def test_restart_bde(self):
"""Test restarting ARC and attaining reaction a rate coefficient"""
restart_path = os.path.join(ARC_PATH, 'arc', 'testing', 'restart',
'3_restart_bde', 'restart.yml')
input_dict = read_yaml_file(path=restart_path)
arc1 = ARC(**input_dict)
arc1.execute()
report_path = os.path.join(ARC_PATH, 'Projects', 'test_restart_bde',
'output', 'BDE_report.txt')
with open(report_path, 'r') as f:
lines = f.readlines()
self.assertIn(' BDE report for anilino_radical:\n', lines)
self.assertIn(' (1, 9) N - H 353.92\n', lines)
self.assertIn(' (3, 4) C - H 454.12\n', lines)
self.assertIn(' (5, 10) C - H 461.75\n', lines)
def main():
# Parse the command-line arguments (requires the argparse module)
args = parse_command_line_arguments()
input_file = args.file
input_dict = read_file(input_file)
project_directory = os.path.abspath(os.path.dirname(args.file))
try:
input_dict['project']
except KeyError:
print('A project name must be provided!')
verbose = logging.INFO
if args.debug:
verbose = logging.DEBUG
elif args.quiet:
verbose = logging.WARNING
input_dict['verbose'] = input_dict['verbose'] if 'verbose' in input_dict else verbose
arc_object = ARC(input_dict=input_dict, project_directory=project_directory)
arc_object.execute()
def test_restart_rate(self):
"""Test restarting ARC and attaining reaction a rate coefficient"""
restart_path = os.path.join(ARC_PATH, 'arc', 'testing', 'restart',
'2_restart_rate', 'restart.yml')
input_dict = read_yaml_file(path=restart_path)
project = 'arc_project_for_testing_delete_after_usage_restart_rate'
project_directory = os.path.join(ARC_PATH, 'Projects', project)
input_dict['project'], input_dict[
'project_directory'] = project, project_directory
arc1 = ARC(**input_dict)
arc1.execute()
kinetics_library_path = os.path.join(project_directory, 'output',
'RMG libraries', 'kinetics',
'reactions.py')
with open(kinetics_library_path, 'r') as f:
got_rate = False
for line in f.readlines():
if "Arrhenius(A=(0.0636958,'cm^3/(mol*s)'), n=4.07981, Ea=(57.5474,'kJ/mol')" in line:
got_rate = True
break
self.assertTrue(got_rate)
def test_restart(self):
"""
Test restarting ARC through the ARC class in main.py via the input_dict argument of the API
Rather than through ARC.py. Check that all files are in place and tst file content.
"""
restart_path = os.path.join(arc_path, 'arc', 'testing', 'restart(H,H2O2,N2H3,CH3CO2).yml')
project = 'arc_project_for_testing_delete_after_usage2'
project_directory = os.path.join(arc_path, 'Projects', project)
arc1 = ARC(project=project, ess_settings=dict(),
input_dict=restart_path, project_directory=project_directory)
arc1.execute()
with open(os.path.join(project_directory, 'output', 'thermo.info'), 'r') as f:
thermo_sft_ccsdtf12_bac = False
for line in f.readlines():
if 'thermo_DFT_CCSDTF12_BAC' in line:
thermo_sft_ccsdtf12_bac = True
break
self.assertTrue(thermo_sft_ccsdtf12_bac)
with open(os.path.join(project_directory, 'arc_project_for_testing_delete_after_usage2.info'), 'r') as f:
sts, n2h3, oet, lot, ap = False, False, False, False, False
for line in f.readlines():
if 'Considered the following species and TSs:' in line:
sts = True
elif 'Species N2H3' in line:
n2h3 = True
elif 'Overall time since project initiation:' in line:
oet = True
elif 'Levels of theory used:' in line:
lot = True
elif 'ARC project arc_project_for_testing_delete_after_usage2' in line:
ap = True
self.assertTrue(sts)
self.assertTrue(n2h3)
self.assertTrue(oet)
self.assertTrue(lot)
self.assertTrue(ap)
with open(os.path.join(project_directory, 'arc.log'), 'r') as f:
aei, ver, git, spc, rtm, ldb, therm, src, ter = False, False, False, False, False, False, False, False, False
for line in f.readlines():
if 'ARC execution initiated on' in line:
aei = True
elif '# Version:' in line:
ver = True
elif 'The current git HEAD for ARC is:' in line:
git = True
elif 'Considering species: CH3CO2_rad' in line:
spc = True
elif 'All jobs for species N2H3 successfully converged. Run time: 1:16:03' in line:
rtm = True
elif 'Loading the RMG database...' in line:
ldb = True
elif 'Thermodynamics for H2O2:' in line:
therm = True
elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line:
src = True
elif 'ARC execution terminated on' in line:
ter = True
self.assertTrue(aei)
self.assertTrue(ver)
self.assertTrue(git)
self.assertTrue(spc)
self.assertTrue(rtm)
self.assertTrue(ldb)
self.assertTrue(therm)
self.assertTrue(src)
self.assertTrue(ter)
self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'thermo_parity_plots.pdf')))
with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'species_dictionary.txt'), 'r') as f:
lines = f.readlines()
adj_list = str(''.join([line for line in lines if (line and 'H2O2' not in line)]))
mol1 = Molecule().fromAdjacencyList(adj_list)
self.assertEqual(mol1.toSMILES(), str('OO'))
thermo_library_path = os.path.join(project_directory, 'output', 'RMG libraries', 'thermo',
'arc_project_for_testing_delete_after_usage2.py')
new_thermo_library_path = os.path.join(settings['database.directory'], 'thermo', 'libraries',
'arc_project_for_testing_delete_after_usage2.py')
# copy the generated library to RMG-database
shutil.copyfile(thermo_library_path, new_thermo_library_path)
db = RMGDatabase()
db.load(
path=settings['database.directory'],
thermoLibraries=[str('arc_project_for_testing_delete_after_usage2')],
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
kineticsFamilies='none',
kineticsDepositories=[],
statmechLibraries=None,
depository=False,
solvation=False,
testing=True,
)
spc2 = Species().fromSMILES(str('CC([O])=O'))
spc2.generate_resonance_structures()
spc2.thermo = db.thermo.getThermoData(spc2)
self.assertAlmostEqual(spc2.getEnthalpy(298), -178003.44650359568, 1)
self.assertAlmostEqual(spc2.getEntropy(298), 283.5983103176096, 1)
self.assertAlmostEqual(spc2.getHeatCapacity(1000), 118.99753808225603, 1)
self.assertTrue('arc_project_for_testing_delete_after_usage2' in spc2.thermo.comment)
# delete the generated library from RMG-database
os.remove(new_thermo_library_path)
def test_restart_thermo(self):
"""
Test restarting ARC through the ARC class in main.py via the input_dict argument of the API
Rather than through ARC.py. Check that all files are in place and the log file content.
"""
restart_path = os.path.join(ARC_PATH, 'arc', 'testing', 'restart',
'1_restart_thermo', 'restart.yml')
input_dict = read_yaml_file(path=restart_path)
project = 'arc_project_for_testing_delete_after_usage_restart_thermo'
project_directory = os.path.join(ARC_PATH, 'Projects', project)
input_dict['project'], input_dict[
'project_directory'] = project, project_directory
arc1 = ARC(**input_dict)
arc1.execute()
self.assertEqual(arc1.freq_scale_factor, 0.988)
self.assertTrue(
os.path.isfile(
os.path.join(project_directory, 'output', 'thermo.info')))
with open(os.path.join(project_directory, 'output', 'thermo.info'),
'r') as f:
thermo_dft_ccsdtf12_bac = False
for line in f.readlines():
if 'thermo_DFT_CCSDTF12_BAC' in line:
thermo_dft_ccsdtf12_bac = True
break
self.assertTrue(thermo_dft_ccsdtf12_bac)
with open(
os.path.join(
project_directory,
'arc_project_for_testing_delete_after_usage_restart_thermo.info'
), 'r') as f:
sts, n2h3, oet, lot, ap = False, False, False, False, False
for line in f.readlines():
if 'Considered the following species and TSs:' in line:
sts = True
elif 'Species N2H3' in line:
n2h3 = True
elif 'Overall time since project initiation:' in line:
oet = True
elif 'Levels of theory used:' in line:
lot = True
elif 'ARC project arc_project_for_testing_delete_after_usage_restart_thermo' in line:
ap = True
self.assertTrue(sts)
self.assertTrue(n2h3)
self.assertTrue(oet)
self.assertTrue(lot)
self.assertTrue(ap)
with open(os.path.join(project_directory, 'arc.log'), 'r') as f:
aei, ver, git, spc, rtm, ldb, therm, src, ter =\
False, False, False, False, False, False, False, False, False
for line in f.readlines():
if 'ARC execution initiated on' in line:
aei = True
elif '# Version:' in line:
ver = True
elif 'The current git HEAD for ARC is:' in line:
git = True
elif 'Considering species: CH3CO2_rad' in line:
spc = True
elif 'All jobs for species N2H3 successfully converged. Run time' in line:
rtm = True
elif 'Loading the RMG database...' in line:
ldb = True
elif 'Thermodynamics for H2O2' in line:
therm = True
elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line:
src = True
elif 'ARC execution terminated on' in line:
ter = True
self.assertTrue(aei)
self.assertTrue(ver)
self.assertTrue(git)
self.assertTrue(spc)
self.assertTrue(rtm)
self.assertTrue(ldb)
self.assertTrue(therm)
self.assertTrue(src)
self.assertTrue(ter)
self.assertTrue(
os.path.isfile(
os.path.join(project_directory, 'output',
'thermo_parity_plots.pdf')))
status = read_yaml_file(
os.path.join(project_directory, 'output', 'status.yml'))
self.assertEqual(
status['CH3CO2_rad']['isomorphism'],
'opt passed isomorphism check; '
'Conformers optimized and compared at b3lyp/6-31g(d,p) empiricaldispersion=gd3bj; '
)
self.assertTrue(status['CH3CO2_rad']['job_types']['sp'])
with open(
os.path.join(project_directory, 'output', 'Species', 'H2O2',
'arkane', 'species_dictionary.txt'), 'r') as f:
lines = f.readlines()
adj_list = ''
for line in lines:
if 'H2O2' not in line:
adj_list += line
if line == '\n':
break
mol1 = Molecule().from_adjacency_list(adj_list)
self.assertEqual(mol1.to_smiles(), 'OO')
thermo_library_path = os.path.join(
project_directory, 'output', 'RMG libraries', 'thermo',
'arc_project_for_testing_delete_after_usage_restart_thermo.py')
new_thermo_library_path = os.path.join(
rmg_settings['database.directory'], 'thermo', 'libraries',
'arc_project_for_testing_delete_after_usage_restart_thermo.py')
# copy the generated library to RMG-database
shutil.copyfile(thermo_library_path, new_thermo_library_path)
db = RMGDatabase()
db.load(
path=rmg_settings['database.directory'],
thermo_libraries=[
'arc_project_for_testing_delete_after_usage_restart_thermo'
],
transport_libraries=[],
reaction_libraries=[],
seed_mechanisms=[],
kinetics_families='none',
kinetics_depositories=[],
statmech_libraries=None,
depository=False,
solvation=False,
testing=True,
)
spc2 = Species(smiles='CC([O])=O')
spc2.generate_resonance_structures()
spc2.thermo = db.thermo.get_thermo_data(spc2)
self.assertAlmostEqual(spc2.get_enthalpy(298), -212439.26998495663, 1)
self.assertAlmostEqual(spc2.get_entropy(298), 283.3972662956835, 1)
self.assertAlmostEqual(spc2.get_heat_capacity(1000), 118.751379824224,
1)
self.assertTrue(
'arc_project_for_testing_delete_after_usage_restart_thermo' in
spc2.thermo.comment)
# delete the generated library from RMG-database
os.remove(new_thermo_library_path)
