deleted useless storage of data resulting in partial speed-up.
large datasets (>1 mio elements) cannot be processed at the moment---investigation required, why each element eats about 20kB of memory?
This commit is contained in:
Philip Eisenlohr
parent
97a0146672
commit
6ac2b4cf88
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@ -61,8 +61,6 @@ class MPIEspectral_result: # mimic py_post result object
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N_elements = 0
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N_element_scalars = 0
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N_element_tensors = 0
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theNodes = []
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theElements = []
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def __init__(self,filename):
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@ -76,23 +74,7 @@ class MPIEspectral_result: # mimic py_post result object
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self.resolution = self._keyedPackedArray('resolution',3,'i')
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self.N_nodes = (self.resolution[0]+1)*(self.resolution[1]+1)*(self.resolution[2]+1)
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self.N_elements = self.resolution[0]*self.resolution[1]*self.resolution[2]
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self.dimension = self._keyedPackedArray('dimension',3,'d')
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a = self.resolution[0]+1
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b = self.resolution[1]+1
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c = self.resolution[2]+1
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for n in range(self.N_nodes):
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self.theNodes.append(vector([self.dimension[0] * (n%a) / self.resolution[0],
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self.dimension[1] * ((n/a)%b) / self.resolution[1],
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self.dimension[2] * ((n/a/b)%c) / self.resolution[2],
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]))
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for e in range(self.N_elements):
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basenode = e+e/self.resolution[0] + e/self.resolution[0]/self.resolution[1]*a
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basenode2 = basenode+a*b
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self.theElements.append(element([basenode ,basenode+1 ,basenode+a+1 ,basenode+a,
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basenode2,basenode2+1,basenode2+a+1,basenode2+a,
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],117))
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self.file.seek(0)
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self.dataOffset = self.file.read(2048).find('eoh')+7
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@ -150,20 +132,33 @@ class MPIEspectral_result: # mimic py_post result object
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def extrapolation(self,value):
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self.extrapolate = value
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def node_sequence(self,node):
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return node
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def node_sequence(self,n):
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return n
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def node_id(self,node):
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return node+1
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def node_id(self,n):
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return n+1
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def node(self,node):
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return self.theNodes[node]
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def node(self,n):
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a = self.resolution[0]+1
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b = self.resolution[1]+1
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c = self.resolution[2]+1
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return vector([self.dimension[0] * (n%a) / self.resolution[0],
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self.dimension[1] * ((n/a)%b) / self.resolution[1],
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self.dimension[2] * ((n/a/b)%c) / self.resolution[2],
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])
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def element_id(self,elem):
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return elem+1
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def element_id(self,e):
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return e+1
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def element(self,elem):
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return self.theElements[elem]
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def element(self,e):
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a = self.resolution[0]+1
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b = self.resolution[1]+1
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c = self.resolution[2]+1
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basenode = e+e/self.resolution[0] + e/self.resolution[0]/self.resolution[1]*a
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basenode2 = basenode+a*b
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return (element([basenode ,basenode+1 ,basenode+a+1 ,basenode+a,
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basenode2,basenode2+1,basenode2+a+1,basenode2+a,
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],117))
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def increments(self):
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return self.N_increments
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@ -180,10 +175,10 @@ class MPIEspectral_result: # mimic py_post result object
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def element_scalars(self):
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return self.N_element_scalars
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def element_scalar(self,elem,idx):
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self.file.seek(self.dataOffset+(self.increment*(4+self.N_elements*self.N_element_scalars*8+4) + 4+(elem*self.N_element_scalars + idx)*8))
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def element_scalar(self,e,idx):
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self.file.seek(self.dataOffset+(self.increment*(4+self.N_elements*self.N_element_scalars*8+4) + 4+(e*self.N_element_scalars + idx)*8))
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value = struct.unpack('d',self.file.read(8))[0]
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return [elemental_scalar(node,value) for node in self.theElements[elem].items]
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return [elemental_scalar(node,value) for node in self.element(e).items]
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def element_scalar_label(elem,idx):
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return 'User Defined Variable %i'%(idx+1)
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@ -221,7 +216,7 @@ class backgroundMessage(threading.Thread):
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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.symbols = ['- ', '\ ', '| ', '/ ',]
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self.waittime = 0.5
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def __quit__(self):
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@ -529,9 +524,10 @@ def ParsePostfile(p,filename, outputFormat):
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def SummarizePostfile(stat,where=sys.stdout):
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# -----------------------------
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where.write('\n\n')
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where.write('title:\t%s'%stat['Title'] + '\n\n')
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where.write('extraplation:\t%s'%stat['Extrapolation'] + '\n\n')
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where.write('increments:\t%i+1'%(stat['NumberOfIncrements']-1) + '\n\n')
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where.write('increments:\t%i'%(stat['NumberOfIncrements']) + '\n\n')
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where.write('nodes:\t%i'%stat['NumberOfNodes'] + '\n\n')
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where.write('elements:\t%i'%stat['NumberOfElements'] + '\n\n')
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where.write('nodal scalars:\t%i'%stat['NumberOfNodalScalars'] + '\n\n ' + '\n '.join(stat['LabelOfNodalScalar']) + '\n\n')
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@ -625,7 +621,7 @@ parser.set_defaults(inc = False)
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parser.set_defaults(time = False)
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parser.set_defaults(separateFiles = False)
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(options, file) = parser.parse_args()
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(options, files) = parser.parse_args()
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options.filetype = options.filetype.lower()
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@ -658,19 +654,15 @@ else:
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bg = backgroundMessage()
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bg.start()
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# --- sanity checks
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if file == []:
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if files == []:
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parser.print_help()
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parser.error('no file specified...')
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if not os.path.exists(file[0]):
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if not os.path.exists(files[0]):
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parser.print_help()
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parser.error('invalid file "%s" specified...'%file[0])
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parser.error('invalid file "%s" specified...'%files[0])
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if options.filetype not in ['marc','spectral']:
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parser.print_help()
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@ -686,11 +678,14 @@ if options.nodalScalar and ( options.elementalScalar or options.elementalTenso
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parser.error('not allowed to mix nodal with elemental results...')
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# --- start background messaging
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bg = backgroundMessage()
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bg.start()
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# --- parse .output and .t16 files
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bg.set_message('parsing .output and result files...')
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filename = os.path.splitext(file[0])[0]
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filename = os.path.splitext(files[0])[0]
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dirname = os.path.abspath(os.path.dirname(filename))+os.sep+options.directory
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if not os.path.isdir(dirname):
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os.mkdir(dirname,0755)
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@ -701,6 +696,9 @@ me = {
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'Crystallite': options.cryst,
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'Constitutive': options.phase,
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}
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bg.set_message('parsing .output files...')
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for what in me:
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outputFormat[what] = ParseOutputFormat(filename, what, me[what])
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if not '_id' in outputFormat[what]['specials']:
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@ -708,9 +706,12 @@ for what in me:
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print '\n'.join(map(lambda x:' '+x, outputFormat[what]['specials']['brothers']))
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sys.exit(1)
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bg.set_message('opening result file...')
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p = OpenPostfile(filename,options.filetype)
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bg.set_message('parsing result file...')
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stat = ParsePostfile(p, filename, outputFormat)
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if options.filetype == 'marc':
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stat['NumberOfIncrements'] -= 1 # t16 contains one "virtual" increment (at 0)
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# --- sanity check for output variables
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# for mentat variables (nodalScalar,elementalScalar,elementalTensor) we simply have to check whether the label is found in the stat[indexOfLabel] dictionary
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@ -729,7 +730,7 @@ for opt in ['nodalScalar','elementalScalar','elementalTensor','homogenizationRes
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if options.info:
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if options.filetype == 'marc':
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print '\nMentat release %s\n'%release
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print '\n\nMentat release %s'%release
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SummarizePostfile(stat,sys.stderr)
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@ -745,12 +746,19 @@ if options.info:
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# --- get output data from .t16 file
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if options.range:
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increments = range( max(0,options.range[0]),
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min(stat['NumberOfIncrements'],options.range[1]+1),
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options.range[2])
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increments = range(stat['NumberOfIncrements'])
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if options.filetype == 'marc':
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offset_inc = 1
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else:
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increments = range(stat['NumberOfIncrements']-1)
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offset_inc = 0
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if options.range:
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options.range = list(options.range)
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if options.filetype == 'spectral':
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options.range[0] -= 1
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options.range[1] -= 1
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increments = range( max(0,options.range[0]),
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min(stat['NumberOfIncrements'],options.range[1]+1),
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options.range[2])
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fileOpen = False
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assembleHeader = True
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@ -759,40 +767,22 @@ header = []
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element_scalar = {}
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element_tensor = {}
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# --- store geometry information
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p.moveto(0)
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nodeID = [ 0 for n in range(stat['NumberOfNodes'])]
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nodeCoordinates = [[] for n in range(stat['NumberOfNodes'])]
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elemID = [ 0 for e in range(stat['NumberOfElements'])]
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elemNodeID = [[] for e in range(stat['NumberOfElements'])]
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ipCoordinates = [[] for e in range(stat['NumberOfElements'])]
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for n in range(stat['NumberOfNodes']):
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nodeID[n] = p.node_id(n)
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nodeCoordinates[n] = [p.node(n).x, p.node(n).y, p.node(n).z]
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for e in range(stat['NumberOfElements']):
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elemID[e] = p.element_id(e)
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elemNodeID[e] = p.element(e).items
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ipCoordinates[e] = ipCoords(p.element(e).type, map(lambda node: [node.x, node.y, node.z], map(p.node, map(p.node_sequence,p.element(e).items))))
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# --- loop over increments
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time_start = time.time()
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for incCount,increment in enumerate(increments):
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p.moveto(increment+1)
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time_delta = (len(increments)-incCount)*(time.time()-time_start)/max(1.0,incCount)
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bg.set_message('(%02i:%02i:%02i) read data from increment %i...'%(time_delta//3600,time_delta%3600//60,time_delta%60,increment))
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p.moveto(increment+offset_inc)
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data = {}
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if options.nodalScalar:
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for n in range(stat['NumberOfNodes']):
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myNodeID = nodeID[n]
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myNodeCoordinates = nodeCoordinates[n]
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if n%100 == 0:
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time_delta = (len(increments)-incCount)*(time.time()-time_start)/max(1.0,incCount)
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bg.set_message('(%02i:%02i:%02i) read node %i from increment %i...'%(time_delta//3600,time_delta%3600//60,time_delta%60,n,increment))
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myNodeID = p.node_id(n)
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myNodeCoordinates = [p.node(n).x, p.node(n).y, p.node(n).z]
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myElemID = 0
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myGrainID = 0
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@ -827,9 +817,12 @@ for incCount,increment in enumerate(increments):
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else:
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for e in range(stat['NumberOfElements']):
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myElemID = elemID[e]
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myIpCoordinates = ipCoordinates[e]
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for n,myNodeID in enumerate(elemNodeID[e]):
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if e%100 == 0:
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time_delta = (len(increments)-incCount)*(time.time()-time_start)/max(1.0,incCount)
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bg.set_message('(%02i:%02i:%02i) read elem %i from increment %i...'%(time_delta//3600,time_delta%3600//60,time_delta%60,e,increment))
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myElemID = p.element_id(e)
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myIpCoordinates = ipCoords(p.element(e).type, map(lambda node: [node.x, node.y, node.z], map(p.node, map(p.node_sequence,p.element(e).items))))
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for n,myNodeID in enumerate(p.element(e).items):
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for g in range(('GrainCount' in stat['IndexOfLabel'] and int(p.element_scalar(e, stat['IndexOfLabel']['GrainCount'])[0].value))
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or 1):
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myGrainID = g + 1
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