Merge pull request #348 from libAtoms/err_calc_stress_virial_voigt

Convert virial/stress to Voigt-6 when computing error table

.github/workflows/pytests.yml

@@ -14,10 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.10" ]
       max-parallel: 5
     env:
-      coverage-on-version: "3.9"
+      coverage-on-version: "3.10"
       use-mpi: True
       PIP_CONSTRAINT: pip_constraint.txt
     defaults:
@@ -42,13 +42,15 @@ jobs:
         run: |
           echo "numpy<2" >> $PIP_CONSTRAINT
           python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit==2024.3.3 flake8 pytest pytest-cov requests
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install latest ASE from pypi
         run: |
           echo PIP_CONSTRAINT $PIP_CONSTRAINT
           python3 -m pip install ase
           echo -n "ASE VERSION "
           python3 -c "import ase; print(ase.__file__, ase.__version__)"
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install intel-oneapi-mkl for phono3py
         run: |
@@ -61,6 +63,7 @@ jobs:
           sudo apt update
           sudo apt install intel-oneapi-mkl
           sudo apt install intel-oneapi-mkl-devel
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install phono3py from source
         run: |
@@ -90,16 +93,22 @@ jobs:
             cd phono3py
             python3 -m pip install -e . -vvv
             cd ..
+            python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install Quippy from PyPI
-        run: python3 -m pip install quippy-ase
+        run: |
+            python3 -m pip install quippy-ase
+            python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install xTB (before things that need pandas like MACE and wfl, since it will break pandas-numpy compatibility by downgrading numpy)
         run: |
+          # force compatible numpy version
+          conda install 'numpy<2'
           conda install -c conda-forge xtb-python
           python3 -m pip install typing-extensions
           # install pandas now to encourage compatible numpy version after conda regressed it
           python3 -m pip install pandas
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: MACE
         run: |
@@ -136,9 +145,11 @@ jobs:
           fi
           echo "found torch version ${torch_version}+cpu, installing"
           python3 -m pip install torch==${torch_version}+cpu -f https://download.pytorch.org/whl/torch_stable.html
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
           echo "installing mace"
           python3 -m pip install git+https://github.com/ACEsuit/mace.git@main
-          python3 -c "import mace; print(mace.__file__)"
+          python3 -c "import mace; print('mace file', mace.__file__)"
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Julia and ace fit
         run: |
@@ -148,19 +159,24 @@ jobs:
           # note that this hardwires a particular compatible ACE1pack version
           echo 'using Pkg; pkg"registry add https://github.com/JuliaRegistries/General"; pkg"registry add https://github.com/JuliaMolSim/MolSim.git"; pkg"add [email protected], ACE1, JuLIP, IPFitting, ASE"' > ace1pack_install.jl
           ${PWD}/julia-1.8.1/bin/julia ace1pack_install.jl
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install wfl (expyre and universalSOAP are dependencies)
-        run: python3 -m pip install .
+        run: |
+            python3 -m pip install .
+            python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install Quantum Espresso
         run: |
           sudo apt-get install --no-install-recommends quantum-espresso
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install MOPAC
         run: |
-          wget http://openmopac.net/mopac-22.1.1-linux.tar.gz
+          wget https://github.com/openmopac/mopac/releases/download/v22.1.1/mopac-22.1.1-linux.tar.gz
           tar -xzvf mopac-22.1.1-linux.tar.gz
           echo $GITHUB_WORKSPACE/mopac-22.1.1-linux/bin >> $GITHUB_PATH
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install buildcell
         run: |
@@ -172,6 +188,7 @@ jobs:
           mkdir -p $HOME/bin
           cp src/buildcell/src/buildcell $HOME/bin/
           cd ..
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Add buildcell to system path
         run: |
@@ -183,6 +200,7 @@ jobs:
           # this can eaily be turned off if needed
           conda install -c conda-forge mpi4py openmpi pytest-mpi
           python3 -m pip install mpipool
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Install and configure slurm and ExPyRe
         run: |
@@ -206,6 +224,7 @@ jobs:
           sinfo -s --long
           mkdir $HOME/.expyre
           cp .github/workflows_assets/config.json $HOME/.expyre
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Set up pw.x for running in wfl
         run: |
@@ -221,6 +240,7 @@ jobs:
 
           echo 'post-espresso $HOME/.config/ase/config.ini'
           cat $HOME/.config/ase/config.ini
+          python3 -c "import numpy; print('numpy version', numpy.__version__)"
 
       - name: Lint with flake8
         run: |
@@ -234,6 +254,8 @@ jobs:
         run: |
           rm -rf $HOME/pytest_plain
           mkdir $HOME/pytest_plain
+          # attempt to work around mkl/numpy issue
+          export MKL_THREADING_LAYER=GNU
           #
           export EXPYRE_PYTEST_SYSTEMS=github
           export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell
@@ -247,6 +269,8 @@ jobs:
         run: |
           rm -rf $HOME/pytest_cov
           mkdir $HOME/pytest_cov
+          # attempt to work around mkl/numpy issue
+          export MKL_THREADING_LAYER=GNU
           #
           export EXPYRE_PYTEST_SYSTEMS=github
           export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell

tests/test_error.py

@@ -5,6 +5,7 @@
 import pytest
 from ase.atoms import Atoms
 from ase.calculators.lj import LennardJones
+from ase.stress import voigt_6_to_full_3x3_stress
 from pytest import approx
 
 from pprint import pprint
@@ -103,6 +104,17 @@ def test_err_from_calc(ref_atoms):
     assert ref_err_dict['virial/atom/comp']['_ALL_']["count"] == 10 * 6
 
 
+def test_err_stress_shape(ref_atoms):
+    ref_atoms_calc = generic_calc(ref_atoms, OutputSpec(), LennardJones(sigma=0.75), output_prefix='calc_')
+    ref_err_dict, _, _ = ref_err_calc(ref_atoms_calc, ref_property_prefix='REF_', calc_property_prefix='calc_')
+
+    for at in ref_atoms_calc:
+        at.info["REF_stress"] = voigt_6_to_full_3x3_stress(at.info["REF_stress"])
+    ref_err_dict_shape, _, _ = ref_err_calc(ref_atoms_calc, ref_property_prefix='REF_', calc_property_prefix='calc_')
+
+    assert ref_err_dict == ref_err_dict_shape
+
+
 def test_error_properties(ref_atoms):
     ref_atoms_calc = generic_calc(ref_atoms, OutputSpec(), LennardJones(sigma=0.75), output_prefix='calc_')
     # both energy and per atom

tests/test_md.py

@@ -268,7 +268,7 @@ def test_md_attach_logger(cu_slab, tmp_path, monkeypatch):
     workdir = Path(os.getcwd())
 
     assert len(atoms_traj) == 602
-    assert all([Path(workdir / "test_log.item_0").is_file(), Path(workdir / "test_log.item_1").is_file()])
+    assert all([Path(workdir / "test_log.config_0").is_file(), Path(workdir / "test_log.config_1").is_file()])
 
 
 def test_md_attach_logger_stdout(cu_slab, tmp_path, monkeypatch, capsys):

wfl/fit/error.py

@@ -7,6 +7,8 @@
 from matplotlib.figure import Figure
 from matplotlib.pyplot import get_cmap
 
+from ase.stress import full_3x3_to_voigt_6_stress
+
 
 def calc(inputs, calc_property_prefix, ref_property_prefix,
          config_properties=None, atom_properties=None, category_keys="config_type",
@@ -83,8 +85,21 @@ def _reshape_normalize(quant, prop, atoms, per_atom):
         quant: 2-d array containing reshaped quantity, with leading dimension 1 for per-config
             or len(atoms) for per-atom
         """
-        # convert scalars or lists into arrays
-        quant = np.asarray(quant)
+
+        # fix shape of stress/virial
+        if prop.startswith("stress") or prop.startswith("virial"):
+            if prop.split("/")[0] in ["stress", "virial"]:
+                if quant.shape != (6,):
+                    if quant.shape not in [(9,), (3,3)]:
+                        raise ValueError(f"Prop '{prop}' has unknown shape of quant {quant.shape}")
+                    quant = full_3x3_to_voigt_6_stress(quant.reshape((3, 3)))
+            elif prop.split("/")[0] in ["stresses", "virials"]:
+                eff_quant_shape = quant.shape[1:]
+                if eff_quant_shape != (6,):
+                    if eff_quant_shape not in [(9,), (3,3)]:
+                        raise ValueError(f"Prop '{prop}' has unknown shape of quant {quant.shape}")
+                    quant = [full_3x3_to_voigt_6_stress(q.reshape((3, 3))) for q in quant]
+                    quant = np.asarray(quant)
 
         # Reshape to 2-d, with leading dimension 1 for per-config, and len(atoms) for per-atom.
         # This is the right shape to work with later flattening for per-property and norm calculation
@@ -150,6 +165,10 @@ def _reshape_normalize(quant, prop, atoms, per_atom):
 
                 continue
 
+            # make a copy so normalization doesn't affect original
+            ref_quant = np.asarray(ref_quant).copy()
+            calc_quant = np.asarray(calc_quant).copy()
+
             if virial_from_stress:
                 # ref quant was actually stress, automatically convert
                 ref_quant *= -at.get_volume()

wfl/fit/utils.py

@@ -5,7 +5,7 @@
 import shlex
 import warnings
 
-from ase.constraints import voigt_6_to_full_3x3_stress
+from ase.stress import voigt_6_to_full_3x3_stress
 
 from wfl.utils.julia import julia_exec_path