adopted use of general damask package
This commit is contained in:
Philip Eisenlohr
parent
a8dece8694
commit
fb7adf7b89
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,string,damask_tools
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import os,re,sys,math,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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@ -67,7 +67,7 @@ else:
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id: addNorm.py 1118 2011-11-23 14:54:53Z MPIE\p.eisenlohr $','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,numpy,string,damask_tools
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import os,re,sys,math,numpy,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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@ -75,7 +75,7 @@ else:
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,string,damask_tools
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import os,re,sys,math,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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@ -79,7 +79,7 @@ else:
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,numpy,string
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import os,re,sys,math,numpy,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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@ -31,7 +31,7 @@ def Mises(what,tensor):
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{
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'stress': 3.0/2.0,
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'strain': 2.0/3.0,
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}[what])
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}[what.lower()])
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# --------------------------------------------------------------------
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@ -45,14 +45,11 @@ Add vonMises equivalent values for symmetric part of requested strains and/or st
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)
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parser.add_option('-m','--memory', dest='memory', action='store_true', \
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help='load complete file into memory [%default]')
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parser.add_option('-e','--strain', dest='strain', action='extend', type='string', \
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help='heading(s) of columns containing strain tensors')
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parser.add_option('-s','--stress', dest='stress', action='extend', type='string', \
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help='heading(s) of columns containing stress tensors')
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parser.set_defaults(memory = False)
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parser.set_defaults(strain = [])
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parser.set_defaults(stress = [])
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@ -86,30 +83,12 @@ else:
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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print file['name']
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if file['name'] != 'STDIN': print file['name']
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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headerlines = int(m.group(1))
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passOn = [file['input'].readline() for i in range(1,headerlines)]
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headers = file['input'].readline().split()
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else:
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headerlines = 1
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passOn = []
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headers = firstline.split()
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if options.memory:
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data = file['input'].readlines()
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else:
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data = []
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for i,l in enumerate(headers):
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if l.startswith('1_'):
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if re.match('\d+_',l[2:]) or i == len(headers)-1 or not headers[i+1].endswith(l[2:]):
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headers[i] = l[2:]
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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active = {}
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column = {}
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@ -119,57 +98,37 @@ for file in files:
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for label in info['label']:
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key = {True :'1_%s',
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False:'%s' }[info['len']>1]%label
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if key not in headers:
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = headers.index(key)
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head.append('Mises(%s)'%label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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table.labels_append('Mises(%s)'%label) # extend ASCII header with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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output = '%i\theader'%(headerlines+1) + '\n' + \
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''.join(passOn) + \
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string.replace('$Id$','\n','\\n')+ '\t' + \
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' '.join(sys.argv[1:]) + '\n' + \
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'\t'.join(headers + head) + '\n' # build extended header
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table.head_write()
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if not options.memory:
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file['output'].write(output)
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output = ''
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# ------------------------------------------ process data ---------------------------------------
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# ------------------------------------------ read file ---------------------------------------
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for line in {True : data,
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False : file['input']}[options.memory]:
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items = line.split()[:len(headers)]
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if len(items) < len(headers):
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continue
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while table.data_read(): # read next data line of ASCII table
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output += '\t'.join(items)
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested norms
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table.data_append(Mises(datatype,
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numpy.array(map(float,items[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3)))
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for datatype,labels in active.items():
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for label in labels:
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theMises = Mises(datatype,
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numpy.array(map(float,items[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3))
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output += '\t%f'%theMises
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table.data_write() # output processed line
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output += '\n'
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if not options.memory:
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file['output'].write(output)
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output = ''
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file['input'].close()
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# ------------------------------------------ output result ---------------------------------------
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if options.memory:
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file['output'].write(output)
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table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table
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if file['name'] != 'STDIN':
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file['output'].close
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os.rename(file['name']+'_tmp',file['name'])
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file['output'].close # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -1,6 +1,6 @@
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#!/usr/bin/python
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import os,re,sys,math,string,damask_tools
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import os,re,sys,math,string,damask
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from optparse import OptionParser, Option
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# -----------------------------
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@ -79,7 +79,7 @@ else:
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace('$Id$','\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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@ -2,10 +2,9 @@
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# Makes postprocessing routines acessible from everywhere.
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import os,sys,glob,string
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import os,sys,glob,string,damask
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from optparse import OptionParser, Option
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import damask_tools
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# -----------------------------
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class extendableOption(Option):
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@ -52,10 +51,9 @@ else:
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acml_subdir='%s64/lib'%options.compiler
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#getting pathinfo
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damask_variables = damask_tools.DAMASK_TOOLS()
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baseDir = damask_variables.relPath('processing/')
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codeDir = damask_variables.relPath('code/')
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damaskEnv = damask.Environment()
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baseDir = damaskEnv.relPath('processing/')
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codeDir = damaskEnv.relPath('code/')
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#define ToDo list
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bin_link = { \
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@ -101,7 +99,7 @@ compile = { \
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execute = { \
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'postMath' : [
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'rm %s'%(os.path.join(damask_variables.relPath('lib/'),'DAMASK.so')),
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'rm %s'%(os.path.join(damaskEnv.relPath('lib/'),'DAMASK.so')),
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# The following command is used to compile math.f90 and make the functions defined in DAMASK_math.pyf
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# available for python in the module DAMASK_math.so
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# It uses the fortran wrapper f2py that is included in the numpy package to construct the
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@ -112,9 +110,9 @@ execute = { \
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'-c --fcompiler=%s '%(f2py_compiler) +\
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'%s ' %(os.path.join(codeDir,'DAMASK2Python_helper.f90'))+\
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'%s ' %(os.path.join(codeDir,'math.f90'))+\
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'%s ' %(os.path.join(damask_variables.pathInfo['fftw'],'libfftw3.a'))+\
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'%s' %(os.path.join(damask_variables.pathInfo['acml'],acml_subdir,'libacml.a'),
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'mv %s %s' %(os.path.join(codeDir,'DAMASK.so'),damask_variables.relPath('lib/')),
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'%s ' %(os.path.join(damaskEnv.pathInfo['fftw'],'libfftw3.a'))+\
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'%s' %(os.path.join(damaskEnv.pathInfo['acml'],acml_subdir,'libacml.a')),
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'mv %s %s' %(os.path.join(codeDir,'DAMASK.so'),damaskEnv.relPath('lib/')),
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]
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}
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@ -135,7 +133,7 @@ os.chdir(codeDir) # needed for compilation with gfortran and f
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for tasks in execute:
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for cmd in execute[tasks]:
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os.system(cmd)
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os.chdir(damask_variables.relPath('processing/setup/'))
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os.chdir(damaskEnv.relPath('processing/setup/'))
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modules = glob.glob('*.mod')
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for module in modules:
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@ -146,16 +144,11 @@ for dir in bin_link:
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for file in bin_link[dir]:
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src = os.path.abspath(os.path.join(baseDir,dir,file))
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if (file == ''):
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sym_link = os.path.abspath(os.path.join(damask_variables.binDir(),dir))
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),dir))
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else:
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sym_link = os.path.abspath(os.path.join(damask_variables.binDir(),os.path.splitext(file)[0]))
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),os.path.splitext(file)[0]))
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print sym_link,'-->',src
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if os.path.lexists(sym_link):
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os.remove(sym_link)
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os.symlink(src,sym_link)
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#--- uncomment next lines to remove your old symbolic links in ~/bin
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#old_link=sym_link.replace(damask_root,os.getenv('HOME'))
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#if os.path.lexists(old_link):
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# os.remove(old_link)
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