Parallel md1

docs/advanced/input_files/input-main.md

@@ -8,6 +8,7 @@
   - [System variables](#system-variables)
     - [suffix](#suffix)
     - [ntype](#ntype)
+    - [replicate](#replicate)
     - [calculation](#calculation)
     - [esolver\_type](#esolver_type)
     - [symmetry](#symmetry)
@@ -580,6 +581,12 @@
 - **Description**: Number of different atom species in the calculation.
 - **Default**: 0
 
+### replicate
+
+- **Type**: Three Integers
+- **Description**: Replicate the input STRU by Na, Nb, and Nc along its lattice vectors for distributed MDCell workflows. The default is 1 1 1, which preserves the input structure.
+- **Default**: 1 1 1
+
 ### calculation
 
 - **Type**: String

docs/parameters.yaml

@@ -17,6 +17,14 @@ parameters:
     default_value: "0"
     unit: ""
     availability: ""
+  - name: replicate
+    category: System variables
+    type: Three Integers
+    description: |
+      Replicate the input STRU by Na, Nb, and Nc along its lattice vectors for distributed MDCell workflows. The default is 1 1 1, which preserves the input structure.
+    default_value: 1 1 1
+    unit: ""
+    availability: ""
   - name: calculation
     category: System variables
     type: String

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 +1,39 @@
+#ifndef COMMUNICATION_DOMAIN_H
+#define COMMUNICATION_DOMAIN_H
+
+#ifdef __MPI
+#include <mpi.h>
+#endif
+
+namespace ModuleBase
+{
+/**
+ * @brief A non-owning MPI communication domain supplied to a subsystem.
+ *
+ * The creator remains responsible for the lifetime of the MPI communicator.
+ */
+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_base/parallel_comm.cpp

@@ -1,6 +1,7 @@
+#include "parallel_comm.h"
+
 #if defined __MPI
 
-#include "mpi.h"
 #include "parallel_global.h"
 
 MPI_Comm POOL_WORLD; //groups for different plane waves. In this group, only plane waves are different. K-points and bands are the same.
@@ -52,4 +53,4 @@ void MPICommGroup::divide_group_comm(const int& ngroup, const bool assert_even)
     }
 }
 
-#endif
+#endif

source/source_base/parallel_comm.h

@@ -42,4 +42,4 @@ class MPICommGroup
 
 #endif
 
-#endif // PARALLEL_COMM_H
+#endif // PARALLEL_COMM_H

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

source/source_cell/base_cell.h

@@ -3,6 +3,8 @@
 
 #include "source_base/matrix3.h"
 
+#include <cstdint>
+
 class BaseCell
 {
 public:
@@ -19,7 +21,7 @@ class BaseCell
         return get_kind();
     }
 
-    int nat() const
+    std::int64_t nat() const
     {
         return get_nat();
     }
@@ -48,7 +50,7 @@ class BaseCell
 
 private:
     virtual Kind get_kind() const = 0;
-    virtual int get_nat() const = 0;
+    virtual std::int64_t get_nat() const = 0;
     virtual double get_lat0() const = 0;
     virtual double get_omega() const = 0;
     virtual const ModuleBase::Matrix3& get_latvec() const = 0;