bump lammps to stable_2Aug2023 (deepmodeling#2717)

Signed-off-by: Jinzhe Zeng <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

doc/install/install-lammps.md

@@ -14,12 +14,12 @@ make lammps
 DeePMD-kit will generate a module called `USER-DEEPMD` in the `build` directory, which supports either double or single float precision interface. Now download the LAMMPS code, and uncompress it.
 ```bash
 cd /some/workspace
-wget https://github.com/lammps/lammps/archive/stable_23Jun2022_update4.tar.gz
-tar xf stable_23Jun2022_update4.tar.gz
+wget https://github.com/lammps/lammps/archive/stable_2Aug2023.tar.gz
+tar xf stable_2Aug2023.tar.gz
 ```
-The source code of LAMMPS is stored in the directory `lammps-stable_23Jun2022_update4`. Now go into the LAMMPS code and copy the DeePMD-kit module like this
+The source code of LAMMPS is stored in the directory `lammps-stable_2Aug2023`. Now go into the LAMMPS code and copy the DeePMD-kit module like this
 ```bash
-cd lammps-stable_23Jun2022_update4/src/
+cd lammps-stable_2Aug2023/src/
 cp -r $deepmd_source_dir/source/build/USER-DEEPMD .
 make yes-kspace
 make yes-extra-fix
@@ -46,15 +46,15 @@ Starting from `8Apr2021`, LAMMPS also provides a plugin mode, allowing one to bu
 Now download the LAMMPS code (`8Apr2021` or later), and uncompress it:
 ```bash
 cd /some/workspace
-wget https://github.com/lammps/lammps/archive/stable_23Jun2022_update4.tar.gz
-tar xf stable_23Jun2022_update4.tar.gz
+wget https://github.com/lammps/lammps/archive/stable_2Aug2023.tar.gz
+tar xf stable_2Aug2023.tar.gz
 ```
 
-The source code of LAMMPS is stored in the directory `lammps-stable_23Jun2022_update4`. The directory of the source code should be specified as the CMAKE argument `LAMMPS_SOURCE_ROOT` during installation of the DeePMD-kit C++ interface. Now go into the LAMMPS directory and create a directory called `build`
+The source code of LAMMPS is stored in the directory `lammps-stable_2Aug2023`. The directory of the source code should be specified as the CMAKE argument `LAMMPS_SOURCE_ROOT` during installation of the DeePMD-kit C++ interface. Now go into the LAMMPS directory and create a directory called `build`
 
 ```bash
-mkdir -p lammps-stable_23Jun2022_update4/build/
-cd lammps-stable_23Jun2022_update4/build/
+mkdir -p lammps-stable_2Aug2023/build/
+cd lammps-stable_2Aug2023/build/
 ```
 Now build LAMMPS. Note that `PLUGIN` and `KSPACE` packages must be enabled, and `BUILD_SHARED_LIBS` must be set to `yes`. You can install any other package you want.
 ```bash

pyproject.toml

@@ -76,7 +76,7 @@ manylinux-x86_64-image = "quay.io/pypa/manylinux_2_28_x86_64:2022-11-19-1b19e81"
 manylinux-aarch64-image = "quay.io/pypa/manylinux_2_28_aarch64:2022-11-19-1b19e81"
 
 [tool.cibuildwheel.macos]
-environment = { PIP_PREFER_BINARY="1", DP_LAMMPS_VERSION="stable_23Jun2022_update4", DP_ENABLE_IPI="1" }
+environment = { PIP_PREFER_BINARY="1", DP_LAMMPS_VERSION="stable_2Aug2023", DP_ENABLE_IPI="1" }
 before-all = [
  """if [[ "$CIBW_BUILD" != *macosx_arm64* ]]; then brew install mpich; fi""",
 ]
@@ -88,7 +88,7 @@ repair-wheel-command = """if [[ "$CIBW_BUILD" == *macosx_arm64* ]]; then rm -rf
 [tool.cibuildwheel.linux]
 repair-wheel-command = "auditwheel repair --exclude libtensorflow_framework.so.2 --exclude libtensorflow_framework.so.1 --exclude libtensorflow_framework.so --exclude _pywrap_tensorflow_internal.so --exclude libtensorflow_cc.so.2 -w {dest_dir} {wheel}"
 environment-pass = ["CIBW_BUILD", "DP_VARIANT"]
-environment = { PIP_PREFER_BINARY="1", DP_VARIANT="cuda", DP_LAMMPS_VERSION="stable_23Jun2022_update4", DP_ENABLE_IPI="1", MPI_HOME="/usr/lib64/mpich", PATH="/usr/lib64/mpich/bin:$PATH" }
+environment = { PIP_PREFER_BINARY="1", DP_VARIANT="cuda", DP_LAMMPS_VERSION="stable_2Aug2023", DP_ENABLE_IPI="1", MPI_HOME="/usr/lib64/mpich", PATH="/usr/lib64/mpich/bin:$PATH" }
 before-all = [
  """{ if [ "$(uname -m)" = "x86_64" ] ; then curl https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_520.61.05_linux.run -O && bash cuda_11.8.0_520.61.05_linux.run --silent --toolkit; fi }""",
  "yum install -y mpich-devel",

setup.py

@@ -134,8 +134,8 @@ def get_tag(self):
  "sphinxcontrib-bibtex",
  ],
  "lmp": [
- "lammps~=2022.6.23.4.0; platform_system=='Linux'",
- "lammps~=2022.6.23.4.0; platform_system!='Linux'",
+ "lammps~=2023.8.2.0.0; platform_system=='Linux'",
+ "lammps~=2023.8.2.0.0; platform_system!='Linux'",
  *find_libpython_requires,
  ],
  "ipi": [

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} -DUSE_TF_PYTHON_LIBS=TRUE ${CUDA_ARGS} -DLAMMPS_VERSION=stable_23Jun2022_update4 ..
+cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DUSE_TF_PYTHON_LIBS=TRUE ${CUDA_ARGS} -DLAMMPS_VERSION=stable_2Aug2023 ..
 make -j${NPROC}
 make install
 

source/install/build_from_c.sh

@@ -13,7 +13,7 @@ NPROC=$(nproc --all)
 BUILD_TMP_DIR=${SCRIPT_PATH}/../build
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
-cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DDEEPMD_C_ROOT=${DEEPMD_C_ROOT} -DLAMMPS_VERSION=stable_23Jun2022_update4 ..
+cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DDEEPMD_C_ROOT=${DEEPMD_C_ROOT} -DLAMMPS_VERSION=stable_2Aug2023 ..
 make -j${NPROC}
 make install
 make lammps

source/install/build_lammps.sh

@@ -14,7 +14,7 @@ BUILD_TMP_DIR=${SCRIPT_PATH}/../build_lammps
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
 # download LAMMMPS
-LAMMPS_VERSION=stable_23Jun2022_update4
+LAMMPS_VERSION=stable_2Aug2023
 if [ ! -d "lammps-${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

source/install/test_cc.sh

@@ -11,7 +11,7 @@ INSTALL_PREFIX=${SCRIPT_PATH}/../../dp_test
 BUILD_TMP_DIR=${SCRIPT_PATH}/../build_tests
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
-cmake -DINSTALL_TENSORFLOW=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DTENSORFLOW_ROOT=${INSTALL_PREFIX} -DBUILD_TESTING:BOOL=TRUE -DLAMMPS_VERSION=stable_23Jun2022_update4 ..
+cmake -DINSTALL_TENSORFLOW=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DTENSORFLOW_ROOT=${INSTALL_PREFIX} -DBUILD_TESTING:BOOL=TRUE -DLAMMPS_VERSION=stable_2Aug2023 ..
 make -j${NPROC}
 make install
 

source/install/test_cc_local.sh

@@ -12,7 +12,7 @@ INSTALL_PREFIX=${SCRIPT_PATH}/../../dp_test
 BUILD_TMP_DIR=${SCRIPT_PATH}/../build_tests
 mkdir -p ${BUILD_TMP_DIR}
 cd ${BUILD_TMP_DIR}
-cmake -DINSTALL_TENSORFLOW=FALSE -DUSE_TF_PYTHON_LIBS=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DBUILD_TESTING:BOOL=TRUE -DLAMMPS_VERSION=stable_23Jun2022_update4 ..
+cmake -DINSTALL_TENSORFLOW=FALSE -DUSE_TF_PYTHON_LIBS=TRUE -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DBUILD_TESTING:BOOL=TRUE -DLAMMPS_VERSION=stable_2Aug2023 ..
 make -j${NPROC}
 make install
 

source/lmp/tests/test_deeptensor.py

@@ -99,7 +99,9 @@ def _lammps(data_file) -> PyLammps:
 
 @pytest.fixture
 def lammps():
- yield _lammps(data_file=data_file)
+ lmp = _lammps(data_file=data_file)
+ yield lmp
+ lmp.close()
 
 
 # @pytest.fixture
@@ -114,4 +116,7 @@ def test_compute_deeptensor_atom(lammps):
  lammps.variable("tensor atom c_tensor[1]")
  lammps.dump("1 all custom 1 dump id c_tensor[1]")
  lammps.run(0)
- assert np.array(lammps.variables["tensor"].value) == pytest.approx(expected_d)
+ idx_map = lammps.lmp.numpy.extract_atom("id") - 1
+ assert np.array(lammps.variables["tensor"].value) == pytest.approx(
+ expected_d[idx_map]
+ )

source/lmp/tests/test_dplr.py

@@ -296,7 +296,9 @@ def _lammps(data_file) -> PyLammps:
 
 @pytest.fixture
 def lammps():
- yield _lammps(data_file=data_file)
+ lmp = _lammps(data_file=data_file)
+ yield lmp
+ lmp.close()
 
 
 def test_pair_deepmd_sr(lammps):
@@ -350,12 +352,18 @@ def test_pair_deepmd_lr(lammps):
  lammps.fix(f"0 all dplr model {pb_file.resolve()} type_associate 1 3 bond_type 1")
  lammps.fix_modify("0 virial yes")
  lammps.run(0)
- for ii in range(2):
- assert lammps.atoms[6 + ii].position == pytest.approx(expected_WC[ii])
+ for ii in range(8):
+ if lammps.atoms[ii].id > 6:
+ assert lammps.atoms[ii].position == pytest.approx(
+ expected_WC[lammps.atoms[ii].id - 7]
+ )
  assert lammps.eval("elong") == pytest.approx(expected_e_kspace)
  assert lammps.eval("pe") == pytest.approx(expected_e_lr)
- for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f_lr[ii])
+ for ii in range(8):
+ if lammps.atoms[ii].id <= 6:
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f_lr[lammps.atoms[ii].id - 1]
+ )
  lammps.run(1)
 
 
@@ -443,8 +451,12 @@ def test_min_dplr(lammps):
  lammps.min_style("cg")
  lammps.minimize("0 1.0e-6 2 2")
  for ii in range(8):
- assert lammps.atoms[ii].position == pytest.approx(expected_x_min_step1[ii])
+ assert lammps.atoms[ii].position == pytest.approx(
+ expected_x_min_step1[lammps.atoms[ii].id - 1]
+ )
  assert lammps.eval("pe") == pytest.approx(expected_e_min_step1)
  assert lammps.eval("elong") == pytest.approx(expected_e_kspace_min_step1)
  for ii in range(8):
- assert lammps.atoms[ii].force == pytest.approx(expected_f_min_step1[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f_min_step1[lammps.atoms[ii].id - 1]
+ )

source/lmp/tests/test_lammps.py

@@ -261,12 +261,16 @@ def _lammps(data_file) -> PyLammps:
 
 @pytest.fixture
 def lammps():
- yield _lammps(data_file=data_file)
+ lmp = _lammps(data_file=data_file)
+ yield lmp
+ lmp.close()
 
 
 @pytest.fixture
 def lammps_type_map():
- yield _lammps(data_file=data_type_map_file)
+ lmp = _lammps(data_file=data_type_map_file)
+ yield lmp
+ lmp.close()
 
 
 def test_pair_deepmd(lammps):
@@ -275,7 +279,9 @@ def test_pair_deepmd(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  lammps.run(1)
 
 
@@ -292,11 +298,14 @@ def test_pair_deepmd_virial(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
+ idx_map = lammps.lmp.numpy.extract_atom("id") - 1
  for ii in range(9):
  assert np.array(
  lammps.variables[f"virial{ii}"].value
- ) / nktv2p == pytest.approx(expected_v[:, ii])
+ ) / nktv2p == pytest.approx(expected_v[idx_map, ii])
 
 
 def test_pair_deepmd_model_devi(lammps):
@@ -309,7 +318,9 @@ def test_pair_deepmd_model_devi(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  # load model devi
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
@@ -342,11 +353,14 @@ def test_pair_deepmd_model_devi_virial(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
+ idx_map = lammps.lmp.numpy.extract_atom("id") - 1
  for ii in range(9):
  assert np.array(
  lammps.variables[f"virial{ii}"].value
- ) / nktv2p == pytest.approx(expected_v[:, ii])
+ ) / nktv2p == pytest.approx(expected_v[idx_map, ii])
  # load model devi
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
@@ -373,7 +387,9 @@ def test_pair_deepmd_model_devi_atomic_relative(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  # load model devi
  md = np.loadtxt(md_file.resolve())
  norm = np.linalg.norm(np.mean([expected_f, expected_f2], axis=0), axis=1)
@@ -402,7 +418,9 @@ def test_pair_deepmd_model_devi_atomic_relative_v(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
  assert md[7:] == pytest.approx(expected_md_f)
@@ -430,5 +448,7 @@ def test_pair_deepmd_type_map(lammps_type_map):
  lammps_type_map.run(0)
  assert lammps_type_map.eval("pe") == pytest.approx(expected_e)
  for ii in range(6):
- assert lammps_type_map.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps_type_map.atoms[ii].force == pytest.approx(
+ expected_f[lammps_type_map.atoms[ii].id - 1]
+ )
  lammps_type_map.run(1)

source/lmp/tests/test_lammps_3types.py

@@ -288,12 +288,16 @@ def _lammps(data_file) -> PyLammps:
 
 @pytest.fixture
 def lammps():
- yield _lammps(data_file=data_file)
+ lmp = _lammps(data_file=data_file)
+ yield lmp
+ lmp.close()
 
 
 @pytest.fixture
 def lammps_type_map():
- yield _lammps(data_file=data_type_map_file)
+ lmp = _lammps(data_file=data_type_map_file)
+ yield lmp
+ lmp.close()
 
 
 def test_pair_deepmd(lammps):
@@ -302,7 +306,9 @@ def test_pair_deepmd(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  lammps.run(1)
 
 
@@ -319,11 +325,14 @@ def test_pair_deepmd_virial(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
+ idx_map = lammps.lmp.numpy.extract_atom("id") - 1
  for ii in range(9):
  assert np.array(
  lammps.variables[f"virial{ii}"].value
- ) / nktv2p == pytest.approx(expected_v[:, ii])
+ ) / nktv2p == pytest.approx(expected_v[idx_map, ii])
 
 
 def test_pair_deepmd_model_devi(lammps):
@@ -336,7 +345,9 @@ def test_pair_deepmd_model_devi(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  # load model devi
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
@@ -369,11 +380,14 @@ def test_pair_deepmd_model_devi_virial(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
+ idx_map = lammps.lmp.numpy.extract_atom("id") - 1
  for ii in range(9):
  assert np.array(
  lammps.variables[f"virial{ii}"].value
- ) / nktv2p == pytest.approx(expected_v[:, ii])
+ ) / nktv2p == pytest.approx(expected_v[idx_map, ii])
  # load model devi
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
@@ -400,7 +414,9 @@ def test_pair_deepmd_model_devi_atomic_relative(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  # load model devi
  md = np.loadtxt(md_file.resolve())
  norm = np.linalg.norm(np.mean([expected_f, expected_f2], axis=0), axis=1)
@@ -429,7 +445,9 @@ def test_pair_deepmd_model_devi_atomic_relative_v(lammps):
  lammps.run(0)
  assert lammps.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps.atoms[ii].force == pytest.approx(
+ expected_f[lammps.atoms[ii].id - 1]
+ )
  md = np.loadtxt(md_file.resolve())
  expected_md_f = np.linalg.norm(np.std([expected_f, expected_f2], axis=0), axis=1)
  assert md[7:] == pytest.approx(expected_md_f)
@@ -457,5 +475,7 @@ def test_pair_deepmd_type_map(lammps_type_map):
  lammps_type_map.run(0)
  assert lammps_type_map.eval("pe") == pytest.approx(expected_e)
  for ii in range(7):
- assert lammps_type_map.atoms[ii].force == pytest.approx(expected_f[ii])
+ assert lammps_type_map.atoms[ii].force == pytest.approx(
+ expected_f[lammps_type_map.atoms[ii].id - 1]
+ )
  lammps_type_map.run(1)