Small fix in get_random_packed_structure

.github/workflows/deploy.yml

@@ -28,8 +28,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/docs.yml

@@ -33,8 +33,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/testing.yml

@@ -23,7 +23,10 @@ jobs:
 
       - uses: pre-commit/action@v3.0.0
 
-  test:
+  test-non-ase:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
     services:
       local_mongodb:
         image: mongo:4.0
@@ -37,6 +40,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
+        split: [1, 2, 3]
 
     steps:
       - name: Check out repo
@@ -72,20 +76,30 @@ jobs:
           micromamba activate a2
           uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
-      - name: Test
+      - name: Test split ${{ matrix.split }}
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
+
+        # regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations`
+        # Note the use of `--splitting-algorithm least_duration`.
+        # This helps prevent a test split having no tests to run, and then the GH action failing, see:
+        # https://github.com/jerry-git/pytest-split/issues/95
+        # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
         run: |
           micromamba activate a2
-          pytest --ignore=tests/ase --cov=atomate2 --cov-report=xml
+          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --cov=atomate2 --cov-report=xml
 
       - uses: codecov/codecov-action@v1
         if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          name: coverage${{ matrix.split }}
           file: ./coverage.xml
 
   test-notebooks-and-ase:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
     # It seems like anything torch-dependent and tblite can't be installed in the same environment
     # without the tblite tests failing in CI, see, e.g.:
     # https://github.com/tblite/tblite/issues/116
@@ -143,7 +157,7 @@ jobs:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          pytest --cov=atomate2 --cov-report=xml tests/ase
+          pytest --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase
 
       - uses: codecov/codecov-action@v1
         if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
@@ -172,7 +186,7 @@ jobs:
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test, docs]
+    needs: [lint, test-non-ase, test-notebooks-and-ase, docs]
     runs-on: ubuntu-latest
 
     permissions:

CHANGELOG.md

@@ -1,5 +1,22 @@
 # Change log
 
+## v0.0.17
+
+### Bug Fixes 🐛
+
+* Fix `prev_dir` behavior in input set generator of `MPGGAStaticMaker` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/996
+
+### Documentation 📖
+
+* Bump min supported Python to 3.10 by @janosh in https://github.com/materialsproject/atomate2/pull/992
+
+### House-Keeping 🧹
+
+* Excise openff dependency from OpenMM testing by @orionarcher in https://github.com/materialsproject/atomate2/pull/993
+* Use `pytest-split` to parallelize across 3 runners and speedup CI by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/985
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.16...v0.0.17
+
 ## v0.0.16
 
 This release brings lots of new workflows and support for all ASE calculators.

pyproject.toml

@@ -87,6 +87,7 @@ tests = [
     "nbmake==1.5.4",
     "pytest-cov==5.0.0",
     "pytest-mock==3.14.0",
+    "pytest-split==0.9.0",
     "pytest==8.3.3",
 ]
 strict = [

src/atomate2/common/jobs/mpmorph.py

@@ -224,9 +224,11 @@ def get_average_volume_from_icsd(
     def get_entry_from_dict(chem_env: str) -> dict | None:
         data = icsd_avg_vols[icsd_avg_vols["chem_env"] == chem_env]
         data = data[
-            data["with_oxi"]
-            if (not ignore_oxi_states and len(data[data["with_oxi"]]) > 0)
-            else ~data["with_oxi"]
+            (
+                data["with_oxi"]
+                if (not ignore_oxi_states and len(data[data["with_oxi"]]) > 0)
+                else ~data["with_oxi"]
+            )
         ]
         if len(data) > 0:
             return {k: data[k].squeeze() for k in ("avg_vol", "count")}
@@ -315,6 +317,8 @@ def get_random_packed_structure(
         )
     if isinstance(composition, str):
         composition = Composition(composition)
+    if isinstance(composition, dict):
+        composition = Composition.from_dict(composition)
 
     struct_db = (
         vol_per_atom_source.lower() if isinstance(vol_per_atom_source, str) else None

src/atomate2/openmm/flows/core.py

@@ -8,7 +8,7 @@
 from typing import TYPE_CHECKING
 
 from emmet.core.openmm import Calculation, OpenMMInterchange, OpenMMTaskDocument
-from jobflow import Flow, Job, Response
+from jobflow import Flow, Job, Maker, Response
 from monty.json import MontyDecoder, MontyEncoder
 
 from atomate2.openmm.jobs.base import openmm_job
@@ -68,7 +68,7 @@ def collect_outputs(
 
 
 @dataclass
-class OpenMMFlowMaker:
+class OpenMMFlowMaker(Maker):
     """Run a production simulation.
 
     This flexible flow links together any flows of OpenMM jobs in

src/atomate2/openmm/jobs/base.py

@@ -225,7 +225,7 @@ def make(
 
         # Run the simulation
         start = time.time()
-        self.run_openmm(sim)
+        self.run_openmm(sim, dir_name)
         elapsed_time = time.time() - start
 
         self._update_interchange(interchange, sim, prev_task)
@@ -303,6 +303,7 @@ def _add_reporters(
         traj_file_name = self._resolve_attr("traj_file_name", prev_task)
         traj_file_type = self._resolve_attr("traj_file_type", prev_task)
         report_velocities = self._resolve_attr("report_velocities", prev_task)
+        wrap_traj = self._resolve_attr("wrap_traj", prev_task)
 
         if has_steps & (traj_interval > 0):
             writer_kwargs = {}
@@ -327,7 +328,7 @@ def _add_reporters(
             kwargs = dict(
                 file=str(dir_name / f"{self.traj_file_name}.{traj_file_type}"),
                 reportInterval=traj_interval,
-                enforcePeriodicBox=self._resolve_attr("wrap_traj", prev_task),
+                enforcePeriodicBox=wrap_traj,
             )
             if report_velocities:
                 # assert package version
@@ -364,7 +365,7 @@ def _add_reporters(
             )
             sim.reporters.append(state_reporter)
 
-    def run_openmm(self, simulation: Simulation) -> NoReturn:
+    def run_openmm(self, sim: Simulation, dir_name: Path) -> NoReturn:
         """Abstract method for running the OpenMM simulation.
 
         This method should be implemented by subclasses to
@@ -524,6 +525,11 @@ def _update_interchange(
             interchange.box = state.getPeriodicBoxVectors(asNumpy=True)
         elif isinstance(interchange, OpenMMInterchange):
             interchange.state = XmlSerializer.serialize(state)
+        else:
+            raise TypeError(
+                f"Interchange must be an Interchange or "
+                f"OpenMMInterchange object, got {type(interchange).__name__}"
+            )
 
     def _create_structure(
         self, sim: Simulation, prev_task: OpenMMTaskDocument | None = None
@@ -607,8 +613,10 @@ def _create_task_doc(
 
         prev_task = prev_task or OpenMMTaskDocument()
 
-        interchange_json = interchange.json()
-        # interchange_bytes = interchange_json.encode("utf-8")
+        if isinstance(interchange, Interchange):
+            interchange_json = interchange.json()
+        else:
+            interchange_json = interchange.model_dump_json()
 
         return OpenMMTaskDocument(
             tags=tags,

src/atomate2/openmm/jobs/core.py

@@ -7,12 +7,15 @@
 
 import numpy as np
 from openmm import Integrator, LangevinMiddleIntegrator, MonteCarloBarostat
+from openmm.app import StateDataReporter
 from openmm.unit import atmosphere, kelvin, kilojoules_per_mole, nanometer, picoseconds
 
 from atomate2.openmm.jobs.base import BaseOpenMMMaker
 from atomate2.openmm.utils import create_list_summing_to
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     from emmet.core.openmm import OpenMMTaskDocument
     from openmm.app import Simulation
 
@@ -41,7 +44,7 @@ class EnergyMinimizationMaker(BaseOpenMMMaker):
     tolerance: float = 10
     max_iterations: int = 0
 
-    def run_openmm(self, sim: Simulation) -> None:
+    def run_openmm(self, sim: Simulation, dir_name: Path) -> None:
         """Run the energy minimization with OpenMM.
 
         This method performs energy minimization on the molecular system using
@@ -62,6 +65,28 @@ def run_openmm(self, sim: Simulation) -> None:
             maxIterations=self.max_iterations,
         )
 
+        if self.state_interval > 0:
+            state = sim.context.getState(
+                getPositions=True,
+                getVelocities=True,
+                getForces=True,
+                getEnergy=True,
+                enforcePeriodicBox=self.wrap_traj,
+            )
+
+            state_reporter = StateDataReporter(
+                file=f"{dir_name / self.state_file_name}.csv",
+                reportInterval=0,
+                step=True,
+                potentialEnergy=True,
+                kineticEnergy=True,
+                totalEnergy=True,
+                temperature=True,
+                volume=True,
+                density=True,
+            )
+            state_reporter.report(sim, state)
+
 
 @dataclass
 class NPTMaker(BaseOpenMMMaker):
@@ -87,7 +112,7 @@ class NPTMaker(BaseOpenMMMaker):
     pressure: float = 1
     pressure_update_frequency: int = 10
 
-    def run_openmm(self, sim: Simulation) -> None:
+    def run_openmm(self, sim: Simulation, dir_name: Path) -> None:
         """Evolve the simulation for self.n_steps in the NPT ensemble.
 
         This adds a Monte Carlo barostat to the system to put it into NPT, runs the
@@ -138,7 +163,7 @@ class NVTMaker(BaseOpenMMMaker):
     name: str = "nvt simulation"
     n_steps: int = 1_000_000
 
-    def run_openmm(self, sim: Simulation) -> None:
+    def run_openmm(self, sim: Simulation, dir_name: Path) -> None:
         """Evolve the simulation with OpenMM for self.n_steps.
 
         Parameters
@@ -177,7 +202,7 @@ class TempChangeMaker(BaseOpenMMMaker):
     temp_steps: int | None = None
     starting_temperature: float | None = None
 
-    def run_openmm(self, sim: Simulation) -> None:
+    def run_openmm(self, sim: Simulation, dir_name: Path) -> None:
         """Evolve the simulation while gradually changing the temperature.
 
         self.temperature is the final temperature. self.temp_steps

src/atomate2/openmm/utils.py

@@ -2,15 +2,23 @@
 
 from __future__ import annotations
 
+import io
 import re
 import tempfile
 import time
 import warnings
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import numpy as np
+import openmm.unit as omm_unit
+from emmet.core.openmm import OpenMMInterchange
+from openmm import LangevinMiddleIntegrator, XmlSerializer
+from openmm.app import PDBFile
+
 if TYPE_CHECKING:
     from emmet.core.openmm import OpenMMTaskDocument
+    from openff.interchange import Interchange
 
 
 def download_opls_xml(
@@ -132,3 +140,34 @@ def task_reports(task: OpenMMTaskDocument, traj_or_state: str = "traj") -> bool:
     else:
         raise ValueError("traj_or_state must be 'traj' or 'state'")
     return calc_input.n_steps >= report_freq
+
+
+def openff_to_openmm_interchange(
+    openff_interchange: Interchange,
+) -> OpenMMInterchange:
+    """Convert an OpenFF Interchange object to an OpenMM Interchange object."""
+    integrator = LangevinMiddleIntegrator(
+        300 * omm_unit.kelvin,
+        10.0 / omm_unit.picoseconds,
+        1.0 * omm_unit.femtoseconds,
+    )
+    sim = openff_interchange.to_openmm_simulation(integrator)
+    state = sim.context.getState(
+        getPositions=True,
+        getVelocities=True,
+        enforcePeriodicBox=True,
+    )
+    with io.StringIO() as buffer:
+        PDBFile.writeFile(
+            sim.topology,
+            np.zeros(shape=(sim.topology.getNumAtoms(), 3)),
+            file=buffer,
+        )
+        buffer.seek(0)
+        pdb = buffer.read()
+
+        return OpenMMInterchange(
+            system=XmlSerializer.serialize(sim.system),
+            state=XmlSerializer.serialize(state),
+            topology=pdb,
+        )

src/atomate2/vasp/jobs/mp.py

@@ -55,7 +55,9 @@ class MPGGARelaxMaker(BaseVaspMaker):
 
     name: str = "MP GGA relax"
     input_set_generator: VaspInputGenerator = field(
-        default_factory=lambda: MPRelaxSet(force_gamma=True, auto_metal_kpoints=True)
+        default_factory=lambda: MPRelaxSet(
+            force_gamma=True, auto_metal_kpoints=True, inherit_incar=False
+        )
     )
 
 
@@ -90,7 +92,9 @@ class MPGGAStaticMaker(BaseVaspMaker):
 
     name: str = "MP GGA static"
     input_set_generator: VaspInputGenerator = field(
-        default_factory=lambda: MPStaticSet(force_gamma=True, auto_metal_kpoints=True)
+        default_factory=lambda: MPStaticSet(
+            force_gamma=True, auto_metal_kpoints=True, inherit_incar=False
+        )
     )
 
 
@@ -127,6 +131,7 @@ class MPPreRelaxMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=lambda: MPScanRelaxSet(
             auto_ismear=False,
+            inherit_incar=False,
             user_incar_settings={
                 "EDIFFG": -0.05,
                 "GGA": "PS",
@@ -172,6 +177,7 @@ class MPMetaGGARelaxMaker(BaseVaspMaker):
     input_set_generator: VaspInputGenerator = field(
         default_factory=lambda: MPScanRelaxSet(
             auto_ismear=False,
+            inherit_incar=False,
             user_incar_settings={
                 "GGA": None,  # unset GGA, shouldn't be set anyway but best be sure
                 "LCHARG": True,