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Merged
Fraser-Birks merged 6 commits into from
Mar 25, 2026
Merged

Merge main into devel #13

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99603ab
Bump requests from 2.32.3 to 2.32.4
dependabot[bot] Jun 10, 2025
e39f4d4
Merge pull request #10 from kermodegroup/dependabot/pip/requests-2.32.4
Fraser-Birks Jun 11, 2025
59055e8
Update requirements.txt
Fraser-Birks Jun 12, 2025
cc08567
made dump deterministic
Fraser-Birks Mar 24, 2026
fa0135c
sort arrays properly
Fraser-Birks Mar 24, 2026
49168c7
update ci
Fraser-Birks Mar 25, 2026
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319 changes: 176 additions & 143 deletions .github/workflows/ci.yml
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Expand Up @@ -5,152 +5,185 @@ on: [push, pull_request]
jobs:
build-python-lammps:
runs-on: ubuntu-latest

steps:
- name: Checkout code
uses: actions/checkout@v4

- name: Install dependencies
run: |
sudo apt-get install -y build-essential cmake git libfftw3-dev libopenmpi-dev mpi-default-bin mpi-default-dev

- name: Get LAMMPS stable branch commit hash
run: |
LAMMPS_VERSION=$(git ls-remote https://github.com/lammps/lammps.git refs/heads/stable | awk '{print $1}')
echo "LAMMPS_VERSION=$LAMMPS_VERSION" >> $GITHUB_ENV

- name: Set up python
uses: actions/setup-python@v5
with:
python-version: '3.10'

- name: Cache LAMMPS
id: lammps-cache
uses: actions/cache@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-${{ env.LAMMPS_VERSION }}-new_venv

- name: Restore cached virtual environment
id: venv-cache
uses: actions/cache@v4
with:
path: venv
key: venv-${{ runner.os }}-${{ hashFiles('requirements.txt') }}
restore-keys: venv-${{ runner.os }}-

- name: Create python venv (if venv cache misses)
if: ${{ steps.venv-cache.outputs.cache-hit != 'true' }}
run: |
python -m venv test_venv
source test_venv/bin/activate
pip install -r requirements.txt
deactivate


- name: Clone and build LAMMPS (if lammps cache misses)
if: ${{ steps.lammps-cache.outputs.cache-hit != 'true' }}
run: |
source test_venv/bin/activate
git clone -b stable https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build
wget -O libpace.tar.gz https://github.com/wcwitt/lammps-user-pace/archive/main.tar.gz
cmake ../cmake -D PKG_PLUGIN=on\
-D BUILD_SHARED_LIBS=on\
-D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \
-D PKG_ML-PACE=yes \
-D PACELIB_MD5=$(md5sum libpace.tar.gz | awk '{print $1}') \
-D PKG_ML-UF3=yes \
-D PKG_EXTRA-PAIR=yes \
-D PKG_MOLECULE=yes \
-D PKG_MANYBODY=yes \
../cmake

cmake --build . -j 20

cmake --install .

make install-python

cd ../..

- name: add LAMMPS to venv (if lammps cache hits, but venv misses)
if: ${{ steps.lammps-cache.outputs.cache-hit == 'true' && steps.venv-cache.outputs.cache-hit != 'true' }}
run: |
source test_venv/bin/activate
cd lammps/build
make install-python
cd ../..

- name: Update LAMMPS cache after build (if cache miss)
if: ${{ steps.lammps-cache.outputs.cache-hit != 'true' }}
uses: actions/cache@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-${{ env.LAMMPS_VERSION }}-new_venv

- name: Upload venv cache after build (if cache miss or venv rebuilt)
if: ${{ steps.venv-cache.outputs.cache-hit != 'true' }}
uses: actions/cache@v4
with:
path: test_venv
key: venv-${{ runner.os }}-${{ hashFiles('requirements.txt') }}


# - name: Upload LAMMPS as an artifact for other tests
# uses: actions/upload-artifact@v4
# with:
# name: lammps
# path: lammps
- name: Checkout code
uses: actions/checkout@v4

- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y \
build-essential cmake git wget \
libfftw3-dev libopenmpi-dev mpi-default-bin mpi-default-dev

- name: Get LAMMPS stable branch commit hash
run: |
LAMMPS_VERSION=$(git ls-remote https://github.com/lammps/lammps.git refs/heads/stable | awk '{print $1}')
echo "LAMMPS_VERSION=$LAMMPS_VERSION" >> "$GITHUB_ENV"

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.10"

- name: Restore venv cache
id: venv-cache
uses: actions/cache/restore@v4
with:
path: test_venv
key: ${{ runner.os }}-py310-venv-${{ hashFiles('requirements.txt') }}

- name: Create venv
if: steps.venv-cache.outputs.cache-hit != 'true'
run: |
python -m venv test_venv
source test_venv/bin/activate
python -m pip install --upgrade pip
pip install -r requirements.txt

- name: Restore LAMMPS source/build cache
id: lammps-src-cache
uses: actions/cache/restore@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-src-${{ env.LAMMPS_VERSION }}

- name: Restore LAMMPS install cache
id: lammps-install-cache
uses: actions/cache/restore@v4
with:
path: .cache/lammps-install
key: ${{ runner.os }}-lammps-install-${{ env.LAMMPS_VERSION }}

- name: Clone LAMMPS
if: steps.lammps-src-cache.outputs.cache-hit != 'true'
run: |
git clone -b stable https://github.com/lammps/lammps.git

- name: Build and install LAMMPS
if: steps.lammps-install-cache.outputs.cache-hit != 'true'
run: |
source test_venv/bin/activate
mkdir -p .cache/lammps-install
cd lammps
mkdir -p build
cd build

wget -O libpace.tar.gz https://github.com/wcwitt/lammps-user-pace/archive/main.tar.gz

cmake ../cmake \
-D PKG_PLUGIN=on \
-D BUILD_SHARED_LIBS=on \
-D CMAKE_INSTALL_PREFIX="$GITHUB_WORKSPACE/.cache/lammps-install" \
-D PKG_ML-PACE=yes \
-D PACELIB_MD5=$(md5sum libpace.tar.gz | awk '{print $1}') \
-D PKG_ML-UF3=yes \
-D PKG_EXTRA-PAIR=yes \
-D PKG_MOLECULE=yes \
-D PKG_MANYBODY=yes

cmake --build . -j"$(nproc)"
cmake --install .

# install Python wrapper into the venv
make install-python

- name: Reinstall Python wrapper into venv from cached LAMMPS build
if: steps.lammps-install-cache.outputs.cache-hit == 'true'
run: |
source test_venv/bin/activate
cd lammps/build
make install-python

- name: Expose cached LAMMPS install to runtime
run: |
echo "$GITHUB_WORKSPACE/.cache/lammps-install/bin" >> "$GITHUB_PATH"
echo "LD_LIBRARY_PATH=$GITHUB_WORKSPACE/.cache/lammps-install/lib:${LD_LIBRARY_PATH}" >> "$GITHUB_ENV"

- name: Save venv cache
if: steps.venv-cache.outputs.cache-hit != 'true'
uses: actions/cache/save@v4
with:
path: test_venv
key: ${{ runner.os }}-py310-venv-${{ hashFiles('requirements.txt') }}

- name: Save LAMMPS source/build cache
if: steps.lammps-src-cache.outputs.cache-hit != 'true'
uses: actions/cache/save@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-src-${{ env.LAMMPS_VERSION }}

- name: Save LAMMPS install cache
if: steps.lammps-install-cache.outputs.cache-hit != 'true'
uses: actions/cache/save@v4
with:
path: .cache/lammps-install
key: ${{ runner.os }}-lammps-install-${{ env.LAMMPS_VERSION }}

run-tests:
runs-on: ubuntu-latest
needs: build-python-lammps
needs: build-python-lammps

steps:
- name: Checkout code
uses: actions/checkout@v4

- name: Install dependencies
run: |
sudo apt-get install -y build-essential cmake git libfftw3-dev libopenmpi-dev mpi-default-bin mpi-default-dev

- name: Get LAMMPS stable branch commit hash
run: |
LAMMPS_VERSION=$(git ls-remote https://github.com/lammps/lammps.git refs/heads/stable | awk '{print $1}')
echo "LAMMPS_VERSION=$LAMMPS_VERSION" >> $GITHUB_ENV

- name: Download LAMMPS cache
uses: actions/cache@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-${{ env.LAMMPS_VERSION }}-new_venv


- name: Build Plugin
run: |
cd lammps/src
LAMMPS_SRC_DIR=$(pwd)
cd ../../LAMMPS_plugin
mkdir build
cd build
cmake ../cmake \
-D LAMMPS_SOURCE_DIR=$LAMMPS_SRC_DIR \
-D BUILD_SHARED_LIBS=on

cmake --build . -j 1

- name: Restore cached virtual environment
uses: actions/cache@v4
with:
path: test_venv
key: venv-${{ runner.os }}-${{ hashFiles('requirements.txt') }}
restore-keys: venv-${{ runner.os }}-

- name: Activate virtual environment and run tests
run: |
source test_venv/bin/activate
cd tests/
pip install pytest
python -m pytest -s -v
- name: Checkout code
uses: actions/checkout@v4

- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y \
build-essential cmake git wget \
libfftw3-dev libopenmpi-dev mpi-default-bin mpi-default-dev

- name: Get LAMMPS stable branch commit hash
run: |
LAMMPS_VERSION=$(git ls-remote https://github.com/lammps/lammps.git refs/heads/stable | awk '{print $1}')
echo "LAMMPS_VERSION=$LAMMPS_VERSION" >> "$GITHUB_ENV"

- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.10"

- name: Restore venv cache
uses: actions/cache/restore@v4
with:
path: test_venv
key: ${{ runner.os }}-py310-venv-${{ hashFiles('requirements.txt') }}

- name: Restore LAMMPS source/build cache
uses: actions/cache/restore@v4
with:
path: lammps
key: ${{ runner.os }}-lammps-src-${{ env.LAMMPS_VERSION }}

- name: Restore LAMMPS install cache
uses: actions/cache/restore@v4
with:
path: .cache/lammps-install
key: ${{ runner.os }}-lammps-install-${{ env.LAMMPS_VERSION }}

- name: Expose cached LAMMPS install to runtime
run: |
echo "$GITHUB_WORKSPACE/.cache/lammps-install/bin" >> "$GITHUB_PATH"
echo "LD_LIBRARY_PATH=$GITHUB_WORKSPACE/.cache/lammps-install/lib:${LD_LIBRARY_PATH}" >> "$GITHUB_ENV"

- name: Build plugin
run: |
cd lammps/src
LAMMPS_SRC_DIR=$(pwd)
cd ../../LAMMPS_plugin
mkdir -p build
cd build
cmake ../cmake \
-D LAMMPS_SOURCE_DIR="$LAMMPS_SRC_DIR" \
-D BUILD_SHARED_LIBS=on
cmake --build . -j1

- name: Run tests
run: |
source test_venv/bin/activate
cd tests
python -m pytest -s -v
2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -59,4 +59,4 @@ tqdm==4.67.1
typing_extensions==4.12.2
tzdata==2025.1
uncertainties==3.2.2
urllib3==2.3.0
urllib3==2.3.0
1 change: 1 addition & 0 deletions tests/shared/build_regions.py
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Expand Up @@ -45,6 +45,7 @@ def build_regions_lammps(lmps,
seed_atoms = get_seed_atoms(struct)
# set up dump
lmps.command(f'dump dump1 all custom 1 {path}/dump.lammpstrj id type x y z fx fy fz {dump_string}')
lmps.command('dump_modify dump1 sort id')
lmps.command(f'dump_modify dump1 format float %20.15g')
lmps.command(f'group seed_atoms id {" ".join([str(i+1) for i in seed_atoms])}')
command = f'fix mlml_fix all mlml {nevery} {r_core} {r_buff} {r_blend}'
Expand Down
7 changes: 5 additions & 2 deletions tests/test_hysteresis_lammps.py
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Expand Up @@ -106,6 +106,7 @@ def hysteresis_test(verbose=False,
if pick_seed_with == 'group':
lmps.command('delete_atoms group seed_atoms compress no')
seed_atoms = get_seed_atoms(struct)
print(seed_atoms)
d2_eval_lammps = np.delete(d2_eval_lammps, seed_atoms, axis=0)


Expand All @@ -124,6 +125,7 @@ def hysteresis_test(verbose=False,


lmps.command(f'dump decaydump all custom 1 {data_path}/dump_{pick_seed_with}.lammpstrj id type x y z fx fy fz i2_potential[1] i2_potential[2] d2_eval[1] d2_eval[2]')
lmps.command('dump_modify decaydump sort id')
lmps.command('run 20')

if rank == 0:
Expand All @@ -133,15 +135,16 @@ def hysteresis_test(verbose=False,
# first check the initial step matches
if pick_seed_with == 'group':
d2_eval_prev = d2_eval_lammps[:,0]
print(d2_eval_prev)
d2_eval_target = np.zeros_like(d2_eval_prev)
d2_eval_predicted = predict_d2_eval(d2_eval_prev, d2_eval_target, nevery, dt, hysteresis_time_in, hysteresis_time_out)
print(d2_eval_predicted)
next_d2_eval = dump[0].arrays['d2_eval[1]']
print(next_d2_eval)
assert np.allclose(d2_eval_predicted, next_d2_eval), f"Prediction failed at step 0"
elif pick_seed_with == 'fix':
assert np.allclose(dump[0].arrays['d2_eval[1]'], np.ones_like(d2_eval_lammps[:,0])), f"Prediction failed at step 0"



for i in range(len(dump)-1):
if pick_seed_with != 'group':
if i < fix_nevery:
Expand Down
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