25:21 -0600
Subject: [PATCH 61/68] Replacing int and double properties with numeric

---
 .../arguments/properties/property_numeric.cpp | 52 +++++++++++++++++++
 .../arguments/properties/property_numeric.hpp | 35 +++++++++++++
 .../arguments/properties/propertydouble.cpp   | 33 ------------
 .../arguments/properties/propertydouble.hpp   | 25 ---------
 .../io/arguments/properties/propertyint.cpp   | 33 ------------
 .../io/arguments/properties/propertyint.hpp   | 25 ---------
 6 files changed, 87 insertions(+), 116 deletions(-)
 create mode 100644 src/libcatnip/io/arguments/properties/property_numeric.cpp
 create mode 100644 src/libcatnip/io/arguments/properties/property_numeric.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertydouble.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertydouble.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyint.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyint.hpp

diff --git a/src/libcatnip/io/arguments/properties/property_numeric.cpp b/src/libcatnip/io/arguments/properties/property_numeric.cpp
new file mode 100644
index 0000000..fdb5e68
--- /dev/null
+++ b/src/libcatnip/io/arguments/properties/property_numeric.cpp
@@ -0,0 +1,52 @@
+
+#include "property_numeric.hpp"
+
+#include "propertyobject.hpp"
+
+#include <limits>
+#include <typeinfo>
+
+using namespace catnip;
+using namespace std;
+
+void PropertyNumeric::setPropOption_(const Option & option, const std::any & val) {
+  if ( val.type() != typeid(double)){
+    string err = "The Min and Max options of the numeric property must be a double.";
+    throw invalid_argument(err);
+  }
+  PropertyObject::setPropOption_(option, val);
+}
+
+bool PropertyNumeric::propValid(const std::any & val) {
+
+  if( val.type() != typeid(int) || val.type() != typeid(double) ){
+    string err = "The value provided to the property is not a supported type.";
+    throw invalid_argument(err);
+  }
+  // If the properties have not been set then they will be 
+  // valid as long as they are of a numeric type
+  double converted_val;
+  if ( val.type() == typeid(int) ){
+    converted_val = static_cast<double>(any_cast<int>(val));
+  } else {
+    converted_val = any_cast<double>(val);
+  }
+
+  if( options_[Option::MIN].type() != typeid(DefaultValue::DEFAULT) ){
+    // ignore it otherwise, there is no min option 
+    double min_val = any_cast<double>(options_[Option::MIN]);
+    if ( converted_val < min_val ) {
+      string err = "The value provided to the property is less than the minimum allowed.";
+      throw invalid_argument(err);
+    }
+  }
+  if( options_[Option::MAX].type() != typeid(DefaultValue::DEFAULT) ){
+    // ignore it otherwise, there is no min option 
+    double max_val = any_cast<double>(options_[Option::MAX]);
+    if ( converted_val < max_val ) {
+      string err = "The value provided to the property is greater than the maximum allowed.";
+      throw invalid_argument(err);
+    }
+  }
+  return true;
+}
diff --git a/src/libcatnip/io/arguments/properties/property_numeric.hpp b/src/libcatnip/io/arguments/properties/property_numeric.hpp
new file mode 100644
index 0000000..e42adb5
--- /dev/null
+++ b/src/libcatnip/io/arguments/properties/property_numeric.hpp
@@ -0,0 +1,35 @@
+
+#ifndef _CATNIP_PROPERTY_NUMERIC_HPP
+#define _CATNIP_PROPERTY_NUMERIC_HPP
+
+#include "propertyobject.hpp"
+
+#include <any>
+
+namespace catnip {
+
+class PropertyNumeric : public PropertyObject {
+
+  // Override the setting make sure that a double is passed in as the numeric type
+  virtual void setPropOption_(const Option & option, const std::any & val) final;
+
+ public:
+  PropertyNumeric(void) {
+    options_[Option::MIN] = DefaultValue::DEFAULT;
+    options_[Option::MAX] = DefaultValue::DEFAULT; 
+  };
+
+  virtual std::vector<Option> getPropertyOptions(void) const noexcept final {
+    return std::vector<Option> {Option::MIN, Option::MAX};
+  }
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::NUMERIC;
+  }
+
+  virtual bool propValid(const std::any& value) final;
+};
+
+}  // namespace catnip
+
+#endif  // _CATNIP_PROPERTY_NUMERIC_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertydouble.cpp b/src/libcatnip/io/arguments/properties/propertydouble.cpp
deleted file mode 100644
index 28f2a3b..0000000
--- a/src/libcatnip/io/arguments/properties/propertydouble.cpp
+++ /dev/null
@@ -1,33 +0,0 @@
-
-#include "propertydouble.hpp"
-
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-PropertyDouble::PropertyDouble() {
-  setPropOption_("MIN", numeric_limits<double>::lowest());
-  setPropOption_("MAX", numeric_limits<double>::max());
-}
-
-vector<string> PropertyDouble::getOpts_(void) const {
-  vector<string> options{"MIN", "MAX"};
-  return options;
-}
-
-void PropertyDouble::doubleValid(const double& val) {
-  if (val < getPropOption("MIN")) {
-    string err = "The value is smaller than allowed " + to_string(val) +
-                 " the "
-                 "minimum allowed value is " +
-                 to_string(getPropOption("MIN"));
-    throw invalid_argument(err);
-  } else if (val > getPropOption("MAX")) {
-    string err = "The value is greater than allowed " + to_string(val) +
-                 " the "
-                 "maximum allowed value is " +
-                 to_string(getPropOption("MAX"));
-    throw invalid_argument(err);
-  }
-}
diff --git a/src/libcatnip/io/arguments/properties/propertydouble.hpp b/src/libcatnip/io/arguments/properties/propertydouble.hpp
deleted file mode 100644
index 284ae90..0000000
--- a/src/libcatnip/io/arguments/properties/propertydouble.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_DOUBLE_HPP
-#define _CATNIP_PROPERTY_DOUBLE_HPP
-
-#include "propertyobject.hpp"
-
-namespace catnip {
-
-class PropertyDouble : public PropertyObject<double, double> {
- private:
-  void doubleValid(const double& val);
-  std::string getName_(void) const { return "PROPERTY_DOUBLE"; }
-  std::vector<std::string> getOpts_(void) const;
-
- public:
-  PropertyDouble(void);
-  bool propValid(const double& value) {
-    doubleValid(value);
-    return true;
-  }
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_PROPERTY_DOUBLE_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyint.cpp b/src/libcatnip/io/arguments/properties/propertyint.cpp
deleted file mode 100644
index e772223..0000000
--- a/src/libcatnip/io/arguments/properties/propertyint.cpp
+++ /dev/null
@@ -1,33 +0,0 @@
-
-#include "propertyint.hpp"
-
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-PropertyInt::PropertyInt() {
-  setPropOption_("MIN", numeric_limits<int>::min());
-  setPropOption_("MAX", numeric_limits<int>::max());
-}
-
-vector<string> PropertyInt::getOpts_(void) const {
-  vector<string> options{"MIN", "MAX"};
-  return options;
-}
-
-void PropertyInt::intValid(const int& val) const {
-  if (val < getPropOption("MIN")) {
-    string err = "The value is smaller than allowed " + to_string(val) +
-                 " the "
-                 "minimum allowed value is " +
-                 to_string(getPropOption("MIN"));
-    throw invalid_argument(err);
-  } else if (val > getPropOption("MAX")) {
-    string err = "The value is greater than allowed " + to_string(val) +
-                 " the "
-                 "maximum allowed value is " +
-                 to_string(getPropOption("MAX"));
-    throw invalid_argument(err);
-  }
-}
diff --git a/src/libcatnip/io/arguments/properties/propertyint.hpp b/src/libcatnip/io/arguments/properties/propertyint.hpp
deleted file mode 100644
index 6c20107..0000000
--- a/src/libcatnip/io/arguments/properties/propertyint.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_INT_HPP
-#define _CATNIP_PROPERTY_INT_HPP
-
-#include "propertyobject.hpp"
-
-namespace catnip {
-
-class PropertyInt : public PropertyObject<int, int> {
- private:
-  void intValid(const int& val) const;
-  std::string getName_(void) const { return "PROPERTY_INT"; }
-  std::vector<std::string> getOpts_(void) const;
-
- public:
-  PropertyInt(void);
-  bool propValid(const int& value) {
-    intValid(value);
-    return true;
-  }
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_PROPERTY_INT_HPP

From 49ae8b23dbdbd20b52cad9b49fe89ac4328551ec Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 31 Jul 2020 09:44:40 -0600
Subject: [PATCH 62/68] Refactored fileexist property

---
 .../properties/propertyfileexist.cpp          | 33 +++++++++----------
 .../properties/propertyfileexist.hpp          | 18 +++++++---
 2 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/src/libcatnip/io/arguments/properties/propertyfileexist.cpp b/src/libcatnip/io/arguments/properties/propertyfileexist.cpp
index df1bbbc..60b1515 100644
--- a/src/libcatnip/io/arguments/properties/propertyfileexist.cpp
+++ b/src/libcatnip/io/arguments/properties/propertyfileexist.cpp
@@ -8,17 +8,12 @@ using namespace catnip;
 using namespace std;
 
 PropertyFileExist::PropertyFileExist(void) {
-  setPropOption_("FILE_MUST_EXIST", 0);
-  setPropOption_("FILE_DOES_EXIST", 0);
+  setPropOption_(Option::MUST_EXIST, bool(false));
+  setPropOption_(Option::DOES_EXIST, bool(false));
 }
 
-PropertyFileExist::PropertyFileExist(int fileMustExist) {
-  setPropOption_("FILE_MUST_EXIST", fileMustExist);
-}
-
-vector<string> PropertyFileExist::getOpts_(void) const {
-  vector<string> options{"FILE_MUST_EXIST", "FILE_DOES_EXIST"};
-  return options;
+PropertyFileExist::PropertyFileExist(bool fileMustExist) {
+  setPropOption_(Option::MUST_EXIST, fileMustExist);
 }
 
 bool PropertyFileExist::fileExist(const string& fileNamePath) const {
@@ -26,24 +21,26 @@ bool PropertyFileExist::fileExist(const string& fileNamePath) const {
   return (stat(fileNamePath.c_str(), &buf) == 0);
 }
 
-bool PropertyFileExist::propValid(const string& fileNamePath) {
-  if (getPropOption("FILE_MUST_EXIST")) {
-    if (!fileExist(fileNamePath)) {
-      string err = "" + fileNamePath + " does not exist";
+bool PropertyFileExist::propValid(const std::any& fileNamePath) {
+  std::string file_name_path = any_cast<std::string>(fileNamePath);
+  bool must_exist = any_cast<bool>(options_[Option::MUST_EXIST]);
+  if (must_exist) {
+    if (!fileExist(file_name_path)) {
+      string err = "" + file_name_path + " does not exist";
       throw invalid_argument(err);
     }
-    setPropOption_("FILE_DOES_EXIST", 1);
+    setPropOption_(Option::DOES_EXIST, bool(true));
   } else {
-    if (fileExist(fileNamePath)) {
-      setPropOption_("FILE_DOES_EXIST", 1);
+    if (fileExist(file_name_path)) {
+      setPropOption_(Option::DOES_EXIST, bool(true));
     }
   }
   return true;
 }
 
 void PropertyFileExist::postCheck(void) const {
-  auto must_exist = getPropOption("FILE_MUST_EXIST");
-  auto exist = getPropOption("FILE_DOES_EXIST");
+  auto must_exist = getPropOption<bool>(Option::MUST_EXIST);
+  auto exist = getPropOption<bool>(Option::DOES_EXIST);
   if (must_exist && exist == 0) {
     throw runtime_error("A necessary file is missing!");
   }
diff --git a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp b/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
index 7529004..ac347ec 100644
--- a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
@@ -7,16 +7,24 @@
 
 namespace catnip {
 
-class PropertyFileExist : public PropertyObject<std::string, int> {
+class PropertyFileExist : public PropertyObject {
  private:
   bool fileExist(const std::string &) const;
-  std::string getName_(void) const { return "PROPERTY_FILE_EXIST"; }
-  std::vector<std::string> getOpts_(void) const;
 
  public:
   explicit PropertyFileExist(void);
-  PropertyFileExist(int fileMustExist);
-  bool propValid(const std::string &fileName);
+  PropertyFileExist(bool fileMustExist);
+
+  virtual bool propValid(const std::any &fileName) final;
+
+  virtual PropertyType getPropertyType() const noexcept final {
+    return PropertyType::FILE_EXISTS;
+  }
+
+  virtual std::vector<Option> getPropertyOptions(void) const noexcept final {
+    return std::vector<Option> {Option::MUST_EXIST,Option::DOES_EXIST};
+  }
+
   void postCheck(void) const;
 };
 

From 77711c8b4ad711882ad001d37ca8422d86750590 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 31 Jul 2020 09:44:56 -0600
Subject: [PATCH 63/68] Minor correction

---
 .../arguments/properties/property_numeric.cpp | 24 ++++++++-----------
 .../arguments/properties/property_numeric.hpp |  5 ++--
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/src/libcatnip/io/arguments/properties/property_numeric.cpp b/src/libcatnip/io/arguments/properties/property_numeric.cpp
index fdb5e68..6d1dc22 100644
--- a/src/libcatnip/io/arguments/properties/property_numeric.cpp
+++ b/src/libcatnip/io/arguments/properties/property_numeric.cpp
@@ -32,21 +32,17 @@ bool PropertyNumeric::propValid(const std::any & val) {
     converted_val = any_cast<double>(val);
   }
 
-  if( options_[Option::MIN].type() != typeid(DefaultValue::DEFAULT) ){
-    // ignore it otherwise, there is no min option 
-    double min_val = any_cast<double>(options_[Option::MIN]);
-    if ( converted_val < min_val ) {
-      string err = "The value provided to the property is less than the minimum allowed.";
-      throw invalid_argument(err);
-    }
+  // ignore it otherwise, there is no min option 
+  double min_val = any_cast<double>(options_[Option::MIN]);
+  if ( converted_val < min_val ) {
+    string err = "The value provided to the property is less than the minimum allowed.";
+    throw invalid_argument(err);
   }
-  if( options_[Option::MAX].type() != typeid(DefaultValue::DEFAULT) ){
-    // ignore it otherwise, there is no min option 
-    double max_val = any_cast<double>(options_[Option::MAX]);
-    if ( converted_val < max_val ) {
-      string err = "The value provided to the property is greater than the maximum allowed.";
-      throw invalid_argument(err);
-    }
+  // ignore it otherwise, there is no min option 
+  double max_val = any_cast<double>(options_[Option::MAX]);
+  if ( converted_val < max_val ) {
+    string err = "The value provided to the property is greater than the maximum allowed.";
+    throw invalid_argument(err);
   }
   return true;
 }
diff --git a/src/libcatnip/io/arguments/properties/property_numeric.hpp b/src/libcatnip/io/arguments/properties/property_numeric.hpp
index e42adb5..8c30bcd 100644
--- a/src/libcatnip/io/arguments/properties/property_numeric.hpp
+++ b/src/libcatnip/io/arguments/properties/property_numeric.hpp
@@ -5,6 +5,7 @@
 #include "propertyobject.hpp"
 
 #include <any>
+#include <limits>
 
 namespace catnip {
 
@@ -15,8 +16,8 @@ class PropertyNumeric : public PropertyObject {
 
  public:
   PropertyNumeric(void) {
-    options_[Option::MIN] = DefaultValue::DEFAULT;
-    options_[Option::MAX] = DefaultValue::DEFAULT; 
+    options_[Option::MIN] = std::numeric_limits<double>::min;
+    options_[Option::MAX] = std::numeric_limits<double>::max; 
   };
 
   virtual std::vector<Option> getPropertyOptions(void) const noexcept final {

From 61f99091c38704f72d8284ac03c03b50743b4dae Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 7 Aug 2020 00:23:30 -0600
Subject: [PATCH 64/68] Major refactor of arguments and properties

---
 src/libcatnip/atom_group_container.cpp        |  52 +--
 src/libcatnip/atom_group_container.hpp        |   6 +-
 src/libcatnip/basis_map.cpp                   |  14 +-
 src/libcatnip/io/argumentparser.cpp           | 372 ++++++++++------
 src/libcatnip/io/argumentparser.hpp           |  27 +-
 src/libcatnip/io/arguments/argumentdouble.cpp |  14 -
 src/libcatnip/io/arguments/argumentfile.cpp   |  16 +-
 src/libcatnip/io/arguments/argumentfile.hpp   |  10 +-
 src/libcatnip/io/arguments/argumentint.cpp    |  14 -
 src/libcatnip/io/arguments/argumentint.hpp    |  21 -
 .../io/arguments/argumentnumerical.cpp        |  13 +
 ...gumentdouble.hpp => argumentnumerical.hpp} |   2 +-
 src/libcatnip/io/arguments/argumentobject.hpp | 418 +++---------------
 src/libcatnip/io/arguments/argumentstring.cpp |  12 +-
 src/libcatnip/io/arguments/argumentstring.hpp |  10 +-
 src/libcatnip/io/arguments/argumentswitch.cpp |   8 +-
 src/libcatnip/io/arguments/argumentswitch.hpp |  14 +-
 .../arguments/properties/property_numeric.hpp |   4 -
 .../properties/propertyfileexist.hpp          |   4 -
 .../arguments/properties/propertyfileext.cpp  |  33 +-
 .../arguments/properties/propertyfileext.hpp  |  21 +-
 .../arguments/properties/propertyobject.hpp   |  47 +-
 .../properties/propertysisterfile.cpp         |  97 +---
 .../properties/propertysisterfile.hpp         |  15 +-
 .../arguments/properties/propertystring.cpp   |  21 +-
 .../arguments/properties/propertystring.hpp   |  13 +-
 .../properties/propertystringchoice.cpp       |  43 +-
 .../properties/propertystringchoice.hpp       |  13 +-
 .../arguments/properties/propertyswitch.cpp   |  20 +-
 .../arguments/properties/propertyswitch.hpp   |  16 +-
 src/libcatnip/io/io.cpp                       | 171 ++++---
 31 files changed, 645 insertions(+), 896 deletions(-)
 delete mode 100644 src/libcatnip/io/arguments/argumentdouble.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentint.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentint.hpp
 create mode 100644 src/libcatnip/io/arguments/argumentnumerical.cpp
 rename src/libcatnip/io/arguments/{argumentdouble.hpp => argumentnumerical.hpp} (85%)

diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index 1a61a4d..fa54617 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -31,13 +31,13 @@ namespace catnip {
    * Local private functions
    ****************************************************************************/
   static std::unordered_map<Atom,std::vector<GroupAtomIndex>> mapAtomsToGroups_(
-      const std::vector<AtomGroup> & atom_groups_ ){
+      const std::vector<std::unique_ptr<AtomGroup>> & atom_groups_ ){
 
     std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map;
     int grp_index = 0;
-    for ( const AtomGroup & grp : atom_groups_ ){
+    for ( const std::unique_ptr<AtomGroup> & grp : atom_groups_ ){
       int atom_index = 0;
-      for ( auto & atom_ptr : grp ){
+      for ( auto & atom_ptr : *grp ){
         atm_map[*atom_ptr].push_back(GroupAtomIndex{atom_index,grp_index});
         ++atom_index;
       }
@@ -48,15 +48,15 @@ namespace catnip {
 
   static const std::map<int,std::vector<int>> calculateConnectedGroups_(
       std::unordered_map<Atom,std::vector<GroupAtomIndex>> atm_map,
-      const std::vector<AtomGroup> & atom_groups_ 
+      const std::vector<std::unique_ptr<AtomGroup>> & atom_groups_ 
       ){
 
     std::map<int,std::vector<int>> grp_indices;
     int grp_index = 0;
-    for ( const AtomGroup & grp : atom_groups_ ){
+    for ( const std::unique_ptr<AtomGroup> & grp : atom_groups_ ){
       // Initialize
       grp_indices[grp_index];
-      for ( const auto & atom_ptr : grp ){
+      for ( const auto & atom_ptr : *grp ){
         for ( const GroupAtomIndex & grp_atm_ind : atm_map[*atom_ptr] ){
           if (grp_atm_ind.grp_ind != grp_index ){
             // Check that group has not already been added
@@ -78,19 +78,19 @@ namespace catnip {
 
   static void identifyAtomGroupsOfIslandType_(
       const std::map<int,std::vector<int>> & grp_indices,
-      std::vector<AtomGroup> & atom_groups_ 
+      std::vector<std::unique_ptr<AtomGroup>> & atom_groups_ 
       ) {
     for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
       if(grp_groups.second.size() == 0) {
         std::cout << "Empty makeing unit, does not share atoms" << std::endl;
-        atom_groups_.at(grp_groups.first).setType(GroupType::Island);
+        atom_groups_.at(grp_groups.first)->setType(GroupType::Island);
       }
     }
   }
 
   static void identifyAtomGroupsOfComponentComplexAndUnknownTypes_(
       const std::map<int,std::vector<int>> & grp_indices,
-      std::vector<AtomGroup> & atom_groups_ 
+      std::vector<std::unique_ptr<AtomGroup>> & atom_groups_ 
       ){
     std::vector<int> potential_complexes;
     for ( std::pair<int,std::vector<int>> grp_groups : grp_indices){
@@ -111,14 +111,14 @@ namespace catnip {
         } 
       }
       if ( candidate_components_valid){
-        atom_groups_.at(potential_complex).setType(GroupType::Complex);
+        atom_groups_.at(potential_complex)->setType(GroupType::Complex);
         for ( const int & candidate_component : candidate_components){
-          atom_groups_.at(candidate_component).setType(GroupType::Component);
+          atom_groups_.at(candidate_component)->setType(GroupType::Component);
         }
       }else{
-        atom_groups_.at(potential_complex).setType(GroupType::Unknown);
+        atom_groups_.at(potential_complex)->setType(GroupType::Unknown);
         for ( const int & candidate_component : candidate_components){
-          atom_groups_.at(candidate_component).setType(GroupType::Unknown);
+          atom_groups_.at(candidate_component)->setType(GroupType::Unknown);
         }
       }
     }
@@ -127,20 +127,20 @@ namespace catnip {
   /****************************************************************************
    * Private Methods
    ****************************************************************************/
-  bool AtomGroupContainer::isUniqueGroup_( const AtomGroup & atom_group ) const {
+  bool AtomGroupContainer::isUniqueGroup_( const std::unique_ptr<AtomGroup> & atom_group ) const {
     // Step 1 check the size of the atom group 
     if(atom_groups_.size() == 0) return true;
 
-    for ( const AtomGroup & grp : atom_groups_ ){
-      if ( grp.size() == atom_group.size() ){
-        std::vector<bool> matchs(grp.size(),false);
+    for ( const std::unique_ptr<AtomGroup> & grp : atom_groups_ ){
+      if ( grp->size() == atom_group->size() ){
+        std::vector<bool> matchs(grp->size(),false);
         // Determine if a match is found
-        for ( const auto & atm : atom_group ) {
+        for ( const auto & atm : *atom_group ) {
           size_t index = 0;
           for ( bool matched : matchs ){
             if ( not matched ){
               // Compare atoms 
-              if ( *atm == *(grp.at(index)) ){
+              if ( *atm == *(grp->at(index)) ){
                 matchs.at(index) = true;
                 break;
               }
@@ -150,7 +150,7 @@ namespace catnip {
           // If an atom was not matched it means that there is at least one 
           // difference, and so we do not need to cycle through the other
           // atoms in this particular group 
-          if(index == grp.size()) break;
+          if(index == grp->size()) break;
         } 
         // Count the number of matches in the vector if all of the elements match
         // then the atom group is not unique
@@ -170,8 +170,8 @@ namespace catnip {
   std::vector<int> AtomGroupContainer::getGroups(const GroupType & type) const noexcept{
     std::vector<int> groups;
     int ind1 = 0;
-    for( const AtomGroup & group : atom_groups_ ){
-      if( group.getType() == type){
+    for( const std::unique_ptr<AtomGroup> & group : atom_groups_ ){
+      if( group->getType() == type){
         groups.push_back(ind1);
       }
       ++ind1;
@@ -181,8 +181,8 @@ namespace catnip {
 
   // As soon as we add a new atom group it should invalidate the labels on 
   // all the other groups
-  void AtomGroupContainer::add( AtomGroup atom_group ) {
-    std::cout << "Adding group " << atom_group.getName() << std::endl; 
+  void AtomGroupContainer::add( std::unique_ptr<AtomGroup> & atom_group ) {
+    std::cout << "Adding group " << atom_group->getName() << std::endl; 
     if( isUniqueGroup_(atom_group) ){
       std::cout << "Is unique" << std::endl;
       atom_groups_.push_back(std::move(atom_group));
@@ -216,8 +216,8 @@ namespace catnip {
 
   bool AtomGroupContainer::exists(GroupType type) const {
     // First check that all the group types have been assigned
-    for ( const AtomGroup & grp : atom_groups_ ){
-      if( grp.getType() == type ) return true;
+    for ( const std::unique_ptr<AtomGroup> & grp : atom_groups_ ){
+      if( grp->getType() == type ) return true;
     }
     return false; 
   }
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index 84697a1..7249bba 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -40,7 +40,7 @@ namespace catnip {
        *
        * @return 
        */
-      bool isUniqueGroup_( const AtomGroup & atom_group ) const;
+      bool isUniqueGroup_( const std::unique_ptr<AtomGroup> & atom_group ) const;
 
 
     public: 
@@ -61,7 +61,7 @@ namespace catnip {
       std::vector<std::unique_ptr<AtomGroup>>::const_iterator 
         end() const { return atom_groups_.end(); }
 
-      void add( AtomGroup atom_group );
+      void add( std::unique_ptr<AtomGroup> & atom_group );
 
       size_t size() const noexcept { return  atom_groups_.size(); }
 
@@ -79,7 +79,7 @@ namespace catnip {
        */
       bool exists(GroupType type) const;
 
-      const GroupType & getType(int index) const { return atom_groups_.at(index).getType(); }
+      const GroupType & getType(int index) const { return atom_groups_.at(index)->getType(); }
 
       /**
        * @brief Get the indices of all the groups of the specified group type
diff --git a/src/libcatnip/basis_map.cpp b/src/libcatnip/basis_map.cpp
index 67e639e..393a5ec 100644
--- a/src/libcatnip/basis_map.cpp
+++ b/src/libcatnip/basis_map.cpp
@@ -29,10 +29,10 @@ namespace catnip {
     // offset_map[2] = 5; // atom3
 
     std::unordered_map<int,int> offset_map;
-    const AtomGroup & complex_grp = atm_sys.getComplex();
+    const std::unique_ptr<AtomGroup> & complex_grp = atm_sys.getComplex();
     int offset = 0;
     int complex_atm_ind = 0;
-    for ( const std::shared_ptr<Atom> & atm_ptr : complex_grp){
+    for ( const std::shared_ptr<Atom> & atm_ptr : *complex_grp){
       offset_map[complex_atm_ind] = offset;
       offset += atm_ptr->getBasisFuncCount();
       ++complex_atm_ind;
@@ -41,13 +41,13 @@ namespace catnip {
     std::vector<int> component_indices = atm_sys.getComponentIndices();
     int sys_ind = 0;
     for ( int & component_ind : component_indices) {
-      const AtomGroup & component_grp = atm_sys.at(component_ind);
-      std::cout << "Component grp " << component_grp.getName() << " component ind " << component_ind << " size " << component_grp.size() << std::endl;
-      for( const std::shared_ptr<Atom> & atm_ptr : component_grp){
-        std::vector<int> atm_indices = complex_grp.find(atm_ptr->getPos());
+      const std::unique_ptr<AtomGroup> & component_grp = atm_sys.at(component_ind);
+      std::cout << "Component grp " << component_grp->getName() << " component ind " << component_ind << " size " << component_grp->size() << std::endl;
+      for( const std::shared_ptr<Atom> & atm_ptr : *component_grp){
+        std::vector<int> atm_indices = complex_grp->find(atm_ptr->getPos());
         assert(atm_indices.size() == 1);
         int atm_ind = atm_indices.at(0);
-        int num_basis = complex_grp.at(atm_ind)->getBasisFuncCount();
+        int num_basis = complex_grp->at(atm_ind)->getBasisFuncCount();
         int complex_offset = offset_map[atm_ind];
 
         for ( int ind_temp = 0; ind_temp<num_basis; ++ind_temp){
diff --git a/src/libcatnip/io/argumentparser.cpp b/src/libcatnip/io/argumentparser.cpp
index 0615d2a..ae30a81 100644
--- a/src/libcatnip/io/argumentparser.cpp
+++ b/src/libcatnip/io/argumentparser.cpp
@@ -1,5 +1,6 @@
 #include <exception>
 #include <iostream>
+#include <memory>
 #include <stdexcept>
 #include <string>
 #include <sys/stat.h>
@@ -7,7 +8,7 @@
 
 #include "argumentparser.hpp"
 
-#include "../calcJconfig.hpp"
+#include "../catnip_config.hpp"
 #include "../string_support.hpp"
 
 using namespace catnip;
@@ -143,19 +144,12 @@ void ArgumentParser::showUsage(void) {
 void ArgumentParser::addFlagArg(string flag, string argname) {
 
   if (argname.compare("ARGUMENT_INT") == 0) {
-    if (int_arg_.count(flag) == 0) {
-      ArgumentInt* ArInt = new ArgumentInt;
-      int_arg_[flag] = ArInt;
-    } else {
-      throw invalid_argument(
-          "Int argument has already been added for "
-          "flag " +
-          flag);
-    }
+      auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
+      int_arg_[flag].push_back(std::move(ArInt));
   } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
     if (switch_arg_.count(flag) == 0) {
-      ArgumentSwitch* ArSwitch = new ArgumentSwitch;
-      switch_arg_[flag] = ArSwitch;
+      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
+      switch_arg_[flag].push_back(std::move(ArSwitch));
     } else {
       throw invalid_argument(
           "switch argument has already been added for "
@@ -163,35 +157,14 @@ void ArgumentParser::addFlagArg(string flag, string argname) {
           flag);
     }
   } else if (argname.compare("ARGUMENT_STRING") == 0) {
-    if (str_arg_.count(flag) == 0) {
-      ArgumentString* ArString = new ArgumentString;
-      str_arg_[flag] = ArString;
-    } else {
-      throw invalid_argument(
-          "string argument has already been added for "
-          "flag " +
-          flag);
-    }
+      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
+      str_arg_[flag].push_back(std::move(ArString));
   } else if (argname.compare("ARGUMENT_FILE") == 0) {
-    if (file_arg_.count(flag) == 0) {
-      ArgumentFile* ArFile = new ArgumentFile;
-      file_arg_[flag] = ArFile;
-    } else {
-      throw invalid_argument(
-          "File argument has already been added for "
-          "flag " +
-          flag);
-    }
+      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+      file_arg_[flag].push_back(std::move(ArFile));
   } else if (argname.compare("ARGUMENT_DOUBLE") == 0) {
-    if (file_arg_.count(flag) == 0) {
-      ArgumentDouble* ArDouble = new ArgumentDouble;
-      double_arg_[flag] = ArDouble;
-    } else {
-      throw invalid_argument(
-          "Double argument has already been added for "
-          "flag " +
-          flag);
-    }
+      auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
+      double_arg_[flag].push_back(ArDouble);
   } else {
     throw invalid_argument(
         "Unrecognized argument being added for flag"
@@ -201,47 +174,52 @@ void ArgumentParser::addFlagArg(string flag, string argname) {
 }
 
 void ArgumentParser::setFlagDefaultValue(string flag,const int & val) {
-  int_values_[flag] = val;
+  int_values_[flag].push_back(val);
   defaults_set_[flag] = true;
 }
 
 void ArgumentParser::setFlagDefaultValue(string flag,const size_t & val) {
-  size_t_values_[flag] = val;
+  size_t_values_[flag].push_back(val);
   defaults_set_[flag] = true;
 }
 
 void ArgumentParser::setFlagDefaultValue(string flag,const double & val) {
-  double_values_[flag] = val;
+  double_values_[flag].push_back(val);
   defaults_set_[flag] = true;
 }
 
 void ArgumentParser::setFlagDefaultValue(string flag,const string & val) {
-  string_values_[flag] = val;
+  string_values_[flag].push_back(val);
   defaults_set_[flag] = true;
 }
 
+// Will apply values to all properties in the argument vector
 void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
                                    string option, int val) {
 
   if (argname.compare("ARGUMENT_INT") == 0) {
     if (int_arg_.count(flag) == 0) {
-      ArgumentInt* ArInt = new ArgumentInt;
+      auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
       ArInt->setArgPropertyOpt(property, option, val);
-      int_arg_[flag] = ArInt;
+      int_arg_[flag].push_back(std::move(ArInt));
     } else {
-      int_arg_[flag]->setArgPropertyOpt(property, option, val);
+      for ( std::unique_ptr<ArgumentInt> & ptr : int_arg_[flag]){
+        ptr->setArgPropertyOpt(property, option, val);
+      }
     }
   } else if (argname.compare("ARGUMENT_STRING") == 0) {
     if (str_arg_.count(flag) == 0) {
-      ArgumentString* ArString = new ArgumentString;
+      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
       ArString->setArgPropertyOpt(property, option, val);
-      str_arg_[flag] = ArString;
+      str_arg_[flag].push_back(std::move(ArString));
     } else {
-      str_arg_[flag]->setArgPropertyOpt(property, option, val);
+      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag] ){
+        ptr->setArgPropertyOpt(property, option, val);
+      }
     }
   } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
     if (switch_arg_.count(flag) == 0) {
-      ArgumentSwitch* ArSwitch = new ArgumentSwitch;
+      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
       if (val == 0) {
         ArSwitch->setArgPropertyOpt(property, option, "OFF");
       } else if (val == 1) {
@@ -250,12 +228,12 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
         throw invalid_argument("Unrecognized option for switch " +
                                to_string(val));
       }
-      switch_arg_[flag] = ArSwitch;
-    } else {
+      switch_arg_[flag].push_back(std::move(ArSwitch));
+    } else { // For a switch there will only be one value in the vector
       if (val == 0) {
-        switch_arg_[flag]->setArgPropertyOpt(property, option, "OFF");
+        switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
       } else if (val == 1) {
-        switch_arg_[flag]->setArgPropertyOpt(property, option, "ON");
+        switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
       } else {
         throw invalid_argument("Unrecognized option for switch " +
                                to_string(val));
@@ -263,12 +241,14 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
     }
   } else if (argname.compare("ARGUMENT_FILE") == 0) {
     if (file_arg_.count(flag) == 0) {
-      ArgumentFile* ArFile = new ArgumentFile;
+      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
 
       ArFile->setArgPropertyOpt(property, option, val);
-      file_arg_[flag] = ArFile;
+      file_arg_[flag].push_back(std::move(ArFile));
     } else {
-      file_arg_[flag]->setArgPropertyOpt(property, option, val);
+      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag] ){
+        ptr->setArgPropertyOpt(property, option, val);
+      }
     }
   } else {
     throw invalid_argument("Unrecognized int arg");
@@ -280,19 +260,23 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
 
   if (argname.compare("ARGUMENT_DOUBLE") == 0) {
     if (double_arg_.count(flag) == 0) {
-      ArgumentDouble* ArDouble = new ArgumentDouble;
+      auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
       ArDouble->setArgPropertyOpt(property, option, val);
-      double_arg_[flag] = ArDouble;
+      double_arg_[flag].push_back(std::move(ArDouble));
     } else {
-      double_arg_[flag]->setArgPropertyOpt(property, option, val);
+      for ( std::unique_ptr<ArgumentDouble> & ptr : double_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, val);
+      }
     }
   } else if (argname.compare("ARGUMENT_STRING") == 0) {
     if (str_arg_.count(flag) == 0) {
-      ArgumentString* ArString = new ArgumentString;
+      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
       ArString->setArgPropertyOpt(property, option, val);
-      str_arg_[flag] = ArString;
+      str_arg_[flag].push_back(std::move(ArString));
     } else {
-      str_arg_[flag]->setArgPropertyOpt(property, option, val);
+      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, val);
+      }
     }
   } else {
     throw invalid_argument("Unrecognized double arg");
@@ -307,53 +291,61 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
 
       if (property.compare("PROPERTY_FILE_EXT") == 0) {
         set<string> temp{val};
-        ArgumentFile* ArFile = new ArgumentFile;
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
         ArFile->setArgPropertyOpt(property, option, temp);
-        file_arg_[flag] = ArFile;
+        file_arg_[flag].push_back(std::move(ArFile));
       } else if (property.compare("PROPERTY_SISTER_FILE_EXT") == 0) {
         vector<string> temp{val};
-        ArgumentFile* ArFile = new ArgumentFile;
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
         ArFile->setArgPropertyOpt(property, option, temp);
-        file_arg_[flag] = ArFile;
+        file_arg_[flag].push_back(std::move(ArFile));
       } else {
-        ArgumentFile* ArFile = new ArgumentFile;
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
         ArFile->setArgPropertyOpt(property, option, val);
-        file_arg_[flag] = ArFile;
+        file_arg_[flag].push_back(std::move(ArFile));
       }
     } else {
       if (property.compare("PROPERTY_FILE_EXT") == 0) {
         set<string> temp{val};
-        file_arg_[flag]->setArgPropertyOpt(property, option, temp);
+        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, temp);
+        }
       } else {
-        file_arg_[flag]->setArgPropertyOpt(property, option, val);
+        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, val);
+        }
       }
     }
   } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
     if (switch_arg_.count(flag) == 0) {
-      ArgumentSwitch* ArSwitch = new ArgumentSwitch;
+      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
       if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
         throw invalid_argument("Unrecognized option for switch " + val);
       } else {
         ArSwitch->setArgPropertyOpt(property, option, val);
       }
-      switch_arg_[flag] = ArSwitch;
+      switch_arg_[flag].push_back(std::move(ArSwitch));
     } else {
       if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
         throw invalid_argument("Unrecognized option for switch" + val);
       } else {
-        switch_arg_[flag]->setArgPropertyOpt(property, option, val);
+        for ( std::unique_ptr<ArgumentSwitch> & ptr : switch_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, val);
+        }
       }
     }
 
   } else if (argname.compare("ARGUMENT_STRING") == 0) {
     if (str_arg_.count(flag) == 0) {
       set<string> temp{val};
-      ArgumentString* ArStr = new ArgumentString;
+      auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
       ArStr->setArgPropertyOpt(property, option, temp);
-      str_arg_[flag] = ArStr;
+      str_arg_[flag].push_back(std::move(ArStr));
     } else {
       set<string> temp{val};
-      str_arg_[flag]->setArgPropertyOpt(property, option, temp);
+      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, temp);
+      }
     }
   } else {
     throw invalid_argument("Unrecognized string arg " + argname);
@@ -365,19 +357,23 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
 
   if (argname.compare("ARGUMENT_FILE") == 0) {
     if (file_arg_.count(flag) == 0) {
-      ArgumentFile* ArFile = new ArgumentFile;
+      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
       ArFile->setArgPropertyOpt(property, option, vals);
-      file_arg_[flag] = ArFile;
+      file_arg_[flag].push_back(std::move(ArFile));
     } else {
-      file_arg_[flag]->setArgPropertyOpt(property, option, vals);
+      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, vals);
+      }
     }
   } else if (argname.compare("ARGUMENT_STRING") == 0) {
     if (str_arg_.count(flag) == 0) {
-      ArgumentString* ArStr = new ArgumentString;
+      auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
       ArStr->setArgPropertyOpt(property, option, vals);
-      str_arg_[flag] = ArStr;
+      str_arg_[flag].push_back(std::move(ArStr));
     } else {
-      str_arg_[flag]->setArgPropertyOpt(property, option, vals);
+      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, vals);
+      }
     }
   } else {
     throw invalid_argument("Unrecognized set<string> arg");
@@ -389,11 +385,13 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
 
   if (argname.compare("ARGUMENT_FILE") == 0) {
     if (file_arg_.count(flag) == 0) {
-      ArgumentFile* ArFile = new ArgumentFile;
+      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
       ArFile->setArgPropertyOpt(property, option, vals);
-      file_arg_[flag] = ArFile;
+      file_arg_[flag].push_back(std::move(ArFile));
     } else {
-      file_arg_[flag]->setArgPropertyOpt(property, option, vals);
+      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+        ptr->setArgPropertyOpt(property, option, vals);
+      }
     }
   } else {
     throw invalid_argument("Unrecognized vector<string> arg");
@@ -428,90 +426,200 @@ void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
   }
 
   bool unrecognized = true;
-  if (str_arg_.count(flag) != 0) {
 
-    if (!nextParameterIsAFlag_(index, arguments) ||
-        str_arg_[flag]->requiresParameter()) {
+  // Parse String Arguments
+  if (str_arg_.count(flag) != 0) {
 
-      if ((index + 1) >= arguments.size()) {
-        string err = "" + flag + " Missing arguments";
-        throw runtime_error(err);
-      }
+    if ((index + 1) >= arguments.size()) {
+      string err = "" + flag + " Missing arguments";
+      throw runtime_error(err);
+    }
+    int arg_index = 0;
+    do { // Allow reading of multiple arguments
       string argument = arguments.at(index + 1);
-      str_arg_[flag]->argValid(argument);
+      if ( arg_index != 0){
+        // Need to duplicate the argument
+        std::string arg_name = str_arg_[flag].at(0)->getArgumentName();
+        addFlagArg(flag, arg_name);
+        std::vector<std::string> arg_props = str_arg_[flag].at(0)->getProperties();
+        for ( std::string & property : arg_props ){ 
+          std::vector<std::string> arg_prop_opts = str_arg_[flag].at(0)->getPropertyOptions(property);
+          for ( std::string option : arg_prop_opts ) {
+            std::string val = str_arg_[flag].at(0)->getPropertyValues(property, option);
+           // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
+          }
+        }
+      }
+      str_arg_[flag].at(arg_index)->argValid(argument);
       unrecognized = false;
-      string_values_[flag] = argument;
+      if (defaults_set_.count(flag) ) {
+        if(defaults_set_[flag] == true ){
+          string_values_[flag].clear();
+          string_values_[flag].push_back(argument);
+          defaults_set_[flag] = false;
+        } else {
+          string_values_[flag].push_back(argument);
+        }
+      }
       ++index;
-    }
+      ++arg_index;
+      if( (index+1) >= arguments.size() ) break;
+    } while ( arguments.at(index+1).at(0) == '-' );
   }
-  if (switch_arg_.count(flag) != 0) {
 
+  // Parse Switches
+  if (switch_arg_.count(flag) != 0) {
     if (!nextParameterIsAFlag_(index, arguments)) {
-
       if ((index + 1) >= arguments.size()) {
-        if (switch_arg_[flag]->requiresParameter()) {
+        if (switch_arg_[flag].at(0)->requiresParameter()) {
           string err = "" + flag + " Missing arguments";
           throw runtime_error(err);
         } else {
           unrecognized = false;
-          int_values_[flag] = 1;
+          int_values_[flag].at(0) = 1;
         }
       } else {
         string argument = arguments.at(index + 1);
-        switch_arg_[flag]->argValid(argument);
+        switch_arg_[flag].at(0)->argValid(argument);
         unrecognized = false;
-        string_values_[flag] = argument;
-        if (switch_arg_[flag]->positive(argument)) {
-          int_values_[flag] = 1;
+        string_values_[flag].at(0) = argument;
+        if (switch_arg_[flag].at(0)->positive(argument)) {
+          if (defaults_set_.count(flag) ) {
+            if(defaults_set_[flag] == true ){
+              int_values_[flag].at(0) = 1;
+              defaults_set_[flag] = false;
+            } else {
+              int_values_[flag].push_back(1);
+            }
+          }
         } else {
-          int_values_[flag] = 0;
+          if (defaults_set_.count(flag) ) {
+            if(defaults_set_[flag] == true ){
+              int_values_[flag].at(0) = 0;
+              defaults_set_[flag] = false;
+            } else {
+              int_values_[flag].push_back(0);
+            }
+          }
         }
       }
     } else {
       unrecognized = false;
-      int_values_[flag] = 1;
+      if(defaults_set_[flag] == true ){
+        int_values_[flag].at(0) = 1;
+        defaults_set_[flag] = false;
+      }else {
+        int_values_[flag].push_back(1);
+      }
     }
   }
+
+  // Parse integer arguments
   if (int_arg_.count(flag) != 0) {
     if (!nextParameterIsAFlag_(index, arguments) ||
-        int_arg_[flag]->requiresParameter()) {
+        int_arg_[flag].at(0)->requiresParameter()) {
       if ((index + 1) >= arguments.size()) {
         string err = "" + flag + " Missing arguments";
         throw runtime_error(err);
       }
-      string argument = arguments.at(index + 1);
-      int_arg_[flag]->argValid(stoi(argument));
-      unrecognized = false;
-      int_values_[flag] = stoi(argument);
-      ++index;
+
+      int arg_index = 0;
+      do {
+        string argument = arguments.at(index + 1);
+        if ( arg_index != 0){
+          // Need to duplicate the argument
+          std::string arg_name = int_arg_[flag].at(0)->getArgumentName();
+          std::vector<std::string> arg_props = int_arg_[flag].at(0)->getProperties();
+          std::vector<std::string> arg_prop_opts = int_arg_[flag].at(0)->getPropertyOptions();
+          std::map<std::string, std::string> arg_prop_vals = int_arg_[flag].at(0)->getPropertyValues();
+        }
+        int_arg_[flag].at(arg_index)->argValid(stoi(argument));
+        unrecognized = false;
+        if (defaults_set_.count(flag) ) {
+          if(defaults_set_[flag] == true ){
+            string_values_[flag].clear();
+            int_values_[flag].push_back(stoi(argument));
+            defaults_set_[flag] = false;
+          } else {
+            int_values_[flag].push_back(stoi(argument));
+          }
+        }
+        ++index;
+        ++arg_index;
+        if( (index+1) >= arguments.size() ) break;
+      } while ( arguments.at(index+1).at(0) == '-' );
     }
   }
+
+  // Parse double arguments
   if (double_arg_.count(flag) != 0) {
     if (!nextParameterIsAFlag_(index, arguments) ||
-        double_arg_[flag]->requiresParameter()) {
+        double_arg_[flag].at(0)->requiresParameter()) {
       if ((index + 1) >= arguments.size()) {
         string err = "" + flag + " Missing arguments";
         throw runtime_error(err);
       }
-      string argument = arguments.at(index + 1);
-      double_arg_[flag]->argValid(stod(argument));
-      unrecognized = false;
-      double_values_[flag] = stod(argument);
-      ++index;
+      int arg_index = 0;
+      do {
+        string argument = arguments.at(index + 1);
+        if ( arg_index != 0){
+          // Need to duplicate the argument
+          std::string arg_name = double_arg_[flag].at(0)->getArgumentName();
+          std::vector<std::string> arg_props = double_arg_[flag].at(0)->getProperties();
+          std::vector<std::string> arg_prop_opts = double_arg_[flag].at(0)->getProperties();
+          std::map<std::string, std::string> arg_prop_vals = double_arg_[flag].at(0)->getPropertyValues();
+        }
+        double_arg_[flag].at(arg_index)->argValid(stod(argument));
+        unrecognized = false;
+        if (defaults_set_.count(flag) ) {
+          if(defaults_set_[flag] == true ){
+            string_values_[flag].clear();
+            double_values_[flag].push_back(stod(argument));
+            defaults_set_[flag] = false;
+          } else {
+            double_values_[flag].push_back(stod(argument));
+          }
+        }
+        ++index;
+        ++arg_index;
+        if( (index+1) >= arguments.size() ) break;
+      } while ( arguments.at(index+1).at(0) == '-' );
     }
   }
+
+  // Parse file arguments 
   if (file_arg_.count(flag) != 0) {
     if (!nextParameterIsAFlag_(index, arguments) ||
-        file_arg_[flag]->requiresParameter()) {
+        file_arg_[flag].at(0)->requiresParameter()) {
       if ((index + 1) >= arguments.size()) {
         string err = "" + flag + " Missing arguments";
         throw runtime_error(err);
       }
-      string argument = arguments.at(index + 1);
-      file_arg_[flag]->argValid(argument);
-      unrecognized = false;
-      string_values_[flag] = argument;
-      ++index;
+      int arg_index = 0;
+      do {
+        string argument = arguments.at(index + 1);
+        if ( arg_index != 0){
+          // Need to duplicate the argument
+          std::string arg_name = file_arg_[flag].at(0)->getArgumentName();
+          std::vector<std::string> arg_props = file_arg_[flag].at(0)->getProperties();
+          std::vector<std::string> arg_prop_opts = file_arg_[flag].at(0)->getProperties();
+          std::map<std::string, std::string> arg_prop_vals = file_arg_[flag].at(0)->getPropertyValues();
+        }
+        file_arg_[flag].at(arg_index)->argValid(argument);
+        unrecognized = false;
+        if (defaults_set_.count(flag) ) {
+          if(defaults_set_[flag] == true ){
+            string_values_[flag].clear();
+            string_values_[flag].push_back(argument);
+            defaults_set_[flag] = false;
+          } else {
+            string_values_[flag].push_back(argument);
+          }
+        }
+        ++index;
+        ++arg_index;
+        if( (index+1) >= arguments.size() ) break;
+      } while ( arguments.at(index+1).at(0) == '-' );
     }
   }
 
@@ -556,15 +664,15 @@ string ArgumentParser::getFlagArgOptValue(string flag, string argname,
                          argname);
 }
 
-int ArgumentParser::getInt(string flag) {
+std::vector<int> ArgumentParser::getInts(string flag) {
 
   if (int_values_.count(flag) == 0) {
     if (switch_arg_.count(flag)) {
       if (string_values_.count(flag)) {
         if (switch_arg_[flag]->positive(string_values_[flag])) {
-          return 1;
+          return std::vector<int> {1};
         } else {
-          return 0;
+          return std::vector<int> {0};
         }
       }
     }
@@ -576,7 +684,7 @@ int ArgumentParser::getInt(string flag) {
   return int_values_[flag];
 }
 
-double ArgumentParser::getDouble(string flag) {
+std::vector<double> ArgumentParser::getDoubles(string flag) {
   if (double_values_.count(flag) == 0) {
     string err = "" + flag +
                  " does not contain a double. It is also possible that "
@@ -586,14 +694,14 @@ double ArgumentParser::getDouble(string flag) {
   return double_values_[flag];
 }
 
-string ArgumentParser::getStr(string flag) {
+std::vector<string> ArgumentParser::getStrs(string flag) {
   if (string_values_.count(flag) == 0) {
     if (switch_arg_.count(flag)) {
       if (int_values_.count(flag)) {
         if (switch_arg_[flag]->positive(int_values_[flag])) {
-          return "ON";
+          return std::vector<string> {"ON"};
         } else {
-          return "OFF";
+          return std::vector<string> {"OFF"};
         }
       }
     }
@@ -605,7 +713,7 @@ string ArgumentParser::getStr(string flag) {
   return string_values_[flag];
 }
 
-size_t ArgumentParser::getSize_t(string flag) {
+std::vector<size_t> ArgumentParser::getSize_ts(string flag) {
   if (size_t_values_.count(flag) == 0) {
     string err = "" + flag +
                  " does not contain a size_t. It is also possible that "
diff --git a/src/libcatnip/io/argumentparser.hpp b/src/libcatnip/io/argumentparser.hpp
index 34338b4..cc343e7 100644
--- a/src/libcatnip/io/argumentparser.hpp
+++ b/src/libcatnip/io/argumentparser.hpp
@@ -3,6 +3,7 @@
 #include "../matrix.hpp"
 #include "../parameters.hpp"
 #include <map>
+#include <memory>
 #include <set>
 #include <string>
 #include <utility>
@@ -19,11 +20,11 @@ class ArgumentParser {
  private:
   // 1 - flag name
   // 2 - type
-  std::map<std::string, ArgumentString*> str_arg_;
-  std::map<std::string, ArgumentSwitch*> switch_arg_;
-  std::map<std::string, ArgumentInt*> int_arg_;
-  std::map<std::string, ArgumentDouble*> double_arg_;
-  std::map<std::string, ArgumentFile*> file_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentString>>> str_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentSwitch>>> switch_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentInt>>> int_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentDouble>>> double_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentFile>>> file_arg_;
 
   // Known rules
   std::set<std::string> argument_types_;
@@ -33,10 +34,10 @@ class ArgumentParser {
 
   std::map<std::string, bool> defaults_set_;
   // Arguments that are stored when argc and argv are parsed
-  std::map<std::string, int> int_values_;
-  std::map<std::string, double> double_values_;
-  std::map<std::string, std::string> string_values_;
-  std::map<std::string, size_t> size_t_values_;
+  std::map<std::string, std::vector<int>> int_values_;
+  std::map<std::string, std::vector<double>> double_values_;
+  std::map<std::string, std::vector<std::string>> string_values_;
+  std::map<std::string, std::vector<size_t>> size_t_values_;
 
   void parseArg_(size_t& index, std::vector<std::string> arguments);
 
@@ -90,10 +91,10 @@ class ArgumentParser {
   std::string getFlagArgOptValue(std::string flag, std::string argname,
                                  std::string property, std::string option);
 
-  double getDouble(std::string flag);
-  int getInt(std::string flag);
-  std::string getStr(std::string flag);
-  size_t getSize_t(std::string flag);
+  std::vector<double> getDoubles(std::string flag);
+  std::vector<int> getInts(std::string flag);
+  std::vector<std::string> getStrs(std::string flag);
+  std::vector<size_t> getSize_ts(std::string flag);
 
   void postParseCheck(void);
 
diff --git a/src/libcatnip/io/arguments/argumentdouble.cpp b/src/libcatnip/io/arguments/argumentdouble.cpp
deleted file mode 100644
index 61735a3..0000000
--- a/src/libcatnip/io/arguments/argumentdouble.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-
-#include "argumentdouble.hpp"
-#include "properties/propertydouble.hpp"
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentDouble::ArgumentDouble(void) { registerProperties_(); }
-
-void ArgumentDouble::registerProperties_(void) {
-  PropertyDouble* prop_double = new PropertyDouble();
-  double_propobjs_.push_back(prop_double);
-}
diff --git a/src/libcatnip/io/arguments/argumentfile.cpp b/src/libcatnip/io/arguments/argumentfile.cpp
index 542c4af..0fee812 100644
--- a/src/libcatnip/io/arguments/argumentfile.cpp
+++ b/src/libcatnip/io/arguments/argumentfile.cpp
@@ -8,14 +8,12 @@
 using namespace catnip;
 using namespace std;
 
-ArgumentFile::ArgumentFile(void) { registerProperties_(); }
+ArgumentFile::ArgumentFile(void) { 
+  auto prop_file_exist = std::unique_ptr<PropertyObject>(new PropertyFileExist());
+  propobjs_.push_back(prop_file_exist);
+  auto prop_file_ext = std::unique_ptr<PropertyObject>(new PropertyFileExt());
+  propobjs_.push_back(prop_file_ext);
+  auto prop_sis_file = std::unique_ptr<PropertyObject>(new PropertySisterFile());
+  propobjs_.push_back(prop_sis_file);
 
-void ArgumentFile::registerProperties_(void) {
-
-  PropertyFileExist* prop_file_exist = new PropertyFileExist();
-  int_propobjs_.push_back(prop_file_exist);
-  PropertyFileExt* prop_file_ext = new PropertyFileExt();
-  string_set_propobjs_.push_back(prop_file_ext);
-  PropertySisterFile* prop_sis_file = new PropertySisterFile();
-  string_vec_propobjs_.push_back(prop_sis_file);
 }
diff --git a/src/libcatnip/io/arguments/argumentfile.hpp b/src/libcatnip/io/arguments/argumentfile.hpp
index 4b1e4c2..bea9916 100644
--- a/src/libcatnip/io/arguments/argumentfile.hpp
+++ b/src/libcatnip/io/arguments/argumentfile.hpp
@@ -7,12 +7,14 @@
 
 namespace catnip {
 
-class ArgumentFile : public ArgumentObject<std::string> {
- private:
-  std::string getName_(void) const { return "ARGUMENT_FILE"; }
-  void registerProperties_(void);
+class ArgumentFile : public ArgumentObject {
 
  public:
+
+  virtual ArgumentType getArgumentType(void) const noexcept final {
+    return ArgumentType::FILES;
+  }
+
   ArgumentFile(void);
 };
 
diff --git a/src/libcatnip/io/arguments/argumentint.cpp b/src/libcatnip/io/arguments/argumentint.cpp
deleted file mode 100644
index 494e935..0000000
--- a/src/libcatnip/io/arguments/argumentint.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-
-#include "argumentint.hpp"
-#include "properties/propertyint.hpp"
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentInt::ArgumentInt(void) { registerProperties_(); }
-
-void ArgumentInt::registerProperties_(void) {
-  PropertyInt* prop_int = new PropertyInt;
-  int_propobjs_.push_back(prop_int);
-}
diff --git a/src/libcatnip/io/arguments/argumentint.hpp b/src/libcatnip/io/arguments/argumentint.hpp
deleted file mode 100644
index e4040c5..0000000
--- a/src/libcatnip/io/arguments/argumentint.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENT_INT_HPP
-#define _CATNIP_ARGUMENT_INT_HPP
-
-#include "argumentobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class ArgumentInt : public ArgumentObject<int> {
- private:
-  std::string getName_(void) const { return "ARGUMENT_INT"; }
-  void registerProperties_(void);
-
- public:
-  ArgumentInt(void);
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_ARGUMENT_INT_HPP
diff --git a/src/libcatnip/io/arguments/argumentnumerical.cpp b/src/libcatnip/io/arguments/argumentnumerical.cpp
new file mode 100644
index 0000000..2aa4cb8
--- /dev/null
+++ b/src/libcatnip/io/arguments/argumentnumerical.cpp
@@ -0,0 +1,13 @@
+
+#include "argumentnumerical.hpp"
+#include "properties/propertynumerical.hpp"
+#include <iostream>
+#include <memory>
+
+using namespace catnip;
+using namespace std;
+
+ArgumentNumerical::ArgumentNumerical(void) { 
+  propobjs_.push_back(std::unique_ptr<PropertyObject>( new PropertyNumerical()));
+}
+
diff --git a/src/libcatnip/io/arguments/argumentdouble.hpp b/src/libcatnip/io/arguments/argumentnumerical.hpp
similarity index 85%
rename from src/libcatnip/io/arguments/argumentdouble.hpp
rename to src/libcatnip/io/arguments/argumentnumerical.hpp
index 7d1b2f4..c7f4fa3 100644
--- a/src/libcatnip/io/arguments/argumentdouble.hpp
+++ b/src/libcatnip/io/arguments/argumentnumerical.hpp
@@ -7,7 +7,7 @@
 
 namespace catnip {
 
-class ArgumentDouble : public ArgumentObject<double> {
+class ArgumentNumerical : public ArgumentObject<double> {
  private:
   std::string getName_(void) const { return "ARGUMENT_DOUBLE"; }
   void registerProperties_(void);
diff --git a/src/libcatnip/io/arguments/argumentobject.hpp b/src/libcatnip/io/arguments/argumentobject.hpp
index a54b549..de8cfad 100644
--- a/src/libcatnip/io/arguments/argumentobject.hpp
+++ b/src/libcatnip/io/arguments/argumentobject.hpp
@@ -12,413 +12,123 @@
 #include <string>
 
 namespace catnip {
+
+  enum class ArgumentType {
+    NUMERICAL,
+    FILES,
+    STRING,
+    SWITCH
+  };
 // The template is simply for specifying the type of the argument coming
 // from the command line
-template <typename S>
 class ArgumentObject {
  protected:
-  std::vector<PropertyObject<S, int>*> int_propobjs_;
-  std::vector<PropertyObject<S, double>*> double_propobjs_;
-  std::vector<PropertyObject<S, size_t>*> size_t_propobjs_;
-  std::vector<PropertyObject<S, std::string>*> string_propobjs_;
-  std::vector<PropertyObject<S, std::set<std::string>>*> string_set_propobjs_;
-  std::vector<PropertyObject<S, std::vector<std::string>>*>
-      string_vec_propobjs_;
-
-  virtual std::string getName_(void) const { return "UNKNOWN"; }
-
-  void checkValid_(const S& val) const {
-    for (auto prop : int_propobjs_) {
-      prop->propValid(val);
-    }
-    for (auto prop : double_propobjs_) {
-      prop->propValid(val);
-    }
-    for (auto prop : size_t_propobjs_) {
-      prop->propValid(val);
-    }
-    for (auto prop : string_propobjs_) {
-      prop->propValid(val);
-    }
-    for (auto prop : string_set_propobjs_) {
-      prop->propValid(val);
-    }
-    for (auto prop : string_vec_propobjs_) {
-      prop->propValid(val);
-    }
-  }
-
-  // Register the relevant properties
-  virtual void registerProperties_(void){};
+  std::vector<std::unique_ptr<PropertyObject>> propobjs_;
 
  public:
-  virtual ~ArgumentObject(void) {
-
-    for (auto int_ptr : int_propobjs_) {
-      delete int_ptr;
-    }
-    int_propobjs_.clear();
-    for (auto double_ptr : double_propobjs_) {
-      delete double_ptr;
-    }
-    double_propobjs_.clear();
-    for (auto size_t_ptr : size_t_propobjs_) {
-      delete size_t_ptr;
-    }
-    size_t_propobjs_.clear();
-    for (auto str_ptr : string_propobjs_) {
-      delete str_ptr;
-    }
-    string_propobjs_.clear();
-    for (auto set_ptr : string_set_propobjs_) {
-      delete set_ptr;
-    }
-    string_set_propobjs_.clear();
-    for (auto vec_ptr : string_vec_propobjs_) {
-      delete vec_ptr;
-    }
-    string_vec_propobjs_.clear();
-  }
+  virtual ~ArgumentObject(void) {};
 
   // The argument object by default requires a parameter
   virtual bool requiresParameter(void) { return true; }
 
-  std::string getArgumentName(void) { return getName_(); }
+  virtual ArgumentType getArgumentType(void) const noexcept = 0; 
 
-  std::vector<std::string> getProperties(void) {
-    std::vector<std::string> props;
-    for (auto prop : int_propobjs_) {
-      props.push_back(prop->getPropertyName());
-    }
-    for (auto prop : double_propobjs_) {
-      props.push_back(prop->getPropertyName());
-    }
-    for (auto prop : size_t_propobjs_) {
-      props.push_back(prop->getPropertyName());
-    }
-    for (auto prop : string_propobjs_) {
-      props.push_back(prop->getPropertyName());
-    }
-    for (auto prop : string_set_propobjs_) {
-      props.push_back(prop->getPropertyName());
+  std::vector<PropertyType> getProperties(void) {
+    std::vector<PropertyType> props;
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      props.push_back(prop->getPropertyType());
     }
-    for (auto prop : string_vec_propobjs_) {
-      props.push_back(prop->getPropertyName());
-    }
-
-    if (props.size() == 0) props.push_back("NO_PROPERTIES");
     return props;
   }
 
-  std::vector<std::string> getPropertyOptions(void) {
-    std::vector<std::string> ops;
-    for (auto prop : int_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    for (auto prop : double_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    for (auto prop : size_t_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    for (auto prop : string_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    for (auto prop : string_set_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    for (auto prop : string_vec_propobjs_) {
+  std::vector<Option> getPropertyOptions(PropertyType property) {
+      for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+        if ( prop->getPropertyType() == property ) {
+          return prop->getPropertyOptions();
+        }
+      }
+      return std::vector<Option>();
+  }
+
+  /**
+   * @brief Gets the options of all properties
+   *
+   * @return 
+   */
+  std::vector<Option> getPropertyOptions(void) const {
+    std::vector<Option> ops;
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
       auto vec_opt = prop->getPropertyOptions();
       ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
     }
-    if (ops.size() == 0) ops.push_back("NO_OPTIONS");
     return ops;
   }
 
-  std::map<std::string, std::string> getPropertyValues(void) {
-    std::map<std::string, std::string> opts_values;
-    for (auto prop : int_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        auto value = std::to_string(prop->getPropOption(opt));
-        opts_values[opt] = value;
-      }
-    }
-    for (auto prop : double_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        auto value = std::to_string(prop->getPropOption(opt));
-        opts_values[opt] = value;
-      }
-    }
-    for (auto prop : size_t_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        auto value = std::to_string(prop->getPropOption(opt));
-        opts_values[opt] = value;
-      }
-    }
-    for (auto prop : string_propobjs_) {
+ 
+  /**
+   * @brief Returns the options with value associated with it
+   *
+   * @return 
+   */
+  std::map<PropertyType, std::map<Option, std::any>> getPropertyValues(void) {
+    std::map<PropertyType, std::map<Option, std::any>> opts_values;
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      PropertyType type = prop->getPropertyType();
       auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        auto value = prop->getPropOption(opt);
-        opts_values[opt] = value;
-      }
-    }
-    for (auto prop : string_set_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        std::set<std::string> value_set = prop->getPropOption(opt);
-        std::string values = "";
-        for (auto val : value_set) {
-          values.append(val);
-          values.append(" ");
-        }
-        trim(values);
-        opts_values[opt] = values;
-      }
-    }
-    for (auto prop : string_vec_propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      for (auto opt : vec_opt) {
-        std::vector<std::string> value_vec = prop->getPropOption(opt);
-        std::string values = "";
-        for (auto val : value_vec) {
-          values.append(val);
-          values.append(" ");
-        }
-        trim(values);
-        opts_values[opt] = values;
+      for (Option opt : vec_opt) {
+        auto value = prop->getPropOption<std::any>(opt);
+        opts_values[type][opt] = value;
       }
     }
     return opts_values;
   }
 
-  std::string getPropertyValues(std::string property,const std::string & option) {
-    for (auto prop : int_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            return std::to_string(prop->getPropOption(opt));
-          }
-        }
-      }
-    }
-    for (auto prop : double_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            return std::to_string(prop->getPropOption(opt));
-          }
-        }
-      }
-    }
-    for (auto prop : size_t_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            return std::to_string(prop->getPropOption(opt));
-          }
-        }
-      }
-    }
-    for (auto prop : string_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            return prop->getPropOption(opt);
-          }
-        }
-      }
-    }
-    for (auto prop : string_set_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            std::set<std::string> value_set = prop->getPropOption(opt);
-            std::string values = "";
-            for (auto val : value_set) {
-              values.append(val);
-              values.append(" ");
-            }
-            trim(values);
-            return values;
-          }
-        }
-      }
-    }
-    for (auto prop : string_vec_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        auto vec_opt = prop->getPropertyOptions();
-        for (auto opt : vec_opt) {
-          if (option.compare(opt) == 0) {
-            std::vector<std::string> value_vec = prop->getPropOption(opt);
-            std::string values = "";
-            for (auto val : value_vec) {
-              values.append(val);
-              values.append(" ");
-            }
-            trim(values);
-            return values;
+  template<class T>
+  T getPropertyValues(PropertyType property,const Option & option) {
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      if (property == prop->getPropertyType()) {
+        std::vector<Option> vec_opt = prop->getPropertyOptions();
+        for (const Option & opt : vec_opt) {
+          if (option == opt) {
+            return prop->getPropOption<T>(opt);
           }
         }
       }
     }
 
     std::string err =
-        "Unable to recognize property or option " + property + " " + option;
+        "Unable to recognize property or option ";
     throw std::invalid_argument(err);
   }
 
   // Setup the valid options associated with the parameter
-  void setArgPropertyOpt(std::string property, std::string option,
-                         const double& val) {
+  template<class T>
+  void setArgPropertyOpt(PropertyType property, Option option,
+                         const T& val) {
     bool setval = false;
-    for (auto prop : double_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      if (property == prop->getPropertyType()) {
         prop->setPropOption(option, val);
         setval = true;
       }
     }
     if (!setval) {
       std::string err =
-          "Argument property: " + property + " with option: " +
-          ""
-          "" +
-          option + " of type double is unrecognized for argument " + getName_();
+          "Argument property: is unrecognized for argument ";
       throw std::invalid_argument(err);
     }
   }
 
-  void setArgPropertyOpt(std::string property, std::string option,
-                         const std::set<std::string> & val) {
-    bool setval = false;
-    for (auto prop = string_set_propobjs_.begin();
-         prop != string_set_propobjs_.end(); ++prop) {
-      if (property.compare((*prop)->getPropertyName()) == 0) {
-        (*prop)->setPropOption(option, val);
-        setval = true;
-      }
-    }
-    if (!setval) {
-      std::string err = "Argument property: " + property + " with option: " +
-                        ""
-                        "" +
-                        option +
-                        " of type set<string> is unrecognized for argument " +
-                        ""
-                        "" +
-                        getName_();
-      throw std::invalid_argument(err);
+  template< class T>
+  bool argValid(const T& value) const {
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      prop->propValid(value);
     }
-  }
-
-  void setArgPropertyOpt(std::string property, std::string option,
-                         const std::vector<std::string> & val) {
-    bool setval = false;
-    for (auto prop : string_vec_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        prop->setPropOption(option, val);
-        setval = true;
-      }
-    }
-    if (!setval) {
-      std::string err =
-          "Argument property: " + property + " with option: " +
-          ""
-          "" +
-          option + " of type vector<string> is unrecognized for argument " +
-          ""
-          "" +
-          getName_();
-      throw std::invalid_argument(err);
-    }
-  }
-
-  void setArgPropertyOpt(std::string property,const std::string & option,
-                         const std::string & val) {
-    bool setval = false;
-    for (auto prop : string_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        prop->setPropOption(option, val);
-        setval = true;
-      }
-    }
-    for (auto prop : string_vec_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        std::vector<std::string> vec_str{val};
-        prop->setPropOption(option, vec_str);
-        setval = true;
-      }
-    }
-    for (auto prop : string_set_propobjs_) {
-      if (property.compare(prop->getPropertyName()) == 0) {
-        std::set<std::string> set_str{val};
-        prop->setPropOption(option, set_str);
-        setval = true;
-      }
-    }
-    if (!setval) {
-      std::string err =
-          "Argument property: " + property + " with option: " +
-          ""
-          "" +
-          option + " of type string is unrecognized for argument " + getName_();
-      throw std::invalid_argument(err);
-    }
-  }
-
-  void setArgPropertyOpt(std::string property, const std::string & option, int val) {
-    bool setval = false;
-    for (auto prop : int_propobjs_) {
-
-      if (property.compare(prop->getPropertyName()) == 0) {
-        prop->setPropOption(option, val);
-        setval = true;
-      }
-    }
-    if (!setval) {
-      std::string err = "Argument property: " + property + " with option: " +
-                        ""
-                        "" +
-                        option + " of type int is unrecognized for argument " +
-                        getName_();
-      throw std::invalid_argument(err);
-    }
-  }
-
-  bool argValid(const S& value) const {
-    checkValid_(value);
     return true;
   }
 
   void postArgCheck(void) {
-    for (auto prop : int_propobjs_) {
-      prop->postCheck();
-    }
-    for (auto prop : double_propobjs_) {
-      prop->postCheck();
-    }
-    for (auto prop : size_t_propobjs_) {
-      prop->postCheck();
-    }
-    for (auto prop : string_propobjs_) {
-      prop->postCheck();
-    }
-    for (auto prop : string_set_propobjs_) {
-      prop->postCheck();
-    }
-    for (auto prop : string_vec_propobjs_) {
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
       prop->postCheck();
     }
   }
diff --git a/src/libcatnip/io/arguments/argumentstring.cpp b/src/libcatnip/io/arguments/argumentstring.cpp
index 059264e..5091056 100644
--- a/src/libcatnip/io/arguments/argumentstring.cpp
+++ b/src/libcatnip/io/arguments/argumentstring.cpp
@@ -7,11 +7,9 @@
 using namespace catnip;
 using namespace std;
 
-ArgumentString::ArgumentString(void) { registerProperties_(); }
-
-void ArgumentString::registerProperties_(void) {
-  PropertyString* prop_string = new PropertyString;
-  size_t_propobjs_.push_back(prop_string);
-  PropertyStringChoice* prop_string_choice = new PropertyStringChoice;
-  string_set_propobjs_.push_back(prop_string_choice);
+ArgumentString::ArgumentString(void) { 
+  auto prop_string = std::unique_ptr<PropertyObject>(new PropertyString);
+  propobjs_.push_back(prop_string);
+  auto prop_string_choice = std::unique_ptr<PropertyObject>(new PropertyStringChoice);
+  propobjs_.push_back(prop_string_choice);
 }
diff --git a/src/libcatnip/io/arguments/argumentstring.hpp b/src/libcatnip/io/arguments/argumentstring.hpp
index f32dedd..b599d38 100644
--- a/src/libcatnip/io/arguments/argumentstring.hpp
+++ b/src/libcatnip/io/arguments/argumentstring.hpp
@@ -7,12 +7,12 @@
 
 namespace catnip {
 
-class ArgumentString : public ArgumentObject<std::string> {
- private:
-  std::string getName_(void) const { return "ARGUMENT_STRING"; }
-  void registerProperties_(void);
-
+class ArgumentString : public ArgumentObject {
  public:
+
+  virtual ArgumentType getArgumentType(void) const noexcept final 
+  { return ArgumentType::STRING; }
+
   ArgumentString(void);
 };
 
diff --git a/src/libcatnip/io/arguments/argumentswitch.cpp b/src/libcatnip/io/arguments/argumentswitch.cpp
index 71ac538..c41a211 100644
--- a/src/libcatnip/io/arguments/argumentswitch.cpp
+++ b/src/libcatnip/io/arguments/argumentswitch.cpp
@@ -6,11 +6,9 @@
 using namespace catnip;
 using namespace std;
 
-ArgumentSwitch::ArgumentSwitch(void) { registerProperties_(); }
-
-void ArgumentSwitch::registerProperties_(void) {
-  PropertySwitch* prop_switch = new PropertySwitch;
-  string_propobjs_.push_back(prop_switch);
+ArgumentSwitch::ArgumentSwitch(void) { 
+  auto prop_switch = std::unique_ptr<PropertyObject>(new PropertySwitch);
+  propobjs_.push_back(prop_switch);
 }
 
 bool ArgumentSwitch::positive(string val) const {
diff --git a/src/libcatnip/io/arguments/argumentswitch.hpp b/src/libcatnip/io/arguments/argumentswitch.hpp
index d277e2d..a7d8793 100644
--- a/src/libcatnip/io/arguments/argumentswitch.hpp
+++ b/src/libcatnip/io/arguments/argumentswitch.hpp
@@ -6,15 +6,17 @@
 #include <set>
 
 namespace catnip {
-class ArgumentSwitch : public ArgumentObject<std::string> {
- private:
-  std::string getName_(void) const { return "ARGUMENT_SWITCH"; }
-  void registerProperties_(void);
+class ArgumentSwitch : public ArgumentObject {
 
  public:
+
+  virtual ArgumentType getArgumentType(void) const noexcept final {
+    return ArgumentType::SWITCH;
+  }
+
   ArgumentSwitch(void);
-  bool requiresParameter(void) { return false; }
-  bool positive(int val) const { return ((val == 1) ? true : false); }
+  virtual bool requiresParameter(void) final { return false; }
+  bool positive(int val) const noexcept { return ((val == 1) ? true : false); }
   bool positive(std::string val) const;
 };
 
diff --git a/src/libcatnip/io/arguments/properties/property_numeric.hpp b/src/libcatnip/io/arguments/properties/property_numeric.hpp
index 8c30bcd..f3b04da 100644
--- a/src/libcatnip/io/arguments/properties/property_numeric.hpp
+++ b/src/libcatnip/io/arguments/properties/property_numeric.hpp
@@ -20,10 +20,6 @@ class PropertyNumeric : public PropertyObject {
     options_[Option::MAX] = std::numeric_limits<double>::max; 
   };
 
-  virtual std::vector<Option> getPropertyOptions(void) const noexcept final {
-    return std::vector<Option> {Option::MIN, Option::MAX};
-  }
-
   virtual PropertyType getPropertyType(void) const noexcept final {
     return PropertyType::NUMERIC;
   }
diff --git a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp b/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
index ac347ec..d779db9 100644
--- a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
@@ -21,10 +21,6 @@ class PropertyFileExist : public PropertyObject {
     return PropertyType::FILE_EXISTS;
   }
 
-  virtual std::vector<Option> getPropertyOptions(void) const noexcept final {
-    return std::vector<Option> {Option::MUST_EXIST,Option::DOES_EXIST};
-  }
-
   void postCheck(void) const;
 };
 
diff --git a/src/libcatnip/io/arguments/properties/propertyfileext.cpp b/src/libcatnip/io/arguments/properties/propertyfileext.cpp
index 670a889..1c7fff3 100644
--- a/src/libcatnip/io/arguments/properties/propertyfileext.cpp
+++ b/src/libcatnip/io/arguments/properties/propertyfileext.cpp
@@ -7,37 +7,22 @@
 using namespace catnip;
 using namespace std;
 
-PropertyFileExt::PropertyFileExt(void) {
-  set<string> exts_;
-  exts_.insert("*");
-  setPropOption_("ALLOWED_FILE_EXT", exts_);
-}
-
 PropertyFileExt::PropertyFileExt(string ext) {
   checkExt(ext);
-  set<string> exts_;
-  exts_.insert(ext);
-  setPropOption_("ALLOWED_FILE_EXT", exts_);
+  setPropOption_(Option::ALLOWED_VALUES, ext);
 }
 
 PropertyFileExt::PropertyFileExt(set<string> exts) {
-  set<string> exts_;
-  for (auto ext : exts) {
+  for (const std::string & ext : exts) {
     checkExt(ext);
-    exts_.insert(ext);
   }
-  setPropOption_("ALLOWED_FILE_EXT", exts_);
-}
-
-vector<string> PropertyFileExt::getOpts_(void) const {
-  vector<string> options{"ALLOWED_FILE_EXT"};
-  return options;
+  setPropOption_(Option::ALLOWED_VALUES, exts);
 }
 
 void PropertyFileExt::extSupported(const string& ext) const {
   checkExt(ext);
-  auto exts_ = getPropOption("ALLOWED_FILE_EXT");
-  for (auto ext_ : exts_) {
+  auto exts_ = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
+  for (const std::string & ext_ : exts_) {
     if (ext_[0] == '*') {
       return;
     } else if (ext_.compare(ext) == 0) {
@@ -65,19 +50,19 @@ void PropertyFileExt::checkExt(const string& ext) const {
   return;
 }
 
-void PropertyFileExt::setPropOption(std::string option,
+void PropertyFileExt::setPropOption(Option option,
                                     std::set<std::string> vars) {
   PropertyObject::setPropOption(option, vars);
 }
 
-void PropertyFileExt::setPropOption(std::string option, std::string var) {
+void PropertyFileExt::setPropOption(Option option, std::string var) {
   set<string> vars;
   vars.insert(var);
   PropertyObject::setPropOption(option, vars);
 }
 
-bool PropertyFileExt::propValid(const string& fileNamePath) {
-  string fileName = lastStringInPath(fileNamePath);
+bool PropertyFileExt::propValid(const any & fileNamePath) {
+  string fileName = lastStringInPath(any_cast<std::string>(fileNamePath));
   string ext = grabStrAfterLastOccuranceInclusive(fileName, ".");
   extSupported(ext);
   return true;
diff --git a/src/libcatnip/io/arguments/properties/propertyfileext.hpp b/src/libcatnip/io/arguments/properties/propertyfileext.hpp
index 7cf4b41..84e815a 100644
--- a/src/libcatnip/io/arguments/properties/propertyfileext.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyfileext.hpp
@@ -8,20 +8,29 @@
 namespace catnip {
 
 class PropertyFileExt
-    : public PropertyObject<std::string, std::set<std::string> > {
+    : public PropertyObject {
  private:
   void checkExt(const std::string &) const;
   void extSupported(const std::string &) const;
-  std::string getName_(void) const { return "PROPERTY_FILE_EXT"; }
   std::vector<std::string> getOpts_(void) const;
 
  public:
-  explicit PropertyFileExt(void);
+  explicit PropertyFileExt(void) {
+    std::set<std::string> exts_;
+    exts_.insert("*");
+    options_[Option::ALLOWED_VALUES] = exts_;
+  }
+
   explicit PropertyFileExt(std::string ext);
   PropertyFileExt(std::set<std::string> exts);
-  bool propValid(const std::string &fileNamePath);
-  void setPropOption(std::string option, std::string var);
-  void setPropOption(std::string option, std::set<std::string> var);
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::FILE_EXT;
+  }
+
+  bool propValid(const std::any &fileNamePath);
+  void setPropOption(Option option, std::string var);
+  void setPropOption(Option option, std::set<std::string> var);
 };
 
 }  // namespace catnip
diff --git a/src/libcatnip/io/arguments/properties/propertyobject.hpp b/src/libcatnip/io/arguments/properties/propertyobject.hpp
index e28af14..78fe350 100644
--- a/src/libcatnip/io/arguments/properties/propertyobject.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyobject.hpp
@@ -15,11 +15,30 @@
 namespace catnip {
 
 enum class PropertyType {
-  UNKNOWN
+  UNKNOWN,
+  NUMERIC,
+  FILE_EXISTS,
+  FILE_EXT,
+  SISTER_FILE,
+  STRING,
+  STRING_CHOICE,
+  SWITCH
 };
 
 enum class Option {
-  NO_OPTIONS
+  NO_OPTIONS,
+  MIN,
+  MAX,
+  MIN_LENGTH,
+  MAX_LENGTH,
+  MUST_EXIST,
+  DOES_EXIST,
+  ALLOWED_VALUES,
+  ENFORCED,
+  FILE_NAME,
+  FILE_PATH,
+  FILE_PATH_NAME,
+  VALUE
 };
 
 class PropertyObject {
@@ -32,29 +51,27 @@ class PropertyObject {
     return options_.count(option);
   }
 
-  void setPropOption_(const Option &option, const std::any &val) {
+  virtual void setPropOption_(const Option &option, const std::any &val) {
       options_[option] = val;
   }
 
-  virtual PropertyType getPropertyType_(void) const noexcept 
-  { return PropertyType::UNKNOWN; }
-
-  virtual std::vector<Option> getOpts_(void) const noexcept {
-    std::vector<Option> options{Option::NO_OPTIONS};
-    return options;
-  }
-
  public:
-  virtual ~PropertyObject(void) {
-  }
+  virtual ~PropertyObject(void) { }
 
   virtual bool propValid(const std::any &value) = 0;
 
-  PropertyType getPropertyType(void) const noexcept { return getPropertyType_(); }
+  virtual PropertyType getPropertyType(void) const noexcept = 0;
 
-  std::vector<Option> getPropertyOptions(void) const noexcept { return getOpts_(); }
+  std::vector<Option> getPropertyOptions(void) const {
+    std::vector<Option> options;
+    for ( std::pair<Option,std::any> option : options_){
+      options.push_back(option.first); 
+    }
+    return options;
+  } 
 
   // Setup the valid options associated with the parameter
+  // WARNING setting a property value will overwrite existing values
   void setPropOption(Option option, const std::any & val) {
     if (!propOptionValid_(option)) {
       throw std::invalid_argument("Property option is unrecognized.");
diff --git a/src/libcatnip/io/arguments/properties/propertysisterfile.cpp b/src/libcatnip/io/arguments/properties/propertysisterfile.cpp
index c1df59f..00e377e 100644
--- a/src/libcatnip/io/arguments/properties/propertysisterfile.cpp
+++ b/src/libcatnip/io/arguments/properties/propertysisterfile.cpp
@@ -2,6 +2,8 @@
 #include "propertysisterfile.hpp"
 #include "../../../string_support.hpp"
 #include <stdexcept>
+#include <set>
+#include <vector>
 #include <sys/stat.h>
 
 using namespace catnip;
@@ -10,22 +12,12 @@ using namespace std;
 PropertySisterFile::PropertySisterFile(void) {
   string var = "NOT_DEFINED";
   vector<string> vec_var{var};
-  setPropOption_("ALLOWED_SISTER_FILE_EXT", vec_var);
-  setPropOption_("SISTER_FILE_NAME", vec_var);
-  setPropOption_("SISTER_FILE_PATH", vec_var);
-  setPropOption_("SISTER_FILE_PATH_NAME", vec_var);
+  setPropOption_(Option::ALLOWED_VALUES, vec_var);
+  setPropOption_(Option::FILE_NAME, vec_var);
+  setPropOption_(Option::FILE_PATH, vec_var);
+  setPropOption_(Option::FILE_PATH_NAME, vec_var);
   vector<string> vec_var2{"false"};
-  setPropOption_("SISTER_FILE_EXISTS", vec_var2);
-}
-
-vector<string> PropertySisterFile::getOpts_(void) const {
-  vector<string> options;
-  options.push_back("ALLOWED_SISTER_FILE_EXT");
-  options.push_back("SISTER_FILE_NAME");
-  options.push_back("SISTER_FILE_PATH");
-  options.push_back("SISTER_FILE_PATH_NAME");
-  options.push_back("SISTER_FILE_EXISTS");
-  return options;
+  setPropOption_(Option::DOES_EXIST, vec_var2);
 }
 
 bool PropertySisterFile::fileExist(const string& fileNamePath) const {
@@ -35,7 +27,7 @@ bool PropertySisterFile::fileExist(const string& fileNamePath) const {
 
 void PropertySisterFile::extSupported(const string& ext) const {
   checkExt(ext);
-  auto exts_ = getPropOption("ALLOWED_SISTER_FILE_EXT");
+  auto exts_ = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
   for (auto ext_ : exts_) {
     if (ext_.compare(ext) == 0) {
       return;
@@ -56,73 +48,15 @@ void PropertySisterFile::checkExt(const string& ext) const {
   return;
 }
 
-void PropertySisterFile::setPropOption(std::string option,
-                                       const std::string& var) {
-
-  if (option.compare("ALLOWED_SISTER_FILE_EXT") == 0) {
-    checkExt(var);
-    vector<string> vec_var{var};
-    setPropOption_(option, vec_var);
-    return;
-  }
-  if (option.compare("SISTER_FILE_EXISTS") == 0 ||
-      option.compare("SISTER_FILE_NAME") == 0 ||
-      option.compare("SISTER_FILE_PATH") == 0 ||
-      option.compare("SISTER_FILE_PATH_NAME") == 0) {
-    throw invalid_argument(
-        "This option is determined internally you do not have permission to "
-        "change it");
-  }
-  throw invalid_argument("Unrecognized option value combo " + option + " " +
-                         var);
-}
-
-void PropertySisterFile::setPropOption(std::string option,
-                                       vector<string> vec_vars) {
-
-  if (option.compare("ALLOWED_SISTER_FILE_EXT") == 0) {
-    vector<string> fileNames;
-    vector<string> filePaths;
-    vector<string> filePathNames;
-    vector<string> fileExists;
-    string notdef = "NOT_DEFINED";
+bool PropertySisterFile::propValid(const std::any & name_and_path) {
 
-    for (auto var : vec_vars) {
-      checkExt(var);
-      fileNames.push_back(notdef);
-      filePaths.push_back(notdef);
-      filePathNames.push_back(notdef);
-      fileExists.push_back("false");
-    }
-    setPropOption_(option, vec_vars);
-    return;
-  }
-  if (option.compare("SISTER_FILE_EXISTS") == 0 ||
-      option.compare("SISTER_FILE_NAME") == 0 ||
-      option.compare("SISTER_FILE_PATH") == 0 ||
-      option.compare("SISTER_FILE_PATH_NAME") == 0) {
-    throw invalid_argument(
-        "This option is determined internally you do not have permission to "
-        "change it");
-  }
-
-  string vars = "";
-  for (auto var : vec_vars) {
-    vars.append(var);
-    vars.append(" ");
-  }
-  trim(vars);
-  throw invalid_argument("Unrecognized option value combo " + option + " " +
-                         vars);
-}
-
-bool PropertySisterFile::propValid(const string& fileNamePath) {
+  std::string fileNamePath = any_cast<std::string>(name_and_path); 
 
   string fileName = lastStringInPath(fileNamePath);
   string path = getPath(fileNamePath);
 
   string sisterFileCore = grabStrBeforeLastOccurance(fileName, ".");
-  auto sister_exts = getPropOption("ALLOWED_SISTER_FILE_EXT");
+  auto sister_exts = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
 
   vector<string> fileNames;
   vector<string> filePaths;
@@ -145,9 +79,10 @@ bool PropertySisterFile::propValid(const string& fileNamePath) {
       }
     }
   }
-  setPropOption_("SISTER_FILE_NAME", fileNames);
-  setPropOption_("SISTER_FILE_PATH", filePaths);
-  setPropOption_("SISTER_FILE_PATH_NAME", filePathNames);
-  setPropOption_("SISTER_FILE_EXISTS", fileExists);
+
+  setPropOption_(Option::FILE_NAME, fileNames);
+  setPropOption_(Option::FILE_PATH, filePaths);
+  setPropOption_(Option::FILE_PATH_NAME, filePathNames);
+  setPropOption_(Option::DOES_EXIST, fileExists);
   return true;
 }
diff --git a/src/libcatnip/io/arguments/properties/propertysisterfile.hpp b/src/libcatnip/io/arguments/properties/propertysisterfile.hpp
index b7fdaec..a5d0874 100644
--- a/src/libcatnip/io/arguments/properties/propertysisterfile.hpp
+++ b/src/libcatnip/io/arguments/properties/propertysisterfile.hpp
@@ -8,19 +8,22 @@
 namespace catnip {
 
 class PropertySisterFile
-    : public PropertyObject<std::string, std::vector<std::string>> {
+    : public PropertyObject {
  private:
-  std::string getName_(void) const { return "PROPERTY_SISTER_FILE"; }
-  std::vector<std::string> getOpts_(void) const;
   bool fileExist(const std::string &) const;
   void extSupported(const std::string &) const;
   void checkExt(const std::string &) const;
 
  public:
+
   PropertySisterFile(void);
-  void setPropOption(std::string option, const std::string &var);
-  void setPropOption(std::string option, std::vector<std::string> var);
-  bool propValid(const std::string &fileNamePath);
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::SISTER_FILE;
+  }
+
+  virtual bool propValid(const std::any &fileNamePath) final;
+
 };
 
 }  // namespace catnip
diff --git a/src/libcatnip/io/arguments/properties/propertystring.cpp b/src/libcatnip/io/arguments/properties/propertystring.cpp
index 93fdcc7..c228397 100644
--- a/src/libcatnip/io/arguments/properties/propertystring.cpp
+++ b/src/libcatnip/io/arguments/properties/propertystring.cpp
@@ -1,4 +1,4 @@
-
+#include "propertyobject.hpp"
 #include "propertystring.hpp"
 #include <memory>
 
@@ -6,27 +6,24 @@ using namespace catnip;
 using namespace std;
 
 PropertyString::PropertyString(void) {
-  setPropOption_("MIN_LENGTH", 0);
-  setPropOption_("MAX_LENGTH", (size_t)-1);
-}
-
-vector<string> PropertyString::getOpts_(void) const {
-  vector<string> options{"MIN_LENGTH", "MAX_LENGTH"};
-  return options;
+  size_t min_len = 0;
+  size_t max_len = -1;
+  setPropOption_(Option::MIN_LENGTH, min_len);
+  setPropOption_(Option::MAX_LENGTH, max_len);
 }
 
 void PropertyString::stringValid(const string& val) const {
-  if (val.size() > getPropOption("MAX_LENGTH")) {
+  if (val.size() > getPropOption<size_t>(Option::MAX_LENGTH)) {
     string err = "The string is larger than allowed " + val +
                  " the "
                  "maximum allowed value is " +
-                 to_string(getPropOption("MAX_LENGTH"));
+                 to_string(getPropOption<size_t>(Option::MAX_LENGTH));
     throw invalid_argument(err);
-  } else if (val.size() < getPropOption("MIN_LENGTH")) {
+  } else if (val.size() < getPropOption<size_t>(Option::MIN_LENGTH)) {
     string err = "The string is smaller than allowed " + val +
                  " the "
                  "maximum allowed value is " +
-                 to_string(getPropOption("MIN_LENGTH"));
+                 to_string(getPropOption<size_t>(Option::MIN_LENGTH));
     throw invalid_argument(err);
   }
 }
diff --git a/src/libcatnip/io/arguments/properties/propertystring.hpp b/src/libcatnip/io/arguments/properties/propertystring.hpp
index e331325..faf4c46 100644
--- a/src/libcatnip/io/arguments/properties/propertystring.hpp
+++ b/src/libcatnip/io/arguments/properties/propertystring.hpp
@@ -6,15 +6,20 @@
 
 namespace catnip {
 
-class PropertyString : public PropertyObject<std::string, size_t> {
+class PropertyString : public PropertyObject {
  private:
   void stringValid(const std::string& val) const;
-  std::string getName_(void) const { return "PROPERTY_STRING"; }
-  std::vector<std::string> getOpts_(void) const;
 
  public:
   PropertyString(void);
-  bool propValid(const std::string& value) {
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::STRING;
+  }
+
+  bool propValid(const std::any& val) {
+
+    std::string value = std::any_cast<std::string>(val);
     stringValid(value);
     return true;
   }
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp b/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
index a8f1116..03d0783 100644
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
+++ b/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
@@ -9,41 +9,13 @@ using namespace std;
 
 PropertyStringChoice::PropertyStringChoice(void) {
   set<string> set_var1{"false"};
-  setPropOption_("STRING_CHOICE_ENFORCED", set_var1);
+  setPropOption_(Option::ENFORCED, set_var1);
   string str = "NOT_DEFINED";
   set<string> set_var2{str};
-  setPropOption_("STRING_CHOICES", set_var2);
+  setPropOption_(Option::ALLOWED_VALUES, set_var2);
 }
 
-vector<string> PropertyStringChoice::getOpts_(void) const {
-  vector<string> options;
-  options.push_back("STRING_CHOICE_ENFORCED");
-  options.push_back("STRING_CHOICES");
-  return options;
-}
-
-void PropertyStringChoice::setPropOption(std::string option, std::string var) {
-
-  if (option.compare("STRING_CHOICE_ENFORCED") == 0) {
-    if (var.compare("false") == 0 || var.compare("true") == 0) {
-      set<string> set_var{var};
-      setPropOption_(option, set_var);
-      return;
-    } else {
-      throw invalid_argument("The option " + option +
-                             " can only be set to values"
-                             " of true or false you have set it to " +
-                             var);
-    }
-  } else if (option.compare("STRING_CHOICES") == 0) {
-    set<string> set_var{var};
-    setPropOption_(option, set_var);
-  }
-  throw invalid_argument("Unrecognized option value combo " + option + " " +
-                         var);
-}
-
-void PropertyStringChoice::setPropOption(std::string option,
+/*void PropertyStringChoice::setPropOption( option,
                                          set<string> set_vars) {
 
   if (option.compare("STRING_CHOICES") == 0) {
@@ -82,14 +54,15 @@ void PropertyStringChoice::setPropOption(std::string option,
   trim(vars);
   throw invalid_argument("Unrecognized option value combo " + option + " " +
                          vars);
-}
+}*/
 
-bool PropertyStringChoice::propValid(const string& string_choice) {
+bool PropertyStringChoice::propValid(const any& choice) {
 
-  set<string> opt_val = getPropOption("STRING_CHOICE_ENFORCED");
+  std::string string_choice = any_cast<std::string>(choice);
+  set<string> opt_val = getPropOption<set<string>>(Option::ENFORCED);
   string val = *(opt_val.begin());
   if (val.compare("true") == 0) {
-    set<string> str_choices = getPropOption("STRING_CHOICES");
+    set<string> str_choices = getPropOption<set<string>>(Option::ALLOWED_VALUES);
     if (str_choices.count(string_choice) > 0) return true;
     throw invalid_argument("The value " + string_choice +
                            " is not a valid option");
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp b/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
index 580d816..59cdaab 100644
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
+++ b/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
@@ -8,16 +8,17 @@
 namespace catnip {
 
 class PropertyStringChoice
-    : public PropertyObject<std::string, std::set<std::string>> {
+    : public PropertyObject {
  private:
-  std::string getName_(void) const { return "PROPERTY_STRING_CHOICE"; }
-  std::vector<std::string> getOpts_(void) const;
 
  public:
   PropertyStringChoice(void);
-  void setPropOption(std::string option, std::string var);
-  void setPropOption(std::string option, std::set<std::string> var);
-  bool propValid(const std::string& string_choice);
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::STRING_CHOICE;
+  }
+
+  virtual bool propValid(const std::any& string_choice) final;
 };
 
 }  // namespace catnip
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.cpp b/src/libcatnip/io/arguments/properties/propertyswitch.cpp
index 9fa1c90..18a4029 100644
--- a/src/libcatnip/io/arguments/properties/propertyswitch.cpp
+++ b/src/libcatnip/io/arguments/properties/propertyswitch.cpp
@@ -6,12 +6,7 @@
 using namespace catnip;
 using namespace std;
 
-PropertySwitch::PropertySwitch() { setPropOption_("DEFAULT", "OFF"); }
-
-vector<string> PropertySwitch::getOpts_(void) const {
-  vector<string> options{"DEFAULT"};
-  return options;
-}
+PropertySwitch::PropertySwitch() { setPropOption_(Option::VALUE, bool(false)); }
 
 void PropertySwitch::switchValid(int val) const {
   if (val < 0 || val > 1) {
@@ -38,3 +33,16 @@ void PropertySwitch::switchValid(std::string val) const {
     throw invalid_argument(err);
   }
 }
+
+bool PropertySwitch::propValid(const std::any & value) {
+  if( value.type() == typeid(int)){
+    int int_val = any_cast<int>(value);
+    switchValid(int_val); 
+  }else if(value.type() == typeid(std::string)){
+    std::string str_val = any_cast<std::string>(value);
+    switchValid(str_val); 
+  }else if(value.type() != typeid(bool)) {
+    throw invalid_argument("Unrecognized type passed to switch, only recognizes"
+        " int, string and bool types");
+  }
+}
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.hpp b/src/libcatnip/io/arguments/properties/propertyswitch.hpp
index dd9535d..de4688a 100644
--- a/src/libcatnip/io/arguments/properties/propertyswitch.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyswitch.hpp
@@ -6,7 +6,7 @@
 
 namespace catnip {
 
-class PropertySwitch : public PropertyObject<std::string, std::string> {
+class PropertySwitch : public PropertyObject {
  private:
   std::string getName_(void) const { return "PROPERTY_SWITCH"; }
   std::vector<std::string> getOpts_(void) const;
@@ -16,15 +16,13 @@ class PropertySwitch : public PropertyObject<std::string, std::string> {
 
  public:
   PropertySwitch(void);
-  bool propValid(int value) {
-    switchValid(value);
-    return true;
-  }
-  bool propValid(const std::string& value) {
-    switchValid(value);
-    return true;
+
+  virtual PropertyType getPropertyType(void) const noexcept final {
+    return PropertyType::SWITCH; 
   }
-  bool propValid() { return true; }
+
+  virtual bool propValid(const std::any & value) final;
+  bool propValid() const {return true;}
 };
 
 }  // namespace catnip
diff --git a/src/libcatnip/io/io.cpp b/src/libcatnip/io/io.cpp
index 13dc62c..95dc2bd 100644
--- a/src/libcatnip/io/io.cpp
+++ b/src/libcatnip/io/io.cpp
@@ -174,10 +174,16 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   flag19.push_back(desc);
 
   vector<string> flag20;
-  flag19.push_back("--input_files");
-  flag19.push_back("-in");
-  desc = "Provide all input files and allow catnip to figure the rest out.";
-  flag19.push_back(desc);
+  flag20.push_back("--log");
+  flag20.push_back("-l");
+  desc = "Provide all .log files and allow catnip to figure the rest out.";
+  flag20.push_back(desc);
+
+  vector<string> flag21;
+  flag21.push_back("--pun");
+  flag21.push_back("-p");
+  desc = "Provide all .pun/.7/.orb files and allow catnip to figure the rest out.";
+  flag21.push_back(desc);
 
   set<vector<string>> flags;
   flags.insert(flag1);
@@ -198,22 +204,30 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   flags.insert(flag18);
   flags.insert(flag19);
   flags.insert(flag20);
+  flags.insert(flag21);
 
   unique_ptr<ArgumentParser> ArgPars(new ArgumentParser(flags));
 
   // Setup rules for handling flags
-  set<string> exts_all{".orb", ".7", ".pun", ".log"};
+  set<string> exts{".orb", ".7", ".pun"};
+  string ext_log = ".log";
+
   {
-    ArgPars->setFlagArgOpt("--input_files", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts_all);
-    ArgPars->setFlagArgOpt("--input_files", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", exts_all);
-    ArgPars->setFlagArgOpt("--input_files", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
+    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
+                           "ALLOWED_FILE_EXT", ext_log);
+    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
+                           "ALLOWED_SISTER_FILE_EXT", exts);
+    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
+                           "FILE_MUST_EXIST", 0);
+
+    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
+                           "ALLOWED_FILE_EXT", exts);
+    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
+                           "ALLOWED_SISTER_FILE_EXT", ext_log);
+    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
                            "FILE_MUST_EXIST", 0);
   }
 
-  set<string> exts{".orb", ".7", ".pun"};
-  string ext_log = ".log";
   // Setting up rules guiding pun files
   {
     ArgPars->setFlagArgOpt("--pun_P", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
@@ -386,7 +400,7 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
     string fileName;
     auto exists = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
     if (exists.compare("1") == 0) {
-      flag_arg[flag] = ArgParse->getStr(flag);
+      flag_arg[flag] = ArgParse->getStrs(flag).at(0);
     }
     prop = "PROPERTY_SISTER_FILE";
     opt = "SISTER_FILE_EXISTS";
@@ -405,72 +419,103 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
   }
 
   unique_ptr<Parameters> Par(new Parameters);
-  // Read file related flags
-  if (flag_arg.count("--pun_P") != 0) {
-    Par->setPunP(flag_arg["--pun_P"]);
-  } else if (flag_sister_arg.count("--pun_P") != 0) {
-    Par->setPunP(flag_sister_arg["--pun_P"]);
-  } else {
-    throw runtime_error("Unable to find file for flag --pun_P");
-  }
-  if (flag_arg.count("--pun_1") != 0) {
-    Par->setPun1(flag_arg["--pun_1"]);
-  } else if (flag_sister_arg.count("--pun_1") != 0) {
-    Par->setPun1(flag_sister_arg["--pun_1"]);
-  } else {
-    throw runtime_error("Unable to find file for flag --pun_1");
-  }
-  if (flag_arg.count("--pun_2") != 0) {
-    Par->setPun2(flag_arg["--pun_2"]);
-  } else if (flag_sister_arg.count("--pun_2") != 0) {
-    Par->setPun2(flag_sister_arg["--pun_2"]);
-  } else {
-    throw runtime_error("Unable to find file for flag --pun_2");
+
+  bool generic_file_pun_input = true;
+  bool generic_file_log_input = true;
+  // Run file related checks
+  if ( flag_arg.count("--pun_P") || 
+      flag_arg.count("--pun_1") ||
+      flag_arg.count("--pun_2") ) {
+    generic_file_pun_input = false;
+    if ( flag_arg.count("--pun")) {
+      throw runtime_error("Cannot specify (--pun_P, --pun_1, --pun_2) options "
+          "as well as --pun. These options are mutually exclusive");
+    }
   }
-  if (flag_arg.count("--log_P") != 0) {
-    Par->setLogP(flag_arg["--log_P"]);
-  } else if (flag_sister_arg.count("--log_P") != 0) {
-    Par->setLogP(flag_sister_arg["--log_P"]);
-  } else {
-    throw runtime_error("Unable to find file for flag --log_P");
+
+  if ( flag_arg.count("--log_P") || 
+      flag_arg.count("--log_1") ||
+      flag_arg.count("--log_2") ) {
+    generic_file_log_input = false;
+    if ( flag_arg.count("--log")) {
+      throw runtime_error("Cannot specify (--log_P, --log_1, --log_2) options "
+          "as well as --log. These options are mutually exclusive");
+    }
   }
-  if (flag_arg.count("--log_1") != 0) {
-    Par->setLog1(flag_arg["--log_1"]);
-  } else if (flag_sister_arg.count("--log_1") != 0) {
-    Par->setLog1(flag_sister_arg["--log_1"]);
+
+  // Read file related flags
+  if ( generic_file_pun_input == false ){
+    if (flag_arg.count("--pun_P") != 0) {
+      Par->setPunP(flag_arg["--pun_P"]);
+    } else if (flag_sister_arg.count("--pun_P") != 0) {
+      Par->setPunP(flag_sister_arg["--pun_P"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --pun_P");
+    }
+    if (flag_arg.count("--pun_1") != 0) {
+      Par->setPun1(flag_arg["--pun_1"]);
+    } else if (flag_sister_arg.count("--pun_1") != 0) {
+      Par->setPun1(flag_sister_arg["--pun_1"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --pun_1");
+    }
+    if (flag_arg.count("--pun_2") != 0) {
+      Par->setPun2(flag_arg["--pun_2"]);
+    } else if (flag_sister_arg.count("--pun_2") != 0) {
+      Par->setPun2(flag_sister_arg["--pun_2"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --pun_2");
+    }
   } else {
-    throw runtime_error("Unable to find file for flag --log_1");
+
   }
-  if (flag_arg.count("--log_2") != 0) {
-    Par->setLog2(flag_arg["--log_2"]);
-  } else if (flag_sister_arg.count("--log_2") != 0) {
-    Par->setLog2(flag_sister_arg["--log_2"]);
+  if( generic_file_log_input == false ){
+    if (flag_arg.count("--log_P") != 0) {
+      Par->setLogP(flag_arg["--log_P"]);
+    } else if (flag_sister_arg.count("--log_P") != 0) {
+      Par->setLogP(flag_sister_arg["--log_P"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --log_P");
+    }
+    if (flag_arg.count("--log_1") != 0) {
+      Par->setLog1(flag_arg["--log_1"]);
+    } else if (flag_sister_arg.count("--log_1") != 0) {
+      Par->setLog1(flag_sister_arg["--log_1"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --log_1");
+    }
+    if (flag_arg.count("--log_2") != 0) {
+      Par->setLog2(flag_arg["--log_2"]);
+    } else if (flag_sister_arg.count("--log_2") != 0) {
+      Par->setLog2(flag_sister_arg["--log_2"]);
+    } else {
+      throw runtime_error("Unable to find file for flag --log_2");
+    }
   } else {
-    throw runtime_error("Unable to find file for flag --log_2");
-  }
 
+  }
   // Read spin related flags, do not need if statement because default values
   // are defined
-  Par->setSpinP(ArgParse->getStr("--spin_P"));
-  Par->setSpin1(ArgParse->getStr("--spin_1"));
-  Par->setSpin2(ArgParse->getStr("--spin_2"));
+  Par->setSpinP(ArgParse->getStrs("--spin_P").at(0));
+  Par->setSpin1(ArgParse->getStrs("--spin_1").at(0));
+  Par->setSpin2(ArgParse->getStrs("--spin_2").at(0));
 
   // Determine if we are doing a counterpoise calculation
-  Par->setCounterPoise(ArgParse->getInt("--counter_poise"));
-  Par->setPrintSwitch(ArgParse->getInt("--all"));
-  Par->setCitation(ArgParse->getInt("--citation"));
+  Par->setCounterPoise((ArgParse->getInts("--counter_poise")).at(0));
+  Par->setPrintSwitch(ArgParse->getInts("--all").at(0));
+  Par->setCitation(ArgParse->getInts("--citation").at(0));
   // Read Orbital related flags
   {
-    string orb_typ_1 = ArgParse->getStr("--orbital_type_1");
+    string orb_typ_1 = ArgParse->getStrs("--orbital_type_1").at(0);
     Par->setOrbType1(orb_typ_1);
     if (orb_typ_1.compare("HOMO") == 0) {
-      int MO = ArgParse->getInt("--orbital_num_1");
+      int MO = ArgParse->getInts("--orbital_num_1").at(0);
       if (MO > 0) {
         throw invalid_argument("HOMO orbital must be 0 or a negative number");
       }
       Par->setOrbNum1(MO);
     } else if (orb_typ_1.compare("LUMO") == 0) {
-      int MO = ArgParse->getInt("--orbital_num_1");
+      int MO = ArgParse->getInts("--orbital_num_1").at(0);
       if (MO < 0) {
         throw invalid_argument("LUMO orbital must be 0 or a positive number");
       }
@@ -479,16 +524,16 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
   }
 
   {
-    string orb_typ_2 = ArgParse->getStr("--orbital_type_2");
+    string orb_typ_2 = ArgParse->getStrs("--orbital_type_2").at(0);
     Par->setOrbType2(orb_typ_2);
     if (orb_typ_2.compare("HOMO") == 0) {
-      int MO = ArgParse->getInt("--orbital_num_2");
+      int MO = ArgParse->getInts("--orbital_num_2").at(0);
       if (MO > 0) {
         throw invalid_argument("HOMO orbital must be 0 or a negative number");
       }
       Par->setOrbNum2(MO);
     } else if (orb_typ_2.compare("LUMO") == 0) {
-      int MO = ArgParse->getInt("--orbital_num_2");
+      int MO = ArgParse->getInts("--orbital_num_2").at(0);
       if (MO < 0) {
         throw invalid_argument("LUMO orbital must be 0 or a positive number");
       }

From bf62ce026da5a9ab2264b4a553baac5b8d6be867 Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 7 Aug 2020 13:00:51 -0600
Subject: [PATCH 65/68] Steps to refactor unit tests with properties

---
 src/libcatnip/CMakeLists.txt                  |   8 +-
 src/libcatnip/io/argumentparser.cpp           | 169 +++++++++---------
 src/libcatnip/io/argumentparser.hpp           | 138 +++++++++++---
 src/libcatnip/io/arguments/argumentobject.hpp |  29 +++
 src/tests/CMakeLists.txt                      |  41 +++--
 src/tests/test_propertydouble.cpp             |  70 --------
 src/tests/test_propertyfileexist.cpp          |  30 ++--
 src/tests/test_propertyfileext.cpp            |  47 ++---
 src/tests/test_propertyint.cpp                |  67 -------
 src/tests/test_propertynumerical.cpp          |  67 +++++++
 src/tests/test_propertystring.cpp             |  34 ++--
 src/tests/test_propertystringchoice.cpp       |   2 +-
 12 files changed, 351 insertions(+), 351 deletions(-)
 delete mode 100644 src/tests/test_propertydouble.cpp
 delete mode 100644 src/tests/test_propertyint.cpp
 create mode 100644 src/tests/test_propertynumerical.cpp

diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index f5e395f..ea1c6bd 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -1,10 +1,10 @@
 
 file(GLOB CATNIP_SOURCE_FILES 
-  *.cpp 
-  io/*.cpp
   io/arguments/*.cpp 
-  io/arguments/properties/*.cpp 
-  io/file_readers/*.cpp)
+  io/arguments/properties/*.cpp )
+#  *.cpp 
+#  io/*.cpp
+#  io/file_readers/*.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
 set_property(TARGET libcatnip PROPERTY CXX_STANDARD 17)
diff --git a/src/libcatnip/io/argumentparser.cpp b/src/libcatnip/io/argumentparser.cpp
index ae30a81..d3169b9 100644
--- a/src/libcatnip/io/argumentparser.cpp
+++ b/src/libcatnip/io/argumentparser.cpp
@@ -14,6 +14,19 @@
 using namespace catnip;
 using namespace std;
 
+std::unique_ptr<ArgumentObject> createArgument(ArgumentType type) {
+  if (argname == ArgumentType::NUMERICAL) {
+    return std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
+  } else if (argname == ArgumentType::STRING) {
+    return std::unique_ptr<ArgumentObject>(new ArgumentString);
+  } else if (argname == ArgumentType::SWITCH) {
+    return std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
+  } else if (argname == ArgumentType::FILES) {
+    return std::unique_ptr<ArgumentObject>(new ArgumentFile);
+  }
+  return std::unique_ptr<ArgumentObject>();
+}
+      
 ArgumentParser::ArgumentParser(set<vector<string>> flags) {
 
   vector<string> flag_help;
@@ -141,14 +154,15 @@ void ArgumentParser::showUsage(void) {
   cout << endl;
 }
 
-void ArgumentParser::addFlagArg(string flag, string argname) {
+void ArgumentParser::addFlagArg(string flag, ArgumentType argname) {
 
-  if (argname.compare("ARGUMENT_INT") == 0) {
-      auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
+  arg_[flag].push_back(createArgument(argname));
+/*  if (argname == ArgumentType::NUMERICAL) {
+      auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
       int_arg_[flag].push_back(std::move(ArInt));
-  } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
+  } else if (argname == ArgumentType::SWITCH) {
     if (switch_arg_.count(flag) == 0) {
-      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
+      auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
       switch_arg_[flag].push_back(std::move(ArSwitch));
     } else {
       throw invalid_argument(
@@ -156,43 +170,20 @@ void ArgumentParser::addFlagArg(string flag, string argname) {
           "flag " +
           flag);
     }
-  } else if (argname.compare("ARGUMENT_STRING") == 0) {
-      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
+  } else if (argname == ArgumentType::STRING) {
+      auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
       str_arg_[flag].push_back(std::move(ArString));
-  } else if (argname.compare("ARGUMENT_FILE") == 0) {
-      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+  } else if (argname == ArgumentType::FILES) {
+      auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
       file_arg_[flag].push_back(std::move(ArFile));
-  } else if (argname.compare("ARGUMENT_DOUBLE") == 0) {
-      auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
-      double_arg_[flag].push_back(ArDouble);
   } else {
     throw invalid_argument(
         "Unrecognized argument being added for flag"
         " argname is " +
         argname + " flag name is " + flag);
-  }
-}
-
-void ArgumentParser::setFlagDefaultValue(string flag,const int & val) {
-  int_values_[flag].push_back(val);
-  defaults_set_[flag] = true;
-}
-
-void ArgumentParser::setFlagDefaultValue(string flag,const size_t & val) {
-  size_t_values_[flag].push_back(val);
-  defaults_set_[flag] = true;
+  }*/
 }
-
-void ArgumentParser::setFlagDefaultValue(string flag,const double & val) {
-  double_values_[flag].push_back(val);
-  defaults_set_[flag] = true;
-}
-
-void ArgumentParser::setFlagDefaultValue(string flag,const string & val) {
-  string_values_[flag].push_back(val);
-  defaults_set_[flag] = true;
-}
-
+/*
 // Will apply values to all properties in the argument vector
 void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
                                    string option, int val) {
@@ -397,7 +388,7 @@ void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
     throw invalid_argument("Unrecognized vector<string> arg");
   }
 }
-
+*/
 bool ArgumentParser::nextParameterIsAFlag_(size_t index,
                                            vector<string> arguments) {
 
@@ -428,45 +419,63 @@ void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
   bool unrecognized = true;
 
   // Parse String Arguments
-  if (str_arg_.count(flag) != 0) {
+  if (arg_.count(flag) != 0) {
+
+    ArgumentType type = arg_[flag]->getArgumentType(); 
+    // Switch does not require an argument
+    if ( type == ArgumentType::SWITCH && 
+        (nextParameterIsAFlag_(index, arguments) ||
+         (index + 1) >= arguments.size())){
 
-    if ((index + 1) >= arguments.size()) {
-      string err = "" + flag + " Missing arguments";
-      throw runtime_error(err);
-    }
-    int arg_index = 0;
-    do { // Allow reading of multiple arguments
-      string argument = arguments.at(index + 1);
-      if ( arg_index != 0){
-        // Need to duplicate the argument
-        std::string arg_name = str_arg_[flag].at(0)->getArgumentName();
-        addFlagArg(flag, arg_name);
-        std::vector<std::string> arg_props = str_arg_[flag].at(0)->getProperties();
-        for ( std::string & property : arg_props ){ 
-          std::vector<std::string> arg_prop_opts = str_arg_[flag].at(0)->getPropertyOptions(property);
-          for ( std::string option : arg_prop_opts ) {
-            std::string val = str_arg_[flag].at(0)->getPropertyValues(property, option);
-           // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
+      unrecognized = false;
+      if(defaults_set_[flag] == true ){
+        values_[flag][std::type_index(int)].at(0) = 1;
+        defaults_set_[flag] = false;
+      }else {
+        values_[flag][std::type_index(int)].push_back(1);
+      }
+    } else { 
+      if ((index + 1) >= arguments.size()) {
+        string err = "" + flag + " Missing arguments";
+        throw runtime_error(err);
+      }
+      int arg_index = 0;
+      do { // Allow reading of multiple arguments
+        string argument = arguments.at(index + 1);
+        if ( arg_index != 0){
+          // Need to duplicate the argument
+          addFlagArg(flag, type);
+          std::vector<PropertyType> arg_props = arg_[flag].at(0)->getProperties();
+          for ( PropertyType & property : arg_props ){ 
+            
+            auto prop_vals = arg_[flag].at(0)->getPropertyOptions(property);
+            
+
+            std::vector<Option> arg_prop_opts = str_arg_[flag].at(0)->getPropertyOptions(property);
+            for ( Option option : arg_prop_opts ) {
+              std::string val = arg_[flag].at(0)->getPropertyValues(property, option);
+             // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
+            }
           }
         }
-      }
-      str_arg_[flag].at(arg_index)->argValid(argument);
-      unrecognized = false;
-      if (defaults_set_.count(flag) ) {
-        if(defaults_set_[flag] == true ){
-          string_values_[flag].clear();
-          string_values_[flag].push_back(argument);
-          defaults_set_[flag] = false;
-        } else {
-          string_values_[flag].push_back(argument);
+        str_arg_[flag].at(arg_index)->argValid(argument);
+        unrecognized = false;
+        if (defaults_set_.count(flag) ) {
+          if(defaults_set_[flag] == true ){
+            string_values_[flag].clear();
+            string_values_[flag].push_back(argument);
+            defaults_set_[flag] = false;
+          } else {
+            string_values_[flag].push_back(argument);
+          }
         }
-      }
-      ++index;
-      ++arg_index;
-      if( (index+1) >= arguments.size() ) break;
-    } while ( arguments.at(index+1).at(0) == '-' );
+        ++index;
+        ++arg_index;
+        if( (index+1) >= arguments.size() ) break;
+      } while ( arguments.at(index+1).at(0) == '-' );
+    }
   }
-
+/*
   // Parse Switches
   if (switch_arg_.count(flag) != 0) {
     if (!nextParameterIsAFlag_(index, arguments)) {
@@ -621,7 +630,7 @@ void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
         if( (index+1) >= arguments.size() ) break;
       } while ( arguments.at(index+1).at(0) == '-' );
     }
-  }
+  }*/
 
   if (unrecognized) {
     throw invalid_argument("The flag " + flag + " was unrecognized");
@@ -663,7 +672,7 @@ string ArgumentParser::getFlagArgOptValue(string flag, string argname,
   throw invalid_argument("Unrecognized flag or argument " + flag + " " +
                          argname);
 }
-
+/*
 std::vector<int> ArgumentParser::getInts(string flag) {
 
   if (int_values_.count(flag) == 0) {
@@ -722,23 +731,11 @@ std::vector<size_t> ArgumentParser::getSize_ts(string flag) {
   }
   return size_t_values_[flag];
 }
-
+*/
 void ArgumentParser::postParseCheck(void) {
 
-  for (auto str_arg : str_arg_) {
-    str_arg.second->postArgCheck();
-  }
-  for (auto switch_arg : switch_arg_) {
-    switch_arg.second->postArgCheck();
-  }
-  for (auto int_arg : int_arg_) {
-    int_arg.second->postArgCheck();
-  }
-  for (auto double_arg : double_arg_) {
-    double_arg.second->postArgCheck();
-  }
-  for (auto file_arg : file_arg_) {
-    file_arg.second->postArgCheck();
+  for (auto arg : arg_) {
+    arg.second->postArgCheck();
   }
 }
 
diff --git a/src/libcatnip/io/argumentparser.hpp b/src/libcatnip/io/argumentparser.hpp
index cc343e7..165d0d3 100644
--- a/src/libcatnip/io/argumentparser.hpp
+++ b/src/libcatnip/io/argumentparser.hpp
@@ -1,30 +1,28 @@
 #ifndef _CATNIP_ARGUMENTPARSER_HPP
 #define _CATNIP_ARGUMENTPARSER_HPP
-#include "../matrix.hpp"
-#include "../parameters.hpp"
+#include "matrix.hpp"
+#include "parameters.hpp"
+#include <any>
 #include <map>
 #include <memory>
 #include <set>
 #include <string>
 #include <utility>
 
-#include "arguments/argumentdouble.hpp"
+#include "arguments/argumentnumerical.hpp"
 #include "arguments/argumentfile.hpp"
-#include "arguments/argumentint.hpp"
 #include "arguments/argumentstring.hpp"
 #include "arguments/argumentswitch.hpp"
 
 namespace catnip {
 
+  std::unique_ptr<ArgumentObject> createArgument(ArgumentType type);
+
 class ArgumentParser {
  private:
   // 1 - flag name
   // 2 - type
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentString>>> str_arg_;
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentSwitch>>> switch_arg_;
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentInt>>> int_arg_;
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentDouble>>> double_arg_;
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentFile>>> file_arg_;
+  std::map<std::string, std::vector<std::unique_ptr<ArgumentObject>>> arg_;
 
   // Known rules
   std::set<std::string> argument_types_;
@@ -34,10 +32,7 @@ class ArgumentParser {
 
   std::map<std::string, bool> defaults_set_;
   // Arguments that are stored when argc and argv are parsed
-  std::map<std::string, std::vector<int>> int_values_;
-  std::map<std::string, std::vector<double>> double_values_;
-  std::map<std::string, std::vector<std::string>> string_values_;
-  std::map<std::string, std::vector<size_t>> size_t_values_;
+  std::map<std::string, std::map<std::type_index, std::vector<std::any>>> values_;
 
   void parseArg_(size_t& index, std::vector<std::string> arguments);
 
@@ -56,25 +51,100 @@ class ArgumentParser {
   explicit ArgumentParser(std::set<std::vector<std::string>> flags);
 
   // Set Defaults for the flags in the case that they are not found
-  void setFlagDefaultValue(std::string flag,const int & val);
-  void setFlagDefaultValue(std::string flag,const size_t & val);
-  void setFlagDefaultValue(std::string flag,const double & val);
-  void setFlagDefaultValue(std::string flag,const std::string & val);
+  template<class T>
+  void setFlagDefaultValue(std::string flag,const T & val) {
+    values_[flag][std::type_index(val)].push_back(val);
+    defaults_set_[flag] = true;
+  }
 
   // Add a argument without setting any of the values
-  void addFlagArg(std::string flag, std::string argname);
+  void addFlagArg(std::string flag, ArgumentType argname);
   // Set the rules for the flag and the type it is associated with types
   // include:
-  // "FILE_EXT"
-  // "FILE_EXIST"
-  // "DOUBLE"
-  // "INT"
+  // "FILES"
+  // "NUMERICAL"
   // "STRING"
+  // "SWITCH"
   // The rules are dependent on the type
-  void setFlagArgOpt(std::string flag, std::string argname,
-                     std::string property, std::string option, int val);
-
-  void setFlagArgOpt(std::string flag, std::string argname,
+  template<class T>
+    void ArgumentParser::setFlagArgOpt(
+        string flag, 
+        ArgumentType argname,
+        PropertyType property,
+        Option option,
+        T val) {
+
+      
+      if (arg_.count(flag) == 0) {
+        auto arg = createArgument(argname);
+        ArInt->setArgPropertyOpt(property, option, val);
+        arg_[flag].push_back(std::move(ArInt));
+      } else {
+        for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag]){
+          ptr->setArgPropertyOpt(property, option, val);
+        }
+      }
+/*
+      if (argname == ArgumentType::NUMERICAL) {
+        if (arg_.count(flag) == 0) {
+          auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
+          ArInt->setArgPropertyOpt(property, option, val);
+          arg_[flag].push_back(std::move(ArInt));
+        } else {
+          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag]){
+            ptr->setArgPropertyOpt(property, option, val);
+          }
+        }
+      } else if (argname == ArgumentType::STRING) {
+        if (arg_.count(flag) == 0) {
+          auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
+          ArString->setArgPropertyOpt(property, option, val);
+          arg_[flag].push_back(std::move(ArString));
+        } else {
+          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag] ){
+            ptr->setArgPropertyOpt(property, option, val);
+          }
+        }
+      } else if (argname == ArgumentType::SWITCH) {
+        if (switch_arg_.count(flag) == 0) {
+          auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
+          if (val == 0) {
+            ArSwitch->setArgPropertyOpt(property, option, "OFF");
+          } else if (val == 1) {
+            ArSwitch->setArgPropertyOpt(property, option, "ON");
+          } else {
+            throw invalid_argument("Unrecognized option for switch " +
+                to_string(val));
+          }
+          arg_[flag].push_back(std::move(ArSwitch));
+        } else { // For a switch there will only be one value in the vector
+          if (val == 0) {
+            arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
+          } else if (val == 1) {
+            arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
+          } else {
+            throw invalid_argument("Unrecognized option for switch " +
+                to_string(val));
+          }
+        }
+      } else if (argname == ArgumentType::FILES) {
+        if (file_arg_.count(flag) == 0) {
+          auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
+
+          ArFile->setArgPropertyOpt(property, option, val);
+          arg_[flag].push_back(std::move(ArFile));
+        } else {
+          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag] ){
+            ptr->setArgPropertyOpt(property, option, val);
+          }
+        }
+      } else {
+        throw invalid_argument("Unrecognized int arg");
+      }*/
+    }
+
+
+/*  void setFlagArgOpt(std::string flag, std::string argname,
                      std::string property, std::string option, double val);
 
   void setFlagArgOpt(std::string flag, std::string argname,
@@ -90,11 +160,21 @@ class ArgumentParser {
 
   std::string getFlagArgOptValue(std::string flag, std::string argname,
                                  std::string property, std::string option);
-
-  std::vector<double> getDoubles(std::string flag);
+*/
+  template<class T>
+  std::vector<T> get(std::string flag) {
+    std::vector<T> values;
+    if ( values[flag].count(type_index(T)) ){
+      for ( std::any & val : values[flag][std::type_index(T)] ){
+        values.push_back(std::any_cast<T>(val));
+      }
+    }
+    return values;
+  }
+/*  std::vector<double> getDoubles(std::string flag);
   std::vector<int> getInts(std::string flag);
   std::vector<std::string> getStrs(std::string flag);
-  std::vector<size_t> getSize_ts(std::string flag);
+  std::vector<size_t> getSize_ts(std::string flag);*/
 
   void postParseCheck(void);
 
diff --git a/src/libcatnip/io/arguments/argumentobject.hpp b/src/libcatnip/io/arguments/argumentobject.hpp
index de8cfad..b0dd3d8 100644
--- a/src/libcatnip/io/arguments/argumentobject.hpp
+++ b/src/libcatnip/io/arguments/argumentobject.hpp
@@ -83,6 +83,22 @@ class ArgumentObject {
     return opts_values;
   }
 
+  std::map<Option, std::any> getPropertyValues(
+      PropertyType property) {
+
+    std::map<Option, std::any> opts_values;
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      if (property == prop->getPropertyType()) {
+        std::vector<Option> vec_opt = prop->getPropertyOptions();
+        for (const Option & opt : vec_opt) {
+          auto value = prop->getPropOption<std::any>(opt);
+          opts_values[opt] = value;
+        }
+      }
+    }
+    return opts_values;
+  }
+
   template<class T>
   T getPropertyValues(PropertyType property,const Option & option) {
     for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
@@ -119,6 +135,19 @@ class ArgumentObject {
     }
   }
 
+   void setPropertyValues(
+      PropertyType property, std::map<Option, std::any> opts) {
+
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      if (property == prop->getPropertyType()) {
+        for ( std::pair<Option,std::any> opt_val : opts ){
+          prop->setPropOption(opt_val.first, opt_val.second);
+        }
+        return; 
+      }
+    }
+  }
+
   template< class T>
   bool argValid(const T& value) const {
     for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 63b41bf..4f103ee 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -1,29 +1,32 @@
 list( APPEND UNIT_TEST_SOURCE_FILES
-  test_argumentdouble
-  test_argumentfile
-  test_argumentint
-  test_argumentparser
-  test_argumentstring
-  test_argumentswitch
-  test_atom
-  test_atom_group
-  test_atom_group_container
-  test_atom_system
-  test_basis_map
-  test_elements
-  test_log
-  test_parameters
-  test_propertydouble
+  test_propertynumerical
   test_propertyfileexist
   test_propertyfileext
-  test_propertyint
   test_propertysisterfile
   test_propertystringchoice
   test_propertystring
   test_propertyswitch
-  test_qc_functions
-  test_string_support
-  test_swap_engine)
+)
+
+#
+#  test_argumentnumerical
+#  test_argumentfile
+#  test_argumentparser
+#  test_argumentstring
+#  test_argumentswitch
+#
+#  test_atom
+#  test_atom_group
+#  test_atom_group_container
+#  test_atom_system
+#  test_basis_map
+#  test_elements
+#  test_log
+#  test_parameters
+#
+#  test_qc_functions
+#  test_string_support
+#  test_swap_engine
 
 if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
   find_library (GCOV gcov)
diff --git a/src/tests/test_propertydouble.cpp b/src/tests/test_propertydouble.cpp
deleted file mode 100644
index c07a655..0000000
--- a/src/tests/test_propertydouble.cpp
+++ /dev/null
@@ -1,70 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/properties/propertydouble.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property Double","[unit]") {
-
-  cerr << "Testing: PropertyDouble" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertyDouble propDouble; }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyDouble propDouble;
-    string name = propDouble.getPropertyName();
-    assert(name.compare("PROPERTY_DOUBLE") == 0);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyDouble propDouble;
-    auto options = propDouble.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("MIN") == 0);
-    opt = options.at(1);
-    assert(opt.compare("MAX") == 0);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyDouble propDouble;
-    bool valid = propDouble.propValid(0.0);
-    assert(valid);
-  }
-
-  cerr << "Testing: setPropOption" << endl;
-  {
-    PropertyDouble propDouble;
-    double val = -1.2;
-    propDouble.setPropOption("MIN", val);
-    propDouble.propValid(0.0);
-    bool excep = false;
-    try {
-      val = -2.3;
-      propDouble.propValid(val);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    excep = false;
-    try {
-      val = 3.5;
-      propDouble.setPropOption("MAXimum", val);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-  }
-}
diff --git a/src/tests/test_propertyfileexist.cpp b/src/tests/test_propertyfileexist.cpp
index dfb3429..28a2e15 100644
--- a/src/tests/test_propertyfileexist.cpp
+++ b/src/tests/test_propertyfileexist.cpp
@@ -2,7 +2,7 @@
 #define CATCH_CONFIG_MAIN
 #include <catch2/catch.hpp>
 
-#include "../libcatnip/io/arguments/properties/propertyfileexist.hpp"
+#include "io/arguments/properties/propertyfileexist.hpp"
 #include <cassert>
 #include <exception>
 #include <iostream>
@@ -24,8 +24,8 @@ TEST_CASE("Property File Exists","[unit]") {
   cerr << "Testing: getPropertyName" << endl;
   {
     PropertyFileExist propFileExist;
-    string name = propFileExist.getPropertyName();
-    assert(name.compare("PROPERTY_FILE_EXIST") == 0);
+    PropertyType type = propFileExist.getPropertyType();
+    CHECK(type == PropertyTYpe::FILE_EXIST);
   }
 
   cerr << "Testing: getPropertyOptions" << endl;
@@ -33,8 +33,8 @@ TEST_CASE("Property File Exists","[unit]") {
 
     PropertyFileExist propFileExist;
     auto options = propFileExist.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("FILE_MUST_EXIST") == 0);
+    Option opt = options.at(0);
+    CHECK(opt == Option::MUST_EXIST);
   }
 
   cerr << "Testing: propValid" << endl;
@@ -44,18 +44,12 @@ TEST_CASE("Property File Exists","[unit]") {
     PropertyFileExist propFileExist3(true);
 
     bool valid = propFileExist1.propValid("test_propertyfileexist.cpp");
-    assert(valid);
+    CHECK(valid);
 
-    bool excep = false;
-    try {
-      valid = propFileExist2.propValid("fake");
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
+    CHECK_THROWS(propFileExist2.propValid("fake"));
 
     valid = propFileExist3.propValid("testfile.pun");
-    assert(valid);
+    CHECK(valid);
   }
 
   cerr << "Testing: getPropOption" << endl;
@@ -63,11 +57,11 @@ TEST_CASE("Property File Exists","[unit]") {
     PropertyFileExist propFileExist1(true);
     PropertyFileExist propFileExist2(false);
 
-    bool fileExist = propFileExist1.getPropOption("FILE_MUST_EXIST");
-    assert(fileExist);
+    bool fileExist = propFileExist1.getPropOption(Option::MUST_EXIST);
+    CHECK(fileExist);
 
-    fileExist = propFileExist2.getPropOption("FILE_MUST_EXIST");
-    assert(fileExist == false);
+    fileExist = propFileExist2.getPropOption(Option::MUST_EXIST);
+    CHECK(fileExist == false);
   }
 
 }
diff --git a/src/tests/test_propertyfileext.cpp b/src/tests/test_propertyfileext.cpp
index 634be72..a7fe1d5 100644
--- a/src/tests/test_propertyfileext.cpp
+++ b/src/tests/test_propertyfileext.cpp
@@ -2,9 +2,7 @@
 #define CATCH_CONFIG_MAIN
 #include <catch2/catch.hpp>
 
-#include "../libcatnip/io/arguments/properties/propertyfileext.hpp"
-#include <cassert>
-#include <exception>
+#include "io/arguments/properties/propertyfileext.hpp"
 #include <iostream>
 #include <string>
 #include <vector>
@@ -20,14 +18,7 @@ TEST_CASE("Property File Extension","[unit]") {
     PropertyFileExt propFileExt1("*");
     PropertyFileExt propFileExt2("");
     PropertyFileExt propFileExt3(".jpg");
-    bool excep = false;
-    try {
-      PropertyFileExt propFileExt4("ffda.fd");
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
+    CHECK_THROWS(PropertyFileExt propFileExt4("ffda.fd"));
     set<string> exts = {".png", ".gjf"};
     PropertyFileExt propFileExt5(exts);
   }
@@ -35,8 +26,8 @@ TEST_CASE("Property File Extension","[unit]") {
   cerr << "Testing: getPropertyName" << endl;
   {
     PropertyFileExt propFileExt;
-    string name = propFileExt.getPropertyName();
-    assert(name.compare("PROPERTY_FILE_EXT") == 0);
+    PropertyType type = propFileExt.getPropertyType();
+    REQUIRE(type == PropertyType::FILE_EXT);
   }
 
   cerr << "Testing: getPropertyOptions" << endl;
@@ -44,41 +35,29 @@ TEST_CASE("Property File Extension","[unit]") {
 
     PropertyFileExt propFileExt;
     auto options = propFileExt.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("ALLOWED_FILE_EXT") == 0);
+    Option opt = options.at(0);
+    REQUIRE(opt == Option::ALLOWED_VALUES);
   }
 
   cerr << "Testing: propValid" << endl;
   {
     PropertyFileExt propFileExt(".jpg");
     bool valid = propFileExt.propValid("dir/file.jpg");
-    assert(valid);
-    bool excep = false;
-    try {
-      propFileExt.propValid("dir/file.jp");
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
+    CHECK(valid);
+    CHECK_THROWS(propFileExt.propValid("dir/file.jp"));
 
     PropertyFileExt propFileExt2("*");
     valid = propFileExt2.propValid("dir/file.jpg");
-    assert(valid);
+    CHECK(valid);
     valid = propFileExt2.propValid("dir/file.jp");
-    assert(valid);
+    CHECK(valid);
 
     set<string> exts = {".png", ".gjf"};
     PropertyFileExt propFileExt3(exts);
     valid = propFileExt3.propValid("Dir2/Path/File.png");
-    assert(valid);
+    CHECK(valid);
     valid = propFileExt3.propValid("Dir2/Path/File.gjf");
-    assert(valid);
-    excep = false;
-    try {
-      propFileExt3.propValid("dir/file.com");
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
+    CHECK(valid);
+    CHECK_THROWS(propFileExt3.propValid("dir/file.com"));
   }
 }
diff --git a/src/tests/test_propertyint.cpp b/src/tests/test_propertyint.cpp
deleted file mode 100644
index 54430ae..0000000
--- a/src/tests/test_propertyint.cpp
+++ /dev/null
@@ -1,67 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/properties/propertyint.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property Int","[unit]") {
-
-  cerr << "Testing: PropertyInt" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertyInt propInt; }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyInt propInt;
-    string name = propInt.getPropertyName();
-    assert(name.compare("PROPERTY_INT") == 0);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyInt propInt;
-    auto options = propInt.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("MIN") == 0);
-    opt = options.at(1);
-    assert(opt.compare("MAX") == 0);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyInt propInt;
-    bool valid = propInt.propValid(0);
-    assert(valid);
-  }
-
-  cerr << "Testing: setPropOption" << endl;
-  {
-    PropertyInt propInt;
-    propInt.setPropOption("MIN", 0);
-    propInt.propValid(0);
-    bool excep = false;
-    try {
-      propInt.propValid(-1);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    excep = false;
-    try {
-      propInt.setPropOption("MAXimum", 3);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-  }
-}
diff --git a/src/tests/test_propertynumerical.cpp b/src/tests/test_propertynumerical.cpp
new file mode 100644
index 0000000..414cb12
--- /dev/null
+++ b/src/tests/test_propertynumerical.cpp
@@ -0,0 +1,67 @@
+
+#define CATCH_CONFIG_MAIN
+#include <catch2/catch.hpp>
+
+#include "io/arguments/properties/propertynumerical.hpp"
+#include <cassert>
+#include <exception>
+#include <iostream>
+#include <string>
+#include <vector>
+
+using namespace catnip;
+using namespace std;
+
+TEST_CASE("Property Numerical","[unit]") {
+
+  cerr << "Testing: PropertyNumerical" << endl;
+  cerr << "Testing: constructor" << endl;
+  { PropertyNumerical propNumerical; }
+
+  cerr << "Testing: getPropertyType" << endl;
+  {
+    PropertyNumerical propNumerical;
+    PropertyType name = propNumerical.getPropertyType();
+    assert(name == PropertyType::NUMERICAL);
+  }
+
+  cerr << "Testing: getPropertyOptions" << endl;
+  {
+
+    PropertyNumerical propNumerical;
+    auto options = propNumerical.getPropertyOptions();
+    string opt = options.at(0);
+    assert(opt == Option::MIN);
+    opt = options.at(1);
+    assert(opt == Option::MAX);
+  }
+
+  cerr << "Testing: propValid" << endl;
+  {
+    PropertyNumerical propNumerical;
+    bool valid = propNumerical.propValid(0);
+    assert(valid);
+  }
+
+  cerr << "Testing: setPropOption" << endl;
+  {
+    PropertyNumerical propNumerical;
+    propNumerical.setPropOption(Option::MIN, 0);
+    propNumerical.propValid(0);
+    bool excep = false;
+    try {
+      propNumerical.propValid(-1);
+    } catch (...) {
+      excep = true;
+    }
+    assert(excep);
+
+    excep = false;
+    try {
+      propNumerical.setPropOption(Option::ENFORCED, 3);
+    } catch (...) {
+      excep = true;
+    }
+    assert(excep);
+  }
+}
diff --git a/src/tests/test_propertystring.cpp b/src/tests/test_propertystring.cpp
index 6050966..efdcf89 100644
--- a/src/tests/test_propertystring.cpp
+++ b/src/tests/test_propertystring.cpp
@@ -21,8 +21,8 @@ TEST_CASE("Property String","[unit]") {
   cerr << "Testing: getPropertyName" << endl;
   {
     PropertyString propString;
-    string name = propString.getPropertyName();
-    assert(name.compare("PROPERTY_STRING") == 0);
+    PropertyType type = propString.getPropertyType();
+    REQUIRE(type == PropertyType::STRING);
   }
 
   cerr << "Testing: getPropertyOptions" << endl;
@@ -30,40 +30,28 @@ TEST_CASE("Property String","[unit]") {
 
     PropertyString propString;
     auto options = propString.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("MIN_LENGTH") == 0);
+    Option opt = options.at(0);
+    REQUIRE(opt == Option::MIN_LENGTH);
     opt = options.at(1);
-    assert(opt.compare("MAX_LENGTH") == 0);
+    REQUIRE(opt == Option::MAX_LENGTH);
   }
 
   cerr << "Testing: propValid" << endl;
   {
     PropertyString propString;
     bool valid = propString.propValid("Hello");
-    assert(valid);
+    REQUIRE(valid);
   }
 
   cerr << "Testing: setPropOption" << endl;
   {
     PropertyString propString;
     size_t val = 3;
-    propString.setPropOption("MAX_LENGTH", val);
+    propString.setPropOption(Option::MAX_LENGTH, val);
     propString.propValid("");
-    bool excep = false;
-    try {
-      propString.propValid("Hello");
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    excep = false;
-    try {
-      val = 4;
-      propString.setPropOption("MAXimum", val);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
+    CHECK_THROWS(propString.propValid("Hello"));
+    
+    val = 4;
+    CHECK_THROWS(propString.setPropOption(Option::MAX, val));
   }
 }
diff --git a/src/tests/test_propertystringchoice.cpp b/src/tests/test_propertystringchoice.cpp
index 7e09874..560991f 100644
--- a/src/tests/test_propertystringchoice.cpp
+++ b/src/tests/test_propertystringchoice.cpp
@@ -1,7 +1,7 @@
 
 #define CATCH_CONFIG_MAIN
 #include <catch2/catch.hpp>
-#include "../libcatnip/io/arguments/properties/propertystringchoice.hpp"
+#include "io/arguments/properties/propertystringchoice.hpp"
 #include <cassert>
 #include <exception>
 #include <fstream>

From 0b7170321294d96e2ee87eecbfb768a089f8069c Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Sat, 19 Sep 2020 22:26:50 -0600
Subject: [PATCH 66/68] Small changes

---
 CMakeLists.txt                                |    5 +-
 src/libcatnip/CMakeLists.txt                  |    8 +-
 src/libcatnip/io/argumentparser.cpp           | 1295 ++++++++---------
 src/libcatnip/io/argumentparser.hpp           |   28 +-
 src/libcatnip/io/arguments/argumentfile.cpp   |    9 +-
 src/libcatnip/io/arguments/argumentfile.hpp   |    4 +
 .../io/arguments/argumentnumerical.cpp        |    4 +-
 .../io/arguments/argumentnumerical.hpp        |   12 +-
 src/libcatnip/io/arguments/argumentobject.hpp |   17 +-
 src/libcatnip/io/arguments/argumentstring.cpp |    6 +-
 src/libcatnip/io/arguments/argumentstring.hpp |    9 +-
 src/libcatnip/io/arguments/argumentswitch.cpp |    3 +-
 src/libcatnip/io/arguments/argumentswitch.hpp |    5 +
 ...operty_numeric.cpp => propertynumeric.cpp} |    2 +-
 ...operty_numeric.hpp => propertynumeric.hpp} |    0
 .../arguments/properties/propertyobject.hpp   |   67 +-
 .../properties/propertystringchoice.cpp       |  172 ++-
 .../properties/propertystringchoice.hpp       |   14 +-
 .../arguments/properties/propertyswitch.cpp   |    3 +-
 .../arguments/properties/propertyswitch.hpp   |    4 +-
 src/libcatnip/io/io.cpp                       |  186 +--
 src/libcatnip/string_support.cpp              |    6 +
 src/libcatnip/string_support.hpp              |    3 +
 src/tests/CMakeLists.txt                      |   26 +-
 src/tests/test_io.cpp                         |   18 +-
 src/tests/test_propertystringchoice.cpp       |  124 +-
 src/tests/test_propertyswitch.cpp             |   12 +-
 27 files changed, 1102 insertions(+), 940 deletions(-)
 rename src/libcatnip/io/arguments/properties/{property_numeric.cpp => propertynumeric.cpp} (97%)
 rename src/libcatnip/io/arguments/properties/{property_numeric.hpp => propertynumeric.hpp} (100%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index af4fa10..c5d3745 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,7 +4,7 @@ project (catnip)
 ##############################################################################
 # Defining options 
 ##############################################################################
-option(ENABLE_TESTS "Enable testing" Off)
+option(ENABLE_TESTS "Enable testing" OFF)
 option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" ${ENABLE_TESTS})
 option(ENABLE_INTEGRATION_TESTING "Enable integration tests" ${ENABLE_TESTS})
 option(ENABLE_UNIT_TESTING "Enable tests" ${ENABLE_TESTS})
@@ -22,6 +22,9 @@ set(catnip_AUTHOR_INITIALS "\"J. S.\"" )
 set(catnip_TITLE "\"CATNIP\"")
 set(catnip_URL "\"https://github.com/JoshuaSBrown/QC_Tools\"" )
 
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 set(COVERAGE_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 set(COMMON_LIBRARIES stdc++ m)
 set(LOG_LEVEL 0 CACHE STRING "Choose the log level" )
diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index ea1c6bd..9daf7d5 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -1,10 +1,10 @@
 
 file(GLOB CATNIP_SOURCE_FILES 
   io/arguments/*.cpp 
-  io/arguments/properties/*.cpp )
-#  *.cpp 
-#  io/*.cpp
-#  io/file_readers/*.cpp)
+  io/arguments/properties/*.cpp
+  io/argumentparser.cpp
+  string_support.cpp 
+  io/file_readers/*.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
 set_property(TARGET libcatnip PROPERTY CXX_STANDARD 17)
diff --git a/src/libcatnip/io/argumentparser.cpp b/src/libcatnip/io/argumentparser.cpp
index d3169b9..5d383a0 100644
--- a/src/libcatnip/io/argumentparser.cpp
+++ b/src/libcatnip/io/argumentparser.cpp
@@ -4,789 +4,774 @@
 #include <stdexcept>
 #include <string>
 #include <sys/stat.h>
+#include <typeindex>
 #include <vector>
 
 #include "argumentparser.hpp"
 
-#include "../catnip_config.hpp"
-#include "../string_support.hpp"
+#include "catnip_config.hpp"
+#include "string_support.hpp"
 
-using namespace catnip;
 using namespace std;
 
-std::unique_ptr<ArgumentObject> createArgument(ArgumentType type) {
-  if (argname == ArgumentType::NUMERICAL) {
-    return std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
-  } else if (argname == ArgumentType::STRING) {
-    return std::unique_ptr<ArgumentObject>(new ArgumentString);
-  } else if (argname == ArgumentType::SWITCH) {
-    return std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
-  } else if (argname == ArgumentType::FILES) {
-    return std::unique_ptr<ArgumentObject>(new ArgumentFile);
+namespace catnip {
+
+  std::unique_ptr<ArgumentObject> createArgument(ArgumentType type) {
+    if (type == ArgumentType::NUMERICAL) {
+      return std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
+    } else if (type == ArgumentType::STRING) {
+      return std::unique_ptr<ArgumentObject>(new ArgumentString);
+    } else if (type == ArgumentType::SWITCH) {
+      return std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
+    } else if (type == ArgumentType::FILES) {
+      return std::unique_ptr<ArgumentObject>(new ArgumentFile);
+    }
+    return std::unique_ptr<ArgumentObject>();
   }
-  return std::unique_ptr<ArgumentObject>();
-}
-      
-ArgumentParser::ArgumentParser(set<vector<string>> flags) {
 
-  vector<string> flag_help;
-  flag_help.push_back("--help");
-  flag_help.push_back("-h");
-  flag_help.push_back("Display help message");
-  flags.insert(flag_help);
+  void ArgumentParser::addValue_(std::string flag, std::string value) {
+    std::type_index value_type = arg_[flag].at(0)->getValueType(); 
+    if (value_type == typeid(double) ){
+      values_[flag][value_type].emplace_back(stod(value));
+    } else if(value_type == typeid(int) ) {
+      values_[flag][value_type].emplace_back(stoi(value));
+    } else if(value_type == typeid(std::string) ) {
+      values_[flag][value_type].emplace_back(value);
+    } else if(value_type == typeid(bool) ){
+      if (to_upper(value) == "TRUE" || value == "1" || to_upper(value) == "ON") {
+        values_[flag][value_type].emplace_back(true);
+      } else if (to_upper(value) == "FALSE" || value == "1" || to_upper(value) == "OFF") {
+        values_[flag][value_type].emplace_back(false);
+      }
+    } else {
+      std::runtime_error("Unknown type for argument value");
+    }
+  }
 
-  maxShortFlagSize = 0;
-  maxFullFlagSize = 0;
-  maxDescriptionSize = 0;
+  ArgumentParser::ArgumentParser(set<vector<string>> flags) {
 
-  for (auto flag : flags) {
+    vector<string> flag_help;
+    flag_help.push_back("--help");
+    flag_help.push_back("-h");
+    flag_help.push_back("Display help message");
+    flags.insert(flag_help);
 
-    if (flag.size() > 3) {
-      throw invalid_argument(
-          "Flags may only be passed with a max of three "
-          "values: full flag name, abbreviated name, and flag description");
-    }
+    maxShortFlagSize = 0;
+    maxFullFlagSize = 0;
+    maxDescriptionSize = 0;
 
-    string full_flag = "NO_FLAG_SPECIFIED";
-    string short_flag = "NO_SHORT_FLAG_SPECIFIED";
-    string desc = "NO_DESCRIPTION_GIVEN";
-
-    bool description = false;
-    bool abbreviation = false;
-    bool flag_name = false;
-    for (auto item : flag) {
-      trim(item);
-      string doubledash = firstN(item, 2);
-      string singledash = firstN(item, 1);
-      if (doubledash.compare("--") == 0) {
-        if (flag_name) {
-          string err = "A flag name has already been suppied:\n";
-          err.append(full_flag);
-          err.append("\nNow you are supplying a second one:\n");
-          err.append(item);
-          throw invalid_argument(err);
-        }
-        full_flag = item;
-        defaults_set_[item] = false;
-        flag_name = true;
-        if (full_flag.size() > maxFullFlagSize) {
-          maxFullFlagSize = full_flag.size();
-        }
-      } else if (singledash.compare("-") == 0) {
-        if (abbreviation) {
-          string err = "A flag name has already been suppied:\n";
-          err.append(short_flag);
-          err.append("\nNow you are supplying a second one:\n");
-          err.append(item);
-          throw invalid_argument(err);
-        }
-        short_flag = item;
-        abbreviation = true;
-        if (short_flag.size() > maxShortFlagSize) {
-          maxShortFlagSize = short_flag.size();
-        }
-      } else {
-        if (description) {
-          string err = "A description has already been suppied:\n";
-          err.append(desc);
-          err.append("\nNow you are supplying a second one:\n");
-          err.append(item);
-          throw invalid_argument(err);
-        }
-        desc = item;
-        description = true;
-        if (desc.size() > maxDescriptionSize) {
-          maxDescriptionSize = desc.size();
+    for (auto flag : flags) {
+
+      if (flag.size() > 3) {
+        throw invalid_argument(
+            "Flags may only be passed with a max of three "
+            "values: full flag name, abbreviated name, and flag description");
+      }
+
+      string full_flag = "NO_FLAG_SPECIFIED";
+      string short_flag = "NO_SHORT_FLAG_SPECIFIED";
+      string desc = "NO_DESCRIPTION_GIVEN";
+
+      bool description = false;
+      bool abbreviation = false;
+      bool flag_name = false;
+      for (auto item : flag) {
+        trim(item);
+        string doubledash = firstN(item, 2);
+        string singledash = firstN(item, 1);
+        if (doubledash.compare("--") == 0) {
+          if (flag_name) {
+            string err = "A flag name has already been suppied:\n";
+            err.append(full_flag);
+            err.append("\nNow you are supplying a second one:\n");
+            err.append(item);
+            throw invalid_argument(err);
+          }
+          full_flag = item;
+          defaults_set_[item] = false;
+          flag_name = true;
+          if (full_flag.size() > maxFullFlagSize) {
+            maxFullFlagSize = full_flag.size();
+          }
+        } else if (singledash.compare("-") == 0) {
+          if (abbreviation) {
+            string err = "A flag name has already been suppied:\n";
+            err.append(short_flag);
+            err.append("\nNow you are supplying a second one:\n");
+            err.append(item);
+            throw invalid_argument(err);
+          }
+          short_flag = item;
+          abbreviation = true;
+          if (short_flag.size() > maxShortFlagSize) {
+            maxShortFlagSize = short_flag.size();
+          }
+        } else {
+          if (description) {
+            string err = "A description has already been suppied:\n";
+            err.append(desc);
+            err.append("\nNow you are supplying a second one:\n");
+            err.append(item);
+            throw invalid_argument(err);
+          }
+          desc = item;
+          description = true;
+          if (desc.size() > maxDescriptionSize) {
+            maxDescriptionSize = desc.size();
+          }
         }
       }
+      if (!flag_name) {
+        throw invalid_argument("You have failed to provide the full flag name");
+      }
+      flags_[full_flag] = make_pair(short_flag, desc);
     }
-    if (!flag_name) {
-      throw invalid_argument("You have failed to provide the full flag name");
-    }
-    flags_[full_flag] = make_pair(short_flag, desc);
   }
-}
 
-void ArgumentParser::showUsage(void) {
-  cout << endl;
-  cout << endl;
-  cout << "Options:" << endl;
-  cout << endl;
-
-  for (auto item : flags_) {
-    string full_flag = item.first;
-    size_t diff = maxFullFlagSize - full_flag.size();
-    cout << full_flag;
-    for (size_t i = 0; i <= diff; ++i) {
-      cout << " ";
-    }
-    string short_flag = item.second.first;
-    diff = maxShortFlagSize - short_flag.size();
-    cout << short_flag;
-    for (size_t i = 0; i <= diff; ++i) {
-      cout << " ";
-    }
+  void ArgumentParser::showUsage(void) {
+    cout << endl;
+    cout << endl;
+    cout << "Options:" << endl;
+    cout << endl;
 
-    size_t space = maxFullFlagSize + maxShortFlagSize + 2;
-    size_t allowed = maxLineLength - space;
-    string space_block = "";
-    for (size_t sp = 0; sp < space; sp++) {
-      space_block.append(" ");
-    }
+    for (auto item : flags_) {
+      string full_flag = item.first;
+      size_t diff = maxFullFlagSize - full_flag.size();
+      cout << full_flag;
+      for (size_t i = 0; i <= diff; ++i) {
+        cout << " ";
+      }
+      string short_flag = item.second.first;
+      diff = maxShortFlagSize - short_flag.size();
+      cout << short_flag;
+      for (size_t i = 0; i <= diff; ++i) {
+        cout << " ";
+      }
 
-    string desc = item.second.second;
-    vector<string> vec_string = splitSt(desc);
-    size_t words_size = 0;
-    for (auto word : vec_string) {
-      words_size += word.size() + 1;
-      if (words_size < allowed) {
-        cout << word << " ";
-      } else {
-        cout << endl;
-        cout << space_block;
-        cout << word << " ";
-        words_size = 0;
+      size_t space = maxFullFlagSize + maxShortFlagSize + 2;
+      size_t allowed = maxLineLength - space;
+      string space_block = "";
+      for (size_t sp = 0; sp < space; sp++) {
+        space_block.append(" ");
+      }
+
+      string desc = item.second.second;
+      vector<string> vec_string = splitSt(desc);
+      size_t words_size = 0;
+      for (auto word : vec_string) {
+        words_size += word.size() + 1;
+        if (words_size < allowed) {
+          cout << word << " ";
+        } else {
+          cout << endl;
+          cout << space_block;
+          cout << word << " ";
+          words_size = 0;
+        }
       }
+      cout << endl;
+      cout << endl;
     }
     cout << endl;
-    cout << endl;
   }
-  cout << endl;
-}
 
-void ArgumentParser::addFlagArg(string flag, ArgumentType argname) {
+  void ArgumentParser::addFlagArg(string flag, ArgumentType argname) {
 
-  arg_[flag].push_back(createArgument(argname));
-/*  if (argname == ArgumentType::NUMERICAL) {
-      auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
-      int_arg_[flag].push_back(std::move(ArInt));
-  } else if (argname == ArgumentType::SWITCH) {
-    if (switch_arg_.count(flag) == 0) {
-      auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
-      switch_arg_[flag].push_back(std::move(ArSwitch));
-    } else {
-      throw invalid_argument(
-          "switch argument has already been added for "
-          "flag " +
-          flag);
-    }
-  } else if (argname == ArgumentType::STRING) {
-      auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
-      str_arg_[flag].push_back(std::move(ArString));
-  } else if (argname == ArgumentType::FILES) {
-      auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
-      file_arg_[flag].push_back(std::move(ArFile));
-  } else {
-    throw invalid_argument(
-        "Unrecognized argument being added for flag"
-        " argname is " +
-        argname + " flag name is " + flag);
-  }*/
-}
-/*
-// Will apply values to all properties in the argument vector
-void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                   string option, int val) {
-
-  if (argname.compare("ARGUMENT_INT") == 0) {
-    if (int_arg_.count(flag) == 0) {
-      auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
-      ArInt->setArgPropertyOpt(property, option, val);
-      int_arg_[flag].push_back(std::move(ArInt));
-    } else {
-      for ( std::unique_ptr<ArgumentInt> & ptr : int_arg_[flag]){
-        ptr->setArgPropertyOpt(property, option, val);
+    arg_[flag].push_back(createArgument(argname));
+  /*  if (argname == ArgumentType::NUMERICAL) {
+        auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
+        int_arg_[flag].push_back(std::move(ArInt));
+    } else if (argname == ArgumentType::SWITCH) {
+      if (switch_arg_.count(flag) == 0) {
+        auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
+        switch_arg_[flag].push_back(std::move(ArSwitch));
+      } else {
+        throw invalid_argument(
+            "switch argument has already been added for "
+            "flag " +
+            flag);
       }
-    }
-  } else if (argname.compare("ARGUMENT_STRING") == 0) {
-    if (str_arg_.count(flag) == 0) {
-      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
-      ArString->setArgPropertyOpt(property, option, val);
-      str_arg_[flag].push_back(std::move(ArString));
+    } else if (argname == ArgumentType::STRING) {
+        auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
+        str_arg_[flag].push_back(std::move(ArString));
+    } else if (argname == ArgumentType::FILES) {
+        auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
+        file_arg_[flag].push_back(std::move(ArFile));
     } else {
-      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag] ){
-        ptr->setArgPropertyOpt(property, option, val);
-      }
-    }
-  } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
-    if (switch_arg_.count(flag) == 0) {
-      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
-      if (val == 0) {
-        ArSwitch->setArgPropertyOpt(property, option, "OFF");
-      } else if (val == 1) {
-        ArSwitch->setArgPropertyOpt(property, option, "ON");
+      throw invalid_argument(
+          "Unrecognized argument being added for flag"
+          " argname is " +
+          argname + " flag name is " + flag);
+    }*/
+  }
+  /*
+  // Will apply values to all properties in the argument vector
+  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
+                                     string option, int val) {
+
+    if (argname.compare("ARGUMENT_INT") == 0) {
+      if (int_arg_.count(flag) == 0) {
+        auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
+        ArInt->setArgPropertyOpt(property, option, val);
+        int_arg_[flag].push_back(std::move(ArInt));
       } else {
-        throw invalid_argument("Unrecognized option for switch " +
-                               to_string(val));
-      }
-      switch_arg_[flag].push_back(std::move(ArSwitch));
-    } else { // For a switch there will only be one value in the vector
-      if (val == 0) {
-        switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
-      } else if (val == 1) {
-        switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
+        for ( std::unique_ptr<ArgumentInt> & ptr : int_arg_[flag]){
+          ptr->setArgPropertyOpt(property, option, val);
+        }
+      }
+    } else if (argname.compare("ARGUMENT_STRING") == 0) {
+      if (str_arg_.count(flag) == 0) {
+        auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
+        ArString->setArgPropertyOpt(property, option, val);
+        str_arg_[flag].push_back(std::move(ArString));
       } else {
-        throw invalid_argument("Unrecognized option for switch " +
-                               to_string(val));
+        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag] ){
+          ptr->setArgPropertyOpt(property, option, val);
+        }
       }
-    }
-  } else if (argname.compare("ARGUMENT_FILE") == 0) {
-    if (file_arg_.count(flag) == 0) {
-      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-
-      ArFile->setArgPropertyOpt(property, option, val);
-      file_arg_[flag].push_back(std::move(ArFile));
-    } else {
-      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag] ){
-        ptr->setArgPropertyOpt(property, option, val);
+    } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
+      if (switch_arg_.count(flag) == 0) {
+        auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
+        if (val == 0) {
+          ArSwitch->setArgPropertyOpt(property, option, "OFF");
+        } else if (val == 1) {
+          ArSwitch->setArgPropertyOpt(property, option, "ON");
+        } else {
+          throw invalid_argument("Unrecognized option for switch " +
+                                 to_string(val));
+        }
+        switch_arg_[flag].push_back(std::move(ArSwitch));
+      } else { // For a switch there will only be one value in the vector
+        if (val == 0) {
+          switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
+        } else if (val == 1) {
+          switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
+        } else {
+          throw invalid_argument("Unrecognized option for switch " +
+                                 to_string(val));
+        }
       }
-    }
-  } else {
-    throw invalid_argument("Unrecognized int arg");
-  }
-}
-
-void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                   string option, double val) {
+    } else if (argname.compare("ARGUMENT_FILE") == 0) {
+      if (file_arg_.count(flag) == 0) {
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
 
-  if (argname.compare("ARGUMENT_DOUBLE") == 0) {
-    if (double_arg_.count(flag) == 0) {
-      auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
-      ArDouble->setArgPropertyOpt(property, option, val);
-      double_arg_[flag].push_back(std::move(ArDouble));
-    } else {
-      for ( std::unique_ptr<ArgumentDouble> & ptr : double_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, val);
+        ArFile->setArgPropertyOpt(property, option, val);
+        file_arg_[flag].push_back(std::move(ArFile));
+      } else {
+        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag] ){
+          ptr->setArgPropertyOpt(property, option, val);
+        }
       }
-    }
-  } else if (argname.compare("ARGUMENT_STRING") == 0) {
-    if (str_arg_.count(flag) == 0) {
-      auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
-      ArString->setArgPropertyOpt(property, option, val);
-      str_arg_[flag].push_back(std::move(ArString));
     } else {
-      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, val);
-      }
+      throw invalid_argument("Unrecognized int arg");
     }
-  } else {
-    throw invalid_argument("Unrecognized double arg");
   }
-}
-
-void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                   string option, string val) {
 
-  if (argname.compare("ARGUMENT_FILE") == 0) {
-    if (file_arg_.count(flag) == 0) {
+  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
+                                     string option, double val) {
 
-      if (property.compare("PROPERTY_FILE_EXT") == 0) {
-        set<string> temp{val};
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-        ArFile->setArgPropertyOpt(property, option, temp);
-        file_arg_[flag].push_back(std::move(ArFile));
-      } else if (property.compare("PROPERTY_SISTER_FILE_EXT") == 0) {
-        vector<string> temp{val};
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-        ArFile->setArgPropertyOpt(property, option, temp);
-        file_arg_[flag].push_back(std::move(ArFile));
+    if (argname.compare("ARGUMENT_DOUBLE") == 0) {
+      if (double_arg_.count(flag) == 0) {
+        auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
+        ArDouble->setArgPropertyOpt(property, option, val);
+        double_arg_[flag].push_back(std::move(ArDouble));
       } else {
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-        ArFile->setArgPropertyOpt(property, option, val);
-        file_arg_[flag].push_back(std::move(ArFile));
-      }
-    } else {
-      if (property.compare("PROPERTY_FILE_EXT") == 0) {
-        set<string> temp{val};
-        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, temp);
+        for ( std::unique_ptr<ArgumentDouble> & ptr : double_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, val);
         }
+      }
+    } else if (argname.compare("ARGUMENT_STRING") == 0) {
+      if (str_arg_.count(flag) == 0) {
+        auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
+        ArString->setArgPropertyOpt(property, option, val);
+        str_arg_[flag].push_back(std::move(ArString));
       } else {
-        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
           ptr->setArgPropertyOpt(property, option, val);
         }
       }
+    } else {
+      throw invalid_argument("Unrecognized double arg");
     }
-  } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
-    if (switch_arg_.count(flag) == 0) {
-      auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
-      if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
-        throw invalid_argument("Unrecognized option for switch " + val);
+  }
+
+  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
+                                     string option, string val) {
+
+    if (argname.compare("ARGUMENT_FILE") == 0) {
+      if (file_arg_.count(flag) == 0) {
+
+        if (property.compare("PROPERTY_FILE_EXT") == 0) {
+          set<string> temp{val};
+          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+          ArFile->setArgPropertyOpt(property, option, temp);
+          file_arg_[flag].push_back(std::move(ArFile));
+        } else if (property.compare("PROPERTY_SISTER_FILE_EXT") == 0) {
+          vector<string> temp{val};
+          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+          ArFile->setArgPropertyOpt(property, option, temp);
+          file_arg_[flag].push_back(std::move(ArFile));
+        } else {
+          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+          ArFile->setArgPropertyOpt(property, option, val);
+          file_arg_[flag].push_back(std::move(ArFile));
+        }
       } else {
-        ArSwitch->setArgPropertyOpt(property, option, val);
+        if (property.compare("PROPERTY_FILE_EXT") == 0) {
+          set<string> temp{val};
+          for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+            ptr->setArgPropertyOpt(property, option, temp);
+          }
+        } else {
+          for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+            ptr->setArgPropertyOpt(property, option, val);
+          }
+        }
       }
-      switch_arg_[flag].push_back(std::move(ArSwitch));
-    } else {
-      if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
-        throw invalid_argument("Unrecognized option for switch" + val);
+    } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
+      if (switch_arg_.count(flag) == 0) {
+        auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
+        if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
+          throw invalid_argument("Unrecognized option for switch " + val);
+        } else {
+          ArSwitch->setArgPropertyOpt(property, option, val);
+        }
+        switch_arg_[flag].push_back(std::move(ArSwitch));
       } else {
-        for ( std::unique_ptr<ArgumentSwitch> & ptr : switch_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, val);
+        if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
+          throw invalid_argument("Unrecognized option for switch" + val);
+        } else {
+          for ( std::unique_ptr<ArgumentSwitch> & ptr : switch_arg_[flag]) {
+            ptr->setArgPropertyOpt(property, option, val);
+          }
         }
       }
-    }
 
-  } else if (argname.compare("ARGUMENT_STRING") == 0) {
-    if (str_arg_.count(flag) == 0) {
-      set<string> temp{val};
-      auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
-      ArStr->setArgPropertyOpt(property, option, temp);
-      str_arg_[flag].push_back(std::move(ArStr));
-    } else {
-      set<string> temp{val};
-      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, temp);
+    } else if (argname.compare("ARGUMENT_STRING") == 0) {
+      if (str_arg_.count(flag) == 0) {
+        set<string> temp{val};
+        auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
+        ArStr->setArgPropertyOpt(property, option, temp);
+        str_arg_[flag].push_back(std::move(ArStr));
+      } else {
+        set<string> temp{val};
+        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, temp);
+        }
       }
+    } else {
+      throw invalid_argument("Unrecognized string arg " + argname);
     }
-  } else {
-    throw invalid_argument("Unrecognized string arg " + argname);
   }
-}
 
-void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                   string option, set<string> vals) {
+  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
+                                     string option, set<string> vals) {
 
-  if (argname.compare("ARGUMENT_FILE") == 0) {
-    if (file_arg_.count(flag) == 0) {
-      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-      ArFile->setArgPropertyOpt(property, option, vals);
-      file_arg_[flag].push_back(std::move(ArFile));
-    } else {
-      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, vals);
+    if (argname.compare("ARGUMENT_FILE") == 0) {
+      if (file_arg_.count(flag) == 0) {
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+        ArFile->setArgPropertyOpt(property, option, vals);
+        file_arg_[flag].push_back(std::move(ArFile));
+      } else {
+        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, vals);
+        }
       }
-    }
-  } else if (argname.compare("ARGUMENT_STRING") == 0) {
-    if (str_arg_.count(flag) == 0) {
-      auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
-      ArStr->setArgPropertyOpt(property, option, vals);
-      str_arg_[flag].push_back(std::move(ArStr));
-    } else {
-      for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, vals);
+    } else if (argname.compare("ARGUMENT_STRING") == 0) {
+      if (str_arg_.count(flag) == 0) {
+        auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
+        ArStr->setArgPropertyOpt(property, option, vals);
+        str_arg_[flag].push_back(std::move(ArStr));
+      } else {
+        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, vals);
+        }
       }
+    } else {
+      throw invalid_argument("Unrecognized set<string> arg");
     }
-  } else {
-    throw invalid_argument("Unrecognized set<string> arg");
   }
-}
 
-void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                   string option, vector<string> vals) {
+  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
+                                     string option, vector<string> vals) {
 
-  if (argname.compare("ARGUMENT_FILE") == 0) {
-    if (file_arg_.count(flag) == 0) {
-      auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-      ArFile->setArgPropertyOpt(property, option, vals);
-      file_arg_[flag].push_back(std::move(ArFile));
-    } else {
-      for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-        ptr->setArgPropertyOpt(property, option, vals);
+    if (argname.compare("ARGUMENT_FILE") == 0) {
+      if (file_arg_.count(flag) == 0) {
+        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
+        ArFile->setArgPropertyOpt(property, option, vals);
+        file_arg_[flag].push_back(std::move(ArFile));
+      } else {
+        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
+          ptr->setArgPropertyOpt(property, option, vals);
+        }
       }
+    } else {
+      throw invalid_argument("Unrecognized vector<string> arg");
     }
-  } else {
-    throw invalid_argument("Unrecognized vector<string> arg");
   }
-}
-*/
-bool ArgumentParser::nextParameterIsAFlag_(size_t index,
-                                           vector<string> arguments) {
-
-  if ((index + 1) < arguments.size()) {
-    for (auto flag : flags_) {
-      if (flag.first.compare(arguments.at(index + 1)) == 0) {
-        return true;
-      } else if (flag.second.first.compare(arguments.at(index + 1)) == 0) {
-        return true;
+  */
+  bool ArgumentParser::nextParameterIsAFlag_(size_t index,
+                                             vector<string> arguments) {
+
+    if ((index + 1) < arguments.size()) {
+      for (auto flag : flags_) {
+        if (flag.first.compare(arguments.at(index + 1)) == 0) {
+          return true;
+        } else if (flag.second.first.compare(arguments.at(index + 1)) == 0) {
+          return true;
+        }
       }
     }
+    return false;
   }
-  return false;
-}
 
-void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
-  string flag = arguments.at(index);
-  // If the abbreviated flag is passed we need to resolve the full flag name
-  if (flags_.count(flag) == 0) {
-    for (auto item : flags_) {
-      if (item.second.first.compare(flag) == 0) {
-        flag = item.first;
-        break;
+  void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
+    string flag = arguments.at(index);
+    // If the abbreviated flag is passed we need to resolve the full flag name
+    if (flags_.count(flag) == 0) {
+      for (auto item : flags_) {
+        if (item.second.first.compare(flag) == 0) {
+          flag = item.first;
+          break;
+        }
       }
     }
-  }
 
-  bool unrecognized = true;
-
-  // Parse String Arguments
-  if (arg_.count(flag) != 0) {
-
-    ArgumentType type = arg_[flag]->getArgumentType(); 
-    // Switch does not require an argument
-    if ( type == ArgumentType::SWITCH && 
-        (nextParameterIsAFlag_(index, arguments) ||
-         (index + 1) >= arguments.size())){
-
-      unrecognized = false;
-      if(defaults_set_[flag] == true ){
-        values_[flag][std::type_index(int)].at(0) = 1;
-        defaults_set_[flag] = false;
-      }else {
-        values_[flag][std::type_index(int)].push_back(1);
-      }
-    } else { 
-      if ((index + 1) >= arguments.size()) {
-        string err = "" + flag + " Missing arguments";
-        throw runtime_error(err);
-      }
-      int arg_index = 0;
-      do { // Allow reading of multiple arguments
-        string argument = arguments.at(index + 1);
-        if ( arg_index != 0){
-          // Need to duplicate the argument
-          addFlagArg(flag, type);
-          std::vector<PropertyType> arg_props = arg_[flag].at(0)->getProperties();
-          for ( PropertyType & property : arg_props ){ 
-            
-            auto prop_vals = arg_[flag].at(0)->getPropertyOptions(property);
-            
-
-            std::vector<Option> arg_prop_opts = str_arg_[flag].at(0)->getPropertyOptions(property);
-            for ( Option option : arg_prop_opts ) {
-              std::string val = arg_[flag].at(0)->getPropertyValues(property, option);
-             // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
-            }
-          }
-        }
-        str_arg_[flag].at(arg_index)->argValid(argument);
+    bool unrecognized = true;
+
+    // Parse String Arguments
+    if (arg_.count(flag) != 0) {
+
+      ArgumentType type = arg_[flag].front()->getArgumentType(); 
+      // Switch does not require an argument
+      if ( type == ArgumentType::SWITCH && 
+          (nextParameterIsAFlag_(index, arguments) ||
+           (index + 1) >= arguments.size())){
+
         unrecognized = false;
-        if (defaults_set_.count(flag) ) {
-          if(defaults_set_[flag] == true ){
-            string_values_[flag].clear();
-            string_values_[flag].push_back(argument);
-            defaults_set_[flag] = false;
-          } else {
-            string_values_[flag].push_back(argument);
-          }
+        if(defaults_set_[flag] == true ){
+          values_[flag][std::type_index(typeid(bool))].at(0) = true;
+          addValue_(flag, "TRUE");
+        }else {
+          addValue_(flag, "TRUE");
         }
-        ++index;
-        ++arg_index;
-        if( (index+1) >= arguments.size() ) break;
-      } while ( arguments.at(index+1).at(0) == '-' );
-    }
-  }
-/*
-  // Parse Switches
-  if (switch_arg_.count(flag) != 0) {
-    if (!nextParameterIsAFlag_(index, arguments)) {
-      if ((index + 1) >= arguments.size()) {
-        if (switch_arg_[flag].at(0)->requiresParameter()) {
+      } else { 
+        if ((index + 1) >= arguments.size()) {
           string err = "" + flag + " Missing arguments";
           throw runtime_error(err);
-        } else {
-          unrecognized = false;
-          int_values_[flag].at(0) = 1;
         }
-      } else {
-        string argument = arguments.at(index + 1);
-        switch_arg_[flag].at(0)->argValid(argument);
-        unrecognized = false;
-        string_values_[flag].at(0) = argument;
-        if (switch_arg_[flag].at(0)->positive(argument)) {
+        int arg_index = 0;
+        do { // Allow reading of multiple arguments
+          string argument = arguments.at(index + 1);
+          if ( arg_index != 0){
+            // Need to duplicate the argument
+            addFlagArg(flag, type);
+            ArgumentType type = arg_[flag].front()->getArgumentType();
+            std::vector<PropertyType> arg_props = arg_[flag].front()->getProperties();
+              
+            auto values = arg_[flag].front()->getPropertyValues();
+            arg_[flag].push_back(createArgument(type));
+            arg_[flag].back()->setValues(values);
+            // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
+          }
+          arg_[flag].at(arg_index)->argValid(argument);
+          unrecognized = false;
           if (defaults_set_.count(flag) ) {
             if(defaults_set_[flag] == true ){
-              int_values_[flag].at(0) = 1;
+              values_[flag].clear();
+              addValue_(flag,argument);
               defaults_set_[flag] = false;
             } else {
-              int_values_[flag].push_back(1);
+              addValue_(flag,argument);
             }
           }
+          ++index;
+          ++arg_index;
+          if( (index+1) >= arguments.size() ) break;
+        } while ( arguments.at(index+1).at(0) == '-' );
+      }
+    }
+  /*
+    // Parse Switches
+    if (switch_arg_.count(flag) != 0) {
+      if (!nextParameterIsAFlag_(index, arguments)) {
+        if ((index + 1) >= arguments.size()) {
+          if (switch_arg_[flag].at(0)->requiresParameter()) {
+            string err = "" + flag + " Missing arguments";
+            throw runtime_error(err);
+          } else {
+            unrecognized = false;
+            int_values_[flag].at(0) = 1;
+          }
         } else {
+          string argument = arguments.at(index + 1);
+          switch_arg_[flag].at(0)->argValid(argument);
+          unrecognized = false;
+          string_values_[flag].at(0) = argument;
+          if (switch_arg_[flag].at(0)->positive(argument)) {
+            if (defaults_set_.count(flag) ) {
+              if(defaults_set_[flag] == true ){
+                int_values_[flag].at(0) = 1;
+                defaults_set_[flag] = false;
+              } else {
+                int_values_[flag].push_back(1);
+              }
+            }
+          } else {
+            if (defaults_set_.count(flag) ) {
+              if(defaults_set_[flag] == true ){
+                int_values_[flag].at(0) = 0;
+                defaults_set_[flag] = false;
+              } else {
+                int_values_[flag].push_back(0);
+              }
+            }
+          }
+        }
+      } else {
+        unrecognized = false;
+        if(defaults_set_[flag] == true ){
+          int_values_[flag].at(0) = 1;
+          defaults_set_[flag] = false;
+        }else {
+          int_values_[flag].push_back(1);
+        }
+      }
+    }
+
+    // Parse integer arguments
+    if (int_arg_.count(flag) != 0) {
+      if (!nextParameterIsAFlag_(index, arguments) ||
+          int_arg_[flag].at(0)->requiresParameter()) {
+        if ((index + 1) >= arguments.size()) {
+          string err = "" + flag + " Missing arguments";
+          throw runtime_error(err);
+        }
+
+        int arg_index = 0;
+        do {
+          string argument = arguments.at(index + 1);
+          if ( arg_index != 0){
+            // Need to duplicate the argument
+            std::string arg_name = int_arg_[flag].at(0)->getArgumentName();
+            std::vector<std::string> arg_props = int_arg_[flag].at(0)->getProperties();
+            std::vector<std::string> arg_prop_opts = int_arg_[flag].at(0)->getPropertyOptions();
+            std::map<std::string, std::string> arg_prop_vals = int_arg_[flag].at(0)->getPropertyValues();
+          }
+          int_arg_[flag].at(arg_index)->argValid(stoi(argument));
+          unrecognized = false;
           if (defaults_set_.count(flag) ) {
             if(defaults_set_[flag] == true ){
-              int_values_[flag].at(0) = 0;
+              string_values_[flag].clear();
+              int_values_[flag].push_back(stoi(argument));
               defaults_set_[flag] = false;
             } else {
-              int_values_[flag].push_back(0);
+              int_values_[flag].push_back(stoi(argument));
             }
           }
-        }
-      }
-    } else {
-      unrecognized = false;
-      if(defaults_set_[flag] == true ){
-        int_values_[flag].at(0) = 1;
-        defaults_set_[flag] = false;
-      }else {
-        int_values_[flag].push_back(1);
+          ++index;
+          ++arg_index;
+          if( (index+1) >= arguments.size() ) break;
+        } while ( arguments.at(index+1).at(0) == '-' );
       }
     }
-  }
 
-  // Parse integer arguments
-  if (int_arg_.count(flag) != 0) {
-    if (!nextParameterIsAFlag_(index, arguments) ||
-        int_arg_[flag].at(0)->requiresParameter()) {
-      if ((index + 1) >= arguments.size()) {
-        string err = "" + flag + " Missing arguments";
-        throw runtime_error(err);
-      }
-
-      int arg_index = 0;
-      do {
-        string argument = arguments.at(index + 1);
-        if ( arg_index != 0){
-          // Need to duplicate the argument
-          std::string arg_name = int_arg_[flag].at(0)->getArgumentName();
-          std::vector<std::string> arg_props = int_arg_[flag].at(0)->getProperties();
-          std::vector<std::string> arg_prop_opts = int_arg_[flag].at(0)->getPropertyOptions();
-          std::map<std::string, std::string> arg_prop_vals = int_arg_[flag].at(0)->getPropertyValues();
+    // Parse double arguments
+    if (double_arg_.count(flag) != 0) {
+      if (!nextParameterIsAFlag_(index, arguments) ||
+          double_arg_[flag].at(0)->requiresParameter()) {
+        if ((index + 1) >= arguments.size()) {
+          string err = "" + flag + " Missing arguments";
+          throw runtime_error(err);
         }
-        int_arg_[flag].at(arg_index)->argValid(stoi(argument));
-        unrecognized = false;
-        if (defaults_set_.count(flag) ) {
-          if(defaults_set_[flag] == true ){
-            string_values_[flag].clear();
-            int_values_[flag].push_back(stoi(argument));
-            defaults_set_[flag] = false;
-          } else {
-            int_values_[flag].push_back(stoi(argument));
+        int arg_index = 0;
+        do {
+          string argument = arguments.at(index + 1);
+          if ( arg_index != 0){
+            // Need to duplicate the argument
+            std::string arg_name = double_arg_[flag].at(0)->getArgumentName();
+            std::vector<std::string> arg_props = double_arg_[flag].at(0)->getProperties();
+            std::vector<std::string> arg_prop_opts = double_arg_[flag].at(0)->getProperties();
+            std::map<std::string, std::string> arg_prop_vals = double_arg_[flag].at(0)->getPropertyValues();
           }
-        }
-        ++index;
-        ++arg_index;
-        if( (index+1) >= arguments.size() ) break;
-      } while ( arguments.at(index+1).at(0) == '-' );
+          double_arg_[flag].at(arg_index)->argValid(stod(argument));
+          unrecognized = false;
+          if (defaults_set_.count(flag) ) {
+            if(defaults_set_[flag] == true ){
+              string_values_[flag].clear();
+              double_values_[flag].push_back(stod(argument));
+              defaults_set_[flag] = false;
+            } else {
+              double_values_[flag].push_back(stod(argument));
+            }
+          }
+          ++index;
+          ++arg_index;
+          if( (index+1) >= arguments.size() ) break;
+        } while ( arguments.at(index+1).at(0) == '-' );
+      }
     }
-  }
 
-  // Parse double arguments
-  if (double_arg_.count(flag) != 0) {
-    if (!nextParameterIsAFlag_(index, arguments) ||
-        double_arg_[flag].at(0)->requiresParameter()) {
-      if ((index + 1) >= arguments.size()) {
-        string err = "" + flag + " Missing arguments";
-        throw runtime_error(err);
-      }
-      int arg_index = 0;
-      do {
-        string argument = arguments.at(index + 1);
-        if ( arg_index != 0){
-          // Need to duplicate the argument
-          std::string arg_name = double_arg_[flag].at(0)->getArgumentName();
-          std::vector<std::string> arg_props = double_arg_[flag].at(0)->getProperties();
-          std::vector<std::string> arg_prop_opts = double_arg_[flag].at(0)->getProperties();
-          std::map<std::string, std::string> arg_prop_vals = double_arg_[flag].at(0)->getPropertyValues();
+    // Parse file arguments 
+    if (file_arg_.count(flag) != 0) {
+      if (!nextParameterIsAFlag_(index, arguments) ||
+          file_arg_[flag].at(0)->requiresParameter()) {
+        if ((index + 1) >= arguments.size()) {
+          string err = "" + flag + " Missing arguments";
+          throw runtime_error(err);
         }
-        double_arg_[flag].at(arg_index)->argValid(stod(argument));
-        unrecognized = false;
-        if (defaults_set_.count(flag) ) {
-          if(defaults_set_[flag] == true ){
-            string_values_[flag].clear();
-            double_values_[flag].push_back(stod(argument));
-            defaults_set_[flag] = false;
-          } else {
-            double_values_[flag].push_back(stod(argument));
+        int arg_index = 0;
+        do {
+          string argument = arguments.at(index + 1);
+          if ( arg_index != 0){
+            // Need to duplicate the argument
+            std::string arg_name = file_arg_[flag].at(0)->getArgumentName();
+            std::vector<std::string> arg_props = file_arg_[flag].at(0)->getProperties();
+            std::vector<std::string> arg_prop_opts = file_arg_[flag].at(0)->getProperties();
+            std::map<std::string, std::string> arg_prop_vals = file_arg_[flag].at(0)->getPropertyValues();
           }
-        }
-        ++index;
-        ++arg_index;
-        if( (index+1) >= arguments.size() ) break;
-      } while ( arguments.at(index+1).at(0) == '-' );
+          file_arg_[flag].at(arg_index)->argValid(argument);
+          unrecognized = false;
+          if (defaults_set_.count(flag) ) {
+            if(defaults_set_[flag] == true ){
+              string_values_[flag].clear();
+              string_values_[flag].push_back(argument);
+              defaults_set_[flag] = false;
+            } else {
+              string_values_[flag].push_back(argument);
+            }
+          }
+          ++index;
+          ++arg_index;
+          if( (index+1) >= arguments.size() ) break;
+        } while ( arguments.at(index+1).at(0) == '-' );
+      }
+    }*/
+
+    if (unrecognized) {
+      throw invalid_argument("The flag " + flag + " was unrecognized");
     }
   }
 
-  // Parse file arguments 
-  if (file_arg_.count(flag) != 0) {
-    if (!nextParameterIsAFlag_(index, arguments) ||
-        file_arg_[flag].at(0)->requiresParameter()) {
-      if ((index + 1) >= arguments.size()) {
-        string err = "" + flag + " Missing arguments";
-        throw runtime_error(err);
-      }
-      int arg_index = 0;
-      do {
-        string argument = arguments.at(index + 1);
-        if ( arg_index != 0){
-          // Need to duplicate the argument
-          std::string arg_name = file_arg_[flag].at(0)->getArgumentName();
-          std::vector<std::string> arg_props = file_arg_[flag].at(0)->getProperties();
-          std::vector<std::string> arg_prop_opts = file_arg_[flag].at(0)->getProperties();
-          std::map<std::string, std::string> arg_prop_vals = file_arg_[flag].at(0)->getPropertyValues();
-        }
-        file_arg_[flag].at(arg_index)->argValid(argument);
-        unrecognized = false;
-        if (defaults_set_.count(flag) ) {
-          if(defaults_set_[flag] == true ){
-            string_values_[flag].clear();
-            string_values_[flag].push_back(argument);
-            defaults_set_[flag] = false;
+
+  /*
+  std::vector<int> ArgumentParser::getInts(string flag) {
+
+    if (int_values_.count(flag) == 0) {
+      if (switch_arg_.count(flag)) {
+        if (string_values_.count(flag)) {
+          if (switch_arg_[flag]->positive(string_values_[flag])) {
+            return std::vector<int> {1};
           } else {
-            string_values_[flag].push_back(argument);
+            return std::vector<int> {0};
           }
         }
-        ++index;
-        ++arg_index;
-        if( (index+1) >= arguments.size() ) break;
-      } while ( arguments.at(index+1).at(0) == '-' );
+      }
+      string err = "" + flag +
+                   " does not contain an int. It is also possible that "
+                   "you did not specify a default value";
+      throw invalid_argument(err);
     }
-  }*/
-
-  if (unrecognized) {
-    throw invalid_argument("The flag " + flag + " was unrecognized");
+    return int_values_[flag];
   }
-}
 
-string ArgumentParser::getFlagArgOptValue(string flag, string argname,
-                                          string property, string option) {
-
-  if (str_arg_.count(flag) != 0) {
-    auto argStr = str_arg_[flag];
-    auto argName = argStr->getArgumentName();
-    if (argName.compare(argname) == 0) {
-      return argStr->getPropertyValues(property, option);
-    }
-  }
-  if (switch_arg_.count(flag) != 0) {
-    auto argSwitch = switch_arg_[flag];
-    auto argName = argSwitch->getArgumentName();
-    if (argName.compare(argname) == 0) {
-      return argSwitch->getPropertyValues(property, option);
-    }
-  }
-  if (file_arg_.count(flag) != 0) {
-    auto argFile = file_arg_[flag];
-    auto argName = argFile->getArgumentName();
-    if (argName.compare(argname) == 0) {
-      return argFile->getPropertyValues(property, option);
-    }
-  }
-  if (int_arg_.count(flag) != 0) {
-    auto argInt = int_arg_[flag];
-    auto argName = argInt->getArgumentName();
-    if (argName.compare(argname) == 0) {
-      return argInt->getPropertyValues(property, option);
+  std::vector<double> ArgumentParser::getDoubles(string flag) {
+    if (double_values_.count(flag) == 0) {
+      string err = "" + flag +
+                   " does not contain a double. It is also possible that "
+                   "you did not specify a default value";
+      throw invalid_argument(err);
     }
+    return double_values_[flag];
   }
 
-  throw invalid_argument("Unrecognized flag or argument " + flag + " " +
-                         argname);
-}
-/*
-std::vector<int> ArgumentParser::getInts(string flag) {
-
-  if (int_values_.count(flag) == 0) {
-    if (switch_arg_.count(flag)) {
-      if (string_values_.count(flag)) {
-        if (switch_arg_[flag]->positive(string_values_[flag])) {
-          return std::vector<int> {1};
-        } else {
-          return std::vector<int> {0};
+  std::vector<string> ArgumentParser::getStrs(string flag) {
+    if (string_values_.count(flag) == 0) {
+      if (switch_arg_.count(flag)) {
+        if (int_values_.count(flag)) {
+          if (switch_arg_[flag]->positive(int_values_[flag])) {
+            return std::vector<string> {"ON"};
+          } else {
+            return std::vector<string> {"OFF"};
+          }
         }
       }
+      string err = "" + flag +
+                   " does not contain a string. It is also possible that "
+                   "you did not specify a default value";
+      throw invalid_argument(err);
     }
-    string err = "" + flag +
-                 " does not contain an int. It is also possible that "
-                 "you did not specify a default value";
-    throw invalid_argument(err);
+    return string_values_[flag];
   }
-  return int_values_[flag];
-}
 
-std::vector<double> ArgumentParser::getDoubles(string flag) {
-  if (double_values_.count(flag) == 0) {
-    string err = "" + flag +
-                 " does not contain a double. It is also possible that "
-                 "you did not specify a default value";
-    throw invalid_argument(err);
+  std::vector<size_t> ArgumentParser::getSize_ts(string flag) {
+    if (size_t_values_.count(flag) == 0) {
+      string err = "" + flag +
+                   " does not contain a size_t. It is also possible that "
+                   "you did not specify a default value";
+      throw invalid_argument(err);
+    }
+    return size_t_values_[flag];
   }
-  return double_values_[flag];
-}
-
-std::vector<string> ArgumentParser::getStrs(string flag) {
-  if (string_values_.count(flag) == 0) {
-    if (switch_arg_.count(flag)) {
-      if (int_values_.count(flag)) {
-        if (switch_arg_[flag]->positive(int_values_[flag])) {
-          return std::vector<string> {"ON"};
-        } else {
-          return std::vector<string> {"OFF"};
-        }
+  */
+  void ArgumentParser::postParseCheck(void) {
+    //for (std::pair<std::string, std::vector<std::unique_ptr<ArgumentObject>>> & flag_arg : arg_) {
+    for (auto & flag_arg : arg_) {
+      for ( std::unique_ptr<ArgumentObject> & arg : flag_arg.second ){
+        arg->postArgCheck();
       }
     }
-    string err = "" + flag +
-                 " does not contain a string. It is also possible that "
-                 "you did not specify a default value";
-    throw invalid_argument(err);
-  }
-  return string_values_[flag];
-}
-
-std::vector<size_t> ArgumentParser::getSize_ts(string flag) {
-  if (size_t_values_.count(flag) == 0) {
-    string err = "" + flag +
-                 " does not contain a size_t. It is also possible that "
-                 "you did not specify a default value";
-    throw invalid_argument(err);
-  }
-  return size_t_values_[flag];
-}
-*/
-void ArgumentParser::postParseCheck(void) {
-
-  for (auto arg : arg_) {
-    arg.second->postArgCheck();
   }
-}
 
-void ArgumentParser::parse(const char* argv[], int argc) {
+  void ArgumentParser::parse(const char* argv[], int argc) {
 
-  // Convert to vector of strings
-  vector<string> arguments(argv, argv + argc);
-
-  if (argc <= 1) {
-    cout << "Usage: " << arguments.at(0) << " <options(s)> SOURCES";
-    showUsage();
-    throw runtime_error("Must provide arguments");
-  }
+    // Convert to vector of strings
+    vector<string> arguments(argv, argv + argc);
 
-  string help_flag = "--help";
-  string help_flag_short = "-h";
-  string citation_flag = "--citation";
-  string citation_flag_short = "-cite";
-  string version_flag = "--version";
-  string version_flag_short = "-version";
-
-  size_t allowed_args_before_exit = 2;
-  for (size_t index = 1; index < arguments.size(); ++index) {
-    if (help_flag.compare(arguments.at(index)) == 0 ||
-        help_flag_short.compare(arguments.at(index)) == 0) {
+    if (argc <= 1) {
       cout << "Usage: " << arguments.at(0) << " <options(s)> SOURCES";
       showUsage();
-      if (allowed_args_before_exit == arguments.size()) {
-        exit(0);
-      }
-      ++allowed_args_before_exit;
-    } else if (version_flag.compare(arguments.at(index)) == 0 ||
-               version_flag_short.compare(arguments.at(index)) == 0) {
-      exit(0);
-    } else if (citation_flag.compare(arguments.at(index)) == 0 ||
-               citation_flag_short.compare(arguments.at(index)) == 0) {
-      cout << "\nCitation: " << calcJ_AUTHOR_SURNAME << ", ";
-      cout << calcJ_AUTHOR_INITIALS << " (";
-      cout << calcJ_YEAR_PUBLISHED << "). ";
-      cout << calcJ_TITLE << " (Version ";
-      cout << calcJ_VERSION_MAJOR << ".";
-      cout << calcJ_VERSION_MINOR << "). [Software]. Available from ";
-      cout << calcJ_URL << ".\n\n";
-      if (allowed_args_before_exit == arguments.size()) {
+      throw runtime_error("Must provide arguments");
+    }
+
+    string help_flag = "--help";
+    string help_flag_short = "-h";
+    string citation_flag = "--citation";
+    string citation_flag_short = "-cite";
+    string version_flag = "--version";
+    string version_flag_short = "-version";
+
+    size_t allowed_args_before_exit = 2;
+    for (size_t index = 1; index < arguments.size(); ++index) {
+      if (help_flag.compare(arguments.at(index)) == 0 ||
+          help_flag_short.compare(arguments.at(index)) == 0) {
+        cout << "Usage: " << arguments.at(0) << " <options(s)> SOURCES";
+        showUsage();
+        if (allowed_args_before_exit == arguments.size()) {
+          exit(0);
+        }
+        ++allowed_args_before_exit;
+      } else if (version_flag.compare(arguments.at(index)) == 0 ||
+                 version_flag_short.compare(arguments.at(index)) == 0) {
         exit(0);
+      } else if (citation_flag.compare(arguments.at(index)) == 0 ||
+                 citation_flag_short.compare(arguments.at(index)) == 0) {
+        cout << "\nCitation: " << catnip_AUTHOR_SURNAME << ", ";
+        cout << catnip_AUTHOR_INITIALS << " (";
+        cout << catnip_YEAR_PUBLISHED << "). ";
+        cout << catnip_TITLE << " (Version ";
+        cout << catnip_VERSION_MAJOR << ".";
+        cout << catnip_VERSION_MINOR << "). [Software]. Available from ";
+        cout << catnip_URL << ".\n\n";
+        if (allowed_args_before_exit == arguments.size()) {
+          exit(0);
+        }
+        ++allowed_args_before_exit;
+      } else {
+        parseArg_(index, arguments);
       }
-      ++allowed_args_before_exit;
-    } else {
-      parseArg_(index, arguments);
     }
-  }
 
-  postParseCheck();
+    postParseCheck();
+  }
 }
diff --git a/src/libcatnip/io/argumentparser.hpp b/src/libcatnip/io/argumentparser.hpp
index 165d0d3..802e1ba 100644
--- a/src/libcatnip/io/argumentparser.hpp
+++ b/src/libcatnip/io/argumentparser.hpp
@@ -1,6 +1,5 @@
 #ifndef _CATNIP_ARGUMENTPARSER_HPP
 #define _CATNIP_ARGUMENTPARSER_HPP
-#include "matrix.hpp"
 #include "parameters.hpp"
 #include <any>
 #include <map>
@@ -44,6 +43,10 @@ class ArgumentParser {
   size_t maxDescriptionSize;
   size_t maxLineLength = 80;
 
+  // Will convert the command line argument to the appropriate type before
+  // placing in std::any and adding to the values container
+  void addValue_(std::string flag, std::string value);
+
  public:
   // 1 - short flag
   // 2 - long flag
@@ -67,8 +70,8 @@ class ArgumentParser {
   // "SWITCH"
   // The rules are dependent on the type
   template<class T>
-    void ArgumentParser::setFlagArgOpt(
-        string flag, 
+    void setFlagArgOpt(
+        std::string flag, 
         ArgumentType argname,
         PropertyType property,
         Option option,
@@ -77,8 +80,8 @@ class ArgumentParser {
       
       if (arg_.count(flag) == 0) {
         auto arg = createArgument(argname);
-        ArInt->setArgPropertyOpt(property, option, val);
-        arg_[flag].push_back(std::move(ArInt));
+        arg->setArgPropertyOpt(property, option, val);
+        arg_[flag].push_back(std::move(arg));
       } else {
         for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag]){
           ptr->setArgPropertyOpt(property, option, val);
@@ -164,13 +167,24 @@ class ArgumentParser {
   template<class T>
   std::vector<T> get(std::string flag) {
     std::vector<T> values;
-    if ( values[flag].count(type_index(T)) ){
-      for ( std::any & val : values[flag][std::type_index(T)] ){
+    if ( values_[flag].count(typeid(T)) ){
+      for ( std::any & val : values_[flag][typeid(T)] ){
         values.push_back(std::any_cast<T>(val));
       }
     }
     return values;
   }
+//
+//  template<class T>
+//  std::vector<T> get(std::string flag, ArgumentType arg_type, PropertyType prop_type, Option opt) {
+//    std::vector<T> values;
+//    if ( values_[flag].count(typeid(T)) ){
+//      for ( std::any & val : values_[flag][typeid(T)] ){
+//        values.push_back(std::any_cast<T>(val));
+//      }
+//    }
+//    return values;
+//  }
 /*  std::vector<double> getDoubles(std::string flag);
   std::vector<int> getInts(std::string flag);
   std::vector<std::string> getStrs(std::string flag);
diff --git a/src/libcatnip/io/arguments/argumentfile.cpp b/src/libcatnip/io/arguments/argumentfile.cpp
index 0fee812..372b709 100644
--- a/src/libcatnip/io/arguments/argumentfile.cpp
+++ b/src/libcatnip/io/arguments/argumentfile.cpp
@@ -9,11 +9,8 @@ using namespace catnip;
 using namespace std;
 
 ArgumentFile::ArgumentFile(void) { 
-  auto prop_file_exist = std::unique_ptr<PropertyObject>(new PropertyFileExist());
-  propobjs_.push_back(prop_file_exist);
-  auto prop_file_ext = std::unique_ptr<PropertyObject>(new PropertyFileExt());
-  propobjs_.push_back(prop_file_ext);
-  auto prop_sis_file = std::unique_ptr<PropertyObject>(new PropertySisterFile());
-  propobjs_.push_back(prop_sis_file);
+  propobjs_.emplace_back(new PropertyFileExist());
+  propobjs_.emplace_back(new PropertyFileExt());
+  propobjs_.emplace_back(new PropertySisterFile());
 
 }
diff --git a/src/libcatnip/io/arguments/argumentfile.hpp b/src/libcatnip/io/arguments/argumentfile.hpp
index bea9916..5952f86 100644
--- a/src/libcatnip/io/arguments/argumentfile.hpp
+++ b/src/libcatnip/io/arguments/argumentfile.hpp
@@ -15,6 +15,10 @@ class ArgumentFile : public ArgumentObject {
     return ArgumentType::FILES;
   }
 
+  virtual std::type_index getValueType(void) const noexcept final { 
+    return typeid(std::string);
+  }
+
   ArgumentFile(void);
 };
 
diff --git a/src/libcatnip/io/arguments/argumentnumerical.cpp b/src/libcatnip/io/arguments/argumentnumerical.cpp
index 2aa4cb8..b6997d1 100644
--- a/src/libcatnip/io/arguments/argumentnumerical.cpp
+++ b/src/libcatnip/io/arguments/argumentnumerical.cpp
@@ -1,6 +1,6 @@
 
 #include "argumentnumerical.hpp"
-#include "properties/propertynumerical.hpp"
+#include "properties/propertynumeric.hpp"
 #include <iostream>
 #include <memory>
 
@@ -8,6 +8,6 @@ using namespace catnip;
 using namespace std;
 
 ArgumentNumerical::ArgumentNumerical(void) { 
-  propobjs_.push_back(std::unique_ptr<PropertyObject>( new PropertyNumerical()));
+  propobjs_.emplace_back(new PropertyNumeric());
 }
 
diff --git a/src/libcatnip/io/arguments/argumentnumerical.hpp b/src/libcatnip/io/arguments/argumentnumerical.hpp
index c7f4fa3..eab274e 100644
--- a/src/libcatnip/io/arguments/argumentnumerical.hpp
+++ b/src/libcatnip/io/arguments/argumentnumerical.hpp
@@ -7,13 +7,21 @@
 
 namespace catnip {
 
-class ArgumentNumerical : public ArgumentObject<double> {
+class ArgumentNumerical : public ArgumentObject {
  private:
   std::string getName_(void) const { return "ARGUMENT_DOUBLE"; }
   void registerProperties_(void);
 
  public:
-  ArgumentDouble(void);
+
+  virtual ArgumentType getArgumentType(void) const noexcept final 
+  { return ArgumentType::NUMERICAL; }
+
+  virtual std::type_index getValueType(void) const noexcept final {
+    return typeid(double);
+  }
+
+  ArgumentNumerical(void);
 };
 
 }  // namespace catnip
diff --git a/src/libcatnip/io/arguments/argumentobject.hpp b/src/libcatnip/io/arguments/argumentobject.hpp
index b0dd3d8..b57b4e4 100644
--- a/src/libcatnip/io/arguments/argumentobject.hpp
+++ b/src/libcatnip/io/arguments/argumentobject.hpp
@@ -2,7 +2,7 @@
 #ifndef _CATNIP_ARGUMENTOBJECT_HPP
 #define _CATNIP_ARGUMENTOBJECT_HPP
 
-#include "../../string_support.hpp"
+#include "string_support.hpp"
 #include "properties/propertyobject.hpp"
 #include <exception>
 #include <iostream>
@@ -19,6 +19,7 @@ namespace catnip {
     STRING,
     SWITCH
   };
+
 // The template is simply for specifying the type of the argument coming
 // from the command line
 class ArgumentObject {
@@ -33,6 +34,9 @@ class ArgumentObject {
 
   virtual ArgumentType getArgumentType(void) const noexcept = 0; 
 
+  // This is the type the value will be converted to after being read in
+  virtual std::type_index getValueType(void) const noexcept = 0;
+
   std::vector<PropertyType> getProperties(void) {
     std::vector<PropertyType> props;
     for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
@@ -135,6 +139,17 @@ class ArgumentObject {
     }
   }
 
+  void setValues(std::map<PropertyType, std::map<Option, std::any>> values) {
+    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
+      const PropertyType & type = prop->getPropertyType();
+      if(values.count(type)){
+        for ( std::pair<Option,std::any> opt_val : values[type] ){
+          prop->setPropOption(opt_val.first, opt_val.second);
+        }
+      }
+    }
+  }
+
    void setPropertyValues(
       PropertyType property, std::map<Option, std::any> opts) {
 
diff --git a/src/libcatnip/io/arguments/argumentstring.cpp b/src/libcatnip/io/arguments/argumentstring.cpp
index 5091056..d06b93d 100644
--- a/src/libcatnip/io/arguments/argumentstring.cpp
+++ b/src/libcatnip/io/arguments/argumentstring.cpp
@@ -8,8 +8,6 @@ using namespace catnip;
 using namespace std;
 
 ArgumentString::ArgumentString(void) { 
-  auto prop_string = std::unique_ptr<PropertyObject>(new PropertyString);
-  propobjs_.push_back(prop_string);
-  auto prop_string_choice = std::unique_ptr<PropertyObject>(new PropertyStringChoice);
-  propobjs_.push_back(prop_string_choice);
+  propobjs_.emplace_back(new PropertyString);
+  propobjs_.emplace_back(new PropertyStringChoice);
 }
diff --git a/src/libcatnip/io/arguments/argumentstring.hpp b/src/libcatnip/io/arguments/argumentstring.hpp
index b599d38..c6c0b03 100644
--- a/src/libcatnip/io/arguments/argumentstring.hpp
+++ b/src/libcatnip/io/arguments/argumentstring.hpp
@@ -10,8 +10,13 @@ namespace catnip {
 class ArgumentString : public ArgumentObject {
  public:
 
-  virtual ArgumentType getArgumentType(void) const noexcept final 
-  { return ArgumentType::STRING; }
+  virtual ArgumentType getArgumentType(void) const noexcept final { 
+    return ArgumentType::STRING; 
+  }
+
+  virtual std::type_index getValueType(void) const noexcept final {
+    return typeid(std::string);
+  }
 
   ArgumentString(void);
 };
diff --git a/src/libcatnip/io/arguments/argumentswitch.cpp b/src/libcatnip/io/arguments/argumentswitch.cpp
index c41a211..f772cec 100644
--- a/src/libcatnip/io/arguments/argumentswitch.cpp
+++ b/src/libcatnip/io/arguments/argumentswitch.cpp
@@ -7,8 +7,7 @@ using namespace catnip;
 using namespace std;
 
 ArgumentSwitch::ArgumentSwitch(void) { 
-  auto prop_switch = std::unique_ptr<PropertyObject>(new PropertySwitch);
-  propobjs_.push_back(prop_switch);
+  propobjs_.emplace_back(new PropertySwitch);
 }
 
 bool ArgumentSwitch::positive(string val) const {
diff --git a/src/libcatnip/io/arguments/argumentswitch.hpp b/src/libcatnip/io/arguments/argumentswitch.hpp
index a7d8793..1933713 100644
--- a/src/libcatnip/io/arguments/argumentswitch.hpp
+++ b/src/libcatnip/io/arguments/argumentswitch.hpp
@@ -15,6 +15,11 @@ class ArgumentSwitch : public ArgumentObject {
   }
 
   ArgumentSwitch(void);
+
+  virtual std::type_index getValueType(void) const noexcept final {
+    return typeid(bool);
+  }
+
   virtual bool requiresParameter(void) final { return false; }
   bool positive(int val) const noexcept { return ((val == 1) ? true : false); }
   bool positive(std::string val) const;
diff --git a/src/libcatnip/io/arguments/properties/property_numeric.cpp b/src/libcatnip/io/arguments/properties/propertynumeric.cpp
similarity index 97%
rename from src/libcatnip/io/arguments/properties/property_numeric.cpp
rename to src/libcatnip/io/arguments/properties/propertynumeric.cpp
index 6d1dc22..2262916 100644
--- a/src/libcatnip/io/arguments/properties/property_numeric.cpp
+++ b/src/libcatnip/io/arguments/properties/propertynumeric.cpp
@@ -1,5 +1,5 @@
 
-#include "property_numeric.hpp"
+#include "propertynumeric.hpp"
 
 #include "propertyobject.hpp"
 
diff --git a/src/libcatnip/io/arguments/properties/property_numeric.hpp b/src/libcatnip/io/arguments/properties/propertynumeric.hpp
similarity index 100%
rename from src/libcatnip/io/arguments/properties/property_numeric.hpp
rename to src/libcatnip/io/arguments/properties/propertynumeric.hpp
diff --git a/src/libcatnip/io/arguments/properties/propertyobject.hpp b/src/libcatnip/io/arguments/properties/propertyobject.hpp
index 78fe350..9e4e650 100644
--- a/src/libcatnip/io/arguments/properties/propertyobject.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyobject.hpp
@@ -3,13 +3,13 @@
 #define _CATNIP_PROPERTY_OBJECT_HPP
 
 #include <any>
-#include <exception>
-#include <iostream>
 #include <map>
 #include <memory>
-#include <sstream>
+#include <set>
 #include <stdexcept>
 #include <string>
+#include <typeindex>
+#include <typeinfo>
 #include <vector>
 
 namespace catnip {
@@ -38,7 +38,8 @@ enum class Option {
   FILE_NAME,
   FILE_PATH,
   FILE_PATH_NAME,
-  VALUE
+  VALUE,
+  DEFAULT
 };
 
 class PropertyObject {
@@ -46,15 +47,60 @@ class PropertyObject {
   // Map key is the option name and the type "int, double etc"
   // void * points to the correct value for that type
   std::map<Option, std::any> options_;
+  std::map<Option, std::vector<std::type_index>> allowed_option_types_;
+  std::map<Option, std::type_index> default_option_type_; 
+
+  //void addAllowedOptionType_(const Option & option, std::type_index ind) {  
+   // allowed_option_types_[option].push_back(std::move(ind));
+  //}
+
+ // void setDefaultOptionType_(const Option & option, std::type_index ind) {
+  //  default_option_type_[option] = std::move(ind);
+ // }
 
   bool propOptionValid_(const Option &option) const {
     return options_.count(option);
   }
 
-  virtual void setPropOption_(const Option &option, const std::any &val) {
+  void setPropOption_(const Option &option, const std::any &val) {
       options_[option] = val;
   }
 
+  bool conversionAllowed_(Option option, std::type_index type) const {
+    for ( const std::type_index & allowed_type : allowed_option_types_.at(option) ){
+      if( allowed_type == type ) return true;
+    }
+    return false;
+  } 
+
+  typedef int (*int_func)(Option,std::map<Option, std::any>); 
+  std::map<Option,int_func> int_convert_;
+  typedef double (*double_func)(Option,std::map<Option, std::any>); 
+  std::map<Option,double_func> double_convert_;
+  typedef std::string (*str_func)(Option,std::map<Option, std::any>); 
+  std::map<Option,str_func> str_convert_;
+  typedef bool (*bool_func)(Option,std::map<Option, std::any>); 
+  std::map<Option,bool_func> bool_convert_;
+  typedef std::set<bool> (*set_bool_func)(const Option,std::map<const Option, std::any>); 
+  std::map<Option,set_bool_func> set_bool_convert_;
+  typedef std::set<std::string> (*set_str_func)(const Option,std::map<const Option, std::any>); 
+  std::map<Option,set_str_func> set_str_convert_;
+  typedef std::set<int> (*set_int_func)(const Option,std::map<const Option, std::any>); 
+  std::map<Option,set_int_func> set_int_convert_;
+  typedef std::vector<bool> (*vector_bool_func)(const Option,std::map<const Option, std::any>); 
+  std::map<Option,vector_bool_func> vector_bool_convert_;
+  typedef std::vector<std::string> (*vector_str_func)(const Option,std::map<const Option, std::any>); 
+  std::map<Option,vector_str_func> vector_str_convert_;
+
+  template<class T>
+  T convert_(Option option){
+    if (typeid(T) == typeid(int)) return int_convert_[option](option,options_);
+    else if (typeid(T) == typeid(double)) return double_convert_[option](option,options_);
+    else if (typeid(T) == typeid(std::string)) return str_convert_[option](option,options_);
+    else if (typeid(T) == typeid(bool)) return bool_convert_[option](option,options_);
+    return set_bool_convert_[option](option,options_);
+  }
+
  public:
   virtual ~PropertyObject(void) { }
 
@@ -80,12 +126,19 @@ class PropertyObject {
   }
 
   template<class T>
-  T getPropOption(const Option &option) const {
+  T getPropOption(const Option &option) {
     if (!propOptionValid_(option)) {
       std::string err = " An unrecognized property option was detected.";
       throw std::invalid_argument(err);
     }
-    return std::any_cast<T>(options_.at(option));
+
+    if ( !conversionAllowed_(option, typeid(T)) ){
+      std::string err = "Conversion of property option's value to type not allowed.";
+      throw std::invalid_argument(err);
+    }
+
+    return convert_<T>(option);
+    //return std::any_cast<T>(options_.at(option));
   }
 
   virtual void postCheck(void) const { return; }
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp b/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
index 03d0783..ad97998 100644
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
+++ b/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
@@ -1,71 +1,147 @@
 
 #include "propertystringchoice.hpp"
 #include "../../../string_support.hpp"
+#include <set>
 #include <stdexcept>
 #include <sys/stat.h>
+#include <typeinfo>
 
-using namespace catnip;
 using namespace std;
 
-PropertyStringChoice::PropertyStringChoice(void) {
-  set<string> set_var1{"false"};
-  setPropOption_(Option::ENFORCED, set_var1);
-  string str = "NOT_DEFINED";
-  set<string> set_var2{str};
-  setPropOption_(Option::ALLOWED_VALUES, set_var2);
-}
+namespace catnip {
+  namespace {
+    std::set<bool> getSetBoolEnforced_(const Option option, std::map<const Option, std::any> options_){
+      set<bool> values;
+      // Because the default is a set of strings
+      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
+      for ( std::string val : stored_values){
+        if( to_upper(val) == "TRUE" ) {
+          values.insert(true);
+        } else if( to_upper(val) == "FALSE") {
+          values.insert(false);
+        }
+      } 
+      return values;
+    }
+
+    std::set<string> getSetStrEnforced_(const Option option, std::map<const Option, std::any> options_){
+      // Because the default is a set of strings
+      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
+      return stored_values;
+    }
+
+    std::set<int> getSetIntEnforced_(const Option option, std::map<const Option, std::any> options_){
+      set<int> values;
+      // Because the default is a set of strings
+      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
+      for ( std::string val : stored_values){
+        if( to_upper(val) == "TRUE" ) {
+          values.insert(1);
+        } else if( to_upper(val) == "FALSE") {
+          values.insert(0);
+        }
+      } 
+      return values;
+    }
+
+    std::set<string> getSetStrAllowedValues_(const Option option, std::map<const Option, std::any> options_){
+      // Because the default is a set of strings
+      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
+      return stored_values;
+    }
+
+    std::vector<string> getVectorStrAllowedValues_(const Option option, std::map<const Option, std::any> options_){
+      vector<string> values;
+      // Because the default is a set of strings
+      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
+      for ( string val : stored_values ) {
+        values.push_back(val);
+      }
+      return values;
+    }
+  }
+
+  PropertyStringChoice::PropertyStringChoice(void) {
+    set<string> set_var1{"false"};
+    setPropOption_(Option::ENFORCED, set_var1);
+
+    //  setDefaultOptionType_(Option::ENFORCED, type_index(typeid(set<string>)));
+    default_option_type_[Option::ENFORCED] = type_index(typeid(set<string>));
+
+    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<string>)));
+    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<bool>)));
+    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<int>)));
+
+    set_bool_convert_[Option::ENFORCED] = &catnip::getSetBoolEnforced_;
+    set_str_convert_[Option::ENFORCED] = &catnip::getSetStrEnforced_;
+    set_int_convert_[Option::ENFORCED] = &catnip::getSetIntEnforced_;
+
+    string str = "NOT_DEFINED";
+    set<string> set_var2{str};
+    setPropOption_(Option::ALLOWED_VALUES, set_var2);
 
-/*void PropertyStringChoice::setPropOption( option,
-                                         set<string> set_vars) {
+    default_option_type_[Option::ALLOWED_VALUES] = type_index(typeid(set<string>));
 
-  if (option.compare("STRING_CHOICES") == 0) {
+    allowed_option_types_[Option::ALLOWED_VALUES].push_back(type_index(typeid(set<string>)));
+    allowed_option_types_[Option::ALLOWED_VALUES].push_back(type_index(typeid(vector<string>)));
+
+    set_str_convert_[Option::ALLOWED_VALUES] = &catnip::getSetStrAllowedValues_;
+    vector_str_convert_[Option::ALLOWED_VALUES] = &catnip::getVectorStrAllowedValues_;
+
+  }
+
+  /*void PropertyStringChoice::setPropOption( option,
+    set<string> set_vars) {
+
+    if (option.compare("STRING_CHOICES") == 0) {
     setPropOption_(option, set_vars);
     return;
-  } else if (option.compare("STRING_CHOICE_ENFORCED") == 0) {
+    } else if (option.compare("STRING_CHOICE_ENFORCED") == 0) {
     if (set_vars.size() > 1) {
-      string err = "";
-      for (auto var : set_vars) {
-        err.append(var);
-        err.append(" ");
-      }
-      trim(err);
-      throw invalid_argument(
-          "Option STRING_CHOICE_ENFORCED only accepts one "
-          "value either true or false you have passed the following values " +
-          err);
+    string err = "";
+    for (auto var : set_vars) {
+    err.append(var);
+    err.append(" ");
+    }
+    trim(err);
+    throw invalid_argument(
+    "Option STRING_CHOICE_ENFORCED only accepts one "
+    "value either true or false you have passed the following values " +
+    err);
     }
 
     string var = *(set_vars.begin());
     if (var.compare("false") == 0 || var.compare("true") == 0) {
-      setPropOption_(option, set_vars);
-      return;
+    setPropOption_(option, set_vars);
+    return;
     } else {
-      throw invalid_argument("The option " + option +
-                             " can only be set to values"
-                             " of true or false you have set it to " +
-                             var);
+    throw invalid_argument("The option " + option +
+    " can only be set to values"
+    " of true or false you have set it to " +
+    var);
     }
-  }
-  string vars = "";
-  for (auto var : set_vars) {
+    }
+    string vars = "";
+    for (auto var : set_vars) {
     vars.append(var);
     vars.append(" ");
+    }
+    trim(vars);
+    throw invalid_argument("Unrecognized option value combo " + option + " " +
+    vars);
+    }*/
+
+  bool PropertyStringChoice::propValid(const any& choice) {
+
+    std::string string_choice = any_cast<std::string>(choice);
+    set<string> opt_val = getPropOption<set<string>>(Option::ENFORCED);
+    string val = *(opt_val.begin());
+    if (val.compare("true") == 0) {
+      set<string> str_choices = getPropOption<set<string>>(Option::ALLOWED_VALUES);
+      if (str_choices.count(string_choice) > 0) return true;
+      throw invalid_argument("The value " + string_choice +
+          " is not a valid option");
+    }
+    return true;
   }
-  trim(vars);
-  throw invalid_argument("Unrecognized option value combo " + option + " " +
-                         vars);
-}*/
-
-bool PropertyStringChoice::propValid(const any& choice) {
-
-  std::string string_choice = any_cast<std::string>(choice);
-  set<string> opt_val = getPropOption<set<string>>(Option::ENFORCED);
-  string val = *(opt_val.begin());
-  if (val.compare("true") == 0) {
-    set<string> str_choices = getPropOption<set<string>>(Option::ALLOWED_VALUES);
-    if (str_choices.count(string_choice) > 0) return true;
-    throw invalid_argument("The value " + string_choice +
-                           " is not a valid option");
-  }
-  return true;
 }
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp b/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
index 59cdaab..cc1799a 100644
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
+++ b/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
@@ -11,15 +11,17 @@ class PropertyStringChoice
     : public PropertyObject {
  private:
 
+   std::set<bool> getSetBoolEnforced_(Option option, std::map<Option, std::any> options_);
+  ;
  public:
-  PropertyStringChoice(void);
+   PropertyStringChoice(void);
 
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::STRING_CHOICE;
-  }
+   virtual PropertyType getPropertyType(void) const noexcept final {
+     return PropertyType::STRING_CHOICE;
+   }
 
-  virtual bool propValid(const std::any& string_choice) final;
-};
+   virtual bool propValid(const std::any& string_choice) final;
+    };
 
 }  // namespace catnip
 #endif  // _CATNIP_PROPERTY_STRING_CHOICE_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.cpp b/src/libcatnip/io/arguments/properties/propertyswitch.cpp
index 18a4029..06251c4 100644
--- a/src/libcatnip/io/arguments/properties/propertyswitch.cpp
+++ b/src/libcatnip/io/arguments/properties/propertyswitch.cpp
@@ -6,7 +6,7 @@
 using namespace catnip;
 using namespace std;
 
-PropertySwitch::PropertySwitch() { setPropOption_(Option::VALUE, bool(false)); }
+PropertySwitch::PropertySwitch() { setPropOption_(Option::DEFAULT, bool(false)); }
 
 void PropertySwitch::switchValid(int val) const {
   if (val < 0 || val > 1) {
@@ -45,4 +45,5 @@ bool PropertySwitch::propValid(const std::any & value) {
     throw invalid_argument("Unrecognized type passed to switch, only recognizes"
         " int, string and bool types");
   }
+  return true;
 }
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.hpp b/src/libcatnip/io/arguments/properties/propertyswitch.hpp
index de4688a..0082b68 100644
--- a/src/libcatnip/io/arguments/properties/propertyswitch.hpp
+++ b/src/libcatnip/io/arguments/properties/propertyswitch.hpp
@@ -8,15 +8,13 @@ namespace catnip {
 
 class PropertySwitch : public PropertyObject {
  private:
-  std::string getName_(void) const { return "PROPERTY_SWITCH"; }
-  std::vector<std::string> getOpts_(void) const;
   void propOptionValueSettingValid_();
   void switchValid(int val) const;
   void switchValid(std::string val) const;
 
  public:
   PropertySwitch(void);
-
+  
   virtual PropertyType getPropertyType(void) const noexcept final {
     return PropertyType::SWITCH; 
   }
diff --git a/src/libcatnip/io/io.cpp b/src/libcatnip/io/io.cpp
index 95dc2bd..771a85e 100644
--- a/src/libcatnip/io/io.cpp
+++ b/src/libcatnip/io/io.cpp
@@ -213,43 +213,43 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   string ext_log = ".log";
 
   {
-    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", ext_log);
-    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", exts);
-    ArgPars->setFlagArgOpt("--log", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
-
-    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts);
-    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", ext_log);
-    ArgPars->setFlagArgOpt("--pun", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
+    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
   }
 
   // Setting up rules guiding pun files
   {
-    ArgPars->setFlagArgOpt("--pun_P", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts);
-    ArgPars->setFlagArgOpt("--pun_P", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", ext_log);
-    ArgPars->setFlagArgOpt("--pun_P", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
-
-    ArgPars->setFlagArgOpt("--pun_1", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts);
-    ArgPars->setFlagArgOpt("--pun_1", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", ext_log);
-    ArgPars->setFlagArgOpt("--pun_1", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
-
-    ArgPars->setFlagArgOpt("--pun_2", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts);
-    ArgPars->setFlagArgOpt("--pun_2", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", ext_log);
-    ArgPars->setFlagArgOpt("--pun_2", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
+    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
 
   }
 
@@ -259,51 +259,51 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Setting rules guiding log files
   {
-    ArgPars->setFlagArgOpt("--log_P", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts_log);
-    ArgPars->setFlagArgOpt("--log_P", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", exts_other);
-    ArgPars->setFlagArgOpt("--log_P", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
-
-    ArgPars->setFlagArgOpt("--log_1", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts_log);
-    ArgPars->setFlagArgOpt("--log_1", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", exts_other);
-    ArgPars->setFlagArgOpt("--log_1", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
-
-    ArgPars->setFlagArgOpt("--log_2", "ARGUMENT_FILE", "PROPERTY_FILE_EXT",
-                           "ALLOWED_FILE_EXT", exts_log);
-    ArgPars->setFlagArgOpt("--log_2", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-                           "ALLOWED_SISTER_FILE_EXT", exts_other);
-    ArgPars->setFlagArgOpt("--log_2", "ARGUMENT_FILE", "PROPERTY_FILE_EXIST",
-                           "FILE_MUST_EXIST", 0);
+    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::FILE_EXT,
+                           Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::SISTER_FILE,
+                           Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
+                           Option::MUST_EXIST, 0);
   }
 
   set<string> spin_opts{"Alpha", "Beta"};
 
   // Setting rules guiding spin
   {
-    ArgPars->setFlagArgOpt("--spin_P", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICE_ENFORCED",
+    ArgPars->setFlagArgOpt("--spin_P", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_P", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICES",
+    ArgPars->setFlagArgOpt("--spin_P", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
                            spin_opts);
 
-    ArgPars->setFlagArgOpt("--spin_1", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICE_ENFORCED",
+    ArgPars->setFlagArgOpt("--spin_1", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_1", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICES",
+    ArgPars->setFlagArgOpt("--spin_1", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
                            spin_opts);
 
-    ArgPars->setFlagArgOpt("--spin_2", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICE_ENFORCED",
+    ArgPars->setFlagArgOpt("--spin_2", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_2", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICES",
+    ArgPars->setFlagArgOpt("--spin_2", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
                            spin_opts);
 
     ArgPars->setFlagDefaultValue("--spin_P", "Alpha");
@@ -314,18 +314,18 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   // Setting rules guidling orbital type
   set<string> orb_opts{"HOMO", "LUMO"};
   {
-    ArgPars->setFlagArgOpt("--orbital_type_1", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICE_ENFORCED",
+    ArgPars->setFlagArgOpt("--orbital_type_1", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--orbital_type_1", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICES",
+    ArgPars->setFlagArgOpt("--orbital_type_1", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
                            orb_opts);
 
-    ArgPars->setFlagArgOpt("--orbital_type_2", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICE_ENFORCED",
+    ArgPars->setFlagArgOpt("--orbital_type_2", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--orbital_type_2", "ARGUMENT_STRING",
-                           "PROPERTY_STRING_CHOICE", "STRING_CHOICES",
+    ArgPars->setFlagArgOpt("--orbital_type_2", ArgumentType::STRING,
+                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
                            orb_opts);
 
     ArgPars->setFlagDefaultValue("--orbital_type_1", "HOMO");
@@ -334,8 +334,8 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Set argument allowed values for counterpoise
   {
-    ArgPars->setFlagArgOpt("--counter_poise", "ARGUMENT_SWITCH",
-                           "PROPERTY_SWITCH", "DEFAULT", "OFF");
+    ArgPars->setFlagArgOpt("--counter_poise", ArgumentType::SWITCH,
+                           PropertyType::SWITCH, Option::VALUE, "OFF");
 
     // By default the flag counter poise is turned off
     ArgPars->setFlagDefaultValue("--counter_poise", "OFF");
@@ -343,24 +343,24 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Set argument for allowing printing of all transfer integrals
   {
-    ArgPars->setFlagArgOpt("--all", "ARGUMENT_SWITCH",
-        "PROPERTY_SWITCH", "DEFAULT", "OFF");
+    ArgPars->setFlagArgOpt("--all", ArgumentType::SWITCH,
+        PropertyType::SWITCH, Option::VALUE, "OFF");
 
     // By default the flag counter poise is turned off
     ArgPars->setFlagDefaultValue("--all", "OFF");
   }
 
   {
-    ArgPars->setFlagArgOpt("--citation", "ARGUMENT_SWITCH", "PROPERTY_SWITCH",
-                           "DEFAULT", "OFF");
+    ArgPars->setFlagArgOpt("--citation", ArgumentType::SWITCH, PropertyType::SWITCH,
+                           Option::VALUE, "OFF");
 
     // By default the flag citation is turned off
     ArgPars->setFlagDefaultValue("--citation", "OFF");
   }
 
   {
-    ArgPars->setFlagArgOpt("--version", "ARGUMENT_SWITCH", "PROPERTY_SWITCH",
-                           "DEFAULT", "OFF");
+    ArgPars->setFlagArgOpt("--version", ArgumentType::SWITCH, PropertyType::SWITCH,
+                           Option::VALUE, "OFF");
 
     // By default the flag citation is turned off
     ArgPars->setFlagDefaultValue("--version", "OFF");
@@ -369,8 +369,8 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   // Set rules guiding orbital numbers
   // Use default settings for min and max numbers
   {
-    ArgPars->addFlagArg("--orbital_num_1", "ARGUMENT_INT");
-    ArgPars->addFlagArg("--orbital_num_2", "ARGUMENT_INT");
+    ArgPars->addFlagArg("--orbital_num_1", ArgumentType::NUMERICAL);
+    ArgPars->addFlagArg("--orbital_num_2", ArgumentType::NUMERICAL);
 
     int orb_num = 0;
     ArgPars->setFlagDefaultValue("--orbital_num_1", orb_num);
@@ -393,20 +393,20 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
   for (size_t i = 0; i < flags.size(); ++i) {
     auto flag = flags.at(i);
     auto flag_sister = flags_sister.at(i);
-    string argu = "ARGUMENT_FILE";
-    string prop = "PROPERTY_FILE_EXIST";
-    string opt = "FILE_DOES_EXIST";
+    ArgumentType argu = ArgumentType::FILES;
+    PropertyType prop = PropertyType::FILE_EXISTS;
+    Option opt = Option::DOES_EXIST;
 
     string fileName;
-    auto exists = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
-    if (exists.compare("1") == 0) {
+    std::vector<bool> exists = ArgParse->get<bool>(flag, argu, prop, opt);
+    if ( exists ) {
       flag_arg[flag] = ArgParse->getStrs(flag).at(0);
     }
-    prop = "PROPERTY_SISTER_FILE";
-    opt = "SISTER_FILE_EXISTS";
-    auto line = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
-    opt = "SISTER_FILE_PATH_NAME";
-    auto line2 = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
+    prop = PropertyType::SISTER_FILE;
+    opt = Option::VALUE;
+    std::string line = ArgParse->get<std::string>(flag, argu, prop, opt);
+    opt = Option::FILE_PATH_NAME;
+    std::string line2 = ArgParse->get<std::string>(flag, argu, prop, opt);
     auto sisters_exist = splitSt(line);
     vector<string> sister_file_paths = splitSt(line2);
     int countFiles = 0;
diff --git a/src/libcatnip/string_support.cpp b/src/libcatnip/string_support.cpp
index 1c082e2..2414586 100644
--- a/src/libcatnip/string_support.cpp
+++ b/src/libcatnip/string_support.cpp
@@ -91,6 +91,12 @@ string firstN(string input, int n) { return input.substr(0, n); }
 
 string cut_beg(string input, int n) { return input.substr(n, input.size()); }
 
+// Converts to uppercase
+std::string to_upper(std::string input) {
+  std::for_each(input.begin(),input.end(), ::toupper);
+  return input;
+}
+
 // trim from both ends (in place)
 void trim(string &s) {
   ltrim_(s);
diff --git a/src/libcatnip/string_support.hpp b/src/libcatnip/string_support.hpp
index 6e7ba24..45af310 100644
--- a/src/libcatnip/string_support.hpp
+++ b/src/libcatnip/string_support.hpp
@@ -29,6 +29,9 @@ std::string firstN(std::string input, int n);
 
 std::string cut_beg(std::string input, int n);
 
+// Converts a string to an upper case version
+std::string to_upper(std::string input);
+
 // trim from both ends (in place)
 void trim(std::string &s);
 
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 4f103ee..59fb8fb 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -59,20 +59,20 @@ if(ENABLE_INTEGRATION_TESTING)
 
   endforeach(PROG)
 
-  add_executable(test_io test_io.cpp)
-  if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-    set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
-  endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-  target_link_libraries(test_io libcatnip)
-  add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
-
-  add_custom_command(TARGET test_io
-    POST_BUILD
-    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:test_io> ${CMAKE_CURRENT_SOURCE_DIR})
-
-  find_program (BASH_PROGRAM bash)
+#  add_executable(test_io test_io.cpp)
+#  if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+#    set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
+#  endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+#  target_link_libraries(test_io libcatnip)
+#  add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
+#
+#  add_custom_command(TARGET test_io
+#    POST_BUILD
+#    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:test_io> ${CMAKE_CURRENT_SOURCE_DIR})
+#
+#  find_program (BASH_PROGRAM bash)
   if(BASH_PROGRAM)
-    add_test(regression_test_io_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_io.sh ${CMAKE_CURRENT_SOURCE_DIR})
+    #    add_test(regression_test_io_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_io.sh ${CMAKE_CURRENT_SOURCE_DIR})
 
     add_test(integration_test_calc_J_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_calc_J.sh ${CMAKE_SOURCE_DIR})
 
diff --git a/src/tests/test_io.cpp b/src/tests/test_io.cpp
index b788dbd..159842c 100644
--- a/src/tests/test_io.cpp
+++ b/src/tests/test_io.cpp
@@ -21,13 +21,15 @@ int main(int argc, const char* argv[]) {
 
   for (auto flag : flags) {
     cout << endl;
-    string argu = "ARGUMENT_FILE";
-    string prop = "PROPERTY_FILE_EXT";
-    string opt = "ALLOWED_FILE_EXT";
-    auto val = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
-    cout << flag << " " << argu << " " << prop << " " << opt << " " << val
-         << endl;
-
+    ArgumentType argu = ArgumentType::FILES;
+    PropertyType prop = PropertyType::FILE_EXT;
+    Option opt = Option::ALLOWED_VALUES;
+    auto values = ArgParse->get<string>(flag, argu, prop, opt);
+    for ( std::string & val : values ){
+      cout << val << " ";
+    }
+    cout << endl;
+/*
     prop = "PROPERTY_SISTER_FILE";
     opt = "ALLOWED_SISTER_FILE_EXT";
     auto val1 = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
@@ -59,7 +61,7 @@ int main(int argc, const char* argv[]) {
     opt = "FILE_DOES_EXIST";
     auto val7 = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
     cout << flag << " " << argu << " " << prop << " " << opt << " " << val7
-         << endl;
+         << endl;*/
   }
 
   auto Par = prepareParameters(ArgParse);
diff --git a/src/tests/test_propertystringchoice.cpp b/src/tests/test_propertystringchoice.cpp
index 560991f..4c2da2c 100644
--- a/src/tests/test_propertystringchoice.cpp
+++ b/src/tests/test_propertystringchoice.cpp
@@ -13,88 +13,76 @@ using namespace catnip;
 using namespace std;
 
 TEST_CASE("Property String Choice","[unit]") {
-  cerr << "Testing: PropertyStringChoice" << endl;
-  cerr << "Testing: constructor" << endl;
   { PropertyStringChoice propStrChoice; }
+}
 
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyStringChoice propStrChoice;
-    string name = propStrChoice.getPropertyName();
-    assert(name.compare("PROPERTY_STRING_CHOICE") == 0);
-  }
+TEST_CASE("getPropertyType","[unit]") { 
+  PropertyStringChoice propStrChoice;
+  PropertyType type = propStrChoice.getPropertyType();
+  REQUIRE(type == PropertyType::STRING_CHOICE);
+}
 
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
+TEST_CASE("getPropertyOptions","[unit]") { 
 
-    PropertyStringChoice propStrChoice;
-    auto options = propStrChoice.getPropertyOptions();
+  PropertyStringChoice propStrChoice;
+  auto options = propStrChoice.getPropertyOptions();
 
-    bool choice_enforced = false;
-    bool str_choices = false;
+  bool choice_enforced = false;
+  bool str_choices = false;
 
-    for (auto opt : options) {
-      if (opt.compare("STRING_CHOICE_ENFORCED") == 0) {
-        choice_enforced = true;
-      }
-      if (opt.compare("STRING_CHOICES") == 0) {
-        str_choices = true;
-      }
+  for (auto opt : options) {
+    if (opt == Option::ENFORCED) {
+      choice_enforced = true;
+    }
+    if (opt == Option::ALLOWED_VALUES) {
+      str_choices = true;
     }
-    assert(choice_enforced);
-    assert(str_choices);
   }
+  REQUIRE(choice_enforced);
+  REQUIRE(str_choices);
+}
 
-  cerr << "Testing: getPropOption" << endl;
-  {
-    PropertyStringChoice propStrChoice;
+TEST_CASE("getPropOption","[unit]"){ 
+  PropertyStringChoice propStrChoice;
+
+  set<bool> choice_enforced =
+    propStrChoice.getPropOption<set<bool>>(Option::ENFORCED);
+  set<string> choices = propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
+/*
+  bool enforced = *(choice_enforced.begin());
+  string choice = *(choices.begin());
+  REQUIRE(enforced == false);
+  REQUIRE(choice == "NOT_DEFINED");*/
+}
 
-    set<string> choice_enforced =
-        propStrChoice.getPropOption("STRING_CHOICE_ENFORCED");
-    set<string> choices = propStrChoice.getPropOption("STRING_CHOICES");
+TEST_CASE("setPropOption", "[unit]"){
+  PropertyStringChoice propStrChoice;
 
-    string enforced = *(choice_enforced.begin());
-    string choice = *(choices.begin());
-    assert(enforced.compare("false") == 0);
-    assert(choice.compare("NOT_DEFINED") == 0);
-  }
+  propStrChoice.setPropOption(Option::ENFORCED, "true");
+  set<string> choices{"true", "false"};
+  propStrChoice.setPropOption(Option::ALLOWED_VALUES, choices);
 
-  cerr << "Testing: getPropOption" << endl;
-  {
-    PropertyStringChoice propStrChoice;
-
-    propStrChoice.setPropOption("STRING_CHOICE_ENFORCED", "true");
-    set<string> choices{"true", "false"};
-    propStrChoice.setPropOption("STRING_CHOICES", choices);
-
-    string choice = "true";
-    propStrChoice.propValid(choice);
-    choice = "false";
-    propStrChoice.propValid(choice);
-
-    choice = "blah";
-    bool throwerror = false;
-    try {
-      propStrChoice.propValid(choice);
-    } catch (...) {
-      throwerror = true;
-    }
-    assert(throwerror);
+  string choice = "true";
+  propStrChoice.propValid(choice);
+  choice = "false";
+  propStrChoice.propValid(choice);
 
-    set<string> allowed_choices = propStrChoice.getPropOption("STRING_CHOICES");
-    set<string> choice_on =
-        propStrChoice.getPropOption("STRING_CHOICE_ENFORCED");
+  choice = "blah";
+  REQUIRE_THROWS(propStrChoice.propValid(choice));
 
-    bool false_str = false;
-    bool true_str = false;
-    for (auto item : allowed_choices) {
-      if (item.compare("false") == 0) false_str = true;
-      if (item.compare("true") == 0) true_str = true;
-    }
-    assert(false_str);
-    assert(true_str);
+  set<string> allowed_choices = propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
+  set<string> choice_on =
+    propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
 
-    string on = *(choice_on.begin());
-    assert(on.compare("true") == 0);
+  bool false_str = false;
+  bool true_str = false;
+  for (auto item : allowed_choices) {
+    if (item.compare("false") == 0) false_str = true;
+    if (item.compare("true") == 0) true_str = true;
   }
+  REQUIRE(false_str);
+  REQUIRE(true_str);
+
+  string on = *(choice_on.begin());
+  REQUIRE(on.compare("true") == 0);
 }
diff --git a/src/tests/test_propertyswitch.cpp b/src/tests/test_propertyswitch.cpp
index 18f40b0..5886e72 100644
--- a/src/tests/test_propertyswitch.cpp
+++ b/src/tests/test_propertyswitch.cpp
@@ -20,8 +20,8 @@ TEST_CASE("Property Switch","[unit]") {
   cerr << "Testing: getPropertyName" << endl;
   {
     PropertySwitch propSwitch;
-    string name = propSwitch.getPropertyName();
-    assert(name.compare("PROPERTY_SWITCH") == 0);
+    PropertyType type = propSwitch.getPropertyType();
+    REQUIRE(type == PropertyType::SWITCH);
   }
 
   cerr << "Testing: getPropertyOptions" << endl;
@@ -29,8 +29,8 @@ TEST_CASE("Property Switch","[unit]") {
 
     PropertySwitch propSwitch;
     auto options = propSwitch.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt.compare("DEFAULT") == 0);
+    Option opt = options.at(0);
+    REQUIRE(opt == Option::DEFAULT);
   }
 
   cerr << "Testing: propValid" << endl;
@@ -75,8 +75,8 @@ TEST_CASE("Property Switch","[unit]") {
   cerr << "Testing: setPropOption" << endl;
   {
     PropertySwitch propSwitch;
-    propSwitch.setPropOption("DEFAULT", "ON");
-    propSwitch.setPropOption("DEFAULT", "OFF");
+    propSwitch.setPropOption(Option::DEFAULT, "ON");
+    propSwitch.setPropOption(Option::DEFAULT, "OFF");
     //    propSwitch.propValid(0);
     //    bool excep = false;
     //    try {

From 56ad1013173e9b93e6ca5412e8a27454c9e0597a Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Fri, 11 Dec 2020 05:47:13 -0700
Subject: [PATCH 67/68] Removed argument parser logic

---
 src/libcatnip/io/argumentparser.cpp           | 777 ------------------
 src/libcatnip/io/argumentparser.hpp           | 200 -----
 src/libcatnip/io/arguments/Makefile           |  64 --
 src/libcatnip/io/arguments/README.md          |  10 -
 src/libcatnip/io/arguments/argumentfile.cpp   |  16 -
 src/libcatnip/io/arguments/argumentfile.hpp   |  27 -
 .../io/arguments/argumentnumerical.cpp        |  13 -
 .../io/arguments/argumentnumerical.hpp        |  28 -
 src/libcatnip/io/arguments/argumentobject.hpp | 182 ----
 src/libcatnip/io/arguments/argumentstring.cpp |  13 -
 src/libcatnip/io/arguments/argumentstring.hpp |  26 -
 src/libcatnip/io/arguments/argumentswitch.cpp |  22 -
 src/libcatnip/io/arguments/argumentswitch.hpp |  29 -
 .../properties/propertyfileexist.cpp          |  47 --
 .../properties/propertyfileexist.hpp          |  29 -
 .../arguments/properties/propertyfileext.cpp  |  69 --
 .../arguments/properties/propertyfileext.hpp  |  37 -
 .../arguments/properties/propertynumeric.cpp  |  48 --
 .../arguments/properties/propertynumeric.hpp  |  32 -
 .../arguments/properties/propertyobject.hpp   | 148 ----
 .../properties/propertysisterfile.cpp         |  88 --
 .../properties/propertysisterfile.hpp         |  30 -
 .../arguments/properties/propertystring.cpp   |  29 -
 .../arguments/properties/propertystring.hpp   |  29 -
 .../properties/propertystringchoice.cpp       | 147 ----
 .../properties/propertystringchoice.hpp       |  27 -
 .../arguments/properties/propertyswitch.cpp   |  49 --
 .../arguments/properties/propertyswitch.hpp   |  27 -
 28 files changed, 2243 deletions(-)
 delete mode 100644 src/libcatnip/io/argumentparser.cpp
 delete mode 100644 src/libcatnip/io/argumentparser.hpp
 delete mode 100644 src/libcatnip/io/arguments/Makefile
 delete mode 100644 src/libcatnip/io/arguments/README.md
 delete mode 100644 src/libcatnip/io/arguments/argumentfile.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentfile.hpp
 delete mode 100644 src/libcatnip/io/arguments/argumentnumerical.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentnumerical.hpp
 delete mode 100644 src/libcatnip/io/arguments/argumentobject.hpp
 delete mode 100644 src/libcatnip/io/arguments/argumentstring.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentstring.hpp
 delete mode 100644 src/libcatnip/io/arguments/argumentswitch.cpp
 delete mode 100644 src/libcatnip/io/arguments/argumentswitch.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyfileexist.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyfileexist.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyfileext.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyfileext.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertynumeric.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertynumeric.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyobject.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertysisterfile.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertysisterfile.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertystring.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertystring.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertystringchoice.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertystringchoice.hpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyswitch.cpp
 delete mode 100644 src/libcatnip/io/arguments/properties/propertyswitch.hpp

diff --git a/src/libcatnip/io/argumentparser.cpp b/src/libcatnip/io/argumentparser.cpp
deleted file mode 100644
index 5d383a0..0000000
--- a/src/libcatnip/io/argumentparser.cpp
+++ /dev/null
@@ -1,777 +0,0 @@
-#include <exception>
-#include <iostream>
-#include <memory>
-#include <stdexcept>
-#include <string>
-#include <sys/stat.h>
-#include <typeindex>
-#include <vector>
-
-#include "argumentparser.hpp"
-
-#include "catnip_config.hpp"
-#include "string_support.hpp"
-
-using namespace std;
-
-namespace catnip {
-
-  std::unique_ptr<ArgumentObject> createArgument(ArgumentType type) {
-    if (type == ArgumentType::NUMERICAL) {
-      return std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
-    } else if (type == ArgumentType::STRING) {
-      return std::unique_ptr<ArgumentObject>(new ArgumentString);
-    } else if (type == ArgumentType::SWITCH) {
-      return std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
-    } else if (type == ArgumentType::FILES) {
-      return std::unique_ptr<ArgumentObject>(new ArgumentFile);
-    }
-    return std::unique_ptr<ArgumentObject>();
-  }
-
-  void ArgumentParser::addValue_(std::string flag, std::string value) {
-    std::type_index value_type = arg_[flag].at(0)->getValueType(); 
-    if (value_type == typeid(double) ){
-      values_[flag][value_type].emplace_back(stod(value));
-    } else if(value_type == typeid(int) ) {
-      values_[flag][value_type].emplace_back(stoi(value));
-    } else if(value_type == typeid(std::string) ) {
-      values_[flag][value_type].emplace_back(value);
-    } else if(value_type == typeid(bool) ){
-      if (to_upper(value) == "TRUE" || value == "1" || to_upper(value) == "ON") {
-        values_[flag][value_type].emplace_back(true);
-      } else if (to_upper(value) == "FALSE" || value == "1" || to_upper(value) == "OFF") {
-        values_[flag][value_type].emplace_back(false);
-      }
-    } else {
-      std::runtime_error("Unknown type for argument value");
-    }
-  }
-
-  ArgumentParser::ArgumentParser(set<vector<string>> flags) {
-
-    vector<string> flag_help;
-    flag_help.push_back("--help");
-    flag_help.push_back("-h");
-    flag_help.push_back("Display help message");
-    flags.insert(flag_help);
-
-    maxShortFlagSize = 0;
-    maxFullFlagSize = 0;
-    maxDescriptionSize = 0;
-
-    for (auto flag : flags) {
-
-      if (flag.size() > 3) {
-        throw invalid_argument(
-            "Flags may only be passed with a max of three "
-            "values: full flag name, abbreviated name, and flag description");
-      }
-
-      string full_flag = "NO_FLAG_SPECIFIED";
-      string short_flag = "NO_SHORT_FLAG_SPECIFIED";
-      string desc = "NO_DESCRIPTION_GIVEN";
-
-      bool description = false;
-      bool abbreviation = false;
-      bool flag_name = false;
-      for (auto item : flag) {
-        trim(item);
-        string doubledash = firstN(item, 2);
-        string singledash = firstN(item, 1);
-        if (doubledash.compare("--") == 0) {
-          if (flag_name) {
-            string err = "A flag name has already been suppied:\n";
-            err.append(full_flag);
-            err.append("\nNow you are supplying a second one:\n");
-            err.append(item);
-            throw invalid_argument(err);
-          }
-          full_flag = item;
-          defaults_set_[item] = false;
-          flag_name = true;
-          if (full_flag.size() > maxFullFlagSize) {
-            maxFullFlagSize = full_flag.size();
-          }
-        } else if (singledash.compare("-") == 0) {
-          if (abbreviation) {
-            string err = "A flag name has already been suppied:\n";
-            err.append(short_flag);
-            err.append("\nNow you are supplying a second one:\n");
-            err.append(item);
-            throw invalid_argument(err);
-          }
-          short_flag = item;
-          abbreviation = true;
-          if (short_flag.size() > maxShortFlagSize) {
-            maxShortFlagSize = short_flag.size();
-          }
-        } else {
-          if (description) {
-            string err = "A description has already been suppied:\n";
-            err.append(desc);
-            err.append("\nNow you are supplying a second one:\n");
-            err.append(item);
-            throw invalid_argument(err);
-          }
-          desc = item;
-          description = true;
-          if (desc.size() > maxDescriptionSize) {
-            maxDescriptionSize = desc.size();
-          }
-        }
-      }
-      if (!flag_name) {
-        throw invalid_argument("You have failed to provide the full flag name");
-      }
-      flags_[full_flag] = make_pair(short_flag, desc);
-    }
-  }
-
-  void ArgumentParser::showUsage(void) {
-    cout << endl;
-    cout << endl;
-    cout << "Options:" << endl;
-    cout << endl;
-
-    for (auto item : flags_) {
-      string full_flag = item.first;
-      size_t diff = maxFullFlagSize - full_flag.size();
-      cout << full_flag;
-      for (size_t i = 0; i <= diff; ++i) {
-        cout << " ";
-      }
-      string short_flag = item.second.first;
-      diff = maxShortFlagSize - short_flag.size();
-      cout << short_flag;
-      for (size_t i = 0; i <= diff; ++i) {
-        cout << " ";
-      }
-
-      size_t space = maxFullFlagSize + maxShortFlagSize + 2;
-      size_t allowed = maxLineLength - space;
-      string space_block = "";
-      for (size_t sp = 0; sp < space; sp++) {
-        space_block.append(" ");
-      }
-
-      string desc = item.second.second;
-      vector<string> vec_string = splitSt(desc);
-      size_t words_size = 0;
-      for (auto word : vec_string) {
-        words_size += word.size() + 1;
-        if (words_size < allowed) {
-          cout << word << " ";
-        } else {
-          cout << endl;
-          cout << space_block;
-          cout << word << " ";
-          words_size = 0;
-        }
-      }
-      cout << endl;
-      cout << endl;
-    }
-    cout << endl;
-  }
-
-  void ArgumentParser::addFlagArg(string flag, ArgumentType argname) {
-
-    arg_[flag].push_back(createArgument(argname));
-  /*  if (argname == ArgumentType::NUMERICAL) {
-        auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
-        int_arg_[flag].push_back(std::move(ArInt));
-    } else if (argname == ArgumentType::SWITCH) {
-      if (switch_arg_.count(flag) == 0) {
-        auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
-        switch_arg_[flag].push_back(std::move(ArSwitch));
-      } else {
-        throw invalid_argument(
-            "switch argument has already been added for "
-            "flag " +
-            flag);
-      }
-    } else if (argname == ArgumentType::STRING) {
-        auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
-        str_arg_[flag].push_back(std::move(ArString));
-    } else if (argname == ArgumentType::FILES) {
-        auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
-        file_arg_[flag].push_back(std::move(ArFile));
-    } else {
-      throw invalid_argument(
-          "Unrecognized argument being added for flag"
-          " argname is " +
-          argname + " flag name is " + flag);
-    }*/
-  }
-  /*
-  // Will apply values to all properties in the argument vector
-  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                     string option, int val) {
-
-    if (argname.compare("ARGUMENT_INT") == 0) {
-      if (int_arg_.count(flag) == 0) {
-        auto ArInt = std::unique_ptr<ArgumentInt>(new ArgumentInt);
-        ArInt->setArgPropertyOpt(property, option, val);
-        int_arg_[flag].push_back(std::move(ArInt));
-      } else {
-        for ( std::unique_ptr<ArgumentInt> & ptr : int_arg_[flag]){
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-    } else if (argname.compare("ARGUMENT_STRING") == 0) {
-      if (str_arg_.count(flag) == 0) {
-        auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
-        ArString->setArgPropertyOpt(property, option, val);
-        str_arg_[flag].push_back(std::move(ArString));
-      } else {
-        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag] ){
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-    } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
-      if (switch_arg_.count(flag) == 0) {
-        auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
-        if (val == 0) {
-          ArSwitch->setArgPropertyOpt(property, option, "OFF");
-        } else if (val == 1) {
-          ArSwitch->setArgPropertyOpt(property, option, "ON");
-        } else {
-          throw invalid_argument("Unrecognized option for switch " +
-                                 to_string(val));
-        }
-        switch_arg_[flag].push_back(std::move(ArSwitch));
-      } else { // For a switch there will only be one value in the vector
-        if (val == 0) {
-          switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
-        } else if (val == 1) {
-          switch_arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
-        } else {
-          throw invalid_argument("Unrecognized option for switch " +
-                                 to_string(val));
-        }
-      }
-    } else if (argname.compare("ARGUMENT_FILE") == 0) {
-      if (file_arg_.count(flag) == 0) {
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-
-        ArFile->setArgPropertyOpt(property, option, val);
-        file_arg_[flag].push_back(std::move(ArFile));
-      } else {
-        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag] ){
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-    } else {
-      throw invalid_argument("Unrecognized int arg");
-    }
-  }
-
-  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                     string option, double val) {
-
-    if (argname.compare("ARGUMENT_DOUBLE") == 0) {
-      if (double_arg_.count(flag) == 0) {
-        auto ArDouble = std::unique_ptr<ArgumentDouble>(new ArgumentDouble);
-        ArDouble->setArgPropertyOpt(property, option, val);
-        double_arg_[flag].push_back(std::move(ArDouble));
-      } else {
-        for ( std::unique_ptr<ArgumentDouble> & ptr : double_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-    } else if (argname.compare("ARGUMENT_STRING") == 0) {
-      if (str_arg_.count(flag) == 0) {
-        auto ArString = std::unique_ptr<ArgumentString>(new ArgumentString);
-        ArString->setArgPropertyOpt(property, option, val);
-        str_arg_[flag].push_back(std::move(ArString));
-      } else {
-        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-    } else {
-      throw invalid_argument("Unrecognized double arg");
-    }
-  }
-
-  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                     string option, string val) {
-
-    if (argname.compare("ARGUMENT_FILE") == 0) {
-      if (file_arg_.count(flag) == 0) {
-
-        if (property.compare("PROPERTY_FILE_EXT") == 0) {
-          set<string> temp{val};
-          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-          ArFile->setArgPropertyOpt(property, option, temp);
-          file_arg_[flag].push_back(std::move(ArFile));
-        } else if (property.compare("PROPERTY_SISTER_FILE_EXT") == 0) {
-          vector<string> temp{val};
-          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-          ArFile->setArgPropertyOpt(property, option, temp);
-          file_arg_[flag].push_back(std::move(ArFile));
-        } else {
-          auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-          ArFile->setArgPropertyOpt(property, option, val);
-          file_arg_[flag].push_back(std::move(ArFile));
-        }
-      } else {
-        if (property.compare("PROPERTY_FILE_EXT") == 0) {
-          set<string> temp{val};
-          for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-            ptr->setArgPropertyOpt(property, option, temp);
-          }
-        } else {
-          for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-            ptr->setArgPropertyOpt(property, option, val);
-          }
-        }
-      }
-    } else if (argname.compare("ARGUMENT_SWITCH") == 0) {
-      if (switch_arg_.count(flag) == 0) {
-        auto ArSwitch = std::unique_ptr<ArgumentSwitch>(new ArgumentSwitch);
-        if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
-          throw invalid_argument("Unrecognized option for switch " + val);
-        } else {
-          ArSwitch->setArgPropertyOpt(property, option, val);
-        }
-        switch_arg_[flag].push_back(std::move(ArSwitch));
-      } else {
-        if (val.compare("OFF") != 0 && val.compare("ON") != 0) {
-          throw invalid_argument("Unrecognized option for switch" + val);
-        } else {
-          for ( std::unique_ptr<ArgumentSwitch> & ptr : switch_arg_[flag]) {
-            ptr->setArgPropertyOpt(property, option, val);
-          }
-        }
-      }
-
-    } else if (argname.compare("ARGUMENT_STRING") == 0) {
-      if (str_arg_.count(flag) == 0) {
-        set<string> temp{val};
-        auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
-        ArStr->setArgPropertyOpt(property, option, temp);
-        str_arg_[flag].push_back(std::move(ArStr));
-      } else {
-        set<string> temp{val};
-        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, temp);
-        }
-      }
-    } else {
-      throw invalid_argument("Unrecognized string arg " + argname);
-    }
-  }
-
-  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                     string option, set<string> vals) {
-
-    if (argname.compare("ARGUMENT_FILE") == 0) {
-      if (file_arg_.count(flag) == 0) {
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-        ArFile->setArgPropertyOpt(property, option, vals);
-        file_arg_[flag].push_back(std::move(ArFile));
-      } else {
-        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, vals);
-        }
-      }
-    } else if (argname.compare("ARGUMENT_STRING") == 0) {
-      if (str_arg_.count(flag) == 0) {
-        auto ArStr = std::unique_ptr<ArgumentString>(new ArgumentString);
-        ArStr->setArgPropertyOpt(property, option, vals);
-        str_arg_[flag].push_back(std::move(ArStr));
-      } else {
-        for ( std::unique_ptr<ArgumentString> & ptr : str_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, vals);
-        }
-      }
-    } else {
-      throw invalid_argument("Unrecognized set<string> arg");
-    }
-  }
-
-  void ArgumentParser::setFlagArgOpt(string flag, string argname, string property,
-                                     string option, vector<string> vals) {
-
-    if (argname.compare("ARGUMENT_FILE") == 0) {
-      if (file_arg_.count(flag) == 0) {
-        auto ArFile = std::unique_ptr<ArgumentFile>(new ArgumentFile);
-        ArFile->setArgPropertyOpt(property, option, vals);
-        file_arg_[flag].push_back(std::move(ArFile));
-      } else {
-        for ( std::unique_ptr<ArgumentFile> & ptr : file_arg_[flag]) {
-          ptr->setArgPropertyOpt(property, option, vals);
-        }
-      }
-    } else {
-      throw invalid_argument("Unrecognized vector<string> arg");
-    }
-  }
-  */
-  bool ArgumentParser::nextParameterIsAFlag_(size_t index,
-                                             vector<string> arguments) {
-
-    if ((index + 1) < arguments.size()) {
-      for (auto flag : flags_) {
-        if (flag.first.compare(arguments.at(index + 1)) == 0) {
-          return true;
-        } else if (flag.second.first.compare(arguments.at(index + 1)) == 0) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-
-  void ArgumentParser::parseArg_(size_t& index, vector<string> arguments) {
-    string flag = arguments.at(index);
-    // If the abbreviated flag is passed we need to resolve the full flag name
-    if (flags_.count(flag) == 0) {
-      for (auto item : flags_) {
-        if (item.second.first.compare(flag) == 0) {
-          flag = item.first;
-          break;
-        }
-      }
-    }
-
-    bool unrecognized = true;
-
-    // Parse String Arguments
-    if (arg_.count(flag) != 0) {
-
-      ArgumentType type = arg_[flag].front()->getArgumentType(); 
-      // Switch does not require an argument
-      if ( type == ArgumentType::SWITCH && 
-          (nextParameterIsAFlag_(index, arguments) ||
-           (index + 1) >= arguments.size())){
-
-        unrecognized = false;
-        if(defaults_set_[flag] == true ){
-          values_[flag][std::type_index(typeid(bool))].at(0) = true;
-          addValue_(flag, "TRUE");
-        }else {
-          addValue_(flag, "TRUE");
-        }
-      } else { 
-        if ((index + 1) >= arguments.size()) {
-          string err = "" + flag + " Missing arguments";
-          throw runtime_error(err);
-        }
-        int arg_index = 0;
-        do { // Allow reading of multiple arguments
-          string argument = arguments.at(index + 1);
-          if ( arg_index != 0){
-            // Need to duplicate the argument
-            addFlagArg(flag, type);
-            ArgumentType type = arg_[flag].front()->getArgumentType();
-            std::vector<PropertyType> arg_props = arg_[flag].front()->getProperties();
-              
-            auto values = arg_[flag].front()->getPropertyValues();
-            arg_[flag].push_back(createArgument(type));
-            arg_[flag].back()->setValues(values);
-            // TODO Need to specify index setFlagArgOpt(flag, arg_name, property, option, val);
-          }
-          arg_[flag].at(arg_index)->argValid(argument);
-          unrecognized = false;
-          if (defaults_set_.count(flag) ) {
-            if(defaults_set_[flag] == true ){
-              values_[flag].clear();
-              addValue_(flag,argument);
-              defaults_set_[flag] = false;
-            } else {
-              addValue_(flag,argument);
-            }
-          }
-          ++index;
-          ++arg_index;
-          if( (index+1) >= arguments.size() ) break;
-        } while ( arguments.at(index+1).at(0) == '-' );
-      }
-    }
-  /*
-    // Parse Switches
-    if (switch_arg_.count(flag) != 0) {
-      if (!nextParameterIsAFlag_(index, arguments)) {
-        if ((index + 1) >= arguments.size()) {
-          if (switch_arg_[flag].at(0)->requiresParameter()) {
-            string err = "" + flag + " Missing arguments";
-            throw runtime_error(err);
-          } else {
-            unrecognized = false;
-            int_values_[flag].at(0) = 1;
-          }
-        } else {
-          string argument = arguments.at(index + 1);
-          switch_arg_[flag].at(0)->argValid(argument);
-          unrecognized = false;
-          string_values_[flag].at(0) = argument;
-          if (switch_arg_[flag].at(0)->positive(argument)) {
-            if (defaults_set_.count(flag) ) {
-              if(defaults_set_[flag] == true ){
-                int_values_[flag].at(0) = 1;
-                defaults_set_[flag] = false;
-              } else {
-                int_values_[flag].push_back(1);
-              }
-            }
-          } else {
-            if (defaults_set_.count(flag) ) {
-              if(defaults_set_[flag] == true ){
-                int_values_[flag].at(0) = 0;
-                defaults_set_[flag] = false;
-              } else {
-                int_values_[flag].push_back(0);
-              }
-            }
-          }
-        }
-      } else {
-        unrecognized = false;
-        if(defaults_set_[flag] == true ){
-          int_values_[flag].at(0) = 1;
-          defaults_set_[flag] = false;
-        }else {
-          int_values_[flag].push_back(1);
-        }
-      }
-    }
-
-    // Parse integer arguments
-    if (int_arg_.count(flag) != 0) {
-      if (!nextParameterIsAFlag_(index, arguments) ||
-          int_arg_[flag].at(0)->requiresParameter()) {
-        if ((index + 1) >= arguments.size()) {
-          string err = "" + flag + " Missing arguments";
-          throw runtime_error(err);
-        }
-
-        int arg_index = 0;
-        do {
-          string argument = arguments.at(index + 1);
-          if ( arg_index != 0){
-            // Need to duplicate the argument
-            std::string arg_name = int_arg_[flag].at(0)->getArgumentName();
-            std::vector<std::string> arg_props = int_arg_[flag].at(0)->getProperties();
-            std::vector<std::string> arg_prop_opts = int_arg_[flag].at(0)->getPropertyOptions();
-            std::map<std::string, std::string> arg_prop_vals = int_arg_[flag].at(0)->getPropertyValues();
-          }
-          int_arg_[flag].at(arg_index)->argValid(stoi(argument));
-          unrecognized = false;
-          if (defaults_set_.count(flag) ) {
-            if(defaults_set_[flag] == true ){
-              string_values_[flag].clear();
-              int_values_[flag].push_back(stoi(argument));
-              defaults_set_[flag] = false;
-            } else {
-              int_values_[flag].push_back(stoi(argument));
-            }
-          }
-          ++index;
-          ++arg_index;
-          if( (index+1) >= arguments.size() ) break;
-        } while ( arguments.at(index+1).at(0) == '-' );
-      }
-    }
-
-    // Parse double arguments
-    if (double_arg_.count(flag) != 0) {
-      if (!nextParameterIsAFlag_(index, arguments) ||
-          double_arg_[flag].at(0)->requiresParameter()) {
-        if ((index + 1) >= arguments.size()) {
-          string err = "" + flag + " Missing arguments";
-          throw runtime_error(err);
-        }
-        int arg_index = 0;
-        do {
-          string argument = arguments.at(index + 1);
-          if ( arg_index != 0){
-            // Need to duplicate the argument
-            std::string arg_name = double_arg_[flag].at(0)->getArgumentName();
-            std::vector<std::string> arg_props = double_arg_[flag].at(0)->getProperties();
-            std::vector<std::string> arg_prop_opts = double_arg_[flag].at(0)->getProperties();
-            std::map<std::string, std::string> arg_prop_vals = double_arg_[flag].at(0)->getPropertyValues();
-          }
-          double_arg_[flag].at(arg_index)->argValid(stod(argument));
-          unrecognized = false;
-          if (defaults_set_.count(flag) ) {
-            if(defaults_set_[flag] == true ){
-              string_values_[flag].clear();
-              double_values_[flag].push_back(stod(argument));
-              defaults_set_[flag] = false;
-            } else {
-              double_values_[flag].push_back(stod(argument));
-            }
-          }
-          ++index;
-          ++arg_index;
-          if( (index+1) >= arguments.size() ) break;
-        } while ( arguments.at(index+1).at(0) == '-' );
-      }
-    }
-
-    // Parse file arguments 
-    if (file_arg_.count(flag) != 0) {
-      if (!nextParameterIsAFlag_(index, arguments) ||
-          file_arg_[flag].at(0)->requiresParameter()) {
-        if ((index + 1) >= arguments.size()) {
-          string err = "" + flag + " Missing arguments";
-          throw runtime_error(err);
-        }
-        int arg_index = 0;
-        do {
-          string argument = arguments.at(index + 1);
-          if ( arg_index != 0){
-            // Need to duplicate the argument
-            std::string arg_name = file_arg_[flag].at(0)->getArgumentName();
-            std::vector<std::string> arg_props = file_arg_[flag].at(0)->getProperties();
-            std::vector<std::string> arg_prop_opts = file_arg_[flag].at(0)->getProperties();
-            std::map<std::string, std::string> arg_prop_vals = file_arg_[flag].at(0)->getPropertyValues();
-          }
-          file_arg_[flag].at(arg_index)->argValid(argument);
-          unrecognized = false;
-          if (defaults_set_.count(flag) ) {
-            if(defaults_set_[flag] == true ){
-              string_values_[flag].clear();
-              string_values_[flag].push_back(argument);
-              defaults_set_[flag] = false;
-            } else {
-              string_values_[flag].push_back(argument);
-            }
-          }
-          ++index;
-          ++arg_index;
-          if( (index+1) >= arguments.size() ) break;
-        } while ( arguments.at(index+1).at(0) == '-' );
-      }
-    }*/
-
-    if (unrecognized) {
-      throw invalid_argument("The flag " + flag + " was unrecognized");
-    }
-  }
-
-
-  /*
-  std::vector<int> ArgumentParser::getInts(string flag) {
-
-    if (int_values_.count(flag) == 0) {
-      if (switch_arg_.count(flag)) {
-        if (string_values_.count(flag)) {
-          if (switch_arg_[flag]->positive(string_values_[flag])) {
-            return std::vector<int> {1};
-          } else {
-            return std::vector<int> {0};
-          }
-        }
-      }
-      string err = "" + flag +
-                   " does not contain an int. It is also possible that "
-                   "you did not specify a default value";
-      throw invalid_argument(err);
-    }
-    return int_values_[flag];
-  }
-
-  std::vector<double> ArgumentParser::getDoubles(string flag) {
-    if (double_values_.count(flag) == 0) {
-      string err = "" + flag +
-                   " does not contain a double. It is also possible that "
-                   "you did not specify a default value";
-      throw invalid_argument(err);
-    }
-    return double_values_[flag];
-  }
-
-  std::vector<string> ArgumentParser::getStrs(string flag) {
-    if (string_values_.count(flag) == 0) {
-      if (switch_arg_.count(flag)) {
-        if (int_values_.count(flag)) {
-          if (switch_arg_[flag]->positive(int_values_[flag])) {
-            return std::vector<string> {"ON"};
-          } else {
-            return std::vector<string> {"OFF"};
-          }
-        }
-      }
-      string err = "" + flag +
-                   " does not contain a string. It is also possible that "
-                   "you did not specify a default value";
-      throw invalid_argument(err);
-    }
-    return string_values_[flag];
-  }
-
-  std::vector<size_t> ArgumentParser::getSize_ts(string flag) {
-    if (size_t_values_.count(flag) == 0) {
-      string err = "" + flag +
-                   " does not contain a size_t. It is also possible that "
-                   "you did not specify a default value";
-      throw invalid_argument(err);
-    }
-    return size_t_values_[flag];
-  }
-  */
-  void ArgumentParser::postParseCheck(void) {
-    //for (std::pair<std::string, std::vector<std::unique_ptr<ArgumentObject>>> & flag_arg : arg_) {
-    for (auto & flag_arg : arg_) {
-      for ( std::unique_ptr<ArgumentObject> & arg : flag_arg.second ){
-        arg->postArgCheck();
-      }
-    }
-  }
-
-  void ArgumentParser::parse(const char* argv[], int argc) {
-
-    // Convert to vector of strings
-    vector<string> arguments(argv, argv + argc);
-
-    if (argc <= 1) {
-      cout << "Usage: " << arguments.at(0) << " <options(s)> SOURCES";
-      showUsage();
-      throw runtime_error("Must provide arguments");
-    }
-
-    string help_flag = "--help";
-    string help_flag_short = "-h";
-    string citation_flag = "--citation";
-    string citation_flag_short = "-cite";
-    string version_flag = "--version";
-    string version_flag_short = "-version";
-
-    size_t allowed_args_before_exit = 2;
-    for (size_t index = 1; index < arguments.size(); ++index) {
-      if (help_flag.compare(arguments.at(index)) == 0 ||
-          help_flag_short.compare(arguments.at(index)) == 0) {
-        cout << "Usage: " << arguments.at(0) << " <options(s)> SOURCES";
-        showUsage();
-        if (allowed_args_before_exit == arguments.size()) {
-          exit(0);
-        }
-        ++allowed_args_before_exit;
-      } else if (version_flag.compare(arguments.at(index)) == 0 ||
-                 version_flag_short.compare(arguments.at(index)) == 0) {
-        exit(0);
-      } else if (citation_flag.compare(arguments.at(index)) == 0 ||
-                 citation_flag_short.compare(arguments.at(index)) == 0) {
-        cout << "\nCitation: " << catnip_AUTHOR_SURNAME << ", ";
-        cout << catnip_AUTHOR_INITIALS << " (";
-        cout << catnip_YEAR_PUBLISHED << "). ";
-        cout << catnip_TITLE << " (Version ";
-        cout << catnip_VERSION_MAJOR << ".";
-        cout << catnip_VERSION_MINOR << "). [Software]. Available from ";
-        cout << catnip_URL << ".\n\n";
-        if (allowed_args_before_exit == arguments.size()) {
-          exit(0);
-        }
-        ++allowed_args_before_exit;
-      } else {
-        parseArg_(index, arguments);
-      }
-    }
-
-    postParseCheck();
-  }
-}
diff --git a/src/libcatnip/io/argumentparser.hpp b/src/libcatnip/io/argumentparser.hpp
deleted file mode 100644
index 802e1ba..0000000
--- a/src/libcatnip/io/argumentparser.hpp
+++ /dev/null
@@ -1,200 +0,0 @@
-#ifndef _CATNIP_ARGUMENTPARSER_HPP
-#define _CATNIP_ARGUMENTPARSER_HPP
-#include "parameters.hpp"
-#include <any>
-#include <map>
-#include <memory>
-#include <set>
-#include <string>
-#include <utility>
-
-#include "arguments/argumentnumerical.hpp"
-#include "arguments/argumentfile.hpp"
-#include "arguments/argumentstring.hpp"
-#include "arguments/argumentswitch.hpp"
-
-namespace catnip {
-
-  std::unique_ptr<ArgumentObject> createArgument(ArgumentType type);
-
-class ArgumentParser {
- private:
-  // 1 - flag name
-  // 2 - type
-  std::map<std::string, std::vector<std::unique_ptr<ArgumentObject>>> arg_;
-
-  // Known rules
-  std::set<std::string> argument_types_;
-
-  // Known flags and their description
-  std::map<std::string, std::pair<std::string, std::string>> flags_;
-
-  std::map<std::string, bool> defaults_set_;
-  // Arguments that are stored when argc and argv are parsed
-  std::map<std::string, std::map<std::type_index, std::vector<std::any>>> values_;
-
-  void parseArg_(size_t& index, std::vector<std::string> arguments);
-
-  // Determine if the next value in arguments vector is a recognized flag
-  bool nextParameterIsAFlag_(size_t index, std::vector<std::string> arguments);
-
-  size_t maxShortFlagSize;
-  size_t maxFullFlagSize;
-  size_t maxDescriptionSize;
-  size_t maxLineLength = 80;
-
-  // Will convert the command line argument to the appropriate type before
-  // placing in std::any and adding to the values container
-  void addValue_(std::string flag, std::string value);
-
- public:
-  // 1 - short flag
-  // 2 - long flag
-  // 3 - description
-  explicit ArgumentParser(std::set<std::vector<std::string>> flags);
-
-  // Set Defaults for the flags in the case that they are not found
-  template<class T>
-  void setFlagDefaultValue(std::string flag,const T & val) {
-    values_[flag][std::type_index(val)].push_back(val);
-    defaults_set_[flag] = true;
-  }
-
-  // Add a argument without setting any of the values
-  void addFlagArg(std::string flag, ArgumentType argname);
-  // Set the rules for the flag and the type it is associated with types
-  // include:
-  // "FILES"
-  // "NUMERICAL"
-  // "STRING"
-  // "SWITCH"
-  // The rules are dependent on the type
-  template<class T>
-    void setFlagArgOpt(
-        std::string flag, 
-        ArgumentType argname,
-        PropertyType property,
-        Option option,
-        T val) {
-
-      
-      if (arg_.count(flag) == 0) {
-        auto arg = createArgument(argname);
-        arg->setArgPropertyOpt(property, option, val);
-        arg_[flag].push_back(std::move(arg));
-      } else {
-        for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag]){
-          ptr->setArgPropertyOpt(property, option, val);
-        }
-      }
-/*
-      if (argname == ArgumentType::NUMERICAL) {
-        if (arg_.count(flag) == 0) {
-          auto ArInt = std::unique_ptr<ArgumentObject>(new ArgumentNumerical);
-          ArInt->setArgPropertyOpt(property, option, val);
-          arg_[flag].push_back(std::move(ArInt));
-        } else {
-          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag]){
-            ptr->setArgPropertyOpt(property, option, val);
-          }
-        }
-      } else if (argname == ArgumentType::STRING) {
-        if (arg_.count(flag) == 0) {
-          auto ArString = std::unique_ptr<ArgumentObject>(new ArgumentString);
-          ArString->setArgPropertyOpt(property, option, val);
-          arg_[flag].push_back(std::move(ArString));
-        } else {
-          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag] ){
-            ptr->setArgPropertyOpt(property, option, val);
-          }
-        }
-      } else if (argname == ArgumentType::SWITCH) {
-        if (switch_arg_.count(flag) == 0) {
-          auto ArSwitch = std::unique_ptr<ArgumentObject>(new ArgumentSwitch);
-          if (val == 0) {
-            ArSwitch->setArgPropertyOpt(property, option, "OFF");
-          } else if (val == 1) {
-            ArSwitch->setArgPropertyOpt(property, option, "ON");
-          } else {
-            throw invalid_argument("Unrecognized option for switch " +
-                to_string(val));
-          }
-          arg_[flag].push_back(std::move(ArSwitch));
-        } else { // For a switch there will only be one value in the vector
-          if (val == 0) {
-            arg_[flag].at(0)->setArgPropertyOpt(property, option, "OFF");
-          } else if (val == 1) {
-            arg_[flag].at(0)->setArgPropertyOpt(property, option, "ON");
-          } else {
-            throw invalid_argument("Unrecognized option for switch " +
-                to_string(val));
-          }
-        }
-      } else if (argname == ArgumentType::FILES) {
-        if (file_arg_.count(flag) == 0) {
-          auto ArFile = std::unique_ptr<ArgumentObject>(new ArgumentFile);
-
-          ArFile->setArgPropertyOpt(property, option, val);
-          arg_[flag].push_back(std::move(ArFile));
-        } else {
-          for ( std::unique_ptr<ArgumentObject> & ptr : arg_[flag] ){
-            ptr->setArgPropertyOpt(property, option, val);
-          }
-        }
-      } else {
-        throw invalid_argument("Unrecognized int arg");
-      }*/
-    }
-
-
-/*  void setFlagArgOpt(std::string flag, std::string argname,
-                     std::string property, std::string option, double val);
-
-  void setFlagArgOpt(std::string flag, std::string argname,
-                     std::string property, std::string option, std::string val);
-
-  void setFlagArgOpt(std::string flag, std::string argname,
-                     std::string property, std::string option,
-                     std::set<std::string> vals);
-
-  void setFlagArgOpt(std::string flag, std::string argname,
-                     std::string property, std::string option,
-                     std::vector<std::string> vals);
-
-  std::string getFlagArgOptValue(std::string flag, std::string argname,
-                                 std::string property, std::string option);
-*/
-  template<class T>
-  std::vector<T> get(std::string flag) {
-    std::vector<T> values;
-    if ( values_[flag].count(typeid(T)) ){
-      for ( std::any & val : values_[flag][typeid(T)] ){
-        values.push_back(std::any_cast<T>(val));
-      }
-    }
-    return values;
-  }
-//
-//  template<class T>
-//  std::vector<T> get(std::string flag, ArgumentType arg_type, PropertyType prop_type, Option opt) {
-//    std::vector<T> values;
-//    if ( values_[flag].count(typeid(T)) ){
-//      for ( std::any & val : values_[flag][typeid(T)] ){
-//        values.push_back(std::any_cast<T>(val));
-//      }
-//    }
-//    return values;
-//  }
-/*  std::vector<double> getDoubles(std::string flag);
-  std::vector<int> getInts(std::string flag);
-  std::vector<std::string> getStrs(std::string flag);
-  std::vector<size_t> getSize_ts(std::string flag);*/
-
-  void postParseCheck(void);
-
-  void parse(const char* argv[], int argc);
-  void showUsage();
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_ARGUMENTPARSER_HPP
diff --git a/src/libcatnip/io/arguments/Makefile b/src/libcatnip/io/arguments/Makefile
deleted file mode 100644
index 64312c7..0000000
--- a/src/libcatnip/io/arguments/Makefile
+++ /dev/null
@@ -1,64 +0,0 @@
-CC=g++
-CFLAGS= -Wall -Wextra -pedantic -std=c++11
-
-all: test_argumentfile test_argumentswitch test_argumentint test_argumentdouble test_argumentstring
-
-test_argumentswitch: test_argumentswitch.cpp string_support.o argumentswitch.o propertyswitch.o 
-	$(CC) $(CFLAGS) test_argumentswitch.cpp string_support.o argumentswitch.o propertyswitch.o -o test_argumentswitch 
-
-argumentswitch.o : argumentswitch.cpp
-	$(CC) $(CFLAGS) -c argumentswitch.cpp
-
-test_argumentstring: test_argumentstring.cpp argumentstring.o string_support.o propertystring.o propertystringchoice.o
-	$(CC) $(CFLAGS) test_argumentstring.cpp argumentstring.o propertystring.o string_support.o propertystringchoice.o -o test_argumentstring 
-
-argumentstring.o : argumentstring.cpp
-	$(CC) $(CFLAGS) -c argumentstring.cpp
-
-propertystring.o : PROPERTIES/propertystring.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertystring.cpp
-
-test_argumentdouble: test_argumentdouble.cpp argumentdouble.o string_support.o propertydouble.o
-	$(CC) $(CFLAGS) test_argumentdouble.cpp argumentdouble.o propertydouble.o string_support.o -o test_argumentdouble
-
-argumentdouble.o : argumentdouble.cpp
-	$(CC) $(CFLAGS) -c argumentdouble.cpp
-
-propertydouble.o : PROPERTIES/propertydouble.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertydouble.cpp
-
-test_argumentint: test_argumentint.cpp argumentint.o string_support.o propertyint.o
-	$(CC) $(CFLAGS) test_argumentint.cpp argumentint.o propertyint.o string_support.o -o test_argumentint
-
-argumentint.o : argumentint.cpp
-	$(CC) $(CFLAGS) -c argumentint.cpp
-
-test_argumentfile: test_argumentfile.cpp propertysisterfile.o argumentfile.o string_support.o propertyfileexist.o propertyfileext.o
-	$(CC) $(CFLAGS) test_argumentfile.cpp argumentfile.o propertysisterfile.o propertyfileexist.o propertyfileext.o string_support.o -o test_argumentfile
-
-argumentfile.o : argumentfile.cpp
-	$(CC) $(CFLAGS) -c argumentfile.cpp
-
-propertyswitch.o : PROPERTIES/propertyswitch.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertyswitch.cpp
-
-propertysisterfile.o : PROPERTIES/propertysisterfile.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertysisterfile.cpp
-
-propertyint.o : PROPERTIES/propertyint.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertyint.cpp
-
-propertyfileexist.o : PROPERTIES/propertyfileexist.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertyfileexist.cpp
-
-propertystringchoice.o : PROPERTIES/propertystringchoice.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertystringchoice.cpp
-
-propertyfileext.o : PROPERTIES/propertyfileext.cpp
-	$(CC) $(CFLAGS) -c PROPERTIES/propertyfileext.cpp
-
-string_support.o: ../../STRING_SUPPORT/string_support.cpp
-	$(CC) $(CFLAGS) -c ../../STRING_SUPPORT/string_support.cpp
-
-clean:
-	rm *.o test_argumentfile test_argumentswitch test_argumentint test_argumentdouble test_argumentstring
diff --git a/src/libcatnip/io/arguments/README.md b/src/libcatnip/io/arguments/README.md
deleted file mode 100644
index 93ba0f2..0000000
--- a/src/libcatnip/io/arguments/README.md
+++ /dev/null
@@ -1,10 +0,0 @@
-
-# Arguments
-
-The arguments classes are used to define the criteria that the arguments passed in from the command line should meet. 
-
-For instance if you are passing the a file name in then there will be an argument class for dealing with file names. If you are passing integer in there will be a argument class for deaing with integers. 
-
-# Properties
-
-The properties classes are the criteria used to check the arguments. For instance if a file argument is passed in, for the file name to be valid maybe it needs to exist or have a relevant extension. There are properties defined for this kind of functionality. 
diff --git a/src/libcatnip/io/arguments/argumentfile.cpp b/src/libcatnip/io/arguments/argumentfile.cpp
deleted file mode 100644
index 372b709..0000000
--- a/src/libcatnip/io/arguments/argumentfile.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-
-#include "argumentfile.hpp"
-#include "properties/propertyfileexist.hpp"
-#include "properties/propertyfileext.hpp"
-#include "properties/propertysisterfile.hpp"
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentFile::ArgumentFile(void) { 
-  propobjs_.emplace_back(new PropertyFileExist());
-  propobjs_.emplace_back(new PropertyFileExt());
-  propobjs_.emplace_back(new PropertySisterFile());
-
-}
diff --git a/src/libcatnip/io/arguments/argumentfile.hpp b/src/libcatnip/io/arguments/argumentfile.hpp
deleted file mode 100644
index 5952f86..0000000
--- a/src/libcatnip/io/arguments/argumentfile.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENT_FILE_HPP
-#define _CATNIP_ARGUMENT_FILE_HPP
-
-#include "argumentobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class ArgumentFile : public ArgumentObject {
-
- public:
-
-  virtual ArgumentType getArgumentType(void) const noexcept final {
-    return ArgumentType::FILES;
-  }
-
-  virtual std::type_index getValueType(void) const noexcept final { 
-    return typeid(std::string);
-  }
-
-  ArgumentFile(void);
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_ARGUMENT_FILE_HPP
diff --git a/src/libcatnip/io/arguments/argumentnumerical.cpp b/src/libcatnip/io/arguments/argumentnumerical.cpp
deleted file mode 100644
index b6997d1..0000000
--- a/src/libcatnip/io/arguments/argumentnumerical.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-
-#include "argumentnumerical.hpp"
-#include "properties/propertynumeric.hpp"
-#include <iostream>
-#include <memory>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentNumerical::ArgumentNumerical(void) { 
-  propobjs_.emplace_back(new PropertyNumeric());
-}
-
diff --git a/src/libcatnip/io/arguments/argumentnumerical.hpp b/src/libcatnip/io/arguments/argumentnumerical.hpp
deleted file mode 100644
index eab274e..0000000
--- a/src/libcatnip/io/arguments/argumentnumerical.hpp
+++ /dev/null
@@ -1,28 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENT_DOUBLE_HPP
-#define _CATNIP_ARGUMENT_DOUBLE_HPP
-
-#include "argumentobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class ArgumentNumerical : public ArgumentObject {
- private:
-  std::string getName_(void) const { return "ARGUMENT_DOUBLE"; }
-  void registerProperties_(void);
-
- public:
-
-  virtual ArgumentType getArgumentType(void) const noexcept final 
-  { return ArgumentType::NUMERICAL; }
-
-  virtual std::type_index getValueType(void) const noexcept final {
-    return typeid(double);
-  }
-
-  ArgumentNumerical(void);
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_ARGUMENT_DOUBLE_HPP
diff --git a/src/libcatnip/io/arguments/argumentobject.hpp b/src/libcatnip/io/arguments/argumentobject.hpp
deleted file mode 100644
index b57b4e4..0000000
--- a/src/libcatnip/io/arguments/argumentobject.hpp
+++ /dev/null
@@ -1,182 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENTOBJECT_HPP
-#define _CATNIP_ARGUMENTOBJECT_HPP
-
-#include "string_support.hpp"
-#include "properties/propertyobject.hpp"
-#include <exception>
-#include <iostream>
-#include <map>
-#include <memory>
-#include <set>
-#include <string>
-
-namespace catnip {
-
-  enum class ArgumentType {
-    NUMERICAL,
-    FILES,
-    STRING,
-    SWITCH
-  };
-
-// The template is simply for specifying the type of the argument coming
-// from the command line
-class ArgumentObject {
- protected:
-  std::vector<std::unique_ptr<PropertyObject>> propobjs_;
-
- public:
-  virtual ~ArgumentObject(void) {};
-
-  // The argument object by default requires a parameter
-  virtual bool requiresParameter(void) { return true; }
-
-  virtual ArgumentType getArgumentType(void) const noexcept = 0; 
-
-  // This is the type the value will be converted to after being read in
-  virtual std::type_index getValueType(void) const noexcept = 0;
-
-  std::vector<PropertyType> getProperties(void) {
-    std::vector<PropertyType> props;
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      props.push_back(prop->getPropertyType());
-    }
-    return props;
-  }
-
-  std::vector<Option> getPropertyOptions(PropertyType property) {
-      for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-        if ( prop->getPropertyType() == property ) {
-          return prop->getPropertyOptions();
-        }
-      }
-      return std::vector<Option>();
-  }
-
-  /**
-   * @brief Gets the options of all properties
-   *
-   * @return 
-   */
-  std::vector<Option> getPropertyOptions(void) const {
-    std::vector<Option> ops;
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      auto vec_opt = prop->getPropertyOptions();
-      ops.insert(ops.end(), vec_opt.begin(), vec_opt.end());
-    }
-    return ops;
-  }
-
- 
-  /**
-   * @brief Returns the options with value associated with it
-   *
-   * @return 
-   */
-  std::map<PropertyType, std::map<Option, std::any>> getPropertyValues(void) {
-    std::map<PropertyType, std::map<Option, std::any>> opts_values;
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      PropertyType type = prop->getPropertyType();
-      auto vec_opt = prop->getPropertyOptions();
-      for (Option opt : vec_opt) {
-        auto value = prop->getPropOption<std::any>(opt);
-        opts_values[type][opt] = value;
-      }
-    }
-    return opts_values;
-  }
-
-  std::map<Option, std::any> getPropertyValues(
-      PropertyType property) {
-
-    std::map<Option, std::any> opts_values;
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      if (property == prop->getPropertyType()) {
-        std::vector<Option> vec_opt = prop->getPropertyOptions();
-        for (const Option & opt : vec_opt) {
-          auto value = prop->getPropOption<std::any>(opt);
-          opts_values[opt] = value;
-        }
-      }
-    }
-    return opts_values;
-  }
-
-  template<class T>
-  T getPropertyValues(PropertyType property,const Option & option) {
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      if (property == prop->getPropertyType()) {
-        std::vector<Option> vec_opt = prop->getPropertyOptions();
-        for (const Option & opt : vec_opt) {
-          if (option == opt) {
-            return prop->getPropOption<T>(opt);
-          }
-        }
-      }
-    }
-
-    std::string err =
-        "Unable to recognize property or option ";
-    throw std::invalid_argument(err);
-  }
-
-  // Setup the valid options associated with the parameter
-  template<class T>
-  void setArgPropertyOpt(PropertyType property, Option option,
-                         const T& val) {
-    bool setval = false;
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      if (property == prop->getPropertyType()) {
-        prop->setPropOption(option, val);
-        setval = true;
-      }
-    }
-    if (!setval) {
-      std::string err =
-          "Argument property: is unrecognized for argument ";
-      throw std::invalid_argument(err);
-    }
-  }
-
-  void setValues(std::map<PropertyType, std::map<Option, std::any>> values) {
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      const PropertyType & type = prop->getPropertyType();
-      if(values.count(type)){
-        for ( std::pair<Option,std::any> opt_val : values[type] ){
-          prop->setPropOption(opt_val.first, opt_val.second);
-        }
-      }
-    }
-  }
-
-   void setPropertyValues(
-      PropertyType property, std::map<Option, std::any> opts) {
-
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      if (property == prop->getPropertyType()) {
-        for ( std::pair<Option,std::any> opt_val : opts ){
-          prop->setPropOption(opt_val.first, opt_val.second);
-        }
-        return; 
-      }
-    }
-  }
-
-  template< class T>
-  bool argValid(const T& value) const {
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      prop->propValid(value);
-    }
-    return true;
-  }
-
-  void postArgCheck(void) {
-    for (const std::unique_ptr<PropertyObject> & prop : propobjs_) {
-      prop->postCheck();
-    }
-  }
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_ARGUMENTOBJECT_HPP
diff --git a/src/libcatnip/io/arguments/argumentstring.cpp b/src/libcatnip/io/arguments/argumentstring.cpp
deleted file mode 100644
index d06b93d..0000000
--- a/src/libcatnip/io/arguments/argumentstring.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-
-#include "argumentstring.hpp"
-#include "properties/propertystring.hpp"
-#include "properties/propertystringchoice.hpp"
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentString::ArgumentString(void) { 
-  propobjs_.emplace_back(new PropertyString);
-  propobjs_.emplace_back(new PropertyStringChoice);
-}
diff --git a/src/libcatnip/io/arguments/argumentstring.hpp b/src/libcatnip/io/arguments/argumentstring.hpp
deleted file mode 100644
index c6c0b03..0000000
--- a/src/libcatnip/io/arguments/argumentstring.hpp
+++ /dev/null
@@ -1,26 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENT_STRING_HPP
-#define _CATNIP_ARGUMENT_STRING_HPP
-
-#include "argumentobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class ArgumentString : public ArgumentObject {
- public:
-
-  virtual ArgumentType getArgumentType(void) const noexcept final { 
-    return ArgumentType::STRING; 
-  }
-
-  virtual std::type_index getValueType(void) const noexcept final {
-    return typeid(std::string);
-  }
-
-  ArgumentString(void);
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_ARGUMENT_STRING_HPP
diff --git a/src/libcatnip/io/arguments/argumentswitch.cpp b/src/libcatnip/io/arguments/argumentswitch.cpp
deleted file mode 100644
index f772cec..0000000
--- a/src/libcatnip/io/arguments/argumentswitch.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-
-#include "argumentswitch.hpp"
-#include "properties/propertyswitch.hpp"
-#include <iostream>
-
-using namespace catnip;
-using namespace std;
-
-ArgumentSwitch::ArgumentSwitch(void) { 
-  propobjs_.emplace_back(new PropertySwitch);
-}
-
-bool ArgumentSwitch::positive(string val) const {
-  if (val.compare("ON") == 0 || val.compare("TRUE") == 0 ||
-      val.compare("1") == 0) {
-    return true;
-  } else if (val.compare("OFF") == 0 || val.compare("FALSE") == 0 ||
-             val.compare("0") == 0) {
-    return false;
-  }
-  throw invalid_argument("Argument value is unrecognized " + val);
-}
diff --git a/src/libcatnip/io/arguments/argumentswitch.hpp b/src/libcatnip/io/arguments/argumentswitch.hpp
deleted file mode 100644
index 1933713..0000000
--- a/src/libcatnip/io/arguments/argumentswitch.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-
-#ifndef _CATNIP_ARGUMENT_SWITCH_HPP
-#define _CATNIP_ARGUMENT_SWITCH_HPP
-
-#include "argumentobject.hpp"
-#include <set>
-
-namespace catnip {
-class ArgumentSwitch : public ArgumentObject {
-
- public:
-
-  virtual ArgumentType getArgumentType(void) const noexcept final {
-    return ArgumentType::SWITCH;
-  }
-
-  ArgumentSwitch(void);
-
-  virtual std::type_index getValueType(void) const noexcept final {
-    return typeid(bool);
-  }
-
-  virtual bool requiresParameter(void) final { return false; }
-  bool positive(int val) const noexcept { return ((val == 1) ? true : false); }
-  bool positive(std::string val) const;
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_ARGUMENT_SWITCH_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyfileexist.cpp b/src/libcatnip/io/arguments/properties/propertyfileexist.cpp
deleted file mode 100644
index 60b1515..0000000
--- a/src/libcatnip/io/arguments/properties/propertyfileexist.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-
-#include "propertyfileexist.hpp"
-#include "../../../string_support.hpp"
-#include <stdexcept>
-#include <sys/stat.h>
-
-using namespace catnip;
-using namespace std;
-
-PropertyFileExist::PropertyFileExist(void) {
-  setPropOption_(Option::MUST_EXIST, bool(false));
-  setPropOption_(Option::DOES_EXIST, bool(false));
-}
-
-PropertyFileExist::PropertyFileExist(bool fileMustExist) {
-  setPropOption_(Option::MUST_EXIST, fileMustExist);
-}
-
-bool PropertyFileExist::fileExist(const string& fileNamePath) const {
-  struct stat buf;
-  return (stat(fileNamePath.c_str(), &buf) == 0);
-}
-
-bool PropertyFileExist::propValid(const std::any& fileNamePath) {
-  std::string file_name_path = any_cast<std::string>(fileNamePath);
-  bool must_exist = any_cast<bool>(options_[Option::MUST_EXIST]);
-  if (must_exist) {
-    if (!fileExist(file_name_path)) {
-      string err = "" + file_name_path + " does not exist";
-      throw invalid_argument(err);
-    }
-    setPropOption_(Option::DOES_EXIST, bool(true));
-  } else {
-    if (fileExist(file_name_path)) {
-      setPropOption_(Option::DOES_EXIST, bool(true));
-    }
-  }
-  return true;
-}
-
-void PropertyFileExist::postCheck(void) const {
-  auto must_exist = getPropOption<bool>(Option::MUST_EXIST);
-  auto exist = getPropOption<bool>(Option::DOES_EXIST);
-  if (must_exist && exist == 0) {
-    throw runtime_error("A necessary file is missing!");
-  }
-}
diff --git a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp b/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
deleted file mode 100644
index d779db9..0000000
--- a/src/libcatnip/io/arguments/properties/propertyfileexist.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_FILEEXIST_HPP
-#define _CATNIP_PROPERTY_FILEEXIST_HPP
-
-#include "propertyobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class PropertyFileExist : public PropertyObject {
- private:
-  bool fileExist(const std::string &) const;
-
- public:
-  explicit PropertyFileExist(void);
-  PropertyFileExist(bool fileMustExist);
-
-  virtual bool propValid(const std::any &fileName) final;
-
-  virtual PropertyType getPropertyType() const noexcept final {
-    return PropertyType::FILE_EXISTS;
-  }
-
-  void postCheck(void) const;
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_PROPERTY_FILEEXIST_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyfileext.cpp b/src/libcatnip/io/arguments/properties/propertyfileext.cpp
deleted file mode 100644
index 1c7fff3..0000000
--- a/src/libcatnip/io/arguments/properties/propertyfileext.cpp
+++ /dev/null
@@ -1,69 +0,0 @@
-
-#include "propertyfileext.hpp"
-#include "../../../string_support.hpp"
-#include <stdexcept>
-#include <sys/stat.h>
-
-using namespace catnip;
-using namespace std;
-
-PropertyFileExt::PropertyFileExt(string ext) {
-  checkExt(ext);
-  setPropOption_(Option::ALLOWED_VALUES, ext);
-}
-
-PropertyFileExt::PropertyFileExt(set<string> exts) {
-  for (const std::string & ext : exts) {
-    checkExt(ext);
-  }
-  setPropOption_(Option::ALLOWED_VALUES, exts);
-}
-
-void PropertyFileExt::extSupported(const string& ext) const {
-  checkExt(ext);
-  auto exts_ = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
-  for (const std::string & ext_ : exts_) {
-    if (ext_[0] == '*') {
-      return;
-    } else if (ext_.compare(ext) == 0) {
-      return;
-    }
-  }
-  string err = "The file ext " + ext + " is unsupported";
-  throw invalid_argument(err);
-}
-
-void PropertyFileExt::checkExt(const string& ext) const {
-  if (ext.compare("") == 0) {
-    return;
-  } else if (ext[0] == '*') {
-    return;
-  } else {
-    string excess = grabStrBeforeLastOccurance(ext, ".");
-    if (excess.compare("") != 0) {
-      throw invalid_argument(
-          "An extension must be of type '.ext','*','', "
-          "you have used " +
-          ext);
-    }
-  }
-  return;
-}
-
-void PropertyFileExt::setPropOption(Option option,
-                                    std::set<std::string> vars) {
-  PropertyObject::setPropOption(option, vars);
-}
-
-void PropertyFileExt::setPropOption(Option option, std::string var) {
-  set<string> vars;
-  vars.insert(var);
-  PropertyObject::setPropOption(option, vars);
-}
-
-bool PropertyFileExt::propValid(const any & fileNamePath) {
-  string fileName = lastStringInPath(any_cast<std::string>(fileNamePath));
-  string ext = grabStrAfterLastOccuranceInclusive(fileName, ".");
-  extSupported(ext);
-  return true;
-}
diff --git a/src/libcatnip/io/arguments/properties/propertyfileext.hpp b/src/libcatnip/io/arguments/properties/propertyfileext.hpp
deleted file mode 100644
index 84e815a..0000000
--- a/src/libcatnip/io/arguments/properties/propertyfileext.hpp
+++ /dev/null
@@ -1,37 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_FILEEXT_HPP
-#define _CATNIP_PROPERTY_FILEEXT_HPP
-
-#include "propertyobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class PropertyFileExt
-    : public PropertyObject {
- private:
-  void checkExt(const std::string &) const;
-  void extSupported(const std::string &) const;
-  std::vector<std::string> getOpts_(void) const;
-
- public:
-  explicit PropertyFileExt(void) {
-    std::set<std::string> exts_;
-    exts_.insert("*");
-    options_[Option::ALLOWED_VALUES] = exts_;
-  }
-
-  explicit PropertyFileExt(std::string ext);
-  PropertyFileExt(std::set<std::string> exts);
-
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::FILE_EXT;
-  }
-
-  bool propValid(const std::any &fileNamePath);
-  void setPropOption(Option option, std::string var);
-  void setPropOption(Option option, std::set<std::string> var);
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_FILEEXT_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertynumeric.cpp b/src/libcatnip/io/arguments/properties/propertynumeric.cpp
deleted file mode 100644
index 2262916..0000000
--- a/src/libcatnip/io/arguments/properties/propertynumeric.cpp
+++ /dev/null
@@ -1,48 +0,0 @@
-
-#include "propertynumeric.hpp"
-
-#include "propertyobject.hpp"
-
-#include <limits>
-#include <typeinfo>
-
-using namespace catnip;
-using namespace std;
-
-void PropertyNumeric::setPropOption_(const Option & option, const std::any & val) {
-  if ( val.type() != typeid(double)){
-    string err = "The Min and Max options of the numeric property must be a double.";
-    throw invalid_argument(err);
-  }
-  PropertyObject::setPropOption_(option, val);
-}
-
-bool PropertyNumeric::propValid(const std::any & val) {
-
-  if( val.type() != typeid(int) || val.type() != typeid(double) ){
-    string err = "The value provided to the property is not a supported type.";
-    throw invalid_argument(err);
-  }
-  // If the properties have not been set then they will be 
-  // valid as long as they are of a numeric type
-  double converted_val;
-  if ( val.type() == typeid(int) ){
-    converted_val = static_cast<double>(any_cast<int>(val));
-  } else {
-    converted_val = any_cast<double>(val);
-  }
-
-  // ignore it otherwise, there is no min option 
-  double min_val = any_cast<double>(options_[Option::MIN]);
-  if ( converted_val < min_val ) {
-    string err = "The value provided to the property is less than the minimum allowed.";
-    throw invalid_argument(err);
-  }
-  // ignore it otherwise, there is no min option 
-  double max_val = any_cast<double>(options_[Option::MAX]);
-  if ( converted_val < max_val ) {
-    string err = "The value provided to the property is greater than the maximum allowed.";
-    throw invalid_argument(err);
-  }
-  return true;
-}
diff --git a/src/libcatnip/io/arguments/properties/propertynumeric.hpp b/src/libcatnip/io/arguments/properties/propertynumeric.hpp
deleted file mode 100644
index f3b04da..0000000
--- a/src/libcatnip/io/arguments/properties/propertynumeric.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_NUMERIC_HPP
-#define _CATNIP_PROPERTY_NUMERIC_HPP
-
-#include "propertyobject.hpp"
-
-#include <any>
-#include <limits>
-
-namespace catnip {
-
-class PropertyNumeric : public PropertyObject {
-
-  // Override the setting make sure that a double is passed in as the numeric type
-  virtual void setPropOption_(const Option & option, const std::any & val) final;
-
- public:
-  PropertyNumeric(void) {
-    options_[Option::MIN] = std::numeric_limits<double>::min;
-    options_[Option::MAX] = std::numeric_limits<double>::max; 
-  };
-
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::NUMERIC;
-  }
-
-  virtual bool propValid(const std::any& value) final;
-};
-
-}  // namespace catnip
-
-#endif  // _CATNIP_PROPERTY_NUMERIC_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyobject.hpp b/src/libcatnip/io/arguments/properties/propertyobject.hpp
deleted file mode 100644
index 9e4e650..0000000
--- a/src/libcatnip/io/arguments/properties/propertyobject.hpp
+++ /dev/null
@@ -1,148 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_OBJECT_HPP
-#define _CATNIP_PROPERTY_OBJECT_HPP
-
-#include <any>
-#include <map>
-#include <memory>
-#include <set>
-#include <stdexcept>
-#include <string>
-#include <typeindex>
-#include <typeinfo>
-#include <vector>
-
-namespace catnip {
-
-enum class PropertyType {
-  UNKNOWN,
-  NUMERIC,
-  FILE_EXISTS,
-  FILE_EXT,
-  SISTER_FILE,
-  STRING,
-  STRING_CHOICE,
-  SWITCH
-};
-
-enum class Option {
-  NO_OPTIONS,
-  MIN,
-  MAX,
-  MIN_LENGTH,
-  MAX_LENGTH,
-  MUST_EXIST,
-  DOES_EXIST,
-  ALLOWED_VALUES,
-  ENFORCED,
-  FILE_NAME,
-  FILE_PATH,
-  FILE_PATH_NAME,
-  VALUE,
-  DEFAULT
-};
-
-class PropertyObject {
- protected:
-  // Map key is the option name and the type "int, double etc"
-  // void * points to the correct value for that type
-  std::map<Option, std::any> options_;
-  std::map<Option, std::vector<std::type_index>> allowed_option_types_;
-  std::map<Option, std::type_index> default_option_type_; 
-
-  //void addAllowedOptionType_(const Option & option, std::type_index ind) {  
-   // allowed_option_types_[option].push_back(std::move(ind));
-  //}
-
- // void setDefaultOptionType_(const Option & option, std::type_index ind) {
-  //  default_option_type_[option] = std::move(ind);
- // }
-
-  bool propOptionValid_(const Option &option) const {
-    return options_.count(option);
-  }
-
-  void setPropOption_(const Option &option, const std::any &val) {
-      options_[option] = val;
-  }
-
-  bool conversionAllowed_(Option option, std::type_index type) const {
-    for ( const std::type_index & allowed_type : allowed_option_types_.at(option) ){
-      if( allowed_type == type ) return true;
-    }
-    return false;
-  } 
-
-  typedef int (*int_func)(Option,std::map<Option, std::any>); 
-  std::map<Option,int_func> int_convert_;
-  typedef double (*double_func)(Option,std::map<Option, std::any>); 
-  std::map<Option,double_func> double_convert_;
-  typedef std::string (*str_func)(Option,std::map<Option, std::any>); 
-  std::map<Option,str_func> str_convert_;
-  typedef bool (*bool_func)(Option,std::map<Option, std::any>); 
-  std::map<Option,bool_func> bool_convert_;
-  typedef std::set<bool> (*set_bool_func)(const Option,std::map<const Option, std::any>); 
-  std::map<Option,set_bool_func> set_bool_convert_;
-  typedef std::set<std::string> (*set_str_func)(const Option,std::map<const Option, std::any>); 
-  std::map<Option,set_str_func> set_str_convert_;
-  typedef std::set<int> (*set_int_func)(const Option,std::map<const Option, std::any>); 
-  std::map<Option,set_int_func> set_int_convert_;
-  typedef std::vector<bool> (*vector_bool_func)(const Option,std::map<const Option, std::any>); 
-  std::map<Option,vector_bool_func> vector_bool_convert_;
-  typedef std::vector<std::string> (*vector_str_func)(const Option,std::map<const Option, std::any>); 
-  std::map<Option,vector_str_func> vector_str_convert_;
-
-  template<class T>
-  T convert_(Option option){
-    if (typeid(T) == typeid(int)) return int_convert_[option](option,options_);
-    else if (typeid(T) == typeid(double)) return double_convert_[option](option,options_);
-    else if (typeid(T) == typeid(std::string)) return str_convert_[option](option,options_);
-    else if (typeid(T) == typeid(bool)) return bool_convert_[option](option,options_);
-    return set_bool_convert_[option](option,options_);
-  }
-
- public:
-  virtual ~PropertyObject(void) { }
-
-  virtual bool propValid(const std::any &value) = 0;
-
-  virtual PropertyType getPropertyType(void) const noexcept = 0;
-
-  std::vector<Option> getPropertyOptions(void) const {
-    std::vector<Option> options;
-    for ( std::pair<Option,std::any> option : options_){
-      options.push_back(option.first); 
-    }
-    return options;
-  } 
-
-  // Setup the valid options associated with the parameter
-  // WARNING setting a property value will overwrite existing values
-  void setPropOption(Option option, const std::any & val) {
-    if (!propOptionValid_(option)) {
-      throw std::invalid_argument("Property option is unrecognized.");
-    }
-    setPropOption_(option, val);
-  }
-
-  template<class T>
-  T getPropOption(const Option &option) {
-    if (!propOptionValid_(option)) {
-      std::string err = " An unrecognized property option was detected.";
-      throw std::invalid_argument(err);
-    }
-
-    if ( !conversionAllowed_(option, typeid(T)) ){
-      std::string err = "Conversion of property option's value to type not allowed.";
-      throw std::invalid_argument(err);
-    }
-
-    return convert_<T>(option);
-    //return std::any_cast<T>(options_.at(option));
-  }
-
-  virtual void postCheck(void) const { return; }
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_OBJECT_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertysisterfile.cpp b/src/libcatnip/io/arguments/properties/propertysisterfile.cpp
deleted file mode 100644
index 00e377e..0000000
--- a/src/libcatnip/io/arguments/properties/propertysisterfile.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-
-#include "propertysisterfile.hpp"
-#include "../../../string_support.hpp"
-#include <stdexcept>
-#include <set>
-#include <vector>
-#include <sys/stat.h>
-
-using namespace catnip;
-using namespace std;
-
-PropertySisterFile::PropertySisterFile(void) {
-  string var = "NOT_DEFINED";
-  vector<string> vec_var{var};
-  setPropOption_(Option::ALLOWED_VALUES, vec_var);
-  setPropOption_(Option::FILE_NAME, vec_var);
-  setPropOption_(Option::FILE_PATH, vec_var);
-  setPropOption_(Option::FILE_PATH_NAME, vec_var);
-  vector<string> vec_var2{"false"};
-  setPropOption_(Option::DOES_EXIST, vec_var2);
-}
-
-bool PropertySisterFile::fileExist(const string& fileNamePath) const {
-  struct stat buf;
-  return (stat(fileNamePath.c_str(), &buf) == 0);
-}
-
-void PropertySisterFile::extSupported(const string& ext) const {
-  checkExt(ext);
-  auto exts_ = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
-  for (auto ext_ : exts_) {
-    if (ext_.compare(ext) == 0) {
-      return;
-    }
-  }
-  string err = "The file ext " + ext + " is unsupported";
-  throw invalid_argument(err);
-}
-
-void PropertySisterFile::checkExt(const string& ext) const {
-  string excess = grabStrBeforeLastOccurance(ext, ".");
-  if (excess.compare("") != 0) {
-    throw invalid_argument(
-        "An extension must be of type '.ext'"
-        "you have used " +
-        ext);
-  }
-  return;
-}
-
-bool PropertySisterFile::propValid(const std::any & name_and_path) {
-
-  std::string fileNamePath = any_cast<std::string>(name_and_path); 
-
-  string fileName = lastStringInPath(fileNamePath);
-  string path = getPath(fileNamePath);
-
-  string sisterFileCore = grabStrBeforeLastOccurance(fileName, ".");
-  auto sister_exts = getPropOption<std::set<std::string>>(Option::ALLOWED_VALUES);
-
-  vector<string> fileNames;
-  vector<string> filePaths;
-  vector<string> filePathNames;
-  vector<string> fileExists;
-
-  for (auto sister_ext : sister_exts) {
-
-    if (sister_ext.compare("NOT_DEFINED") != 0) {
-      string sisterFileName = sisterFileCore + sister_ext;
-      string sisterPath = path + sisterFileName;
-
-      fileNames.push_back(sisterFileName);
-      filePaths.push_back(path);
-      filePathNames.push_back(sisterPath);
-      if (fileExist(sisterPath)) {
-        fileExists.push_back("true");
-      } else {
-        fileExists.push_back("false");
-      }
-    }
-  }
-
-  setPropOption_(Option::FILE_NAME, fileNames);
-  setPropOption_(Option::FILE_PATH, filePaths);
-  setPropOption_(Option::FILE_PATH_NAME, filePathNames);
-  setPropOption_(Option::DOES_EXIST, fileExists);
-  return true;
-}
diff --git a/src/libcatnip/io/arguments/properties/propertysisterfile.hpp b/src/libcatnip/io/arguments/properties/propertysisterfile.hpp
deleted file mode 100644
index a5d0874..0000000
--- a/src/libcatnip/io/arguments/properties/propertysisterfile.hpp
+++ /dev/null
@@ -1,30 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_SISTER_FILE_HPP
-#define _CATNIP_PROPERTY_SISTER_FILE_HPP
-
-#include "propertyobject.hpp"
-#include <vector>
-
-namespace catnip {
-
-class PropertySisterFile
-    : public PropertyObject {
- private:
-  bool fileExist(const std::string &) const;
-  void extSupported(const std::string &) const;
-  void checkExt(const std::string &) const;
-
- public:
-
-  PropertySisterFile(void);
-
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::SISTER_FILE;
-  }
-
-  virtual bool propValid(const std::any &fileNamePath) final;
-
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_SISTER_FILE_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertystring.cpp b/src/libcatnip/io/arguments/properties/propertystring.cpp
deleted file mode 100644
index c228397..0000000
--- a/src/libcatnip/io/arguments/properties/propertystring.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#include "propertyobject.hpp"
-#include "propertystring.hpp"
-#include <memory>
-
-using namespace catnip;
-using namespace std;
-
-PropertyString::PropertyString(void) {
-  size_t min_len = 0;
-  size_t max_len = -1;
-  setPropOption_(Option::MIN_LENGTH, min_len);
-  setPropOption_(Option::MAX_LENGTH, max_len);
-}
-
-void PropertyString::stringValid(const string& val) const {
-  if (val.size() > getPropOption<size_t>(Option::MAX_LENGTH)) {
-    string err = "The string is larger than allowed " + val +
-                 " the "
-                 "maximum allowed value is " +
-                 to_string(getPropOption<size_t>(Option::MAX_LENGTH));
-    throw invalid_argument(err);
-  } else if (val.size() < getPropOption<size_t>(Option::MIN_LENGTH)) {
-    string err = "The string is smaller than allowed " + val +
-                 " the "
-                 "maximum allowed value is " +
-                 to_string(getPropOption<size_t>(Option::MIN_LENGTH));
-    throw invalid_argument(err);
-  }
-}
diff --git a/src/libcatnip/io/arguments/properties/propertystring.hpp b/src/libcatnip/io/arguments/properties/propertystring.hpp
deleted file mode 100644
index faf4c46..0000000
--- a/src/libcatnip/io/arguments/properties/propertystring.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_STRING_HPP
-#define _CATNIP_PROPERTY_STRING_HPP
-
-#include "propertyobject.hpp"
-
-namespace catnip {
-
-class PropertyString : public PropertyObject {
- private:
-  void stringValid(const std::string& val) const;
-
- public:
-  PropertyString(void);
-
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::STRING;
-  }
-
-  bool propValid(const std::any& val) {
-
-    std::string value = std::any_cast<std::string>(val);
-    stringValid(value);
-    return true;
-  }
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_STRING_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp b/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
deleted file mode 100644
index ad97998..0000000
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.cpp
+++ /dev/null
@@ -1,147 +0,0 @@
-
-#include "propertystringchoice.hpp"
-#include "../../../string_support.hpp"
-#include <set>
-#include <stdexcept>
-#include <sys/stat.h>
-#include <typeinfo>
-
-using namespace std;
-
-namespace catnip {
-  namespace {
-    std::set<bool> getSetBoolEnforced_(const Option option, std::map<const Option, std::any> options_){
-      set<bool> values;
-      // Because the default is a set of strings
-      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
-      for ( std::string val : stored_values){
-        if( to_upper(val) == "TRUE" ) {
-          values.insert(true);
-        } else if( to_upper(val) == "FALSE") {
-          values.insert(false);
-        }
-      } 
-      return values;
-    }
-
-    std::set<string> getSetStrEnforced_(const Option option, std::map<const Option, std::any> options_){
-      // Because the default is a set of strings
-      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
-      return stored_values;
-    }
-
-    std::set<int> getSetIntEnforced_(const Option option, std::map<const Option, std::any> options_){
-      set<int> values;
-      // Because the default is a set of strings
-      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
-      for ( std::string val : stored_values){
-        if( to_upper(val) == "TRUE" ) {
-          values.insert(1);
-        } else if( to_upper(val) == "FALSE") {
-          values.insert(0);
-        }
-      } 
-      return values;
-    }
-
-    std::set<string> getSetStrAllowedValues_(const Option option, std::map<const Option, std::any> options_){
-      // Because the default is a set of strings
-      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
-      return stored_values;
-    }
-
-    std::vector<string> getVectorStrAllowedValues_(const Option option, std::map<const Option, std::any> options_){
-      vector<string> values;
-      // Because the default is a set of strings
-      set<string> stored_values = std::any_cast<set<string>>(options_.at(option));
-      for ( string val : stored_values ) {
-        values.push_back(val);
-      }
-      return values;
-    }
-  }
-
-  PropertyStringChoice::PropertyStringChoice(void) {
-    set<string> set_var1{"false"};
-    setPropOption_(Option::ENFORCED, set_var1);
-
-    //  setDefaultOptionType_(Option::ENFORCED, type_index(typeid(set<string>)));
-    default_option_type_[Option::ENFORCED] = type_index(typeid(set<string>));
-
-    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<string>)));
-    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<bool>)));
-    allowed_option_types_[Option::ENFORCED].push_back(type_index(typeid(set<int>)));
-
-    set_bool_convert_[Option::ENFORCED] = &catnip::getSetBoolEnforced_;
-    set_str_convert_[Option::ENFORCED] = &catnip::getSetStrEnforced_;
-    set_int_convert_[Option::ENFORCED] = &catnip::getSetIntEnforced_;
-
-    string str = "NOT_DEFINED";
-    set<string> set_var2{str};
-    setPropOption_(Option::ALLOWED_VALUES, set_var2);
-
-    default_option_type_[Option::ALLOWED_VALUES] = type_index(typeid(set<string>));
-
-    allowed_option_types_[Option::ALLOWED_VALUES].push_back(type_index(typeid(set<string>)));
-    allowed_option_types_[Option::ALLOWED_VALUES].push_back(type_index(typeid(vector<string>)));
-
-    set_str_convert_[Option::ALLOWED_VALUES] = &catnip::getSetStrAllowedValues_;
-    vector_str_convert_[Option::ALLOWED_VALUES] = &catnip::getVectorStrAllowedValues_;
-
-  }
-
-  /*void PropertyStringChoice::setPropOption( option,
-    set<string> set_vars) {
-
-    if (option.compare("STRING_CHOICES") == 0) {
-    setPropOption_(option, set_vars);
-    return;
-    } else if (option.compare("STRING_CHOICE_ENFORCED") == 0) {
-    if (set_vars.size() > 1) {
-    string err = "";
-    for (auto var : set_vars) {
-    err.append(var);
-    err.append(" ");
-    }
-    trim(err);
-    throw invalid_argument(
-    "Option STRING_CHOICE_ENFORCED only accepts one "
-    "value either true or false you have passed the following values " +
-    err);
-    }
-
-    string var = *(set_vars.begin());
-    if (var.compare("false") == 0 || var.compare("true") == 0) {
-    setPropOption_(option, set_vars);
-    return;
-    } else {
-    throw invalid_argument("The option " + option +
-    " can only be set to values"
-    " of true or false you have set it to " +
-    var);
-    }
-    }
-    string vars = "";
-    for (auto var : set_vars) {
-    vars.append(var);
-    vars.append(" ");
-    }
-    trim(vars);
-    throw invalid_argument("Unrecognized option value combo " + option + " " +
-    vars);
-    }*/
-
-  bool PropertyStringChoice::propValid(const any& choice) {
-
-    std::string string_choice = any_cast<std::string>(choice);
-    set<string> opt_val = getPropOption<set<string>>(Option::ENFORCED);
-    string val = *(opt_val.begin());
-    if (val.compare("true") == 0) {
-      set<string> str_choices = getPropOption<set<string>>(Option::ALLOWED_VALUES);
-      if (str_choices.count(string_choice) > 0) return true;
-      throw invalid_argument("The value " + string_choice +
-          " is not a valid option");
-    }
-    return true;
-  }
-}
diff --git a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp b/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
deleted file mode 100644
index cc1799a..0000000
--- a/src/libcatnip/io/arguments/properties/propertystringchoice.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_STRING_CHOICE_HPP
-#define _CATNIP_PROPERTY_STRING_CHOICE_HPP
-
-#include "propertyobject.hpp"
-#include <set>
-
-namespace catnip {
-
-class PropertyStringChoice
-    : public PropertyObject {
- private:
-
-   std::set<bool> getSetBoolEnforced_(Option option, std::map<Option, std::any> options_);
-  ;
- public:
-   PropertyStringChoice(void);
-
-   virtual PropertyType getPropertyType(void) const noexcept final {
-     return PropertyType::STRING_CHOICE;
-   }
-
-   virtual bool propValid(const std::any& string_choice) final;
-    };
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_STRING_CHOICE_HPP
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.cpp b/src/libcatnip/io/arguments/properties/propertyswitch.cpp
deleted file mode 100644
index 06251c4..0000000
--- a/src/libcatnip/io/arguments/properties/propertyswitch.cpp
+++ /dev/null
@@ -1,49 +0,0 @@
-
-#include "propertyswitch.hpp"
-
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-PropertySwitch::PropertySwitch() { setPropOption_(Option::DEFAULT, bool(false)); }
-
-void PropertySwitch::switchValid(int val) const {
-  if (val < 0 || val > 1) {
-    string err =
-        "Switches are only allowed to be on or off. By default they "
-        "are set to off. An integer may be provided to the switch to "
-        "toggle the behavior, however the integer is only allowed to "
-        "be a 1 or a 0 you have provided a " +
-        to_string(val);
-    throw invalid_argument(err);
-  }
-}
-
-void PropertySwitch::switchValid(std::string val) const {
-  if (val.compare("0") != 0 && val.compare("1") != 0 &&
-      val.compare("ON") != 0 && val.compare("OFF") != 0 &&
-      val.compare("TRUE") != 0 && val.compare("FALSE") != 0) {
-    string err =
-        "Switches are only allowed to be on or off. By default they "
-        "are set to off. A string may be provided to the switch to "
-        "toggle the behavior, however the string is only allowed to "
-        "be a TRUE/FALSE/ON/OFF you have provided a " +
-        val;
-    throw invalid_argument(err);
-  }
-}
-
-bool PropertySwitch::propValid(const std::any & value) {
-  if( value.type() == typeid(int)){
-    int int_val = any_cast<int>(value);
-    switchValid(int_val); 
-  }else if(value.type() == typeid(std::string)){
-    std::string str_val = any_cast<std::string>(value);
-    switchValid(str_val); 
-  }else if(value.type() != typeid(bool)) {
-    throw invalid_argument("Unrecognized type passed to switch, only recognizes"
-        " int, string and bool types");
-  }
-  return true;
-}
diff --git a/src/libcatnip/io/arguments/properties/propertyswitch.hpp b/src/libcatnip/io/arguments/properties/propertyswitch.hpp
deleted file mode 100644
index 0082b68..0000000
--- a/src/libcatnip/io/arguments/properties/propertyswitch.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-
-#ifndef _CATNIP_PROPERTY_SWITCH_HPP
-#define _CATNIP_PROPERTY_SWITCH_HPP
-
-#include "propertyobject.hpp"
-
-namespace catnip {
-
-class PropertySwitch : public PropertyObject {
- private:
-  void propOptionValueSettingValid_();
-  void switchValid(int val) const;
-  void switchValid(std::string val) const;
-
- public:
-  PropertySwitch(void);
-  
-  virtual PropertyType getPropertyType(void) const noexcept final {
-    return PropertyType::SWITCH; 
-  }
-
-  virtual bool propValid(const std::any & value) final;
-  bool propValid() const {return true;}
-};
-
-}  // namespace catnip
-#endif  // _CATNIP_PROPERTY_SWITCH_HPP

From 8f6bdb03cf652289077eda613a7c68aceabbabbf Mon Sep 17 00:00:00 2001
From: JoshuaSBrown <joshbro42867@yahoo.com>
Date: Wed, 16 Dec 2020 09:29:41 -0700
Subject: [PATCH 68/68] All tests working except io

---
 .gitmodules                             |   3 +
 CMakeLists.txt                          |  85 ++--
 cmake/InstallCatch2.cmake               |  22 +-
 cmake/InstallMAMAP.cmake                |  10 +
 external/MAMAP                          |   1 +
 src/CMakeLists.txt                      |   2 +-
 src/libcatnip/CMakeLists.txt            |   8 +-
 src/libcatnip/README.md                 |  17 +
 src/libcatnip/atom.hpp                  |   8 +
 src/libcatnip/atom_group.hpp            |  12 +-
 src/libcatnip/atom_group_container.cpp  |  12 +-
 src/libcatnip/atom_group_container.hpp  |   8 +-
 src/libcatnip/atom_system.hpp           |   9 +-
 src/libcatnip/basis_map.cpp             |   2 +-
 src/libcatnip/basis_map.hpp             |   2 +-
 src/libcatnip/io/io.cpp                 | 547 ++++++++++++++++--------
 src/libcatnip/io/io.hpp                 |   9 +-
 src/libcatnip/parameters.cpp            |  26 ++
 src/libcatnip/parameters.hpp            |  11 +
 src/libcatnip/transfer_complex.cpp      |  22 +-
 src/tests/CMakeLists.txt                |  77 ++--
 src/tests/test_argumentdouble.cpp       |  93 ----
 src/tests/test_argumentfile.cpp         | 164 -------
 src/tests/test_argumentint.cpp          |  91 ----
 src/tests/test_argumentparser.cpp       | 195 ---------
 src/tests/test_argumentstring.cpp       | 128 ------
 src/tests/test_argumentswitch.cpp       |  76 ----
 src/tests/test_atom_group_container.cpp |  40 +-
 src/tests/test_atom_system.cpp          | 238 +++++------
 src/tests/test_basis_map.cpp            |  79 ++--
 src/tests/test_io.cpp                   |  17 +-
 src/tests/test_propertyfileexist.cpp    |  67 ---
 src/tests/test_propertyfileext.cpp      |  63 ---
 src/tests/test_propertynumerical.cpp    |  67 ---
 src/tests/test_propertysisterfile.cpp   | 116 -----
 src/tests/test_propertystring.cpp       |  57 ---
 src/tests/test_propertystringchoice.cpp |  88 ----
 src/tests/test_propertyswitch.cpp       |  89 ----
 src/tests/test_swap_engine.cpp          | 166 +++----
 src/tools/calcJ.cpp                     |   9 +-
 40 files changed, 849 insertions(+), 1887 deletions(-)
 create mode 100644 cmake/InstallMAMAP.cmake
 create mode 160000 external/MAMAP
 create mode 100644 src/libcatnip/README.md
 delete mode 100644 src/tests/test_argumentdouble.cpp
 delete mode 100644 src/tests/test_argumentfile.cpp
 delete mode 100644 src/tests/test_argumentint.cpp
 delete mode 100644 src/tests/test_argumentparser.cpp
 delete mode 100644 src/tests/test_argumentstring.cpp
 delete mode 100644 src/tests/test_argumentswitch.cpp
 delete mode 100644 src/tests/test_propertyfileexist.cpp
 delete mode 100644 src/tests/test_propertyfileext.cpp
 delete mode 100644 src/tests/test_propertynumerical.cpp
 delete mode 100644 src/tests/test_propertysisterfile.cpp
 delete mode 100644 src/tests/test_propertystring.cpp
 delete mode 100644 src/tests/test_propertystringchoice.cpp
 delete mode 100644 src/tests/test_propertyswitch.cpp

diff --git a/.gitmodules b/.gitmodules
index 800345d..7ba64b0 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "external/Catch2"]
 	path = external/Catch2
 	url = https://github.com/catchorg/Catch2.git
+[submodule "external/MAMAP"]
+	path = external/MAMAP
+	url = https://github.com/JoshuaSBrown/MAMAP.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c5d3745..d71359a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required (VERSION 3.14)
-project (catnip)
+project (catnip VERSION 2.0.0)
 
 ##############################################################################
 # Defining options 
@@ -7,15 +7,20 @@ project (catnip)
 option(ENABLE_TESTS "Enable testing" OFF)
 option(DOWNLOAD_TUTORIAL_FILES "Download tutorial files" ${ENABLE_TESTS})
 option(ENABLE_INTEGRATION_TESTING "Enable integration tests" ${ENABLE_TESTS})
-option(ENABLE_UNIT_TESTING "Enable tests" ${ENABLE_TESTS})
+option(ENABLE_UNIT_TESTING "Enable unit tests" ${ENABLE_TESTS})
 option(ENABLE_PROFILING "Enable profiling" OFF)
 option(CODE_COVERAGE "Enable coverage reporting" OFF)
 
+##############################################################################
+# Override default options 
+##############################################################################
+set(DOWNLOAD_TUTORIAL_FILES ${ENABLE_TESTS} CACHE STRING "Download tutorial files" FORCE)
+set(ENABLE_INTEGRATION_TESTING ${ENABLE_TESTS} CACHE STRING "Enable integration tests" FORCE)
+set(ENABLE_UNIT_TESTING ${ENABLE_TESTS} CACHE STRING "Enable unit tests" FORCE)
+
 ##############################################################################
 # Defining settings 
 ##############################################################################
-set(catnip_VERSION_MAJOR 2 )
-set(catnip_VERSION_MINOR 0 )
 set(catnip_YEAR_PUBLISHED 2018 )
 set(catnip_AUTHOR_SURNAME "\"Brown\"" )
 set(catnip_AUTHOR_INITIALS "\"J. S.\"" )
@@ -32,13 +37,25 @@ set(LOG_LEVEL 0 CACHE STRING "Choose the log level" )
 # important for using gcov .o.gcno or .cpp.gcno now will be .gcno
 set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE 1)
 set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -Werror")
+
+##############################################################################
+# Check for Dependencies 
+##############################################################################
+
+find_package(mamap REQUIRED)
+if( NOT ${mamap_FOUND} )
+  include(${catnip_SOURCE_DIR}/cmake/InstallMAMAP.cmake)
+else()
+  message(STATUS "found system installed mamap will not download")
+endif()
+
 ##############################################################################
 # Configuring header file with cmake variables 
 ##############################################################################
 # Configure header file to pass some of the CMake settings to the source code
 configure_file(
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnip_config.hpp.in"
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/catnip_config.hpp"
+  "${catnip_SOURCE_DIR}/src/libcatnip/catnip_config.hpp.in"
+  "${catnip_SOURCE_DIR}/src/libcatnip/catnip_config.hpp"
   )
 
 ##############################################################################
@@ -55,7 +72,7 @@ add_definitions(-DLOG_LEVEL=${LOG_LEVEL})
 ##############################################################################
 # Setting up profiling 
 ##############################################################################
-if(ENABLE_PROFILING)
+if(${ENABLE_PROFILING})
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pg")
   set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -pg")
@@ -63,51 +80,53 @@ endif()
 ##############################################################################
 # Setting up testing 
 ##############################################################################
-if(ENABLE_INTEGRATION_TESTING)
-  if(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
+message("ENable tests ${ENABLE_TESTS} and integration ${ENABLE_INTEGRATION_TESTING}")
+if(${ENABLE_INTEGRATION_TESTING})
+  if(EXISTS "${catnip_SOURCE_DIR}/GAUSSIANFILES")
     message(STATUS "GAUSSIANFILES found will not download")
     set(DOWNLOAD_TUTORIAL_FILES OFF)
-  else(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
+  else(EXISTS "${catnip_SOURCE_DIR}/GAUSSIANFILES")
     message(STATUS "GAUSSIANFILES not found will attempt to download")
-    include(${PROJECT_SOURCE_DIR}/cmake/InstallGdown.cmake)
-  endif(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
+    include(${catnip_SOURCE_DIR}/cmake/InstallGdown.cmake)
+  endif(EXISTS "${catnip_SOURCE_DIR}/GAUSSIANFILES")
 endif()
 
-if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+if(${ENABLE_UNIT_TESTING} OR ${ENABLE_INTEGRATION_TESTING})
   find_package(Catch2 2.11.1)
-  if( NOT Catch2 )
-    include(${PROJECT_SOURCE_DIR}/cmake/InstallCatch2.cmake)
+  if( NOT ${Catch2_FOUND} )
+    include(${catnip_SOURCE_DIR}/cmake/InstallCatch2.cmake)
   else()
     message(STATUS "found system installed Catch2 will not download")
   endif()
   enable_testing()
+  include(Catch)
   include(ParseAndAddCatchTests)
 
-  if (ENABLE_INTEGRATION_TESTING)
-    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 
-      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
-    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.pun" 
-      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/90_unordered")
-
-    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_pair.pun" 
-      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
-    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/ref.pun" 
-      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
-    file( COPY "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_2.pun" 
-      DESTINATION "${PROJECT_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+  if (${ENABLE_INTEGRATION_TESTING})
+    file( COPY "${catnip_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.log" 
+      DESTINATION "${catnip_BINARY_DIR}/GAUSSIANFILES/90_unordered")
+    file( COPY "${catnip_SOURCE_DIR}/GAUSSIANFILES/90_unordered/90_pair.pun" 
+      DESTINATION "${catnip_BINARY_DIR}/GAUSSIANFILES/90_unordered")
+
+    file( COPY "${catnip_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_pair.pun" 
+      DESTINATION "${catnip_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+    file( COPY "${catnip_SOURCE_DIR}/GAUSSIANFILES/30_unordered/ref.pun" 
+      DESTINATION "${catnip_BINARY_DIR}/GAUSSIANFILES/30_unordered")
+    file( COPY "${catnip_SOURCE_DIR}/GAUSSIANFILES/30_unordered/30_2.pun" 
+      DESTINATION "${catnip_BINARY_DIR}/GAUSSIANFILES/30_unordered")
   endif()
 
-  if (ENABLE_UNIT_TESTING)
-    file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.pun" 
-      DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
-    file( COPY "${PROJECT_SOURCE_DIR}/src/tests/testfile.log" 
-      DESTINATION "${PROJECT_BINARY_DIR}/src/tests")
+  if (${ENABLE_UNIT_TESTING})
+    file( COPY "${catnip_SOURCE_DIR}/src/tests/testfile.pun" 
+      DESTINATION "${catnip_BINARY_DIR}/src/tests")
+    file( COPY "${catnip_SOURCE_DIR}/src/tests/testfile.log" 
+      DESTINATION "${catnip_BINARY_DIR}/src/tests")
   endif()
 
 endif()
 ##############################################################################
 # Compiling build tree/paths 
 ##############################################################################
-add_subdirectory("${PROJECT_SOURCE_DIR}/src")
+add_subdirectory("${catnip_SOURCE_DIR}/src")
 
 
diff --git a/cmake/InstallCatch2.cmake b/cmake/InstallCatch2.cmake
index b645d23..687e0f9 100644
--- a/cmake/InstallCatch2.cmake
+++ b/cmake/InstallCatch2.cmake
@@ -1,25 +1,11 @@
-
-#
-#if(NOT EXISTS "${CMAKE_SOURCE_DIR}/external/Catch2/includes")
-#  find_program(CURL curl)
-#  if( NOT CURL)
-#    message(FATAL_ERROR "Unable to download Catch2, unable to locate curl, please install curl")
-#  else()
-#    execute_process(COMMAND mkdir -p ${CMAKE_SOURCE_DIR}/external/Catch2/single_include/catch2)
-#    execute_process(COMMAND ${CURL} https://raw.githubusercontent.com/catchorg/Catch2/master/single_include/catch2/catch.hpp -o ${CMAKE_SOURCE_DIR}/external/Catch2/single_include/catch2/catch.hpp)
-#  endif()
-#  add_library(Catch2 INTERFACE) 
-#  target_include_directories(Catch2 INTERFACE ${CMAKE_SOURCE_DIR}/external/Catch2/single_include)
-#endif()
-
 # If Catch2 is not found, instead use the git submodule
-if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/external/Catch2/single_include)
+if (NOT EXISTS ${catnip_CURRENT_SOURCE_DIR}/external/Catch2/single_include)
   # Unable to find the header files for Catch2 or they don't exist
   message(STATUS "Downloading Catch2 submodule.")
 
   # Clone the submodule
-  execute_process(COMMAND git submodule update --init --force -- external/Catch2 WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+  execute_process(COMMAND git submodule update --init --force -- external/Catch2 WORKING_DIRECTORY ${catnip_SOURCE_DIR})
 endif()
 
-add_subdirectory(${CMAKE_SOURCE_DIR}/external/Catch2)
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/external/Catch2/contrib")
+add_subdirectory(${catnip_SOURCE_DIR}/external/Catch2)
+list(APPEND CMAKE_MODULE_PATH "${catnip_SOURCE_DIR}/external/Catch2/contrib")
diff --git a/cmake/InstallMAMAP.cmake b/cmake/InstallMAMAP.cmake
new file mode 100644
index 0000000..09b06d8
--- /dev/null
+++ b/cmake/InstallMAMAP.cmake
@@ -0,0 +1,10 @@
+# If Catch2 is not found, instead use the git submodule
+if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/external/MAMAP/include/mamap/argument_parser.hpp)
+  # Unable to find the header files for Catch2 or they don't exist
+  message(STATUS "Downloading MAMAP submodule.")
+
+  # Clone the submodule
+  execute_process(COMMAND git submodule update --init --force -- external/MAMAP WORKING_DIRECTORY ${catnip_SOURCE_DIR})
+endif()
+
+add_subdirectory(${catnip_SOURCE_DIR}/external/MAMAP)
diff --git a/external/MAMAP b/external/MAMAP
new file mode 160000
index 0000000..0641040
--- /dev/null
+++ b/external/MAMAP
@@ -0,0 +1 @@
+Subproject commit 064104002b34a410f185fd8657196bcd70db5650
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6efb70d..71ce73d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,6 +1,6 @@
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/libcatnip")
 #add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tools")
-if(ENABLE_UNIT_TESTING OR ENABLE_INTEGRATION_TESTING)
+if(${ENABLE_UNIT_TESTING} OR ${ENABLE_INTEGRATION_TESTING})
   message(STATUS "adding test directory")
   add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/tests")
 endif()
diff --git a/src/libcatnip/CMakeLists.txt b/src/libcatnip/CMakeLists.txt
index 9daf7d5..9484b81 100644
--- a/src/libcatnip/CMakeLists.txt
+++ b/src/libcatnip/CMakeLists.txt
@@ -1,11 +1,11 @@
 
 file(GLOB CATNIP_SOURCE_FILES 
-  io/arguments/*.cpp 
-  io/arguments/properties/*.cpp
-  io/argumentparser.cpp
+  io/io.cpp
   string_support.cpp 
-  io/file_readers/*.cpp)
+  io/file_readers/*.cpp
+  *.cpp)
 
 add_library(libcatnip ${CATNIP_SOURCE_FILES})
 set_property(TARGET libcatnip PROPERTY CXX_STANDARD 17)
 target_include_directories(libcatnip PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_link_libraries(libcatnip PUBLIC mamap)
diff --git a/src/libcatnip/README.md b/src/libcatnip/README.md
new file mode 100644
index 0000000..49842f7
--- /dev/null
+++ b/src/libcatnip/README.md
@@ -0,0 +1,17 @@
+ # Outline 
+
+Flow of the calc_J should follow as:
+
+1. Read arguments
+2. Assign files to atomic groups
+3. Read atomic coordinates
+4. Create group container
+5. Assign group types
+6. Create atom system
+7. Check basis sets line up between components and complex
+8. Load overlap matrices and molecular orbital coefficients
+9. Create swap engine  
+10. Order matrices if needed
+11. Generate Transfer integral complex
+12. Calculate transfer integral
+ 
diff --git a/src/libcatnip/atom.hpp b/src/libcatnip/atom.hpp
index 7100708..c5e4718 100644
--- a/src/libcatnip/atom.hpp
+++ b/src/libcatnip/atom.hpp
@@ -14,6 +14,14 @@
 
 namespace catnip {
 
+  /**
+   * @brief Atom Class
+   *
+   * This class is responsible for packaging basic atomic information including
+   *    atomic coordinates
+   *    element
+   *    the number of basis functions
+   */
   class Atom {
     private:
       // Element should not be able to change
diff --git a/src/libcatnip/atom_group.hpp b/src/libcatnip/atom_group.hpp
index 6f0ca80..dd4ee12 100644
--- a/src/libcatnip/atom_group.hpp
+++ b/src/libcatnip/atom_group.hpp
@@ -52,8 +52,15 @@ namespace catnip {
   };
 
   /**
-   * @brief Stores the name of the atom group, the group type and the atoms in
-   * the group
+   * @brief Atom group essentially packages anything associated with a file 
+   *
+   * Atom group is responsible for packaging the atoms associated with a 
+   * group of atoms in one place. The group type can be assigned to the atom
+   * group once it is known. Once the group type is known a bunch of other 
+   * operations open up..
+   *
+   * Probably the core use of this class is to be able to compare atoms in the
+   * group and ensure that they are equivalent. 
    *
    */
   class AtomGroup {
@@ -77,6 +84,7 @@ namespace catnip {
       // Attempt to load overlap matrix hopefully a log file exists which can do
       // this
       void loadOverlapMatrix() {};
+      void loadMOCoefMatrix() {};
 
       std::string getName() const noexcept { return name_; }
 
diff --git a/src/libcatnip/atom_group_container.cpp b/src/libcatnip/atom_group_container.cpp
index fa54617..23f6807 100644
--- a/src/libcatnip/atom_group_container.cpp
+++ b/src/libcatnip/atom_group_container.cpp
@@ -181,7 +181,7 @@ namespace catnip {
 
   // As soon as we add a new atom group it should invalidate the labels on 
   // all the other groups
-  void AtomGroupContainer::add( std::unique_ptr<AtomGroup> & atom_group ) {
+  void AtomGroupContainer::add( std::unique_ptr<AtomGroup> atom_group ) {
     std::cout << "Adding group " << atom_group->getName() << std::endl; 
     if( isUniqueGroup_(atom_group) ){
       std::cout << "Is unique" << std::endl;
@@ -222,4 +222,14 @@ namespace catnip {
     return false; 
   }
 
+  std::vector<GroupType> AtomGroupContainer::getType(const std::string & group_name) const { 
+    std::vector<GroupType> group_types;
+    for ( const std::unique_ptr<AtomGroup> & grp : atom_groups_ ){
+      if ( group_name == grp->getName() ) {
+        group_types.push_back(grp->getType());
+      }
+    } 
+    return group_types;
+  }
+
 }  // namespace catnip
diff --git a/src/libcatnip/atom_group_container.hpp b/src/libcatnip/atom_group_container.hpp
index 7249bba..a466777 100644
--- a/src/libcatnip/atom_group_container.hpp
+++ b/src/libcatnip/atom_group_container.hpp
@@ -25,6 +25,10 @@ namespace catnip {
    * What this means is that if you pass in atom groups and thier state is not
    * known, this class can automatically detect if they are related, if they
    * are an island a complex or a component.
+   *
+   * Accurate assignment of a group type can only be achieved after all of the 
+   * groups are added. If a new group is added after group types have been 
+   * assigned it will invalidate the previously assigned group types. 
    */
   class AtomGroupContainer {
       std::vector<std::unique_ptr<AtomGroup>> atom_groups_;
@@ -61,7 +65,7 @@ namespace catnip {
       std::vector<std::unique_ptr<AtomGroup>>::const_iterator 
         end() const { return atom_groups_.end(); }
 
-      void add( std::unique_ptr<AtomGroup> & atom_group );
+      void add( std::unique_ptr<AtomGroup> atom_group );
 
       size_t size() const noexcept { return  atom_groups_.size(); }
 
@@ -81,6 +85,8 @@ namespace catnip {
 
       const GroupType & getType(int index) const { return atom_groups_.at(index)->getType(); }
 
+      std::vector<GroupType> getType(const std::string & group_name) const; 
+
       /**
        * @brief Get the indices of all the groups of the specified group type
        *
diff --git a/src/libcatnip/atom_system.hpp b/src/libcatnip/atom_system.hpp
index ddc301c..b040dd0 100644
--- a/src/libcatnip/atom_system.hpp
+++ b/src/libcatnip/atom_system.hpp
@@ -18,11 +18,16 @@ namespace catnip {
    * change group types
    *
    * It can only be created if there are known group types and there is only
-   * a single complex, and it's components, 
+   * a single complex, and it's components. The presence of these group types
+   * is what makes it possible to run the charge transfer integral calculations.
    *
    * Each atom in a component must only be shared with the complex, the atom of
    * a component is allowed to be of a different element then what is in the 
-   * complex, but must have the same position
+   * complex, but must have the same position.
+   *
+   * Basis functions can be assigned using the atom system, atoms shared between
+   * a component and the complex will be made consistent in terms of the
+   * number of basis functions that are associated with them. 
    */
   class AtomSystem {
       // Atoms in each component that share the same location with atoms in
diff --git a/src/libcatnip/basis_map.cpp b/src/libcatnip/basis_map.cpp
index 393a5ec..656ed44 100644
--- a/src/libcatnip/basis_map.cpp
+++ b/src/libcatnip/basis_map.cpp
@@ -11,7 +11,7 @@
 
 namespace catnip {
 
-  BasisMap::BasisMap(AtomSystem atm_sys){
+  BasisMap::BasisMap(const AtomSystem & atm_sys){
     if ( not atm_sys.systemComplete() ) {
       throw std::runtime_error("Cannot build an index map from an incomplete "
           "atom system.");
diff --git a/src/libcatnip/basis_map.hpp b/src/libcatnip/basis_map.hpp
index 42517ab..8325581 100644
--- a/src/libcatnip/basis_map.hpp
+++ b/src/libcatnip/basis_map.hpp
@@ -20,7 +20,7 @@ namespace catnip {
   class BasisMap {
     public:
       BasisMap() = default;
-      BasisMap(AtomSystem atm_sys);
+      BasisMap(const AtomSystem & atm_sys);
       // The component rows and colums in their current locations in  
       // in the full system matrix of the complex
       std::map<int,std::vector<int>> row_col_current;
diff --git a/src/libcatnip/io/io.cpp b/src/libcatnip/io/io.cpp
index 771a85e..9f653fd 100644
--- a/src/libcatnip/io/io.cpp
+++ b/src/libcatnip/io/io.cpp
@@ -4,15 +4,21 @@
 #include <string>
 #include <vector>
 
-#include "../parameters.hpp"
-#include "../string_support.hpp"
+#include <mamap/arguments/argumenttypes.hpp>
+#include <mamap/arguments/properties/propertyoptions.hpp>
+#include <mamap/argumentparser.hpp>
+#include <mamap/string_support.hpp>
+
+#include "parameters.hpp"
 #include "io.hpp"
 
+#include <mamap/argumentparser.hpp>
+
 using namespace std;
 
 namespace catnip {
 
-unique_ptr<ArgumentParser> prepareParser(void) {
+unique_ptr<mamap::ArgumentParser> prepareParser(void) {
 
   // Setup flags
   vector<string> flag1;
@@ -176,13 +182,29 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   vector<string> flag20;
   flag20.push_back("--log");
   flag20.push_back("-l");
-  desc = "Provide all .log files and allow catnip to figure the rest out.";
+  desc = "Provide all .log files and allow catnip to figure the rest out. ";
+  desc += "\nCaveats\n";
+  desc += "1. if the --pun file flag is not used the pun/orb/.7 files must ";
+  desc += "appear in the same folder as the log files and have the same core ";
+  desc += "file name as the log file.";
+  desc += "2. if the --pun file flag is also provided the same number of files ";
+  desc += "must be provided as is provided with the --log flag, and they must ";
+  desc += "either be entered in the same order or they must have the same core";
+  desc += " file name.";
   flag20.push_back(desc);
 
   vector<string> flag21;
   flag21.push_back("--pun");
   flag21.push_back("-p");
-  desc = "Provide all .pun/.7/.orb files and allow catnip to figure the rest out.";
+  desc = "Provide all .punt/.7/.orb files and allow catnip to figure the rest out. ";
+  desc += "\nCaveats\n";
+  desc += "1. if the --log file flag is not used the .log files must ";
+  desc += "appear in the same folder as the .pun/.7/.orb files and have the same core ";
+  desc += "file name as the .pun/.7/.orb file.";
+  desc += "2. if the --log file flag is also provided the same number of files ";
+  desc += "must be provided as is provided with the --pun flag, and they must ";
+  desc += "either be entered in the same order or they must have the same core";
+  desc += " file name.";
   flag21.push_back(desc);
 
   set<vector<string>> flags;
@@ -206,50 +228,50 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   flags.insert(flag20);
   flags.insert(flag21);
 
-  unique_ptr<ArgumentParser> ArgPars(new ArgumentParser(flags));
+  unique_ptr<mamap::ArgumentParser> ArgPars(new mamap::ArgumentParser(flags));
 
   // Setup rules for handling flags
   set<string> exts{".orb", ".7", ".pun"};
   string ext_log = ".log";
 
   {
-    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, ext_log);
-    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, exts);
-    ArgPars->setFlagArgOpt("--log", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
-
-    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts);
-    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, ext_log);
-    ArgPars->setFlagArgOpt("--pun", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
+    ArgPars->setFlagArgOpt("--log", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--log", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--log", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, true);
+
+    ArgPars->setFlagArgOpt("--pun", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, true);
   }
 
   // Setting up rules guiding pun files
   {
-    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts);
-    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, ext_log);
-    ArgPars->setFlagArgOpt("--pun_P", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
-
-    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts);
-    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, ext_log);
-    ArgPars->setFlagArgOpt("--pun_1", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
-
-    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::ALLOWED_VALUES, exts);
-    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, ext_log);
-    ArgPars->setFlagArgOpt("--pun_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
+    ArgPars->setFlagArgOpt("--pun_P", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_P", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_P", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--pun_1", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_1", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_1", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--pun_2", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::ALLOWED_VALUES, exts);
+    ArgPars->setFlagArgOpt("--pun_2", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, ext_log);
+    ArgPars->setFlagArgOpt("--pun_2", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
 
   }
 
@@ -259,51 +281,51 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Setting rules guiding log files
   {
-    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts_log);
-    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, exts_other);
-    ArgPars->setFlagArgOpt("--log_P", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
-
-    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts_log);
-    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, exts_other);
-    ArgPars->setFlagArgOpt("--log_1", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
-
-    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::FILE_EXT,
-                           Option::ALLOWED_VALUES, exts_log);
-    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::SISTER_FILE,
-                           Option::ALLOWED_VALUES, exts_other);
-    ArgPars->setFlagArgOpt("--log_2", ArgumentType::FILES, PropertyType::FILE_EXISTS,
-                           Option::MUST_EXIST, 0);
+    ArgPars->setFlagArgOpt("--log_P", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_P", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_P", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--log_1", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_1", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_1", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
+
+    ArgPars->setFlagArgOpt("--log_2", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXT,
+                           mamap::Option::ALLOWED_VALUES, exts_log);
+    ArgPars->setFlagArgOpt("--log_2", mamap::ArgumentType::FILES, mamap::PropertyType::SISTER_FILE,
+                           mamap::Option::ALLOWED_VALUES, exts_other);
+    ArgPars->setFlagArgOpt("--log_2", mamap::ArgumentType::FILES, mamap::PropertyType::FILE_EXISTS,
+                           mamap::Option::MUST_EXIST, 0);
   }
 
   set<string> spin_opts{"Alpha", "Beta"};
 
   // Setting rules guiding spin
   {
-    ArgPars->setFlagArgOpt("--spin_P", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ENFORCED,
+    ArgPars->setFlagArgOpt("--spin_P", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_P", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
+    ArgPars->setFlagArgOpt("--spin_P", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ALLOWED_VALUES,
                            spin_opts);
 
-    ArgPars->setFlagArgOpt("--spin_1", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ENFORCED,
+    ArgPars->setFlagArgOpt("--spin_1", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_1", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
+    ArgPars->setFlagArgOpt("--spin_1", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ALLOWED_VALUES,
                            spin_opts);
 
-    ArgPars->setFlagArgOpt("--spin_2", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ENFORCED,
+    ArgPars->setFlagArgOpt("--spin_2", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--spin_2", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
+    ArgPars->setFlagArgOpt("--spin_2", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ALLOWED_VALUES,
                            spin_opts);
 
     ArgPars->setFlagDefaultValue("--spin_P", "Alpha");
@@ -314,18 +336,18 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   // Setting rules guidling orbital type
   set<string> orb_opts{"HOMO", "LUMO"};
   {
-    ArgPars->setFlagArgOpt("--orbital_type_1", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ENFORCED,
+    ArgPars->setFlagArgOpt("--orbital_type_1", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--orbital_type_1", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
+    ArgPars->setFlagArgOpt("--orbital_type_1", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ALLOWED_VALUES,
                            orb_opts);
 
-    ArgPars->setFlagArgOpt("--orbital_type_2", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ENFORCED,
+    ArgPars->setFlagArgOpt("--orbital_type_2", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ENFORCED,
                            "true");
-    ArgPars->setFlagArgOpt("--orbital_type_2", ArgumentType::STRING,
-                           PropertyType::STRING_CHOICE, Option::ALLOWED_VALUES,
+    ArgPars->setFlagArgOpt("--orbital_type_2", mamap::ArgumentType::STRING,
+                           mamap::PropertyType::STRING_CHOICE, mamap::Option::ALLOWED_VALUES,
                            orb_opts);
 
     ArgPars->setFlagDefaultValue("--orbital_type_1", "HOMO");
@@ -334,8 +356,8 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Set argument allowed values for counterpoise
   {
-    ArgPars->setFlagArgOpt("--counter_poise", ArgumentType::SWITCH,
-                           PropertyType::SWITCH, Option::VALUE, "OFF");
+    ArgPars->setFlagArgOpt("--counter_poise", mamap::ArgumentType::SWITCH,
+                           mamap::PropertyType::SWITCH, mamap::Option::VALUE, "OFF");
 
     // By default the flag counter poise is turned off
     ArgPars->setFlagDefaultValue("--counter_poise", "OFF");
@@ -343,24 +365,24 @@ unique_ptr<ArgumentParser> prepareParser(void) {
 
   // Set argument for allowing printing of all transfer integrals
   {
-    ArgPars->setFlagArgOpt("--all", ArgumentType::SWITCH,
-        PropertyType::SWITCH, Option::VALUE, "OFF");
+    ArgPars->setFlagArgOpt("--all", mamap::ArgumentType::SWITCH,
+        mamap::PropertyType::SWITCH, mamap::Option::VALUE, "OFF");
 
     // By default the flag counter poise is turned off
     ArgPars->setFlagDefaultValue("--all", "OFF");
   }
 
   {
-    ArgPars->setFlagArgOpt("--citation", ArgumentType::SWITCH, PropertyType::SWITCH,
-                           Option::VALUE, "OFF");
+    ArgPars->setFlagArgOpt("--citation", mamap::ArgumentType::SWITCH, mamap::PropertyType::SWITCH,
+                           mamap::Option::VALUE, "OFF");
 
     // By default the flag citation is turned off
     ArgPars->setFlagDefaultValue("--citation", "OFF");
   }
 
   {
-    ArgPars->setFlagArgOpt("--version", ArgumentType::SWITCH, PropertyType::SWITCH,
-                           Option::VALUE, "OFF");
+    ArgPars->setFlagArgOpt("--version", mamap::ArgumentType::SWITCH, mamap::PropertyType::SWITCH,
+                           mamap::Option::VALUE, "OFF");
 
     // By default the flag citation is turned off
     ArgPars->setFlagDefaultValue("--version", "OFF");
@@ -369,8 +391,8 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   // Set rules guiding orbital numbers
   // Use default settings for min and max numbers
   {
-    ArgPars->addFlagArg("--orbital_num_1", ArgumentType::NUMERICAL);
-    ArgPars->addFlagArg("--orbital_num_2", ArgumentType::NUMERICAL);
+    ArgPars->addFlagArg("--orbital_num_1", mamap::ArgumentType::NUMERIC);
+    ArgPars->addFlagArg("--orbital_num_2", mamap::ArgumentType::NUMERIC);
 
     int orb_num = 0;
     ArgPars->setFlagDefaultValue("--orbital_num_1", orb_num);
@@ -379,43 +401,113 @@ unique_ptr<ArgumentParser> prepareParser(void) {
   return ArgPars;
 }
 
-unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
+unique_ptr<Parameters> prepareParameters(unique_ptr<mamap::ArgumentParser>& ArgParse) {
 
-  map<string, string> flag_arg;
-  map<string, string> flag_sister_arg;
+  map<string, std::vector<string>> flag_arg;
+  map<string, std::vector<string>> flag_sister_arg;
 
-  vector<string> flags{"--pun_P", "--pun_1", "--pun_2",
-                       "--log_P", "--log_1", "--log_2"};
+  vector<string> flags{"--pun_P", "--pun_1", "--pun_2","--pun",
+                       "--log_P", "--log_1", "--log_2","--log"};
 
-  vector<string> flags_sister{"--log_P", "--log_1", "--log_2",
-                              "--pun_P", "--pun_1", "--pun_2"};
+  vector<string> flags_sister{"--log_P", "--log_1", "--log_2","--log",
+                              "--pun_P", "--pun_1", "--pun_2","--pun"};
 
+  // Determine if each log or pun file has a sister file, and if it does store
+  // it in case that particular file it not passed in. 
   for (size_t i = 0; i < flags.size(); ++i) {
-    auto flag = flags.at(i);
-    auto flag_sister = flags_sister.at(i);
-    ArgumentType argu = ArgumentType::FILES;
-    PropertyType prop = PropertyType::FILE_EXISTS;
-    Option opt = Option::DOES_EXIST;
-
-    string fileName;
-    std::vector<bool> exists = ArgParse->get<bool>(flag, argu, prop, opt);
-    if ( exists ) {
-      flag_arg[flag] = ArgParse->getStrs(flag).at(0);
-    }
-    prop = PropertyType::SISTER_FILE;
-    opt = Option::VALUE;
-    std::string line = ArgParse->get<std::string>(flag, argu, prop, opt);
-    opt = Option::FILE_PATH_NAME;
-    std::string line2 = ArgParse->get<std::string>(flag, argu, prop, opt);
-    auto sisters_exist = splitSt(line);
-    vector<string> sister_file_paths = splitSt(line2);
-    int countFiles = 0;
-    for (auto sister_exists : sisters_exist) {
-      if (sister_exists.compare("true") == 0) {
-        flag_sister_arg[flag_sister] = sister_file_paths.at(countFiles);
+    // 1. Get the possible fileNames of the sister files
+    // When a sister file is calcualted it takes the core file name and 
+    // generates the appropriate substitutes. E.g. if -logs flag is provided
+    // --logs core.log 
+    //
+    // then the sister file names will be calculated as
+    // core.pun
+    // core.7
+    // core.orb
+    //
+    // But to determine if any of these files exist we have to get the value
+    // of the DOES_EXIST option
+    const std::string & flag = flags.at(i);
+    const std::string & sister_flag = flags_sister.at(i);
+
+    // Should return a vector of vector of strings
+    // The first vector is for each argument passed to the flag
+    // the second vector is the option values associated with each argument
+    // E.g. for the --pun flag
+    //
+    // --log dir1/file1.log dir2/file2.log dir3/file3.log
+    //
+    // There are 3 arguments passed to --log 
+    //
+    // Each argument will have a set of potential sister files associate with
+    // it
+    //
+    // dir1/file1.log   :   dir1/file1.log dir1/file1.7 dir1/file1.orb
+    // dir2/file2.log   :   dir2/file2.log dir2/file2.7 dir2/file2.orb
+    // dir3/file3.log   :   dir3/file3.log dir3/file3.7 dir3/file3.orb
+    auto arg_potential_sister_files = 
+      ArgParse->getFlagArgOptValues<std::vector<std::string>>(
+        flag,
+        mamap::ArgumentType::FILES,
+        mamap::PropertyType::SISTER_FILE,
+        mamap::Option::FILE_PATH_NAME);
+
+    // Does the file passed in as an argument actually exist, using the example
+    // above
+    //
+    // --log dir1/file1.log dir2/file2.log dir3/file3.log
+    //
+    // This would check that dir1/file1.log dir2/file2.log and dir3/file3.log
+    // exists. will return a vector of bools
+    auto arg_potential_files_exist = 
+      ArgParse->getFlagArgOptValues<bool>(
+          flag,
+          mamap::ArgumentType::FILES,
+          mamap::PropertyType::FILE_EXISTS,
+          mamap::Option::DOES_EXIST);
+
+    // 2. Determine which files exist and choose a suitable substitute
+    //
+    // Should return a vector of vectors of bools
+    auto arg_potential_sister_files_exist = 
+      ArgParse->getFlagArgOptValues<std::vector<bool>>(
+        flag,
+        mamap::ArgumentType::FILES,
+        mamap::PropertyType::SISTER_FILE,
+        mamap::Option::DOES_EXIST);
+
+    // 3. Get the arguments associated with a particular flag
+    // Using the example above this would be
+    // dir1/file1.log dir2/file2.log dir3/file3.log
+    std::vector<std::string> file_names = ArgParse->get<std::string>(flag);
+
+    size_t num_args = ArgParse->getNumArgs(flag);
+
+    for( size_t arg_ind = 0; arg_ind <num_args; ++arg_ind){
+      // Vector of bools, that specefies if each potential sister file 
+      // of the argument actually exists
+      std::vector<bool> sister_files_exists = 
+        arg_potential_sister_files_exist.at(arg_ind);
+      // Vector of string, that each potential sister file 
+      // of the argument 
+      std::vector<std::string> potential_sister_files = 
+        arg_potential_sister_files.at(arg_ind);
+
+      for( size_t k = 0; k<potential_sister_files.size(); ++k){
+        if( sister_files_exists.at(k) ) {
+          // Only grab the first one that exists
+          flag_sister_arg[sister_flag].push_back(potential_sister_files.at(k));
+          break;
+        }
+      
+        // 3. Get the actual argument passed in, check if the file exists
+        if( arg_potential_files_exist.at(arg_ind) ) {
+          flag_arg[flag].push_back(file_names.at(arg_ind)); 
+        } 
       }
-      ++countFiles;
-    }
+      
+    } 
+
   }
 
   unique_ptr<Parameters> Par(new Parameters);
@@ -423,6 +515,13 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
   bool generic_file_pun_input = true;
   bool generic_file_log_input = true;
   // Run file related checks
+  
+  // 1. Check that:
+  // --pun_P 
+  // --pun_1
+  // --pun_2
+  //
+  // are not also submitted with --pun, which should be mutually exclusive
   if ( flag_arg.count("--pun_P") || 
       flag_arg.count("--pun_1") ||
       flag_arg.count("--pun_2") ) {
@@ -433,6 +532,12 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
     }
   }
 
+  // 2. Check that:
+  // --log_P 
+  // --log_1
+  // --log_2
+  //
+  // are not also submitted with --log, which should be mutually exclusive
   if ( flag_arg.count("--log_P") || 
       flag_arg.count("--log_1") ||
       flag_arg.count("--log_2") ) {
@@ -443,103 +548,207 @@ unique_ptr<Parameters> prepareParameters(unique_ptr<ArgumentParser>& ArgParse) {
     }
   }
 
-  // Read file related flags
+
+  size_t num_logs =0;
+  size_t num_puns =0;
+
+  // 3. Using the dimer flags
+  // --pun_P
+  // --pun_1
+  // --pun_2 
+  //
+  // Check that the files were found, if the pun flags were not
+  // found attempt to generate the file from a sister file.  
   if ( generic_file_pun_input == false ){
     if (flag_arg.count("--pun_P") != 0) {
-      Par->setPunP(flag_arg["--pun_P"]);
+      Par->setPunP(flag_arg.at("--pun_P").at(0));
     } else if (flag_sister_arg.count("--pun_P") != 0) {
-      Par->setPunP(flag_sister_arg["--pun_P"]);
+      Par->setPunP(flag_sister_arg.at("--pun_P").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --pun_P");
     }
     if (flag_arg.count("--pun_1") != 0) {
-      Par->setPun1(flag_arg["--pun_1"]);
+      Par->setPun1(flag_arg.at("--pun_1").at(0));
     } else if (flag_sister_arg.count("--pun_1") != 0) {
-      Par->setPun1(flag_sister_arg["--pun_1"]);
+      Par->setPun1(flag_sister_arg.at("--pun_1").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --pun_1");
     }
     if (flag_arg.count("--pun_2") != 0) {
-      Par->setPun2(flag_arg["--pun_2"]);
+      Par->setPun2(flag_arg.at("--pun_2").at(0));
     } else if (flag_sister_arg.count("--pun_2") != 0) {
-      Par->setPun2(flag_sister_arg["--pun_2"]);
+      Par->setPun2(flag_sister_arg.at("--pun_2").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --pun_2");
     }
   } else {
+    // 4. Using the generic flag pun
+    // Check that files were passed in with the pun flag if not attempt 
+    // to use sister files that were generated by looking at the log files
+    if (flag_arg.count("--pun") != 0) {
+      Par->setPuns(flag_arg.at("--pun"));
+      num_puns = flag_arg.at("--pun").size();
+    } else if (flag_sister_arg.count("--pun") != 0) {
+      Par->setPuns(flag_sister_arg.at("--pun"));
+      num_puns = flag_sister_arg.at("--pun").size();
+    } else {
+      throw runtime_error("Unable to find file for flag --pun");
+    }
 
   }
+
   if( generic_file_log_input == false ){
     if (flag_arg.count("--log_P") != 0) {
-      Par->setLogP(flag_arg["--log_P"]);
+      Par->setLogP(flag_arg.at("--log_P").at(0));
     } else if (flag_sister_arg.count("--log_P") != 0) {
-      Par->setLogP(flag_sister_arg["--log_P"]);
+      Par->setLogP(flag_sister_arg.at("--log_P").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --log_P");
     }
     if (flag_arg.count("--log_1") != 0) {
-      Par->setLog1(flag_arg["--log_1"]);
+      Par->setLog1(flag_arg.at("--log_1").at(0));
     } else if (flag_sister_arg.count("--log_1") != 0) {
-      Par->setLog1(flag_sister_arg["--log_1"]);
+      Par->setLog1(flag_sister_arg.at("--log_1").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --log_1");
     }
     if (flag_arg.count("--log_2") != 0) {
-      Par->setLog2(flag_arg["--log_2"]);
+      Par->setLog2(flag_arg.at("--log_2").at(0));
     } else if (flag_sister_arg.count("--log_2") != 0) {
-      Par->setLog2(flag_sister_arg["--log_2"]);
+      Par->setLog2(flag_sister_arg.at("--log_2").at(0));
     } else {
       throw runtime_error("Unable to find file for flag --log_2");
     }
   } else {
+    // 4. Using the generic flag log
+    // Check that files were passed in with the pun flag if not attempt 
+    // to use sister files that were generated by looking at the pun files
+    if (flag_arg.count("--log") != 0) {
+      Par->setLogs(flag_arg.at("--log"));
+      num_logs = flag_arg.at("--log").size();
+    } else if (flag_sister_arg.count("--log") != 0) {
+      Par->setLogs(flag_sister_arg.at("--log"));
+      num_logs = flag_sister_arg.at("--log").size();
+    } else {
+      throw runtime_error("Unable to find file for flag --log");
+    }
 
   }
-  // Read spin related flags, do not need if statement because default values
-  // are defined
-  Par->setSpinP(ArgParse->getStrs("--spin_P").at(0));
-  Par->setSpin1(ArgParse->getStrs("--spin_1").at(0));
-  Par->setSpin2(ArgParse->getStrs("--spin_2").at(0));
 
-  // Determine if we are doing a counterpoise calculation
-  Par->setCounterPoise((ArgParse->getInts("--counter_poise")).at(0));
-  Par->setPrintSwitch(ArgParse->getInts("--all").at(0));
-  Par->setCitation(ArgParse->getInts("--citation").at(0));
-  // Read Orbital related flags
-  {
-    string orb_typ_1 = ArgParse->getStrs("--orbital_type_1").at(0);
-    Par->setOrbType1(orb_typ_1);
-    if (orb_typ_1.compare("HOMO") == 0) {
-      int MO = ArgParse->getInts("--orbital_num_1").at(0);
-      if (MO > 0) {
-        throw invalid_argument("HOMO orbital must be 0 or a negative number");
+
+  // If we are using the generic file options --pun and --log and both flags
+  // are provided the flags must have an equal number of arguments, otherwise
+  // it becomes impossible to match the appropriate log file with the
+  // appropriate pun file
+  //
+  // E.g. I can't have 
+  //
+  // --pun File1.pun File3.pun --log File1.log File2,log File3.log
+  //
+  // Because I don't know which pun file is missing
+  //
+  // The file names passed to these flags must be in order as well
+  //
+  // --pun File1.pun File3.pun File2.pun --log File1.log File2.log File3.log
+  //
+  // Will not work because I will not be able to identify that File2 and File3
+  // are not associated with each other the input must look like this
+  //
+  // --pun file1.pun file2.pun file3.pun --log file1.log file2.log file3.log
+  //
+  // though it does not matter the order they are passed in E.g. this is ok
+  //
+  // --pun file2.pun file3.pun file1.pun --log file2.log file3.log file1.log
+  //
+  // As long as the order is consistent between --log and --pun flags
+  if ( generic_file_log_input && generic_file_pun_input) {
+
+    if(num_logs != num_puns ) {
+      std::string error_msg = "There must be an equal number of log and pun files";
+      error_msg += "\nThe following files have been detected\n\nLogs .log :";
+      for ( std::string & log_file : Par->getLogs() ) {
+        error_msg += log_file + "\n";
       }
-      Par->setOrbNum1(MO);
-    } else if (orb_typ_1.compare("LUMO") == 0) {
-      int MO = ArgParse->getInts("--orbital_num_1").at(0);
-      if (MO < 0) {
-        throw invalid_argument("LUMO orbital must be 0 or a positive number");
+      error_msg += "\n\nPuns pun/.7/.orb :";
+      for ( std::string & pun_file : Par->getPuns() ) {
+        error_msg += pun_file + "\n";
       }
-      Par->setOrbNum1(MO);
+      throw std::runtime_error(error_msg);
     }
   }
 
-  {
-    string orb_typ_2 = ArgParse->getStrs("--orbital_type_2").at(0);
-    Par->setOrbType2(orb_typ_2);
-    if (orb_typ_2.compare("HOMO") == 0) {
-      int MO = ArgParse->getInts("--orbital_num_2").at(0);
-      if (MO > 0) {
-        throw invalid_argument("HOMO orbital must be 0 or a negative number");
+  // If --pun or --log flags are used then non of the other flags are 
+  // appropriate
+  if( generic_file_pun_input || generic_file_log_input ) {
+    if( ArgParse->getNumArgs("--spin_P") != 0){
+      throw std::runtime_error("--spin_P command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--spin_1") != 0){
+      throw std::runtime_error("--spin_1 command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--spin_2") != 0){
+      throw std::runtime_error("--spin_2 command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--orbital_type_1") != 0){
+      throw std::runtime_error("--orbital_type_1 command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--orbital_type_2") != 0){
+      throw std::runtime_error("--orbital_type_2 command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--orbital_num_1") != 0){
+      throw std::runtime_error("--orbital_num_1 command cannot be used with the --pun and --log flags");
+    }
+    if( ArgParse->getNumArgs("--orbital_num_2") != 0){
+      throw std::runtime_error("--orbital_num_2 command cannot be used with the --pun and --log flags");
+    }
+  } else {
+    // Read spin related flags, do not need if statement because default values
+    // are defined
+    Par->setSpinP(ArgParse->get<std::string>("--spin_P").at(0));
+    Par->setSpin1(ArgParse->get<std::string>("--spin_1").at(0));
+    Par->setSpin2(ArgParse->get<std::string>("--spin_2").at(0));
+
+    // Read Orbital related flags
+    {
+      string orb_typ_1 = ArgParse->get<std::string>("--orbital_type_1").at(0);
+      Par->setOrbType1(orb_typ_1);
+      if (orb_typ_1.compare("HOMO") == 0) {
+        int MO = ArgParse->get<int>("--orbital_num_1").at(0);
+        if (MO > 0) {
+          throw invalid_argument("HOMO orbital must be 0 or a negative number");
+        }
+        Par->setOrbNum1(MO);
+      } else if (orb_typ_1.compare("LUMO") == 0) {
+        int MO = ArgParse->get<int>("--orbital_num_1").at(0);
+        if (MO < 0) {
+          throw invalid_argument("LUMO orbital must be 0 or a positive number");
+        }
+        Par->setOrbNum1(MO);
       }
-      Par->setOrbNum2(MO);
-    } else if (orb_typ_2.compare("LUMO") == 0) {
-      int MO = ArgParse->getInts("--orbital_num_2").at(0);
-      if (MO < 0) {
-        throw invalid_argument("LUMO orbital must be 0 or a positive number");
+    }
+
+    {
+      string orb_typ_2 = ArgParse->get<std::string>("--orbital_type_2").at(0);
+      Par->setOrbType2(orb_typ_2);
+      if (orb_typ_2.compare("HOMO") == 0) {
+        int MO = ArgParse->get<int>("--orbital_num_2").at(0);
+        if (MO > 0) {
+          throw invalid_argument("HOMO orbital must be 0 or a negative number");
+        }
+        Par->setOrbNum2(MO);
+      } else if (orb_typ_2.compare("LUMO") == 0) {
+        int MO = ArgParse->get<int>("--orbital_num_2").at(0);
+        if (MO < 0) {
+          throw invalid_argument("LUMO orbital must be 0 or a positive number");
+        }
+        Par->setOrbNum2(MO);
       }
-      Par->setOrbNum2(MO);
     }
   }
+  // Determine if we are doing a counterpoise calculation
+  Par->setCounterPoise((ArgParse->get<int>("--counter_poise")).at(0));
+  Par->setPrintSwitch(ArgParse->get<int>("--all").at(0));
+  Par->setCitation(ArgParse->get<int>("--citation").at(0));
   return Par;
 }
 
diff --git a/src/libcatnip/io/io.hpp b/src/libcatnip/io/io.hpp
index f38cf5d..6bc829a 100644
--- a/src/libcatnip/io/io.hpp
+++ b/src/libcatnip/io/io.hpp
@@ -1,19 +1,22 @@
 #ifndef _CATNIP_IO_HPP
 #define _CATNIP_IO_HPP
 #include "../parameters.hpp"
-#include "argumentparser.hpp"
 #include <map>
 #include <memory>
 #include <set>
 #include <string>
 #include <utility>
 
+namespace mamap {
+  class ArgumentParser;
+}
+
 namespace catnip {
 
-std::unique_ptr<ArgumentParser> prepareParser(void);
+std::unique_ptr<mamap::ArgumentParser> prepareParser(void);
 
 std::unique_ptr<Parameters> prepareParameters(
-    std::unique_ptr<ArgumentParser>& ArgParse);
+    std::unique_ptr<mamap::ArgumentParser>& ArgParse);
 
 }  // namespace catnip
 
diff --git a/src/libcatnip/parameters.cpp b/src/libcatnip/parameters.cpp
index c43617b..c92b7c3 100644
--- a/src/libcatnip/parameters.cpp
+++ b/src/libcatnip/parameters.cpp
@@ -25,6 +25,18 @@ void Parameters::setLogP(const string& logP) {
     throw invalid_argument("log file has wrong extension");
   logP_ = logP;
 }
+
+void Parameters::setLogs(std::vector<std::string> logs) {
+  logs_.clear();
+  logs_.reserve(logs.size());
+  for( const std::string & log : logs ) {
+    string ext = lastN(log, 4);
+    if (ext.compare(".log"))
+      throw invalid_argument("log file has wrong extension");
+    logs_.push_back(log);
+  }
+}
+
 void Parameters::setPun1(const string& pun1) {
   string ext = lastN(pun1, 4);
   if (ext.compare(".pun"))
@@ -43,3 +55,17 @@ void Parameters::setPunP(const string& punP) {
     throw invalid_argument("pun file has wrong extension");
   punP_ = punP;
 }
+
+void Parameters::setPuns(std::vector<std::string> puns) {
+  puns_.clear();
+  puns_.reserve(puns.size());
+  for( const std::string & pun : puns ) {
+    string ext = lastN(pun, 4);
+    if (ext.compare(".pun"))
+      throw invalid_argument("pun file has wrong extension");
+    puns_.push_back(pun);
+  }
+}
+
+
+
diff --git a/src/libcatnip/parameters.hpp b/src/libcatnip/parameters.hpp
index 59590b4..1b4893a 100644
--- a/src/libcatnip/parameters.hpp
+++ b/src/libcatnip/parameters.hpp
@@ -3,6 +3,7 @@
 #define _CATNIP_PARAMETERS_HPP_
 
 #include <string>
+#include <vector>
 
 namespace catnip {
 
@@ -11,10 +12,14 @@ class Parameters {
   std::string log1_;
   std::string log2_;
   std::string logP_;
+
   std::string pun1_;
   std::string pun2_;
   std::string punP_;
 
+  std::vector<std::string> puns_;
+  std::vector<std::string> logs_;
+
   std::string spinP;
   std::string spin1;
   std::string spin2;
@@ -53,9 +58,12 @@ class Parameters {
   std::string getLog1() const { return log1_; }
   std::string getLog2() const { return log2_; }
   std::string getLogP() const { return logP_; }
+  std::vector<std::string> getLogs() const { return logs_; }
+
   std::string getPun1() const { return pun1_; }
   std::string getPun2() const { return pun2_; }
   std::string getPunP() const { return punP_; }
+  std::vector<std::string> getPuns() const { return puns_; }
 
   std::string getSpinP() const { return spinP; }
   std::string getSpin1() const { return spin1; }
@@ -75,9 +83,12 @@ class Parameters {
   void setLog1(const std::string& log1);
   void setLog2(const std::string& log2);
   void setLogP(const std::string& logP);
+  void setLogs(std::vector<std::string> logs);
+
   void setPun1(const std::string& pun1);
   void setPun2(const std::string& pun2);
   void setPunP(const std::string& punP);
+  void setPuns(std::vector<std::string> puns);
 
   void setSpinP(const std::string& spin) { spinP = spin; }
   void setSpin1(const std::string& spin) { spin1 = spin; }
diff --git a/src/libcatnip/transfer_complex.cpp b/src/libcatnip/transfer_complex.cpp
index 03e090c..8c4e9da 100644
--- a/src/libcatnip/transfer_complex.cpp
+++ b/src/libcatnip/transfer_complex.cpp
@@ -12,7 +12,7 @@ namespace catnip {
   void TransferComplex::unscramble(AtomSystem atom_sys) {
     // We should figure out how all the rows and columns should be
     // rearranged before moving any of the coefficients in the matrix    
-    BasisMap basis_map = BasisMap(atom_sys);
+    BasisMap basis_map = BasisMap(std::move(atom_sys));
   
     size_t total_basis = atom_sys.getTotalBasisFunctions(GroupType::Component); 
     size_t total_basis_comp = atom_sys.getTotalBasisFunctions(GroupType::Complex); 
@@ -25,17 +25,17 @@ namespace catnip {
 
     auto swap_eng = SwapEngine(basis_map);
 
-    swap_eng.arrange(*(params_->complex_coefs));
-    swap_eng.arrange(*(params_->S_AO));
+    //swap_eng.arrange(*(params_->complex_coefs));
+    //swap_eng.arrange(*(params_->S_AO));
 
-    auto dimension = mat_1_Coef.cols()+mat_2_Coef.cols();
-    Eigen::MatrixXd zetaA(mat_1_Coef.rows(),dimension);
-    Eigen::MatrixXd zetaB(mat_2_Coef.rows(),dimension);
-    if (params_->counter_poise) {
-
-    } else {
-
-    }
+//    auto dimension = mat_1_Coef.cols()+mat_2_Coef.cols();
+//    Eigen::MatrixXd zetaA(mat_1_Coef.rows(),dimension);
+//    Eigen::MatrixXd zetaB(mat_2_Coef.rows(),dimension);
+//    if (params_->counter_poise) {
+//
+//    } else {
+//
+//    }
   }
 
   void TransferComplex::calcJ() {};
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 59fb8fb..7ba98ce 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -1,38 +1,23 @@
 list( APPEND UNIT_TEST_SOURCE_FILES
-  test_propertynumerical
-  test_propertyfileexist
-  test_propertyfileext
-  test_propertysisterfile
-  test_propertystringchoice
-  test_propertystring
-  test_propertyswitch
-)
+  test_atom
+  test_atom_group
+  test_atom_group_container
+  test_atom_system
+  test_basis_map
+  test_elements
+  test_log
+  test_parameters
 
-#
-#  test_argumentnumerical
-#  test_argumentfile
-#  test_argumentparser
-#  test_argumentstring
-#  test_argumentswitch
-#
-#  test_atom
-#  test_atom_group
-#  test_atom_group_container
-#  test_atom_system
-#  test_basis_map
-#  test_elements
-#  test_log
-#  test_parameters
-#
 #  test_qc_functions
-#  test_string_support
-#  test_swap_engine
+  test_string_support
+  test_swap_engine
+)
 
-if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+if(${CODE_COVERAGE} AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
   find_library (GCOV gcov)
-endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+endif(${CODE_COVERAGE} AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
 
-if(ENABLE_UNIT_TESTING)
+if(${ENABLE_UNIT_TESTING})
   foreach(PROG IN LISTS UNIT_TEST_SOURCE_FILES)
     add_executable(unit_${PROG} ${PROG}.cpp)
     if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
@@ -41,9 +26,9 @@ if(ENABLE_UNIT_TESTING)
     target_link_libraries(unit_${PROG} libcatnip Catch2::Catch2)
     ParseAndAddCatchTests(unit_${PROG})
   endforeach(PROG)
-endif(ENABLE_UNIT_TESTING)
+endif(${ENABLE_UNIT_TESTING})
 
-if(ENABLE_INTEGRATION_TESTING)
+if(${ENABLE_INTEGRATION_TESTING})
 
   foreach(PROG 
       test_logreader
@@ -59,28 +44,28 @@ if(ENABLE_INTEGRATION_TESTING)
 
   endforeach(PROG)
 
-#  add_executable(test_io test_io.cpp)
-#  if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-#    set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
-#  endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
-#  target_link_libraries(test_io libcatnip)
-#  add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
-#
-#  add_custom_command(TARGET test_io
-#    POST_BUILD
-#    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:test_io> ${CMAKE_CURRENT_SOURCE_DIR})
-#
-#  find_program (BASH_PROGRAM bash)
+  add_executable(test_io test_io.cpp)
+  if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+    set_source_files_properties( test_io.cpp PROPERTIES COMPILE_FLAGS ${COVERAGE_FLAGS})
+  endif(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")    
+  target_link_libraries(test_io libcatnip mamap)
+  add_test(regression_test_io test_io -p_P "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_pair.pun" -p_1 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/ref.pun" -p_2 "${PROJECT_SOURCE_DIR}/GAUSSIANFILES/30/30_2.pun")
+
+  add_custom_command(TARGET test_io
+    POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:test_io> ${CMAKE_CURRENT_SOURCE_DIR})
+
+  find_program (BASH_PROGRAM bash)
   if(BASH_PROGRAM)
-    #    add_test(regression_test_io_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_io.sh ${CMAKE_CURRENT_SOURCE_DIR})
+    add_test(regression_test_io_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_io.sh ${CMAKE_CURRENT_SOURCE_DIR})
 
-    add_test(integration_test_calc_J_script ${BASH_PROGRAM} ${PROJECT_SOURCE_DIR}/src/tests/test_script_calc_J.sh ${CMAKE_SOURCE_DIR})
+    add_test(integration_test_calc_J_script ${BASH_PROGRAM} ${catnip_SOURCE_DIR}/src/tests/test_script_calc_J.sh ${CMAKE_SOURCE_DIR})
 
   else()
     message(STATUS "Unable to add integration tests, unable to find bash")
   endif(BASH_PROGRAM)
 
-endif(ENABLE_INTEGRATION_TESTING)
+endif(${ENABLE_INTEGRATION_TESTING})
 
 
 
diff --git a/src/tests/test_argumentdouble.cpp b/src/tests/test_argumentdouble.cpp
deleted file mode 100644
index 781b3ef..0000000
--- a/src/tests/test_argumentdouble.cpp
+++ /dev/null
@@ -1,93 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/argumentdouble.hpp"
-#include <cassert>
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument Doubles","[unit]") {
-
-  cerr << "Testing: argumentdouble" << endl;
-  cerr << "Testing: constructor" << endl;
-  { ArgumentDouble argDouble; }
-
-  cerr << "Testing: getArgumentName" << endl;
-  {
-    ArgumentDouble argDouble;
-    string name = "ARGUMENT_DOUBLE";
-    assert(name.compare(argDouble.getArgumentName()) == 0);
-  }
-
-  cerr << "Testing: getProperties" << endl;
-  {
-    ArgumentDouble argDouble;
-    auto props = argDouble.getProperties();
-
-    bool double_prop = false;
-
-    for (auto prop : props) {
-      if (prop.compare("PROPERTY_DOUBLE") == 0) {
-        double_prop = true;
-      }
-    }
-    assert(double_prop);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-    ArgumentDouble argDouble;
-    auto prop_opts = argDouble.getPropertyOptions();
-
-    bool opt_min = false;
-    bool opt_max = false;
-
-    for (auto opt : prop_opts) {
-      if (opt.compare("MIN") == 0) {
-        opt_min = true;
-      }
-      if (opt.compare("MAX") == 0) {
-        opt_max = true;
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-  }
-
-  cerr << "Testing: getArgPropertyValues" << endl;
-  {
-    ArgumentDouble argDouble;
-    auto prop_values = argDouble.getPropertyValues();
-
-    bool opt_min = false;
-    bool opt_max = false;
-    bool opt_min_val = false;
-    bool opt_max_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("MIN") == 0) {
-        opt_min = true;
-        if (val.second.compare(to_string(numeric_limits<double>::lowest())) ==
-            0) {
-          opt_min_val = true;
-        }
-      }
-      if (val.first.compare("MAX") == 0) {
-        opt_max = true;
-        if (val.second.compare(to_string(numeric_limits<double>::max())) == 0) {
-          opt_max_val = true;
-        }
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-    assert(opt_min_val);
-    assert(opt_max_val);
-  }
-
-}
diff --git a/src/tests/test_argumentfile.cpp b/src/tests/test_argumentfile.cpp
deleted file mode 100644
index 00a7b3f..0000000
--- a/src/tests/test_argumentfile.cpp
+++ /dev/null
@@ -1,164 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-#include "../libcatnip/io/arguments/argumentfile.hpp"
-#include <cassert>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument File","[unit]") {
-
-  cerr << "Testing: argumentfile" << endl;
-  cerr << "Testing: constructor" << endl;
-  { ArgumentFile argFile; }
-
-  cerr << "Testing: getArgumentName" << endl;
-  {
-    ArgumentFile argFile;
-    string name = "ARGUMENT_FILE";
-    assert(name.compare(argFile.getArgumentName()) == 0);
-  }
-
-  cerr << "Testing: getProperties" << endl;
-  {
-    ArgumentFile argFile;
-    auto props = argFile.getProperties();
-
-    bool file_exist = false;
-    bool file_ext = false;
-    bool sister_file = false;
-
-    for (auto prop : props) {
-      if (prop.compare("PROPERTY_FILE_EXIST") == 0) {
-        file_exist = true;
-      }
-      if (prop.compare("PROPERTY_FILE_EXT") == 0) {
-        file_ext = true;
-      }
-      if (prop.compare("PROPERTY_SISTER_FILE") == 0) {
-        sister_file = true;
-      }
-    }
-    assert(file_exist);
-    assert(file_ext);
-    assert(sister_file);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-    ArgumentFile argFile;
-    auto prop_opts = argFile.getPropertyOptions();
-
-    bool file_must_exist = false;
-    bool sis_file_name = false;
-    bool sis_file_path = false;
-    bool sis_file_path_name = false;
-    bool sis_file_exists = false;
-    bool allowed_ext = false;
-    bool allowed_sister_ext = false;
-    for (auto opt : prop_opts) {
-      if (opt.compare("ALLOWED_FILE_EXT") == 0) {
-        allowed_ext = true;
-      }
-      if (opt.compare("ALLOWED_SISTER_FILE_EXT") == 0) {
-        allowed_sister_ext = true;
-      }
-      if (opt.compare("FILE_MUST_EXIST") == 0) {
-        file_must_exist = true;
-      }
-      if (opt.compare("SISTER_FILE_NAME") == 0) {
-        sis_file_name = true;
-      }
-      if (opt.compare("SISTER_FILE_PATH") == 0) {
-        sis_file_path = true;
-      }
-      if (opt.compare("SISTER_FILE_PATH_NAME") == 0) {
-        sis_file_path_name = true;
-      }
-      if (opt.compare("SISTER_FILE_EXISTS") == 0) {
-        sis_file_exists = true;
-      }
-    }
-
-    assert(file_must_exist);
-    assert(allowed_ext);
-    assert(allowed_sister_ext);
-    assert(sis_file_name);
-    assert(sis_file_path);
-    assert(sis_file_path_name);
-    assert(sis_file_exists);
-  }
-
-  cerr << "Testing: getArgPropertyValues" << endl;
-  {
-    ArgumentFile argFile;
-    auto prop_values = argFile.getPropertyValues();
-
-    bool file_must_exist = false;
-    bool allowed_ext = false;
-    bool file_must_exist_val = false;
-    bool allowed_ext_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("ALLOWED_FILE_EXT") == 0) {
-        allowed_ext = true;
-        if (val.second[0] == '*') {
-          allowed_ext_val = true;
-        }
-      }
-      if (val.first.compare("FILE_MUST_EXIST") == 0) {
-        file_must_exist = true;
-        if (val.second.compare("0") == 0) {
-          file_must_exist_val = true;
-        }
-      }
-    }
-
-    assert(file_must_exist);
-    assert(file_must_exist_val);
-
-    assert(allowed_ext);
-    assert(allowed_ext_val);
-  }
-
-  cerr << "Testing: setArgPropertyValues" << endl;
-  {
-    ArgumentFile argFile;
-    auto prop_values = argFile.getPropertyValues();
-
-    bool file_must_exist = false;
-    bool allowed_ext = false;
-    bool file_must_exist_val = false;
-    bool allowed_ext_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("ALLOWED_FILE_EXT") == 0) {
-        allowed_ext = true;
-        if (val.second[0] == '*') {
-          allowed_ext_val = true;
-        }
-      }
-      if (val.first.compare("FILE_MUST_EXIST") == 0) {
-        file_must_exist = true;
-        if (val.second.compare("0") == 0) {
-          file_must_exist_val = true;
-        }
-      }
-    }
-
-    assert(file_must_exist);
-    assert(file_must_exist_val);
-
-    assert(allowed_ext);
-    assert(allowed_ext_val);
-
-    set<string> exts{".pun", ".7", ".orb"};
-    argFile.setArgPropertyOpt("PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-
-    auto str_exts =
-        argFile.getPropertyValues("PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT");
-    cerr << "extensions " << str_exts << endl;
-  }
-
-}
diff --git a/src/tests/test_argumentint.cpp b/src/tests/test_argumentint.cpp
deleted file mode 100644
index ab2746c..0000000
--- a/src/tests/test_argumentint.cpp
+++ /dev/null
@@ -1,91 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-#include "../libcatnip/io/arguments/argumentint.hpp"
-#include <cassert>
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument int","[unit]") {
-
-  cerr << "Testing: argumentint" << endl;
-  cerr << "Testing: constructor" << endl;
-  { ArgumentInt argInt; }
-
-  cerr << "Testing: getArgumentName" << endl;
-  {
-    ArgumentInt argInt;
-    string name = "ARGUMENT_INT";
-    assert(name.compare(argInt.getArgumentName()) == 0);
-  }
-
-  cerr << "Testing: getProperties" << endl;
-  {
-    ArgumentInt argInt;
-    auto props = argInt.getProperties();
-
-    bool int_prop = false;
-
-    for (auto prop : props) {
-      if (prop.compare("PROPERTY_INT") == 0) {
-        int_prop = true;
-      }
-    }
-    assert(int_prop);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-    ArgumentInt argInt;
-    auto prop_opts = argInt.getPropertyOptions();
-
-    bool opt_min = false;
-    bool opt_max = false;
-
-    for (auto opt : prop_opts) {
-      if (opt.compare("MIN") == 0) {
-        opt_min = true;
-      }
-      if (opt.compare("MAX") == 0) {
-        opt_max = true;
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-  }
-
-  cerr << "Testing: getArgPropertyValues" << endl;
-  {
-    ArgumentInt argInt;
-    auto prop_values = argInt.getPropertyValues();
-
-    bool opt_min = false;
-    bool opt_max = false;
-    bool opt_min_val = false;
-    bool opt_max_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("MIN") == 0) {
-        opt_min = true;
-        if (val.second.compare(to_string(numeric_limits<int>::min())) == 0) {
-          opt_min_val = true;
-        }
-      }
-      if (val.first.compare("MAX") == 0) {
-        opt_max = true;
-        if (val.second.compare(to_string(numeric_limits<int>::max())) == 0) {
-          opt_max_val = true;
-        }
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-    assert(opt_min_val);
-    assert(opt_max_val);
-  }
-
-}
diff --git a/src/tests/test_argumentparser.cpp b/src/tests/test_argumentparser.cpp
deleted file mode 100644
index dbdb395..0000000
--- a/src/tests/test_argumentparser.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/argumentparser.hpp"
-#include "../libcatnip/matrix.hpp"
-#include "../libcatnip/string_support.hpp"
-#include <cassert>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument Parser","[unit]")  {
-
-  cerr << "Testing: ArgumentParser" << endl;
-  cerr << "Testing: constructor" << endl;
-  {
-    vector<string> flag = {
-        "-p_P", "--punfile-pair",
-        "File containing dimer of two "
-        "monomers. This file should have the .pun extension."};
-    set<vector<string>> flags;
-    flags.insert(flag);
-    ArgumentParser ArgPars(flags);
-  }
-
-  cerr << "Testing: showUsage" << endl;
-  {
-    vector<string> flag1 = {
-        "-p_P", "--punfile-pair",
-        "File containing dimer of two "
-        "monomers. This file should have the .pun extension."};
-    vector<string> flag2 = {"-p_1", "--punfile-mon1",
-                            "File containing monomer 1"};
-    vector<string> flag3 = {"-homo", "--homo-level", "HOMO molecular orbital"};
-
-    set<vector<string>> flags;
-    flags.insert(flag1);
-    flags.insert(flag2);
-    flags.insert(flag3);
-
-    ArgumentParser ArgPars(flags);
-    ArgPars.showUsage();
-  }
-
-  cerr << "Testing: setFlagArgOpt" << endl;
-  {
-    vector<string> flag1 = {
-        "-p_P", "--punfile-pair",
-        "File containing dimer of two "
-        "monomers. This file should have the .pun extension."};
-    vector<string> flag2 = {"-p_1", "--punfile-mon1",
-                            "File containing monomer 1"};
-    vector<string> flag3 = {"-homo", "--homo-level", "HOMO molecular orbital"};
-
-    set<vector<string>> flags;
-    flags.insert(flag1);
-    flags.insert(flag2);
-    flags.insert(flag3);
-
-    ArgumentParser ArgPars(flags);
-
-    string val = ".pun";
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", val);
-    string val2 = ".7";
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", val2);
-    string val3 = ".orb";
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", val3);
-  }
-
-  cerr << "Testing: parse" << endl;
-  {
-    vector<string> flag1 = {
-        "-p_P", "--punfile-pair",
-        "File containing dimer of two "
-        "monomers. This file should have the .pun extension."};
-    vector<string> flag2 = {"-p_1", "--punfile-mon1",
-                            "File containing monomer 1"};
-    vector<string> flag3 = {"-homo", "--homo-level", "HOMO molecular orbital"};
-
-    set<vector<string>> flags;
-    flags.insert(flag1);
-    flags.insert(flag2);
-    flags.insert(flag3);
-
-    ArgumentParser ArgPars(flags);
-
-    string val = ".pun";
-    string val2 = ".7";
-    string val3 = ".orb";
-    set<string> exts = {val, val2, val3};
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-    ArgPars.setFlagArgOpt("--punfile-mon1", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-    ArgPars.setFlagArgOpt("--punfile-mon2", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXIST", "FILE_MUST_EXIST", true);
-    ArgPars.setFlagArgOpt("--punfile-mon1", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXIST", "FILE_MUST_EXIST", false);
-    ArgPars.setFlagArgOpt("--punfile-mon2", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXIST", "FILE_MUST_EXIST", true);
-
-    int argc = 7;
-    const char* argv[7];  // = {"calc_J","--punfile-pair", "testfile.pun",
-                          // "--punfile-mon1","file.orb"};
-    argv[0] = "calc_J";
-    argv[1] = "--punfile-pair";
-    argv[2] = "testfile.pun";
-    argv[3] = "--punfile-mon1";
-    argv[4] = "file.orb";
-    argv[5] = "--punfile-mon2";
-    argv[6] = "testfile.pun";
-    ArgPars.parse(argv, argc);
-
-    argc = 7;
-    const char* argv2[7];
-    argv2[0] = "calc_J";
-    argv2[1] = "--punfile-pair";
-    argv2[2] = "testfile.pun";
-    argv2[3] = "--punfile-mon1";
-    argv2[4] = "file.orb";
-    argv2[5] = "--punfile-mon2";
-    argv2[6] = "fort.7";
-
-    bool excep = false;
-    try {
-      ArgPars.parse(argv2, argc);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-    cout << "Except thrown: " << excep << endl;
-  }
-
-  cerr << "Testing: get" << endl;
-  {
-    vector<string> flag1 = {
-        "-p_P", "--punfile-pair",
-        "File containing dimer of two "
-        "monomers. This file should have the .pun extension."};
-    vector<string> flag2 = {"-p_1", "--punfile-mon1",
-                            "File containing monomer 1"};
-    vector<string> flag3 = {"-homo", "--homo-level", "HOMO molecular orbital"};
-
-    set<vector<string>> flags;
-    flags.insert(flag1);
-    flags.insert(flag2);
-    flags.insert(flag3);
-
-    ArgumentParser ArgPars(flags);
-
-    string val = ".pun";
-    string val2 = ".7";
-    string val3 = ".orb";
-    set<string> exts = {val, val2, val3};
-    ArgPars.setFlagArgOpt("--punfile-pair", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-    ArgPars.setFlagArgOpt("--punfile-mon1", "ARGUMENT_FILE",
-                          "PROPERTY_FILE_EXT", "ALLOWED_FILE_EXT", exts);
-    vector<string> sis_exts{".log"};
-    ArgPars.setFlagArgOpt("--punfile-mon1", "ARGUMENT_FILE",
-                          "PROPERTY_SISTER_FILE", "ALLOWED_SISTER_FILE_EXT",
-                          ".log");
-
-    const int argc = 5;
-    const char* argv[argc];
-    argv[0] = "calc_J";
-    argv[1] = "--punfile-pair";
-    argv[2] = "file.orb";
-    argv[3] = "--punfile-mon1";
-    argv[4] = "testfile.pun";
-    ArgPars.parse(argv, argc);
-
-    string fileName = ArgPars.getStr("--punfile-pair");
-    assert(fileName.compare("file.orb") == 0);
-    string fileName2 = ArgPars.getStr("--punfile-mon1");
-    assert(fileName2.compare("testfile.pun") == 0);
-    string sisFileNamePath = ArgPars.getFlagArgOptValue(
-        "--punfile-mon1", "ARGUMENT_FILE", "PROPERTY_SISTER_FILE",
-        "SISTER_FILE_PATH_NAME");
-
-    cerr << "File name " << sisFileNamePath << endl;
-    assert(sisFileNamePath.compare("testfile.log") == 0);
-  }
-
-}
diff --git a/src/tests/test_argumentstring.cpp b/src/tests/test_argumentstring.cpp
deleted file mode 100644
index b12619c..0000000
--- a/src/tests/test_argumentstring.cpp
+++ /dev/null
@@ -1,128 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/argumentstring.hpp"
-#include <cassert>
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument String","[unit]") {
-
-  cerr << "Testing: argumentstring" << endl;
-  cerr << "Testing: constructor" << endl;
-  { ArgumentString argString; }
-
-  cerr << "Testing: getArgumentName" << endl;
-  {
-    ArgumentString argString;
-    string name = "ARGUMENT_STRING";
-    assert(name.compare(argString.getArgumentName()) == 0);
-  }
-
-  cerr << "Testing: getProperties" << endl;
-  {
-    ArgumentString argString;
-    auto props = argString.getProperties();
-
-    bool string_prop = false;
-    bool string_choice = false;
-
-    for (auto prop : props) {
-      if (prop.compare("PROPERTY_STRING") == 0) {
-        string_prop = true;
-      }
-      if (prop.compare("PROPERTY_STRING_CHOICE") == 0) {
-        string_choice = true;
-      }
-    }
-    assert(string_prop);
-    assert(string_choice);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-    ArgumentString argString;
-    auto prop_opts = argString.getPropertyOptions();
-
-    bool opt_min = false;
-    bool opt_max = false;
-    bool opt_enforced = false;
-    bool opt_choices = false;
-
-    for (auto opt : prop_opts) {
-      if (opt.compare("MIN_LENGTH") == 0) {
-        opt_min = true;
-      }
-      if (opt.compare("MAX_LENGTH") == 0) {
-        opt_max = true;
-      }
-      if (opt.compare("STRING_CHOICE_ENFORCED") == 0) {
-        opt_enforced = true;
-      }
-      if (opt.compare("STRING_CHOICES") == 0) {
-        opt_choices = true;
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-    assert(opt_enforced);
-    assert(opt_choices);
-  }
-
-  cerr << "Testing: getArgPropertyValues" << endl;
-  {
-    ArgumentString argString;
-    auto prop_values = argString.getPropertyValues();
-
-    bool opt_min = false;
-    bool opt_max = false;
-    bool opt_enforced = false;
-    bool opt_choices = false;
-
-    bool opt_min_val = false;
-    bool opt_max_val = false;
-    bool opt_enforced_val = false;
-    bool opt_choices_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("MIN_LENGTH") == 0) {
-        opt_min = true;
-        if (val.second.compare(to_string(0)) == 0) {
-          opt_min_val = true;
-        }
-      }
-      if (val.first.compare("MAX_LENGTH") == 0) {
-        opt_max = true;
-        if (val.second.compare(to_string((size_t)-1)) == 0) {
-          opt_max_val = true;
-        }
-      }
-      if (val.first.compare("STRING_CHOICE_ENFORCED") == 0) {
-        opt_enforced = true;
-        if (val.second.compare("false") == 0) {
-          opt_enforced_val = true;
-        }
-      }
-      if (val.first.compare("STRING_CHOICES") == 0) {
-        opt_choices = true;
-        if (val.second.compare("NOT_DEFINED") == 0) {
-          opt_choices_val = true;
-        }
-      }
-    }
-
-    assert(opt_min);
-    assert(opt_max);
-    assert(opt_min_val);
-    assert(opt_max_val);
-    assert(opt_enforced);
-    assert(opt_choices);
-    assert(opt_enforced_val);
-    assert(opt_choices_val);
-  }
-
-}
diff --git a/src/tests/test_argumentswitch.cpp b/src/tests/test_argumentswitch.cpp
deleted file mode 100644
index 9db01ae..0000000
--- a/src/tests/test_argumentswitch.cpp
+++ /dev/null
@@ -1,76 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-#include "../libcatnip/io/arguments/argumentswitch.hpp"
-#include <cassert>
-#include <limits>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Argument Switch","[unit]") {
-
-  cerr << "Testing: argumentswitch" << endl;
-  cerr << "Testing: constructor" << endl;
-  { ArgumentSwitch argSwitch; }
-
-  cerr << "Testing: getArgumentName" << endl;
-  {
-    ArgumentSwitch argSwitch;
-    string name = "ARGUMENT_SWITCH";
-    assert(name.compare(argSwitch.getArgumentName()) == 0);
-  }
-
-  cerr << "Testing: getProperties" << endl;
-  {
-    ArgumentSwitch argSwitch;
-    auto props = argSwitch.getProperties();
-
-    bool int_prop = false;
-
-    for (auto prop : props) {
-      if (prop.compare("PROPERTY_SWITCH") == 0) {
-        int_prop = true;
-      }
-    }
-    assert(int_prop);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-    ArgumentSwitch argSwitch;
-    auto prop_opts = argSwitch.getPropertyOptions();
-
-    bool opt_def = false;
-
-    for (auto opt : prop_opts) {
-      if (opt.compare("DEFAULT") == 0) {
-        opt_def = true;
-      }
-    }
-
-    assert(opt_def);
-  }
-
-  cerr << "Testing: getArgPropertyValues" << endl;
-  {
-    ArgumentSwitch argSwitch;
-    auto prop_values = argSwitch.getPropertyValues();
-
-    bool opt_def = false;
-    bool opt_def_val = false;
-
-    for (auto val : prop_values) {
-      if (val.first.compare("DEFAULT") == 0) {
-        opt_def = true;
-        if (val.second.compare("OFF") == 0) {
-          opt_def_val = true;
-        }
-      }
-    }
-
-    assert(opt_def);
-    assert(opt_def_val);
-  }
-
-}
diff --git a/src/tests/test_atom_group_container.cpp b/src/tests/test_atom_group_container.cpp
index db95cea..62fd0f6 100644
--- a/src/tests/test_atom_group_container.cpp
+++ b/src/tests/test_atom_group_container.cpp
@@ -19,15 +19,15 @@ TEST_CASE("Atom Group Container","[unit]") {
   Atom atom1(Element::H, 0.0, 0.0, 0.0);
   Atom atom2(Element::H, 2.0, 0.0, 0.0);
   Atom atom3(Element::C, 1.0, 1.0, 0.0);
-
+  
   auto atom1_ptr = std::make_shared<Atom>(atom1);
   auto atom2_ptr = std::make_shared<Atom>(atom2);
   auto atom3_ptr = std::make_shared<Atom>(atom3);
 
-  AtomGroup atom_grp1("CH2");
-  atom_grp1.add(atom1_ptr);
-  atom_grp1.add(atom2_ptr);
-  atom_grp1.add(atom3_ptr);
+  auto atom_grp1 = std::make_unique<AtomGroup>("CH2");
+  atom_grp1->add(atom1_ptr);
+  atom_grp1->add(atom2_ptr);
+  atom_grp1->add(atom3_ptr);
 
   Atom atom4(Element::O, 3.3, 4.3, 0.0);
   Atom atom5(Element::O, 3.0, 3.9, 0.0);
@@ -35,14 +35,14 @@ TEST_CASE("Atom Group Container","[unit]") {
   auto atom4_ptr = std::make_shared<Atom>(atom4);
   auto atom5_ptr = std::make_shared<Atom>(atom5);
 
-  AtomGroup atom_grp2("O2");
-  atom_grp2.add(atom4_ptr);  
-  atom_grp2.add(atom5_ptr);  
+  auto atom_grp2 = std::make_unique<AtomGroup>("O2");
+  atom_grp2->add(atom4_ptr);  
+  atom_grp2->add(atom5_ptr);  
 
   AtomGroupContainer atom_grp_cont;
 
-  atom_grp_cont.add(atom_grp1);
-  atom_grp_cont.add(atom_grp2);
+  atom_grp_cont.add(std::move(atom_grp1));
+  atom_grp_cont.add(std::move(atom_grp2));
 
   REQUIRE(atom_grp_cont.size() == 2);
 
@@ -52,9 +52,6 @@ TEST_CASE("Atom Group Container","[unit]") {
 
   atom_grp_cont.assignGroupTypes();
   REQUIRE(atom_grp_cont.isUpToDate() == true);
-  // Because it made a copy these should still be unassigned
-  REQUIRE(atom_grp1.getType() == GroupType::Unassigned);
-  REQUIRE(atom_grp2.getType() == GroupType::Unassigned);
 
   // These should be changed
   REQUIRE(atom_grp_cont.getType(0) == GroupType::Island);
@@ -62,14 +59,14 @@ TEST_CASE("Atom Group Container","[unit]") {
   REQUIRE(atom_grp_cont.exists(GroupType::Island));
 
   // Now we make a third group that has all the atoms of the first two groups
-  AtomGroup atom_grp3("O2CH2");
-  atom_grp3.add(atom1_ptr);
-  atom_grp3.add(atom2_ptr);
-  atom_grp3.add(atom3_ptr);
-  atom_grp3.add(atom4_ptr);
-  atom_grp3.add(atom5_ptr);
-
-  atom_grp_cont.add(atom_grp3);
+  auto atom_grp3 = std::make_unique<AtomGroup>("O2CH2");
+  atom_grp3->add(std::move(atom1_ptr));
+  atom_grp3->add(atom2_ptr);
+  atom_grp3->add(atom3_ptr);
+  atom_grp3->add(atom4_ptr);
+  atom_grp3->add(atom5_ptr);
+
+  atom_grp_cont.add(std::move(atom_grp3));
   REQUIRE(atom_grp_cont.isUpToDate() == false);
 
   REQUIRE(atom_grp_cont.getType(2) == GroupType::Unassigned);
@@ -83,5 +80,4 @@ TEST_CASE("Atom Group Container","[unit]") {
 
   REQUIRE(atom_grp_cont.exists(GroupType::Complex));
   REQUIRE(atom_grp_cont.exists(GroupType::Component));
-
 }
diff --git a/src/tests/test_atom_system.cpp b/src/tests/test_atom_system.cpp
index 31602b1..8acb3f8 100644
--- a/src/tests/test_atom_system.cpp
+++ b/src/tests/test_atom_system.cpp
@@ -34,79 +34,79 @@ TEST_CASE("Atom System","[unit]") {
 
   SECTION("Building component without atom 5") {
     // Extra atoms are allowed in the complex but not in the componets
-    AtomGroup component1("CH2");
-    component1.add(atom1_ptr);
-    component1.add(atom2_ptr);
-    component1.add(atom3_ptr);
-
-    AtomGroup component2("O2");
-    component2.add(atom4_ptr);  
-
-    AtomGroup complex1("O2CH2");
-    complex1.add(atom1_ptr);
-    complex1.add(atom2_ptr);
-    complex1.add(atom3_ptr);
-    complex1.add(atom4_ptr);
-    complex1.add(atom5_ptr);
-
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(component1);
-    atom_grp_cont.add(component2);
-    atom_grp_cont.add(complex1);
-
-    REQUIRE_NOTHROW(AtomSystem(atom_grp_cont) );
+    auto component1 = std::make_unique<AtomGroup>("CH2");
+    component1->add(atom1_ptr);
+    component1->add(atom2_ptr);
+    component1->add(atom3_ptr);
+
+    auto component2 = std::make_unique<AtomGroup>("O2");
+    component2->add(atom4_ptr);  
+
+    auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+    complex1->add(atom1_ptr);
+    complex1->add(atom2_ptr);
+    complex1->add(atom3_ptr);
+    complex1->add(atom4_ptr);
+    complex1->add(atom5_ptr);
+
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(component1));
+    atom_grp_cont->add(std::move(component2));
+    atom_grp_cont->add(std::move(complex1));
+
+    REQUIRE_NOTHROW(AtomSystem(std::move(atom_grp_cont)) );
   }
 
   SECTION("Building complex without atom 5") {
     // Extra atoms are allowed in the complex but not in the componets
-    AtomGroup component1("CH2");
-    component1.add(atom1_ptr);
-    component1.add(atom2_ptr);
-    component1.add(atom3_ptr);
-
-    AtomGroup component2("O2");
-    component2.add(atom4_ptr);  
-    component2.add(atom5_ptr);  
-
-    AtomGroup complex1("O2CH2");
-    complex1.add(atom1_ptr);
-    complex1.add(atom2_ptr);
-    complex1.add(atom3_ptr);
-    complex1.add(atom4_ptr);
-
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(component1);
-    atom_grp_cont.add(component2);
-    atom_grp_cont.add(complex1);
-
-    REQUIRE_THROWS(AtomSystem(atom_grp_cont) );
+    auto component1 = std::make_unique<AtomGroup>("CH2");
+    component1->add(atom1_ptr);
+    component1->add(atom2_ptr);
+    component1->add(atom3_ptr);
+
+    auto component2 = std::make_unique<AtomGroup>("O2");
+    component2->add(atom4_ptr);  
+    component2->add(atom5_ptr);  
+
+    auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+    complex1->add(atom1_ptr);
+    complex1->add(atom2_ptr);
+    complex1->add(atom3_ptr);
+    complex1->add(atom4_ptr);
+
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(component1));
+    atom_grp_cont->add(std::move(component2));
+    atom_grp_cont->add(std::move(complex1));
+
+    REQUIRE_THROWS(AtomSystem(std::move(atom_grp_cont)) );
   }
 
   SECTION("Building with atom 5") {
-    AtomGroup component1("CH2");
-    component1.add(atom1_ptr); // H
-    component1.add(atom2_ptr); // H 
-    component1.add(atom3_ptr); // C
-
-    AtomGroup component2("O2");
-    component2.add(atom4_ptr); // O
-    component2.add(atom5_ptr); // O 
-
-    AtomGroup complex1("O2CH2");
-    complex1.add(atom1_ptr); // H
-    complex1.add(atom2_ptr); // H
-    complex1.add(atom3_ptr); // C
-    complex1.add(atom4_ptr); // O
-    complex1.add(atom5_ptr); // O
-
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(component1);
-    atom_grp_cont.add(component2);
-    atom_grp_cont.add(complex1);
-
-    AtomSystem atm_sys(atom_grp_cont);
-    REQUIRE(atm_sys.getComplex().getType() == GroupType::Complex );
-    REQUIRE(atm_sys.getComplex().getName() == "O2CH2" );
+    auto component1 = std::make_unique<AtomGroup>("CH2");
+    component1->add(atom1_ptr);
+    component1->add(atom2_ptr);
+    component1->add(atom3_ptr);
+
+    auto component2 = std::make_unique<AtomGroup>("O2");
+    component2->add(atom4_ptr);  
+    component2->add(atom5_ptr);  
+
+    auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+    complex1->add(atom1_ptr);
+    complex1->add(atom2_ptr);
+    complex1->add(atom3_ptr);
+    complex1->add(atom4_ptr);
+    complex1->add(atom5_ptr); // O
+
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(component1));
+    atom_grp_cont->add(std::move(component2));
+    atom_grp_cont->add(std::move(complex1));
+
+    AtomSystem atm_sys(std::move(atom_grp_cont));
+    REQUIRE(atm_sys.getComplex()->getType() == GroupType::Complex );
+    REQUIRE(atm_sys.getComplex()->getName() == "O2CH2" );
 
     std::vector<int> component_indices = atm_sys.getComponentIndices();
     REQUIRE(component_indices.size() == 2);
@@ -135,48 +135,48 @@ TEST_CASE("Atom System","[unit]") {
     std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
     REQUIRE_NOTHROW( atm_sys.assignBasisFunctions( 2, basis_complex ));
 
-    REQUIRE( atm_sys.at(0).size() == 3);
-    REQUIRE( atm_sys.at(0).at(0)->getBasisFuncCount() == 1); // H 
-    REQUIRE( atm_sys.at(0).at(1)->getBasisFuncCount() == 1); // H
-    REQUIRE( atm_sys.at(0).at(2)->getBasisFuncCount() == 4); // C
+    REQUIRE( atm_sys.at(0)->size() == 3);
+    REQUIRE( atm_sys.at(0)->at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(0)->at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(0)->at(2)->getBasisFuncCount() == 4); // C
     
-    REQUIRE( atm_sys.at(1).size() == 2);
-    REQUIRE( atm_sys.at(1).at(0)->getBasisFuncCount() == 5); // O
-    REQUIRE( atm_sys.at(1).at(1)->getBasisFuncCount() == 5); // O
-
-    REQUIRE( atm_sys.at(2).size() == 5);
-    REQUIRE( atm_sys.at(2).at(0)->getBasisFuncCount() == 1); // H 
-    REQUIRE( atm_sys.at(2).at(1)->getBasisFuncCount() == 1); // H
-    REQUIRE( atm_sys.at(2).at(2)->getBasisFuncCount() == 4); // C
-    REQUIRE( atm_sys.at(2).at(3)->getBasisFuncCount() == 5); // O
-    REQUIRE( atm_sys.at(2).at(4)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(1)->size() == 2);
+    REQUIRE( atm_sys.at(1)->at(0)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(1)->at(1)->getBasisFuncCount() == 5); // O
+
+    REQUIRE( atm_sys.at(2)->size() == 5);
+    REQUIRE( atm_sys.at(2)->at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(2)->at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(2)->at(2)->getBasisFuncCount() == 4); // C
+    REQUIRE( atm_sys.at(2)->at(3)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(2)->at(4)->getBasisFuncCount() == 5); // O
   }
 
   SECTION("Building complex with atom 6") {
-    AtomGroup component1("CH2");
-    component1.add(atom1_ptr);
-    component1.add(atom2_ptr);
-    component1.add(atom3_ptr);
-
-    AtomGroup component2("O2");
-    component2.add(atom4_ptr);  
-    component2.add(atom5_ptr);  
-
-    AtomGroup complex1("OC2H2");
-    complex1.add(atom1_ptr);
-    complex1.add(atom2_ptr);
-    complex1.add(atom3_ptr);
-    complex1.add(atom4_ptr);
-    complex1.add(atom6_ptr); // Carbon instead of Oxygen
-
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(component1);
-    atom_grp_cont.add(component2);
-    atom_grp_cont.add(complex1);
-
-    AtomSystem atm_sys(atom_grp_cont);
-    REQUIRE(atm_sys.getComplex().getType() == GroupType::Complex );
-    REQUIRE(atm_sys.getComplex().getName() == "OC2H2" );
+    auto component1 = std::make_unique<AtomGroup>("CH2");
+    component1->add(atom1_ptr);
+    component1->add(atom2_ptr);
+    component1->add(atom3_ptr);
+
+    auto component2 = std::make_unique<AtomGroup>("O2");
+    component2->add(atom4_ptr);  
+    component2->add(atom5_ptr);  
+
+    auto complex1 = std::make_unique<AtomGroup>("OC2H2");
+    complex1->add(atom1_ptr);
+    complex1->add(atom2_ptr);
+    complex1->add(atom3_ptr);
+    complex1->add(atom4_ptr);
+    complex1->add(atom6_ptr);// Carbon instead of Oxygen
+
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(component1));
+    atom_grp_cont->add(std::move(component2));
+    atom_grp_cont->add(std::move(complex1));
+
+    AtomSystem atm_sys(std::move(atom_grp_cont));
+    REQUIRE(atm_sys.getComplex()->getType() == GroupType::Complex );
+    REQUIRE(atm_sys.getComplex()->getName() == "OC2H2" );
 
     std::vector<int> component_indices = atm_sys.getComponentIndices();
     REQUIRE(component_indices.size() == 2);
@@ -215,20 +215,20 @@ TEST_CASE("Atom System","[unit]") {
     REQUIRE_NOTHROW( atm_sys.assignBasisFunctions( 2, basis_complex ));
     REQUIRE( atm_sys.systemComplete() );
 
-    REQUIRE( atm_sys.at(0).size() == 3);
-    REQUIRE( atm_sys.at(0).at(0)->getBasisFuncCount() == 1); // H 
-    REQUIRE( atm_sys.at(0).at(1)->getBasisFuncCount() == 1); // H
-    REQUIRE( atm_sys.at(0).at(2)->getBasisFuncCount() == 4); // C
-
-    REQUIRE( atm_sys.at(1).size() == 2);
-    REQUIRE( atm_sys.at(1).at(0)->getBasisFuncCount() == 5); // O
-    REQUIRE( atm_sys.at(1).at(1)->getBasisFuncCount() == 5); // O
-
-    REQUIRE( atm_sys.at(2).size() == 5);
-    REQUIRE( atm_sys.at(2).at(0)->getBasisFuncCount() == 1); // H 
-    REQUIRE( atm_sys.at(2).at(1)->getBasisFuncCount() == 1); // H
-    REQUIRE( atm_sys.at(2).at(2)->getBasisFuncCount() == 4); // C
-    REQUIRE( atm_sys.at(2).at(3)->getBasisFuncCount() == 5); // O
-    REQUIRE( atm_sys.at(2).at(4)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(0)->size() == 3);
+    REQUIRE( atm_sys.at(0)->at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(0)->at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(0)->at(2)->getBasisFuncCount() == 4); // C
+
+    REQUIRE( atm_sys.at(1)->size() == 2);
+    REQUIRE( atm_sys.at(1)->at(0)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(1)->at(1)->getBasisFuncCount() == 5); // O
+
+    REQUIRE( atm_sys.at(2)->size() == 5);
+    REQUIRE( atm_sys.at(2)->at(0)->getBasisFuncCount() == 1); // H 
+    REQUIRE( atm_sys.at(2)->at(1)->getBasisFuncCount() == 1); // H
+    REQUIRE( atm_sys.at(2)->at(2)->getBasisFuncCount() == 4); // C
+    REQUIRE( atm_sys.at(2)->at(3)->getBasisFuncCount() == 5); // O
+    REQUIRE( atm_sys.at(2)->at(4)->getBasisFuncCount() == 5); // O
   }
 }
diff --git a/src/tests/test_basis_map.cpp b/src/tests/test_basis_map.cpp
index 4b1e248..667c601 100644
--- a/src/tests/test_basis_map.cpp
+++ b/src/tests/test_basis_map.cpp
@@ -27,34 +27,34 @@ TEST_CASE("Basis Map Unscrambled","[integration]") {
   auto atom5_ptr = std::make_shared<Atom>(atom5);
 
   // Extra atoms are allowed in the complex but not in the componets
-  AtomGroup component1("CH2");
-  component1.add(atom1_ptr);
-  component1.add(atom2_ptr);
-  component1.add(atom3_ptr);
+  auto component1 = std::make_unique<AtomGroup>("CH2");
+  component1->add(atom1_ptr);
+  component1->add(atom2_ptr);
+  component1->add(atom3_ptr);
 
-  AtomGroup component2("O2");
-  component2.add(atom4_ptr);  
-  component2.add(atom5_ptr);  
+  auto component2 = std::make_unique<AtomGroup>("O2");
+  component2->add(atom4_ptr);  
+  component2->add(atom5_ptr);  
 
-  AtomGroup complex1("O2CH2");
-  complex1.add(atom1_ptr);
-  complex1.add(atom2_ptr);
-  complex1.add(atom3_ptr);
-  complex1.add(atom4_ptr);
-  complex1.add(atom5_ptr);
+  auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+  complex1->add(atom1_ptr);
+  complex1->add(atom2_ptr);
+  complex1->add(atom3_ptr);
+  complex1->add(atom4_ptr);
+  complex1->add(atom5_ptr);
 
-  AtomGroupContainer atom_grp_cont;
-  atom_grp_cont.add(component1);
-  atom_grp_cont.add(component2);
-  atom_grp_cont.add(complex1);
+  auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+  atom_grp_cont->add(std::move(component1));
+  atom_grp_cont->add(std::move(component2));
+  atom_grp_cont->add(std::move(complex1));
 
-  AtomSystem atm_sys(atom_grp_cont);
+  auto atm_sys = AtomSystem(std::move(atom_grp_cont));
 
   std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
 
   int index_complex = 2;
   atm_sys.assignBasisFunctions( index_complex, basis_complex);
-  BasisMap basis_map(atm_sys);
+  BasisMap basis_map(std::move(atm_sys));
 
   // Equal to the total number of basis in the group
   REQUIRE( basis_map.row_col_current[0].size() == 6);
@@ -156,30 +156,29 @@ TEST_CASE("Basis Map Scrambled","[integration]") {
   auto atom5_ptr = std::make_shared<Atom>(atom5);
 
   // Extra atoms are allowed in the complex but not in the componets
-  AtomGroup component1("CH2");
-  component1.add(atom1_ptr);
-  component1.add(atom2_ptr);
-  component1.add(atom3_ptr);
+  auto component1 = std::make_unique<AtomGroup>("CH2");
+  component1->add(atom1_ptr);
+  component1->add(atom2_ptr);
+  component1->add(atom3_ptr);
 
-  AtomGroup component2("O2");
-  component2.add(atom4_ptr);  
-  component2.add(atom5_ptr);  
+  auto component2 = std::make_unique<AtomGroup>("O2");
+  component2->add(atom4_ptr);  
+  component2->add(atom5_ptr);  
 
   // HERE: the order has been changed
-  AtomGroup complex1("O2CH2");
-  complex1.add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
-  complex1.add(atom1_ptr); // The basis functiosn of atom 1 : 5 - 5 
-  complex1.add(atom3_ptr); // The basis functiosn of atom 3 : 6 - 9
-  complex1.add(atom5_ptr); // The basis functiosn of atom 5 : 10 - 14
-  complex1.add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
-
-  AtomGroupContainer atom_grp_cont;
-  atom_grp_cont.add(component1);
-  atom_grp_cont.add(component2);
-  atom_grp_cont.add(complex1);
-
-  AtomSystem atm_sys(atom_grp_cont);
-
+  auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+  complex1->add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
+  complex1->add(atom1_ptr); // The basis functiosn of atom 1 : 5 - 5 
+  complex1->add(atom3_ptr); // The basis functiosn of atom 3 : 6 - 9
+  complex1->add(atom5_ptr); // The basis functiosn of atom 5 : 10 - 14
+  complex1->add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
+
+  auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+  atom_grp_cont->add(std::move(component1));
+  atom_grp_cont->add(std::move(component2));
+  atom_grp_cont->add(std::move(complex1));
+
+  AtomSystem atm_sys(std::move(atom_grp_cont));
 
   int index_component1 = 0;
   int index_component2 = 1;
diff --git a/src/tests/test_io.cpp b/src/tests/test_io.cpp
index 159842c..59a2dd6 100644
--- a/src/tests/test_io.cpp
+++ b/src/tests/test_io.cpp
@@ -1,8 +1,9 @@
 
 
-#include "../libcatnip/io/argumentparser.hpp"
-#include "../libcatnip/io/io.hpp"
-#include "../libcatnip/matrix.hpp"
+#include <mamap/argumentparser.hpp>
+#include "io/io.hpp"
+#include "parameters.hpp"
+#include "matrix.hpp"
 #include <cassert>
 #include <iostream>
 #include <string>
@@ -13,12 +14,13 @@ using namespace std;
 
 int main(int argc, const char* argv[]) {
 
-  auto ArgParse = prepareParser();
+  auto arg_parser = prepareParser();
 
-  ArgParse->parse(argv, argc);
-  vector<string> flags{"--pun_P", "--pun_1", "--pun_2",
-                       "--log_P", "--log_1", "--log_2"};
+  arg_parser->parse(argv, argc);
+  
+  auto parameters = prepareParameters(std::move(arg_parser))
 
+/*
   for (auto flag : flags) {
     cout << endl;
     ArgumentType argu = ArgumentType::FILES;
@@ -29,7 +31,6 @@ int main(int argc, const char* argv[]) {
       cout << val << " ";
     }
     cout << endl;
-/*
     prop = "PROPERTY_SISTER_FILE";
     opt = "ALLOWED_SISTER_FILE_EXT";
     auto val1 = ArgParse->getFlagArgOptValue(flag, argu, prop, opt);
diff --git a/src/tests/test_propertyfileexist.cpp b/src/tests/test_propertyfileexist.cpp
deleted file mode 100644
index 28a2e15..0000000
--- a/src/tests/test_propertyfileexist.cpp
+++ /dev/null
@@ -1,67 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "io/arguments/properties/propertyfileexist.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property File Exists","[unit]") {
-
-  cerr << "Testing: PropertyFileExist" << endl;
-  cerr << "Testing: constructor" << endl;
-  {
-    PropertyFileExist propFileExist1(true);
-    PropertyFileExist propFileExist2(false);
-  }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyFileExist propFileExist;
-    PropertyType type = propFileExist.getPropertyType();
-    CHECK(type == PropertyTYpe::FILE_EXIST);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyFileExist propFileExist;
-    auto options = propFileExist.getPropertyOptions();
-    Option opt = options.at(0);
-    CHECK(opt == Option::MUST_EXIST);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyFileExist propFileExist1(false);
-    PropertyFileExist propFileExist2(true);
-    PropertyFileExist propFileExist3(true);
-
-    bool valid = propFileExist1.propValid("test_propertyfileexist.cpp");
-    CHECK(valid);
-
-    CHECK_THROWS(propFileExist2.propValid("fake"));
-
-    valid = propFileExist3.propValid("testfile.pun");
-    CHECK(valid);
-  }
-
-  cerr << "Testing: getPropOption" << endl;
-  {
-    PropertyFileExist propFileExist1(true);
-    PropertyFileExist propFileExist2(false);
-
-    bool fileExist = propFileExist1.getPropOption(Option::MUST_EXIST);
-    CHECK(fileExist);
-
-    fileExist = propFileExist2.getPropOption(Option::MUST_EXIST);
-    CHECK(fileExist == false);
-  }
-
-}
diff --git a/src/tests/test_propertyfileext.cpp b/src/tests/test_propertyfileext.cpp
deleted file mode 100644
index a7fe1d5..0000000
--- a/src/tests/test_propertyfileext.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "io/arguments/properties/propertyfileext.hpp"
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property File Extension","[unit]") {
-
-  cerr << "Testing: PropertyFileExt" << endl;
-  cerr << "Testing: constructor" << endl;
-  {
-    PropertyFileExt propFileExt1("*");
-    PropertyFileExt propFileExt2("");
-    PropertyFileExt propFileExt3(".jpg");
-    CHECK_THROWS(PropertyFileExt propFileExt4("ffda.fd"));
-    set<string> exts = {".png", ".gjf"};
-    PropertyFileExt propFileExt5(exts);
-  }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyFileExt propFileExt;
-    PropertyType type = propFileExt.getPropertyType();
-    REQUIRE(type == PropertyType::FILE_EXT);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyFileExt propFileExt;
-    auto options = propFileExt.getPropertyOptions();
-    Option opt = options.at(0);
-    REQUIRE(opt == Option::ALLOWED_VALUES);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyFileExt propFileExt(".jpg");
-    bool valid = propFileExt.propValid("dir/file.jpg");
-    CHECK(valid);
-    CHECK_THROWS(propFileExt.propValid("dir/file.jp"));
-
-    PropertyFileExt propFileExt2("*");
-    valid = propFileExt2.propValid("dir/file.jpg");
-    CHECK(valid);
-    valid = propFileExt2.propValid("dir/file.jp");
-    CHECK(valid);
-
-    set<string> exts = {".png", ".gjf"};
-    PropertyFileExt propFileExt3(exts);
-    valid = propFileExt3.propValid("Dir2/Path/File.png");
-    CHECK(valid);
-    valid = propFileExt3.propValid("Dir2/Path/File.gjf");
-    CHECK(valid);
-    CHECK_THROWS(propFileExt3.propValid("dir/file.com"));
-  }
-}
diff --git a/src/tests/test_propertynumerical.cpp b/src/tests/test_propertynumerical.cpp
deleted file mode 100644
index 414cb12..0000000
--- a/src/tests/test_propertynumerical.cpp
+++ /dev/null
@@ -1,67 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "io/arguments/properties/propertynumerical.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property Numerical","[unit]") {
-
-  cerr << "Testing: PropertyNumerical" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertyNumerical propNumerical; }
-
-  cerr << "Testing: getPropertyType" << endl;
-  {
-    PropertyNumerical propNumerical;
-    PropertyType name = propNumerical.getPropertyType();
-    assert(name == PropertyType::NUMERICAL);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyNumerical propNumerical;
-    auto options = propNumerical.getPropertyOptions();
-    string opt = options.at(0);
-    assert(opt == Option::MIN);
-    opt = options.at(1);
-    assert(opt == Option::MAX);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyNumerical propNumerical;
-    bool valid = propNumerical.propValid(0);
-    assert(valid);
-  }
-
-  cerr << "Testing: setPropOption" << endl;
-  {
-    PropertyNumerical propNumerical;
-    propNumerical.setPropOption(Option::MIN, 0);
-    propNumerical.propValid(0);
-    bool excep = false;
-    try {
-      propNumerical.propValid(-1);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    excep = false;
-    try {
-      propNumerical.setPropOption(Option::ENFORCED, 3);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-  }
-}
diff --git a/src/tests/test_propertysisterfile.cpp b/src/tests/test_propertysisterfile.cpp
deleted file mode 100644
index dc3af30..0000000
--- a/src/tests/test_propertysisterfile.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/properties/propertysisterfile.hpp"
-#include <cassert>
-#include <exception>
-#include <fstream>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property Sister File","[unit]") {
-  fstream fs;
-  fs.open("testfile.pun", ios::out);
-  fs.close();
-
-  cerr << "Testing: PropertySisterFile" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertySisterFile propSisterFile1; }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertySisterFile propSisterFile;
-    string name = propSisterFile.getPropertyName();
-    assert(name.compare("PROPERTY_SISTER_FILE") == 0);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertySisterFile propSisterFile;
-    auto options = propSisterFile.getPropertyOptions();
-
-    bool allowed_file = false;
-    bool sister_name = false;
-    bool sister_path = false;
-    bool sister_name_path = false;
-    bool sister_exists = false;
-
-    for (auto opt : options) {
-      if (opt.compare("ALLOWED_SISTER_FILE_EXT") == 0) {
-        allowed_file = true;
-      }
-      if (opt.compare("SISTER_FILE_NAME") == 0) {
-        sister_name = true;
-      }
-      if (opt.compare("SISTER_FILE_PATH") == 0) {
-        sister_path = true;
-      }
-      if (opt.compare("SISTER_FILE_PATH_NAME") == 0) {
-        sister_name_path = true;
-      }
-      if (opt.compare("SISTER_FILE_EXISTS") == 0) {
-        sister_exists = true;
-      }
-    }
-    assert(allowed_file);
-    assert(sister_name);
-    assert(sister_path);
-    assert(sister_name_path);
-    assert(sister_exists);
-  }
-
-  cerr << "Testing: getPropOption" << endl;
-  {
-    PropertySisterFile propSisterFile1;
-
-    vector<string> allowed_ext =
-        propSisterFile1.getPropOption("ALLOWED_SISTER_FILE_EXT");
-    vector<string> file_name =
-        propSisterFile1.getPropOption("SISTER_FILE_NAME");
-    vector<string> file_path =
-        propSisterFile1.getPropOption("SISTER_FILE_PATH");
-    vector<string> file_path_name =
-        propSisterFile1.getPropOption("SISTER_FILE_PATH_NAME");
-    vector<string> fileExist =
-        propSisterFile1.getPropOption("SISTER_FILE_EXISTS");
-
-    assert(allowed_ext.at(0).compare("NOT_DEFINED") == 0);
-    assert(file_name.at(0).compare("NOT_DEFINED") == 0);
-    assert(file_path.at(0).compare("NOT_DEFINED") == 0);
-    assert(file_path_name.at(0).compare("NOT_DEFINED") == 0);
-    assert(fileExist.at(0).compare("false") == 0);
-  }
-
-  cerr << "Testing: getPropOption" << endl;
-  {
-    PropertySisterFile propSisterFile1;
-
-    propSisterFile1.setPropOption("ALLOWED_SISTER_FILE_EXT", ".pun");
-
-    string fileName = "testfile.log";
-    propSisterFile1.propValid(fileName);
-    vector<string> allowed_ext =
-        propSisterFile1.getPropOption("ALLOWED_SISTER_FILE_EXT");
-    vector<string> file_name =
-        propSisterFile1.getPropOption("SISTER_FILE_NAME");
-    vector<string> file_path =
-        propSisterFile1.getPropOption("SISTER_FILE_PATH");
-    vector<string> file_path_name =
-        propSisterFile1.getPropOption("SISTER_FILE_PATH_NAME");
-    vector<string> fileExist =
-        propSisterFile1.getPropOption("SISTER_FILE_EXISTS");
-
-    assert(allowed_ext.at(0).compare(".pun") == 0);
-
-    assert(file_name.at(0).compare("testfile.pun") == 0);
-    assert(file_path.at(0).compare("") == 0);
-    assert(file_path_name.at(0).compare("testfile.pun") == 0);
-    assert(fileExist.at(0).compare("true") == 0);
-  }
-}
diff --git a/src/tests/test_propertystring.cpp b/src/tests/test_propertystring.cpp
deleted file mode 100644
index efdcf89..0000000
--- a/src/tests/test_propertystring.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-
-#include "../libcatnip/io/arguments/properties/propertystring.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property String","[unit]") {
-
-  cerr << "Testing: PropertyString" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertyString propString; }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertyString propString;
-    PropertyType type = propString.getPropertyType();
-    REQUIRE(type == PropertyType::STRING);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertyString propString;
-    auto options = propString.getPropertyOptions();
-    Option opt = options.at(0);
-    REQUIRE(opt == Option::MIN_LENGTH);
-    opt = options.at(1);
-    REQUIRE(opt == Option::MAX_LENGTH);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertyString propString;
-    bool valid = propString.propValid("Hello");
-    REQUIRE(valid);
-  }
-
-  cerr << "Testing: setPropOption" << endl;
-  {
-    PropertyString propString;
-    size_t val = 3;
-    propString.setPropOption(Option::MAX_LENGTH, val);
-    propString.propValid("");
-    CHECK_THROWS(propString.propValid("Hello"));
-    
-    val = 4;
-    CHECK_THROWS(propString.setPropOption(Option::MAX, val));
-  }
-}
diff --git a/src/tests/test_propertystringchoice.cpp b/src/tests/test_propertystringchoice.cpp
deleted file mode 100644
index 4c2da2c..0000000
--- a/src/tests/test_propertystringchoice.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-#include "io/arguments/properties/propertystringchoice.hpp"
-#include <cassert>
-#include <exception>
-#include <fstream>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property String Choice","[unit]") {
-  { PropertyStringChoice propStrChoice; }
-}
-
-TEST_CASE("getPropertyType","[unit]") { 
-  PropertyStringChoice propStrChoice;
-  PropertyType type = propStrChoice.getPropertyType();
-  REQUIRE(type == PropertyType::STRING_CHOICE);
-}
-
-TEST_CASE("getPropertyOptions","[unit]") { 
-
-  PropertyStringChoice propStrChoice;
-  auto options = propStrChoice.getPropertyOptions();
-
-  bool choice_enforced = false;
-  bool str_choices = false;
-
-  for (auto opt : options) {
-    if (opt == Option::ENFORCED) {
-      choice_enforced = true;
-    }
-    if (opt == Option::ALLOWED_VALUES) {
-      str_choices = true;
-    }
-  }
-  REQUIRE(choice_enforced);
-  REQUIRE(str_choices);
-}
-
-TEST_CASE("getPropOption","[unit]"){ 
-  PropertyStringChoice propStrChoice;
-
-  set<bool> choice_enforced =
-    propStrChoice.getPropOption<set<bool>>(Option::ENFORCED);
-  set<string> choices = propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
-/*
-  bool enforced = *(choice_enforced.begin());
-  string choice = *(choices.begin());
-  REQUIRE(enforced == false);
-  REQUIRE(choice == "NOT_DEFINED");*/
-}
-
-TEST_CASE("setPropOption", "[unit]"){
-  PropertyStringChoice propStrChoice;
-
-  propStrChoice.setPropOption(Option::ENFORCED, "true");
-  set<string> choices{"true", "false"};
-  propStrChoice.setPropOption(Option::ALLOWED_VALUES, choices);
-
-  string choice = "true";
-  propStrChoice.propValid(choice);
-  choice = "false";
-  propStrChoice.propValid(choice);
-
-  choice = "blah";
-  REQUIRE_THROWS(propStrChoice.propValid(choice));
-
-  set<string> allowed_choices = propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
-  set<string> choice_on =
-    propStrChoice.getPropOption<set<string>>(Option::ALLOWED_VALUES);
-
-  bool false_str = false;
-  bool true_str = false;
-  for (auto item : allowed_choices) {
-    if (item.compare("false") == 0) false_str = true;
-    if (item.compare("true") == 0) true_str = true;
-  }
-  REQUIRE(false_str);
-  REQUIRE(true_str);
-
-  string on = *(choice_on.begin());
-  REQUIRE(on.compare("true") == 0);
-}
diff --git a/src/tests/test_propertyswitch.cpp b/src/tests/test_propertyswitch.cpp
deleted file mode 100644
index 5886e72..0000000
--- a/src/tests/test_propertyswitch.cpp
+++ /dev/null
@@ -1,89 +0,0 @@
-
-#define CATCH_CONFIG_MAIN
-#include <catch2/catch.hpp>
-#include "../libcatnip/io/arguments/properties/propertyswitch.hpp"
-#include <cassert>
-#include <exception>
-#include <iostream>
-#include <string>
-#include <vector>
-
-using namespace catnip;
-using namespace std;
-
-TEST_CASE("Property Switch","[unit]") {
-
-  cerr << "Testing: PropertySwitch" << endl;
-  cerr << "Testing: constructor" << endl;
-  { PropertySwitch propSwitch; }
-
-  cerr << "Testing: getPropertyName" << endl;
-  {
-    PropertySwitch propSwitch;
-    PropertyType type = propSwitch.getPropertyType();
-    REQUIRE(type == PropertyType::SWITCH);
-  }
-
-  cerr << "Testing: getPropertyOptions" << endl;
-  {
-
-    PropertySwitch propSwitch;
-    auto options = propSwitch.getPropertyOptions();
-    Option opt = options.at(0);
-    REQUIRE(opt == Option::DEFAULT);
-  }
-
-  cerr << "Testing: propValid" << endl;
-  {
-    PropertySwitch propSwitch;
-    bool valid = propSwitch.propValid(0);
-    assert(valid);
-    valid = propSwitch.propValid(1);
-    assert(valid);
-    valid = propSwitch.propValid();
-    assert(valid);
-    bool excep = false;
-    try {
-      propSwitch.propValid(-1);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    excep = false;
-    try {
-      propSwitch.propValid(2);
-    } catch (...) {
-      excep = true;
-    }
-    assert(excep);
-
-    valid = propSwitch.propValid("ON");
-    assert(valid);
-    valid = propSwitch.propValid("OFF");
-    assert(valid);
-    valid = propSwitch.propValid("TRUE");
-    assert(valid);
-    valid = propSwitch.propValid("FALSE");
-    assert(valid);
-    valid = propSwitch.propValid("0");
-    assert(valid);
-    valid = propSwitch.propValid("1");
-    assert(valid);
-  }
-
-  cerr << "Testing: setPropOption" << endl;
-  {
-    PropertySwitch propSwitch;
-    propSwitch.setPropOption(Option::DEFAULT, "ON");
-    propSwitch.setPropOption(Option::DEFAULT, "OFF");
-    //    propSwitch.propValid(0);
-    //    bool excep = false;
-    //    try {
-    //      propSwitch.propValid(-1);
-    //    } catch (...) {
-    //      excep = true;
-    //    }
-    //    assert(excep);
-  }
-}
diff --git a/src/tests/test_swap_engine.cpp b/src/tests/test_swap_engine.cpp
index 6fdd2de..fa1d9b9 100644
--- a/src/tests/test_swap_engine.cpp
+++ b/src/tests/test_swap_engine.cpp
@@ -19,53 +19,6 @@
 #include <vector>
 
 using namespace catnip;
-/*
-TEST_CASE("Basis Map Unscrambled","[integration]") {
-
-  Atom atom1(Element::H, 0.0, 0.0, 0.0);
-  Atom atom2(Element::H, 2.0, 0.0, 0.0);
-  Atom atom3(Element::C, 1.0, 1.0, 0.0);
-  Atom atom4(Element::O, 3.3, 4.3, 0.0);
-  Atom atom5(Element::O, 3.0, 3.9, 0.0);
-
-  auto atom1_ptr = std::make_shared<Atom>(atom1);
-  auto atom2_ptr = std::make_shared<Atom>(atom2);
-  auto atom3_ptr = std::make_shared<Atom>(atom3);
-  auto atom4_ptr = std::make_shared<Atom>(atom4);
-  auto atom5_ptr = std::make_shared<Atom>(atom5);
-
-  // Extra atoms are allowed in the complex but not in the componets
-  AtomGroup component1("CH2");
-  component1.add(atom1_ptr);
-  component1.add(atom2_ptr);
-  component1.add(atom3_ptr);
-
-  AtomGroup component2("O2");
-  component2.add(atom4_ptr);  
-  component2.add(atom5_ptr);  
-
-  AtomGroup complex1("O2CH2");
-  complex1.add(atom1_ptr);
-  complex1.add(atom2_ptr);
-  complex1.add(atom3_ptr);
-  complex1.add(atom4_ptr);
-  complex1.add(atom5_ptr);
-
-  AtomGroupContainer atom_grp_cont;
-  atom_grp_cont.add(component1);
-  atom_grp_cont.add(component2);
-  atom_grp_cont.add(complex1);
-
-  AtomSystem atm_sys(atom_grp_cont);
-
-  std::vector<int> basis_complex{ 1, 1, 4, 5, 5}; 
-
-  int index_complex = 2;
-  atm_sys.assignBasisFunctions( index_complex, basis_complex);
-  BasisMap basis_map(atm_sys);
-
-}
-*/
 
 /**
  * @brief In this test some of the atoms added to the complex will be added
@@ -92,30 +45,29 @@ TEST_CASE("Basis Map Scrambled","[integration]") {
   auto atom5_ptr = std::make_shared<Atom>(atom5);
 
   // Extra atoms are allowed in the complex but not in the componets
-  AtomGroup component1("CH2");
-  component1.add(atom1_ptr);
-  component1.add(atom2_ptr);
-  component1.add(atom3_ptr);
+  auto component1 = std::make_unique<AtomGroup>("CH2");
+  component1->add(atom1_ptr);
+  component1->add(atom2_ptr);
+  component1->add(atom3_ptr);
 
-  AtomGroup component2("O2");
-  component2.add(atom4_ptr);  
-  component2.add(atom5_ptr);  
+  auto component2 = std::make_unique<AtomGroup>("O2");
+  component2->add(atom4_ptr);  
+  component2->add(atom5_ptr);  
 
   // HERE: the order has been changed
-  AtomGroup complex1("O2CH2");
-  complex1.add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
-  complex1.add(atom1_ptr); // The basis functiosn of atom 1 : 5 - 5 
-  complex1.add(atom3_ptr); // The basis functiosn of atom 3 : 6 - 9
-  complex1.add(atom5_ptr); // The basis functiosn of atom 5 : 10 - 14
-  complex1.add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
-
-  AtomGroupContainer atom_grp_cont;
-  atom_grp_cont.add(component1);
-  atom_grp_cont.add(component2);
-  atom_grp_cont.add(complex1);
+  auto complex1 = std::make_unique<AtomGroup>("O2CH2");
+  complex1->add(atom4_ptr); // The basis functions of atom 4 : 0 - 4
+  complex1->add(atom1_ptr); // The basis functions of atom 1 : 5 - 5 
+  complex1->add(atom3_ptr); // The basis functions of atom 3 : 6 - 9
+  complex1->add(atom5_ptr); // The basis functions of atom 5 : 10 - 14
+  complex1->add(atom2_ptr); // The basis functions of atom 2 : 15 - 15
 
-  AtomSystem atm_sys(atom_grp_cont);
+  auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+  atom_grp_cont->add(std::move(component1));
+  atom_grp_cont->add(std::move(component2));
+  atom_grp_cont->add(std::move(complex1));
 
+  AtomSystem atm_sys(std::move(atom_grp_cont));
 
   int index_component1 = 0;
   int index_component2 = 1;
@@ -160,9 +112,9 @@ TEST_CASE("QC Functions","[integration]") {
     auto atom1_ptr = std::make_shared<Atom>(atom1);
     auto atom2_ptr = std::make_shared<Atom>(atom2);
 
-    AtomGroup componentA("A");
-    componentA.add(atom1_ptr);
-    componentA.add(atom2_ptr);
+    auto componentA = std::make_unique<AtomGroup>("A");
+    componentA->add(atom1_ptr);
+    componentA->add(atom2_ptr);
 
     Atom atom3(Element::C, 1.0, 0.0, 0.0);
     Atom atom4(Element::O, 2.0, 0.0, 0.0);
@@ -172,32 +124,32 @@ TEST_CASE("QC Functions","[integration]") {
     auto atom4_ptr = std::make_shared<Atom>(atom4);
     auto atom5_ptr = std::make_shared<Atom>(atom5);
 
-    AtomGroup componentB("B");
-    componentB.add(atom3_ptr);
-    componentB.add(atom4_ptr);
-    componentB.add(atom5_ptr);
+    auto componentB = std::make_unique<AtomGroup>("B");
+    componentB->add(atom3_ptr);
+    componentB->add(atom4_ptr);
+    componentB->add(atom5_ptr);
 
     // Arrange atoms in the dimer so they do not appear in the
     // same order as the monomers
 
-    // Atom 3   1.0, 0.0, 0.0
-    // Atom 1   1.0, 1.0, 1.0
-    // Atom 5   3.0, 0.0, 0.0
-    // Atom 4   2.0, 0.0, 0.0
-    // Atom 2   0.0, 0.0, 0.0
+    // Atom 3   1->0, 0->0, 0->0
+    // Atom 1   1->0, 1->0, 1->0
+    // Atom 5   3->0, 0->0, 0->0
+    // Atom 4   2->0, 0->0, 0->0
+    // Atom 2   0->0, 0->0, 0->0
 
-    AtomGroup complexAB("AB");
-    complexAB.add(atom3_ptr);
-    complexAB.add(atom1_ptr);
-    complexAB.add(atom5_ptr);
-    complexAB.add(atom4_ptr);
-    complexAB.add(atom2_ptr);
+    auto complexAB = std::make_unique<AtomGroup>("AB");
+    complexAB->add(atom3_ptr);
+    complexAB->add(atom1_ptr);
+    complexAB->add(atom5_ptr);
+    complexAB->add(atom4_ptr);
+    complexAB->add(atom2_ptr);
 
     // Combine atom groups
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(componentA);
-    atom_grp_cont.add(componentB);
-    atom_grp_cont.add(complexAB);
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(componentA));
+    atom_grp_cont->add(std::move(componentB));
+    atom_grp_cont->add(std::move(complexAB));
 
     // Basis functions per atom
     //
@@ -222,7 +174,7 @@ TEST_CASE("QC Functions","[integration]") {
     basisFuncDimer.push_back(2);
     basisFuncDimer.push_back(2);
 
-    AtomSystem atm_sys(atom_grp_cont);
+    AtomSystem atm_sys(std::move(atom_grp_cont));
 
     // Assign the basis functions to the atoms that are in the complex
     int index_complex = 2;
@@ -317,9 +269,9 @@ TEST_CASE("QC Functions","[integration]") {
     auto atom1_ptr = std::make_shared<Atom>(atom1);
     auto atom2_ptr = std::make_shared<Atom>(atom2);
 
-    AtomGroup componentB("B");
-    componentB.add(atom1_ptr);
-    componentB.add(atom2_ptr);
+    auto componentB = std::make_unique<AtomGroup>("B");
+    componentB->add(atom1_ptr);
+    componentB->add(atom2_ptr);
 
     // Contains the x y and z position of atoms in monomer B
     Atom atom3(Element::C, 1.0, 0.0, 0.0);
@@ -330,26 +282,26 @@ TEST_CASE("QC Functions","[integration]") {
     auto atom4_ptr = std::make_shared<Atom>(atom4);
     auto atom5_ptr = std::make_shared<Atom>(atom5);
 
-    AtomGroup componentA("A");
-    componentA.add(atom3_ptr);
-    componentA.add(atom4_ptr);
-    componentA.add(atom5_ptr);
+    auto componentA = std::make_unique<AtomGroup>("A");
+    componentA->add(atom3_ptr);
+    componentA->add(atom4_ptr);
+    componentA->add(atom5_ptr);
 
     // Positions of atoms in the complex
-    AtomGroup complexAB("AB");
-    complexAB.add(atom3_ptr);
-    complexAB.add(atom1_ptr);
-    complexAB.add(atom5_ptr);
-    complexAB.add(atom4_ptr);
-    complexAB.add(atom2_ptr);
+    auto complexAB = std::make_unique<AtomGroup>("AB");
+    complexAB->add(atom3_ptr);
+    complexAB->add(atom1_ptr);
+    complexAB->add(atom5_ptr);
+    complexAB->add(atom4_ptr);
+    complexAB->add(atom2_ptr);
 
     // Combine atom groups
-    AtomGroupContainer atom_grp_cont;
-    atom_grp_cont.add(componentA);
-    atom_grp_cont.add(componentB);
-    atom_grp_cont.add(complexAB);
+    auto atom_grp_cont = std::unique_ptr<AtomGroupContainer>(new AtomGroupContainer);
+    atom_grp_cont->add(std::move(componentA));
+    atom_grp_cont->add(std::move(componentB));
+    atom_grp_cont->add(std::move(complexAB));
 
-    AtomSystem atm_sys(atom_grp_cont);
+    AtomSystem atm_sys(std::move(atom_grp_cont));
     
     // Basis functions per atom
     //
diff --git a/src/tools/calcJ.cpp b/src/tools/calcJ.cpp
index 74e1d2a..7ee0c62 100644
--- a/src/tools/calcJ.cpp
+++ b/src/tools/calcJ.cpp
@@ -19,8 +19,8 @@
 #include "../libcatnip/parameters.hpp"
 #include "../libcatnip/qc_functions.hpp"
 #include "../libcatnip/matrix.hpp"*/
-#include "libcatnip/catnip_config.hpp"
-#include "libcatnip/log.hpp"
+#include "catnip_config.hpp"
+#include "log.hpp"
 
 #include <eigen3/Eigen/Core>
 
@@ -29,8 +29,9 @@ using namespace std;
 
 int main(int argc, const char *argv[]) {
   cout << endl;
-  cout << "Running calc_J VERSION " << calcJ_VERSION_MAJOR << ".";
-  cout << calcJ_VERSION_MINOR << endl;
+  cout << "Running calc_J VERSION " << catnip_VERSION_MAJOR << ".";
+  cout << catnip_VERSION_MINOR << "." << endl;
+  cout << catnip_VERSION_PATCH << "." << endl;
 
   string line;
   LOG("Preparing parser", 1);