WIP Refactor Version 2.0

.gitmodules

@@ -0,0 +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

.travis.yml

@@ -4,6 +4,7 @@ dist: xenial
 addons:
   apt:
     update: true
+    packages: libeigen3-dev
 
 language: cpp
 
@@ -17,6 +18,7 @@ jobs:
       compiler: gcc
       script: ./scripts/deploy.bash
       apt:
+        packages: libeigen3-dev
         packages: gcov
         packages: lcov
 

CMakeLists.txt

@@ -1,120 +1,132 @@
-cmake_minimum_required (VERSION 2.8)
-project (calc_J)
+cmake_minimum_required (VERSION 3.14)
+project (catnip VERSION 2.0.0)
 
 ##############################################################################
 # 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_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 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(calcJ_VERSION_MAJOR 1 )
-set(calcJ_VERSION_MINOR 9 )
-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_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(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 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)
-set(CMAKE_CXX_FLAGS "-Wall -Wextra -std=c++11 -pedantic -Werror")
+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(
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/calcJconfig.hpp.in"
-  "${PROJECT_SOURCE_DIR}/src/libcatnip/calcJconfig.hpp"
+  "${catnip_SOURCE_DIR}/src/libcatnip/catnip_config.hpp.in"
+  "${catnip_SOURCE_DIR}/src/libcatnip/catnip_config.hpp"
   )
 
 ##############################################################################
 # 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)
+#  message("-- Eigen found")
+#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 
 ##############################################################################
-if(ENABLE_INTEGRATION_TESTS)
-  if(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-    message("GAUSSIANFILES found will not download")
+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")
-    message("GAUSSIANFILES not found will download")
-    set(DOWNLOAD_TUTORIAL_FILES ON)
-  endif(EXISTS "${PROJECT_SOURCE_DIR}/GAUSSIANFILES")
-endif()
-
-if(DOWNLOAD_TUTORIAL_FILES)
-  message("Downloading gaussian tutorial files")
-  execute_process(COMMAND ${PROJECT_SOURCE_DIR}/scripts/test_suite_install.bash "${PROJECT_SOURCE_DIR}" )
+  else(EXISTS "${catnip_SOURCE_DIR}/GAUSSIANFILES")
+    message(STATUS "GAUSSIANFILES not found will attempt to download")
+    include(${catnip_SOURCE_DIR}/cmake/InstallGdown.cmake)
+  endif(EXISTS "${catnip_SOURCE_DIR}/GAUSSIANFILES")
 endif()
 
-if(ENABLE_TESTS OR ENABLE_INTEGRATION_TESTS)
+if(${ENABLE_UNIT_TESTING} OR ${ENABLE_INTEGRATION_TESTING})
+  find_package(Catch2 2.11.1)
+  if( NOT ${Catch2_FOUND} )
+    include(${catnip_SOURCE_DIR}/cmake/InstallCatch2.cmake)
+  else()
+    message(STATUS "found system installed Catch2 will not download")
+  endif()
   enable_testing()
-  add_subdirectory("${PROJECT_SOURCE_DIR}/src/tests")
-endif()
+  include(Catch)
+  include(ParseAndAddCatchTests)
 
-if (ENABLE_INTEGRATION_TESTS)
-  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()
+  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")
 
-if (ENABLE_TESTS)
-  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()
+    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 (${ENABLE_UNIT_TESTING})
+    file( COPY "${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 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")
-
-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/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 ${COMMON_LIBRARIES})
-install( TARGETS calc_J DESTINATION bin)
+add_subdirectory("${catnip_SOURCE_DIR}/src")
+
+

cmake/InstallCatch2.cmake

@@ -0,0 +1,11 @@
+# If Catch2 is not found, instead use the git submodule
+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 ${catnip_SOURCE_DIR})
+endif()
+
+add_subdirectory(${catnip_SOURCE_DIR}/external/Catch2)
+list(APPEND CMAKE_MODULE_PATH "${catnip_SOURCE_DIR}/external/Catch2/contrib")

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()

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)

src/CMakeLists.txt

@@ -0,0 +1,8 @@
+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()
+
+

src/libcatnip/CMakeLists.txt

@@ -1,9 +1,11 @@
 
 file(GLOB CATNIP_SOURCE_FILES 
-  *.cpp 
-  io/*.cpp
-  io/arguments/*.cpp 
-  io/arguments/properties/*.cpp 
-  io/file_readers/*.cpp)
+  io/io.cpp
+  string_support.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)

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
+

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;
+  }
+}