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_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