mirror of
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Make CUDA the default compute platform (#1576)
* Make CUDA the default compute platform
This commit is contained in:
Irfan Alibay
GitHub
24
news/cuda.rst
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24
news/cuda.rst
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@@ -0,0 +1,24 @@
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**Added:**
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* <news item>
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**Changed:**
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* The default platform for OpenMM-based Protocols is now CUDA and will fail
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by default on a non-Nvidia GPU enabled system.
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>
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@@ -314,10 +314,13 @@ class OpenMMEngineSettings(SettingsBaseModel):
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* In the future make precision and deterministic forces user defined too.
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"""
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compute_platform: Optional[str] = None
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compute_platform: Optional[str] = 'cuda'
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"""
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OpenMM compute platform to perform MD integration with. If ``None``, will
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choose fastest available platform. Default ``None``.
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choose fastest available platform.
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Allowed platforms are; ``cuda``, ``opencl``, ``cpu``.
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Default ``cuda``.
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"""
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gpu_device_index: Optional[list[int]] = None
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"""
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@@ -332,6 +335,15 @@ class OpenMMEngineSettings(SettingsBaseModel):
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Default ``None``.
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"""
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@field_validator('compute_platform')
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def supported_sampler(cls, v):
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supported = ['cpu', 'opencl', 'cuda']
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if v is not None and v.lower() not in supported:
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errmsg = ("Only the following OpenMM compute backends are "
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f"supported: {supported}")
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raise ValueError(errmsg)
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return v
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class IntegratorSettings(SettingsBaseModel):
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"""Settings for the `LangevinDynamicsMove integrator <https://openmmtools.readthedocs.io/en/latest/api/generated/openmmtools.mcmc.LangevinDynamicsMove.html>`_.
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@@ -29,6 +29,15 @@ from openfe.protocols.openmm_utils.charge_generation import (
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)
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@pytest.fixture()
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def protocol_dry_settings():
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settings = AbsoluteSolvationProtocol.default_settings()
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settings.vacuum_engine_settings.compute_platform = None
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settings.solvent_engine_settings.compute_platform = None
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settings.protocol_repeats = 1
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return settings
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@pytest.fixture()
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def default_settings():
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return AbsoluteSolvationProtocol.default_settings()
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@@ -55,14 +64,16 @@ def test_serialize_protocol(default_settings):
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@pytest.mark.parametrize('method', [
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'repex', 'sams', 'independent', 'InDePeNdENT'
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])
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def test_dry_run_vac_benzene(benzene_modifications,
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method, tmpdir):
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.vacuum_simulation_settings.sampler_method = method
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def test_dry_run_vac_benzene(
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benzene_modifications,
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method,
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protocol_dry_settings,
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tmpdir
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):
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protocol_dry_settings.vacuum_simulation_settings.sampler_method = method
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -98,13 +109,10 @@ def test_dry_run_vac_benzene(benzene_modifications,
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assert not vac_sampler.is_periodic
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def test_confgen_fail_AFE(benzene_modifications, tmpdir):
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def test_confgen_fail_AFE(benzene_modifications, protocol_dry_settings, tmpdir):
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# check system parametrisation works even if confgen fails
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -134,13 +142,13 @@ def test_confgen_fail_AFE(benzene_modifications, tmpdir):
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assert vac_sampler
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def test_dry_run_solv_benzene(benzene_modifications, tmpdir):
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.solvent_output_settings.output_indices = "resname UNK"
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def test_dry_run_solv_benzene(
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benzene_modifications, protocol_dry_settings, tmpdir
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):
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protocol_dry_settings.solvent_output_settings.output_indices = "resname UNK"
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -179,24 +187,24 @@ def test_dry_run_solv_benzene(benzene_modifications, tmpdir):
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assert pdb.n_atoms == 12
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def test_dry_run_solv_benzene_tip4p(benzene_modifications, tmpdir):
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s = AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.vacuum_forcefield_settings.forcefields = [
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def test_dry_run_solv_benzene_tip4p(
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benzene_modifications, protocol_dry_settings, tmpdir
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):
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protocol_dry_settings.vacuum_forcefield_settings.forcefields = [
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"amber/ff14SB.xml", # ff14SB protein force field
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"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
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"amber/phosaa10.xml", # Handles THE TPO
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]
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s.solvent_forcefield_settings.forcefields = [
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protocol_dry_settings.solvent_forcefield_settings.forcefields = [
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"amber/ff14SB.xml", # ff14SB protein force field
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"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
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"amber/phosaa10.xml", # Handles THE TPO
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]
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s.solvation_settings.solvent_model = 'tip4pew'
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s.integrator_settings.reassign_velocities = True
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protocol_dry_settings.solvation_settings.solvent_model = 'tip4pew'
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protocol_dry_settings.integrator_settings.reassign_velocities = True
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protocol = AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -226,13 +234,12 @@ def test_dry_run_solv_benzene_tip4p(benzene_modifications, tmpdir):
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def test_dry_run_solv_benzene_noncubic(
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benzene_modifications, tmpdir
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benzene_modifications, protocol_dry_settings, tmpdir
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):
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s = AbsoluteSolvationProtocol.default_settings()
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s.solvation_settings.solvent_padding = 1.5 * offunit.nanometer
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s.solvation_settings.box_shape = 'dodecahedron'
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protocol_dry_settings.solvation_settings.solvent_padding = 1.5 * offunit.nanometer
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protocol_dry_settings.solvation_settings.box_shape = 'dodecahedron'
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protocol = AbsoluteSolvationProtocol(settings=s)
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protocol = AbsoluteSolvationProtocol(settings=protocol_dry_settings)
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stateA = ChemicalSystem({
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'benzene': benzene_modifications['benzene'],
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@@ -276,17 +283,16 @@ def test_dry_run_solv_benzene_noncubic(
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)
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def test_dry_run_solv_user_charges_benzene(benzene_modifications, tmpdir):
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def test_dry_run_solv_user_charges_benzene(
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benzene_modifications, protocol_dry_settings, tmpdir
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):
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"""
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Create a test system with fictitious user supplied charges and
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ensure that they are properly passed through to the constructed
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alchemical system.
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"""
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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def assign_fictitious_charges(offmol):
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@@ -385,19 +391,18 @@ def test_dry_run_solv_user_charges_benzene(benzene_modifications, tmpdir):
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),
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])
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def test_dry_run_charge_backends(
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CN_molecule, tmpdir, method, backend, ref_key, am1bcc_ref_charges
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CN_molecule, tmpdir, method, backend, ref_key,
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protocol_dry_settings, am1bcc_ref_charges
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):
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"""
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Check that partial charge generation with different backends
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works as expected.
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"""
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.partial_charge_settings.partial_charge_method = method
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s.partial_charge_settings.off_toolkit_backend = backend
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s.partial_charge_settings.nagl_model = 'openff-gnn-am1bcc-0.1.0-rc.1.pt'
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protocol_dry_settings.partial_charge_settings.partial_charge_method = method
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protocol_dry_settings.partial_charge_settings.off_toolkit_backend = backend
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protocol_dry_settings.partial_charge_settings.nagl_model = 'openff-gnn-am1bcc-0.1.0-rc.1.pt'
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protocol = openmm_afe.AbsoluteSolvationProtocol(settings=s)
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protocol = openmm_afe.AbsoluteSolvationProtocol(settings=protocol_dry_settings)
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# Create ChemicalSystems
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stateA = ChemicalSystem({
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@@ -441,14 +446,12 @@ def test_dry_run_charge_backends(
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)
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def test_high_timestep(benzene_modifications, tmpdir):
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s = AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.solvent_forcefield_settings.hydrogen_mass = 1.0
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s.vacuum_forcefield_settings.hydrogen_mass = 1.0
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def test_high_timestep(benzene_modifications, protocol_dry_settings, tmpdir):
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protocol_dry_settings.solvent_forcefield_settings.hydrogen_mass = 1.0
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protocol_dry_settings.vacuum_forcefield_settings.hydrogen_mass = 1.0
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protocol = AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -474,11 +477,10 @@ def test_high_timestep(benzene_modifications, tmpdir):
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@pytest.fixture
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def benzene_solvation_dag(benzene_modifications):
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s = AbsoluteSolvationProtocol.default_settings()
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def benzene_solvation_dag(benzene_modifications, protocol_dry_settings):
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protocol_dry_settings.protocol_repeats = 3
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -672,20 +674,21 @@ class TestProtocolResult:
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[[100 * offunit.picosecond, None],
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[None, None],
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[None, 100 * offunit.picosecond]])
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def test_dry_run_vacuum_write_frequency(benzene_modifications,
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positions_write_frequency,
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velocities_write_frequency,
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tmpdir):
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s = openmm_afe.AbsoluteSolvationProtocol.default_settings()
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s.protocol_repeats = 1
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s.solvent_output_settings.output_indices = "resname UNK"
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s.solvent_output_settings.positions_write_frequency = positions_write_frequency
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s.solvent_output_settings.velocities_write_frequency = velocities_write_frequency
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s.vacuum_output_settings.positions_write_frequency = positions_write_frequency
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s.vacuum_output_settings.velocities_write_frequency = velocities_write_frequency
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def test_dry_run_vacuum_write_frequency(
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benzene_modifications,
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positions_write_frequency,
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velocities_write_frequency,
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protocol_dry_settings,
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tmpdir
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):
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protocol_dry_settings.solvent_output_settings.output_indices = "resname UNK"
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protocol_dry_settings.solvent_output_settings.positions_write_frequency = positions_write_frequency
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protocol_dry_settings.solvent_output_settings.velocities_write_frequency = velocities_write_frequency
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protocol_dry_settings.vacuum_output_settings.positions_write_frequency = positions_write_frequency
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protocol_dry_settings.vacuum_output_settings.velocities_write_frequency = velocities_write_frequency
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protocol = openmm_afe.AbsoluteSolvationProtocol(
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settings=s,
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settings=protocol_dry_settings,
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)
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stateA = ChemicalSystem({
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@@ -26,6 +26,14 @@ import logging
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from openfe.tests.conftest import HAS_ESPALOMA
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@pytest.fixture()
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def vac_settings():
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settings = PlainMDProtocol.default_settings()
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settings.forcefield_settings.nonbonded_method = 'nocutoff'
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settings.engine_settings.compute_platform = None
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return settings
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def test_create_default_settings():
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settings = PlainMDProtocol.default_settings()
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@@ -87,10 +95,7 @@ def test_create_independent_repeat_ids(benzene_system):
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assert len(repeat_ids) == 6
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def test_dry_run_default_vacuum(benzene_vacuum_system, tmpdir):
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vac_settings = PlainMDProtocol.default_settings()
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
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def test_dry_run_default_vacuum(benzene_vacuum_system, vac_settings, tmpdir):
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protocol = PlainMDProtocol(
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settings=vac_settings,
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@@ -112,10 +117,8 @@ def test_dry_run_default_vacuum(benzene_vacuum_system, tmpdir):
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protocol.settings.thermo_settings.temperature)).barostat is None
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def test_dry_run_logger_output(benzene_vacuum_system, tmpdir, caplog):
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def test_dry_run_logger_output(benzene_vacuum_system, vac_settings, tmpdir, caplog):
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vac_settings = PlainMDProtocol.default_settings()
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
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vac_settings.simulation_settings.equilibration_length_nvt = 1 * unit.picosecond
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vac_settings.simulation_settings.equilibration_length = 1 * unit.picosecond
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vac_settings.simulation_settings.production_length = 1 * unit.picosecond
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@@ -143,10 +146,8 @@ def test_dry_run_logger_output(benzene_vacuum_system, tmpdir, caplog):
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assert "running production phase" in messages
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def test_dry_run_ffcache_none_vacuum(benzene_vacuum_system, tmpdir):
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def test_dry_run_ffcache_none_vacuum(benzene_vacuum_system, vac_settings, tmpdir):
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vac_settings = PlainMDProtocol.default_settings()
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
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vac_settings.output_settings.forcefield_cache = None
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protocol = PlainMDProtocol(
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@@ -166,9 +167,7 @@ def test_dry_run_ffcache_none_vacuum(benzene_vacuum_system, tmpdir):
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dag_unit.run(dry=True)['debug']['system']
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def test_dry_run_gaff_vacuum(benzene_vacuum_system, tmpdir):
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vac_settings = PlainMDProtocol.default_settings()
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
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def test_dry_run_gaff_vacuum(benzene_vacuum_system, vac_settings, tmpdir):
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vac_settings.forcefield_settings.small_molecule_forcefield = 'gaff-2.11'
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protocol = PlainMDProtocol(
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@@ -187,9 +186,7 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, tmpdir):
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@pytest.mark.skipif(not HAS_ESPALOMA, reason='espaloma is not available')
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def test_dry_run_espaloma_vacuum(benzene_vacuum_system, tmpdir):
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vac_settings = PlainMDProtocol.default_settings()
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
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def test_dry_run_espaloma_vacuum(benzene_vacuum_system, vac_settings, tmpdir):
|
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vac_settings.forcefield_settings.small_molecule_forcefield = 'espaloma-0.3.2'
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protocol = PlainMDProtocol(
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@@ -230,10 +227,8 @@ def test_dry_run_espaloma_vacuum(benzene_vacuum_system, tmpdir):
|
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),
|
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])
|
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def test_dry_run_charge_backends(
|
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CN_molecule, tmpdir, method, backend, ref_key, am1bcc_ref_charges
|
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CN_molecule, tmpdir, method, backend, ref_key, vac_settings, am1bcc_ref_charges
|
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):
|
||||
vac_settings = PlainMDProtocol.default_settings()
|
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vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.partial_charge_settings.partial_charge_method = method
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vac_settings.partial_charge_settings.off_toolkit_backend = backend
|
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vac_settings.partial_charge_settings.nagl_model = "openff-gnn-am1bcc-0.1.0-rc.1.pt"
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@@ -268,6 +263,7 @@ def test_dry_many_molecules_solvent(
|
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A basic test flushing "will it work if you pass multiple molecules"
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"""
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||||
settings = PlainMDProtocol.default_settings()
|
||||
settings.engine_settings.compute_platform = None
|
||||
|
||||
protocol = PlainMDProtocol(
|
||||
settings=settings,
|
||||
@@ -357,6 +353,7 @@ def test_dry_run_ligand_tip4p(benzene_system, tmpdir):
|
||||
environment (waters)
|
||||
"""
|
||||
settings = PlainMDProtocol.default_settings()
|
||||
settings.engine_settings.compute_platform = None
|
||||
settings.forcefield_settings.forcefields = [
|
||||
"amber/ff14SB.xml", # ff14SB protein force field
|
||||
"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
|
||||
@@ -386,6 +383,7 @@ def test_dry_run_ligand_tip4p(benzene_system, tmpdir):
|
||||
def test_dry_run_complex(benzene_complex_system, tmpdir):
|
||||
# this will be very time consuming
|
||||
settings = PlainMDProtocol.default_settings()
|
||||
settings.engine_settings.compute_platform = None
|
||||
|
||||
protocol = PlainMDProtocol(
|
||||
settings=settings,
|
||||
|
||||
@@ -44,6 +44,23 @@ from openfe.protocols.openmm_utils.charge_generation import (
|
||||
)
|
||||
|
||||
|
||||
@pytest.fixture()
|
||||
def vac_settings():
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
settings.engine_settings.compute_platform = None
|
||||
settings.protocol_repeats = 1
|
||||
return settings
|
||||
|
||||
|
||||
@pytest.fixture()
|
||||
def solv_settings():
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.engine_settings.compute_platform = None
|
||||
settings.protocol_repeats = 1
|
||||
return settings
|
||||
|
||||
|
||||
def test_compute_platform_warn():
|
||||
with pytest.warns(UserWarning, match="Non-CUDA platform selected: CPU"):
|
||||
omm_compute.get_openmm_platform('CPU')
|
||||
@@ -188,13 +205,11 @@ def test_validate_alchemical_components_missing_alchem_comp(
|
||||
@pytest.mark.parametrize('method', [
|
||||
'repex', 'sams', 'independent', 'InDePeNdENT'
|
||||
])
|
||||
def test_dry_run_default_vacuum(benzene_vacuum_system, toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping, method, tmpdir, benzene_toluene_topology):
|
||||
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
def test_dry_run_default_vacuum(
|
||||
benzene_vacuum_system, toluene_vacuum_system, benzene_to_toluene_mapping,
|
||||
method, vac_settings, tmpdir, benzene_toluene_topology
|
||||
):
|
||||
vac_settings.simulation_settings.sampler_method = method
|
||||
vac_settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=vac_settings,
|
||||
@@ -248,10 +263,10 @@ def test_dry_run_default_vacuum(benzene_vacuum_system, toluene_vacuum_system,
|
||||
assert_allclose(new_positions.value_in_unit(omm_unit.angstrom), htf._new_positions.value_in_unit(omm_unit.angstrom))
|
||||
|
||||
|
||||
def test_dry_run_gaff_vacuum(benzene_vacuum_system, toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
def test_dry_run_gaff_vacuum(
|
||||
benzene_vacuum_system, toluene_vacuum_system, benzene_to_toluene_mapping,
|
||||
vac_settings, tmpdir
|
||||
):
|
||||
vac_settings.forcefield_settings.small_molecule_forcefield = 'gaff-2.11'
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
@@ -271,16 +286,17 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, toluene_vacuum_system,
|
||||
|
||||
@pytest.mark.slow
|
||||
def test_dry_many_molecules_solvent(
|
||||
benzene_many_solv_system, toluene_many_solv_system,
|
||||
benzene_to_toluene_mapping, tmpdir
|
||||
benzene_many_solv_system,
|
||||
toluene_many_solv_system,
|
||||
benzene_to_toluene_mapping,
|
||||
solv_settings,
|
||||
tmpdir
|
||||
):
|
||||
"""
|
||||
A basic test flushing "will it work if you pass multiple molecules"
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
|
||||
# create DAG from protocol and take first (and only) work unit from within
|
||||
@@ -361,7 +377,7 @@ $$$$
|
||||
"""
|
||||
|
||||
|
||||
def test_dry_core_element_change(tmpdir):
|
||||
def test_dry_core_element_change(vac_settings, tmpdir):
|
||||
|
||||
benz = openfe.SmallMoleculeComponent(Chem.MolFromMolBlock(BENZ, removeHs=False))
|
||||
pyr = openfe.SmallMoleculeComponent(Chem.MolFromMolBlock(PYRIDINE, removeHs=False))
|
||||
@@ -371,11 +387,8 @@ def test_dry_core_element_change(tmpdir):
|
||||
{0: 0, 1: 10, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 8, 10: 7, 11: 6}
|
||||
)
|
||||
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=vac_settings,
|
||||
)
|
||||
|
||||
dag = protocol.create(
|
||||
@@ -403,16 +416,16 @@ def test_dry_core_element_change(tmpdir):
|
||||
|
||||
|
||||
@pytest.mark.parametrize('method', ['repex', 'sams', 'independent'])
|
||||
def test_dry_run_ligand(benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, method, tmpdir):
|
||||
def test_dry_run_ligand(
|
||||
benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, method, solv_settings, tmpdir
|
||||
):
|
||||
# this might be a bit time consuming
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.simulation_settings.sampler_method = method
|
||||
settings.protocol_repeats = 1
|
||||
settings.output_settings.output_indices = 'resname UNK'
|
||||
solv_settings.simulation_settings.sampler_method = method
|
||||
solv_settings.output_settings.output_indices = 'resname UNK'
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_system,
|
||||
@@ -434,15 +447,14 @@ def test_dry_run_ligand(benzene_system, toluene_system,
|
||||
assert pdb.n_atoms == 16
|
||||
|
||||
|
||||
def test_confgen_mocked_fail(benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
def test_confgen_mocked_fail(
|
||||
benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, solv_settings, tmpdir
|
||||
):
|
||||
"""
|
||||
Check that even if conformer generation fails, we can still perform a sim
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings=settings)
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings=solv_settings)
|
||||
|
||||
dag = protocol.create(stateA=benzene_system, stateB=toluene_system,
|
||||
mapping=benzene_to_toluene_mapping)
|
||||
@@ -464,6 +476,7 @@ def tip4p_hybrid_factory(
|
||||
Hybrid system with virtual sites in the environment (waters)
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.engine_settings.compute_platform = None
|
||||
settings.forcefield_settings.forcefields = [
|
||||
"amber/ff14SB.xml", # ff14SB protein force field
|
||||
"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
|
||||
@@ -578,17 +591,17 @@ def test_tip4p_check_vsite_parameters(tip4p_hybrid_factory):
|
||||
0.9 * unit.nanometer]
|
||||
)
|
||||
def test_dry_run_ligand_system_cutoff(
|
||||
cutoff, benzene_system, toluene_system, benzene_to_toluene_mapping, tmpdir
|
||||
cutoff, benzene_system, toluene_system, benzene_to_toluene_mapping,
|
||||
solv_settings, tmpdir
|
||||
):
|
||||
"""
|
||||
Test that the right nonbonded cutoff is propagated to the hybrid system.
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
|
||||
settings.forcefield_settings.nonbonded_cutoff = cutoff
|
||||
solv_settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
|
||||
solv_settings.forcefield_settings.nonbonded_cutoff = cutoff
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_system,
|
||||
@@ -633,11 +646,9 @@ def test_dry_run_ligand_system_cutoff(
|
||||
),
|
||||
])
|
||||
def test_dry_run_charge_backends(
|
||||
CN_molecule, tmpdir, method, backend, ref_key, am1bcc_ref_charges
|
||||
CN_molecule, tmpdir, method, backend, ref_key,
|
||||
vac_settings, am1bcc_ref_charges
|
||||
):
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.protocol_repeats = 1
|
||||
vac_settings.partial_charge_settings.partial_charge_method = method
|
||||
vac_settings.partial_charge_settings.off_toolkit_backend = backend
|
||||
vac_settings.partial_charge_settings.nagl_model = 'openff-gnn-am1bcc-0.1.0-rc.1.pt'
|
||||
@@ -702,16 +713,12 @@ def test_dry_run_charge_backends(
|
||||
|
||||
|
||||
@pytest.mark.flaky(reruns=3) # bad minimisation can happen
|
||||
def test_dry_run_user_charges(benzene_modifications, tmpdir):
|
||||
def test_dry_run_user_charges(benzene_modifications, vac_settings, tmpdir):
|
||||
"""
|
||||
Create a hybrid system with a set of fictitious user supplied charges
|
||||
and ensure that they are properly passed through to the constructed
|
||||
hybrid topology.
|
||||
"""
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=vac_settings,
|
||||
)
|
||||
@@ -828,26 +835,27 @@ def test_dry_run_user_charges(benzene_modifications, tmpdir):
|
||||
np.testing.assert_allclose(c_offsets[i], c_exp)
|
||||
|
||||
|
||||
def test_virtual_sites_no_reassign(benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
def test_virtual_sites_no_reassign(
|
||||
benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, solv_settings, tmpdir
|
||||
):
|
||||
"""
|
||||
Because of some as-of-yet not fully identified issue, not reassigning
|
||||
velocities will cause systems to NaN.
|
||||
See https://github.com/choderalab/openmmtools/issues/695
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.forcefield_settings.forcefields = [
|
||||
solv_settings.forcefield_settings.forcefields = [
|
||||
"amber/ff14SB.xml", # ff14SB protein force field
|
||||
"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
|
||||
"amber/phosaa10.xml", # Handles THE TPO
|
||||
]
|
||||
settings.solvation_settings.solvent_padding = 1.0 * unit.nanometer
|
||||
settings.forcefield_settings.nonbonded_cutoff = 0.9 * unit.nanometer
|
||||
settings.solvation_settings.solvent_model = 'tip4pew'
|
||||
settings.integrator_settings.reassign_velocities = False
|
||||
solv_settings.solvation_settings.solvent_padding = 1.0 * unit.nanometer
|
||||
solv_settings.forcefield_settings.nonbonded_cutoff = 0.9 * unit.nanometer
|
||||
solv_settings.solvation_settings.solvent_model = 'tip4pew'
|
||||
solv_settings.integrator_settings.reassign_velocities = False
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_system,
|
||||
@@ -862,15 +870,16 @@ def test_virtual_sites_no_reassign(benzene_system, toluene_system,
|
||||
dag_unit.run(dry=True)
|
||||
|
||||
|
||||
def test_dodecahdron_ligand_box(benzene_system, toluene_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
def test_dodecahdron_ligand_box(
|
||||
benzene_system, toluene_system, benzene_to_toluene_mapping,
|
||||
solv_settings, tmpdir
|
||||
):
|
||||
"""
|
||||
Test that a hybrid system with a dodechadron is built properly.
|
||||
"""
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
|
||||
settings.solvation_settings.box_shape = 'dodecahedron'
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings=settings)
|
||||
solv_settings.solvation_settings.solvent_padding = 1.5 * unit.nanometer
|
||||
solv_settings.solvation_settings.box_shape = 'dodecahedron'
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings=solv_settings)
|
||||
|
||||
dag = protocol.create(
|
||||
stateA=benzene_system,
|
||||
@@ -902,16 +911,16 @@ def test_dodecahdron_ligand_box(benzene_system, toluene_system,
|
||||
|
||||
@pytest.mark.slow
|
||||
@pytest.mark.parametrize('method', ['repex', 'sams', 'independent'])
|
||||
def test_dry_run_complex(benzene_complex_system, toluene_complex_system,
|
||||
benzene_to_toluene_mapping, method, tmpdir):
|
||||
def test_dry_run_complex(
|
||||
benzene_complex_system, toluene_complex_system,
|
||||
benzene_to_toluene_mapping, method, solv_settings, tmpdir
|
||||
):
|
||||
# this will be very time consuming
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.simulation_settings.sampler_method = method
|
||||
settings.protocol_repeats = 1
|
||||
settings.output_settings.output_indices = 'protein or resname UNK'
|
||||
solv_settings.simulation_settings.sampler_method = method
|
||||
solv_settings.output_settings.output_indices = 'protein or resname UNK'
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -945,15 +954,17 @@ def test_lambda_schedule(windows):
|
||||
assert len(lambdas.lambda_schedule) == windows
|
||||
|
||||
|
||||
def test_hightimestep(benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
def test_hightimestep(
|
||||
benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
vac_settings,
|
||||
tmpdir
|
||||
):
|
||||
vac_settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
|
||||
p = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=vac_settings,
|
||||
)
|
||||
|
||||
dag = p.create(
|
||||
@@ -969,15 +980,17 @@ def test_hightimestep(benzene_vacuum_system,
|
||||
dag_unit.run(dry=True)
|
||||
|
||||
|
||||
def test_n_replicas_not_n_windows(benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
def test_n_replicas_not_n_windows(
|
||||
benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
vac_settings,
|
||||
tmpdir
|
||||
):
|
||||
# For PR #125 we pin such that the number of lambda windows
|
||||
# equals the numbers of replicas used - TODO: remove limitation
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
# default lambda windows is 11
|
||||
settings.simulation_settings.n_replicas = 13
|
||||
settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.simulation_settings.n_replicas = 13
|
||||
|
||||
errmsg = ("Number of replicas 13 does not equal the number of "
|
||||
"lambda windows 11")
|
||||
@@ -985,7 +998,7 @@ def test_n_replicas_not_n_windows(benzene_vacuum_system,
|
||||
with tmpdir.as_cwd():
|
||||
with pytest.raises(ValueError, match=errmsg):
|
||||
p = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=vac_settings,
|
||||
)
|
||||
dag = p.create(
|
||||
stateA=benzene_vacuum_system,
|
||||
@@ -1178,11 +1191,10 @@ def test_element_change_warning(atom_mapping_basic_test_files):
|
||||
)
|
||||
|
||||
|
||||
def test_ligand_overlap_warning(benzene_vacuum_system, toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping, tmpdir):
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
|
||||
def test_ligand_overlap_warning(
|
||||
benzene_vacuum_system, toluene_vacuum_system, benzene_to_toluene_mapping,
|
||||
vac_settings, tmpdir
|
||||
):
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=vac_settings,
|
||||
)
|
||||
@@ -1521,13 +1533,14 @@ def tyk2_xml(tmp_path_factory):
|
||||
29: 23, 30: 24, 31: 25, 32: 26, 33: 27}
|
||||
)
|
||||
|
||||
settings: openmm_rfe.RelativeHybridTopologyProtocolSettings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.forcefield_settings.small_molecule_forcefield = 'openff-2.0.0'
|
||||
settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
settings.forcefield_settings.hydrogen_mass = 3.0
|
||||
settings.protocol_repeats = 1
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.engine_settings.compute_platform = None
|
||||
vac_settings.forcefield_settings.small_molecule_forcefield = 'openff-2.0.0'
|
||||
vac_settings.forcefield_settings.hydrogen_mass = 3.0
|
||||
vac_settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(settings)
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(vac_settings)
|
||||
|
||||
dag = protocol.create(
|
||||
stateA=openfe.ChemicalSystem({'ligand': lig23}),
|
||||
@@ -2070,7 +2083,9 @@ def _assert_total_charge(system, atom_classes, chgA, chgB):
|
||||
assert chgB == pytest.approx(np.sum(stateB_charges))
|
||||
|
||||
|
||||
def test_dry_run_alchemwater_solvent(benzene_to_benzoic_mapping, tmpdir):
|
||||
def test_dry_run_alchemwater_solvent(
|
||||
benzene_to_benzoic_mapping, solv_settings, tmpdir
|
||||
):
|
||||
stateA_system = openfe.ChemicalSystem(
|
||||
{'ligand': benzene_to_benzoic_mapping.componentA,
|
||||
'solvent': openfe.SolventComponent()}
|
||||
@@ -2079,7 +2094,6 @@ def test_dry_run_alchemwater_solvent(benzene_to_benzoic_mapping, tmpdir):
|
||||
{'ligand': benzene_to_benzoic_mapping.componentB,
|
||||
'solvent': openfe.SolventComponent()}
|
||||
)
|
||||
solv_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
solv_settings.alchemical_settings.explicit_charge_correction = True
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=solv_settings,
|
||||
@@ -2116,7 +2130,7 @@ def test_dry_run_alchemwater_solvent(benzene_to_benzoic_mapping, tmpdir):
|
||||
])
|
||||
def test_dry_run_complex_alchemwater_totcharge(
|
||||
mapping_name, chgA, chgB, correction, core_atoms,
|
||||
new_uniq, old_uniq, tmpdir, request, T4_protein_component,
|
||||
new_uniq, old_uniq, tmpdir, request, T4_protein_component, solv_settings
|
||||
):
|
||||
mapping = request.getfixturevalue(mapping_name)
|
||||
solvent = openfe.SolventComponent()
|
||||
@@ -2131,13 +2145,12 @@ def test_dry_run_complex_alchemwater_totcharge(
|
||||
'protein': T4_protein_component}
|
||||
)
|
||||
|
||||
settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
settings.solvation_settings.solvent_padding="0.9 nm"
|
||||
settings.solvation_settings.box_shape="dodecahedron"
|
||||
settings.alchemical_settings.explicit_charge_correction = correction
|
||||
solv_settings.solvation_settings.solvent_padding="0.9 nm"
|
||||
solv_settings.solvation_settings.box_shape="dodecahedron"
|
||||
solv_settings.alchemical_settings.explicit_charge_correction = correction
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=settings,
|
||||
settings=solv_settings,
|
||||
)
|
||||
|
||||
# create DAG from protocol and take first (and only) work unit from within
|
||||
@@ -2174,19 +2187,17 @@ def test_structural_analysis_error(tmpdir):
|
||||
[[100 * unit.picosecond, None],
|
||||
[None, None],
|
||||
[None, 100 * unit.picosecond]])
|
||||
def test_dry_run_vacuum_write_frequency(benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
positions_write_frequency,
|
||||
velocities_write_frequency,
|
||||
tmpdir,
|
||||
):
|
||||
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
def test_dry_run_vacuum_write_frequency(
|
||||
benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
positions_write_frequency,
|
||||
velocities_write_frequency,
|
||||
vac_settings,
|
||||
tmpdir,
|
||||
):
|
||||
vac_settings.output_settings.positions_write_frequency = positions_write_frequency
|
||||
vac_settings.output_settings.velocities_write_frequency = velocities_write_frequency
|
||||
vac_settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=vac_settings,
|
||||
@@ -2216,19 +2227,18 @@ def test_dry_run_vacuum_write_frequency(benzene_vacuum_system,
|
||||
@pytest.mark.parametrize('positions_write_frequency,velocities_write_frequency',
|
||||
[[100.1 * unit.picosecond, 100 * unit.picosecond],
|
||||
[100 * unit.picosecond, 100.1 * unit.picosecond]])
|
||||
def test_pos_write_frequency_not_divisible(benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
positions_write_frequency,
|
||||
velocities_write_frequency,
|
||||
tmpdir,
|
||||
):
|
||||
def test_pos_write_frequency_not_divisible(
|
||||
benzene_vacuum_system,
|
||||
toluene_vacuum_system,
|
||||
benzene_to_toluene_mapping,
|
||||
positions_write_frequency,
|
||||
velocities_write_frequency,
|
||||
tmpdir,
|
||||
vac_settings,
|
||||
):
|
||||
|
||||
vac_settings = openmm_rfe.RelativeHybridTopologyProtocol.default_settings()
|
||||
vac_settings.forcefield_settings.nonbonded_method = 'nocutoff'
|
||||
vac_settings.output_settings.positions_write_frequency = positions_write_frequency
|
||||
vac_settings.output_settings.velocities_write_frequency = velocities_write_frequency
|
||||
vac_settings.protocol_repeats = 1
|
||||
|
||||
protocol = openmm_rfe.RelativeHybridTopologyProtocol(
|
||||
settings=vac_settings,
|
||||
|
||||
@@ -49,9 +49,19 @@ EPSILON0 = (
|
||||
ONE_4PI_EPS0 = 1 / (4 * np.pi * EPSILON0) * EPSILON0.unit * 10.0 # nm -> angstrom
|
||||
|
||||
|
||||
@pytest.fixture()
|
||||
def protocol_dry_settings():
|
||||
# a set of settings for dry run tests
|
||||
s = SepTopProtocol.default_settings()
|
||||
s.engine_settings.compute_platform = None
|
||||
s.protocol_repeats = 1
|
||||
return s
|
||||
|
||||
|
||||
@pytest.fixture()
|
||||
def default_settings():
|
||||
return SepTopProtocol.default_settings()
|
||||
s = SepTopProtocol.default_settings()
|
||||
return s
|
||||
|
||||
|
||||
def test_create_default_settings():
|
||||
@@ -637,10 +647,9 @@ class TestNonbondedInteractions:
|
||||
def benzene_toluene_dag(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
default_settings.protocol_repeats = 1
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
return protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -710,18 +719,17 @@ def test_dry_run_methods(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
method,
|
||||
):
|
||||
|
||||
default_settings.solvent_simulation_settings.sampler_method = method
|
||||
default_settings.complex_simulation_settings.sampler_method = method
|
||||
default_settings.protocol_repeats = 1
|
||||
default_settings.complex_output_settings.output_indices = 'resname UNK'
|
||||
default_settings.solvent_output_settings.output_indices = 'resname UNK'
|
||||
protocol_dry_settings.solvent_simulation_settings.sampler_method = method
|
||||
protocol_dry_settings.complex_simulation_settings.sampler_method = method
|
||||
protocol_dry_settings.complex_output_settings.output_indices = 'resname UNK'
|
||||
protocol_dry_settings.solvent_output_settings.output_indices = 'resname UNK'
|
||||
|
||||
protocol = SepTopProtocol(
|
||||
settings=default_settings,
|
||||
settings=protocol_dry_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -765,16 +773,16 @@ def test_dry_run_ligand_system_pressure(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
"""
|
||||
Test that the right nonbonded cutoff is propagated to the system.
|
||||
"""
|
||||
# openfe settings requires openff/pint units
|
||||
default_settings.thermo_settings.pressure = pressure * offunit.bar
|
||||
protocol_dry_settings.thermo_settings.pressure = pressure * offunit.bar
|
||||
|
||||
protocol = SepTopProtocol(
|
||||
settings=default_settings,
|
||||
settings=protocol_dry_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -801,22 +809,21 @@ def test_virtual_sites_no_reassign(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
"""
|
||||
Test that an error is raised when not reassigning velocities
|
||||
in a system with virtual site.
|
||||
"""
|
||||
default_settings.protocol_repeats = 1
|
||||
default_settings.forcefield_settings.forcefields = [
|
||||
protocol_dry_settings.forcefield_settings.forcefields = [
|
||||
"amber/ff14SB.xml",
|
||||
"amber/tip4pew_standard.xml", # FF with VS
|
||||
]
|
||||
default_settings.solvent_solvation_settings.solvent_model = 'tip4pew'
|
||||
default_settings.integrator_settings.reassign_velocities = False
|
||||
protocol_dry_settings.solvent_solvation_settings.solvent_model = 'tip4pew'
|
||||
protocol_dry_settings.integrator_settings.reassign_velocities = False
|
||||
|
||||
protocol = SepTopProtocol(
|
||||
settings=default_settings,
|
||||
settings=protocol_dry_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -841,18 +848,18 @@ def test_dry_run_ligand_system_cutoff(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
"""
|
||||
Test that the right nonbonded cutoff is propagated to the system.
|
||||
"""
|
||||
default_settings.solvent_solvation_settings.solvent_padding = (
|
||||
protocol_dry_settings.solvent_solvation_settings.solvent_padding = (
|
||||
1.9 * offunit.nanometer
|
||||
)
|
||||
default_settings.forcefield_settings.nonbonded_cutoff = cutoff
|
||||
protocol_dry_settings.forcefield_settings.nonbonded_cutoff = cutoff
|
||||
|
||||
protocol = SepTopProtocol(
|
||||
settings=default_settings,
|
||||
settings=protocol_dry_settings,
|
||||
)
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -881,18 +888,17 @@ def test_dry_run_benzene_toluene_tip4p(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
default_settings.protocol_repeats = 1
|
||||
default_settings.forcefield_settings.forcefields = [
|
||||
protocol_dry_settings.forcefield_settings.forcefields = [
|
||||
"amber/ff14SB.xml", # ff14SB protein force field
|
||||
"amber/tip4pew_standard.xml", # FF we are testsing with the fun VS
|
||||
"amber/phosaa10.xml", # Handles THE TPO
|
||||
]
|
||||
default_settings.solvent_solvation_settings.solvent_model = "tip4pew"
|
||||
default_settings.integrator_settings.reassign_velocities = True
|
||||
protocol_dry_settings.solvent_solvation_settings.solvent_model = "tip4pew"
|
||||
protocol_dry_settings.integrator_settings.reassign_velocities = True
|
||||
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
# Create DAG from protocol, get the solvent units
|
||||
# and eventually dry run the first solvent unit
|
||||
@@ -926,15 +932,14 @@ def test_dry_run_benzene_toluene_noncubic(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
default_settings.protocol_repeats = 1
|
||||
default_settings.solvent_solvation_settings.solvent_padding = (
|
||||
protocol_dry_settings.solvent_solvation_settings.solvent_padding = (
|
||||
1.5 * offunit.nanometer
|
||||
)
|
||||
default_settings.solvent_solvation_settings.box_shape = "dodecahedron"
|
||||
protocol_dry_settings.solvent_solvation_settings.box_shape = "dodecahedron"
|
||||
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
# Create DAG from protocol, get the vacuum and solvent units
|
||||
# and eventually dry run the first solvent unit
|
||||
@@ -977,16 +982,14 @@ def test_dry_run_solv_user_charges_benzene_toluene(
|
||||
benzene_modifications,
|
||||
T4_protein_component,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
"""
|
||||
Create a test system with fictitious user supplied charges and
|
||||
ensure that they are properly passed through to the constructed
|
||||
alchemical system.
|
||||
"""
|
||||
default_settings.protocol_repeats = 1
|
||||
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
def assign_fictitious_charges(offmol):
|
||||
"""
|
||||
@@ -1091,13 +1094,12 @@ def test_high_timestep(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmpdir,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
default_settings.protocol_repeats = 1
|
||||
default_settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
default_settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
protocol_dry_settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
protocol_dry_settings.forcefield_settings.hydrogen_mass = 1.0
|
||||
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
@@ -1117,14 +1119,14 @@ def T4L_xml(
|
||||
benzene_complex_system,
|
||||
toluene_complex_system,
|
||||
tmp_path_factory,
|
||||
default_settings,
|
||||
protocol_dry_settings,
|
||||
):
|
||||
# Fixing the number of solvent molecules in the solvent settings
|
||||
# to test against reference xml
|
||||
default_settings.solvent_solvation_settings.solvent_padding = None
|
||||
default_settings.solvent_solvation_settings.number_of_solvent_molecules = 364
|
||||
default_settings.forcefield_settings.small_molecule_forcefield = "openff-2.1.1"
|
||||
protocol = SepTopProtocol(settings=default_settings)
|
||||
protocol_dry_settings.solvent_solvation_settings.solvent_padding = None
|
||||
protocol_dry_settings.solvent_solvation_settings.number_of_solvent_molecules = 364
|
||||
protocol_dry_settings.forcefield_settings.small_molecule_forcefield = "openff-2.1.1"
|
||||
protocol = SepTopProtocol(settings=protocol_dry_settings)
|
||||
|
||||
dag = protocol.create(
|
||||
stateA=benzene_complex_system,
|
||||
|
||||
@@ -22,7 +22,9 @@ import mdtraj as md
|
||||
|
||||
@pytest.fixture()
|
||||
def default_settings():
|
||||
return SepTopProtocol.default_settings()
|
||||
s = SepTopProtocol.default_settings()
|
||||
s.engine_settings.compute_platform = None
|
||||
return s
|
||||
|
||||
|
||||
def compare_energies(alchemical_system, positions):
|
||||
|
||||
@@ -94,3 +94,15 @@ class TestOpenMMSolvationSettings:
|
||||
|
||||
with pytest.raises(ValueError, match="must be a 1-D array"):
|
||||
s.box_size = np.array([[1, 2, 3], [1, 2, 3]]) * unit.angstrom
|
||||
|
||||
|
||||
class TestOpenMMEngineSettings:
|
||||
@pytest.mark.parametrize('platform', ['CUDA', 'OpenCL', 'cPu'])
|
||||
def test_ok_platforms(self, platform):
|
||||
s = omm_settings.OpenMMEngineSettings(compute_platform=platform)
|
||||
assert isinstance(s, omm_settings.OpenMMEngineSettings)
|
||||
|
||||
def test_fail_platform(self):
|
||||
with pytest.raises(ValueError, match="OpenMM compute backends"):
|
||||
_ = omm_settings.OpenMMEngineSettings(compute_platform="foo")
|
||||
|
||||
|
||||
Reference in New Issue
Block a user