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lmp2xyz.py
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Sun, Nov 17, 00:32

lmp2xyz.py
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Info="""
Module name: lmp2xyz.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@caltech.edu
Project: pEFF
Version: August 2009
Extracts the xyz from a lammps trajectory dump of style custom:
dump 1 all custom period dump_file id type x y z spin radius ...
Usage: python lmp2xyz.py lammps_dump_filename xyz_filename
"""
import os, sys
from math import log10
from numpy import zeros
mass={"1.00794":"H","4.002602":"He","6.941":"Li","9.012182":"Be","10.811":"B","12.0107":"C","1.00":"Au","0.0005486":"Au"}
def lmp2xyz(lammps,xyz):
print "\nGenerating %s file"%(xyz)
fin=open(lammps,'r')
fout=open(xyz,'w')
header=9
lines=fin.readlines()
numatoms=lines[3].split()[0]
fsize=os.system("wc -l %s> lines"%(lammps))
tmp=open('lines','r')
tlines=tmp.readline()
tmp.close()
flines=int(tlines.split()[0])
snaps=flines/(int(numatoms)+header)
countsnap=1
coords=zeros((int(numatoms),4),dtype=float)
sys.stdout.write("Writing [%d]: "%(snaps))
sys.stdout.flush()
read_atoms=1
for line in lines:
if line.find('ITEM: TIMESTEP')==0:
read_atom_flag=False
sys.stdout.write("%d "%(countsnap))
sys.stdout.flush()
fout.writelines("%s\nAtoms\n"%(numatoms))
countsnap+=1
continue
if line.find('ITEM: ATOMS')==0:
read_atom_flag=True
continue
if read_atom_flag==True:
read_atoms+=1
parse=line.split()
if parse[0]!="":
coords[int(parse[0])-1][0]=int(parse[1])
coords[int(parse[0])-1][1]=float(parse[2])
coords[int(parse[0])-1][2]=float(parse[3])
coords[int(parse[0])-1][3]=float(parse[4])
if read_atoms==int(numatoms):
read_atoms=0
for i in range(int(numatoms)):
fout.writelines("%d %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
print "\nDone converting to xyz!!\n"
fin.close()
fout.close()
return
if __name__ == '__main__':
# if no input, print help and exit
if len(sys.argv) < 2:
print Info()
sys.exit(1)
inputfile=sys.argv[1]
outfile=sys.argv[2]
lmp2xyz(inputfile,outfile.split()[0])

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