def test_given_esps(self, nme2ala2, methylammonium,
methylammonium_nme2ala2_charge_constraints, stage_2,
restraint_height, red_charges, job_esps, job_grids):
resp_options = RespOptions(stage_2=stage_2,
restraint_height_stage_1=restraint_height)
job = Job(
molecules=[methylammonium, nme2ala2],
charge_constraints=methylammonium_nme2ala2_charge_constraints,
resp_options=resp_options)
for mol in job.molecules:
for conf in mol.conformers:
for orient in conf.orientations:
fname = orient.qcmol.get_hash()
orient.esp = job_esps[fname]
orient.grid = job_grids[fname]
job.charge_constraints.split_conformers = False
job.compute_charges()
charges = np.concatenate(job.charges)
assert_allclose(charges[[0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14,
15]].sum(),
0,
atol=1e-7)
assert_allclose(charges[[27, 28, 29, 30, 31, 32]].sum(), 0, atol=1e-7)
assert_allclose(charges[25], 0.6163)
assert_allclose(charges[26], -0.5722)
assert_allclose(charges[18], charges[22])
for calculated, reference in zip(job.charges[::-1], red_charges[::-1]):
assert_allclose(calculated, reference, atol=1e-3)
def test_add_constraints_from_charges(self):
pytest.importorskip("psi4")
job = Job.parse_file(DMSO_JOB_WITH_ORIENTATION_ENERGIES)
charge_options = job.charge_constraints
assert len(charge_options.charge_sum_constraints) == 0
assert len(charge_options.charge_equivalence_constraints) == 0
constraints = job.generate_molecule_charge_constraints()
assert len(constraints.charge_sum_constraints) == 0
assert len(constraints.charge_equivalence_constraints) == 2
constraints.add_constraints_from_charges([
-0.43877469, 0.14814998, 0.17996033, 0.18716814, 0.35743529,
-0.5085439, -0.46067469, 0.19091725, 0.15500465, 0.18935764
])
assert len(constraints.charge_sum_constraints) == 2
assert len(constraints.charge_equivalence_constraints) == 2
surface_constraints = job.construct_surface_constraint_matrix()
assert surface_constraints.matrix.shape == (12, 11)
matrix = SparseGlobalConstraintMatrix.from_constraints(
surface_constraints, constraints)
ref_a = np.loadtxt(DMSO_STAGE_2_A)
ref_b = np.loadtxt(DMSO_STAGE_2_B)
assert_allclose(matrix.coefficient_matrix.toarray(), ref_a)
assert_allclose(matrix.constant_vector, ref_b)
def test_load_job_from_json():
job = Job.parse_file(TRIFLUOROETHANOL_JOB)
assert len(job.molecules) == 1
orientation = job.molecules[0].conformers[0].orientations[0]
assert_allclose(orientation.esp[0], 0.0054845008310878)
assert_allclose(orientation.esp[-1], 0.0290851723179761)
assert job.charges is None
def test_restrained(self, dmso, fractal_client):
options = RespOptions(stage_2=True, restrained_fit=True)
job = Job(molecules=[dmso], resp_options=options)
job.run(client=fractal_client)
resp_1 = [[
-0.31436216, 0.11376836, 0.14389443, 0.15583112, 0.30951582,
-0.50568553, -0.33670393, 0.15982115, 0.12029174, 0.153629
]]
resp_2 = [[
-0.25158642, 0.11778735, 0.11778735, 0.11778735, 0.30951582,
-0.50568553, -0.29298059, 0.12912489, 0.12912489, 0.12912489
]]
assert_allclose(job.stage_1_charges.restrained_charges,
resp_1,
atol=1e-5)
assert_allclose(job.stage_2_charges.restrained_charges,
resp_2,
atol=1e-5)
def test_symmetric_constraints(tmpdir):
pytest.importorskip("rdkit")
# formic smiles: "[H:4][C:2](=[O:1])[O-:3]"
mol = psiresp.Molecule.parse_file(FORMIC_ACID_JSON)
with tmpdir.as_cwd():
shutil.copytree(FORMIC_ACID_WKDIR, "psiresp_working_directory")
not_equiv = Job(molecules=[mol],
charge_constraints=dict(
symmetric_atoms_are_equivalent=False)).run()[0]
# 0 and 2 are the oxygens
assert not np.allclose(not_equiv[0], not_equiv[2])
equiv = Job(molecules=[mol],
charge_constraints=dict(
symmetric_atoms_are_equivalent=True)).run()[0]
assert_allclose(equiv[0], equiv[2])
def test_conformer_splitting_one_conf(self, jobfile, n_mol, n_confs,
nosplit, split):
job = Job.parse_file(jobfile)
charge_options = job.charge_constraints
assert len(job.molecules) == n_mol
assert [mol.n_conformers for mol in job.molecules] == n_confs
charge_options.split_conformers = False
surface_constraints = job.construct_surface_constraint_matrix()
assert surface_constraints.matrix.shape == nosplit
charge_options.split_conformers = True
surface_constraints = job.construct_surface_constraint_matrix()
assert surface_constraints.matrix.shape == split
def test_unrestrained(self, dmso, fractal_client):
options = RespOptions(stage_2=True, restrained_fit=False)
job = Job(molecules=[dmso], resp_options=options)
job.run(client=fractal_client)
esp_1 = [[
-0.43877469, 0.14814998, 0.17996033, 0.18716814, 0.35743529,
-0.5085439, -0.46067469, 0.19091725, 0.15500465, 0.18935764
]]
esp_2 = [[
-0.39199538, 0.15716631, 0.15716631, 0.15716631, 0.35743529,
-0.5085439, -0.43701446, 0.16953984, 0.16953984, 0.16953984
]]
assert_allclose(job.stage_1_charges.unrestrained_charges,
esp_1,
atol=1e-7)
assert_allclose(job.stage_2_charges.unrestrained_charges,
esp_2,
atol=1e-7)
chgrepr = """<RespCharges(restraint_height=0.0005, restraint_slope=0.1, restrained_fit=False, exclude_hydrogens=True) with 0 charge constraints; unrestrained_charges=[array([-0.43877, 0.14815, 0.17996, 0.18717, 0.35744, -0.50854,
-0.46067, 0.19092, 0.155 , 0.18936])], restrained_charges=None>"""
assert repr(job.stage_1_charges) == chgrepr
def test_run_manual(self, nme2ala2_empty, methylammonium_empty, tmpdir):
pytest.importorskip("rdkit")
nme2ala2_empty.optimize_geometry = True
methylammonium_empty.optimize_geometry = True
assert len(nme2ala2_empty.conformers) == 2
assert len(methylammonium_empty.conformers) == 1
job = Job(molecules=[methylammonium_empty, nme2ala2_empty])
data_wkdir = pathlib.Path(MANUAL_JOBS_WKDIR)
with tmpdir.as_cwd():
# OPTIMIZATION
assert not job.working_directory.exists()
with pytest.raises(SystemExit, match="Exiting to allow running"):
job.run()
assert job.working_directory.exists()
# check run file contents
runfile = job.qm_optimization_options.get_run_file(
job.working_directory)
assert str(
runfile
) == "psiresp_working_directory/optimization/run_optimization.sh"
with runfile.open() as f:
optlines = [x.strip() for x in f.readlines()]
assert len(optlines) == 4
# check existence and copy completed files in
opt_filenames = glob.glob(str(data_wkdir / "optimization/*"))
assert len(opt_filenames) == 4
for file in opt_filenames:
path = pathlib.Path(file.split("manual_jobs/")[1])
assert path.exists()
if file.endswith("msgpack"):
assert f"psi4 --qcschema {path.name}" in optlines
shutil.copyfile(file, path)
assert all(not conf.is_optimized for conf in job.iter_conformers())
# SINGLE POINT
assert not job.qm_esp_options.get_working_directory(
job.working_directory).exists()
with pytest.raises(SystemExit, match="Exiting to allow running"):
job.run()
assert all(conf.is_optimized for conf in job.iter_conformers())
# check run file contents
runfile = job.qm_esp_options.get_run_file(job.working_directory)
assert str(
runfile
) == "psiresp_working_directory/single_point/run_single_point.sh"
with runfile.open() as f:
splines = [x.strip() for x in f.readlines()]
assert len(splines) == 11
# check existence and copy completed files in
opt_filenames = glob.glob(str(data_wkdir / "single_point/*"))
assert len(opt_filenames) == 11
for file in opt_filenames:
path = pathlib.Path(file.split("manual_jobs/")[1])
assert path.exists()
if file.endswith("msgpack"):
assert f"psi4 --qcschema {path.name}" in splines
shutil.copyfile(file, path)
job.run()
methylammonium_charges = [
-0.281849, 0.174016, 0.174016, 0.174016, -0.528287, 0.215501,
0.857086, 0.215501
]
nme2ala2_charges = [
4.653798, -1.174226, -1.1742263, -1.1742263, -1.2224316,
0.1732717, -3.9707787, 0.8309516, 8.291471, 4.749616,
-1.870866, -1.870866, -1.870866, 2.275405, -1.3199896,
-1.3199896, -1.3199896, 1.6195477, -1.5787892, -14.898019,
2.9755072, 30.303230, -7.035844, -7.035844, -7.035844
]
assert_allclose(job.charges[0], methylammonium_charges, atol=1e-6)
assert_allclose(job.charges[1], nme2ala2_charges, atol=1e-6)