def setUp(self):
arkane = Arkane()
jobList = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'methoxy.py'))
pdepjob = jobList[-1]
self.kineticsjob = jobList[0]
pdepjob.activeJRotor = True
network = pdepjob.network
self.Nisom = len(network.isomers)
self.Nreac = len(network.reactants)
self.Nprod = len(network.products)
self.Npath = len(network.pathReactions)
self.PathReaction2 = network.pathReactions[2]
self.TminValue = pdepjob.Tmin.value
self.Tmaxvalue = pdepjob.Tmax.value
self.TmaxUnits = pdepjob.Tmax.units
self.TlistValue = pdepjob.Tlist.value
self.PminValue = pdepjob.Pmin.value
self.Pcount = pdepjob.Pcount
self.Tcount = pdepjob.Tcount
self.GenTlist = pdepjob.generateTemperatureList()
self.PlistValue = pdepjob.Plist.value
self.maximumGrainSizeValue = pdepjob.maximumGrainSize.value
self.method = pdepjob.method
self.rmgmode = pdepjob.rmgmode
def setUp(cls):
"""A method that is run before each unit test in this class"""
arkane = Arkane()
job_list = arkane.load_input_file(
os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data',
'methoxy.py'))
pdepjob = job_list[-1]
cls.kineticsjob = job_list[0]
pdepjob.active_j_rotor = True
network = pdepjob.network
cls.Nisom = len(network.isomers)
cls.Nreac = len(network.reactants)
cls.Nprod = len(network.products)
cls.Npath = len(network.path_reactions)
cls.PathReaction2 = network.path_reactions[2]
cls.TminValue = pdepjob.Tmin.value
cls.Tmaxvalue = pdepjob.Tmax.value
cls.TmaxUnits = pdepjob.Tmax.units
cls.TlistValue = pdepjob.Tlist.value
cls.PminValue = pdepjob.Pmin.value
cls.Pcount = pdepjob.Pcount
cls.Tcount = pdepjob.Tcount
cls.GenTlist = pdepjob.generate_T_list()
cls.PlistValue = pdepjob.Plist.value
cls.maximum_grain_size_value = pdepjob.maximum_grain_size.value
cls.method = pdepjob.method
cls.rmgmode = pdepjob.rmgmode
def setUp(self):
arkane = Arkane()
jobList = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'methoxy.py'))
pdepjob = jobList[-1]
self.kineticsjob = jobList[0]
pdepjob.activeJRotor = True
network = pdepjob.network
self.Nisom = len(network.isomers)
self.Nreac = len(network.reactants)
self.Nprod = len(network.products)
self.Npath = len(network.pathReactions)
self.PathReaction2 = network.pathReactions[2]
self.TminValue = pdepjob.Tmin.value
self.Tmaxvalue = pdepjob.Tmax.value
self.TmaxUnits = pdepjob.Tmax.units
self.TlistValue = pdepjob.Tlist.value
self.PminValue = pdepjob.Pmin.value
self.Pcount = pdepjob.Pcount
self.Tcount = pdepjob.Tcount
self.GenTlist = pdepjob.generateTemperatureList()
self.PlistValue = pdepjob.Plist.value
self.maximumGrainSizeValue = pdepjob.maximumGrainSize.value
self.method = pdepjob.method
self.rmgmode = pdepjob.rmgmode
def setUpClass(cls):
arkane = Arkane()
cls.jobList = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),'data','methoxy_explore.py'))
for job in cls.jobList:
if not isinstance(job,ExplorerJob):
job.execute(outputFile=None, plot=None)
else:
thermoLibrary,kineticsLibrary,speciesList = arkane.getLibraries()
job.execute(outputFile=None, plot=None, speciesList=speciesList, thermoLibrary=thermoLibrary, kineticsLibrary=kineticsLibrary)
cls.thermoLibrary = thermoLibrary
cls.kineticsLibrary = kineticsLibrary
cls.explorerjob = cls.jobList[-1]
cls.pdepjob = cls.jobList[-2]
def setUpClass(cls):
"""A method that is run before each unit test in this class"""
arkane = Arkane()
cls.job_list = arkane.load_input_file(
os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'methoxy_explore.py'))
for job in cls.job_list:
if not isinstance(job, ExplorerJob):
job.execute(output_file=None, plot=None)
else:
thermo_library, kinetics_library, species_list = arkane.get_libraries()
job.execute(output_file=None, plot=None, thermo_library=thermo_library,
kinetics_library=kinetics_library)
cls.thermo_library = thermo_library
cls.kinetics_library = kinetics_library
cls.explorer_job = cls.job_list[-1]
cls.pdep_job = cls.job_list[-2]
def test_arkane_examples(self):
for example_type in self.example_types:
example_type_path = os.path.join(self.base_path, example_type)
for example in sorted(os.listdir(example_type_path)):
path = os.path.join(example_type_path, example)
arkane = Arkane(inputFile=os.path.join(path, 'input.py'), outputDirectory=path)
arkane.plot = True
logging.info("running {}".format(example))
arkane.execute()
with open(os.path.join(path, 'arkane.log'), 'r') as f:
log = f.readlines()
for line in log[::-1]:
if 'execution terminated' in line:
break
else:
self.failed.append([example_type, example])
error_message = 'Arkane example(s) failed: '
for example_type, example_name in self.failed:
error_message += '{1} in {0}; '.format(example_name, example_type)
self.assertFalse(self.failed, error_message)
def test_arkane_examples(self):
for example_type in self.example_types:
example_type_path = os.path.join(self.base_path, example_type)
for example in os.listdir(example_type_path):
path = os.path.join(example_type_path, example)
arkane = Arkane(inputFile=os.path.join(path, 'input.py'),
outputDirectory=path)
arkane.plot = True
arkane.execute()
with open(os.path.join(path, 'arkane.log'), 'r') as f:
log = f.readlines()
for line in log[::-1]:
if 'execution terminated' in line:
break
else:
self.failed.append([example_type, example])
error_message = 'Arkane example(s) failed: '
for example_type, example_name in self.failed:
error_message += '{1} in {0}; '.format(example_name, example_type)
self.assertFalse(self.failed, error_message)
def test_arkane_examples(self):
for example_type in self.example_types:
example_type_path = os.path.join(self.base_path, example_type)
for example in sorted(os.listdir(example_type_path)):
path = os.path.join(example_type_path, example)
arkane = Arkane(input_file=os.path.join(path, 'input.py'), output_directory=path)
arkane.plot = example_type != 'bac' # Don't plot BAC examples because they require a lot of memory
logging.info("running {}".format(example))
arkane.execute()
with open(os.path.join(path, 'arkane.log'), 'r') as f:
log = f.readlines()
for line in log[::-1]:
if 'execution terminated' in line:
break
else:
self.failed.append([example_type, example])
error_message = 'Arkane example(s) failed: '
for example_type, example_name in self.failed:
error_message += '{1} in {0}; '.format(example_name, example_type)
self.assertFalse(self.failed, error_message)
def test_arkane_two_parameter_arrhenius_fit(self):
test_path = os.path.join(self.test_base_path,
'two_parameter_arrhenius_fit')
file_to_remove = [
'output.py', 'chem.inp', 'supporting_information.csv'
]
for file in file_to_remove:
if os.path.exists(os.path.join(test_path, file)):
os.remove(os.path.join(test_path, file))
arkane = Arkane(input_file=os.path.join(test_path, 'input.py'),
output_directory=test_path)
arkane.plot = False
arkane.save_rmg_libraries = False
arkane.execute()
with open(os.path.join(test_path, 'output.py'), 'r') as f:
output = f.readlines()
reverse_output = output[::-1]
for i, line in enumerate(reverse_output):
if 'kinetics fitted using' in line:
msg_output = line.rstrip()
n_output = reverse_output[i - 5].split('=')[1].strip().replace(
',', '')
break
msg_expected = '# kinetics fitted using the two-parameter Arrhenius equation k = A * exp(-Ea/RT)'
self.assertEqual(msg_output, msg_expected)
n_expected = '0'
self.assertEqual(n_output, n_expected)
def setUpClass(cls):
"""
A method that is run ONCE before all unit tests in this class.
"""
cls.arkane = Arkane()
path = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)),
'examples', 'arkane', 'species')
cls.dump_path = os.path.join(path, 'C2H6')
cls.dump_input_path = os.path.join(cls.dump_path, 'input.py')
cls.dump_output_file = os.path.join(cls.dump_path, 'output.py')
cls.dump_yaml_file = os.path.join(cls.dump_path, 'species', 'C2H6.yml')
cls.load_path = os.path.join(path, 'C2H6_from_yaml')
cls.load_input_path = os.path.join(cls.load_path, 'input.py')
cls.load_output_file = os.path.join(cls.load_path, 'output.py')
if os.path.exists(cls.dump_yaml_file):
logging.debug('removing existing yaml file {0} before running tests'.format(cls.dump_yaml_file))
os.remove(cls.dump_yaml_file)
def setUp(cls):
"""A method that is run before each unit test in this class"""
arkane = Arkane()
cls.job_list = arkane.load_input_file(
os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data',
'Benzyl', 'input.py'))
def setUp(self):
arkane = Arkane()
self.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'Benzyl', 'input.py'))
def setUp(self):
arkane = Arkane()
self.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data', 'Benzyl', 'input.py'))