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ODB2VTK+.py
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#-*-coding:UTF-8-*-
'''
The script is developed by Qingbin Liu
E-mail: [email protected]
'''
#import necessary modules which support operations
from odbAccess import *
from textRepr import *
#from string import *
from time import *
from math import *
import copy
import multiprocessing
import numpy as np
#Dictionary of label and name of variables
#It can be modified if necessary
VARIABLEDICT = {'U':"Spatial_displacement", 'A':"Spatial_acceleration", 'V':"Spatial_velocity",'RF':"Reaction_force",\
'S':"Stress", 'LE':"Logarithmic_strain", 'PE':"Plastic_strain",'PEEQ':"Equivalent_plastic_strain",\
'MISES':"Mises", 'MAX_PRINCIPAL':"Max_Principal", 'MID_PRINCIPAL':"Mid_Principal", 'MIN_PRINCIPAL':"Min_Principal",\
'TRESCA':"Tresca", 'PRESS':"Pressure", 'INV3':"Third_Invariant"}
###==============================Sub=Function=============================###
#-----------------------------Read Configuration----------------------------#
#To get the parameters from configuration file
def GetConfig(filename = 'odb2vtk.cfg'):
# Check if filename points to existing file
if not os.path.isfile(filename):
print 'Parameter file "%s" not found'%(filename)
sys.exit(2)
#get parameters from configuration file
config = open(filename,'r')
read = config.read()
input = read.split("'")
#get odb file's path
odb_path = input[1]
#get odb file's name
odb_name = input[3]
#get the output vtk files' path
vtk_path = input[5]
#get the mesh type ( ex: Hexahedron, Tetrahedron, etc. )
mesh_type = input[7]
mesh_conner = 0
if (mesh_type == 'Hexahedron'):
mesh_conner = 8
mesh_type = 12
mesh_name = "Hexahedron"
if (mesh_type == 'Tetrahedron'):
mesh_conner = 4
mesh_type = 10
mesh_name = "Tetrahedron"
if (mesh_conner == 0):
print("Mesh type error or unidentified")
os._exit(0)
#get the selection of partition method (ex: Random, Regular, CenterPoint, etc.)
partition_method = input[9]
#get the parameters of partition, such as quantity and its distribution
temp_partition_parameter = input[11]
if(partition_method == 'Random'):
partition_parameter = int(temp_partition_parameter)
piece_number = int(temp_partition_parameter)
elif(partition_method == 'Regular'):
partition_parameter = temp_partition_parameter.split(',')
piece_number = int(partition_parameter[0]) * int(partition_parameter[1]) * int(partition_parameter[2])
elif(partition_method == 'CenterPoint'):
temppoint = temp_partition_parameter.split(',')
piece_number = int(len(temppoint) / 3)
partition_parameter = np.zeros(piece_number * 3).reshape(piece_number ,3)
for i in range(piece_number):
for j in range(3):
partition_parameter[i][j] = float(temppoint[i * 3 + j])
else:
print "partition method " + partition_method + " doesn't exist, it must be 'Random','Regular' or 'CenterPoint', Please Check!"
os._exit(0)
#get the frame to transfer
input_frame = input[13].split("-")
input_frame = range(int(input_frame[0]),int(input_frame[1])+1)
#get the step to transfer
input_step = input[15].split(",")
#get the instance to transfer
input_instance = input[17].split(",")
#get the variables to transfer
output_scalar = input[19].split(",")
output_vector = input[21].split(",")
output_tensor = input[23].split(",")
#get the multiprocessing set
parallel_partition = input[25]
partition_processing_number = int(input[27])
parallel_frame = input[29]
frame_processing_number = int(input[31])
#end reding and close odb2vtk file
config.close()
#display the reading result of odb2vtk file
print "Basic Information:"
print "Model:",odb_name,"; Mesh type:",mesh_name
print "Partition method:",partition_method,"; partition_parameter:",partition_parameter
print "Convert frames: ",input_frame[0]," to ",input_frame[-1]
print "Step & Instance : ",str(input_step),", ",str(input_instance)
print "Parallel partition : ", parallel_partition
print "parallel_frame : ", parallel_frame
return{'odb_path':odb_path,'odbname':odb_name,'vtk_path':vtk_path,'mesh_type':mesh_type,'mesh_conner':mesh_conner,\
'partition_method':partition_method,'partition_parameter':partition_parameter,'piece_number':piece_number,\
'input_frame':input_frame,'input_step':input_step,'input_instance':input_instance,
'output_scalar':output_scalar,'output_vector':output_vector,'output_tensor':output_tensor,
'parallel_partition':parallel_partition,'partition_processing_number':partition_processing_number,\
'parallel_frame':parallel_frame,'frame_processing_number':frame_processing_number}
#-----------------------------Read Configuration----------------------------#
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#------------------------------Read Attribution-----------------------------#
#To Read nodes' coordination, return a (n*3)numpy
def ReadNode(node = '', max_nodelabel = 0):
node_coordination = np.zeros(max_nodelabel*3).reshape(max_nodelabel,3)
for i_node in node:
node_coordination[i_node.label-1] = i_node.coordinates
return node_coordination
#To read scalar variable, return a (1*n)numpy
def ReadScalarAtInt(odbscalar = '',outputlength = 0):
nodal_fieldvalues = odbscalar.getSubset(position=ELEMENT_NODAL)
fieldValues = nodal_fieldvalues.values
acount = np.zeros(outputlength)
scalaroutput = np.zeros(outputlength)
for scalar_value in fieldValues :
acount[scalar_value.nodeLabel-1] += 1
scalaroutput[scalar_value.nodeLabel-1] += scalar_value.data
for i in range(outputlength):
if(acount[i] != 0):
scalaroutput[i] = scalaroutput[i]/acount[i]
return scalaroutput
#To read vector variable, return a (n*3)numpy
def ReadVector(odbvector = '',outputlength = 0):
fieldvalues = odbvector.values
vectoroutput = np.zeros(outputlength*3).reshape(outputlength,3)
for vector_value in fieldvalues :
vectoroutput[vector_value.nodeLabel-1] = vector_value.data
return vectoroutput
#To read tensor vriable, transfer the variable from integration point to nodal point,
#return a dicrtionary with two numpy:
#the first is tensor(), the second is invariant()
#modify the function can read tensor variable with different invariant
def ReadTensorAtIntS(odbtensor = '',invariantamount = 0,outputlength = 0):
nodal_fieldvalues = odbtensor.getSubset(position=ELEMENT_NODAL)
fieldvalues = nodal_fieldvalues.values
acount = np.zeros(outputlength)
outputtensor = np.zeros(outputlength*6).reshape(outputlength,6)
outputinvariant = np.zeros(outputlength*invariantamount).reshape(outputlength,invariantamount)
for tensor_value in fieldvalues:
acount[tensor_value.nodeLabel-1] += 1
outputtensor[tensor_value.nodeLabel-1] += tensor_value.data
#modification!!!
outputinvariant[tensor_value.nodeLabel-1][0] += tensor_value.mises
outputinvariant[tensor_value.nodeLabel-1][1] += tensor_value.maxPrincipal
outputinvariant[tensor_value.nodeLabel-1][2] += tensor_value.midPrincipal
outputinvariant[tensor_value.nodeLabel-1][3] += tensor_value.minPrincipal
outputinvariant[tensor_value.nodeLabel-1][4] += tensor_value.press
outputinvariant[tensor_value.nodeLabel-1][5] += tensor_value.tresca
outputinvariant[tensor_value.nodeLabel-1][6] += tensor_value.inv3
for i in range(outputlength):
if(acount[i] != 0):
outputtensor[i] = outputtensor[i]/acount[i]
outputinvariant[i] = outputinvariant[i]/acount[i]
listinvariant = ['MISES', 'MAX_PRINCIPAL', 'MID_PRINCIPAL', 'MIN_PRINCIPAL', 'TRESCA', 'PRESS', 'INV3']
return {'tensor':outputtensor,'invariant':outputinvariant,'validinvariant':listinvariant}
def ReadTensorAtIntE(odbtensor = '',invariantamount = 0,outputlength = 0):
nodal_fieldvalues = odbtensor.getSubset(position=ELEMENT_NODAL)
fieldvalues = nodal_fieldvalues.values
acount = np.zeros(outputlength)
outputtensor = np.zeros(outputlength*6).reshape(outputlength,6)
outputinvariant = np.zeros(outputlength*invariantamount).reshape(outputlength,invariantamount)
for tensor_value in fieldvalues:
acount[tensor_value.nodeLabel-1] += 1
outputtensor[tensor_value.nodeLabel-1] += tensor_value.data
#modification!!!
outputinvariant[tensor_value.nodeLabel-1][0] += tensor_value.maxPrincipal
outputinvariant[tensor_value.nodeLabel-1][1] += tensor_value.minPrincipal
for i in range(outputlength):
if(acount[i] != 0):
outputtensor[i] = outputtensor[i]/acount[i]
outputinvariant[i] = outputinvariant[i]/acount[i]
listinvariant = ['MAX_PRINCIPAL', 'MIN_PRINCIPAL']
return {'tensor':outputtensor,'invariant':outputinvariant,'validinvariant':listinvariant}
#------------------------------Read Attribution-----------------------------#
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#-------------------------Partition & Reorganization------------------------#
#---------------------Random Partition & Reorganization---------------------#
#Partition model into pieces by the label of element which might be random
def PartitionRandom(config = {}, element_amount = 0):
piecenum = config['piece_number']
element_piece_amount = element_amount/piecenum
last_element_piece_amount = element_amount - (element_piece_amount*(piecenum-1)) #last block
piecelist = []
for i in range(piecenum):
piecelist.append(str(i))
piecedict = dict.fromkeys(piecelist)
for i_piece in range(piecenum):
if(i_piece == piecenum-1):
piecedict[str(i_piece)] = copy.deepcopy(np.arange(i_piece*element_piece_amount,element_amount))
else:
piecedict[str(i_piece)] = copy.deepcopy(np.arange(i_piece*element_piece_amount,(i_piece+1)*element_piece_amount))
return piecedict
#Reorganize model partitioned by random method in serial
def ReorganizeRandomNodeElementSerial(config = {}, piecedict = {},element = '', max_nodelabel = 0):
mesh_conner = config['mesh_conner']
piecelist = piecedict.keys()
newmodel = dict.fromkeys(piecelist)
#reorganize the node and element (reconstruct the mesh)
for i_keys in piecelist:
#nodeexisted: mark the nodes which have already existed in new model
nodeexisted = np.zeros(max_nodelabel,dtype=np.int32)
nodeexisted = -1
#elementnode: store the reorganized element
elementnode = np.zeros(0,dtype=np.int32)
#newnode: store the reorganized node
newnode = np.zeros(0,dtype=np.int32)
nodecount = 0
#reorganize each piece
i_piece = piecedict[i_keys]
for i in i_piece:
i_element = element[i]
for j in range(mesh_conner):
k = i_element.connectivity[j] - 1
if(nodeexisted[k] < 0):
nodeexisted[k] = nodecount
newnode = np.append(newnode,k)
elementnode = np.append(elementnode,nodecount)
nodecount += 1
else:
elementnode = np.append(elementnode,nodeexisted[k])
newmodel[i_keys] = {'node':copy.deepcopy(newnode),'element':copy.deepcopy(elementnode)}
return newmodel
#Reorganize model partitioned by random method in parallel
def ReorganizeRandomNodeElementParallel(config = {}, piecedict = {}, instancename = '', max_nodelabel = 0):
piecelist = piecedict.keys()
manager = multiprocessing.Manager()
newmodel = manager.dict()
#reorganize the node and element (reconstruct the mesh)
#control the process
piecelist_length = len(piecelist)
process_munber = config['partition_processing_number']
piece_each_process = piecelist_length/process_munber
control_dict = {}
#distribute pieces to process
for i in range(process_munber-1):
control_dict[str(i)] = piecelist[i*piece_each_process:(i+1)*piece_each_process]
control_dict[str(process_munber-1)] = piecelist[(process_munber-1)*piece_each_process : piecelist_length]
print "Partition by multiprocessing......"
processlist = []
for i in range(process_munber):
P = multiprocessing.Process(target = ReorganizeRandomNodeElementSubFunction,\
args = (newmodel,piecedict,control_dict[str(i)],config,instancename,max_nodelabel))
processlist.append(P)
P.start()
print "process-ID: ",P.pid
for i in processlist:
P.join()
for i in processlist:
P.terminate()
return newmodel
def ReorganizeRandomNodeElementSubFunction(newmodel,piecedict,controllist,config,instancename,max_nodelabel):
odb = openOdb(os.path.join(config['odb_path'],config['odbname'])+'.odb',readOnly=True)
element = odb.rootAssembly.instances[instancename].elements
for i_keys in controllist:
#nodeexisted: mark the nodes which have already existed in new model
nodeexisted = np.zeros(max_nodelabel,dtype=np.int32)
nodeexisted[:] = -1
#elementnode: store the reorganized element
elementnode = np.zeros(0,dtype=np.int32)
#newnode: store the reorganized node
newnode = np.zeros(0,dtype=np.int32)
nodecount = 0
#reorganize each piece
i_piece = piecedict[i_keys]
for i in i_piece:
i_element = element[i]
for j in range(config['mesh_conner']):
k = i_element.connectivity[j] - 1
if(nodeexisted[k] < 0):
nodeexisted[k] = nodecount
newnode = np.append(newnode,k)
elementnode = np.append(elementnode,nodecount)
nodecount += 1
else:
elementnode = np.append(elementnode,nodeexisted[k])
newmodel[i_keys] = {'node':copy.deepcopy(newnode),'element':copy.deepcopy(elementnode)}
#-------------------------------Regular Partition---------------------------#
#Partition model into pieces by regular partitoin method in serial
def PartitionRegularSerial(config = {},node_coordination = [], element = ''):
piecesize = config['partition_parameter']
mesh_conner = config['mesh_conner']
x_size = int(piecesize[0])
y_size = int(piecesize[1])
z_size = int(piecesize[2])
node_coordination = node_coordination.T
x_max = np.max(node_coordination[0])
x_min = np.min(node_coordination[0])
y_max = np.max(node_coordination[1])
y_min = np.min(node_coordination[1])
z_max = np.max(node_coordination[2])
z_min = np.min(node_coordination[2])
node_coordination = node_coordination.T
x_interval = (x_max - x_min) / x_size
y_interval = (y_max - y_min) / y_size
z_interval = (z_max - z_min) / z_size
x_limit = np.zeros(x_size + 1)
y_limit = np.zeros(y_size + 1)
z_limit = np.zeros(z_size + 1)
for i in range(x_limit.shape[0]):
x_limit[i] = x_min + (i * x_interval)
x_limit[0] = x_min - 10
x_limit[x_limit.shape[0] - 1] = x_max + 10
for i in range(y_limit.shape[0]):
y_limit[i] = y_min + (i * y_interval)
y_limit[0] = y_min - 10
y_limit[y_limit.shape[0] - 1] = y_max + 10
for i in range(z_limit.shape[0]):
z_limit[i] = z_min + (i * z_interval)
z_limit[0] = z_min - 10
z_limit[z_limit.shape[0] - 1] = z_max + 10
#create the dictionary of partition piece, storing the element label in each piece
piecelist = []
for i in range(x_size):
for j in range(y_size):
for k in range(z_size):
piecelist.append(str(i)+str(j)+str(k))
piecedict = dict.fromkeys(piecelist)
for i in range(x_size):
for j in range(y_size):
for k in range(z_size):
piecedict[str(i)+str(j)+str(k)] = copy.deepcopy(np.zeros(0))
#create the numpy for storing the connectivity of each element
element_connectivity = np.zeros(len(element)*mesh_conner,dtype=np.int32).reshape(len(element),mesh_conner)
tempcoordinate = np.zeros(3)
for i_element in element:
label = i_element.label
element_connectivity[label - 1] = i_element.connectivity
tempcoordinate[:] = 0
for elementnode in range(mesh_conner):
k = i_element.connectivity[elementnode] - 1
tempcoordinate += node_coordination[k]
tempcoordinate = tempcoordinate / mesh_conner
i = 0
j = x_size
x = tempcoordinate[0]
while( (j - i) > 1):
k = (i + j) / 2
if (x > x_limit[k]):
i = k
else:
j = k
i_x = i
i = 0
j = y_size
y = tempcoordinate[1]
while( (j - i) > 1):
k = (i + j) / 2
if (y > y_limit[k]):
i = k
else:
j = k
i_y = i
i = 0
j = z_size
z = tempcoordinate[2]
while( (j - i) > 1):
k = (i + j) / 2
if (z > z_limit[k]):
i = k
else:
j = k
i_z = i
tempkey = str(i_x)+str(i_y)+str(i_z)
piecedict[tempkey] = np.append(piecedict[tempkey], label)
return piecedict,element_connectivity
#Partition model into pieces by regular partitoin method in parallel
def PartitionRegularParallel(config = {}, node_coordination = [], instancename = ''):
odb = openOdb(os.path.join(config['odb_path'],config['odbname'])+'.odb',readOnly=True)
element = odb.rootAssembly.instances[instancename].elements
mesh_conner = config['mesh_conner']
piecesize = config['partition_parameter']
x_size = int(piecesize[0])
y_size = int(piecesize[1])
z_size = int(piecesize[2])
node_coordination = node_coordination.T
x_max = np.max(node_coordination[0])
x_min = np.min(node_coordination[0])
y_max = np.max(node_coordination[1])
y_min = np.min(node_coordination[1])
z_max = np.max(node_coordination[2])
z_min = np.min(node_coordination[2])
node_coordination = node_coordination.T
x_interval = (x_max - x_min) / x_size
y_interval = (y_max - y_min) / y_size
z_interval = (z_max - z_min) / z_size
x_limit = np.zeros(x_size + 1)
y_limit = np.zeros(y_size + 1)
z_limit = np.zeros(z_size + 1)
for i in range(x_limit.shape[0]):
x_limit[i] = x_min + (i * x_interval)
x_limit[0] = x_min - 10
x_limit[x_limit.shape[0] - 1] = x_max + 10
for i in range(y_limit.shape[0]):
y_limit[i] = y_min + (i * y_interval)
y_limit[0] = y_min - 10
y_limit[y_limit.shape[0] - 1] = y_max + 10
for i in range(z_limit.shape[0]):
z_limit[i] = z_min + (i * z_interval)
z_limit[0] = z_min - 10
z_limit[z_limit.shape[0] - 1] = z_max + 10
#create the dictionary of partition piece, storing the element label in each piece
manager = multiprocessing.Manager()
piecedict = manager.dict()
for i in range(x_size):
for j in range(y_size):
for k in range(z_size):
piecedict[str(i)+str(j)+str(k)] = copy.deepcopy(np.zeros(0,dtype=np.int32))
element_length = len(element)
elementdict = manager.dict()
elementpiecedict = manager.dict()
#control the process
process_munber = config['partition_processing_number']
element_each_process = element_length/process_munber
control_dict = {}
#distribute elements to process
for i in range(process_munber-1):
control_dict[str(i)] = range(i*element_each_process, (i+1)*element_each_process)
control_dict[str(process_munber-1)] = range((process_munber-1)*element_each_process, element_length)
processlist = []
for i in range(process_munber):
P = multiprocessing.Process(target = PartitionRegularSubfunction, args = (config,elementpiecedict,elementdict,control_dict[str(i)],node_coordination,instancename,x_limit,y_limit,z_limit,x_size,y_size,z_size))
processlist.append(P)
P.start()
print "process-ID: ",P.pid
for i in processlist:
P.join()
for i in processlist:
P.terminate()
print('Parallel Finish')
element_connectivity = np.zeros(element_length*mesh_conner,dtype=np.int32).reshape(element_length,mesh_conner)
for i in range(element_length):
element_connectivity[i] = elementdict[str(i)]
tmpkey = elementpiecedict[str(i)]
piecedict[tmpkey] = np.append(piecedict[tmpkey] , i + 1)
print('return piecedict,element_connectivity')
return piecedict, element_connectivity
def PartitionRegularSubfunction(config,elementpiecedict,elementdict,controllist,node_coordination,instancename,x_limit,y_limit,z_limit,x_size,y_size,z_size):
odb = openOdb(os.path.join(config['odb_path'],config['odbname'])+'.odb',readOnly=True)
element = odb.rootAssembly.instances[instancename].elements
mesh_conner = config['mesh_conner']
tempcoordinate = np.zeros(3)
for ie_label in controllist:
i_element = element[ie_label]
label = i_element.label
elementdict[str(label - 1)] = i_element.connectivity
tempcoordinate[:] = 0
for elementnode in range(mesh_conner):
k = i_element.connectivity[elementnode] - 1
tempcoordinate += node_coordination[k]
# get the center point coordinates of element
tempcoordinate = tempcoordinate / mesh_conner
i = 0
j = x_size
x = tempcoordinate[0]
while( (j - i) > 1):
k = (i + j) / 2
if (x > x_limit[k]):
i = k
else:
j = k
i_x = i
i = 0
j = y_size
y = tempcoordinate[1]
while( (j - i) > 1):
k = (i + j) / 2
if (y > y_limit[k]):
i = k
else:
j = k
i_y = i
i = 0
j = z_size
z = tempcoordinate[2]
while( (j - i) > 1):
k = (i + j) / 2
if (z > z_limit[k]):
i = k
else:
j = k
i_z = i
tempkey = str(i_x)+str(i_y)+str(i_z)
elementpiecedict[str(label - 1)] = tempkey
#-----------------------------CenterPoint Partition-------------------------#
#Partition model into pieces by indentifing the center point of the piece in serial
def PartitionPointCenterSerial(config = {}, node_coordination = [], element = ''):
centerpoint = config['partition_parameter']
mesh_conner = config['mesh_conner']
piece_number = config['piece_number']
for i in range(piece_number):
piecelist = piecelist.append(str(i))
for i in piecelist:
piecedict[i] = copy.deepcopy(np.zeros(0))
element_connectivity = np.zeros(len(element)*mesh_conner,dtype=np.int32).reshape(len(element),mesh_conner)
tempcoordinate = np.zeros(3)
tempdistance = np.zeros(piecenum)
tempkey = ''
for i_element in element:
label = i_element.label
element_connectivity[label - 1] = i_element.connectivity
tempcoordinate[:] = 0
for elementnode in range(mesh_conner):
k = i_element.connectivity[elementnode] - 1
tempcoordinate += node_coordination[k]
tempcoordinate = tempcoordinate / mesh_conner
for i in range(piecenum):
tempdistance[i] = PointDistance(tempcoordinate,centerpoint[i])
tempkey = np.argmin(tempdistance)
tempkey = str(tempkey)
piecedict[tempkey] = np.append(piecedict[tempkey], label)
return piecedict,element_connectivity
#Partition model into pieces by indentifing the center point of the piece in parallel
def PartitionPointCenterParallel(config = {}, node_coordination = [], instancename = ''):
#Open ODB
odb = openOdb(os.path.join(config['odb_path'],config['odbname'])+'.odb',readOnly=True)
element = odb.rootAssembly.instances[instancename].elements
element_length = len(element)
centerpoint = config['partition_parameter']
mesh_conner = config['mesh_conner']
piece_number = config['piece_number']
manager = multiprocessing.Manager()
piecedict = manager.dict()
for i in range(piece_number):
piecelist = piecelist.append(str(i))
for i in piecelist:
piecedict[i] = copy.deepcopy(np.zeros(0))
elementdict = manager.dict()
for i in range(len(element)):
elementdict[str(i)] = copy.deepcopy(np.zeros(mesh_conner,dtype=np.int32))
#control the process
process_munber = config['partition_processing_number']
element_each_process = element_length/process_munber
control_dict = {}
#distribute elements to process
for i in range(process_munber-1):
control_dict[str(i)] = range(i*element_each_process, (i+1)*element_each_process)
control_dict[str(process_munber-1)] = range((process_munber-1)*element_each_process, element_length)
processlist = []
for i in range(process_munber):
P = multiprocessing.Process(target = PartitionPointCenterSubfunction, \
args = (config,piecedict,elementdict,control_dict[str(i)],node_coordination,instancename,centerpoint))
processlist.append(P)
P.start()
print "process-ID: ",P.pid
for i in processlist:
P.join()
for i in processlist:
P.terminate()
element_connectivity = np.zeros(element_length*mesh_conner,dtype=np.int32).reshape(element_length,mesh_conner)
for i in range(element_length):
element_connectivity[i] = elementdict[str(i)]
print('return piecedict,element_connectivity')
return piecedict,element_connectivity
def PartitionPointCenterSubfunction(config,piecedict,elementdict,controllist,node_coordination,instancename,centerpoint):
odb = openOdb(os.path.join(config['odb_path'],config['odbname'])+'.odb',readOnly=True)
element = odb.rootAssembly.instances[instancename].elements
mesh_conner = config['mesh_conner']
piece_number = config['piece_number']
tempcoordinate = np.zeros(3)
tempdistance = np.zeros(piece_number)
tempkey = ''
for ie_label in controllist:
i_element = element[ie_label]
label = i_element.label
elementdict[label - 1] = i_element.connectivity
tempcoordinate[:] = 0
for elementnode in range(mesh_conner):
k = i_element.connectivity[elementnode] - 1
tempcoordinate += node_coordination[k]
tempcoordinate = tempcoordinate / mesh_conner
for i in range(piece_number):
tempdistance[i] = PointDistance(tempcoordinate,centerpoint[i])
tempkey = np.argmin(tempdistance)
tempkey = str(tempkey)
piecedict[tempkey] = np.append(piecedict[tempkey], label)
def PointDistance(Point1 = [], Point2 = []):
return sqrt(np.sum(np.square(Point1-Point2)))
#------------------------------Reorganization------------------------------#
#Reorganize partitioned model in serial
def ReorganizeNodeElementSerial(config = {}, piecedict = {}, element_connectivity = [], max_nodelabel = 0):
mesh_conner = config['mesh_conner']
piecelist = piecedict.keys()
newmodel = dict.fromkeys(piecelist)
#reorganize the node and element (reconstruct the mesh)
for i_keys in piecelist:
i_piece = piecedict[i_keys]
#nodeexisted: estimate whether the node has already existed
nodeexisted = np.zeros(max_nodelabel, dtype=np.int32)
nodeexisted[:] = -1
#elementnode: store the reorganized node for element
elementnode = np.zeros(0,dtype=np.int32)
#newnode: store the reorganized node for node
newnode = np.zeros(0,dtype=np.int32)
nodecount = 0
for i in i_piece:
connectivity = element_connectivity[i-1]
for j in range(mesh_conner):
k = connectivity[j] - 1
if(nodeexisted[k] < 0):
nodeexisted[k] = nodecount
newnode = np.append(newnode,k)
elementnode = np.append(elementnode,nodecount)
nodecount += 1
else:
elementnode = np.append(elementnode,nodeexisted[k])
newmodel[i_keys] = {'node':copy.deepcopy(newnode),'element':copy.deepcopy(elementnode)}
return newmodel
#Reorganize partitioned model in parallel
def ReorganizeNodeElementParallel(config = {}, piecedict = {}, element_connectivity = [], max_nodelabel = 0):
piecelist = piecedict.keys()
manager = multiprocessing.Manager()
newmodel = manager.dict()
#reorganize the node and element (reconstruct the mesh)
#control the process
piecelist_length = len(piecelist)
process_munber = config['partition_processing_number']
piece_each_process = piecelist_length/process_munber
control_dict = {}
#distribute pieces to process
for i in range(process_munber-1):
control_dict[str(i)] = piecelist[i*piece_each_process:(i+1)*piece_each_process]
control_dict[str(process_munber-1)] = piecelist[(process_munber-1)*piece_each_process : piecelist_length]
print "Reorganize by multiprocessing......"
processlist = []
for i in range(process_munber):
P = multiprocessing.Process(target = ReorganizeNodeElementSubfunction,\
args = (newmodel,piecedict,element_connectivity,control_dict[str(i)],config,max_nodelabel))
processlist.append(P)
P.start()
print "process-ID: ",P.pid
for i in processlist:
P.join()
for i in processlist:
P.terminate()
return newmodel
def ReorganizeNodeElementSubfunction(newmodel, piecedict, element_connectivity, controllist, config, max_nodelabel):
mesh_conner = config['mesh_conner']
#reorganize the node and element (reconstruct the mesh)
for i_keys in controllist:
i_piece = piecedict[i_keys]
#nodeexisted: estimate whether the node has already existed
nodeexisted = np.zeros(max_nodelabel, dtype=np.int32)
nodeexisted[:] = -1
#elementnode: store the reorganized node for element
elementnode = np.zeros(0,dtype=np.int32)
#newnode: store the reorganized node for node
newnode = np.zeros(0,dtype=np.int32)
nodecount = 0
for i in i_piece:
connectivity = element_connectivity[i-1]
for j in range(mesh_conner):
k = connectivity[j] - 1
if(nodeexisted[k] < 0):
nodeexisted[k] = nodecount
newnode = np.append(newnode,k)
elementnode = np.append(elementnode,nodecount)
nodecount += 1
else:
elementnode = np.append(elementnode,nodeexisted[k])
newmodel[i_keys] = {'node':copy.deepcopy(newnode),'element':copy.deepcopy(elementnode)}
#-------------------------Partition & Reorganization------------------------#
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#---------------------Read Attribution and Output to VTK--------------------#
#Read attribution from each frame and write to VTK file format in serial
def WriteToVTKSerial(config = {}, frame = '', newmodel = {}, node_coordination = [], stepname = '', instancename = '', max_nodelabel = 0):
frame_list = config['input_frame']
for i_frame in frame_list:
#Detect whether the input frame is out of range
try:
TRY = frame[int(i_frame)]
except:
print "input frame exceeds the range of frames"
os._exit(0)
#Access a frame
n_frame = frame[int(i_frame)]
print "Frame:",i_frame
#Access Vector: Spatial displacement, acceleration, velocity and reaction force
vectorlist = config['output_vector']
print "Reading"+str(vectorlist)+" ......"
time1 = time()
vector_amount = len(vectorlist)
vector_dict = dict.fromkeys(vectorlist)
for vector_name in vectorlist:
tempvector = ReadVector(n_frame.fieldOutputs[vector_name],max_nodelabel)
vector_dict[vector_name] = copy.deepcopy(tempvector)
print "Time elapsed: ", time() - time1, "s"
#modification
#Access Tensor: Stress components, Logarithmic strain components and Plastic strain components
tensorlist = config['output_tensor']
tensor_dict = dict.fromkeys(tensorlist)
print "Reading"+str(tensorlist)+"......"
time1 = time()
#access Stress components
tensor_dict[tensorlist[0]] = ReadTensorAtIntS(n_frame.fieldOutputs[tensorlist[0]],7,max_nodelabel)
#Logarithmic strain components
tensor_dict[tensorlist[1]] = ReadTensorAtIntE(n_frame.fieldOutputs[tensorlist[1]],2,max_nodelabel)
#Plastic strain components
tensor_dict[tensorlist[2]] = ReadTensorAtIntE(n_frame.fieldOutputs[tensorlist[2]],2,max_nodelabel)
print "Time elapsed: ", time() - time1, "s"
#Access Saclar: Equivalent plastic strain
saclarlist = config['output_scalar']
scalar_dict = dict.fromkeys(saclarlist)
print "Reading"+str(saclarlist)+"......"
#Equivalent plastic strain
time1 = time()
scalar_dict[saclarlist[0]] = ReadScalarAtInt(n_frame.fieldOutputs[saclarlist[0]],max_nodelabel)
print "Time elapsed: ", time() - time1, "s"
piecekey = newmodel.keys()
for pn in piecekey:
print "Create .vtu file for piece " + pn + "......"
#create and open a VTK(.vtu) files
if(config['piece_number'] > 1):
outfile = open (os.path.join(config['vtk_path'],config['odbname'])+'_'+stepname+'_'+instancename+'f%03d'%int(i_frame)+' '+'p'+str(pn)+'.vtu','w')
if(config['piece_number'] == 1):
outfile = open (os.path.join(config['vtk_path'],config['odbname'])+'_'+stepname+'_'+instancename+'f%03d'%int(i_frame)+'.vtu','w')
#<VTKFile>, including the type of mesh, version, and byte_order
outfile.write('<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">'+'\n')
#<UnstructuredGrid>
outfile.write('<UnstructuredGrid>'+'\n')
#get the partitioned model
newnode = newmodel[pn]['node']
newelement = newmodel[pn]['element']
#compute point & element quantity
newelementamount = newelement.shape[0] / config['mesh_conner']
newnodeamount = newnode.shape[0]
newnodeamount_N = range(0,newnodeamount)
#<Piece>, including the number of points and cells
outfile.write('<Piece NumberOfPoints="'+str(newnodeamount)+'"'+' '+'NumberOfCells="'+str(newelementamount)+'">'+'\n')
#<Points> Write nodes into vtk files
tempvector = vector_dict['U']
outfile.write('<Points>'+'\n')
outfile.write('<DataArray type="Float64" NumberOfComponents="3" format="ascii">'+'\n')
for i in newnodeamount_N:
k = newnode[i]
X,Y,Z = node_coordination[k]+tempvector[k]
outfile.write(' '+'%11.8e'%X+' '+'%11.8e'%Y+' '+'%11.8e'%Z+'\n')
outfile.write('</DataArray>'+'\n')
outfile.write('</Points>'+'\n')
#</Points>
#<PointData> Write results data into vtk files
templist = []
templist.append("<PointData ")
templist.append("Tensors="+'"')
for tensorkey in tensorlist:
templist.append(VARIABLEDICT[tensorkey])
templist.append(',')
templist.pop()
templist.append('"'+" ")
templist.append("Vevtors="+'"')
for vectorkey in vectorlist:
templist.append(VARIABLEDICT[vectorkey])
templist.append(',')
templist.pop()
templist.append('"'+" ")
templist.append("Scalars="+'"')
for scalarkey in saclarlist:
templist.append(VARIABLEDICT[scalarkey])
templist.append(',')
for tensorkey in tensorlist:
for invariantkey in tensor_dict[tensorkey]['validinvariant']:
templist.append(VARIABLEDICT[tensorkey]+VARIABLEDICT[invariantkey])
templist.append(',')
templist.append('"'+">"+'\n')
outfile.write("".join(templist))
#Tensor: Stress components, Logarithmic strain components, Plastic strain components <DataArray>
for tensorkey in tensorlist:
temptensor = tensor_dict[tensorkey]['tensor']
outfile.write("<"+"DataArray"+" "+"type="+'"'+"Float32"+'"'+" "+"Name="+'"'+VARIABLEDICT[tensorkey]+'"'+" "+"NumberOfComponents="+'"'+"9"+'"'+" "+"format="+'"'+"ascii"+'"'+">"+'\n')
for i in newnodeamount_N:
k = newnode[i]
#XX,XY,XZ,YY,YZ,ZZ = temptensor[k][0],temptensor[k][3],temptensor[k][5],temptensor[k][1],temptensor[k][4],temptensor[k][2]
XX,YY,ZZ,XY,YZ,XZ = temptensor[k]
YX,ZY,ZX = temptensor[k][3], temptensor[k][4], temptensor[k][5]
outfile.write('%11.8e'%XX+' '+'%11.8e'%XY+' '+'%11.8e'%XZ+' '+'%11.8e'%YX+' '+'%11.8e'%YY+' '+'%11.8e'%YZ+' '+'%11.8e'%ZX+' '+'%11.8e'%ZY+' '+'%11.8e'%ZZ+'\n')
outfile.write("</DataArray>"+'\n')
#</DataArray>
#Vector: Spatial displacement, acceleration, velocity, Reaction force <DataArray>
for vectorkey in vectorlist:
tempvector = vector_dict[vectorkey]
outfile.write("<"+"DataArray"+" "+"type="+'"'+"Float32"+'"'+" "+"Name="+'"'+VARIABLEDICT[vectorkey]+'"'+" "+"NumberOfComponents="+'"'+"3"+'"'+" "+"format="+'"'+"ascii"+'"'+">"+'\n')
for i in newnodeamount_N:
k = newnode[i]
X,Y,Z = tempvector[k]
outfile.write('%11.8e'%X+' '+'%11.8e'%Y+' '+'%11.8e'%Z+'\n')
outfile.write("</DataArray>"+'\n')
#</DataArray>
#Scalar: Equivalent plastic strain, <DataArray>
for scalarkey in saclarlist:
tempscalar = scalar_dict[scalarkey]
outfile.write("<"+"DataArray"+" "+"type="+'"'+"Float32"+'"'+" "+"Name="+'"'+VARIABLEDICT[scalarkey]+'"'+" "+"format="+'"'+"ascii"+'"'+">"+'\n')
for i in newnodeamount_N:
k = newnode[i]
X = tempscalar[k]
outfile.write('%11.8e'%X+'\n')
outfile.write('</DataArray>'+'\n')
#</DataArray>
#Invariant in Tensor: Stress Mises, Stress Max.Principal, Stress Mid.Principal, Stress Min.Principal,
#Stress Min.Principal, Stress Pressure, Stress Tresca,Stress Third_Invariant,Logarithmic_strain_Max_Principal
#Logarithmic strain Min.Principal, Plastic strain Max.Principal, Plastic strain Min.Principal<DataArray>
for tensorkey in tensorlist:
invariant = tensor_dict[tensorkey]['invariant']
i_validinvariant = 0
for invariantkey in tensor_dict[tensorkey]['validinvariant']:
outfile.write("<"+"DataArray"+" "+"type="+'"'+"Float32"+'"'+" "+"Name="+'"'+VARIABLEDICT[tensorkey]+VARIABLEDICT[invariantkey]+'"'+" "+"format="+'"'+"ascii"+'"'+">"+'\n')
for i in newnodeamount_N:
k = newnode[i]
X = invariant[k][i_validinvariant]
outfile.write('%11.8e'%X+'\n')
outfile.write('</DataArray>'+'\n')
i_validinvariant = i_validinvariant + 1
#</DataArray>
outfile.write("</PointData>"+'\n')
#</PointData>
#<Cells> Write cells into vtk files
outfile.write('<Cells>'+'\n')
#Connectivity
outfile.write('<DataArray type="Int32" Name="connectivity" format="ascii">'+'\n')
if (config['mesh_type'] == 12):
for i in range(len(newelement)/8):
outfile.write(str(newelement[i*8])+' '+str(newelement[i*8+1])+' '+str(newelement[i*8+2])+' '+str(newelement[i*8+3])+' '+str(newelement[i*8+4])+' '+str(newelement[i*8+5])+' '+str(newelement[i*8+6])+' '+str(newelement[i*8+7])+'\n')
if (config['mesh_type'] == 10):
for i in range(len(newelement)/4):
outfile.write(str(newelement[i*4])+' '+str(newelement[i*4+1])+' '+str(newelement[i*4+2])+' '+str(newelement[i*4+3])+'\n')
outfile.write('</DataArray>'+'\n')
#Offsets
outfile.write('<DataArray type="Int32" Name="offsets" format="ascii">'+'\n')
for i in range(len(newelement)/config['mesh_conner']):
outfile.write(str(i*config['mesh_conner']+config['mesh_conner'])+'\n')
outfile.write('</DataArray>'+'\n')
#Type
outfile.write('<DataArray type="UInt8" Name="types" format="ascii">'+'\n')
for i in range(len(newelement)/config['mesh_conner']):
outfile.write(str(config['mesh_type'])+'\n')
outfile.write('</DataArray>'+'\n')
outfile.write('</Cells>'+'\n')
#</Cells>
#</Piece>
outfile.write('</Piece>'+'\n')
#</UnstructuredGrid>
outfile.write('</UnstructuredGrid>'+'\n')
#</VTKFile>
outfile.write('</VTKFile>'+'\n')
outfile.close()
print "Time elapsed: ", time() - time1, "s"
#====================================写入.pvtu文件=======================================#
print "Creating .pvtu file for frame ", i_frame," ......"
time1 = time()
#create .pvtu files for parallel visualization
if ( config['piece_number'] > 1 ):
outfile = open (os.path.join(config['vtk_path'],config['odbname'])+'_'+stepname+'_'+'f%03d'%int(i_frame)+'.pvtu','w')
#write the basic information for .pvtu files
outfile.write('<?xml version="1.0"?>'+'\n')
outfile.write('<VTKFile type="PUnstructuredGrid" version="0.1" byte_order="LittleEndian">'+'\n')
outfile.write("<PUnstructuredGrid GhostLevel="+'"'+str(config['piece_number'])+'"'+">"+'\n')
#pointdata
#<PointData> Write results data into vtk files
templist = []
templist.append("<PPointData ")
templist.append("Tensors="+'"')
for tensorkey in tensorlist:
templist.append(VARIABLEDICT[tensorkey])
templist.append(',')
templist.pop()
templist.append('"'+" ")
templist.append("Vevtors="+'"')
for vectorkey in vectorlist:
templist.append(VARIABLEDICT[vectorkey])
templist.append(',')
templist.pop()
templist.append('"'+" ")
templist.append("Scalars="+'"')