added addCurl.py, not sure if it works correctly. still in old (eq. to addDivergence.py) style
This commit is contained in:
Krishna Komerla
parent
b12c6672d6
commit
f463c2da70
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@ -75,7 +75,7 @@ python module DAMASK ! in
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complex*16, dimension(res[0],res[1],res[2],3,3), depend(res[0],res[1],res[2]) :: defgrad_fft
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complex*16, dimension(res[0],res[1],res[2],3,3), depend(res[0],res[1],res[2]) :: defgrad_fft
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end subroutine deformed_fft
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end subroutine deformed_fft
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subroutine curl_fft(res,geomdim,vec_tens,field,curl_fft) ! in :math:math.f90
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subroutine curl_fft(res,geomdim,vec_tens,field,curl_field) ! in :math:math.f90
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! input variables
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! input variables
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integer, dimension(3), intent(in) :: res
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integer, dimension(3), intent(in) :: res
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real*8, dimension(3), intent(in) :: geomdim
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real*8, dimension(3), intent(in) :: geomdim
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@ -1,6 +1,6 @@
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# possible options are MSC, FFTW, IKML, ACML, LAPACK
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# possible options are MSC, FFTW, IKML, ACML, LAPACK
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#ACML /opt/acml5.0.0
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ACML /opt/acml4.4.0
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LAPACK /usr
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LAPACK /usr
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FFTW ./fftw
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FFTW ./fftw
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MSC /msc
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MSC /msc
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@ -0,0 +1,207 @@
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#!/usr/bin/python
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import os,re,sys,math,string,numpy,DAMASK
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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def location(idx,res):
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return ( idx % res[0], \
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(idx // res[0]) % res[1], \
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(idx // res[0] // res[1]) % res[2] )
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def index(location,res):
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return ( location[0] % res[0] + \
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(location[1] % res[1]) * res[0] + \
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(location[2] % res[2]) * res[0] * res[1] )
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def prefixMultiply(what,len):
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return {True: ['%i_%s'%(i+1,what) for i in range(len)],
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False:[what]}[len>1]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing curl of requested column(s).
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Operates on periodic ordered three-dimensional data sets.
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Deals with both vector- and tensor-valued fields.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-v','--vector', dest='vector', action='extend', type='string', \
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help='heading of columns containing vector field values')
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parser.add_option('-t','--tensor', dest='tensor', action='extend', type='string', \
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help='heading of columns containing tensor field values')
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parser.add_option('-d','--dimension', dest='dim', type='float', nargs=3, \
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help='physical dimension of data set in x (fast) y z (slow) [%default]')
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parser.add_option('-r','--resolution', dest='res', type='int', nargs=3, \
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help='resolution of data set in x (fast) y z (slow)')
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parser.set_defaults(vector = [])
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parser.set_defaults(tensor = [])
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parser.set_defaults(dim = [])
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parser.set_defaults(skip = [0,0,0])
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(options,filenames) = parser.parse_args()
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if len(options.vector) + len(options.tensor) == 0:
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parser.error('no data column specified...')
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if len(options.dim) < 3:
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parser.error('improper dimension specification...')
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if not options.res or len(options.res) < 3:
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parser.error('improper resolution specification...')
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resSkip = map(lambda (a,b): a+b,zip(options.res,options.skip))
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datainfo = { # list of requested labels per datatype
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'vector': {'len':3,
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'label':[]},
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'tensor': {'len':9,
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'label':[]},
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}
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if options.vector != None: datainfo['vector']['label'] += options.vector
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if options.tensor != None: datainfo['tensor']['label'] += options.tensor
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'handle':sys.stdin})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'handle':open(name)})
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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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content = file['handle'].readlines()
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file['handle'].close()
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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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headerlines = 1
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m = re.search('(\d+)\s*head', content[0].lower())
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if m:
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headerlines = int(m.group(1))
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passOn = content[1:headerlines]
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headers = content[headerlines].split()
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data = content[headerlines+1:]
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regexp = re.compile('1_\d+_')
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for i,l in enumerate(headers):
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if regexp.match(l):
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headers[i] = l[2:]
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active = {}
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column = {}
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values = {}
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curl_field ={}
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head = []
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for datatype,info in datainfo.items():
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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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print 'column %s not found...'%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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if datatype not in values: values[datatype] = {}
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if datatype not in curl_field: curl_field[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = headers.index(key)
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values[datatype][label] = numpy.array([0.0 for i in xrange(datainfo[datatype]['len']*\
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options.res[0]*options.res[1]*options.res[2])]).\
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reshape((options.res[0],options.res[1],options.res[2],\
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3,datainfo[datatype]['len']//3))
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head += prefixMultiply('curlfft(%s)'%(label),datainfo[datatype]['len'])
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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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# ------------------------------------------ read value field ---------------------------------------
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idx = 0
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for line in data:
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items = line.split()[:len(headers)]
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if len(items) < len(headers): # skip too short lines (probably comments or invalid)
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continue
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locSkip = location(idx,resSkip)
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if ( locSkip[0] < options.res[0]
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and locSkip[1] < options.res[1]
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and locSkip[2] < options.res[2] ): # only take values that are not periodic images
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for datatype,labels in active.items():
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for label in labels:
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values[datatype][label][locSkip[0]][locSkip[1]][locSkip[2]]\
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= numpy.reshape(items[column[datatype][label]:
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column[datatype][label]+datainfo[datatype]['len']],(3,datainfo[datatype]['len']//3))
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idx += 1
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else:
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for datatype,labels in active.items():
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for label in labels:
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if label not in curl_field[datatype]: curl_field[datatype][label] = {}
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curl_field[datatype][label] = numpy.array([0.0 for i in range((datainfo[datatype]['len'])*\
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options.res[0]*options.res[1]*options.res[2])]).\
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reshape(options.res[0],options.res[1],options.res[2],\
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3,datainfo[datatype]['len']//3)
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curl_field[datatype][label] = DAMASK.math.curl_fft(options.res,options.dim,datainfo[datatype]['len']//3,values[datatype][label])
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idx = 0
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for line in data:
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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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output += '\t'.join(items)
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for datatype,labels in active.items():
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for label in labels:
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for i in range(3):
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for j in range(datainfo[datatype]['len']//3):
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output += '\t%f'%curl_field[datatype][label][location(idx,options.res)[0]][location(idx,options.res)[1]][location(idx,options.res)[2]][i][j]
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output += '\n'
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idx += 1
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# ------------------------------------------ output result ---------------------------------------
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if file['name'] == 'STDIN':
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print output
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else:
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file['handle'] = open(file['name']+'_tmp','w')
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try:
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file['handle'].write(output)
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file['handle'].close()
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os.rename(file['name']+'_tmp',file['name'])
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except:
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print 'error during writing',file['name']+'_tmp'
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@ -76,6 +76,7 @@ bin_link = { \
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'addCalculation.py',
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'addCalculation.py',
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'addDeterminant.py',
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'addDeterminant.py',
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'addDivergence.py',
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'addDivergence.py',
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'addCurl.py',
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'addMises.py',
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'addMises.py',
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'addNorm.py',
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'addNorm.py',
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'addStrainTensors.py',
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'addStrainTensors.py',
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@ -111,7 +112,8 @@ execute = { \
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'-c --fcompiler=%s '%(f2py_compiler) +\
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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,'DAMASK2Python_helper.f90'))+\
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'%s ' %(os.path.join(codeDir,'math.f90'))+\
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'%s ' %(os.path.join(codeDir,'math.f90'))+\
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'%s ' %(os.path.join(damaskEnv.pathInfo['fftw'],'libfftw3.a'))+\
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'%s '
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%(os.path.join(damaskEnv.pathInfo['fftw'],'lib/libfftw3.a'))+\
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'%s' %(os.path.join(damaskEnv.pathInfo['acml'],acml_subdir,'libacml.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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'mv %s %s' %(os.path.join(codeDir,'DAMASK.so'),damaskEnv.relPath('lib/')),
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]
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]
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