implementation of esolver_dp and esolver_lj (#1406)

* feature: make dir for HS matrix output in md

* refactor: add para istep for afterscf()

* feature: md output HS matrix in a subdir

* fix: fix typo

* Refactor: use esolver_lj to classic MD

* fix: fix esolver_lj

* feature: esolver_dp for MD

* update makefile for DP potential

* fix: fix Makefile and DP virial

* fix: fix memory leak of DP

* update Makefile for DP

* fix: update head file for DP

* update CmakeLists.txt for DP potential

* remove useless functions and __LCAO in module_md

* add para for DP model

* fix: fix init of ESolver_DP

* update docs and tests for esolver lj and dp

* docs: update docs for esolver_dp

Author: YuLiu98

CMakeLists.txt

@@ -249,6 +249,32 @@ if(ENABLE_LIBXC)
   endif()
 endif()
 
+if(DEFINED DeePMD_DIR)
+  add_compile_definitions(
+    __DPMD 
+    HIGH_PREC
+  )
+  add_compile_options(-Wl,--no-as-needed)
+  find_package(DeePMD REQUIRED)
+  include_directories(${DeePMD_DIR}/include)
+  target_link_libraries(${ABACUS_BIN_NAME} 
+    DeePMD::deepmd_cc
+    DeePMD::deepmd_op
+    DeePMD::deepmd_op_cuda
+    DeePMD::tensorflow_cc
+  )
+  if(NOT DEFINED TensorFlow_DIR)
+    message(FATAL_ERROR "Please define TensorFlow_DIR!")
+  endif()
+endif()
+
+if(DEFINED TensorFlow_DIR)
+  include_directories(${TensorFlow_DIR}/include)
+  if(NOT DEFINED DeePMD_DIR)
+    message(FATAL_ERROR "Please define DeePMD_DIR!")
+  endif()
+endif()
+
 add_compile_definitions(
   __EXX
   __FFTW3

docs/advanced/input_files/input-main.md

@@ -42,7 +42,7 @@
 
 - [Molecular dynamics](#molecular-dynamics)
 
-    [md_type](#md_type) | [md_nstep](#md_nstep) | [md_ensolver](#md_ensolver) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_mnhc](#md_mnhc) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp)
+    [md_type](#md_type) | [md_nstep](#md_nstep) | [md_ensolver](#md_ensolver) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_mnhc](#md_mnhc) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [pot_file](#pot_file) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp)
 
 - [vdW correction](#vdw-correction)
 
@@ -1380,6 +1380,12 @@ temperature will fluctuate violently; if it is too small, the temperature will t
 - **Description**: The value of sigma for Leonard Jones potential (angstrom).
 - **Default**: 3.405 (for He)
 
+### pot_file
+
+- **Type**: String
+- **Description**: The filename of potential files for CMD such as DP.
+- **Default**: graph.pb
+
 ### msst_direction
 
 - **Type**: Integer

docs/advanced/install.md

@@ -26,6 +26,18 @@ If DeePKS feature is requied for [DeePKS-kit](https://github.com/deepmodeling/de
 cmake -B build -DENABLE_DEEPKS=1 -DTorch_DIR=~/libtorch/share/cmake/Torch/ -Dlibnpy_INCLUDE_DIR=~/libnpy/include
 ```
 
+## Build with DeePMD-kit
+If the Deep Potential model is employed in Molecule Dynamics calculations, the following prerequisites and steps are needed:
+
+### Extra prerequisites
+
+- [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit)
+- [TensorFlow](https://www.tensorflow.org/)
+
+```bash
+cmake -B build -DDeePMD_DIR=~/deepmd-kit -DTensorFlow_DIR=~/tensorflow
+```
+
 ## Build Unit Tests
 To build tests for ABACUS, define `BUILD_TESTING` flag. You can also specify path to local installation of [Googletest](https://github.com/google/googletest) by setting `GTEST_DIR` flags. If not found in local, the configuration process will try to download it automatically.
 
@@ -60,6 +72,10 @@ CC = mpiicpc
 # g++:       compile gnu serial version
 # make: FFTW_DIR, OPENBLAS_LIB_DIR, SCALAPACK_LIB_DIR, ELPA_DIR, ELPA_INCLUDE_DIR, CEREAL_DIR must also be set.
 # make pw: FFTW_DIR, OPENBLAS_LIB_DIR must be set.
+
+# GPU = OFF  #We do not support GPU yet
+# OFF:  do not use GPU
+# CUDA: use CUDA
 #======================================================================
 
 #-------  FOR INTEL COMPILER  ------------
@@ -96,6 +112,17 @@ CEREAL_DIR    = /public/soft/cereal
 # LIBXC_DIR    		= /public/soft/libxc
 # directory of libxc(>5.1.7), which contains include and lib/libxc.a
 # add LIBXC_DIR to use libxc to compile ABACUS
+
+# DeePMD_DIR = ${deepmd_root}
+# TensorFlow_DIR = ${tensorflow_root}
+# add them to use DEEPMD
+
+# NP = 14 # It is not supported. use make -j14 or make -j to parallelly compile
+
+# DEBUG = OFF
+# Only for developers
+# ON:   use gnu compiler and check segmental defaults
+# OFF:  nothing
 #======================================================================
 ```
 
@@ -164,3 +191,11 @@ To compile ABACUS with DEEPKS, you need to define `LIBTORCH_DIR` and `LIBNPY_DIR
 make LIBTORCH_DIR=/opt/libtorch/ LIBNPY_DIR=/opt/libnpy/
 ```
 directly.
+
+### Add DeePMD-kit Support
+
+To compile ABACUS with DeePMD-kit, you need to define `DeePMD_DIR` and `TensorFlow_DIR` in the file `Makefile.vars` or use 
+```makefile
+make DeePMD_DIR=~/deepmd-kit TensorFlow_DIR=~/tensorflow
+``` 
+directly.

docs/advanced/md.md

@@ -13,6 +13,9 @@ By setting `calculation` to be `md` or `sto-md`, ABACUS currently provides six d
 
 Furthermore, ABACUS also provides a [list of keywords](./input_files/input-main.md#molecular-dynamics) to control relevant parmeters used in MD simulations.
 
+To employ CMD calculations, `md_ensolver` should be set to be `LJ` or `DP`.
+If DP model is selected, the filename of DP model is specified by keyword `pot_file`.
+
 [Examples](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/md/lcao_gammaonly_Sn64) of MD simulations are also provided.
 There are six INPUT files corresponding to six different MD evolution methods in the directory.
 For examlpe, `INPUT_0` shows how to employ the NVE simulation.

modules/FindDeePMD.cmake

@@ -0,0 +1,78 @@
+###############################################################################
+# - Find DeePMD
+# Find the native DeePMD headers and libraries.
+#
+#  DeePMD_FOUND        - True if lib is found.
+#  DeePMD_LIBRARIES    - List of libraries
+#  DeePMD_INCLUDE_DIR  - Where to find DeePMD headers.
+#
+
+find_path(DeePMD_INCLUDE_DIR
+    deepmd/DeepPot.h
+    HINTS ${DeePMD_DIR}
+    PATH_SUFFIXES "include"
+    )
+find_library(deepmd_cc
+    NAMES deepmd_cc
+    HINTS ${DeePMD_DIR}
+    PATH_SUFFIXES "lib"
+    )
+find_library(deepmd_op
+    NAMES deepmd_op
+    HINTS ${DeePMD_DIR}
+    PATH_SUFFIXES "lib"
+    )
+find_library(deepmd_op_cuda
+    NAMES deepmd_op_cuda
+    HINTS ${DeePMD_DIR}
+    PATH_SUFFIXES "lib"
+    )
+find_library(tensorflow_cc
+    NAMES tensorflow_cc
+    HINTS ${DeePMD_DIR}
+    PATH_SUFFIXES "lib"
+    )
+
+# Handle the QUIET and REQUIRED arguments and
+# set DeePMD_FOUND to TRUE if all variables are non-zero.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(DeePMD DEFAULT_MSG deepmd_cc deepmd_op deepmd_op_cuda tensorflow_cc DeePMD_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(DeePMD_FOUND)
+    #set(DeePMD_LIBRARIES ${DeePMD_LIBRARY})
+    set(DeePMD_INCLUDE_DIR ${DeePMD_INCLUDE_DIR})
+
+    if(NOT TARGET DeePMD::deepmd_cc)
+        add_library(DeePMD::deepmd_cc UNKNOWN IMPORTED)
+        set_target_properties(DeePMD::deepmd_cc PROPERTIES
+           IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+           IMPORTED_LOCATION "${deepmd_cc}"
+           INTERFACE_INCLUDE_DIRECTORIES "${DeePMD_INCLUDE_DIR}")
+    endif()
+    if(NOT TARGET DeePMD::deepmd_op)
+        add_library(DeePMD::deepmd_op UNKNOWN IMPORTED)
+        set_target_properties(DeePMD::deepmd_op PROPERTIES
+           IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+           IMPORTED_LOCATION "${deepmd_op}"
+           INTERFACE_INCLUDE_DIRECTORIES "${DeePMD_INCLUDE_DIR}")
+    endif()
+    if(NOT TARGET DeePMD::deepmd_op_cuda)
+        add_library(DeePMD::deepmd_op_cuda UNKNOWN IMPORTED)
+        set_target_properties(DeePMD::deepmd_op_cuda PROPERTIES
+           IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+           IMPORTED_LOCATION "${deepmd_op_cuda}"
+           INTERFACE_INCLUDE_DIRECTORIES "${DeePMD_INCLUDE_DIR}")
+    endif()
+    if(NOT TARGET DeePMD::tensorflow_cc)
+        add_library(DeePMD::tensorflow_cc UNKNOWN IMPORTED)
+        set_target_properties(DeePMD::tensorflow_cc PROPERTIES
+           IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+           IMPORTED_LOCATION "${tensorflow_cc}"
+           INTERFACE_INCLUDE_DIRECTORIES "${DeePMD_INCLUDE_DIR}")
+    endif()
+endif()
+
+set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${DeePMD_INCLUDE_DIR})
+
+mark_as_advanced(DeePMD_INCLUDE_DIR deepmd_cc deepmd_op deepmd_op_cuda tensorflow_cc)

source/Makefile

@@ -115,6 +115,26 @@ ifdef LIBTORCH_DIR
   endif
 endif
 
+ifdef DeePMD_DIR
+    HONG  += -D__DPMD -DHIGH_PREC 
+    OPTS  += -Wl,--no-as-needed
+    ##==========================
+    ## DeePMD-kit package
+    ##==========================
+    DeeP_LIB_DIR = ${DeePMD_DIR}/lib
+    LIBS += -L${DeeP_LIB_DIR} -ldeepmd_cc -ldeepmd_op -ldeepmd_op_cuda -Wl,-rpath=${DeeP_LIB_DIR}
+    DeeP_INCLUDE_DIR = ${DeePMD_DIR}/include
+    INCLUDES += -I${DeeP_INCLUDE_DIR}
+
+    #==========================
+    # TensorFlow package
+    #==========================
+    TensorFlow_LIB_DIR = ${TensorFlow_DIR}/lib
+    LIBS += -L${TensorFlow_LIB_DIR} -ltensorflow_cc -Wl,-rpath=${TensorFlow_LIB_DIR}
+    TensorFlow_INCLUDE_DIR = ${TensorFlow_DIR}/include
+    INCLUDES += -I${TensorFlow_INCLUDE_DIR}
+endif
+
 include Makefile.Objects
 
 #==========================

source/Makefile.vars

@@ -21,28 +21,28 @@ CC = mpiicpc
 
 
 #-------  FOR INTEL COMPILER  ------------
-ELPA_DIR      = /pubilc/soft/elpa_21.05.002
+ELPA_DIR      = /public/soft/elpa_21.05.002
 ELPA_INCLUDE_DIR = ${ELPA_DIR}/include/elpa-2021.05.002
 # directory of elpa, which contains include and lib/libelpa.a
 
-CEREAL_DIR    = /pubilc/soft/cereal
+CEREAL_DIR    = /public/soft/cereal
 # directory of cereal, which contains a include directory in it.
 
 #-------  FOR GNU COMPILER  ---------------
-# FFTW_DIR = /pubilc/soft/fftw
+# FFTW_DIR = /public/soft/fftw_3.3.8
 # # directory of fftw package, which contains lib/libfftw3.a. Only used when CC = mpicxx/g++
 
-# OPENBLAS_LIB_DIR   = /pubilc/soft/openblas/lib
+# OPENBLAS_LIB_DIR   = /public/soft/openblas/lib
 # # directory of libopenblas.a, only used when CC = mpicxx/g++
 
-# SCALAPACK_LIB_DIR  = /pubilc/soft/openblas/lib
+# SCALAPACK_LIB_DIR  = /public/soft/openblas/lib
 # # directory of libscalapack.a, only used when CC = mpicxx/g++
 
-# ELPA_DIR      = /pubilc/soft/elpa_21.05.002
+# ELPA_DIR      = /public/soft/elpa_21.05.002
 # ELPA_INCLUDE_DIR = ${ELPA_DIR}/include/elpa-2021.05.002
 # # directory of elpa, which contains include and lib/libelpa.a
 
-# CEREAL_DIR    = /pubilc/soft/cereal
+# CEREAL_DIR    = /public/soft/cereal
 # # directory of cereal, which contains a include directory in it.
 
 
@@ -52,10 +52,14 @@ CEREAL_DIR    = /pubilc/soft/cereal
 # LIBNPY_DIR    = /usr/local
 # add them to use DEEPKS
 
-# LIBXC_DIR    		= /pubilc/soft/libxc
+# LIBXC_DIR    		= /public/soft/libxc
 # directory of libxc(5.1.7), which contains include and lib/libxc.a
 # add LIBXC_DIR to use libxc to compile ABACUS
 
+# DeePMD_DIR = ${deepmd_root}
+# TensorFlow_DIR = ${tensorflow_root}
+# add them to use DEEPMD
+
 # NP = 14 # It is not supported. use make -j14 or make -j to parallelly compile
 
 # DEBUG = OFF

source/driver_run.cpp

@@ -6,6 +6,7 @@
 #include "src_io/print_info.h"
 #include "src_lcao/run_md_lcao.h"
 #include "src_pw/run_md_pw.h"
+#include "module_md/run_md_classic.h"
 
 // This is the driver function which defines the workflow of ABACUS calculations
 // It relies on the class Esolver, which is a class that organizes workflows of single point calculations.
@@ -56,6 +57,11 @@ void Driver::driver_run()
         run_md_lcao.opt_ions(p_esolver);
 #endif
     }
+    else if(INPUT.mdp.md_ensolver == "LJ" || INPUT.mdp.md_ensolver == "DP")
+    {
+        Run_MD_CLASSIC run_md_classic;
+        run_md_classic.classic_md_line(GlobalC::ucell, p_esolver);
+    }
     else if(GlobalV::CALCULATION == "md" || GlobalV::CALCULATION == "sto-md")
     {
         Run_MD_PW run_md_pw;

source/input.cpp

@@ -18,6 +18,7 @@
 #include <stdio.h>
 #include <string.h>
 #include <vector>
+#include <unistd.h>
 Input INPUT;
 
 void Input::Init(const std::string &fn)
@@ -1257,6 +1258,10 @@ bool Input::Read(const std::string &fn)
         {
             read_value(ifs, mdp.md_damp);
         }
+        else if (strcmp("pot_file", word) == 0)
+        {
+            read_value(ifs, mdp.pot_file);
+        }
         //----------------------------------------------------------
         // efield and dipole correction
         // Yu Liu add 2022-05-18
@@ -2204,6 +2209,7 @@ void Input::Bcast()
     Parallel_Common::bcast_double(mdp.msst_tscale);
     Parallel_Common::bcast_double(mdp.md_tfreq);
     Parallel_Common::bcast_double(mdp.md_damp);
+    Parallel_Common::bcast_string(mdp.pot_file);
     // Yu Liu add 2022-05-18
     Parallel_Common::bcast_bool(efield_flag);
     Parallel_Common::bcast_bool(dip_cor_flag);
@@ -2547,6 +2553,13 @@ void Input::Check(void)
                 ModuleBase::WARNING_QUIT("Input::Check", "msst_qmass must be greater than 0!");
             }
         }
+        if(mdp.md_ensolver == "DP")
+        {
+            if (access(mdp.pot_file.c_str(), 0) == -1)
+            {
+                ModuleBase::WARNING_QUIT("Input::Check", "Can not find DP model !");
+            }
+        }
         // if(mdp.md_tfirst!=mdp.md_tlast)
         // {
         //     std::ifstream file1;

source/module_esolver/esolver.cpp

@@ -90,7 +90,7 @@ namespace ModuleESolver
         }
         else if (esolver_type == "dp_pot")
         {
-            p_esolver = new ESolver_DP();
+            p_esolver = new ESolver_DP(INPUT.mdp.pot_file);
         }
     }