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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9183 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-01-02 16:45:47 +00:00
parent f4cc8c35bb
commit 5b9c57e438
1 changed files with 9 additions and 10 deletions
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19
tools/eff/lmp2xyz.py
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@ -57,14 +57,15 @@ def lmp2xyz(lammps,xyz,xpos):
countsnap=1
if data!='n': coords={}
else: coords=zeros((int(numatoms),4),dtype=float)
sys.stdout.write("Writing [%d]: "%(snaps))
sys.stdout.flush()
# 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()
# sys.stdout.write("%d "%(countsnap))
# sys.stdout.flush()
fout.writelines("%s\nAtoms\n"%(numatoms))
countsnap+=1
continue
@ -75,13 +76,11 @@ def lmp2xyz(lammps,xyz,xpos):
read_atoms+=1
parse=line.split()
if parse[0]!="":
# 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])]
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])