feat: add distributed MdCell domain decomposition (#7768)

* feat: add distributed MdCell domain decomposition

* fix: update NeighborAtom test construction

* refactor: generalize distributed MDCell reader

* fix: restore distributed MDCell build integration

* fix: preserve MDCell build and MPI ownership

* refactor: simplify MDCell construction

* refactor: pass MD communication domain

* fix: pass communication domain to LJ solver

* fix: restore neighbor search serial initialization

* refactor: restore serial neighbor list implementation

---------

Co-authored-by: Fei Yang <2501213217@stu.pku.edu.cn>
Co-authored-by: Mohan Chen <mohanchen@pku.edu.cn>

Author: 3 people

source/Makefile.Objects

@@ -217,6 +217,8 @@ OBJS_CELL=atom_pseudo.o\
     read_pp_ucell.o\
     cal_wfc.o\
     cal_ux.o\
+    distributed_mdcell_reader.o\
+    md_cell.o\
     cif_io.o\
     ucell_io.o\
 
@@ -437,7 +439,6 @@ OBJS_NEIGHBOR_SEARCH=neighbor_search.o\
     bin_manager.o\
     domain_decomposition.o\
     page_allocator.o\
-    unitcell_lite.o\
 
 
 OBJS_ORBITAL=orb_atomic.o\

source/source_base/CMakeLists.txt

@@ -51,6 +51,7 @@ add_library(
     tool_title.cpp
     ylm.cpp
     parallel_common.cpp
+    communication_domain.cpp
     parallel_global.cpp
     parallel_comm.cpp
     parallel_reduce.cpp

source/source_base/communication_domain.cpp

@@ -0,0 +1,43 @@
+#include "source_base/communication_domain.h"
+
+namespace ModuleBase
+{
+CommunicationDomain::CommunicationDomain()
+{
+}
+
+#ifdef __MPI
+CommunicationDomain::CommunicationDomain(MPI_Comm communicator) : communicator_(communicator)
+{
+    if (communicator_ != MPI_COMM_NULL)
+    {
+        MPI_Comm_rank(communicator_, &rank_);
+        MPI_Comm_size(communicator_, &size_);
+    }
+}
+
+MPI_Comm CommunicationDomain::communicator() const
+{
+    return communicator_;
+}
+#endif
+
+int CommunicationDomain::rank() const
+{
+    return rank_;
+}
+
+int CommunicationDomain::size() const
+{
+    return size_;
+}
+
+CommunicationDomain world_communication_domain()
+{
+#ifdef __MPI
+    return CommunicationDomain(MPI_COMM_WORLD);
+#else
+    return CommunicationDomain();
+#endif
+}
+} // namespace ModuleBase

source/source_base/communication_domain.h

@@ -0,0 +1,32 @@
+#ifndef COMMUNICATION_DOMAIN_H
+#define COMMUNICATION_DOMAIN_H
+
+#ifdef __MPI
+#include <mpi.h>
+#endif
+
+namespace ModuleBase
+{
+class CommunicationDomain
+{
+public:
+    CommunicationDomain();
+#ifdef __MPI
+    explicit CommunicationDomain(MPI_Comm communicator);
+    MPI_Comm communicator() const;
+#endif
+    int rank() const;
+    int size() const;
+
+private:
+#ifdef __MPI
+    MPI_Comm communicator_ = MPI_COMM_NULL;
+#endif
+    int rank_ = 0;
+    int size_ = 1;
+};
+
+CommunicationDomain world_communication_domain();
+} // namespace ModuleBase
+
+#endif

source/source_cell/CMakeLists.txt

@@ -15,6 +15,8 @@ add_library(
     read_pp_upf201.cpp
     read_pp_blps.cpp
     read_pp_vwr.cpp
+    distributed_mdcell_reader.cpp
+    md_cell.cpp
     unitcell.cpp
     read_atoms.cpp
     read_atoms_helper.cpp