Merge branch 'main' into orca-update

.github/workflows/pytests.yml

@@ -41,12 +41,12 @@ jobs:
       - name: Install dependencies from pip
         run: |
           echo "numpy<2" >> $PIP_CONSTRAINT
-          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests
+          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit==2024.3.3 flake8 pytest pytest-cov requests
 
       - name: Install latest ASE from pypi
         run: |
           echo PIP_CONSTRAINT $PIP_CONSTRAINT
-          python3 -m pip install ase 
+          python3 -m pip install ase
           echo -n "ASE VERSION "
           python3 -c "import ase; print(ase.__file__, ase.__version__)"
 
@@ -105,15 +105,27 @@ jobs:
         run: |
           echo "search for torch version"
           set +o pipefail
+
+          # echo "torch versions"
+          # python3 -m pip install torch==
+          # echo "torch versions to search"
+          # python3 -m pip install torch== 2>&1 | fgrep 'from versions' |
+          #                      sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac
+
           # search for available torch version with +cpu support
-          for torch_version_test in $( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | 
-                                       sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac ); do
+          # for torch_version_test in $( python3 -m pip install torch== 2>&1 | fgrep 'from versions' |
+          #                              sed -e 's/.*from versions: //' -e 's/)//' -e 's/,[ ]*/\n/g' | tac ); do
+          wget https://pypi.org/pypi/torch/json -O torch_versions
+          for torch_version_test in $( python3 -c "import json; print(' '.join(json.load(open('torch_versions'))['releases'].keys()))" | sed 's/ /\n/g' | tac ); do
+              echo "check torch_version_test $torch_version_test"
               set +e
               python3 -m pip install --dry-run torch==${torch_version_test}+cpu \
-                                     -f https://download.pytorch.org/whl/torch_stable.html > /dev/null 2>&1
+                                     -f https://download.pytorch.org/whl/torch_stable.html 2>&1
               search_stat=$?
+              echo "got search_stat $search_stat"
               set -e
               if [ $search_stat == 0 ]; then
+                  echo "got valid +cpu version, exiting"
                   torch_version=${torch_version_test}
                   break
               fi

tests/calculators/test_ase_fileio_caching.py

@@ -0,0 +1,78 @@
+import os
+
+import pytest
+
+from ase.atoms import Atoms
+
+
+########################
+# test Vasp calculator
+
+from tests.calculators.test_vasp import test_vasp_mark
+@pytest.mark.skipif(test_vasp_mark, reason='Vasp testing env vars missing')
+def test_vasp_cache_timing(tmp_path, monkeypatch):
+    from ase.calculators.vasp import Vasp as Vasp_ase
+    from wfl.calculators.vasp import Vasp as Vasp_wrap
+
+    config = Atoms('Si', positions=[[0, 0, 9]], cell=[2, 2, 2], pbc=[True, True, True])
+    kwargs_ase = {'encut': 200, 'pp': os.environ['PYTEST_VASP_POTCAR_DIR']}
+    kwargs_wrapper = {'workdir': tmp_path}
+    # make sure 'pp' is relative to correct dir (see wfl.calculators.vasp)
+    if os.environ['PYTEST_VASP_POTCAR_DIR'].startswith('/'):
+        monkeypatch.setenv("VASP_PP_PATH", "/.")
+    else:
+        monkeypatch.setenv("VASP_PP_PATH", ".")
+    cache_timing(config, Vasp_ase, kwargs_ase, Vasp_wrap, kwargs_wrapper, tmp_path, monkeypatch)
+
+########################
+# test quantum espresso calculator
+from tests.calculators.test_qe import espresso_avail, qe_pseudo
+@pytest.mark.skipif(not espresso_avail, reason='qe testing env vars missing')
+def test_qe_cache_timing(tmp_path, monkeypatch, qe_pseudo):
+    from ase.calculators.espresso import Espresso as Espresso_ASE
+    from wfl.calculators.espresso import Espresso as Espresso_wrap
+
+    config = Atoms('Si', positions=[[0, 0, 9]], cell=[2, 2, 2], pbc=[True, True, True])
+
+    pspot = qe_pseudo
+    kwargs_ase =  dict(
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
+        input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
+        kpts=(2, 3, 4),
+        conv_thr=0.0001,
+        workdir=tmp_path
+    )
+
+    kwargs_wrapper = {}
+    cache_timing(config, Espresso_ASE, kwargs_ase, Espresso_wrap, kwargs_wrapper, tmp_path, monkeypatch)
+
+
+########################
+# generic code used by all calculators
+
+import time
+
+from wfl.configset import ConfigSet, OutputSpec
+from wfl.calculators import generic
+
+def cache_timing(config, calc_ase, kwargs_ase, calc_wfl, kwargs_wrapper, rundir, monkeypatch):
+    (rundir / "run_calc_ase").mkdir()
+
+    calc = calc_ase(**kwargs_ase)
+    config.calc = calc
+
+    monkeypatch.chdir(rundir / "run_calc_ase")
+    t0 = time.time()
+    E = config.get_potential_energy()
+    ase_time = time.time() - t0
+
+    monkeypatch.chdir(rundir)
+    t0 = time.time()
+    _ = generic.calculate(inputs=ConfigSet(config), outputs=OutputSpec(),
+                          calculator=calc_wfl(**kwargs_wrapper, **kwargs_ase))
+    wfl_time = time.time() - t0
+
+    print("ASE", ase_time, "WFL", wfl_time)
+
+    assert wfl_time < ase_time * 1.25

tests/calculators/test_calc_generic.py

@@ -139,7 +139,6 @@ def test_generic_autopara_defaults():
     sys.stderr = sys.__stderr__
     assert "num_inputs_per_python_subprocess=3" in l_stderr.getvalue()
 
-@pytest.mark.xfail(reason="Waiting for update to work with ASE3.23")
 def test_generic_DFT_autopara_defaults(tmp_path, monkeypatch):
     ats = [Atoms('Al2', positions=[[0,0,0], [1,1,1]], cell=[10]*3, pbc=[True]*3) for _ in range(50)]
 
@@ -151,6 +150,6 @@ def test_generic_DFT_autopara_defaults(tmp_path, monkeypatch):
     # try with a calculator that overrides an autopara default, namely a DFT calculator
     # that sets num_inputs_per_python_subprocess=1
     sys.stderr = l_stderr
-    at_proc = generic.calculate(ci, os, Espresso(calculator_exec="_DUMMY_EXEC_", pseudo_dir="_DUMMY_DIR_", workdir=tmp_path))
+    at_proc = generic.calculate(ci, os, Espresso(workdir=tmp_path))
     sys.stderr = sys.__stderr__
     assert "num_inputs_per_python_subprocess=1" in l_stderr.getvalue()

tests/calculators/test_vasp.py

@@ -13,10 +13,11 @@
 from wfl.calculators import generic
 from wfl.configset import ConfigSet, OutputSpec
 
-pytestmark = pytest.mark.skipif('ASE_VASP_COMMAND' not in os.environ or
-                                'ASE_VASP_COMMAND_GAMMA' not in os.environ or
-                                'PYTEST_VASP_POTCAR_DIR' not in os.environ,
-                                reason='missing env var ASE_VASP_COMMAND or ASE_VASP_COMMAND_GAMMA or PYTEST_VASP_POTCAR_DIR')
+test_vasp_mark = ('ASE_VASP_COMMAND' not in os.environ or
+                  'ASE_VASP_COMMAND_GAMMA' not in os.environ or
+                  'PYTEST_VASP_POTCAR_DIR' not in os.environ)
+pytestmark = pytest.mark.skipif(test_vasp_mark, reason='missing env var ASE_VASP_COMMAND or ASE_VASP_COMMAND_GAMMA '
+                                                       'or PYTEST_VASP_POTCAR_DIR')
 
 
 def test_vasp_gamma(tmp_path, monkeypatch):

tests/calculators/test_wrapped_calculator.py

@@ -0,0 +1,30 @@
+import pytest
+from ase.atoms import Atoms
+from wfl.configset import ConfigSet, OutputSpec
+from wfl.calculators import generic
+
+########################
+# test a RuntimeWarning is raised when using the Espresso Calculator directly from ase
+from tests.calculators.test_qe import espresso_avail, qe_pseudo
+@pytest.mark.skipif(not espresso_avail, reason='qe testing env vars missing')
+def test_wrapped_qe(tmp_path, qe_pseudo):
+    from ase.calculators.espresso import Espresso as Espresso_ASE
+    from wfl.calculators.espresso import Espresso as Espresso_wrap
+
+    config = Atoms('Si', positions=[[0, 0, 9]], cell=[2, 2, 2], pbc=[True, True, True])
+
+    pspot = qe_pseudo
+    kwargs =  dict(
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
+        input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
+        kpts=(2, 3, 4),
+        conv_thr=0.0001,
+        workdir=tmp_path,
+        tstress=True,
+        tprnfor=True
+    )
+
+    direct_calc = (Espresso_ASE, [],  kwargs)
+    kwargs_generic = dict(inputs=ConfigSet(config), outputs=OutputSpec(), calculator=direct_calc)
+    pytest.warns(RuntimeWarning, generic.calculate, **kwargs_generic)

wfl/calculators/generic.py

@@ -150,6 +150,20 @@ def calculate(*args, **kwargs):
     if calculator is None:
         calculator = args[2]
 
+    #check if calculator should be wrapped
+    if type(calculator) == tuple:
+        from ase.calculators.espresso import Espresso as ASE_Espresso
+        from ase.calculators.vasp.vasp import Vasp as ASE_Vasp
+        from ase.calculators.aims import Aims as ASE_Aims
+        from ase.calculators.castep import Castep as ASE_Castep
+        from ase.calculators.mopac import MOPAC as ASE_MOPAC
+        from ase.calculators.orca import ORCA as ASE_ORCA
+        wrapped_types = [ASE_Espresso, ASE_Vasp, ASE_Aims, ASE_Castep, ASE_MOPAC, ASE_ORCA]
+
+        calc = calculator[0]
+        if calc in wrapped_types:
+            warnings.warn(f"{calc} should be imported from wfl.calculators rather than ase. Using {calc} directly can lead to duplicated singlepoints", RuntimeWarning)
+
     default_autopara_info = getattr(calculator, "wfl_generic_default_autopara_info", {"num_inputs_per_python_subprocess": 10})
 
     return autoparallelize(_run_autopara_wrappable, *args, default_autopara_info=default_autopara_info, **kwargs)