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DAMASK_EICMD
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Merge remote-tracking branch 'refs/remotes/origin/development' 

Conflicts:
	lib/damask/test/test.py
This commit is contained in:
Philip Eisenlohr 2016-09-04 18:49:49 -04:00
parent cde7de4e9f 6ea7eeee08
commit 6f843ce85b
4 changed files with 82 additions and 67 deletions
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1
code/math.f90
View File

@ -178,7 +178,6 @@ subroutine math_init
use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment) use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
use prec, only: tol_math_check use prec, only: tol_math_check
use numerics, only: & use numerics, only: &
worldrank, &
fixedSeed fixedSeed
use IO, only: IO_error, IO_timeStamp use IO, only: IO_error, IO_timeStamp

107
lib/damask/test/test.py
View File

@ -93,10 +93,9 @@ class Test():
def feasible(self): def feasible(self):
"""Check whether test is possible or not (e.g. no license available).""" """Check whether test is possible or not (e.g. no license available)."""
return True return True
def clean(self): def clean(self):
"""Delete directory tree containing current results.""" """Delete directory tree containing current results."""
try: try:
shutil.rmtree(self.dirCurrent()) shutil.rmtree(self.dirCurrent())
except: except:
@ -116,7 +115,7 @@ class Test():
def prepare(self,variant): def prepare(self,variant):
"""Do all necessary preparations for the run of each test variant""" """Do all necessary preparations for the run of each test variant"""
return True return True
def run(self,variant): def run(self,variant):
"""Execute the requested test variant.""" """Execute the requested test variant."""
@ -148,17 +147,17 @@ class Test():
"""Directory containing current results of the test.""" """Directory containing current results of the test."""
return os.path.normpath(os.path.join(self.dirBase,'current/')) return os.path.normpath(os.path.join(self.dirBase,'current/'))
def dirProof(self): def dirProof(self):
"""Directory containing human readable proof of correctness for the test.""" """Directory containing human readable proof of correctness for the test."""
return os.path.normpath(os.path.join(self.dirBase,'proof/')) return os.path.normpath(os.path.join(self.dirBase,'proof/'))
def fileInRoot(self,dir,file): def fileInRoot(self,dir,file):
"""Path to a file in the root directory of DAMASK.""" """Path to a file in the root directory of DAMASK."""
return os.path.join(damask.Environment().rootDir(),dir,file) return os.path.join(damask.Environment().rootDir(),dir,file)
def fileInReference(self,file): def fileInReference(self,file):
"""Path to a file in the refrence directory for the test.""" """Path to a file in the refrence directory for the test."""
return os.path.join(self.dirReference(),file) return os.path.join(self.dirReference(),file)
@ -168,7 +167,7 @@ class Test():
"""Path to a file in the current results directory for the test.""" """Path to a file in the current results directory for the test."""
return os.path.join(self.dirCurrent(),file) return os.path.join(self.dirCurrent(),file)
def fileInProof(self,file): def fileInProof(self,file):
"""Path to a file in the proof directory for the test.""" """Path to a file in the proof directory for the test."""
return os.path.join(self.dirProof(),file) return os.path.join(self.dirProof(),file)
@ -185,58 +184,58 @@ class Test():
for source,target in zip(map(mapA,A),map(mapB,B)): for source,target in zip(map(mapA,A),map(mapB,B)):
try: try:
shutil.copy2(source,target) shutil.copy2(source,target)
except: except:
logging.critical('error copying {} to {}'.format(source,target)) logging.critical('error copying {} to {}'.format(source,target))
def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]): def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Reference2Current: Unable to copy file "{}"'.format(file)) logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]): def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir)) source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
if len(targetfiles) == 0: targetfiles = sourcefiles if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i])) shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.error(os.path.join(source,file)) logging.error(os.path.join(source,file))
logging.critical('Base2Current: Unable to copy file "{}"'.format(file)) logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]): def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i])) shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
except: except:
logging.critical('Current2Reference: Unable to copy file "{}"'.format(file)) logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]): def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
if len(targetfiles) == 0: targetfiles = sourcefiles if len(targetfiles) == 0: targetfiles = sourcefiles
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Proof2Current: Unable to copy file "{}"'.format(file)) logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
def copy_Current2Current(self,sourcefiles=[],targetfiles=[]): def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
for i,file in enumerate(sourcefiles): for i,file in enumerate(sourcefiles):
try: try:
shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i])) shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
except: except:
logging.critical('Current2Current: Unable to copy file "{}"'.format(file)) logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
@ -248,11 +247,11 @@ class Test():
logging.info(error) logging.info(error)
logging.debug(out) logging.debug(out)
return out,error
return out,error
def compare_Array(self,File1,File2): def compare_Array(self,File1,File2):
import numpy as np import numpy as np
@ -283,28 +282,28 @@ class Test():
def compare_ArrayRefCur(self,ref,cur=''): def compare_ArrayRefCur(self,ref,cur=''):
if cur =='': cur = ref if cur =='': cur = ref
refName = self.fileInReference(ref) refName = self.fileInReference(ref)
curName = self.fileInCurrent(cur) curName = self.fileInCurrent(cur)
return self.compare_Array(refName,curName) return self.compare_Array(refName,curName)
def compare_ArrayCurCur(self,cur0,cur1): def compare_ArrayCurCur(self,cur0,cur1):
cur0Name = self.fileInCurrent(cur0) cur0Name = self.fileInCurrent(cur0)
cur1Name = self.fileInCurrent(cur1) cur1Name = self.fileInCurrent(cur1)
return self.compare_Array(cur0Name,cur1Name) return self.compare_Array(cur0Name,cur1Name)
def compare_Table(self,headings0,file0,headings1,file1,normHeadings='',normType=None, def compare_Table(self,headings0,file0,headings1,file1,normHeadings='',normType=None,
absoluteTolerance=False,perLine=False,skipLines=[]): absoluteTolerance=False,perLine=False,skipLines=[]):
import numpy as np import numpy as np
logging.info('\n '.join(['comparing ASCII Tables',file0,file1])) logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
if normHeadings == '': normHeadings = headings0 if normHeadings == '': normHeadings = headings0
# check if comparison is possible and determine lenght of columns # check if comparison is possible and determine lenght of columns
if len(headings0) == len(headings1) == len(normHeadings): if len(headings0) == len(headings1) == len(normHeadings):
dataLength = len(headings0) dataLength = len(headings0)
length = [1 for i in xrange(dataLength)] length = [1 for i in xrange(dataLength)]
shape = [[] for i in xrange(dataLength)] shape = [[] for i in xrange(dataLength)]
@ -312,14 +311,14 @@ class Test():
maxError = [0.0 for i in xrange(dataLength)] maxError = [0.0 for i in xrange(dataLength)]
absTol = [absoluteTolerance for i in xrange(dataLength)] absTol = [absoluteTolerance for i in xrange(dataLength)]
column = [[1 for i in xrange(dataLength)] for j in xrange(2)] column = [[1 for i in xrange(dataLength)] for j in xrange(2)]
norm = [[] for i in xrange(dataLength)] norm = [[] for i in xrange(dataLength)]
normLength = [1 for i in xrange(dataLength)] normLength = [1 for i in xrange(dataLength)]
normShape = [[] for i in xrange(dataLength)] normShape = [[] for i in xrange(dataLength)]
normColumn = [1 for i in xrange(dataLength)] normColumn = [1 for i in xrange(dataLength)]
for i in xrange(dataLength): for i in xrange(dataLength):
if headings0[i]['shape'] != headings1[i]['shape']: if headings0[i]['shape'] != headings1[i]['shape']:
raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label'])) raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
shape[i] = headings0[i]['shape'] shape[i] = headings0[i]['shape']
for j in xrange(np.shape(shape[i])[0]): for j in xrange(np.shape(shape[i])[0]):
@ -335,7 +334,7 @@ class Test():
table0 = damask.ASCIItable(name=file0,readonly=True) table0 = damask.ASCIItable(name=file0,readonly=True)
table0.head_read() table0.head_read()
table1 = damask.ASCIItable(name=file1,readonly=True) table1 = damask.ASCIItable(name=file1,readonly=True)
table1.head_read() table1.head_read()
for i in xrange(dataLength): for i in xrange(dataLength):
key0 = ('1_' if length[i]>1 else '') + headings0[i]['label'] key0 = ('1_' if length[i]>1 else '') + headings0[i]['label']
@ -351,7 +350,7 @@ class Test():
column[0][i] = table0.label_index(key0) column[0][i] = table0.label_index(key0)
column[1][i] = table1.label_index(key1) column[1][i] = table1.label_index(key1)
normColumn[i] = table0.label_index(normKey) normColumn[i] = table0.label_index(normKey)
line0 = 0 line0 = 0
while table0.data_read(): # read next data line of ASCII table while table0.data_read(): # read next data line of ASCII table
if line0 not in skipLines: if line0 not in skipLines:
@ -366,7 +365,7 @@ class Test():
else: else:
norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType)) norm[i] = np.append(norm[i],np.linalg.norm(np.reshape(normData,normShape[i]),normType))
line0 += 1 line0 += 1
for i in xrange(dataLength): for i in xrange(dataLength):
if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))] if not perLine: norm[i] = [np.max(norm[i]) for j in xrange(line0-len(skipLines))]
data[i] = np.reshape(data[i],[line0-len(skipLines),length[i]]) data[i] = np.reshape(data[i],[line0-len(skipLines),length[i]])
@ -437,14 +436,14 @@ class Test():
logging.info(files[i]+':'+','.join(columns[i])) logging.info(files[i]+':'+','.join(columns[i]))
if len(files) < 2: return True # single table is always close to itself... if len(files) < 2: return True # single table is always close to itself...
data = [] data = []
for table,labels in zip(tables,columns): for table,labels in zip(tables,columns):
table.data_readArray(labels) table.data_readArray(labels)
data.append(table.data) data.append(table.data)
table.close() table.close()
for i in xrange(1,len(data)): for i in xrange(1,len(data)):
delta = data[i]-data[i-1] delta = data[i]-data[i-1]
normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5 normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5
@ -453,7 +452,7 @@ class Test():
std = np.amax(np.std(normedDelta,0)) std = np.amax(np.std(normedDelta,0))
logging.info('mean: {:f}'.format(mean)) logging.info('mean: {:f}'.format(mean))
logging.info('std: {:f}'.format(std)) logging.info('std: {:f}'.format(std))
return (mean<meanTol) & (std < stdTol) return (mean<meanTol) & (std < stdTol)
@ -525,10 +524,10 @@ class Test():
return allclose return allclose
def compare_TableRefCur(self,headingsRef,ref,headingsCur='',cur='',normHeadings='',normType=None,\ def compare_TableRefCur(self,headingsRef,ref,headingsCur='',cur='',normHeadings='',normType=None,\
absoluteTolerance=False,perLine=False,skipLines=[]): absoluteTolerance=False,perLine=False,skipLines=[]):
if cur == '': cur = ref if cur == '': cur = ref
if headingsCur == '': headingsCur = headingsRef if headingsCur == '': headingsCur = headingsRef
refName = self.fileInReference(ref) refName = self.fileInReference(ref)
@ -536,10 +535,10 @@ class Test():
return self.compare_Table(headingsRef,refName,headingsCur,curName,normHeadings,normType, return self.compare_Table(headingsRef,refName,headingsCur,curName,normHeadings,normType,
absoluteTolerance,perLine,skipLines) absoluteTolerance,perLine,skipLines)
def compare_TableCurCur(self,headingsCur0,Cur0,Cur1,headingsCur1='',normHeadings='',normType=None,\ def compare_TableCurCur(self,headingsCur0,Cur0,Cur1,headingsCur1='',normHeadings='',normType=None,\
absoluteTolerance=False,perLine=False,skipLines=[]): absoluteTolerance=False,perLine=False,skipLines=[]):
if headingsCur1 == '': headingsCur1 = headingsCur0 if headingsCur1 == '': headingsCur1 = headingsCur0
cur0Name = self.fileInCurrent(Cur0) cur0Name = self.fileInCurrent(Cur0)
cur1Name = self.fileInCurrent(Cur1) cur1Name = self.fileInCurrent(Cur1)
@ -548,15 +547,17 @@ class Test():
def report_Success(self,culprit): def report_Success(self,culprit):
ret = culprit
if culprit == 0: if culprit == 0:
logging.critical(('The test' if len(self.variants) == 1 else 'All {} tests'.format(len(self.variants))) + ' passed') msg = 'The test passed' if len(self.variants) == 1 \
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n') else 'All {} tests passed.'.format(len(self.variants))
return 0 elif culprit == -1:
if culprit == -1: msg = 'Warning: Could not start test...'
logging.warning('Warning: Could not start test') ret = 0
return 0
else: else:
logging.critical(' ********\n * Test {} failed...\n ********'.format(culprit)) msg = ' * Test "{}" failed.'.format(self.variants[culprit-1])
logging.critical('\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n')
return culprit logging.critical('\n'.join(['*'*40,msg,'*'*40]) + '\n')
return ret

14
processing/post/vtk_addPointcloudData.py
View File

@ -3,6 +3,7 @@
import os,vtk import os,vtk
import damask import damask
import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
@ -131,11 +132,14 @@ for name in filenames:
for datatype,labels in active.items(): # loop over scalar,color for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings theData = [float(table.data[i]) for i in table.label_indexrange(me)] # read strings
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*x),theData))
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData)) elif datatype == 'scalar': VTKarray[me].InsertNextValue(theData[0])
elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*map(float,theData)) elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*theData)
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0])) elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
np.array(theData) \
.reshape(3,3).T \
.reshape(9)))
table.input_close() # close input ASCII table table.input_close() # close input ASCII table

27
processing/post/vtk_addRectilinearGridData.py
View File

@ -3,6 +3,7 @@
import os,vtk import os,vtk
import damask import damask
import numpy as np
from collections import defaultdict from collections import defaultdict
from optparse import OptionParser from optparse import OptionParser
@ -38,6 +39,10 @@ parser.add_option('-v', '--vector',
dest = 'vector', dest = 'vector',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'vector value label(s)') help = 'vector value label(s)')
parser.add_option('-t', '--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color', parser.add_option('-c', '--color',
dest = 'color', dest = 'color',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
@ -45,6 +50,7 @@ parser.add_option('-c', '--color',
parser.set_defaults(scalar = [], parser.set_defaults(scalar = [],
vector = [], vector = [],
tensor = [],
color = [], color = [],
inplace = False, inplace = False,
render = False, render = False,
@ -92,9 +98,10 @@ for name in filenames:
errors = [] errors = []
VTKarray = {} VTKarray = {}
active = defaultdict(list) active = defaultdict(list)
for datatype,dimension,label in [['scalar',1,options.scalar], for datatype,dimension,label in [['scalar',1,options.scalar],
['vector',3,options.vector], ['vector',3,options.vector],
['tensor',9,options.tensor],
['color',3,options.color], ['color',3,options.color],
]: ]:
for i,dim in enumerate(table.label_dimension(label)): for i,dim in enumerate(table.label_dimension(label)):
@ -105,7 +112,7 @@ for name in filenames:
remarks.append('adding {} "{}"...'.format(datatype,me)) remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me) active[datatype].append(me)
if datatype in ['scalar','vector']: VTKarray[me] = vtk.vtkDoubleArray() if datatype in ['scalar','vector','tensor']: VTKarray[me] = vtk.vtkDoubleArray()
elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray() elif datatype == 'color': VTKarray[me] = vtk.vtkUnsignedCharArray()
VTKarray[me].SetNumberOfComponents(dimension) VTKarray[me].SetNumberOfComponents(dimension)
@ -117,7 +124,7 @@ for name in filenames:
table.close(dismiss = True) table.close(dismiss = True)
continue continue
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ---------------------------------------
datacount = 0 datacount = 0
@ -128,12 +135,16 @@ for name in filenames:
for me in labels: # loop over all requested items for me in labels: # loop over all requested items
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData)) if datatype == 'color': VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData))
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0])) elif datatype == 'scalar': VTKarray[me].InsertNextValue(float(theData[0]))
elif datatype == 'vector': VTKarray[me].InsertNextTuple3(*map(float,theData))
elif datatype == 'tensor': VTKarray[me].InsertNextTuple9(*0.5*(np.array(theData)+
np.array(theData) \
.reshape(3,3).T \
.reshape(9)))
table.close() # close input ASCII table table.close() # close input ASCII table
# ------------------------------------------ add data --------------------------------------- # ------------------------------------------ add data ---------------------------------------
if datacount == Npoints: mode = 'point' if datacount == Npoints: mode = 'point'
elif datacount == Ncells: mode = 'cell' elif datacount == Ncells: mode = 'cell'
@ -154,7 +165,7 @@ for name in filenames:
rGrid.Modified() rGrid.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update() if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update()
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result ---------------------------------------
writer = vtk.vtkXMLRectilinearGridWriter() writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetDataModeToBinary() writer.SetDataModeToBinary()
@ -164,7 +175,7 @@ for name in filenames:
else: writer.SetInputData(rGrid) else: writer.SetInputData(rGrid)
writer.Write() writer.Write()
# ------------------------------------------ render result --------------------------------------- # ------------------------------------------ render result ---------------------------------------
if options.render: if options.render:
mapper = vtk.vtkDataSetMapper() mapper = vtk.vtkDataSetMapper()
@ -188,7 +199,7 @@ if options.render:
iren = vtk.vtkRenderWindowInteractor() iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin) iren.SetRenderWindow(renWin)
iren.Initialize() iren.Initialize()
renWin.Render() renWin.Render()
iren.Start() iren.Start()