Exit CP2K applications more reliably

examol/simulate/ase/__init__.py

@@ -54,8 +54,11 @@
     METHOD $METHOD$
   &END QS
   &SCF
+    &MIXING
+       NBUFFER 8
+    &END MIXING
     &OUTER_SCF
-      MAX_SCF 5
+      MAX_SCF 3
     &END OUTER_SCF
     &OT T
       PRECONDITIONER FULL_ALL
@@ -174,7 +177,7 @@ def create_configuration(self, name: str, xyz: str, charge: int, solvent: str |
             }
         elif name.startswith('cp2k_'):
             # Get the name the basis set
-            xc_name, basis_set_id = name.rsplit('_', 2)[-2:]
+            xc_name, basis_set_id = name[5:].rsplit('_', 1)
             xc_name = xc_name.upper()
 
             # Determine the proper basis set, pseudopotential, and method
@@ -237,7 +240,7 @@ def create_configuration(self, name: str, xyz: str, charge: int, solvent: str |
                     uks=charge != 0,
                     inp=inp,
                     cutoff=cutoff * units.Ry,
-                    max_scf=32,
+                    max_scf=64,
                     basis_set_file=str(basis_set_file),
                     basis_set=basis_set_name,
                     pseudo_potential=potential,
@@ -401,14 +404,17 @@ def compute_energy(self, mol_key: str, xyz: str, config_name: str, charge: int =
                 # Make any changes to cell needed by the calculator
                 self._prepare_atoms(atoms, charge, calc_cfg)
 
+                # Remove the previous output file, if any
+                cp2k_output = Path('cp2k.out')
+                cp2k_output.unlink(True)
+
                 # Run a single point
                 atoms.calc = calc
                 forces = atoms.get_forces() if forces else None
                 energy = atoms.get_potential_energy()
 
                 # If CP2K, make sure it converged
                 if config_name.startswith('cp2k'):
-                    cp2k_output = (run_path / 'cp2k.out')
                     assert cp2k_output.is_file(), f'Cannot find output at: {cp2k_output.absolute()}'
                     if ':: SCF run NOT converged ***' in cp2k_output.read_text():  # pragma: no-coverage
                         raise ValueError('CP2K computation did not converge')

examol/simulate/ase/utils.py

@@ -38,19 +38,8 @@ def make_ephemeral_calculator(calc: Calculator | dict) -> Iterator[Calculator]:
     name = calc['name'].lower()
     if name == 'cp2k':
         from ase.calculators.cp2k import CP2K
-        calc = CP2K(*calc.get('args', []), **calc.get('kwargs', {}))
-        yield calc
-
-        # Kill the calculator by deleting the object to stop the underlying
-        #  shell and then set the `_shell` parameter of the object so that the
-        #  calculator object's destructor will skip the shell shutdown process
-        #  when the object is finally garbage collected
-        try:
-            calc.__del__()
-        except AssertionError as e:  # pragma: no-coverage
-            logger.info(f'CP2K was noisy on failure: {e}')
-            pass
-        calc._shell = None
+        with CP2K(*args, **kwargs) as calc:
+            yield calc
     elif name == 'gaussian':
         from ase.calculators.gaussian import Gaussian
         yield Gaussian(*args, **kwargs)

examol/store/recipes.py

@@ -153,7 +153,7 @@ def suggest_computations(self, record: MoleculeRecord) -> list[SimulationRequest
             # Determine if the geometry has been computed
             matching_conformers = [
                 (x.get_energy(geometry.config_name, geometry.charge, solvent=None), x) for x in record.conformers
-                if x.source == 'relaxation' and x.config_name == geometry.config_name and x.charge == geometry.charge
+                if x.config_name == geometry.config_name and x.charge == geometry.charge
             ]
             if len(matching_conformers) > 0:
                 _, conformer = min(matching_conformers)

examples/redoxmers/run/report.md

@@ -1,12 +1,12 @@
 # Run Report
-Report time: 2023-10-18 17:38:06.910593
+Report time: 2023-11-30 14:02:53.333870
 
 ## Task Summary
 Measures how many tasks have run as part of the application
 
 | Task Type   |   Count |   Node Hours | Failures   |
 |-------------|---------|--------------|------------|
-| simulation  |       2 |      0.00041 | 0 (0.0%)   |
+| simulation  |       2 |       0.0017 | 0 (0.0%)   |
 
 ## Outcomes over Time
 The property of the molecules over time.

tests/simulation/test_ase.py

@@ -19,6 +19,7 @@
 
 try:
     import xtb  # noqa: F401
+
     has_xtb = True
 except ImportError:
     has_xtb = False
@@ -31,12 +32,22 @@
 cp2k_configs_to_test = ['cp2k_b3lyp_svp', 'cp2k_blyp_szv', 'cp2k_wb97x_d3_tzvpd']
 
 
+class FakeShell:
+
+    def __del__(self):
+        return
+
+
 class FakeCP2K(LennardJones):
+    _shell = FakeShell()
 
     def __init__(self, *args, **kwargs):
         super().__init__()
 
-    def __del__(self):
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
         return
 
 
@@ -67,6 +78,14 @@ def test_cp2k_configs(tmpdir, strc):
     assert 'GAPW' in config['kwargs']['inp']
     assert Path(config['kwargs']['basis_set_file']).is_file()
 
+    # With wb97x-d3
+    config = sim.create_configuration('cp2k_wb97x_d3_tzvpd', strc, charge=1, solvent=None)
+    assert config['kwargs']['cutoff'] == 600 * units.Ry
+    assert config['kwargs']['charge'] == 1
+    assert config['kwargs']['uks']
+    assert 'GAPW' in config['kwargs']['inp']
+    assert Path(config['kwargs']['basis_set_file']).is_file()
+
     # With an undefined basis set
     with raises(AssertionError):
         sim.create_configuration('cp2k_blyp_notreal', strc, charge=1, solvent=None)

tests/steer/conftest.py

@@ -1,4 +1,4 @@
-from concurrent.futures import ProcessPoolExecutor
+from concurrent.futures import ThreadPoolExecutor
 from pathlib import Path
 import sys
 
@@ -57,7 +57,7 @@ def simulator(tmp_path) -> ASESimulator:
 
 @fixture()
 def pool():
-    yield ProcessPoolExecutor()
+    yield ThreadPoolExecutor(max_workers=1)
 
 
 @fixture()

tests/steer/test_multi.py

@@ -86,26 +86,26 @@ def test_detect_level(thinker, recipe):
 def test_iterator(thinker, recipe, mocker):
     # Make sure we return xTB regardless of what the system asks for
     for choice in [0, 1]:
-        with mocker.patch('numpy.random.choice', return_value=choice):
-            thinker.task_queue = [('C', 0)]
-            record, recipes, request = next(thinker.task_iterator)
-            assert record.identifier.smiles == 'C'
-            assert request.config_name == 'xtb'
-            assert recipes[0].level == 'xtb-vertical'
-            assert len(thinker.task_queue) == 0
+        mocker.patch('numpy.random.choice', return_value=choice)
+        thinker.task_queue = [('C', 0)]
+        record, recipes, request = next(thinker.task_iterator)
+        assert record.identifier.smiles == 'C'
+        assert request.config_name == 'xtb'
+        assert recipes[0].level == 'xtb-vertical'
+        assert len(thinker.task_queue) == 0
 
     # Test after we add data for C
     #  We should default to C if it's the only item in the task queue
     thinker.database.get_or_make_record('C').properties[recipe.name] = {'xtb-vertical': 1}
     assert thinker.get_level('C') == 1
     for choice in [0, 1]:
-        with mocker.patch('numpy.random.choice', return_value=choice):
-            thinker.task_queue = [('C', 0)]
-            record, recipes, request = next(thinker.task_iterator)
-            assert record.identifier.smiles == 'C'
-            assert recipes[0].level == 'mopac_pm7-vertical'
-            assert request.config_name == 'mopac_pm7', f'choice={choice}'
-            assert len(thinker.task_queue) == 0
+        mocker.patch('numpy.random.choice', return_value=choice)
+        thinker.task_queue = [('C', 0)]
+        record, recipes, request = next(thinker.task_iterator)
+        assert record.identifier.smiles == 'C'
+        assert recipes[0].level == 'mopac_pm7-vertical'
+        assert request.config_name == 'mopac_pm7', f'choice={choice}'
+        assert len(thinker.task_queue) == 0
 
 
 @mark.timeout(120)