added addCurl.py, not sure if it works correctly. still in old (eq. to addDivergence.py) style

This commit is contained in:
Krishna Komerla 2011-12-21 17:25:31 +00:00
parent b12c6672d6
commit f463c2da70
4 changed files with 212 additions and 3 deletions

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@ -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

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@ -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

207
processing/post/addCurl.py Executable file
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@ -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'

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@ -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/')),
]