Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Philip Eisenlohr
commit
88809863ba
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@ -1,3 +1,4 @@
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.noH5py
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*.pyc
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*.mod
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*.o
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2
LICENSE
2
LICENSE
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@ -1,4 +1,4 @@
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Copyright 2011-16 Max-Planck-Institut für Eisenforschung GmbH
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Copyright 2011-17 Max-Planck-Institut für Eisenforschung GmbH
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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@ -1716,7 +1716,7 @@ subroutine lattice_initializeStructure(myPhase,CoverA,CoverA_trans,a_fcc,a_bcc)
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lattice_trans_C66(1:6,1:6,myPhase) = math_Mandel3333to66(lattice_trans_C3333(1:3,1:3,1:3,1:3,myPhase))
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do i = 1_pInt, 6_pInt
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if (abs(lattice_trans_C66(i,i,myPhase))<tol_math_check) &
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call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip"')
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call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip" in fcc-->bcc transformation')
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enddo
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case (LATTICE_hex_ID)
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c11bar = (lattice_C66(1,1,myPhase) + lattice_C66(1,2,myPhase) + 2.0_pReal*lattice_C66(4,4,myPhase))/2.0_pReal
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@ -1749,7 +1749,7 @@ subroutine lattice_initializeStructure(myPhase,CoverA,CoverA_trans,a_fcc,a_bcc)
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lattice_trans_C66(1:6,1:6,myPhase) = math_Mandel3333to66(lattice_trans_C3333(1:3,1:3,1:3,1:3,myPhase))
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do i = 1_pInt, 6_pInt
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if (abs(lattice_trans_C66(i,i,myPhase))<tol_math_check) &
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call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip"')
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call IO_error(135_pInt,el=i,ip=myPhase,ext_msg='matrix diagonal "el"ement of phase "ip" in fcc-->hex transformation')
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enddo
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end select
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end select
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@ -58,4 +58,4 @@ ask_delete=OFF
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# Remove the temporary names from the namespace
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del fortCmd
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del DAMASKVERSION
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@ -58,4 +58,4 @@ ask_delete=OFF
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# Remove the temporary names from the namespace
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del fortCmd
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del DAMASKVERSION
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@ -203,58 +203,63 @@ class Test():
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shutil.copy2(source,target)
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except:
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logging.critical('error copying {} to {}'.format(source,target))
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raise
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def copy_Reference2Current(self,sourcefiles=[],targetfiles=[]):
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if len(targetfiles) == 0: targetfiles = sourcefiles
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for i,file in enumerate(sourcefiles):
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
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shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Reference2Current: Unable to copy file "{}"'.format(file))
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logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
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raise
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def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
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source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
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if len(targetfiles) == 0: targetfiles = sourcefiles
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for i,file in enumerate(sourcefiles):
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(os.path.join(source,file),self.fileInCurrent(targetfiles[i]))
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shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
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except:
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logging.error(os.path.join(source,file))
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logging.critical('Base2Current: Unable to copy file "{}"'.format(file))
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logging.error(os.path.join(source,f))
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logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
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raise
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def copy_Current2Reference(self,sourcefiles=[],targetfiles=[]):
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if len(targetfiles) == 0: targetfiles = sourcefiles
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for i,file in enumerate(sourcefiles):
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInCurrent(file),self.fileInReference(targetfiles[i]))
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shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
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except:
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logging.critical('Current2Reference: Unable to copy file "{}"'.format(file))
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logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
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raise
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def copy_Proof2Current(self,sourcefiles=[],targetfiles=[]):
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if len(targetfiles) == 0: targetfiles = sourcefiles
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for i,file in enumerate(sourcefiles):
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInProof(file),self.fileInCurrent(targetfiles[i]))
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shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Proof2Current: Unable to copy file "{}"'.format(file))
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logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
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raise
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def copy_Current2Current(self,sourcefiles=[],targetfiles=[]):
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for i,file in enumerate(sourcefiles):
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for i,f in enumerate(sourcefiles):
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try:
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shutil.copy2(self.fileInReference(file),self.fileInCurrent(targetfiles[i]))
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shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
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except:
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logging.critical('Current2Current: Unable to copy file "{}"'.format(file))
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logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
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raise
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def execute_inCurrentDir(self,cmd,streamIn=None):
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@ -9,8 +9,6 @@ import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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oversampling = 2.
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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@ -50,14 +48,17 @@ parser.add_option( '--degrees', dest='degrees', action='store_true',
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help = 'angle is given in degrees [%default]')
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parser.add_option( '--nonperiodic', dest='periodic', action='store_false',
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help = 'wrap around edges [%default]')
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parser.add_option( '--voxelspace', dest='voxelspace', action='store_true',
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help = '-c and -d are given in (0 to grid) coordinates instead of (origin to origin+size) \
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coordinates [%default]')
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parser.set_defaults(center = [0,0,0],
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fill = 0,
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quaternion = [],
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angleaxis = [],
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degrees = False,
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exponent = [1e10,1e10,1e10], # box shape by default
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periodic = True
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periodic = True,
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voxelspace = False
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)
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(options, filenames) = parser.parse_args()
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@ -73,6 +74,7 @@ else:
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rotation = damask.Quaternion()
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options.center = np.array(options.center)
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options.dimension = np.array(options.dimension)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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@ -119,36 +121,64 @@ for name in filenames:
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# If we have a negative dimension, make it an ellipsoid for backwards compatibility
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options.exponent = np.where(np.array(options.dimension) > 0, options.exponent, 2)
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microstructure = microstructure.reshape(info['grid'],order='F')
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# coordinates given in real space (default) vs voxel space
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if not options.voxelspace:
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options.center += info['origin']
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options.center *= np.array(info['grid']) / np.array(info['size'])
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options.dimension *= np.array(info['grid']) / np.array(info['size'])
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size = microstructure.shape
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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if options.periodic: # use padding to achieve periodicity
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(X, Y, Z) = np.meshgrid(np.arange(-size[0]/2, (3*size[0])/2, dtype=np.float32), # 50% padding on each side
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np.arange(-size[1]/2, (3*size[1])/2, dtype=np.float32),
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np.arange(-size[2]/2, (3*size[2])/2, dtype=np.float32),
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indexing='ij')
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# Padding handling
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X = np.roll(np.roll(np.roll(X,
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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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Y = np.roll(np.roll(np.roll(Y,
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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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Z = np.roll(np.roll(np.roll(Z,
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-size[0]/2, axis=0),
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-size[1]/2, axis=1),
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-size[2]/2, axis=2)
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else: # nonperiodic, much lighter on resources
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(Y, X, Z) = np.meshgrid(np.arange(-size[0], 2*size[0], dtype=np.float64),
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np.arange(-size[1], 2*size[1], dtype=np.float64),
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np.arange(-size[2], 2*size[2], dtype=np.float64))
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# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
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X -= options.center[0] - 0.5
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Y -= options.center[1] - 0.5
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Z -= options.center[2] - 0.5
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# and then by applying the quaternion
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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(X, Y, Z) = rotation * (X, Y, Z)
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# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
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X /= options.dimension[0] * 0.5
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Y /= options.dimension[1] * 0.5
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Z /= options.dimension[2] * 0.5
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(X, Y, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float32),
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np.arange(0, size[1], dtype=np.float32),
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np.arange(0, size[2], dtype=np.float32),
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indexing='ij')
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# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
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old_settings = np.seterr()
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np.seterr(over='ignore', under='ignore')
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# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
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X -= options.center[0] - 0.5
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Y -= options.center[1] - 0.5
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Z -= options.center[2] - 0.5
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# and then by applying the quaternion
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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(X, Y, Z) = rotation * (X, Y, Z)
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# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
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X /= options.dimension[0] * 0.5
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Y /= options.dimension[1] * 0.5
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Z /= options.dimension[2] * 0.5
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# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
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old_settings = np.seterr()
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np.seterr(over='ignore', under='ignore')
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if options.periodic: # use padding to achieve periodicity
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inside = np.zeros(size, dtype=bool)
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for i in range(3):
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for j in range(3):
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for k in range(3):
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for i in range(2):
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for j in range(2):
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for k in range(2):
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inside = inside | ( # Most of this is handling the padding
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np.abs(X[size[0] * i : size[0] * (i+1),
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size[1] * j : size[1] * (j+1),
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@ -161,33 +191,13 @@ for name in filenames:
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size[2] * k : size[2] * (k+1)])**options.exponent[2] < 1)
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microstructure = np.where(inside, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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else: # nonperiodic, much lighter on resources
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# change to coordinate space where the primitive is the unit sphere/cube/etc
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(Y, X, Z) = np.meshgrid(np.arange(0, size[0], dtype=np.float64),
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np.arange(0, size[1], dtype=np.float64),
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np.arange(0, size[2], dtype=np.float64))
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# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
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X -= options.center[0] - 0.5
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Y -= options.center[1] - 0.5
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Z -= options.center[2] - 0.5
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# and then by applying the quaternion (the implementation of quat. does q*v*q.conj)
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# this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
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(X, Y, Z) = rotation * (X, Y, Z)
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# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
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X /= options.dimension[0] * 0.5
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Y /= options.dimension[1] * 0.5
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Z /= options.dimension[2] * 0.5
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# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
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old_settings = np.seterr()
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np.seterr(over='ignore', under='ignore')
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microstructure = np.where(np.abs(X)**options.exponent[0] +
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np.abs(Y)**options.exponent[1] +
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np.abs(Z)**options.exponent[2] < 1, options.fill, microstructure)
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np.seterr(**old_settings) # Reset warnings to old state
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np.seterr(**old_settings) # Reset warnings to old state
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newInfo['microstructures'] = microstructure.max()
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# --- report ---------------------------------------------------------------------------------------
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