Wikiadmin: /* data script */

2024-12-18T07:05:08Z

data script

Wikiadmin: Created page with "=data script= script to extract data and print in a format to paste into the template excel sheet used for the database simply copy and paste this script into a file get_dat..."

2020-11-25T04:24:40Z

Created page with "=data script= *script to extract data and print in a format to paste into the template excel sheet used for the database *simply copy and paste this script into a file get_dat..."

New page

=data script=
*script to extract data and print in a format to paste into the template excel sheet used for the database
*simply copy and paste this script into a file get_data.py
*then run with "python getdata.py file_name.log"
<pre>
#
# getdata.py
#
# python3 script to
# extract key data from gaussian log files for input into
# excell spreadsheets for our database
#
# to run the script type
# python3 getdata.py file.log
#
import sys
filein=str(sys.argv[1])
f = open(filein,'r')

enstring = 'SCF Done'
gstring = 'Sum of electronic and thermal Free Energies='
hstring = 'Sum of electronic and thermal Enthalpies='
zpestring = 'Zero-point correction='
freqstring = 'Low frequencies ---'
freqlist = []

line=f.readline()
while line:
if enstring in line:
enval = line[(len(enstring)+16):(len(enstring)+31)]

if gstring in line:
gval = line[(len(gstring)+9):(len(gstring)+21)]

if hstring in line:
hval = line[(len(hstring)+12):(len(hstring)+24)]

if zpestring in line:
zpeval = line[(len(zpestring)+27):(len(zpestring)+36)]

pos = line.find(freqstring)
if pos != -1:
freqval = line[(len(freqstring)+1):]
freqs = freqval.split()
freqlist = freqlist + freqs;

line=f.readline()
#endwhile

newval=float(hval)-float(gval)
newval=str(round(newval,10))

f.close()

s='input file is '
print('\n {0:}{1:}'.format(s,filein))

se='SCF energy'
sg='Gibbs free energy'
sh='Enthalpy'
ss='Entropy'
sz='ZPE'
print(' {0:}={1:} \n {2:}={3:} \n {4:}={5:} \n {6:}={7:} \n {8:}={9:}'.format \
(se,enval,sg,gval,sh,hval,ss,newval,sz,zpeval))

sf='low modes:'
print(' {0:} {1[0]:}, {1[1]:}, {1[2]:}, {1[3]:}, {1[4]:}, {1[5]:}'.format(sf,freqlist))

s='suitable for copying to excel:'
print('{0:} \n'.format(s))
print('{0:}, , ,{1:}, ,{2:}, ,{3:}, ,{4:}, ,{5:},{6[0]:},{6[1]:},{6[2]:},{6[3]:},{6[4]:},{6[5]:}'.format(filein,enval,gval,hval,newval,zpeval,freqlist))

# finish up
f.close()
sys.exit()
</pre>

@@ Line 1: / Line 1: @@
 =data script=
 *script to extract data and print in a format to paste into the template excel sheet used for the database
-*simply copy and paste this script into a file get_data.py
+*simply copy and paste this script into a file getdata.py
 *then run with "python getdata.py file_name.log"
 <pre>
@@ Line 15: / Line 15: @@
+#
 import sys
-filein=str(sys.argv[1])
+import os
-f = open(filein,'r')
-enstring = 'SCF Done'
+scfstring = 'SCF Done:'
 gstring = 'Sum of electronic and thermal Free Energies='
 freqstring = 'Low frequencies ---'
 freqlist = []
@@ Line 27: / Line 40: @@
 line=f.readline()
 while line:
-         if enstring in line:
+         if scfstring in line:
-                enval = line[(len(enstring)+16):(len(enstring)+31)]
+           tmp=line.rstrip().split()
-         if gstring in line:
+         if zpestring in line:
-                gval = line[(len(gstring)+9):(len(gstring)+21)]
+           tmp=line.rstrip().split()
          if hstring in line:
-                hval = line[(len(hstring)+12):(len(hstring)+24)]
+           tmp=line.rstrip().split()
-         if zpestring in line:
+         if gstring in line:
-                zpeval = line[(len(zpestring)+27):(len(zpestring)+36)]
+           tmp=line.rstrip().split()
          pos = line.find(freqstring)
@@ Line 48: / Line 74: @@
 #endwhile
-newval=float(hval)-float(gval)
+entval=hval-gval
-newval=str(round(newval,10))
+entval=round(entval,10)
 f.close()
 s='input file is '
-print('\n {0:}{1:}'.format(s,filein))
+print('\n {0:}{1:}'.format(s,log_file))
 se='SCF energy'
 sg='Gibbs free energy'
 sh='Enthalpy'
 ss='Entropy'
 sz='ZPE'
-print(' {0:}={1:} \n {2:}={3:} \n {4:}={5:} \n {6:}={7:} \n {8:}={9:}'.format \
+#enscf = scf energy
-      (se,enval,sg,gval,sh,hval,ss,newval,sz,zpeval))
+#zpeval = ZPE correction
-sf='low modes:'
+sf=' low modes:'
-print(' {0:} {1[0]:}, {1[1]:}, {1[2]:}, {1[3]:}, {1[4]:}, {1[5]:}'.format(sf,freqlist))
+sf1=' no modes!'
-s='suitable for copying to excel:'
+s='\n suitable for copying to excel:'
-print('{0:} \n'.format(s))
+print('{0:}'.format(s))
-print('{0:}, , ,{1:}, ,{2:}, ,{3:}, ,{4:}, ,{5:},{6[0]:},{6[1]:},{6[2]:},{6[3]:},{6[4]:},{6[5]:}'.format(filein,enval,gval,hval,newval,zpeval,freqlist))
+print('{0:},,{1:}, ,{2:}, ,{3:}, ,{4:}, ,{5:},{6:}, ,{7[0]:},{7[1]:},{7[2]:},{7[3]:},{7[4]:},{7[5]:} \n'.format(log_file,enscf,gval,hval,entval,zpeval,enzpeval,freqlist))
 # finish up

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

Wikiadmin: /* data script */

Wikiadmin: Created page with "=data script= *script to extract data and print in a format to paste into the template excel sheet used for the database *simply copy and paste this script into a file get_dat..."

Wikiadmin: Created page with "=data script= script to extract data and print in a format to paste into the template excel sheet used for the database simply copy and paste this script into a file get_dat..."