Merge branch 'development' into using-submodules

VERSION

@@ -1 +1 @@
-v2.0.3-2872-g0a2d3046
+v2.0.3-2881-gc07efe84

env/DAMASK.csh

@@ -9,7 +9,7 @@ source $ENV_ROOT/CONFIG
 
 set path = ($DAMASK_ROOT/bin $path)
 
-set SOLVER=`which DAMASK_spectral`                                                          
+set SOLVER=`which DAMASK_grid`
 if ( "x$DAMASK_NUM_THREADS" == "x" ) then
   set DAMASK_NUM_THREADS=1
 endif

env/DAMASK.sh

@@ -35,7 +35,7 @@ cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd
 
 PATH=${DAMASK_ROOT}/bin:$PATH
 
-SOLVER=$(type -p DAMASK_spectral || true 2>/dev/null)
+SOLVER=$(type -p DAMASK_grid || true 2>/dev/null)
 [ "x$SOLVER" == "x" ] && SOLVER=$(blink 'Not found!')
 
 [ "x$DAMASK_NUM_THREADS" == "x" ] && DAMASK_NUM_THREADS=1

env/DAMASK.zsh

@@ -27,7 +27,7 @@ cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd
 
 PATH=${DAMASK_ROOT}/bin:$PATH
 
-SOLVER=$(which DAMASK_spectral || true 2>/dev/null)
+SOLVER=$(which DAMASK_grid || true 2>/dev/null)
 [[ "x$SOLVER" == "x" ]] && SOLVER=$(blink 'Not found!')
 
 [[ "x$DAMASK_NUM_THREADS" == "x" ]] && DAMASK_NUM_THREADS=1

examples/SpectralMethod/Polycrystal/numerics.config

@@ -1,2 +0,0 @@
-itmin 4
-itmax 40

examples/SpectralMethod/Polycrystal/numerics.yaml

@@ -0,0 +1,3 @@
+grid:
+  itmin: 4
+  itmax: 40

installation/mods_MarcMentat/2018.1/Marc_tools/comp_damask_hmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018.1/Marc_tools/comp_damask_lmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018.1/Marc_tools/comp_damask_mp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018.1/Marc_tools/run_damask_hmp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2018.1/Marc_tools/run_damask_lmp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2018.1/Marc_tools/run_damask_mp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2018/Marc_tools/comp_damask_hmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018/Marc_tools/comp_damask_lmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018/Marc_tools/comp_damask_mp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2018/Marc_tools/run_damask_hmp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2018/Marc_tools/run_damask_lmp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2018/Marc_tools/run_damask_mp

@@ -3267,6 +3267,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3599,6 +3600,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3933,6 +3935,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2019/Marc_tools/comp_damask_hmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2019/Marc_tools/comp_damask_lmp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2019/Marc_tools/comp_damask_mp

@@ -49,4 +49,5 @@ echo "program: $program"
     exit 1
     }
     /bin/rm $userobj
-	/bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.mod
+    /bin/rm $DIRJOB/*.smod

installation/mods_MarcMentat/2019/Marc_tools/run_damask_hmp

@@ -3241,6 +3241,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3573,6 +3574,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3907,6 +3909,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2019/Marc_tools/run_damask_lmp

@@ -3241,6 +3241,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3573,6 +3574,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3907,6 +3909,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

installation/mods_MarcMentat/2019/Marc_tools/run_damask_mp

@@ -3241,6 +3241,7 @@ else
 fi
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3573,6 +3574,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 
 #
 # run marc
@@ -3907,6 +3909,7 @@ else # if test $link
 fi   # if test $link
 /bin/rm $userobj 2>/dev/null
 /bin/rm $DIRJOB/*.mod 2>/dev/null
+/bin/rm $DIRJOB/*.smod 2>/dev/null
 # done if no job id given
 if test -z "$jid"
 then

python/damask/_rotation.py

@@ -805,7 +805,7 @@ class Rotation:
         """Rotation matrix to Bunge-Euler angles."""
         with np.errstate(invalid='ignore',divide='ignore'):
             zeta = 1.0/np.sqrt(1.0-om[...,2,2:3]**2)
-            eu = np.where(np.isclose(np.abs(om[...,2,2:3]),1.0,1e-9),
+            eu = np.where(np.isclose(np.abs(om[...,2,2:3]),1.0,0.0),
                           np.block([np.arctan2(om[...,0,1:2],om[...,0,0:1]),
                                     np.pi*0.5*(1-om[...,2,2:3]),
                                     np.zeros(om.shape[:-2]+(1,)),

python/tests/test_Rotation.py

@@ -150,7 +150,7 @@ def om2qu(a):
 
 def om2eu(om):
     """Rotation matrix to Bunge-Euler angles."""
-    if not np.isclose(np.abs(om[2,2]),1.0,1.e-9):
+    if not np.isclose(np.abs(om[2,2]),1.0,0.0):
         zeta = 1.0/np.sqrt(1.0-om[2,2]**2)
         eu = np.array([np.arctan2(om[2,0]*zeta,-om[2,1]*zeta),
                        np.arccos(om[2,2]),

src/CPFEM.f90

@@ -248,7 +248,7 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
     endif validCalculation
 
     if (debugCPFEM%extensive &
-         .and. (debugCPFEM%element == elCP .and. debugCPFEM%ip == ip) .or. .not. debugCPFEM%selective) then
+         .and. ((debugCPFEM%element == elCP .and. debugCPFEM%ip == ip) .or. .not. debugCPFEM%selective)) then
         write(6,'(a,i8,1x,i2,/,12x,6(f10.3,1x)/)') &
           '<< CPFEM >> stress/MPa at elFE ip ',   elFE, ip, CPFEM_cs(1:6,ip,elCP)*1.0e-6_pReal
         write(6,'(a,i8,1x,i2,/,6(12x,6(f10.3,1x)/))') &

src/IO.f90

@@ -529,6 +529,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
       msg = 'unknown material parameter:'
     case (211)
       msg = 'material parameter out of bounds:'
+    case (212)
+      msg = 'nonlocal model not supported'
 
 !--------------------------------------------------------------------------------------------------
 ! numerics error messages

src/constitutive.f90

@@ -15,7 +15,8 @@ module constitutive
   use results
   use lattice
   use discretization
-  use geometry_plastic_nonlocal
+  use geometry_plastic_nonlocal, only: &
+    geometry_plastic_nonlocal_disable
 
   implicit none
   private

src/constitutive_plastic_nonlocal.f90

@@ -386,7 +386,11 @@ module subroutine plastic_nonlocal_init
 
     call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
 
-    plasticState(p)%nonlocal         = config%KeyExists('/nonlocal/')
+    plasticState(p)%nonlocal = config%KeyExists('/nonlocal/')
+    if(plasticState(p)%nonlocal .and. .not. allocated(IPneighborhood)) &
+      call IO_error(212,ext_msg='IPneighborhood does not exist')
+
+
     plasticState(p)%offsetDeltaState = 0                                                            ! ToDo: state structure does not follow convention
 
     st0%rho => plasticState(p)%state0                             (0*prm%sum_N_sl+1:10*prm%sum_N_sl,:)

src/grid/discretization_grid.f90

@@ -118,6 +118,7 @@ subroutine discretization_grid_init(restart)
     call results_addAttribute('origin',origin,  'geometry')
     call results_closeJobFile
   endif
+
 !--------------------------------------------------------------------------------------------------
 ! geometry information required by the nonlocal CP model
   call geometry_plastic_nonlocal_setIPvolume(reshape([(product(mySize/real(myGrid,pReal)),j=1,product(myGrid))], &

src/marc/discretization_marc.f90

@@ -119,6 +119,7 @@ subroutine discretization_marc_init
   unscaledNormals = IPareaNormal(elem,nElems,connectivity_cell,node0_cell)
   call geometry_plastic_nonlocal_setIParea(norm2(unscaledNormals,1))
   call geometry_plastic_nonlocal_setIPareaNormal(unscaledNormals/spread(norm2(unscaledNormals,1),1,3))
+  !call geometry_plastic_nonlocal_setIPneighborhood                                                 ToDo: Support nonlocal
   call geometry_plastic_nonlocal_results
 
 end subroutine discretization_marc_init
@@ -492,8 +493,8 @@ subroutine inputRead_mapNodes(FEM2DAMASK, &
     chunkPos = IO_stringPos(fileContent(l))
     if(chunkPos(1) < 1) cycle
     if(IO_lc(IO_stringValue(fileContent(l),chunkPos,1)) == 'coordinates') then
+      chunkPos = [1,1,10]
       do i = 1,nNodes
-        chunkPos = IO_stringPos(fileContent(l+1+i))
         map_unsorted(:,i) = [IO_intValue(fileContent(l+1+i),chunkPos,1),i]
       enddo
       exit
@@ -528,8 +529,8 @@ subroutine inputRead_elemNodes(nodes, &
     chunkPos = IO_stringPos(fileContent(l))
     if(chunkPos(1) < 1) cycle
     if(IO_lc(IO_stringValue(fileContent(l),chunkPos,1)) == 'coordinates') then
+      chunkPos = [4,1,10,11,30,31,50,51,70]
       do i=1,nNode
-        chunkPos = IO_stringPos(fileContent(l+1+i))
         m = mesh_FEM2DAMASK_node(IO_intValue(fileContent(l+1+i),chunkPos,1))
         do j = 1,3
           nodes(j,m) = mesh_unitlength * IO_floatValue(fileContent(l+1+i),chunkPos,j+1)
@@ -732,7 +733,7 @@ end subroutine inputRead_microstructureAndHomogenization
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief Calculates cell node coordinates from element node coordinates
+!> @brief Determine cell connectivity and definition of cell nodes
 !--------------------------------------------------------------------------------------------------
 subroutine buildCells(connectivity_cell,cellNodeDefinition, &
                       elem,connectivity_elem)
@@ -746,7 +747,8 @@ subroutine buildCells(connectivity_cell,cellNodeDefinition, &
   integer,dimension(:),     allocatable :: candidates_local
   integer,dimension(:,:),   allocatable :: parentsAndWeights,candidates_global
 
-  integer :: e, n, c, p, s,i,m,j,nParentNodes,nCellNode,Nelem,candidateID
+  integer :: e,n,c,p,s,i,m,j,&
+             nParentNodes,nCellNode,Nelem,candidateID
 
   Nelem = size(connectivity_elem,2)
 
@@ -760,9 +762,7 @@ subroutine buildCells(connectivity_cell,cellNodeDefinition, &
   do e = 1, Nelem
     do c = 1, elem%NcellNodes
       realNode: if (count(elem%cellNodeParentNodeWeights(:,c) /= 0) == 1) then
-        where(connectivity_cell(:,:,e) == -c)
-          connectivity_cell(:,:,e) = connectivity_elem(c,e)
-        end where
+        where(connectivity_cell(:,:,e) == -c) connectivity_cell(:,:,e) = connectivity_elem(c,e)
       endif realNode
     enddo
   enddo
@@ -889,7 +889,7 @@ end subroutine buildCells
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief Calculates cell node coordinates from element node coordinates
+!> @brief Calculate cell node coordinates from element node coordinates
 !--------------------------------------------------------------------------------------------------
 subroutine buildCellNodes(node_cell, &
                           definition,node_elem)
@@ -919,7 +919,7 @@ end subroutine buildCellNodes
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief Calculates IP coordinates as center of cell
+!> @brief Calculate IP coordinates as center of cell
 !--------------------------------------------------------------------------------------------------
 subroutine buildIPcoordinates(IPcoordinates, &
                               connectivity_cell,node_cell)

src/quaternions.f90

@@ -464,6 +464,8 @@ subroutine selfTest
   real(pReal), dimension(4) :: qu
   type(quaternion)          :: q, q_2
 
+  if(dNeq(abs(P),1.0_pReal))                           call IO_error(0,ext_msg='P not in {-1,+1}')
+
   call random_number(qu)
   qu = (qu-0.5_pReal) * 2.0_pReal
   q  = quaternion(qu)

src/rotations.f90

@@ -574,6 +574,7 @@ end function om2qu
 !---------------------------------------------------------------------------------------------------
 !> @author Marc De Graef, Carnegie Mellon University
 !> @brief orientation matrix to Euler angles
+!> @details Two step check for special cases to avoid invalid operations (not needed for python)
 !---------------------------------------------------------------------------------------------------
 pure function om2eu(om) result(eu)
 
@@ -581,16 +582,16 @@ pure function om2eu(om) result(eu)
   real(pReal),             dimension(3)   :: eu
   real(pReal)                             :: zeta
 
-  if (abs(om(3,3)) < 1.0_pReal) then
-    zeta = 1.0_pReal/sqrt(1.0_pReal-om(3,3)**2.0_pReal)
+  if    (dNeq(abs(om(3,3)),1.0_pReal,1.e-8_pReal)) then
+    zeta = 1.0_pReal/sqrt(math_clip(1.0_pReal-om(3,3)**2.0_pReal,1e-64_pReal,1.0_pReal))
     eu = [atan2(om(3,1)*zeta,-om(3,2)*zeta), &
-          acos(om(3,3)), &
+          acos(math_clip(om(3,3),-1.0_pReal,1.0_pReal)), &
           atan2(om(1,3)*zeta, om(2,3)*zeta)]
   else
     eu = [atan2(om(1,2),om(1,1)), 0.5_pReal*PI*(1.0_pReal-om(3,3)),0.0_pReal ]
   end if
-
-  where(eu<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
+  where(abs(eu) < 1.e-8_pReal) eu = 0.0_pReal
+  where(eu<0.0_pReal)          eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
 
 end function om2eu