Merge branch 'improvements' into 'development'

misc improvements.

See merge request damask/DAMASK!974

.gitlab/issue_templates/new_release.md

@@ -13,6 +13,7 @@ Detailed instructions for each step are documented in the [wiki](https://git.dam
    - [ ] PyPi package (wheel)
    - [ ] Arch Linux (PKGBUILD)
    - [ ] Ubuntu (Launchpad)
+   - [ ] Flatpak (Flathub)
    - Open build service
      - [ ] Debian
      - [ ] Fedora/Suse

LICENSE

@@ -1,3 +1,4 @@
+Copyright 2024 Max-Planck-Institut für Nachhaltige Materialien GmbH
 Copyright 2011-2024 Max-Planck-Institut für Eisenforschung GmbH
 
 DAMASK is free software: you can redistribute it and/or modify

README.md

@@ -21,7 +21,7 @@ The site is primarily meant to provide a forum for [Discussions](https://github.
 
 ## Contact Information
 
-Max-Planck-Institut für Eisenforschung GmbH  
+Max-Planck-Institut für Nachhaltige Materialien GmbH
 Max-Planck-Str. 1  
 40237 Düsseldorf  
 Germany  

cmake/Compiler-IntelLLVM.cmake

@@ -19,7 +19,7 @@ endif ()
 set (STANDARD_CHECK "-stand f18 -assume nostd_mod_proc_name")
 set (LINKER_FLAGS   "${LINKER_FLAGS} -shared-intel")
 # Link against shared Intel libraries instead of static ones
-set (LINKER_FLAGS   "${LINKER_FLAGS} -shared-intel -fc=ifx")
+set (LINKER_FLAGS   "${LINKER_FLAGS} -fc=ifx")
 # enforce use of ifx for MPI wrapper
 
 #------------------------------------------------------------------------------------------------

env/DAMASK.sh

@@ -27,8 +27,10 @@ cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd
 
 PATH=${DAMASK_ROOT}/bin:$PATH
 
-SOLVER=$(type -p DAMASK_grid || true 2>/dev/null)
-[ "x$SOLVER" == "x" ] && SOLVER=$(blink 'Not found!')
+SOLVER_GRID=$(type -p DAMASK_grid || true 2>/dev/null)
+[ "x$SOLVER_GRID" == "x" ] && SOLVER_GRID=$(blink 'Not found!')
+SOLVER_MESH=$(type -p DAMASK_mesh || true 2>/dev/null)
+[ "x$SOLVER_MESH" == "x" ] && SOLVER_MESH=$(blink 'Not found!')
 
 
 # currently, there is no information that unlimited stack size causes problems
@@ -42,12 +44,13 @@ ulimit -s unlimited 2>/dev/null # maximum stack size (kB)
 if [ ! -z "$PS1" ]; then
   echo
   echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
+  echo Max-Planck-Institut für Nachhaltige Materialien GmbH, Düsseldorf
   echo https://damask.mpie.de
   echo
   echo Using environment with ...
   echo "DAMASK             $DAMASK_ROOT $BRANCH"
-  echo "Grid Solver        $SOLVER"
+  echo "Grid Solver        $SOLVER_GRID"
+  echo "Mesh Solver        $SOLVER_MESH"
   if [ "x$PETSC_DIR"   != "x" ]; then
     echo -n "PETSc location     "
     [ -d $PETSC_DIR ] && echo $PETSC_DIR || blink $PETSC_DIR

env/DAMASK.zsh

@@ -17,8 +17,10 @@ cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd
 
 PATH=${DAMASK_ROOT}/bin:$PATH
 
-SOLVER=$(which DAMASK_grid || true 2>/dev/null)
-[[ "x$SOLVER" == "x" ]] && SOLVER=$(blink 'Not found!')
+SOLVER_GRID=$(which DAMASK_grid || true 2>/dev/null)
+[[ "x$SOLVER_GRID" == "x" ]] && SOLVER_GRID=$(blink 'Not found!')
+SOLVER_MESH=$(which DAMASK_mesh || true 2>/dev/null)
+[[ "x$SOLVER_MESH" == "x" ]] && SOLVER_MESH=$(blink 'Not found!')
 
 
 # currently, there is no information that unlimited stack size causes problems
@@ -32,12 +34,13 @@ ulimit -s unlimited 2>/dev/null # maximum stack size (kB)
 if [ ! -z "$PS1" ]; then
   echo
   echo Düsseldorf Advanced Materials Simulation Kit --- DAMASK
-  echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
+  echo Max-Planck-Institut für Nachhaltige Materialien GmbH, Düsseldorf
   echo https://damask.mpie.de
   echo
   echo "Using environment with ..."
   echo "DAMASK             $DAMASK_ROOT $BRANCH"
-  echo "Grid Solver        $SOLVER"
+  echo "Grid Solver        $SOLVER_GRID"
+  echo "Mesh Solver        $SOLVER_MESH"
   if [ "x$PETSC_DIR" != "x" ]; then
     echo -n "PETSc location     "
     [ -d $PETSC_DIR ] && echo $PETSC_DIR || blink $PETSC_DIR

python/damask/_crystal.py

@@ -685,13 +685,33 @@ def symmetry_operations(self) -> Rotation:
         """
         Return symmetry operations.
 
+        Notes
+        -----
+        The symmetry operations defined here only consider Rotations.
+        More specifically, for each crystal family, an enantiomorphic
+        point symmetry is selected. In case that there are multiple
+        point groups with enantiomorphic point symmetry, the one with
+        the highest order is chosen:
+
+        Overview of crystal classes and point group in Hermann-Mauguin
+        notation used for definition of symmetry operations.
+        - tricinic: 1
+        - monoclinic: 2
+        - orthorhombic: 222
+        - tetragonal: 422
+        - hexagonal: 622
+        - cubic: 432
+
+
         References
         ----------
         U.F. Kocks et al.,
-        Texture and Anisotropy:
-        Preferred Orientations in Polycrystals and their Effect on Materials Properties.
+        Texture and Anisotropy: Preferred Orientations in Polycrystals
+        and their Effect on Materials Properties.
         Cambridge University Press 1998. Table II
 
+        https://en.wikipedia.org/wiki/Crystal_system#Crystal_classes
+
         """
         _symmetry_operations: Dict[CrystalFamily, List]  = {
             'cubic':         [
@@ -719,7 +739,7 @@ def symmetry_operations(self) -> Rotation:
                               [-0.5*np.sqrt(2), 0.0,           -0.5*np.sqrt(2), 0.0            ],
                               [-0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0,            0.0            ],
                               [-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0,            0.0            ],
-                            ],
+                            ], # 432
             'hexagonal':    [
                               [ 1.0,            0.0,            0.0,            0.0            ],
                               [-0.5*np.sqrt(3), 0.0,            0.0,           -0.5            ],
@@ -733,7 +753,7 @@ def symmetry_operations(self) -> Rotation:
                               [ 0.0,            0.0,            1.0,            0.0            ],
                               [ 0.0,           -0.5,           -0.5*np.sqrt(3), 0.0            ],
                               [ 0.0,            0.5*np.sqrt(3), 0.5,            0.0            ],
-                            ],
+                            ], # 622
             'tetragonal':   [
                               [ 1.0,            0.0,            0.0,            0.0            ],
                               [ 0.0,            1.0,            0.0,            0.0            ],
@@ -743,20 +763,20 @@ def symmetry_operations(self) -> Rotation:
                               [ 0.0,           -0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0            ],
                               [ 0.5*np.sqrt(2), 0.0,            0.0,            0.5*np.sqrt(2) ],
                               [-0.5*np.sqrt(2), 0.0,            0.0,            0.5*np.sqrt(2) ],
-                            ],
+                            ], # 422
             'orthorhombic': [
                               [ 1.0,0.0,0.0,0.0 ],
                               [ 0.0,1.0,0.0,0.0 ],
                               [ 0.0,0.0,1.0,0.0 ],
                               [ 0.0,0.0,0.0,1.0 ],
-                            ],
+                            ], # 222
             'monoclinic':   [
                               [ 1.0,0.0,0.0,0.0 ],
                               [ 0.0,0.0,1.0,0.0 ],
-                            ],
+                            ], # 2
             'triclinic':    [
                               [ 1.0,0.0,0.0,0.0 ],
-                            ]}
+                            ]} # 1
         return Rotation.from_quaternion(_symmetry_operations[self.family],accept_homomorph=True)
 
 

python/damask/_geomgrid.py

@@ -476,6 +476,10 @@ def from_Laguerre_tessellation(cells: IntSequence,
         periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
+        Notes
+        -----
+        damask.seeds contains functionality for seed generation.
+
         Returns
         -------
         new : damask.GeomGrid
@@ -537,6 +541,27 @@ def from_Voronoi_tessellation(cells: IntSequence,
         new : damask.GeomGrid
             Grid-based geometry from tessellation.
 
+        Notes
+        -----
+        damask.seeds contains functionality for seed generation.
+
+        Examples
+        --------
+        Generate microstructure with three grains.
+
+        >>> import numpy as np
+        >>> import damask
+        >>> seeds = np.array([[0.30828, 0.64020, 0.65237],
+        ...                   [0.62200, 0.56858, 0.32842],
+        ...                   [0.57315, 0.94534, 0.87531]])*1e-6
+        >>> damask.GeomGrid.from_Voronoi_tessellation(cells=[10,10,10],
+        ...                                           size=[1e-6]*3,
+        ...                                           seeds=seeds)
+        cells:  10 × 10 × 10
+        size:   1e-06 × 1e-06 × 1e-06 m³
+        origin: 0.0   0.0   0.0 m
+        # materials: 3
+
         """
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
         tree = spatial.cKDTree(seeds,boxsize=size) if periodic else \
@@ -882,7 +907,7 @@ def flip(self,
 
         Invariance of flipping a (fully) mirrored grid.
 
-        >>> g.mirror('x',True) == g.mirror('x',True).flip('x')
+        >>> g.mirror('x',reflect=True) == g.mirror('x',reflect=True).flip('x')
         True
 
         """
@@ -1183,6 +1208,14 @@ def add_primitive(self,
         """
         Insert a primitive geometric object at a given position.
 
+        The shape of the object is defined as
+
+        .. math::
+
+           |x|^{2^a} + |y|^{2^b} + |z|^{2^c} < 1
+
+        where dimension = (x,y,z) and exponent = (a,b,c).
+
         Parameters
         ----------
         dimension : sequence of int or float, len (3)

src/grid/DAMASK_grid.f90

@@ -97,15 +97,15 @@ program DAMASK_grid
   type(tLoadCase), allocatable, dimension(:) :: loadCases                                           !< array of all load cases
   type(tSolutionState), allocatable, dimension(:) :: solres
   procedure(grid_mechanical_spectral_basic_init), pointer :: &
-    mechanical_init
+    grid_mechanical_init
   procedure(grid_mechanical_spectral_basic_forward), pointer :: &
-    mechanical_forward
+    grid_mechanical_forward
   procedure(grid_mechanical_spectral_basic_solution), pointer :: &
-    mechanical_solution
+    grid_mechanical_solution
   procedure(grid_mechanical_spectral_basic_updateCoords), pointer :: &
-    mechanical_updateCoords
+    grid_mechanical_updateCoords
   procedure(grid_mechanical_spectral_basic_restartWrite), pointer :: &
-    mechanical_restartWrite
+    grid_mechanical_restartWrite
 
   external :: &
     quit
@@ -160,35 +160,35 @@ program DAMASK_grid
   nActiveFields = 1
   select case (solver%get_asStr('mechanical'))
     case ('spectral_basic')
-      mechanical_init         => grid_mechanical_spectral_basic_init
-      mechanical_forward      => grid_mechanical_spectral_basic_forward
-      mechanical_solution     => grid_mechanical_spectral_basic_solution
-      mechanical_updateCoords => grid_mechanical_spectral_basic_updateCoords
-      mechanical_restartWrite => grid_mechanical_spectral_basic_restartWrite
+      grid_mechanical_init         => grid_mechanical_spectral_basic_init
+      grid_mechanical_forward      => grid_mechanical_spectral_basic_forward
+      grid_mechanical_solution     => grid_mechanical_spectral_basic_solution
+      grid_mechanical_updateCoords => grid_mechanical_spectral_basic_updateCoords
+      grid_mechanical_restartWrite => grid_mechanical_spectral_basic_restartWrite
       active_Gamma = .true.
 
     case ('spectral_polarization')
-      mechanical_init         => grid_mechanical_spectral_polarization_init
-      mechanical_forward      => grid_mechanical_spectral_polarization_forward
-      mechanical_solution     => grid_mechanical_spectral_polarization_solution
-      mechanical_updateCoords => grid_mechanical_spectral_polarization_updateCoords
-      mechanical_restartWrite => grid_mechanical_spectral_polarization_restartWrite
+      grid_mechanical_init         => grid_mechanical_spectral_polarization_init
+      grid_mechanical_forward      => grid_mechanical_spectral_polarization_forward
+      grid_mechanical_solution     => grid_mechanical_spectral_polarization_solution
+      grid_mechanical_updateCoords => grid_mechanical_spectral_polarization_updateCoords
+      grid_mechanical_restartWrite => grid_mechanical_spectral_polarization_restartWrite
       active_Gamma = .true.
 
     case ('spectral_Galerkin')
-      mechanical_init         => grid_mechanical_spectral_Galerkin_init
-      mechanical_forward      => grid_mechanical_spectral_Galerkin_forward
-      mechanical_solution     => grid_mechanical_spectral_Galerkin_solution
-      mechanical_updateCoords => grid_mechanical_spectral_Galerkin_updateCoords
-      mechanical_restartWrite => grid_mechanical_spectral_Galerkin_restartWrite
+      grid_mechanical_init         => grid_mechanical_spectral_Galerkin_init
+      grid_mechanical_forward      => grid_mechanical_spectral_Galerkin_forward
+      grid_mechanical_solution     => grid_mechanical_spectral_Galerkin_solution
+      grid_mechanical_updateCoords => grid_mechanical_spectral_Galerkin_updateCoords
+      grid_mechanical_restartWrite => grid_mechanical_spectral_Galerkin_restartWrite
       active_G = .true.
 
     case ('FEM')
-      mechanical_init         => grid_mechanical_FEM_init
-      mechanical_forward      => grid_mechanical_FEM_forward
-      mechanical_solution     => grid_mechanical_FEM_solution
-      mechanical_updateCoords => grid_mechanical_FEM_updateCoords
-      mechanical_restartWrite => grid_mechanical_FEM_restartWrite
+      grid_mechanical_init         => grid_mechanical_FEM_init
+      grid_mechanical_forward      => grid_mechanical_FEM_forward
+      grid_mechanical_solution     => grid_mechanical_FEM_solution
+      grid_mechanical_updateCoords => grid_mechanical_FEM_updateCoords
+      grid_mechanical_restartWrite => grid_mechanical_FEM_restartWrite
 
     case default
       call IO_error(error_ID = 891, ext_msg = trim(solver%get_asStr('mechanical')))
@@ -232,7 +232,7 @@ program DAMASK_grid
     end select
   end do
 
-  call mechanical_init(num_grid)
+  call grid_mechanical_init(num_grid)
   call config_numerics_deallocate()
 
 !--------------------------------------------------------------------------------------------------
@@ -302,7 +302,7 @@ program DAMASK_grid
           do field = 1, nActiveFields
             select case(ID(field))
               case(FIELD_MECH_ID)
-                call mechanical_forward (&
+                call grid_mechanical_forward (&
                         cutBack,guess,Delta_t,Delta_t_prev,t_remaining, &
                         deformation_BC = loadCases(l)%deformation, &
                         stress_BC      = loadCases(l)%stress, &
@@ -324,7 +324,7 @@ program DAMASK_grid
             do field = 1, nActiveFields
               select case(ID(field))
                 case(FIELD_MECH_ID)
-                  solres(field) = mechanical_solution(incInfo)
+                  solres(field) = grid_mechanical_solution(incInfo)
                 case(FIELD_THERMAL_ID)
                   solres(field) = grid_thermal_spectral_solution(Delta_t)
                 case(FIELD_DAMAGE_ID)
@@ -344,7 +344,7 @@ program DAMASK_grid
 ! check solution and either advance or retry with smaller timestep
 
           if (all(solres(:)%converged .and. solres(:)%stagConverged)) then                          ! converged and acceptable solution found
-            call mechanical_updateCoords()
+            call grid_mechanical_updateCoords()
             Delta_t_prev = Delta_t
             cutBack = .false.
             guess = .true.                                                                          ! start guessing after first converged (sub)inc
@@ -389,7 +389,7 @@ program DAMASK_grid
           do field = 1, nActiveFields
             select case (ID(field))
               case(FIELD_MECH_ID)
-                call mechanical_restartWrite()
+                call grid_mechanical_restartWrite()
               case(FIELD_THERMAL_ID)
                 call grid_thermal_spectral_restartWrite()
               case(FIELD_DAMAGE_ID)
@@ -538,7 +538,7 @@ function parseLoadsteps(load_steps) result(loadCases)
                  transpose(loadCases(l)%rot%asMatrix())
 
       if (loadCases(l)%r <= 0.0_pREAL) errorID = 833
-      if (loadCases(l)%t < 0.0_pREAL)  errorID = 834
+      if (loadCases(l)%t <= 0.0_pREAL) errorID = 834
       if (loadCases(l)%N < 1)          errorID = 835
       if (loadCases(l)%f_out < 1)      errorID = 836
       if (loadCases(l)%f_restart < 1)  errorID = 839

src/grid/grid_damage_spectral.f90

@@ -237,7 +237,7 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
 
   call SNESGetDM(SNES_damage,DM_damage,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(DM_damage,phi_PETSc,phi,err_PETSc)                                        ! returns 0-indexed phi
+  call DMDAVecGetArrayReadF90(DM_damage,phi_PETSc,phi,err_PETSc)                                    ! returns 0-indexed phi
   CHKERRQ(err_PETSc)
 
   stagNorm = maxval(abs(phi - phi_stagInc))
@@ -250,7 +250,7 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
 
   call homogenization_set_phi(reshape(phi,[product(cells(1:2))*cells3]))
 
-  call DMDAVecRestoreArrayF90(DM_damage,phi_PETSc,phi,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(DM_damage,phi_PETSc,phi,err_PETSc)
   CHKERRQ(err_PETSc)
 
   if (solution%converged) &