Merge branch 'development' into CCodeUse

DAMASK_env.sh

@@ -53,7 +53,10 @@ if [ ! -z "$PS1" ]; then
   [[ "x$SOLVER"       != "x" ]] && echo "Spectral Solver    $SOLVER" 
   [[ "x$PROCESSING"   != "x" ]] && echo "Post Processing    $PROCESSING"
   echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  [[ "x$PETSC_DIR"   != "x" ]] && echo "PETSc location     $PETSC_DIR"
+  if [ "x$PETSC_DIR"   != "x" ]; then
+    echo "PETSc location     $PETSC_DIR"
+    [[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo "               ~~> "`readlink -f $PETSC_DIR`
+  fi
   [[ "x$PETSC_ARCH"  != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
   echo "MSC.Marc/Mentat    $MSC_ROOT"
   echo

DAMASK_env.zsh

@@ -51,7 +51,10 @@ if [ ! -z "$PS1" ]; then
   [[ "x$SOLVER"       != "x" ]] && echo "Spectral Solver    $SOLVER" 
   [[ "x$PROCESSING"   != "x" ]] && echo "Post Processing    $PROCESSING"
   echo "Multithreading     DAMASK_NUM_THREADS=$DAMASK_NUM_THREADS"
-  [[ "x$PETSC_DIR"   != "x" ]] && echo "PETSc location     $PETSC_DIR"
+  if [ "x$PETSC_DIR"   != "x" ]; then
+    echo "PETSc location     $PETSC_DIR"
+    [[ `readlink -f $PETSC_DIR` == $PETSC_DIR ]] || echo "               ~~> "`readlink -f $PETSC_DIR`
+  fi
   [[ "x$PETSC_ARCH"  != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
   echo "MSC.Marc/Mentat    $MSC_ROOT"
   echo

VERSION

@@ -1 +1 @@
-revision3813-1036-g5233236
+v2.0.0-15-g3898fb2

code/.gitignore

@@ -1 +1,2 @@
 DAMASK_marc*.f90
+quit__genmod.f90

code/DAMASK_spectral.f90

@@ -329,7 +329,7 @@ program DAMASK_spectral
              errorID = 838_pInt                                                                     ! no rotation is allowed by stress BC
      write(6,'(2x,a)') 'stress / GPa:'
      do i = 1_pInt, 3_pInt; do j = 1_pInt, 3_pInt
-       if(loadCases(currentLoadCase)%deformation%maskLogical(i,j)) then
+       if(loadCases(currentLoadCase)%P%maskLogical(i,j)) then
          write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%P%values(i,j)*1e-9_pReal
        else
          write(6,'(2x,12a)',advance='no') '    *       '

code/plastic_isotropic.f90

@@ -184,14 +184,13 @@ subroutine plastic_isotropic_init(fileUnit)
    if (IO_getTag(line,'[',']') /= '') then                                                          ! next section
      phase = phase + 1_pInt                                                                         ! advance section counter
      if (phase_plasticity(phase) == PLASTICITY_ISOTROPIC_ID) then
-       instance = phase_plasticityInstance(phase)
+       instance = phase_plasticityInstance(phase)                                                   ! count instances of my constitutive law
-
+       allocate(param(instance)%outputID(phase_Noutput(phase)))                                     ! allocate space for IDs of every requested output
      endif
      cycle                                                                                          ! skip to next line
    endif
    if (phase > 0_pInt) then; if (phase_plasticity(phase) == PLASTICITY_ISOTROPIC_ID) then           ! one of my phases. Do not short-circuit here (.and. between if-statements), it's not safe in Fortran
      instance = phase_plasticityInstance(phase)                                                     ! which instance of my plasticity is present phase
-     allocate(param(instance)%outputID(phase_Noutput(phase)))                                       ! allocate space for IDs of every requested output
      chunkPos = IO_stringPos(line) 
      tag = IO_lc(IO_stringValue(line,chunkPos,1_pInt))                                              ! extract key
      extmsg = trim(tag)//' ('//PLASTICITY_ISOTROPIC_label//')'                                      ! prepare error message identifier

config/numerics.config

@@ -54,12 +54,12 @@ discrepancyPower_RGC      5.0
 fixed_seed                0            # put any number larger than zero, integer, if you want to have a pseudo random distribution
 
 ## spectral parameters ##
-err_div_tolAbs            1.0e-3       # relative tolerance for fulfillment of stress equilibrium
+err_div_tolAbs            1.0e-3       # absolute tolerance for fulfillment of stress equilibrium
-err_div_tolRel            5.0e-4       # absolute tolerance for fulfillment of stress equilibrium
+err_div_tolRel            5.0e-4       # relative tolerance for fulfillment of stress equilibrium
-err_curl_tolAbs           1.0e-12      # relative tolerance for fulfillment of strain compatibility
+err_curl_tolAbs           1.0e-12      # absolute tolerance for fulfillment of strain compatibility
-err_curl_tolRel           5.0e-4       # absolute tolerance for fulfillment of strain compatibility
+err_curl_tolRel           5.0e-4       # relative tolerance for fulfillment of strain compatibility
-err_stress_tolrel         0.01         # relative tolerance for fulfillment of stress BC
+err_stress_tolAbs         1.0e3        # absolute tolerance for fulfillment of stress BC
-err_stress_tolabs         1.0e3        # absolute tolerance for fulfillment of stress BC
+err_stress_tolRel         0.01         # relative tolerance for fulfillment of stress BC
 fftw_timelimit           -1.0          # timelimit of plan creation for FFTW, see manual on www.fftw.org, Default -1.0: disable timelimit
 rotation_tol              1.0e-12      # tolerance of rotation specified in loadcase, Default 1.0e-12: first guess
 fftw_plan_mode            FFTW_PATIENT # reads the planing-rigor flag, see manual on www.fftw.org, Default FFTW_PATIENT: use patient planner flag    

processing/post/addGrainID.py

@@ -110,7 +110,7 @@ for name in filenames:
   remarks = []
   
   if table.label_dimension(options.coords) != 3:       errors.append('coordinates {} are not a vector.'.format(options.coords))
-  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} has wrong dimension {}.'.format(label,dim))
+  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} does not have dimension {}.'.format(label,dim))
   else:  column = table.label_index(label)
 
   if remarks != []: damask.util.croak(remarks)

processing/post/addIPFcolor.py

@@ -99,7 +99,7 @@ for name in filenames:
 # ------------------------------------------ sanity checks ----------------------------------------
 
   if not np.all(table.label_dimension(label) == dim):
-    damask.util.croak('input {} has wrong dimension {}.'.format(label,dim))
+    damask.util.croak('input {} does not have dimension {}.'.format(label,dim))
     table.close(dismiss = True)                                                                     # close ASCIItable and remove empty file
     continue
 

processing/post/addOrientations.py

@@ -113,7 +113,7 @@ for name in filenames:
   errors  = []
   remarks = []
   
-  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} has wrong dimension {}.'.format(label,dim))
+  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} does not have dimension {}.'.format(label,dim))
   else:  column = table.label_index(label)
 
   if remarks != []: damask.util.croak(remarks)

processing/post/addPole.py

@@ -101,7 +101,7 @@ for name in filenames:
   errors  = []
   remarks = []
   
-  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} has wrong dimension {}.'.format(label,dim))
+  if not np.all(table.label_dimension(label) == dim):  errors.append('input {} does not have dimension {}.'.format(label,dim))
   else:  column = table.label_index(label)
 
   if remarks != []: damask.util.croak(remarks)

processing/post/addQuaternions.py

@@ -1,100 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: UTF-8 no BOM -*-
-
-import os,sys,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 options [file[s]]', description = """
-Add Quaternions based on Crystal Frame Coordinates.
-
-""", version = scriptID)
-
-parser.add_option('-f','--frame',
-                  dest='frame', nargs=4, type='string', metavar='<string string string string>',
-                  help='heading of columns containing b* vector components and three frame vectors in that order')
-parser.add_option('-s','--symmetry',
-                  dest='crysym', nargs=1,type='string',metavar='<string>',
-                  help='crystal symmetry definition')                                        
-parser.set_defaults(frame = None)
-
-(options,filenames) = parser.parse_args()
-
-if options.frame is None:
-  parser.error('no data column specified...')
-
-datainfo = {'len':4,
-            'label':[]
-           }
-
-if options.frame  is not None:    datainfo['label']  += options.frame
-
-# --- 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)
-
-  table.head_read()                                                                                 # read ASCII header info
-
-# --------------- figure out columns to process  ---------------------------------------------------
-  active = []
-  column = {}
-
-  for label in datainfo['label']:
-    key = '1_'+label if datainfo['len'] > 1 else label                                              # non-special labels have to start with '1_'
-    if key in table.labels:
-        active.append(label)
-        column[label] = table.labels.index(key)                                                     # remember columns of requested data
-    else:
-      damask.util.croak('column %s not found...'%label)
-
-# ------------------------------------------ assemble header ---------------------------------------
-  
-  table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
-  table.labels_append(['Q_%i'%(i+1) for i in xrange(4)])                              # extend ASCII header with new labels [1 real, 3 imaginary components]
-  table.head_write()
-  
-# ------------------------------------------ process data ------------------------------------------
-  outputAlive = True
-  while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    vec    = np.zeros([4,3])
-    for i,label in enumerate(active):
-      vec[i,:] = np.array(table.data[column[label]:
-                                     column[label]+3])
-      
-    if sys.argv[1:][6]=='hexagonal':                                                      # Ensure Input matrix is orthogonal
-      M=np.dot(vec[0,:],vec[2,:])
-      vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
-      vec[2,:]=M*(vec[0,:]/np.linalg.norm(vec[0,:]))
-      vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
-    else:
-      vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
-      vec[2,:]=vec[2,:]/np.linalg.norm(vec[2,:])
-      vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
-     
-    
-    Ori=damask.Orientation(matrix=vec[1:,:],symmetry=sys.argv[1:][6])
-   
-    table.data_append(np.asarray(Ori.asQuaternion()))
-    
-    
-    outputAlive = table.data_write()                                                                # output processed line
-
-# ------------------------------------------ output result -----------------------------------------
-  outputAlive and table.output_flush()                                                              # just in case of buffered ASCII table
-
-  table.close()                                                                                     # close ASCII tables

processing/post/imageDataRGB.py

@@ -98,7 +98,7 @@ for name in filenames:
     errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '',
                                                  ', '.join(missing_labels)))
   if table.label_dimension(options.label) != 3:
-    errors.append('column {} has wrong dimension'.format(options.label))
+    errors.append('column {} does not have dimension'.format(options.label))
 
   if errors != []:
     damask.util.croak(errors)

processing/pre/geom_fromVoronoiTessellation.py

@@ -276,10 +276,10 @@ for name in filenames:
   grid = np.vstack(meshgrid2(x, y, z)).reshape(3,-1).T
   indices = laguerreTessellation(grid, coords, weights, grains, options.nonperiodic, options.cpus)
     
-# --- write header ---------------------------------------------------------------------------------
+# --- write header ------------------------------------------------------------------------
 
-  grainIDs = np.intersect1d(grainIDs,indices)
+  usedGrainIDs = np.intersect1d(grainIDs,indices)
-  info['microstructures'] = len(grainIDs)
+  info['microstructures'] = len(usedGrainIDs)
 
   if info['homogenization'] == 0: info['homogenization'] = options.homogenization
   
@@ -292,13 +292,13 @@ for name in filenames:
                    ])
 
   config_header = []
-  formatwidth = 1+int(math.log10(info['microstructures']))
+  formatwidth = 1+int(math.log10(NgrainIDs))
 
-  phase = options.phase * np.ones(info['microstructures'],'i')
+  phase = options.phase * np.ones(NgrainIDs,'i')
   if int(options.secondphase*info['microstructures']) > 0:
-    phase[0:int(options.secondphase*info['microstructures'])] += 1
+    phase[0:int(options.secondphase*info['microstructures'])] += 1                                # alter fraction 'options.secondphase' of used grainIDs
-    randomSeed = int(os.urandom(4).encode('hex'), 16)  if options.randomSeed is None \
+    randomSeed = options.randomSeed if options.randomSeed \
-                                                       else options.randomSeed                      # random seed for second phase
+                 else int(os.urandom(4).encode('hex'), 16)                                        # random seed for second phase
     np.random.seed(randomSeed)
     np.random.shuffle(phase)
     config_header += ['# random seed (phase shuffling): {}'.format(randomSeed)]