Merge pull request #6 from mir-group/develop

v0.5.1
mir-group · Mar 8, 2022 · 86d44d2 · 86d44d2
2 parents 80cd63e + bbae0c5
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -0,0 +1,69 @@
+name: Run LAMMPS-Python tests
+
+on:
+  push:
+    branches:
+    - main
+    - develop
+
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+        torch-version: [1.10.0]
+        nequip-branch: ["develop"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      env:
+        TORCH: "${{ matrix.torch-version }}"
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        python -m pip install --upgrade pip
+        pip install torch==${TORCH} -f https://download.pytorch.org/whl/cpu/torch_stable.html
+        pip install pytest
+        pip install pytest-xdist[psutil]
+        pip install mkl-include
+    - name: Install NequIP
+      env:
+          NEQUIP: "${{ matrix.nequip-branch }}"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install "https://github.com/mir-group/nequip/archive/${NEQUIP}.zip"
+    - name: Fetch and build LAMMPS
+      run: |
+        mkdir lammps_dir/
+        cd lammps_dir/
+        wget -nv "https://github.com/lammps/lammps/archive/release.zip"
+        unzip -q release.zip
+        mv lammps-release/ lammps/
+        rm release.zip
+        cd ..
+        ./patch_lammps.sh lammps_dir/lammps/
+        cd lammps_dir/lammps/
+        mkdir build/
+        cd build/
+        cmake ../cmake -DCMAKE_PREFIX_PATH=`python -c 'import torch;print(torch.utils.cmake_prefix_path)'` -DMKL_INCLUDE_DIR=`python -c "import sysconfig;from pathlib import Path;print(Path(sysconfig.get_paths()[\"include\"]).parent)"`
+        make -j$(nproc)
+        echo "LAMMPS in dir"
+        pwd
+        ls lmp
+        cd ../../..
+        echo "Now in dir"
+        pwd
+    - name: Run tests with pytest
+      run: |
+        # See https://github.com/pytest-dev/pytest/issues/1075
+        PYTHONHASHSEED=0 LAMMPS=`pwd`/lammps_dir/lammps/build/lmp pytest -n auto tests/
diff --git a/.gitignore b/.gitignore
@@ -32,4 +32,62 @@
 *.out
 *.app
 
-.vscode/
+.vscode/*
+!.vscode/settings.json
+
+
+# ---------- Python .gigignores-----------
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,7 @@
+{
+    "editor.formatOnSave": false,
+    "[python]": {
+        "editor.formatOnSave": true
+    },
+    "python.formatting.provider": "black"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,15 @@ Most recent change on the bottom.
 
 ## [Unreleased]
 
+## [0.5.1]
+### Added
+- Full suite of unit tests
+
+### Fixed
+- edge duplication issue
+
+## [0.5.0] - 11/24/2021
+
 ### Changed
 - The mapping from LAMMPS to NequIP types is now explicitly provided
 - Don't print full config in LAMMPS log

diff --git a/README.md b/README.md
@@ -6,8 +6,7 @@ This pair style allows you to use NequIP models in LAMMPS simulations.
 
 ## Pre-requisites
 
-* NequIP >= 0.4.0
-* Pytorch or LibTorch >= 1.9.0
+* PyTorch or LibTorch >= 1.10.0
 
 ## Usage in LAMMPS
 
@@ -17,8 +16,8 @@ pair_coeff	* * deployed.pth <type name 1> <type name 2> ...
 ```
 where `deployed.pth` is the filename of your trained model.
 
-The names after the model path indicate, in order, the names of the NequIP model's atom types to use for LAMMPS atom types 1, 2, and so on. The number of names given must be equal to the number of atom types in the lammps configuration (not the NequIP model!). 
-The element string should be consistent with the names specified in the NequIP training YAML in `chemical_symbol_to_type` or `type_names`.
+The names after the model path `deployed.pth` indicate, in order, the names of the NequIP model's atom types to use for LAMMPS atom types 1, 2, and so on. The number of names given must be equal to the number of atom types in the LAMMPS configuration (not the NequIP model!). 
+The given names must be consistent with the names specified in the NequIP training YAML in `chemical_symbol_to_type` or `type_names`.
 
 ## Building LAMMPS with this pair style
 
@@ -73,13 +72,22 @@ cmake ../cmake -DCMAKE_PREFIX_PATH=/path/to/libtorch
 ```
 CMake will look for MKL and, optionally, CUDA and cuDNN. You may have to explicitly provide the path for your CUDA installation (e.g. `-DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/cuda/`) and your MKL installation (e.g. `-DMKL_INCLUDE_DIR=/usr/include/`).
 
-Note that the CUDA that comes with PyTorch when installed with `conda` (the `cudatoolkit` package) may not be sufficient (see [here](https://github.com/pytorch/extension-cpp/issues/26), for example) and you may have to install full CUDA seperately.
-
 Pay attention to warnings and error messages.
 
+**MKL:** If `MKL_INCLUDE_DIR` is not found and you are using a Python environment, a simple solution is to run `conda install mkl-include` or `pip install mkl-include` and append:
+```
+-DMKL_INCLUDE_DIR="$CONDA_PREFIX/include"
+```
+to the `cmake` command if using a `conda` environment, or
+```
+-DMKL_INCLUDE_DIR=`python -c "import sysconfig;from pathlib import Path;print(Path(sysconfig.get_paths()[\"include\"]).parent)"`
+```
+if using plain Python and `pip`.
+
+**CUDA:** Note that the CUDA that comes with PyTorch when installed with `conda` (the `cudatoolkit` package) is usually insufficient (see [here](https://github.com/pytorch/extension-cpp/issues/26), for example) and you may have to install full CUDA seperately. A minor version mismatch between the available full CUDA version and the version of `cudatoolkit` is usually *not* a problem, as long as the system CUDA is equal or newer. (For example, PyTorch's requested `cudatoolkit==11.3` with a system CUDA of 11.4 works, but a system CUDA 11.1 will likely fail.)
+
 ### Build LAMMPS
 ```bash
 make -j$(nproc)
 ```
 This gives `lammps/build/lmp`, which can be run as usual with `/path/to/lmp -in in.script`. If you specify `-DCMAKE_INSTALL_PREFIX=/somewhere/in/$PATH` (the default is `$HOME/.local`), you can do `make install` and just run `lmp -in in.script`.
-
diff --git a/pair_nequip.cpp b/pair_nequip.cpp
@@ -47,9 +47,10 @@
 // (see https://github.com/pytorch/pytorch/blob/dfbd030854359207cb3040b864614affeace11ce/torch/csrc/jit/api/module.cpp#L479)
 // is wrong, and we have ro "reimplement" the function
 // to get around that...
-// it's broken in 1.8 and 1.9 so the < check is correct.
-// This appears to be fixed in 1.10.
-#if (TORCH_VERSION_MAJOR == 1 && TORCH_VERSION_MINOR < 10)
+// it's broken in 1.8 and 1.9
+// BUT the internal logic in the function is wrong in 1.10
+// So we only use torch::jit::freeze in >=1.11
+#if (TORCH_VERSION_MAJOR == 1 && TORCH_VERSION_MINOR <= 10)
   #define DO_TORCH_FREEZE_HACK
   // For the hack, need more headers:
   #include <torch/csrc/jit/passes/freeze_module.h>
@@ -194,7 +195,8 @@ void PairNEQUIP::coeff(int narg, char **arg) {
       auto out_mod = freeze_module(
         model, {}
       );
-      auto graph = model.get_method("forward").graph();
+      // See 1.11 bugfix in https://github.com/pytorch/pytorch/pull/71436
+      auto graph = out_mod.get_method("forward").graph();
       OptimizeFrozenGraph(graph, optimize_numerics);
       model = out_mod;
     #else
@@ -394,14 +396,15 @@ void PairNEQUIP::compute(int eflag, int vflag){
           edge_counter++;
 
           if (debug_mode){
-              printf("%d %d %g %g %g %g %g %g %g %g %g %g\n", itag-1, jtag-1,
+              printf("%d %d %.10g %.10g %.10g %.10g %.10g %.10g %.10g %.10g %.10g %.10g\n", itag-1, jtag-1,
                 pos[itag-1][0],pos[itag-1][1],pos[itag-1][2],pos[jtag-1][0],pos[jtag-1][1],pos[jtag-1][2],
                 e_vec[0],e_vec[1],e_vec[2],sqrt(rsq));
           }
 
       }
     }
   }
+  if (debug_mode) printf("end NEQUIP edges\n");
 
   // shorten the list before sending to nequip
   torch::Tensor edges_tensor = torch::zeros({2,edge_counter}, torch::TensorOptions().dtype(torch::kInt64));

diff --git a/test/check_result.py b/test/check_result.py
diff --git a/tests/test_data/Cu-cubic.xyz b/tests/test_data/Cu-cubic.xyz
@@ -0,0 +1,90 @@
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.017391652023890813 free_energy=-0.017391652023890813 pbc="T T T"
+Cu       0.01764052       0.00400157       0.00978738      -0.08717844       0.04962473      -0.12179229      -0.00472427
+Cu       0.02240893       1.82367558       1.79522722      -0.12285307      -0.13375551       0.17188324      -0.00362717
+Cu       1.81450088      -0.00151357       1.80396781       0.08501339       0.09035482       0.10694376      -0.00469092
+Cu       1.80910599       1.80644044       0.01454274       0.12501812      -0.00622404      -0.15703471      -0.00434929
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.015905094412799414 free_energy=-0.015905094412799414 pbc="T T T"
+Cu       0.01624345      -0.00611756      -0.00528172      -0.06246748       0.14140106      -0.03262814      -0.00437084
+Cu      -0.01072969       1.81365408       1.78198461       0.13723509      -0.12500316       0.07279520      -0.00412798
+Cu       1.82244812      -0.00761207       1.80819039      -0.11120998       0.15286120      -0.12108536      -0.00357991
+Cu       1.80250630       1.81962108      -0.02060141       0.03644236      -0.16925910       0.08091829      -0.00382637
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.01528731937769301 free_energy=-0.01528731937769301 pbc="T T T"
+Cu      -0.00416758      -0.00056267      -0.02136196       0.01148580      -0.04169084       0.08236991      -0.00512480
+Cu       0.01640271       1.78706564       1.79658253      -0.14132134       0.08420319       0.07401279      -0.00350296
+Cu       1.81002881      -0.01245288       1.79442048       0.01247261       0.04689613       0.08984380      -0.00391347
+Cu       1.79590992       1.81051454       0.02292208       0.11736294      -0.08940848      -0.24622650      -0.00274609
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.01887755101138211 free_energy=-0.01887755101138211 pbc="T T T"
+Cu       0.01788628       0.00436510       0.00096497      -0.15444665      -0.09501731      -0.02555193      -0.00454935
+Cu      -0.01863493       1.80222612       1.80145241       0.11584357       0.01712771       0.06618692      -0.00503852
+Cu       1.80417259      -0.00627001       1.80456182       0.00463158      -0.01619046       0.04319703      -0.00488369
+Cu       1.80022782       1.79186135       0.00884622       0.03397150       0.09408005      -0.08383203      -0.00440599
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.020128104148323445 free_energy=-0.020128104148323445 pbc="T T T"
+Cu       0.00050562       0.00499951      -0.00995909      -0.07686553      -0.03193870       0.02688282      -0.00520543
+Cu       0.00693599       1.80081698       1.78915423      -0.12450754       0.07391750       0.07765346      -0.00475940
+Cu       1.79852293       0.00598575       1.80832250       0.08218191      -0.03926083      -0.06416069      -0.00518652
+Cu       1.79352523       1.81118670      -0.00087987       0.11919115      -0.00271797      -0.04037558      -0.00497675
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.020154675346251594 free_energy=-0.020154675346251594 pbc="T T T"
+Cu       0.00441227      -0.00330870       0.02430771      -0.08239901      -0.01596948      -0.11560842      -0.00482879
+Cu      -0.00252092       1.80609610       1.82082481      -0.03096779      -0.04175481      -0.03348025      -0.00521007
+Cu       1.79590768      -0.00591637       1.80687603       0.07820172       0.00326506       0.06975380      -0.00487497
+Cu       1.80170130       1.79307235      -0.00204877       0.03516508       0.05445923       0.07933486      -0.00524084
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.01482573303385415 free_energy=-0.01482573303385415 pbc="T T T"
+Cu      -0.00311784       0.00729004       0.00217821       0.05397007      -0.04615605       0.08312341      -0.00388045
+Cu      -0.00899092       1.78013219       1.81413252       0.09728569       0.15265900      -0.04201865      -0.00425637
+Cu       1.81627064      -0.01514093       1.82139291      -0.13314014       0.11989754      -0.09607516      -0.00301817
+Cu       1.80070106       1.83131281       0.00601822      -0.01811562      -0.22640049       0.05497041      -0.00367074
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.021005203893530222 free_energy=-0.021005203893530222 pbc="T T T"
+Cu       0.01690526      -0.00465937       0.00032820      -0.10681903      -0.01566386       0.03841762      -0.00519367
+Cu       0.00407516       1.79711077       1.80502066      -0.01195269      -0.02590150      -0.00836358      -0.00557351
+Cu       1.80499110      -0.01754724       1.81517658       0.08162914       0.07959041      -0.08354024      -0.00494696
+Cu       1.81100499       1.79874571      -0.00171548       0.03714257      -0.03802506       0.05348620      -0.00529107
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.004108154437133749 free_energy=-0.004108154437133749 pbc="T T T"
+Cu       0.00091205       0.01091283      -0.01946970       0.10455948      -0.22944333       0.27304574      -0.00116755
+Cu      -0.01386350       1.78203508       1.82909834       0.21498056       0.31338220      -0.18956466       0.00087501
+Cu       1.82227836       0.02204556       1.81294828      -0.18865295      -0.31150667      -0.06864456      -0.00045239
+Cu       1.81476421       1.79316573       0.01916364      -0.13088708       0.22756779      -0.01483652      -0.00336323
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.019378981209557722 free_energy=-0.019378981209557722 pbc="T T T"
+Cu       0.00001109      -0.00289544      -0.01116066      -0.08585694       0.03365348       0.05228967      -0.00526449
+Cu      -0.00012883       1.80121639       1.80018865      -0.08489222      -0.00366840       0.06224814      -0.00489394
+Cu       1.78982669      -0.00490872       1.80259319       0.11746446       0.04869625       0.04446378      -0.00464278
+Cu       1.79852053       1.81135891       0.01740117       0.05328471      -0.07868133      -0.15900158      -0.00457777
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.02045229620204303 free_energy=-0.02045229620204303 pbc="T T T"
+Cu       0.01331587       0.00715279      -0.01545400      -0.09836036      -0.01328786       0.08680352      -0.00509484
+Cu      -0.00008384       1.81121336       1.79779914       0.00068210      -0.01608512       0.04158748      -0.00522638
+Cu       1.80765512       0.00108549       1.80504291       0.03263030       0.03155436      -0.01202871      -0.00515197
+Cu       1.80325400       1.80933026       0.01203037       0.06504795      -0.00218138      -0.11636230      -0.00497910
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.018290814060376803 free_energy=-0.018290814060376803 pbc="T T T"
+Cu       0.01749455      -0.00286073      -0.00484565      -0.19061190      -0.01456145       0.04251433      -0.00438217
+Cu      -0.02653319       1.80491715       1.80180369       0.13511600       0.00423319      -0.01469846      -0.00510239
+Cu       1.79963371       0.00315403       1.80921051       0.00818829      -0.05888333      -0.06960037      -0.00441341
+Cu       1.79434397       1.79613760      -0.00475733       0.04730761       0.06921159       0.04178450      -0.00439284
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.014445625580108867 free_energy=-0.014445625580108867 pbc="T T T"
+Cu       0.00472986      -0.00681426       0.00242439       0.08237017       0.05878299      -0.11269540      -0.00449715
+Cu      -0.01700736       1.81253143       1.78965279       0.24383637      -0.08787004       0.14938555      -0.00237017
+Cu       1.80505127      -0.00120228       1.79693018      -0.05672510       0.01724830       0.09417810      -0.00506256
+Cu       1.83371819       1.79902177       0.00472457      -0.26948144       0.01183874      -0.13086824      -0.00251574
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.0176633526467036 free_energy=-0.0176633526467036 pbc="T T T"
+Cu      -0.00712391       0.00753766      -0.00044503       0.06557173      -0.03798336       0.08665333      -0.00473434
+Cu       0.00451812       1.81845102       1.81032338      -0.02074291      -0.03687740      -0.09653905      -0.00501509
+Cu       1.81850188       0.00861211       1.81978686      -0.11099053      -0.04625615      -0.16681003      -0.00395624
+Cu       1.79454623       1.79711011      -0.01261606       0.06616171       0.12111690       0.17669574      -0.00395768
+4
+Lattice="3.61 0.0 0.0 0.0 3.61 0.0 0.0 0.0 3.61" Properties=species:S:1:pos:R:3:forces:R:3:energies:R:1 energy=-0.018288343723298794 free_energy=-0.018288343723298794 pbc="T T T"
+Cu       0.01551339       0.00079186       0.00173977      -0.13521265      -0.09341389      -0.02995679      -0.00426431
+Cu      -0.00072337       1.78495671       1.80644678      -0.01536463       0.16563008      -0.00209572      -0.00447119
+Cu       1.78998831       0.00211109       1.79941795       0.17102355      -0.10330832       0.04999955      -0.00401561
+Cu       1.81584529       1.80313711       0.00014661      -0.02044627       0.03109214      -0.01794704      -0.00553723