Mod:Hunt Research Group:model freq script2 - Revision history

Hashmi at 03:36, 1 August 2024

2024-08-01T03:36:27Z

Wikiadmin at 08:31, 30 July 2024

2024-07-30T08:31:22Z

Hashmi: /* Script to Extract Thermochemistry Data from all the log files in PWD */

2024-07-30T06:01:59Z

Script to Extract Thermochemistry Data from all the log files in PWD

New page

=data script=
*script to extract data and directly produce a csv file that can be opened in MS Excel. It runs and uses all the log files (*.log) in the current directory.
*simply copy and paste this script into a file get_frequencies_data.py
*then run with "python3 get_frequencies_data.py"
<pre>
import glob
import os
import sys
import csv

print("#=====================================================================================#")
print("#-------------------------------------------------------------------------------------#")
print("# A Script to Extract ΔE, ΔG, ΔH, TΔS, and ZPE from Gaussian Output Files #")
print("#-------------------------------------------------------------------------------------#")
print("#=====================================================================================#")
print("\n")

#---------------------------------------------------------------------------------------------------------------------------------------#
# A function to take out SCF & Gibb's Free Energy Values from a Gaussian log file and save the Filename., SCF E, & Gibb's E to a list #
#---------------------------------------------------------------------------------------------------------------------------------------#
#---------- Start of Function ----------#
def Extract_Energies(input_file):
SCF_Energy = "--NOT FOUND--"
Gibbs_Energy = "--NOT FOUND--"
Rxn_Enthalpy_H = "--NOT FOUND--"
Zero_point_energy = "--NOT FOUND--"
TDS = "--NOT FOUND--"
SCF_E_kJ = "--NOT FOUND--"
Gibbs_E_kJ = "--NOT FOUND--"
Enthalpy_of_Rxn_kJ = "--NOT FOUND--"
ZPE_kJ = "--NOT FOUND--"
found_low_frequencies = False
f = open(input_file, 'r')
input = f.readlines()
filename=os.path.splitext(os.path.basename(input_file))[0]
for line in input:
if "SCF Done:" in line:
complete_line = line.split()
SCF_Energy = complete_line[4] # ΔE
SCF_E_kJ = float(SCF_Energy)*2625.50
if "Sum of electronic and thermal Free Energies" in line:
gibbs_line = line.split()
Gibbs_Energy = gibbs_line[7] # ΔG
Gibbs_E_kJ = float(Gibbs_Energy) * 2625.50
if "Sum of electronic and thermal Enthalpies" in line:
enthalpies_line = line.split()
Rxn_Enthalpy_H = enthalpies_line[6] # ΔH
Enthalpy_of_Rxn_kJ = float(Rxn_Enthalpy_H) * 2625.50
#TDS_au = float(Rxn_Enthalpy_H) - float(Gibbs_Energy)
#print('Here is the TDS value', TDS_au)
if "Zero-point correction=" in line:
complete_line = line.split()
Zero_point_energy = complete_line[2] # ZPE
ZPE_kJ = float(Zero_point_energy)*2625.50
if "Low frequencies ---" in line:
if found_low_frequencies:
continue # Skip processing if already found
complete_line = line.split()
LF01 = complete_line[3]
LF02 = complete_line[4]
LF03 = complete_line[5]
LF04 = complete_line[6]
LF05 = complete_line[7]
LF06 = complete_line[8]
found_low_frequencies = True
return [filename, SCF_Energy, SCF_E_kJ, Gibbs_Energy, Gibbs_E_kJ, Rxn_Enthalpy_H, Enthalpy_of_Rxn_kJ, round(float(Rxn_Enthalpy_H) - float(Gibbs_Energy),10), round((float(Rxn_Enthalpy_H) - float(Gibbs_Energy))*2625.50,10), Zero_point_energy, float(SCF_Energy)+float(Zero_point_energy), (float(SCF_Energy)+float(Zero_point_energy))*2625.50, LF01, LF02, LF03, LF04, LF05, LF06]
#---------- End of Function ----------#

#Define the user input for input files (log files)
#input_files = input('Enter the names of input files or a range (e.g. *.log): ')
input_files = '*.log'
Final_Energies_List = [['File Name', 'SCF Energy (a.u.)', u'Δ'+'E (KJ/mol)', u'Δ'+'G (a.u.)', u'Δ'+'G (KJ/mol)', u'Δ'+'H (a.u)', u'Δ'+'H (KJ/mol)', 'T'+u'Δ'+'S (a.u)', 'T'+u'Δ'+'S (kJ/mol)', 'ZPE (a.u.)', u'Δ'+'E+ZPE (a.u.)', u'Δ'+'E+ZPE (kJ/mol)', 'Low Frequencies', ' ', ' ', ' ', ' ', ' ']] # A list which will contain all the data from all log files

#-------------------------------------------------------------------------------------------------------------------------#
# A for loop to go through all the .log files in the current directory and use the function defined above on all of them #
#-------------------------------------------------------------------------------------------------------------------------#
#Uncomment below if your log files are located in the same directory or use the loop below if log files are in multiple subdirectories.
for files in glob.glob(input_files):
Final_Energies_List.append(Extract_Energies(files))

#-----------------------------------------------------------------------------------------------------------------------------------#
# A for loop to go through all the subdirectories in the current directory and use the function defined above on all the log files #
#-----------------------------------------------------------------------------------------------------------------------------------#
'''for files in glob.iglob(os.path.join('*', '*.log')):
Final_Energies_List.append(SCF_and_Gibbs_Energy(files))'''

print("Here are the ΔE, ΔG, ΔH, TΔS, and ZPE of all the Files\n")
for i in Final_Energies_List:
print(
" {:<20} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<16} {:<10} {:<10} {:<10} {:<10} {:<10}".format(i[0], i[1], i[2], i[3],
i[4], i[5], i[6], i[7], i[8], i[9], i[10], i[11], i[12], i[13], i[14], i[15], i[16], i[17]))

print("\nAll Done Boss :)")

# ------------------------------------------#
# A loop to write the output to a csv file #
# ------------------------------------------#
with open('frequencies_database.csv', 'w', newline='', encoding='utf-8-sig') as csvfile:
writer = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL) # Defining general csv writing template
for i in Final_Energies_List:
writer.writerow(i)

print("\n")
print("#-------------------------------------------------------#")
print("# A Script by Dr. Muhammad Ali Hashmi (30-July-2024) #")
print("#-------------------------------------------------------#")

</pre>

@@ Line 1: / Line 1: @@
-=test=
+=Extract thermodynamic data and low frequencies from all the log files in a folder to a csv file for the database=
-*script to extract data and directly produce a csv file that can be opened in MS Excel. It runs and uses all the log files (*.log) in the current directory.
+*Here is a script to extract data from all the log files in a folder and directly produce a csv file that can be opened in MS Excel. It runs and uses all the log files (*.log) in the current directory.
-*simply copy and paste this script into a file get_frequencies_data.py
+*To use, simply copy and paste this script into a file get_frequencies_data.py
-*then run with "python3 get_frequencies_data.py"
+*Then run the file in any folder with the command "python3 get_frequencies_data.py"
 <pre>
-import glob
+import glob, os, sys, csv
 print("#=====================================================================================#")
 print("#-------------------------------------------------------------------------------------#")
-print("#       A Script to Extract ΔE, ΔG, ΔH, TΔS, and ZPE from Gaussian Output Files       #")
+print("#       A Script to Extract SCF E, ΔG, ΔH, TΔS, and ZPE from Gaussian Output Files       #")
 print("#-------------------------------------------------------------------------------------#")
 print("#=====================================================================================#")
@@ Line 26: / Line 24: @@
      Zero_point_energy = "--NOT FOUND--"
      TDS = "--NOT FOUND--"
      SCF_E_kJ = "--NOT FOUND--"
      Gibbs_E_kJ = "--NOT FOUND--"
@@ Line 64: / Line 63: @@
              LF06 = complete_line[8]
              found_low_frequencies = True
-     return [filename, SCF_Energy, SCF_E_kJ, Gibbs_Energy, Gibbs_E_kJ, Rxn_Enthalpy_H, Enthalpy_of_Rxn_kJ, round(float(Rxn_Enthalpy_H) - float(Gibbs_Energy),10), round((float(Rxn_Enthalpy_H) - float(Gibbs_Energy))*2625.50,10), Zero_point_energy, float(SCF_Energy)+float(Zero_point_energy), (float(SCF_Energy)+float(Zero_point_energy))*2625.50, LF01, LF02, LF03, LF04, LF05, LF06]
+     return [filename, SCF_Energy, SCF_E_kJ, delta_E, Gibbs_Energy, Gibbs_E_kJ, Rxn_Enthalpy_H, Enthalpy_of_Rxn_kJ, round(float(Rxn_Enthalpy_H) - float(Gibbs_Energy),10), round((float(Rxn_Enthalpy_H) - float(Gibbs_Energy))*2625.50,10), Zero_point_energy, float(SCF_Energy)+float(Zero_point_energy), (float(SCF_Energy)+float(Zero_point_energy))*2625.50, LF01, LF02, LF03, LF04, LF05, LF06]
 #---------- End of Function ----------#
@@ Line 70: / Line 69: @@
 #input_files = input('Enter the names of input files or a range (e.g. *.log):  ')
 input_files = '*.log'
-Final_Energies_List = [['File Name', 'SCF Energy (a.u.)', u'Δ'+'E (KJ/mol)', u'Δ'+'G (a.u.)', u'Δ'+'G (KJ/mol)', u'Δ'+'H (a.u)', u'Δ'+'H (KJ/mol)', 'T'+u'Δ'+'S (a.u)', 'T'+u'Δ'+'S (kJ/mol)', 'ZPE (a.u.)', u'Δ'+'E+ZPE (a.u.)', u'Δ'+'E+ZPE (kJ/mol)', 'Low Frequencies', ' ', ' ', ' ', ' ', ' ']] # A list which will contain all the data from all log files
+Final_Energies_List = [['File Name', 'SCF Energy (a.u.)', 'SCF Energy (KJ/mol)', u'Δ'+'E (kJ/mol)' , 'G (a.u.)', 'G (KJ/mol)', 'H (a.u)', 'H (KJ/mol)', 'T'+u'Δ'+'S (a.u)', 'T'+u'Δ'+'S (kJ/mol)', 'ZPE (a.u.)', 'E+ZPE (a.u.)', 'E+ZPE (kJ/mol)', 'Low Frequencies', ' ', ' ', ' ', ' ', ' ']] # A list which will contain all the data from all log files
 #-------------------------------------------------------------------------------------------------------------------------#
@@ Line 85: / Line 84: @@
      Final_Energies_List.append(SCF_and_Gibbs_Energy(files))'''
-print("Here are the ΔE, ΔG, ΔH, TΔS, and ZPE of all the Files\n")
+print("Here are the SCF E, ΔG, ΔH, TΔS, and ZPE of all the Files\n")
 for i in Final_Energies_List:
      print(
-         " {:<20}  {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<10}   {:<10}   {:<10}   {:<10}   {:<10}".format(i[0], i[1], i[2], i[3],
+         " {:<20}  {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<16}   {:<10}   {:<10}   {:<10}   {:<10}   {:<10}   {:<10}".format(i[0], i[1], i[2], i[3],
-                                                                                                 i[4], i[5], i[6], i[7], i[8], i[9], i[10], i[11], i[12], i[13], i[14], i[15], i[16], i[17]))
+                                                                                                 i[4], i[5], i[6], i[7], i[8], i[9], i[10], i[11], i[12], i[13], i[14], i[15], i[16], i[17], i[18]))
 print("\nAll Done Boss :)")
@@ Line 104: / Line 103: @@
 print("\n")
 print("#-------------------------------------------------------#")
-print("# A Script by Dr. Muhammad Ali Hashmi (30-July-2024)    #")
+print("# A Script by Dr. Muhammad Ali Hashmi (01-August-2024)  #")
 print("#-------------------------------------------------------#")
 </pre>