def vib_calc(vib_file, temp_r):
"""Description Needed
Parameters
----------
vib_file : type
description
temp_r : type
description
zpe_true : type
description
ent_true : type
description
Returns
-------
zpe :
description
svib :
description
"""
vib_prop = ut.read_vibdata(vib_file)
new_temp = ut.build_tempgrid(temp_r, vib_prop['Frequencies'])
freq = ut.build_freqgrid(vib_prop['Frequencies'], temp_r)
zpe = 0
zpe = zpe_calc(vib_prop)
svib = entropy_calc(freq, new_temp, vib_prop)
return zpe, svib
def test_entropy_calc(self):
vib_prop = ut.read_vibdata(test_data)
new_temp = ut.build_tempgrid(np.arange(10), vib_prop['Frequencies'])
freq = ut.build_freqgrid(vib_prop['Frequencies'], np.arange(10))
svib = vd.entropy_calc(freq, new_temp, vib_prop)[0]
avib = vd.entropy_calc(freq, new_temp, vib_prop)[1]
assert_approx_equal(svib[1], 4.5220660932E-05)
assert_approx_equal(avib[1], -1.492071248040480E-05)
def vib_calc(vib_file, temp_r):
"""Calculates and returns the Zero Point Energy (ZPE) and vibrational entropy for the temperature range provided.
Parameters
----------
vib_file : :py:attr:`str`):
yaml file containing vibrational frequencies
temp_r : :py:attr:`array_like`
Temperature range at which the vibrational entropy is calculated
Returns
-------
zpe : :py:attr:`float`
Zero Point energy for the system
svib : :py:attr:`array_like`
Vibrational entropy for the system calculated using the temperature range provided.
"""
vib_prop = ut.read_vibdata(vib_file)
new_temp = ut.build_tempgrid(temp_r, vib_prop['Frequencies'])
freq = ut.build_freqgrid(vib_prop['Frequencies'], temp_r)
zpe = 0
zpe = zpe_calc(vib_prop)
svib, avib = entropy_calc(freq, new_temp, vib_prop)
return zpe, svib, avib
def test_build_freqgrid(self):
x = ut.build_freqgrid(np.arange(10), np.arange(10))
assert np.array_equal(x[0], np.arange(10))
def test_entropy_calc(self):
vib_prop = ut.read_vibdata(test_data)
new_temp = ut.build_tempgrid(np.arange(10), vib_prop['Frequencies'])
freq = ut.build_freqgrid(vib_prop['Frequencies'], np.arange(10))
svib = vd.entropy_calc(freq, new_temp, vib_prop)
assert svib[1] == 5.77204564238144e-05