def test_temperature_corrections_QH(QS, E, ZPE, H, qhH, TS, TqhS, G, qhG):
temp = 200
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, spc, invert = True, 100.0, 100.0, 1.0, 'none', False, False
bbe298 = GV.calc_bbe(datapath('Al_298K.out'), QS, QH, s_freq_cutoff,
h_freq_cutoff, temp, conc, freq_scale_factor, solv,
spc, invert)
bbe400 = GV.calc_bbe(datapath('Al_400K.out'), QS, QH, s_freq_cutoff,
h_freq_cutoff, temp, conc, freq_scale_factor, solv,
spc, invert)
precision = 6
assert E == round(bbe298.scf_energy, precision) == round(
bbe400.scf_energy, precision)
assert ZPE == round(bbe298.zpe, precision) == round(bbe400.zpe, precision)
assert H == round(bbe298.enthalpy, precision) == round(
bbe400.enthalpy, precision)
assert qhH == round(bbe298.qh_enthalpy, precision) == round(
bbe400.qh_enthalpy, precision)
assert TS == round(temp * bbe298.entropy, precision) == round(
temp * bbe400.entropy, precision)
assert TqhS == round(temp * bbe298.qh_entropy, precision) == round(
temp * bbe400.qh_entropy, precision)
assert G == round(bbe298.gibbs_free_energy, precision) == round(
bbe400.gibbs_free_energy, precision)
assert qhG == round(bbe298.qh_gibbs_free_energy, precision) == round(
bbe400.qh_gibbs_free_energy, precision)
def test_temperature_corrections(QH, E, ZPE, H, TS, TqhS, G, qhG):
temp = 200
conc = GV.atmos / (GV.GAS_CONSTANT * temp)
freq_cutoff, freq_scale_factor, solv, spc = 100.0, 1.0, 'none', False
bbe298 = GV.calc_bbe(datapath('Al_298K.out'), QH, freq_cutoff, temp, conc, freq_scale_factor, solv, spc)
bbe400 = GV.calc_bbe(datapath('Al_400K.out'), QH, freq_cutoff, temp, conc, freq_scale_factor, solv, spc)
precision = 6
assert E == round(bbe298.scf_energy, precision) == round(bbe400.scf_energy, precision)
assert ZPE == round(bbe298.zpe, precision) == round(bbe400.zpe, precision)
assert H == round(bbe298.enthalpy, precision) == round(bbe400.enthalpy, precision)
assert TS == round(temp * bbe298.entropy, precision) == round(temp * bbe400.entropy, precision)
assert TqhS == round(temp * bbe298.qh_entropy, precision) == round(temp * bbe400.qh_entropy, precision)
assert G == round(bbe298.gibbs_free_energy, precision) == round(bbe400.gibbs_free_energy, precision)
assert qhG == round(bbe298.qh_gibbs_free_energy, precision) == round(bbe400.qh_gibbs_free_energy, precision)
def test_pes(E, ZPE, H, TS, TqhS, GT, qhGT):
temp = 298.15
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
QS, QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, invert, d3 = 'grimme', False, 100.0, 100.0, 1.0, 'none', False, 0
invert, spc, gconf = False, False, True
precision = 2
files = [
'pes/Int-III_Oax_cis_a.log', 'pes/Int-II_Oax_cis_a.log',
'pes/Int-I_Oax.log', 'pes/TolS.log', 'pes/TolSH.log'
]
files = [datapath(file) for file in files]
log = GV.Logger("GoodVibes", 'test', False)
bbe_vals = []
for file in files: # loop over all specified output files and compute thermochemistry
bbe = GV.calc_bbe(file, QS, QH, s_freq_cutoff, h_freq_cutoff, temp,
conc, freq_scale_factor, solv, spc, invert, d3)
bbe_vals.append(bbe)
fileList = [file for file in files]
thermo_data = dict(zip(
fileList, bbe_vals)) # the collected thermochemical data for all files
pes = GV.get_pes(datapath('pes/Cis_complete_pathway.yaml'), thermo_data,
log, temp, gconf, QH)
zero_vals = [
pes.e_zero[0][0], pes.zpe_zero[0][0], pes.h_zero[0][0],
temp * pes.ts_zero[0][0], temp * pes.qhts_zero[0][0], pes.g_zero[0][0],
pes.qhg_zero[0][0]
]
for i, path in enumerate(pes.path):
for j, e_abs in enumerate(pes.e_abs[i]):
species = [
pes.e_abs[i][j], pes.zpe_abs[i][j], pes.h_abs[i][j],
temp * pes.s_abs[i][j], temp * pes.qs_abs[i][j],
pes.g_abs[i][j], pes.qhg_abs[i][j]
]
relative = [
species[x] - zero_vals[x] for x in range(len(zero_vals))
]
formatted_list = [GV.KCAL_TO_AU * x for x in relative]
assert E[j] == round(formatted_list[0], precision)
assert ZPE[j] == round(formatted_list[1], precision)
assert H[j] == round(formatted_list[2], precision)
assert TS[j] == round(formatted_list[3], precision)
assert TqhS[j] == round(formatted_list[4], precision)
assert GT[j] == round(formatted_list[5], precision)
assert qhGT[j] == round(formatted_list[6], precision)
log.finalize()
def test_media_correction(path, conc, media, E, ZPE, H, TS, TqhS, G, qhG):
path = datapath(path)
QH, QS, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, temp, solv, spc, invert = False, "grimme", 100.0, 100.0, 1.0, 298.15, 'none', False, False
bbe = GV.calc_bbe(path, QS, QH, s_freq_cutoff, h_freq_cutoff, temp, conc,
freq_scale_factor, solv, spc, invert)
precision = 6
media_correction = 0.0
if media is not False:
MW_solvent = solvents[media][0]
density_solvent = solvents[media][1]
concentration_solvent = (density_solvent * 1000) / MW_solvent
media_correction = -(GV.GAS_CONSTANT /
GV.J_TO_AU) * math.log(concentration_solvent)
assert E == round(bbe.scf_energy, precision)
if hasattr(bbe, "gibbs_free_energy"):
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * (bbe.entropy + media_correction), precision)
assert TqhS == round(temp * (bbe.qh_entropy + media_correction),
precision)
assert G == round(bbe.gibbs_free_energy + (temp * (-media_correction)),
precision)
assert qhG == round(
bbe.qh_gibbs_free_energy + (temp * (-media_correction)), precision)
def __init__(self, file):
# default values for thermochemical calculations
if '.log' not in file:
raise TypeError('A g16 .log file must be provided')
self.file=file
self.name=os.path.basename(file)
QH, freq_cutoff, temperature, freq_scale_factor, solv, spc = 'grimme', 100.0, 298.15, 1.0, 'none', False
conc = GV.atmos / GV.GAS_CONSTANT / temperature
self.get_termination() and self.getCPU()
self.get_error() and self.getCPU()
try:
#pybel molecule object
self._pybel_mol = next(readfile('g09', file))
except:
raise Exception('You log file is too bad to generate a molecule')
else:
self.get_charge()
self.get_route()
self.get_coords()
self.freq = pq.getoutData(file)
if self.termination:
bbe = GV.calc_bbe(file, QH, freq_cutoff, temperature, conc, freq_scale_factor, solv, spc)
if hasattr(bbe, 'scf_energy'): self._pybel_mol.data['scf_energy'] = bbe.scf_energy
if hasattr(bbe, 'enthalpy'): self._pybel_mol.data['enthalpy'] = bbe.enthalpy
if hasattr(bbe, 'im_freq'): self._pybel_mol.data['im_freq'] = len(bbe.im_freq)
if hasattr(self, 'CPU'):
cpu = self.CPU[0]*3600*24 + self.CPU[1]*3600 + self.CPU[2]*60 + self.CPU[3]
self._pybel_mol.data['CPU'] = '{}s'.format(cpu)
self.get_rdkit_mol()
def test_scaling_factor_search(filename, freq_scale_factor, zpe):
temp = 298.15
conc = GV.atmos / (GV.GAS_CONSTANT * temp)
QH, freq_cutoff, solv, spc = 'grimme', 100.0, 'none', False
precision = 6
bbe = GV.calc_bbe(datapath('ethane.out'), QH, freq_cutoff, temp, conc, freq_scale_factor, solv, spc)
assert zpe == round(bbe.zpe, precision)
def test_scaling_factor_search(filename, freq_scale_factor, zpe):
temp = 298.15
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
QS, QH, s_freq_cutoff, h_freq_cutoff, solv, spc, invert = 'grimme', True, 100.0, 100.0, 'none', False, False
precision = 6
bbe = GV.calc_bbe(datapath('ethane.out'), QS, QH, s_freq_cutoff,
h_freq_cutoff, temp, conc, freq_scale_factor, solv, spc,
invert)
assert zpe == round(bbe.zpe, precision)
def test_all(path, QH, temp, E, ZPE, H, TS, TqhS, G, qhG):
# Defaults, no temp interval, no conc interval
path = datapath(path)
conc = GV.atmos / (GV.GAS_CONSTANT * temp)
freq_cutoff, freq_scale_factor, solv, spc = 100.0, 1.0, 'none', False
bbe = GV.calc_bbe(path, QH, freq_cutoff, temp, conc, freq_scale_factor, solv, spc)
precision = 6 # if temp == 298.15 else 4e-4
assert E == round(bbe.scf_energy, precision)
if hasattr(bbe, "gibbs_free_energy"):
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * bbe.entropy, precision)
assert TqhS == round(temp * bbe.qh_entropy, precision)
assert G == round(bbe.gibbs_free_energy, precision)
assert qhG == round(bbe.qh_gibbs_free_energy, precision)
def test_concentration_correction(path, conc, QS, E, ZPE, H, TS, TqhS, G, qhG):
path = datapath(path)
QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, temp, solv, spc, invert = False, 100.0, 100.0, 1.0, 298.15, 'none', False, False
if conc == False:
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
bbe = GV.calc_bbe(path, QS, QH, s_freq_cutoff, h_freq_cutoff, temp, conc,
freq_scale_factor, solv, spc, invert)
precision = 6
assert E == round(bbe.scf_energy, precision)
if hasattr(bbe, "gibbs_free_energy"):
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * bbe.entropy, precision)
assert TqhS == round(temp * bbe.qh_entropy, precision)
assert G == round(bbe.gibbs_free_energy, precision)
assert qhG == round(bbe.qh_gibbs_free_energy, precision)
def test_QS(path, QS, temp, E, ZPE, H, TS, TqhS, G, qhG):
# Defaults, no temp interval, no conc interval
path = datapath(path)
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, spc, invert = False, 100.0, 100.0, 1.0, 'none', False, False
bbe = GV.calc_bbe(path, QS, QH, s_freq_cutoff, h_freq_cutoff, temp, conc,
freq_scale_factor, solv, spc, invert)
precision = 6 # if temp == 298.15 else 4e-4
assert E == round(bbe.scf_energy, precision)
if hasattr(bbe, "gibbs_free_energy"):
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * bbe.entropy, precision)
assert TqhS == round(temp * bbe.qh_entropy, precision)
assert G == round(bbe.gibbs_free_energy, precision)
assert qhG == round(bbe.qh_gibbs_free_energy, precision)
def test_single_point_correction(spc, E_spc, E, ZPE, H, TS, TqhS, GT, qhGT):
temp = 298.15
conc = GV.atmos / (GV.GAS_CONSTANT * temp)
QH, freq_cutoff, freq_scale_factor, solv = 'grimme', 100.0, 1.0, 'none'
precision = 6
bbe = GV.calc_bbe(datapath('ethane.out'), QH, freq_cutoff, temp, conc, freq_scale_factor, solv, spc)
if E_spc:
assert E_spc == round(bbe.sp_energy, precision)
assert E == round(bbe.scf_energy, precision)
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * bbe.entropy, precision)
assert TqhS == round(temp * bbe.qh_entropy, precision)
assert GT == round(bbe.gibbs_free_energy, precision)
assert qhGT == round(bbe.qh_gibbs_free_energy, precision)
def test_single_point_correction(spc, E_spc, E, ZPE, H, TS, TqhS, GT, qhGT):
temp = 298.15
conc = GV.atmos / (GV.GAS_CONSTANT * temp)
QH, freq_cutoff, freq_scale_factor, solv = 'grimme', 100.0, 1.0, 'none'
precision = 6
bbe = GV.calc_bbe(datapath('ethane.out'), QH, freq_cutoff, temp, conc,
freq_scale_factor, solv, spc)
if E_spc:
assert E_spc == round(bbe.sp_energy, precision)
assert E == round(bbe.scf_energy, precision)
assert ZPE == round(bbe.zpe, precision)
assert H == round(bbe.enthalpy, precision)
assert TS == round(temp * bbe.entropy, precision)
assert TqhS == round(temp * bbe.qh_entropy, precision)
assert GT == round(bbe.gibbs_free_energy, precision)
assert qhGT == round(bbe.qh_gibbs_free_energy, precision)
def test_temperature_interval(path, ti, H, TS, TqhS, GT, qhGT):
QS, QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, spc, invert, d3 = 'grimme', False, 100.0, 100.0, 1.0, 'none', False, False, 0
precision = 6
temperature_interval = [float(temp) for temp in ti.split(',')]
interval = range(int(temperature_interval[0]),
int(temperature_interval[1] + 1),
int(temperature_interval[2]))
for i in range(len(interval)):
temp = float(interval[i])
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
bbe = GV.calc_bbe(datapath(path), QS, QH, s_freq_cutoff, h_freq_cutoff,
temp, conc, freq_scale_factor, solv, spc, invert, d3)
assert H[i] == round(bbe.enthalpy, precision)
assert TS[i] == round(temp * bbe.entropy, precision)
assert TqhS[i] == round(temp * bbe.qh_entropy, precision)
assert GT[i] == round(bbe.gibbs_free_energy, precision)
assert qhGT[i] == round(bbe.qh_gibbs_free_energy, precision)
def test_pes(E, ZPE, H, TS, TqhS, GT, qhGT):
temp = 298.15
conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
QS, QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, invert = 'grimme', False, 100.0, 100.0, 1.0, 'none', False
invert, spc, gconf = False, False, True
precision = 6
files = [
'pes/Int-III_Oax_cis_a.log', 'pes/Int-II_Oax_cis_a.log',
'pes/Int-I_Oax.log', 'pes/TolS.log', 'pes/TolSH.log'
]
files = [datapath(file) for file in files]
log = GV.Logger("GoodVibes", 'test', False)
bbe_vals = []
for file in files: # loop over all specified output files and compute thermochemistry
bbe = GV.calc_bbe(file, QS, QH, s_freq_cutoff, h_freq_cutoff, temp,
conc, freq_scale_factor, solv, spc, invert)
bbe_vals.append(bbe)
fileList = [file for file in files]
thermo_data = dict(zip(
fileList, bbe_vals)) # the collected thermochemical data for all files
pes = GV.get_pes(datapath('pes/Cis_complete_pathway.yaml'), thermo_data,
log, temp, gconf, QH)
zero_vals = [
pes.e_zero[0][0], pes.zpe_zero[0][0], pes.h_zero[0][0],
temp * pes.ts_zero[0][0], temp * pes.qhts_zero[0][0], pes.g_zero[0][0],
pes.qhg_zero[0][0]
]
for i, path in enumerate(pes.path):
for j, e_abs in enumerate(pes.e_abs[i]):
species = [
pes.e_abs[i][j], pes.zpe_abs[i][j], pes.h_abs[i][j],
temp * pes.s_abs[i][j], temp * pes.qs_abs[i][j],
pes.g_abs[i][j], pes.qhg_abs[i][j]
]
relative = [
species[x] - zero_vals[x] for x in range(len(zero_vals))
]
formatted_list = [GV.KCAL_TO_AU * x for x in relative]
assert E[j] == round(formatted_list[0], precision)
assert ZPE[j] == round(formatted_list[1], precision)
assert H[j] == round(formatted_list[2], precision)
assert TS[j] == round(formatted_list[3], precision)
assert TqhS[j] == round(formatted_list[4], precision)
assert GT[j] == round(formatted_list[5], precision)
assert qhGT[j] == round(formatted_list[6], precision)
log.Finalize()
# @pytest.mark.parametrize("yaml, gconf, E, ZPE, H, TS, TqhS, GT, qhGT", [
# #test cat conformers
# ('gconf_ee_boltz/gconf_TS.yaml', True, [0.0,5.053763],[0.0,-0.497994],[0.0,3.936414],[0.0,-14.426341],[0.0,-15.107289],[0.0,18.362755],[0.0,19.043703]),
# ('gconf_ee_boltz/gconf_TS.yaml', False, [0.0,5.053763],[0.0,-0.497994],[0.0,3.936414],[0.0,-14.823888],[0.0,-15.504836],[0.0,18.760302],[0.0,19.44125]),
# #test TS conformers
# ('gconf_ee_boltz/gconf_aminox_cat.yaml', True, [0.0,4.716292],[0.0,-0.460919],[0.0,3.534549],[0.0,-15.852617],[0.0,-16.367881],[0.0,19.387166],[0.0,19.90243]),
# ('gconf_ee_boltz/gconf_aminox_cat.yaml', False, [0.0,4.716292],[0.0,-0.460919],[0.0,3.534549],[0.0,-15.245404],[0.0,-15.760668],[0.0,18.779954],[0.0,19.295218])
#
# ])
# def test_gconf(yaml, gconf, E, ZPE, H, TS, TqhS, GT, qhGT):
# temp = 298.15
# conc = GV.ATMOS / (GV.GAS_CONSTANT * temp)
# QS, QH, s_freq_cutoff, h_freq_cutoff, freq_scale_factor, solv, invert = 'grimme', False, 100.0, 100.0, 1.0, 'none', False
# invert, spc = False, False
# files = ['gconf_ee_boltz/Aminoxylation_TS1_R.log', 'gconf_ee_boltz/Aminoxylation_TS2_S.log', 'gconf_ee_boltz/aminox_cat_conf212_S.log', 'gconf_ee_boltz/aminox_cat_conf280_R.log', 'gconf_ee_boltz/aminox_cat_conf65_S.log','gconf_ee_boltz/aminox_subs_conf713.log']
# files = [datapath(file) for file in files]
# log = GV.Logger("GoodVibes",'test',False)
# yaml = datapath(yaml)
#
# bbe_vals = []
# for file in files: # loop over all specified output files and compute thermochemistry
# bbe = GV.calc_bbe(file, QS, QH, s_freq_cutoff, h_freq_cutoff, temp,
# conc, freq_scale_factor, solv, spc, invert)
# bbe_vals.append(bbe)
# fileList = [file for file in files]
# thermo_data = dict(zip(fileList, bbe_vals)) # the collected thermochemical data for all files
#
# pes = GV.get_pes(yaml,thermo_data,log,temp,gconf,QH)
#
# zero_vals = [pes.e_zero[0][0], pes.zpe_zero[0][0], pes.h_zero[0][0], temp * pes.ts_zero[0][0], temp * pes.qhts_zero[0][0], pes.g_zero[0][0], pes.qhg_zero[0][0]]
#
# for i, path in enumerate(pes.path):
# for j, e_abs in enumerate(pes.e_abs[i]):
# species = [pes.e_abs[i][j], pes.zpe_abs[i][j], pes.h_abs[i][j], temp * pes.s_abs[i][j], temp * pes.qs_abs[i][j], pes.g_abs[i][j], pes.qhg_abs[i][j]]
# relative = [species[x]-zero_vals[x] for x in range(len(zero_vals))]
# formatted_list = [GV.KCAL_TO_AU * x for x in relative]
# assert '{:13.2f}'.format(E[j]) == '{:13.2f}'.format(formatted_list[0])
# assert '{:13.2f}'.format(ZPE[j]) == '{:13.2f}'.format(formatted_list[1])
# assert '{:13.2f}'.format(H[j]) == '{:13.2f}'.format(formatted_list[2])
# assert '{:13.2f}'.format(TS[j]) == '{:13.2f}'.format(formatted_list[3])
# assert '{:13.2f}'.format(TqhS[j]) == '{:13.2f}'.format(formatted_list[4])
# assert '{:13.2f}'.format(GT[j]) == '{:13.2f}'.format(formatted_list[5])
# assert '{:13.2f}'.format(qhGT[j]) == '{:13.2f}'.format(formatted_list[6])
# log.Finalize()
# let guys could run Goodvibes by python -m goodvibes <args>
# Copied from __main__.py in pip
from __future__ import absolute_import
import os
import sys
# If we are running from a wheel, add the wheel to sys.path
# This allows the usage python pip-*.whl/pip install pip-*.whl
if __package__ == '':
path = os.path.dirname(os.path.dirname(__file__))
sys.path.insert(0, path)
from goodvibes import GoodVibes # noqa
if __name__ == '__main__':
sys.exit(GoodVibes.main())
def sp_energy(self):
sp = GV.sp_energy(self.file)
return sp
