- Save the following as script_name.py wherever you want.
- Follow the instructions to run
- Feel free to improve!
import os
import glob
import sys
############
#HOW TO RUN#
############
#go to the folder with frequency log files in
#this script currently doesn't work if there are .log file present which don't contain frequency analysis, you will have to change it yourself if you want that.
#this script outputs various data from the frequency files to the terminal including relative values, which are calculated relative to the reference_file.log
#run as follows:
#python path/to/script.py reference_file.log
##################################################################
#setting the reference file, this file is the 0 level for all relative values
ref_file = sys.argv[1]
print "ref_file = " + (ref_file)
#making a list of all .log files in current directory
log_files = []
for log_file in glob.glob('*.log'):
if log_file != ref_file:
log_files.append(log_file)
print "list of files: "
print log_files
#defining the strings which will be searched for in each file
e_elec_string = 'SCF Done'
zpe_string = 'Zero-point correction='
e_string = 'Sum of electronic and thermal Energies='
h_string = 'Sum of electronic and thermal Enthalpies='
g_string = 'Sum of electronic and thermal Free Energies='
freq_string = 'Low frequencies ---'
im_freq_string = 'imaginary frequencies (negative Signs)'
conver_string = 'Stationary point found.'
#fetching all data for the reference file
f = open(ref_file, 'r')
low_freqs_list = []
conver = 'no'
im_freq_num = '0'
for line in f:
if e_elec_string in line:
ref_e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
ref_e_elec_au = float(ref_e_elec_au)
if zpe_string in line:
ref_zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
ref_zpe_au = float(ref_zpe_au)
if e_string in line:
ref_e_au = line[(len(e_string)+1):(len(e_string)+35)]
ref_e_au = float(ref_e_au)
if h_string in line:
ref_h_au = line[(len(h_string)+1):(len(h_string)+35)]
ref_h_au = float(ref_h_au)
if g_string in line:
ref_g_au = line[(len(g_string)+1):(len(g_string)+35)]
ref_g_au = float(ref_g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))
f.close()
#assigning/calculating all data fields to print for the reference file
ref_low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
ref_low_freqs.append(low_freq)
low_freqs_string = ",".join(ref_low_freqs)
ref_e_elec_kj = str(ref_e_elec_au*2625.5)
ref_zpe_kj = str(ref_zpe_au*2625.5)
ref_e_kj = str(ref_e_au*2625.5)
ref_h_kj = str(ref_h_au*2625.5)
ref_ts_au = ref_h_au - ref_g_au
ref_ts_kj = str(ref_ts_au*2625.5)
ref_g_kj = str(ref_g_au*2625.5)
#printing header and reference rows
print "Filename,E_elec,DE_elec,zpe,Dzpe,E,DE,H,DH,TS,TDS,G,DG,Low freqencies,,,,,,,,,Converged?,# of imaginary frequencies"
print ref_file+','+ref_e_elec_kj+',0.00,'+ref_zpe_kj+',0.00,'+ref_e_kj+',0.00,'+ref_h_kj+',0.00,'+ref_ts_kj+',0.00,'+ref_g_kj+',0.00,'+low_freqs_string+','+conver+','+im_freq_num
#doing the other files
for log_file in log_files:
##resetting the variables
low_freqs_list = []
conver = 'no'
im_freq_num = '0'
e_elec_au = 'ERROR'
de_elec_au = 'ERROR'
zpe_au = 'ERROR'
dzpe_au = 'ERROR'
e_au = 'ERROR'
de_au = 'ERROR'
h_au = 'ERROR'
dh_au = 'ERROR'
ts_au = 'ERROR'
ts_au = 'ERROR'
tds_au = 'ERROR'
g_au = 'ERROR'
dg_au = 'ERROR'
##fetching all data for the file
f = open(log_file, 'r')
file_name = log_file
for line in f:
if e_elec_string in line:
e_elec_au = line[(len(e_elec_string)+15):(len(e_elec_string)+35)]
e_elec_au = float(e_elec_au)
if zpe_string in line:
zpe_au = line[(len(zpe_string)+1):(len(zpe_string)+37)]
zpe_au = float(zpe_au)
if e_string in line:
e_au = line[(len(e_string)+1):(len(e_string)+35)]
e_au = float(e_au)
if h_string in line:
h_au = line[(len(h_string)+1):(len(h_string)+35)]
h_au = float(h_au)
if g_string in line:
g_au = line[(len(g_string)+1):(len(g_string)+35)]
g_au = float(g_au)
if freq_string in line:
low_freqs = line[(len(freq_string)+1):]
low_freqs = low_freqs.split()
low_freqs_list = low_freqs_list + low_freqs;
if conver_string in line:
conver = 'yes'
if im_freq_string in line:
im_freq_num = line[7:12]
im_freq_num = str(int(im_freq_num))
##assigning/calculating all data fields to print for the file
e_elec_kj = str(e_elec_au*2625.5)
de_elec_kj = str(round(((e_elec_au - ref_e_elec_au)*2625.5),2))
zpe_kj = str(zpe_au*2625.5)
dzpe_kj = str(round(((zpe_au - ref_zpe_au)*2625.5),2))
e_kj = str(e_au*2625.5)
de_kj = str(round(((e_au - ref_e_au)*2625.5),2))
h_kj = str(h_au*2625.5)
dh_kj = str(round(((h_au - ref_h_au)*2625.5),2))
ts_au = h_au - g_au
ts_kj = str(ts_au*2625.5)
tds_kj = str(round(((ts_au - ref_ts_au)*2625.5),2))
g_kj = str(g_au*2625.5)
dg_kj = str(round(((g_au - ref_g_au)*2625.5),2))
low_freqs = []
for low_freq in low_freqs_list:
low_freq = str(int(round(float(low_freq))))
low_freqs.append(low_freq)
low_freqs_string = ",".join(low_freqs)
##printing file row
print file_name+','+e_elec_kj+','+de_elec_kj+','+zpe_kj+','+dzpe_kj+','+e_kj+','+de_kj+','+h_kj+','+dh_kj+','+ts_kj+','+tds_kj+','+g_kj+','+dg_kj+','+low_freqs_string+','+conver+','+im_freq_num
f.close()
