fixed a nasty bug in reading the header of spectral files
file type is guessed from extension script tries to gracefully continue when data is missing but not crucial ASCII file splitting now has correct increment (not position) in its name: poop_inc123.txt refers to true increment 123 not to position 123 in the result file anymore...
This commit is contained in:
Onur Guevenc
parent
b6b02f6cf9
commit
daa45306f2
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@ -3,7 +3,13 @@
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import pdb, os, sys, gc, math, re, threading, time, struct, string
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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releases = {'2010':['linux64',''],
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fileExtensions = { \
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'marc': ['.t16',],
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'spectral': ['.spectralOut',],
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}
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releases = { \
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'2010':['linux64',''],
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'2008r1':[''],
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'2007r1':[''],
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'2005r3':[''],
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@ -75,16 +81,16 @@ class MPIEspectral_result: # mimic py_post result object
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self.theTitle = self._keyedString('load')
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self.wd = self._keyedString('workingdir')
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self.geometry = self._keyedString('geometry')
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self.N_loadcases = self._keyedInt('loadcases',default=1)
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self._frequencies = self._keyedInts('frequencies',self.N_loadcases,1)
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self._increments = self._keyedInts('increments',self.N_loadcases)
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self.N_loadcases = self._keyedPackedArray('loadcases',count=1,type='i',default=1)[0]
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self._frequencies = self._keyedPackedArray('frequencies',count=self.N_loadcases,type='i',default=1)
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self._increments = self._keyedPackedArray('increments',count=self.N_loadcases,type='i')
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self._increments[0] -= 1 # delete zero'th entry
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self._times = self._keyedFloats('times',self.N_loadcases,0.0)
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self.dimension = self._keyedPackedArray('dimension',3,'d')
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self.resolution = self._keyedPackedArray('resolution',3,'i')
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self._times = self._keyedPackedArray('times',count=self.N_loadcases,type='d',default=0.0)
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self.dimension = self._keyedPackedArray('dimension',count=3,type='d')
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self.resolution = self._keyedPackedArray('resolution',count=3,type='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.N_element_scalars = self._keyedInt('materialpoint_sizeResults')
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self.N_element_scalars = self._keyedPackedArray('materialpoint_sizeResults',count=1,type='i',default=0)[0]
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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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@ -97,60 +103,43 @@ class MPIEspectral_result: # mimic py_post result object
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def __str__(self):
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return '\n'.join([
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'title: %s'%self.theTitle,
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'workdir: %s'%self.wd,
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'geometry: %s'%self.geometry,
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'extrapolation: %s'%self.extrapolate,
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'loadcases: %i'%self.N_loadcases,
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'increments: %i'%self.N_increments,
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'increment: %i'%self.increment,
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'position: %i'%self.position,
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'time: %i'%self.time,
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'nodes: %i'%self.N_nodes,
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'resolution: %s'%(','.join(map(str,self.resolution))),
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'dimension: %s'%(','.join(map(str,self.dimension))),
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'elements: %i'%self.N_elements,
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'nodal_scalars: %i'%self.N_node_scalars,
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'elemental scalars: %i'%self.N_element_scalars,
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'elemental tensors: %i'%self.N_element_tensors,
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'header size: %i'%self.dataOffset,
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'file size: %i'%(self.dataOffset+self.N_increments*(8+self.N_elements*self.N_element_scalars*8)),
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]
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)
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def _keyedPackedArray(self,identifier,length = 3,type = 'd'):
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match = {'d': 8,'i': 4}
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self.file.seek(0)
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m = re.search('%s%s'%(identifier,'(.{%i})'%(match[type])*length),self.file.read(2048),re.DOTALL)
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values = []
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if m:
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for i in m.groups():
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values.append(struct.unpack(type,i)[0])
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def locateKeyValue(self,identifier):
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key = {'name':'','pos':0}
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filepos = 0
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while key['name'] != identifier and key['name'] != 'eoh' and filepos < 2048:
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self.file.seek(filepos)
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tag = self.file.read(4) # read the starting/ending tag
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key['name'] = self.file.read(len(identifier)) # anticipate identifier
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key['pos'] = self.file.tell() # remember position right after identifier
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self.file.seek(filepos+4) # start looking after opening tag
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filepos += 4 + self.file.read(2048).find(tag) + 4 # locate end of closing tag
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return key
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def _keyedPackedArray(self,identifier,count = 3,type = 'd',default = None):
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bytecount = {'d': 8,'i': 4}
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values = [default]*count
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key = self.locateKeyValue(identifier)
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if key['name'] == identifier:
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self.file.seek(key['pos'])
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for i in range(count):
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values[i] = struct.unpack(type,self.file.read(bytecount[type]))[0]
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return values
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def _keyedInt(self,identifier,default=None):
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value = default
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self.file.seek(0)
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m = re.search('%s%s'%(identifier,'(.{4})'),self.file.read(2048),re.DOTALL)
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if m:
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value = struct.unpack('i',m.group(1))[0]
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return value
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def _keyedInts(self,identifier,number=1,default=None):
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values = [default]*number
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self.file.seek(0)
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m = re.search('%s%s'%(identifier,'(.{4})'*number),self.file.read(2048),re.DOTALL)
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if m:
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for i in range(number):
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values[i] = struct.unpack('i',m.group(1+i))[0]
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return values
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def _keyedFloats(self,identifier,number=1,default=None):
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values = [default]*number
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self.file.seek(0)
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m = re.search('%s%s'%(identifier,'(.{8})'*number),self.file.read(2048),re.DOTALL)
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if m:
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for i in range(number):
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values[i] = struct.unpack('d',m.group(1+i))[0]
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return values
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def _keyedString(self,identifier,default=None):
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value = default
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@ -229,7 +218,12 @@ class MPIEspectral_result: # mimic py_post result object
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def element_scalar(self,e,idx):
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self.file.seek(self.dataOffset+(self.position*(4+self.N_elements*self.N_element_scalars*8+4) + 4+(e*self.N_element_scalars + idx)*8))
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try:
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value = struct.unpack('d',self.file.read(8))[0]
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except:
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print 'seeking',self.dataOffset+(self.position*(4+self.N_elements*self.N_element_scalars*8+4) + 4+(e*self.N_element_scalars + idx)*8)
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print 'e',e,'idx',idx
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sys.exit(1)
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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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@ -434,13 +428,7 @@ def OpenPostfile(name,type):
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p = {\
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'spectral': MPIEspectral_result,\
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'marc': post_open,\
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}[type]\
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(name+
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{\
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'marc': '.t16',\
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'spectral': '.spectralOut',\
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}[type]
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)
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}[type](name)
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p.extrapolation('translate')
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p.moveto(1)
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@ -555,6 +543,7 @@ def ParsePostfile(p,filename, outputFormat):
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stat['IndexOfLabel']['%s'%(var[0])] = startIndex + offset + 1
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offset += var[1]
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if '(ngrains)' in outputFormat['Homogenization']['specials']:
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for grain in range(outputFormat['Homogenization']['specials']['(ngrains)']):
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stat['IndexOfLabel']['%i_CrystalliteCount'%(grain+1)] = startIndex + offset + 1
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offset += 1
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@ -580,7 +569,7 @@ def ParsePostfile(p,filename, outputFormat):
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# -----------------------------
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def SummarizePostfile(stat,where=sys.stdout):
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def SummarizePostfile(stat,where=sys.stdout,format='marc'):
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# -----------------------------
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where.write('\n\n')
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@ -638,9 +627,8 @@ parser.add_option('-m','--map', dest='func', type='string', \
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help='data reduction mapping ["%default"] out of min, max, avg, sum, abssum or user-lambda')
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parser.add_option('-p','--type', dest='filetype', type='string', \
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help = 'type of result file [%default]')
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group_material = OptionGroup(parser,'Material identifier')
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group_special = OptionGroup(parser,'Special outputs')
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group_general = OptionGroup(parser,'General outputs')
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group_material.add_option('--homogenization', dest='homog', type='string', \
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help='homogenization identifier (as string or integer [%default])')
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@ -649,6 +637,8 @@ group_material.add_option('--crystallite', dest='cryst', type='string', \
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group_material.add_option('--phase', dest='phase', type='string', \
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help='phase identifier (as string or integer [%default])')
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group_special = OptionGroup(parser,'Special outputs')
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group_special.add_option('-t','--time', action='store_true', dest='time', \
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help='output time of increment [%default]')
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group_special.add_option('-f','--filter', dest='filter', type='string', \
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@ -658,6 +648,8 @@ group_special.add_option('--separation', action='extend', dest='separation', typ
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group_special.add_option('--sort', action='extend', dest='sort', type='string', \
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help='properties to sort results [%default]')
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group_general = OptionGroup(parser,'General outputs')
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group_general.add_option('--ns', action='extend', dest='nodalScalar', type='string', \
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help='list of nodal scalars to extract')
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group_general.add_option('--es', action='extend', dest='elementalScalar', type='string', \
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@ -679,7 +671,7 @@ parser.set_defaults(info = False)
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parser.set_defaults(sloppy = False)
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parser.set_defaults(prefix = '')
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parser.set_defaults(directory = 'postProc')
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parser.set_defaults(filetype = 'marc')
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parser.set_defaults(filetype = None)
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parser.set_defaults(func = 'avg')
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parser.set_defaults(homog = '1')
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parser.set_defaults(cryst = '1')
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@ -693,8 +685,33 @@ parser.set_defaults(separateFiles = False)
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(options, files) = parser.parse_args()
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# --- basic sanity checks
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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(files[0]):
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parser.print_help()
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parser.error('invalid file "%s" specified...'%files[0])
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# --- figure out filetype
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if options.filetype == None:
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ext = os.path.splitext(files[0])[1]
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for theType in fileExtensions.keys():
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if ext in fileExtensions[theType]:
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options.filetype = theType
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break
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options.filetype = options.filetype.lower()
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# --- more sanity checks
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if options.filetype not in ['marc','spectral']:
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parser.print_help()
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parser.error('file type "%s" not supported...'%options.filetype)
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if options.filetype == 'marc':
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try:
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file = open('%s/../MSCpath'%os.path.dirname(os.path.realpath(sys.argv[0])))
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@ -722,22 +739,6 @@ else:
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def post_open():
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return
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# --- sanity checks
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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(files[0]):
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parser.print_help()
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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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parser.error('file type "%s" not supported...'%options.filetype)
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if options.constitutiveResult and not options.phase:
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parser.print_help()
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parser.error('constitutive results require phase...')
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@ -764,7 +765,12 @@ bg.start()
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# --- parse .output and .t16 files
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if os.path.splitext(files[0])[1] == '':
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filename = files[0]
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extension = fileExtensions[options.filetype]
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else:
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filename = os.path.splitext(files[0])[0]
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extension = os.path.splitext(files[0])[1]
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outputFormat = {}
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me = {
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@ -782,7 +788,7 @@ for what in me:
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print '\n'.join(map(lambda x:' '+x, outputFormat[what]['specials']['brothers']))
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bg.set_message('opening result file...')
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p = OpenPostfile(filename,options.filetype)
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p = OpenPostfile(filename+extension,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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@ -806,6 +812,8 @@ 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 '\n\nMentat release %s'%release
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if options.filetype == 'spectral':
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print '\n\n',p
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SummarizePostfile(stat,sys.stderr)
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@ -837,24 +845,24 @@ for l in elementsOfNode.values():
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# --- get output data from .t16 file
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increments = range(stat['NumberOfIncrements'])
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positions = range(stat['NumberOfIncrements'])
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if options.filetype == 'marc':
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offset_inc = 1
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offset_pos = 1
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else:
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offset_inc = 0
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offset_pos = 0
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if options.range:
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options.range = list(options.range)
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if options.sloppy:
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increments = range(options.range[0],options.range[1]+1,options.range[2])
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positions = range(options.range[0],options.range[1]+1,options.range[2])
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else:
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increments = range( max(0,options.range[0]),
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positions = 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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# --------------------------- build group membership --------------------------------
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p.moveto(increments[0]+offset_inc)
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p.moveto(positions[0]+offset_pos)
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index = {}
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groups = []
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groupCount = 0
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@ -982,19 +990,26 @@ standard = ['inc'] + \
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{True: ['node.x','node.y','node.z'],
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False:['ip.x','ip.y','ip.z']}[options.nodalScalar != []]
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# --------------------------- loop over increments --------------------------------
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# --------------------------- loop over positions --------------------------------
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bg.set_message('getting increments...')
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increments = [None]*len(positions)
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for incCount,position in enumerate(positions):
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p.moveto(position+offset_pos)
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increments[incCount] = p.increment # remember "real" increment at this position
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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+offset_inc)
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for incCount,position in enumerate(positions):
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p.moveto(position+offset_pos)
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# --------------------------- file management --------------------------------
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if options.separateFiles:
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if fileOpen:
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file.close()
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fileOpen = False
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outFilename = eval('"'+eval("'%%s_inc%%0%ii.txt'%(math.log10(max(increments+[1]))+1)")+'"%(dirname + os.sep + options.prefix + os.path.split(filename)[1],increment)')
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outFilename = eval('"'+eval("'%%s_inc%%0%ii.txt'%(math.log10(max(increments+[1]))+1)")+'"%(dirname + os.sep + options.prefix + os.path.split(filename)[1],increments[incCount])')
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else:
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outFilename = '%s.txt'%(dirname + os.sep + options.prefix + os.path.split(filename)[1])
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@ -1017,8 +1032,8 @@ for incCount,increment in enumerate(increments):
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for (e,n,i,g,n_local) in group[1:]: # loop over group members
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member += 1
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if member%1000 == 0:
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time_delta = ((len(increments)*memberCount)/float(member+incCount*memberCount)-1.0)*(time.time()-time_start)
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bg.set_message('(%02i:%02i:%02i) processing point %i of %i from increment %i...'%(time_delta//3600,time_delta%3600//60,time_delta%60,member,memberCount,increment))
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time_delta = ((len(positions)*memberCount)/float(member+incCount*memberCount)-1.0)*(time.time()-time_start)
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bg.set_message('(%02i:%02i:%02i) processing point %i of %i from position %i...'%(time_delta//3600,time_delta%3600//60,time_delta%60,member,memberCount,position))
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newby = [] # current member's data
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