def setUp(self):
unittest.TestCase.setUp(self)
H2_thermo = BaseThermo(name='H2',
phase='G',
elements={'H': 2},
thermo_model=IdealGasThermo,
T_ref=c.T0('K'),
HoRT_ref=0.,
vib_energies=np.array([4306.1793]) *
c.c('cm/s') * c.h('eV s'),
potentialenergy=-6.7598,
geometry='linear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2'))
H2O_thermo = BaseThermo(
name='H2O',
phase='G',
elements={
'H': 2,
'O': 1
},
thermo_model=IdealGasThermo,
T_ref=c.T0('K'),
HoRT_ref=-241.826 / (c.R('kJ/mol/K') * c.T0('K')),
vib_energies=np.array([3825.434, 3710.264, 1582.432]) *
c.c('cm/s') * c.h('eV s'),
potentialenergy=-14.2209,
geometry='nonlinear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2O'))
O2_thermo = BaseThermo(name='H2O',
phase='G',
elements={'O': 2},
thermo_model=IdealGasThermo,
T_ref=c.T0('K'),
HoRT_ref=0.,
vib_energies=np.array([2205.]) * c.c('cm/s') *
c.h('eV s'),
potentialenergy=-9.86,
geometry='linear',
symmetrynumber=2,
spin=1,
atoms=molecule('O2'))
self.references = References(
references=[H2_thermo, H2O_thermo, O2_thermo])
species_path = '{}/thermdat_input.xlsx'.format(base_path)
T_low = 200.
T_high = 1100. #K
#Output information
thermdat_path = '{}/thermdat'.format(base_path)
#Miscellaneous options
show_plot = True
write_date = True
'''
Processing References
'''
#Import from excel
refs_input = read_excel(io=refs_path)
refs = References([BaseThermo(**ref_input) for ref_input in refs_input])
print('Reference Input:')
pprint(refs_input)
'''
Processing Input Species
'''
#Import from excel
species_data = read_excel(io=species_path)
species = [
Nasa(references=refs,
T_low=T_low,
T_high=T_high,
T_ref=c.T0('K'),
**specie_data) for specie_data in species_data
]
print('Species Input:')
#Input information
species_path = '{}/input_data.xlsx'.format(base_path)
T_low = 100.
T_high = 1500. #K
#Output information
thermdat_path = '{}/thermdat'.format(base_path)
#Miscellaneous options
show_plot = True
'''
Processing References
'''
#Import from excel
refs_data = read_excel(io=refs_path)
refs = References([BaseThermo(**ref_data) for ref_data in refs_data])
'''
Processing Surfaces
'''
surfaces_data = read_excel(io=surfaces_path)
'''
Processing Input Species
'''
#Import from excel
species_data = read_excel(io=species_path)
#Adjust potential energy to subtract contribution from surface
for specie_data in species_data:
#Find appropriate surface
for surface_data in surfaces_data:
if surface_data['name'] in specie_data['notes']:
specie_data['potentialenergy'] -= surface_data['potentialenergy']
T_low = 200.
T_high = 1100. #K
#Output information
thermdat_path = '{}/thermdat'.format(base_path)
#Miscellaneous options
show_plot = True
write_date = True
'''
Processing References
'''
#Import from excel
refs_input = read_excel(io=refs_path)
pprint(refs_input)
refs = References([Reference(**ref_input) for ref_input in refs_input])
print('Reference Input:')
pprint(refs_input)
print('Reference Data:')
pprint(refs[0])
'''
Processing Input Species
'''
#Import from excel
species_data = read_excel(io=species_path)
# pprint([specie_data['elements'] for specie_data in species_data])
species = []
for specie_data in species_data:
species.append(
Nasa.from_statmech(references=refs,
T_low=T_low,
#Input information
species_path = '{}/input_data.xlsx'.format(base_path)
T_low = 100.
T_high = 1500. #K
#Output information
thermdat_path = '{}/thermdat'.format(base_path)
#Miscellaneous options
save_plot = True
'''
Processing References
'''
#Import from excel
refs_data = read_excel(io=refs_path)
refs = References([Reference(**ref_data) for ref_data in refs_data])
'''
Processing Surfaces
'''
surfaces_data = read_excel(io=surfaces_path)
'''
Processing Input Species
'''
#Import from excel
species_data = read_excel(io=species_path)
#Adjust potential energy to subtract contribution from surface
for specie_data in species_data:
#Find appropriate surface
for surface_data in surfaces_data:
if surface_data['name'] in specie_data['notes']:
specie_data['potentialenergy'] -= surface_data['potentialenergy']
def setUp(self):
unittest.TestCase.setUp(self)
H2_thermo = Reference(name='H2',
phase='G',
elements={'H': 2},
T_ref=c.T0('K'),
HoRT_ref=0.,
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([4306.1793]),
potentialenergy=-6.7598,
geometry='linear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2'))
H2O_thermo = Reference(
name='H2O',
phase='G',
elements={
'H': 2,
'O': 1
},
T_ref=c.T0('K'),
HoRT_ref=-241.826 / (c.R('kJ/mol/K') * c.T0('K')),
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([3825.434, 3710.264, 1582.432]),
potentialenergy=-14.2209,
geometry='nonlinear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2O'))
O2_thermo = Reference(name='H2O',
phase='G',
elements={'O': 2},
T_ref=c.T0('K'),
HoRT_ref=0.,
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([2205.]),
potentialenergy=-9.86,
geometry='linear',
symmetrynumber=2,
spin=1,
atoms=molecule('O2'))
self.references = References(
references=[H2_thermo, H2O_thermo, O2_thermo])
class TestReferences(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
H2_thermo = Reference(name='H2',
phase='G',
elements={'H': 2},
T_ref=c.T0('K'),
HoRT_ref=0.,
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([4306.1793]),
potentialenergy=-6.7598,
geometry='linear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2'))
H2O_thermo = Reference(
name='H2O',
phase='G',
elements={
'H': 2,
'O': 1
},
T_ref=c.T0('K'),
HoRT_ref=-241.826 / (c.R('kJ/mol/K') * c.T0('K')),
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([3825.434, 3710.264, 1582.432]),
potentialenergy=-14.2209,
geometry='nonlinear',
symmetrynumber=2,
spin=0,
atoms=molecule('H2O'))
O2_thermo = Reference(name='H2O',
phase='G',
elements={'O': 2},
T_ref=c.T0('K'),
HoRT_ref=0.,
statmech_model=StatMech,
trans_model=trans.IdealTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.IdealElec,
rot_model=rot.RigidRotor,
vib_wavenumbers=np.array([2205.]),
potentialenergy=-9.86,
geometry='linear',
symmetrynumber=2,
spin=1,
atoms=molecule('O2'))
self.references = References(
references=[H2_thermo, H2O_thermo, O2_thermo])
def test_get_elements(self):
self.assertEqual(self.references.get_elements(), ('H', 'O'))
def test_get_elements_matrix(self):
elements_matrix = np.array([[2, 0], [2, 1], [0, 2]])
np.testing.assert_array_equal(self.references.get_elements_matrix(),
elements_matrix)
def test_calc_offset(self):
expected_element_offset = {'H': -123.10868373, 'O': -186.72503046}
calculated_element_offset = self.references.HoRT_element_offset
#Assess whether the keys are the same
self.assertSetEqual(set(expected_element_offset.keys()),
set(calculated_element_offset.keys()))
#Assess whether the values assigned to the keys are the close
for element in expected_element_offset.keys():
self.assertAlmostEqual(expected_element_offset[element],
calculated_element_offset[element])
def test_get_specie_offset(self):
elements = {'H': 2, 'O': 2}
self.assertAlmostEqual(
self.references.get_HoRT_offset(elements=elements),
619.6674284923677)
with self.assertWarns(RuntimeWarning):
self.assertEqual(
self.references.get_HoRT_offset(
elements={'non-referenced element': 1}), 0.)