Change names of MD subroutines and files

source/Makefile.Objects

@@ -195,7 +195,7 @@ OBJS_BASE=assoc_laguerre.o\
     orb_io.o\
 
 OBJS_CELL=atom_pseudo.o\
-    base_cell.o\
+    basecell.o\
     qlist.o\
     atom_spec.o\
     pseudo.o\
@@ -225,8 +225,8 @@ OBJS_CELL=atom_pseudo.o\
     read_pp_ucell.o\
     cal_wfc.o\
     cal_ux.o\
-    distributed_mdcell_reader.o\
-    md_cell.o\
+    mdcell_reader.o\
+    mdcell.o\
     cif_io.o\
     ucell_io.o\
 

source/source_base/parallel_cell.cpp

@@ -24,12 +24,12 @@ int CommunicationDomain::rank() const
     return rank_;
 }
 
-CommunicationDomain world_communication_domain()
+CommunicationDomain world_comm_domain()
 {
-    CommunicationDomain communication_domain;
+    CommunicationDomain comm_domain;
 #ifdef __MPI
-    communication_domain.initialize(MPI_COMM_WORLD);
+    comm_domain.initialize(MPI_COMM_WORLD);
 #endif
-    return communication_domain;
+    return comm_domain;
 }
 } // namespace ModuleBase

source/source_base/parallel_cell.h

@@ -24,7 +24,7 @@ class CommunicationDomain
     int rank_ = 0;
 };
 
-CommunicationDomain world_communication_domain();
+CommunicationDomain world_comm_domain();
 } // namespace ModuleBase
 
 #endif

source/source_cell/CMakeLists.txt

@@ -5,7 +5,7 @@ add_subdirectory(module_neighlist)
 add_library(
     cell
     OBJECT
-    base_cell.cpp
+    basecell.cpp
     atom_pseudo.cpp
     atom_spec.cpp
     pseudo.cpp
@@ -15,8 +15,8 @@ add_library(
     read_pp_upf201.cpp
     read_pp_blps.cpp
     read_pp_vwr.cpp
-    distributed_mdcell_reader.cpp
-    md_cell.cpp
+    mdcell_reader.cpp
+    mdcell.cpp
     unitcell.cpp
     read_atoms.cpp
     read_atoms_helper.cpp

source/source_cell/base_cell.cpp → source/source_cell/basecell.cpp

@@ -1,12 +1,12 @@
-#include "source_cell/base_cell.h"
+#include "source_cell/basecell.h"
 
 #include "source_base/tool_quit.h"
 
 void BaseCell::require_kind(const Kind& expected, const char* caller) const
 {
     if (this->kind() != expected)
     {
-        const char* required_cell = expected == Kind::unit_cell ? "UnitCell" : "MDCell";
+        const char* required_cell = expected == Kind::unitcell ? "UnitCell" : "MDCell";
         ModuleBase::WARNING_QUIT(caller, std::string("This operation only supports ") + required_cell + ".");
     }
 }

source/source_cell/base_cell.h → source/source_cell/basecell.h

@@ -1,5 +1,5 @@
-#ifndef BASE_CELL_H
-#define BASE_CELL_H
+#ifndef BASECELL_H
+#define BASECELL_H
 
 #include "source_base/matrix3.h"
 
@@ -10,8 +10,8 @@ class BaseCell
 public:
     enum class Kind
     {
-        unit_cell,
-        md_cell
+        unitcell,
+        mdcell
     };
 
     virtual ~BaseCell() = default;

source/source_cell/md_cell.cpp → source/source_cell/mdcell.cpp

@@ -1,4 +1,4 @@
-#include "source_cell/md_cell.h"
+#include "source_cell/mdcell.h"
 
 #include "source_base/parallel_cell.h"
 #include "source_cell/unitcell.h"
@@ -180,12 +180,12 @@ void MDCell::initialize_from_owned_atoms_(double cutoff, double skin)
 void MDCell::initialize_from_unitcell(UnitCell& ucell,
                                       double cutoff,
                                       double skin,
-                                      const ModuleBase::CommunicationDomain& communication_domain)
+                                      const ModuleBase::CommunicationDomain& comm_domain)
 {
 #ifdef __MPI
-    initialize_from_ucell_(ucell, communication_domain.communicator(), cutoff, skin);
+    initialize_from_ucell_(ucell, comm_domain.communicator(), cutoff, skin);
 #else
-    static_cast<void>(communication_domain);
+    static_cast<void>(comm_domain);
     initialize_from_ucell_(ucell, cutoff, skin);
 #endif
 }
@@ -201,7 +201,7 @@ void MDCell::initialize_from_owned_atoms(const ModuleBase::Matrix3& latvec,
                                          const std::vector<std::int64_t>& type_atom_counts,
                                          double cutoff,
                                          double skin,
-                                         const ModuleBase::CommunicationDomain& communication_domain)
+                                         const ModuleBase::CommunicationDomain& comm_domain)
 {
     latvec_ = latvec;
     gt_ = gt;
@@ -213,9 +213,9 @@ void MDCell::initialize_from_owned_atoms(const ModuleBase::Matrix3& latvec,
     type_masses_ = type_masses;
     type_atom_counts_ = type_atom_counts;
 #ifdef __MPI
-    initialize_from_owned_atoms_(communication_domain.communicator(), cutoff, skin);
+    initialize_from_owned_atoms_(comm_domain.communicator(), cutoff, skin);
 #else
-    static_cast<void>(communication_domain);
+    static_cast<void>(comm_domain);
     initialize_from_owned_atoms_(cutoff, skin);
 #endif
 }
@@ -556,7 +556,7 @@ void MDCell::sync_backing_unitcell()
 
 BaseCell::Kind MDCell::get_kind() const
 {
-    return Kind::md_cell;
+    return Kind::mdcell;
 }
 
 std::int64_t MDCell::get_nat() const

source/source_cell/md_cell.h → source/source_cell/mdcell.h

@@ -1,7 +1,8 @@
-#ifndef MD_CELL_H
-#define MD_CELL_H
+#ifndef MDCELL_H
+#define MDCELL_H
 
-#include "source_cell/base_cell.h"
+#include "source_cell/basecell.h"
+#include "source_cell/strumeta.h"
 #include "source_cell/module_neighlist/local_atom.h"
 
 #ifdef __MPI
@@ -33,7 +34,7 @@ class MDCell : public BaseCell
     void initialize_from_unitcell(UnitCell& ucell,
                                   double cutoff,
                                   double skin,
-                                  const ModuleBase::CommunicationDomain& communication_domain);
+                                  const ModuleBase::CommunicationDomain& comm_domain);
     void initialize_from_owned_atoms(const ModuleBase::Matrix3& latvec,
                                      const ModuleBase::Matrix3& gt,
                                      double lat0,
@@ -45,7 +46,7 @@ class MDCell : public BaseCell
                                      const std::vector<std::int64_t>& type_atom_counts,
                                      double cutoff,
                                      double skin,
-                                     const ModuleBase::CommunicationDomain& communication_domain);
+                                     const ModuleBase::CommunicationDomain& comm_domain);
 
 #ifdef __MPI
     int mpi_rank() const;
@@ -68,6 +69,8 @@ class MDCell : public BaseCell
     const std::vector<std::string>& type_labels() const { return type_labels_; }
     const std::vector<double>& type_masses() const { return type_masses_; }
     const std::vector<std::int64_t>& type_atom_counts() const { return type_atom_counts_; }
+    StruMeta& mutable_stru_meta() { return stru_meta_; }
+    const StruMeta& stru_meta() const { return stru_meta_; }
     std::vector<LocalAtom>& mutable_owned_atoms();
     std::vector<LocalAtom>& mutable_ghost_atoms();
 
@@ -110,6 +113,7 @@ class MDCell : public BaseCell
     std::vector<std::string> type_labels_;
     std::vector<double> type_masses_;
     std::vector<std::int64_t> type_atom_counts_;
+    StruMeta stru_meta_;
     double cutoff_ = 0.0;
     double skin_ = 0.0;
     std::unique_ptr<NeighborSearch> neighbor_search_;

source/source_cell/distributed_mdcell_reader.cpp → source/source_cell/mdcell_reader.cpp

@@ -1,9 +1,9 @@
-#include "source_cell/distributed_mdcell_reader.h"
+#include "source_cell/mdcell_reader.h"
 
 #include "source_base/constants.h"
 #include "source_base/parallel_cell.h"
 #include "source_base/vector3.h"
-#include "source_cell/md_cell.h"
+#include "source_cell/mdcell.h"
 
 #ifdef __MPI
 #include "source_cell/module_neighlist/domain_decomposition.h"
@@ -30,7 +30,7 @@ struct StruMetadata
     std::vector<std::string> labels;
     std::vector<double> masses;
     std::vector<std::int64_t> type_atom_counts;
-    MdStruFileMetadata stru_file_metadata;
+    StruMeta stru_meta;
 };
 
 std::string next_data_line(std::ifstream& ifs, const char* context)
@@ -130,15 +130,15 @@ StruMetadata parse_stru_metadata(std::ifstream& ifs)
         }
         if (line == "NUMERICAL_ORBITAL")
         {
-            for (std::size_t it = 0; it < metadata.stru_file_metadata.species.size(); ++it)
+            for (std::size_t it = 0; it < metadata.stru_meta.species.size(); ++it)
             {
-                metadata.stru_file_metadata.species[it].orbital_file = next_data_line(ifs, "NUMERICAL_ORBITAL body");
+                metadata.stru_meta.species[it].orbital_file = next_data_line(ifs, "NUMERICAL_ORBITAL body");
             }
             continue;
         }
         if (line == "NUMERICAL_DESCRIPTOR")
         {
-            metadata.stru_file_metadata.descriptor_file = next_data_line(ifs, "NUMERICAL_DESCRIPTOR body");
+            metadata.stru_meta.descriptor_file = next_data_line(ifs, "NUMERICAL_DESCRIPTOR body");
             continue;
         }
 
@@ -153,9 +153,9 @@ StruMetadata parse_stru_metadata(std::ifstream& ifs)
 
         metadata.labels.push_back(label);
         metadata.masses.push_back(parse_double(mass_token, "atomic mass"));
-        MdStruFileSpecies species;
+        StruSpecies species;
         iss >> species.pseudo_file >> species.pseudo_type;
-        metadata.stru_file_metadata.species.push_back(species);
+        metadata.stru_meta.species.push_back(species);
     }
 
     expect_keyword(ifs, "LATTICE_CONSTANT");
@@ -190,13 +190,13 @@ std::vector<LocalAtom> read_owned_atoms(std::ifstream& ifs,
                                          double cutoff,
                                          double skin,
                                          std::int64_t& nat,
-                                         const ModuleBase::CommunicationDomain& communication_domain)
+                                         const ModuleBase::CommunicationDomain& comm_domain)
 {
     int rank = 0;
 #ifdef __MPI
     DomainDecomposition decomposition;
-    decomposition.init(communication_domain.communicator(), metadata.latvec, metadata.lat0, cutoff, skin);
-    rank = communication_domain.rank();
+    decomposition.init(comm_domain.communicator(), metadata.latvec, metadata.lat0, cutoff, skin);
+    rank = comm_domain.rank();
 #endif
 
     int begin[3] = {0, 0, 0};
@@ -232,7 +232,7 @@ std::vector<LocalAtom> read_owned_atoms(std::ifstream& ifs,
             throw std::runtime_error("ATOMIC_POSITIONS label order does not match ATOMIC_SPECIES.");
         }
         std::istringstream magnetism(next_data_line(ifs, "magnetism"));
-        magnetism >> metadata.stru_file_metadata.species[it].start_mag;
+        magnetism >> metadata.stru_meta.species[it].start_mag;
         const std::int64_t nat_type = parse_int64(next_data_line(ifs, "atom count"), "atom count");
 
         for (std::int64_t ia = 0; ia < nat_type; ++ia)
@@ -323,12 +323,11 @@ std::vector<LocalAtom> read_owned_atoms(std::ifstream& ifs,
 }
 } // namespace
 
-MDCell DistributedMDCellReader::read_stru(const std::string& stru_file,
+MDCell MDCellReader::read_stru(const std::string& stru_file,
                                           const std::vector<int>& cell_replica,
                                           double cutoff,
                                           double skin,
-                                          MdStruFileMetadata& stru_metadata,
-                                          const ModuleBase::CommunicationDomain& communication_domain)
+                                          const ModuleBase::CommunicationDomain& comm_domain)
 {
     if (cutoff <= 0.0)
     {
@@ -355,7 +354,7 @@ MDCell DistributedMDCellReader::read_stru(const std::string& stru_file,
     metadata.omega = std::abs(metadata.latvec.Det()) * metadata.lat0 * metadata.lat0 * metadata.lat0;
     std::int64_t nat = 0;
     const std::vector<LocalAtom> owned_atoms = read_owned_atoms(ifs, metadata, primitive_latvec, primitive_gt,
-                                                                  cell_replica, cutoff, skin, nat, communication_domain);
+                                                                  cell_replica, cutoff, skin, nat, comm_domain);
     MDCell mdcell;
     mdcell.initialize_from_owned_atoms(metadata.latvec,
                                        metadata.gt,
@@ -368,7 +367,7 @@ MDCell DistributedMDCellReader::read_stru(const std::string& stru_file,
                                        metadata.type_atom_counts,
                                        cutoff,
                                        skin,
-                                       communication_domain);
-    stru_metadata = metadata.stru_file_metadata;
+                                       comm_domain);
+    mdcell.mutable_stru_meta() = metadata.stru_meta;
     return mdcell;
 }

source/source_cell/distributed_mdcell_reader.h → source/source_cell/mdcell_reader.h

@@ -1,7 +1,5 @@
-#ifndef DISTRIBUTED_MDCELL_READER_H
-#define DISTRIBUTED_MDCELL_READER_H
-
-#include "source_cell/md_stru_file_metadata.h"
+#ifndef MDCELL_READER_H
+#define MDCELL_READER_H
 
 #include <string>
 #include <vector>
@@ -12,15 +10,14 @@ namespace ModuleBase
 class CommunicationDomain;
 }
 
-class DistributedMDCellReader
+class MDCellReader
 {
 public:
     static MDCell read_stru(const std::string& stru_file,
                             const std::vector<int>& cell_replica,
                             double cutoff,
                             double skin,
-                            MdStruFileMetadata& stru_metadata,
-                            const ModuleBase::CommunicationDomain& communication_domain);
+                            const ModuleBase::CommunicationDomain& comm_domain);
 };
 
 #endif

source/source_cell/module_neighlist/neighbor_search.cpp

@@ -1,5 +1,5 @@
 #include "source_cell/module_neighlist/neighbor_search.h"
-#include "source_cell/md_cell.h"
+#include "source_cell/mdcell.h"
 #include "source_cell/unitcell.h"
 
 #include <cmath>
@@ -146,14 +146,14 @@ void NeighborSearch::init_from_unitcell_(const UnitCell& ucell, double sr)
 
 void NeighborSearch::init(BaseCell& cell, double sr)
 {
-    if (cell.kind() == BaseCell::Kind::md_cell)
+    if (cell.kind() == BaseCell::Kind::mdcell)
     {
-        MDCell& md_cell = static_cast<MDCell&>(cell);
-        init_from_mdcell_(md_cell, sr);
+        MDCell& mdcell = static_cast<MDCell&>(cell);
+        init_from_mdcell_(mdcell, sr);
         return;
     }
 
-    assert(cell.kind() == BaseCell::Kind::unit_cell);
+    assert(cell.kind() == BaseCell::Kind::unitcell);
     UnitCell& ucell = static_cast<UnitCell&>(cell);
     init_from_unitcell_(ucell, sr);
 }

source/source_cell/module_neighlist/neighbor_search.h

@@ -5,7 +5,7 @@
 #include "source_cell/module_neighlist/bin_manager.h"
 #include "source_cell/module_neighlist/neighbor_list.h"
 #include "source_cell/module_neighlist/local_atom.h"
-#include "source_cell/base_cell.h"
+#include "source_cell/basecell.h"
 
 class MDCell;
 class UnitCell;