428 lines
14 KiB
Python
Executable File
428 lines
14 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# This script is used for the post processing of the results achieved by the spectral method.
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# As it reads in the data coming from "materialpoint_results", it can be adopted to the data
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# computed using the FEM solvers. Until now, its capable to handle elements with one IP in a regular order
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# written by M. Diehl, m.diehl@mpie.de
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import os,sys,threading,re,numpy,time,string,postprocessingMath
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# -----------------------------
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class backgroundMessage(threading.Thread):
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# -----------------------------
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def __init__(self):
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threading.Thread.__init__(self)
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self.message = ''
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self.new_message = ''
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self.counter = 0
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self.symbols = ['- ', '\ ', '| ', '/ ']
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self.waittime = 0.5
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def __quit__(self):
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length = len(self.message) + len(self.symbols[self.counter])
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sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length)
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sys.stderr.write('')
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def run(self):
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while not threading.enumerate()[0]._Thread__stopped:
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time.sleep(self.waittime)
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self.update_message()
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self.__quit__()
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def set_message(self, new_message):
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self.new_message = new_message
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self.print_message()
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def print_message(self):
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length = len(self.message) + len(self.symbols[self.counter])
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sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) # delete former message
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sys.stderr.write(self.symbols[self.counter] + self.new_message) # print new message
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self.message = self.new_message
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def update_message(self):
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self.counter = (self.counter + 1)%len(self.symbols)
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self.print_message()
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def outStdout(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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print cmd
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else:
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print cmd
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return
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def outFile(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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locals['filepointer'].write(cmd+'\n')
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else:
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locals['filepointer'].write(cmd+'\n')
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return
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def output(cmds,locals,dest):
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for cmd in cmds:
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if isinstance(cmd,list):
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output(cmd,locals,dest)
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else:
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{\
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'File': outFile,\
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'Stdout': outStdout,\
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}[dest](str(cmd),locals)
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return
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def transliterateToFloat(x):
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try:
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return float(x)
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except:
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return 0.0
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_mesh(mesh,data,res):
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a hexahedral mesh (geometry) """
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N1 = (res[0]+1)*(res[1]+1)*(res[2]+1)
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N = res[0]*res[1]*res[2]
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cmds = [\
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'# vtk DataFile Version 3.1',
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string.replace('powered by $Id$','\n','\\n'),
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N1,
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[[['\t'.join(map(str,mesh[i,j,k])) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)],
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'CELLS %i %i'%(N,N*9),
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]
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# cells
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for z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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cmds.append('8 '+'\t'.join(map(str,[ \
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base,
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base+1,
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base+res[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+1,
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])))
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cmds += [\
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'CELL_TYPES %i'%N,
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['12']*N,
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'CELL_DATA %i'%N,
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]
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for type in data:
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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]:
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cmds += [\
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'%s %s float'%(type.upper()+plural,item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])],
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]
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return cmds
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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def gmsh_writeASCII_mesh(mesh,data,res):
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a hexahedral mesh (geometry) """
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N1 = (res[0]+1)*(res[1]+1)*(res[2]+1)
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N = res[0]*res[1]*res[2]
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cmds = [\
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'$MeshFormat',
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'2.1 0 8',
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'$EndMeshFormat',
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'$Nodes',
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'%i float'%N1,
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[[['\t'.join(map(str,l,mesh[i,j,k])) for l in range(1,N1+1) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)],
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'$EndNodes',
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'$Elements',
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'%i'%N,
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]
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# cells
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n_elem = 0
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for z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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n_elem +=1
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cmds.append('\t'.join(map(str,[ \
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n_elem,
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'5',
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base,
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base+1,
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base+res[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+1,
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])))
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cmds += [\
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'ElementData',
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'1',
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'%s'%item, # name of the view
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'0.0', # thats the time value
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'3',
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'0', # time step
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'1',
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'%i'%N
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]
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for type in data:
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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]:
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cmds += [\
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'%s %s float'%(type.upper()+plural,item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])],
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]
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return cmds
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_points(coordinates,data,res):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a point field """
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N = res[0]*res[1]*res[2]
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by $Id$',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N,
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[[['\t'.join(map(str,coordinates[i,j,k])) for i in range(res[0])] for j in range(res[1])] for k in range(res[2])],
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'CELLS %i %i'%(N,N*2),
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['1\t%i'%i for i in range(N)],
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'CELL_TYPES %i'%N,
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['1']*N,
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'POINT_DATA %i'%N,
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]
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for type in data:
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plural = {True:'',False:'S'}[type.lower().endswith('s')]
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for item in data[type]:
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cmds += [\
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'%s %s float'%(type.upper()+plural,item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])]
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]
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return cmds
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_box(diag,defgrad):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++++
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""" corner box for the average defgrad """
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points = numpy.array([\
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[0.0,0.0,0.0,],\
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[diag[0],0.0,0.0,],\
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[diag[0],diag[1],0.0,],\
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[0.0,diag[1],0.0,],\
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[0.0,0.0,diag[2],],\
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[diag[0],0.0,diag[2],],\
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[diag[0],diag[1],diag[2],],\
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[0.0,diag[1],diag[2],],\
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])
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by $Id$',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS 8 float',
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['\t'.join(map(str,numpy.dot(defgrad_av,points[p]))) for p in range(8)],
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'CELLS 8 16',
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['1\t%i'%i for i in range(8)],
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'CELL_TYPES 8',
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['1']*8,
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]
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return cmds
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# ----------------------- MAIN -------------------------------
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parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile[s]', description = """
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Produce VTK file from data field. Coordinates are taken from (consecutive) ip.x, ip.y, and ip.z columns.
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$Id$
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""")
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parser.add_option('-s', '--scalar', action='extend', dest='scalar', type='string', \
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help='list of scalars to visualize')
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parser.add_option('-d', '--deformation', dest='defgrad', type='string', \
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help='heading of deformation gradient columns [%default]')
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(scalar = [])
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parser.set_defaults(vector = [])
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parser.set_defaults(tensor = [])
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(options, args) = parser.parse_args()
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for filename in args:
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if not os.path.exists(filename):
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continue
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file = open(filename)
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content = file.readlines()
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file.close()
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m = re.search('(\d+)\shead',content[0],re.I)
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if m == None:
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continue
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print filename,
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sys.stdout.flush()
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headrow = int(m.group(1))
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headings = content[headrow].split()
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column = {}
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maxcol = 0
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for col,head in enumerate(headings):
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if head == 'ip.x':
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ipcol = col
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maxcol = max(maxcol,col+3)
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break
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if ipcol < 0:
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print 'missing ip coordinates..!'
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continue
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column['tensor'] = {}
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for label in [options.defgrad] + options.tensor:
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column['tensor'][label] = -1
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for col,head in enumerate(headings):
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if head == label or head == '1_%s'%label:
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column['tensor'][label] = col
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maxcol = max(maxcol,col+9)
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break
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if column['tensor'][options.defgrad] < 0:
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print 'missing deformation gradient "%s"..!'%options.defgrad
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continue
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column['vector'] = {}
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for label in options.vector:
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column['vector'][label] = -1
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for col,head in enumerate(headings):
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if head == label or head == '1_%s'%label:
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column['vector'][label] = col
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maxcol = max(maxcol,col+3)
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break
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column['scalar'] = {}
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for label in options.scalar:
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column['scalar'][label] = -1
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for col,head in enumerate(headings):
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if head == label:
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column['scalar'][label] = col
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maxcol = max(maxcol,col+1)
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break
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values = numpy.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
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key=lambda x:(x[ipcol+0],x[ipcol+1],x[ipcol+2])), # sort with z as fastest and x as slowest index
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'd')
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N = len(values)
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grid = [{},{},{}]
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for j in range(3):
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for i in range(N):
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grid[j][str(values[i,ipcol+j])] = True
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res = numpy.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i')
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dim = numpy.ones(3)
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for i,r in enumerate(res):
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if r > 1:
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dim[i] = (max(map(float,grid[i].keys()))-min(map(float,grid[i].keys())))*r/(r-1.0)
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print res,dim
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defgrad_av = postprocessingMath.tensor_avg(res[0],res[1],res[2],\
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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centroids = postprocessingMath.deformed_fft(res[0],res[1],res[2],dim,\
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)),defgrad_av,1.0)
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ms = postprocessingMath.mesh(res[0],res[1],res[2],dim,defgrad_av,centroids)
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fields = {\
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'tensor': {},\
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'vector': {},\
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'scalar': {},\
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}
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reshape = {\
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'tensor': (3,3),\
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'vector': (3),\
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'scalar': (),\
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}
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length = {\
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'tensor': 9,\
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'vector': 3,\
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'scalar': 1,\
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}
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for datatype in fields.keys():
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print '\n%s:'%datatype,
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for what in eval('options.%s'%datatype):
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col = column[datatype][what]
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if col != -1:
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print what,
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fields[datatype][what] = numpy.reshape(values[:,col:col+length[datatype]],(res[0],res[1],res[2])+reshape[datatype])
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print '\n'
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out = {}
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out['mesh'] = vtk_writeASCII_mesh(ms,fields,res)
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out['points'] = vtk_writeASCII_points(centroids,fields,res)
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out['box'] = vtk_writeASCII_box(dim,defgrad_av)
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for what in out.keys():
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print what
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(head,tail) = os.path.split(filename)
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vtk = open(os.path.join(head,'%s_'%what+os.path.splitext(tail)[0]+'.vtk'), 'w')
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output(out[what],{'filepointer':vtk},'File')
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vtk.close()
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print
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