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.,
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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')),
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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.,
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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_descriptors(self):
self.assertEqual(self.references.get_descriptors(), ('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_descriptors_matrix(),
elements_matrix)
def test_calc_offset(self):
expected_element_offset = {'H': -123.10868373, 'O': -186.72503046}
calculated_element_offset = self.references.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_HoRT(self):
elements = {'H': 2, 'O': 2}
self.assertAlmostEqual(self.references.get_HoRT(descriptors=elements),
619.6674284923677)
with self.assertWarns(RuntimeWarning):
self.assertEqual(
self.references.get_HoRT(
descriptors={'non-referenced element': 1}), 0.)
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.,
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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')),
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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.,
model=StatMech,
trans_model=trans.FreeTrans,
n_degrees=3,
vib_model=vib.HarmonicVib,
elec_model=elec.GroundStateElec,
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])
3027.6062, 2984.8436, 2966.1692,
2963.4684, 2959.7431, 1462.5683,
1457.4221, 1446.858, 1442.0357,
1438.7871, 1369.6901, 1352.6287,
1316.215, 1273.9426, 1170.4456,
1140.9699, 1049.3866, 902.8507,
885.3209, 865.5958, 735.1924,
362.7372, 266.3928, 221.4547],
symmetrynumber=2,
potentialenergy=-57.0864,
spin=0,
T_ref=298.15,
HoRT_ref=-42.2333,
**idealgas_defaults)
refs = References(references=[ethane_ref, propane_ref])
print(refs.offset)
# Passing the ``References`` object when we make our ``Nasa`` object produces a value closer to the one listed above.
# In[10]:
butane_nasa_ref = Nasa.from_statmech(name='butane',
statmech_model=butane_statmech,
T_low=298.,
T_high=800.,
elements={'C': 4, 'H': 10},
references=refs)
H_nasa_ref = butane_nasa_ref.get_H(T=298., units='kJ/mol')
H2O_ref = Reference(name='H2O',
elements={
'H': 2,
'O': 1
},
potentialenergy=-14.2209,
symmetrynumber=2,
spin=0.,
atoms=molecule('H2O'),
vib_wavenumbers=[3825.434, 3710.2642, 1582.432],
T_ref=298.,
HoRT_ref=-97.60604334,
**presets['idealgas'])
refs = References(references=[H2_ref, H2O_ref])
H2O_statmech = StatMech(name='H2O',
phase='G',
atoms=molecule('H2O'),
potentialenergy=-14.2209,
symmetrynumber=2,
spin=0,
references=refs,
vib_wavenumbers=[3825.434, 3710.264, 1582.432],
**presets['idealgas'])
H2O_TS_statmech = StatMech(name='H2O',
elements={
'H': 2,
'O': 1
# Print the properties of the catalyst site pprint(cat_site.to_dict()) # ### Reading reference species # In[2]: from pmutt.empirical.references import Reference, References references_data = read_excel(io=excel_path, sheet_name='refs') # Convert data to Reference objects and put them in a list refs_list = [Reference(**ref_data) for ref_data in references_data] # Assign the Reference objects to a References object so offsets can be calculated refs = References(references=refs_list) # Print out the offsets calculated print(refs.offset) # ### Reading species # In[3]: from pmutt.empirical.nasa import Nasa # Range of data to fit the Nasa polynomials T_low = 298. # K T_high = 800. # K species_data = read_excel(io=excel_path, sheet_name='species')
from pathlib import Path
from pmutt.io.excel import read_excel
from pmutt.empirical.references import Reference, References
# Find the location of Jupyter notebook
# Note that normally Python scripts have a __file__ variable but Jupyter notebook doesn't.
# Using pathlib can overcome this limiation
#notebook_path = Path().resolve()
notebook_path = os.path.dirname(__file__)
os.chdir(notebook_path)
input_path = './inputs/NH3_Input_Data.xlsx'
refs_data = read_excel(io=input_path, sheet_name='refs')
refs = [Reference(**ref_data) for ref_data in refs_data]
refs = References(references=refs)
# ### Reading Species
# In[3]:
from pmutt.empirical.nasa import Nasa
# Lower and higher temperatures
T_low = 298. # K
T_high = 800. # K
species_data = read_excel(io=input_path, sheet_name='species')
species = []
species_phases = {}
for ind_species_data in species_data:
# In[2]:
refs_input = read_excel(io='references.xlsx')
pprint(refs_input)
# Now that we've imported the data, we can make a ``References`` object, which is made of ``Reference`` objects using the following syntax.
# In[3]:
from pmutt.empirical.references import Reference, References
refs = References(descriptor='elements',
references=[Reference(**ref_input)
for ref_input in refs_input])
print(refs.offset)
# The ``References`` object calculated the offset between C, H, and O.
# ## Initialize the Nasa objects
# The ``from_statmech`` method allows us to initialize the Nasa objects from the data.
# In[4]:
from pmutt.empirical.nasa import Nasa
T_low = 300. # K