def test_compute_dataset(fractal_compute_server):
client = portal.FractalClient(fractal_compute_server.get_address(""))
ds_name = "He_PES"
ds = portal.collections.Dataset(ds_name, client, ds_type="ie")
# Adds options
option = portal.data.get_options("psi_default")
opt_ret = client.add_options([option])
opt_key = option["name"]
# Add two helium dimers to the DB at 4 and 8 bohr
He1 = portal.Molecule([[2, 0, 0, -2], [2, 0, 0, 2]], dtype="numpy", units="bohr", frags=[1])
ds.add_ie_rxn("He1", He1, attributes={"r": 4}, reaction_results={"default": {"Benchmark": 0.0009608501557}})
# Save the DB and re-acquire via classmethod
r = ds.save()
ds = portal.collections.Dataset.from_server(client, ds_name)
assert "Dataset(" in str(ds)
# Test collection lists
ret = client.list_collections()
assert ret == {"dataset": [ds_name]}
ret = client.list_collections("dataset")
assert ret == [ds_name]
He2 = portal.Molecule([[2, 0, 0, -4], [2, 0, 0, 4]], dtype="numpy", units="bohr", frags=[1])
ds.add_ie_rxn("He2", He2, attributes={"r": 4}, reaction_results={"default": {"Benchmark": -0.00001098794749}})
# Save the DB and overwrite the result, reacquire via client
r = ds.save(overwrite=True)
ds = client.get_collection("dataset", ds_name)
# Compute SCF/sto-3g
ret = ds.compute("SCF", "STO-3G")
assert len(ret["submitted"]) == 3
fractal_compute_server.objects["queue_nanny"].await_results()
# Query computed results
assert ds.query("SCF", "STO-3G")
assert pytest.approx(0.6024530476071095, 1.e-5) == ds.df.loc["He1", "SCF/STO-3G"]
assert pytest.approx(-0.006895035942673289, 1.e-5) == ds.df.loc["He2", "SCF/STO-3G"]
# Check results
assert ds.query("Benchmark", "", reaction_results=True)
assert pytest.approx(0.00024477933196125805, 1.e-5) == ds.statistics("MUE", "SCF/STO-3G")
def test_service_torsiondrive(dask_server_fixture):
client = portal.FractalClient(dask_server_fixture.get_address())
# Add a HOOH
hooh = portal.data.get_molecule("hooh.json")
mol_ret = client.add_molecules({"hooh": hooh})
# Geometric options
torsiondrive_options = {
"torsiondrive_meta": {
"dihedrals": [[0, 1, 2, 3]],
"grid_spacing": [90]
},
"optimization_meta": {
"program": "geometric",
"coordsys": "tric",
},
"qc_meta": {
"driver": "gradient",
"method": "UFF",
"basis": "",
"options": "none",
"program": "rdkit",
},
}
ret = client.add_service("torsiondrive", [mol_ret["hooh"]],
torsiondrive_options)
compute_key = ret[0]
# Manually handle the compute
nanny = dask_server_fixture.objects["queue_nanny"]
nanny.await_services(max_iter=5)
assert len(nanny.list_current_tasks()) == 0
# Get a TorsionDriveORM result and check data
result = client.get_procedures({"procedure": "torsiondrive"})[0]
assert isinstance(str(result), str) # Check that repr runs
assert pytest.approx(0.002597541340221565,
1e-5) == result.final_energies(0)
assert pytest.approx(0.000156553761859276,
1e-5) == result.final_energies(90)
assert pytest.approx(0.000156553761859271,
1e-5) == result.final_energies(-90)
assert pytest.approx(0.000753492556057886,
1e-5) == result.final_energies(180)
def torsiondrive_fixture(dask_server_fixture):
# Cannot use this fixture without these services. Also cannot use `mark` and `fixture` decorators
pytest.importorskip("torsiondrive")
pytest.importorskip("geometric")
pytest.importorskip("rdkit")
client = portal.FractalClient(dask_server_fixture.get_address())
# Add a HOOH
hooh = portal.data.get_molecule("hooh.json")
mol_ret = client.add_molecules({"hooh": hooh})
default_grid_spacing = 90
# Geometric options
torsiondrive_options = {
"torsiondrive_meta": {
"dihedrals": [[0, 1, 2, 3]],
"grid_spacing": [default_grid_spacing]
},
"optimization_meta": {
"program": "geometric",
"coordsys": "tric",
},
"qc_meta": {
"driver": "gradient",
"method": "UFF",
"basis": "",
"options": "none",
"program": "rdkit",
},
}
def spin_up_test(grid_spacing=default_grid_spacing, **keyword_augments):
instance_options = copy.deepcopy(torsiondrive_options)
instance_options["torsiondrive_meta"]["grid_spacing"] = [grid_spacing]
# instance_options = {**instance_options, **keyword_augments}
recursive_dict_merge(instance_options, keyword_augments)
ret = client.add_service("torsiondrive", [mol_ret["hooh"]],
instance_options)
nanny = dask_server_fixture.objects["queue_nanny"]
nanny.await_services(max_iter=5)
assert len(nanny.list_current_tasks()) == 0
return ret
yield spin_up_test, client
def test_compute_biofragment(fractal_compute_server):
# Obtain a client and build a BioFragment
client = portal.FractalClient(fractal_compute_server.get_address(""))
butane = portal.data.get_molecule("butane.json")
frag = portal.collections.BioFragment("CCCC", butane, client=client)
# Options
torsiondrive_options = {
"torsiondrive_meta": {
"internal_grid_spacing": [90],
"terminal_grid_spacing": [90],
},
"optimization_meta": {
"program": "geometric",
"coordsys": "tric",
},
"qc_meta": {
"driver": "gradient",
"method": "UFF",
"basis": "",
"options": "none",
"program": "rdkit",
},
}
frag.add_options_set("torsiondrive", "v1", torsiondrive_options)
# Required torsions
needed_torsions = {
"internal": [
[[0, 2, 3, 1]],
],
"terminal": [
[[3, 2, 0, 4]],
[[2, 3, 1, 7]],
]
} # yapf: disable
def test_compute_openffworkflow(fractal_compute_server):
# Obtain a client and build a BioFragment
client = portal.FractalClient(fractal_compute_server.get_address(""))
nanny = fractal_compute_server.objects["queue_nanny"]
openff_workflow_options = {
# Blank Fragmenter options
"enumerate_states": {},
"enumerate_fragments": {},
"torsiondrive_input": {},
# TorsionDrive, Geometric, and QC options
"torsiondrive_meta": {},
"optimization_meta": {
"program": "geometric",
"coordsys": "tric",
},
"qc_meta": {
"driver": "gradient",
"method": "UFF",
"basis": "",
"options": "none",
"program": "rdkit",
}
}
wf = portal.collections.OpenFFWorkflow("Workflow1", client=client, options=openff_workflow_options)
# Add a fragment and wait for the compute
hooh = portal.data.get_molecule("hooh.json")
fragment_input = {
"label1": {
"initial_molecule": hooh.to_json(),
"grid_spacing": [120],
"dihedrals": [[0, 1, 2, 3]],
},
}
wf.add_fragment("HOOH", fragment_input, provenance={})
assert set(wf.list_fragments()) == {"HOOH"}
nanny.await_services(max_iter=5)
final_energies = wf.list_final_energies()
assert final_energies.keys() == {"HOOH"}
assert final_energies["HOOH"].keys() == {"label1"}
final_molecules = wf.list_final_molecules()
assert final_molecules.keys() == {"HOOH"}
assert final_molecules["HOOH"].keys() == {"label1"}
# Add a second fragment
butane = portal.data.get_molecule("butane.json")
butane_id = butane.identifiers["canonical_isomeric_explicit_hydrogen_mapped_smiles"]
fragment_input = {
"label1": {
"initial_molecule": butane.to_json(),
"grid_spacing": [90],
"dihedrals": [[0, 2, 3, 1]],
},
}
wf.add_fragment(butane_id, fragment_input, provenance={})
assert set(wf.list_fragments()) == {butane_id, "HOOH"}
final_energies = wf.list_final_energies()
assert final_energies.keys() == {butane_id, "HOOH"}
assert final_energies[butane_id].keys() == {"label1"}
assert final_energies[butane_id]["label1"] is None