add LAMMPS plugin

.github/workflows/build_cc.yml

@@ -9,14 +9,8 @@ jobs:
     strategy:  
       matrix:
         include:
-        - float_prec: high
-          variant: cpu
-        - float_prec: low
-          variant: cpu
-        - float_prec: high
-          variant: cuda
-        - float_prec: low
-          variant: cuda
+        - variant: cpu
+        - variant: cuda
     steps:
     - uses: actions/checkout@master
       with:
@@ -26,12 +20,6 @@ jobs:
       if: matrix.variant == 'cuda'
     - run: source/install/build_cc.sh
       env:
-        FLOAT_PREC: ${{ matrix.float_prec }}
         DP_VARIANT: ${{ matrix.variant }}
         CC: gcc-7
         CXX: g++-7
-    - run: source/install/build_lammps.sh
-      env:
-        FLOAT_PREC: ${{ matrix.float_prec }}
-        CC: gcc-7
-        CXX: g++-7

doc/getting-started.md

@@ -414,6 +414,12 @@ Note that the model for MD simulations is required to be compatible with the Dee
 
 ### Run MD with LAMMPS
 
+Firstly, enable DeePMD-kit package in LAMMPS with `plugin` command:
+
+```
+plugin load path/to/deepmd/lib/libdeepmd_lmp.so
+```
+
 #### pair_style `deepmd`
 
 The DeePMD-kit package provides the pair_style `deepmd`

doc/install.md

@@ -2,7 +2,7 @@
 
 - [Easy installation methods](#easy-installation-methods)
 - [Install from source code](#install-from-source-code)
-- [Install i-PI](#install-i-pi)
+- [Install third-party packages](#install-third-party-packages)
 - [Building conda packages](#building-conda-packages)
 
 ## Easy installation methods
@@ -204,6 +204,7 @@ One may add the following arguments to `cmake`:
 | -DCUDA_TOOLKIT_ROOT_DIR=<value> | Path         | Detected automatically | The path to the CUDA toolkit directory. |
 | -DUSE_ROCM_TOOLKIT=<value> | `TRUE` or `FALSE` | `FALSE`       | If `TRUE`, Build GPU support with ROCM toolkit. |
 | -DROCM_ROOT=<value> | Path         | Detected automatically | The path to the ROCM toolkit directory. |
+| -LAMMPS_SOURCE_ROOT=<value> | Path         | - | The path to the LAMMPS source code (later than 8Apr2021). |
 
 If the cmake has executed successfully, then 
 ```bash
@@ -215,46 +216,40 @@ The option `-j4` means using 4 processes in parallel. You may want to use a diff
 If everything works fine, you will have the following executable and libraries installed in `$deepmd_root/bin` and `$deepmd_root/lib`
 ```bash
 $ ls $deepmd_root/bin
-dp_ipi
+dp_ipi      dp_ipi_low
 $ ls $deepmd_root/lib
-libdeepmd_ipi.so  libdeepmd_op.so  libdeepmd.so
+libdeepmd_cc_low.so  libdeepmd_ipi_low.so  libdeepmd_lmp_low.so  libdeepmd_low.so          libdeepmd_op_cuda.so  libdeepmd_op.so
+libdeepmd_cc.so      libdeepmd_ipi.so      libdeepmd_lmp.so      libdeepmd_op_cuda_low.so  libdeepmd_op_low.so   libdeepmd.so
 ```
 
-### Install LAMMPS's DeePMD-kit module
-DeePMD-kit provide module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.
-```bash
-cd $deepmd_source_dir/source/build
-make lammps
-```
-DeePMD-kit will generate a module called `USER-DEEPMD` in the `build` directory. If you need low precision version, move `env_low.sh` to `env.sh` in the directory. Now download the LAMMPS code (`29Oct2020` or later), and uncompress it:
+## Install third-party packages
+### Install LAMMPS
+DeePMD-kit provide module for running MD simulation with LAMMPS.
+
+DeePMD-kit will generate a module called `USER-DEEPMD` in the `build` directory. If you need low precision version, move `env_low.sh` to `env.sh` in the directory. Now download the LAMMPS code (`8Apr2021` or later), and uncompress it:
 ```bash
 cd /some/workspace
-wget https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz
-tar xf stable_29Oct2020.tar.gz
-```
-The source code of LAMMPS is stored in directory `lammps-stable_29Oct2020`. Now go into the LAMMPS code and copy the DeePMD-kit module like this
-```bash
-cd lammps-stable_29Oct2020/src/
-cp -r $deepmd_source_dir/source/build/USER-DEEPMD .
+wget https://github.com/lammps/lammps/archive/patch_30Jul2021.tar.gz
+tar xf patch_30Jul2021.tar.gz
 ```
-Now build LAMMPS
+The source code of LAMMPS is stored in directory `lammps-patch_30Jul2021`. Now go into the LAMMPS code and create a directory called `build`
 ```bash
-make yes-kspace
-make yes-user-deepmd
-make mpi -j4
+mkdir -p lammps-patch_30Jul2021/build/
+cd lammps-patch_30Jul2021/build/
 ```
-
-If everything works fine, you will end up with an executable `lmp_mpi`.
+Now build LAMMPS. Note that `PLUGIN` and `KSPACE` package must be enabled, and `BUILD_SHARED_LIBS` must be set to `yes`.
 ```bash
-./lmp_mpi -h
+cmake -D PKG_PLUGIN=ON -D PKG_KSPACE=ON -D LAMMPS_INSTALL_RPATH=ON -D BUILD_SHARED_LIBS=yes -D CMAKE_INSTALL_PREFIX=${deepmd_root} ../cmake
+make -j4
+make install
 ```
 
-The DeePMD-kit module can be removed from LAMMPS source code by 
+If everything works fine, you will end up with an executable `${deepmd_root}/lmp`.
 ```bash
-make no-user-deepmd
+${deepmd_root}/lmp -h
 ```
 
-## Install i-PI
+### Install i-PI
 The i-PI works in a client-server model. The i-PI provides the server for integrating the replica positions of atoms, while the DeePMD-kit provides a client named `dp_ipi` that computes the interactions (including energy, force and virial). The server and client communicates via the Unix domain socket or the Internet socket. A full instruction of i-PI can be found [here](http://ipi-code.org/). The source code and a complete installation instructions of i-PI can be found [here](https://github.com/i-pi/i-pi).
 To use i-PI with already existing drivers, install and update using Pip:
 ```bash

doc/troubleshooting/index.md

@@ -6,7 +6,6 @@ If other unexpected problems occur, you're welcome to contact us for help.
 ## Trouble shooting
 - [Installation](installation.md)
 - [The temperature undulates violently during early stages of MD](md-energy-undulation.md)
-- [MD: cannot run LAMMPS after installing a new version of DeePMD-kit](md-version-compatibility.md)
 - [Model compatability](model-compatability.md)
 
 ## Parameters setting

examples/water/lmp/in.lammps

@@ -11,8 +11,9 @@ read_data	water.lmp
 mass 		1 16
 mass		2 2
 
+plugin load ../../../dp/lib/libdeepmd_lmp.so
 pair_style	deepmd frozen_model.pb
-pair_coeff	
+pair_coeff  * *	
 
 velocity        all create 330.0 23456789
 

source/CMakeLists.txt

@@ -146,16 +146,6 @@ if (USE_TTM)
   set(TTM_DEF "-DUSE_TTM")
 endif (USE_TTM)
 
-# old pppm interface
-if(NOT DEFINED OLD_LMP_PPPM)
-  set(OLD_LMP_PPPM FALSE)
-endif(NOT DEFINED OLD_LMP_PPPM)
-if (OLD_LMP_PPPM)
-  set(OLD_LMP_PPPM_DEF "-DOLD_LMP_PPPM")
-  message(STATUS "Use old lammps pppm interface")
-endif()
-add_definitions (${OLD_LMP_PPPM_DEF})
-
 # define build type
 if ((NOT DEFINED CMAKE_BUILD_TYPE) OR CMAKE_BUILD_TYPE STREQUAL "")
    set (CMAKE_BUILD_TYPE release)

source/install/build_cc.sh

@@ -20,7 +20,7 @@ NPROC=$(nproc --all)
 BUILD_TMP_DIR=${SCRIPT_PATH}/../build
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
-cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DINSTALL_TENSORFLOW=TRUE ${CUDA_ARGS} ..
+cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -D LAMMPS_INSTALL_RPATH=ON -DINSTALL_TENSORFLOW=TRUE ${CUDA_ARGS} -DLAMMPS_VERSION=patch_30Jul2021 -DUSE_TTM=TRUE ..
 make -j${NPROC}
 make install
 

source/install/build_lammps.sh

@@ -1,21 +1,5 @@
 set -e
 
-# You need to first run ./build_cc.sh
-
-if [ -z "$FLOAT_PREC" ]
-then
-  FLOAT_PREC=high
-fi
-
-if [ ${FLOAT_PREC} == "high" ]; then
-    PREC_DEF="-DHIGH_PREC"
-    PREC_SUFFIX=""
-else
-    PREC_DEF="-DLOW_PREC"
-    PREC_SUFFIX="_low"
-fi
-#------------------
-
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 if [ -z "$INSTALL_PREFIX" ]
 then
@@ -25,33 +9,23 @@ mkdir -p ${INSTALL_PREFIX}
 echo "Installing LAMMPS to ${INSTALL_PREFIX}"
 NPROC=$(nproc --all)
 
-#------------------
-# copy lammps plugin
-BUILD_TMP_DIR2=${SCRIPT_PATH}/../build
-cd ${BUILD_TMP_DIR2}
-make lammps
-
 #------------------
 
 BUILD_TMP_DIR=${SCRIPT_PATH}/../build_lammps
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
 # download LAMMMPS
-LAMMPS_VERSION=stable_29Oct2020
+LAMMPS_VERSION=patch_30Jul2021
 if [ ! -d "lammps-${LAMMPS_VERSION}" ]
 then
 	curl -L -o lammps.tar.gz https://github.com/lammps/lammps/archive/refs/tags/${LAMMPS_VERSION}.tar.gz
 	tar vxzf lammps.tar.gz
 fi
-curl -L -o lammps.patch https://github.com/deepmd-kit-recipes/lammps-dp-feedstock/raw/fdd954a1af4fadabe5c0dd2f3bed260a484175a4/recipe/deepmd.patch
-cd ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}
-patch -f -p1 < ../lammps.patch || true 
-mkdir -p ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}/src/USER-DEEPMD
-cp -r ${BUILD_TMP_DIR2}/USER-DEEPMD/* ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}/src/USER-DEEPMD
 
+cd ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}
 mkdir -p ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}/build
 cd ${BUILD_TMP_DIR}/lammps-${LAMMPS_VERSION}/build
-cmake -C ../cmake/presets/all_off.cmake -D PKG_USER-DEEPMD=ON -D PKG_KSPACE=ON -D CMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -D CMAKE_CXX_FLAGS="${PREC_DEF} -I${INSTALL_PREFIX}/include -L${INSTALL_PREFIX}/lib -Wl,--no-as-needed -lrt -ldeepmd_cc${PREC_SUFFIX} -ltensorflow_cc -ltensorflow_framework" ../cmake
+cmake -C ../cmake/presets/all_off.cmake -D PKG_PLUGIN=ON -D PKG_KSPACE=ON -D BUILD_SHARED_LIBS=yes -D LAMMPS_INSTALL_RPATH=ON -D CMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} ../cmake
 
 make -j${NPROC}
 make install

source/lmp/CMakeLists.txt

@@ -1,3 +1,10 @@
+add_subdirectory(plugin)
+if (NOT DEFINED LAMMPS_VERSION_NUMBER)
+    # set the default to 29 Oct 2020
+    set(LAMMPS_VERSION_NUMBER 20201029)
+endif()
+message(STATUS "LAMMPS version is ${LAMMPS_VERSION_NUMBER}")
+
 file(GLOB LMP_HEADER *.h)
 file(GLOB LMP_SRC *.cpp)
 file(GLOB LMP_SHSCRIPT *.sh)

source/lmp/compute_deeptensor_atom.h

@@ -9,7 +9,11 @@ ComputeStyle(deeptensor/atom,ComputeDeeptensorAtom)
 
 #include "compute.h"
 #include "pair_deepmd.h"
+#ifdef LMPPLUGIN
+#include "DeepTensor.h"
+#else
 #include "deepmd/DeepTensor.h"
+#endif
 
 namespace LAMMPS_NS {
 

source/lmp/env.sh.in

@@ -6,6 +6,6 @@ TF_INCLUDE_DIRS=`echo $TENSORFLOW_INCLUDE_DIRS | sed "s/;/ -I/g"`
 TF_LIBRARY_PATH=`echo $TENSORFLOW_LIBRARY_PATH | sed "s/;/ -L/g"`
 TF_RPATH=`echo $TENSORFLOW_LIBRARY_PATH | sed "s/;/ -Wl,-rpath=/g"`
 
-NNP_INC=" -std=c++11 -D@prec_def@ @TTM_DEF@ @OLD_LMP_PPPM_DEF@ -I$TF_INCLUDE_DIRS -I$DEEPMD_ROOT/include/ "
+NNP_INC=" -std=c++11 -D@prec_def@ @TTM_DEF@ -DLAMMPS_VERSION_NUMBER=@LAMMPS_VERSION_NUMBER@ -I$TF_INCLUDE_DIRS -I$DEEPMD_ROOT/include/ "
 NNP_PATH=" -L$TF_LIBRARY_PATH -L$DEEPMD_ROOT/lib"
 NNP_LIB=" -Wl,--no-as-needed -l@LIB_DEEPMD_CC@@variant_name@ -ltensorflow_cc -ltensorflow_framework -Wl,-rpath=$TF_RPATH -Wl,-rpath=$DEEPMD_ROOT/lib"

source/lmp/fix_dplr.cpp

@@ -41,7 +41,13 @@ FixDPLR::FixDPLR(LAMMPS *lmp, int narg, char **arg)
      efield_fsum_all(4, 0.0), 
      efield_force_flag(0)
 {
+#if LAMMPS_VERSION_NUMBER>=20210702
+  // lammps/lammps#2560
+  energy_global_flag = 1;
+  virial_global_flag = 1;
+#else
   virial_flag = 1;
+#endif
 
   if (strcmp(update->unit_style,"metal") != 0) {
     error->all(FLERR,"Pair deepmd requires metal unit, please set it by \"units metal\"");
@@ -117,7 +123,10 @@ FixDPLR::FixDPLR(LAMMPS *lmp, int narg, char **arg)
 int FixDPLR::setmask()
 {
   int mask = 0;
+#if LAMMPS_VERSION_NUMBER<20210702
+  // THERMO_ENERGY removed in lammps/lammps#2560
   mask |= THERMO_ENERGY;
+#endif
   mask |= POST_INTEGRATE;
   mask |= PRE_FORCE;
   mask |= POST_FORCE;

source/lmp/fix_dplr.h

@@ -10,8 +10,13 @@ FixStyle(dplr,FixDPLR)
 #include <stdio.h>
 #include "fix.h"
 #include "pair_deepmd.h"
+#ifdef LMPPLUGIN
+#include "DeepTensor.h"
+#include "DataModifier.h"
+#else
 #include "deepmd/DeepTensor.h"
 #include "deepmd/DataModifier.h"
+#endif
 
 #ifdef HIGH_PREC
 #define FLOAT_PREC double

source/lmp/pair_deepmd.h.in

@@ -8,7 +8,11 @@ PairStyle(deepmd,PairDeepMD)
 #define LMP_PAIR_NNP_H
 
 #include "pair.h"
+#ifdef LMPPLUGIN
+#include "DeepPot.h"
+#else
 #include "deepmd/DeepPot.h"
+#endif
 #include <iostream>
 #include <fstream>
 

source/lmp/plugin/CMakeLists.txt

@@ -0,0 +1,84 @@
+if (DEFINED LAMMPS_SOURCE_ROOT OR DEFINED LAMMPS_VERSION)
+  add_library(lammps_interface INTERFACE)
+  if (DEFINED LAMMPS_VERSION)
+    cmake_minimum_required(VERSION 3.11)
+    include(FetchContent)
+    FetchContent_Declare(lammps_download
+      GIT_REPOSITORY    https://github.com/lammps/lammps
+      GIT_TAG           ${LAMMPS_VERSION}
+    )
+    FetchContent_GetProperties(lammps_download)
+    if(NOT lammps_download_POPULATED)
+      FetchContent_Populate(lammps_download)
+      set(LAMMPS_SOURCE_ROOT ${lammps_download_SOURCE_DIR})
+    endif()
+  endif()
+  set(LAMMPS_HEADER_DIR ${LAMMPS_SOURCE_ROOT}/src)
+  message(STATUS "LAMMPS_HEADER_DIR is ${LAMMPS_HEADER_DIR}")
+
+  target_include_directories(lammps_interface INTERFACE ${LAMMPS_HEADER_DIR})
+
+  find_package(MPI)
+  if(MPI_FOUND)
+    set(LAMMPS_MPI_INCLUDE_DIRS ${MPI_CXX_INCLUDE_DIRS})
+    target_link_libraries(lammps_interface INTERFACE MPI::MPI_CXX)
+  else()
+    # Use LAMMPS serial mpi.h header
+    target_include_directories(lammps_interface INTERFACE "${LAMMPS_HEADER_DIR}/STUBS")
+  endif()
+
+  # get_lammps_version
+  # https://github.com/lammps/lammps/blob/c2a12f97c5f665852fb38fdd4922f7dd2e77a0a1/cmake/Modules/LAMMPSUtils.cmake#L27-L46
+  include(${LAMMPS_SOURCE_ROOT}/cmake/Modules/LAMMPSUtils.cmake)
+  get_lammps_version(${LAMMPS_HEADER_DIR}/version.h LAMMPS_VERSION_NUMBER)
+  set(LAMMPS_VERSION_NUMBER ${LAMMPS_VERSION_NUMBER} PARENT_SCOPE)
+
+  configure_file("../pair_deepmd.h.in" "${CMAKE_CURRENT_BINARY_DIR}/pair_deepmd.h" @ONLY)
+
+  file(GLOB LMP_SRC
+    deepmdplugin.cpp
+    ../*.cpp
+    ${LAMMPS_SOURCE_ROOT}/src/kspace.cpp # for pppm_dplr
+    ${LAMMPS_SOURCE_ROOT}/src/KSPACE/pppm.cpp
+  )
+
+  function(_add_lmp_plugin_variant variant_name prec_def)
+  set (libname "deepmd_lmp${variant_name}")
+
+  add_library(${libname} MODULE ${LMP_SRC})
+
+  # link: libdeepmd libtensorflow_cc libtensorflow_framework
+  target_link_libraries (${libname} PUBLIC
+    lammps_interface
+    ${LIB_DEEPMD_CC}${variant_name}
+    ${TensorFlow_LIBRARY}
+    ${TensorFlowFramework_LIBRARY}
+  )
+  target_include_directories(${libname} PRIVATE
+    ${CMAKE_CURRENT_BINARY_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/..
+    ${TensorFlow_INCLUDE_DIRS}
+    ${LAMMPS_SOURCE_ROOT}/src/PLUGIN
+    ${LAMMPS_SOURCE_ROOT}/src/KSPACE
+    ${LAMMPS_SOURCE_ROOT}/src
+  )
+
+  set_target_properties(
+    ${libname} 
+    PROPERTIES 
+    INSTALL_RPATH "$ORIGIN;${TensorFlow_LIBRARY_PATH}"
+    LINK_FLAGS "-rdynamic"
+  )
+  target_compile_definitions(${libname}
+    PUBLIC ${prec_def}
+    PRIVATE "LMPPLUGIN" # fix header path
+    PRIVATE "LAMMPS_VERSION_NUMBER=${LAMMPS_VERSION_NUMBER}"
+  )
+
+  install(TARGETS ${libname} DESTINATION lib/)
+
+  endfunction()
+  _add_lmp_plugin_variant("${HIGH_PREC_VARIANT}" "${HIGH_PREC_DEF}")
+  _add_lmp_plugin_variant("${LOW_PREC_VARIANT}" "${LOW_PREC_DEF}")
+
+endif()