merge devel into master (#2725)

Author: amcadmus

.clang-format

@@ -1,4 +1,5 @@
 ---
 BasedOnStyle: Google
 BinPackParameters: false
+InsertBraces: true
 ...

.github/labeler.yml

@@ -1,5 +1,6 @@
 Python:
 - deepmd/**/*
+- deepmd_cli/**/*
 - source/tests/**/*
 Docs: doc/**/*
 Examples: examples/**/*

.github/workflows/build_wheel.yml

@@ -22,6 +22,11 @@ jobs:
             python: 311
             platform_id: macosx_x86_64
             dp_variant: cpu
+          # macos-arm64
+          - os: macos-latest
+            python: 311
+            platform_id: macosx_arm64
+            dp_variant: cpu
           # win-64
           - os: windows-2019
             python: 311
@@ -42,7 +47,7 @@ jobs:
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.14
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -95,20 +100,20 @@ jobs:
           name: artifact
           path: source/install/docker/dist
       - name: Log in to the Container registry
-        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@c4ee3adeed93b1fa6a762f209fb01608c1a22f1e
+        uses: docker/metadata-action@818d4b7b91585d195f67373fd9cb0332e31a7175
         with:
           images: ghcr.io/deepmodeling/deepmd-kit
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        uses: docker/build-push-action@2eb1c1961a95fc15694676618e422e8ba1d63825
         with:
           context: source/install/docker
           push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' }}

.github/workflows/test_cc.yml

@@ -23,9 +23,11 @@ jobs:
         TF_INTER_OP_PARALLELISM_THREADS: 1
         LMP_CXX11_ABI_0: 1
     # test lammps
+    # ASE issue: https://gitlab.com/ase/ase/-/merge_requests/2843
+    # TODO: remove ase version when ase has new release
     - run: |
         python -m pip install -U pip
-        python -m pip install -e .[cpu,test,lmp]
+        python -m pip install -e .[cpu,test,lmp] "ase @ https://github.com/rosswhitfield/ase/archive/edd03571aff6944b77b4a4b055239f3c3e4eeb66.zip"
       env:
         DP_BUILD_TESTING: 1
     - run: pytest --cov=deepmd source/lmp/tests
@@ -35,6 +37,14 @@ jobs:
         TF_INTER_OP_PARALLELISM_THREADS: 1
         LAMMPS_PLUGIN_PATH: ${{ github.workspace }}/dp_test/lib/deepmd_lmp
         LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
+    # test ipi
+    - run: pytest --cov=deepmd source/ipi/tests
+      env:
+        OMP_NUM_THREADS: 1
+        TF_INTRA_OP_PARALLELISM_THREADS: 1
+        TF_INTER_OP_PARALLELISM_THREADS: 1
+        PATH: ${{ github.workspace }}/dp_test/bin:$PATH
+        LD_LIBRARY_PATH: ${{ github.workspace }}/dp_test/lib
     - uses: codecov/codecov-action@v3
       with:
         gcov: true

.github/workflows/test_python.yml

@@ -42,10 +42,11 @@ jobs:
         TENSORFLOW_VERSION: ${{ matrix.tf }}
         DP_BUILD_TESTING: 1
     - run: dp --version
-    - run: pytest --cov=deepmd source/tests --durations=0
+    - run: pytest --cov=deepmd --cov=deepmd_cli source/tests --durations=0
     - uses: codecov/codecov-action@v3
       with:
         gcov: true
+        gcov_executable: gcov-${{ matrix.gcc }}
   pass:
     name: Pass testing Python
     needs: [testpython]

.license-header.txt

@@ -0,0 +1 @@
+SPDX-License-Identifier: LGPL-3.0-or-later

.pre-commit-config.yaml

@@ -11,22 +11,29 @@ repos:
     -   id: check-yaml
     #-   id: check-json
     -   id: check-added-large-files
+        args: ['--maxkb=1024', '--enforce-all']
+        # TODO: remove the following after resolved
+        exclude: |
+            (?x)^(
+                source/tests/infer/dipolecharge_e.pbtxt|
+                source/tests/infer/deeppolar_new.pbtxt
+            )$
     -   id: check-merge-conflict
     -   id: check-symlinks
     -   id: check-toml
 # Python
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
     -   id: black-jupyter
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
     - id: isort
       files: \.py$
--   repo: https://github.com/charliermarsh/ruff-pre-commit
+-   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.269
+    rev: v0.0.280
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -38,12 +45,12 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.15.0
     hooks:
     -   id: blacken-docs
 # C++
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v16.0.4
+    rev: v16.0.6
     hooks:
     -   id: clang-format
         exclude: ^source/3rdparty|source/lib/src/cuda/cudart/.+\.inc
@@ -54,7 +61,7 @@ repos:
     -   id: csslint
 # Shell
 - repo: https://github.com/scop/pre-commit-shfmt
-  rev: v3.6.0-2
+  rev: v3.7.0-1
   hooks:
     - id: shfmt
 # CMake
@@ -63,5 +70,46 @@ repos:
   hooks:
     - id: cmake-format
     #- id: cmake-lint
+# license header
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.1
+  hooks:
+    # C++, js
+    -   id: insert-license
+        files: \.(c|cc|cpp|js|ts|h|hpp)$
+        args:
+        - --license-filepath
+        - .license-header.txt
+        - --comment-style
+        - //
+        - --no-extra-eol
+        exclude: ^source/3rdparty|source/lib/src/cuda/cudart/.+\.inc
+    # CSS
+    -   id: insert-license
+        files: \.(css|scss)$
+        args:
+        - --license-filepath
+        - .license-header.txt
+        - --comment-style
+        - /*| *| */
+        - --no-extra-eol
+    # Python
+    -   id: insert-license
+        files: \.(py|pyx)$
+        args:
+        - --license-filepath
+        - .license-header.txt
+        - --comment-style
+        - "#"
+        - --no-extra-eol
+    # HTML
+    -   id: insert-license
+        files: \.(html|vue|xml)$
+        args:
+        - --license-filepath
+        - .license-header.txt
+        - --comment-style
+        - <!--|  ~|  -->
+        - --no-extra-eol
 ci:
   autoupdate_branch: devel

CITATIONS.bib

@@ -15,27 +15,29 @@ @article{Wang_ComputPhysCommun_2018_v228_p178
     pages = {178--184},
 }
 
-@misc{Zeng_arXiv_2023,
+@Article{Zeng_JChemPhys_2023_v159_p054801,
     annote = {general purpose},
-    title = {{DeePMD-kit v2: A software package for Deep Potential models}},
-    author = {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and
-            Zeyu Li and Yixiao Chen and Marián Rynik and Li'ang Huang and
-            Ziyao Li and Shaochen Shi and Yingze Wang and Haotian Ye and
-            Ping Tuo and Jiabin Yang and Ye Ding and Yifan Li and Davide
-            Tisi and Qiyu Zeng and Han Bao and Yu Xia and Jiameng Huang
-            and Koki Muraoka and Yibo Wang and Junhan Chang and Fengbo
-            Yuan and Sigbjørn Løland Bore and Chun Cai and Yinnian Lin
-            and Bo Wang and Jiayan Xu and Jia-Xin Zhu and Chenxing Luo and
-            Yuzhi Zhang and Rhys E. A. Goodall and Wenshuo Liang and Anurag
-            Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
-            Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and
-            Darrin M. York and Weinan E and Roberto Car and Linfeng Zhang
-            and Han Wang},
-    year = {2023},
-    archivePrefix = {arXiv},
-    doi = {10.48550/arXiv.2304.09409}
+    title  = {{DeePMD-kit v2: A software package for deep potential models}},
+    author =   {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and Zeyu Li
+             and Yixiao Chen and Mari{\'a}n Rynik and Li'ang Huang and Ziyao Li and
+             Shaochen Shi and Yingze Wang and Haotian Ye and Ping Tuo and Jiabin
+             Yang and Ye Ding and Yifan Li and Davide Tisi and Qiyu Zeng and Han
+             Bao and Yu Xia and Jiameng Huang and Koki Muraoka and Yibo Wang and
+             Junhan Chang and Fengbo Yuan and Sigbj{\o}rn L{\o}land Bore and Chun
+             Cai and Yinnian Lin and Bo Wang and Jiayan Xu and Jia-Xin Zhu and
+             Chenxing Luo and Yuzhi Zhang and Rhys E A Goodall and Wenshuo Liang
+             and Anurag Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
+             Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and Darrin M
+             York and Weinan E and Roberto Car and Linfeng Zhang and Han Wang},
+    journal =  {J. Chem. Phys.},
+    volume =   159,
+    issue =    5,
+    year =    2023,
+    pages  =   054801,
+    doi =      {10.1063/5.0155600},
 }
 
+
 @article{Lu_CompPhysCommun_2021_v259_p107624,
     annote = {GPU support},
     title={{86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million

MANIFEST.in

@@ -0,0 +1,9 @@
+prune source/tests
+prune source/api_c/tests
+prune source/api_cc/tests
+prune source/lib/tests
+prune source/lmp/tests
+prune doc
+prune examples
+prune data
+prune .github

README.md

@@ -5,8 +5,6 @@
 <span style="font-size:larger;">DeePMD-kit Manual</span>
 ========
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/deepmd-kit.svg?maxAge=86400)](https://github.com/deepmodeling/deepmd-kit/releases)
-[![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2020.107206)
-[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
 [![offline packages](https://img.shields.io/github/downloads/deepmodeling/deepmd-kit/total?label=offline%20packages)](https://github.com/deepmodeling/deepmd-kit/releases)
 [![conda-forge](https://img.shields.io/conda/dn/conda-forge/deepmd-kit?color=red&label=conda-forge&logo=conda-forge)](https://anaconda.org/conda-forge/deepmd-kit)
 [![pip install](https://img.shields.io/pypi/dm/deepmd-kit?label=pip%20install)](https://pypi.org/project/deepmd-kit)
@@ -49,7 +47,11 @@ For more information, check the [documentation](https://deepmd.readthedocs.io/).
 The project DeePMD-kit is licensed under [GNU LGPLv3.0](./LICENSE).
 If you use this code in any future publications, please cite the following publications for general purpose:
 - Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. "DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics." Computer Physics Communications 228 (2018): 178-184.
-- Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang. "DeePMD-kit v2: A software package for Deep Potential models." [arXiv:2304.09409](https://doi.org/10.48550/arXiv.2304.09409).
+[![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2018.03.016)
+[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
+- Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang. "DeePMD-kit v2: A software package for deep potential models." J. Chem. Phys. 159 (2023): 054801.
+[![doi:10.1063/5.0155600](https://img.shields.io/badge/DOI-10.1063%2F5.0155600-blue)](https://doi.org/10.1063/5.0155600)
+[![Citations](https://citations.njzjz.win/10.1063/5.0155600)](https://badge.dimensions.ai/details/doi/10.1063/5.0155600)
 
 In addition, please follow [the bib file](CITATIONS.bib) to cite the methods you used.
 
@@ -105,7 +107,7 @@ A full [document](doc/train/train-input-auto.rst) on options in the training inp
     - [Fit energy](doc/model/train-energy.md)
     - [Fit spin energy](doc/model/train-energy-spin.md)
     - [Fit `tensor` like `Dipole` and `Polarizability`](doc/model/train-fitting-tensor.md)
-- [Fit electronic density of states (DOS)](doc/model/train-fitting-dos.md)
+    - [Fit electronic density of states (DOS)](doc/model/train-fitting-dos.md)
     - [Train a Deep Potential model using `type embedding` approach](doc/model/train-se-e2-a-tebd.md)
     - [Deep potential long-range](doc/model/dplr.md)
     - [Deep Potential - Range Correction (DPRc)](doc/model/dprc.md)