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_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_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_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()