Add CI for LPC3D

.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+name: LPC3D CI
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lpc3d-cpu:
+    name: LPC3D (CPU) - ${{ matrix.case }} - Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"]
+        case:
+          - bulk
+          - supercapacitor
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # LPC3D uses pystencils.session, removed in pystencils 2.x
+          pip install "pystencils<2" numba ipython matplotlib pyevtk
+          pip freeze > pip-freeze.txt
+
+      - name: Prepare run directory
+        run: |
+          mkdir -p run
+          cp tests/ci/${{ matrix.case }}/lattice_gas.inpt run/
+          if [ "${{ matrix.case }}" = "supercapacitor" ]; then
+            cp examples/short-test/psd.txt examples/short-test/pore_dens_freq_2neg.txt run/
+          fi
+
+      - name: Run LPC3D
+        working-directory: run
+        env:
+          OMP_NUM_THREADS: "2"
+          NUMBA_NUM_THREADS: "2"
+        run: |
+          set -o pipefail
+          python3 ../LPC3D.py -i lattice_gas.inpt | tee log.lpc3d
+
+      - name: Check outputs
+        run: |
+          if [ "${{ matrix.case }}" = "supercapacitor" ]; then NB=3; else NB=1; fi
+          python3 tests/ci/check_outputs.py run $NB
+
+      - name: Upload outputs and environment
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: lpc3d-${{ matrix.case }}-py${{ matrix.python-version }}
+          path: |
+            run/
+            pip-freeze.txt

LPC3D.py

@@ -492,7 +492,9 @@ 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:

README.md

@@ -10,6 +10,10 @@ Here, a manual and example input files are provided.
 
 Compared to the previous version of the program, written in C and serial (https://github.com/cmerlet/LPC3D-C-serial), this code is written using pystencils (https://pypi.org/project/pystencils/), is parallel and can use CPU and GPU.
 
+## Continuous integration
+
+![CI](https://github.com/multixscale/LPC3D/actions/workflows/ci.yml/badge.svg)
+
 ## Multiscale coupling with LAMMPS
 
 The `LAMMPS-LPC3D/` folder contains a coupled version of the code, in which LPC3D drives an ensemble of independent LAMMPS simulations, one for each pore size. The pore-resolved densities obtained from molecular dynamics are transferred on the fly to the lattice gas model. The coupling is implemented in Python with mpi4py and the LAMMPS Python interface, and can be run on CPU or GPU (LAMMPS with Kokkos). Examples for both modes are provided in `LAMMPS-LPC3D/Examples/`, and the installation, input format and usage are described in the manual.

tests/ci/bulk/lattice_gas.inpt

@@ -0,0 +1,21 @@
+cpu
+10 10 10
+true true true
+1.0
+5e-6
+1
+298
+282
+100
+0.0
+0
+bulk
+1
+
+bulk
+1 10
+1 10
+1 10
+0.296297
+0.000
+

tests/ci/check_outputs.py

@@ -0,0 +1,48 @@
+"""Check that an LPC3D run produced the expected, valid output files.
+
+Usage: python3 check_outputs.py <run_directory> <number_of_blocks>
+"""
+import sys
+from pathlib import Path
+
+import numpy as np
+
+
+def main():
+    run_dir = Path(sys.argv[1])
+    nblocks = int(sys.argv[2])
+    errors = []
+
+    for b in range(1, nblocks + 1):
+        expected = [
+            f"density_{b}.txt",
+            f"vacf_{b}.txt",
+            f"Diffusion_coeff_x_{b}.txt",
+            f"Diffusion_coeff_y_{b}.txt",
+            f"Diffusion_coeff_z_{b}.txt",
+            f"FT_signal-1-bloc-{b}.dat",
+            f"Normalised_spectrum-1-bloc-{b}.dat",
+        ]
+        for name in expected:
+            path = run_dir / name
+            if not path.is_file() or path.stat().st_size == 0:
+                errors.append(f"missing or empty: {name}")
+                continue
+            try:
+                data = np.loadtxt(path, ndmin=1)
+            except ValueError as exc:
+                errors.append(f"unreadable: {name} ({exc})")
+                continue
+            if not np.all(np.isfinite(data)):
+                errors.append(f"NaN or Inf values in: {name}")
+
+    if errors:
+        print("Output check FAILED:")
+        for e in errors:
+            print("  -", e)
+        sys.exit(1)
+    print(f"Output check passed for {nblocks} block(s) in {run_dir}")
+
+
+if __name__ == "__main__":
+    main()

tests/ci/supercapacitor/lattice_gas.inpt

@@ -0,0 +1,37 @@
+cpu
+10 10 30
+true true false
+1.0
+5e-6
+1
+298
+282
+100
+0.0
+0
+porous_carbon
+3
+
+electrode
+1
+1 10
+1 10
+1 10
+psd.txt
+pore_dens_freq_2neg.txt
+
+bulk
+1 10
+1 10
+11 20
+0.296297
+0.000
+
+electrode
+1
+1 10
+1 10
+21 30
+psd.txt
+pore_dens_freq_2neg.txt
+