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
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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'
|
||||
|
|
@ -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/')),
|
||||
]
|
||||
|
|
|
|||
Loading…
Reference in New Issue