Merge branch 'housekeeping_2025-10-22' into 'development'

housekeeping 2025-10-22

See merge request damask/DAMASK!1150

Author: dmentock

.gitlab-ci.yml

@@ -12,8 +12,8 @@ variables:
   GIT_SUBMODULE_STRATEGY: normal
   # Shortcut names
   MARC_VERSION: '2025.1'
-  PETSC_GCC_LATEST: '2025.09.30'
-  PETSC_ONEAPI_LATEST: '2025.09.30'
+  PETSC_GCC_LATEST: '2025.11.13'
+  PETSC_ONEAPI_LATEST: '2025.11.13'
   PYTHON_LATEST: '2025.06.05'
 
 ####################################################################################################

PRIVATE

@@ -232,6 +232,20 @@ def from_image_data(cells: IntSequence,
         -------
         new : damask.VTK
             VTK-based geometry without nodal or cell data.
+
+        Examples
+        --------
+        Create image data with larger spacing along z-direction:
+
+        >>> import damask
+        >>> cells = (16,8,4)
+        >>> size = (1.0,0.5,.4)
+        >>> print(v := damask.VTK.from_image_data(cells=cells,size=size))
+        vtkImageData
+        <BLANKLINE>
+        # cells: 512
+        <BLANKLINE>
+        # points: 765
         """
         vtk_data = vtkImageData()
         vtk_data.SetDimensions(*(np.array(cells)+1))
@@ -267,6 +281,21 @@ def from_unstructured_grid(nodes: np.ndarray,
         -------
         new : damask.VTK
             VTK-based geometry without nodal or cell data.
+
+        Examples
+        --------
+        Create a first-order tetrahedron:
+
+        >>> import damask
+        >>> import numpy as np
+        >>> nodes = np.array([[0,0,0],[1,0,0],[1,1,0],[0,0,1]])
+        >>> connectivity = np.array([[0,1,2,3]])
+        >>> print(v := damask.VTK.from_unstructured_grid(nodes,connectivity,'TETRAHEDRON'))
+        vtkUnstructuredGrid
+        <BLANKLINE>
+        # cells: 1
+        <BLANKLINE>
+        # points: 4
         """
         vtk_nodes = vtkPoints()
         vtk_nodes.SetData(numpy_to_vtk(np.ascontiguousarray(nodes)))
@@ -529,6 +558,24 @@ def set(self,
         Notes
         -----
         If the number of cells equals the number of points, the data is added to both.
+
+
+        Examples
+        --------
+        Add a constant tensor field called 'F' to image data:
+
+        >>> import numpy as np
+        >>> import damask
+        >>> cells = (16,8,16)
+        >>> size = (1.0,0.5,1.0)
+        >>> v = damask.VTK.from_image_data(cells=cells,size=size)
+        >>> print(v := v.set(label='F',data=np.broadcast_to(np.eye(3),(np.prod(cells),3,3))))
+        vtkImageData
+        <BLANKLINE>
+        # cells: 2048
+          - F
+        <BLANKLINE>
+        # points: 2601
         """
 
         def _add_array(vtk_data,

python/damask/_vtk.py

@@ -372,7 +372,6 @@ subroutine IO_error_new(error_ID, &
                         info_1,info_2,info_3,info_4,info_5,info_6,info_7,info_8,info_9, &
                         emph)
 
-
   integer(pI16),      intent(in) :: error_ID        ! should go back to default integer after completed migration.
   class(*), optional, intent(in) :: info_1,info_2,info_3,info_4,info_5,info_6,info_7,info_8,info_9
   integer, dimension(:), optional, intent(in) :: emph                                               !< which info(s) to emphasize
@@ -595,7 +594,6 @@ subroutine IO_warning_new(warning_ID, &
                           info_1,info_2,info_3,info_4,info_5,info_6,info_7,info_8,info_9, &
                           emph)
 
-
   integer(pI16),      intent(in) :: warning_ID        ! should go back to default integer after completed migration.
   class(*), optional, intent(in) :: info_1,info_2,info_3,info_4,info_5,info_6,info_7,info_8,info_9
   integer, dimension(:), optional, intent(in) :: emph                                              !< which info(s) to emphasize
@@ -969,15 +967,15 @@ subroutine panel(paneltype,ID,msg, &
 
   end select
 
-  info_extra = as_str(info_1,is_emph(1)) &
-            // as_str(info_2,is_emph(2)) &
-            // as_str(info_3,is_emph(3)) &
-            // as_str(info_4,is_emph(4)) &
-            // as_str(info_5,is_emph(5)) &
-            // as_str(info_6,is_emph(6)) &
-            // as_str(info_7,is_emph(7)) &
-            // as_str(info_8,is_emph(8)) &
-            // as_str(info_9,is_emph(9))
+  info_extra = as_str(info_1,is_emph(1,emph)) &
+            // as_str(info_2,is_emph(2,emph)) &
+            // as_str(info_3,is_emph(3,emph)) &
+            // as_str(info_4,is_emph(4,emph)) &
+            // as_str(info_5,is_emph(5,emph)) &
+            // as_str(info_6,is_emph(6,emph)) &
+            // as_str(info_7,is_emph(7,emph)) &
+            // as_str(info_8,is_emph(8,emph)) &
+            // as_str(info_9,is_emph(9,emph))
 
 
   !$OMP CRITICAL (write2out)
@@ -1006,55 +1004,61 @@ subroutine panel(paneltype,ID,msg, &
   flush(IO_STDERR)
   !$OMP END CRITICAL (write2out)
 
-  contains
+end subroutine panel
 
-    !-----------------------------------------------------------------------------------------------
-    !> @brief Convert to string with white space prefix and optional emphasis.
-    !-----------------------------------------------------------------------------------------------
-    function as_str(info,emph)
-
-      character(len=:), allocatable :: as_str
-      class(*), optional, intent(in) :: info
-      logical, intent(in) :: emph
-
-
-      if (present(info)) then
-        select type(info)
-          type is (character(*))
-            as_str = info
-          type is (integer)
-            as_str = IO_intAsStr(info)
-          type is (real(pREAL))
-            as_str = IO_realAsStr(info)
-          class default
-            error stop 'cannot convert info argument to string'
-        end select
-
-        if (emph) then
-          if (IO_isaTTY(IO_STDERR)) then
-            as_str = IO_EMPH//as_str//IO_FORMATRESET
-          else
-            as_str = IO_QUOTES(2:2)//as_str//IO_QUOTES(2:2)
-          end if
-        end if
-        as_str = ' '//as_str
-      else
-        as_str = ''
-      end if
 
-    end function as_str
+!-----------------------------------------------------------------------------------------------
+!> @brief Convert to string with white space prefix and optional emphasis.
+!-----------------------------------------------------------------------------------------------
+function as_str(info,emph)
+
+  character(len=:), allocatable :: as_str
+  class(*), optional, intent(in) :: info
+  logical, intent(in) :: emph
+
 
-    pure logical function is_emph(i)
-      integer, intent(in) :: i
+  if (present(info)) then
+    select type(info)
+      type is (character(*))
+        as_str = info
+      type is (integer)
+        as_str = IO_intAsStr(info)
+      type is (real(pREAL))
+        as_str = IO_realAsStr(info)
+      class default
+        error stop 'cannot convert info argument to string'
+    end select
 
-      if (present(emph)) then
-        is_emph = any(emph == i)
+    if (emph) then
+      if (IO_isaTTY(IO_STDERR)) then
+        as_str = IO_EMPH//as_str//IO_FORMATRESET
       else
-        is_emph = .false.
+        as_str = IO_QUOTES(2:2)//as_str//IO_QUOTES(2:2)
       end if
-    end function is_emph
+    end if
+    as_str = ' '//as_str
+  else
+    as_str = ''
+  end if
 
-end subroutine panel
+end function as_str
+
+!-----------------------------------------------------------------------------------------------
+!> @brief Convert to string with white space prefix and optional emphasis.
+!-----------------------------------------------------------------------------------------------
+pure logical function is_emph(idx,emph)
+
+  integer, intent(in) :: idx
+  integer, dimension(:), optional, intent(in) :: emph                                               !< which info(s) to emphasize
+
+
+  if (present(emph)) then
+    is_emph = any(emph == idx)
+  else
+    is_emph = .false.
+  end if
+
+end function is_emph
 
 
 end module IO

src/IO.f90

@@ -303,7 +303,7 @@ subroutine discretization_mesh_init()
                            reshape(x_p,[3,int(mesh_maxNips*mesh_nElems)]), &
                            x_n)
 
-#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>24)
+#if (PETSC_VERSION_MINOR>24 || (PETSC_VERSION_MINOR==24 && PETSC_VERSION_SUBMINOR>=1))
   call writeGeometry(reshape(x_p,[3,int(mesh_maxNips*mesh_nElems)]),x_n,T_e)
 #else
   call writeGeometry(reshape(x_p,[3,int(mesh_maxNips*mesh_nElems)]),x_n)
@@ -561,7 +561,7 @@ subroutine build_nodes_and_connectivity(x_n, p_s)
 #if (PETSC_VERSION_MINOR>24 || (PETSC_VERSION_MINOR==24 && PETSC_VERSION_SUBMINOR>=1))
   PetscCall(DMPlexGetHeightStratum(coordDM, 0_pPETSCINT, cellStart, cellEnd, ierr))
   PetscCall(DMPlexGetCellType(coordDM, cellStart, cell_type, ierr))
-  node_map = PETSc_to_VTK_node_order(cell_type, p_s)
+  node_map = PETSc_to_VTK_node_order(cell_type, int(p_s))
 
   allocate(T_e(nCellNodes, cellEnd - cellStart), source = -1_pPETSCINT)
   do cell = cellStart, cellEnd - 1_pPETSCINT

src/mesh/discretization_mesh.f90

@@ -62,7 +62,8 @@ module phase
     DAMAGE_ISOBRITTLE, &
     DAMAGE_ANISOBRITTLE, &
     THERMAL_SOURCE_DISSIPATION, &
-    THERMAL_SOURCE_EXTERNALHEAT
+    THERMAL_SOURCE_EXTERNALHEAT, &
+    CHEMICAL_QUADENERGY
   end enum
 
 

src/phase.f90

@@ -7,12 +7,7 @@
     real(pREAL) ::                 V_m = 0.0_pREAL                                                  !< molar volume
   end type tChemicalParameters
 
-  enum, bind(c); enumerator :: &
-    CHEMICAL_UNDEFINED_ID ,&
-    CHEMICAL_QUADENERGY_ID
-  end enum
-
-  integer(kind(CHEMICAL_UNDEFINED_ID)),  dimension(:), allocatable :: &
+  integer(kind(UNDEFINED)),  dimension(:), allocatable :: &
     chemical_energy
 
   type :: tDataContainer             ! ?? not very telling name. Better: "fieldQuantities" ??
@@ -85,8 +80,7 @@ module subroutine chemical_init(phases)
   print'(/,a)', ' <<<+-  phase:chemical init  -+>>>'
 
   allocate(current(size(phases)))
-  !allocate(chemicalState(size(phases)))
-  allocate(chemical_energy(size(phases)),source=CHEMICAL_UNDEFINED_ID)
+  allocate(chemical_energy(size(phases)),source=UNDEFINED)
   allocate(param(size(phases)))
 
   phases => config_material%get_dict('phase')
@@ -97,11 +91,11 @@ module subroutine chemical_init(phases)
   end do
 
   !initialize chemical energy model
-  where(quadEnergy_init())       chemical_energy = CHEMICAL_QUADENERGY_ID
+  where(quadEnergy_init())       chemical_energy = CHEMICAL_QUADENERGY
 
   do ph = 1,size(phases)
     Nmembers = count(material_ID_phase == ph)
-    if (chemical_energy(ph) == CHEMICAL_UNDEFINED_ID) then
+    if (chemical_energy(ph) == UNDEFINED) then
       allocate(current(ph)%C(1,Nmembers),source=0.0_pREAL)
       allocate(current(ph)%dot_C(1,Nmembers),source=0.0_pREAL)
       allocate(current(ph)%C0(1,Nmembers),source=0.0_pREAL)
@@ -116,6 +110,7 @@ end subroutine chemical_init
 !< @brief Calculates composition for constituent.
 !----------------------------------------------------------------------------------------------
 module function phase_calculate_composition(mu,co,ce) result(conc)
+
   real(pREAL), intent(in), dimension(:) :: mu
   integer, intent(in) :: co, ce
   real(pREAL), dimension(:), allocatable :: conc
@@ -124,49 +119,51 @@ module function phase_calculate_composition(mu,co,ce) result(conc)
   integer :: &
     ph, en
 
+
   ph = material_ID_phase(co,ce)
   en = material_entry_phase(co,ce)
 
   mu_chemical = mu
   chemicalEnergyType: select case (chemical_energy(ph))
 
-    case (CHEMICAL_QUADENERGY_ID)
-      conc =  quadEnergy_composition(mu_chemical,ph,en)
-    case default
-      conc = [0.0_pREAL]
+    case (CHEMICAL_QUADENERGY)
+      conc = quadEnergy_composition(mu_chemical,ph,en)
 
   end select chemicalEnergyType
 
 end function phase_calculate_composition
 
 
 !----------------------------------------------------------------------------------------------
-!< @brief Retrieves composition for constituent
+!< @brief Retrieves composition for constituent.
 !----------------------------------------------------------------------------------------------
 module function phase_get_mobility(co,ce) result(mobility)
+
   integer, intent(in) :: co, ce
   real(pREAL), dimension(:,:),allocatable :: mobility
 
   integer :: &
     ph, en
 
+
   ph = material_ID_phase(co,ce)
   en = material_entry_phase(co,ce)
 
   chemicalEnergyType: select case (chemical_energy(ph))
 
-    case (CHEMICAL_QUADENERGY_ID)
-      mobility =  quadEnergy_mobility(ph,en)
+    case (CHEMICAL_QUADENERGY)
+      mobility = quadEnergy_mobility(ph,en)
 
   end select chemicalEnergyType
 
 end function phase_get_mobility
 
 
 !----------------------------------------------------------------------------------------------
-!< @brief Retrieves composition tangent for constituent
+!< @brief Retrieves composition tangent for constituent.
 !----------------------------------------------------------------------------------------------
 module function phase_compositionTangent(mu,co,ce) result(comp_tangent)
+
   real(pREAL), dimension(:), intent(in) :: mu
   integer, intent(in) :: co, ce
   real(pREAL), dimension(:,:),allocatable :: comp_tangent
@@ -175,14 +172,15 @@ module function phase_compositionTangent(mu,co,ce) result(comp_tangent)
   integer :: &
     ph, en
 
+
   ph = material_ID_phase(co,ce)
   en = material_entry_phase(co,ce)
 
   mu_chemical = mu
   chemicalEnergyType: select case (chemical_energy(ph))
 
-    case (CHEMICAL_QUADENERGY_ID)
-      comp_tangent =  quadEnergy_compositionTangent(mu_chemical,ph,en)
+    case (CHEMICAL_QUADENERGY)
+      comp_tangent = quadEnergy_compositionTangent(mu_chemical,ph,en)
 
   end select chemicalEnergyType
 
@@ -212,12 +210,12 @@ module subroutine chemical_result(group,ph)
   integer,          intent(in) :: ph
 
 
-  if (chemical_energy(ph) /= CHEMICAL_UNDEFINED_ID) &
+  if (chemical_energy(ph) /= UNDEFINED) &
     call result_closeGroup(result_addGroup(group//'chemical'))
 
   chemicalEnergyType: select case (chemical_energy(ph))
 
-    case (CHEMICAL_QUADENERGY_ID)
+    case (CHEMICAL_QUADENERGY)
       call quadEnergy_results(ph,current(ph)%C,group//'chemical/')
 
   end select chemicalEnergyType