Fix relative tolerance (#604)

* add nobatch

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* add fix

* add helper test functions

* add test data

* Revert "add fix"

This reverts commit 3d9f043.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Revert "Revert "add fix""

This reverts commit 79a8bea.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>

Author: 3 people

openff/evaluator/_tests/test_full_workflows/conftest.py

@@ -0,0 +1,55 @@
+import pytest
+from openff.units import unit
+
+from openff.evaluator.datasets import (
+    MeasurementSource,
+    PhysicalPropertyDataSet,
+    PropertyPhase,
+)
+from openff.evaluator.properties import Density, EnthalpyOfMixing
+from openff.evaluator.substances import Substance
+from openff.evaluator.thermodynamics import ThermodynamicState
+
+
+@pytest.fixture
+def dummy_enthalpy_of_mixing():
+    thermodynamic_state = ThermodynamicState(
+        temperature=298.15 * unit.kelvin,
+        pressure=101.325 * unit.kilopascal,
+    )
+
+    return EnthalpyOfMixing(
+        thermodynamic_state=thermodynamic_state,
+        phase=PropertyPhase.Liquid,
+        value=1.0 * EnthalpyOfMixing.default_unit(),
+        uncertainty=1.0 * EnthalpyOfMixing.default_unit(),
+        source=MeasurementSource(doi=" "),
+        substance=Substance.from_components("CCCO", "O"),
+    )
+
+
+@pytest.fixture
+def dummy_density():
+    thermodynamic_state = ThermodynamicState(
+        temperature=298.15 * unit.kelvin,
+        pressure=101.325 * unit.kilopascal,
+    )
+
+    return Density(
+        thermodynamic_state=thermodynamic_state,
+        phase=PropertyPhase.Liquid,
+        value=1.0 * Density.default_unit(),
+        uncertainty=1.0 * Density.default_unit(),
+        source=MeasurementSource(doi=" "),
+        substance=Substance.from_components("CCCO"),
+    )
+
+
+@pytest.fixture
+def dummy_dataset(dummy_density, dummy_enthalpy_of_mixing):
+    dataset = PhysicalPropertyDataSet()
+    dataset.add_properties(dummy_density, dummy_enthalpy_of_mixing)
+
+    for i, prop in enumerate(dataset.properties):
+        prop.id = f"{i}"
+    return dataset

openff/evaluator/_tests/test_full_workflows/test_simulation.py

@@ -0,0 +1,179 @@
+import os
+import pathlib
+
+import pytest
+
+from openff.evaluator._tests.utils import (
+    _copy_property_working_data,
+    _write_force_field,
+)
+from openff.evaluator.backends.dask import DaskLocalCluster
+from openff.evaluator.client import BatchMode, EvaluatorClient, RequestOptions
+from openff.evaluator.forcefield import SmirnoffForceFieldSource
+from openff.evaluator.layers.simulation import SimulationLayer
+from openff.evaluator.properties import Density, EnthalpyOfMixing
+from openff.evaluator.server.server import EvaluatorServer
+from openff.evaluator.storage.localfile import LocalFileStorage
+from openff.evaluator.workflow import Workflow
+
+
+def _get_simulation_request_options(
+    n_molecules: int = 256,
+):
+    dhmix_schema = EnthalpyOfMixing.default_simulation_schema(
+        n_molecules=n_molecules,
+        relative_tolerance=0.2,
+    )
+    density_schema = Density.default_simulation_schema(
+        n_molecules=n_molecules,
+        relative_tolerance=0.2,
+    )
+
+    options = RequestOptions()
+    options.calculation_layers = ["SimulationLayer"]
+
+    options.add_schema(
+        "SimulationLayer",
+        "Density",
+        density_schema,
+    )
+    options.add_schema(
+        "SimulationLayer",
+        "EnthalpyOfMixing",
+        dhmix_schema,
+    )
+    return options
+
+
+class TestSimulationLayer:
+
+    @pytest.fixture
+    def dhmix_density_CCCO(self, tmp_path_factory):
+        path = tmp_path_factory.mktemp("dhmix-density-CCCO")
+        path.mkdir(exist_ok=True, parents=True)
+
+        _copy_property_working_data(
+            "test/workflows/simulation/dhmix-density-CCCO",
+            uuid_prefix=["0", "1"],
+            destination_directory=path,
+        )
+        return path
+
+    def test_simulation(self, dummy_enthalpy_of_mixing, dhmix_density_CCCO):
+        """
+        Test direct execution of an EnthalpyOfMixing protocol
+        """
+        os.chdir(dhmix_density_CCCO)
+
+        _write_force_field()
+        schema = EnthalpyOfMixing.default_simulation_schema(
+            n_molecules=256,
+            relative_tolerance=0.2,
+        )
+
+        metadata = Workflow.generate_default_metadata(
+            dummy_enthalpy_of_mixing, "force-field.json"
+        )
+        metadata.update(
+            SimulationLayer._get_workflow_metadata(
+                ".",
+                dummy_enthalpy_of_mixing,
+                "force-field.json",
+                [],
+                LocalFileStorage(),
+                schema,
+            )
+        )
+
+        workflow_schema = schema.workflow_schema
+        workflow_schema.replace_protocol_types(
+            {"BaseBuildSystem": "BuildSmirnoffSystem"}
+        )
+        uuid_prefix = "1"
+        workflow = Workflow.from_schema(
+            workflow_schema, metadata=metadata, unique_id=uuid_prefix
+        )
+        workflow_graph = workflow.to_graph()
+        protocol_graph = workflow_graph._protocol_graph
+
+        previous_output_paths = []
+
+        for name, protocol in workflow_graph.protocols.items():
+            path = name.replace("|", "_")
+            if "conditional" not in name:
+                output = protocol_graph._execute_protocol(
+                    path,
+                    protocol,
+                    True,
+                    *previous_output_paths,
+                    available_resources=None,
+                    safe_exceptions=False,
+                )
+                previous_output_paths.append(output)
+
+        # delete existing output so we can re-create it
+        pattern = "*conditional*/*conditional*output.json"
+        for file in pathlib.Path(".").rglob(pattern):
+            file.unlink()
+
+        for name, protocol in workflow_graph.protocols.items():
+            path = name.replace("|", "_")
+            if "conditional" in name:
+                output = protocol_graph._execute_protocol(
+                    path,
+                    protocol,
+                    True,
+                    *previous_output_paths,
+                    available_resources=None,
+                    safe_exceptions=False,
+                )
+                previous_output_paths.append(output)
+
+    def test_simulation_with_server(self, dummy_dataset, dhmix_density_CCCO):
+        """
+        Test the full workflow with a server
+        """
+        force_field_path = "openff-2.1.0.offxml"
+        force_field_source = SmirnoffForceFieldSource.from_path(force_field_path)
+
+        os.chdir(dhmix_density_CCCO)
+        options = _get_simulation_request_options(
+            n_molecules=256,
+        )
+        options.batch_mode = BatchMode.NoBatch
+
+        batch_path = pathlib.Path("SimulationLayer") / "batch_0000"
+        batch_path.mkdir(parents=True, exist_ok=True)
+        _copy_property_working_data(
+            "test/workflows/simulation/dhmix-density-CCCO",
+            uuid_prefix="0",
+            destination_directory=batch_path,
+        )
+        _copy_property_working_data(
+            "test/workflows/simulation/dhmix-density-CCCO",
+            uuid_prefix="1",
+            destination_directory=batch_path,
+        )
+
+        with DaskLocalCluster(number_of_workers=1) as calculation_backend:
+            server = EvaluatorServer(
+                calculation_backend=calculation_backend,
+                working_directory=".",
+                delete_working_files=False,
+            )
+            with server:
+                client = EvaluatorClient()
+                request, error = client.request_estimate(
+                    dummy_dataset, force_field_source, options
+                )
+
+                assert error is None
+                results, exception = request.results(
+                    synchronous=True, polling_interval=30
+                )
+
+                assert exception is None
+                assert len(results.queued_properties) == 0
+                assert len(results.estimated_properties) == 2
+                assert len(results.unsuccessful_properties) == 0
+                assert len(results.exceptions) == 0

openff/evaluator/_tests/utils.py

@@ -1,8 +1,12 @@
 import os
+import pathlib
+import shutil
 import uuid
 from contextlib import contextmanager
 
+from openff.toolkit import ForceField
 from openff.units import unit
+from openff.utilities.utilities import get_data_dir_path
 
 from openff.evaluator.datasets import (
     CalculationSource,
@@ -238,3 +242,56 @@ def build_tip3p_smirnoff_force_field():
     )
 
     return SmirnoffForceFieldSource.from_object(smirnoff_force_field_with_tip3p)
+
+
+def _write_force_field(force_field: str = "openff-2.0.0.offxml"):
+    """
+    Write a force field file to disk.
+    """
+    ff = ForceField(force_field)
+    with open("force-field.json", "w") as file:
+        file.write(SmirnoffForceFieldSource.from_object(ff).json())
+
+
+def _copy_property_working_data(
+    source_directory: str,
+    uuid_prefix: str | list[str],
+    destination_directory: str = ".",
+    include_data_files: bool = False,
+):
+    """
+    Copy test data from one directory to another.
+    This is typically working data in a *Layer directory.
+
+    Parameters
+    ----------
+    source_directory : str
+        The directory to copy data from.
+        This should be relative to to the data directory.
+        For tests, the path will typically start with `test`.
+    uuid_prefix : str or list[str]
+        The prefix of the UUID/s to copy.
+    destination_directory : str
+        The directory to copy data to.
+        This should be relative to the current working directory.
+        Default is the current working directory.
+    """
+    if isinstance(uuid_prefix, str):
+        uuid_prefix = [uuid_prefix]
+
+    # locate our saved test data
+    data_directory = pathlib.Path(
+        get_data_dir_path(source_directory, "openff.evaluator")
+    )
+    abs_path = data_directory.resolve()
+    destination_directory = pathlib.Path(destination_directory)
+
+    # copy data files over from data_directory
+    for path in abs_path.iterdir():
+        if path.name.startswith(tuple(uuid_prefix)) and path.is_dir():
+            dest_dir = destination_directory / path.name
+            shutil.copytree(path, dest_dir)
+
+    if include_data_files:
+        for path in abs_path.glob("data*.json"):
+            shutil.copy(path, destination_directory)

openff/evaluator/data/test/workflows/simulation/dhmix-density-CCCO/0_decorrelate_observables/0|decorrelate_observables_output.json

@@ -0,0 +1 @@
+{".output_trajectory_path": "0_decorrelate_trajectory/uncorrelated_trajectory.dcd"}

openff/evaluator/data/test/workflows/simulation/dhmix-density-CCCO/0_decorrelate_trajectory/0|decorrelate_trajectory_output.json

@@ -0,0 +1 @@
+

openff/evaluator/data/test/workflows/simulation/dhmix-density-CCCO/0_decorrelate_trajectory/uncorrelated_trajectory.dcd

@@ -0,0 +1 @@
+{".result": {"value": {"value": {"value": -4.5574468423925065, "unit": "kilojoule / mole", "@type": "openff.evaluator.unit.Quantity"}, "error": {"value": 0.029844082370627523, "unit": "kilojoule / mole", "@type": "openff.evaluator.unit.Quantity"}, "@type": "openff.evaluator.unit.Measurement"}, "gradients": [], "@type": "openff.evaluator.utils.observables.Observable"}}

openff/evaluator/data/test/workflows/simulation/dhmix-density-CCCO/1_add_component_observables/1|add_component_observables_output.json

@@ -0,0 +1 @@
+{".output_number_of_molecules": 256, ".output_substance": {"components": [{"smiles": "CCCO", "role": {"value": "solv", "@type": "openff.evaluator.substances.components.Component.Role"}, "@type": "openff.evaluator.substances.components.Component"}], "amounts": {"CCCO{solv}": [{"value": 1.0, "@type": "openff.evaluator.substances.amounts.MoleFraction"}]}, "@type": "openff.evaluator.substances.substances.Substance"}, ".assigned_residue_names": {"CCCO{solv}": "UFX"}, ".coordinate_file_path": "1_build_coordinates_component_0/output.pdb"}