def setUp(self):
unittest.TestCase.setUp(self)
# Using Cl2 as an example
molecular_weight = 71.
self.trans_1D = trans.FreeTrans(molecular_weight=molecular_weight,
n_degrees=1)
self.trans_2D = trans.FreeTrans(molecular_weight=molecular_weight,
n_degrees=2)
self.trans_3D = trans.FreeTrans(molecular_weight=molecular_weight,
n_degrees=3)
self.trans_3D_dict = {
'class': "<class 'pmutt.statmech.trans.FreeTrans'>",
'molecular_weight': 71.,
'n_degrees': 3
}
self.T = 300 # K
self.P = 0.99768 # bar
# - rigid rotor rotations
# - ground state electronic structure -
# - ground state nuclear structure).
#
# <img src="images/butane.png" width=300>
# In[2]:
from ase.build import molecule
from pmutt.statmech import StatMech, trans, vib, rot, elec
butane_atoms = molecule('trans-butane')
'''Translational'''
butane_trans = trans.FreeTrans(n_degrees=3, atoms=butane_atoms)
'''Vibrational'''
butane_vib = vib.HarmonicVib(vib_wavenumbers=[3054.622862, 3047.573455, 3037.53448,
3030.21322, 3029.947329, 2995.758708,
2970.12166, 2968.142985, 2951.122942,
2871.560685, 1491.354921, 1456.480829,
1455.224163, 1429.084081, 1423.153673,
1364.456094, 1349.778994, 1321.137752,
1297.412109, 1276.969173, 1267.783512,
1150.401492, 1027.841298, 1018.203753,
945.310074, 929.15992, 911.661049,
808.685354, 730.986587, 475.287654,
339.164649, 264.682213, 244.584138,
219.956713, 115.923768, 35.56194])
# - no contribution from nuclear modes.
#
# <img src="images/H2_1.jpg" width=200>
# <a id='section_5_2'></a>
# ## 5.2. Initializing StatMech modes individually
# In[5]:
from ase.build import molecule
from pmutt.statmech import StatMech, trans, vib, rot, elec
H2_atoms = molecule('H2')
'''Translational'''
H2_trans = trans.FreeTrans(n_degrees=3, atoms=H2_atoms)
'''Vibrational'''
H2_vib = vib.HarmonicVib(vib_wavenumbers=[4342.]) # vib_wavenumbers in cm-1
'''Rotational'''
H2_rot = rot.RigidRotor(symmetrynumber=2, atoms=H2_atoms)
'''Electronic'''
H2_elec = elec.GroundStateElec(potentialenergy=-6.77,
spin=0) # potentialenergy in eV
'''StatMech Initialization'''
H2_statmech = StatMech(name='H2',
trans_model=H2_trans,
vib_model=H2_vib,
rot_model=H2_rot,
elec_model=H2_elec)
'''Calculate thermodynamic properties'''
H_statmech = H2_statmech.get_H(T=298., units='kJ/mol')