diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 927349d..6bf46f0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -63,3 +63,63 @@ jobs: path: | run/ pip-freeze.txt + + lammps-lpc3d-cpu: + # Workflow test of the LAMMPS-LPC3D coupling on a reduced system: + # 2 pore sizes, 10% of the molecules, 100 NPT + 200 NVT steps, 4 MPI ranks. + # The densities are not physically meaningful; the test checks that the + # calls (fftool, packmol, LAMMPS, centre of mass, LPC3D) and the MPI + # workflow run end to end. + name: LAMMPS-LPC3D coupling (CPU, MPI) + runs-on: ubuntu-latest + timeout-minutes: 45 + defaults: + run: + shell: bash -el {0} + + steps: + - uses: actions/checkout@v4 + + - name: Set up conda environment (LAMMPS, mpi4py, packmol) + uses: mamba-org/setup-micromamba@v2 + with: + environment-file: tests/ci/coupling/environment.yml + cache-environment: true + + - name: Check LAMMPS installation + run: | + python -c "from lammps import lammps; l = lammps(cmdargs=['-log', 'none']); print('LAMMPS', l.version(), 'MPI:', l.has_mpi_support); missing = {'MOLECULE', 'KSPACE', 'RIGID'} - set(l.installed_packages); assert not missing, f'missing LAMMPS packages: {missing}'" + micromamba env export > conda-env.yml + + - name: Prepare reduced coupled run + run: bash tests/ci/coupling/prepare.sh run + + - name: Run LAMMPS-LPC3D + working-directory: run + env: + OMP_NUM_THREADS: "1" + run: | + set -o pipefail + mpirun --oversubscribe -np 4 python3 LAMMPS-LPC3D.py -i lattice_gas.inpt 2>&1 | tee log.lpc3d + + - name: Check LAMMPS side of the coupling + run: python3 tests/ci/coupling/check_coupling.py run + + - name: Check LPC3D outputs + run: python3 tests/ci/check_outputs.py run 3 + + - name: Upload outputs and environment + if: always() + uses: actions/upload-artifact@v4 + with: + name: lammps-lpc3d-cpu + path: | + run/log.lpc3d + run/all_densities.dat + run/*.txt + run/*.dat + run/simulation_*/log.lammps + run/simulation_*/packmol.log + run/simulation_*/fftool.log* + run/simulation_*/NVT/log.lammps + conda-env.yml diff --git a/LAMMPS-LPC3D/LAMMPS-LPC3D.py b/LAMMPS-LPC3D/LAMMPS-LPC3D.py index 562a0a0..17f0a6c 100644 --- a/LAMMPS-LPC3D/LAMMPS-LPC3D.py +++ b/LAMMPS-LPC3D/LAMMPS-LPC3D.py @@ -478,7 +478,9 @@ def fourier_transform(ReGtotsmp, ImGtotsmp, Nvalues, dwell, larmorfreq, tau, nsa minvalue = np.min(NMR_spec) NMR_spec -= minvalue - save = np.trapz(NMR_spec, NMR_freq) + # np.trapz was renamed np.trapezoid in NumPy 2.0 and later removed + trapezoid = getattr(np, "trapezoid", None) or np.trapz + save = trapezoid(NMR_spec, NMR_freq) name = f"Normalised_spectrum-{nsample}-bloc-{nb}.dat" with open(name, "w") as outFT: diff --git a/ci-fix.patch b/ci-fix.patch new file mode 100644 index 0000000..421325c --- /dev/null +++ b/ci-fix.patch @@ -0,0 +1,40 @@ +diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml +index 79f7dc3..927349d 100644 +--- a/.github/workflows/ci.yml ++++ b/.github/workflows/ci.yml +@@ -29,7 +29,8 @@ jobs: + - name: Install dependencies + run: | + python -m pip install --upgrade pip +- pip install pystencils numba ipython matplotlib pyevtk ++ # LPC3D uses pystencils.session, removed in pystencils 2.x ++ pip install "pystencils<2" numba ipython matplotlib pyevtk + pip freeze > pip-freeze.txt + + - name: Prepare run directory +@@ -45,7 +46,9 @@ jobs: + env: + OMP_NUM_THREADS: "2" + NUMBA_NUM_THREADS: "2" +- run: python3 ../LPC3D.py -i lattice_gas.inpt | tee log.lpc3d ++ run: | ++ set -o pipefail ++ python3 ../LPC3D.py -i lattice_gas.inpt | tee log.lpc3d + + - name: Check outputs + run: | +diff --git a/LPC3D.py b/LPC3D.py +index ac43f4d..e0cc7ab 100644 +--- a/LPC3D.py ++++ b/LPC3D.py +@@ -492,7 +492,9 @@ def main(): + minvalue = np.min(NMR_spec) + NMR_spec -= minvalue + +- save = np.trapz(NMR_spec, NMR_freq) ++ # np.trapz was renamed np.trapezoid in NumPy 2.0 and later removed ++ trapezoid = getattr(np, "trapezoid", None) or np.trapz ++ save = trapezoid(NMR_spec, NMR_freq) + + name = f"Normalised_spectrum-{nsample}-bloc-{nb}.dat" + with open(name, "w") as outFT: diff --git a/ci-lammps.patch b/ci-lammps.patch new file mode 100644 index 0000000..e734291 --- /dev/null +++ b/ci-lammps.patch @@ -0,0 +1,334 @@ +diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml +index 927349d..6bf46f0 100644 +--- a/.github/workflows/ci.yml ++++ b/.github/workflows/ci.yml +@@ -63,3 +63,63 @@ jobs: + path: | + run/ + pip-freeze.txt ++ ++ lammps-lpc3d-cpu: ++ # Workflow test of the LAMMPS-LPC3D coupling on a reduced system: ++ # 2 pore sizes, 10% of the molecules, 100 NPT + 200 NVT steps, 4 MPI ranks. ++ # The densities are not physically meaningful; the test checks that the ++ # calls (fftool, packmol, LAMMPS, centre of mass, LPC3D) and the MPI ++ # workflow run end to end. ++ name: LAMMPS-LPC3D coupling (CPU, MPI) ++ runs-on: ubuntu-latest ++ timeout-minutes: 45 ++ defaults: ++ run: ++ shell: bash -el {0} ++ ++ steps: ++ - uses: actions/checkout@v4 ++ ++ - name: Set up conda environment (LAMMPS, mpi4py, packmol) ++ uses: mamba-org/setup-micromamba@v2 ++ with: ++ environment-file: tests/ci/coupling/environment.yml ++ cache-environment: true ++ ++ - name: Check LAMMPS installation ++ run: | ++ python -c "from lammps import lammps; l = lammps(cmdargs=['-log', 'none']); print('LAMMPS', l.version(), 'MPI:', l.has_mpi_support); missing = {'MOLECULE', 'KSPACE', 'RIGID'} - set(l.installed_packages); assert not missing, f'missing LAMMPS packages: {missing}'" ++ micromamba env export > conda-env.yml ++ ++ - name: Prepare reduced coupled run ++ run: bash tests/ci/coupling/prepare.sh run ++ ++ - name: Run LAMMPS-LPC3D ++ working-directory: run ++ env: ++ OMP_NUM_THREADS: "1" ++ run: | ++ set -o pipefail ++ mpirun --oversubscribe -np 4 python3 LAMMPS-LPC3D.py -i lattice_gas.inpt 2>&1 | tee log.lpc3d ++ ++ - name: Check LAMMPS side of the coupling ++ run: python3 tests/ci/coupling/check_coupling.py run ++ ++ - name: Check LPC3D outputs ++ run: python3 tests/ci/check_outputs.py run 3 ++ ++ - name: Upload outputs and environment ++ if: always() ++ uses: actions/upload-artifact@v4 ++ with: ++ name: lammps-lpc3d-cpu ++ path: | ++ run/log.lpc3d ++ run/all_densities.dat ++ run/*.txt ++ run/*.dat ++ run/simulation_*/log.lammps ++ run/simulation_*/packmol.log ++ run/simulation_*/fftool.log* ++ run/simulation_*/NVT/log.lammps ++ conda-env.yml +diff --git a/LAMMPS-LPC3D/LAMMPS-LPC3D.py b/LAMMPS-LPC3D/LAMMPS-LPC3D.py +index 562a0a0..17f0a6c 100644 +--- a/LAMMPS-LPC3D/LAMMPS-LPC3D.py ++++ b/LAMMPS-LPC3D/LAMMPS-LPC3D.py +@@ -478,7 +478,9 @@ def main(): + minvalue = np.min(NMR_spec) + NMR_spec -= minvalue + +- save = np.trapz(NMR_spec, NMR_freq) ++ # np.trapz was renamed np.trapezoid in NumPy 2.0 and later removed ++ trapezoid = getattr(np, "trapezoid", None) or np.trapz ++ save = trapezoid(NMR_spec, NMR_freq) + + name = f"Normalised_spectrum-{nsample}-bloc-{nb}.dat" + with open(name, "w") as outFT: +diff --git a/tests/ci/coupling/check_coupling.py b/tests/ci/coupling/check_coupling.py +new file mode 100644 +index 0000000..ef45705 +--- /dev/null ++++ b/tests/ci/coupling/check_coupling.py +@@ -0,0 +1,67 @@ ++"""Check the LAMMPS side of a reduced LAMMPS-LPC3D run. ++ ++For every pore size in psd.txt, checks that the LAMMPS simulations ran ++(NPT and NVT logs completed, centre-of-mass file written), and that the ++densities passed back to LPC3D (all_densities.dat) are finite, non-negative ++and not all zero. ++ ++Usage: python3 check_coupling.py ++""" ++import sys ++from pathlib import Path ++ ++import numpy as np ++ ++ ++def main(): ++ run_dir = Path(sys.argv[1]) ++ errors = [] ++ ++ pore_sizes = np.unique(np.loadtxt(run_dir / "psd.txt", usecols=0, ndmin=1)) ++ ++ for p in pore_sizes: ++ sim = run_dir / f"simulation_{p:g}" ++ if not sim.is_dir(): ++ # the folder name follows Python's str() of the pore size ++ sim = run_dir / f"simulation_{float(p)}" ++ if not sim.is_dir(): ++ errors.append(f"missing simulation folder for pore size {p:g}") ++ continue ++ for log in (sim / "log.lammps", sim / "NVT" / "log.lammps"): ++ if not log.is_file() or "Total wall time" not in log.read_text(): ++ errors.append(f"LAMMPS run did not complete: {log.relative_to(run_dir)}") ++ cm = sim / "NVT" / "CM_positions.xyz" ++ if not cm.is_file() or cm.stat().st_size == 0: ++ errors.append(f"missing or empty: {cm.relative_to(run_dir)}") ++ ++ dens_file = run_dir / "all_densities.dat" ++ if not dens_file.is_file(): ++ errors.append("missing: all_densities.dat") ++ else: ++ dens = np.loadtxt(dens_file, ndmin=2) ++ if dens.shape[0] != len(pore_sizes): ++ errors.append( ++ f"all_densities.dat has {dens.shape[0]} rows, expected {len(pore_sizes)}" ++ ) ++ values = dens[:, 1:] ++ if not np.all(np.isfinite(values)): ++ errors.append("NaN or Inf in all_densities.dat") ++ elif np.any(values < 0): ++ errors.append("negative density in all_densities.dat") ++ elif not np.any(values > 0): ++ errors.append("all densities are zero in all_densities.dat") ++ ++ log = run_dir / "log.lpc3d" ++ if log.is_file() and "still not equilibrated" in log.read_text(): ++ errors.append("LPC3D reported that the system is not equilibrated") ++ ++ if errors: ++ print("Coupling check FAILED:") ++ for e in errors: ++ print(" -", e) ++ sys.exit(1) ++ print(f"Coupling check passed for {len(pore_sizes)} pore size(s) in {run_dir}") ++ ++ ++if __name__ == "__main__": ++ main() +diff --git a/tests/ci/coupling/environment.yml b/tests/ci/coupling/environment.yml +new file mode 100644 +index 0000000..1e2a094 +--- /dev/null ++++ b/tests/ci/coupling/environment.yml +@@ -0,0 +1,21 @@ ++# Environment for the LAMMPS-LPC3D CI test (CPU only). ++# LAMMPS, mpi4py and packmol come from conda-forge so that LAMMPS and mpi4py ++# are built against the same MPI library (OpenMPI). ++name: lpc3d-lammps ++channels: ++ - conda-forge ++dependencies: ++ - python=3.12 ++ - lammps=2025.07.22=*openmpi* ++ - openmpi ++ - mpi4py ++ - packmol ++ - numpy ++ - pip ++ - pip: ++ # LPC3D uses pystencils.session, removed in pystencils 2.x ++ - pystencils<2 ++ - numba ++ - ipython ++ - matplotlib ++ - pyevtk +diff --git a/tests/ci/coupling/lattice_gas.inpt b/tests/ci/coupling/lattice_gas.inpt +new file mode 100644 +index 0000000..2e8a465 +--- /dev/null ++++ b/tests/ci/coupling/lattice_gas.inpt +@@ -0,0 +1,43 @@ ++cpu ++10 10 30 ++true true true ++1.0 ++5e-6 ++1 ++298 ++282 ++100 ++0.0 ++0 ++porouscarbon ++psd.txt ++3 ++ ++electrode ++1 ++1 10 ++1 10 ++1 10 ++pore_freq_neg.txt ++ ++bulk ++1 10 ++1 10 ++11 20 ++0.05 ++0.0 ++ ++electrode ++1 ++1 10 ++1 10 ++21 30 ++pore_freq_pos.txt ++ ++H2O.zmat 1000 ++H2O.zmat 1000 ++H2O.zmat 3000 ++1 ++npt_in.lmp ++nvt_in.lmp ++ +diff --git a/tests/ci/coupling/pore_freq_neg.txt b/tests/ci/coupling/pore_freq_neg.txt +new file mode 100644 +index 0000000..dd39885 +--- /dev/null ++++ b/tests/ci/coupling/pore_freq_neg.txt +@@ -0,0 +1,2 @@ ++20.0 0.0 0.0 0.0 ++26.0 0.0 0.0 0.0 +diff --git a/tests/ci/coupling/pore_freq_pos.txt b/tests/ci/coupling/pore_freq_pos.txt +new file mode 100644 +index 0000000..dd39885 +--- /dev/null ++++ b/tests/ci/coupling/pore_freq_pos.txt +@@ -0,0 +1,2 @@ ++20.0 0.0 0.0 0.0 ++26.0 0.0 0.0 0.0 +diff --git a/tests/ci/coupling/prepare.sh b/tests/ci/coupling/prepare.sh +new file mode 100644 +index 0000000..a0de3ec +--- /dev/null ++++ b/tests/ci/coupling/prepare.sh +@@ -0,0 +1,41 @@ ++#!/usr/bin/env bash ++# Prepare a reduced LAMMPS-LPC3D run for CI. ++# Usage: tests/ci/coupling/prepare.sh ++# ++# The code and molecular files are taken from LAMMPS-LPC3D/ so the test always ++# follows the real workflow. Only the size of the problem is reduced: ++# - 2 pore sizes (psd.txt), so 2 LAMMPS simulations ++# - 5000 water molecules instead of 50000 (lattice_gas.inpt, sites2cm.inpt) ++# - 100 NPT steps and 200 NVT steps instead of 10000 and 100000 ++# - 10x10x30 lattice, no equilibration ++set -euo pipefail ++ ++REPO="$(cd "$(dirname "$0")/../../.." && pwd)" ++SRC="$REPO/LAMMPS-LPC3D" ++CI="$REPO/tests/ci/coupling" ++RUN="$1" ++ ++mkdir -p "$RUN" ++ ++for f in LAMMPS-LPC3D.py mpi4py_lammps.py fftool il.ff H2O.zmat CG1.xyz CG2.xyz \ ++ npt_in.lmp nvt_in.lmp; do ++ cp "$SRC/$f" "$RUN/" ++done ++for f in lattice_gas.inpt psd.txt pore_freq_neg.txt pore_freq_pos.txt sites2cm.inpt; do ++ cp "$CI/$f" "$RUN/" ++done ++ ++# The workflow calls ./packmol in each simulation folder ++cp "$(command -v packmol)" "$RUN/packmol" ++chmod +x "$RUN/fftool" "$RUN/packmol" ++ ++# Shorten the MD runs, and fail loudly if the scripts change ++shorten() { ++ local file="$1" old="$2" new="$3" ++ grep -q "^run $old\$" "$RUN/$file" || { echo "Expected 'run $old' in $file" >&2; exit 1; } ++ sed -i "s/^run $old\$/run $new/" "$RUN/$file" ++} ++shorten npt_in.lmp 10000 100 ++shorten nvt_in.lmp 100000 200 ++ ++echo "Reduced coupled test prepared in $RUN" +diff --git a/tests/ci/coupling/psd.txt b/tests/ci/coupling/psd.txt +new file mode 100644 +index 0000000..a587a82 +--- /dev/null ++++ b/tests/ci/coupling/psd.txt +@@ -0,0 +1,2 @@ ++20.0 0.5 ++26.0 0.5 +diff --git a/tests/ci/coupling/sites2cm.inpt b/tests/ci/coupling/sites2cm.inpt +new file mode 100644 +index 0000000..6b65813 +--- /dev/null ++++ b/tests/ci/coupling/sites2cm.inpt +@@ -0,0 +1,25 @@ ++2 ++2 ++5 ++3 ++3 ++1000 ++12.01 ++1.01 ++1.01 ++3 ++1000 ++12.01 ++1.01 ++1.01 ++3 ++3000 ++12.01 ++1.01 ++1.01 ++1 ++776 ++12.01 ++1 ++776 ++12.01 diff --git a/examples/mathieu/Density_Energy_out_00000001.vti b/examples/mathieu/Density_Energy_out_00000001.vti new file mode 100644 index 0000000..c8d37c6 Binary files /dev/null and b/examples/mathieu/Density_Energy_out_00000001.vti differ diff --git a/examples/mathieu/Density_Energy_out_00000002.vti b/examples/mathieu/Density_Energy_out_00000002.vti new file mode 100644 index 0000000..3f246cf Binary files /dev/null and b/examples/mathieu/Density_Energy_out_00000002.vti differ diff --git a/examples/mathieu/Diffusion_coeff_x_1.txt b/examples/mathieu/Diffusion_coeff_x_1.txt new file mode 100644 index 0000000..fa78164 --- /dev/null +++ b/examples/mathieu/Diffusion_coeff_x_1.txt @@ -0,0 +1,46 @@ +2.757337695312500000e+04 2.703098828125000000e+04 2.856964453125000000e+04 2.711946093750000000e+04 +2.760213476562500000e+04 2.655249804687500000e+04 2.723667773437500000e+04 2.901706445312500000e+04 +2.653138476562500000e+04 2.686302343750000000e+04 2.745084960937500000e+04 2.528028515625000000e+04 +2.916399218750000000e+04 2.821592968750000000e+04 2.918313476562500000e+04 3.009300195312500000e+04 +2.822171289062500000e+04 2.760741406250000000e+04 2.753368554687500000e+04 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+2.948162187500000000e+05 +2.940599375000000000e+05 +2.933060937500000000e+05 +2.925548125000000000e+05 +2.918059687500000000e+05 +2.910595625000000000e+05 +2.903155937500000000e+05 diff --git a/lpc3d-ci.zip b/lpc3d-ci.zip new file mode 100644 index 0000000..7337c4b Binary files /dev/null and b/lpc3d-ci.zip differ diff --git a/tests/ci/coupling/check_coupling.py b/tests/ci/coupling/check_coupling.py new file mode 100644 index 0000000..ef45705 --- /dev/null +++ b/tests/ci/coupling/check_coupling.py @@ -0,0 +1,67 @@ +"""Check the LAMMPS side of a reduced LAMMPS-LPC3D run. + +For every pore size in psd.txt, checks that the LAMMPS simulations ran +(NPT and NVT logs completed, centre-of-mass file written), and that the +densities passed back to LPC3D (all_densities.dat) are finite, non-negative +and not all zero. + +Usage: python3 check_coupling.py +""" +import sys +from pathlib import Path + +import numpy as np + + +def main(): + run_dir = Path(sys.argv[1]) + errors = [] + + pore_sizes = np.unique(np.loadtxt(run_dir / "psd.txt", usecols=0, ndmin=1)) + + for p in pore_sizes: + sim = run_dir / f"simulation_{p:g}" + if not sim.is_dir(): + # the folder name follows Python's str() of the pore size + sim = run_dir / f"simulation_{float(p)}" + if not sim.is_dir(): + errors.append(f"missing simulation folder for pore size {p:g}") + continue + for log in (sim / "log.lammps", sim / "NVT" / "log.lammps"): + if not log.is_file() or "Total wall time" not in log.read_text(): + errors.append(f"LAMMPS run did not complete: {log.relative_to(run_dir)}") + cm = sim / "NVT" / "CM_positions.xyz" + if not cm.is_file() or cm.stat().st_size == 0: + errors.append(f"missing or empty: {cm.relative_to(run_dir)}") + + dens_file = run_dir / "all_densities.dat" + if not dens_file.is_file(): + errors.append("missing: all_densities.dat") + else: + dens = np.loadtxt(dens_file, ndmin=2) + if dens.shape[0] != len(pore_sizes): + errors.append( + f"all_densities.dat has {dens.shape[0]} rows, expected {len(pore_sizes)}" + ) + values = dens[:, 1:] + if not np.all(np.isfinite(values)): + errors.append("NaN or Inf in all_densities.dat") + elif np.any(values < 0): + errors.append("negative density in all_densities.dat") + elif not np.any(values > 0): + errors.append("all densities are zero in all_densities.dat") + + log = run_dir / "log.lpc3d" + if log.is_file() and "still not equilibrated" in log.read_text(): + errors.append("LPC3D reported that the system is not equilibrated") + + if errors: + print("Coupling check FAILED:") + for e in errors: + print(" -", e) + sys.exit(1) + print(f"Coupling check passed for {len(pore_sizes)} pore size(s) in {run_dir}") + + +if __name__ == "__main__": + main() diff --git a/tests/ci/coupling/environment.yml b/tests/ci/coupling/environment.yml new file mode 100644 index 0000000..1e2a094 --- /dev/null +++ b/tests/ci/coupling/environment.yml @@ -0,0 +1,21 @@ +# Environment for the LAMMPS-LPC3D CI test (CPU only). +# LAMMPS, mpi4py and packmol come from conda-forge so that LAMMPS and mpi4py +# are built against the same MPI library (OpenMPI). +name: lpc3d-lammps +channels: + - conda-forge +dependencies: + - python=3.12 + - lammps=2025.07.22=*openmpi* + - openmpi + - mpi4py + - packmol + - numpy + - pip + - pip: + # LPC3D uses pystencils.session, removed in pystencils 2.x + - pystencils<2 + - numba + - ipython + - matplotlib + - pyevtk diff --git a/tests/ci/coupling/lattice_gas.inpt b/tests/ci/coupling/lattice_gas.inpt new file mode 100644 index 0000000..2e8a465 --- /dev/null +++ b/tests/ci/coupling/lattice_gas.inpt @@ -0,0 +1,43 @@ +cpu +10 10 30 +true true true +1.0 +5e-6 +1 +298 +282 +100 +0.0 +0 +porouscarbon +psd.txt +3 + +electrode +1 +1 10 +1 10 +1 10 +pore_freq_neg.txt + +bulk +1 10 +1 10 +11 20 +0.05 +0.0 + +electrode +1 +1 10 +1 10 +21 30 +pore_freq_pos.txt + +H2O.zmat 1000 +H2O.zmat 1000 +H2O.zmat 3000 +1 +npt_in.lmp +nvt_in.lmp + diff --git a/tests/ci/coupling/pore_freq_neg.txt b/tests/ci/coupling/pore_freq_neg.txt new file mode 100644 index 0000000..dd39885 --- /dev/null +++ b/tests/ci/coupling/pore_freq_neg.txt @@ -0,0 +1,2 @@ +20.0 0.0 0.0 0.0 +26.0 0.0 0.0 0.0 diff --git a/tests/ci/coupling/pore_freq_pos.txt b/tests/ci/coupling/pore_freq_pos.txt new file mode 100644 index 0000000..dd39885 --- /dev/null +++ b/tests/ci/coupling/pore_freq_pos.txt @@ -0,0 +1,2 @@ +20.0 0.0 0.0 0.0 +26.0 0.0 0.0 0.0 diff --git a/tests/ci/coupling/prepare.sh b/tests/ci/coupling/prepare.sh new file mode 100644 index 0000000..a0de3ec --- /dev/null +++ b/tests/ci/coupling/prepare.sh @@ -0,0 +1,41 @@ +#!/usr/bin/env bash +# Prepare a reduced LAMMPS-LPC3D run for CI. +# Usage: tests/ci/coupling/prepare.sh +# +# The code and molecular files are taken from LAMMPS-LPC3D/ so the test always +# follows the real workflow. Only the size of the problem is reduced: +# - 2 pore sizes (psd.txt), so 2 LAMMPS simulations +# - 5000 water molecules instead of 50000 (lattice_gas.inpt, sites2cm.inpt) +# - 100 NPT steps and 200 NVT steps instead of 10000 and 100000 +# - 10x10x30 lattice, no equilibration +set -euo pipefail + +REPO="$(cd "$(dirname "$0")/../../.." && pwd)" +SRC="$REPO/LAMMPS-LPC3D" +CI="$REPO/tests/ci/coupling" +RUN="$1" + +mkdir -p "$RUN" + +for f in LAMMPS-LPC3D.py mpi4py_lammps.py fftool il.ff H2O.zmat CG1.xyz CG2.xyz \ + npt_in.lmp nvt_in.lmp; do + cp "$SRC/$f" "$RUN/" +done +for f in lattice_gas.inpt psd.txt pore_freq_neg.txt pore_freq_pos.txt sites2cm.inpt; do + cp "$CI/$f" "$RUN/" +done + +# The workflow calls ./packmol in each simulation folder +cp "$(command -v packmol)" "$RUN/packmol" +chmod +x "$RUN/fftool" "$RUN/packmol" + +# Shorten the MD runs, and fail loudly if the scripts change +shorten() { + local file="$1" old="$2" new="$3" + grep -q "^run $old\$" "$RUN/$file" || { echo "Expected 'run $old' in $file" >&2; exit 1; } + sed -i "s/^run $old\$/run $new/" "$RUN/$file" +} +shorten npt_in.lmp 10000 100 +shorten nvt_in.lmp 100000 200 + +echo "Reduced coupled test prepared in $RUN" diff --git a/tests/ci/coupling/psd.txt b/tests/ci/coupling/psd.txt new file mode 100644 index 0000000..a587a82 --- /dev/null +++ b/tests/ci/coupling/psd.txt @@ -0,0 +1,2 @@ +20.0 0.5 +26.0 0.5 diff --git a/tests/ci/coupling/sites2cm.inpt b/tests/ci/coupling/sites2cm.inpt new file mode 100644 index 0000000..6b65813 --- /dev/null +++ b/tests/ci/coupling/sites2cm.inpt @@ -0,0 +1,25 @@ +2 +2 +5 +3 +3 +1000 +12.01 +1.01 +1.01 +3 +1000 +12.01 +1.01 +1.01 +3 +3000 +12.01 +1.01 +1.01 +1 +776 +12.01 +1 +776 +12.01