Merge branch '404-units-of-size-and-origin-missing' into 'development'

DADF5 1.1

Closes #404

See merge request damask/DAMASK!946

python/damask/_result.py

@@ -2113,11 +2113,16 @@ def export_DADF5(self,
  Names of the datasets to export.
  Defaults to '*', in which case all visible datasets are exported.
  mapping : numpy.ndarray of int, shape (:,:,:), optional
- Indices for regridding.
+ Indices for regridding. Only applicable for grid
+ solver results.
 
  """
  if Path(fname).expanduser().absolute() == self.fname:
- raise PermissionError(f'cannot overwrite {self.fname}')
+ raise PermissionError(f'cannot overwrite "{self.fname}"')
+
+ if mapping is not None and not self.structured:
+ raise PermissionError('cannot regrid unstructured mesh')
+
 
  def cp(path_in,path_out,label,mapping):
  if mapping is None:
@@ -2135,7 +2140,11 @@ def cp(path_in,path_out,label,mapping):
  if mapping is not None:
  cells = mapping.shape
  mapping_flat = mapping.flatten(order='F')
+
  f_out['geometry'].attrs['cells'] = cells
+ if self.version_major == 1 and self.version_minor > 0:
+ f_out['geometry']['cells'][...] = cells
+
  f_out.create_group('cell_to') # ToDo: attribute missing
  mappings = {'phase':{},'homogenization':{}} # type: ignore
 

src/HDF5_utilities.f90

@@ -981,7 +981,7 @@ end subroutine HDF5_read_int5
 
 #if defined(__GFORTRAN__)
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 1 dimension
+!> @brief Write dataset of type real with 1 dimension.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real1(dataset,loc_id,datasetName,parallel)
 
@@ -1018,7 +1018,7 @@ subroutine HDF5_write_real1(dataset,loc_id,datasetName,parallel)
 end subroutine HDF5_write_real1
 
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 2 dimensions
+!> @brief Write dataset of type real with 2 dimensions.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real2(dataset,loc_id,datasetName,parallel)
 
@@ -1055,7 +1055,7 @@ subroutine HDF5_write_real2(dataset,loc_id,datasetName,parallel)
 end subroutine HDF5_write_real2
 
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 3 dimensions
+!> @brief Write dataset of type real with 3 dimensions.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real3(dataset,loc_id,datasetName,parallel)
 
@@ -1092,7 +1092,7 @@ subroutine HDF5_write_real3(dataset,loc_id,datasetName,parallel)
 end subroutine HDF5_write_real3
 
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 4 dimensions
+!> @brief Write dataset of type real with 4 dimensions.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real4(dataset,loc_id,datasetName,parallel)
 
@@ -1130,7 +1130,7 @@ end subroutine HDF5_write_real4
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 5 dimensions
+!> @brief Write dataset of type real with 5 dimensions.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real5(dataset,loc_id,datasetName,parallel)
 
@@ -1169,7 +1169,7 @@ end subroutine HDF5_write_real5
 #else
 
 !--------------------------------------------------------------------------------------------------
-!> @brief write dataset of type real with 1-5 dimension
+!> @brief Write dataset of type real with 1-5 dimensions.
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_write_real(dataset,loc_id,datasetName,parallel)
 

src/grid/discretization_grid.f90

@@ -19,6 +19,8 @@ module discretization_grid
  use CLI
  use IO
  use config
+ use HDF5
+ use HDF5_utilities
  use result
  use discretization
  use geometry_plastic_nonlocal
@@ -73,6 +75,7 @@ subroutine discretization_grid_init(restart)
  displs, sendcounts
  character(len=:), allocatable :: &
  fileContent, fname
+ integer(HID_T) :: handle
 
 
  print'(/,1x,a)', '<<<+- discretization_grid init -+>>>'; flush(IO_STDOUT)
@@ -145,12 +148,19 @@ subroutine discretization_grid_init(restart)
 
 !--------------------------------------------------------------------------------------------------
 ! store geometry information for post processing
- if (.not. restart) then
- call result_openJobFile()
- call result_closeGroup(result_addGroup('geometry'))
- call result_addAttribute('cells', cells, '/geometry')
- call result_addAttribute('size', geomSize,'/geometry')
- call result_addAttribute('origin',origin, '/geometry')
+ if (.not. restart .and. worldrank == 0) then
+ call result_openJobFile(parallel=.false.)
+ handle = result_addGroup('geometry')
+ call HDF5_write(cells, handle,'cells', .false.)
+ call HDF5_write(geomSize,handle,'size', .false.)
+ call HDF5_write(origin, handle,'origin',.false.)
+ call HDF5_addAttribute(handle,'unit','1','cells')
+ call HDF5_addAttribute(handle,'unit','m³','size')
+ call HDF5_addAttribute(handle,'unit','m','origin')
+ call result_addAttribute('cells', cells, '/geometry') ! legacy for DADF5 1.x
+ call result_addAttribute('size', geomSize,'/geometry') ! legacy for DADF5 1.x
+ call result_addAttribute('origin',origin, '/geometry') ! legacy for DADF5 1.x
+ call result_closeGroup(handle)
  call result_closeJobFile()
  end if
 

src/result.f90

@@ -90,12 +90,21 @@ subroutine result_init(restart)
  if (.not. restart) then
  resultFile = HDF5_openFile(getSolverJobName()//'.hdf5','w')
  call result_addAttribute('DADF5_version_major',1)
- call result_addAttribute('DADF5_version_minor',0)
+ call result_addAttribute('DADF5_version_minor',1)
  call get_command_argument(0,commandLine)
  call result_addAttribute('creator',trim(commandLine)//' '//DAMASKVERSION)
  call result_addAttribute('created',now())
  call get_command(commandLine)
  call result_addAttribute('call',trim(commandLine))
+#ifdef DAMASK_GRID
+ call result_addAttribute('solver','grid')
+#endif
+#ifdef DAMASK_MESH
+ call result_addAttribute('solver','mesh')
+#endif
+#ifdef MARC4DAMASK
+ call result_addAttribute('solver','Marc')
+#endif
  call result_closeGroup(result_addGroup('cell_to'))
  call result_addAttribute('description','mappings to place data in space','cell_to')
  call result_closeGroup(result_addGroup('setup'))
@@ -118,7 +127,7 @@ end subroutine result_init
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief opens the result file to append data
+!> @brief Open the result file to append data.
 !--------------------------------------------------------------------------------------------------
 subroutine result_openJobFile(parallel)
 
@@ -131,7 +140,7 @@ end subroutine result_openJobFile
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief closes the result file
+!> @brief Close the result file.
 !--------------------------------------------------------------------------------------------------
 subroutine result_closeJobFile
 
@@ -141,7 +150,7 @@ end subroutine result_closeJobFile
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief creates the group of increment and adds time as attribute to the file
+!> @brief Creates a group for the increment and add time as attribute to the file.
 !--------------------------------------------------------------------------------------------------
 subroutine result_addIncrement(inc,time)
 
@@ -160,8 +169,8 @@ end subroutine result_addIncrement
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief finalize increment
-!> @details remove soft link
+!> @brief Finalize increment.
+!> @details Remove soft link.
 !--------------------------------------------------------------------------------------------------
 subroutine result_finalizeIncrement
 
@@ -478,7 +487,7 @@ end subroutine result_writeTensorDataset_int
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief adds the unique mapping from spatial position and constituent ID to results
+!> @brief Add the unique mapping from spatial position and constituent ID to results.
 !--------------------------------------------------------------------------------------------------
 subroutine result_mapping_phase(ID,entry,label)
 
@@ -631,7 +640,7 @@ end subroutine result_mapping_phase
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief adds the unique mapping from spatial position and constituent ID to results
+!> @brief Add the unique mapping from spatial position and constituent ID to results.
 !--------------------------------------------------------------------------------------------------
 subroutine result_mapping_homogenization(ID,entry,label)