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_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()