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lmp2xyz.py
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Tue, May 28, 11:35

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,floor
from numpy import zeros
masses={"1.00794":"H","4.002602":"He","6.941":"Li","9.012182":"Be","10.811":"B","12.0107":"C","1.00":"Au","0.0005486":"Au"}
mass_floor={1:"H",4:"He",6:"Li",9:"Be",10:"B",12:"C",0:"Au",28:"Si"}
def lmp2xyz(lammps,xyz,xpos):
print "\nGenerating %s file"%(xyz)
fin=open(lammps,'r')
fout=open(xyz,'w')
data=raw_input("Do you have a corresponding data file? please enter filename or 'n': ")
count=1
if data!='n':
dataf=open(data,'r')
datafile=dataf.readlines()
dataf.close()
for line in datafile:
if line.find("atom types")>=0:
numtypes=int(line.split()[0])
mass=zeros(numtypes,dtype=float)
elif line.find("Masses")>=0:
count+=1+datafile.index(line)
elif line.find("Atoms")>=0:
break
for i in range(numtypes):
mass[i]=float(datafile[count].split()[1])
count+=1
else:
print "\nWill continue without a data file specification"
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()
os.system("rm lines")
flines=int(tlines.split()[0])
snaps=flines/(int(numatoms)+header)
countsnap=1
if data!='n': coords={}
else: coords=zeros((int(numatoms),4),dtype=float)
# sys.stdout.write("Writing %d snapshots\n"%(snaps))
# sys.stdout.flush()
read_atoms=0
types={}
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]!="":
if data!='n':
if parse[1] not in types.keys():
type=raw_input("Atom name for type %s: "%parse[1])
types[parse[1]]=type
coords[int(parse[0])-1]=[types[parse[1]],float(parse[xpos-1]),float(parse[xpos]),float(parse[xpos+1])]
else:
coords[int(parse[0])-1][0]=int(parse[1])
coords[int(parse[0])-1][1]=float(parse[xpos-1])
coords[int(parse[0])-1][2]=float(parse[xpos])
coords[int(parse[0])-1][3]=float(parse[xpos+1])
if read_atoms==int(numatoms):
read_atoms=0
for i in range(int(numatoms)):
if data!='n': fout.writelines("%s %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
else: 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]
if len(sys.argv)==4:
xpos=sys.arv[3]-1
else: xpos=5
lmp2xyz(inputfile,outfile.split()[0],xpos)

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