Merge branch 'modernize-testing' into 'development'

Modernize testing

See merge request damask/DAMASK!289

.gitlab-ci.yml

@@ -2,14 +2,10 @@
 stages:
   - prepareAll
   - python
-  - preprocessing
+  - deprecated
-  - postprocessing
+  - compile
-  - compilePETSc
-  - prepareGrid
   - grid
-  - compileMarc
   - marc
-  - example
   - performance
   - createPackage
   - createDocumentation
@@ -111,71 +107,70 @@ Pytest_python:
 
 ###################################################################################################
 Pre_SeedGeneration:
-  stage: preprocessing
+  stage: deprecated
   script: PreProcessing_SeedGeneration/test.py
   except:
     - master
     - release
 
 Pre_GeomGeneration:
-  stage: preprocessing
+  stage: deprecated
   script: PreProcessing_GeomGeneration/test.py
   except:
     - master
     - release
 
 Pre_GeomModification:
-  stage: preprocessing
+  stage: deprecated
   script: PreProcessing_GeomModification/test.py
   except:
     - master
     - release
 
 Pre_General:
-  stage: preprocessing
+  stage: deprecated
   script: PreProcessing/test.py
   except:
     - master
     - release
 
-###################################################################################################
 Post_General:
-  stage: postprocessing
+  stage: deprecated
   script: PostProcessing/test.py
   except:
     - master
     - release
 
 Post_GeometryReconstruction:
-  stage: postprocessing
+  stage: deprecated
   script: spectral_geometryReconstruction/test.py
   except:
     - master
     - release
 
 Post_addCurl:
-  stage: postprocessing
+  stage: deprecated
   script: addCurl/test.py
   except:
     - master
     - release
 
 Post_addDivergence:
-  stage: postprocessing
+  stage: deprecated
   script: addDivergence/test.py
   except:
     - master
     - release
 
 Post_addGradient:
-  stage: postprocessing
+  stage: deprecated
   script: addGradient/test.py
   except:
     - master
     - release
 
 Post_OrientationAverageMisorientation:
-  stage: postprocessing
+  stage: deprecated
   script:
     - OrientationAverageMisorientation/test.py
   except:
@@ -183,8 +178,8 @@ Post_OrientationAverageMisorientation:
     - release
 
 ###################################################################################################
-grid_mech_compile_Intel:
+compile_grid_Intel:
-  stage: compilePETSc
+  stage: compile
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd pytest
@@ -193,8 +188,8 @@ grid_mech_compile_Intel:
     - master
     - release
 
-Compile_FEM_Intel:
+compile_mesh_Intel:
-  stage: compilePETSc
+  stage: compile
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
     - cd pytest
@@ -203,8 +198,8 @@ Compile_FEM_Intel:
     - master
     - release
 
-grid_mech_compile_GNU:
+compile_grid_GNU:
-  stage: compilePETSc
+  stage: compile
   script:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
     - cd pytest
@@ -213,8 +208,8 @@ grid_mech_compile_GNU:
     - master
     - release
 
-Compile_FEM_GNU:
+compile_mesh_GNU:
-  stage: compilePETSc
+  stage: compile
   script:
     - module load $GNUCompiler $MPICH_GNU $PETSc_MPICH_GNU
     - cd pytest
@@ -223,13 +218,36 @@ Compile_FEM_GNU:
     - master
     - release
 
-###################################################################################################
+compile_MARC:
-Compile_Intel_Prepare:
+  stage: compile
-  stage: prepareGrid
+  script:
+    - module load $IntelMarc $HDF5Marc $MSC
+    - cd pytest
+    - pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
+  except:
+    - master
+    - release
+
+setup_grid:
+  stage: compile
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
-    - cd $DAMASKROOT
+    - BUILD_DIR=$(mktemp -d)
-    - make clean grid processing
+    - cd ${BUILD_DIR}
+    - cmake -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${DAMASKROOT} ${DAMASKROOT}
+    - make -j2 all install
+  except:
+    - master
+    - release
+
+setup_mesh:
+  stage: compile
+  script:
+    - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel
+    - BUILD_DIR=$(mktemp -d)
+    - cd ${BUILD_DIR}
+    - cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${DAMASKROOT} ${DAMASKROOT}
+    - make -j2 all install
   except:
     - master
     - release
@@ -252,13 +270,6 @@ Thermal:
     - master
     - release
 
-grid_parsingArguments:
-  stage: grid
-  script: grid_parsingArguments/test.py
-  except:
-    - master
-    - release
-
 Nonlocal_Damage_DetectChanges:
   stage: grid
   script: Nonlocal_Damage_DetectChanges/test.py
@@ -280,16 +291,6 @@ Phenopowerlaw_singleSlip:
     - master
     - release
 
-###################################################################################################
-Marc_compileIfort:
-  stage: compileMarc
-  script:
-    - module load $IntelMarc $HDF5Marc $MSC
-    - cd pytest
-    - pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
-  except:
-    - master
-    - release
 
 ###################################################################################################
 Hex_elastic:
@@ -337,14 +338,6 @@ Marc_elementLib:
     - master
     - release
 
-###################################################################################################
-grid_all_example:
-  stage: example
-  script: grid_all_example/test.py
-  except:
-    - master
-    - release
-
 ###################################################################################################
 SpectralRuntime:
   stage: performance

PRIVATE

@@ -1 +1 @@
-Subproject commit 8bd09b5511d1e0e0ea288b47d16ce4924d75adcd
+Subproject commit a6be226f2ab08cfa44adabf37168f4d952d6174f

processing/post/addCompatibilityMismatch.py

@@ -13,85 +13,6 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-def volTetrahedron(coords):
-  """
-  Return the volume of the tetrahedron with given vertices or sides.
-
-  If vertices are given they must be in a NumPy array with shape (4,3): the
-  position vectors of the 4 vertices in 3 dimensions; if the six sides are
-  given, they must be an array of length 6. If both are given, the sides
-  will be used in the calculation.
-
-  This method implements
-  Tartaglia's formula using the Cayley-Menger determinant:
-              |0   1    1    1    1  |
-              |1   0   s1^2 s2^2 s3^2|
-    288 V^2 = |1  s1^2  0   s4^2 s5^2|
-              |1  s2^2 s4^2  0   s6^2|
-              |1  s3^2 s5^2 s6^2  0  |
-  where s1, s2, ..., s6 are the tetrahedron side lengths.
-
-  from http://codereview.stackexchange.com/questions/77593/calculating-the-volume-of-a-tetrahedron
-  """
-  # The indexes of rows in the vertices array corresponding to all
-  # possible pairs of vertices
-  vertex_pair_indexes = np.array(((0, 1), (0, 2), (0, 3),
-                                  (1, 2), (1, 3), (2, 3)))
-
-  # Get all the squares of all side lengths from the differences between
-  # the 6 different pairs of vertex positions
-  vertices =  np.concatenate((coords[0],coords[1],coords[2],coords[3])).reshape(4,3)
-  vertex1, vertex2 = vertex_pair_indexes[:,0], vertex_pair_indexes[:,1]
-  sides_squared = np.sum((vertices[vertex1] - vertices[vertex2])**2,axis=-1)
-
-
-  # Set up the Cayley-Menger determinant
-  M = np.zeros((5,5))
-  # Fill in the upper triangle of the matrix
-  M[0,1:] = 1
-  # The squared-side length elements can be indexed using the vertex
-  # pair indices (compare with the determinant illustrated above)
-  M[tuple(zip(*(vertex_pair_indexes + 1)))] = sides_squared
-
-  # The matrix is symmetric, so we can fill in the lower triangle by
-  # adding the transpose
-  M = M + M.T
-  return np.sqrt(np.linalg.det(M) / 288)
-
-
-def volumeMismatch(size,F,nodes):
-  """
-  Calculates the volume mismatch.
-
-  volume mismatch is defined as the difference between volume of reconstructed
-  (compatible) cube and determinant of deformation gradient at Fourier point.
-  """
-  coords = np.empty([8,3])
-  vMismatch = np.empty(F.shape[:3])
-
-#--------------------------------------------------------------------------------------------------
-# calculate actual volume and volume resulting from deformation gradient
-  for k in range(grid[0]):
-    for j in range(grid[1]):
-      for i in range(grid[2]):
-        coords[0,0:3] = nodes[k,  j,  i  ,0:3]
-        coords[1,0:3] = nodes[k  ,j,  i+1,0:3]
-        coords[2,0:3] = nodes[k  ,j+1,i+1,0:3]
-        coords[3,0:3] = nodes[k,  j+1,i  ,0:3]
-        coords[4,0:3] = nodes[k+1,j,  i  ,0:3]
-        coords[5,0:3] = nodes[k+1,j,  i+1,0:3]
-        coords[6,0:3] = nodes[k+1,j+1,i+1,0:3]
-        coords[7,0:3] = nodes[k+1,j+1,i  ,0:3]
-        vMismatch[k,j,i] = \
-        (  abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[7,0:3],coords[3,0:3]])) \
-         + abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[7,0:3],coords[4,0:3]])) \
-         + abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[2,0:3],coords[3,0:3]])) \
-         + abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[2,0:3],coords[1,0:3]])) \
-         + abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[5,0:3]])) \
-         + abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[0,0:3]]))) \
-        /np.linalg.det(F[k,j,i,0:3,0:3])
-  return vMismatch/(size.prod()/grid.prod())
-
 
 def shapeMismatch(size,F,nodes,centres):
   """
@@ -101,35 +22,16 @@ def shapeMismatch(size,F,nodes,centres):
   the corners of reconstructed (combatible) volume element and the vectors calculated by deforming
   the initial volume element with the  current deformation gradient.
   """
-  sMismatch     = np.empty(F.shape[:3])
-
-#--------------------------------------------------------------------------------------------------
-# initial positions
   delta = size/grid*.5
-  coordsInitial = np.vstack((delta * np.array((-1,-1,-1)),
-                             delta * np.array((+1,-1,-1)),
-                             delta * np.array((+1,+1,-1)),
-                             delta * np.array((-1,+1,-1)),
-                             delta * np.array((-1,-1,+1)),
-                             delta * np.array((+1,-1,+1)),
-                             delta * np.array((+1,+1,+1)),
-                             delta * np.array((-1,+1,+1))))
 
-#--------------------------------------------------------------------------------------------------
+  return + np.linalg.norm(nodes[:-1,:-1,:-1] -centres - np.dot(F,delta * np.array((-1,-1,-1))),axis=-1)\
-# compare deformed original and deformed positions to actual positions
+         + np.linalg.norm(nodes[+1:,:-1,:-1] -centres - np.dot(F,delta * np.array((+1,-1,-1))),axis=-1)\
-  for k in range(grid[0]):
+         + np.linalg.norm(nodes[+1:,+1:,:-1] -centres - np.dot(F,delta * np.array((+1,+1,-1))),axis=-1)\
-    for j in range(grid[1]):
+         + np.linalg.norm(nodes[:-1,+1:,:-1] -centres - np.dot(F,delta * np.array((-1,+1,-1))),axis=-1)\
-      for i in range(grid[2]):
+         + np.linalg.norm(nodes[:-1,:-1,+1:] -centres - np.dot(F,delta * np.array((-1,-1,+1))),axis=-1)\
-       sMismatch[k,j,i] = \
+         + np.linalg.norm(nodes[+1:,:-1,+1:] -centres - np.dot(F,delta * np.array((+1,-1,+1))),axis=-1)\
-         + np.linalg.norm(nodes[k,  j,  i  ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[0,0:3]))\
+         + np.linalg.norm(nodes[+1:,+1:,+1:] -centres - np.dot(F,delta * np.array((+1,+1,+1))),axis=-1)\
-         + np.linalg.norm(nodes[k+1,j,  i  ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\
+         + np.linalg.norm(nodes[:-1,+1:,+1:] -centres - np.dot(F,delta * np.array((-1,+1,+1))),axis=-1)
-         + np.linalg.norm(nodes[k+1,j+1,i  ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\
-         + np.linalg.norm(nodes[k,  j+1,i  ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[3,0:3]))\
-         + np.linalg.norm(nodes[k,  j,  i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\
-         + np.linalg.norm(nodes[k+1,j,  i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[5,0:3]))\
-         + np.linalg.norm(nodes[k+1,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[6,0:3]))\
-         + np.linalg.norm(nodes[k  ,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3]))
-  return sMismatch
 
 
 # --------------------------------------------------------------------
@@ -155,10 +57,6 @@ parser.add_option('--no-shape','-s',
                   dest = 'shape',
                   action = 'store_false',
                   help = 'omit shape mismatch')
-parser.add_option('--no-volume','-v',
-                  dest = 'volume',
-                  action = 'store_false',
-                  help = 'omit volume mismatch')
 parser.set_defaults(pos     = 'pos',
                     defgrad = 'f',
                     shape   = True,
@@ -185,10 +83,4 @@ for name in filenames:
                       shapeMismatch.reshape(-1,1,order='F'),
                       scriptID+' '+' '.join(sys.argv[1:]))
 
-  if options.volume:
+  table.save((sys.stdout if name is None else name))
-    volumeMismatch = volumeMismatch(size,F,nodes)
-    table = table.add('volMismatch(({}))'.format(options.defgrad),
-                      volumeMismatch.reshape(-1,1,order='F'),
-                      scriptID+' '+' '.join(sys.argv[1:]))
-
-  table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addCurl.py

@@ -55,4 +55,4 @@ for name in filenames:
                           curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.save((sys.stdout if name is None else name), legacy=True)
+    table.save((sys.stdout if name is None else name))

processing/post/addDerivative.py

@@ -1,74 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from io import StringIO
-from optparse import OptionParser
-
-import numpy as np
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-def derivative(coordinates,what):
-
-  result = np.empty_like(what)
-
-  # use differentiation by interpolation
-  # as described in http://www2.math.umd.edu/~dlevy/classes/amsc466/lecture-notes/differentiation-chap.pdf
-
-  result[1:-1,:] = + what[1:-1,:] * (2.*coordinates[1:-1]-coordinates[:-2]-coordinates[2:]) / \
-                     ((coordinates[1:-1]-coordinates[:-2])*(coordinates[1:-1]-coordinates[2:])) \
-                   + what[2:,:] * (coordinates[1:-1]-coordinates[:-2]) / \
-                     ((coordinates[2:]-coordinates[1:-1])*(coordinates[2:]-coordinates[:-2])) \
-                   + what[:-2,:] * (coordinates[1:-1]-coordinates[2:]) / \
-                     ((coordinates[:-2]-coordinates[1:-1])*(coordinates[:-2]-coordinates[2:])) \
-
-  result[0,:]    = (what[0,:] - what[1,:]) / \
-                   (coordinates[0] - coordinates[1])
-  result[-1,:]   = (what[-1,:] - what[-2,:]) / \
-                   (coordinates[-1] - coordinates[-2])
-
-  return result
-
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Add column(s) containing numerical derivative of requested column(s) with respect to given coordinates.
-
-""", version = scriptID)
-
-parser.add_option('-c','--coordinates',
-                  dest = 'coordinates',
-                  type = 'string', metavar='string',
-                  help = 'heading of coordinate column')
-parser.add_option('-l','--label',
-                  dest = 'labels',
-                  action = 'extend', metavar = '<string LIST>',
-                  help = 'heading of column(s) to differentiate')
-
-
-(options,filenames) = parser.parse_args()
-if filenames == []: filenames = [None]
-
-if options.coordinates is None:
-    parser.error('no coordinate column specified.')
-if options.labels is None:
-    parser.error('no data column specified.')
-
-for name in filenames:
-    damask.util.report(scriptName,name)
-
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    for label in options.labels:
-        table = table.add('d({})/d({})'.format(label,options.coordinates),
-                          derivative(table.get(options.coordinates),table.get(label)),
-                          scriptID+' '+' '.join(sys.argv[1:]))
-
-    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addDisplacement.py

@@ -60,7 +60,7 @@ for name in filenames:
               .add('fluct({}).{}'.format(options.f,options.pos),
                    damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
                     scriptID+' '+' '.join(sys.argv[1:]))\
-               .save((sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt'), legacy=True)
+               .save((sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt'))
     else:
         table.add('avg({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
@@ -68,4 +68,4 @@ for name in filenames:
              .add('fluct({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))\
-             .save((sys.stdout if name is None else name), legacy=True)
+             .save((sys.stdout if name is None else name))

processing/post/addDivergence.py

@@ -55,4 +55,4 @@ for name in filenames:
                           div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.save((sys.stdout if name is None else name), legacy=True)
+    table.save((sys.stdout if name is None else name))

processing/post/addEuclideanDistance.py

@@ -184,4 +184,4 @@ for name in filenames:
                           distance[i,:],
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.save((sys.stdout if name is None else name), legacy=True)
+    table.save((sys.stdout if name is None else name))

processing/post/addGradient.py

@@ -55,4 +55,4 @@ for name in filenames:
                           grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.save((sys.stdout if name is None else name), legacy=True)
+    table.save((sys.stdout if name is None else name))

processing/post/addOrientations.py

@@ -1,150 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-from io import StringIO
-from optparse import OptionParser
-
-import numpy as np
-
-import damask
-
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Add quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
-Orientation is given by quaternion, Euler angles, rotation matrix, or crystal frame coordinates
-(i.e. component vectors of rotation matrix).
-Additional (globally fixed) rotations of the lab frame and/or crystal frame can be applied.
-
-""", version = scriptID)
-
-representations = ['quaternion', 'rodrigues', 'eulers', 'matrix', 'axisangle']
-
-
-parser.add_option('-o',
-                  '--output',
-                  dest = 'output',
-                  action = 'extend', metavar = '<string LIST>',
-                  help = 'output orientation formats {{{}}}'.format(', '.join(representations)))
-parser.add_option('-d',
-                  '--degrees',
-                  dest = 'degrees',
-                  action = 'store_true',
-                  help = 'all angles in degrees')
-parser.add_option('-R',
-                  '--labrotation',
-                  dest='labrotation',
-                  type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'axis and angle of additional lab frame rotation [%default]')
-parser.add_option('-r',
-                  '--crystalrotation',
-                  dest='crystalrotation',
-                  type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'axis and angle of additional crystal frame rotation [%default]')
-parser.add_option('--eulers',
-                  dest = 'eulers',
-                  metavar = 'string',
-                  help = 'Euler angles label')
-parser.add_option('--rodrigues',
-                  dest = 'rodrigues',
-                  metavar = 'string',
-                  help = 'Rodrigues vector label')
-parser.add_option('--matrix',
-                  dest = 'matrix',
-                  metavar = 'string',
-                  help = 'orientation matrix label')
-parser.add_option('--quaternion',
-                  dest = 'quaternion',
-                  metavar = 'string',
-                  help = 'quaternion label')
-parser.add_option('-x',
-                  dest = 'x',
-                  metavar = 'string',
-                  help = 'label of lab x vector (expressed in crystal coords)')
-parser.add_option('-y',
-                  dest = 'y',
-                  metavar = 'string',
-                  help = 'label of lab y vector (expressed in crystal coords)')
-parser.add_option('-z',
-                  dest = 'z',
-                  metavar = 'string',
-                  help = 'label of lab z vector (expressed in crystal coords)')
-parser.add_option('--lattice',
-                  dest = 'lattice',
-                  metavar = 'string',
-                  help = 'lattice structure to reduce rotation into fundamental zone')
-
-parser.set_defaults(output = [],
-                    labrotation     = (1.,1.,1.,0.),                                                # no rotation about (1,1,1)
-                    crystalrotation = (1.,1.,1.,0.),                                                # no rotation about (1,1,1)
-                    lattice = None,
-                   )
-
-(options, filenames) = parser.parse_args()
-if filenames == []: filenames = [None]
-
-if options.output == [] or (not set(options.output).issubset(set(representations))):
-    parser.error('output must be chosen from {}.'.format(', '.join(representations)))
-
-input = [options.eulers     is not None,
-         options.rodrigues  is not None,
-         options.x          is not None and \
-         options.y          is not None and \
-         options.z          is not None,
-         options.matrix     is not None,
-         options.quaternion is not None,
-        ]
-
-if np.sum(input) != 1: parser.error('needs exactly one input format.')
-
-r = damask.Rotation.from_axis_angle(np.array(options.crystalrotation),options.degrees,normalize=True)
-R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degrees,normalize=True)
-
-for name in filenames:
-    damask.util.report(scriptName,name)
-
-    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-
-    if   options.eulers is not None:
-        label = options.eulers
-        print(np.max(table.get(options.eulers),axis=0))
-        o = damask.Rotation.from_Euler_angles(table.get(options.eulers), options.degrees)
-    elif options.rodrigues is not None:
-        label = options.rodrigues
-        o = damask.Rotation.from_Rodrigues_vector(table.get(options.rodrigues))
-    elif options.matrix is not None:
-        label = options.matrix
-        o = damask.Rotation.from_matrix(table.get(options.matrix).reshape(-1,3,3))
-    elif options.x is not None:
-        label = '<{},{},{}>'.format(options.x,options.y,options.z)
-        M = np.block([table.get(options.x),table.get(options.y),table.get(options.z)]).reshape(-1,3,3)
-        o = damask.Rotation.from_matrix(M/np.linalg.norm(M,axis=0))
-    elif options.quaternion is not None:
-        label = options.quaternion
-        o = damask.Rotation.from_quaternion(table.get(options.quaternion))
-
-    o = r.broadcast_to(o.shape) @ o @ R.broadcast_to(o.shape)
-
-    #if options.lattice is not None:
-    #  o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
-
-
-    if 'rodrigues' in options.output:
-        table = table.add('ro({})'.format(label),o.as_Rodrigues_vector(),           scriptID+' '+' '.join(sys.argv[1:]))
-    if 'eulers' in options.output:
-        table = table.add('eu({})'.format(label),o.as_Euler_angles(options.degrees),scriptID+' '+' '.join(sys.argv[1:]))
-    if 'quaternion' in options.output:
-        table = table.add('qu({})'.format(label),o.as_quaternion(),                 scriptID+' '+' '.join(sys.argv[1:]))
-    if 'matrix' in options.output:
-        table = table.add('om({})'.format(label),o.as_matrix(),                     scriptID+' '+' '.join(sys.argv[1:]))
-    if 'axisangle' in options.output:
-        table = table.add('om({})'.format(label),o.as_axis_angle(options.degrees),  scriptID+' '+' '.join(sys.argv[1:]))
-
-    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addSchmidfactors.py

@@ -14,84 +14,9 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 slipSystems = {
-'fcc':
+'fcc': damask.lattice.kinematics['cF']['slip'][:12],
-    np.array([
+'bcc': damask.lattice.kinematics['cI']['slip'],
-    [+0,+1,-1 , +1,+1,+1],
+'hex': damask.lattice.kinematics['hP']['slip'],
-    [-1,+0,+1 , +1,+1,+1],
-    [+1,-1,+0 , +1,+1,+1],
-    [+0,-1,-1 , -1,-1,+1],
-    [+1,+0,+1 , -1,-1,+1],
-    [-1,+1,+0 , -1,-1,+1],
-    [+0,-1,+1 , +1,-1,-1],
-    [-1,+0,-1 , +1,-1,-1],
-    [+1,+1,+0 , +1,-1,-1],
-    [+0,+1,+1 , -1,+1,-1],
-    [+1,+0,-1 , -1,+1,-1],
-    [-1,-1,+0 , -1,+1,-1],
-   ],'d'),
-'bcc':
-    np.array([
-    [+1,-1,+1 , +0,+1,+1],
-    [-1,-1,+1 , +0,+1,+1],
-    [+1,+1,+1 , +0,-1,+1],
-    [-1,+1,+1 , +0,-1,+1],
-    [-1,+1,+1 , +1,+0,+1],
-    [-1,-1,+1 , +1,+0,+1],
-    [+1,+1,+1 , -1,+0,+1],
-    [+1,-1,+1 , -1,+0,+1],
-    [-1,+1,+1 , +1,+1,+0],
-    [-1,+1,-1 , +1,+1,+0],
-    [+1,+1,+1 , -1,+1,+0],
-    [+1,+1,-1 , -1,+1,+0],
-    [-1,+1,+1 , +2,+1,+1],
-    [+1,+1,+1 , -2,+1,+1],
-    [+1,+1,-1 , +2,-1,+1],
-    [+1,-1,+1 , +2,+1,-1],
-    [+1,-1,+1 , +1,+2,+1],
-    [+1,+1,-1 , -1,+2,+1],
-    [+1,+1,+1 , +1,-2,+1],
-    [-1,+1,+1 , +1,+2,-1],
-    [+1,+1,-1 , +1,+1,+2],
-    [+1,-1,+1 , -1,+1,+2],
-    [-1,+1,+1 , +1,-1,+2],
-    [+1,+1,+1 , +1,+1,-2],
-   ],'d'),
-'hex':
-    np.array([
-    [+2,-1,-1,+0 , +0,+0,+0,+1],
-    [-1,+2,-1,+0 , +0,+0,+0,+1],
-    [-1,-1,+2,+0 , +0,+0,+0,+1],
-    [+2,-1,-1,+0 , +0,+1,-1,+0],
-    [-1,+2,-1,+0 , -1,+0,+1,+0],
-    [-1,-1,+2,+0 , +1,-1,+0,+0],
-    [-1,+1,+0,+0 , +1,+1,-2,+0],
-    [+0,-1,+1,+0 , -2,+1,+1,+0],
-    [+1,+0,-1,+0 , +1,-2,+1,+0],
-    [-1,+2,-1,+0 , +1,+0,-1,+1],
-    [-2,+1,+1,+0 , +0,+1,-1,+1],
-    [-1,-1,+2,+0 , -1,+1,+0,+1],
-    [+1,-2,+1,+0 , -1,+0,+1,+1],
-    [+2,-1,-1,+0 , +0,-1,+1,+1],
-    [+1,+1,-2,+0 , +1,-1,+0,+1],
-    [-2,+1,+1,+3 , +1,+0,-1,+1],
-    [-1,-1,+2,+3 , +1,+0,-1,+1],
-    [-1,-1,+2,+3 , +0,+1,-1,+1],
-    [+1,-2,+1,+3 , +0,+1,-1,+1],
-    [+1,-2,+1,+3 , -1,+1,+0,+1],
-    [+2,-1,-1,+3 , -1,+1,+0,+1],
-    [+2,-1,-1,+3 , -1,+0,+1,+1],
-    [+1,+1,-2,+3 , -1,+0,+1,+1],
-    [+1,+1,-2,+3 , +0,-1,+1,+1],
-    [-1,+2,-1,+3 , +0,-1,+1,+1],
-    [-1,+2,-1,+3 , +1,-1,+0,+1],
-    [-2,+1,+1,+3 , +1,-1,+0,+1],
-    [-1,-1,+2,+3 , +1,+1,-2,+2],
-    [+1,-2,+1,+3 , -1,+2,-1,+2],
-    [+2,-1,-1,+3 , -2,+1,+1,+2],
-    [+1,+1,-2,+3 , -1,-1,+2,+2],
-    [-1,+2,-1,+3 , +1,-2,+1,+2],
-    [-2,+1,+1,+3 , +2,-1,-1,+2],
-   ],'d'),
 }
 
 # --------------------------------------------------------------------
@@ -189,4 +114,4 @@ for name in filenames:
     for i,label in enumerate(labels):
         table = table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.save((sys.stdout if name is None else name), legacy=True)
+    table.save((sys.stdout if name is None else name))