void
ComputeResidualThread::onBoundary(const Elem *elem, unsigned int side, BoundaryID bnd_id)
{
std::vector<IntegratedBC *> bcs = _sys._bcs[_tid].activeIntegrated(bnd_id);
if (bcs.size() > 0)
{
_fe_problem.reinitElemFace(elem, side, bnd_id, _tid);
unsigned int subdomain = elem->subdomain_id();
if (subdomain != _subdomain)
_fe_problem.subdomainSetupSide(subdomain, _tid);
_fe_problem.reinitMaterialsFace(elem->subdomain_id(), _tid);
_fe_problem.reinitMaterialsBoundary(bnd_id, _tid);
// Set the active boundary id so that BoundaryRestrictable::_boundary_id is correct
_fe_problem.setCurrentBoundaryID(bnd_id);
for (std::vector<IntegratedBC *>::iterator it = bcs.begin(); it != bcs.end(); ++it)
{
IntegratedBC * bc = (*it);
if (bc->shouldApply())
bc->computeResidual();
}
_fe_problem.swapBackMaterialsFace(_tid);
// Set active boundary id to invalid
_fe_problem.setCurrentBoundaryID(Moose::INVALID_BOUNDARY_ID);
}
}
void
ComputeResidualThread::subdomainChanged()
{
_fe_problem.subdomainSetup(_subdomain, _tid);
_sys._kernels[_tid].updateActiveKernels(_subdomain);
if (_sys._doing_dg)
_sys._dg_kernels[_tid].updateActiveDGKernels(_fe_problem.time(), _fe_problem.dt());
std::set<MooseVariable *> needed_moose_vars;
const std::vector<KernelBase *> & kernels = _sys._kernels[_tid].active();
for (std::vector<KernelBase *>::const_iterator it = kernels.begin(); it != kernels.end(); ++it)
{
const std::set<MooseVariable *> & mv_deps = (*it)->getMooseVariableDependencies();
needed_moose_vars.insert(mv_deps.begin(), mv_deps.end());
}
// Boundary Condition Dependencies
const std::set<unsigned int> & subdomain_boundary_ids = _mesh.getSubdomainBoundaryIds(_subdomain);
for (std::set<unsigned int>::const_iterator id_it = subdomain_boundary_ids.begin();
id_it != subdomain_boundary_ids.end();
++id_it)
{
std::vector<IntegratedBC *> bcs = _sys._bcs[_tid].activeIntegrated(*id_it);
if (bcs.size() > 0)
{
for (std::vector<IntegratedBC *>::iterator it = bcs.begin(); it != bcs.end(); ++it)
{
IntegratedBC * bc = (*it);
if (bc->shouldApply())
{
const std::set<MooseVariable *> & mv_deps = bc->getMooseVariableDependencies();
needed_moose_vars.insert(mv_deps.begin(), mv_deps.end());
}
}
}
}
// DG Kernel dependencies
{
std::vector<DGKernel *> dgks = _sys._dg_kernels[_tid].active();
for (std::vector<DGKernel *>::iterator it = dgks.begin(); it != dgks.end(); ++it)
{
const std::set<MooseVariable *> & mv_deps = (*it)->getMooseVariableDependencies();
needed_moose_vars.insert(mv_deps.begin(), mv_deps.end());
}
}
_fe_problem.setActiveElementalMooseVariables(needed_moose_vars, _tid);
_fe_problem.prepareMaterials(_subdomain, _tid);
}
void
ComputeJacobianBlockThread::operator() (const ConstElemRange & range, bool bypass_threading/*=false*/)
{
ParallelUniqueId puid;
_tid = bypass_threading ? 0 : puid.id;
unsigned int subdomain = std::numeric_limits<unsigned int>::max();
const DofMap & dof_map = _precond_system.get_dof_map();
std::vector<unsigned int> dof_indices;
ConstElemRange::const_iterator range_end = range.end();
for (ConstElemRange::const_iterator el = range.begin() ; el != range_end; ++el)
{
const Elem* elem = *el;
unsigned int cur_subdomain = elem->subdomain_id();
dof_map.dof_indices(elem, dof_indices);
if (dof_indices.size())
{
_fe_problem.prepare(elem, _ivar, _jvar, dof_indices, _tid);
_fe_problem.reinitElem(elem, _tid);
if (cur_subdomain != subdomain)
{
subdomain = cur_subdomain;
_fe_problem.subdomainSetup(subdomain, _tid);
_nl._kernels[_tid].updateActiveKernels(cur_subdomain);
}
_fe_problem.reinitMaterials(cur_subdomain, _tid);
//Kernels
std::vector<KernelBase *> kernels = _nl._kernels[_tid].active();
for (std::vector<KernelBase *>::const_iterator it = kernels.begin(); it != kernels.end(); it++)
{
KernelBase * kernel = *it;
if (kernel->variable().index() == _ivar)
{
kernel->subProblem().prepareShapes(_jvar, _tid);
kernel->computeOffDiagJacobian(_jvar);
}
}
_fe_problem.swapBackMaterials(_tid);
for (unsigned int side = 0; side < elem->n_sides(); side++)
{
std::vector<BoundaryID> boundary_ids = _mesh.boundaryIDs(elem, side);
if (boundary_ids.size() > 0)
{
for (std::vector<BoundaryID>::iterator it = boundary_ids.begin(); it != boundary_ids.end(); ++it)
{
BoundaryID bnd_id = *it;
std::vector<IntegratedBC *> bcs = _nl._bcs[_tid].activeIntegrated(bnd_id);
if (bcs.size() > 0)
{
_fe_problem.prepareFace(elem, _tid);
_fe_problem.reinitElemFace(elem, side, bnd_id, _tid);
_fe_problem.reinitMaterialsFace(elem->subdomain_id(), _tid);
_fe_problem.reinitMaterialsBoundary(bnd_id, _tid);
for (std::vector<IntegratedBC *>::iterator it = bcs.begin(); it != bcs.end(); ++it)
{
IntegratedBC * bc = *it;
if (bc->variable().index() == _ivar)
{
if (bc->shouldApply())
{
bc->subProblem().prepareFaceShapes(_jvar, _tid);
bc->computeJacobianBlock(_jvar);
}
}
}
_fe_problem.swapBackMaterialsFace(_tid);
}
}
}
if (elem->neighbor(side) != NULL)
{
// on internal edge
// Pointer to the neighbor we are currently working on.
const Elem * neighbor = elem->neighbor(side);
// Get the global id of the element and the neighbor
const unsigned int elem_id = elem->id();
const unsigned int neighbor_id = neighbor->id();
if ((neighbor->active() && (neighbor->level() == elem->level()) && (elem_id < neighbor_id)) || (neighbor->level() < elem->level()))
{
std::vector<DGKernel *> dgks = _nl._dg_kernels[_tid].active();
if (dgks.size() > 0)
{
_fe_problem.prepareFace(elem, _tid);
_fe_problem.reinitNeighbor(elem, side, _tid);
_fe_problem.reinitMaterialsFace(elem->subdomain_id(), _tid);
_fe_problem.reinitMaterialsNeighbor(neighbor->subdomain_id(), _tid);
for (std::vector<DGKernel *>::iterator it = dgks.begin(); it != dgks.end(); ++it)
{
DGKernel * dg = *it;
if (dg->variable().index() == _ivar)
{
dg->subProblem().prepareFaceShapes(_jvar, _tid);
dg->subProblem().prepareNeighborShapes(_jvar, _tid);
dg->computeOffDiagJacobian(_jvar);
}
}
_fe_problem.swapBackMaterialsFace(_tid);
_fe_problem.swapBackMaterialsNeighbor(_tid);
std::vector<unsigned int> neighbor_dof_indices;
dof_map.dof_indices(neighbor, neighbor_dof_indices);
{
Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
_fe_problem.addJacobianNeighbor(_jacobian, _ivar, _jvar, dof_map, dof_indices, neighbor_dof_indices, _tid);
}
}
}
}
}
{
Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
_fe_problem.addJacobianBlock(_jacobian, _ivar, _jvar, dof_map, dof_indices, _tid);
}
}
}
}
void
ComputeFullJacobianThread::computeFaceJacobian(BoundaryID bnd_id)
{
std::vector<std::pair<MooseVariable *, MooseVariable *> > & ce = _fe_problem.couplingEntries(_tid);
for (std::vector<std::pair<MooseVariable *, MooseVariable *> >::iterator it = ce.begin(); it != ce.end(); ++it)
{
MooseVariable & ivar = *(*it).first;
MooseVariable & jvar = *(*it).second;
if (ivar.activeOnSubdomain(_subdomain) && jvar.activeOnSubdomain(_subdomain))
{
// only if there are dofs for j-variable (if it is subdomain restricted var, there may not be any)
std::vector<IntegratedBC *> bcs = _sys._bcs[_tid].getBCs(bnd_id);
for (std::vector<IntegratedBC *>::iterator jt = bcs.begin(); jt != bcs.end(); ++jt)
{
IntegratedBC * bc = *jt;
if (bc->shouldApply() && bc->variable().index() == ivar.index() && bc->isImplicit())
{
bc->subProblem().prepareFaceShapes(jvar.index(), _tid);
bc->computeJacobianBlock(jvar.index());
}
}
}
}
const std::vector<MooseVariableScalar *> & scalar_vars = _sys.getScalarVariables(_tid);
if (scalar_vars.size() > 0)
{
// go over nl-variables (non-scalar)
const std::vector<MooseVariable *> & vars = _sys.getVariables(_tid);
for (std::vector<MooseVariable *>::const_iterator it = vars.begin(); it != vars.end(); it++)
{
MooseVariable & ivar = *(*it);
if (ivar.activeOnSubdomain(_subdomain) > 0)
{
// for each variable get the list of active kernels
std::vector<IntegratedBC *> bcs = _sys._bcs[_tid].activeIntegrated(bnd_id);
for (std::vector<IntegratedBC *>::iterator kt = bcs.begin(); kt != bcs.end(); ++kt)
{
IntegratedBC * bc = *kt;
if (bc->variable().index() == ivar.index() && bc->isImplicit())
{
// now, get the list of coupled scalar vars and compute their off-diag jacobians
const std::vector<MooseVariableScalar *> coupled_scalar_vars = bc->getCoupledMooseScalarVars();
for (std::vector<MooseVariableScalar *>::const_iterator jt = coupled_scalar_vars.begin(); jt != coupled_scalar_vars.end(); jt++)
{
MooseVariableScalar & jvar = *(*jt);
// Do: dvar / dscalar_var
if (_sys.hasScalarVariable(jvar.name())) // want to process only nl-variables (not aux ones)
bc->computeJacobianBlockScalar(jvar.index());
}
}
}
}
}
}
}