Merge deepmd-pytorch into main repo (deepmodeling#3180)

Merge the deepmd-pytorch into main repo🎉
Add the following directories:

- deepmd/pt : main implementations of deepmd-pytorch
- source/tests/pt: UTs for deepmd-pytorch

TODO list:
- [x] examples added for water/se_e2_a, water/se_atten, water/dpa2
- [x] README updated (need modified)
- [x] Paths in each files have been adapted. 
- [x] pyproject.toml needed to be merge

---------

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

.github/workflows/test_cuda.yml

@@ -37,7 +37,7 @@ jobs:
       run: python -m pip config --user set global.index-url https://mirrors.aliyun.com/pypi/simple/
     - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
     - run: python -m pip install "tensorflow>=2.15.0rc0"
-    - run: python -m pip install -v -e .[gpu,test,lmp,cu12] "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
+    - run: python -m pip install -v -e .[gpu,test,lmp,cu12,torch] "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
       env:
         DP_BUILD_TESTING: 1
         DP_VARIANT: cuda

.github/workflows/test_python.yml

@@ -9,12 +9,12 @@ jobs:
     strategy:
       matrix:
         include:
-          - python: 3.7
-            tf: 1.14
           - python: 3.8
             tf:
+            torch:
           - python: "3.11"
             tf:
+            torch:
 
     steps:
     - uses: actions/checkout@v4
@@ -23,22 +23,25 @@ jobs:
         python-version: ${{ matrix.python }}
         cache: 'pip'
     - uses: mpi4py/setup-mpi@v1
-      if: ${{ matrix.tf == '' }}
       with:
         mpi: openmpi
     # https://github.com/pypa/pip/issues/11770
     - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
-    - run: pip install -e .[cpu,test]
+    - run: python -m pip install -U "torch==${{ matrix.torch }}" "numpy<1.20"
+      if: matrix.torch != ''
+    - run: pip install -e .[cpu,test,torch]
       env:
         TENSORFLOW_VERSION: ${{ matrix.tf }}
         DP_BUILD_TESTING: 1
     - run: pip install horovod mpi4py
-      if: ${{ matrix.tf == '' }}
       env:
         HOROVOD_WITH_TENSORFLOW: 1
+        HOROVOD_WITHOUT_PYTORCH: 1
         HOROVOD_WITHOUT_GLOO: 1
     - run: dp --version
     - run: pytest --cov=deepmd source/tests --durations=0
+      env:
+        NUM_WORKERS: 0
     - uses: codecov/codecov-action@v3
       with:
         gcov: true

.gitignore

@@ -13,6 +13,7 @@
 *.bz2
 *.pyc
 *.pb
+*.DS_Store
 tmp*
 CMakeCache.txt
 CMakeFiles

README.md

@@ -93,7 +93,6 @@ The code is organized as follows:
 
 See [DeePMD-kit Contributing Guide](CONTRIBUTING.md) to become a contributor! 🤓
 
-
 [1]: https://arxiv.org/abs/1707.01478
 [2]: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.143001
 [3]: https://arxiv.org/abs/1805.09003

backend/dynamic_metadata.py

@@ -88,4 +88,8 @@ def dynamic_metadata(
                 "nvidia-cudnn-cu12",
                 "nvidia-cuda-nvcc-cu12",
             ],
+            "torch": [
+                "torch>=2a",
+                "tqdm",
+            ],
         }

deepmd/pt/__init__.py

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

deepmd/pt/entrypoints/__init__.py

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