Simplify MDCell helper functions

Author: Fei Yang

source/source_cell/distributed_mdcell_reader.cpp

@@ -33,37 +33,27 @@ struct StruMetadata
     MdStruFileMetadata stru_file_metadata;
 };
 
-std::string trim_copy(const std::string& value)
-{
-    std::size_t begin = 0;
-    while (begin < value.size() && std::isspace(static_cast<unsigned char>(value[begin])))
-    {
-        ++begin;
-    }
-    std::size_t end = value.size();
-    while (end > begin && std::isspace(static_cast<unsigned char>(value[end - 1])))
-    {
-        --end;
-    }
-    return value.substr(begin, end - begin);
-}
-
-std::string strip_comment(const std::string& line)
-{
-    const std::size_t pos = line.find('#');
-    return trim_copy(pos == std::string::npos ? line : line.substr(0, pos));
-}
-
 std::string next_data_line(std::ifstream& ifs, const char* context)
 {
     std::string line;
     while (std::getline(ifs, line))
     {
-        line = strip_comment(line);
-        if (!line.empty())
+        const std::size_t comment = line.find('#');
+        if (comment != std::string::npos)
+        {
+            line.erase(comment);
+        }
+        std::size_t begin = 0;
+        while (begin < line.size() && std::isspace(static_cast<unsigned char>(line[begin])))
+        {
+            ++begin;
+        }
+        std::size_t end = line.size();
+        while (end > begin && std::isspace(static_cast<unsigned char>(line[end - 1])))
         {
-            return line;
+            --end;
         }
+        if (begin != end) return line.substr(begin, end - begin);
     }
     throw std::runtime_error(std::string("Unexpected EOF while reading ") + context + ".");
 }
@@ -258,17 +248,13 @@ std::vector<LocalAtom> read_owned_atoms(std::ifstream& ifs,
             }
 
             ModuleBase::Vector3<double> frac;
-            ModuleBase::Vector3<double> cart;
             if (is_cartesian)
             {
-                cart.set(c1, c2, c3);
-                frac = wrap_fractional(cart * primitive_gt);
-                cart = frac * primitive_latvec;
+                frac = wrap_fractional(ModuleBase::Vector3<double>(c1, c2, c3) * primitive_gt);
             }
             else
             {
                 frac = wrap_fractional(ModuleBase::Vector3<double>(c1, c2, c3));
-                cart = frac * primitive_latvec;
             }
 
             ModuleBase::Vector3<int> mbl(1, 1, 1);

source/source_cell/print_cell.cpp

@@ -252,23 +252,21 @@ std::string mdcell_type_header(const MDCell& cell, const MdStruFileMetadata& met
     return output.str();
 }
 
-std::string mdcell_atom_line(const LocalAtom& atom)
-{
-    std::ostringstream output;
-    output << std::fixed << std::setprecision(10)
-           << atom.cart.x << " " << atom.cart.y << " " << atom.cart.z
-           << " m " << atom.mbl.x << " " << atom.mbl.y << " " << atom.mbl.z
-           << " v " << atom.vel.x << " " << atom.vel.y << " " << atom.vel.z << "\n";
-    return output.str();
-}
-
 std::string local_mdcell_atoms(const MDCell& cell, const std::size_t type)
 {
     std::string output;
     for (std::size_t iat = 0; iat < cell.owned_atoms().size(); ++iat)
     {
         const LocalAtom& atom = cell.owned_atoms()[iat];
-        if (atom.type == static_cast<int>(type)) output += mdcell_atom_line(atom);
+        if (atom.type == static_cast<int>(type))
+        {
+            std::ostringstream atom_output;
+            atom_output << std::fixed << std::setprecision(10)
+                        << atom.cart.x << " " << atom.cart.y << " " << atom.cart.z
+                        << " m " << atom.mbl.x << " " << atom.mbl.y << " " << atom.mbl.z
+                        << " v " << atom.vel.x << " " << atom.vel.y << " " << atom.vel.z << "\n";
+            output += atom_output.str();
+        }
     }
     return output;
 }

source/source_md/nhchain.cpp

@@ -6,22 +6,6 @@
 #endif
 #include "source_base/timer.h"
 
-namespace
-{
-ModuleBase::matrix global_temp_tensor(const MDCell& mdcell)
-{
-    ModuleBase::matrix t_vector(3, 3);
-    for (const LocalAtom& atom : mdcell.owned_atoms())
-        for (int i = 0; i < 3; ++i)
-            for (int j = 0; j < 3; ++j)
-                t_vector(i, j) += atom.mass * atom.vel[i] * atom.vel[j];
-#ifdef __MPI
-    MPI_Allreduce(MPI_IN_PLACE, t_vector.c, t_vector.nr * t_vector.nc, MPI_DOUBLE, MPI_SUM, mdcell.communicator());
-#endif
-    return t_vector;
-}
-}
-
 Nose_Hoover::Nose_Hoover(const Parameter& param_in, MDCell& mdcell_in) : MD_base(param_in, mdcell_in)
 {
     const double unit_transform = ModuleBase::HARTREE_SI / pow(ModuleBase::BOHR_RADIUS_SI, 3) * 1.0e-8;
@@ -659,7 +643,14 @@ void Nose_Hoover::update_baro()
     }
     else
     {
-        const ModuleBase::matrix t_vector = global_temp_tensor(mdcell);
+        ModuleBase::matrix t_vector(3, 3);
+        for (const LocalAtom& atom : mdcell.owned_atoms())
+            for (int i = 0; i < 3; ++i)
+                for (int j = 0; j < 3; ++j)
+                    t_vector(i, j) += atom.mass * atom.vel[i] * atom.vel[j];
+#ifdef __MPI
+        MPI_Allreduce(MPI_IN_PLACE, t_vector.c, t_vector.nr * t_vector.nc, MPI_DOUBLE, MPI_SUM, mdcell.communicator());
+#endif
 
         for (int i = 0; i < 3; ++i)
         {