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adjusting to PETSc 3.9.x

This commit is contained in:
Martin Diehl 2018-08-18 14:05:57 +02:00
parent d4bcfae82b
commit 0d8f17cbe6
2 changed files with 23 additions and 290 deletions
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288
src/FEM_mech.f90
View File

@ -5,6 +5,10 @@
!> @brief FEM PETSc solver
!--------------------------------------------------------------------------------------------------
module FEM_mech
#include <petsc/finclude/petsc.h>
use PETScdmda
use PETScsnes
use prec, only: &
pInt, &
pReal
@ -23,7 +27,6 @@ module FEM_mech
implicit none
private
#include <petsc/finclude/petsc.h>
!--------------------------------------------------------------------------------------------------
! derived types
@ -40,7 +43,7 @@ module FEM_mech
SNES, private :: mech_snes
Vec, private :: solution, solution_rate, solution_local
PetscInt, private :: dimPlex, cellDof, nQuadrature, nBasis
PetscReal, allocatable, target, private :: qPoints(:), qWeights(:)
PetscReal, allocatable, target,dimension(:), private :: qPoints, qWeights
MatNullSpace, private :: matnull
!--------------------------------------------------------------------------------------------------
@ -55,32 +58,11 @@ module FEM_mech
FEM_mech_init, &
FEM_mech_solution ,&
FEM_mech_forward, &
FEM_mech_output, &
FEM_mech_destroy
external :: &
MPI_abort, &
MPI_Allreduce, &
VecCopy, &
VecSet, &
VecISSet, &
VecScale, &
VecWAXPY, &
VecAXPY, &
VecGetSize, &
VecAssemblyBegin, &
VecAssemblyEnd, &
VecView, &
VecDestroy, &
MatSetOption, &
MatSetLocalToGlobalMapping, &
MatSetNearNullSpace, &
MatZeroEntries, &
MatZeroRowsColumnsLocalIS, &
MatAssemblyBegin, &
MatAssemblyEnd, &
MatScale, &
MatNullSpaceCreateRigidBody, &
PetscQuadratureCreate, &
PetscFECreateDefault, &
PetscFESetQuadrature, &
@ -92,39 +74,14 @@ module FEM_mech
PetscDSGetTotalDimension, &
PetscDSGetDiscretization, &
PetscDualSpaceGetFunctional, &
DMClone, &
DMCreateGlobalVector, &
DMGetDS, &
DMGetDimension, &
DMGetDefaultSection, &
DMGetDefaultGlobalSection, &
DMGetLocalToGlobalMapping, &
DMGetLocalVector, &
DMGetLabelSize, &
DMPlexCopyCoordinates, &
DMPlexGetHeightStratum, &
DMPlexGetDepthStratum, &
DMLocalToGlobalBegin, &
DMLocalToGlobalEnd, &
DMGlobalToLocalBegin, &
DMGlobalToLocalEnd, &
DMRestoreLocalVector, &
DMSNESSetFunctionLocal, &
DMSNESSetJacobianLocal, &
SNESCreate, &
SNESSetOptionsPrefix, &
SNESSetDM, &
SNESSetMaxLinearSolveFailures, &
SNESSetConvergenceTest, &
SNESSetTolerances, &
SNESSetFromOptions, &
SNESGetDM, &
SNESGetConvergedReason, &
SNESGetIterationNumber, &
SNESSolve, &
SNESDestroy, &
PetscViewerHDF5PushGroup, &
PetscViewerHDF5PopGroup, &
PetscObjectSetName
contains
@ -177,12 +134,10 @@ subroutine FEM_mech_init(fieldBC)
PetscInt :: cellStart, cellEnd, cell, basis
character(len=7) :: prefix = 'mechFE_'
PetscErrorCode :: ierr
if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- FEM_mech init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
write(6,'(/,a)') ' <<<+- FEM_mech init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif
!--------------------------------------------------------------------------------------------------
! Setup FEM mech mesh
@ -248,13 +203,13 @@ subroutine FEM_mech_init(fieldBC)
call ISRestoreIndicesF90(bcPoint,pBcPoint,ierr); CHKERRQ(ierr)
call ISDestroy(bcPoint,ierr); CHKERRQ(ierr)
else
call ISCreateGeneral(PETSC_COMM_WORLD,0,0,PETSC_COPY_VALUES,bcPoints(numBC),ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,0,[0],PETSC_COPY_VALUES,bcPoints(numBC),ierr)
CHKERRQ(ierr)
endif
endif
enddo; enddo
call DMPlexCreateSection(mech_mesh,dimPlex,1,pNumComp,pNumDof, &
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_OBJECT, &
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_VEC, &
section,ierr)
CHKERRQ(ierr)
call DMSetDefaultSection(mech_mesh,section,ierr); CHKERRQ(ierr)
@ -270,12 +225,12 @@ subroutine FEM_mech_init(fieldBC)
call DMCreateGlobalVector(mech_mesh,solution ,ierr); CHKERRQ(ierr) !< locally owned displacement Dofs
call DMCreateGlobalVector(mech_mesh,solution_rate ,ierr); CHKERRQ(ierr) !< locally owned velocity Dofs to guess solution at next load step
call DMCreateLocalVector (mech_mesh,solution_local ,ierr); CHKERRQ(ierr) !< locally owned velocity Dofs to guess solution at next load step
call DMSNESSetFunctionLocal(mech_mesh,FEM_mech_formResidual,PETSC_NULL_OBJECT,ierr) !< function to evaluate residual forces
call DMSNESSetFunctionLocal(mech_mesh,FEM_mech_formResidual,PETSC_NULL_VEC,ierr) !< function to evaluate residual forces
CHKERRQ(ierr)
call DMSNESSetJacobianLocal(mech_mesh,FEM_mech_formJacobian,PETSC_NULL_OBJECT,ierr) !< function to evaluate stiffness matrix
call DMSNESSetJacobianLocal(mech_mesh,FEM_mech_formJacobian,PETSC_NULL_VEC,ierr) !< function to evaluate stiffness matrix
CHKERRQ(ierr)
call SNESSetMaxLinearSolveFailures(mech_snes, huge(1), ierr); CHKERRQ(ierr) !< ignore linear solve failures
call SNESSetConvergenceTest(mech_snes,FEM_mech_converged,PETSC_NULL_OBJECT,PETSC_NULL_FUNCTION,ierr)
call SNESSetConvergenceTest(mech_snes,FEM_mech_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,ierr)
CHKERRQ(ierr)
call SNESSetTolerances(mech_snes,1.0,0.0,0.0,itmax,itmax,ierr)
CHKERRQ(ierr)
@ -357,7 +312,7 @@ type(tSolutionState) function FEM_mech_solution( &
params%timeincOld = timeinc_old
params%fieldBC = fieldBC
call SNESSolve(mech_snes,PETSC_NULL_OBJECT,solution,ierr); CHKERRQ(ierr) ! solve mech_snes based on solution guess (result in solution)
call SNESSolve(mech_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr) ! solve mech_snes based on solution guess (result in solution)
call SNESGetConvergedReason(mech_snes,reason,ierr); CHKERRQ(ierr) ! solution converged?
terminallyIll = .false.
@ -370,10 +325,8 @@ type(tSolutionState) function FEM_mech_solution( &
CHKERRQ(ierr)
endif
if (worldrank == 0) then
write(6,'(/,a)') ' ==========================================================================='
flush(6)
endif
write(6,'(/,a)') ' ==========================================================================='
flush(6)
end function FEM_mech_solution
@ -765,215 +718,6 @@ subroutine FEM_mech_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reason,dumm
end subroutine FEM_mech_converged
!--------------------------------------------------------------------------------------------------
!> @brief output routine
!--------------------------------------------------------------------------------------------------
subroutine FEM_mech_output(inc,fieldBC)
use material, only: &
material_Nhomogenization, &
material_Ncrystallite, &
material_Nphase, &
homogenization_maxNgrains, &
homogenization_name, &
crystallite_name, &
phase_name
use homogenization, only: &
homogOutput, &
crystalliteOutput, &
phaseOutput
use numerics, only: &
integrationOrder
use FEM_utilities, only: &
resUnit, &
coordinatesVec, &
homogenizationResultsVec, &
crystalliteResultsVec, &
phaseResultsVec
implicit none
integer(pInt), intent(in) :: inc
type(tFieldBC),intent(in) :: fieldBC
DM :: dm_local
PetscDS :: prob
Vec :: localVec
PetscScalar, dimension(:), pointer :: x_scal, coordinates, results
PetscSection :: section
PetscReal, pointer :: basisField(:), basisFieldDer(:)
PetscInt :: nodeStart, nodeEnd, node
PetscInt :: faceStart, faceEnd, face
PetscInt :: cellStart, cellEnd, cell
PetscInt :: field, qPt, qOffset, fOffset, dim, gType, cSize
PetscInt :: homog, cryst, grain, phase, res, resSize
PetscErrorCode :: ierr
character(len=1024) :: resultPartition, incPartition, homogPartition, &
crystPartition, phasePartition, &
grainStr
integer(pInt) :: ctr
write(incPartition,'(a11,i0)') '/Increment_',inc
call PetscViewerHDF5PushGroup(resUnit, trim(incPartition), ierr); CHKERRQ(ierr)
call SNESGetDM(mech_snes,dm_local,ierr); CHKERRQ(ierr) !< retrieve mesh info from mech_snes into dm_local
call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr) !< retrieve discretization from mesh and store in prob
call DMGetDefaultSection(dm_local,section,ierr); CHKERRQ(ierr) !< retrieve section (degrees of freedom)
call DMGetLocalVector(dm_local,localVec,ierr); CHKERRQ(ierr) !< retrieve local vector
call VecCopy(solution_local,localVec,ierr); CHKERRQ(ierr)
call VecGetArrayF90(coordinatesVec, coordinates, ierr); CHKERRQ(ierr)
ctr = 1_pInt
select case (integrationOrder)
case(1_pInt) !< first order quadrature
call DMPlexGetDepthStratum(dm_local,0,nodeStart,nodeEnd,ierr); CHKERRQ(ierr) !< get index range of entities at dimension 0 (i.e., all nodes)
do node = nodeStart, nodeEnd-1 !< loop over all nodes in mesh
call DMPlexVecGetClosure(dm_local,section,localVec,node,x_scal,ierr) !< x_scal = localVec (i.e. solution) at node
CHKERRQ(ierr)
do dim = 1, dimPlex
coordinates(ctr) = x_scal(dim); ctr = ctr + 1_pInt !< coordinates of node
enddo
call DMPlexVecRestoreClosure(dm_local,section,localVec,node,x_scal,ierr) !< disassociate x_scal pointer
CHKERRQ(ierr)
enddo
case(2_pInt) !< second order quadrature
call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr) !< get index range of highest dimension object (i.e. cells of mesh) TODO 3D assumption!!
CHKERRQ(ierr)
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexVecGetClosure(dm_local,section,localVec,cell,x_scal,ierr)
CHKERRQ(ierr)
do dim = 1, dimPlex
coordinates(ctr) = sum(x_scal(dim:cellDof:dimPlex))/real(nBasis) !< coordinates of cell center
ctr = ctr + 1_pInt
enddo
call DMPlexVecRestoreClosure(dm_local,section,localVec,cell,x_scal,ierr)
CHKERRQ(ierr)
enddo
call DMPlexGetDepthStratum(dm_local,0,nodeStart,nodeEnd,ierr) !< get index range of entities at dimension 0 (i.e., all nodes)
CHKERRQ(ierr)
do node = nodeStart, nodeEnd-1 !< loop over all nodes
call DMPlexVecGetClosure(dm_local,section,localVec,node,x_scal,ierr)
CHKERRQ(ierr)
do dim = 1, dimPlex
coordinates(ctr) = x_scal(dim) !< coordinates of cell corners
ctr = ctr + 1_pInt
enddo
call DMPlexVecRestoreClosure(dm_local,section,localVec,node,x_scal,ierr)
CHKERRQ(ierr)
enddo
do gType = 1, dimPlex-1
call DMPlexGetHeightStratum(dm_local,gType,faceStart,faceEnd,ierr) !< get index range of entities at dimension N-1 (i.e., all faces)
CHKERRQ(ierr)
do face = faceStart, faceEnd-1 !< loop over all elements
call DMPlexVecGetClosure(dm_local,section,localVec,face,x_scal,ierr)
CHKERRQ(ierr)
cSize = size(x_scal)
do dim = 1, dimPlex
coordinates(ctr) = sum(x_scal(dim:cSize:dimPlex))/real(cSize/dimPlex) !< coordinates of edge/face centers TODO quadratic element assumption used here!
ctr = ctr + 1_pInt
enddo
call DMPlexVecRestoreClosure(dm_local,section,localVec,face,x_scal,ierr)
CHKERRQ(ierr)
enddo
enddo
case default
call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr) !< get index range of elements (mesh cells)
CHKERRQ(ierr)
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexVecGetClosure(dm_local, & !< mesh
section, & !< distribution of DoF on mesh
localVec, & !< overall solution vector (i.e. all DoFs)...
cell, & !< ...at this cell
x_scal, & !< store all DoFs of closure (faces, edges, nodes if present) into x_scal
ierr) !< --> get coordinates of closure entities with DoFs
CHKERRQ(ierr)
qOffset = 0
do qPt = 1, nQuadrature !< loop over each quad point in cell
fOffset = 0
do field = 0, dimPlex-1 !< loop over each solution field (e.g., x,y,z coordinates)
call PetscDSGetTabulation(prob,field,basisField,basisFieldDer,ierr) !< retrieve shape function at each quadrature point for field
CHKERRQ(ierr)
coordinates(ctr) = real(sum(basisField(qOffset+1:qOffset+nBasis)* &
x_scal(fOffset+1:fOffset+nBasis)), pReal) !< interpolate field value (in x_scal) to quad points
ctr = ctr + 1_pInt
fOffset = fOffset + nBasis !< wind forward by one field
enddo
qOffset = qOffset + nBasis !< wind forward by one quad point
enddo
call DMPlexVecRestoreClosure(dm_local,section,localVec,cell,x_scal,ierr)
CHKERRQ(ierr)
enddo
end select
call VecRestoreArrayF90(coordinatesVec, coordinates, ierr); CHKERRQ(ierr)
call VecAssemblyBegin(coordinatesVec, ierr); CHKERRQ(ierr)
call VecAssemblyEnd (coordinatesVec, ierr); CHKERRQ(ierr)
call VecView(coordinatesVec, resUnit, ierr); CHKERRQ(ierr)
call DMRestoreLocalVector(dm_local,localVec,ierr); CHKERRQ(ierr)
do homog = 1, material_Nhomogenization
call VecGetSize(homogenizationResultsVec(homog),resSize,ierr)
if (resSize > 0) then
homogPartition = trim(incPartition)//'/Homog_'//trim(homogenization_name(homog))
call PetscViewerHDF5PushGroup(resUnit, homogPartition, ierr)
CHKERRQ(ierr)
do res = 1, homogOutput(homog)%sizeResults
write(resultPartition,'(a12,i0)') 'homogResult_',res
call PetscObjectSetName(homogenizationResultsVec(homog),trim(resultPartition),ierr)
CHKERRQ(ierr)
call VecGetArrayF90(homogenizationResultsVec(homog),results,ierr);CHKERRQ(ierr)
results = homogOutput(homog)%output(res,:)
call VecRestoreArrayF90(homogenizationResultsVec(homog), results, ierr)
CHKERRQ(ierr)
call VecAssemblyBegin(homogenizationResultsVec(homog), ierr); CHKERRQ(ierr)
call VecAssemblyEnd (homogenizationResultsVec(homog), ierr); CHKERRQ(ierr)
call VecView(homogenizationResultsVec(homog), resUnit, ierr); CHKERRQ(ierr)
enddo
call PetscViewerHDF5PopGroup(resUnit, ierr); CHKERRQ(ierr)
endif
enddo
do cryst = 1, material_Ncrystallite; do grain = 1, homogenization_maxNgrains
call VecGetSize(crystalliteResultsVec(cryst,grain),resSize,ierr)
if (resSize > 0) then
write(grainStr,'(a,i0)') 'Grain',grain
crystPartition = trim(incPartition)//'/Crystallite_'//trim(crystallite_name(cryst))//'_'//trim(grainStr)
call PetscViewerHDF5PushGroup(resUnit, crystPartition, ierr)
CHKERRQ(ierr)
do res = 1, crystalliteOutput(cryst,grain)%sizeResults
write(resultPartition,'(a18,i0)') 'crystalliteResult_',res
call PetscObjectSetName(crystalliteResultsVec(cryst,grain),trim(resultPartition),ierr)
CHKERRQ(ierr)
call VecGetArrayF90(crystalliteResultsVec(cryst,grain),results,ierr)
CHKERRQ(ierr)
results = crystalliteOutput(cryst,grain)%output(res,:)
call VecRestoreArrayF90(crystalliteResultsVec(cryst,grain), results, ierr)
CHKERRQ(ierr)
call VecAssemblyBegin(crystalliteResultsVec(cryst,grain), ierr);CHKERRQ(ierr)
call VecAssemblyEnd (crystalliteResultsVec(cryst,grain), ierr);CHKERRQ(ierr)
call VecView(crystalliteResultsVec(cryst,grain), resUnit, ierr);CHKERRQ(ierr)
enddo
call PetscViewerHDF5PopGroup(resUnit, ierr); CHKERRQ(ierr)
endif
enddo; enddo
do phase = 1, material_Nphase; do grain = 1, homogenization_maxNgrains
call VecGetSize(phaseResultsVec(phase,grain),resSize,ierr)
if (resSize > 0) then
write(grainStr,'(a,i0)') 'Grain',grain
phasePartition = trim(incPartition)//'/Phase_'//trim(phase_name(phase))//'_'//trim(grainStr)
call PetscViewerHDF5PushGroup(resUnit, phasePartition, ierr)
CHKERRQ(ierr)
do res = 1, phaseOutput(phase,grain)%sizeResults
write(resultPartition,'(a12,i0)') 'phaseResult_',res
call PetscObjectSetName(phaseResultsVec(phase,grain),trim(resultPartition),ierr)
CHKERRQ(ierr)
call VecGetArrayF90(phaseResultsVec(phase,grain),results,ierr);CHKERRQ(ierr)
results = phaseOutput(phase,grain)%output(res,:)
call VecRestoreArrayF90(phaseResultsVec(phase,grain), results, ierr)
CHKERRQ(ierr)
call VecAssemblyBegin(phaseResultsVec(phase,grain), ierr); CHKERRQ(ierr)
call VecAssemblyEnd (phaseResultsVec(phase,grain), ierr); CHKERRQ(ierr)
call VecView(phaseResultsVec(phase,grain), resUnit, ierr); CHKERRQ(ierr)
enddo
call PetscViewerHDF5PopGroup(resUnit, ierr); CHKERRQ(ierr)
endif
enddo; enddo
end subroutine FEM_mech_output
!--------------------------------------------------------------------------------------------------
!> @brief destroy routine

25
src/FEM_utilities.f90
View File

@ -3,8 +3,7 @@
!> @brief Utilities used by the FEM solver
!--------------------------------------------------------------------------------------------------
module FEM_utilities
#include <petsc/finclude/petscis.h>
#include <petsc/finclude/petscdmda.h>
#include <petsc/finclude/petsc.h>
use prec, only: pReal, pInt
use PETScdmda
@ -12,7 +11,6 @@ use PETScis
implicit none
private
#include <petsc/finclude/petsc.h>
!--------------------------------------------------------------------------------------------------
!
logical, public :: cutBack = .false. !< cut back of BVP solver in case convergence is not achieved or a material point is terminally ill
@ -187,14 +185,9 @@ subroutine utilities_init()
use mesh, only: &
mesh_NcpElemsGlobal, &
mesh_maxNips, &
geomMesh, &
mesh_element
geomMesh
use material, only: &
homogenization_Ngrains, &
homogenization_maxNgrains, &
material_homog, &
material_phase, &
microstructure_crystallite
material_homog
implicit none
@ -204,17 +197,13 @@ subroutine utilities_init()
PetscInt, dimension(:), pointer :: points
PetscInt, allocatable :: nEntities(:), nOutputCells(:), nOutputNodes(:), mappingCells(:)
PetscInt :: cellStart, cellEnd, cell, ip, dim, ctr, qPt
PetscInt :: homog, cryst, grain, phase
PetscInt, allocatable :: connectivity(:,:)
Vec :: connectivityVec
PetscScalar, dimension(:), pointer :: results
PetscErrorCode :: ierr
if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- DAMASK_FEM_utilities init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
write(6,'(/,a)') ' <<<+- DAMASK_FEM_utilities init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif
!--------------------------------------------------------------------------------------------------
! set debugging parameters
@ -738,8 +727,8 @@ end subroutine utilities_indexActiveSet
!> @brief cleans up
!--------------------------------------------------------------------------------------------------
subroutine utilities_destroy()
use material, only: &
homogenization_Ngrains
!use material, only: &
! homogenization_Ngrains
!implicit none
!PetscInt :: homog, cryst, grain, phase