Say you've done a computation along the lines of this:
and want the data in a neat data file, like this:#P rBP86/GEN 5D Pseudo(Read) Opt=() Freq=() SCF=(MaxCycle=999 ) Punch=(MO) Pop=()
33.237 0.0023 0.0536 39.9976 0.0043 0.8305 69.7345 0.0129 0.3348 84.7005 0.0173 0.7027 [..] 3133.0068 6.2938 0.6114 3143.8021 6.3551 0.3775 3164.9242 6.4685 0.8829 3221.8787 6.6972 4.6005
Then you can use the following python (2.x) script, g09freq:
#!/usr/bin/python
# Compatible with python 2.7
# Reads frequency output from a g09 (gaussian) calculation
# Usage ex.: g09freq g09.log ir.dat
import sys
def ints2float(integerlist):
for n in range(0,len(integerlist)):
integerlist[n]=float(integerlist[n])
return integerlist
def parse_in(infile):
g09output=open(infile,'r')
captured=[]
for line in g09output:
if ('Frequencies' in line) or ('Frc consts' in line) or ('IR Inten' in line):
captured+=[line.strip('\n')]
g09output.close()
return captured
def format_captured(captured):
vibmatrix=[]
steps=len(captured)
for n in range(0,steps,3):
freqs=ints2float(filter(None,captured[n].split(' '))[2:5])
forces=ints2float(filter(None,captured[n+1].split(' '))[3:6])
intensities=ints2float(filter(None,captured[n+2].split(' '))[3:6])
for m in range(0,3):
vibmatrix+=[[freqs[m],forces[m],intensities[m]]]
return vibmatrix
def write_matrix(vibmatrix,outfile):
f=open(outfile,'w')
for n in range(0,len(vibmatrix)):
item=vibmatrix[n]
f.write(str(item[0])+'\t'+str(item[1])+'\t'+str(item[2])+'\n')
f.close()
return 0
if __name__ == "__main__":
infile=sys.argv[1]
outfile=sys.argv[2]
captured=parse_in(infile)
if len(captured)%3==0:
vibmatrix=format_captured(captured)
else:
print 'Number of elements not divisible by 3 (freq+force+intens=3)'
exit()
success=write_matrix(vibmatrix,outfile)
if success==0:
print 'Read %s, parsed it, and wrote %s'%(infile,outfile)
Run it as e.g.
g09freq g09.log test.out
The output is compatible with gnuplot:
gnuplot> set xrange [3500:0] gnuplot> set yrange [10:-1] gnuplot> plot './test.out' u 1:2 w impulse
It's trivial to add gaussian broadening (see e.g. this post)
