def test_conformers(self):
"""Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
label = 'methylamine'
self.job1.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_0.out')
self.job1.job_status = ['done', 'done']
self.job2.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_1.out')
self.job2.job_status = ['done', 'done']
self.sched1.job_dict[label] = dict()
self.sched1.job_dict[label]['conformers'] = dict()
self.sched1.job_dict[label]['conformers'][0] = self.job1
self.sched1.job_dict[label]['conformers'][1] = self.job2
self.sched1.species_dict[label].conformer_energies = [None, None]
self.sched1.species_dict[label].conformers = [None, None]
self.sched1.parse_conformer_energy(job=self.job1, label=label, i=0)
self.sched1.parse_conformer_energy(job=self.job2, label=label, i=1)
expecting = [-251596443.5088726, -254221943.3698632]
self.assertEqual(self.sched1.species_dict[label].conformer_energies,
expecting)
self.sched1.species_dict[label].conformers[
0] = parser.parse_xyz_from_file(
self.job1.local_path_to_output_file)
self.sched1.species_dict[label].conformers[
1] = parser.parse_xyz_from_file(
self.job2.local_path_to_output_file)
self.sched1.determine_most_stable_conformer(label=label)
expecting = """N -0.75555952 -0.12937106 0.00000000
C 0.70855440 0.03887206 0.00000000
H 1.06395135 1.08711266 0.00000000
H 1.12732348 -0.45978507 0.88433277
H 1.12732348 -0.45978507 -0.88433277
H -1.16566701 0.32023496 0.81630508
H -1.16566701 0.32023496 -0.81630508
"""
self.assertEqual(self.sched1.species_dict[label].initial_xyz,
expecting)
methylamine_conf_path = os.path.join(
self.sched1.project_directory, 'output', 'Species', 'methylamine',
'geometry', 'conformers_after_optimization.txt')
self.assertTrue(os.path.isfile(methylamine_conf_path))
with open(methylamine_conf_path, 'r') as f:
lines = f.readlines()
self.assertTrue('conformers optimized at' in lines[0])
self.assertEqual(lines[11], 'SMILES: CN\n')
self.assertTrue('Relative Energy:' in lines[12])
self.assertEqual(lines[16][0], 'N')
self.sched1.run_conformer_jobs()
self.sched1.save_conformers_file(label='C2H6')
c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output',
'Species', 'C2H6', 'geometry',
'conformers_before_optimization.txt')
self.assertTrue(os.path.isfile(c2h6_conf_path))
with open(c2h6_conf_path, 'r') as f:
lines = f.readlines()
self.assertEqual(lines[1][0], 'C')
self.assertEqual(lines[9], '\n')
self.assertEqual(lines[17][0], 'H')
def check_converge_and_geom_consist(spc,
job_types=['composite', 'freq'],
basis_job='composite'):
basis_xyz = None
done = determine_convergence(spc[basis_job], basis_job, spc['ts'])
if done:
try:
basis_xyz = parse_xyz_from_file(spc[basis_job])
except:
pass
else:
if 'species' in spc \
and not spc['species'].check_xyz_isomorphism(xyz=basis_xyz):
basis_xyz = None
if not basis_xyz:
return
spc['geom'] = basis_xyz
spc['final_xyz'] = basis_xyz
spc['checkfile'] = ''
spc['charge'], spc['multiplicity'] = parse_charge_and_mult(spc[basis_job])
try:
spc['smiles'] = xyz_to_mol(spc['geom']).to_smiles()
except:
try:
spc['smiles'] = molecules_from_xyz(spc['geom'],
spc['multiplicity'],
spc['charge'])[0].to_smiles()
except:
spc['smiles'] = ''
logging.warning(f"Cannot generate SMILES for {spc['label']}")
# Assume checkfile is located under the same dir and named check.chk
check_path = os.path.join(os.path.dirname(spc[basis_job]), 'check.chk')
if os.path.isfile(check_path):
spc['checkfile'] = check_path
for job_type in job_types:
if job_type == basis_job:
continue
xyz_to_compare = None
done = determine_convergence(spc[job_type], job_type, spc['ts'])
if done:
try:
xyz_to_compare = parse_xyz_from_file(spc[job_type])
except:
pass
if not xyz_to_compare or not compare_confs(basis_xyz, xyz_to_compare):
# It seems like only basis job is well done
spc[job_type] = ''
continue
return spc
def xyz_to_mol(xyz):
if isinstance(xyz, dict):
string = xyz_to_xyz_file_format(xyz)
elif isinstance(xyz, str):
if not xyz[0].isdigit():
atom_num = len(xyz.splitlines())
string = f'{atom_num}\n\n' + xyz
else:
string = xyz
elif os.path.isfile(xyz):
string = xyz_to_xyz_file_format(parse_xyz_from_file(xyz))
else:
raise ValueError(f'Invalid xyz input, got: {xyz}')
molecule = pybel.readstring('xyz', string)
mol = Molecule()
from_ob_mol(mol, molecule.OBMol)
return mol
def generate_geom_info(spc, xyz_file=None):
if not 'geom' in spc:
xyz_file = xyz_file or os.path.join(spc['directory'], 'xyz.txt')
try:
spc['geom'] = parse_xyz_from_file(xyz_file)
except:
return
try:
mol = xyz_to_mol(spc['geom'])
except:
return
spc['smiles'] = mol.to_smiles()
spc['mol'] = mol.to_adjacency_list()
spc['bond_dict'] = enumerate_bonds(mol)
spc['atom_dict'] = mol.get_element_count()
spc['linear'] = is_linear(coordinates=np.array(spc['geom']['coords']))
spc['external_symmetry'], spc['optical_isomers'] = determine_symmetry(
spc['geom'])
return spc
def test_parse_xyz_from_file(self):
"""Test parsing xyz from a file"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.gjf')
path2 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.xyz')
path3 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'AIBN.gjf')
path4 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'molpro.in')
path5 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'qchem.in')
path6 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'qchem_output.out')
path7 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'TS.gjf')
xyz1 = parser.parse_xyz_from_file(path1)
xyz2 = parser.parse_xyz_from_file(path2)
xyz3 = parser.parse_xyz_from_file(path3)
xyz4 = parser.parse_xyz_from_file(path4)
xyz5 = parser.parse_xyz_from_file(path5)
xyz6 = parser.parse_xyz_from_file(path6)
xyz7 = parser.parse_xyz_from_file(path7)
self.assertEqual(xyz1.rstrip(), xyz2.rstrip())
self.assertTrue(
'C 1.40511900 0.21728200 0.07675200' in xyz1)
self.assertTrue(
'O -0.79314200 1.04818800 0.18134200' in xyz1)
self.assertTrue(
'H -0.43701200 -1.34990600 0.92900600' in xyz2)
self.assertTrue(
'C 2.12217963 -0.66843078 1.04808732' in
xyz3)
self.assertTrue(
'N 2.41731872 -1.07916417 2.08039935' in
xyz3)
spc3 = ARCSpecies(label='AIBN', xyz=xyz3)
self.assertEqual(len(spc3.mol.atoms), 24)
self.assertTrue(
'S -0.4204682221 -0.3909949822 0.0245352116'
in xyz4)
self.assertTrue(
'N -1.99742564 0.38106573 0.09139807' in
xyz5)
self.assertTrue(
'N -1.17538406 0.34366165 0.03265021' in xyz6)
self.assertEqual(len(xyz7.strip().splitlines()), 34)
def test_parse_xyz_from_file(self):
"""Test parsing xyz from a file"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.gjf')
path2 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.xyz')
path3 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'AIBN.gjf')
path4 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'molpro.in')
path5 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'qchem.in')
path6 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'qchem_output.out')
path7 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'TS.gjf')
path8 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'formaldehyde_coords.xyz')
path9 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'optim_traj_terachem.xyz') # test trajectories
path10 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'ethane_minimize_terachem_output.out')
path11 = os.path.join(arc_path, 'arc', 'testing',
'orca_example_opt.log')
xyz1 = parser.parse_xyz_from_file(path1)
xyz2 = parser.parse_xyz_from_file(path2)
xyz3 = parser.parse_xyz_from_file(path3)
xyz4 = parser.parse_xyz_from_file(path4)
xyz5 = parser.parse_xyz_from_file(path5)
xyz6 = parser.parse_xyz_from_file(path6)
xyz7 = parser.parse_xyz_from_file(path7)
xyz8 = parser.parse_xyz_from_file(path8)
xyz9 = parser.parse_xyz_from_file(path9)
xyz10 = parser.parse_xyz_from_file(path10)
xyz11 = parser.parse_xyz_from_file(path11)
self.assertEqual(xyz1, xyz2)
xyz1_str = xyz_to_str(xyz1)
xyz2_str = xyz_to_str(xyz2)
xyz3_str = xyz_to_str(xyz3)
xyz4_str = xyz_to_str(xyz4)
xyz5_str = xyz_to_str(xyz5)
xyz6_str = xyz_to_str(xyz6)
xyz9_str = xyz_to_str(xyz9)
xyz11_str = xyz_to_str(xyz11)
self.assertTrue(
'C 1.40511900 0.21728200 0.07675200' in xyz1_str)
self.assertTrue(
'O -0.79314200 1.04818800 0.18134200' in xyz1_str)
self.assertTrue(
'H -0.43701200 -1.34990600 0.92900600' in xyz2_str)
self.assertTrue(
'C 2.12217963 -0.66843078 1.04808732' in xyz3_str)
self.assertTrue(
'N 2.41731872 -1.07916417 2.08039935' in xyz3_str)
spc3 = ARCSpecies(label='AIBN', xyz=xyz3)
self.assertEqual(len(spc3.mol.atoms), 24)
self.assertTrue(
'S -0.42046822 -0.39099498 0.02453521' in xyz4_str)
self.assertTrue(
'N -1.99742564 0.38106573 0.09139807' in xyz5_str)
self.assertTrue(
'N -1.17538406 0.34366165 0.03265021' in xyz6_str)
self.assertEqual(len(xyz7['symbols']), 34)
self.assertEqual(len(xyz8['symbols']), 4)
expected_xyz_9 = """N -0.67665958 0.74524340 -0.41319355
H -1.26179357 1.52577220 -0.13687665
H 0.28392722 1.06723640 -0.44163375
N -0.75345799 -0.33268278 0.51180786
H -0.97153041 -0.02416219 1.45398654
H -1.48669570 -0.95874053 0.20627423
N 2.28178508 -0.42455356 0.14404399
H 1.32677989 -0.80557411 0.33156013"""
self.assertEqual(xyz9_str, expected_xyz_9)
self.assertIsNone(xyz10)
expected_xyz_11 = """C 0.00917900 -0.00000000 -0.00000000
O 1.20814900 -0.00000000 0.00000000
H -0.59436200 0.94730400 0.00000000
H -0.59436200 -0.94730400 0.00000000"""
self.assertEqual(xyz11_str, expected_xyz_11)
def test_conformers(self):
"""Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
label = 'methylamine'
self.job1.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_0.out')
self.job1.job_status = [
'done', {
'status': 'done',
'keywords': list(),
'error': '',
'line': ''
}
]
self.job2.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_1.out')
self.job2.job_status = [
'done', {
'status': 'done',
'keywords': list(),
'error': '',
'line': ''
}
]
self.sched1.job_dict[label] = dict()
self.sched1.job_dict[label]['conformers'] = dict()
self.sched1.job_dict[label]['conformers'][0] = self.job1
self.sched1.job_dict[label]['conformers'][1] = self.job2
self.sched1.species_dict[label].conformer_energies = [None, None]
self.sched1.species_dict[label].conformers = [None, None]
self.sched1.parse_conformer(job=self.job1, label=label, i=0)
self.sched1.parse_conformer(job=self.job2, label=label, i=1)
expecting = [-251596.4435088726, -254221.9433698632]
self.assertAlmostEqual(
self.sched1.species_dict[label].conformer_energies[0],
expecting[0], 5)
self.assertAlmostEqual(
self.sched1.species_dict[label].conformer_energies[1],
expecting[1], 5)
self.sched1.species_dict[label].conformers[
0] = parser.parse_xyz_from_file(
self.job1.local_path_to_output_file)
self.sched1.species_dict[label].conformers[
1] = parser.parse_xyz_from_file(
self.job2.local_path_to_output_file)
self.sched1.determine_most_stable_conformer(label=label)
expecting = {
'symbols': ('N', 'C', 'H', 'H', 'H', 'H', 'H'),
'isotopes': (14, 12, 1, 1, 1, 1, 1),
'coords':
((-0.75555952, -0.12937106, 0.0), (0.7085544, 0.03887206, 0.0),
(1.06395135, 1.08711266,
0.0), (1.12732348, -0.45978507,
0.88433277), (1.12732348, -0.45978507, -0.88433277),
(-1.16566701, 0.32023496, 0.81630508), (-1.16566701, 0.32023496,
-0.81630508))
}
self.assertTrue(
almost_equal_coords_lists(
self.sched1.species_dict[label].initial_xyz, expecting))
methylamine_conf_path = os.path.join(
self.sched1.project_directory, 'output', 'Species', 'methylamine',
'geometry', 'conformers', 'conformers_after_optimization.txt')
self.assertTrue(os.path.isfile(methylamine_conf_path))
with open(methylamine_conf_path, 'r') as f:
lines = f.readlines()
self.assertTrue(
'Conformers for methylamine, optimized at the wb97xd/def2svp level'
in lines[0])
self.assertEqual(lines[11], 'SMILES: CN\n')
self.assertTrue('Relative Energy:' in lines[12])
self.assertEqual(lines[16][0], 'N')
self.sched1.output['C2H6'] = {
'info': '',
'paths': {
'composite': '',
'freq': '',
'geo': ''
},
'isomorphism': '',
'warnings': '',
'errors': '',
'job_types': {
'opt': False,
'composite': False,
'sp': False,
'fine_grid': False,
'freq': False,
'conformers': False
},
'convergence': True,
'conformers': '',
'restart': ''
}
self.sched1.run_conformer_jobs()
save_conformers_file(project_directory=self.sched1.project_directory,
label='C2H6',
xyzs=self.sched1.species_dict['C2H6'].conformers,
level_of_theory=Level(method='CBS-QB3'),
multiplicity=1,
charge=0)
c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output',
'Species', 'C2H6', 'geometry',
'conformers',
'conformers_before_optimization.txt')
self.assertTrue(os.path.isfile(c2h6_conf_path))
with open(c2h6_conf_path, 'r') as f:
lines = f.readlines()
self.assertEqual(lines[0], 'conformer 0:\n')
self.assertEqual(lines[1][0], 'C')
self.assertEqual(lines[9], '\n')
self.assertEqual(lines[10], 'SMILES: CC\n')
def test_conformers(self):
"""Test the parse_conformer_energy() and determine_most_stable_conformer() methods"""
label = 'methylamine'
self.job1.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_0.out')
self.job1.job_status = [
'done', {
'status': 'done',
'keywords': list(),
'error': '',
'line': ''
}
]
self.job2.local_path_to_output_file = os.path.join(
arc_path, 'arc', 'testing', 'methylamine_conformer_1.out')
self.job2.job_status = [
'done', {
'status': 'done',
'keywords': list(),
'error': '',
'line': ''
}
]
self.sched1.job_dict[label] = dict()
self.sched1.job_dict[label]['conformers'] = dict()
self.sched1.job_dict[label]['conformers'][0] = self.job1
self.sched1.job_dict[label]['conformers'][1] = self.job2
self.sched1.species_dict[label].conformer_energies = [None, None]
self.sched1.species_dict[label].conformers = [None, None]
self.sched1.parse_conformer(job=self.job1, label=label, i=0)
self.sched1.parse_conformer(job=self.job2, label=label, i=1)
expecting = [-251596.4435088726, -254221.9433698632]
self.assertAlmostEqual(
self.sched1.species_dict[label].conformer_energies[0],
expecting[0], 5)
self.assertAlmostEqual(
self.sched1.species_dict[label].conformer_energies[1],
expecting[1], 5)
self.sched1.species_dict[label].conformers[
0] = parser.parse_xyz_from_file(
self.job1.local_path_to_output_file)
self.sched1.species_dict[label].conformers[
1] = parser.parse_xyz_from_file(
self.job2.local_path_to_output_file)
self.sched1.determine_most_stable_conformer(label=label)
expecting = """N -0.75555952 -0.12937106 0.00000000
C 0.70855440 0.03887206 0.00000000
H 1.06395135 1.08711266 0.00000000
H 1.12732348 -0.45978507 0.88433277
H 1.12732348 -0.45978507 -0.88433277
H -1.16566701 0.32023496 0.81630508
H -1.16566701 0.32023496 -0.81630508"""
self.assertEqual(self.sched1.species_dict[label].initial_xyz,
expecting)
methylamine_conf_path = os.path.join(
self.sched1.project_directory, 'output', 'Species', 'methylamine',
'geometry', 'conformers', 'conformers_after_optimization.txt')
self.assertTrue(os.path.isfile(methylamine_conf_path))
with open(methylamine_conf_path, 'r') as f:
lines = f.readlines()
self.assertTrue(
'Conformers for methylamine, optimized at the b3lyp/6-31g(d,p) EmpiricalDispersion=GD3BJ level'
in lines[0])
self.assertEqual(lines[10], 'SMILES: CN\n')
self.assertTrue('Relative Energy:' in lines[11])
self.assertEqual(lines[15][0], 'N')
self.sched1.output['C2H6'] = {
'info': '',
'paths': {
'composite': '',
'freq': '',
'geo': ''
},
'isomorphism': '',
'warnings': '',
'errors': '',
'job_types': {
'opt': False,
'composite': False,
'sp': False,
'fine_grid': False,
'freq': False,
'conformers': False
},
'convergence': True,
'conformers': '',
'restart': ''
}
self.sched1.run_conformer_jobs()
save_conformers_file(project_directory=self.sched1.project_directory,
label='C2H6',
xyzs=self.sched1.species_dict['C2H6'].conformers,
level_of_theory='level1',
multiplicity=1,
charge=0)
c2h6_conf_path = os.path.join(self.sched1.project_directory, 'output',
'Species', 'C2H6', 'geometry',
'conformers',
'conformers_before_optimization.txt')
self.assertTrue(os.path.isfile(c2h6_conf_path))
with open(c2h6_conf_path, 'r') as f:
lines = f.readlines()
self.assertEqual(lines[1][0], 'C')
self.assertEqual(lines[9], '\n')
self.assertEqual(lines[10], 'SMILES: CC\n')
