From f463c2da70d0fc203a1735eb1cd6d31e3b24a091 Mon Sep 17 00:00:00 2001 From: Krishna Komerla Date: Wed, 21 Dec 2011 17:25:31 +0000 Subject: [PATCH] added addCurl.py, not sure if it works correctly. still in old (eq. to addDivergence.py) style --- code/DAMASK.pyf | 2 +- lib/pathinfo | 2 +- processing/post/addCurl.py | 207 +++++++++++++++++++++++++++ processing/setup/setup_processing.py | 4 +- 4 files changed, 212 insertions(+), 3 deletions(-) create mode 100755 processing/post/addCurl.py diff --git a/code/DAMASK.pyf b/code/DAMASK.pyf index a3d741957..6510d94b5 100644 --- a/code/DAMASK.pyf +++ b/code/DAMASK.pyf @@ -75,7 +75,7 @@ python module DAMASK ! in complex*16, dimension(res[0],res[1],res[2],3,3), depend(res[0],res[1],res[2]) :: defgrad_fft end subroutine deformed_fft - subroutine curl_fft(res,geomdim,vec_tens,field,curl_fft) ! in :math:math.f90 + subroutine curl_fft(res,geomdim,vec_tens,field,curl_field) ! in :math:math.f90 ! input variables integer, dimension(3), intent(in) :: res real*8, dimension(3), intent(in) :: geomdim diff --git a/lib/pathinfo b/lib/pathinfo index 096885ef5..68f6c040e 100644 --- a/lib/pathinfo +++ b/lib/pathinfo @@ -1,6 +1,6 @@ # possible options are MSC, FFTW, IKML, ACML, LAPACK -#ACML /opt/acml5.0.0 +ACML /opt/acml4.4.0 LAPACK /usr FFTW ./fftw MSC /msc diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py new file mode 100755 index 000000000..51afbfedc --- /dev/null +++ b/processing/post/addCurl.py @@ -0,0 +1,207 @@ +#!/usr/bin/python + +import os,re,sys,math,string,numpy,DAMASK +from optparse import OptionParser, Option + +# ----------------------------- +class extendableOption(Option): +# ----------------------------- +# used for definition of new option parser action 'extend', which enables to take multiple option arguments +# taken from online tutorial http://docs.python.org/library/optparse.html + + ACTIONS = Option.ACTIONS + ("extend",) + STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) + TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) + ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) + + def take_action(self, action, dest, opt, value, values, parser): + if action == "extend": + lvalue = value.split(",") + values.ensure_value(dest, []).extend(lvalue) + else: + Option.take_action(self, action, dest, opt, value, values, parser) + +def location(idx,res): + return ( idx % res[0], \ + (idx // res[0]) % res[1], \ + (idx // res[0] // res[1]) % res[2] ) + +def index(location,res): + return ( location[0] % res[0] + \ + (location[1] % res[1]) * res[0] + \ + (location[2] % res[2]) * res[0] * res[1] ) + +def prefixMultiply(what,len): + return {True: ['%i_%s'%(i+1,what) for i in range(len)], + False:[what]}[len>1] + + +# -------------------------------------------------------------------- +# MAIN +# -------------------------------------------------------------------- + +parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ +Add column(s) containing curl of requested column(s). +Operates on periodic ordered three-dimensional data sets. +Deals with both vector- and tensor-valued fields. + +""" + string.replace('$Id$','\n','\\n') +) + + +parser.add_option('-v','--vector', dest='vector', action='extend', type='string', \ + help='heading of columns containing vector field values') +parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \ + help='heading of columns containing tensor field values') +parser.add_option('-d','--dimension', dest='dim', type='float', nargs=3, \ + help='physical dimension of data set in x (fast) y z (slow) [%default]') +parser.add_option('-r','--resolution', dest='res', type='int', nargs=3, \ + help='resolution of data set in x (fast) y z (slow)') + +parser.set_defaults(vector = []) +parser.set_defaults(tensor = []) +parser.set_defaults(dim = []) +parser.set_defaults(skip = [0,0,0]) + +(options,filenames) = parser.parse_args() + +if len(options.vector) + len(options.tensor) == 0: + parser.error('no data column specified...') +if len(options.dim) < 3: + parser.error('improper dimension specification...') +if not options.res or len(options.res) < 3: + parser.error('improper resolution specification...') + +resSkip = map(lambda (a,b): a+b,zip(options.res,options.skip)) +datainfo = { # list of requested labels per datatype + 'vector': {'len':3, + 'label':[]}, + 'tensor': {'len':9, + 'label':[]}, + } + +if options.vector != None: datainfo['vector']['label'] += options.vector +if options.tensor != None: datainfo['tensor']['label'] += options.tensor + +# ------------------------------------------ setup file handles --------------------------------------- + +files = [] +if filenames == []: + files.append({'name':'STDIN', 'handle':sys.stdin}) +else: + for name in filenames: + if os.path.exists(name): + files.append({'name':name, 'handle':open(name)}) + +# ------------------------------------------ loop over input files --------------------------------------- + +for file in files: + print file['name'] + + content = file['handle'].readlines() + file['handle'].close() + + # get labels by either read the first row, or - if keyword header is present - the last line of the header + + headerlines = 1 + m = re.search('(\d+)\s*head', content[0].lower()) + if m: + headerlines = int(m.group(1)) + passOn = content[1:headerlines] + headers = content[headerlines].split() + data = content[headerlines+1:] + + regexp = re.compile('1_\d+_') + for i,l in enumerate(headers): + if regexp.match(l): + headers[i] = l[2:] + + active = {} + column = {} + values = {} + curl_field ={} + head = [] + + for datatype,info in datainfo.items(): + for label in info['label']: + key = {True :'1_%s', + False:'%s' }[info['len']>1]%label + if key not in headers: + print 'column %s not found...'%key + else: + if datatype not in active: active[datatype] = [] + if datatype not in column: column[datatype] = {} + if datatype not in values: values[datatype] = {} + if datatype not in curl_field: curl_field[datatype] = {} + active[datatype].append(label) + column[datatype][label] = headers.index(key) + values[datatype][label] = numpy.array([0.0 for i in xrange(datainfo[datatype]['len']*\ + options.res[0]*options.res[1]*options.res[2])]).\ + reshape((options.res[0],options.res[1],options.res[2],\ + 3,datainfo[datatype]['len']//3)) + + head += prefixMultiply('curlfft(%s)'%(label),datainfo[datatype]['len']) + +# ------------------------------------------ assemble header --------------------------------------- + + output = '%i\theader'%(headerlines+1) + '\n' + \ + ''.join(passOn) + \ + string.replace('$Id$','\n','\\n')+ '\t' + \ + ' '.join(sys.argv[1:]) + '\n' + \ + '\t'.join(headers + head) + '\n' # build extended header + +# ------------------------------------------ read value field --------------------------------------- + + idx = 0 + for line in data: + items = line.split()[:len(headers)] + if len(items) < len(headers): # skip too short lines (probably comments or invalid) + continue + locSkip = location(idx,resSkip) + if ( locSkip[0] < options.res[0] + and locSkip[1] < options.res[1] + and locSkip[2] < options.res[2] ): # only take values that are not periodic images + for datatype,labels in active.items(): + for label in labels: + values[datatype][label][locSkip[0]][locSkip[1]][locSkip[2]]\ + = numpy.reshape(items[column[datatype][label]: + column[datatype][label]+datainfo[datatype]['len']],(3,datainfo[datatype]['len']//3)) + idx += 1 + else: + for datatype,labels in active.items(): + for label in labels: + if label not in curl_field[datatype]: curl_field[datatype][label] = {} + curl_field[datatype][label] = numpy.array([0.0 for i in range((datainfo[datatype]['len'])*\ + options.res[0]*options.res[1]*options.res[2])]).\ + reshape(options.res[0],options.res[1],options.res[2],\ + 3,datainfo[datatype]['len']//3) + curl_field[datatype][label] = DAMASK.math.curl_fft(options.res,options.dim,datainfo[datatype]['len']//3,values[datatype][label]) + idx = 0 + for line in data: + items = line.split()[:len(headers)] + if len(items) < len(headers): + continue + + output += '\t'.join(items) + + for datatype,labels in active.items(): + for label in labels: + for i in range(3): + for j in range(datainfo[datatype]['len']//3): + output += '\t%f'%curl_field[datatype][label][location(idx,options.res)[0]][location(idx,options.res)[1]][location(idx,options.res)[2]][i][j] + output += '\n' + idx += 1 + + +# ------------------------------------------ output result --------------------------------------- + + if file['name'] == 'STDIN': + print output + else: + file['handle'] = open(file['name']+'_tmp','w') + try: + file['handle'].write(output) + file['handle'].close() + os.rename(file['name']+'_tmp',file['name']) + except: + print 'error during writing',file['name']+'_tmp' diff --git a/processing/setup/setup_processing.py b/processing/setup/setup_processing.py index f77cc0529..999dec934 100755 --- a/processing/setup/setup_processing.py +++ b/processing/setup/setup_processing.py @@ -76,6 +76,7 @@ bin_link = { \ 'addCalculation.py', 'addDeterminant.py', 'addDivergence.py', + 'addCurl.py', 'addMises.py', 'addNorm.py', 'addStrainTensors.py', @@ -111,7 +112,8 @@ execute = { \ '-c --fcompiler=%s '%(f2py_compiler) +\ '%s ' %(os.path.join(codeDir,'DAMASK2Python_helper.f90'))+\ '%s ' %(os.path.join(codeDir,'math.f90'))+\ - '%s ' %(os.path.join(damaskEnv.pathInfo['fftw'],'libfftw3.a'))+\ + '%s ' + %(os.path.join(damaskEnv.pathInfo['fftw'],'lib/libfftw3.a'))+\ '%s' %(os.path.join(damaskEnv.pathInfo['acml'],acml_subdir,'libacml.a')), 'mv %s %s' %(os.path.join(codeDir,'DAMASK.so'),damaskEnv.relPath('lib/')), ]