Merge remote-tracking branch 'origin/development' into 302-dimension-mismatch-when-passing-a-flattened-f-array-to-utilities_updatecoords

VERSION

@@ -1 +1 @@
-3.0.0-alpha7-604-g65fa62b3f
+3.0.0-alpha7-610-g716600299

python/damask/_result.py

@@ -1201,7 +1201,7 @@ class Result:
                 'label': f"epsilon_{t}^{m}({F['label']})",
                 'meta':  {
                           'unit':        F['meta']['unit'],
-                          'description': f'strain tensor of order {m} based on {side} stretch tensor '+\
+                          'description': f'Seth-Hill strain tensor of order {m} based on {side} stretch tensor '+\
                                          f"of {F['label']} ({F['meta']['description']})",
                           'creator':     'add_strain'
                           }
@@ -1210,10 +1210,11 @@ class Result:
                    F: str = 'F',
                    t: Literal['V', 'U'] = 'V',
                    m: float = 0.0):
-        """
+        r"""
-        Add strain tensor of a deformation gradient.
+        Add strain tensor (Seth-Hill family) of a deformation gradient.
 
-        For details, see damask.mechanics.strain.
+        By default, the logarithmic strain based on the
+        left stretch tensor is added.
 
         Parameters
         ----------
@@ -1247,6 +1248,23 @@ class Result:
         spatial/Eulerian strain measures (based on 'V') for elastic strains
         when calculating averages.
 
+        The strain is defined as:
+
+        .. math::
+
+            m = 0 \\\\
+            \vb*{\epsilon}_V^{(0)} = \ln (\vb{V}) \\\\
+            \vb*{\epsilon}_U^{(0)} = \ln (\vb{U}) \\\\
+
+            m \neq 0 \\\\
+            \vb*{\epsilon}_V^{(m)} = \frac{1}{2m} (\vb{V}^{2m} - \vb{I}) \\\\
+            \vb*{\epsilon}_U^{(m)} = \frac{1}{2m} (\vb{U}^{2m} - \vb{I})
+
+        References
+        ----------
+        | https://en.wikipedia.org/wiki/Finite_strain_theory
+        | https://de.wikipedia.org/wiki/Verzerrungstensor
+
         """
         self._add_generic_pointwise(self._add_strain,{'F':F},{'t':t,'m':m})
 

src/grid/grid_damage_spectral.f90

@@ -307,7 +307,7 @@ end subroutine grid_damage_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief Write current solver and constitutive data for restart to file.
 !--------------------------------------------------------------------------------------------------
-subroutine grid_damage_spectral_restartWrite
+subroutine grid_damage_spectral_restartWrite()
 
   PetscErrorCode :: err_PETSc
   DM :: dm_local
@@ -316,7 +316,7 @@ subroutine grid_damage_spectral_restartWrite
 
   call SNESGetDM(SNES_damage,dm_local,err_PETSc);
   CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(dm_local,solution_vec,phi,err_PETSc);
+  call DMDAVecGetArrayReadF90(dm_local,solution_vec,phi,err_PETSc);
   CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'saving damage solver data required for restart'; flush(IO_STDOUT)
@@ -328,7 +328,7 @@ subroutine grid_damage_spectral_restartWrite
   call HDF5_closeGroup(groupHandle)
   call HDF5_closeFile(fileHandle)
 
-  call DMDAVecRestoreArrayF90(dm_local,solution_vec,phi,err_PETSc);
+  call DMDAVecRestoreArrayReadF90(dm_local,solution_vec,phi,err_PETSc);
   CHKERRQ(err_PETSc)
 
 end subroutine grid_damage_spectral_restartWrite

src/grid/grid_mech_FEM.f90

@@ -351,15 +351,8 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
     rotation_BC
 
   PetscErrorCode :: err_PETSc
-  PetscScalar, pointer, dimension(:,:,:,:) :: &
-    u,u_lastInc
 
 
-  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u,err_PETSc)
-  CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
-  CHKERRQ(err_PETSc)
-
   if (cutBack) then
     C_volAvg = C_volAvgLastInc
   else
@@ -408,10 +401,6 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
 
   call VecAXPY(solution_current,Delta_t,solution_rate,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u,err_PETSc)
-  CHKERRQ(err_PETSc)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
-  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! set module wide available data
@@ -425,7 +414,7 @@ end subroutine grid_mechanical_FEM_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief Update coordinates
 !--------------------------------------------------------------------------------------------------
-subroutine grid_mechanical_FEM_updateCoords
+subroutine grid_mechanical_FEM_updateCoords()
 
   call utilities_updateCoords(F)
 
@@ -435,16 +424,16 @@ end subroutine grid_mechanical_FEM_updateCoords
 !--------------------------------------------------------------------------------------------------
 !> @brief Write current solver and constitutive data for restart to file
 !--------------------------------------------------------------------------------------------------
-subroutine grid_mechanical_FEM_restartWrite
+subroutine grid_mechanical_FEM_restartWrite()
 
   PetscErrorCode :: err_PETSc
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: u,u_lastInc
 
 
-  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u,err_PETSc)
+  call DMDAVecGetArrayReadF90(mechanical_grid,solution_current,u,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  call DMDAVecGetArrayReadF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
   CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'saving solver data required for restart'; flush(IO_STDOUT)
@@ -471,9 +460,9 @@ subroutine grid_mechanical_FEM_restartWrite
     call HDF5_closeFile(fileHandle)
   end if
 
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(mechanical_grid,solution_current,u,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
   CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_FEM_restartWrite
@@ -566,7 +555,7 @@ subroutine formResidual(da_local,x_local, &
 
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
+  call DMDAVecGetArrayReadF90(da_local,x_local,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
   do k = cells3Offset+1, cells3Offset+cells3; do j = 1, cells(2); do i = 1, cells(1)
     ctr = 0
@@ -576,7 +565,7 @@ subroutine formResidual(da_local,x_local, &
     end do; end do; end do
     F(1:3,1:3,i,j,k-cells3Offset) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   end do; end do; end do
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da_local,x_local,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
@@ -596,7 +585,7 @@ subroutine formResidual(da_local,x_local, &
 ! constructing residual
   call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
+  call DMDAVecGetArrayReadF90(da_local,x_local,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
   ele = 0
   r = 0.0_pREAL
@@ -617,7 +606,7 @@ subroutine formResidual(da_local,x_local, &
       r(0:2,i+ii,j+jj,k+kk) = r(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
     end do; end do; end do
   end do; end do; end do
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da_local,x_local,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_basic.f90

@@ -382,11 +382,10 @@ subroutine grid_mechanical_spectral_basic_updateCoords()
   PetscErrorCode :: err_PETSc
   real(pREAL), dimension(:,:,:,:), pointer :: F
 
-
+  call DMDAVecGetArrayReadF90(da,solution_vec,F,err_PETSc)
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
   call utilities_updateCoords(reshape(F,[3,3,size(F,2),size(F,3),size(F,4)]))
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_updateCoords
@@ -401,8 +400,7 @@ subroutine grid_mechanical_spectral_basic_restartWrite()
   integer(HID_T) :: fileHandle, groupHandle
   real(pREAL), dimension(:,:,:,:), pointer :: F
 
-
+  call DMDAVecGetArrayReadF90(da,solution_vec,F,err_PETSc)
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
 
   if (num%update_gamma) C_minMaxAvgRestart = C_minMaxAvg
@@ -430,7 +428,7 @@ subroutine grid_mechanical_spectral_basic_restartWrite()
     call HDF5_closeFile(fileHandle)
   end if
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_restartWrite

src/grid/grid_mech_spectral_polarisation.f90

@@ -439,11 +439,10 @@ subroutine grid_mechanical_spectral_polarisation_updateCoords()
   PetscErrorCode :: err_PETSc
   real(pREAL), dimension(:,:,:,:), pointer :: FandF_tau
 
-
+  call DMDAVecGetArrayReadF90(da,solution_vec,FandF_tau,err_PETSc)
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
   CHKERRQ(err_PETSc)
   call utilities_updateCoords(reshape(FandF_tau(0:8,:,:,:),[3,3,size(FandF_tau,2),size(FandF_tau,3),size(FandF_tau,4)]))
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da,solution_vec,FandF_tau,err_PETSc)
   CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_polarisation_updateCoords
@@ -458,8 +457,7 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite()
   integer(HID_T) :: fileHandle, groupHandle
   real(pREAL), dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
 
-
+  call DMDAVecGetArrayReadF90(da,solution_vec,FandF_tau,err_PETSc)
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
   CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
@@ -491,7 +489,7 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite()
     call HDF5_closeFile(fileHandle)
   end if
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  call DMDAVecRestoreArrayReadF90(da,solution_vec,FandF_tau,err_PETSc)
   CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_polarisation_restartWrite

src/grid/grid_thermal_spectral.f90

@@ -285,7 +285,7 @@ end subroutine grid_thermal_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief Write current solver and constitutive data for restart to file.
 !--------------------------------------------------------------------------------------------------
-subroutine grid_thermal_spectral_restartWrite
+subroutine grid_thermal_spectral_restartWrite()
 
   PetscErrorCode :: err_PETSc
   DM :: dm_local
@@ -294,7 +294,7 @@ subroutine grid_thermal_spectral_restartWrite
 
   call SNESGetDM(SNES_thermal,dm_local,err_PETSc);
   CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(dm_local,solution_vec,T,err_PETSc);
+  call DMDAVecGetArrayReadF90(dm_local,solution_vec,T,err_PETSc);
   CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'saving thermal solver data required for restart'; flush(IO_STDOUT)
@@ -307,7 +307,7 @@ subroutine grid_thermal_spectral_restartWrite
   call HDF5_closeGroup(groupHandle)
   call HDF5_closeFile(fileHandle)
 
-  call DMDAVecRestoreArrayF90(dm_local,solution_vec,T,err_PETSc);
+  call DMDAVecRestoreArrayReadF90(dm_local,solution_vec,T,err_PETSc);
   CHKERRQ(err_PETSc)
 
 end subroutine grid_thermal_spectral_restartWrite