void
MechanicalContactConstraint::computeOffDiagJacobian(unsigned int jvar)
{
getConnectedDofIndices(jvar);
_Kee.resize(_test_slave.size(), _connected_dof_indices.size());
DenseMatrix<Number> & Knn = _assembly.jacobianBlockNeighbor(Moose::NeighborNeighbor, _master_var.number(), jvar);
for (_i=0; _i<_test_slave.size(); _i++)
// Loop over the connected dof indices so we can get all the jacobian contributions
for (_j=0; _j<_connected_dof_indices.size(); _j++)
_Kee(_i,_j) += computeQpOffDiagJacobian(Moose::SlaveSlave, jvar);
if (_master_slave_jacobian)
{
DenseMatrix<Number> & Ken = _assembly.jacobianBlockNeighbor(Moose::ElementNeighbor, _var.number(), jvar);
for (_i=0; _i<_test_slave.size(); _i++)
for (_j=0; _j<_phi_master.size(); _j++)
Ken(_i,_j) += computeQpOffDiagJacobian(Moose::SlaveMaster, jvar);
_Kne.resize(_test_master.size(), _connected_dof_indices.size());
if (_Kne.m() && _Kne.n())
for (_i=0; _i<_test_master.size(); _i++)
// Loop over the connected dof indices so we can get all the jacobian contributions
for (_j=0; _j<_connected_dof_indices.size(); _j++)
_Kne(_i,_j) += computeQpOffDiagJacobian(Moose::MasterSlave, jvar);
}
for (_i=0; _i<_test_master.size(); _i++)
for (_j=0; _j<_phi_master.size(); _j++)
Knn(_i,_j) += computeQpOffDiagJacobian(Moose::MasterMaster, jvar);
}
void
KernelValue::computeOffDiagJacobian(unsigned int jvar)
{
// Moose::perf_log.push("computeOffDiagJacobian()",_name);
DenseMatrix<Number> & Ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_j=0; _j<_phi.size(); _j++)
for (_qp=0; _qp<_qrule->n_points(); _qp++)
{
if (jvar == _var.number())
{
_value = _coord[_qp]*precomputeQpJacobian();
for (_i=0; _i<_test.size(); _i++)
Ke(_i,_j) += _JxW[_qp]*_coord[_qp]*_value*_test[_i][_qp];
}
else
{
for (_i=0; _i<_test.size(); _i++)
{
_value = _coord[_qp]*computeQpOffDiagJacobian(jvar);
Ke(_i,_j) += _JxW[_qp]*_coord[_qp]*_value;
}
}
}
// Moose::perf_log.pop("computeOffDiagJacobian()",_name);
}
void
DiracKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
{
computeJacobian();
}
else
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
const std::vector<unsigned int> * multiplicities = _drop_duplicate_points ? NULL : &_local_dirac_kernel_info.getPoints()[_current_elem].second;
unsigned int local_qp = 0;
Real multiplicity = 1.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
_current_point = _physical_point[_qp];
if (isActiveAtPoint(_current_elem, _current_point))
{
if (!_drop_duplicate_points)
multiplicity = (*multiplicities)[local_qp++];
for (_i=0; _i<_test.size(); _i++)
for (_j=0; _j<_phi.size(); _j++)
ke(_i, _j) += multiplicity * computeQpOffDiagJacobian(jvar);
}
}
}
}
void
NodeFaceConstraint::computeOffDiagJacobian(unsigned int jvar)
{
getConnectedDofIndices(jvar);
_Kee.resize(_test_slave.size(), _connected_dof_indices.size());
_Kne.resize(_test_master.size(), _connected_dof_indices.size());
DenseMatrix<Number> & Ken = _assembly.jacobianBlockNeighbor(Moose::ElementNeighbor, _var.number(), jvar);
DenseMatrix<Number> & Knn = _assembly.jacobianBlockNeighbor(Moose::NeighborNeighbor, _master_var.number(), jvar);
_phi_slave.resize(_connected_dof_indices.size());
_qp = 0;
// Fill up _phi_slave so that it is 1 when j corresponds to this dof and 0 for every other dof
// This corresponds to evaluating all of the connected shape functions at _this_ node
for (unsigned int j=0; j<_connected_dof_indices.size(); j++)
{
_phi_slave[j].resize(1);
if (_connected_dof_indices[j] == _var.nodalDofIndex())
_phi_slave[j][_qp] = 1.0;
else
_phi_slave[j][_qp] = 0.0;
}
for (_i=0; _i<_test_slave.size(); _i++)
// Loop over the connected dof indices so we can get all the jacobian contributions
for (_j=0; _j<_connected_dof_indices.size(); _j++)
_Kee(_i,_j) += computeQpOffDiagJacobian(Moose::SlaveSlave, jvar);
for (_i=0; _i<_test_slave.size(); _i++)
for (_j=0; _j<_phi_master.size(); _j++)
Ken(_i,_j) += computeQpOffDiagJacobian(Moose::SlaveMaster, jvar);
if (_Kne.m() && _Kne.n())
for (_i=0; _i<_test_master.size(); _i++)
// Loop over the connected dof indices so we can get all the jacobian contributions
for (_j=0; _j<_connected_dof_indices.size(); _j++)
_Kne(_i,_j) += computeQpOffDiagJacobian(Moose::MasterSlave, jvar);
for (_i=0; _i<_test_master.size(); _i++)
for (_j=0; _j<_phi_master.size(); _j++)
Knn(_i,_j) += computeQpOffDiagJacobian(Moose::MasterMaster, jvar);
}
void
StressDivergenceRZ::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
if (_volumetric_locking_correction)
{
// calculate volume averaged value of shape function derivative
_avg_grad_test.resize(_test.size());
for (_i = 0; _i < _test.size(); _i++)
{
_avg_grad_test[_i].resize(2);
_avg_grad_test[_i][_component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
if (_component == 0)
_avg_grad_test[_i][_component] += (_grad_test[_i][_qp](_component) + _test[_i][_qp] / _q_point[_qp](0)) * _JxW[_qp] * _coord[_qp];
else
_avg_grad_test[_i][_component] += _grad_test[_i][_qp](_component) * _JxW[_qp] * _coord[_qp];
}
_avg_grad_test[_i][_component] /= _current_elem_volume;
}
_avg_grad_phi.resize(_phi.size());
for (_i = 0; _i < _phi.size(); _i++)
{
_avg_grad_phi[_i].resize(3);
for (unsigned int component = 0; component < 2; component++)
{
_avg_grad_phi[_i][component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
if (component == 0)
_avg_grad_phi[_i][component] += (_grad_phi[_i][_qp](component) + _phi[_i][_qp] / _q_point[_qp](0)) * _JxW[_qp] * _coord[_qp];
else
_avg_grad_phi[_i][component] += _grad_phi[_i][_qp](component) * _JxW[_qp] * _coord[_qp];
}
_avg_grad_phi[_i][component] /= _current_elem_volume;
}
}
}
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < _phi.size(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
}
void
IntegratedBC::computeJacobianBlockScalar(unsigned int jvar)
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
MooseVariableScalar & jv = _sys.getScalarVariable(_tid, jvar);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < jv.order(); _j++)
ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
void
IntegratedBC::computeJacobianBlockScalar(unsigned int jvar)
{
prepareMatrixTag(_assembly, _var.number(), jvar);
MooseVariableScalar & jv = _sys.getScalarVariable(_tid, jvar);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < jv.order(); _j++)
_local_ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
accumulateTaggedLocalMatrix();
}
void
KernelGrad::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
DenseMatrix<Number> & Ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_j = 0; _j < _phi.size(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
Ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
}
void
ODEKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (_sys.isScalarVariable(jvar))
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
MooseVariableScalar & var_j = _sys.getScalarVariable(_tid, jvar);
for (_i = 0; _i < _var.order(); _i++)
for (_j = 0; _j < var_j.order(); _j++)
{
if (jvar != _var.number())
ke(_i, _j) += computeQpOffDiagJacobian(jvar);
}
}
}
void
NodalKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
_assembly.cacheJacobianContribution(cached_row, cached_col, cached_val);
}
}
void
DGKernel::computeOffDiagElemNeighJacobian(Moose::DGJacobianType type,unsigned int jvar)
{
const VariableTestValue & test_space = ( type == Moose::ElementElement || type == Moose::ElementNeighbor ) ?
_test : _test_neighbor;
const VariableTestValue & loc_phi = ( type == Moose::ElementElement || type == Moose::NeighborElement ) ?
_phi : _phi_neighbor;
DenseMatrix<Number> & Kxx = type == Moose::ElementElement ? _assembly.jacobianBlock(_var.number(), jvar) :
type == Moose::ElementNeighbor ? _assembly.jacobianBlockNeighbor(Moose::ElementNeighbor, _var.number(), jvar) :
type == Moose::NeighborElement ? _assembly.jacobianBlockNeighbor(Moose::NeighborElement, _var.number(), jvar) :
_assembly.jacobianBlockNeighbor(Moose::NeighborNeighbor, _var.number(), jvar);
for (_qp=0; _qp<_qrule->n_points(); _qp++)
for (_i=0; _i<test_space.size(); _i++)
for (_j=0; _j<loc_phi.size(); _j++)
Kxx(_i,_j) += _JxW[_qp]*_coord[_qp]*computeQpOffDiagJacobian(type, jvar);
}
void
NodalBC::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
// Cache the user's computeQpJacobian() value for later use.
_fe_problem.assembly(0).cacheNodalBCJacobianEntry(cached_row, cached_col, cached_val);
}
}
void
StressDivergence::computeOffDiagJacobian(MooseVariableFEBase & jvar)
{
size_t jvar_num = jvar.number();
if (jvar_num == _var.number())
computeJacobian();
else
{
if (_volumetric_locking_correction)
{
// calculate volume averaged value of shape function derivative
_avg_grad_test.resize(_test.size());
for (_i = 0; _i < _test.size(); _i++)
{
_avg_grad_test[_i].resize(3);
_avg_grad_test[_i][_component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
_avg_grad_test[_i][_component] +=
_grad_test[_i][_qp](_component) * _JxW[_qp] * _coord[_qp];
_avg_grad_test[_i][_component] /= _current_elem_volume;
}
_avg_grad_phi.resize(jvar.phiSize());
for (_i = 0; _i < jvar.phiSize(); _i++)
{
_avg_grad_phi[_i].resize(3);
for (unsigned int component = 0; component < _mesh.dimension(); component++)
{
_avg_grad_phi[_i][component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
_avg_grad_phi[_i][component] += _grad_phi[_i][_qp](component) * _JxW[_qp] * _coord[_qp];
_avg_grad_phi[_i][component] /= _current_elem_volume;
}
}
}
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar_num);
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < jvar.phiSize(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar_num);
}
}
void
IntegratedBC::computeJacobianBlock(MooseVariableFEBase & jvar)
{
size_t jvar_num = jvar.number();
prepareMatrixTag(_assembly, _var.number(), jvar_num);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < jvar.phiFaceSize(); _j++)
{
if (_var.number() == jvar_num)
_local_ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpJacobian();
else
_local_ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar_num);
}
accumulateTaggedLocalMatrix();
}
void
ODEKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (_sys.isScalarVariable(jvar))
{
prepareMatrixTag(_assembly, _var.number(), jvar);
MooseVariableScalar & var_j = _sys.getScalarVariable(_tid, jvar);
for (_i = 0; _i < _var.order(); _i++)
for (_j = 0; _j < var_j.order(); _j++)
{
if (jvar != _var.number())
_local_ke(_i, _j) += computeQpOffDiagJacobian(jvar);
}
accumulateTaggedLocalMatrix();
}
}
void
IntegratedBC::computeJacobianBlock(unsigned int jvar)
{
// Moose::perf_log.push("computeJacobianBlock()","IntegratedBC");
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_qp=0; _qp<_qrule->n_points(); _qp++)
for (_i=0; _i<_test.size(); _i++)
for (_j=0; _j<_phi.size(); _j++)
{
if (_var.number() == jvar)
ke(_i,_j) += _JxW[_qp]*_coord[_qp]*computeQpJacobian();
else
ke(_i,_j) += _JxW[_qp]*_coord[_qp]*computeQpOffDiagJacobian(jvar);
}
// Moose::perf_log.pop("computeJacobianBlock()","IntegratedBC");
}
void
IntegratedBC::computeJacobianBlock(unsigned int jvar)
{
mooseDeprecated("The computeJacobianBlock method signature has changed. Developers, please "
"pass in a MooseVariableFEBase reference instead of the variable number");
prepareMatrixTag(_assembly, _var.number(), jvar);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < _phi.size(); _j++)
{
if (_var.number() == jvar)
_local_ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpJacobian();
else
_local_ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
accumulateTaggedLocalMatrix();
}
void
DiracKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
{
computeJacobian();
}
else
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
_current_point = _physical_point[_qp];
if (isActiveAtPoint(_current_elem, _current_point))
for (_i=0; _i<_test.size(); _i++)
for (_j=0; _j<_phi.size(); _j++)
ke(_i, _j) += computeQpOffDiagJacobian(jvar);
}
}
}
void
NodalBC::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = 0.0;
cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
// Cache the user's computeQpJacobian() value for later use.
for (auto tag : _matrix_tags)
if (_sys.hasMatrix(tag))
_fe_problem.assembly(0).cacheJacobianContribution(cached_row, cached_col, cached_val, tag);
}
}
Real
PorousFlowHeatConduction::computeQpJacobian()
{
return computeQpOffDiagJacobian(_var.number());
}
Real
PlasticHeatEnergy::computeQpJacobian()
{
return computeQpOffDiagJacobian(_var.number());
}
