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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1693 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-03-31 22:39:55 +00:00
parent 386dec94ae
commit 13643a8314
1 changed files with 9 additions and 4 deletions
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13
tools/python/dump2pdb.py
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@ -2,11 +2,13 @@
# Script: dump2pdb.py # Script: dump2pdb.py
# Purpose: convert a LAMMPS dump file to PDB format # Purpose: convert a LAMMPS dump file to PDB format
# Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile # Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile template
# dumpfile = LAMMPS dump file in native LAMMPS format # dumpfile = LAMMPS dump file in native LAMMPS format
# Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z # Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z
# (usually 1,2,3,4,5) # (usually 1,2,3,4,5)
# pdbfile = new PDB file # pdbfile = new PDB file
# template = PDB file to use as template for creating new PDB file
# this arg is optional, if not used a generic PDB file is created
# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov # Author: Steve Plimpton (Sandia), sjplimp at sandia.gov
import sys,os import sys,os
@ -15,8 +17,8 @@ sys.path.append(path)
from dump import dump from dump import dump
from pdbfile import pdbfile from pdbfile import pdbfile
if len(sys.argv) != 8: if len(sys.argv) != 8 and len(sys.argv) != 9:
raise StandardError, "Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile" raise StandardError, "Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile template"
dumpfile = sys.argv[1] dumpfile = sys.argv[1]
nid = int(sys.argv[2]) nid = int(sys.argv[2])
@ -25,8 +27,11 @@ nx = int(sys.argv[4])
ny = int(sys.argv[5]) ny = int(sys.argv[5])
nz = int(sys.argv[6]) nz = int(sys.argv[6])
pfile = sys.argv[7] pfile = sys.argv[7]
if len(sys.argv) == 9: template = sys.argv[8]
else: template = ""
d = dump(dumpfile) d = dump(dumpfile)
d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z") d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z")
p = pdbfile(d) if template: p = pdbfile(template,d)
else: p = pdbfile(d)
p.one(pfile) p.one(pfile)