# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# ensight tool
oneline = "Convert LAMMPS snapshots or meshes to Ensight format"
docstr = """
e = ensight(d) d = object with atoms or elements (dump,data,mdump)
e.change = 1 set to 1 if element nodal xyz change with time (def = 0)
e.maxtype = 10 max particle type, set if query to data will be bad
e.one()
e.one("new")
e.one("cns","Centro","eng","Energy")
e.one("new","cns","Centro","eng","Energy")
write all snapshots as an Ensight data set
Ensight header file = tmp.case (no 1st arg) or new.case
Ensight coord file = tmp.xyz or new.xyz
additional pairs of args create auxiliary files:
tmp.cns, tmp.eng or new.cns, new.eng
cns,eng = column name in dump file and file name suffix
Centro,Energy = Ensight name for the variable
e.increment() same args as one(), but process dump out-of-core
e.many() same args as one(), but create multiple Ensight files
tmp0000.xyz, tmp0001.xyz, etc
new0000.cns, new0001.cns, etc
new0000.eng, new0001.eng, etc
e.single(N) same args as one() prepended by N, but write a single snap
"""
# History
# 10/06, Steve Plimpton (SNL): original version
# ToDo list
# binary files
# create vector or tensor variable files, not just scalar
# via pair of args like ["vx","vy","vz"],"vel"
# Variables
# data = data file to read from
# which = 0 for particles, 1 for elements
# change = 0 for unchanging mesh coords, 1 for changing mesh coords (def = 0)
# Imports and external programs
import sys, types
# Class definition
class ensight:
# --------------------------------------------------------------------
def __init__(self,data):
self.change = 0
self.maxtype = 0
self.data = data
if type(data) is types.InstanceType and ".dump" in str(data.__class__):
self.which = 0
elif type(data) is types.InstanceType and ".data" in str(data.__class__):
self.which = 0
elif type(data) is types.InstanceType and ".mdump" in str(data.__class__):
self.which = 1
elif type(data) is types.InstanceType and ".cdata" in str(data.__class__):
self.which = 1
else:
raise StandardError,"unrecognized object passed to ensight"
# --------------------------------------------------------------------
def one(self,*args):
if len(args) % 2 == 0: root = "tmp"
else:
root = args[0]
args = args[1:]
pairs = []
for i in range(0,len(args),2): pairs.append([args[i],args[i+1]])
# max # of types for all steps in Ensight files
if self.which == 0 and self.maxtype == 0:
self.maxtype = self.data.maxtype()
# write Ensight *.case header file
f = open("%s.case" % root,"w")
times = self.data.time()
self.case_file(f,root,pairs,0,len(times),times)
f.close()
# open additional files
f = open(root + ".xyz","w")
vfiles = []
for pair in pairs: vfiles.append(open(root + "." + pair[0],"w"))
# loop over snapshots
# write coords into xyz file, variables into their files
first = 1
n = flag = etype = 0
while 1:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
if self.which == 0:
print >>f,"BEGIN TIME STEP"
time,box,atoms,bonds,tris,lines = self.data.viz(which)
self.coord_file_atoms(f,box,atoms)
print >>f,"END TIME STEP"
elif self.change == 0 and first:
print >>f,"BEGIN TIME STEP"
time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
first = 0
print >>f,"END TIME STEP"
elif self.change:
print >>f,"BEGIN TIME STEP"
time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
print >>f,"END TIME STEP"
for i in range(len(pairs)):
print >>vfiles[i],"BEGIN TIME STEP"
values = self.data.vecs(time,pairs[i][0])
if self.which == 0:
self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values)
else:
self.variable_file_elements(vfiles[i],pairs[i][1],etype,values)
print >>vfiles[i],"END TIME STEP"
print time,
sys.stdout.flush()
n += 1
# close additional files
f.close()
for f in vfiles: f.close()
print "\nwrote %s snapshots in Ensight format" % n
# --------------------------------------------------------------------
def increment(self,*args):
if len(args) % 2 == 0: root = "tmp"
else:
root = args[0]
args = args[1:]
pairs = []
for i in range(0,len(args),2): pairs.append([args[i],args[i+1]])
# max # of types for all steps in Ensight files
if self.which == 0 and self.maxtype == 0:
self.maxtype = self.data.maxtype()
# open additional files
f = open(root + ".xyz","w")
vfiles = []
for pair in pairs: vfiles.append(open(root + "." + pair[0],"w"))
# loop over snapshots
# write coords into xyz file, variables into their files
times = []
first = 1
n = etype = 0
while 1:
time = self.data.next()
if time == -1: break
times.append(time)
self.data.tselect.one(time)
self.data.delete()
if self.which == 0:
print >>f,"BEGIN TIME STEP"
time,box,atoms,bonds,tris,lines = self.data.viz(0)
self.coord_file_atoms(f,box,atoms)
print >>f,"END TIME STEP"
elif self.change == 0 and first:
print >>f,"BEGIN TIME STEP"
time,box,nodes,elements,nvalues,evalues = self.data.mviz(0)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
first = 0
print >>f,"END TIME STEP"
elif self.change:
print >>f,"BEGIN TIME STEP"
time,box,nodes,elements,nvalues,evalues = self.data.mviz(0)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
print >>f,"END TIME STEP"
for i in range(len(pairs)):
print >>vfiles[i],"BEGIN TIME STEP"
values = self.data.vecs(time,pairs[i][0])
if self.which == 0:
self.variable_file_atoms(vfiles[i],pairs[i][1],atoms,values)
else:
self.variable_file_elements(vfiles[i],pairs[i][1],etype,values)
print >>vfiles[i],"END TIME STEP"
print time,
sys.stdout.flush()
n += 1
# close additional files
f.close()
for f in vfiles: f.close()
# write Ensight *.case header file now that know all timesteps
f = open("%s.case" % root,"w")
self.case_file(f,root,pairs,0,len(times),times)
f.close()
print "\nwrote %s snapshots in Ensight format" % n
# --------------------------------------------------------------------
def many(self,*args):
if len(args) % 2 == 0: root = "tmp"
else:
root = args[0]
args = args[1:]
pairs = []
for i in range(0,len(args),2): pairs.append([args[i],args[i+1]])
# max # of types for all steps in Ensight files
if self.which == 0 and self.maxtype == 0:
self.maxtype = self.data.maxtype()
# write Ensight *.case header file
f = open("%s.case" % root,"w")
times = self.data.time()
self.case_file(f,root,pairs,1,len(times),times)
f.close()
# loop over snapshots
# generate unique filenames
# write coords into one xyz file per snapshot, variables into their files
first = 1
n = flag = etype = 0
while 1:
which,time,flag = self.data.iterator(flag)
if flag == -1: break
files = []
if n < 10:
file = root + "000" + str(n) + ".xyz"
for pair in pairs:
files.append(root + "000" + str(n) + "." + pair[0])
elif n < 100:
file = root + "00" + str(n) + ".xyz"
for pair in pairs:
files.append(root + "00" + str(n) + "." + pair[0])
elif n < 1000:
file = root + "0" + str(n) + ".xyz"
for pair in pairs:
files.append(root + "0" + str(n) + "." + pair[0])
else:
file = root + str(n) + ".xyz"
for pair in pairs:
files.append(root + str(n) + "." + pair[0])
if self.which == 0:
f = open(file,"w")
time,box,atoms,bonds,tris,lines = self.data.viz(which)
self.coord_file_atoms(f,box,atoms)
f.close()
elif self.change == 0 and first:
f = open(root + ".xyz","w")
time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
first = 0
f.close()
elif self.change:
f = open(file,"w")
time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
f.close()
for i in range(len(pairs)):
values = self.data.vecs(time,pairs[i][0])
f = open(files[i],"w")
if self.which == 0:
self.variable_file_atoms(f,pairs[i][1],atoms,values)
else:
self.variable_file_elements(f,pairs[i][1],etype,values)
f.close()
print time,
sys.stdout.flush()
n += 1
print "\nwrote %s snapshots in Ensight format" % n
# --------------------------------------------------------------------
def single(self,time,*args):
if len(args) % 2 == 0: root = "tmp"
else:
root = args[0]
args = args[1:]
pairs = []
for i in range(0,len(args),2): pairs.append([args[i],args[i+1]])
# max # of types for all steps in Ensight files
if self.which == 0 and self.maxtype == 0:
self.maxtype = self.data.maxtype()
# write Ensight *.case header file
f = open("%s.case" % root,"w")
self.case_file(f,root,pairs,0,1,[time])
f.close()
# write coords into xyz file, variables into their files
which = self.data.findtime(time)
etype = 0
f = open(root + ".xyz","w")
if self.which == 0:
time,box,atoms,bonds,tris,lines = self.data.viz(which)
self.coord_file_atoms(f,box,atoms)
else:
time,box,nodes,elements,nvalues,evalues = self.data.mviz(which)
self.coord_file_elements(f,box,nodes,elements)
etype = len(elements[0])
f.close()
for i in range(len(pairs)):
values = self.data.vecs(time,pairs[i][0])
f = open(root + "." + pairs[i][0],"w")
if self.which == 0:
self.variable_file_atoms(f,pairs[i][1],atoms,values)
else:
self.variable_file_elements(f,pairs[i][1],etype,values)
f.close()
# --------------------------------------------------------------------
# write Ensight case file
def case_file(self,f,root,pairs,multifile,nsnaps,times):
print >>f,"# Ensight case file\n"
print >>f,"FORMAT\ntype: ensight gold\n"
if self.which == 0:
if multifile:
# print >>f,"GEOMETRY\nmodel: %s****.xyz change_coords_only\n" % root
print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root
else:
# print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz change_coords_only\n" % root
print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root
else:
if self.change == 0:
print >>f,"GEOMETRY\nmodel: %s.xyz\n" % root
elif multifile:
print >>f,"GEOMETRY\nmodel: %s****.xyz\n" % root
else:
print >>f,"GEOMETRY\nmodel: 1 1 %s.xyz\n" % root
if len(pairs):
print >>f,"VARIABLE"
for pair in pairs:
if self.which == 0:
if multifile:
print >>f,"scalar per node: %s %s****.%s" % (pair[1],root,pair[0])
else:
print >>f,"scalar per node: 1 1 %s %s.%s" % (pair[1],root,pair[0])
else:
if multifile:
print >>f,"scalar per element: %s %s****.%s" % (pair[1],root,pair[0])
else:
print >>f,"scalar per element: 1 1 %s %s.%s" % (pair[1],root,pair[0])
print >>f
print >>f,"TIME"
print >>f,"time set: 1"
print >>f,"number of steps:",nsnaps
print >>f,"filename start number: 0"
print >>f,"filename increment: 1"
print >>f,"time values:"
for i in range(nsnaps):
print >>f,times[i],
if i % 10 == 9: print >>f
print >>f
print >>f
if not multifile:
print >>f,"FILE"
print >>f,"file set: 1"
print >>f,"number of steps:",nsnaps
# --------------------------------------------------------------------
# write Ensight coordinates for atoms
# partition into "parts"
# one part = coords for all atoms of a single type
def coord_file_atoms(self,f,box,atoms):
print >>f,"Particle geometry\nfor a collection of atoms"
print >>f,"node id given"
print >>f,"element id off"
print >>f,"extents"
print >>f,"%12.5e%12.5e" % (box[0],box[3])
print >>f,"%12.5e%12.5e" % (box[1],box[4])
print >>f,"%12.5e%12.5e" % (box[2],box[5])
for type in xrange(1,self.maxtype+1):
print >>f,"part"
print >>f,"%10d" % type
print >>f,"type",type
print >>f,"coordinates"
group = [atom for atom in atoms if int(atom[1]) == type]
print >>f,"%10d" % len(group)
for atom in group: print >>f,"%10d" % int(atom[0])
for atom in group: print >>f,"%12.5e" % atom[2]
for atom in group: print >>f,"%12.5e" % atom[3]
for atom in group: print >>f,"%12.5e" % atom[4]
print >>f,"point"
print >>f,"%10d" % len(group)
for i in xrange(1,len(group)+1): print >>f,"%10d" % i
# --------------------------------------------------------------------
# write Ensight coordinates for elements
def coord_file_elements(self,f,box,nodes,elements):
print >>f,"Element geometry\nfor a collection of elements"
print >>f,"node id given"
print >>f,"element id given"
print >>f,"extents"
print >>f,"%12.5e%12.5e" % (box[0],box[3])
print >>f,"%12.5e%12.5e" % (box[1],box[4])
print >>f,"%12.5e%12.5e" % (box[2],box[5])
print >>f,"part"
print >>f,"%10d" % 1
print >>f,"all elements"
print >>f,"coordinates"
print >>f,"%10d" % len(nodes)
for node in nodes: print >>f,"%10d" % int(node[0])
for node in nodes: print >>f,"%12.5e" % node[2]
for node in nodes: print >>f,"%12.5e" % node[3]
for node in nodes: print >>f,"%12.5e" % node[4]
if len(elements[0]) == 5: print >>f,"tria3"
elif len(elements[0]) == 6: print >>f,"tetra4"
else: raise StandardError,"unrecognized element type"
print >>f,"%10d" % len(elements)
for element in elements: print >>f,"%10d" % int(element[0])
if len(elements[0]) == 5:
for element in elements:
print >>f,"%10d%10d%10d" % \
(int(element[2]),int(element[3]),int(element[4]))
elif len(elements[0]) == 6:
for element in elements:
print >>f,"%10d%10d%10d%10d" % \
(int(element[2]),int(element[3]),int(element[4]),int(element[5]))
# --------------------------------------------------------------------
# write Ensight variable values for atoms
# partition into "parts"
# one part = values for all atoms of a single type
def variable_file_atoms(self,f,name,atoms,values):
print >>f,"Particle %s" % name
for type in xrange(1,self.maxtype+1):
print >>f,"part"
print >>f,"%10d" % type
print >>f,"coordinates"
group = [values[i] for i in xrange(len(atoms))
if int(atoms[i][1]) == type]
for value in group: print >>f,"%12.5e" % value
# --------------------------------------------------------------------
# write Ensight variable values for elements
def variable_file_elements(self,f,name,etype,values):
print >>f,"Element %s" % name
print >>f,"part"
print >>f,"%10d" % 1
if etype == 5: print >>f,"tria3"
elif etype == 6: print >>f,"tetra4"
for value in values: print >>f,"%12.5e" % value
