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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5712 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-02-22 22:32:28 +00:00
parent 46104f1588
commit 49b72ac36e
8 changed files with 162 additions and 49 deletions
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57
tools/eff/lmp2xyz.py
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@ -15,15 +15,35 @@ Usage: python lmp2xyz.py lammps_dump_filename xyz_filename
"""
import os, sys
from math import log10
from math import log10,floor
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"}
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):
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]
@ -31,13 +51,15 @@ def lmp2xyz(lammps,xyz):
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
coords=zeros((int(numatoms),4),dtype=float)
if data!='n': coords={}
else: coords=zeros((int(numatoms),4),dtype=float)
sys.stdout.write("Writing [%d]: "%(snaps))
sys.stdout.flush()
read_atoms=1
read_atoms=0
for line in lines:
if line.find('ITEM: TIMESTEP')==0:
read_atom_flag=False
@ -53,14 +75,23 @@ def lmp2xyz(lammps,xyz):
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])
# print [mass_floor[int(floor(mass[int(parse[1])-1]))],float(parse[xpos-1]),float(parse[xpos]),float(parse[xpos+1])]
if data!='n':
if mass[int(parse[1])-1]==1.0:
type='Au'
else:
type=mass_floor[int(floor(mass[int(parse[1])-1]))]
coords[int(parse[0])-1]=[type,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)):
fout.writelines("%d %2.4f %2.4f %2.4f\n"%(coords[i][0],coords[i][1],coords[i][2],coords[i][3]))
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()
@ -76,6 +107,8 @@ if __name__ == '__main__':
inputfile=sys.argv[1]
outfile=sys.argv[2]
lmp2xyz(inputfile,outfile.split()[0])
if len(sys.argv)==4:
xpos=sys.arv[3]-1
else: xpos=5
lmp2xyz(inputfile,outfile.split()[0],xpos)