Merge remote-tracking branch 'origin/development' into allocatable-strings

VERSION

@@ -1 +1 @@
-3.0.0-alpha7-291-gd2ad37e7f
+3.0.0-alpha7-302-g56ff8c769

python/damask/_rotation.py

@@ -902,7 +902,8 @@ class Rotation:
         return Rotation(Rotation._om2qu(om))
 
     @staticmethod
-    def from_matrix(R: np.ndarray) -> 'Rotation':
+    def from_matrix(R: np.ndarray,
+                    normalize: bool = False) -> 'Rotation':
         """
         Initialize from rotation matrix.
 
@@ -910,13 +911,17 @@ class Rotation:
         ----------
         R : numpy.ndarray, shape (...,3,3)
             Rotation matrix with det(R) = 1 and R.T ∙ R = I.
+        normalize : bool, optional
+            Rescales rotation matrix to unit determinant. Defaults to False.
 
         Returns
         -------
         new : damask.Rotation
 
         """
-        return Rotation.from_basis(R)
+        return Rotation.from_basis(np.array(R,dtype=float) * (np.linalg.det(R)**(-1./3.))[...,np.newaxis,np.newaxis]
+                                   if normalize else
+                                   R)
 
     @staticmethod
     def from_parallel(a: np.ndarray,

python/tests/test_Rotation.py

@@ -774,9 +774,11 @@ class TestRotation:
                             ).all()
 
 
-    def test_matrix(self,multidim_rotations):
+    @pytest.mark.parametrize('normalize',[True,False])
+    def test_matrix(self,multidim_rotations,normalize):
         m = multidim_rotations
-        o = Rotation.from_matrix(m.as_matrix())
+        o = Rotation.from_matrix(m.as_matrix()*(0.9 if normalize else 1.0),
+                                 normalize=normalize)
         f = Rotation(np.where(np.isclose(m.as_quaternion()[...,0],0.0,atol=atol)[...,np.newaxis],~o,o))
         assert np.logical_or(m.isclose(o,atol=atol),
                              m.isclose(f,atol=atol)

python/tests/test_util.py

@@ -286,18 +286,6 @@ p2 : str, optional
 
             Remaining description
         """
-        invalid_docstring = """
-            Function description
-
-            Parameters ----------
-            p0 : numpy.ndarray, shape (...,4)
-                p0 description 1
-                p0 description 2
-            p1 : int, optional
-                p1 description
-
-            Remaining description
-        """
         expected = """
             Function description
 

src/grid/grid_mech_spectral_basic.f90

@@ -77,6 +77,7 @@ module grid_mechanical_spectral_basic
     C_volAvgLastInc = 0.0_pReal, &                                                                  !< previous volume average stiffness
     C_minMaxAvg = 0.0_pReal, &                                                                      !< current (min+max)/2 stiffness
     C_minMaxAvgLastInc = 0.0_pReal, &                                                               !< previous (min+max)/2 stiffness
+    C_minMaxAvgRestart = 0.0_pReal, &                                                               !< (min+max)/2 stiffnes (restart)
     S = 0.0_pReal                                                                                   !< current compliance (filled up with zeros)
 
   real(pReal) :: &
@@ -256,21 +257,17 @@ subroutine grid_mechanical_spectral_basic_init()
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
     call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call HDF5_read(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
+    call MPI_Bcast(C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
 
-    call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
-                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,status,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_close(fileUnit,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if restartRead2
 
   call utilities_updateGamma(C_minMaxAvg)
-  call utilities_saveReferenceStiffness
+  C_minMaxAvgRestart = C_minMaxAvg
 
 end subroutine grid_mechanical_spectral_basic_init
 
@@ -420,6 +417,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
   call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
 
+  if (num%update_gamma) C_minMaxAvgRestart = C_minMaxAvg
+
   print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
   fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
@@ -438,13 +437,11 @@ subroutine grid_mechanical_spectral_basic_restartWrite
     call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
     call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
     call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call HDF5_write(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
+    call HDF5_write(C_minMaxAvgRestart,groupHandle,'C_minMaxAvg',.false.)
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
   end if
 
-  if (num%update_gamma) call utilities_saveReferenceStiffness
-
   call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
   CHKERRQ(err_PETSc)
 

src/grid/grid_mech_spectral_polarisation.f90

@@ -85,6 +85,7 @@ module grid_mechanical_spectral_polarisation
     C_volAvgLastInc = 0.0_pReal, &                                                                  !< previous volume average stiffness
     C_minMaxAvg = 0.0_pReal, &                                                                      !< current (min+max)/2 stiffness
     C_minMaxAvgLastInc = 0.0_pReal, &                                                               !< previous (min+max)/2 stiffness
+    C_minMaxAvgRestart = 0.0_pReal, &                                                              !< (min+max)/2 stiffnes (restart)
     S = 0.0_pReal, &                                                                                !< current compliance (filled up with zeros)
     C_scale = 0.0_pReal, &
     S_scale = 0.0_pReal
@@ -283,21 +284,17 @@ subroutine grid_mechanical_spectral_polarisation_init()
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
     call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call HDF5_read(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
+    call MPI_Bcast(C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
 
-    call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
-                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,status,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_close(fileUnit,err_MPI)
-    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if restartRead2
 
   call utilities_updateGamma(C_minMaxAvg)
-  call utilities_saveReferenceStiffness
+  C_minMaxAvgRestart = C_minMaxAvg
   C_scale = C_minMaxAvg
   S_scale = math_invSym3333(C_minMaxAvg)
 
@@ -477,6 +474,8 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
+  if (num%update_gamma) C_minMaxAvgRestart = C_minMaxAvg
+
   print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
   fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
@@ -497,12 +496,11 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
     call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
     call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
     call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
+    call HDF5_write(C_minMaxAvgRestart,groupHandle,'C_minMaxAvg',.false.)
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
   end if
 
-  if (num%update_gamma) call utilities_saveReferenceStiffness
-
   call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
   CHKERRQ(err_PETSc)
 

src/grid/spectral_utilities.f90

@@ -126,8 +126,7 @@ module spectral_utilities
     utilities_constitutiveResponse, &
     utilities_calculateRate, &
     utilities_forwardField, &
-    utilities_updateCoords, &
+    utilities_updateCoords
-    utilities_saveReferenceStiffness
 
 contains
 
@@ -1098,27 +1097,6 @@ subroutine utilities_updateCoords(F)
 end subroutine utilities_updateCoords
 
 
-!---------------------------------------------------------------------------------------------------
-!> @brief Write out the current reference stiffness for restart.
-!---------------------------------------------------------------------------------------------------
-subroutine utilities_saveReferenceStiffness()
-
-  integer :: &
-    fileUnit,ierr
-
-
-  if (worldrank == 0) then
-    print'(/,1x,a)', '... writing reference stiffness data required for restart to file .........'; flush(IO_STDOUT)
-    open(newunit=fileUnit, file=getSolverJobName()//'.C_ref',&
-         status='replace',access='stream',action='write',iostat=ierr)
-    if (ierr /=0) call IO_error(100,ext_msg='could not open file '//getSolverJobName()//'.C_ref')
-    write(fileUnit) C_ref*wgt
-    close(fileUnit)
-  end if
-
-end subroutine utilities_saveReferenceStiffness
-
-
 !--------------------------------------------------------------------------------------------------
 !> @brief Check correctness of forward-backward transform.
 !--------------------------------------------------------------------------------------------------

src/lattice.f90

@@ -405,13 +405,13 @@ module lattice
 contains
 
 !--------------------------------------------------------------------------------------------------
-!> @brief Module initialization
+!> @brief Run self test.
 !--------------------------------------------------------------------------------------------------
-subroutine lattice_init
+subroutine lattice_init()
 
   print'(/,1x,a)', '<<<+-  lattice init  -+>>>'; flush(IO_STDOUT)
 
-  call selfTest
+  call selfTest()
 
 end subroutine lattice_init
 
@@ -2330,14 +2330,14 @@ subroutine selfTest
           lattice_isotropic_nu(C_tI,'isostress','tI'),1.0e-12_pReal)) error stop 'isotropic_nu/isostress/tI'
 
   call random_number(C)
-  C = lattice_symmetrize_C66(C,'cI')
+  C = lattice_symmetrize_C66(C+math_eye(6),'cI')
-  if (dNeq(lattice_isotropic_mu(C,'isostrain','cI'), lattice_isotropic_mu(C,'isostrain','hP'), 5.0e-9_pReal)) &
+  if (dNeq(lattice_isotropic_mu(C,'isostrain','cI'), lattice_isotropic_mu(C,'isostrain','hP'), 1.0e-12_pReal)) &
     error stop 'isotropic_mu/isostrain/cI-hP'
-  if (dNeq(lattice_isotropic_nu(C,'isostrain','cF'), lattice_isotropic_nu(C,'isostrain','cI'), 5.0e-9_pReal)) &
+  if (dNeq(lattice_isotropic_nu(C,'isostrain','cF'), lattice_isotropic_nu(C,'isostrain','cI'), 1.0e-12_pReal)) &
     error stop 'isotropic_nu/isostrain/cF-tI'
-  if (dNeq(lattice_isotropic_mu(C,'isostress','cI'), lattice_isotropic_mu(C,'isostress'), 5.0e-9_pReal)) &
+  if (dNeq(lattice_isotropic_mu(C,'isostress','cI'), lattice_isotropic_mu(C,'isostress'), 1.0e-12_pReal)) &
     error stop 'isotropic_mu/isostress/cI-hP'
-  if (dNeq(lattice_isotropic_nu(C,'isostress','cF'), lattice_isotropic_nu(C,'isostress'), 5.0e-9_pReal)) &
+  if (dNeq(lattice_isotropic_nu(C,'isostress','cF'), lattice_isotropic_nu(C,'isostress'), 1.0e-12_pReal)) &
     error stop 'isotropic_nu/isostress/cF-tI'
 
 end subroutine selfTest