You can extract the Cartesian coordinate (XYZ) of the final optimized structure using Python code. Go to gau2xyz.py and download g09-cartesian-extract.py or download directly to your Linux machine using the command
wget https://raw.githubusercontent.com/rangsimanketkaew/compchem/main/gaussian/gau2xyz.py
Follow README for how to use this Python code.
Usage:
chmod +x gau2xyz.py
python gau2xyz.py Gaussian_output.log
Source code:
#!/usr/bin/env python3
## Rangsiman Ketkaew
## https://github.com/rangsimanketkaew/compchem
##
## -------------------------Usage-------------------------
## $ chmod +x gau2xyz.py
## $ python3 gau2xyz.py Gaussian_output.log
## -------------------------------------------------------
import sys
import re
import numpy
start = 0
end = 0
filename = sys.argv[1]
newfile = str(filename) + ".final.opt.xyz"
openold = open(filename,"r")
opennew = open(newfile,"w")
rline = openold.readlines()
for i in range (len(rline)):
if "Standard orientation:" in rline[i]:
start = i
for m in range (start + 5, len(rline)):
if "---" in rline[m]:
end = m
break
## Convert to Cartesian coordinates format
## convert atomic number to atomic symbol
for line in rline[start+5 : end] :
words = line.split()
word1 = int(words[1])
word3 = str(words[3])
if word1 == 1 : word1 = "H"
elif word1 == 2 : word1 = "He"
elif word1 == 3 : word1 = "Li"
elif word1 == 4 : word1 = "Be"
elif word1 == 5 : word1 = "B"
elif word1 == 6 : word1 = "C"
elif word1 == 7 : word1 = "N"
elif word1 == 8 : word1 = "O"
elif word1 == 9 : word1 = "F"
elif word1 == 10 : word1 = "Ne"
elif word1 == 11 : word1 = "Na"
elif word1 == 12 : word1 = "Mg"
elif word1 == 13 : word1 = "Al"
elif word1 == 14 : word1 = "Si"
elif word1 == 15 : word1 = "P"
elif word1 == 16 : word1 = "S"
elif word1 == 17 : word1 = "Cl"
elif word1 == 18 : word1 = "Ar"
elif word1 == 19 : word1 = "K"
elif word1 == 20 : word1 = "Ca"
elif word1 == 21 : word1 = "Sc"
elif word1 == 22 : word1 = "Ti"
elif word1 == 23 : word1 = "V"
elif word1 == 24 : word1 = "Cr"
elif word1 == 25 : word1 = "Mn"
elif word1 == 26 : word1 = "Fe"
elif word1 == 27 : word1 = "Co"
elif word1 == 28 : word1 = "Ni"
elif word1 == 29 : word1 = "Cu"
elif word1 == 30 : word1 = "Zn"
elif word1 == 31 : word1 = "Ga"
elif word1 == 32 : word1 = "Ge"
elif word1 == 33 : word1 = "As"
elif word1 == 34 : word1 = "Se"
elif word1 == 35 : word1 = "Br"
elif word1 == 36 : word1 = "Kr"
elif word1 == 37 : word1 = "Rb"
elif word1 == 38 : word1 = "Sr"
elif word1 == 39 : word1 = "Y"
elif word1 == 40 : word1 = "Zr"
elif word1 == 41 : word1 = "Nb"
elif word1 == 42 : word1 = "Mo"
elif word1 == 43 : word1 = "Tc"
elif word1 == 44 : word1 = "Ru"
elif word1 == 45 : word1 = "Rh"
elif word1 == 46 : word1 = "Pd"
elif word1 == 47 : word1 = "Ag"
elif word1 == 48 : word1 = "Cd"
elif word1 == 49 : word1 = "In"
elif word1 == 50 : word1 = "Sn"
elif word1 == 51 : word1 = "Sb"
elif word1 == 52 : word1 = "Te"
elif word1 == 53 : word1 = "I"
elif word1 == 54 : word1 = "Xe"
elif word1 == 55 : word1 = "Cs"
elif word1 == 56 : word1 = "Ba"
elif word1 == 57 : word1 = "La"
elif word1 == 58 : word1 = "Ce"
elif word1 == 59 : word1 = "Pr"
elif word1 == 60 : word1 = "Nd"
elif word1 == 61 : word1 = "Pm"
elif word1 == 62 : word1 = "Sm"
elif word1 == 63 : word1 = "Eu"
elif word1 == 64 : word1 = "Gd"
elif word1 == 65 : word1 = "Tb"
elif word1 == 66 : word1 = "Dy"
elif word1 == 67 : word1 = "Ho"
elif word1 == 68 : word1 = "Er"
elif word1 == 69 : word1 = "Tm"
elif word1 == 70 : word1 = "Yb"
elif word1 == 71 : word1 = "Lu"
elif word1 == 72 : word1 = "Hf"
elif word1 == 73 : word1 = "Ta"
elif word1 == 74 : word1 = "W"
elif word1 == 75 : word1 = "Re"
elif word1 == 76 : word1 = "Os"
elif word1 == 77 : word1 = "Ir"
elif word1 == 78 : word1 = "Pt"
elif word1 == 79 : word1 = "Au"
elif word1 == 80 : word1 = "Hg"
elif word1 == 81 : word1 = "Tl"
elif word1 == 82 : word1 = "Pb"
elif word1 == 83 : word1 = "Bi"
elif word1 == 84 : word1 = "Po"
elif word1 == 85 : word1 = "At"
elif word1 == 86 : word1 = "Rn"
elif word1 == 87 : word1 = "Fe"
elif word1 == 88 : word1 = "Ra"
elif word1 == 89 : word1 = "Ac"
elif word1 == 90 : word1 = "Th"
## copy from atom list.
print("%s%s" % (word1,line[30:-1]), file=opennew)
openold.close()
opennew.close()
print("#"*10 + " Done " + "#"*10)
Rangsiman Ketkaew