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Now doesn't crash with failed Gaussian calculation - returns the fina…
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…l energy

and skips thermochemical analysis
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@bobbypaton
bobbypaton committed Apr 18, 2016
1 parent e0db9f7 commit 5a8d0ce
Showing 1 changed file with 70 additions and 74 deletions.
144 changes: 70 additions & 74 deletions GoodVibes.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -308,63 +308,62 @@ def __init__(self, file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor,s
# look for thermal corrections, paying attention to point group symmetry
if line.strip().startswith('Zero-point correction='): self.zero_point_corr = float(line.strip().split()[2])
if line.strip().find('Multiplicity') > -1: mult = float(line.strip().split()[5])
if line.strip().startswith('Thermal correction to Energy='): self.energy_corr = float(line.strip().split()[4])
if line.strip().startswith('Thermal correction to Enthalpy='): enthalpy_corr = float(line.strip().split()[4])
if line.strip().startswith('Thermal correction to Gibbs Free Energy='): gibbs_corr = float(line.strip().split()[6])
if line.strip().startswith('Molecular mass:'): molecular_mass = float(line.strip().split()[2])
if line.strip().startswith('Rotational symmetry number'): symmno = int((line.strip().split()[3]).split(".")[0])
if line.strip().startswith('Full point group'):
if line.strip().split()[3] == 'D*H' or line.strip().split()[3] == 'C*V': linear_mol = 1
if line.strip().startswith('Rotational constants'): roconst = [float(line.strip().split()[3]), float(line.strip().split()[4]), float(line.strip().split()[5])]

# create an array of frequencies equal to cut-off value
cutoffs = []
for j in range(0,len(frequency_wn)): cutoffs.append(FREQ_CUTOFF)

# Calculate Translational, Rotational and Vibrational contributions to the energy
Utrans = calc_translational_energy(temperature)
Urot = calc_rotational_energy(self.zero_point_corr, symmno, temperature,linear_mol)
Uvib = calc_vibrational_energy(frequency_wn, temperature,freq_scale_factor)
ZPE = calc_zeropoint_energy(frequency_wn, freq_scale_factor)

# Calculate Translational, Rotational and Vibrational contributions to the entropy
Strans = calc_translational_entropy(molecular_mass, conc, temperature, solv)
Selec = calc_electronic_entropy(mult)
Srot = calc_rotational_entropy(self.zero_point_corr, linear_mol, symmno, roconst, temperature)

# Calculate harmonic entropy, free-rotor entropy and damping function for each frequency
Svib_rrho = calc_rrho_entropy(frequency_wn, temperature,freq_scale_factor)
if FREQ_CUTOFF > 0.0: Svib_rrqho = calc_rrho_entropy(cutoffs, temperature,1.0)
Svib_free_rot = calc_freerot_entropy(frequency_wn, temperature,freq_scale_factor)
damp = calc_damp(frequency_wn, FREQ_CUTOFF)

# Compute entropy (cal/mol/K) using the two values and damping function
vib_entropy = []
for j in range(0,len(frequency_wn)):
if QH == "grimme": vib_entropy.append(Svib_rrho[j] * damp[j] + (1-damp[j]) * Svib_free_rot[j])
elif QH == "truhlar" and FREQ_CUTOFF > 0.0:
if frequency_wn[j] > FREQ_CUTOFF: vib_entropy.append(Svib_rrho[j])
else: vib_entropy.append(Svib_rrqho[j])

# Add all terms to get Free energy - perform separately for harmonic and quasi-harmonic values out of interest
qh_Svib = sum(vib_entropy)
h_Svib = sum(Svib_rrho)
self.enthalpy = self.scf_energy + (Utrans + Urot + Uvib + GAS_CONSTANT*temperature/kjtokcal/1000.0)/autokcal
self.zpe = ZPE/autokcal
self.entropy = (Strans + Srot + h_Svib + Selec)/autokcal/1000.0
self.qh_entropy = (Strans + Srot + qh_Svib + Selec)/autokcal/1000.0
self.gibbs_free_energy = self.enthalpy - temperature * self.entropy
self.qh_gibbs_free_energy = self.enthalpy - temperature * self.qh_entropy

#Uncomment to compute the magnitude of the quasi-harmonic correction to the RRHO entropy
#QH_correction = h_Svib - qh_Svib
# self.QH_correction = -QH_correction * temperature/1000.0

#Uncomment to compute the magnitude of the haptic (i.e. concentration-dependent) correction to the RRHO entropy
#Strans1atm = calc_translational_entropy(molecular_mass, atmos/(GAS_CONSTANT*temperature), temperature, solv)
#conc_correction = Strans - Strans1atm
#self.conc_correction = -conc_correction * temperature/1000.0

# skip the next steps if unable to parse the frequencies or zpe from the output file
if len(frequency_wn) > 0 and hasattr(self, "zero_point_corr"):

# create an array of frequencies equal to cut-off value
cutoffs = []
for j in range(0,len(frequency_wn)): cutoffs.append(FREQ_CUTOFF)

# Calculate Translational, Rotational and Vibrational contributions to the energy
Utrans = calc_translational_energy(temperature)
Urot = calc_rotational_energy(self.zero_point_corr, symmno, temperature,linear_mol)
Uvib = calc_vibrational_energy(frequency_wn, temperature,freq_scale_factor)
ZPE = calc_zeropoint_energy(frequency_wn, freq_scale_factor)

# Calculate Translational, Rotational and Vibrational contributions to the entropy
Strans = calc_translational_entropy(molecular_mass, conc, temperature, solv)
Selec = calc_electronic_entropy(mult)
Srot = calc_rotational_entropy(self.zero_point_corr, linear_mol, symmno, roconst, temperature)

# Calculate harmonic entropy, free-rotor entropy and damping function for each frequency
Svib_rrho = calc_rrho_entropy(frequency_wn, temperature,freq_scale_factor)
if FREQ_CUTOFF > 0.0: Svib_rrqho = calc_rrho_entropy(cutoffs, temperature,1.0)
Svib_free_rot = calc_freerot_entropy(frequency_wn, temperature,freq_scale_factor)
damp = calc_damp(frequency_wn, FREQ_CUTOFF)

# Compute entropy (cal/mol/K) using the two values and damping function
vib_entropy = []
for j in range(0,len(frequency_wn)):
if QH == "grimme": vib_entropy.append(Svib_rrho[j] * damp[j] + (1-damp[j]) * Svib_free_rot[j])
elif QH == "truhlar" and FREQ_CUTOFF > 0.0:
if frequency_wn[j] > FREQ_CUTOFF: vib_entropy.append(Svib_rrho[j])
else: vib_entropy.append(Svib_rrqho[j])

# Add all terms to get Free energy - perform separately for harmonic and quasi-harmonic values out of interest
qh_Svib = sum(vib_entropy)
h_Svib = sum(Svib_rrho)
self.enthalpy = self.scf_energy + (Utrans + Urot + Uvib + GAS_CONSTANT*temperature/kjtokcal/1000.0)/autokcal
self.zpe = ZPE/autokcal
self.entropy = (Strans + Srot + h_Svib + Selec)/autokcal/1000.0
self.qh_entropy = (Strans + Srot + qh_Svib + Selec)/autokcal/1000.0
self.gibbs_free_energy = self.enthalpy - temperature * self.entropy
self.qh_gibbs_free_energy = self.enthalpy - temperature * self.qh_entropy

#Uncomment to compute the magnitude of the quasi-harmonic correction to the RRHO entropy
#QH_correction = h_Svib - qh_Svib
# self.QH_correction = -QH_correction * temperature/1000.0

#Uncomment to compute the magnitude of the haptic (i.e. concentration-dependent) correction to the RRHO entropy
#Strans1atm = calc_translational_entropy(molecular_mass, atmos/(GAS_CONSTANT*temperature), temperature, solv)
#conc_correction = Strans - Strans1atm
#self.conc_correction = -conc_correction * temperature/1000.0

if __name__ == "__main__":
# Takes arguments: cutoff_freq g09_output_files
Expand All @@ -386,8 +385,6 @@ def __init__(self, file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor,s
if len(sys.argv[i].split(".")) > 1:
if sys.argv[i].split(".")[1] == "out" or sys.argv[i].split(".")[1] == "log":
files.append(sys.argv[i])
name_of_file=str(sys.argv[i].split(".")[0])

freespace = get_free_space(solv)

start = time.strftime("%Y/%m/%d %H:%M:%S", time.localtime())
Expand Down Expand Up @@ -424,28 +421,27 @@ def __init__(self, file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor,s
log.Write("\n\n "+"".ljust(30)+"E/au".rjust(12)+ " ZPE/au".rjust(12)+ " H/au".rjust(12)+ " T.S/au".rjust(12)+ " T.qh-S/au".rjust(12)+ " G(T)/au".rjust(12)+ " qh-G(T)/au".rjust(12))
log.Write("\n"+stars)
for file in files:
bbe = calc_bbe(file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor, solv)
log.Write("\no ")
log.Write((file.split(".")[0]).ljust(30))
if not hasattr(bbe,"gibbs_free_energy"): log.Write("Warning! Job did not finish normally!\n")
else:
if hasattr(bbe, "scf_energy"): log.Write("%.6f" % bbe.scf_energy)
else: log.Write("N/A ")
if hasattr(bbe, "zero_point_corr"): log.Write(" %.6f" % (bbe.zpe))
else: log.Write("N/A ")
if hasattr(bbe, "enthalpy"): log.Write(" %.6f" % (bbe.enthalpy))
else: log.Write("N/A ")
if hasattr(bbe, "entropy"): log.Write(" %.6f" % (temperature * bbe.entropy))
else: log.Write("N/A ")
if hasattr(bbe, "qh_entropy"): log.Write(" %.6f" % (temperature * bbe.qh_entropy))
else: log.Write("N/A ")
if hasattr(bbe, "gibbs_free_energy"): log.Write(" %.6f" % (bbe.gibbs_free_energy))
else: log.Write("N/A ")
if hasattr(bbe, "qh_gibbs_free_energy"): log.Write(" %.6f" % (bbe.qh_gibbs_free_energy))
else: log.Write("N/A")
bbe = calc_bbe(file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor, solv)
log.Write("\no ")
log.Write((file.split(".")[0]).ljust(30))
if hasattr(bbe, "scf_energy"): log.Write("%.6f" % bbe.scf_energy)
else: log.Write("N/A ")
if not hasattr(bbe,"gibbs_free_energy"): log.Write(" Warning! Couldn't find frequency information ...\n")
else:
if hasattr(bbe, "zero_point_corr"): log.Write(" %.6f" % (bbe.zpe))
else: log.Write("N/A ")
if hasattr(bbe, "enthalpy"): log.Write(" %.6f" % (bbe.enthalpy))
else: log.Write("N/A ")
if hasattr(bbe, "entropy"): log.Write(" %.6f" % (temperature * bbe.entropy))
else: log.Write("N/A ")
if hasattr(bbe, "qh_entropy"): log.Write(" %.6f" % (temperature * bbe.qh_entropy))
else: log.Write("N/A ")
if hasattr(bbe, "gibbs_free_energy"): log.Write(" %.6f" % (bbe.gibbs_free_energy))
else: log.Write("N/A ")
if hasattr(bbe, "qh_gibbs_free_energy"): log.Write(" %.6f" % (bbe.qh_gibbs_free_energy))
else: log.Write("N/A")
log.Write("\n")


#Running a variable temperature analysis of the enthalpy, entropy and the free energy
if len(temperature_interval) != 0:
# If no temperature step was defined, divide the region into 10
Expand All @@ -465,7 +461,7 @@ def __init__(self, file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor,s
log.Write("o "+file+" @"+" %.1f " % (temperature))
if conc_ini == "None": conc = atmos/(GAS_CONSTANT*temperature)
bbe = calc_bbe(file, QH, FREQ_CUTOFF, temperature, conc, freq_scale_factor, solv)
if not hasattr(bbe,"gibbs_free_energy"): log.Write("Warning! Job did not finish normally!\n")
if not hasattr(bbe,"gibbs_free_energy"): log.Write("Warning! Couldn't find frequency information ...\n")
else:
if hasattr(bbe, "enthalpy"): log.Write(" %.6f" % (bbe.enthalpy))
else: log.Write("N/A ")
Expand Down

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