- copy the code into a script called "extract_steps.py"
- to execute the script type "python3 extract_steps.py file_name (without .log extension)
- this will print some info to the terminal and create a file file_name.xyz
- the Standard Orientaion is extracted
#
# extract_steps.py
#
# python script to extract and print the standard orintation of the optimised structure for each step of a scan
# from a gaussian log file
# to run the script type python extract_steps.py input_file_name (without extension)
#
import sys
import os
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python extract_structure.py input_file_name \(without extension\)')
sys.exit()
else:
base=str(sys.argv[1])
file=base+'.log'
out=base+'.xyz'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='output file is '
print('{0:}{1:}'.format(s,out))
#close if
#
# set some defaults
col_num=[]
col_atom=[]
col_type=[]
col_x=[]
col_y=[]
col_z=[]
step_num=[]
step_atom=[]
step_type=[]
step_x=[]
step_y=[]
step_z=[]
n=0
scan_step=0
n_step=0
no_atoms=0
ntotal=0
nstep=0
go=False
ntotal=0
rewind=0
# open file and read lines one by one
f=open(file,"r")
line =f.readline()
while line :
line =f.readline()
#==extract GEOMETRY ==
# check for standard orientation text set go if the text appears
if 'Standard orientation:' in line:
go=True
# s='Standard orientation found '
# print('{0:}'.format(s))
no_atoms=0
n=0
# close if
#
# if go is on then save the structure
while go:
n = n+1
m = 0
line =f.readline()
if 'Rotational constants (GHZ):' in line: m=-1
if '---------' in line: m=1
# s1='n= '
# s2=' m= '
# print('{0:}{1:}{2:}{3:}'.format(s1,n,s2,m))
if n > 4 and m == 0 :
# print(line)
no_atoms = no_atoms+1
ntotal=ntotal+1
a1,b1,c1,d1,e1,f1=line.rstrip().split()
col_num.append(int(a1))
col_atom.append(int(b1))
col_type.append(int(c1))
col_x.append(float(d1))
col_y.append(float(e1))
col_z.append(float(f1))
# s='number of atoms '
# print('{0:}{1:}'.format(s,no_atoms))
if m == -1 : go=False
# close while
#
# now check to see if this is a completed opt step, if it is
# then save the last geometry stored
#
# scan_step is the surrent scan step number
# no_atoms is the total number of atoms
# ntotal is the total number in the col array at this point
# rewind takes us back to the previous set of coordinated
# m is the local atom counter
# n is the current counter for the position in the col array
# n_step is the current counter for the position in the step array
m=0
if ' ! Optimized Parameters !' in line:
s='Optimised structure found '
print('{0:}'.format(s))
scan_step=scan_step+1
rewind=ntotal-(no_atoms+1)
# s='rewind '
# print('{0:}{1:}'.format(s,rewind))
while m < no_atoms :
m=m+1
n=rewind+m
# s1=' scan step ='
# s2=' step n='
# s3=' col n='
# s4=' local m='
# print('{0:}{1:}{2:}{3:}{4:}{5:}{6:}{7:}'.format(s1,scan_step,s2,nstep,s3,n,s4,m))
step_num.append(col_num[n])
step_atom.append(col_atom[n])
step_type.append(col_type[n])
step_x.append(col_x[n])
step_y.append(col_y[n])
step_z.append(col_z[n])
# print('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f}'.format(step_atom[nstep],step_x[nstep],step_y[nstep],step_z[nstep]))
nstep=nstep+1
# close while
# close if
#close while
#
# now write to the .xyz file
c=open(out,"w")
s='number of atoms '
print('{0:}{1:}'.format(s,no_atoms))
#c.write('{0:}{1:} \n'.format(s,no_atoms))
s='number of scan steps '
print('{0:}{1:}'.format(s,scan_step))
#c.write('{0:}{1:} \n'.format(s,scan_step))
s='file format: atomic no, xyz coords'
print('{0:}'.format(s))
#c.write('{0:} \n'.format(s))
#s='array counter total '
#print('{0:}{1:}'.format(s,ntotal))
#
# scan_step is the total number of scan steps
# no_atoms is the total number of atoms
# step_n is the scan step
# m is the local atom counter
# n is the current number in the overall array
step_n=0
m=0
n=0
while step_n < scan_step :
step_n=step_n+1
m=0
s='print step '
print('{0:}{1:}'.format(s,step_n))
c.write('{0:} \n'.format(step_n))
while m < no_atoms :
m=m+1
s1=' step='
s3=' array n='
s2=' local m='
# print('{0:}{1:}{2:}{3:}{4:}{5:}'.format(s1,step_n,s2,m,s3,n))
# print('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f}'.format(step_atom[n],step_x[n],step_y[n],step_z[n]))
c.write('{0:>4d} {1: 09.6f} {2: 09.6f} {3: 09.6f} \n'.format(step_atom[n],step_x[n],step_y[n],step_z[n]))
n=n+1
# close while
#close while
# close all open files
f.close()
c.close()
