190 lines
6.1 KiB
Python
190 lines
6.1 KiB
Python
# Pizza.py toolkit, https://lammps.github.io/pizza
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# LAMMPS development team: developers@lammps.org
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#
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# Copyright (2005) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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from __future__ import print_function
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# cfg tool
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oneline = "Convert LAMMPS snapshots to AtomEye CFG format"
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docstr = """
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c = cfg(d) d = object containing atom coords (dump, data)
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c.one() write all snapshots to tmp.cfg
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c.one("new") write all snapshots to new.cfg
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c.many() write snapshots to tmp0000.cfg, tmp0001.cfg, etc
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c.many("new") write snapshots to new0000.cfg, new0001.cfg, etc
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c.single(N) write snapshot for timestep N to tmp.cfg
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c.single(N,"file") write snapshot for timestep N to file.cfg
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"""
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# History
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# 11/06, Aidan Thompson (SNL): original version
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# ToDo list
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# should decide if dump is scaled or not, since CFG prints in scaled coords
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# this creates a simple AtomEye CFG format
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# there is more complex format we could write out
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# which allows for extra atom info, e.g. to do atom coloring on
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# how to dump for a triclinic box, since AtomEye accepts this
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# Variables
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# data = data file to read from
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# Imports and external programs
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import sys
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# Class definition
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class cfg:
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# --------------------------------------------------------------------
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def __init__(self,data):
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self.data = data
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# --------------------------------------------------------------------
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def one(self,*args):
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if len(args) == 0: file = "tmp.cfg"
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elif args[0][-4:] == ".cfg": file = args[0]
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else: file = args[0] + ".cfg"
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f = open(file,"w")
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n = flag = 0
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while 1:
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which,time,flag = self.data.iterator(flag)
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if flag == -1: break
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time,box,atoms,bonds,tris,lines = self.data.viz(which)
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xlen = box[3]-box[0]
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ylen = box[4]-box[1]
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zlen = box[5]-box[2]
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print("Number of particles = %d " % len(atoms), file=f)
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print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
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print("H0(1,1) = %20.10f A " % xlen, file=f)
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print("H0(1,2) = 0.0 A ", file=f)
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print("H0(1,3) = 0.0 A ", file=f)
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print("H0(2,1) = 0.0 A ", file=f)
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print("H0(2,2) = %20.10f A " % ylen, file=f)
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print("H0(2,3) = 0.0 A ", file=f)
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print("H0(3,1) = 0.0 A ", file=f)
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print("H0(3,2) = 0.0 A ", file=f)
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print("H0(3,3) = %20.10f A " % zlen, file=f)
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print("#", file=f)
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for atom in atoms:
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itype = int(atom[1])
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xfrac = (atom[2]-box[0])/xlen
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yfrac = (atom[3]-box[1])/ylen
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zfrac = (atom[4]-box[2])/zlen
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# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
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print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
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print(time)
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sys.stdout.flush()
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n += 1
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f.close()
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print("\nwrote %d snapshots to %s in CFG format" % (n,file))
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# --------------------------------------------------------------------
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def many(self,*args):
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if len(args) == 0: root = "tmp"
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else: root = args[0]
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n = flag = 0
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while 1:
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which,time,flag = self.data.iterator(flag)
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if flag == -1: break
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time,box,atoms,bonds,tris,lines = self.data.viz(which)
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if n < 10:
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file = root + "000" + str(n)
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elif n < 100:
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file = root + "00" + str(n)
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elif n < 1000:
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file = root + "0" + str(n)
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else:
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file = root + str(n)
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file += ".cfg"
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f = open(file,"w")
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xlen = box[3]-box[0]
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ylen = box[4]-box[1]
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zlen = box[5]-box[2]
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print("Number of particles = %d " % len(atoms), file=f)
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print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
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print("H0(1,1) = %20.10f A " % xlen, file=f)
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print("H0(1,2) = 0.0 A ", file=f)
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print("H0(1,3) = 0.0 A ", file=f)
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print("H0(2,1) = 0.0 A ", file=f)
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print("H0(2,2) = %20.10f A " % ylen, file=f)
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print("H0(2,3) = 0.0 A ", file=f)
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print("H0(3,1) = 0.0 A ", file=f)
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print("H0(3,2) = 0.0 A ", file=f)
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print("H0(3,3) = %20.10f A " % zlen, file=f)
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print("#", file=f)
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for atom in atoms:
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itype = int(atom[1])
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xfrac = (atom[2]-box[0])/xlen
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yfrac = (atom[3]-box[1])/ylen
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zfrac = (atom[4]-box[2])/zlen
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# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
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print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
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print(time)
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sys.stdout.flush()
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f.close()
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n += 1
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print("\nwrote %s snapshots in CFG format" % n)
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# --------------------------------------------------------------------
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def single(self,time,*args):
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if len(args) == 0: file = "tmp.cfg"
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elif args[0][-4:] == ".cfg": file = args[0]
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else: file = args[0] + ".cfg"
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which = self.data.findtime(time)
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time,box,atoms,bonds,tris,lines = self.data.viz(which)
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f = open(file,"w")
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xlen = box[3]-box[0]
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ylen = box[4]-box[1]
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zlen = box[5]-box[2]
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print("Number of particles = %d " % len(atoms), file=f)
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print("# Timestep %d \n#\nA = 1.0 Angstrom" % time, file=f)
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print("H0(1,1) = %20.10f A " % xlen, file=f)
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print("H0(1,2) = 0.0 A ", file=f)
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print("H0(1,3) = 0.0 A ", file=f)
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print("H0(2,1) = 0.0 A ", file=f)
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print("H0(2,2) = %20.10f A " % ylen, file=f)
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print("H0(2,3) = 0.0 A ", file=f)
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print("H0(3,1) = 0.0 A ", file=f)
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print("H0(3,2) = 0.0 A ", file=f)
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print("H0(3,3) = %20.10f A " % zlen, file=f)
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print("#", file=f)
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for atom in atoms:
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itype = int(atom[1])
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xfrac = (atom[2]-box[0])/xlen
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yfrac = (atom[3]-box[1])/ylen
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zfrac = (atom[4]-box[2])/zlen
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# print("1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]), file=f)
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print("1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac), file=f)
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f.close()
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