A script to convert a PL_POLY HISTORY file to an xyz file
- copy and paste the script into a file called his2xyz.py
- you will need to alter the atomList to match the 3letter names for your atoms!
- run by typing: python his2xyz.py HISTORY_file XYZ_file
- once you have downloaded it remove the .rtf extension and save with the simple filename "HISTORY"
#!/usr/bin/env python
import sys,string
#run this script by typing python his2xyz.py his_file *.xyz
# his_file is the input HISTORY file
# *.xyz is the output xyz coordinates file
# a list of the atom labels that can be read
# you will need to change these for your file!
# watch out for missing one or two, then the number of atoms in the *.xyz file will be wrong
atomList=['NA','CR','CW','C1','CE','HCR','HCW','HC','H1','OBT','SBT','NBT','FSI']
# arguments from running the file,
# argv[1]=HISTORY file
# argv[2]=output *.xyz file
inputFile=open(sys.argv[1],'r')
outFile=open(sys.argv[2],'w')
#HISTORY file foromat is
#title line (a80)
#data line (3i10)
# example: 0 1 7168 30000 430200002
# this is (traj key) (periodic boundry key) (number of atoms in cell)
# don't know what the rest is
#
#then lines repeat for each timestep with the following
#data line (a8,4i10,f12.6)
# example: timestep 1 7168 0 1 0.001000 0.001000
# (timestep) (current time step) (number of atoms in cell) i
# (traj key) (periodic boundry key) (timestep) (current time)
#cell parameters (3g12.4)
# example: 44.0395918372 0.0000000000 0.0000000000
# one line each for a,b,c cell unit vectors in x,y,z coords
# so a cubic cell will only have values on the diagonals
#then series of lines for the atoms (a8,i10,2f12.6)
# example:NA 1 14.007000 0.150000 0.010361
# atomic label, atom index, atomic mass, atomic charge
#then the coordinates x,y,z (3e12.4)
# example: -10.59313518 -14.80289434 2.774588572
#then the forces x,y,z (3e12.4)
# but only if trajectory key is greater than one
#the VMD xyz file format is
#number of atoms
#comment (normally the time step)
#atom_name x y z
#
#read the first line of history file
title=inputFile.readline()
#print(title)
#read second line of history file
#and break the stings up into their constituents
#print out the total atoms and totoal number of frames
line=inputFile.readline()
#print(line)
line=line.rstrip().split()
#print(line[0])
if line[0]=='0':
total_steps=line[3]
print('total number of steps is {0}'.format(total_steps))
total_atoms=line[2]+'\n'
print('total atoms {0}'.format(total_atoms))
#read a new line
#now loop through reading the lines
#if this line has content do the following
#otherwise quit
line=inputFile.readline()
line=line.rstrip().split()
while line:
#if the first component if the line is the word timestep
#then identify the timestep
#and write the total atoms and timestep to the output *.xyz file
if line[0]=='timestep':
time_step=line[1]+'\n'
print('timestep is {0}'.format(time_step))
outFile.write('{0}'.format(total_atoms))
outFile.write('time step {0}'.format(time_step))
exit
#extract everything before the 3rd character from the line string
#if this letter combination is found in the atomList array
#then write this atomName into the *.xyz file
#and read and write out the xys coorinates on the same line (ie use \t ranther than \n)
#
if line[0][:3] in atomList:
atom_name=line[0]+'\t'
# print('atom name is {0}'.format(atom_name))
outFile.write(atom_name)
xyzline=inputFile.readline()
outFile.write(xyzline)
#read another line from the input file
#and cycle back in the while loop
line=inputFile.readline()
line=line.rstrip().split()
# print(line)
#close the open files
inputFile.close()
outFile.close()
