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Updated the frequency scale factor assignemt
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- Corrected scaling factors which were for ZPE instead of freq
- Organized the references
- Removed commented out levels
- Added some more levels (one of which calculated by Duminda, as noted)
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@alongd
alongd committed Jun 16, 2019
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118 changes: 59 additions & 59 deletions arkane/statmech.py
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Expand Up @@ -1227,79 +1227,79 @@ def projectRotors(conformer, F, rotors, linear, is_ts, label):
return np.sqrt(eig[-Nvib:]) / (2 * math.pi * constants.c * 100)


def assign_frequency_scale_factor(model_chemistry):
def assign_frequency_scale_factor(freq_level):
"""
Assign the frequency scaling factor according to the model chemistry.
Refer to https://comp.chem.umn.edu/freqscale/index.html for future updates of these factors
Sources:
[1] I.M. Alecu, J. Zheng, Y. Zhao, D.G. Truhlar, J. Chem. Theory Comput. 2010, 6, 2872, DOI: 10.1021/ct100326h
[2] http://cccbdb.nist.gov/vibscalejust.asp
[3] http://comp.chem.umn.edu/freqscale/190107_Database_of_Freq_Scale_Factors_v4.pdf
[4] Calculated as described in 10.1021/ct100326h
[5] J.A. Montgomery, M.J. Frisch, J. Chem. Phys. 1999, 110, 2822–2827, DOI: 10.1063/1.477924
Args:
model_chemistry (str, unicode): The frequency level of theory.
freq_level (str, unicode): The frequency level of theory.
Returns:
float: The frequency scaling factor (1 by default).
"""
freq_dict = {'cbs-qb3': 0.99, # J. Chem. Phys. 1999, 110, 2822–2827
'cbs-qb3-paraskevas': 0.99,
# 'g3': ,
'm08so/mg3s*': 0.983, # DOI: 10.1021/ct100326h, taken as 'M08-SO/MG3S'
'm06-2x/cc-pvtz': 0.955, # http://cccbdb.nist.gov/vibscalejust.asp
# 'klip_1': ,
# 'klip_2': ,
# 'klip_3': ,
# 'klip_2_cc': ,
# 'ccsd(t)-f12/cc-pvdz-f12_h-tz': ,
# 'ccsd(t)-f12/cc-pvdz-f12_h-qz': ,
'ccsd(t)-f12/cc-pvdz-f12': 0.979,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/cc-pvdz'
'ccsd(t)-f12/cc-pvtz-f12': 0.984,
# Taken from https://comp.chem.umn.edu/freqscale/version3b2.htm as CCSD(T)-F12a/cc-pVTZ-F12
'ccsd(t)-f12/cc-pvqz-f12': 0.970,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/cc-pvqz'
'ccsd(t)-f12/cc-pcvdz-f12': 0.971,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/cc-pcvdz'
'ccsd(t)-f12/cc-pcvtz-f12': 0.966,
# 'ccsd(t)-f12/cc-pcvqz-f12': ,
# 'ccsd(t)-f12/cc-pvtz-f12(-pp)': ,
# 'ccsd(t)/aug-cc-pvtz(-pp)': ,
'ccsd(t)-f12/aug-cc-pvdz': 0.963,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/aug-cc-pvdz'
'ccsd(t)-f12/aug-cc-pvtz': 0.970,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/aug-cc-pvtz'
'ccsd(t)-f12/aug-cc-pvqz': 0.975,
# http://cccbdb.nist.gov/vibscalejust.asp, taken as 'ccsd(t)/aug-cc-pvqz'
# 'b-ccsd(t)-f12/cc-pvdz-f12': ,
# 'b-ccsd(t)-f12/cc-pvtz-f12': ,
# 'b-ccsd(t)-f12/cc-pvqz-f12': ,
# 'b-ccsd(t)-f12/cc-pcvdz-f12': ,
# 'b-ccsd(t)-f12/cc-pcvtz-f12': ,
# 'b-ccsd(t)-f12/cc-pcvqz-f12': ,
# 'b-ccsd(t)-f12/aug-cc-pvdz': ,
# 'b-ccsd(t)-f12/aug-cc-pvtz': ,
# 'b-ccsd(t)-f12/aug-cc-pvqz': ,
'mp2_rmp2_pvdz': 0.953, # http://cccbdb.nist.gov/vibscalejust.asp, taken as ',p2/cc-pvdz'
'mp2_rmp2_pvtz': 0.950, # http://cccbdb.nist.gov/vibscalejust.asp, taken as ',p2/cc-pvdz'
'mp2_rmp2_pvqz': 0.962, # http://cccbdb.nist.gov/vibscalejust.asp, taken as ',p2/cc-pvdz'
'ccsd-f12/cc-pvdz-f12': 0.947, # http://cccbdb.nist.gov/vibscalejust.asp, taken as ccsd/cc-pvdz
# 'ccsd(t)-f12/cc-pvdz-f12_noscale': ,
# 'g03_pbepbe_6-311++g_d_p': ,
# 'fci/cc-pvdz': ,
# 'fci/cc-pvtz': ,
# 'fci/cc-pvqz': ,
# 'bmk/cbsb7': ,
# 'bmk/6-311g(2d,d,p)': ,
'b3lyp/6-31g**': 0.961, # http://cccbdb.nist.gov/vibscalejust.asp
'b3lyp/6-311+g(3df,2p)': 0.967, # http://cccbdb.nist.gov/vibscalejust.asp
'wb97x-d/aug-cc-pvtz': 0.974,
# Taken from https://comp.chem.umn.edu/freqscale/version3b2.htm as ωB97X-D/maug-cc-pVTZ
freq_dict = {'hf/sto-3g': 0.817, # [2]
'hf/6-31g': 0.903, # [2]
'hf/6-31g(d)': 0.899, # [2]
'hf/6-31g(d,p)': 0.903, # [2]
'hf/6-31g+(d,p)': 0.904, # [2]
'hf/6-31+g(d,p)': 0.915 * 1.014, # [1] Table 7
'pm3': 0.940 * 1.014, # [1] Table 7, the 0.940 value is the ZPE scale factor
'pm6': 1.078 * 1.014, # [1] Table 7, the 1.078 value is the ZPE scale factor
'b3lyp/6-31g(d,p)': 0.961, # [2]
'b3lyp/6-311g(d,p)': 0.967, # [2]
'b3lyp/6-311+g(3df,2p)': 0.967, # [2]
'b3lyp/6-311+g(3df,2pd)': 0.970, # [2]
'm06-2x/6-31g(d,p)': 0.952, # [2]
'm06-2x/6-31+g(d,p)': 0.979, # [3]
'm06-2x/6-311+g(d,p)': 0.983, # [3]
'm06-2x/6-311++g(d,p)': 0.983, # [3]
'm06-2x/cc-pvtz': 0.955, # [2]
'm06-2x/aug-cc-pvdz': 0.993, # [3]
'm06-2x/aug-cc-pvtz': 0.985, # [1] Table 3, [3]
'm06-2x/def2-tzvp': 0.984, # [3]
'm06-2x/def2-qzvp': 0.983, # [3]
'm06-2x/def2-tzvpp': 0.983, # [1] Table 3, [3]
'm08so/mg3s*': 0.995, # [1] Table 3, taken as 'M08-SO/MG3S'
'wb97x-d/aug-cc-pvtz': 0.988, # [3], taken as 'ωB97X-D/maug-cc-pVTZ'
'wb97xd/6-311++g(d,p)': 0.988, # [4]
'mp2_rmp2_pvdz': 0.953, # [2], taken as 'MP2/cc-pVDZ'
'mp2_rmp2_pvtz': 0.950, # [2], taken as 'MP2/cc-pVTZ'
'mp2_rmp2_pvqz': 0.962, # [2], taken as 'MP2/cc-pVQZ'
'cbs-qb3': 0.99 * 1.014, # [5], the 0.99 value is the ZPE scale factor of CBS-QB3
'cbs-qb3-paraskevas': 0.99 * 1.014, # [5], the 0.99 value is the ZPE scale factor of CBS-QB3
'ccsd-f12/cc-pvdz-f12': 0.947, # [2], taken as 'CCSD/cc-pVDZ'
'ccsd(t)/cc-pvdz': 0.979, # [2]
'ccsd(t)/cc-pvtz': 0.975, # [2]
'ccsd(t)/cc-pvqz': 0.970, # [2]
'ccsd(t)/aug-cc-pvdz': 0.963, # [2]
'ccsd(t)/aug-cc-pvtz': 1.001, # [3]
'ccsd(t)/aug-cc-pvqz': 0.975, # [2]
'ccsd(t)/cc-pv(t+d)z': 0.965, # [2]
'ccsd(t)-f12/cc-pvdz-f12': 0.997, # [3], taken as 'CCSD(T)-F12a/cc-pVDZ-F12'
'ccsd(t)-f12/cc-pvtz-f12': 0.998, # [3], taken as 'CCSD(T)-F12a/cc-pVTZ-F12'
'ccsd(t)-f12/cc-pvqz-f12': 0.998, # [3], taken as 'CCSD(T)-F12b/VQZF12//CCSD(T)-F12a/TZF'
'ccsd(t)-f12/cc-pcvdz-f12': 0.997, # [3], taken as 'CCSD(T)-F12a/cc-pVDZ-F12'
'ccsd(t)-f12/cc-pcvtz-f12': 0.998, # [3], taken as 'CCSD(T)-F12a/cc-pVTZ-F12'
'ccsd(t)-f12/aug-cc-pvdz': 0.997, # [3], taken as 'CCSD(T)/cc-pVDZ'
'ccsd(t)-f12/aug-cc-pvtz': 0.998, # [3], taken as CCSD(T)-F12a/cc-pVTZ-F12
'ccsd(t)-f12/aug-cc-pvqz': 0.998, # [3], taken as 'CCSD(T)-F12b/VQZF12//CCSD(T)-F12a/TZF'
}
scaling_factor = freq_dict.get(model_chemistry.lower(), 1)
scaling_factor = freq_dict.get(freq_level.lower(), 1)
if scaling_factor == 1:
logging.warning('No frequency scaling factor found for model chemistry {0}. Assuming a value of unity. '
'This will affect the partition function and all quantities derived from it '
'(thermo quantities and rate coefficients).'.format(model_chemistry))
'(thermo quantities and rate coefficients).'.format(freq_level))
else:
logging.info('Assigned a frequency scale factor of {0} for model chemistry {1}'.format(
scaling_factor, model_chemistry))
logging.info('Assigned a frequency scale factor of {0} for the frequency level of theory {1}'.format(
scaling_factor, freq_level))
return scaling_factor


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