Parallel MD (deepmodeling#7812)

* feat: enable MDCell runtime workflows

* Fix MDCell force output and default RNG seeding

* Add MDCell output controls

* Move MDCell force logging to IO

* Update random MD references

* Clean up MDCell runtime state

* Avoid redundant MDCell force storage

* Fix MD test velocity setup

* Update Langevin MD test references

* Optimize MDCell migration output

* Fix rebase integration and parameter metadata

* Localize MDCell ghost force communication

* Add reusable MDCell neighbor skin

* Preserve legacy velocity initialization for MD fallback

* Simplify MDCell helper functions

* Rerun abacuslite MPI check

* Remove legacy UnitCell velocity initialization

* Remove unused UnitCell MD helpers

* docs: clarify MDCell input availability

* fix: add parallel cell to Makefile build

---------

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

Author: 19hello

docs/advanced/input_files/input-main.md

@@ -8,6 +8,7 @@
   - [System variables](#system-variables)
     - [suffix](#suffix)
     - [ntype](#ntype)
+    - [cell\_replica](#cell_replica)
     - [calculation](#calculation)
     - [esolver\_type](#esolver_type)
     - [symmetry](#symmetry)
@@ -356,6 +357,8 @@
     - [md\_restart](#md_restart)
     - [md\_restartfreq](#md_restartfreq)
     - [md\_dumpfreq](#md_dumpfreq)
+    - [md\_neighbor\_skin](#md_neighbor_skin)
+    - [md\_out\_force](#md_out_force)
     - [dump\_force](#dump_force)
     - [dump\_vel](#dump_vel)
     - [dump\_virial](#dump_virial)
@@ -601,6 +604,12 @@
 - **Description**: Number of different atom species in the calculation.
 - **Default**: 0
 
+### cell_replica
+
+- **Type**: Three Integers
+- **Description**: Replicate the input STRU by Na, Nb, and Nc along its lattice vectors for distributed MDCell workflows. This parameter is only used for classical potentials or machine-learned interatomic potentials. The default is 1 1 1, which preserves the input structure.
+- **Default**: 1 1 1
+
 ### calculation
 
 - **Type**: String
@@ -3504,15 +3513,28 @@
 ### md_restartfreq
 
 - **Type**: Integer
-- **Description**: The output frequency of OUT.{suffix}/STRIU/, which are used to restart molecular dynamics calculations, see md_restart in detail.
+- **Description**: The output frequency of OUT.{suffix}/STRU_MD_*, which are used to restart molecular dynamics calculations, see md_restart in detail. Set to 0 to disable MD restart output.
 - **Default**: 5
 
 ### md_dumpfreq
 
 - **Type**: Integer
-- **Description**: The output frequency of OUT.${suffix}/MD_dump in molecular dynamics calculations, which including the information of lattices and atoms.
+- **Description**: The output frequency of OUT.${suffix}/MD_dump in molecular dynamics calculations, which includes lattice and atomic information. Set to 0 to disable MD_dump output.
 - **Default**: 1
 
+### md_neighbor_skin
+
+- **Type**: Real
+- **Description**: The extra neighbor-list radius in Angstrom for MDCell molecular dynamics. This parameter is only used for classical potentials or machine-learned interatomic potentials. A positive value reuses the cutoff-plus-skin candidate list until an atom has moved by half this distance; 0 rebuilds the list every force evaluation.
+- **Default**: 0.0
+- **Unit**: Angstrom
+
+### md_out_force
+
+- **Type**: Boolean
+- **Description**: Whether to output the TOTAL-FORCE table in OUT.${suffix}/running_md.log for MDCell molecular dynamics. This does not affect force calculation or molecular dynamics integration.
+- **Default**: True
+
 ### dump_force
 
 - **Type**: Boolean
@@ -3535,8 +3557,8 @@
 
 - **Type**: Integer
 - **Description**: The random seed to initialize random numbers used in molecular dynamics calculations.
-  - < 0: No srand() function is called.
-  - >= 0: The function srand(md_seed) is called.
+  - < 0: Each MPI rank uses the default seed 1 plus its rank.
+  - >= 0: Each MPI rank uses md_seed plus its rank.
 - **Default**: -1
 
 ### md_tfreq

docs/parameters.yaml

@@ -17,6 +17,14 @@ parameters:
     default_value: "0"
     unit: ""
     availability: ""
+  - name: cell_replica
+    category: System variables
+    type: Three Integers
+    description: |
+      Replicate the input STRU by Na, Nb, and Nc along its lattice vectors for distributed MDCell workflows. This parameter is only used for classical potentials or machine-learned interatomic potentials. 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
@@ -1449,18 +1457,34 @@ parameters:
     category: Molecular dynamics
     type: Integer
     description: |
-      The output frequency of OUT.{suffix}/STRIU/, which are used to restart molecular dynamics calculations, see md_restart in detail.
+      The output frequency of OUT.{suffix}/STRU_MD_*, which are used to restart molecular dynamics calculations, see md_restart in detail. Set to 0 to disable MD restart output.
     default_value: "5"
     unit: ""
     availability: ""
   - name: md_dumpfreq
     category: Molecular dynamics
     type: Integer
     description: |
-      The output frequency of OUT.${suffix}/MD_dump in molecular dynamics calculations, which including the information of lattices and atoms.
+      The output frequency of OUT.${suffix}/MD_dump in molecular dynamics calculations, which includes lattice and atomic information. Set to 0 to disable MD_dump output.
     default_value: "1"
     unit: ""
     availability: ""
+  - name: md_neighbor_skin
+    category: Molecular dynamics
+    type: Real
+    description: |
+      The extra neighbor-list radius in Angstrom for MDCell molecular dynamics. This parameter is only used for classical potentials or machine-learned interatomic potentials. A positive value reuses the cutoff-plus-skin candidate list until an atom has moved by half this distance; 0 rebuilds the list every force evaluation.
+    default_value: "0.0"
+    unit: Angstrom
+    availability: ""
+  - name: md_out_force
+    category: Molecular dynamics
+    type: Boolean
+    description: |
+      Whether to output the TOTAL-FORCE table in OUT.${suffix}/running_md.log for MDCell molecular dynamics. This does not affect force calculation or molecular dynamics integration.
+    default_value: "True"
+    unit: ""
+    availability: ""
   - name: dump_force
     category: Molecular dynamics
     type: Boolean
@@ -1490,8 +1514,8 @@ parameters:
     type: Integer
     description: |
       The random seed to initialize random numbers used in molecular dynamics calculations.
-      * < 0: No srand() function is called.
-      * >= 0: The function srand(md_seed) is called.
+      * < 0: Each MPI rank uses the default seed 1 plus its rank.
+      * >= 0: Each MPI rank uses md_seed plus its rank.
     default_value: "-1"
     unit: ""
     availability: ""

source/Makefile.Objects

@@ -772,7 +772,7 @@ OBJS_MODULE_RI=conv_coulomb_pot_k.o\
       singular_value.o\
 
 OBJS_PARALLEL=parallel_common.o\
-    communication_domain.o\
+    parallel_cell.o\
     parallel_global.o\
     parallel_comm.o\
     parallel_grid.o\

source/source_base/CMakeLists.txt

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

…rce/source_base/communication_domain.cpp source/source_base/parallel_cell.cppsource/source_base/communication_domain.cpp renamed to source/source_base/parallel_cell.cpp source/source_base/communication_domain.cpp renamed to source/source_base/parallel_cell.cpp

@@ -1,4 +1,4 @@
-#include "source_base/communication_domain.h"
+#include "source_base/parallel_cell.h"
 
 namespace ModuleBase
 {
@@ -12,7 +12,6 @@ CommunicationDomain::CommunicationDomain(MPI_Comm communicator) : communicator_(
     if (communicator_ != MPI_COMM_NULL)
     {
         MPI_Comm_rank(communicator_, &rank_);
-        MPI_Comm_size(communicator_, &size_);
     }
 }
 
@@ -27,11 +26,6 @@ int CommunicationDomain::rank() const
     return rank_;
 }
 
-int CommunicationDomain::size() const
-{
-    return size_;
-}
-
 CommunicationDomain world_communication_domain()
 {
 #ifdef __MPI

source/source_base/communication_domain.h source/source_base/parallel_cell.hsource/source_base/communication_domain.h renamed to source/source_base/parallel_cell.h

@@ -1,5 +1,5 @@
-#ifndef COMMUNICATION_DOMAIN_H
-#define COMMUNICATION_DOMAIN_H
+#ifndef PARALLEL_CELL_H
+#define PARALLEL_CELL_H
 
 #ifdef __MPI
 #include <mpi.h>
@@ -16,14 +16,12 @@ class CommunicationDomain
     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();

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;