Merge branch 'MiscImprovements' into 'development'

Misc improvements

See merge request damask/DAMASK!76

processing/post/DADF5_postResults.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 no BOM -*-
+
+import os
+import numpy as np
+import argparse
+import damask
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+parser = argparse.ArgumentParser()
+
+#ToDo:  We need to decide on a way of handling arguments of variable lentght
+#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python
+
+#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
+parser.add_argument('filenames', nargs='+',
+                    help='DADF5 files')
+parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
+                    help='name of subdirectory to hold output')
+
+options = parser.parse_args()
+
+options.labels = ['Fe','Fp','xi_sl']
+
+# --- loop over input files ------------------------------------------------------------------------
+
+for filename in options.filenames:
+  results = damask.DADF5(filename)
+  
+  if not results.structured: continue
+  delta = results.size/results.grid*0.5
+  x, y, z = np.meshgrid(np.linspace(delta[2],results.size[2]-delta[2],results.grid[2]),
+                        np.linspace(delta[1],results.size[1]-delta[1],results.grid[1]),
+                        np.linspace(delta[0],results.size[0]-delta[0],results.grid[0]),
+                        indexing = 'ij')
+
+  coords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) 
+  
+  for i,inc in enumerate(results.increments):
+    print('Output step {}/{}'.format(i+1,len(results.increments)))
+
+    header = '1 header\n'
+    
+    data = np.array([inc['inc'] for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])
+    header+= 'inc'
+    
+    data = np.concatenate((data,np.array([j+1 for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])),1)
+    header+=' node'
+
+    coords = coords.reshape([np.product(results.grid),3])
+    data = np.concatenate((data,coords),1)
+    header+=' 1_pos 2_pos 3_pos'
+        
+    results.active['increments'] = [inc]
+    for label in options.labels:
+      for o in results.c_output_types:
+        results.active['c_output_types'] = [o]
+        for c in results.constituents:
+          results.active['constituents'] = [c]
+          x = results.get_dataset_location(label)
+          if len(x) == 0:
+            continue
+          label = x[0].split('/')[-1]
+          array = results.read_dataset(x,0)
+          d = np.product(np.shape(array)[1:])
+          array = np.reshape(array,[np.product(results.grid),d])
+          data = np.concatenate((data,array),1)
+          
+          header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
+
+
+    dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
+    try:
+      os.mkdir(dirname)
+    except FileExistsError:
+      pass
+    file_out = '{}_inc{:04d}.txt'.format(filename.split('.')[0],inc['inc'])
+    np.savetxt(os.path.join(dirname,file_out),data,header=header,comments='')

processing/post/DADF5_vtk_cells.py

@@ -21,6 +21,8 @@ parser = argparse.ArgumentParser()
 #parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
 parser.add_argument('filenames', nargs='+',
                     help='DADF5 files')
+parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
+                    help='name of subdirectory to hold output')
 
 options = parser.parse_args()
 
@@ -80,12 +82,17 @@ for filename in options.filenames:
     if results.structured:
       writer = vtk.vtkXMLRectilinearGridWriter()
 
+
+    dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
+    try:
+      os.mkdir(dirname)
+    except FileExistsError:
+      pass
+    file_out = '{}_inc{:04d}.{}'.format(filename.split('.')[0],inc['inc'],writer.GetDefaultFileExtension())
+    
     writer.SetCompressorTypeToZLib()
     writer.SetDataModeToBinary()
-    writer.SetFileName(os.path.join(os.path.split(filename)[0],
+    writer.SetFileName(os.path.join(dirname,file_out))
-                                    os.path.splitext(os.path.split(filename)[1])[0] +
-                                    '_inc{:04d}'.format(i) +                                        # ToDo: adjust to length of increments
-                                    '.' + writer.GetDefaultFileExtension()))
     if results.structured:
       writer.SetInputData(rGrid)
     

python/damask/dadf5.py

@@ -20,14 +20,14 @@ class DADF5():
       
     with h5py.File(filename,'r') as f:
       
-      if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 1:
+      if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 2:
         raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
     
-      self.structured = 'grid' in f['mapping'].attrs.keys()
+      self.structured = 'grid' in f['geometry'].attrs.keys()
     
       if self.structured:
-        self.grid = f['mapping'].attrs['grid']
+        self.grid = f['geometry'].attrs['grid']
-        self.size = f['mapping'].attrs['size']
+        self.size = f['geometry'].attrs['size']
         
       r=re.compile('inc[0-9]+')
       self.increments = [{'inc':  int(u[3:]),

src/CPFEM.f90

@@ -47,7 +47,8 @@ module CPFEM
 
  public :: &
    CPFEM_general, &
-   CPFEM_initAll
+   CPFEM_initAll, &
+   CPFEM_results
 
 contains
 
@@ -633,4 +634,35 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
 
 end subroutine CPFEM_general
 
+
+!--------------------------------------------------------------------------------------------------
+!> @brief triggers writing of the results
+!--------------------------------------------------------------------------------------------------
+subroutine CPFEM_results(inc,time)
+ use prec, only: &
+   pInt
+#ifdef DAMASK_HDF5
+ use results
+ use HDF5_utilities
+#endif
+ use constitutive, only: &
+   constitutive_results
+ use crystallite, only: &
+   crystallite_results
+
+ implicit none
+ integer(pInt), intent(in) :: inc
+ real(pReal),   intent(in) :: time
+
+#ifdef DAMASK_HDF5
+ call results_openJobFile
+ call results_addIncrement(inc,time)
+ call constitutive_results
+ call crystallite_results
+ call results_removeLink('current') ! ToDo: put this into closeJobFile
+ call results_closeJobFile
+#endif
+
+end subroutine CPFEM_results
+
 end module CPFEM

src/CPFEM2.f90

@@ -290,6 +290,7 @@ subroutine CPFEM_age()
 
 end subroutine CPFEM_age
 
+
 !--------------------------------------------------------------------------------------------------
 !> @brief triggers writing of the results
 !--------------------------------------------------------------------------------------------------

src/DAMASK_interface.f90

@@ -45,7 +45,7 @@ contains
 !> @brief initializes the solver by interpreting the command line arguments. Also writes
 !! information on computation to screen
 !--------------------------------------------------------------------------------------------------
-subroutine DAMASK_interface_init()
+subroutine DAMASK_interface_init
   use, intrinsic :: &
     iso_fortran_env
   use, intrinsic :: &
@@ -130,11 +130,11 @@ subroutine DAMASK_interface_init()
   call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,mpi_err)
   if (mpi_err /= 0) call quit(1)
   if (threadLevel<MPI_THREAD_FUNNELED) then
-    write(6,'(a)') ' MPI library does not support OpenMP'
+    write(6,'(/,a)') ' ERROR: MPI library does not support OpenMP'
     call quit(1)
   endif
 #endif
-  call PETScInitialize(PETSC_NULL_CHARACTER,petsc_err)                                              ! according to PETSc manual, that should be the first line in the code
+  call PETScInitializeNoArguments(petsc_err)                                                        ! according to PETSc manual, that should be the first line in the code
   CHKERRQ(petsc_err)                                                                                ! this is a macro definition, it is case sensitive
 
   call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,mpi_err)
@@ -144,11 +144,11 @@ subroutine DAMASK_interface_init()
 
   mainProcess: if (worldrank == 0) then
     if (output_unit /= 6) then
-      write(output_unit,'(a)') ' STDOUT != 6'
+      write(output_unit,'(/,a)') ' ERROR: STDOUT != 6'
       call quit(1)
     endif
     if (error_unit /= 0) then
-      write(output_unit,'(a)') ' STDERR != 0'
+      write(output_unit,'(/,a)') ' ERROR: STDERR != 0'
       call quit(1)
     endif
   else mainProcess
@@ -254,14 +254,14 @@ subroutine DAMASK_interface_init()
         call get_command_argument(i+1,arg)
         read(arg,*,iostat=stat) interface_restartInc
         if (interface_restartInc < 0 .or. stat /=0) then
-          write(6,'(a)') ' Could not parse restart increment: '//trim(arg)
+          write(6,'(/,a)') ' ERROR: Could not parse restart increment: '//trim(arg)
           call quit(1)
         endif
     end select
   enddo
 
   if (len_trim(loadcaseArg) == 0 .or. len_trim(geometryArg) == 0) then
-    write(6,'(a)') ' Please specify geometry AND load case (-h for help)'
+    write(6,'(/,a)') ' ERROR: Please specify geometry AND load case (-h for help)'
     call quit(1)
   endif
 
@@ -324,7 +324,7 @@ subroutine setWorkingDirectory(workingDirectoryArg)
   workingDirectory = trim(rectifyPath(workingDirectory))
   error = setCWD(trim(workingDirectory))
   if(error) then
-    write(6,'(a20,a,a16)') ' Working directory "',trim(workingDirectory),'" does not exist'
+    write(6,'(/,a)') ' ERROR: Working directory "'//trim(workingDirectory)//'" does not exist'
     call quit(1)
   endif
 
@@ -374,7 +374,7 @@ character(len=1024) function getGeometryFile(geometryParameter)
 
   inquire(file=trim(getGeometryFile), exist=file_exists)
   if (.not. file_exists) then
-    write(6,'(a)') ' Geometry file does not exists ('//trim(getGeometryFile)//')'
+    write(6,'(/,a)') ' ERROR: Geometry file does not exists ('//trim(getGeometryFile)//')'
     call quit(1)
   endif
 
@@ -399,7 +399,7 @@ character(len=1024) function getLoadCaseFile(loadCaseParameter)
 
   inquire(file=trim(getLoadCaseFile), exist=file_exists)
   if (.not. file_exists) then
-    write(6,'(a)') ' Load case file does not exists ('//trim(getLoadCaseFile)//')'
+    write(6,'(/,a)') ' ERROR: Load case file does not exists ('//trim(getLoadCaseFile)//')'
     call quit(1)
   endif
 

src/DAMASK_marc.f90

@@ -16,6 +16,7 @@
 !> @details  Marc subroutines used:
 !> @details   - hypela2
 !> @details   - plotv
+!> @details   - uedinc
 !> @details   - flux
 !> @details   - quit
 !> @details  Marc common blocks included:
@@ -273,26 +274,20 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
        outdatedByNewInc = .false.                                                                   ! no aging of state
        calcMode = .false.                                                                           ! pretend last step was collection
        lastLovl = lovl                                                                              ! pretend that this is NOT the first after a lovl change
-       !$OMP CRITICAL (write2out)
+       write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
-         write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
+       flush(6)
-         flush(6)
-       !$OMP END CRITICAL (write2out)
      else if (inc - theInc > 1) then                                                                ! >> restart of broken analysis <<
        lastIncConverged = .false.                                                                   ! no Jacobian backup
        outdatedByNewInc = .false.                                                                   ! no aging of state
        calcMode = .true.                                                                            ! pretend last step was calculation
-       !$OMP CRITICAL (write2out)
+       write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
-         write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
+       flush(6)
-         flush(6)
-       !$OMP END CRITICAL (write2out)
      else                                                                                           ! >> just the next inc <<
        lastIncConverged = .true.                                                                    ! request Jacobian backup
        outdatedByNewInc = .true.                                                                    ! request aging of state
        calcMode = .true.                                                                            ! assure last step was calculation
-       !$OMP CRITICAL (write2out)
+       write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
-         write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
+       flush(6)
-         flush(6)
-       !$OMP END CRITICAL (write2out)
      endif
    else if ( timinc < theDelta ) then                                                               ! >> cutBack <<
      lastIncConverged = .false.                                                                     ! no Jacobian backup
@@ -300,10 +295,8 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
      terminallyIll = .false.
      cycleCounter = -1                                                                              ! first calc step increments this to cycle = 0
      calcMode = .true.                                                                              ! pretend last step was calculation
-     !$OMP CRITICAL (write2out)
+     write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
-       write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
+     flush(6)
-       flush(6)
-     !$OMP END CRITICAL (write2out)
    endif                                                                                            ! convergence treatment end
 
 
@@ -365,7 +358,6 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
  lastLovl = lovl                                                                                    ! record lovl
 
  call CPFEM_general(computationMode,usePingPong,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
-
 !     Mandel: 11, 22, 33, SQRT(2)*12, SQRT(2)*23, SQRT(2)*13
 !     Marc:   11, 22, 33, 12, 23, 13
 !     Marc:   11, 22, 33, 12
@@ -407,6 +399,26 @@ subroutine flux(f,ts,n,time)
  end subroutine flux
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief sets user defined output variables for Marc
+!> @details select a variable contour plotting (user subroutine).
+!--------------------------------------------------------------------------------------------------
+subroutine uedinc(inc,incsub)
+  use prec, only: &
+    pReal, &
+    pInt
+  use CPFEM, only: &
+    CPFEM_results
+
+  implicit none
+  integer, intent(in) :: inc, incsub
+#include QUOTE(PASTE(./MarcInclude/creeps,Marc4DAMASK))                                             ! creeps is needed for timinc (time increment)
+
+  call CPFEM_results(inc,cptim)
+
+end subroutine uedinc
+
+
 !--------------------------------------------------------------------------------------------------
 !> @brief sets user defined output variables for Marc
 !> @details select a variable contour plotting (user subroutine).

src/grid/DAMASK_grid.f90

@@ -77,6 +77,7 @@ program DAMASK_spectral
  use grid_mech_FEM
  use grid_damage_spectral
  use grid_thermal_spectral
+ use HDF5_utilities
  use results
 
  implicit none
@@ -155,8 +156,6 @@ program DAMASK_spectral
  write(6,'(/,a)') ' Shanthraj et al., Handbook of Mechanics of Materials, 2019'
  write(6,'(a)')   ' https://doi.org/10.1007/978-981-10-6855-3_80'
 
- call results_openJobFile()
- call results_closeJobFile()
 !--------------------------------------------------------------------------------------------------
 ! initialize field solver information
  nActiveFields = 1
@@ -301,7 +300,7 @@ program DAMASK_spectral
 
    reportAndCheck: if (worldrank == 0) then
      write (loadcase_string, '(i6)' ) currentLoadCase
-     write(6,'(1x,a,i6)') 'load case: ', currentLoadCase
+     write(6,'(/,1x,a,i6)') 'load case: ', currentLoadCase
      if (.not. newLoadCase%followFormerTrajectory) write(6,'(2x,a)') 'drop guessing along trajectory'
      if (newLoadCase%deformation%myType == 'l') then
        do j = 1_pInt, 3_pInt
@@ -348,10 +347,10 @@ program DAMASK_spectral
      if (newLoadCase%time < 0.0_pReal) errorID = 834_pInt                                           ! negative time increment
      write(6,'(2x,a,f12.6)') 'time:       ', newLoadCase%time
      if (newLoadCase%incs < 1_pInt)    errorID = 835_pInt                                           ! non-positive incs count
-     write(6,'(2x,a,i5)')    'increments: ', newLoadCase%incs
+     write(6,'(2x,a,i5)')  'increments: ', newLoadCase%incs
      if (newLoadCase%outputfrequency < 1_pInt)  errorID = 836_pInt                                  ! non-positive result frequency
-     write(6,'(2x,a,i5)')    'output  frequency:  ', newLoadCase%outputfrequency
+     write(6,'(2x,a,i5)')  'output  frequency:  ', newLoadCase%outputfrequency
-     write(6,'(2x,a,i5,/)')  'restart frequency:  ', newLoadCase%restartfrequency
+     write(6,'(2x,a,i5)')  'restart frequency:  ', newLoadCase%restartfrequency
      if (errorID > 0_pInt) call IO_error(error_ID = errorID, ext_msg = loadcase_string)             ! exit with error message
    endif reportAndCheck
    loadCases = [loadCases,newLoadCase]                                                              ! load case is ok, append it
@@ -359,8 +358,9 @@ program DAMASK_spectral
  close(fileUnit)
 
  call results_openJobFile
- call results_addAttribute('grid',grid,'mapping')
+ call HDF5_closeGroup(results_addGroup('geometry'))
- call results_addAttribute('size',geomSize,'mapping')
+ call results_addAttribute('grid',grid,'geometry')
+ call results_addAttribute('size',geomSize,'geometry')
  call results_closeJobFile
 
 !--------------------------------------------------------------------------------------------------

src/quit.f90

@@ -34,13 +34,13 @@ subroutine quit(stop_id)
 #endif
  
  call date_and_time(values = dateAndTime)
- write(6,'(/,a)') 'DAMASK terminated on:'
+ write(6,'(/,a)') ' DAMASK terminated on:'
- write(6,'(a,2(i2.2,a),i4.4)') 'Date:               ',dateAndTime(3),'/',&
+ write(6,'(a,2(i2.2,a),i4.4)') ' Date:               ',dateAndTime(3),'/',&
-                                                      dateAndTime(2),'/',&
+                                                       dateAndTime(2),'/',&
-                                                      dateAndTime(1)
+                                                       dateAndTime(1)
- write(6,'(a,2(i2.2,a),i2.2)') 'Time:               ',dateAndTime(5),':',&
+ write(6,'(a,2(i2.2,a),i2.2)') ' Time:               ',dateAndTime(5),':',&
-                                                      dateAndTime(6),':',&
+                                                       dateAndTime(6),':',&
-                                                      dateAndTime(7)
+                                                       dateAndTime(7)
 
  if (stop_id == 0 .and. ierr == 0 .and. error == 0) stop 0                                          ! normal termination
  if (stop_id == 2 .and. ierr == 0 .and. error == 0) stop 2                                          ! not all incs converged

src/results.f90

@@ -66,9 +66,9 @@ subroutine results_init
   write(6,'(a)')   ' https://doi.org/10.1007/s40192-018-0118-7'
 
   resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
-  call HDF5_addAttribute(resultsFile,'DADF5-version',0.1)
+  call HDF5_addAttribute(resultsFile,'DADF5-version',0.2)
   call HDF5_addAttribute(resultsFile,'DADF5-major',0)
-  call HDF5_addAttribute(resultsFile,'DADF5-minor',1)
+  call HDF5_addAttribute(resultsFile,'DADF5-minor',2)
   call HDF5_addAttribute(resultsFile,'DAMASK',DAMASKVERSION)
   call get_command(commandLine)
   call HDF5_addAttribute(resultsFile,'call',trim(commandLine))
@@ -103,7 +103,7 @@ end subroutine results_closeJobFile
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief closes the results file
+!> @brief creates the group of increment and adds time as attribute to the file
 !--------------------------------------------------------------------------------------------------
 subroutine results_addIncrement(inc,time)
  
@@ -250,6 +250,8 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &
@@ -277,6 +279,8 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &
@@ -305,6 +309,8 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &
@@ -333,6 +339,8 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &
@@ -347,7 +355,7 @@ end subroutine results_writeVectorDataset_int
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a vector dataset in a group
+!> @brief stores a tensor dataset in a group
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit)
 
@@ -361,6 +369,8 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &
@@ -375,7 +385,7 @@ end subroutine results_writeTensorDataset_int
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief stores a vector dataset in a group
+!> @brief stores a scalar dataset in a group
 !--------------------------------------------------------------------------------------------------
 subroutine results_writeScalarDataset_rotation(group,dataset,label,description,lattice_structure)
   use rotations, only: &
@@ -391,6 +401,8 @@ subroutine results_writeScalarDataset_rotation(group,dataset,label,description,l
   
 #ifdef PETSc
   call HDF5_write(groupHandle,dataset,label,.true.)
+#else
+  call HDF5_write(groupHandle,dataset,label,.false.)
 #endif
   
   if (HDF5_objectExists(groupHandle,label)) &