Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

VERSION

@@ -1 +1 @@
-v2.0.1-148-gfb23c49
+v2.0.1-150-g5345b42

code/C_routines.c

@@ -9,6 +9,14 @@
 
 /* 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)
+    return 0;
+  return S_ISDIR(statbuf.st_mode);
+}
+
+
 void getcurrentworkdir_c(char cwd[], int *stat ){
   char cwd_tmp[1024];
   if(getcwd(cwd_tmp, sizeof(cwd_tmp)) == cwd_tmp){
@@ -20,9 +28,14 @@ void getcurrentworkdir_c(char cwd[], int *stat ){
   }
 }
 
-int isdirectory_c(const char *dir){
+
-  struct stat statbuf;
+void gethostname_c(char hostname[], int *stat ){
-  if(stat(dir, &statbuf) != 0)
+  char hostname_tmp[1024];
-    return 0;
+  if(gethostname(hostname_tmp, sizeof(hostname_tmp)) == 0){
-  return S_ISDIR(statbuf.st_mode);
+    strcpy(hostname,hostname_tmp);
+    *stat = 0;
+  }
+  else{
+    *stat = 1;
+  }
 }

code/IO.f90

@@ -1568,8 +1568,6 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
    msg = 'math_check: R*v == q*v failed'
  case (410_pInt)
    msg = 'eigenvalues computation error'
- case (450_pInt)
-   msg = 'unknown symmetry type specified'
 
 !-------------------------------------------------------------------------------------------------
 ! homogenization errors

code/math.f90

@@ -1864,37 +1864,29 @@ end function math_sampleGaussVar
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief symmetrically equivalent Euler angles for given sample symmetry 1:triclinic, 2:monoclinic, 4:orthotropic
+!> @brief symmetrically equivalent Euler angles for given sample symmetry 
+!> @detail 1 (equivalent to != 2 and !=4):triclinic, 2:monoclinic, 4:orthotropic
 !--------------------------------------------------------------------------------------------------
 pure function math_symmetricEulers(sym,Euler)
 
  implicit none
- integer(pInt), intent(in) :: sym
+ integer(pInt), intent(in) :: sym                                                                   !< symmetry Class
  real(pReal), dimension(3), intent(in) :: Euler
  real(pReal), dimension(3,3) :: math_symmetricEulers
- integer(pInt) :: i,j
 
- math_symmetricEulers(1,1) = PI+Euler(1)
+ math_symmetricEulers = transpose(reshape([PI+Euler(1), PI-Euler(1), 2.0_pReal*PI-Euler(1), &
- math_symmetricEulers(2,1) = Euler(2)
+                                              Euler(2), PI-Euler(2), PI          -Euler(2), &
- math_symmetricEulers(3,1) = Euler(3)
+                                              Euler(3), PI+Euler(3), PI          +Euler(3)],[3,3])) ! transpose is needed to have symbolic notation instead of column-major
 
- math_symmetricEulers(1,2) = PI-Euler(1)
+ math_symmetricEulers = modulo(math_symmetricEulers,2.0_pReal*pi)
- math_symmetricEulers(2,2) = PI-Euler(2)
- math_symmetricEulers(3,2) = PI+Euler(3)
-
- math_symmetricEulers(1,3) = 2.0_pReal*PI-Euler(1)
- math_symmetricEulers(2,3) = PI-Euler(2)
- math_symmetricEulers(3,3) = PI+Euler(3)
-
- forall (i=1_pInt:3_pInt,j=1_pInt:3_pInt) math_symmetricEulers(j,i) = modulo(math_symmetricEulers(j,i),2.0_pReal*pi)
 
  select case (sym)
-   case (4_pInt) ! all done
+   case (4_pInt)                                                                                    ! orthotropic: all done
 
-   case (2_pInt)  ! return only first
+   case (2_pInt)                                                                                    ! monoclinic: return only first
      math_symmetricEulers(1:3,2:3) = 0.0_pReal
 
-   case default         ! return blank
+   case default                                                                                     ! triclinic: return blank
      math_symmetricEulers = 0.0_pReal
  end select
 

code/spectral_interface.f90

@@ -20,6 +20,7 @@ module DAMASK_interface
    geometryFile = '', &                                                                             !< parameter given for geometry file
    loadCaseFile = ''                                                                                !< parameter given for load case file
  character(len=1024), private           :: workingDirectory                                         !< accessed by getSolverWorkingDirectoryName for compatibility reasons
+ character,           private,parameter :: pathSep = '/'
 
  public :: &
    getSolverWorkingDirectoryName, &
@@ -31,7 +32,6 @@ module DAMASK_interface
    getLoadCaseFile, &
    rectifyPath, &
    makeRelativePath, &
-   getPathSep, &
    IIO_stringValue, &
    IIO_intValue, &
    IIO_lc, &
@@ -44,6 +44,8 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine DAMASK_interface_init()
  use, intrinsic :: iso_fortran_env                                                                  ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
+ use system_routines, only: &
+   getHostName
 
  implicit none
  character(len=1024) :: &
@@ -64,6 +66,7 @@ subroutine DAMASK_interface_init()
  integer, dimension(8) :: &
    dateAndTime                                                                                      ! type default integer
  PetscErrorCode :: ierr
+ logical        :: error
  external :: &
    quit,&
    MPI_Comm_rank,&
@@ -116,7 +119,6 @@ subroutine DAMASK_interface_init()
    tag = IIO_lc(IIO_stringValue(commandLine,chunkPos,i))                                            ! extract key
    select case(tag)
      case ('-h','--help')
-       mainProcess2: if (worldrank == 0) then
        write(6,'(a)')  ' #######################################################################'
        write(6,'(a)')  ' DAMASK_spectral:'
        write(6,'(a)')  ' The spectral method boundary value problem solver for'
@@ -163,7 +165,6 @@ subroutine DAMASK_interface_init()
        write(6,'(/,a)')'   --help'
        write(6,'(a,/)')'        Prints this message and exits'
        call quit(0_pInt)                                                                        ! normal Termination
-       endif mainProcess2
      case ('-l', '--load', '--loadcase')
        loadcaseArg = IIO_stringValue(commandLine,chunkPos,i+1_pInt)
      case ('-g', '--geom', '--geometry')
@@ -185,12 +186,11 @@ subroutine DAMASK_interface_init()
  geometryFile = getGeometryFile(geometryArg)
  loadCaseFile = getLoadCaseFile(loadCaseArg)
 
- call get_environment_variable('HOSTNAME',hostName)
  call get_environment_variable('USER',userName)
- mainProcess3: if (worldrank == 0) then
+ error = getHostName(hostName)
  write(6,'(a,a)')      ' Host name:             ', trim(hostName)
  write(6,'(a,a)')      ' User name:             ', trim(userName)
-   write(6,'(a,a)')      ' Path separator:        ', getPathSep()
+ write(6,'(a,a)')      ' Path separator:        ', pathSep
  write(6,'(a,a)')      ' Command line call:     ', trim(commandLine)
  if (len(trim(workingDirArg))>0) &
    write(6,'(a,a)')    ' Working dir argument:  ', trim(workingDirArg)
@@ -203,7 +203,6 @@ subroutine DAMASK_interface_init()
  if (SpectralRestartInc > 1_pInt) &
    write(6,'(a,i6.6)') ' Restart at increment:  ', spectralRestartInc
  write(6,'(a,l1,/)')   ' Append to result file: ', appendToOutFile
- endif mainProcess3
 
 end subroutine DAMASK_interface_init
 
@@ -222,11 +221,9 @@ character(len=1024) function storeWorkingDirectory(workingDirectoryArg,geometryA
  character(len=*),  intent(in) :: workingDirectoryArg                                               !< working directory argument
  character(len=*),  intent(in) :: geometryArg                                                       !< geometry argument
  character(len=1024)           :: cwd
- character                     :: pathSep
  logical                       :: error
  external                      :: quit
 
- pathSep = getPathSep()
  wdGiven: if (len(workingDirectoryArg)>0) then
    absolutePath: if (workingDirectoryArg(1:1) == pathSep) then
      storeWorkingDirectory = workingDirectoryArg
@@ -262,6 +259,7 @@ end function storeWorkingDirectory
 character(len=1024) function getSolverWorkingDirectoryName()
 
  implicit none
+
  getSolverWorkingDirectoryName = workingDirectory
 
 end function getSolverWorkingDirectoryName
@@ -274,10 +272,8 @@ character(len=1024) function getSolverJobName()
 
  implicit none
  integer :: posExt,posSep
- character :: pathSep
  character(len=1024) :: tempString 
 
- pathSep = getPathSep()
 
  tempString = geometryFile
  posExt = scan(tempString,'.',back=.true.)
@@ -308,11 +304,9 @@ character(len=1024) function getGeometryFile(geometryParameter)
    cwd
  integer :: posExt, posSep
  logical :: error
- character :: pathSep
  external  :: quit
 
  getGeometryFile = geometryParameter
- pathSep = getPathSep()
  posExt = scan(getGeometryFile,'.',back=.true.)
  posSep = scan(getGeometryFile,pathSep,back=.true.)
 
@@ -344,11 +338,9 @@ character(len=1024) function getLoadCaseFile(loadCaseParameter)
    cwd
  integer :: posExt, posSep
  logical :: error
- character :: pathSep
  external  :: quit
 
  getLoadCaseFile = loadcaseParameter
- pathSep = getPathSep()
  posExt = scan(getLoadCaseFile,'.',back=.true.)
  posSep = scan(getLoadCaseFile,pathSep,back=.true.)
 
@@ -374,11 +366,8 @@ function rectifyPath(path)
  implicit none
  character(len=*) :: path
  character(len=len_trim(path)) :: rectifyPath
- character :: pathSep
  integer :: i,j,k,l                                                                                 ! no pInt
 
- pathSep = getPathSep()
-
 !--------------------------------------------------------------------------------------------------
 ! remove /./ from path
  l = len_trim(path)
@@ -415,10 +404,8 @@ character(len=1024) function makeRelativePath(a,b)
 
  implicit none
  character (len=*) :: a,b
- character :: pathSep
  integer :: i,posLastCommonSlash,remainingSlashes !no pInt
 
- pathSep = getPathSep()
  posLastCommonSlash = 0
  remainingSlashes = 0
 
@@ -434,35 +421,6 @@ character(len=1024) function makeRelativePath(a,b)
 end function makeRelativePath
 
 
-!--------------------------------------------------------------------------------------------------
-!> @brief counting / and \ in $PATH System variable the character occuring more often is assumed
-! to be the path separator
-!--------------------------------------------------------------------------------------------------
-character function getPathSep()
-
- implicit none
- character(len=2048) :: &
-   path
- integer(pInt) :: &
-   backslash = 0_pInt, &
-   slash = 0_pInt
- integer :: i
-
- call get_environment_variable('PATH',path)
- do i=1, len(trim(path))
-   if (path(i:i)=='/') slash     =     slash + 1_pInt
-   if (path(i:i)=='\') backslash = backslash + 1_pInt
- enddo
-
- if (backslash>slash) then
-   getPathSep = '\'
- else
-   getPathSep = '/'
- endif
-
-end function getPathSep
-
-
 !--------------------------------------------------------------------------------------------------
 !> @brief taken from IO, check IO_stringValue for documentation 
 !--------------------------------------------------------------------------------------------------

code/system_routines.f90

@@ -9,7 +9,8 @@ module system_routines
  
  public :: &
    isDirectory, &
-   getCWD
+   getCWD, &
+   getHostName
 
 interface
 
@@ -29,6 +30,14 @@ interface
    integer(C_INT),intent(out)         :: stat
   end subroutine getCurrentWorkDir_C
 
+ subroutine getHostName_C(str, stat) bind(C)
+   use, intrinsic :: ISO_C_Binding, only: &
+     C_INT, &
+     C_CHAR
+   character(kind=C_CHAR), dimension(1024), intent(out)  :: str                                     ! C string is an array
+   integer(C_INT),intent(out)         :: stat
+  end subroutine getHostName_C
+
 end interface
 
 
@@ -85,5 +94,34 @@ logical function getCWD(str)
 
 end function getCWD
 
+
+!--------------------------------------------------------------------------------------------------
+!> @brief gets the current host name
+!--------------------------------------------------------------------------------------------------
+logical function getHostName(str)
+  use, intrinsic :: ISO_C_Binding, only: &
+    C_INT, &
+    C_CHAR, &
+    C_NULL_CHAR
+
+  implicit none
+  character(len=*), intent(out) :: str
+  character(kind=C_CHAR), dimension(1024) :: strFixedLength                                         ! C string is an array
+  integer(C_INT) :: stat
+  integer :: i
+
+  str = repeat('',len(str))
+  call getHostName_C(strFixedLength,stat)
+  do i=1,1024                                                                                       ! copy array components until Null string is found
+    if (strFixedLength(i) /= C_NULL_CHAR) then
+      str(i:i)=strFixedLength(i)
+    else
+      exit
+    endif
+  enddo
+  getHostName=merge(.True.,.False.,stat /= 0_C_INT)
+
+end function getHostName
+
 end module system_routines
 

examples/ConfigFiles/Phase_Nonlocal_Aluminum.config

@@ -8,32 +8,20 @@ plasticity              nonlocal
 (output)                rho_edge
 (output)                rho_screw
 (output)                rho_sgl
-(output)                rho_sgl_edge
 (output)                rho_sgl_edge_pos
 (output)                rho_sgl_edge_neg
-(output)                rho_sgl_screw
 (output)                rho_sgl_screw_pos
 (output)                rho_sgl_screw_neg
-(output)                rho_sgl_mobile
-(output)                rho_sgl_edge_mobile
 (output)                rho_sgl_edge_pos_mobile
 (output)                rho_sgl_edge_neg_mobile
-(output)                rho_sgl_screw_mobile
 (output)                rho_sgl_screw_pos_mobile
 (output)                rho_sgl_screw_neg_mobile
-(output)                rho_sgl_immobile
-(output)                rho_sgl_edge_immobile
 (output)                rho_sgl_edge_pos_immobile
 (output)                rho_sgl_edge_neg_immobile
-(output)                rho_sgl_screw_immobile
 (output)                rho_sgl_screw_pos_immobile
 (output)                rho_sgl_screw_neg_immobile
-(output)                rho_dip
 (output)                rho_dip_edge
 (output)                rho_dip_screw
-(output)                excess_rho
-(output)                excess_rho_edge
-(output)                excess_rho_screw
 (output)                rho_forest
 (output)                delta
 (output)                delta_sgl
@@ -47,10 +35,8 @@ plasticity              nonlocal
 (output)                rho_dot_sgl
 (output)                rho_dot_sgl_mobile
 (output)                rho_dot_dip
-(output)                rho_dot_gen
 (output)                rho_dot_gen_edge
 (output)                rho_dot_gen_screw
-(output)                rho_dot_sgl2dip
 (output)                rho_dot_sgl2dip_edge
 (output)                rho_dot_sgl2dip_screw
 (output)                rho_dot_ann_ath
@@ -66,24 +52,6 @@ plasticity              nonlocal
 (output)                velocity_edge_neg
 (output)                velocity_screw_pos
 (output)                velocity_screw_neg
-(output)                slipdirection.x
-(output)                slipdirection.y
-(output)                slipdirection.z
-(output)                slipnormal.x
-(output)                slipnormal.y
-(output)                slipnormal.z
-(output)                fluxDensity_edge_pos.x
-(output)                fluxDensity_edge_pos.y
-(output)                fluxDensity_edge_pos.z
-(output)                fluxDensity_edge_neg.x
-(output)                fluxDensity_edge_neg.y
-(output)                fluxDensity_edge_neg.z
-(output)                fluxDensity_screw_pos.x
-(output)                fluxDensity_screw_pos.y
-(output)                fluxDensity_screw_pos.z
-(output)                fluxDensity_screw_neg.x
-(output)                fluxDensity_screw_neg.y
-(output)                fluxDensity_screw_neg.z
 (output)                maximumDipoleHeight_edge
 (output)                maximumDipoleHeight_screw
 (output)                accumulated_shear

examples/ConfigFiles/Phase_Nonlocal_Nickel.config

@@ -14,8 +14,6 @@ plasticity              nonlocal
 (output)                rho_dip_edge
 (output)                rho_dip_screw
 (output)                rho_forest
-(output)                excess_rho_edge
-(output)                excess_rho_screw
 (output)                accumulatedshear
 (output)                shearrate
 (output)                resolvedstress
@@ -30,24 +28,6 @@ plasticity              nonlocal
 (output)                rho_dot_edgejogs
 (output)                rho_dot_flux_edge
 (output)                rho_dot_flux_screw
-(output)                slipdirection.x
-(output)                slipdirection.y
-(output)                slipdirection.z
-(output)                slipnormal.x
-(output)                slipnormal.y
-(output)                slipnormal.z
-(output)                fluxdensity_edge_pos.x
-(output)                fluxdensity_edge_pos.y
-(output)                fluxdensity_edge_pos.z
-(output)                fluxdensity_edge_neg.x
-(output)                fluxdensity_edge_neg.y
-(output)                fluxdensity_edge_neg.z
-(output)                fluxdensity_screw_pos.x
-(output)                fluxdensity_screw_pos.y
-(output)                fluxdensity_screw_pos.z
-(output)                fluxdensity_screw_neg.x
-(output)                fluxdensity_screw_neg.y
-(output)                fluxdensity_screw_neg.z
 
 lattice_structure       fcc
 Nslip                   12               # number of slip systems per family

examples/ConfigFiles/Phase_Phenopowerlaw_Aluminum.config

@@ -7,11 +7,6 @@ plasticity              phenopowerlaw
 (output)                resolvedstress_slip
 (output)                accumulated_shear_slip
 (output)                totalshear
-(output)                resistance_twin
-(output)                shearrate_twin
-(output)                resolvedstress_twin
-(output)                accumulated_shear_twin
-(output)                totalvolfrac_twin
 
 lattice_structure       fcc
 Nslip                   12                # per family
@@ -26,19 +21,6 @@ n_slip                  20
 tau0_slip                 31e6                # per family
 tausat_slip               63e6                # per family
 a_slip                  2.25
-gdot0_twin              0.001
-n_twin                  20
-tau0_twin                 31e6                # per family
-s_pr                    0                     # push-up factor for slip saturation due to twinning
-twin_b                  0
-twin_c                  0
-twin_d                  0
-twin_e                  0
 h0_slipslip             75e6
-h0_twinslip             0
-h0_twintwin             0
 interaction_slipslip    1 1 1.4 1.4 1.4 1.4
-interaction_sliptwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twinslip    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-interaction_twintwin    1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
 atol_resistance         1

lib/damask/test/test.py

@@ -23,6 +23,8 @@ class Test():
                 'keep':          False,
                 'accept':        False,
                 'updateRequest': False,
+                'show':          False,
+                'select':        None,
                 }
     for arg in defaults.keys():
       setattr(self,arg,kwargs.get(arg) if kwargs.get(arg) else defaults[arg])
@@ -58,10 +60,18 @@ class Test():
                            action = "store_true",
                            dest   = "accept",
                            help   = "calculate results but always consider test as successfull")
-
+    self.parser.add_option("-l",   "--list",
+                           action = "store_true",
+                           dest   = "show",
+                           help   = "show all test variants and do no calculation")
+    self.parser.add_option("-s",   "--select",
+                           dest   = "select",
+                           help   = "run test of given name only")
     self.parser.set_defaults(keep   = self.keep,
                              accept = self.accept,
                              update = self.updateRequest,
+                             show   = self.show,
+                             select = self.select,
                             )
 
     
@@ -73,6 +83,11 @@ class Test():
       self.prepareAll()
 
     for variant,name in enumerate(self.variants):
+      if self.options.show:
+        logging.critical('{}: {}'.format(variant,name))
+      elif self.options.select is not None and name != self.options.select:
+        pass
+      else:
         try:
           if not self.options.keep:
             self.prepare(variant)

processing/pre/geom_check.sh

@@ -11,7 +11,7 @@ do
   < $geom \
   | \
   vtk_addRectilinearGridData \
-    --scalar microstructure \
+    --data microstructure \
     --inplace \
     --vtk ${geom%.*}.vtk
   rm ${geom%.*}.vtk

processing/pre/patchFromReconstructedBoundaries.py

@@ -270,7 +270,6 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
         myWalk = point['segments'].pop()
         grainLegs = [myWalk]
         myEnd = segments[myWalk][1 if segments[myWalk][0] == myStart else 0]
-
         while (myEnd != pointId):
           myV = [points[myEnd]['coords'][0]-points[myStart]['coords'][0],
                  points[myEnd]['coords'][1]-points[myStart]['coords'][1]]
@@ -281,13 +280,13 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
             if peek == myWalk:
               continue                                                                              # do not go back same path
             peekEnd = segments[peek][1 if segments[peek][0] == myEnd else 0]
-            peekV = [points[myEnd]['coords'][0]-points[peekEnd]['coords'][0],
+            peekV = [points[peekEnd]['coords'][0]-points[myEnd]['coords'][0],
-                     points[myEnd]['coords'][1]-points[peekEnd]['coords'][1]]
+                     points[peekEnd]['coords'][1]-points[myEnd]['coords'][1]]
             peekLen = math.sqrt(peekV[0]**2+peekV[1]**2)
             if peekLen == 0.0: damask.util.croak('peeklen is zero: peek point {}'.format(peek))
             crossproduct = (myV[0]*peekV[1] - myV[1]*peekV[0])/myLen/peekLen
             dotproduct   = (myV[0]*peekV[0] + myV[1]*peekV[1])/myLen/peekLen
-            innerAngle = crossproduct*(dotproduct+1.0)
+            innerAngle = math.copysign(1.0,crossproduct)*(dotproduct-1.0)
             if innerAngle >= best['product']:                                    # takes sharpest left turn
               best['product'] = innerAngle
               best['peek'] = peek
@@ -301,7 +300,7 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
           if myWalk in points[myStart]['segments']:
             points[myStart]['segments'].remove(myWalk)
           else:
-            damask.utilcroak('{} not in segments of point {}'.format(myWalk,myStart))
+            damask.util.croak('{} not in segments of point {}'.format(myWalk,myStart))
           grainDraw.append(points[myStart]['coords'])
           grainLegs.append(myWalk)
           
@@ -311,7 +310,6 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
         else:
           grains['box'] = grainLegs
 
-  
 # build overall data structure
 
   rcData = {'dimension':[dX,dY],
@@ -772,8 +770,8 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):
              'dimension':(xsize,ysize,zsize)}
   
   frameindex=len(rcData['grain'])+1                                          # calculate frame index as largest grain index plus one 
-  dx = xsize/(xres+1)                                                        # calculate step sizes
+  dx = xsize/(xres)                                                          # calculate step sizes
-  dy = ysize/(yres+1)
+  dy = ysize/(yres)
  
   grainpoints = []
   for segments in rcData['grain']:                                           # get segments of each grain
@@ -788,11 +786,10 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):
     grainpoints.append([])                                                   # start out blank for current grain
     for p in sorted(points, key=points.get):                                 # loop thru set of sorted points
       grainpoints[-1].append([rcData['point'][p][0],rcData['point'][p][1]])  # append x,y of point
- 
   bestGuess = 0                                                              # assume grain 0 as best guess
   for i in range(int(xres*yres)):                                            # walk through all points in xy plane
     xtest = -xframe+((i%xres)+0.5)*dx                                        # calculate coordinates
-    ytest = -yframe+(int(i/xres)+0.5)*dy
+    ytest = -yframe+((i//xres)+0.5)*dy
     if(xtest < 0 or xtest > maxX):                                           # check wether part of frame
       if( ytest < 0 or ytest > maxY):                                        # part of edges
         fftdata['fftpoints'].append(frameindex+2)                            # append frameindex to result array

processing/pre/seeds_check.sh

@@ -5,7 +5,7 @@ do
   vtk_pointcloud $seeds
 
   vtk_addPointcloudData $seeds \
-    --scalar microstructure,weight \
+    --data microstructure,weight \
     --inplace \
     --vtk ${seeds%.*}.vtp \