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readGauss.py
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#!/usr/bin/python -u
# 2016.4.20 09:29
__author__ = 'TQC'
import os
import re
import sys
import numpy as np
def extract():
lat = []
litem = []
temp = []
templat = []
a2b = 1.0/0.529177
hartrees2eV = 27.21
if os.path.exists('goutput'):
fileOpen = 'goutput'
else:
print 'Error: no input file: goutput'
exit(0)
f = open(fileOpen, 'r')
nstru = 0
while True:
line = f.readline()
if len(line) == 0:
break
if 'NAtoms=' in line:
litem = line.split()
natom = int(litem[1])
if 'Multiplicity' in line:
line = f.readline()
name = line.split()[0]
if 'Coordinates' in line:
nstru = nstru + 1
#if nstru==0:
# continue
fw = open(str(nstru)+'_g.xyz','w')
#fw.write("%s\n" % name)
#fw.write("%15.10f\n" % 1.0)
trtreesemp = f.readline()
temp = f.readline()
fw.write("%d\n" % natom)
fw.write("\n")
for i in range(natom):
templat = f.readline().split()
#lat.append(map(float,templat[0:3]))
lat = (map(float,templat[3:6]))
fw.write(str(name) + ' ')
fw.write("%15.10f\t%15.10f\t%15.10f\n" % tuple(lat[0:3]))
#fw.write("%s\n" % name)
fw.write("\n" )
if 'E(' in line:
linelat = line.strip().split()
#print linelat
fw.write("%s\n" % 'Energy(eV)')
ene = float(linelat[4])*hartrees2eV/natom
fw.write("%15.10f\n" % ene)
if 'Forces (Hartrees/Bohr)' in line:
temp = f.readline()
temp = f.readline()
fw.write("%s\n" % 'Forces (eV/A)')
for i in range(natom):
templat = f.readline().split()
lat = np.array(templat[2:5],float)
lat1 = lat[0:3]*hartrees2eV*a2b
fw.write("%15.10f\t%15.10f\t%15.10f\n" % tuple(lat1))
fw.close()
'''
if 'in kB' in line:
stress_temp = map(float,line.split()[2:8])
stress_sort = [0.0,0.0,0.0,0.0,0.0,0.0]
stress_sort[0] = stress_temp[0]
stress_sort[1] = stress_temp[3]
stress_sort[2] = stress_temp[5]
stress_sort[3] = stress_temp[1]
stress_sort[4] = stress_temp[4]
stress_sort[5] = stress_temp[2]
stress = stress_sort
#print stress
#fw.write("%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\n" % tuple(stress))
if 'POSITION' in line:
f.readline()
for i in range(natom):
litem = map(float,f.readline().split())
fw.write("%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\n" % tuple(litem))
#fw.write(" %s\n" % "F")
#fw.write("%15.10f\t%15.10f\t%15.10f\n" % tuple(litem[0:3]))
if 'energy without entropy' in line:
energy = float(line.split()[3].strip())
fw.write("%15.11f %15.11f\n" % (energy,energy/natom))
#fw.write(" %s\n" % "E")
fw.write("%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\t%15.10f\n" % tuple(stress))
#fw.write(" %s\n" % "S")
fw.close()'''
#f.close()
def extract_last():
lat = []
litem = []
temp = []
templat = []
pos = []
a2b = 1.0/0.529177
hartrees2eV = 27.21
if os.path.exists('goutput'):
fileOpen = 'goutput'
else:
print 'Error: no input file: goutput'
exit(0)
f = open(fileOpen, 'r')
nstru = 0
ns = int(os.popen("grep 'E(' goutput | wc -l").read().split()[0])
ns += 1
while True:
line = f.readline()
if len(line) == 0:
break
if 'NAtoms=' in line:
litem = line.split()
natom = int(litem[1])
if 'Multiplicity' in line:
line = f.readline()
name = line.split()[0]
if 'Coordinates' in line:
nstru = nstru + 1
if nstru == ns:
#fw = open('glast.xyz','w')
f.readline()
f.readline()
for i in range(natom):
templat = f.readline().split()
lat = (map(float,templat[3:6]))
pos.append(lat)
pos = np.array(pos,float)
#print pos,name
return (name,pos)
if __name__ == '__main__':
#nns = int(sys.argv[1])
#print nns
extract()