merged and added correction to FreeSurface.config example

.gitlab-ci.yml

@@ -7,9 +7,9 @@ stages:
   - compilePETScGNU
   - prepareSpectral
   - spectral
-  - compileMarc2018_1
+  - compileMarc
   - marc
-  - compileAbaqus2017
+  - compileAbaqus
   - example
   - performance
   - createPackage
@@ -51,39 +51,37 @@ variables:
   # Names of module files to load
   # ===============================================================================================
   # ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++
-  IntelCompiler16_0:               "Compiler/Intel/16.0 Libraries/IMKL/2016"
+  IntelCompiler16_4:               "Compiler/Intel/16.4 Libraries/IMKL/2016"
-  IntelCompiler16_4:               "Compiler/Intel/16.4 Libraries/IMKL/2016-4"
+  IntelCompiler17_8:               "Compiler/Intel/17.8 Libraries/IMKL/2017"
-  IntelCompiler17_0:               "Compiler/Intel/17.0 Libraries/IMKL/2017"
+  IntelCompiler18_4:               "Compiler/Intel/18.4 Libraries/IMKL/2018"
-  IntelCompiler18_1:               "Compiler/Intel/18.1 Libraries/IMKL/2018"
+  GNUCompiler8_2:                  "Compiler/GNU/8.2"
-  GNUCompiler7_3:                  "Compiler/GNU/7.3"
   # ------------ Defaults ----------------------------------------------
-  IntelCompiler:                   "$IntelCompiler18_1"
+  IntelCompiler:                   "$IntelCompiler18_4"
-  GNUCompiler:                     "$GNUCompiler7_3"
+  GNUCompiler:                     "$GNUCompiler8_2"
   # ++++++++++++ MPI +++++++++++++++++++++++++++++++++++++++++++++++++++
-  MPICH3_2Intel18_1:               "MPI/Intel/18.1/MPICH/3.2.1"
+  IMPI2018Intel18_4:               "MPI/Intel/18.4/IntelMPI/2018"
-  MPICH3_2GNU7_3:                  "MPI/GNU/7.3/MPICH/3.2.1"
+  MPICH3_3GNU8_2:                  "MPI/GNU/8.2/MPICH/3.3"
   # ------------ Defaults ----------------------------------------------
-  MPICH_Intel:                     "$MPICH3_2Intel18_1"
+  MPICH_Intel:                     "$IMPI2018Intel18_4"
-  MPICH_GNU:                       "$MPICH3_2GNU7_3"
+  MPICH_GNU:                       "$MPICH3_3GNU8_2"
   # ++++++++++++ PETSc +++++++++++++++++++++++++++++++++++++++++++++++++
-  PETSc3_10_0MPICH3_2Intel18_1:    "Libraries/PETSc/3.10.0/Intel-18.1-MPICH-3.2.1"
+  PETSc3_10_3IMPI2018Intel18_4:    "Libraries/PETSc/3.10.3/Intel-18.4-IntelMPI-2018"
-  PETSc3_10_0MPICH3_2GNU7_3:       "Libraries/PETSc/3.10.0/GNU-7.3-MPICH-3.2.1"
+  PETSc3_10_3MPICH3_3GNU8_2:       "Libraries/PETSc/3.10.3/GNU-8.2-MPICH-3.3"
   # ------------ Defaults ----------------------------------------------
-  PETSc_MPICH_Intel:               "$PETSc3_10_0MPICH3_2Intel18_1"
+  PETSc_MPICH_Intel:               "$PETSc3_10_3IMPI2018Intel18_4"
-  PETSc_MPICH_GNU:                 "$PETSc3_10_0MPICH3_2GNU7_3"
+  PETSc_MPICH_GNU:                 "$PETSc3_10_3MPICH3_3GNU8_2"
   # ++++++++++++ FEM +++++++++++++++++++++++++++++++++++++++++++++++++++
-  Abaqus2017:                      "FEM/Abaqus/2017"
+  Abaqus2019:                      "FEM/Abaqus/2019"
   MSC2018_1:                       "FEM/MSC/2018.1"
-  MSC2017:                         "FEM/MSC/2017"
   # ------------ Defaults ----------------------------------------------
-  Abaqus:                          "$Abaqus2017"
+  Abaqus:                          "$Abaqus2019"
   MSC:                             "$MSC2018_1"
-  IntelMarc:                       "$IntelCompiler17_0"
+  IntelMarc:                       "$IntelCompiler17_8"
   IntelAbaqus:                     "$IntelCompiler16_4"
   # ++++++++++++ Documentation +++++++++++++++++++++++++++++++++++++++++
-  Doxygen1_8_13:                   "Documentation/Doxygen/1.8.13"
+  Doxygen1_8_15:                   "Documentation/Doxygen/1.8.15"
   # ------------ Defaults ----------------------------------------------
-  Doxygen:                         "$Doxygen1_8_13"
+  Doxygen:                         "$Doxygen1_8_15"
 
 
 ###################################################################################################
@@ -158,6 +156,13 @@ Post_AverageDown:
     - master
     - release
 
+Post_ASCIItable:
+  stage: postprocessing
+  script: ASCIItable/test.py
+  except:
+    - master
+    - release
+
 Post_General:
   stage: postprocessing
   script: PostProcessing/test.py
@@ -202,7 +207,9 @@ Post_ParaviewRelated:
 
 Post_OrientationConversion:
   stage: postprocessing
-  script: OrientationConversion/test.py
+  script:
+    - OrientationConversion/test.py
+    - OrientationConversion/test2.py
   except:
     - master
     - release
@@ -383,9 +390,9 @@ TextureComponents:
 
 ###################################################################################################
 Marc_compileIfort2018_1:
-  stage: compileMarc2018_1
+  stage: compileMarc
   script:
-    - module load $IntelCompiler17_0 $MSC2018_1
+    - module load $IntelMarc $MSC
     - Marc_compileIfort/test.py -m 2018.1
   except:
     - master
@@ -430,11 +437,11 @@ J2_plasticBehavior:
     - release
 
 ###################################################################################################
-Abaqus_compile2017:
+Abaqus_compile:
-  stage: compileAbaqus2017
+  stage: compileAbaqus
   script:
-    - module load $IntelCompiler16_4 $Abaqus2017
+    - module load $IntelAbaqus $Abaqus
-    - Abaqus_compileIfort/test.py -a 2017
+    - Abaqus_compileIfort/test.py
   except:
     - master
     - release
@@ -477,24 +484,40 @@ AbaqusStd:
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
     - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT abaqus
-  only:
+  except:
-    - development
+    - master
+    - release
 
 Marc:
   stage: createDocumentation
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
     - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT marc
-  only:
+  except:
-    - development
+    - master
+    - release
 
 Spectral:
   stage: createDocumentation
   script:
     - module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
     - $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT spectral
-  only:
+  except:
-    - development
+    - master
+    - release
+
+Processing:
+  stage: createDocumentation
+  script:
+    - cd $DAMASKROOT/processing/pre
+    - rm abq_addUserOutput.py marc_addUserOutput.py
+    - $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py
+    - cd $DAMASKROOT/processing/post
+    - rm marc_to_vtk.py vtk2ang.py
+    - $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py
+  except:
+    - master
+    - release
 
 ##################################################################################################
 backupData:
@@ -503,11 +526,10 @@ backupData:
     - cd $TESTROOT/performance                                                                      # location of new runtime results
     - git commit -am"${CI_PIPELINE_ID}_${CI_COMMIT_SHA}"
     - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
-    - cp $TESTROOT/performance/time.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $TESTROOT/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - cp $TESTROOT/performance/memory.txt $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $TESTROOT/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
+    - mv $DAMASKROOT/processing $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   only:
     - development
 

CMakeLists.txt

@@ -445,6 +445,33 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
 
   # Additional options
   # -fdefault-integer-8: Use it to set precision to 8 bytes for integer, don't use it for the standard case of pInt=4 (there is no -fdefault-integer-4)
+
+
+###################################################################################################
+# PGI Compiler
+###################################################################################################
+elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "PGI")
+
+  if (OPTIMIZATION STREQUAL "OFF")
+    set (OPTIMIZATION_FLAGS "-O0"       )
+  elseif (OPTIMIZATION STREQUAL "DEFENSIVE")
+    set (OPTIMIZATION_FLAGS "-O2")
+  elseif (OPTIMIZATION STREQUAL "AGGRESSIVE")
+    set (OPTIMIZATION_FLAGS "-O3")
+  endif ()
+
+
+#------------------------------------------------------------------------------------------------
+# Fine tuning compilation options
+  set (COMPILE_FLAGS "${COMPILE_FLAGS} -Mpreprocess")
+  # preprocessor
+
+  set (STANDARD_CHECK "-Mallocatable=03")
+
+#------------------------------------------------------------------------------------------------
+# Runtime debugging
+  set (DEBUG_FLAGS "${DEBUG_FLAGS} -g")
+  # Includes debugging information in the object module; sets the optimization level to zero unless a -⁠O option is present on the command line
 else ()
   message (FATAL_ERROR "Compiler type (CMAKE_Fortran_COMPILER_ID) not recognized")
 endif ()

CONFIG

@@ -8,6 +8,6 @@ set DAMASK_NUM_THREADS    = 4
 set MSC_ROOT              = /opt/msc
 set MARC_VERSION          = 2018.1
 
-set ABAQUS_VERSION        = 2017
+set ABAQUS_VERSION        = 2019
 
 set DAMASK_HDF5           = OFF

PRIVATE

@@ -1 +1 @@
-Subproject commit beb9682fff7d4d6c65aba12ffd04c7441dc6ba6b
+Subproject commit def4081e837539dba7c4760abbb340553be66d3c

README

@@ -10,3 +10,4 @@ Germany
 
 Email: DAMASK@mpie.de
 https://damask.mpie.de
+https://magit1.mpie.de

VERSION

@@ -1 +1 @@
-v2.0.2-1614-g8764c615
+v2.0.2-1961-g07eff8eb

examples/ConfigFiles/Crystallite_All.config

@@ -3,7 +3,6 @@
 (output) texture
 (output) volume
 (output) orientation    # quaternion
-(output) eulerangles    # orientation as Bunge triple in degree
 (output) grainrotation  # deviation from initial orientation as axis (1-3) and angle in degree (4) in crystal reference coordinates
 (output) f              # deformation gradient tensor
 (output) fe             # elastic deformation gradient tensor

examples/ConfigFiles/Phase_Isotropic_FreeSurface.config

@@ -13,13 +13,13 @@ plasticity              isotropic
 (output)                strainrate
 
 lattice_structure       isotropic
-c11                     110.9e9
+c11                     10e9
 c12                     0.0
-taylorfactor            3
-tau0                    31e6
 gdot0                   0.001
-n                       20
+tau0                    0.3e6
-h0                      75e6
+tausat                  0.6e6
-tausat                  63e6
+h0                      1e6
-w0                      2.25
+n                       5
+m                       3
+a                       2
 atol_resistance         1

examples/SpectralMethod/Polycrystal/material.config

@@ -13,7 +13,6 @@ mech	none
 (output) texture
 (output) volume
 (output) orientation    # quaternion
-(output) eulerangles    # orientation as Bunge triple
 (output) grainrotation  # deviation from initial orientation as axis (1-3) and angle in degree (4)
 (output) f              # deformation gradient tensor; synonyms: "defgrad"
 (output) fe             # elastic deformation gradient tensor

processing/misc/DREAM3D_toTable.py

@@ -1,84 +0,0 @@
-#!/usr/bin/env python2.7
-# -*- coding: UTF-8 no BOM -*-
-
-import os,h5py
-import numpy as np
-from optparse import OptionParser
-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 [dream3dfile[s]]', description = """
-Convert DREAM3D file to ASCIItable. Works for 3D datasets, but, hey, its not called DREAM2D ;)
-
-""", version = scriptID)
-
-parser.add_option('-d','--data',
-                  dest = 'data',
-                  action = 'extend', metavar = '<string LIST>',
-                  help = 'data to extract from DREAM3D file')
-parser.add_option('-c','--container',
-                  dest = 'container', metavar = 'string',
-                  help = 'root container(group) in which data is stored [%default]')
-
-parser.set_defaults(container="ImageDataContainer",
-                   )
-
-(options, filenames) = parser.parse_args()
-
-if options.data is None:
-  parser.error('No data selected')
-
-rootDir ='DataContainers/'+options.container
-
-# --- loop over input files -------------------------------------------------------------------------
-
-if filenames == []: parser.error('no input file specified.')
-
-for name in filenames:
-  try:
-    table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt',
-                              buffered = False
-                              )
-  except: continue
-  damask.util.report(scriptName,name)
-
-  inFile = h5py.File(name, 'r')
-  try:
-    grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
-  except:
-    damask.util.croak('Group {} not found'.format(options.container))
-    table.close(dismiss = True)
-    continue
-  
-# --- read comments --------------------------------------------------------------------------------
-                    
-  coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T                             
-  table.data = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
-             + inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
-             + inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
-  labels = ['1_pos','2_pos','3_pos']
-  for data in options.data:
-    try:
-      l = np.prod(inFile[rootDir+'/CellData/'+data].shape[3:])
-      labels+=['{}_{}'.format(i+1,data.replace(' ','')) for i in range(l)] if l >1 else [data.replace(' ','')]
-    except KeyError:
-      damask.util.croak('Data {} not found'.format(data))
-      pass
-    table.data = np.hstack((table.data,
-                            inFile[rootDir+'/CellData/'+data][...].reshape(grid.prod(),l)))
-    
-# ------------------------------------------ assemble header ---------------------------------------
-  table.labels_clear()
-  table.labels_append(labels,reset = True)
-  table.head_write()
-  
-# ------------------------------------------ finalize output ---------------------------------------
-  table.data_writeArray()
-  table.close()

processing/misc/OIMgrainFile_toTable.py

@@ -1,48 +0,0 @@
-#!/usr/bin/env python2.7
-# -*- coding: UTF-8 no BOM -*-
-
-import os,sys
-from optparse import OptionParser
-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 [file[s]]', description = """
-Adds header to OIM grain file type 1 to make it accesible as ASCII table
-
-""", version = scriptID)
-
-
-(options, filenames) = parser.parse_args()
-
-# --- loop over input files -------------------------------------------------------------------------
-
-if filenames == []: filenames = [None]
-
-for name in filenames:
-  try:
-    table = damask.ASCIItable(name = name,
-                              buffered = False,
-                              labeled = False)
-  except: continue
-  damask.util.report(scriptName,name)
-  table.head_read()
-  data = []
-  while  table.data_read():
-    data.append(table.data[0:9])
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  table.labels_append(['1_euler','2_euler','3_euler','1_pos','2_pos','IQ','CI','Fit','GrainID'])
-  table.head_write()
-  for i in data:
-    table.data = i
-    table.data_write()
-
-# --- output finalization --------------------------------------------------------------------------
-
-  table.close()                                                                                     # close ASCII table

processing/post/addAPS34IDEstrainCoords.py

@@ -14,19 +14,14 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Transform X,Y,Z,F APS BeamLine 34 coordinates to x,y,z APS strain coordinates.
 
 """, version = scriptID)
 
-parser.add_option('-f',
+parser.add_option('-f','--frame',dest='frame', metavar='string',
-                  '--frame',
+                                 help='label of APS X,Y,Z coords')
-                  dest='frame',
+parser.add_option('--depth',     dest='depth',          metavar='string',
-                  metavar='string',
-                  help='APS X,Y,Z coords')
-parser.add_option('--depth',
-                  dest='depth',
-                  metavar='string',
                                  help='depth')
 
 (options,filenames) = parser.parse_args()

processing/post/addCalculation.py

@@ -18,7 +18,7 @@ def listify(x):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add or alter column(s) with derived values according to user-defined arithmetic operation between column(s).
 Column labels are tagged by '#label#' in formulas. Use ';' for ',' in functions.
 Numpy is available as 'np'.
@@ -41,10 +41,7 @@ parser.add_option('-f','--formula',
 
 parser.add_option('-c','--condition',
                   dest   = 'condition', metavar='string',
-                  help   = 'condition to alter existing column data')
+                  help   = 'condition to alter existing column data (optional)')
-
-parser.set_defaults(condition = None,
-                   )
 
 (options,filenames) = parser.parse_args()
 

processing/post/addCauchy.py

@@ -13,8 +13,8 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Add column(s) containing Cauchy stress based on given column(s) of deformation gradient and first Piola--Kirchhoff stress.
+Add column containing Cauchy stress based on deformation gradient and first Piola--Kirchhoff stress.
 
 """, version = scriptID)
 

processing/post/addCompatibilityMismatch.py

@@ -209,7 +209,7 @@ def shapeMismatch(size,F,nodes,centres):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing the shape and volume mismatch resulting from given deformation gradient.
 Operates on periodic three-dimensional x,y,z-ordered data sets.
 

processing/post/addCumulative.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add cumulative (sum of first to current row) values for given label(s).
 """, version = scriptID)
 
@@ -22,12 +22,9 @@ parser.add_option('-l','--label',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'columns to cumulate')
 
-parser.set_defaults(label = [],
-                   )
-                    
 (options,filenames) = parser.parse_args()
 
-if len(options.label) == 0:
+if options.label is None:
   parser.error('no data column(s) specified.')
 
 # --- loop over input files -------------------------------------------------------------------------

processing/post/addCurl.py

@@ -49,14 +49,14 @@ def curlFFT(geomdim,field):
 
   curl_fourier = np.einsum(einsums[n],e,k_s,field_fourier)*TWOPIIMG
 
-  return np.fft.irfftn(curl_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n])
+  return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
 
 
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing curl of requested column(s).
 Operates on periodic ordered three-dimensional data sets
 of vector and tensor fields.

processing/post/addDerivative.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -34,7 +34,7 @@ def derivative(coordinates,what):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+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)

processing/post/addDeterminant.py

@@ -20,7 +20,7 @@ def determinant(m):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing determinant of requested tensor column(s).
 
 """, version = scriptID)

processing/post/addDeviator.py

@@ -23,7 +23,7 @@ def deviator(m,spherical = False):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(2)]', description = """
 Add column(s) containing deviator of requested tensor column(s).
 
 """, version = scriptID)

processing/post/addDisplacement.py

@@ -87,7 +87,7 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] [ASCIItable(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add displacments resulting from deformation gradient field.
 Operates on periodic three-dimensional x,y,z-ordered data sets.
 Outputs at cell centers or cell nodes (into separate file).
@@ -111,7 +111,6 @@ parser.add_option('--nodal',
 
 parser.set_defaults(defgrad = 'f',
                     pos     = 'pos',
-                    nodal   = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/addDivergence.py

@@ -45,7 +45,7 @@ def divFFT(geomdim,field):
 
   div_fourier = np.einsum(einsums[n],k_s,field_fourier)*TWOPIIMG
 
-  return np.fft.irfftn(div_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n//3])
+  return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n//3])
 
 
 # --------------------------------------------------------------------

processing/post/addEhkl.py

@@ -30,7 +30,7 @@ def E_hkl(stiffness,vec):   # stiffness = (c11,c12,c44)
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing directional stiffness based on given cubic stiffness values C11, C12, and C44 in consecutive columns.
 
 """, version = scriptID)

processing/post/addEuclideanDistance.py

@@ -83,7 +83,7 @@ neighborhoods = {
                                       ])
                 }
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing Euclidean distance to grain structural features: boundaries, triple lines, and quadruple points.
 
 """, version = scriptID)

processing/post/addGaussian.py

@@ -15,7 +15,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
 Add column(s) containing Gaussian filtered values of requested column(s).
 Operates on periodic and non-periodic ordered three-dimensional data sets.
 For details see scipy.ndimage documentation.
@@ -34,12 +34,12 @@ parser.add_option('-o','--order',
                   dest = 'order',
                   type = int,
                   metavar = 'int',
-                  help = 'order of the filter')
+                  help = 'order of the filter [%default]')
 parser.add_option('--sigma',
                   dest = 'sigma',
                   type = float,
                   metavar = 'float',
-                  help = 'standard deviation')
+                  help = 'standard deviation [%default]')
 parser.add_option('--periodic',
                   dest = 'periodic',
                   action = 'store_true',
@@ -50,7 +50,6 @@ parser.add_option('--periodic',
 parser.set_defaults(pos = 'pos',
                     order = 0,
                     sigma = 1,
-                    periodic = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/addGradient.py

@@ -45,14 +45,14 @@ def gradFFT(geomdim,field):
   k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')                           
   grad_fourier = np.einsum(einsums[n],field_fourier,k_s)*TWOPIIMG
 
-  return np.fft.irfftn(grad_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,3*n])
+  return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
 
 
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
 Add column(s) containing gradient of requested column(s).
 Operates on periodic ordered three-dimensional data sets
 of vector and scalar fields.

processing/post/addGrainID.py

@@ -1,176 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
-
-import os,sys,copy
-import numpy as np
-import damask
-from optparse import OptionParser
-from scipy import spatial
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
-Add grain index based on similiarity of crystal lattice orientation.
-
-""", version = scriptID)
-
-parser.add_option('-r',
-                  '--radius',
-                  dest = 'radius',
-                  type = 'float', metavar = 'float',
-                  help = 'search radius')
-parser.add_option('-d',
-                  '--disorientation',
-                  dest = 'disorientation',
-                  type = 'float', metavar = 'float',
-                  help = 'disorientation threshold in degrees [%default]')
-parser.add_option('-s',
-                  '--symmetry',
-                  dest = 'symmetry',
-                  metavar = 'string',
-                  help = 'crystal symmetry [%default]')
-parser.add_option('-o',
-                  '--orientation',
-                  dest = 'quaternion',
-                  metavar = 'string',
-                  help = 'label of crystal orientation given as unit quaternion [%default]')
-parser.add_option('-p',
-                  '--pos', '--position',
-                  dest = 'pos',
-                  metavar = 'string',
-                  help = 'label of coordinates [%default]')
-parser.add_option('--quiet',
-                  dest='verbose',
-                  action = 'store_false',
-                  help = 'hide status bar (useful when piping to file)')
-
-parser.set_defaults(disorientation = 5,
-                    verbose = True,
-                    quaternion = 'orientation',
-                    symmetry = 'cubic',
-                    pos      = 'pos',
-                   )
-
-(options, filenames) = parser.parse_args()
-
-if options.radius is None:
-  parser.error('no radius specified.')
-
-cos_disorientation = np.cos(np.radians(options.disorientation/2.))                                  # cos of half the disorientation angle
-
-# --- loop over input files -------------------------------------------------------------------------
-
-if filenames == []: filenames = [None]
-
-for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
-                                    buffered = False)
-  except: continue
-  damask.util.report(scriptName,name)
-
-# ------------------------------------------ read header -------------------------------------------  
-
-  table.head_read()
-
-# ------------------------------------------ sanity checks -----------------------------------------
-
-  errors  = []
-  remarks = []
-  
-  if not 3 >= table.label_dimension(options.pos) >= 1:
-    errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
-  if not np.all(table.label_dimension(options.quaternion) == 4):
-    errors.append('input "{}" does not have dimension 4.'.format(options.quaternion))
-  else:  column = table.label_index(options.quaternion)
-
-  if remarks != []: damask.util.croak(remarks)
-  if errors  != []:
-    damask.util.croak(errors)
-    table.close(dismiss = True)
-    continue
-
-# ------------------------------------------ assemble header ---------------------------------------
-
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  table.labels_append('grainID_{}@{:g}'.format(options.quaternion,options.disorientation))          # report orientation source and disorientation
-  table.head_write()
-
-# ------------------------------------------ build KD tree -----------------------------------------
-
-  table.data_readArray(options.pos)                                                                 # read position vectors
-  grainID = -np.ones(len(table.data),dtype=int)
-  Npoints = table.data.shape[0]
-  kdtree = spatial.KDTree(copy.deepcopy(table.data))
-
-# ------------------------------------------ assign grain IDs --------------------------------------
-
-  orientations = []                                                                                 # quaternions found for grain
-  memberCounts = []                                                                                 # number of voxels in grain
-  p = 0                                                                                             # point counter
-  g = 0                                                                                             # grain counter
-  matchedID = -1
-  lastDistance = np.dot(kdtree.data[-1]-kdtree.data[0],kdtree.data[-1]-kdtree.data[0])              # (arbitrarily) use diagonal of cloud
-
-  table.data_rewind()
-  while table.data_read():                                                                          # read next data line of ASCII table
-
-    if options.verbose and Npoints > 100 and p%(Npoints//100) == 0:                                 # report in 1% steps if possible and avoid modulo by zero
-      damask.util.progressBar(iteration=p,total=Npoints)
-
-    o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))),
-                           symmetry   = options.symmetry).reduced()
-
-    matched        = False
-    alreadyChecked = {}
-    candidates     = []
-    bestDisorientation = damask.Quaternion([0,0,0,1])                                               # initialize to 180 deg rotation as worst case
-
-    for i in kdtree.query_ball_point(kdtree.data[p],options.radius):                                # check all neighboring points
-      gID = grainID[i]
-      if gID != -1 and gID not in alreadyChecked:                                                   # indexed point belonging to a grain not yet tested?
-        alreadyChecked[gID] = True                                                                  # remember not to check again
-        disorientation = o.disorientation(orientations[gID],SST = False)[0]                         # compare against other orientation
-        if disorientation.quaternion.q >  cos_disorientation:                                       # within threshold ...
-          candidates.append(gID)                                                                    # remember as potential candidate
-          if disorientation.quaternion.q >= bestDisorientation.q:                                   # ... and better than current best? 
-            matched = True
-            matchedID = gID                                                                         # remember that grain
-            bestDisorientation = disorientation.quaternion
-
-    if matched:                                                                                     # did match existing grain
-      memberCounts[matchedID] += 1
-      if len(candidates) > 1:                                                                       # ambiguity in grain identification?
-        largestGrain = sorted(candidates,key=lambda x:memberCounts[x])[-1]                          # find largest among potential candidate grains
-        matchedID    = largestGrain
-        for c in [c for c in candidates if c != largestGrain]:                                      # loop over smaller candidates
-          memberCounts[largestGrain] += memberCounts[c]                                             # reassign member count of smaller to largest
-          memberCounts[c] = 0
-        grainID = np.where(np.in1d(grainID,candidates), largestGrain, grainID)                      # relabel grid points of smaller candidates as largest one
-      
-    else:                                                                                           # no match -> new grain found
-      orientations += [o]                                                                           # initialize with current orientation
-      memberCounts += [1]                                                                           # start new membership counter
-      matchedID = g
-      g += 1                                                                                        # increment grain counter
-
-    grainID[p] = matchedID                                                                          # remember grain index assigned to point
-    p += 1                                                                                          # increment point
-
-  grainIDs = np.where(np.array(memberCounts) > 0)[0]                                                # identify "live" grain identifiers
-  packingMap = dict(zip(list(grainIDs),range(len(grainIDs))))                                       # map to condense into consecutive IDs
-  
-  table.data_rewind()
-
-  outputAlive = True
-  p = 0
-  damask.util.progressBar(iteration=1,total=1)
-  while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    table.data_append(1+packingMap[grainID[p]])                                                     # add (condensed) grain ID
-    outputAlive = table.data_write()                                                                # output processed line
-    p += 1
-
-# ------------------------------------------ output finalization -----------------------------------  
-
-  table.close()                                                                                     # close ASCII tables

processing/post/addIPFcolor.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
 
 """, version = scriptID)
@@ -41,6 +41,10 @@ parser.set_defaults(pole = (0.0,0.0,1.0),
 
 (options, filenames) = parser.parse_args()
 
+# damask.Orientation requires Bravais lattice, but we are only interested in symmetry
+symmetry2lattice={'cubic':'bcc','hexagonal':'hex','tetragonal':'bct'}
+lattice = symmetry2lattice[options.symmetry]
+
 pole = np.array(options.pole)
 pole /= np.linalg.norm(pole)
 
@@ -78,8 +82,8 @@ for name in filenames:
 
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))),
+    o = damask.Orientation(np.array(list(map(float,table.data[column:column+4]))),
-                           symmetry   = options.symmetry).reduced()
+                           lattice   = lattice).reduced()
 
     table.data_append(o.IPFcolor(pole))
     outputAlive = table.data_write()                                                                # output processed line

processing/post/addIndexed.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add data in column(s) of mapped ASCIItable selected from the row indexed by the value in a mapping column.
 Row numbers start at 1.
 

processing/post/addInfo.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add info lines to ASCIItable header.
 
 """, version = scriptID)
@@ -23,11 +23,12 @@ parser.add_option('-i',
                   dest = 'info', action = 'extend', metavar = '<string LIST>',
                   help    = 'items to add')
 
-parser.set_defaults(info = [],
-                   )
 
 (options,filenames) = parser.parse_args()
 
+if options.info is None:
+  parser.error('no info specified.')
+
 # --- loop over input files ------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]

processing/post/addLinked.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add data of selected column(s) from (first) row of linked ASCIItable that shares the linking column value.
 
 """, version = scriptID)
@@ -21,7 +21,7 @@ Add data of selected column(s) from (first) row of linked ASCIItable that shares
 parser.add_option('--link',
                   dest = 'link', nargs = 2,
                   type = 'string', metavar = 'string string',
-                  help = 'column labels containing linked values')
+                  help = 'column labels of table and linked table containing linking values')
 parser.add_option('-l','--label',
                   dest = 'label',
                   action = 'extend', metavar = '<string LIST>',
@@ -105,7 +105,8 @@ for name in filenames:
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
     try:
-      table.data_append(data[np.argwhere(np.all((map(float,table.data[myLink:myLink+myLinkDim]) - index)==0,axis=1))[0]])  # add data of first matching line
+      table.data_append(data[np.argwhere(np.all((list(map(float,table.data[myLink:myLink+myLinkDim])) - index)==0,
+                                                 axis=1))[0]])                                      # add data of first matching line
     except IndexError:
       table.data_append(np.nan*np.ones_like(data[0]))                                               # or add NaNs
     outputAlive = table.data_write()                                                                # output processed line

processing/post/addMises.py

@@ -24,7 +24,7 @@ def Mises(what,tensor):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add vonMises equivalent values for symmetric part of requested strains and/or stresses.
 
 """, version = scriptID)
@@ -41,10 +41,9 @@ parser.add_option('-s','--stress',
 parser.set_defaults(strain = [],
                     stress = [],
                    )
-
 (options,filenames) = parser.parse_args()
 
-if len(options.stress+options.strain) == 0:
+if options.stress is [] and options.strain is []:
   parser.error('no data column specified...')
 
 # --- loop over input files -------------------------------------------------------------------------

processing/post/addNorm.py

@@ -9,6 +9,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 # definition of element-wise p-norms for matrices
+# ToDo: better use numpy.linalg.norm
 
 def norm(which,object):
 
@@ -18,12 +19,14 @@ def norm(which,object):
     return math.sqrt(sum([x*x for x in object]))
   elif which == 'Max':                                                                              # p = inf
     return max(map(abs, object))
+  else:
+    return -1
 
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing norm of requested column(s) being either vectors or tensors.
 
 """, version = scriptID)
@@ -43,6 +46,8 @@ parser.set_defaults(norm = 'frobenius',
 
 (options,filenames) = parser.parse_args()
 
+if options.norm.lower() not in normChoices:
+  parser.error('invalid norm ({}) specified.'.format(options.norm))
 if options.label is None:
   parser.error('no data column specified.')
 

processing/post/addOrientations.py

@@ -9,36 +9,11 @@ import damask
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
-# --------------------------------------------------------------------
-#                     convention conformity checks
-# --------------------------------------------------------------------
-
-def check_Eulers(eulers):
-  if np.any(eulers < 0.0) or np.any(eulers > 2.0*np.pi) or eulers[1] > np.pi:                       # Euler angles within valid range?
-    raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π].\n{} {} {}.'.format(*eulers))
-  return eulers
-
-def check_quaternion(q):
-  if q[0] < 0.0:                                                                                    # positive first quaternion component?
-    raise ValueError('quaternion has negative first component.\n{}'.format(q[0]))
-  if not np.isclose(np.linalg.norm(q), 1.0):                                                        # unit quaternion?
-    raise ValueError('quaternion is not of unit length.\n{} {} {} {}'.format(*q))
-  return q
- 
-def check_matrix(M):
-  if not np.isclose(np.linalg.det(M),1.0):                                                          # proper rotation?
-    raise ValueError('matrix is not a proper rotation.\n{}'.format(M))
-  if    not np.isclose(np.dot(M[0],M[1]), 0.0) \
-     or not np.isclose(np.dot(M[1],M[2]), 0.0) \
-     or not np.isclose(np.dot(M[2],M[0]), 0.0):                                                     # all orthogonal?
-    raise ValueError('matrix is not orthogonal.\n{}'.format(M))
-  return M
-
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+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).
@@ -46,9 +21,9 @@ Additional (globally fixed) rotations of the lab frame and/or crystal frame can
 
 """, version = scriptID)
 
-outputChoices = {
+representations = {
-                  'quaternion': ['quat',4],
+                  'quaternion': ['quat',4], #ToDo: Use here Rowenhorst names (qu/ro/om/ax?)
-                  'rodrigues':  ['rodr',3],
+                  'rodrigues':  ['rodr',4],
                   'eulers':     ['eulr',3],
                   'matrix':     ['mtrx',9],
                   'angleaxis':  ['aaxs',4],
@@ -58,7 +33,7 @@ parser.add_option('-o',
                   '--output',
                   dest = 'output',
                   action = 'extend', metavar = '<string LIST>',
-                  help = 'output orientation formats {{{}}}'.format(', '.join(outputChoices)))
+                  help = 'output orientation formats {{{}}}'.format(', '.join(representations)))
 parser.add_option('-d',
                   '--degrees',
                   dest = 'degrees',
@@ -68,12 +43,12 @@ parser.add_option('-R',
                   '--labrotation',
                   dest='labrotation',
                   type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'angle and axis of additional lab frame rotation')
+                  help = 'angle and axis of additional lab frame rotation [%default]')
 parser.add_option('-r',
                   '--crystalrotation',
                   dest='crystalrotation',
                   type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
-                  help = 'angle and axis of additional crystal frame rotation')
+                  help = 'angle and axis of additional crystal frame rotation [%default]')
 parser.add_option('--eulers',
                   dest = 'eulers',
                   metavar = 'string',
@@ -104,16 +79,15 @@ parser.add_option('-z',
                   help = 'label of lab z vector (expressed in crystal coords)')
 
 parser.set_defaults(output = [],
-                    labrotation     = (0.,1.,1.,1.),                                                # no rotation about 1,1,1
+                    labrotation     = (0.,1.,0.,0.),                                                # no rotation about 1,0,0
-                    crystalrotation = (0.,1.,1.,1.),                                                # no rotation about 1,1,1
+                    crystalrotation = (0.,1.,0.,0.),                                                # no rotation about 1,0,0
-                    degrees = False,
                    )
 
 (options, filenames) = parser.parse_args()
 
 options.output = list(map(lambda x: x.lower(), options.output))
-if options.output == [] or (not set(options.output).issubset(set(outputChoices))):
+if options.output == [] or (not set(options.output).issubset(set(representations))):
-  parser.error('output must be chosen from {}.'.format(', '.join(outputChoices)))
+  parser.error('output must be chosen from {}.'.format(', '.join(representations)))
 
 input = [options.eulers     is not None,
          options.rodrigues  is not None,
@@ -126,16 +100,18 @@ input = [options.eulers     is not None,
 
 if np.sum(input) != 1: parser.error('needs exactly one input format.')
 
-(label,dim,inputtype) = [(options.eulers,3,'eulers'),
+(label,dim,inputtype) = [(options.eulers,representations['eulers'][1],'eulers'),
-                         (options.rodrigues,3,'rodrigues'),
+                         (options.rodrigues,representations['rodrigues'][1],'rodrigues'),
                          ([options.x,options.y,options.z],[3,3,3],'frame'),
-                         (options.matrix,9,'matrix'),
+                         (options.matrix,representations['matrix'][1],'matrix'),
-                         (options.quaternion,4,'quaternion'),
+                         (options.quaternion,representations['quaternion'][1],'quaternion'),
                         ][np.where(input)[0][0]]                                                    # select input label that was requested
 
-toRadians = np.pi/180.0 if options.degrees else 1.0                                                 # rescale degrees to radians
+crystalrotation = np.array(options.crystalrotation[1:4] + (options.crystalrotation[0],))            # Compatibility hack
-r = damask.Quaternion.fromAngleAxis(toRadians*options.crystalrotation[0],options.crystalrotation[1:]) # crystal frame rotation
+labrotation     = np.array(options.labrotation[1:4]     + (options.labrotation[0],))                # Compatibility hack
-R = damask.Quaternion.fromAngleAxis(toRadians*options.    labrotation[0],options.    labrotation[1:]) #     lab frame rotation
+r = damask.Rotation.fromAxisAngle(crystalrotation,options.degrees)                                  # crystal frame rotation
+R = damask.Rotation.fromAxisAngle(labrotation,options.degrees)                                      #     lab frame rotation
+
 
 # --- loop over input files ------------------------------------------------------------------------
 
@@ -169,9 +145,9 @@ for name in filenames:
 
   table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
   for output in options.output:
-    if output in outputChoices:
+    if output in representations:
-      table.labels_append(['{}_{}({})'.format(i+1,outputChoices[output][0],label) \
+      table.labels_append(['{}_{}({})'.format(i+1,representations[output][0],label) \
-                           for i in range(outputChoices[output][1])])
+                           for i in range(representations[output][1])])
   table.head_write()
 
 # ------------------------------------------ process data ------------------------------------------
@@ -179,30 +155,35 @@ for name in filenames:
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
     if   inputtype == 'eulers':
+      l = representations['eulers'][1]
+      o = damask.Rotation.fromEulers(list(map(float,table.data[column:column+l])),options.degrees)
       
-      o = damask.Orientation(Eulers = check_Eulers(np.array(list(map(float,table.data[column:column+3])))*toRadians))
     elif inputtype == 'rodrigues':
-      o = damask.Orientation(Rodrigues = np.array(list(map(float,table.data[column:column+3]))))
+      l = representations['rodrigues'][1]
-    elif inputtype == 'matrix':
+      o = damask.Rotation.fromRodrigues(list(map(float,table.data[column:column+l])))
+      
+    elif inputtype == 'matrix':
+      l = representations['matrix'][1]
+      o = damask.Rotation.fromMatrix(list(map(float,table.data[column:column+l])))
 
-      o = damask.Orientation(matrix = check_matrix(np.array(list(map(float,table.data[column:column+9]))).reshape(3,3)))
     elif inputtype == 'frame':
       M = np.array(list(map(float,table.data[column[0]:column[0]+3] + \
                                   table.data[column[1]:column[1]+3] + \
                                   table.data[column[2]:column[2]+3]))).reshape(3,3).T
-      o = damask.Orientation(matrix = check_matrix(M/np.linalg.norm(M,axis=0)))
+      o = damask.Rotation.fromMatrix(M/np.linalg.norm(M,axis=0))
+      
     elif inputtype == 'quaternion':
+      l = representations['quaternion'][1]
+      o = damask.Rotation.fromQuaternion(list(map(float,table.data[column:column+l])))
 
-      o = damask.Orientation(quaternion = check_quaternion(np.array(list(map(float,table.data[column:column+4])))))
+    o= r*o*R                                                                                        # apply additional lab and crystal frame rotations
-
-    o.quaternion = r*o.quaternion*R                                                                 # apply additional lab and crystal frame rotations
 
     for output in options.output:
       if   output == 'quaternion': table.data_append(o.asQuaternion())
       elif output == 'rodrigues':  table.data_append(o.asRodrigues())
       elif output == 'eulers':     table.data_append(o.asEulers(degrees=options.degrees))
       elif output == 'matrix':     table.data_append(o.asMatrix())
-      elif output == 'angleaxis':  table.data_append(o.asAngleAxis(degrees=options.degrees,flat=True))
+      elif output == 'angleaxis':  table.data_append(o.asAxisAngle(degrees=options.degrees))
     outputAlive = table.data_write()                                                                # output processed line
 
 # ------------------------------------------ output finalization -----------------------------------  

processing/post/addPK2.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing Second Piola--Kirchhoff stress based on given column(s) of deformation
 gradient and first Piola--Kirchhoff stress.
 

processing/post/addPole.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add coordinates of stereographic projection of given direction (pole) in crystal frame.
 
 """, version = scriptID)
@@ -35,7 +35,6 @@ parser.add_option('-o',
 
 parser.set_defaults(pole = (1.0,0.0,0.0),
                     quaternion = 'orientation',
-                    polar   = False,
                    )
 
 (options, filenames) = parser.parse_args()
@@ -76,9 +75,9 @@ for name in filenames:
 # ------------------------------------------ process data ------------------------------------------
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))))
+    o = damask.Rotation(np.array(list(map(float,table.data[column:column+4]))))
 
-    rotatedPole = o.quaternion*pole                                                                 # rotate pole according to crystal orientation
+    rotatedPole = o*pole                                                                 # rotate pole according to crystal orientation
     (x,y) = rotatedPole[0:2]/(1.+abs(pole[2]))                                                      # stereographic projection
 
     table.data_append([np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y])               # cartesian coordinates

processing/post/addSchmidfactors.py

@@ -103,7 +103,7 @@ slipSystems = {
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
 
 """, version = scriptID)
@@ -115,7 +115,7 @@ parser.add_option('-l',
                   help = 'type of lattice structure [%default] {}'.format(latticeChoices))
 parser.add_option('--covera',
                   dest = 'CoverA', type = 'float', metavar = 'float',
-                  help = 'C over A ratio for hexagonal systems')
+                  help = 'C over A ratio for hexagonal systems [%default]')
 parser.add_option('-f',
                   '--force',
                   dest = 'force',
@@ -212,10 +212,10 @@ for name in filenames:
 
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))))
+    o = damask.Rotation(list(map(float,table.data[column:column+4])))
 
-    table.data_append(  np.abs(  np.sum(slip_direction * (o.quaternion * force) ,axis=1) \
+    table.data_append(  np.abs(  np.sum(slip_direction * (o * force) ,axis=1) \
-                               * np.sum(slip_normal    * (o.quaternion * normal),axis=1)))
+                               * np.sum(slip_normal    * (o * normal),axis=1)))
     outputAlive = table.data_write()                                                                # output processed line
 
 # ------------------------------------------ output finalization -----------------------------------  

processing/post/addSpectralDecomposition.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing eigenvalues and eigenvectors of requested symmetric tensor column(s).
 
 """, version = scriptID)

processing/post/addStrainTensors.py

@@ -25,7 +25,7 @@ def operator(stretch,strain,eigenvalues):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Add column(s) containing given strains based on given stretches of requested deformation gradient column(s).
 
 """, version = scriptID)
@@ -56,16 +56,15 @@ parser.add_option('-f','--defgrad',
                   metavar = '<string LIST>',
                   help = 'heading(s) of columns containing deformation tensor values [%default]')
 
-parser.set_defaults(right       = False,
+parser.set_defaults(
-                    left        = False,
-                    logarithmic = False,
-                    biot        = False,
-                    green       = False,
                     defgrad     = ['f'],
                    )
 
 (options,filenames) = parser.parse_args()
 
+if len(options.defgrad) > 1:
+  options.defgrad = options.defgrad[1:]
+
 stretches = []
 strains = []
 

processing/post/addTable.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -12,7 +12,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Append data of ASCIItable(s).
 
 """, version = scriptID)
@@ -24,6 +24,10 @@ parser.add_option('-a', '--add','--table',
 
 (options,filenames) = parser.parse_args()
 
+if options.table is None:
+  parser.error('no table specified.')
+
+
 # --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]

processing/post/averageDown.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Average each data block of size 'packing' into single values thus reducing the former grid to grid/packing.
 
 """, version = scriptID)
@@ -34,16 +34,14 @@ parser.add_option('--shift',
 parser.add_option('-g', '--grid',
                   dest = 'grid',
                   type = 'int', nargs = 3, metavar = 'int int int',
-                  help = 'grid in x,y,z [autodetect]')
+                  help = 'grid in x,y,z (optional)')
 parser.add_option('-s', '--size',
                   dest = 'size',
                   type = 'float', nargs = 3, metavar = 'float float float',
-                  help = 'size in x,y,z [autodetect]')
+                  help = 'size in x,y,z (optional)')
 parser.set_defaults(pos     = 'pos',
                     packing = (2,2,2),
                     shift   = (0,0,0),
-                    grid    = (0,0,0),
-                    size    = (0.0,0.0,0.0),
                    )
 
 (options,filenames) = parser.parse_args()
@@ -92,7 +90,7 @@ for name in filenames:
 
   table.data_readArray()
 
-  if (any(options.grid) == 0 or any(options.size) == 0.0):
+  if (options.grid is None or options.size is None):
     grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
   else:
     grid   = np.array(options.grid,'i')

processing/post/binXY.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map.
 
 """, version = scriptID)
@@ -37,15 +37,15 @@ parser.add_option('-t','--type',
 parser.add_option('-x','--xrange',
                   dest = 'xrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in x direction [autodetect]')
+                  help = 'min max limits in x direction (optional)')
 parser.add_option('-y','--yrange',
                   dest = 'yrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in y direction [autodetect]')
+                  help = 'min max limits in y direction (optional)')
 parser.add_option('-z','--zrange',
                   dest = 'zrange',
                   type = 'float', nargs = 2, metavar = 'float float',
-                  help = 'min max value in z direction [autodetect]')
+                  help = 'min max limits in z direction (optional)')
 parser.add_option('-i','--invert',
                   dest = 'invert',
                   action = 'store_true',
@@ -64,9 +64,6 @@ parser.set_defaults(bins = (10,10),
                     xrange = (0.0,0.0),
                     yrange = (0.0,0.0),
                     zrange = (0.0,0.0),
-                    invert = False,
-                    normRow = False,
-                    normCol = False,
                    )
 
 (options,filenames) = parser.parse_args()

processing/post/blowUp.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Blows up each value to a surrounding data block of size 'packing' thus increasing the former resolution
 to resolution*packing.
 
@@ -27,10 +27,10 @@ parser.add_option('-p','--packing',
                   help = 'dimension of packed group [%default]')
 parser.add_option('-g','--grid',
                   dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
-                  help = 'resolution in x,y,z [autodetect]')
+                  help = 'grid in x,y,z (optional)')
 parser.add_option('-s','--size',
                   dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
-                  help = 'dimension in x,y,z [autodetect]')
+                  help = 'size in x,y,z (optional)')
 parser.set_defaults(pos  = 'pos',
                     packing = (2,2,2),
                     grid    = (0,0,0),

processing/post/filterTable.py

@@ -30,7 +30,7 @@ def sortingList(labels,whitelistitems):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Filter rows according to condition and columns by either white or black listing.
 
 Examples:

processing/post/groupTable.py

@@ -20,7 +20,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Apply a user-specified function to condense into a single row all those rows for which columns 'label' have identical values.
 Output table will contain as many rows as there are different (unique) values in the grouping column(s).
 Periodic domain averaging of coordinate values is supported.

processing/post/permuteData.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Permute all values in given column(s).
 
 """, version = scriptID)

processing/post/reLabel.py

@@ -12,7 +12,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] dfile[s]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Rename scalar, vectorial, and/or tensorial data header labels.
 
 """, version = scriptID)

processing/post/rotateData.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math
+import os,sys
 import numpy as np
 from optparse import OptionParser
 import damask
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Rotate vector and/or tensor column data by given angle around given axis.
 
 """, version = scriptID)
@@ -29,7 +29,7 @@ parser.add_option('-r', '--rotation',
 parser.add_option('--degrees',
                   dest = 'degrees',
                   action = 'store_true',
-                  help = 'angles are given in degrees [%default]')
+                  help = 'angles are given in degrees')
 
 parser.set_defaults(rotation = (0.,1.,1.,1.),                                                       # no rotation about 1,1,1
                     degrees = False,
@@ -40,9 +40,8 @@ parser.set_defaults(rotation = (0.,1.,1.,1.),
 if options.data is None:
   parser.error('no data column specified.')
 
-toRadians = math.pi/180.0 if options.degrees else 1.0                                               # rescale degrees to radians
+rotation = np.array(options.rotation[1:4]+(options.rotation[0],))                                   # Compatibility hack
-q = damask.Quaternion().fromAngleAxis(toRadians*options.rotation[0],options.rotation[1:])
+r = damask.Rotation.fromAxisAngle(rotation,options.degrees,normalise=True)
-R = q.asMatrix()
 
 # --- loop over input files -------------------------------------------------------------------------
 
@@ -90,12 +89,11 @@ for name in filenames:
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
     for v in active['vector']:
       column = table.label_index(v)
-      table.data[column:column+3] = q * np.array(list(map(float,table.data[column:column+3])))
+      table.data[column:column+3] = r * np.array(list(map(float,table.data[column:column+3])))
     for t in active['tensor']:
       column = table.label_index(t)
-      table.data[column:column+9] = \
+      table.data[column:column+9] = (r * np.array(list(map(float,table.data[column:column+9]))).reshape((3,3))).reshape(9)
-        np.dot(R,np.dot(np.array(list(map(float,table.data[column:column+9]))).reshape((3,3)),
+      
-                        R.transpose())).reshape((9))
     outputAlive = table.data_write()                                                                # output processed line
 
 # ------------------------------------------ output finalization -----------------------------------  

processing/post/scaleData.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Uniformly scale column values by given factor.
 
 """, version = scriptID)

processing/post/shiftData.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Uniformly shift column values by given offset.
 
 """, version = scriptID)

processing/post/sortTable.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Sort rows by given (or all) column label(s).
 
 Examples:

processing/post/viewTable.py

@@ -12,7 +12,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(usage='%prog [options] [file[s]]', description = """
+parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
 Show components of given ASCIItable(s).
 
 """, version = scriptID)

processing/post/vtk_addGridData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk
@@ -17,7 +17,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 msg = "Add scalars, vectors, and/or an RGB tuple from"
 msg += "an ASCIItable to existing VTK grid (.vtr/.vtk/.vtu)."
 parser = OptionParser(option_class=damask.extendableOption,
-                      usage='%prog options [file[s]]',
+                      usage='%prog options [ASCIItable(s)]',
                       description = msg,
                       version = scriptID)
 
@@ -25,10 +25,6 @@ parser.add_option(      '--vtk',
                   dest = 'vtk',
                   type = 'string', metavar = 'string',
                   help = 'VTK file name')
-parser.add_option(      '--inplace',
-                  dest = 'inplace',
-                  action = 'store_true',
-                  help = 'modify VTK file in-place')
 parser.add_option('-r', '--render',
                   dest = 'render',
                   action = 'store_true',
@@ -49,7 +45,6 @@ parser.add_option('-c', '--color',
 parser.set_defaults(data = [],
                     tensor = [],
                     color = [],
-                    inplace = False,
                     render = False,
 )
 
@@ -58,30 +53,32 @@ parser.set_defaults(data = [],
 if not options.vtk:                 parser.error('No VTK file specified.')
 if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
 
-if os.path.splitext(options.vtk)[1] == '.vtr':
+vtk_file,vtk_ext = os.path.splitext(options.vtk)
+
+if vtk_ext == '.vtr':
   reader = vtk.vtkXMLRectilinearGridReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   rGrid = reader.GetOutput()
   writer = vtk.vtkXMLRectilinearGridWriter()
-  writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
+elif vtk_ext == '.vtk':
-elif os.path.splitext(options.vtk)[1] == '.vtk':
   reader = vtk.vtkGenericDataObjectReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   rGrid = reader.GetRectilinearGridOutput()
   writer = vtk.vtkXMLRectilinearGridWriter()
-  writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
+  vtk_ext = '.vtr'
-elif os.path.splitext(options.vtk)[1] == '.vtu':
+elif vtk_ext == '.vtu':
   reader = vtk.vtkXMLUnstructuredGridReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   rGrid = reader.GetOutput()
   writer = vtk.vtkXMLUnstructuredGridWriter()
-  writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtu' if options.inplace else '_added.vtu'))
 else:
   parser.error('Unsupported VTK file type extension.')
 
+writer.SetFileName(vtk_file+vtk_ext)
+
 Npoints = rGrid.GetNumberOfPoints()
 Ncells  = rGrid.GetNumberOfCells()
 
@@ -172,8 +169,7 @@ for name in filenames:
 
   writer.SetDataModeToBinary()
   writer.SetCompressorTypeToZLib()
-  if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
+  writer.SetInputData(rGrid)
-  else:                          writer.SetInputData(rGrid)
   writer.Write()
 
 # ------------------------------------------ render result ---------------------------------------

processing/post/vtk_addPointCloudData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk
@@ -15,7 +15,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 # --------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption,
-                      usage='%prog options [file[s]]',
+                      usage='%prog options [ASCIItable(s)]',
                       description = """Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).""",
                       version = scriptID)
 
@@ -23,10 +23,6 @@ parser.add_option(      '--vtk',
                   dest = 'vtk',
                   type = 'string', metavar = 'string',
                   help = 'VTK file name')
-parser.add_option(      '--inplace',
-                  dest = 'inplace',
-                  action = 'store_true',
-                  help = 'modify VTK file in-place')
 parser.add_option('-r', '--render',
                   dest = 'render',
                   action = 'store_true',
@@ -46,8 +42,6 @@ parser.add_option('-c', '--color',   dest='color', action='extend',
 parser.set_defaults(data = [],
                     tensor = [],
                     color = [],
-                    inplace = False,
-                    render = False,
 )
 
 (options, filenames) = parser.parse_args()
@@ -55,16 +49,19 @@ parser.set_defaults(data = [],
 if not options.vtk:                 parser.error('no VTK file specified.')
 if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
 
-if os.path.splitext(options.vtk)[1] == '.vtp':
+vtk_file,vtk_ext = os.path.splitext(options.vtk)
+
+if vtk_ext == '.vtp':
   reader = vtk.vtkXMLPolyDataReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   Polydata = reader.GetOutput()
-elif os.path.splitext(options.vtk)[1] == '.vtk':
+elif vtk_ext == '.vtk':
   reader = vtk.vtkGenericDataObjectReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   Polydata = reader.GetPolyDataOutput()
+  vtk_ext = '.vtp'
 else:
   parser.error('unsupported VTK file type extension.')
 
@@ -151,14 +148,12 @@ for name in filenames:
 # ------------------------------------------ output result ---------------------------------------
 
   Polydata.Modified()
-  if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
 
   writer = vtk.vtkXMLPolyDataWriter()
   writer.SetDataModeToBinary()
   writer.SetCompressorTypeToZLib()
-  writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtp' if options.inplace else '_added.vtp'))
+  writer.SetFileName(vtk_file+vtk_ext)
-  if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
+  writer.SetInputData(Polydata)
-  else:                          writer.SetInputData(Polydata)
   writer.Write()
 
 # ------------------------------------------ render result ---------------------------------------

processing/post/vtk_addRectilinearGridData.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,vtk
@@ -25,10 +25,6 @@ parser.add_option(      '--vtk',
                   dest = 'vtk',
                   type = 'string', metavar = 'string',
                   help = 'VTK file name')
-parser.add_option(      '--inplace',
-                  dest = 'inplace',
-                  action = 'store_true',
-                  help = 'modify VTK file in-place')
 parser.add_option('-r', '--render',
                   dest = 'render',
                   action = 'store_true',
@@ -49,7 +45,6 @@ parser.add_option('-c', '--color',
 parser.set_defaults(data = [],
                     tensor = [],
                     color = [],
-                    inplace = False,
                     render = False,
 )
 
@@ -58,16 +53,18 @@ parser.set_defaults(data = [],
 if not options.vtk:                 parser.error('no VTK file specified.')
 if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
 
-if os.path.splitext(options.vtk)[1] == '.vtr':
+vtk_file,vtk_ext = os.path.splitext(options.vtk)
+if vtk_ext == '.vtr':
   reader = vtk.vtkXMLRectilinearGridReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   rGrid = reader.GetOutput()
-elif os.path.splitext(options.vtk)[1] == '.vtk':
+elif vtk_ext == '.vtk':
   reader = vtk.vtkGenericDataObjectReader()
   reader.SetFileName(options.vtk)
   reader.Update()
   rGrid = reader.GetRectilinearGridOutput()
+  vtk_ext = '.vtr'
 else:
   parser.error('unsupported VTK file type extension.')
 
@@ -158,16 +155,14 @@ for name in filenames:
       elif mode == 'point': rGrid.GetPointData().AddArray(VTKarray[me])
 
   rGrid.Modified()
-  if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update()
 
 # ------------------------------------------ output result ---------------------------------------
 
   writer = vtk.vtkXMLRectilinearGridWriter()
   writer.SetDataModeToBinary()
   writer.SetCompressorTypeToZLib()
-  writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
+  writer.SetFileName(vtk_file+vtk_ext)
-  if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
+  writer.SetInputData(rGrid)
-  else:                          writer.SetInputData(rGrid)
   writer.Write()
 
 # ------------------------------------------ render result ---------------------------------------

processing/post/vtk_pointCloud.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,vtk
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
 
 """, version = scriptID)
@@ -78,7 +78,6 @@ for name in filenames:
   Polydata.SetPoints(Points)
   Polydata.SetVerts(Vertices)
   Polydata.Modified()
-  if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
  
 # ------------------------------------------ output result ---------------------------------------  
 
@@ -94,8 +93,8 @@ for name in filenames:
     writer.SetHeader('# powered by '+scriptID)
     writer.WriteToOutputStringOn()
   
-  if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
+  
-  else:                          writer.SetInputData(Polydata)
+  writer.SetInputData(Polydata)
 
   writer.Write()
 

processing/post/vtk_rectilinearGrid.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,vtk
@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
 Create regular voxel grid from points in an ASCIItable.
 
 """, version = scriptID)
@@ -125,8 +125,7 @@ for name in filenames:
     writer.SetHeader('# powered by '+scriptID)
     writer.WriteToOutputStringOn()
   
-  if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
+  writer.SetInputData(rGrid)
-  else:                          writer.SetInputData(rGrid)
 
   writer.Write()
 

processing/pre/3DRVEfrom2Dang.py

@@ -1,119 +0,0 @@
-#!/usr/bin/env python2.7
-# -*- coding: UTF-8 no BOM -*-
-
-import os,sys,math
-from optparse import OptionParser
-import damask
-import pipes
-
-scriptName = os.path.splitext(os.path.basename(__file__))[0]
-scriptID   = ' '.join([scriptName,damask.version])
-
-# --------------------------------------------------------------------
-#                                MAIN
-# --------------------------------------------------------------------
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', 
-                      description ='generate 3D RVE from .ang files of EBSD slices .',
-                      version = scriptID)
-
-parser.add_option('--offset',
-                  dest='offset',
-                  type='float',
-                  help='offset of EBSD slices [%default]',
-                  metavar='float')
-parser.add_option('--outname',
-                  dest='outName',
-                  type='string',
-                  help='output file name [%default]',  metavar='string')    
-parser.add_option('--vtr',
-                  action="store_true",
-                  dest='vtr')
-parser.add_option('--geom',
-                  action="store_true",
-                  dest='geom')
-parser.set_defaults(offset = 1.0,
-                    outName = 'RVE3D')
-
-(options,filenames) = parser.parse_args()
-
-numFiles = len(filenames)
-formatwidth = 1+int(math.log10(numFiles))
-
-# copy original files to tmp files to not alter originals
-for i in range(numFiles):
-  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
-  strCommand = 'cp ' + pipes.quote(filenames[i]) + ' ' + sliceID
-  os.system(strCommand)
-
-# modify tmp files
-print('Add z-coordinates')
-for i in range(numFiles):
-  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
-  strCommand = 'OIMgrainFile_toTable ' + sliceID
-  os.system(strCommand)
-  strCommand = 'addCalculation --label 3Dpos --formula "np.array(#pos#.tolist()+[' + str(i*options.offset) + '])" ' + sliceID
-  os.system(strCommand)
-
-# join temp files into one
-
-print('\n Colocate files')
-fileOut = open(options.outName + '.ang','w')
-
-# take header information from 1st file
-sliceID = 'slice' + str(0).zfill(formatwidth) + '.tmp'
-fileRead = open(sliceID)
-data = fileRead.readlines()
-fileRead.close()
-headerLines = int(data[0].split()[0])
-fileOut.write(str(headerLines+1) + '\t header\n')
-for line in data[1:headerLines]:
-  fileOut.write(line)
-fileOut.write(scriptID + '\t' + ' '.join(sys.argv[1:]) + '\n')
-for line in data[headerLines:]:
-  fileOut.write(line)
-
-# append other files content without header
-for i in range(numFiles-1):
-  sliceID = 'slice' + str(i+1).zfill(formatwidth) + '.tmp'
-  fileRead = open(sliceID)
-  data = fileRead.readlines()
-  fileRead.close()
-  headerLines = int(data[0].split()[0])
-  for line in data[headerLines+1:]:
-    fileOut.write(line)
-fileOut.close()
-
-# tidy up and add phase column 
-print('\n Remove temp data and add phase info')
-strCommand = 'filterTable --black pos ' + options.outName + '.ang'
-os.system(strCommand)
-strCommand = 'reLabel --label 3Dpos --substitute pos ' + options.outName + '.ang'
-os.system(strCommand)
-strCommand = 'addCalculation -l phase -f 1 ' + options.outName + '.ang'
-os.system(strCommand)
-
-
-# create geom file when asked for
-if options.geom:
-  print('\n Build geometry file')
-  strCommand = 'geom_fromTable --phase phase --eulers euler --coordinates pos ' + pipes.quote(options.outName) + '.ang'
-  os.system(strCommand)
-
-# create paraview file when asked for
-
-if options.vtr:
-  print('\n Build Paraview file')
-  strCommand = 'addIPFcolor --eulers euler --pole 0.0 0.0 1.0 ' + options.outName + '.ang'
-  os.system(strCommand)
-  strCommand = 'vtk_rectilinearGrid ' + pipes.quote(options.outName) + '.ang'
-  os.system(strCommand)
-  os.rename(pipes.quote(options.outName) + '_pos(cell)'+'.vtr', pipes.quote(options.outName) + '.vtr')
-  strCommand = 'vtk_addRectilinearGridData --vtk '+ pipes.quote(options.outName) + '.vtr --color IPF_001_cubic '\
-               + pipes.quote(options.outName) + '.ang'
-  os.system(strCommand)
-  
-# delete tmp files
-for i in range(numFiles):
-  sliceID = 'slice' + str(i).zfill(formatwidth) + '.tmp'
-  os.remove(sliceID)

processing/pre/geom_addPrimitive.py

@@ -25,7 +25,7 @@ mappings = {
         'microstructures': lambda x: int(x),
           }
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [geomfile(s)]', description = """
 Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
 Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
 
@@ -43,7 +43,7 @@ parser.add_option('-f', '--fill',       dest='fill', type='int', metavar = 'int'
                   help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
 parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4),
                   help = 'rotation of primitive as quaternion')
-parser.add_option('-a', '--angleaxis',  dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4),
+parser.add_option('-a', '--angleaxis',  dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4), type=float,
                   help = 'angle,x,y,z clockwise rotation of primitive about axis by angle')
 parser.add_option(     '--degrees',     dest='degrees', action='store_true',
                   help = 'angle is given in degrees [%default]')
@@ -63,14 +63,12 @@ parser.set_defaults(center = (.0,.0,.0),
 if options.dimension is None:
   parser.error('no dimension specified.')   
 if options.angleaxis is not None:
-  options.angleaxis = list(map(float,options.angleaxis))
+  ax = np.array(options.angleaxis[1:4] + (options.angleaxis[0],))   # Compatibility hack
-  rotation = damask.Quaternion.fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0],
+  rotation = damask.Rotation.fromAxisAngle(ax,options.degrees,normalise=True)
-                                             options.angleaxis[1:4])
 elif options.quaternion is not None:
-  options.quaternion = list(map(float,options.quaternion))
+  rotation = damask.Rotation.fromQuaternion(options.quaternion)
-  rotation = damask.Quaternion(quat=options.quaternion)
 else:
-  rotation = damask.Quaternion()
+  rotation = damask.Rotation()
 
 options.center = np.array(options.center)
 options.dimension = np.array(options.dimension)
@@ -159,8 +157,7 @@ for name in filenames:
   X -= options.center[0] - 0.5
   Y -= options.center[1] - 0.5
   Z -= options.center[2] - 0.5
-  # and then by applying the quaternion
+  # and then by applying the rotation
-  # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script
   (X, Y, Z) = rotation * (X, Y, Z)
   # and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
   X /= options.dimension[0] * 0.5

processing/pre/geom_check.sh

@@ -18,8 +18,8 @@ do
   < $geom \
   | \
   vtk_addRectilinearGridData \
+    --vtk ${geom%.*}.vtk \
     --data microstructure \
-    --inplace \
+
-    --vtk ${geom%.*}.vtk
   rm ${geom%.*}.vtk
 done

processing/pre/geom_clean.py

@@ -18,7 +18,7 @@ def mostFrequent(arr):
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
 Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
 
 """, version=scriptID)

processing/pre/geom_fromDREAM3D.py

@@ -0,0 +1,189 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 no BOM -*-
+
+import os,sys,h5py
+import numpy as np
+from optparse import OptionParser
+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 [dream3dfile[s]]', description = """
+Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
+from grain data (individual grains are segmented). Requires orientation data as quaternion.
+
+""", version = scriptID)
+
+parser.add_option('-b','--basegroup',
+                  dest = 'basegroup', metavar = 'string',
+                  help = 'name of the group in "DataContainers" that contains all the data')
+parser.add_option('-p','--pointwise',
+                  dest = 'pointwise', metavar = 'string',
+                  help = 'name of the group in "DataContainers/<basegroup>" that contains pointwise data [%default]')
+parser.add_option('-a','--average',
+                  dest = 'average', metavar = 'string',
+                  help = 'name of the group in "DataContainers</basegroup>" that contains grain average data. '\
+                       + 'Leave empty for pointwise data')
+parser.add_option('--phase',
+                  dest = 'phase',
+                  type = 'string', metavar = 'string',
+                  help = 'name of the dataset containing pointwise/average phase IDs [%default]')
+parser.add_option('--microstructure',
+                  dest = 'microstructure',
+                  type = 'string', metavar = 'string',
+                  help = 'name of the dataset connecting pointwise and average data [%default]')
+parser.add_option('-q', '--quaternion',
+                  dest = 'quaternion',
+                  type = 'string', metavar='string',
+                  help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
+
+parser.set_defaults(pointwise      = 'CellData',
+                    quaternion     = 'Quats',
+                    phase          = 'Phases',
+                    microstructure = 'FeatureIds',
+                    crystallite    = 1,
+                   )
+
+(options, filenames) = parser.parse_args()
+
+if options.basegroup is None:
+  parser.error('No base group selected')
+
+rootDir ='DataContainers'
+
+# --- loop over input files -------------------------------------------------------------------------
+
+if filenames == []: parser.error('no input file specified.')
+
+for name in filenames:
+  try:
+    table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.geom',
+                              buffered = False, labeled=False,
+                              )
+  except: continue
+  damask.util.report(scriptName,name)
+
+  errors = []
+  
+  info = {}
+  ori  = []
+  inFile = h5py.File(name, 'r')
+  group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
+  try:
+    info['size']   = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
+                   * inFile[os.path.join(group_geom,'SPACING')][...]
+    info['grid']   = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
+    info['origin'] = inFile[os.path.join(group_geom,'ORIGIN')][...]
+  except:
+    errors.append('Geometry data ({}) not found'.format(group_geom))
+    
+    
+  group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
+  if options.average is None:
+    label = 'point'
+    N_microstructure = np.product(info['grid'])
+    
+    dataset = os.path.join(group_pointwise,options.quaternion)
+    try:
+      quats = np.reshape(inFile[dataset][...],(N_microstructure,3))
+    except:
+      errors.append('Pointwise orientation data ({}) not found'.format(dataset))
+      
+    texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
+
+    dataset = os.path.join(group_pointwise,options.phase)
+    try:
+      phase = np.reshape(inFile[dataset][...],(N_microstructure))
+    except:
+      errors.append('Pointwise phase data ({}) not found'.format(dataset))
+
+    
+  else:
+    label = 'grain'
+    
+    dataset = os.path.join(group_pointwise,options.microstructure)
+    try:
+      microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
+      N_microstructure = np.max(microstructure)
+    except:
+      errors.append('Link between pointwise and grain average data ({}) not found'.format(dataset))
+
+    group_average = os.path.join(rootDir,options.basegroup,options.average)
+    
+    dataset = os.path.join(group_average,options.quaternion)
+    try:
+      texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]]     # skip first entry (unindexed)
+    except:
+      errors.append('Average orientation data ({}) not found'.format(dataset))
+      
+    dataset = os.path.join(group_average,options.phase)
+    try:
+      phase = [i[0] for i in inFile[dataset][...]][1:]                                              # skip first entry (unindexed)
+    except:
+      errors.append('Average phase data ({}) not found'.format(dataset))
+
+  if errors != []:
+    damask.util.croak(errors)
+    table.close(dismiss = True)
+    continue
+    
+    
+  mat = damask.Material()
+  mat.verbose = False
+
+  # dummy <homogenization>
+  h = damask.config.material.Homogenization()
+  mat.add_section('Homogenization','none',h)
+  info['homogenization'] = 1
+  
+  # <crystallite> placeholder (same for all microstructures at the moment)
+  c = damask.config.material.Crystallite()
+  mat.add_section('Crystallite','tbd',c)
+  
+  # <phase> placeholders
+  for i in range(np.max(phase)):
+    p = damask.config.material.Phase()
+    mat.add_section('phase','phase{}-tbd'.format(i+1),p)
+
+  # <texture>
+  for i,o in enumerate(texture):
+    t = damask.config.material.Texture()
+    t.add_component('gauss',{'eulers':o.asEulers(degrees=True)})
+    mat.add_section(part='texture', section='{}{}'.format(label,i+1),initialData=t)
+  
+  # <microstructure>
+  for i in range(N_microstructure):
+    m = damask.config.material.Microstructure()
+    mat.add_section('microstructure','{}{}'.format(label,i+1),m)
+    mat.add_microstructure('{}{}'.format(label,i+1),
+                           {'phase':  'phase{}-tbd'.format(phase[i]),
+                            'texture':'{}{}'.format(label,i+1),
+                            'crystallite':'tbd',
+                            'fraction':1
+                            })
+    
+  table.info_append([
+    scriptID + ' ' + ' '.join(sys.argv[1:]),
+    "grid\ta {}\tb {}\tc {}".format(*info['grid']),
+    "size\tx {}\ty {}\tz {}".format(*info['size']),
+    "origin\tx {}\ty {}\tz {}".format(*info['origin']),
+    "homogenization\t{}".format(info['homogenization']),
+    str(mat).split('\n')
+    ])
+  table.head_write()
+  
+  if options.average is None:
+    table.data = [1, 'to', format(N_microstructure)]
+    table.data_write()
+  else:
+    table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
+    table.data_writeArray()
+    
+    
+  table.close()  

processing/pre/geom_fromTable.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
-import os,sys,math,time
+import os,sys,math
-import scipy.spatial, numpy as np
+import numpy as np
 from optparse import OptionParser
 import damask
 
@@ -32,34 +32,6 @@ parser.add_option('--microstructure',
                   dest = 'microstructure',
                   type = 'string', metavar = 'string',
                   help = 'microstructure label')
-parser.add_option('-t', '--tolerance',
-                  dest = 'tolerance',
-                  type = 'float', metavar = 'float',
-                  help = 'angular tolerance for orientation squashing [%default]')
-parser.add_option('-e', '--eulers',
-                  dest = 'eulers',
-                  type = 'string', metavar = 'string',
-                  help = 'Euler angles label')
-parser.add_option('-d', '--degrees',
-                  dest = 'degrees',
-                  action = 'store_true',
-                  help = 'all angles are in degrees')
-parser.add_option('-m', '--matrix',
-                  dest = 'matrix',
-                  type = 'string', metavar = 'string',
-                  help = 'orientation matrix label')
-parser.add_option('-a',
-                  dest='a',
-                  type = 'string', metavar = 'string',
-                  help = 'crystal frame a vector label')
-parser.add_option('-b',
-                  dest='b',
-                  type = 'string', metavar = 'string',
-                  help = 'crystal frame b vector label')
-parser.add_option('-c',
-                  dest = 'c',
-                  type =  'string', metavar='string',
-                  help = 'crystal frame c vector label')
 parser.add_option('-q', '--quaternion',
                   dest = 'quaternion',
                   type = 'string', metavar='string',
@@ -67,11 +39,8 @@ parser.add_option('-q', '--quaternion',
 parser.add_option('--axes',
                   dest = 'axes',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
-                  help = 'orientation coordinate frame in terms of position coordinate frame [same]')
+                  help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
-parser.add_option('-s', '--symmetry',
+
-                  dest = 'symmetry',
-                  action = 'extend', metavar = '<string LIST>',
-                  help = 'crystal symmetry of each phase %default {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
 parser.add_option('--homogenization',
                   dest = 'homogenization',
                   type = 'int', metavar = 'int',
@@ -80,27 +49,16 @@ parser.add_option('--crystallite',
                   dest = 'crystallite',
                   type = 'int', metavar = 'int',
                   help = 'crystallite index to be used [%default]')
-parser.add_option('--verbose',
-                  dest = 'verbose', action = 'store_true',
-                  help = 'output extra info')
 
-parser.set_defaults(symmetry       = [damask.Symmetry.lattices[-1]],
+
-                    tolerance      = 0.0,
+parser.set_defaults(homogenization = 1,
-                    degrees        = False,
-                    homogenization = 1,
                     crystallite    = 1,
-                    verbose        = False,
                     pos            = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
 
-input = [options.eulers     is not None,
+input = [ options.quaternion is not None,
-         options.a          is not None and \
-         options.b          is not None and \
-         options.c          is not None,
-         options.matrix     is not None,
-         options.quaternion is not None,
          options.microstructure is not None,
         ]
 
@@ -109,14 +67,9 @@ if np.sum(input) != 1:
 if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
   parser.error('invalid axes {} {} {}.'.format(*options.axes))
 
-(label,dim,inputtype) = [(options.eulers,3,'eulers'),
+(label,dim,inputtype) = [(options.quaternion,4,'quaternion'),
-                         ([options.a,options.b,options.c],[3,3,3],'frame'),
-                         (options.matrix,9,'matrix'),
-                         (options.quaternion,4,'quaternion'),
                          (options.microstructure,1,'microstructure'),
                         ][np.where(input)[0][0]]                                                    # select input label that was requested
-toRadians = math.pi/180.0 if options.degrees else 1.0                                               # rescale all angles to radians
-threshold = np.cos(options.tolerance/2.*toRadians)                                                  # cosine of (half of) tolerance angle
 
 # --- loop over input files -------------------------------------------------------------------------
 
@@ -157,10 +110,8 @@ for name in filenames:
   
   if coordDim == 2:
     table.data = np.insert(table.data,2,np.zeros(len(table.data)),axis=1)                           # add zero z coordinate for two-dimensional input
-    if options.verbose: damask.util.croak('extending to 3D...')
   if options.phase is None:
     table.data = np.column_stack((table.data,np.ones(len(table.data))))                             # add single phase if no phase column given
-    if options.verbose: damask.util.croak('adding dummy phase info...')
 
 # --------------- figure out size and grid ---------------------------------------------------------
 
@@ -196,17 +147,10 @@ for name in filenames:
     grain = table.data[:,colOri]
     nGrains = len(np.unique(grain))
 
-  else:
+  elif inputtype == 'quaternion':
-
-    if options.verbose: bg = damask.util.backgroundMessage(); bg.start()                            # start background messaging
 
     colPhase = -1                                                                                   # column of phase data comes last
-    if options.verbose: bg.set_message('sorting positions...')
     index  = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2]))                          # index of position when sorting x fast, z slow
-    if options.verbose: bg.set_message('building KD tree...')
-    KDTree = scipy.spatial.KDTree((table.data[index,:3]-mincorner) / delta)                         # build KDTree with dX = dY = dZ = 1 and origin 0,0,0
-  
-    statistics = {'global': 0, 'local': 0}
     grain = -np.ones(N,dtype = 'int32')                                                             # initialize empty microstructure
     orientations = []                                                                               # orientations
     multiplicity = []                                                                               # orientation multiplicity (number of group members)
@@ -215,73 +159,17 @@ for name in filenames:
     existingGrains = np.arange(nGrains)
     myPos   = 0                                                                                     # position (in list) of current grid point
 
-    tick = time.clock()
-    if options.verbose: bg.set_message('assigning grain IDs...')
 
     for z in range(grid[2]):
       for y in range(grid[1]):
         for x in range(grid[0]):
-          if (myPos+1)%(N/500.) < 1:
+
-            time_delta = (time.clock()-tick) * (N - myPos) / myPos
-            if options.verbose: bg.set_message('(%02i:%02i:%02i) processing point %i of %i (grain count %i)...'
-                                            %(time_delta//3600,time_delta%3600//60,time_delta%60,myPos,N,nGrains))
 
           myData = table.data[index[myPos]]                                                         # read data for current grid point
           myPhase = int(myData[colPhase])
-          mySym = options.symmetry[min(myPhase,len(options.symmetry))-1]                            # take last specified option for all with higher index
          
-          if inputtype == 'eulers':
+          o = damask.Rotation(myData[colOri:colOri+4])
-            o = damask.Orientation(Eulers = myData[colOri:colOri+3]*toRadians,
-                                   symmetry = mySym)
-          elif inputtype == 'matrix':
-            o = damask.Orientation(matrix = myData[colOri:colOri+9].reshape(3,3),
-                                   symmetry = mySym)
-          elif inputtype == 'frame':
-            o = damask.Orientation(matrix = np.hstack((myData[colOri[0]:colOri[0]+3],
-                                                       myData[colOri[1]:colOri[1]+3],
-                                                       myData[colOri[2]:colOri[2]+3],
-                                                      )).reshape(3,3),
-                                   symmetry = mySym)
-          elif inputtype == 'quaternion':
-            o = damask.Orientation(quaternion = myData[colOri:colOri+4],
-                                   symmetry = mySym)
           
-          cos_disorientations = -np.ones(1,dtype=float)                                             # largest possible disorientation
-          closest_grain = -1                                                                        # invalid neighbor
-
-          if options.tolerance > 0.0:                                                               # only try to compress orientations if asked to
-            neighbors = np.array(KDTree.query_ball_point([x,y,z], 3))                               # point indices within radius
-# filter neighbors: skip myself, anyone further ahead (cannot yet have a grain ID), and other phases
-            neighbors = neighbors[(neighbors < myPos) & \
-                                  (table.data[index[neighbors],colPhase] == myPhase)]               
-            grains = np.unique(grain[neighbors])                                                    # unique grain IDs among valid neighbors
-
-            if len(grains) > 0:                                                                     # check immediate neighborhood first
-              cos_disorientations = np.array([o.disorientation(orientations[grainID],
-                                                               SST = False)[0].quaternion.q \
-                                              for grainID in grains])                               # store disorientation per grainID
-              closest_grain = np.argmax(cos_disorientations)                                        # grain among grains with closest orientation to myself
-              match = 'local'
-
-            if cos_disorientations[closest_grain] < threshold:                                      # orientation not close enough?
-              grains = existingGrains[np.atleast_1d( (np.array(phases) == myPhase ) & \
-                                                     (np.in1d(existingGrains,grains,invert=True)))] # other already identified grains (of my phase)
-
-              if len(grains) > 0:
-                cos_disorientations = np.array([o.disorientation(orientations[grainID],
-                                                                 SST = False)[0].quaternion.q \
-                                                for grainID in grains])                             # store disorientation per grainID
-                closest_grain = np.argmax(cos_disorientations)                                      # grain among grains with closest orientation to myself
-                match = 'global'
-
-          if cos_disorientations[closest_grain] >= threshold:                                       # orientation now close enough?
-            grainID = grains[closest_grain]
-            grain[myPos] = grainID                                                                  # assign myself to that grain ...
-            orientations[grainID] = damask.Orientation.average([orientations[grainID],o],
-                                                               [multiplicity[grainID],1])           # update average orientation of best matching grain
-            multiplicity[grainID] += 1
-            statistics[match] += 1
-          else:
           grain[myPos] = nGrains                                                                  # assign new grain to me ...
           nGrains += 1                                                                            # ... and update counter
           orientations.append(o)                                                                  # store new orientation for future comparison
@@ -291,11 +179,6 @@ for name in filenames:
 
           myPos += 1
 
-    if options.verbose:
-      bg.stop()
-      bg.join()
-      damask.util.croak("{} seconds total.\n{} local and {} global matches.".\
-                        format(time.clock()-tick,statistics['local'],statistics['global']))
     
     grain += 1                                                                                      # offset from starting index 0 to 1
      

processing/pre/geom_grainGrowth.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys,math
@@ -49,7 +49,7 @@ parser.set_defaults(d = 1,
 
 (options, filenames) = parser.parse_args()
 
-options.immutable = map(int,options.immutable)
+options.immutable = list(map(int,options.immutable))
 
 getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0)                               # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
 struc = ndimage.generate_binary_structure(3,1)                                                     # 3D von Neumann neighborhood
@@ -70,9 +70,9 @@ for name in filenames:
   table.head_read()
   info,extra_header = table.head_getGeom()
   
-  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(map(str,info['grid']))),
+  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  {}'.format(' x '.join(map(str,info['size']))),
+                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  {}'.format(' : '.join(map(str,info['origin']))),
+                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
                      'homogenization:  {}'.format(info['homogenization']),
                      'microstructures: {}'.format(info['microstructures']),
                     ])
@@ -102,9 +102,9 @@ for name in filenames:
     gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
             /np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.,dtype=np.float32)
           
-    gauss[:,:,:grid[2]/2:-1] = gauss[:,:,1:(grid[2]+1)/2]     # trying to cope with uneven (odd) grid size
+    gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2]     # trying to cope with uneven (odd) grid size
-    gauss[:,:grid[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:]
+    gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
-    gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:]
+    gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
     gauss = np.fft.rfftn(gauss).astype(np.complex64)
 
   for smoothIter in range(options.N):
@@ -119,9 +119,9 @@ for name in filenames:
                                                           microstructure,i,axis=0), j,axis=1), k,axis=2)))
 
     # periodically extend interfacial energy array by half a grid size in positive and negative directions
-    periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
+    periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                                grid[1]/2:-grid[1]/2,
+                                                                grid[1]//2:-grid[1]//2,
-                                                                grid[2]/2:-grid[2]/2]
+                                                                grid[2]//2:-grid[2]//2]
 
     # transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
     index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,                                            
@@ -148,15 +148,15 @@ for name in filenames:
                          ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
                                                             structure = struc,
                                                             iterations = int(round(options.d*2.))-1),# fat boundary
-                         periodic_bulkEnergy[grid[0]/2:-grid[0]/2,                                 # retain filled energy on fat boundary...
+                         periodic_bulkEnergy[grid[0]//2:-grid[0]//2,                                 # retain filled energy on fat boundary...
-                                             grid[1]/2:-grid[1]/2,
+                                             grid[1]//2:-grid[1]//2,
-                                             grid[2]/2:-grid[2]/2],                                # ...and zero everywhere else
+                                             grid[2]//2:-grid[2]//2],                                # ...and zero everywhere else
                          0.)).astype(np.complex64) *
                          gauss).astype(np.float32)
 
-      periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
+      periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                                grid[1]/2:-grid[1]/2,
+                                                                grid[1]//2:-grid[1]//2,
-                                                                grid[2]/2:-grid[2]/2]              # periodically extend the smoothed bulk energy
+                                                                grid[2]//2:-grid[2]//2]              # periodically extend the smoothed bulk energy
 
 
     # transform voxels close to interface region
@@ -164,15 +164,15 @@ for name in filenames:
                                                       return_distances = False,
                                                       return_indices = True)                       # want index of closest bulk grain
 
-    periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
+    periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                              grid[1]/2:-grid[1]/2,
+                                                              grid[1]//2:-grid[1]//2,
-                                                              grid[2]/2:-grid[2]/2]                # periodically extend the microstructure
+                                                              grid[2]//2:-grid[2]//2]                # periodically extend the microstructure
 
     microstructure = periodic_microstructure[index[0],
                                              index[1],
-                                             index[2]].reshape(2*grid)[grid[0]/2:-grid[0]/2,
+                                             index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
-                                                                       grid[1]/2:-grid[1]/2,
+                                                                       grid[1]//2:-grid[1]//2,
-                                                                       grid[2]/2:-grid[2]/2]       # extent grains into interface region
+                                                                       grid[2]//2:-grid[2]//2]       # extent grains into interface region
 
     # replace immutable microstructures with closest mutable ones
     index = ndimage.morphology.distance_transform_edt(np.in1d(microstructure,options.immutable).reshape(grid),
@@ -236,3 +236,4 @@ for name in filenames:
 # --- output finalization --------------------------------------------------------------------------
 
   table.close()     
+  

processing/pre/geom_rotate.py

@@ -52,13 +52,14 @@ parser.set_defaults(degrees = False,
 if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) != 1:
   parser.error('not exactly one rotation specified...')
 
-eulers = np.array(damask.orientation.Orientation(
+if options.quaternion is not None:
-                         quaternion = np.array(options.quaternion)  if options.quaternion else None,
+  eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True)
-                         angleAxis  = np.array(options.rotation)    if options.rotation else None,
+if options.rotation is not None:
-                         matrix     = np.array(options.matrix)      if options.matrix else None,
+  eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=True)).asEulers(degrees=True)
-                         Eulers     = np.array(options.eulers)      if options.eulers else None,
+if options.matrix is not None:
-                         degrees    = options.degrees,
+  eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True)
-                  ).asEulers(degrees=True))
+if options.eulers is not None:
+  eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
 
 # --- loop over input files -------------------------------------------------------------------------
 

processing/pre/geom_toTable.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
@@ -48,11 +48,11 @@ for name in filenames:
   table.head_read()
   info,extra_header = table.head_getGeom()
   
-  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
+  damask.util.croak(['grid     a b c:  {}'.format(' x '.join(list(map(str,info['grid'])))),
-                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
+                     'size     x y z:  {}'.format(' x '.join(list(map(str,info['size'])))),
-                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
+                     'origin   x y z:  {}'.format(' : '.join(list(map(str,info['origin'])))),
-                     'homogenization:  %i'%info['homogenization'],
+                     'homogenization:  {}'.format(info['homogenization']),
-                     'microstructures: %i'%info['microstructures'],
+                     'microstructures: {}'.format(info['microstructures']),
                     ])
 
   errors = []
@@ -86,7 +86,7 @@ for name in filenames:
   yy = np.tile(np.repeat(y,info['grid'][0]                ),info['grid'][2])
   zz =         np.repeat(z,info['grid'][0]*info['grid'][1])
 
-  table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)))
+  table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)),axis=0)
   table.data_writeArray()
 
 # ------------------------------------------ finalize output ---------------------------------------

processing/pre/seeds_check.sh

@@ -2,9 +2,9 @@
 
 for seeds in "$@"
 do
-  vtk_pointcloud $seeds
+  vtk_pointCloud $seeds
 
-  vtk_addPointcloudData $seeds \
+  vtk_addPointCloudData $seeds \
     --data microstructure,weight \
     --inplace \
     --vtk ${seeds%.*}.vtp \

processing/pre/seeds_fromDistribution.py

@@ -1,10 +1,11 @@
-#!/usr/bin/env python2.7
+#!/usr/bin/env python3
 # -*- coding: UTF-8 no BOM -*-
 
 import threading,time,os,sys,random
 import numpy as np
 from optparse import OptionParser
-from cStringIO import StringIO
+from io import StringIO
+import binascii
 import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
@@ -96,7 +97,7 @@ class myThread (threading.Thread):
       perturbedGeomVFile = StringIO()
       perturbedSeedsVFile.reset()
       perturbedGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
-                     ' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0])
+                     ' -g '+' '.join(list(map(str, options.grid))),streamIn=perturbedSeedsVFile)[0])
       perturbedGeomVFile.reset()
 
 #--- evaluate current seeds file ----------------------------------------------------------------------
@@ -214,7 +215,7 @@ options = parser.parse_args()[0]
 damask.util.report(scriptName,options.seedFile)
 
 if options.randomSeed is None:
-  options.randomSeed = int(os.urandom(4).encode('hex'), 16)
+  options.randomSeed = int(binascii.hexlify(os.urandom(4)),16)
 damask.util.croak(options.randomSeed)
 delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2])
 baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
@@ -240,17 +241,17 @@ if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'):
     for line in initialSeedFile: bestSeedsVFile.write(line)
 else:
   bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
-                                ' -g '+' '.join(map(str, options.grid))+\
+                                ' -g '+' '.join(list(map(str, options.grid)))+\
                                 ' -r {:d}'.format(options.randomSeed)+\
                                 ' -N '+str(nMicrostructures))[0])
 bestSeedsUpdate = time.time()
 
 # ----------- tessellate initial seed file to get and evaluate geom file
-bestSeedsVFile.reset()
+bestSeedsVFile.seek(0)
 initialGeomVFile = StringIO()
 initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
-                               ' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0])
+                               ' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
-initialGeomVFile.reset()
+initialGeomVFile.seek(0)
 initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)
 initialGeomTable.head_read()
 info,devNull =  initialGeomTable.head_getGeom()

processing/pre/seeds_fromRandom.py

@@ -28,7 +28,7 @@ def kdtree_search(cloud, queryPoints):
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options', description = """
 Distribute given number of points randomly within (a fraction of) the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0].
 Reports positions with random crystal orientations in seeds file format to STDOUT.
 
@@ -90,11 +90,7 @@ group.add_option( '-s',
                   '--selective',
                   action = 'store_true',
                   dest   = 'selective',
-                  help   = 'selective picking of seed points from random seed points [%default]')
+                  help   = 'selective picking of seed points from random seed points')
-group.add_option( '--force',
-                  action = 'store_true',
-                  dest   = 'force',
-                  help   = 'try selective picking despite large seed point number [%default]')
 group.add_option( '--distance',
                   dest = 'distance',
                   type = 'float', metavar = 'float',
@@ -115,7 +111,6 @@ parser.set_defaults(randomSeed = None,
                     sigma = 0.05,
                     microstructure = 1,
                     selective = False,
-                    force = False,
                     distance = 0.2,
                     numCandidates = 10,
                     format = None,
@@ -148,10 +143,11 @@ for name in filenames:
   errors  = []
   if gridSize == 0:
     errors.append('zero grid dimension for {}.'.format(', '.join([['a','b','c'][x] for x in np.where(options.grid == 0)[0]])))
-  if options.N > gridSize/10.: errors.append('seed count exceeds 0.1 of grid points.')
+  if options.N > gridSize/10.:
+    remarks.append('seed count exceeds 0.1 of grid points.')
   if options.selective and 4./3.*math.pi*(options.distance/2.)**3*options.N > 0.5:
-    (remarks if options.force else errors).append('maximum recommended seed point count for given distance is {}.{}'.
+    remarks.append('maximum recommended seed point count for given distance is {}.{}'.
-                             format(int(3./8./math.pi/(options.distance/2.)**3),'..'*options.force))
+                   format(int(3./8./math.pi/(options.distance/2.)**3)))
 
   if remarks != []: damask.util.croak(remarks)
   if errors  != []:

python/damask/Lambert.py

@@ -0,0 +1,125 @@
+# -*- coding: UTF-8 no BOM -*-
+
+####################################################################################################
+# Code below available according to the followin conditions on https://github.com/MarDiehl/3Drotations
+####################################################################################################
+# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
+# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification, are 
+# permitted provided that the following conditions are met:
+#
+#     - Redistributions of source code must retain the above copyright notice, this list 
+#        of conditions and the following disclaimer.
+#     - Redistributions in binary form must reproduce the above copyright notice, this 
+#        list of conditions and the following disclaimer in the documentation and/or 
+#        other materials provided with the distribution.
+#     - Neither the names of Marc De Graef, Carnegie Mellon University nor the names 
+#        of its contributors may be used to endorse or promote products derived from 
+#        this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE 
+# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+####################################################################################################
+
+import numpy as np
+
+sc   = np.pi**(1./6.)/6.**(1./6.)
+beta = np.pi**(5./6.)/6.**(1./6.)/2.
+R1   = (3.*np.pi/4.)**(1./3.)
+
+def CubeToBall(cube):
+  
+    if np.abs(np.max(cube))>np.pi**(2./3.) * 0.5:
+      raise ValueError
+  
+    # transform to the sphere grid via the curved square, and intercept the zero point
+    if np.allclose(cube,0.0,rtol=0.0,atol=1.0e-300):
+      ball = np.zeros(3)
+    else:
+      # get pyramide and scale by grid parameter ratio
+      p = GetPyramidOrder(cube)
+      XYZ = cube[p] * sc
+
+      # intercept all the points along the z-axis
+      if np.allclose(XYZ[0:2],0.0,rtol=0.0,atol=1.0e-300):
+        ball = np.array([0.0, 0.0, np.sqrt(6.0/np.pi) * XYZ[2]])
+      else:
+        order = [1,0] if np.abs(XYZ[1]) <= np.abs(XYZ[0]) else [0,1]
+        q = np.pi/12.0 * XYZ[order[0]]/XYZ[order[1]]
+        c = np.cos(q)
+        s = np.sin(q)
+        q = R1*2.0**0.25/beta * XYZ[order[1]] / np.sqrt(np.sqrt(2.0)-c)
+        T = np.array([ (np.sqrt(2.0)*c - 1.0), np.sqrt(2.0) * s]) * q
+
+        # transform to sphere grid (inverse Lambert)
+        # note that there is no need to worry about dividing by zero, since XYZ[2] can not become zero
+        c = np.sum(T**2)
+        s = c *         np.pi/24.0 /XYZ[2]**2
+        c = c * np.sqrt(np.pi/24.0)/XYZ[2]
+        q = np.sqrt( 1.0 - s )
+        ball = np.array([ T[order[1]] * q, T[order[0]] * q, np.sqrt(6.0/np.pi) * XYZ[2] - c ])
+    
+      # reverse the coordinates back to the regular order according to the original pyramid number
+      ball = ball[p]
+
+    return ball
+
+
+def BallToCube(ball):
+  
+    rs = np.linalg.norm(ball)
+    if rs > R1: 
+      raise ValueError
+  
+    if np.allclose(ball,0.0,rtol=0.0,atol=1.0e-300):
+      cube = np.zeros(3)
+    else:
+      p = GetPyramidOrder(ball)
+      xyz3 = ball[p] 
+
+      # inverse M_3
+      xyz2 = xyz3[0:2] * np.sqrt( 2.0*rs/(rs+np.abs(xyz3[2])) )
+      
+      # inverse M_2
+      qxy = np.sum(xyz2**2)
+      
+      if np.isclose(qxy,0.0,rtol=0.0,atol=1.0e-300):
+        Tinv = np.zeros(2)
+      else:
+        q2 = qxy + np.max(np.abs(xyz2))**2
+        sq2 = np.sqrt(q2)
+        q = (beta/np.sqrt(2.0)/R1) * np.sqrt(q2*qxy/(q2-np.max(np.abs(xyz2))*sq2))
+        tt = np.clip((np.min(np.abs(xyz2))**2+np.max(np.abs(xyz2))*sq2)/np.sqrt(2.0)/qxy,-1.0,1.0)
+        Tinv = np.array([1.0,np.arccos(tt)/np.pi*12.0]) if np.abs(xyz2[1]) <= np.abs(xyz2[0]) else \
+               np.array([np.arccos(tt)/np.pi*12.0,1.0])
+        Tinv = q * np.where(xyz2<0.0,-Tinv,Tinv)
+      
+      # inverse M_1
+      cube = np.array([ Tinv[0], Tinv[1],  (-1.0 if xyz3[2] < 0.0 else 1.0) * rs / np.sqrt(6.0/np.pi) ]) /sc
+
+      # reverse the coordinates back to the regular order according to the original pyramid number
+      cube = cube[p]
+      
+    return cube
+
+def GetPyramidOrder(xyz):
+ 
+    if   (abs(xyz[0])<= xyz[2]) and (abs(xyz[1])<= xyz[2]) or \
+         (abs(xyz[0])<=-xyz[2]) and (abs(xyz[1])<=-xyz[2]):
+      return [0,1,2]
+    elif (abs(xyz[2])<= xyz[0]) and (abs(xyz[1])<= xyz[0]) or \
+         (abs(xyz[2])<=-xyz[0]) and (abs(xyz[1])<=-xyz[0]):
+      return [1,2,0]
+    elif (abs(xyz[0])<= xyz[1]) and (abs(xyz[2])<= xyz[1]) or \
+         (abs(xyz[0])<=-xyz[1]) and (abs(xyz[2])<=-xyz[1]):
+      return [2,0,1]

python/damask/__init__.py

@@ -13,7 +13,7 @@ from .asciitable  import ASCIItable       # noqa
     
 from .config      import Material         # noqa
 from .colormaps   import Colormap, Color  # noqa
-from .orientation import Quaternion, Symmetry, Orientation # noqa
+from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
 
 #from .block       import Block           # only one class
 from .result      import Result           # noqa

python/damask/config/material.py

@@ -77,18 +77,6 @@ class Texture(Section):
                                         )
                         )
 
-    if multiKey == 'fiber':
-      self.add_multiKey(multiKey,'alpha1 %g\talpha2 %g\tbeta1 %g\tbeta2 %g\tscatter %g\tfraction %g'%(
-                                        properties['eulers'][0],
-                                        properties['eulers'][1],
-                                        properties['eulers'][2],
-                                        properties['eulers'][3],
-                                        scatter,
-                                        fraction,
-                                        )
-                        )
-
- 
  
 class Material():
   """Reads, manipulates and writes material.config files"""
@@ -97,10 +85,10 @@ class Material():
     """Generates ordered list of parts"""
     self.parts = [
              'homogenization',
-             'microstructure',
              'crystallite',
              'phase',
              'texture',
+             'microstructure',
             ]
     self.data = {\
               'homogenization': {'__order__': []},
@@ -117,15 +105,12 @@ class Material():
     for part in self.parts:
       if self.verbose: print('processing <{}>'.format(part))
       me += ['',
-             '#-----------------------------#',
+             '#'*100,
              '<{}>'.format(part),
-             '#-----------------------------#',
+             '#'*100,
             ]
       for section in self.data[part]['__order__']:
-        me += ['',
+        me += ['[{}] {}'.format(section,'#'+'-'*max(0,96-len(section)))]
-               '[{}] {}'.format(section,'#'*max(0,27-len(section))),
-               '',
-              ]
         for key in self.data[part][section]['__order__']:
           if key.startswith('(') and key.endswith(')'):                       # multiple (key)
             me += ['{}\t{}'.format(key,' '.join(values)) for values in self.data[part][section][key]]

python/damask/solver/abaqus.py

@@ -2,7 +2,7 @@
 
 from .solver import Solver
 import damask
-import subprocess,re
+import subprocess
 
 class Abaqus(Solver):
 
@@ -15,14 +15,13 @@ class Abaqus(Solver):
 
   def return_run_command(self,model):
     env=damask.Environment()
-    shortVersion = re.sub('[\.,-]', '',self.version)
     try:
-      cmd='abq'+shortVersion
+      cmd='abq'+self.version
-      subprocess.check_output(['abq'+shortVersion,'information=release'])
+      subprocess.check_output([cmd,'information=release'])
     except OSError:                                                                                 # link to abqXXX not existing
       cmd='abaqus'
       process = subprocess.Popen(['abaqus','information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
-      detectedVersion = process.stdout.readlines()[1].split()[1]
+      detectedVersion = process.stdout.readlines()[1].split()[1].decode('utf-8')
       if self.version != detectedVersion:
-        raise Exception('found Abaqus version %s, but requested %s'%(detectedVersion,self.version))
+        raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
-    return '%s -job %s -user %s/src/DAMASK_abaqus interactive'%(cmd,model,env.rootDir())
+    return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,env.rootDir())

src/CMakeLists.txt

@@ -7,6 +7,7 @@ endif()
 
 # The dependency detection in CMake is not functioning for Fortran,
 # hence we declare the dependencies from top to bottom in the following
+
 add_library(C_ROUTINES OBJECT "C_routines.c")
 set(OBJECTFILES $<TARGET_OBJECTS:C_ROUTINES>)
 
@@ -17,6 +18,10 @@ list(APPEND OBJECTFILES $<TARGET_OBJECTS:SYSTEM_ROUTINES>)
 add_library(PREC OBJECT "prec.f90")
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:PREC>)
 
+add_library(ELEMENT OBJECT "element.f90")
+add_dependencies(ELEMENT PREC)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:ELEMENT>)
+
 add_library(QUIT OBJECT "quit.f90")
 add_dependencies(QUIT PREC)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:QUIT>)
@@ -34,7 +39,7 @@ add_dependencies(NUMERICS IO)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:NUMERICS>)
 
 add_library(DEBUG OBJECT "debug.f90")
-add_dependencies(DEBUG NUMERICS)
+add_dependencies(DEBUG IO)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:DEBUG>)
 
 add_library(DAMASK_CONFIG OBJECT "config.f90")
@@ -42,7 +47,7 @@ add_dependencies(DAMASK_CONFIG DEBUG)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:DAMASK_CONFIG>)
 
 add_library(HDF5_UTILITIES OBJECT "HDF5_utilities.f90")
-add_dependencies(HDF5_UTILITIES DAMASK_CONFIG)
+add_dependencies(HDF5_UTILITIES DAMASK_CONFIG NUMERICS)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:HDF5_UTILITIES>)
 
 add_library(RESULTS OBJECT "results.f90")
@@ -50,34 +55,50 @@ add_dependencies(RESULTS HDF5_UTILITIES)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:RESULTS>)
 
 add_library(FEsolving OBJECT "FEsolving.f90")
-add_dependencies(FEsolving RESULTS)
+add_dependencies(FEsolving DEBUG)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:FEsolving>)
 
-add_library(DAMASK_MATH OBJECT "math.f90")
+add_library(MATH OBJECT "math.f90")
-add_dependencies(DAMASK_MATH FEsolving)
+add_dependencies(MATH NUMERICS)
-list(APPEND OBJECTFILES $<TARGET_OBJECTS:DAMASK_MATH>)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:MATH>)
+
+add_library(QUATERNIONS OBJECT "quaternions.f90")
+add_dependencies(QUATERNIONS MATH)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:QUATERNIONS>)
+
+add_library(LAMBERT OBJECT "Lambert.f90")
+add_dependencies(LAMBERT MATH)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:LAMBERT>)
+
+add_library(ROTATIONS OBJECT "rotations.f90")
+add_dependencies(ROTATIONS LAMBERT QUATERNIONS)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:ROTATIONS>)
+
+add_library(MESH_BASE OBJECT "mesh_base.f90")
+add_dependencies(MESH_BASE ELEMENT)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:MESH_BASE>)
 
 # SPECTRAL solver and FEM solver use different mesh files
 if (PROJECT_NAME STREQUAL "DAMASK_spectral")
-      add_library(MESH OBJECT "mesh.f90")
+      add_library(MESH OBJECT "mesh_grid.f90")
-      add_dependencies(MESH DAMASK_MATH)
+      add_dependencies(MESH MESH_BASE MATH FEsolving)
       list(APPEND OBJECTFILES $<TARGET_OBJECTS:MESH>)
 elseif (PROJECT_NAME STREQUAL "DAMASK_FEM")
       add_library(FEZoo OBJECT "FEM_zoo.f90")
-      add_dependencies(FEZoo DAMASK_MATH)
+      add_dependencies(FEZoo IO)
       list(APPEND OBJECTFILES $<TARGET_OBJECTS:FEZoo>)
-      add_library(MESH  OBJECT "meshFEM.f90")
+      add_library(MESH OBJECT "mesh_FEM.f90")
-      add_dependencies(MESH FEZoo)
+      add_dependencies(MESH FEZoo MESH_BASE MATH FEsolving)
       list(APPEND OBJECTFILES $<TARGET_OBJECTS:MESH>)
 endif()
 
 add_library(MATERIAL OBJECT "material.f90")
-add_dependencies(MATERIAL MESH DAMASK_CONFIG)
+add_dependencies(MATERIAL MESH DAMASK_CONFIG ROTATIONS)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:MATERIAL>)
 
-add_library(DAMASK_HELPERS OBJECT "lattice.f90")
+add_library(LATTICE OBJECT "lattice.f90")
-add_dependencies(DAMASK_HELPERS MATERIAL)
+add_dependencies(LATTICE MATERIAL)
-list(APPEND OBJECTFILES $<TARGET_OBJECTS:DAMASK_HELPERS>)
+list(APPEND OBJECTFILES $<TARGET_OBJECTS:LATTICE>)
 
 # For each modular section
 add_library (PLASTIC OBJECT
@@ -88,14 +109,14 @@ add_library (PLASTIC OBJECT
   "plastic_kinematichardening.f90"
   "plastic_nonlocal.f90"
   "plastic_none.f90")
-add_dependencies(PLASTIC DAMASK_HELPERS)
+add_dependencies(PLASTIC LATTICE RESULTS)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:PLASTIC>)
 
 add_library (KINEMATICS OBJECT
   "kinematics_cleavage_opening.f90"
   "kinematics_slipplane_opening.f90"
   "kinematics_thermal_expansion.f90")
-add_dependencies(KINEMATICS DAMASK_HELPERS)
+add_dependencies(KINEMATICS LATTICE RESULTS)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:KINEMATICS>)
 
 add_library (SOURCE OBJECT
@@ -105,7 +126,7 @@ add_library (SOURCE OBJECT
   "source_damage_isoDuctile.f90"
   "source_damage_anisoBrittle.f90"
   "source_damage_anisoDuctile.f90")
-add_dependencies(SOURCE DAMASK_HELPERS)
+add_dependencies(SOURCE LATTICE RESULTS)
 list(APPEND OBJECTFILES $<TARGET_OBJECTS:SOURCE>)
 
 add_library(CONSTITUTIVE OBJECT "constitutive.f90")

src/CPFEM.f90

@@ -140,8 +140,7 @@ subroutine CPFEM_init
    restartRead, &
    modelName
  use mesh, only: &
-   mesh_NcpElems, &
+   theMesh
-   mesh_maxNips
  use material, only: &
    material_phase, &
    homogState, &
@@ -168,10 +167,9 @@ subroutine CPFEM_init
    flush(6)
  endif mainProcess
 
- ! initialize stress and jacobian to zero
+ allocate(CPFEM_cs(               6,theMesh%elem%nIPs,theMesh%Nelems), source= 0.0_pReal)
- allocate(CPFEM_cs(6,mesh_maxNips,mesh_NcpElems)) ;                CPFEM_cs              = 0.0_pReal
+ allocate(CPFEM_dcsdE(          6,6,theMesh%elem%nIPs,theMesh%Nelems), source= 0.0_pReal)
- allocate(CPFEM_dcsdE(6,6,mesh_maxNips,mesh_NcpElems)) ;           CPFEM_dcsdE           = 0.0_pReal
+ allocate(CPFEM_dcsdE_knownGood(6,6,theMesh%elem%nIPs,theMesh%Nelems), source= 0.0_pReal)
- allocate(CPFEM_dcsdE_knownGood(6,6,mesh_maxNips,mesh_NcpElems)) ; CPFEM_dcsdE_knownGood = 0.0_pReal
 
  ! *** restore the last converged values of each essential variable from the binary file
  if (restartRead) then
@@ -289,8 +287,7 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
    math_6toSym33
  use mesh, only: &
    mesh_FEasCP, &
-   mesh_NcpElems, &
+   theMesh, &
-   mesh_maxNips, &
    mesh_element
  use material, only: &
    microstructure_elemhomo, &
@@ -401,7 +398,7 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
    enddo; enddo
    if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0_pInt) then
      write(6,'(a)') '<< CPFEM >> aging states'
-     if (debug_e <= mesh_NcpElems .and. debug_i <= mesh_maxNips) then
+     if (debug_e <= theMesh%Nelems .and. debug_i <= theMesh%elem%nIPs) then
        write(6,'(a,1x,i8,1x,i2,1x,i4,/,(12x,6(e20.8,1x)),/)') &
              '<< CPFEM >> aged state of elFE ip grain',debug_e, debug_i, 1, &
               plasticState(phaseAt(1,debug_i,debug_e))%state(:,phasememberAt(1,debug_i,debug_e))

src/CPFEM2.f90

@@ -95,8 +95,6 @@ subroutine CPFEM_init
  use prec, only: &
    pInt, pReal, pLongInt
  use IO, only: &
-   IO_read_realFile,&
-   IO_read_intFile, &
    IO_timeStamp, &
    IO_error
  use numerics, only: &

src/C_routines.c

@@ -6,9 +6,11 @@
 #include <sys/stat.h>
 #include <stdio.h>
 #include <string.h>
+#include <signal.h>
 
 /* http://stackoverflow.com/questions/30279228/is-there-an-alternative-to-getcwd-in-fortran-2003-2008 */
 
+
 int isdirectory_c(const char *dir){
   struct stat statbuf;
   if(stat(dir, &statbuf) != 0)                                                                      /* error */
@@ -44,3 +46,11 @@ void gethostname_c(char hostname[], int *stat){
 int chdir_c(const char *dir){
   return chdir(dir);
 }
+
+void signalusr1_c(void (*handler)(int)){
+  signal(SIGUSR1, handler);
+}
+
+void signalusr2_c(void (*handler)(int)){
+  signal(SIGUSR2, handler);
+}

src/DAMASK_abaqus.f

@@ -30,6 +30,11 @@ contains
 !> @brief reports and sets working directory
 !--------------------------------------------------------------------------------------------------
 subroutine DAMASK_interface_init
+#if __INTEL_COMPILER >= 1800
+ use, intrinsic :: iso_fortran_env, only: &
+   compiler_version, &
+   compiler_options
+#endif
  use ifport, only: &
    CHDIR
  
@@ -40,16 +45,25 @@ subroutine DAMASK_interface_init
  character(len=256) :: wd
 
  call date_and_time(values = dateAndTime)
- write(6,'(/,a)') ' <<<+-  DAMASK_abaqus_std  -+>>>'
+ write(6,'(/,a)') ' <<<+-  DAMASK_abaqus  -+>>>'
- write(6,'(/,a)') ' Roters et al., Computational Materials Science, 2018'
+ write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
- write(6,'(/,a)')              ' Version: '//DAMASKVERSION
+ write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
- write(6,'(a,2(i2.2,a),i4.4)') ' Date:    ',dateAndTime(3),'/',&
+
-                                            dateAndTime(2),'/',&
+ write(6,'(a,/)')              ' Version: '//DAMASKVERSION
-                                            dateAndTime(1) 
+
- write(6,'(a,2(i2.2,a),i2.2)') ' Time:    ',dateAndTime(5),':',&
+! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
-                                            dateAndTime(6),':',&
+#if __INTEL_COMPILER >= 1800
-                                            dateAndTime(7)  
+ write(6,*) 'Compiled with: ', compiler_version()
- write(6,'(/,a)') ' <<<+-  DAMASK_interface init  -+>>>'
+ write(6,*) 'Compiler options: ', compiler_options()
+#else
+ write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
+                                                    ', build date :', __INTEL_COMPILER_BUILD_DATE
+#endif
+
+ write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
+
+ write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
+ write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
 
  call getoutdir(wd, lenOutDir)
  ierr = CHDIR(wd)

src/DAMASK_interface.f90

@@ -12,9 +12,9 @@
 module DAMASK_interface
  use prec, only: &
    pInt
-
  implicit none
  private
+ logical, public, protected :: SIGUSR1,SIGUSR2
  integer(pInt),       public, protected :: &
    interface_restartInc = 0_pInt                                                                    !< Increment at which calculation starts
  character(len=1024), public, protected :: &
@@ -42,6 +42,8 @@ contains
 subroutine DAMASK_interface_init()
  use, intrinsic :: &
    iso_fortran_env
+ use :: &
+   iso_c_binding
 #include <petsc/finclude/petscsys.h>
 #if defined(__GFORTRAN__) &&  __GNUC__ < 5
 ===================================================================================================
@@ -81,6 +83,8 @@ subroutine DAMASK_interface_init()
 
  use PETScSys
  use system_routines, only: &
+   signalusr1_C, &
+   signalusr2_C, &
    getHostName, &
    getCWD
 
@@ -139,16 +143,27 @@ subroutine DAMASK_interface_init()
 
  call date_and_time(values = dateAndTime)
  write(6,'(/,a)') ' <<<+-  DAMASK_interface init  -+>>>'
- write(6,'(a,/)') ' Roters et al., Computational Materials Science, 2018'
+ write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
- write(6,'(/,a)')              ' Version: '//DAMASKVERSION
+ write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
- write(6,'(a,2(i2.2,a),i4.4)') ' Date:    ',dateAndTime(3),'/',&
+
-                                            dateAndTime(2),'/',&
+ write(6,'(a,/)')              ' Version: '//DAMASKVERSION
-                                            dateAndTime(1) 
+
- write(6,'(a,2(i2.2,a),i2.2)') ' Time:    ',dateAndTime(5),':',&
+! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
-                                            dateAndTime(6),':',&
+#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
-                                            dateAndTime(7)  
+ write(6,*) 'Compiled with: ', compiler_version()
- write(6,'(/,a,i4.1)') ' MPI processes: ',worldsize
+ write(6,*) 'Compiler options: ', compiler_options()
-#include "compilation_info.f90"
+#elif defined(__INTEL_COMPILER)
+ write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
+                                                    ', build date :', __INTEL_COMPILER_BUILD_DATE
+#elif defined(__PGI)
+ write(6,'(a,i4.4,a,i8.8)') ' Compiled with PGI fortran version :', __PGIC__,&
+                                                               '.', __PGIC_MINOR__
+#endif
+
+ write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
+
+ write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
+ write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
  
  call get_command(commandLine)
  chunkPos = IIO_stringPos(commandLine)
@@ -215,9 +230,11 @@ subroutine DAMASK_interface_init()
 
  call get_environment_variable('USER',userName)
  ! ToDo: https://stackoverflow.com/questions/8953424/how-to-get-the-username-in-c-c-in-linux
+ write(6,'(/,a,i4.1)') ' MPI processes: ',worldsize
  write(6,'(a,a)')      ' Host name: ', trim(getHostName())
  write(6,'(a,a)')      ' User name: ', trim(userName)
- write(6,'(a,a)')      ' Command line call:      ', trim(commandLine)
+
+ write(6,'(/a,a)')     ' Command line call:      ', trim(commandLine)
  if (len(trim(workingDirArg)) > 0) &
    write(6,'(a,a)')    ' Working dir argument:   ', trim(workingDirArg)
  write(6,'(a,a)')      ' Geometry argument:      ', trim(geometryArg)
@@ -229,6 +246,12 @@ subroutine DAMASK_interface_init()
  if (interface_restartInc > 0_pInt) &
    write(6,'(a,i6.6)') ' Restart from increment: ', interface_restartInc
 
+ call signalusr1_c(c_funloc(setSIGUSR1))
+ call signalusr2_c(c_funloc(setSIGUSR2))
+ SIGUSR1 = .false.
+ SIGUSR2 = .false.
+
+
 end subroutine DAMASK_interface_init
 
 
@@ -412,6 +435,35 @@ character(len=1024) function makeRelativePath(a,b)
 
 end function makeRelativePath
 
+!--------------------------------------------------------------------------------------------------
+!> @brief sets global variable SIGUSR1 to .true. if program receives SIGUSR1
+!--------------------------------------------------------------------------------------------------
+subroutine setSIGUSR1(signal) bind(C)
+ use :: iso_c_binding
+   
+ implicit none
+ integer(C_INT), value :: signal
+ SIGUSR1 = .true.
+ 
+ write(6,*) 'received signal ',signal, 'set SIGUSR1'
+ 
+end subroutine setSIGUSR1
+ 
+ 
+!--------------------------------------------------------------------------------------------------
+!> @brief sets global variable SIGUSR2 to .true. if program receives SIGUSR2
+!--------------------------------------------------------------------------------------------------
+subroutine setSIGUSR2(signal) bind(C)
+ use :: iso_c_binding
+
+ implicit none
+ integer(C_INT), value :: signal
+ SIGUSR2 = .true.
+
+ write(6,*) 'received signal ',signal, 'set SIGUSR2'
+  
+end subroutine setSIGUSR2
+
 
 !--------------------------------------------------------------------------------------------------
 !> @brief taken from IO, check IO_stringValue for documentation 
@@ -469,7 +521,6 @@ pure function IIO_stringPos(string)
  do while (verify(string(right+1:),SEP)>0)
    left  = right + verify(string(right+1:),SEP)
    right = left + scan(string(left:),SEP) - 2
-   if ( string(left:left) == '#' ) exit
    IIO_stringPos = [IIO_stringPos,int(left, pInt), int(right, pInt)]
    IIO_stringPos(1) = IIO_stringPos(1)+1_pInt
  enddo

src/DAMASK_marc.f90

@@ -43,6 +43,11 @@ contains
 !> @brief reports and sets working directory
 !--------------------------------------------------------------------------------------------------
 subroutine DAMASK_interface_init
+#if __INTEL_COMPILER >= 1800
+ use, intrinsic :: iso_fortran_env, only: &
+   compiler_version, &
+   compiler_options
+#endif
  use ifport, only: &
    CHDIR
 
@@ -53,17 +58,26 @@ subroutine DAMASK_interface_init
  character(len=1024) :: wd
 
  call date_and_time(values = dateAndTime)
- write(6,'(/,a)') ' <<<+-  DAMASK_Marc  -+>>>'
+ write(6,'(/,a)') ' <<<+-  DAMASK_abaqus  -+>>>'
- write(6,'(/,a)') ' Roters et al., Computational Materials Science, 2018'
+ write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
- write(6,'(/,a)')              ' Version: '//DAMASKVERSION
+ write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
- write(6,'(a,2(i2.2,a),i4.4)') ' Date:    ',dateAndTime(3),'/',&
+
-                                            dateAndTime(2),'/',&
+ write(6,'(a,/)')              ' Version: '//DAMASKVERSION
-                                            dateAndTime(1)
+
- write(6,'(a,2(i2.2,a),i2.2)') ' Time:    ',dateAndTime(5),':',&
+! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
-                                            dateAndTime(6),':',&
+#if __INTEL_COMPILER >= 1800
-                                            dateAndTime(7)
+ write(6,*) 'Compiled with: ', compiler_version()
- write(6,'(/,a)') ' <<<+-  DAMASK_interface init  -+>>>'
+ write(6,*) 'Compiler options: ', compiler_options()
-#include "compilation_info.f90"
+#else
+ write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
+                                                    ', build date :', __INTEL_COMPILER_BUILD_DATE
+#endif
+
+ write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
+
+ write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
+ write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
+
  inquire(5, name=wd)                                                                                ! determine inputputfile
  wd = wd(1:scan(wd,'/',back=.true.))
  ierr = CHDIR(wd)
@@ -134,6 +148,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
    debug_info, &
    debug_reset
  use mesh, only: &
+   theMesh, &
    mesh_FEasCP, &
    mesh_element, &
    mesh_node0, &
@@ -141,8 +156,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
    mesh_Ncellnodes, &
    mesh_cellnode, &
    mesh_build_cellnodes, &
-   mesh_build_ipCoordinates, &
+   mesh_build_ipCoordinates
-   FE_Nnodes
  use CPFEM, only: &
    CPFEM_general, &
    CPFEM_init_done, &
@@ -314,7 +328,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
          computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN)                                ! collect and backup Jacobian after convergence
          lastIncConverged = .false.                                                                 ! reset flag
        endif
-       do node = 1,FE_Nnodes(mesh_element(2,cp_en))
+       do node = 1,theMesh%elem%nNodes
          CPnodeID = mesh_element(4_pInt+node,cp_en)
          mesh_node(1:ndeg,CPnodeID) = mesh_node0(1:ndeg,CPnodeID) + numerics_unitlength * dispt(1:ndeg,node)
        enddo

src/FEM_utilities.f90

@@ -162,7 +162,6 @@ subroutine utilities_init()
 
  character(len=1024)                :: petsc_optionsPhysics
  integer(pInt)                      :: dimPlex
- integer(pInt)                      :: headerID = 205_pInt
  PetscInt,    allocatable           :: nEntities(:), nOutputCells(:), nOutputNodes(:)
  PetscInt                           :: dim
  PetscErrorCode                     :: ierr
@@ -213,13 +212,6 @@ subroutine utilities_init()
  nOutputCells(worldrank+1) = count(material_homog > 0_pInt)
  call MPI_Allreduce(MPI_IN_PLACE,nOutputNodes,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)
  call MPI_Allreduce(MPI_IN_PLACE,nOutputCells,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)
- if (worldrank == 0_pInt) then
-   open(unit=headerID, file=trim(getSolverJobName())//'.header', &
-        form='FORMATTED', status='REPLACE')
-   write(headerID, '(a,i0)') 'dimension : ',   dimPlex                                             
-   write(headerID, '(a,i0)') 'number of nodes : ', sum(nOutputNodes)
-   write(headerID, '(a,i0)') 'number of cells : ', sum(nOutputCells)
- endif 
 
 end subroutine utilities_init
 
@@ -503,7 +495,6 @@ subroutine utilities_indexActiveSet(field,section,x_local,f_local,localIS,global
    CHKERRQ(ierr)
    call ISDestroy(dummyIS,ierr); CHKERRQ(ierr)
  endif                      
- deallocate(localIndices)
  
 end subroutine utilities_indexActiveSet
 

src/FEM_zoo.f90

@@ -9,11 +9,11 @@ module FEM_Zoo
  private
  integer(pInt), parameter, public:: &
    maxOrder = 5                                                                            !< current max interpolation set at cubic (intended to be arbitrary)
- real(pReal),   dimension(2,3),       private, protected :: &
+ real(pReal),   dimension(2,3),       private, parameter :: &
    triangle    = reshape([-1.0_pReal, -1.0_pReal, &
                            1.0_pReal, -1.0_pReal, &
                           -1.0_pReal,  1.0_pReal], shape=[2,3])
- real(pReal),   dimension(3,4),       private, protected :: &
+ real(pReal),   dimension(3,4),       private, parameter :: &
    tetrahedron = reshape([-1.0_pReal, -1.0_pReal, -1.0_pReal, &
                            1.0_pReal, -1.0_pReal, -1.0_pReal, &
                           -1.0_pReal,  1.0_pReal, -1.0_pReal, &

src/Lambert.f90

@@ -0,0 +1,217 @@
+! ###################################################################
+! Copyright (c) 2013-2015, Marc De Graef/Carnegie Mellon University
+! Modified      2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
+! All rights reserved.
+!
+! Redistribution and use in source and binary forms, with or without modification, are 
+! permitted provided that the following conditions are met:
+!
+!     - Redistributions of source code must retain the above copyright notice, this list 
+!        of conditions and the following disclaimer.
+!     - Redistributions in binary form must reproduce the above copyright notice, this 
+!        list of conditions and the following disclaimer in the documentation and/or 
+!        other materials provided with the distribution.
+!     - Neither the names of Marc De Graef, Carnegie Mellon University nor the names 
+!        of its contributors may be used to endorse or promote products derived from 
+!        this software without specific prior written permission.
+!
+! THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+! AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+! ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+! LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+! DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+! SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+! CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+! OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE 
+! USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+! ###################################################################
+
+!--------------------------------------------------------------------------
+!> @author Marc De Graef, Carnegie Mellon University
+!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
+!> @brief Mapping homochoric <-> cubochoric 
+!
+!> @details
+!> D. Rosca, A. Morawiec, and M. De Graef. “A new method of constructing a grid 
+!> in the space of 3D rotations and its applications to texture analysis”. 
+!> Modeling and Simulations in Materials Science and Engineering 22, 075013 (2014).
+!--------------------------------------------------------------------------
+module Lambert
+ use math
+ use prec, only: &
+   pReal
+
+ implicit none
+ private
+ real(pReal), parameter, private :: &
+   SPI  = sqrt(PI), &
+   PREF = sqrt(6.0_pReal/PI), &
+   A    = PI**(5.0_pReal/6.0_pReal)/6.0_pReal**(1.0_pReal/6.0_pReal), &
+   AP   = PI**(2.0_pReal/3.0_pReal), &
+   SC   = A/AP, &
+   BETA = A/2.0_pReal, &
+   R1   = (3.0_pReal*PI/4.0_pReal)**(1.0_pReal/3.0_pReal), &
+   R2   = sqrt(2.0_pReal), &
+   PI12 = PI/12.0_pReal, &
+   PREK = R1 * 2.0_pReal**(1.0_pReal/4.0_pReal)/BETA
+
+ public :: &
+   LambertCubeToBall, &
+   LambertBallToCube
+ private :: &
+  GetPyramidOrder
+
+contains
+
+
+!--------------------------------------------------------------------------
+!> @author Marc De Graef, Carnegie Mellon University
+!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
+!> @brief map from 3D cubic grid to 3D ball 
+!--------------------------------------------------------------------------
+function LambertCubeToBall(cube) result(ball)
+ use, intrinsic :: IEEE_ARITHMETIC
+ use prec, only: &
+   pInt, &
+   dEq0
+
+ implicit none
+ real(pReal), intent(in), dimension(3) :: cube
+ real(pReal),             dimension(3) :: ball, LamXYZ, XYZ
+ real(pReal)                 ::  T(2), c, s, q
+ real(pReal), parameter      :: eps = 1.0e-8_pReal
+ integer(pInt), dimension(3) :: p
+ integer(pInt), dimension(2) :: order
+ 
+ if (maxval(abs(cube)) > AP/2.0+eps) then
+   ball = IEEE_value(cube,IEEE_positive_inf)
+   return
+ end if
+ 
+ ! transform to the sphere grid via the curved square, and intercept the zero point
+ center: if (all(dEq0(cube))) then
+   ball  = 0.0_pReal
+ else center
+   ! get pyramide and scale by grid parameter ratio
+   p = GetPyramidOrder(cube)
+   XYZ = cube(p) * sc
+ 
+   ! intercept all the points along the z-axis
+   special: if (all(dEq0(XYZ(1:2)))) then
+     LamXYZ = [ 0.0_pReal, 0.0_pReal, pref * XYZ(3) ]
+   else special
+     order = merge( [2,1], [1,2], abs(XYZ(2)) <= abs(XYZ(1)))                                        ! order of absolute values of XYZ
+     q = PI12 *  XYZ(order(1))/XYZ(order(2))                                                         ! smaller by larger
+     c = cos(q)
+     s = sin(q)
+     q = prek * XYZ(order(2))/ sqrt(R2-c)
+     T = [ (R2*c - 1.0), R2 * s] * q
+ 
+ ! transform to sphere grid (inverse Lambert)
+ ! [note that there is no need to worry about dividing by zero, since XYZ(3) can not become zero]
+     c = sum(T**2)
+     s = Pi * c/(24.0*XYZ(3)**2)
+     c = sPi * c / sqrt(24.0_pReal) / XYZ(3)
+     q = sqrt( 1.0 - s )
+     LamXYZ = [ T(order(2)) * q, T(order(1)) * q, pref * XYZ(3) - c ]
+   endif special
+ 
+ ! reverse the coordinates back to the regular order according to the original pyramid number
+   ball = LamXYZ(p)
+
+ endif center
+
+end function LambertCubeToBall
+
+
+!--------------------------------------------------------------------------
+!> @author Marc De Graef, Carnegie Mellon University
+!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
+!> @brief map from 3D ball to 3D cubic grid  
+!--------------------------------------------------------------------------
+pure function LambertBallToCube(xyz) result(cube)
+ use, intrinsic :: IEEE_ARITHMETIC, only:&
+   IEEE_positive_inf, &
+   IEEE_value
+ use prec, only: &
+   pInt, &
+   dEq0
+
+ implicit none
+ real(pReal), intent(in), dimension(3) :: xyz
+ real(pReal),             dimension(3) :: cube, xyz1, xyz3
+ real(pReal),             dimension(2) :: Tinv, xyz2
+ real(pReal)                           :: rs, qxy, q2, sq2, q, tt
+ integer(pInt),           dimension(3) :: p
+ 
+ rs = norm2(xyz)
+ if (rs > R1) then 
+   cube = IEEE_value(cube,IEEE_positive_inf)
+   return
+ endif
+ 
+ center: if (all(dEq0(xyz))) then 
+   cube = 0.0_pReal
+ else center
+   p = GetPyramidOrder(xyz)
+   xyz3 = xyz(p)
+   
+   ! inverse M_3
+   xyz2 = xyz3(1:2) * sqrt( 2.0*rs/(rs+abs(xyz3(3))) )
+   
+   ! inverse M_2
+   qxy = sum(xyz2**2)
+   
+   special: if (dEq0(qxy)) then 
+     Tinv = 0.0
+   else special
+     q2 = qxy + maxval(abs(xyz2))**2
+     sq2 = sqrt(q2)
+     q = (beta/R2/R1) * sqrt(q2*qxy/(q2-maxval(abs(xyz2))*sq2))
+     tt = (minval(abs(xyz2))**2+maxval(abs(xyz2))*sq2)/R2/qxy 
+     Tinv = q * sign(1.0,xyz2) * merge([ 1.0_pReal, acos(math_clip(tt,-1.0_pReal,1.0_pReal))/PI12], &
+                                       [ acos(math_clip(tt,-1.0_pReal,1.0_pReal))/PI12, 1.0_pReal], &
+                                       abs(xyz2(2)) <= abs(xyz2(1)))
+   endif special
+   
+   ! inverse M_1
+   xyz1 = [ Tinv(1), Tinv(2), sign(1.0,xyz3(3)) * rs / pref ] /sc
+   
+   ! reverst the coordinates back to the regular order according to the original pyramid number
+   cube = xyz1(p)
+
+ endif center
+
+end function LambertBallToCube
+
+
+!--------------------------------------------------------------------------
+!> @author Marc De Graef, Carnegie Mellon University
+!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
+!> @brief determine to which pyramid a point in a cubic grid belongs
+!--------------------------------------------------------------------------
+pure function GetPyramidOrder(xyz)
+ use prec, only: &
+   pInt
+
+ implicit none
+ real(pReal),intent(in),dimension(3) :: xyz
+ integer(pInt),         dimension(3) :: GetPyramidOrder
+
+ if      (((abs(xyz(1)) <=  xyz(3)).and.(abs(xyz(2)) <=  xyz(3))) .or. &
+          ((abs(xyz(1)) <= -xyz(3)).and.(abs(xyz(2)) <= -xyz(3)))) then
+   GetPyramidOrder = [1,2,3]
+ else if (((abs(xyz(3)) <=  xyz(1)).and.(abs(xyz(2)) <=  xyz(1))) .or. &
+          ((abs(xyz(3)) <= -xyz(1)).and.(abs(xyz(2)) <= -xyz(1)))) then
+   GetPyramidOrder = [2,3,1]
+ else if (((abs(xyz(1)) <=  xyz(2)).and.(abs(xyz(3)) <=  xyz(2))) .or. &
+          ((abs(xyz(1)) <= -xyz(2)).and.(abs(xyz(3)) <= -xyz(2)))) then
+   GetPyramidOrder = [3,1,2]
+ else
+   GetPyramidOrder = -1                                                                             ! should be impossible, but might simplify debugging
+ end if
+
+end function GetPyramidOrder
+
+end module Lambert

src/commercialFEM_fileList.f90

@@ -11,8 +11,18 @@
 #include "HDF5_utilities.f90"
 #endif
 #include "math.f90"
+#include "quaternions.f90"
+#include "Lambert.f90"
+#include "rotations.f90"
 #include "FEsolving.f90"
-#include "mesh.f90"
+#include "element.f90"
+#include "mesh_base.f90"
+#ifdef Abaqus
+#include "mesh_abaqus.f90"
+#endif
+#ifdef Marc4DAMASK
+#include "mesh_marc.f90"
+#endif
 #include "material.f90"
 #include "lattice.f90"
 #include "source_thermal_dissipation.f90"

src/compilation_info.f90

@@ -1,10 +0,0 @@
-#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
-  write(6,*) 'Compiled with ', compiler_version()
-  write(6,*) 'With options  ', compiler_options()
-#else
-  write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version ', __INTEL_COMPILER,&
-                                                     ', build date ', __INTEL_COMPILER_BUILD_DATE
-#endif
-write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
-write(6,*)
-flush(6)

src/constitutive.f90

@@ -38,11 +38,6 @@ contains
 !> @brief allocates arrays pointing to array of the various constitutive modules
 !--------------------------------------------------------------------------------------------------
 subroutine constitutive_init()
-#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
- use, intrinsic :: iso_fortran_env, only: &
-   compiler_version, &
-   compiler_options
-#endif
  use prec, only: &
    pReal
  use debug, only: &
@@ -53,15 +48,8 @@ subroutine constitutive_init()
  use IO, only: &
    IO_error, &
    IO_open_file, &
-   IO_checkAndRewind, &
    IO_open_jobFile_stat, &
-   IO_write_jobFile, &
+   IO_write_jobFile
-   IO_write_jobIntFile, &
-   IO_timeStamp
- use config, only: &
-   config_phase
- use mesh, only: &
-   FE_geomtype
  use config, only: &
    material_Nphase, &
    material_localFileExt, &
@@ -141,46 +129,33 @@ subroutine constitutive_init()
  nonlocalConstitutionPresent = .false.
 
 !--------------------------------------------------------------------------------------------------
-! open material.config
+! initialized plasticity
- if (.not. IO_open_jobFile_stat(FILEUNIT,material_localFileExt)) &                                  ! no local material configuration present...
-   call IO_open_file(FILEUNIT,material_configFile)                                                  ! ... open material.config file
-
-!--------------------------------------------------------------------------------------------------
-! parse plasticities from config file
  if (any(phase_plasticity == PLASTICITY_NONE_ID))          call plastic_none_init
  if (any(phase_plasticity == PLASTICITY_ISOTROPIC_ID))     call plastic_isotropic_init
  if (any(phase_plasticity == PLASTICITY_PHENOPOWERLAW_ID)) call plastic_phenopowerlaw_init
  if (any(phase_plasticity == PLASTICITY_KINEHARDENING_ID)) call plastic_kinehardening_init
  if (any(phase_plasticity == PLASTICITY_DISLOTWIN_ID))     call plastic_dislotwin_init
  if (any(phase_plasticity == PLASTICITY_DISLOUCLA_ID))     call plastic_disloucla_init
- if (any(phase_plasticity == PLASTICITY_NONLOCAL_ID)) then
+ if (any(phase_plasticity == PLASTICITY_NONLOCAL_ID))      call plastic_nonlocal_init
-  call plastic_nonlocal_init(FILEUNIT)
-  call plastic_nonlocal_stateInit()
- endif
 
 !--------------------------------------------------------------------------------------------------
-! parse source mechanisms from config file
+! initialize source mechanisms
- call IO_checkAndRewind(FILEUNIT)
+ if (any(phase_source == SOURCE_thermal_dissipation_ID))     call source_thermal_dissipation_init
- if (any(phase_source == SOURCE_thermal_dissipation_ID))     call source_thermal_dissipation_init(FILEUNIT)
+ if (any(phase_source == SOURCE_thermal_externalheat_ID))    call source_thermal_externalheat_init
- if (any(phase_source == SOURCE_thermal_externalheat_ID))    call source_thermal_externalheat_init(FILEUNIT)
+ if (any(phase_source == SOURCE_damage_isoBrittle_ID))       call source_damage_isoBrittle_init
- if (any(phase_source == SOURCE_damage_isoBrittle_ID))       call source_damage_isoBrittle_init(FILEUNIT)
+ if (any(phase_source == SOURCE_damage_isoDuctile_ID))       call source_damage_isoDuctile_init
- if (any(phase_source == SOURCE_damage_isoDuctile_ID))       call source_damage_isoDuctile_init(FILEUNIT)
+ if (any(phase_source == SOURCE_damage_anisoBrittle_ID))     call source_damage_anisoBrittle_init
- if (any(phase_source == SOURCE_damage_anisoBrittle_ID))     call source_damage_anisoBrittle_init(FILEUNIT)
+ if (any(phase_source == SOURCE_damage_anisoDuctile_ID))     call source_damage_anisoDuctile_init
- if (any(phase_source == SOURCE_damage_anisoDuctile_ID))     call source_damage_anisoDuctile_init(FILEUNIT)
  
 !--------------------------------------------------------------------------------------------------
-! parse kinematic mechanisms from config file
+! initialize kinematic mechanisms
- call IO_checkAndRewind(FILEUNIT)
+ if (any(phase_kinematics == KINEMATICS_cleavage_opening_ID))  call kinematics_cleavage_opening_init
- if (any(phase_kinematics == KINEMATICS_cleavage_opening_ID))  call kinematics_cleavage_opening_init(FILEUNIT)
+ if (any(phase_kinematics == KINEMATICS_slipplane_opening_ID)) call kinematics_slipplane_opening_init
- if (any(phase_kinematics == KINEMATICS_slipplane_opening_ID)) call kinematics_slipplane_opening_init(FILEUNIT)
+ if (any(phase_kinematics == KINEMATICS_thermal_expansion_ID)) call kinematics_thermal_expansion_init
- if (any(phase_kinematics == KINEMATICS_thermal_expansion_ID)) call kinematics_thermal_expansion_init(FILEUNIT)
- close(FILEUNIT)
 
  call config_deallocate('material.config/phase')
 
  write(6,'(/,a)')   ' <<<+-  constitutive init  -+>>>'
- write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
-#include "compilation_info.f90"
 
  mainProcess: if (worldrank == 0) then
 !--------------------------------------------------------------------------------------------------
@@ -348,7 +323,7 @@ end function constitutive_homogenizedC
 !--------------------------------------------------------------------------------------------------
 !> @brief calls microstructure function of the different constitutive models
 !--------------------------------------------------------------------------------------------------
-subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
+subroutine constitutive_microstructure(Fe, Fp, ipc, ip, el)
  use prec, only: &
    pReal
  use material, only: &
@@ -363,7 +338,7 @@ subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
    PLASTICITY_disloucla_ID, &
    PLASTICITY_nonlocal_ID
  use plastic_nonlocal, only: &
-   plastic_nonlocal_microstructure
+   plastic_nonlocal_dependentState
  use plastic_dislotwin, only: &
    plastic_dislotwin_dependentState
  use plastic_disloUCLA, only: &
@@ -381,8 +356,6 @@ subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
    ho, &                                                                                            !< homogenization
    tme, &                                                                                           !< thermal member position
    instance, of
- real(pReal),   intent(in), dimension(:,:,:,:) :: &
-   orientations                                                                                     !< crystal orientations as quaternions
 
  ho = material_homogenizationAt(el)
  tme = thermalMapping(ho)%p(ip,el)
@@ -397,7 +370,7 @@ subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
      instance = phase_plasticityInstance(material_phase(ipc,ip,el))
      call plastic_disloUCLA_dependentState(instance,of)
    case (PLASTICITY_NONLOCAL_ID) plasticityType
-     call plastic_nonlocal_microstructure (Fe,Fp,ip,el)
+     call plastic_nonlocal_dependentState (Fe,Fp,ip,el)
  end select plasticityType
 
 end subroutine constitutive_microstructure
@@ -405,15 +378,15 @@ end subroutine constitutive_microstructure
 
 !--------------------------------------------------------------------------------------------------
 !> @brief  contains the constitutive equation for calculating the velocity gradient
+! ToDo: Discuss wheter it makes sense if crystallite handles the configuration conversion, i.e.
+! Mp in, dLp_dMp out
 !--------------------------------------------------------------------------------------------------
-subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, el)
+subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, &
+                                         S, Fi, ipc, ip, el)
  use prec, only: &
    pReal
  use math, only: &
-   math_mul33x33, &
+   math_mul33x33
-   math_6toSym33, &
-   math_sym33to6, &
-   math_99to3333
  use material, only: &
    phasememberAt, &
    phase_plasticity, &
@@ -429,6 +402,8 @@ subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, e
    PLASTICITY_DISLOTWIN_ID, &
    PLASTICITY_DISLOUCLA_ID, &
    PLASTICITY_NONLOCAL_ID
+ use mesh, only: &
+   mesh_ipVolume
  use plastic_isotropic, only: &
    plastic_isotropic_LpAndItsTangent
  use plastic_phenopowerlaw, only: &
@@ -447,9 +422,8 @@ subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, e
    ipc, &                                                                                           !< component-ID of integration point
    ip, &                                                                                            !< integration point
    el                                                                                               !< element
- real(pReal),   intent(in),  dimension(6) :: &
-   S6                                                                                               !< 2nd Piola-Kirchhoff stress (vector notation)
  real(pReal),   intent(in),  dimension(3,3) :: &
+   S, &                                                                                             !< 2nd Piola-Kirchhoff stress
    Fi                                                                                               !< intermediate deformation gradient
  real(pReal),   intent(out), dimension(3,3) :: &
    Lp                                                                                               !< plastic velocity gradient
@@ -458,11 +432,8 @@ subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, e
    dLp_dFi                                                                                          !< derivative of Lp with respect to Fi
  real(pReal), dimension(3,3,3,3) :: &
    dLp_dMp                                                                                          !< derivative of Lp with respect to Mandel stress
- real(pReal), dimension(9,9) :: &
-   dLp_dMp99                                                                                        !< derivative of Lp with respect to Mstar (matrix notation)
  real(pReal), dimension(3,3) :: &
-   Mp, &                                                                                            !< Mandel stress work conjugate with Lp
+   Mp                                                                                               !< Mandel stress work conjugate with Lp
-   S                                                                                                !< 2nd Piola-Kirchhoff stress
  integer(pInt) :: &
    ho, &                                                                                            !< homogenization
    tme                                                                                              !< thermal member position
@@ -472,7 +443,6 @@ subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, e
  ho = material_homogenizationAt(el)
  tme = thermalMapping(ho)%p(ip,el)
 
- S  = math_6toSym33(S6)
  Mp  = math_mul33x33(math_mul33x33(transpose(Fi),Fi),S)
 
  plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
@@ -497,9 +467,8 @@ subroutine constitutive_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, S6, Fi, ipc, ip, e
      call plastic_kinehardening_LpAndItsTangent   (Lp,dLp_dMp, Mp,instance,of)
 
    case (PLASTICITY_NONLOCAL_ID) plasticityType
-     call plastic_nonlocal_LpAndItsTangent        (Lp,dLp_dMp99, math_sym33to6(Mp), &
+     call plastic_nonlocal_LpAndItsTangent        (Lp,dLp_dMp,Mp, &
-                                                   temperature(ho)%p(tme),ip,el)
+                                                   temperature(ho)%p(tme),mesh_ipVolume(ip,el),ip,el)
-     dLp_dMp = math_99to3333(dLp_dMp99)                                                             ! ToDo: We revert here the last statement in plastic_xx_LpAndItsTanget
 
    case (PLASTICITY_DISLOTWIN_ID) plasticityType
      of = phasememberAt(ipc,ip,el)
@@ -534,15 +503,15 @@ end subroutine constitutive_LpAndItsTangents
 !> @brief  contains the constitutive equation for calculating the velocity gradient
 ! ToDo: MD: S is Mi?
 !--------------------------------------------------------------------------------------------------
-subroutine constitutive_LiAndItsTangents(Li, dLi_dS, dLi_dFi, S6, Fi, ipc, ip, el)
+subroutine constitutive_LiAndItsTangents(Li, dLi_dS, dLi_dFi, &
+                                         S, Fi, ipc, ip, el)
  use prec, only: &
    pReal
  use math, only: &
    math_I3, &
    math_inv33, &
    math_det33, &
-   math_mul33x33, &
+   math_mul33x33
-   math_6toSym33
  use material, only: &
    phasememberAt, &
    phase_plasticity, &
@@ -569,8 +538,8 @@ subroutine constitutive_LiAndItsTangents(Li, dLi_dS, dLi_dFi, S6, Fi, ipc, ip, e
    ipc, &                                                                                           !< component-ID of integration point
    ip, &                                                                                            !< integration point
    el                                                                                               !< element
- real(pReal),   intent(in),  dimension(6) :: &
+ real(pReal),   intent(in),  dimension(3,3) :: &
-   S6                                                                                               !< 2nd Piola-Kirchhoff stress (vector notation)
+   S                                                                                                !< 2nd Piola-Kirchhoff stress
  real(pReal),   intent(in),  dimension(3,3) :: &
    Fi                                                                                               !< intermediate deformation gradient
  real(pReal),   intent(out), dimension(3,3) :: &
@@ -599,7 +568,7 @@ subroutine constitutive_LiAndItsTangents(Li, dLi_dS, dLi_dFi, S6, Fi, ipc, ip, e
    case (PLASTICITY_isotropic_ID) plasticityType
      of = phasememberAt(ipc,ip,el)
      instance = phase_plasticityInstance(material_phase(ipc,ip,el))
-     call plastic_isotropic_LiAndItsTangent(my_Li, my_dLi_dS, math_6toSym33(S6),instance,of)
+     call plastic_isotropic_LiAndItsTangent(my_Li, my_dLi_dS, S ,instance,of)
    case default plasticityType
      my_Li = 0.0_pReal
      my_dLi_dS = 0.0_pReal
@@ -611,9 +580,9 @@ subroutine constitutive_LiAndItsTangents(Li, dLi_dS, dLi_dFi, S6, Fi, ipc, ip, e
  KinematicsLoop: do k = 1_pInt, phase_Nkinematics(material_phase(ipc,ip,el))
    kinematicsType: select case (phase_kinematics(k,material_phase(ipc,ip,el)))
      case (KINEMATICS_cleavage_opening_ID) kinematicsType
-       call kinematics_cleavage_opening_LiAndItsTangent(my_Li, my_dLi_dS, S6, ipc, ip, el)
+       call kinematics_cleavage_opening_LiAndItsTangent(my_Li, my_dLi_dS, S, ipc, ip, el)
      case (KINEMATICS_slipplane_opening_ID) kinematicsType
-       call kinematics_slipplane_opening_LiAndItsTangent(my_Li, my_dLi_dS, S6, ipc, ip, el)
+       call kinematics_slipplane_opening_LiAndItsTangent(my_Li, my_dLi_dS, S, ipc, ip, el)
      case (KINEMATICS_thermal_expansion_ID) kinematicsType
        call kinematics_thermal_expansion_LiAndItsTangent(my_Li, my_dLi_dS, ipc, ip, el)
      case default kinematicsType
@@ -645,10 +614,11 @@ pure function constitutive_initialFi(ipc, ip, el)
  use prec, only: &
    pReal
  use math, only: &
-   math_I3, &
+   math_I3
-   math_inv33, &
-   math_mul33x33
  use material, only: &
+   material_phase, &
+   material_homog, &
+   thermalMapping, &
    phase_kinematics, &
    phase_Nkinematics, &
    material_phase, &
@@ -665,14 +635,20 @@ pure function constitutive_initialFi(ipc, ip, el)
    constitutive_initialFi                                                                           !< composite initial intermediate deformation gradient
  integer(pInt) :: &
    k                                                                                                !< counter in kinematics loop
+ integer(pInt) :: &
+   phase, &
+   homog, offset
 
  constitutive_initialFi = math_I3
+ phase = material_phase(ipc,ip,el)
 
- KinematicsLoop: do k = 1_pInt, phase_Nkinematics(material_phase(ipc,ip,el))                        !< Warning: small initial strain assumption
+ KinematicsLoop: do k = 1_pInt, phase_Nkinematics(phase)                                            !< Warning: small initial strain assumption
-   kinematicsType: select case (phase_kinematics(k,material_phase(ipc,ip,el)))
+   kinematicsType: select case (phase_kinematics(k,phase))
      case (KINEMATICS_thermal_expansion_ID) kinematicsType
+       homog = material_homog(ip,el)
+       offset = thermalMapping(homog)%p(ip,el)
        constitutive_initialFi = &
-         constitutive_initialFi + kinematics_thermal_expansion_initialStrain(ipc, ip, el)
+         constitutive_initialFi + kinematics_thermal_expansion_initialStrain(homog,phase,offset)
    end select kinematicsType
  enddo KinematicsLoop
 
@@ -712,7 +688,8 @@ end subroutine constitutive_SandItsTangents
 !> @brief returns the 2nd Piola-Kirchhoff stress tensor and its tangent with respect to
 !> the elastic and intermeidate deformation gradients using Hookes law
 !--------------------------------------------------------------------------------------------------
-subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, Fe, Fi, ipc, ip, el)
+subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, &
+                                              Fe, Fi, ipc, ip, el)
  use prec, only: &
    pReal
  use math, only : &
@@ -776,7 +753,7 @@ end subroutine constitutive_hooke_SandItsTangents
 !--------------------------------------------------------------------------------------------------
 !> @brief contains the constitutive equation for calculating the rate of change of microstructure
 !--------------------------------------------------------------------------------------------------
-subroutine constitutive_collectDotState(S6, FeArray, Fi, FpArray, subdt, subfracArray,ipc, ip, el)
+subroutine constitutive_collectDotState(S, FeArray, Fi, FpArray, subdt, ipc, ip, el)
  use prec, only: &
    pReal, &
    pLongInt
@@ -786,12 +763,9 @@ subroutine constitutive_collectDotState(S6, FeArray, Fi, FpArray, subdt, subfrac
    debug_levelBasic
  use math, only: &
    math_mul33x33, &
-   math_6toSym33, &
-   math_sym33to6, &
    math_mul33x33
  use mesh, only: &
-   mesh_NcpElems, &
+   theMesh
-   mesh_maxNips
  use material, only: &
    phasememberAt, &
    phase_plasticityInstance, &
@@ -842,27 +816,25 @@ subroutine constitutive_collectDotState(S6, FeArray, Fi, FpArray, subdt, subfrac
    el                                                                                               !< element
  real(pReal),  intent(in) :: &
    subdt                                                                                            !< timestep
- real(pReal),  intent(in), dimension(homogenization_maxNgrains,mesh_maxNips,mesh_NcpElems) :: &
+ real(pReal),  intent(in), dimension(3,3,homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems) :: &
-   subfracArray                                                                                     !< subfraction of timestep
- real(pReal),  intent(in), dimension(3,3,homogenization_maxNgrains,mesh_maxNips,mesh_NcpElems) :: &
    FeArray, &                                                                                       !< elastic deformation gradient
    FpArray                                                                                          !< plastic deformation gradient
  real(pReal),  intent(in), dimension(3,3) :: &
    Fi                                                                                               !< intermediate deformation gradient
- real(pReal),  intent(in), dimension(6) :: &
+ real(pReal),  intent(in), dimension(3,3) :: &
-   S6                                                                                               !< 2nd Piola Kirchhoff stress (vector notation)
+   S                                                                                                !< 2nd Piola Kirchhoff stress (vector notation)
  real(pReal),              dimension(3,3) :: &
    Mp
  integer(pInt) :: &
    ho, &                                                                                            !< homogenization
    tme, &                                                                                           !< thermal member position
-   s, &                                                                                             !< counter in source loop
+   i, &                                                                                             !< counter in source loop
    instance, of
 
  ho = material_homogenizationAt(el)
  tme = thermalMapping(ho)%p(ip,el)
 
- Mp  = math_mul33x33(math_mul33x33(transpose(Fi),Fi),math_6toSym33(S6))
+ Mp  = math_mul33x33(math_mul33x33(transpose(Fi),Fi),S)
 
  plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
 
@@ -892,16 +864,16 @@ subroutine constitutive_collectDotState(S6, FeArray, Fi, FpArray, subdt, subfrac
      call plastic_disloucla_dotState    (Mp,temperature(ho)%p(tme),instance,of)
 
    case (PLASTICITY_NONLOCAL_ID) plasticityType
-     call plastic_nonlocal_dotState     (math_sym33to6(Mp),FeArray,FpArray,temperature(ho)%p(tme), &
+     call plastic_nonlocal_dotState     (Mp,FeArray,FpArray,temperature(ho)%p(tme), &
-                                         subdt,subfracArray,ip,el)
+                                         subdt,ip,el)
  end select plasticityType
 
- SourceLoop: do s = 1_pInt, phase_Nsources(material_phase(ipc,ip,el))
+ SourceLoop: do i = 1_pInt, phase_Nsources(material_phase(ipc,ip,el))
 
-   sourceType: select case (phase_source(s,material_phase(ipc,ip,el)))
+   sourceType: select case (phase_source(i,material_phase(ipc,ip,el)))
 
      case (SOURCE_damage_anisoBrittle_ID) sourceType
-       call source_damage_anisoBrittle_dotState (S6, ipc, ip, el) !< correct stress?
+       call source_damage_anisoBrittle_dotState (S, ipc, ip, el) !< correct stress?
 
      case (SOURCE_damage_isoDuctile_ID) sourceType
        call source_damage_isoDuctile_dotState   (         ipc, ip, el)
@@ -931,7 +903,6 @@ subroutine constitutive_collectDeltaState(S, Fe, Fi, ipc, ip, el)
    debug_constitutive, &
    debug_levelBasic
  use math, only: &
-   math_sym33to6, &
    math_mul33x33
  use material, only: &
    phasememberAt, &
@@ -975,7 +946,7 @@ subroutine constitutive_collectDeltaState(S, Fe, Fi, ipc, ip, el)
      call plastic_kinehardening_deltaState(Mp,instance,of)
 
    case (PLASTICITY_NONLOCAL_ID) plasticityType
-     call plastic_nonlocal_deltaState(math_sym33to6(Mp),ip,el)
+     call plastic_nonlocal_deltaState(Mp,ip,el)
 
  end select plasticityType
 
@@ -997,15 +968,11 @@ end subroutine constitutive_collectDeltaState
 !--------------------------------------------------------------------------------------------------
 !> @brief returns array of constitutive results
 !--------------------------------------------------------------------------------------------------
-function constitutive_postResults(S6, Fi, FeArray, ipc, ip, el)
+function constitutive_postResults(S, Fi, ipc, ip, el)
  use prec, only: &
    pReal
  use math, only: &
-  math_6toSym33, &
   math_mul33x33
- use mesh, only: &
-   mesh_NcpElems, &
-   mesh_maxNips
  use material, only: &
    phasememberAt, &
    phase_plasticityInstance, &
@@ -1018,7 +985,6 @@ function constitutive_postResults(S6, Fi, FeArray, ipc, ip, el)
    material_homogenizationAt, &
    temperature, &
    thermalMapping, &
-   homogenization_maxNgrains, &
    PLASTICITY_NONE_ID, &
    PLASTICITY_ISOTROPIC_ID, &
    PLASTICITY_PHENOPOWERLAW_ID, &
@@ -1061,10 +1027,8 @@ function constitutive_postResults(S6, Fi, FeArray, ipc, ip, el)
    constitutive_postResults
  real(pReal),  intent(in), dimension(3,3) :: &
    Fi                                                                                               !< intermediate deformation gradient
- real(pReal),  intent(in), dimension(3,3,homogenization_maxNgrains,mesh_maxNips,mesh_NcpElems) :: &
+ real(pReal),  intent(in), dimension(3,3) :: &
-   FeArray                                                                                          !< elastic deformation gradient
+   S                                                                                                !< 2nd Piola Kirchhoff stress
- real(pReal),  intent(in), dimension(6) :: &
-   S6                                                                                               !< 2nd Piola Kirchhoff stress (vector notation)
  real(pReal), dimension(3,3) :: &
    Mp                                                                                               !< Mandel stress
  integer(pInt) :: &
@@ -1072,11 +1036,11 @@ function constitutive_postResults(S6, Fi, FeArray, ipc, ip, el)
  integer(pInt) :: &
    ho, &                                                                                            !< homogenization
    tme, &                                                                                           !< thermal member position
-   s, of, instance                                                                                  !< counter in source loop
+   i, of, instance                                                                                  !< counter in source loop
 
  constitutive_postResults = 0.0_pReal
 
- Mp  = math_mul33x33(math_mul33x33(transpose(Fi),Fi),math_6toSym33(S6))
+ Mp  = math_mul33x33(math_mul33x33(transpose(Fi),Fi),S)
 
  ho = material_homogenizationAt(el)
  tme = thermalMapping(ho)%p(ip,el)
@@ -1117,22 +1081,24 @@ function constitutive_postResults(S6, Fi, FeArray, ipc, ip, el)
 
    case (PLASTICITY_NONLOCAL_ID) plasticityType
      constitutive_postResults(startPos:endPos) = &
-       plastic_nonlocal_postResults (S6,FeArray,ip,el)
+       plastic_nonlocal_postResults (Mp,ip,el)
  end select plasticityType
 
- SourceLoop: do s = 1_pInt, phase_Nsources(material_phase(ipc,ip,el))
+ SourceLoop: do i = 1_pInt, phase_Nsources(material_phase(ipc,ip,el))
    startPos = endPos + 1_pInt
-   endPos = endPos + sourceState(material_phase(ipc,ip,el))%p(s)%sizePostResults
+   endPos = endPos + sourceState(material_phase(ipc,ip,el))%p(i)%sizePostResults
-   sourceType: select case (phase_source(s,material_phase(ipc,ip,el)))
+   of = phasememberAt(ipc,ip,el)
+   sourceType: select case (phase_source(i,material_phase(ipc,ip,el)))
      case (SOURCE_damage_isoBrittle_ID) sourceType
-       constitutive_postResults(startPos:endPos) = source_damage_isoBrittle_postResults(ipc, ip, el)
+       constitutive_postResults(startPos:endPos) = source_damage_isoBrittle_postResults(material_phase(ipc,ip,el),of)
      case (SOURCE_damage_isoDuctile_ID) sourceType
-       constitutive_postResults(startPos:endPos) = source_damage_isoDuctile_postResults(ipc, ip, el)
+       constitutive_postResults(startPos:endPos) = source_damage_isoDuctile_postResults(material_phase(ipc,ip,el),of)
      case (SOURCE_damage_anisoBrittle_ID) sourceType
-       constitutive_postResults(startPos:endPos) = source_damage_anisoBrittle_postResults(ipc, ip, el)
+       constitutive_postResults(startPos:endPos) = source_damage_anisoBrittle_postResults(material_phase(ipc,ip,el),of)
      case (SOURCE_damage_anisoDuctile_ID) sourceType
-       constitutive_postResults(startPos:endPos) = source_damage_anisoDuctile_postResults(ipc, ip, el)
+       constitutive_postResults(startPos:endPos) = source_damage_anisoDuctile_postResults(material_phase(ipc,ip,el),of)
    end select sourceType
+
  enddo SourceLoop
 
 end function constitutive_postResults

src/damage_local.f90

@@ -225,6 +225,7 @@ subroutine damage_local_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip, el
    homogenization_Ngrains, &
    mappingHomogenization, &
    phaseAt, &
+   phasememberAt, &
    phase_source, &
    phase_Nsources, &
    SOURCE_damage_isoBrittle_ID, &
@@ -249,7 +250,8 @@ subroutine damage_local_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip, el
  integer(pInt) :: &
    phase, &
    grain, &
-   source
+   source, &
+   constituent
  real(pReal) :: &
    phiDot, dPhiDot_dPhi, localphiDot, dLocalphiDot_dPhi  
 
@@ -257,19 +259,20 @@ subroutine damage_local_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip, el
  dPhiDot_dPhi = 0.0_pReal
  do grain = 1, homogenization_Ngrains(mappingHomogenization(2,ip,el))
    phase = phaseAt(grain,ip,el)
+   constituent = phasememberAt(grain,ip,el)
    do source = 1, phase_Nsources(phase)
      select case(phase_source(source,phase))                                                   
        case (SOURCE_damage_isoBrittle_ID)
-        call source_damage_isobrittle_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_isobrittle_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_isoDuctile_ID)
-        call source_damage_isoductile_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_isoductile_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_anisoBrittle_ID)
-        call source_damage_anisobrittle_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_anisobrittle_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_anisoDuctile_ID)
-        call source_damage_anisoductile_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_anisoductile_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case default
         localphiDot = 0.0_pReal

src/damage_nonlocal.f90

@@ -186,6 +186,7 @@ subroutine damage_nonlocal_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip,
    homogenization_Ngrains, &
    mappingHomogenization, &
    phaseAt, &
+   phasememberAt, &
    phase_source, &
    phase_Nsources, &
    SOURCE_damage_isoBrittle_ID, &
@@ -210,7 +211,8 @@ subroutine damage_nonlocal_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip,
  integer(pInt) :: &
    phase, &
    grain, &
-   source
+   source, &
+   constituent
  real(pReal) :: &
    phiDot, dPhiDot_dPhi, localphiDot, dLocalphiDot_dPhi  
 
@@ -218,19 +220,20 @@ subroutine damage_nonlocal_getSourceAndItsTangent(phiDot, dPhiDot_dPhi, phi, ip,
  dPhiDot_dPhi = 0.0_pReal
  do grain = 1, homogenization_Ngrains(mappingHomogenization(2,ip,el))
    phase = phaseAt(grain,ip,el)
+   constituent = phasememberAt(grain,ip,el)
    do source = 1_pInt, phase_Nsources(phase)
      select case(phase_source(source,phase))                                                   
        case (SOURCE_damage_isoBrittle_ID)
-        call source_damage_isobrittle_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_isobrittle_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_isoDuctile_ID)
-        call source_damage_isoductile_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_isoductile_getRateAndItsTangent  (localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_anisoBrittle_ID)
-        call source_damage_anisobrittle_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_anisobrittle_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case (SOURCE_damage_anisoDuctile_ID)
-        call source_damage_anisoductile_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, grain, ip,  el)
+        call source_damage_anisoductile_getRateAndItsTangent(localphiDot, dLocalphiDot_dPhi, phi, phase, constituent)
 
        case default
         localphiDot = 0.0_pReal

src/element.f90

@@ -0,0 +1,921 @@
+!--------------------------------------------------------------------------------------------------
+!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
+!> @author Christoph Koords, Max-Planck-Institut für Eisenforschung GmbH
+!--------------------------------------------------------------------------------------------------
+module element
+ use prec, only: &
+   pInt, &
+   pReal
+
+ implicit none
+ private 
+
+!---------------------------------------------------------------------------------------------------
+!> Properties of a single element (the element used in the mesh)
+!---------------------------------------------------------------------------------------------------
+ type, public :: tElement
+   integer(pInt) :: &
+     elemType, &
+     geomType, &                                                                                    ! geometry type (same for same dimension and same number of integration points)
+     cellType, &
+     Nnodes, &
+     Ncellnodes, &
+     NcellnodesPerCell, &
+     nIPs, &
+     nIPneighbors, &                                                                                   ! ToDo: MD: Do all IPs in one element type have the same number of neighbors?
+     maxNnodeAtIP
+   integer(pInt), dimension(:,:), allocatable :: &
+     Cell, &                                                                                        ! intra-element (cell) nodes that constitute a cell
+     NnodeAtIP, &
+     IPneighbor, &
+     cellFace
+   real(pReal), dimension(:,:), allocatable :: &
+ ! center of gravity of the weighted nodes gives the position of the cell node.
+ ! example: face-centered cell node with face nodes 1,2,5,6 to be used in,
+ !          e.g., an 8 node element, would be encoded:
+ !          1, 1, 0, 0, 1, 1, 0, 0
+     cellNodeParentNodeWeights
+   contains
+     procedure :: init => tElement_init
+ end type
+
+ integer(pInt), parameter, private :: &
+   NELEMTYPE = 13_pInt
+
+ integer(pInt), dimension(NelemType), parameter, private :: NNODE = &
+ int([ &
+      3, & ! 2D 3node 1ip
+      6, & ! 2D 6node 3ip
+      4, & ! 2D 4node 4ip
+      8, & ! 2D 8node 9ip
+      8, & ! 2D 8node 4ip
+      !--------------------
+      4, & ! 3D 4node 1ip
+      5, & ! 3D 5node 4ip
+     10, & ! 3D 10node 4ip
+      6, & ! 3D 6node 6ip
+      8, & ! 3D 8node 1ip
+      8, & ! 3D 8node 8ip
+     20, & ! 3D 20node 8ip
+     20  & ! 3D 20node 27ip
+  ],pInt)                                                                                           !< number of nodes that constitute a specific type of element
+
+ integer(pInt), dimension(NelemType), parameter, public :: GEOMTYPE = &
+ int([ &
+      1, & ! 2D 3node 1ip
+      2, & ! 2D 6node 3ip
+      3, & ! 2D 4node 4ip
+      4, & ! 2D 8node 9ip
+      3, & ! 2D 8node 4ip
+      !--------------------
+      5, & ! 3D 4node 1ip
+      6, & ! 3D 5node 4ip
+      6, & ! 3D 10node 4ip
+      7, & ! 3D 6node 6ip
+      8, & ! 3D 8node 1ip
+      9, & ! 3D 8node 8ip
+      9, & ! 3D 20node 8ip
+     10  & ! 3D 20node 27ip
+  ],pInt)                                                                                           !< geometry type of particular element type
+
+ !integer(pInt), dimension(maxval(geomType)), parameter, private :: NCELLNODE = &                   ! Intel 16.0 complains
+ integer(pInt), dimension(10), parameter, private :: NCELLNODE = &
+ int([ &
+      3, &
+      7, &
+      9, &
+     16, &
+      4, &
+     15, &
+     21, &
+      8, &
+     27, &
+     64  &
+  ],pInt)                                                                                           !< number of cell nodes in a specific geometry type
+
+ !integer(pInt), dimension(maxval(geomType)), parameter, private :: NIP = &                         ! Intel 16.0 complains
+ integer(pInt), dimension(10), parameter, private :: NIP = &
+ int([ &
+      1, & 
+      3, & 
+      4, & 
+      9, & 
+      1, & 
+      4, & 
+      6, & 
+      1, & 
+      8, & 
+     27  & 
+  ],pInt)                                                                                           !< number of IPs in a specific geometry type
+
+ !integer(pInt), dimension(maxval(geomType)), parameter, private  :: CELLTYPE = &                   ! Intel 16.0 complains
+ integer(pInt), dimension(10), parameter, private  :: CELLTYPE = &                                  !< cell type that is used by each geometry type
+ int([ &
+      1, & ! 2D 3node
+      2, & ! 2D 4node
+      2, & ! 2D 4node
+      2, & ! 2D 4node
+      3, & ! 3D 4node
+      4, & ! 3D 8node
+      4, & ! 3D 8node
+      4, & ! 3D 8node
+      4, & ! 3D 8node
+      4  & ! 3D 8node
+  ],pInt)
+ 
+ !integer(pInt), dimension(maxval(cellType)), parameter, private :: nIPNeighbor = &                 ! causes problem with Intel 16.0
+ integer(pInt), dimension(4), parameter, private :: NIPNEIGHBOR = &                                 !< number of ip neighbors / cell faces in a specific cell type
+ int([&
+      3, & ! 2D 3node
+      4, & ! 2D 4node
+      4, & ! 3D 4node
+      6  & ! 3D 8node
+  ],pInt)
+
+ !integer(pInt), dimension(maxval(cellType)), parameter, private :: NCELLNODESPERCELLFACE = &            
+ integer(pInt), dimension(4), parameter, private :: NCELLNODEPERCELLFACE = &                        !< number of cell nodes in a specific cell type
+ int([ &
+      2, & ! 2D 3node
+      2, & ! 2D 4node
+      3, & ! 3D 4node
+      4  & ! 3D 8node
+  ],pInt)
+
+ !integer(pInt), dimension(maxval(geomType)), parameter, private :: maxNodeAtIP = &                 ! causes problem with Intel 16.0
+ integer(pInt), dimension(10), parameter, private :: maxNnodeAtIP = &                               !< maximum number of parent nodes that belong to an IP for a specific type of element
+ int([ &
+      3, &
+      1, &
+      1, &
+      2, &
+      4, &
+      1, &
+      1, &
+      8, &
+      1, &
+      4  &
+  ],pInt)
+
+
+ !integer(pInt), dimension(maxval(CELLTYPE)), parameter, private  :: NCELLNODEPERCELL = &           ! Intel 16.0 complains
+ integer(pInt), dimension(4), parameter, private :: NCELLNODEPERCELL = &                            !< number of cell nodes in a specific cell type
+ int([ &
+      3, & ! 2D 3node
+      4, & ! 2D 4node
+      4, & ! 3D 4node
+      8  & ! 3D 8node
+  ],pInt)
+
+ integer(pInt), dimension(maxNnodeAtIP(1),nIP(1)), parameter, private :: NnodeAtIP1 = &
+    reshape(int([&
+    1,2,3   &
+    ],pInt),[maxNnodeAtIP(1),nIP(1)])
+
+ integer(pInt), dimension(maxNnodeAtIP(2),nIP(2)), parameter, private :: NnodeAtIP2 = &
+    reshape(int([&
+    1,  &
+    2,  &
+    3   &
+    ],pInt),[maxNnodeAtIP(2),nIP(2)])
+
+ integer(pInt), dimension(maxNnodeAtIP(3),nIP(3)), parameter, private :: NnodeAtIP3 = &
+    reshape(int([&
+    1,  &
+    2,  &
+    4,  &
+    3   &
+    ],pInt),[maxNnodeAtIP(3),nIP(3)])
+
+ integer(pInt), dimension(maxNnodeAtIP(4),nIP(4)), parameter, private :: NnodeAtIP4 = &
+    reshape(int([&
+    1,0,  &
+    1,2,  &
+    2,0,  &
+    1,4,  &
+    0,0,  &
+    2,3,  &
+    4,0,  &
+    3,4,  &
+    3,0   &
+    ],pInt),[maxNnodeAtIP(4),nIP(4)])
+
+ integer(pInt), dimension(maxNnodeAtIP(5),nIP(5)), parameter, private :: NnodeAtIP5 = &
+    reshape(int([&
+    1,2,3,4   &
+    ],pInt),[maxNnodeAtIP(5),nIP(5)])
+
+ integer(pInt), dimension(maxNnodeAtIP(6),nIP(6)), parameter, private :: NnodeAtIP6 = &
+    reshape(int([&
+    1,  &
+    2,  &
+    3,  &
+    4   &
+    ],pInt),[maxNnodeAtIP(6),nIP(6)])
+
+ integer(pInt), dimension(maxNnodeAtIP(7),nIP(7)), parameter, private :: NnodeAtIP7 = &
+    reshape(int([&
+    1,  &
+    2,  &
+    3,  &
+    4,  &
+    5,  &
+    6   &
+    ],pInt),[maxNnodeAtIP(7),nIP(7)])
+
+ integer(pInt), dimension(maxNnodeAtIP(8),nIP(8)), parameter, private :: NnodeAtIP8 = &
+    reshape(int([&
+    1,2,3,4,5,6,7,8   &
+    ],pInt),[maxNnodeAtIP(8),nIP(8)])
+
+ integer(pInt), dimension(maxNnodeAtIP(9),nIP(9)), parameter, private :: NnodeAtIP9 = &
+    reshape(int([&
+    1,  &
+    2,  &
+    4,  &
+    3,  &
+    5,  &
+    6,  &
+    8,  &
+    7   &
+    ],pInt),[maxNnodeAtIP(9),nIP(9)])
+
+ integer(pInt), dimension(maxNnodeAtIP(10),nIP(10)), parameter, private :: NnodeAtIP10 = &
+    reshape(int([&
+    1,0, 0,0,  &
+    1,2, 0,0,  &
+    2,0, 0,0,  &
+    1,4, 0,0,  &
+    1,3, 2,4,  &
+    2,3, 0,0,  &
+    4,0, 0,0,  &
+    3,4, 0,0,  &
+    3,0, 0,0,  &
+    1,5, 0,0,  &
+    1,6, 2,5,  &
+    2,6, 0,0,  &
+    1,8, 4,5,  &
+    0,0, 0,0,  &
+    2,7, 3,6,  &
+    4,8, 0,0,  &
+    3,8, 4,7,  &
+    3,7, 0,0,  &
+    5,0, 0,0,  &
+    5,6, 0,0,  &
+    6,0, 0,0,  &
+    5,8, 0,0,  &
+    5,7, 6,8,  &
+    6,7, 0,0,  &
+    8,0, 0,0,  &
+    7,8, 0,0,  &
+    7,0, 0,0   &
+    ],pInt),[maxNnodeAtIP(10),nIP(10)])
+
+ ! *** FE_ipNeighbor ***
+ ! is a list of the neighborhood of each IP.
+ ! It is sorted in (local) +x,-x, +y,-y, +z,-z direction.
+ ! Positive integers denote an intra-FE IP identifier.
+ ! Negative integers denote the interface behind which the neighboring (extra-FE) IP will be located.
+
+
+ integer(pInt), dimension(nIPneighbor(cellType(1)),nIP(1)), parameter, private :: IPneighbor1 = &
+    reshape(int([&
+    -2,-3,-1   &
+    ],pInt),[nIPneighbor(cellType(1)),nIP(1)])
+
+ integer(pInt), dimension(nIPneighbor(cellType(2)),nIP(2)), parameter, private :: IPneighbor2 = &
+     reshape(int([&
+      2,-3, 3,-1,  &
+     -2, 1, 3,-1,  &
+      2,-3,-2, 1   &
+    ],pInt),[nIPneighbor(cellType(2)),nIP(2)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(3)),nIP(3)), parameter, private :: IPneighbor3 = &
+     reshape(int([&
+      2,-4, 3,-1,  &
+     -2, 1, 4,-1,  &
+      4,-4,-3, 1,  &
+     -2, 3,-3, 2   &
+    ],pInt),[nIPneighbor(cellType(3)),nIP(3)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(4)),nIP(4)), parameter, private :: IPneighbor4 = &
+     reshape(int([&
+      2,-4, 4,-1,  &
+      3, 1, 5,-1,  &
+     -2, 2, 6,-1,  &
+      5,-4, 7, 1,  &
+      6, 4, 8, 2,  &
+     -2, 5, 9, 3,  &
+      8,-4,-3, 4,  &
+      9, 7,-3, 5,  &
+     -2, 8,-3, 6   &
+    ],pInt),[nIPneighbor(cellType(4)),nIP(4)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(5)),nIP(5)), parameter, private :: IPneighbor5 = &
+     reshape(int([&
+     -1,-2,-3,-4   &
+    ],pInt),[nIPneighbor(cellType(5)),nIP(5)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(6)),nIP(6)), parameter, private :: IPneighbor6 = &
+     reshape(int([&
+      2,-4, 3,-2, 4,-1,  &
+     -2, 1, 3,-2, 4,-1,  &
+      2,-4,-3, 1, 4,-1,  &
+      2,-4, 3,-2,-3, 1   &
+    ],pInt),[nIPneighbor(cellType(6)),nIP(6)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(7)),nIP(7)), parameter, private :: IPneighbor7 = &
+     reshape(int([&
+      2,-4, 3,-2, 4,-1,  &
+     -3, 1, 3,-2, 5,-1,  &
+      2,-4,-3, 1, 6,-1,  &
+      5,-4, 6,-2,-5, 1,  &
+     -3, 4, 6,-2,-5, 2,  &
+      5,-4,-3, 4,-5, 3   &
+    ],pInt),[nIPneighbor(cellType(7)),nIP(7)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(8)),nIP(8)), parameter, private :: IPneighbor8 = &
+     reshape(int([&
+     -3,-5,-4,-2,-6,-1   &
+    ],pInt),[nIPneighbor(cellType(8)),nIP(8)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(9)),nIP(9)), parameter, private :: IPneighbor9 = &
+     reshape(int([&
+      2,-5, 3,-2, 5,-1,  &
+     -3, 1, 4,-2, 6,-1,  &
+      4,-5,-4, 1, 7,-1,  &
+     -3, 3,-4, 2, 8,-1,  &
+      6,-5, 7,-2,-6, 1,  &
+     -3, 5, 8,-2,-6, 2,  &
+      8,-5,-4, 5,-6, 3,  &
+     -3, 7,-4, 6,-6, 4   &
+    ],pInt),[nIPneighbor(cellType(9)),nIP(9)])
+ 
+ integer(pInt), dimension(nIPneighbor(cellType(10)),nIP(10)), parameter, private :: IPneighbor10 = &
+     reshape(int([&
+      2,-5, 4,-2,10,-1,  &
+      3, 1, 5,-2,11,-1,  &
+     -3, 2, 6,-2,12,-1,  &
+      5,-5, 7, 1,13,-1,  &
+      6, 4, 8, 2,14,-1,  &
+     -3, 5, 9, 3,15,-1,  &
+      8,-5,-4, 4,16,-1,  &
+      9, 7,-4, 5,17,-1,  &
+     -3, 8,-4, 6,18,-1,  &
+     11,-5,13,-2,19, 1,  &
+     12,10,14,-2,20, 2,  &
+     -3,11,15,-2,21, 3,  &
+     14,-5,16,10,22, 4,  &
+     15,13,17,11,23, 5,  &
+     -3,14,18,12,24, 6,  &
+     17,-5,-4,13,25, 7,  &
+     18,16,-4,14,26, 8,  &
+     -3,17,-4,15,27, 9,  &
+     20,-5,22,-2,-6,10,  &
+     21,19,23,-2,-6,11,  &
+     -3,20,24,-2,-6,12,  &
+     23,-5,25,19,-6,13,  &
+     24,22,26,20,-6,14,  &
+     -3,23,27,21,-6,15,  &
+     26,-5,-4,22,-6,16,  &
+     27,25,-4,23,-6,17,  &
+     -3,26,-4,24,-6,18   &
+    ],pInt),[nIPneighbor(cellType(10)),nIP(10)])
+
+
+ real(pReal), dimension(nNode(1),NcellNode(geomType(1))), parameter :: cellNodeParentNodeWeights1 = &
+    reshape(real([&
+    1, 0, 0,  &
+    0, 1, 0,  &
+    0, 0, 1   &
+    ],pReal),[nNode(1),NcellNode(geomType(1))]) ! 2D 3node 1ip
+
+ real(pReal), dimension(nNode(2),NcellNode(geomType(2))), parameter :: cellNodeParentNodeWeights2 = &
+     reshape(real([&
+     1, 0, 0, 0, 0, 0,  &
+     0, 1, 0, 0, 0, 0,  &
+     0, 0, 1, 0, 0, 0,  &
+     0, 0, 0, 1, 0, 0,  &
+     0, 0, 0, 0, 1, 0,  &
+     0, 0, 0, 0, 0, 1,  &
+     1, 1, 1, 2, 2, 2   &
+    ],pReal),[nNode(2),NcellNode(geomType(2))]) ! 2D 6node 3ip
+
+ real(pReal), dimension(nNode(3),NcellNode(geomType(3))), parameter :: cellNodeParentNodeWeights3 = &
+    reshape(real([&
+    1, 0, 0, 0,  &
+    0, 1, 0, 0,  &
+    0, 0, 1, 0,  &
+    0, 0, 0, 1,  &
+    1, 1, 0, 0,  &
+    0, 1, 1, 0,  &
+    0, 0, 1, 1,  &
+    1, 0, 0, 1,  &
+    1, 1, 1, 1   &
+    ],pReal),[nNode(3),NcellNode(geomType(3))]) ! 2D 6node 3ip
+
+ real(pReal), dimension(nNode(4),NcellNode(geomType(4))), parameter :: cellNodeParentNodeWeights4 = &
+    reshape(real([&
+    1, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 1, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 1, 0, 0, 0, 0,  &
+    1, 0, 0, 0, 2, 0, 0, 0,  &
+    0, 1, 0, 0, 2, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 2, 0, 0,  &
+    0, 0, 1, 0, 0, 2, 0, 0,  &
+    0, 0, 1, 0, 0, 0, 2, 0,  &
+    0, 0, 0, 1, 0, 0, 2, 0,  &
+    0, 0, 0, 1, 0, 0, 0, 2,  &
+    1, 0, 0, 0, 0, 0, 0, 2,  &
+    4, 1, 1, 1, 8, 2, 2, 8,  &
+    1, 4, 1, 1, 8, 8, 2, 2,  &
+    1, 1, 4, 1, 2, 8, 8, 2,  &
+    1, 1, 1, 4, 2, 2, 8, 8   &
+    ],pReal),[nNode(4),NcellNode(geomType(4))])  ! 2D 8node 9ip
+
+ real(pReal), dimension(nNode(5),NcellNode(geomType(5))), parameter :: cellNodeParentNodeWeights5 = &
+    reshape(real([&
+    1, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 1, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 1, 0, 0, 0, 0,  &
+    0, 0, 0, 0, 1, 0, 0, 0,  &
+    0, 0, 0, 0, 0, 1, 0, 0,  &
+    0, 0, 0, 0, 0, 0, 1, 0,  &
+    0, 0, 0, 0, 0, 0, 0, 1,  &
+    1, 1, 1, 1, 2, 2, 2, 2   &
+    ],pReal),[nNode(5),NcellNode(geomType(5))])  ! 2D 8node 4ip
+
+ real(pReal), dimension(nNode(6),NcellNode(geomType(6))), parameter :: cellNodeParentNodeWeights6 = &
+    reshape(real([&
+    1, 0, 0, 0,  &
+    0, 1, 0, 0,  &
+    0, 0, 1, 0,  &
+    0, 0, 0, 1   &
+    ],pReal),[nNode(6),NcellNode(geomType(6))]) ! 3D 4node 1ip
+
+ real(pReal), dimension(nNode(7),NcellNode(geomType(7))), parameter :: cellNodeParentNodeWeights7 = &
+    reshape(real([&
+    1, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0,  &
+    0, 0, 1, 0, 0,  &
+    0, 0, 0, 1, 0,  &
+    1, 1, 0, 0, 0,  &
+    0, 1, 1, 0, 0,  &
+    1, 0, 1, 0, 0,  &
+    1, 0, 0, 1, 0,  &
+    0, 1, 0, 1, 0,  &
+    0, 0, 1, 1, 0,  &
+    1, 1, 1, 0, 0,  &
+    1, 1, 0, 1, 0,  &
+    0, 1, 1, 1, 0,  &
+    1, 0, 1, 1, 0,  &
+    0, 0, 0, 0, 1   &
+    ],pReal),[nNode(7),NcellNode(geomType(7))])  ! 3D 5node 4ip
+
+ real(pReal), dimension(nNode(8),NcellNode(geomType(8))), parameter :: cellNodeParentNodeWeights8 = &
+    reshape(real([&
+    1, 0, 0, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 1, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 1, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 0, 1, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 0, 0, 1, 0, 0, 0, 0,  &
+    0, 0, 0, 0, 0, 0, 1, 0, 0, 0,  &
+    0, 0, 0, 0, 0, 0, 0, 1, 0, 0,  &
+    0, 0, 0, 0, 0, 0, 0, 0, 1, 0,  &
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 1,  &
+    1, 1, 1, 0, 2, 2, 2, 0, 0, 0,  &
+    1, 1, 0, 1, 2, 0, 0, 2, 2, 0,  &
+    0, 1, 1, 1, 0, 2, 0, 0, 2, 2,  &
+    1, 0, 1, 1, 0, 0, 2, 2, 0, 2,  &
+    3, 3, 3, 3, 4, 4, 4, 4, 4, 4   &
+    ],pReal),[nNode(8),NcellNode(geomType(8))])  ! 3D 10node 4ip
+
+ real(pReal), dimension(nNode(9),NcellNode(geomType(9))), parameter :: cellNodeParentNodeWeights9 = &
+    reshape(real([&
+    1, 0, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 0,  &
+    0, 0, 1, 0, 0, 0,  &
+    0, 0, 0, 1, 0, 0,  &
+    0, 0, 0, 0, 1, 0,  &
+    0, 0, 0, 0, 0, 1,  &
+    1, 1, 0, 0, 0, 0,  &
+    0, 1, 1, 0, 0, 0,  &
+    1, 0, 1, 0, 0, 0,  &
+    1, 0, 0, 1, 0, 0,  &
+    0, 1, 0, 0, 1, 0,  &
+    0, 0, 1, 0, 0, 1,  &
+    0, 0, 0, 1, 1, 0,  &
+    0, 0, 0, 0, 1, 1,  &
+    0, 0, 0, 1, 0, 1,  &
+    1, 1, 1, 0, 0, 0,  &
+    1, 1, 0, 1, 1, 0,  &
+    0, 1, 1, 0, 1, 1,  &
+    1, 0, 1, 1, 0, 1,  &
+    0, 0, 0, 1, 1, 1,  &
+    1, 1, 1, 1, 1, 1   &
+    ],pReal),[nNode(9),NcellNode(geomType(9))])  ! 3D 6node 6ip
+
+ real(pReal), dimension(nNode(10),NcellNode(geomType(10))), parameter :: cellNodeParentNodeWeights10 = &
+    reshape(real([&
+    1, 0, 0, 0, 0, 0, 0, 0,  &
+    0, 1, 0, 0, 0, 0, 0, 0,  &
+    0, 0, 1, 0, 0, 0, 0, 0,  &
+    0, 0, 0, 1, 0, 0, 0, 0,  &
+    0, 0, 0, 0, 1, 0, 0, 0,  &
+    0, 0, 0, 0, 0, 1, 0, 0,  &
+    0, 0, 0, 0, 0, 0, 1, 0,  &
+    0, 0, 0, 0, 0, 0, 0, 1   &
+    ],pReal),[nNode(10),NcellNode(geomType(10))])  ! 3D 8node 1ip
+ 
+ real(pReal), dimension(nNode(11),NcellNode(geomType(11))), parameter :: cellNodeParentNodeWeights11 = &
+    reshape(real([&
+    1, 0, 0, 0,  0, 0, 0, 0,  &   !
+    0, 1, 0, 0,  0, 0, 0, 0,  &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  &   !
+    0, 0, 0, 0,  1, 0, 0, 0,  &   !  5
+    0, 0, 0, 0,  0, 1, 0, 0,  &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  &   !
+    0, 0, 0, 0,  0, 0, 0, 1,  &   !
+    1, 1, 0, 0,  0, 0, 0, 0,  &   !
+    0, 1, 1, 0,  0, 0, 0, 0,  &   ! 10
+    0, 0, 1, 1,  0, 0, 0, 0,  &   !
+    1, 0, 0, 1,  0, 0, 0, 0,  &   !
+    1, 0, 0, 0,  1, 0, 0, 0,  &   !
+    0, 1, 0, 0,  0, 1, 0, 0,  &   !
+    0, 0, 1, 0,  0, 0, 1, 0,  &   ! 15
+    0, 0, 0, 1,  0, 0, 0, 1,  &   !
+    0, 0, 0, 0,  1, 1, 0, 0,  &   !
+    0, 0, 0, 0,  0, 1, 1, 0,  &   !
+    0, 0, 0, 0,  0, 0, 1, 1,  &   !
+    0, 0, 0, 0,  1, 0, 0, 1,  &   ! 20
+    1, 1, 1, 1,  0, 0, 0, 0,  &   !
+    1, 1, 0, 0,  1, 1, 0, 0,  &   !
+    0, 1, 1, 0,  0, 1, 1, 0,  &   !
+    0, 0, 1, 1,  0, 0, 1, 1,  &   !
+    1, 0, 0, 1,  1, 0, 0, 1,  &   ! 25
+    0, 0, 0, 0,  1, 1, 1, 1,  &   !
+    1, 1, 1, 1,  1, 1, 1, 1   &   !
+    ],pReal),[nNode(11),NcellNode(geomType(11))])  ! 3D 8node 8ip
+ 
+ real(pReal), dimension(nNode(12),NcellNode(geomType(12))), parameter :: cellNodeParentNodeWeights12 = &
+    reshape(real([&
+    1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !  5
+    0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   ! 10
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  1, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 1, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 1, 0, &   ! 15
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 1, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0, &   ! 20
+    1, 1, 1, 1,  0, 0, 0, 0,  2, 2, 2, 2,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    1, 1, 0, 0,  1, 1, 0, 0,  2, 0, 0, 0,  2, 0, 0, 0,  2, 2, 0, 0, &   !
+    0, 1, 1, 0,  0, 1, 1, 0,  0, 2, 0, 0,  0, 2, 0, 0,  0, 2, 2, 0, &   !
+    0, 0, 1, 1,  0, 0, 1, 1,  0, 0, 2, 0,  0, 0, 2, 0,  0, 0, 2, 2, &   !
+    1, 0, 0, 1,  1, 0, 0, 1,  0, 0, 0, 2,  0, 0, 0, 2,  2, 0, 0, 2, &   ! 25
+    0, 0, 0, 0,  1, 1, 1, 1,  0, 0, 0, 0,  2, 2, 2, 2,  0, 0, 0, 0, &   !
+    3, 3, 3, 3,  3, 3, 3, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4  &   !
+    ],pReal),[nNode(12),NcellNode(geomType(12))])  ! 3D 20node 8ip
+ 
+ real(pReal), dimension(nNode(13),NcellNode(geomType(13))), parameter :: cellNodeParentNodeWeights13 = &
+    reshape(real([&
+    1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !  5
+    0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    1, 0, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 1, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   ! 10
+    0, 1, 0, 0,  0, 0, 0, 0,  0, 2, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  0, 2, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 2, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 2, 0,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 2,  0, 0, 0, 0,  0, 0, 0, 0, &   ! 15
+    1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 2,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0, &   !
+    0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 2, 0, 0, &   !
+    0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 2, 0, &   !
+    0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 2, &   ! 20
+    0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 2, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 2, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 2, &   !
+    0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0,  0, 0, 0, 0, &   ! 25
+    0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  2, 0, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 1, 0, 0,  0, 0, 0, 0,  0, 2, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 2, 0, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 1, 0,  0, 0, 0, 0,  0, 0, 2, 0,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 2, 0,  0, 0, 0, 0, &   ! 30
+    0, 0, 0, 0,  0, 0, 0, 1,  0, 0, 0, 0,  0, 0, 0, 2,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  1, 0, 0, 0,  0, 0, 0, 0,  0, 0, 0, 2,  0, 0, 0, 0, &   !
+    4, 1, 1, 1,  0, 0, 0, 0,  8, 2, 2, 8,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    1, 4, 1, 1,  0, 0, 0, 0,  8, 8, 2, 2,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    1, 1, 4, 1,  0, 0, 0, 0,  2, 8, 8, 2,  0, 0, 0, 0,  0, 0, 0, 0, &   ! 35
+    1, 1, 1, 4,  0, 0, 0, 0,  2, 2, 8, 8,  0, 0, 0, 0,  0, 0, 0, 0, &   !
+    4, 1, 0, 0,  1, 1, 0, 0,  8, 0, 0, 0,  2, 0, 0, 0,  8, 2, 0, 0, &   !
+    1, 4, 0, 0,  1, 1, 0, 0,  8, 0, 0, 0,  2, 0, 0, 0,  2, 8, 0, 0, &   !
+    0, 4, 1, 0,  0, 1, 1, 0,  0, 8, 0, 0,  0, 2, 0, 0,  0, 8, 2, 0, &   !
+    0, 1, 4, 0,  0, 1, 1, 0,  0, 8, 0, 0,  0, 2, 0, 0,  0, 2, 8, 0, &   ! 40
+    0, 0, 4, 1,  0, 0, 1, 1,  0, 0, 8, 0,  0, 0, 2, 0,  0, 0, 8, 2, &   !
+    0, 0, 1, 4,  0, 0, 1, 1,  0, 0, 8, 0,  0, 0, 2, 0,  0, 0, 2, 8, &   !
+    1, 0, 0, 4,  1, 0, 0, 1,  0, 0, 0, 8,  0, 0, 0, 2,  2, 0, 0, 8, &   !
+    4, 0, 0, 1,  1, 0, 0, 1,  0, 0, 0, 8,  0, 0, 0, 2,  8, 0, 0, 2, &   !
+    1, 1, 0, 0,  4, 1, 0, 0,  2, 0, 0, 0,  8, 0, 0, 0,  8, 2, 0, 0, &   ! 45
+    1, 1, 0, 0,  1, 4, 0, 0,  2, 0, 0, 0,  8, 0, 0, 0,  2, 8, 0, 0, &   !
+    0, 1, 1, 0,  0, 4, 1, 0,  0, 2, 0, 0,  0, 8, 0, 0,  0, 8, 2, 0, &   !
+    0, 1, 1, 0,  0, 1, 4, 0,  0, 2, 0, 0,  0, 8, 0, 0,  0, 2, 8, 0, &   !
+    0, 0, 1, 1,  0, 0, 4, 1,  0, 0, 2, 0,  0, 0, 8, 0,  0, 0, 8, 2, &   !
+    0, 0, 1, 1,  0, 0, 1, 4,  0, 0, 2, 0,  0, 0, 8, 0,  0, 0, 2, 8, &   ! 50
+    1, 0, 0, 1,  1, 0, 0, 4,  0, 0, 0, 2,  0, 0, 0, 8,  2, 0, 0, 8, &   !
+    1, 0, 0, 1,  4, 0, 0, 1,  0, 0, 0, 2,  0, 0, 0, 8,  8, 0, 0, 2, &   !
+    0, 0, 0, 0,  4, 1, 1, 1,  0, 0, 0, 0,  8, 2, 2, 8,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  1, 4, 1, 1,  0, 0, 0, 0,  8, 8, 2, 2,  0, 0, 0, 0, &   !
+    0, 0, 0, 0,  1, 1, 4, 1,  0, 0, 0, 0,  2, 8, 8, 2,  0, 0, 0, 0, &   ! 55
+    0, 0, 0, 0,  1, 1, 1, 4,  0, 0, 0, 0,  2, 2, 8, 8,  0, 0, 0, 0, &   !
+   24, 8, 4, 8,  8, 4, 3, 4, 32,12,12,32, 12, 4, 4,12, 32,12, 4,12, &   !
+    8,24, 8, 4,  4, 8, 4, 3, 32,32,12,12, 12,12, 4, 4, 12,32,12, 4, &   !
+    4, 8,24, 8,  3, 4, 8, 4, 12,32,32,12,  4,12,12, 4,  4,12,32,12, &   !
+    8, 4, 8,24,  4, 3, 4, 8, 12,12,32,32,  4, 4,12,12, 12, 4,12,32, &   ! 60
+    8, 4, 3, 4, 24, 8, 4, 8, 12, 4, 4,12, 32,12,12,32, 32,12, 4,12, &   !
+    4, 8, 4, 3,  8,24, 8, 4, 12,12, 4, 4, 32,32,12,12, 12,32,12, 4, &   !
+    3, 4, 8, 4,  4, 8,24, 8,  4,12,12, 4, 12,32,32,12,  4,12,32,12, &   !
+    4, 3, 4, 8,  8, 4, 8,24,  4, 4,12,12, 12,12,32,32, 12, 4,12,32  &   !
+    ],pReal),[nNode(13),NcellNode(geomType(13))])  ! 3D 20node 27ip
+
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(1)),NIP(1)), parameter :: CELL1 = &
+    reshape(int([&
+    1,2,3   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(1)),NIP(1)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(2)),NIP(2)), parameter :: CELL2 = &
+    reshape(int([&
+    1, 4, 7, 6,   &
+    2, 5, 7, 4,   &
+    3, 6, 7, 5    &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(2)),NIP(2)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(3)),NIP(3)), parameter :: CELL3 = &
+    reshape(int([&
+    1, 5, 9, 8,   &
+    5, 2, 6, 9,   &
+    8, 9, 7, 4,   &
+    9, 6, 3, 7    &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(3)),NIP(3)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(4)),NIP(4)), parameter :: CELL4 = &
+    reshape(int([&
+    1, 5,13,12,   &
+    5, 6,14,13,   &
+    6, 2, 7,14,   &
+   12,13,16,11,   &
+   13,14,15,16,   &
+   14, 7, 8,15,   &
+   11,16,10, 4,   &
+   16,15, 9,10,   &
+   15, 8, 3, 9    &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(4)),NIP(4)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(5)),NIP(5)), parameter :: CELL5 = &
+    reshape(int([&
+    1, 2, 3, 4   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(5)),NIP(5)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(6)),NIP(6)), parameter :: CELL6 = &
+    reshape(int([&
+    1, 5,11, 7, 8,12,15,14,  &
+    5, 2, 6,11,12, 9,13,15,  &
+    7,11, 6, 3,14,15,13,10,  &
+    8,12,15, 4, 4, 9,13,10   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(6)),NIP(6)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(7)),NIP(7)), parameter :: CELL7 = &
+    reshape(int([&
+    1, 7,16, 9,10,17,21,19,  &
+    7, 2, 8,16,17,11,18,21,  &
+    9,16, 8, 3,19,21,18,12,  &
+   10,17,21,19, 4,13,20,15,  &
+   17,11,18,21,13, 5,14,20,  &
+   19,21,18,12,15,20,14, 6   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(7)),NIP(7)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(8)),NIP(8)), parameter :: CELL8 = &
+    reshape(int([&
+    1, 2, 3, 4, 5, 6, 7, 8   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(8)),NIP(8)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(9)),NIP(9)), parameter :: CELL9 = &
+    reshape(int([&
+    1, 9,21,12,13,22,27,25,  &
+    9, 2,10,21,22,14,23,27,  &
+   12,21,11, 4,25,27,24,16,  &
+   21,10, 3,11,27,23,15,24,  &
+   13,22,27,25, 5,17,26,20,  &
+   22,14,23,27,17, 6,18,26,  &
+   25,27,24,16,20,26,19, 8,  &
+   27,23,15,24,26,18, 7,19   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(9)),NIP(9)])
+
+ integer(pInt), dimension(NCELLNODEPERCELL(CELLTYPE(10)),NIP(10)), parameter :: CELL10 = &
+    reshape(int([&
+    1, 9,33,16,17,37,57,44,  &
+    9,10,34,33,37,38,58,57,  &
+   10, 2,11,34,38,18,39,58,  &
+   16,33,36,15,44,57,60,43,  &
+   33,34,35,36,57,58,59,60,  &
+   34,11,12,35,58,39,40,59,  &
+   15,36,14, 4,43,60,42,20,  &
+   36,35,13,14,60,59,41,42,  &
+   35,12, 3,13,59,40,19,41,  &
+   17,37,57,44,21,45,61,52,  &
+   37,38,58,57,45,46,62,61,  &
+   38,18,39,58,46,22,47,62,  &
+   44,57,60,43,52,61,64,51,  &
+   57,58,59,60,61,62,63,64,  &
+   58,39,40,59,62,47,48,63,  &
+   43,60,42,20,51,64,50,24,  &
+   60,59,41,42,64,63,49,50,  &
+   59,40,19,41,63,48,23,49,  &
+   21,45,61,52, 5,25,53,32,  &
+   45,46,62,61,25,26,54,53,  &
+   46,22,47,62,26, 6,27,54,  &
+   52,61,64,51,32,53,56,31,  &
+   61,62,63,64,53,54,55,56,  &
+   62,47,48,63,54,27,28,55,  &
+   51,64,50,24,31,56,30, 8,  &
+   64,63,49,50,56,55,29,30,  &
+   63,48,23,49,55,28, 7,29   &
+    ],pInt),[NCELLNODEPERCELL(CELLTYPE(10)),NIP(10)])
+
+
+  integer(pInt), dimension(NCELLNODEPERCELLFACE(1),NIPNEIGHBOR(1)), parameter :: CELLFACE1 = &
+    reshape(int([&
+    2,3,  &
+    3,1,  &
+    1,2   &
+    ],pInt),[NCELLNODEPERCELLFACE(1),NIPNEIGHBOR(1)])                   ! 2D 3node, VTK_TRIANGLE (5)
+
+ integer(pInt), dimension(NCELLNODEPERCELLFACE(2),NIPNEIGHBOR(2)), parameter :: CELLFACE2 = &
+    reshape(int([&
+    2,3,  &
+    4,1,  &
+    3,4,  &
+    1,2   &
+    ],pInt),[NCELLNODEPERCELLFACE(2),NIPNEIGHBOR(2)])              ! 2D 4node, VTK_QUAD (9)
+
+ integer(pInt), dimension(NCELLNODEPERCELLFACE(3),NIPNEIGHBOR(3)), parameter :: CELLFACE3 = &
+    reshape(int([&
+    1,3,2,  &
+    1,2,4,  &
+    2,3,4,  &
+    1,4,3   &
+    ],pInt),[NCELLNODEPERCELLFACE(3),NIPNEIGHBOR(3)])                     ! 3D 4node, VTK_TETRA (10)
+
+ integer(pInt), dimension(NCELLNODEPERCELLFACE(4),NIPNEIGHBOR(4)), parameter :: CELLFACE4 = &
+    reshape(int([&
+    2,3,7,6,  &
+    4,1,5,8,  &
+    3,4,8,7,  &
+    1,2,6,5,  &
+    5,6,7,8,  &
+    1,4,3,2   &
+    ],pInt),[NCELLNODEPERCELLFACE(4),NIPNEIGHBOR(4)])              ! 3D 8node, VTK_HEXAHEDRON (12)
+
+
+contains
+
+ subroutine tElement_init(self,elemType)
+   implicit none
+   class(tElement) :: self
+   integer(pInt), intent(in) :: elemType
+   self%elemType = elemType
+
+   self%Nnodes     = Nnode    (self%elemType)
+   self%geomType   = geomType (self%elemType)
+   select case (self%elemType)
+     case(1_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights1
+     case(2_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights2
+     case(3_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights3
+     case(4_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights4
+     case(5_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights5
+     case(6_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights6
+     case(7_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights7
+     case(8_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights8
+     case(9_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights9
+     case(10_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights10
+     case(11_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights11
+     case(12_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights12
+     case(13_pInt)
+       self%cellNodeParentNodeWeights  = cellNodeParentNodeWeights13
+     case default
+       print*, 'Mist'
+  end select
+  
+
+   self%NcellNodes   = NcellNode    (self%geomType)
+   self%maxNnodeAtIP = maxNnodeAtIP (self%geomType) 
+   self%nIPs         = nIP          (self%geomType)
+   self%cellType     = cellType     (self%geomType)
+
+
+   select case (self%geomType)
+     case(1_pInt)
+       self%NnodeAtIP   = NnodeAtIP1
+       self%IPneighbor  = IPneighbor1
+       self%cell        = CELL1
+     case(2_pInt)
+       self%NnodeAtIP   = NnodeAtIP2
+       self%IPneighbor  = IPneighbor2
+       self%cell        = CELL2
+     case(3_pInt)
+       self%NnodeAtIP   = NnodeAtIP3
+       self%IPneighbor  = IPneighbor3
+       self%cell        = CELL3
+     case(4_pInt)
+       self%NnodeAtIP   = NnodeAtIP4
+       self%IPneighbor  = IPneighbor4
+       self%cell        = CELL4
+     case(5_pInt)
+       self%NnodeAtIP   = NnodeAtIP5
+       self%IPneighbor  = IPneighbor5
+       self%cell        = CELL5
+     case(6_pInt)
+       self%NnodeAtIP   = NnodeAtIP6
+       self%IPneighbor  = IPneighbor6
+       self%cell        = CELL6
+     case(7_pInt)
+       self%NnodeAtIP   = NnodeAtIP7
+       self%IPneighbor  = IPneighbor7
+       self%cell        = CELL7
+     case(8_pInt)
+       self%NnodeAtIP   = NnodeAtIP8
+       self%IPneighbor  = IPneighbor8
+       self%cell        = CELL8
+     case(9_pInt)
+       self%NnodeAtIP   = NnodeAtIP9
+       self%IPneighbor  = IPneighbor9
+       self%cell        = CELL9
+     case(10_pInt)
+       self%NnodeAtIP   = NnodeAtIP10
+       self%IPneighbor  = IPneighbor10
+       self%cell        = CELL10
+  end select
+   self%NcellNodesPerCell = NCELLNODEPERCELL(self%cellType)
+ 
+  select case(self%cellType)
+    case(1_pInt)
+      self%cellFace = CELLFACE1
+    case(2_pInt)
+      self%cellFace = CELLFACE2
+    case(3_pInt)
+      self%cellFace = CELLFACE3
+    case(4_pInt)
+      self%cellFace = CELLFACE4
+   end select
+   
+   self%nIPneighbors = size(self%IPneighbor,1)
+   
+   write(6,'(/,a)')   ' <<<+-  element_init  -+>>>'
+   
+   write(6,*)' element type        ',self%elemType
+   write(6,*)'   geom type         ',self%geomType
+   write(6,*)'   cell type         ',self%cellType
+   write(6,*)'   # node            ',self%Nnodes
+   write(6,*)'   # IP              ',self%nIPs
+   write(6,*)'   # cellnode        ',self%Ncellnodes
+   write(6,*)'   # cellnode/cell   ',self%NcellnodesPerCell
+   write(6,*)'   # IP neighbor     ',self%nIPneighbors
+   write(6,*)'   max # node at IP  ',self%maxNnodeAtIP
+   
+ end subroutine tElement_init
+
+end module element

src/homogenization.f90

@@ -71,11 +71,8 @@ subroutine homogenization_init
    debug_e, &
    debug_g
  use mesh, only: &
-   mesh_maxNips, &
+   theMesh, &
-   mesh_NcpElems, &
+   mesh_element
-   mesh_element, &
-   FE_Nips, &
-   FE_geomtype
  use constitutive, only: &
    constitutive_plasticity_maxSizePostResults, &
    constitutive_source_maxSizePostResults
@@ -111,30 +108,18 @@ subroutine homogenization_init
  logical :: valid
 
 
-!--------------------------------------------------------------------------------------------------
-! open material.config
- if (.not. IO_open_jobFile_stat(FILEUNIT,material_localFileExt)) &                                  ! no local material configuration present...
-   call IO_open_file(FILEUNIT,material_configFile)                                                  ! ... open material.config file
-
-!--------------------------------------------------------------------------------------------------
-! parse homogenization from config file 
  if (any(homogenization_type == HOMOGENIZATION_NONE_ID))      call homogenization_none_init
  if (any(homogenization_type == HOMOGENIZATION_ISOSTRAIN_ID)) call homogenization_isostrain_init
  if (any(homogenization_type == HOMOGENIZATION_RGC_ID))       call homogenization_RGC_init
 
-!--------------------------------------------------------------------------------------------------
+ if (any(thermal_type == THERMAL_isothermal_ID)) call thermal_isothermal_init
-! parse thermal from config file
+ if (any(thermal_type == THERMAL_adiabatic_ID))  call thermal_adiabatic_init
- call IO_checkAndRewind(FILEUNIT)
+ if (any(thermal_type == THERMAL_conduction_ID)) call thermal_conduction_init
- if (any(thermal_type == THERMAL_isothermal_ID)) &
-   call thermal_isothermal_init()
- if (any(thermal_type == THERMAL_adiabatic_ID)) &
-   call thermal_adiabatic_init(FILEUNIT)
- if (any(thermal_type == THERMAL_conduction_ID)) &
-   call thermal_conduction_init(FILEUNIT)
 
 !--------------------------------------------------------------------------------------------------
-! parse damage from config file
+! open material.config
- call IO_checkAndRewind(FILEUNIT)
+ if (.not. IO_open_jobFile_stat(FILEUNIT,material_localFileExt)) &                                  ! no local material configuration present...
+   call IO_open_file(FILEUNIT,material_configFile)                                                  ! ... open material.config file
  if (any(damage_type == DAMAGE_none_ID)) &
    call damage_none_init()
  if (any(damage_type == DAMAGE_local_ID)) &
@@ -244,20 +229,20 @@ subroutine homogenization_init
 
 !--------------------------------------------------------------------------------------------------
 ! allocate and initialize global variables
- allocate(materialpoint_dPdF(3,3,3,3,mesh_maxNips,mesh_NcpElems),       source=0.0_pReal)
+ allocate(materialpoint_dPdF(3,3,3,3,theMesh%elem%nIPs,theMesh%nElems),       source=0.0_pReal)
- allocate(materialpoint_F0(3,3,mesh_maxNips,mesh_NcpElems),             source=0.0_pReal)
+ allocate(materialpoint_F0(3,3,theMesh%elem%nIPs,theMesh%nElems),             source=0.0_pReal)
- materialpoint_F0 = spread(spread(math_I3,3,mesh_maxNips),4,mesh_NcpElems)                          ! initialize to identity
+ materialpoint_F0 = spread(spread(math_I3,3,theMesh%elem%nIPs),4,theMesh%nElems)                          ! initialize to identity
- allocate(materialpoint_F(3,3,mesh_maxNips,mesh_NcpElems),              source=0.0_pReal)
+ allocate(materialpoint_F(3,3,theMesh%elem%nIPs,theMesh%nElems),              source=0.0_pReal)
  materialpoint_F = materialpoint_F0                                                                 ! initialize to identity
- allocate(materialpoint_subF0(3,3,mesh_maxNips,mesh_NcpElems),          source=0.0_pReal)
+ allocate(materialpoint_subF0(3,3,theMesh%elem%nIPs,theMesh%nElems),          source=0.0_pReal)
- allocate(materialpoint_subF(3,3,mesh_maxNips,mesh_NcpElems),           source=0.0_pReal)
+ allocate(materialpoint_subF(3,3,theMesh%elem%nIPs,theMesh%nElems),           source=0.0_pReal)
- allocate(materialpoint_P(3,3,mesh_maxNips,mesh_NcpElems),              source=0.0_pReal)
+ allocate(materialpoint_P(3,3,theMesh%elem%nIPs,theMesh%nElems),              source=0.0_pReal)
- allocate(materialpoint_subFrac(mesh_maxNips,mesh_NcpElems),            source=0.0_pReal)
+ allocate(materialpoint_subFrac(theMesh%elem%nIPs,theMesh%nElems),            source=0.0_pReal)
- allocate(materialpoint_subStep(mesh_maxNips,mesh_NcpElems),            source=0.0_pReal)
+ allocate(materialpoint_subStep(theMesh%elem%nIPs,theMesh%nElems),            source=0.0_pReal)
- allocate(materialpoint_subdt(mesh_maxNips,mesh_NcpElems),              source=0.0_pReal)
+ allocate(materialpoint_subdt(theMesh%elem%nIPs,theMesh%nElems),              source=0.0_pReal)
- allocate(materialpoint_requested(mesh_maxNips,mesh_NcpElems),          source=.false.)
+ allocate(materialpoint_requested(theMesh%elem%nIPs,theMesh%nElems),          source=.false.)
- allocate(materialpoint_converged(mesh_maxNips,mesh_NcpElems),          source=.true.)
+ allocate(materialpoint_converged(theMesh%elem%nIPs,theMesh%nElems),          source=.true.)
- allocate(materialpoint_doneAndHappy(2,mesh_maxNips,mesh_NcpElems),     source=.true.)
+ allocate(materialpoint_doneAndHappy(2,theMesh%elem%nIPs,theMesh%nElems),     source=.true.)
 
 !--------------------------------------------------------------------------------------------------
 ! allocate and initialize global state and postresutls variables
@@ -277,7 +262,7 @@ subroutine homogenization_init
                            + homogenization_maxNgrains * (1 + crystallite_maxSizePostResults &      ! crystallite size & crystallite results
                                                         + 1 + constitutive_plasticity_maxSizePostResults &     ! constitutive size & constitutive results
                                                             + constitutive_source_maxSizePostResults)
- allocate(materialpoint_results(materialpoint_sizeResults,mesh_maxNips,mesh_NcpElems))
+ allocate(materialpoint_results(materialpoint_sizeResults,theMesh%elem%nIPs,theMesh%nElems))
 
  write(6,'(/,a)')   ' <<<+-  homogenization init  -+>>>'
  write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
@@ -346,7 +331,6 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
    crystallite_Lp, &
    crystallite_Li0, &
    crystallite_Li, &
-   crystallite_dPdF, &
    crystallite_Tstar0_v, &
    crystallite_Tstar_v, &
    crystallite_partionedF0, &
@@ -614,6 +598,7 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
 ! crystallite integration
 ! based on crystallite_partionedF0,.._partionedF
 ! incrementing by crystallite_dt
+    
     materialpoint_converged = crystallite_stress() !ToDo: MD not sure if that is the best logic
 
 !--------------------------------------------------------------------------------------------------
@@ -898,6 +883,8 @@ function postResults(ip,el)
  use mesh, only: &
    mesh_element
  use material, only: &
+   thermalMapping, &
+   thermal_typeInstance, &
    material_homogenizationAt, &
    homogenization_typeInstance,&
    mappingHomogenization, &
@@ -937,7 +924,7 @@ function postResults(ip,el)
    postResults
  integer(pInt) :: &
    startPos, endPos ,&
-   of, instance
+   of, instance, homog
 
 
  postResults = 0.0_pReal
@@ -957,9 +944,13 @@ function postResults(ip,el)
  chosenThermal: select case (thermal_type(mesh_element(3,el)))
 
    case (THERMAL_adiabatic_ID) chosenThermal
-     postResults(startPos:endPos) = thermal_adiabatic_postResults(ip, el)
+     homog = mappingHomogenization(2,ip,el)
+     postResults(startPos:endPos) = &
+       thermal_adiabatic_postResults(homog,thermal_typeInstance(homog),thermalMapping(homog)%p(ip,el))
    case (THERMAL_conduction_ID) chosenThermal
-     postResults(startPos:endPos) =  thermal_conduction_postResults(ip, el)
+     homog = mappingHomogenization(2,ip,el)
+     postResults(startPos:endPos) = &
+       thermal_conduction_postResults(homog,thermal_typeInstance(homog),thermalMapping(homog)%p(ip,el))
 
  end select chosenThermal
 

src/kinematics_cleavage_opening.f90

@@ -11,20 +11,22 @@ module kinematics_cleavage_opening
 
  implicit none
  private
- integer(pInt),                       dimension(:),           allocatable,         public, protected :: &
+ integer(pInt), dimension(:), allocatable, private :: kinematics_cleavage_opening_instance
-   kinematics_cleavage_opening_sizePostResults, &                                                                !< cumulative size of post results
-   kinematics_cleavage_opening_offset, &                                                                         !< which kinematics is my current damage mechanism?
-   kinematics_cleavage_opening_instance                                                                          !< instance of damage kinematics mechanism
 
- integer(pInt),                       dimension(:,:),         allocatable, target, public  :: &
+ type, private :: tParameters                                                                       !< container type for internal constitutive parameters
-   kinematics_cleavage_opening_sizePostResult                                                                    !< size of each post result output
+   integer(pInt) :: &
-
+     totalNcleavage
- character(len=64),                   dimension(:,:),         allocatable, target, public  :: &
+   integer(pInt), dimension(:),   allocatable :: &
-   kinematics_cleavage_opening_output                                                                            !< name of each post result output
+     Ncleavage                                                                                      !< active number of cleavage systems per family
-   
+   real(pReal) :: &
- integer(pInt),                       dimension(:),           allocatable, target, public  :: &
+     sdot0, &
-   kinematics_cleavage_opening_Noutput                                                                           !< number of outputs per instance of this damage 
+     n
+   real(pReal),   dimension(:),   allocatable :: &
+     critDisp, &
+     critLoad
+ end type
 
+! Begin Deprecated
  integer(pInt),                       dimension(:),           allocatable,         private :: &
    kinematics_cleavage_opening_totalNcleavage                                                                    !< total number of cleavage systems
    
@@ -38,6 +40,7 @@ module kinematics_cleavage_opening
  real(pReal),                         dimension(:,:),         allocatable,         private :: &
    kinematics_cleavage_opening_critDisp, &
    kinematics_cleavage_opening_critLoad
+! End Deprecated
 
  public :: &
    kinematics_cleavage_opening_init, &
@@ -50,7 +53,7 @@ contains
 !> @brief module initialization
 !> @details reads in material parameters, allocates arrays, and does sanity checks
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_cleavage_opening_init(fileUnit)
+subroutine kinematics_cleavage_opening_init()
 #if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
  use, intrinsic :: iso_fortran_env, only: &
    compiler_version, &
@@ -60,41 +63,25 @@ subroutine kinematics_cleavage_opening_init(fileUnit)
    debug_level,&
    debug_constitutive,&
    debug_levelBasic
+ use config, only: &
+   config_phase
  use IO, only: &
-   IO_read, &
-   IO_lc, &
-   IO_getTag, &
-   IO_isBlank, &
-   IO_stringPos, &
-   IO_stringValue, &
-   IO_floatValue, &
-   IO_intValue, &
    IO_warning, &
    IO_error, &
-   IO_timeStamp, &
+   IO_timeStamp
-   IO_EOF
  use material, only: &
    phase_kinematics, &
-   phase_Nkinematics, &
-   phase_Noutput, &
    KINEMATICS_cleavage_opening_label, &
    KINEMATICS_cleavage_opening_ID
- use config, only: &
-   material_Nphase, &
-   MATERIAL_partPhase
  use lattice, only: &
    lattice_maxNcleavageFamily, &
    lattice_NcleavageSystem
 
  implicit none
- integer(pInt), intent(in) :: fileUnit
+ integer(pInt), allocatable, dimension(:) :: tempInt
+ real(pReal), allocatable, dimension(:) :: tempFloat
 
- integer(pInt), allocatable, dimension(:) :: chunkPos
+ integer(pInt) :: maxNinstance,p,instance,kinematics
- integer(pInt) :: maxNinstance,phase,instance,kinematics
- integer(pInt) :: Nchunks_CleavageFamilies = 0_pInt, j   
- character(len=65536) :: &
-   tag  = '', &
-   line = ''
 
  write(6,'(/,a)')   ' <<<+-  kinematics_'//KINEMATICS_cleavage_opening_LABEL//' init  -+>>>'
  write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
@@ -106,21 +93,11 @@ subroutine kinematics_cleavage_opening_init(fileUnit)
  if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt) &
    write(6,'(a16,1x,i5,/)') '# instances:',maxNinstance
  
- allocate(kinematics_cleavage_opening_offset(material_Nphase), source=0_pInt)
+ allocate(kinematics_cleavage_opening_instance(size(config_phase)), source=0_pInt)
- allocate(kinematics_cleavage_opening_instance(material_Nphase), source=0_pInt)
+ do p = 1_pInt, size(config_phase)
- do phase = 1, material_Nphase
+   kinematics_cleavage_opening_instance(p) = count(phase_kinematics(:,1:p) == kinematics_cleavage_opening_ID) ! ToDo: count correct?
-   kinematics_cleavage_opening_instance(phase) = count(phase_kinematics(:,1:phase) == kinematics_cleavage_opening_ID)
-   do kinematics = 1, phase_Nkinematics(phase)
-     if (phase_kinematics(kinematics,phase) == kinematics_cleavage_opening_ID) &
-       kinematics_cleavage_opening_offset(phase) = kinematics
-   enddo    
  enddo
    
- allocate(kinematics_cleavage_opening_sizePostResults(maxNinstance),                      source=0_pInt)
- allocate(kinematics_cleavage_opening_sizePostResult(maxval(phase_Noutput),maxNinstance), source=0_pInt)
- allocate(kinematics_cleavage_opening_output(maxval(phase_Noutput),maxNinstance))
-          kinematics_cleavage_opening_output = ''
- allocate(kinematics_cleavage_opening_Noutput(maxNinstance),                              source=0_pInt) 
  allocate(kinematics_cleavage_opening_critDisp(lattice_maxNcleavageFamily,maxNinstance),  source=0.0_pReal) 
  allocate(kinematics_cleavage_opening_critLoad(lattice_maxNcleavageFamily,maxNinstance),  source=0.0_pReal) 
  allocate(kinematics_cleavage_opening_Ncleavage(lattice_maxNcleavageFamily,maxNinstance), source=0_pInt)
@@ -128,90 +105,51 @@ subroutine kinematics_cleavage_opening_init(fileUnit)
  allocate(kinematics_cleavage_opening_sdot_0(maxNinstance),                               source=0.0_pReal) 
  allocate(kinematics_cleavage_opening_N(maxNinstance),                                    source=0.0_pReal) 
 
- rewind(fileUnit)
+ do p = 1_pInt, size(config_phase)
- phase = 0_pInt
+   if (all(phase_kinematics(:,p) /= KINEMATICS_cleavage_opening_ID)) cycle
- do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= MATERIAL_partPhase)         ! wind forward to <phase>
+   instance = kinematics_cleavage_opening_instance(p)
-   line = IO_read(fileUnit)
+   kinematics_cleavage_opening_sdot_0(instance) = config_phase(p)%getFloat('anisobrittle_sdot0')
- enddo
+   kinematics_cleavage_opening_N(instance)      = config_phase(p)%getFloat('anisobrittle_ratesensitivity')
+   tempInt = config_phase(p)%getInts('ncleavage')     
+   kinematics_cleavage_opening_Ncleavage(1:size(tempInt),instance) = tempInt
 
- parsingFile: do while (trim(line) /= IO_EOF)                                                       ! read through sections of phase part
+   tempFloat = config_phase(p)%getFloats('anisobrittle_criticaldisplacement',requiredSize=size(tempInt))
-   line = IO_read(fileUnit)
+   kinematics_cleavage_opening_critDisp(1:size(tempInt),instance) = tempFloat
-   if (IO_isBlank(line)) cycle                                                                      ! skip empty lines
-   if (IO_getTag(line,'<','>') /= '') then                                                          ! stop at next part
-     line = IO_read(fileUnit, .true.)                                                               ! reset IO_read
-     exit                                                                                           
-   endif   
-   if (IO_getTag(line,'[',']') /= '') then                                                          ! next phase section
-     phase = phase + 1_pInt                                                                         ! advance phase section counter
-     cycle                                                                                          ! skip to next line
-   endif
-   if (phase > 0_pInt ) then; if (any(phase_kinematics(:,phase) == KINEMATICS_cleavage_opening_ID)) then         ! do not short-circuit here (.and. with next if statemen). It's not safe in Fortran
-     instance = kinematics_cleavage_opening_instance(phase)                                                         ! which instance of my damage is present phase
-     chunkPos = IO_stringPos(line)
-     tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt))                                             ! extract key
-     select case(tag)
-       case ('anisobrittle_sdot0')
-         kinematics_cleavage_opening_sdot_0(instance) = IO_floatValue(line,chunkPos,2_pInt)
 
-       case ('anisobrittle_ratesensitivity')
+   tempFloat = config_phase(p)%getFloats('anisobrittle_criticalload',requiredSize=size(tempInt))
-         kinematics_cleavage_opening_N(instance) = IO_floatValue(line,chunkPos,2_pInt)
+   kinematics_cleavage_opening_critLoad(1:size(tempInt),instance) = tempFloat
 
-       case ('ncleavage')  !
-         Nchunks_CleavageFamilies = chunkPos(1) - 1_pInt
-         do j = 1_pInt, Nchunks_CleavageFamilies
-           kinematics_cleavage_opening_Ncleavage(j,instance) = IO_intValue(line,chunkPos,1_pInt+j)
-         enddo
-
-       case ('anisobrittle_criticaldisplacement')
-         do j = 1_pInt, Nchunks_CleavageFamilies
-           kinematics_cleavage_opening_critDisp(j,instance) = IO_floatValue(line,chunkPos,1_pInt+j)
-         enddo
-
-       case ('anisobrittle_criticalload')
-         do j = 1_pInt, Nchunks_CleavageFamilies
-           kinematics_cleavage_opening_critLoad(j,instance) = IO_floatValue(line,chunkPos,1_pInt+j)
-         enddo
-
-     end select
-   endif; endif
- enddo parsingFile
-
-!--------------------------------------------------------------------------------------------------
-!  sanity checks
- sanityChecks: do phase = 1_pInt, material_Nphase   
-   myPhase: if (any(phase_kinematics(:,phase) == KINEMATICS_cleavage_opening_ID)) then
-     instance = kinematics_cleavage_opening_instance(phase)
    kinematics_cleavage_opening_Ncleavage(1:lattice_maxNcleavageFamily,instance) = &
-       min(lattice_NcleavageSystem(1:lattice_maxNcleavageFamily,phase),&                            ! limit active cleavage systems per family to min of available and requested
+       min(lattice_NcleavageSystem(1:lattice_maxNcleavageFamily,p),&                            ! limit active cleavage systems per family to min of available and requested
            kinematics_cleavage_opening_Ncleavage(1:lattice_maxNcleavageFamily,instance))
      kinematics_cleavage_opening_totalNcleavage(instance)  = sum(kinematics_cleavage_opening_Ncleavage(:,instance)) ! how many cleavage systems altogether
      if (kinematics_cleavage_opening_sdot_0(instance) <= 0.0_pReal) &
        call IO_error(211_pInt,el=instance,ext_msg='sdot_0 ('//KINEMATICS_cleavage_opening_LABEL//')')
-     if (any(kinematics_cleavage_opening_critDisp(1:Nchunks_CleavageFamilies,instance) < 0.0_pReal)) &
+     if (any(kinematics_cleavage_opening_critDisp(1:size(tempInt),instance) < 0.0_pReal)) &
        call IO_error(211_pInt,el=instance,ext_msg='critical_displacement ('//KINEMATICS_cleavage_opening_LABEL//')')
-     if (any(kinematics_cleavage_opening_critLoad(1:Nchunks_CleavageFamilies,instance) < 0.0_pReal)) &
+     if (any(kinematics_cleavage_opening_critLoad(1:size(tempInt),instance) < 0.0_pReal)) &
        call IO_error(211_pInt,el=instance,ext_msg='critical_load ('//KINEMATICS_cleavage_opening_LABEL//')')
      if (kinematics_cleavage_opening_N(instance) <= 0.0_pReal) &
        call IO_error(211_pInt,el=instance,ext_msg='rate_sensitivity ('//KINEMATICS_cleavage_opening_LABEL//')')
-   endif myPhase
+ enddo
- enddo sanityChecks
  
 end subroutine kinematics_cleavage_opening_init
 
 !--------------------------------------------------------------------------------------------------
 !> @brief  contains the constitutive equation for calculating the velocity gradient  
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar_v, ipc, ip, el)
+subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar, S, ipc, ip, el)
  use prec, only: &
    tol_math_check
+ use math, only: &
+   math_mul33xx33
  use material, only: &
-   phaseAt, phasememberAt, &
+   material_phase, &
    material_homog, &
    damage, &
    damageMapping
  use lattice, only: &
    lattice_Scleavage, &
-   lattice_Scleavage_v, &
    lattice_maxNcleavageFamily, &
    lattice_NcleavageSystem
  
@@ -220,36 +158,33 @@ subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar
    ipc, &                                                                                           !< grain number
    ip, &                                                                                            !< integration point number
    el                                                                                               !< element number
- real(pReal),   intent(in),  dimension(6) :: &
+ real(pReal),   intent(in),  dimension(3,3) :: &
-   Tstar_v                                                                                          !< 2nd Piola-Kirchhoff stress
+   S
  real(pReal),   intent(out), dimension(3,3) :: &
    Ld                                                                                               !< damage velocity gradient
  real(pReal),   intent(out), dimension(3,3,3,3) :: &
-   dLd_dTstar3333                                                                                   !< derivative of Ld with respect to Tstar (4th-order tensor)
+   dLd_dTstar                                                                                       !< derivative of Ld with respect to Tstar (4th-order tensor)
  integer(pInt) :: &
-   phase, &
+   instance, phase, &
-   constituent, &
-   instance, &
    homog, damageOffset, &
    f, i, index_myFamily, k, l, m, n
  real(pReal) :: &
    traction_d, traction_t, traction_n, traction_crit, &
    udotd, dudotd_dt, udott, dudott_dt, udotn, dudotn_dt
 
- phase = phaseAt(ipc,ip,el)
+ phase = material_phase(ipc,ip,el)
- constituent = phasememberAt(ipc,ip,el)
  instance = kinematics_cleavage_opening_instance(phase)
  homog = material_homog(ip,el)
  damageOffset = damageMapping(homog)%p(ip,el)
  
  Ld = 0.0_pReal
- dLd_dTstar3333 = 0.0_pReal
+ dLd_dTstar = 0.0_pReal
  do f = 1_pInt,lattice_maxNcleavageFamily
    index_myFamily = sum(lattice_NcleavageSystem(1:f-1_pInt,phase))                                   ! at which index starts my family
    do i = 1_pInt,kinematics_cleavage_opening_Ncleavage(f,instance)                                            ! process each (active) cleavage system in family
-     traction_d    = dot_product(Tstar_v,lattice_Scleavage_v(1:6,1,index_myFamily+i,phase))
+     traction_d    = math_mul33xx33(S,lattice_Scleavage(1:3,1:3,1,index_myFamily+i,phase))
-     traction_t    = dot_product(Tstar_v,lattice_Scleavage_v(1:6,2,index_myFamily+i,phase))
+     traction_t    = math_mul33xx33(S,lattice_Scleavage(1:3,1:3,2,index_myFamily+i,phase))
-     traction_n    = dot_product(Tstar_v,lattice_Scleavage_v(1:6,3,index_myFamily+i,phase))
+     traction_n    = math_mul33xx33(S,lattice_Scleavage(1:3,1:3,3,index_myFamily+i,phase))
      traction_crit = kinematics_cleavage_opening_critLoad(f,instance)* &
                      damage(homog)%p(damageOffset)*damage(homog)%p(damageOffset)
      udotd = &
@@ -261,7 +196,7 @@ subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar
        dudotd_dt = sign(1.0_pReal,traction_d)*udotd*kinematics_cleavage_opening_N(instance)/ &
                    max(0.0_pReal, abs(traction_d) - traction_crit)
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudotd_dt*lattice_Scleavage(k,l,1,index_myFamily+i,phase)* &
                      lattice_Scleavage(m,n,1,index_myFamily+i,phase)
      endif                
@@ -275,7 +210,7 @@ subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar
        dudott_dt = sign(1.0_pReal,traction_t)*udott*kinematics_cleavage_opening_N(instance)/ &
                    max(0.0_pReal, abs(traction_t) - traction_crit)  
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudott_dt*lattice_Scleavage(k,l,2,index_myFamily+i,phase)* &
                      lattice_Scleavage(m,n,2,index_myFamily+i,phase)
      endif                
@@ -289,11 +224,10 @@ subroutine kinematics_cleavage_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar
        dudotn_dt = sign(1.0_pReal,traction_n)*udotn*kinematics_cleavage_opening_N(instance)/ &
                    max(0.0_pReal, abs(traction_n) - traction_crit)
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudotn_dt*lattice_Scleavage(k,l,3,index_myFamily+i,phase)* &
                      lattice_Scleavage(m,n,3,index_myFamily+i,phase)
      endif                
-
    enddo
  enddo
  

src/kinematics_slipplane_opening.f90

@@ -11,20 +11,22 @@ module kinematics_slipplane_opening
 
  implicit none
  private
- integer(pInt),                       dimension(:),           allocatable,         public, protected :: &
+ integer(pInt), dimension(:), allocatable, private :: kinematics_slipplane_opening_instance
-   kinematics_slipplane_opening_sizePostResults, &                                                            !< cumulative size of post results
-   kinematics_slipplane_opening_offset, &                                                                     !< which kinematics is my current damage mechanism?
-   kinematics_slipplane_opening_instance                                                                      !< instance of damage kinematics mechanism
    
- integer(pInt),                       dimension(:,:),         allocatable, target, public  :: &
+ type, private :: tParameters                                                                       !< container type for internal constitutive parameters
-   kinematics_slipplane_opening_sizePostResult                                                                !< size of each post result output
+   integer(pInt) :: &
-
+     totalNslip
- character(len=64),                   dimension(:,:),         allocatable, target, public  :: &
+   integer(pInt), dimension(:),   allocatable :: &
-   kinematics_slipplane_opening_output                                                                        !< name of each post result output
+     Nslip                                                                                          !< active number of slip systems per family
-   
+   real(pReal) :: &
- integer(pInt),                       dimension(:),           allocatable, target, public  :: &
+     sdot0, &
-   kinematics_slipplane_opening_Noutput                                                                       !< number of outputs per instance of this damage 
+     n
+   real(pReal),   dimension(:),   allocatable :: &
+     critDisp, &
+     critPlasticStrain
+ end type
 
+! Begin Deprecated
  integer(pInt),                       dimension(:),           allocatable,         private :: &
    kinematics_slipplane_opening_totalNslip                                                                    !< total number of slip systems
 
@@ -38,6 +40,7 @@ module kinematics_slipplane_opening
  real(pReal),                         dimension(:,:),         allocatable,         private :: &
    kinematics_slipplane_opening_critPlasticStrain, &
    kinematics_slipplane_opening_critLoad
+! End Deprecated
    
  public :: &
    kinematics_slipplane_opening_init, &
@@ -50,7 +53,7 @@ contains
 !> @brief module initialization
 !> @details reads in material parameters, allocates arrays, and does sanity checks
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_slipplane_opening_init(fileUnit)
+subroutine kinematics_slipplane_opening_init()
 #if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
  use, intrinsic :: iso_fortran_env, only: &
    compiler_version, &
@@ -60,41 +63,25 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
    debug_level,&
    debug_constitutive,&
    debug_levelBasic
+ use config, only: &
+   config_phase
  use IO, only: &
-   IO_read, &
-   IO_lc, &
-   IO_getTag, &
-   IO_isBlank, &
-   IO_stringPos, &
-   IO_stringValue, &
-   IO_floatValue, &
-   IO_intValue, &
    IO_warning, &
    IO_error, &
-   IO_timeStamp, &
+   IO_timeStamp
-   IO_EOF
  use material, only: &
    phase_kinematics, &
-   phase_Nkinematics, &
-   phase_Noutput, &
    KINEMATICS_slipplane_opening_label, &
    KINEMATICS_slipplane_opening_ID
- use config, only: &
-   material_Nphase, &
-   MATERIAL_partPhase
  use lattice, only: &
    lattice_maxNslipFamily, &
    lattice_NslipSystem
 
  implicit none
- integer(pInt), intent(in) :: fileUnit
+ integer(pInt), allocatable, dimension(:) :: tempInt
+ real(pReal), allocatable, dimension(:) :: tempFloat
 
- integer(pInt), allocatable, dimension(:) :: chunkPos
+ integer(pInt) :: maxNinstance,p,instance,kinematics
- integer(pInt) :: maxNinstance,phase,instance,kinematics
- integer(pInt) :: Nchunks_SlipFamilies = 0_pInt, j   
- character(len=65536) :: &
-   tag  = '', &
-   line = ''
 
  write(6,'(/,a)')   ' <<<+-  kinematics_'//KINEMATICS_slipplane_opening_LABEL//' init  -+>>>'
  write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
@@ -106,21 +93,11 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
  if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt) &
    write(6,'(a16,1x,i5,/)') '# instances:',maxNinstance
  
- allocate(kinematics_slipplane_opening_offset(material_Nphase), source=0_pInt)
+ allocate(kinematics_slipplane_opening_instance(size(config_phase)), source=0_pInt)
- allocate(kinematics_slipplane_opening_instance(material_Nphase), source=0_pInt)
+ do p = 1_pInt, size(config_phase)
- do phase = 1, material_Nphase
+   kinematics_slipplane_opening_instance(p) = count(phase_kinematics(:,1:p) == kinematics_slipplane_opening_ID) ! ToDo: count correct?
-   kinematics_slipplane_opening_instance(phase) = count(phase_kinematics(:,1:phase) == kinematics_slipplane_opening_ID)
-   do kinematics = 1, phase_Nkinematics(phase)
-     if (phase_kinematics(kinematics,phase) == kinematics_slipplane_opening_ID) &
-       kinematics_slipplane_opening_offset(phase) = kinematics
-   enddo    
  enddo
    
- allocate(kinematics_slipplane_opening_sizePostResults(maxNinstance),                     source=0_pInt)
- allocate(kinematics_slipplane_opening_sizePostResult(maxval(phase_Noutput),maxNinstance),source=0_pInt)
- allocate(kinematics_slipplane_opening_output(maxval(phase_Noutput),maxNinstance))
-          kinematics_slipplane_opening_output = ''
- allocate(kinematics_slipplane_opening_Noutput(maxNinstance),                             source=0_pInt) 
  allocate(kinematics_slipplane_opening_critLoad(lattice_maxNslipFamily,maxNinstance),     source=0.0_pReal) 
  allocate(kinematics_slipplane_opening_critPlasticStrain(lattice_maxNslipFamily,maxNinstance),source=0.0_pReal) 
  allocate(kinematics_slipplane_opening_Nslip(lattice_maxNslipFamily,maxNinstance),        source=0_pInt)
@@ -128,61 +105,22 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
  allocate(kinematics_slipplane_opening_N(maxNinstance),                                   source=0.0_pReal) 
  allocate(kinematics_slipplane_opening_sdot_0(maxNinstance),                              source=0.0_pReal) 
 
- rewind(fileUnit)
+ do p = 1_pInt, size(config_phase)
- phase = 0_pInt
+   if (all(phase_kinematics(:,p) /= KINEMATICS_slipplane_opening_ID)) cycle
- do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= MATERIAL_partPhase)         ! wind forward to <phase>
+   instance = kinematics_slipplane_opening_instance(p)
-   line = IO_read(fileUnit)
+   kinematics_slipplane_opening_sdot_0(instance) = config_phase(p)%getFloat('anisoductile_sdot0')
- enddo
+   kinematics_slipplane_opening_N(instance)      = config_phase(p)%getFloat('anisoductile_ratesensitivity')
+   tempInt = config_phase(p)%getInts('ncleavage')     
+   kinematics_slipplane_opening_Nslip(1:size(tempInt),instance) = tempInt
 
- parsingFile: do while (trim(line) /= IO_EOF)                                                       ! read through sections of phase part
+   tempFloat = config_phase(p)%getFloats('anisoductile_criticalplasticstrain',requiredSize=size(tempInt))
-   line = IO_read(fileUnit)
+   kinematics_slipplane_opening_critPlasticStrain(1:size(tempInt),instance) = tempFloat
-   if (IO_isBlank(line)) cycle                                                                      ! skip empty lines
-   if (IO_getTag(line,'<','>') /= '') then                                                          ! stop at next part
-     line = IO_read(fileUnit, .true.)                                                               ! reset IO_read
-     exit                                                                                           
-   endif   
-   if (IO_getTag(line,'[',']') /= '') then                                                          ! next phase section
-     phase = phase + 1_pInt                                                                         ! advance phase section counter
-     cycle                                                                                          ! skip to next line
-   endif
-   if (phase > 0_pInt ) then; if (any(phase_kinematics(:,phase) == KINEMATICS_slipplane_opening_ID)) then ! do not short-circuit here (.and. with next if statemen). It's not safe in Fortran
-     instance = kinematics_slipplane_opening_instance(phase)                                        ! which instance of my damage is present phase
-     chunkPos = IO_stringPos(line)
-     tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt))                                              ! extract key
-     select case(tag)
-       case ('nslip')  !
-         Nchunks_SlipFamilies = chunkPos(1) - 1_pInt
-         do j = 1_pInt, Nchunks_SlipFamilies
-           kinematics_slipplane_opening_Nslip(j,instance) = IO_intValue(line,chunkPos,1_pInt+j)
-         enddo
 
-       case ('anisoductile_sdot0')
+   tempFloat = config_phase(p)%getFloats('anisoductile_criticalload',requiredSize=size(tempInt))
-         kinematics_slipplane_opening_sdot_0(instance) = IO_floatValue(line,chunkPos,2_pInt)
+   kinematics_slipplane_opening_critLoad(1:size(tempInt),instance) = tempFloat
 
-       case ('anisoductile_criticalplasticstrain')
-         do j = 1_pInt, Nchunks_SlipFamilies
-           kinematics_slipplane_opening_critPlasticStrain(j,instance) = IO_floatValue(line,chunkPos,1_pInt+j)
-         enddo
-         
-       case ('anisoductile_ratesensitivity')
-         kinematics_slipplane_opening_N(instance) = IO_floatValue(line,chunkPos,2_pInt)
-
-       case ('anisoductile_criticalload')
-         do j = 1_pInt, Nchunks_SlipFamilies
-           kinematics_slipplane_opening_critLoad(j,instance) = IO_floatValue(line,chunkPos,1_pInt+j)
-         enddo
-         
-     end select
-   endif; endif
- enddo parsingFile
-
-!--------------------------------------------------------------------------------------------------
-!  sanity checks
- sanityChecks: do phase = 1_pInt, material_Nphase   
-   myPhase: if (any(phase_kinematics(:,phase) == KINEMATICS_slipplane_opening_ID)) then
-     instance = kinematics_slipplane_opening_instance(phase)
      kinematics_slipplane_opening_Nslip(1:lattice_maxNslipFamily,instance) = &
-       min(lattice_NslipSystem(1:lattice_maxNslipFamily,phase),&                                    ! limit active cleavage systems per family to min of available and requested
+       min(lattice_NslipSystem(1:lattice_maxNslipFamily,p),&                                    ! limit active cleavage systems per family to min of available and requested
            kinematics_slipplane_opening_Nslip(1:lattice_maxNslipFamily,instance))
          kinematics_slipplane_opening_totalNslip(instance) = sum(kinematics_slipplane_opening_Nslip(:,instance))
      if (kinematics_slipplane_opening_sdot_0(instance) <= 0.0_pReal) &
@@ -191,18 +129,18 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
        call IO_error(211_pInt,el=instance,ext_msg='criticaPlasticStrain ('//KINEMATICS_slipplane_opening_LABEL//')')
      if (kinematics_slipplane_opening_N(instance) <= 0.0_pReal) &
        call IO_error(211_pInt,el=instance,ext_msg='rate_sensitivity ('//KINEMATICS_slipplane_opening_LABEL//')')
-   endif myPhase
+ enddo
- enddo sanityChecks
-  
   
 end subroutine kinematics_slipplane_opening_init
 
 !--------------------------------------------------------------------------------------------------
 !> @brief  contains the constitutive equation for calculating the velocity gradient  
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tstar_v, ipc, ip, el)
+subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar, S, ipc, ip, el)
  use prec, only: &
    tol_math_check
+ use math, only: &
+   math_mul33xx33
  use lattice, only: &
    lattice_maxNslipFamily, &
    lattice_NslipSystem, &
@@ -210,53 +148,41 @@ subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tsta
    lattice_st, &
    lattice_sn
  use material, only: &
-   phaseAt, phasememberAt, &
+   material_phase, &
    material_homog, &
    damage, &
    damageMapping
  use math, only: &
-   math_Plain3333to99, &
+   math_tensorproduct33
-   math_I3, &
-   math_identity4th, &
-   math_symmetric33, &
-   math_Mandel33to6, &
-   math_tensorproduct33, &
-   math_det33, &
-   math_mul33x33
  
  implicit none
  integer(pInt), intent(in) :: &
    ipc, &                                                                                           !< grain number
    ip, &                                                                                            !< integration point number
    el                                                                                               !< element number
- real(pReal),   intent(in),  dimension(6) :: &
+ real(pReal),   intent(in),  dimension(3,3) :: &
-   Tstar_v                                                                                          !< 2nd Piola-Kirchhoff stress
+   S
  real(pReal),   intent(out), dimension(3,3) :: &
    Ld                                                                                               !< damage velocity gradient
  real(pReal),   intent(out), dimension(3,3,3,3) :: &
-   dLd_dTstar3333                                                                                   !< derivative of Ld with respect to Tstar (4th-order tensor)
+   dLd_dTstar                                                                                       !< derivative of Ld with respect to Tstar (4th-order tensor)
  real(pReal),   dimension(3,3) :: &
    projection_d, projection_t, projection_n                                                         !< projection modes 3x3 tensor
- real(pReal),   dimension(6) :: &
-   projection_d_v, projection_t_v, projection_n_v                                                   !< projection modes 3x3 vector
  integer(pInt) :: &
-   phase, &
+   instance, phase, &
-   constituent, &
-   instance, &
    homog, damageOffset, &
    f, i, index_myFamily, k, l, m, n
  real(pReal) :: &
    traction_d, traction_t, traction_n, traction_crit, &
    udotd, dudotd_dt, udott, dudott_dt, udotn, dudotn_dt
    
- phase = phaseAt(ipc,ip,el)
+ phase = material_phase(ipc,ip,el)
- constituent = phasememberAt(ipc,ip,el)
  instance = kinematics_slipplane_opening_instance(phase)
  homog = material_homog(ip,el)
  damageOffset = damageMapping(homog)%p(ip,el)
  
  Ld = 0.0_pReal
- dLd_dTstar3333 = 0.0_pReal
+ dLd_dTstar = 0.0_pReal
  do f = 1_pInt,lattice_maxNslipFamily
    index_myFamily = sum(lattice_NslipSystem(1:f-1_pInt,phase))                                      ! at which index starts my family
    do i = 1_pInt,kinematics_slipplane_opening_Nslip(f,instance)                                              ! process each (active) slip system in family
@@ -267,13 +193,10 @@ subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tsta
      projection_n = math_tensorproduct33(lattice_sn(1:3,index_myFamily+i,phase),&
                                        lattice_sn(1:3,index_myFamily+i,phase))
 
-     projection_d_v(1:6) = math_Mandel33to6(math_symmetric33(projection_d(1:3,1:3)))
-     projection_t_v(1:6) = math_Mandel33to6(math_symmetric33(projection_t(1:3,1:3)))
-     projection_n_v(1:6) = math_Mandel33to6(math_symmetric33(projection_n(1:3,1:3)))
    
-     traction_d    = dot_product(Tstar_v,projection_d_v(1:6))
+     traction_d    = math_mul33xx33(S,projection_d)
-     traction_t    = dot_product(Tstar_v,projection_t_v(1:6))
+     traction_t    = math_mul33xx33(S,projection_t)
-     traction_n    = dot_product(Tstar_v,projection_n_v(1:6))
+     traction_n    = math_mul33xx33(S,projection_n)
      
      traction_crit = kinematics_slipplane_opening_critLoad(f,instance)* &
                      damage(homog)%p(damageOffset)                                                        ! degrading critical load carrying capacity by damage 
@@ -287,7 +210,7 @@ subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tsta
        Ld = Ld + udotd*projection_d
        dudotd_dt = udotd*kinematics_slipplane_opening_N(instance)/traction_d
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudotd_dt*projection_d(k,l)*projection_d(m,n)
      endif                
  
@@ -300,9 +223,10 @@ subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tsta
        Ld = Ld + udott*projection_t
        dudott_dt = udott*kinematics_slipplane_opening_N(instance)/traction_t
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudott_dt*projection_t(k,l)*projection_t(m,n)
      endif
+
      udotn = &
        kinematics_slipplane_opening_sdot_0(instance)* &
        (max(0.0_pReal,traction_n)/traction_crit - &
@@ -311,7 +235,7 @@ subroutine kinematics_slipplane_opening_LiAndItsTangent(Ld, dLd_dTstar3333, Tsta
        Ld = Ld + udotn*projection_n
        dudotn_dt = udotn*kinematics_slipplane_opening_N(instance)/traction_n
        forall (k=1_pInt:3_pInt,l=1_pInt:3_pInt,m=1_pInt:3_pInt,n=1_pInt:3_pInt) &
-         dLd_dTstar3333(k,l,m,n) = dLd_dTstar3333(k,l,m,n) + &
+         dLd_dTstar(k,l,m,n) = dLd_dTstar(k,l,m,n) + &
            dudotn_dt*projection_n(k,l)*projection_n(m,n)
      endif 
    enddo

src/kinematics_thermal_expansion.f90

@@ -10,24 +10,14 @@ module kinematics_thermal_expansion
 
   implicit none
   private
- integer(pInt),                       dimension(:),           allocatable,         public, protected :: &
-   kinematics_thermal_expansion_sizePostResults, &                                                                !< cumulative size of post results
-   kinematics_thermal_expansion_offset, &                                                                         !< which kinematics is my current damage mechanism?
-   kinematics_thermal_expansion_instance                                                                          !< instance of damage kinematics mechanism
  
- integer(pInt),                       dimension(:,:),         allocatable, target, public  :: &
+  type, private :: tParameters
-   kinematics_thermal_expansion_sizePostResult                                                                    !< size of each post result output
+    real(pReal), allocatable, dimension(:,:,:) :: &
+      expansion
+  end type tParameters
  
- character(len=64),                   dimension(:,:),         allocatable, target, public  :: &
+  type(tParameters), dimension(:), allocatable :: param
-   kinematics_thermal_expansion_output                                                                            !< name of each post result output
   
- integer(pInt),                       dimension(:),           allocatable, target, public  :: &
-   kinematics_thermal_expansion_Noutput                                                                           !< number of outputs per instance of this damage 
-
-! enum, bind(c)                                                                                                   ! ToDo kinematics need state machinery to deal with sizePostResult
-!   enumerator :: undefined_ID, &                                                                                 ! possible remedy is to decouple having state vars from having output
-!                 thermalexpansionrate_ID                                                                         ! which means to separate user-defined types tState + tOutput...
-! end enum
   public :: &
     kinematics_thermal_expansion_init, &
     kinematics_thermal_expansion_initialStrain, &
@@ -40,139 +30,70 @@ contains
 !> @brief module initialization
 !> @details reads in material parameters, allocates arrays, and does sanity checks
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_thermal_expansion_init(fileUnit)
+subroutine kinematics_thermal_expansion_init()
-#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
- use, intrinsic :: iso_fortran_env, only: &
-   compiler_version, &
-   compiler_options
-#endif
   use debug, only: &
     debug_level,&
     debug_constitutive,&
     debug_levelBasic
- use IO, only: &
-   IO_read, &
-   IO_lc, &
-   IO_getTag, &
-   IO_isBlank, &
-   IO_stringPos, &
-   IO_stringValue, &
-   IO_floatValue, &
-   IO_intValue, &
-   IO_warning, &
-   IO_error, &
-   IO_timeStamp, &
-   IO_EOF
   use material, only: &
     phase_kinematics, &
-   phase_Nkinematics, &
-   phase_Noutput, &
     KINEMATICS_thermal_expansion_label, &
     KINEMATICS_thermal_expansion_ID
   use config, only: &
-   material_Nphase, &
+    config_phase
-   MATERIAL_partPhase
  
   implicit none
- integer(pInt), intent(in) :: fileUnit
+  integer(pInt) :: &
-
+    Ninstance, &
- integer(pInt), allocatable, dimension(:) :: chunkPos
+    p, i
- integer(pInt) :: maxNinstance,phase,instance,kinematics
+  real(pReal),  dimension(:), allocatable :: &
- character(len=65536) :: &
+    temp
-   tag     = '', &
-   line    = ''
   
   write(6,'(/,a)')   ' <<<+-  kinematics_'//KINEMATICS_thermal_expansion_LABEL//' init  -+>>>'
- write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
-#include "compilation_info.f90"
  
- maxNinstance = int(count(phase_kinematics == KINEMATICS_thermal_expansion_ID),pInt)
+  Ninstance = int(count(phase_kinematics == KINEMATICS_thermal_expansion_ID),pInt)
- if (maxNinstance == 0_pInt) return
   
   if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt) &
-   write(6,'(a16,1x,i5,/)') '# instances:',maxNinstance
+    write(6,'(a16,1x,i5,/)') '# instances:',Ninstance
   
- allocate(kinematics_thermal_expansion_offset(material_Nphase), source=0_pInt)
+  allocate(param(Ninstance))
- allocate(kinematics_thermal_expansion_instance(material_Nphase), source=0_pInt)
+  
- do phase = 1, material_Nphase
+  do p = 1_pInt, size(phase_kinematics)
-   kinematics_thermal_expansion_instance(phase) = count(phase_kinematics(:,1:phase) == kinematics_thermal_expansion_ID)
+    if (all(phase_kinematics(:,p) /= KINEMATICS_thermal_expansion_ID)) cycle
-   do kinematics = 1, phase_Nkinematics(phase)
+    
-     if (phase_kinematics(kinematics,phase) == kinematics_thermal_expansion_ID) &
+    ! ToDo: Here we need to decide how to extend the concept of instances to
-       kinematics_thermal_expansion_offset(phase) = kinematics
+    ! kinetics and sources. I would suggest that the same mechanism exists at maximum once per phase
+    
+    ! read up to three parameters (constant, linear, quadratic with T)
+    temp = config_phase(p)%getFloats('thermal_expansion11')                   
+    !lattice_thermalExpansion33(1,1,1:size(temp),p) = temp
+    temp = config_phase(p)%getFloats('thermal_expansion22', &
+                                     defaultVal=[(0.0_pReal, i=1,size(temp))],requiredSize=size(temp)) 
+    !lattice_thermalExpansion33(2,2,1:size(temp),p) = temp
+    temp = config_phase(p)%getFloats('thermal_expansion33', &
+                                     defaultVal=[(0.0_pReal, i=1,size(temp))],requiredSize=size(temp))
   enddo
- enddo
-   
- allocate(kinematics_thermal_expansion_sizePostResults(maxNinstance),                     source=0_pInt)
- allocate(kinematics_thermal_expansion_sizePostResult(maxval(phase_Noutput),maxNinstance),source=0_pInt)
- allocate(kinematics_thermal_expansion_output(maxval(phase_Noutput),maxNinstance))
-          kinematics_thermal_expansion_output = ''
- allocate(kinematics_thermal_expansion_Noutput(maxNinstance),                             source=0_pInt) 
-
- rewind(fileUnit)
- phase = 0_pInt
- do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= MATERIAL_partPhase)         ! wind forward to <phase>
-   line = IO_read(fileUnit)
- enddo
- 
- parsingFile: do while (trim(line) /= IO_EOF)                                                       ! read through sections of phase part
-   line = IO_read(fileUnit)
-   if (IO_isBlank(line)) cycle                                                                      ! skip empty lines
-   if (IO_getTag(line,'<','>') /= '') then                                                          ! stop at next part
-     line = IO_read(fileUnit, .true.)                                                               ! reset IO_read
-     exit                                                                                           
-   endif   
-   if (IO_getTag(line,'[',']') /= '') then                                                          ! next phase section
-     phase = phase + 1_pInt                                                                         ! advance phase section counter
-     cycle                                                                                          ! skip to next line
-   endif
-   if (phase > 0_pInt ) then; if (any(phase_kinematics(:,phase) == KINEMATICS_thermal_expansion_ID)) then         ! do not short-circuit here (.and. with next if statemen). It's not safe in Fortran
-     instance = kinematics_thermal_expansion_instance(phase)                                                         ! which instance of my damage is present phase
-     chunkPos = IO_stringPos(line)
-     tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt))                                             ! extract key...
-     select case(tag)
-!       case ('(output)')
-!         output = IO_lc(IO_stringValue(line,chunkPos,2_pInt))                                       ! ...and corresponding output
-!         select case(output)
-!           case ('thermalexpansionrate')
-!             kinematics_thermal_expansion_Noutput(instance) = kinematics_thermal_expansion_Noutput(instance) + 1_pInt
-!             kinematics_thermal_expansion_outputID(kinematics_thermal_expansion_Noutput(instance),instance) = &
-!               thermalexpansionrate_ID
-!             kinematics_thermal_expansion_output(kinematics_thermal_expansion_Noutput(instance),instance) = output
-! ToDo add sizePostResult loop afterwards...
-
-     end select
-   endif; endif
- enddo parsingFile
 
 end subroutine kinematics_thermal_expansion_init
 
+
 !--------------------------------------------------------------------------------------------------
 !> @brief  report initial thermal strain based on current temperature deviation from reference
 !--------------------------------------------------------------------------------------------------
-pure function kinematics_thermal_expansion_initialStrain(ipc, ip, el)
+pure function kinematics_thermal_expansion_initialStrain(homog,phase,offset)
   use material, only: &
-   material_phase, &
+    temperature
-   material_homog, &
-   temperature, &
-   thermalMapping
   use lattice, only: &
     lattice_thermalExpansion33, &
     lattice_referenceTemperature
   
   implicit none
   integer(pInt), intent(in) :: &
-   ipc, &                                                                                           !< grain number
-   ip, &                                                                                            !< integration point number
-   el                                                                                               !< element number
- real(pReal), dimension(3,3) :: &
-   kinematics_thermal_expansion_initialStrain                                                       !< initial thermal strain (should be small strain, though)
- integer(pInt) :: &
     phase, &
     homog, offset
+  real(pReal), dimension(3,3) :: &
+    kinematics_thermal_expansion_initialStrain                                                       !< initial thermal strain (should be small strain, though)
  
- phase = material_phase(ipc,ip,el)
- homog = material_homog(ip,el)
- offset = thermalMapping(homog)%p(ip,el)
   
   kinematics_thermal_expansion_initialStrain = &
     (temperature(homog)%p(offset) - lattice_referenceTemperature(phase))**1 / 1. * &
@@ -184,10 +105,11 @@ pure function kinematics_thermal_expansion_initialStrain(ipc, ip, el)
   
 end function kinematics_thermal_expansion_initialStrain
 
+
 !--------------------------------------------------------------------------------------------------
 !> @brief  contains the constitutive equation for calculating the velocity gradient  
 !--------------------------------------------------------------------------------------------------
-subroutine kinematics_thermal_expansion_LiAndItsTangent(Li, dLi_dTstar3333, ipc, ip, el)
+subroutine kinematics_thermal_expansion_LiAndItsTangent(Li, dLi_dTstar, ipc, ip, el)
   use material, only: &
     material_phase, &
     material_homog, &
@@ -206,7 +128,7 @@ subroutine kinematics_thermal_expansion_LiAndItsTangent(Li, dLi_dTstar3333, ipc,
   real(pReal),   intent(out), dimension(3,3) :: &
     Li                                                                                               !< thermal velocity gradient
   real(pReal),   intent(out), dimension(3,3,3,3) :: &
-   dLi_dTstar3333                                                                                   !< derivative of Li with respect to Tstar (4th-order tensor defined to be zero)
+    dLi_dTstar                                                                                       !< derivative of Li with respect to Tstar (4th-order tensor defined to be zero)
   integer(pInt) :: &
     phase, &
     homog, offset
@@ -230,7 +152,7 @@ subroutine kinematics_thermal_expansion_LiAndItsTangent(Li, dLi_dTstar3333, ipc,
              + lattice_thermalExpansion33(1:3,1:3,2,phase)*(T - TRef)**2 / 2. &
              + lattice_thermalExpansion33(1:3,1:3,3,phase)*(T - TRef)**3 / 3. &
        )
- dLi_dTstar3333 = 0.0_pReal 
+  dLi_dTstar = 0.0_pReal 
   
 end subroutine kinematics_thermal_expansion_LiAndItsTangent
 

src/material.f90

@@ -235,6 +235,7 @@ module material
  public :: &
    material_init, &
    material_allocatePlasticState, &
+   material_allocateSourceState, &
    ELASTICITY_hooke_ID ,&
    PLASTICITY_none_ID, &
    PLASTICITY_isotropic_ID, &
@@ -305,9 +306,7 @@ subroutine material_init()
    texture_name
  use mesh, only: &
    mesh_homogenizationAt, &
-   mesh_NipsPerElem, &
+   theMesh
-   mesh_NcpElems, &
-   FE_geomtype
 
  implicit none
  integer(pInt), parameter :: FILEUNIT = 210_pInt
@@ -399,10 +398,10 @@ subroutine material_init()
  call material_populateGrains
 
 ! BEGIN DEPRECATED
- allocate(phaseAt                   (  homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),source=0_pInt)
+ allocate(phaseAt                   (  homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),source=0_pInt)
- allocate(phasememberAt             (  homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),source=0_pInt)
+ allocate(phasememberAt             (  homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),source=0_pInt)
- allocate(mappingHomogenization     (2,                          mesh_nIPsPerElem,mesh_NcpElems),source=0_pInt)
+ allocate(mappingHomogenization     (2,                          theMesh%elem%nIPs,theMesh%Nelems),source=0_pInt)
- allocate(mappingHomogenizationConst(                            mesh_nIPsPerElem,mesh_NcpElems),source=1_pInt)
+ allocate(mappingHomogenizationConst(                            theMesh%elem%nIPs,theMesh%Nelems),source=1_pInt)
 ! END DEPRECATED
 
  allocate(material_homogenizationAt,source=mesh_homogenizationAt)
@@ -410,9 +409,9 @@ subroutine material_init()
  allocate(CounterHomogenization(size(config_homogenization)),source=0_pInt)
 
 ! BEGIN DEPRECATED
- do e = 1_pInt,mesh_NcpElems
+ do e = 1_pInt,theMesh%Nelems
  myHomog = mesh_homogenizationAt(e)
-   do i = 1_pInt, mesh_NipsPerElem
+   do i = 1_pInt, theMesh%elem%nIPs
      CounterHomogenization(myHomog) = CounterHomogenization(myHomog) + 1_pInt
      mappingHomogenization(1:2,i,e) = [CounterHomogenization(myHomog),myHomog]
      do g = 1_pInt,homogenization_Ngrains(myHomog)
@@ -553,7 +552,7 @@ subroutine material_parseMicrostructure
    microstructure_name
  use mesh, only: &
    mesh_microstructureAt, &
-   mesh_NcpElems
+   theMesh
 
  implicit none
  character(len=65536), dimension(:), allocatable :: &
@@ -571,7 +570,7 @@ subroutine material_parseMicrostructure
  if(any(mesh_microstructureAt > size(config_microstructure))) &
   call IO_error(155_pInt,ext_msg='More microstructures in geometry than sections in material.config')
 
- forall (e = 1_pInt:mesh_NcpElems) &
+ forall (e = 1_pInt:theMesh%Nelems) &
    microstructure_active(mesh_microstructureAt(e)) = .true.                                         ! current microstructure used in model? Elementwise view, maximum N operations for N elements
 
  do m=1_pInt, size(config_microstructure)
@@ -922,7 +921,7 @@ subroutine material_allocatePlasticState(phase,NofMyPhase,&
                                          sizeState,sizeDotState,sizeDeltaState,&
                                          Nslip,Ntwin,Ntrans)
  use numerics, only: &
-   numerics_integrator2 => numerics_integrator                                                      ! compatibility hack
+   numerics_integrator
 
  implicit none
  integer(pInt), intent(in) :: &
@@ -934,8 +933,6 @@ subroutine material_allocatePlasticState(phase,NofMyPhase,&
    Nslip, &
    Ntwin, &
    Ntrans
- integer(pInt) :: numerics_integrator                                                               ! compatibility hack
- numerics_integrator = numerics_integrator2(1)                                                      ! compatibility hack
 
  plasticState(phase)%sizeState        = sizeState
  plasticState(phase)%sizeDotState     = sizeDotState
@@ -966,6 +963,47 @@ subroutine material_allocatePlasticState(phase,NofMyPhase,&
 end subroutine material_allocatePlasticState
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief allocates the source state of a phase
+!--------------------------------------------------------------------------------------------------
+subroutine material_allocateSourceState(phase,of,NofMyPhase,&
+                                        sizeState,sizeDotState,sizeDeltaState)
+ use numerics, only: &
+   numerics_integrator
+
+ implicit none
+ integer(pInt), intent(in) :: &
+   phase, &
+   of, &
+   NofMyPhase, &
+   sizeState, sizeDotState,sizeDeltaState
+
+ sourceState(phase)%p(of)%sizeState        = sizeState
+ sourceState(phase)%p(of)%sizeDotState     = sizeDotState
+ sourceState(phase)%p(of)%sizeDeltaState   = sizeDeltaState
+ plasticState(phase)%offsetDeltaState = sizeState-sizeDeltaState                                    ! deltaState occupies latter part of state by definition
+
+ allocate(sourceState(phase)%p(of)%aTolState           (sizeState),                source=0.0_pReal)
+ allocate(sourceState(phase)%p(of)%state0              (sizeState,NofMyPhase),     source=0.0_pReal)
+ allocate(sourceState(phase)%p(of)%partionedState0     (sizeState,NofMyPhase),     source=0.0_pReal)
+ allocate(sourceState(phase)%p(of)%subState0           (sizeState,NofMyPhase),     source=0.0_pReal)
+ allocate(sourceState(phase)%p(of)%state               (sizeState,NofMyPhase),     source=0.0_pReal)
+
+ allocate(sourceState(phase)%p(of)%dotState            (sizeDotState,NofMyPhase),  source=0.0_pReal)
+ if (numerics_integrator == 1_pInt) then
+   allocate(sourceState(phase)%p(of)%previousDotState  (sizeDotState,NofMyPhase),  source=0.0_pReal)
+   allocate(sourceState(phase)%p(of)%previousDotState2 (sizeDotState,NofMyPhase),  source=0.0_pReal)
+ endif
+ if (numerics_integrator == 4_pInt) &
+   allocate(sourceState(phase)%p(of)%RK4dotState       (sizeDotState,NofMyPhase),  source=0.0_pReal)
+ if (numerics_integrator == 5_pInt) &
+   allocate(sourceState(phase)%p(of)%RKCK45dotState  (6,sizeDotState,NofMyPhase),  source=0.0_pReal)
+
+ allocate(sourceState(phase)%p(of)%deltaState        (sizeDeltaState,NofMyPhase),  source=0.0_pReal)
+
+end subroutine material_allocateSourceState
+
+
 !--------------------------------------------------------------------------------------------------
 !> @brief populates the grains
 !> @details populates the grains by identifying active microstructure/homogenization pairs,
@@ -984,13 +1022,10 @@ subroutine material_populateGrains
    math_sampleFiberOri, &
    math_symmetricEulers
  use mesh, only: &
-   mesh_NipsPerElem, &
-   mesh_elemType, &
    mesh_homogenizationAt, &
    mesh_microstructureAt, &
-   mesh_NcpElems, &
+   theMesh, &
-   mesh_ipVolume, &
+   mesh_ipVolume
-   FE_geomtype
  use config, only: &
    config_homogenization, &
    config_microstructure, &
@@ -1026,24 +1061,24 @@ subroutine material_populateGrains
 
  myDebug = debug_level(debug_material)
 
- allocate(material_volume(homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),       source=0.0_pReal)
+ allocate(material_volume(homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),       source=0.0_pReal)
- allocate(material_phase(homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),        source=0_pInt)
+ allocate(material_phase(homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),        source=0_pInt)
- allocate(material_homog(mesh_nIPsPerElem,mesh_NcpElems),                                  source=0_pInt)
+ allocate(material_homog(theMesh%elem%nIPs,theMesh%Nelems),                                  source=0_pInt)
- allocate(material_texture(homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),      source=0_pInt)
+ allocate(material_texture(homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),      source=0_pInt)
- allocate(material_EulerAngles(3,homogenization_maxNgrains,mesh_nIPsPerElem,mesh_NcpElems),source=0.0_pReal)
+ allocate(material_EulerAngles(3,homogenization_maxNgrains,theMesh%elem%nIPs,theMesh%Nelems),source=0.0_pReal)
 
  allocate(Ngrains(size(config_homogenization),size(config_microstructure)),            source=0_pInt)
  allocate(Nelems (size(config_homogenization),size(config_microstructure)),            source=0_pInt)
 
 ! populating homogenization schemes in each
 !--------------------------------------------------------------------------------------------------
- do e = 1_pInt, mesh_NcpElems
+ do e = 1_pInt, theMesh%Nelems
-   material_homog(1_pInt:mesh_NipsPerElem,e) = mesh_homogenizationAt(e)
+   material_homog(1_pInt:theMesh%elem%nIPs,e) = mesh_homogenizationAt(e)
  enddo
 
 !--------------------------------------------------------------------------------------------------
 ! precounting of elements for each homog/micro pair
- do e = 1_pInt, mesh_NcpElems
+ do e = 1_pInt, theMesh%Nelems
    homog = mesh_homogenizationAt(e)
    micro = mesh_microstructureAt(e)
    Nelems(homog,micro) = Nelems(homog,micro) + 1_pInt
@@ -1061,8 +1096,7 @@ subroutine material_populateGrains
 !--------------------------------------------------------------------------------------------------
 ! identify maximum grain count per IP (from element) and find grains per homog/micro pair
  Nelems = 0_pInt                                                                                    ! reuse as counter
- elementLooping: do e = 1_pInt,mesh_NcpElems
+ elementLooping: do e = 1_pInt,theMesh%Nelems
-   t     = mesh_elemType
    homog = mesh_homogenizationAt(e)
    micro = mesh_microstructureAt(e)
    if (homog < 1_pInt .or. homog > size(config_homogenization)) &                                      ! out of bounds
@@ -1072,7 +1106,7 @@ subroutine material_populateGrains
    if (microstructure_elemhomo(micro)) then                                                         ! how many grains are needed at this element?
      dGrains = homogenization_Ngrains(homog)                                                        ! only one set of Ngrains (other IPs are plain copies)
    else
-     dGrains = homogenization_Ngrains(homog) * mesh_NipsPerElem                                     ! each IP has Ngrains
+     dGrains = homogenization_Ngrains(homog) * theMesh%elem%nIPs                                     ! each IP has Ngrains
    endif
    Ngrains(homog,micro) = Ngrains(homog,micro) + dGrains                                            ! total grain count
    Nelems(homog,micro)  = Nelems(homog,micro) + 1_pInt                                              ! total element count
@@ -1106,16 +1140,15 @@ subroutine material_populateGrains
 
        do hme = 1_pInt, Nelems(homog,micro)
          e = elemsOfHomogMicro(homog,micro)%p(hme)                                                  ! my combination of homog and micro, only perform calculations for elements with homog, micro combinations which is indexed in cpElemsindex
-         t = mesh_elemType
          if (microstructure_elemhomo(micro)) then                                                   ! homogeneous distribution of grains over each element's IPs
-           volumeOfGrain(grain+1_pInt:grain+dGrains) = sum(mesh_ipVolume(1:mesh_NipsPerElem,e))/&
+           volumeOfGrain(grain+1_pInt:grain+dGrains) = sum(mesh_ipVolume(1:theMesh%elem%nIPs,e))/&
                                                                          real(dGrains,pReal)        ! each grain combines size of all IPs in that element
            grain = grain + dGrains                                                                  ! wind forward by Ngrains@IP
          else
-           forall (i = 1_pInt:mesh_NipsPerElem) &                                                   ! loop over IPs
+           forall (i = 1_pInt:theMesh%elem%nIPs) &                                                   ! loop over IPs
              volumeOfGrain(grain+(i-1)*dGrains+1_pInt:grain+i*dGrains) = &
                mesh_ipVolume(i,e)/real(dGrains,pReal)                                               ! assign IPvolume/Ngrains@IP to all grains of IP
-           grain = grain + mesh_NipsPerElem * dGrains                                               ! wind forward by Nips*Ngrains@IP
+           grain = grain + theMesh%elem%nIPs * dGrains                                               ! wind forward by Nips*Ngrains@IP
          endif
        enddo
 
@@ -1261,11 +1294,10 @@ subroutine material_populateGrains
 
        do hme = 1_pInt, Nelems(homog,micro)
          e = elemsOfHomogMicro(homog,micro)%p(hme)                                                  ! only perform calculations for elements with homog, micro combinations which is indexed in cpElemsindex
-         t = mesh_elemType
          if (microstructure_elemhomo(micro)) then                                                   ! homogeneous distribution of grains over each element's IPs
            m = 1_pInt                                                                               ! process only first IP
          else
-           m = mesh_NipsPerElem
+           m = theMesh%elem%nIPs
          endif
 
          do i = 1_pInt, m                                                                           ! loop over necessary IPs
@@ -1303,7 +1335,7 @@ subroutine material_populateGrains
 
          enddo
 
-         do i = i, mesh_NipsPerElem                                                                 ! loop over IPs to (possibly) distribute copies from first IP
+         do i = i, theMesh%elem%nIPs                                                                 ! loop over IPs to (possibly) distribute copies from first IP
            material_volume (1_pInt:dGrains,i,e) = material_volume (1_pInt:dGrains,1,e)
            material_phase  (1_pInt:dGrains,i,e) = material_phase  (1_pInt:dGrains,1,e)
            material_texture(1_pInt:dGrains,i,e) = material_texture(1_pInt:dGrains,1,e)

src/math.f90

@@ -70,6 +70,10 @@ module math
 !--------------------------------------------------------------------------------------------------
 ! Provide deprecated names for compatibility
 
+ interface math_cross
+   module procedure math_crossproduct
+ end interface math_cross
+
 ! ToDo MD: Our naming scheme was a little bit odd: We use essentially the re-ordering according to Nye
 ! (convenient because Abaqus and Marc want to have 12 on position 4)
 ! but weight the shear components according to Mandel (convenient for matrix multiplications)
@@ -98,26 +102,19 @@ module math
    module procedure math_99to3333
  end interface math_Plain99to3333
  
- interface math_Mandel3333to66
-   module procedure math_sym3333to66
- end interface math_Mandel3333to66
- 
- interface math_Mandel66to3333
-   module procedure math_66toSym3333
- end interface math_Mandel66to3333
- 
  public :: &
    math_Plain33to9, &
    math_Plain9to33, &
    math_Mandel33to6, &
    math_Mandel6to33, &
    math_Plain3333to99, &
-   math_Plain99to3333, &
+   math_Plain99to3333
-   math_Mandel3333to66, &
-   math_Mandel66to3333
 !---------------------------------------------------------------------------------------------------
 
  public :: &
+#if defined(__PGI)
+   norm2, &
+#endif
    math_init, &
    math_qsort, &
    math_expand, &
@@ -126,6 +123,7 @@ module math
    math_identity4th, &
    math_civita, &
    math_delta, &
+   math_cross, &
    math_crossproduct, &
    math_tensorproduct33, &
    math_mul3x3, &
@@ -351,20 +349,38 @@ end subroutine math_check
 
 !--------------------------------------------------------------------------------------------------
 !> @brief Quicksort algorithm for two-dimensional integer arrays
-! Sorting is done with respect to array(1,:)
+! Sorting is done with respect to array(sort,:) and keeps array(/=sort,:) linked to it.
-! and keeps array(2:N,:) linked to it.
+! default: sort=1
 !--------------------------------------------------------------------------------------------------
-recursive subroutine math_qsort(a, istart, iend)
+recursive subroutine math_qsort(a, istart, iend, sortDim)
 
  implicit none
  integer(pInt), dimension(:,:), intent(inout) :: a
- integer(pInt), intent(in) :: istart,iend
+ integer(pInt), intent(in),optional :: istart,iend, sortDim
- integer(pInt) :: ipivot
+ integer(pInt) :: ipivot,s,e,d
  
- if (istart < iend) then
+ if(present(istart)) then
-   ipivot = qsort_partition(a,istart, iend)
+   s = istart
-   call math_qsort(a, istart, ipivot-1_pInt)
+ else
-   call math_qsort(a, ipivot+1_pInt, iend)
+   s = lbound(a,2)
+ endif
+ 
+ if(present(iend)) then
+   e = iend
+ else
+   e = ubound(a,2)
+ endif
+ 
+  if(present(sortDim)) then
+   d = sortDim
+ else
+   d = 1
+ endif
+  
+ if (s < e) then
+   ipivot = qsort_partition(a,s, e, d)
+   call math_qsort(a, s, ipivot-1_pInt, d)
+   call math_qsort(a, ipivot+1_pInt, e, d)
  endif
 
 !--------------------------------------------------------------------------------------------------
@@ -373,37 +389,34 @@ recursive subroutine math_qsort(a, istart, iend)
  !-------------------------------------------------------------------------------------------------
  !> @brief Partitioning required for quicksort
  !-------------------------------------------------------------------------------------------------
- integer(pInt) function qsort_partition(a, istart, iend)
+ integer(pInt) function qsort_partition(a, istart, iend, sort)
  
    implicit none
    integer(pInt), dimension(:,:), intent(inout) :: a
-   integer(pInt), intent(in) :: istart,iend
+   integer(pInt),                 intent(in)    :: istart,iend,sort
-   integer(pInt) :: i,j,k,tmp
+   integer(pInt), dimension(size(a,1))          :: tmp
+   integer(pInt) :: i,j
   
    do
      ! find the first element on the right side less than or equal to the pivot point
      do j = iend, istart, -1_pInt
-       if (a(1,j) <= a(1,istart)) exit
+       if (a(sort,j) <= a(sort,istart)) exit
      enddo
      ! find the first element on the left side greater than the pivot point
      do i = istart, iend
-       if (a(1,i) > a(1,istart)) exit
+       if (a(sort,i) > a(sort,istart)) exit
-     enddo
-     if (i < j) then ! if the indexes do not cross, exchange values
-       do k = 1_pInt, int(size(a,1_pInt), pInt)
-         tmp = a(k,i)
-         a(k,i) = a(k,j)
-         a(k,j) = tmp
-       enddo
-     else           ! if they do cross, exchange left value with pivot and return with the partition index
-       do k = 1_pInt, int(size(a,1_pInt), pInt)
-         tmp = a(k,istart)
-         a(k,istart) = a(k,j)
-         a(k,j) = tmp
      enddo
+     cross: if (i >= j) then ! if the indices cross, exchange left value with pivot and return with the partition index
+       tmp         = a(:,istart)
+       a(:,istart) = a(:,j)
+       a(:,j)      = tmp
        qsort_partition = j
        return
-     endif
+     else cross ! if they do not cross, exchange values
+       tmp    = a(:,i)
+       a(:,i) = a(:,j)
+       a(:,j) = tmp
+     endif cross
    enddo
  
  end function qsort_partition
@@ -1869,7 +1882,6 @@ function math_sampleGaussOri(center,FWHM)
    math_sampleGaussOri = math_RtoEuler(math_mul33x33(R,math_EulerToR(center)))
  endif
 
-
 end function math_sampleGaussOri
 
 
@@ -2707,4 +2719,19 @@ real(pReal) pure elemental function math_clip(a, left, right)
 
 end function math_clip
 
+
+#if defined(__PGI)
+!--------------------------------------------------------------------------------------------------
+!> @brief substitute for the norm2 intrinsic which is not available in PGI 18.10
+!--------------------------------------------------------------------------------------------------
+real(pReal) pure function norm2(v)
+ 
+ implicit none
+ real(pReal), intent(in), dimension(3) :: v
+ 
+ norm2 = sqrt(sum(v**2))
+
+end function norm2
+#endif
+
 end module math