mirror of
https://github.com/ParticulateFlow/LPP.git
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Committer: ckloss <ckloss@fluid38.(none)>
On branch master Initial commit for lpp, version 2011-10-11
This commit is contained in:
ckloss
435
src/vtk.py
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435
src/vtk.py
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# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
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# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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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# vtk tool
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oneline = "Convert LAMMPS snapshots to VTK format"
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docstr = """
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v = vtk(d) d = object containing atom coords (dump, data)
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v.one() write all snapshots to tmp.vtk
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v.one("new") write all snapshots to new.vtk
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v.many() write snapshots to tmp0000.vtk, tmp0001.vtk, etc
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v.many("new") write snapshots to new0000.vtk, new0001.vtk, etc
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v.single(N) write snapshot for timestep N to tmp.vtk
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v.single(N,"file") write snapshot for timestep N to file.vtk
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surfaces in snapshot will be written to SURF1.vtk, SURF2.vtk, etc
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where each surface (triangle type) is in a different file
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"""
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# History
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# 8/05, Steve Plimpton (SNL): original version
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# ToDo list
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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, re
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# Class definition
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class vtk:
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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.vtk"
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elif args[0][-4:] == ".vtk": file = args[0]
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else: file = args[0] + ".vtk"
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n = flag = 0
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which,time,flag = self.data.iterator(flag)
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time,box,atoms,bonds,tris,lines = self.data.viz(which)
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print time,
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sys.stdout.flush()
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if len(tris): surface(tris)
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allatoms = []
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for atom in atoms:
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allatoms.append(atom)
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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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for atom in atoms: allatoms.append(atom)
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print time,
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sys.stdout.flush()
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n += 1
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particle(file,allatoms)
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print "\nwrote %d snapshots to %s in VTK 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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surfflag = 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 surfflag == 0 and len(tris):
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surfflag = 1
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surface(tris)
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if n < 10:
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file = root + "000" + str(n) + ".vtk"
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elif n < 100:
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file = root + "00" + str(n) + ".vtk"
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elif n < 1000:
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file = root + "0" + str(n) + ".vtk"
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else:
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file = root + str(n) + ".vtk"
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particle(file,atoms)
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print time,
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sys.stdout.flush()
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n += 1
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print "\nwrote %s snapshots in VTK format" % n
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# --------------------------------------------------------------------
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def manyGran(self,*args,**kwargs):
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# check whether to output or not
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outputfl = True
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if "output" in kwargs: outputfl = kwargs["output"]
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# read startIndex (offset for filename due to parallel processing)
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startIndex = 0
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fileNos = []
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if "fileNos" in kwargs:
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fileNos = kwargs["fileNos"]
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else:
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fileNos = range(len(self.data.snaps))
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# output name
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if len(args) == 0: root = "tmp"
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else: root = args[0]
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surfflag = 0
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n = flag = 0
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# iterate over snaps
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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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xlo=self.data.snaps[n].xlo
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xhi=self.data.snaps[n].xhi
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ylo=self.data.snaps[n].ylo
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yhi=self.data.snaps[n].yhi
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zlo=self.data.snaps[n].zlo
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zhi=self.data.snaps[n].zhi
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atoms=self.data.snaps[n].atoms
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names=self.data.names
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if surfflag == 0 and len(tris):
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surfflag = 1
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surface(tris)
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if fileNos[n] < 10:
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file = root + "000" + str(fileNos[n]) + ".vtk"
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file_bb= root + "000" + str(fileNos[n]) + "_boundingBox.vtk"
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file_walls= root + "000" + str(fileNos[n]) + "_walls.vtk"
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elif fileNos[n] < 100:
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file = root + "00" + str(fileNos[n]) + ".vtk"
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file_bb= root + "00" + str(fileNos[n]) + "_boundingBox.vtk"
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file_walls= root + "00" + str(fileNos[n]) + "_walls.vtk"
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elif fileNos[n] < 1000:
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file = root + "0" + str(fileNos[n]) + ".vtk"
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file_bb= root + "0" + str(fileNos[n]) + "_boundingBox.vtk"
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file_walls= root + "0" + str(fileNos[n]) + "_walls.vtk"
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else:
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file = root + str(fileNos[n]) + ".vtk"
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file_bb= root + str(fileNos[n]) + "_boundingBox.vtk"
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file_walls= root + str(fileNos[n]) + "_walls.vtk"
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boundingBox(file_bb,xlo,xhi,ylo,yhi,zlo,zhi)
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nvalues = 0
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try: nvalues = len(self.data.snaps[0].atoms[0])
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except: nvalues = 0
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particleGran(file,atoms,names,nvalues)
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if outputfl: print time,
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if outputfl: sys.stdout.flush()
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n += 1
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if outputfl: print "\nwrote %s granular snapshots in VTK 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.vtk"
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elif args[0][-4:] == ".vtk": file = args[0]
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else: file = args[0] + ".vtk"
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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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if len(tris): surface(tris)
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particle(file,atoms)
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# --------------------------------------------------------------------
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# write list of triangles into VTK surface files: SURF1.vtk, SURF2.vtk, ...
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# all triangles of one type constitute 1 surface = 1 file
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# create list of unique vertices (via dictionary) from triangle list
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def surface(tris):
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ntypes = tris[-1][1]
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for i in xrange(ntypes):
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itype = i+1
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v = {}
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nvert = ntri = 0
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for tri in tris:
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if tri[1] == itype:
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ntri += 1
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vert = (tri[2],tri[3],tri[4])
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if not v.has_key(vert):
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v[vert] = nvert
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nvert += 1
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vert = (tri[5],tri[6],tri[7])
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if not v.has_key(vert):
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v[vert] = nvert
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nvert += 1
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vert = (tri[8],tri[9],tri[10])
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if not v.has_key(vert):
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v[vert] = nvert
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nvert += 1
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keys = v.keys()
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vinverse = {}
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for key in keys:
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vinverse[v[key]] = key
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filename = "SURF" + str(itype) + ".vtk"
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f = open(filename,"w")
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print >>f,"# vtk DataFile Version 3.0"
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print >>f,"Generated by pizza.py"
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print >>f,"ASCII"
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print >>f,"DATASET POLYDATA"
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print >>f,"POINTS %d float" % nvert
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for i in xrange(nvert):
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tuple = vinverse[i]
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print >>f,tuple[0],tuple[1],tuple[2]
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print >>f,"POLYGONS",ntri,4*ntri
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for tri in tris:
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if tri[1] == itype:
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vert = (tri[2],tri[3],tri[4])
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ivert1 = v[vert]
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vert = (tri[5],tri[6],tri[7])
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ivert2 = v[vert]
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vert = (tri[8],tri[9],tri[10])
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ivert3 = v[vert]
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print >>f,3,ivert1,ivert2,ivert3
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print >>f
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print >>f,"CELL_DATA",ntri
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print >>f,"POINT_DATA",nvert
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f.close()
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# --------------------------------------------------------------------
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# write atoms from one snapshot into file in VTK format
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def particle(file,atoms):
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f = open(file,"w")
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print >>f,"# vtk DataFile Version 2.0"
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print >>f,"Generated by pizza.py"
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print >>f,"ASCII"
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print >>f,"DATASET POLYDATA"
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print >>f,"POINTS %d float" % len(atoms)
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for atom in atoms:
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print >>f,atom[2],atom[3],atom[4]
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print >>f,"VERTICES",len(atoms),2*len(atoms)
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for i in xrange(len(atoms)):
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print >>f,1,i
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print >>f,"POINT_DATA",len(atoms)
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print >>f,"SCALARS atom_type int 1"
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print >>f,"LOOKUP_TABLE default"
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for atom in atoms:
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itype = int(atom[1])
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print >>f,itype,
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print >>f
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f.close()
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def boundingBox(file,xlo,xhi,ylo,yhi,zlo,zhi):
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f = open(file,"w")
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print >>f,"# vtk DataFile Version 2.0"
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print >>f,"Generated by pizza.py"
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print >>f,"ASCII"
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print >>f,"DATASET RECTILINEAR_GRID"
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print >>f,"DIMENSIONS 2 2 2"
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print >>f,"X_COORDINATES 2 float"
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print >>f,xlo,xhi
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print >>f,"Y_COORDINATES 2 float"
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print >>f,ylo,yhi
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print >>f,"Z_COORDINATES 2 float"
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print >>f,zlo,zhi
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def typestr(o):
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string = str(type(o))
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sp = string.split('\'')
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return sp[1]
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def particleGran(file,atoms,names,n_values):
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f = open(file,"w")
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# if no atoms are present
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if atoms == None:
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atoms = []
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# find indices of scalars and vectors
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scalars, vectors = findScalarsAndVectors(names)
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# print head
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print >>f,"# vtk DataFile Version 2.0"
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print >>f,"Generated by lpp.py"
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print >>f,"ASCII"
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print >>f,"DATASET POLYDATA"
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print >>f,"POINTS %d float" % len(atoms)
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for atom in atoms:
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print >>f, atom[vectors['x']], atom[vectors['x']+1], atom[vectors['x']+2] #atom[3],atom[4],atom[5] #write x,y,z [atom[0]=id, atom[1]=type]
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print >>f,"VERTICES",len(atoms),2*len(atoms)
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for i in xrange(len(atoms)):
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print >>f,1,i
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print >>f,"POINT_DATA",len(atoms)
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# print VECTORS
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for key in vectors.keys():
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# don't print coodinates again
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if key == 'x':
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continue
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vectortype = 'float'
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if atoms != []:
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vectortype = typestr(atoms[0][vectors[key]])
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if 'float' in vectortype: vectortype = 'float'
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elif 'int' in vectortype: vectortype = 'int'
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else: vectortype = 'float'
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else: # if no atoms are present
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pass
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print >>f,"VECTORS",key,vectortype
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for atom in atoms:
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print >>f, atom[vectors[key]], atom[vectors[key]+1], atom[vectors[key]+2]
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# print SCALARS
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for key in scalars.keys():
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scalartype =''
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if atoms != []:
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scalartype = typestr(atoms[0][scalars[key]])
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if 'float' in scalartype: scalartype = 'float'
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elif 'int' in scalartype: scalartype = 'int'
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else: scalartype = 'int'
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else: # if no atoms are present
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pass
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print >>f,"SCALARS",key,scalartype,1
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print >>f,"LOOKUP_TABLE default"
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for atom in atoms:
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print >>f, atom[scalars[key]]
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print >>f
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f.close()
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def findScalarsAndVectors(names):
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vectors={}
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scalars={}
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# create reversed dictionary {position:name}
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indices = {}
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for name in names:
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indices[names[name]]=name
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# fill missing indices (occurrs e.g. if output is like vx vy vz fx fy fz vx vy vz)
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for i in xrange(max(indices)):
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if i not in indices:
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indices[i]=""
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# compile regexes to find vectors
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regvx = re.compile(".*x")
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regvy = re.compile(".*y")
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regvz = re.compile(".*z")
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regf = re.compile("f_.*\[[0-9]+\]")
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regc = re.compile("c_.*\[[0-9]+\]")
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regv = re.compile("v_.*\[[0-9]+\]")
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# loop over all indices and look if their names represent a vector (if not: it's a scalar)
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i = 0
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while i<= max(indices):
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if i+2 <= max(indices) and regvx.match(indices[i]) != None and regvy.match(indices[i+1]) != None and regvz.match(indices[i+2]) != None:
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newname=''
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if len(indices[i]) == 1:
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newname=indices[i]
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else:
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newname=indices[i][:-1]
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vectors[newname]=i
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i+=3
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continue
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if regf.match(indices[i]) != None or regc.match(indices[i]) != None or regv.match(indices[i]) != None:
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name = indices[i]
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number = int( name.split('[')[1].split(']')[0] )
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nextName = name.split('[')[0]+'['+str(number+1)+']'
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nextButOneName = name.split('[')[0]+'['+str(number+2)+']'
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newname = name[2:-(len(name.split('[')[1])+1)]
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if i+2 <= max(indices) and indices[i+1] == nextName and indices[i+2] == nextButOneName:
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vectors[newname]=i
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i+=3
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continue
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else:
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scalars[newname]=i
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i+=1
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continue
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# program only here if not a vector
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if indices[i] != '':
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newname = indices[i]
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scalars[newname]=i
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i+=1
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if 'x' not in vectors.keys():
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print "vector x y z has to be contained in dump file. please change liggghts input script accordingly."
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exit()
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return scalars, vectors
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