NumericType PostProcessedQuantities<NumericType>::component( const libMesh::FEMContext& context,
unsigned int component,
const libMesh::Point& p,
libMesh::Real /*time*/ )
{
// Check if the Elem is the same between the incoming context and the cached one.
// If not, reinit the cached MultiphysicsSystem context
if( &(context.get_elem()) != &(_multiphysics_context->get_elem()) )
{
_multiphysics_context->pre_fe_reinit(*_multiphysics_sys,&context.get_elem());
_multiphysics_context->elem_fe_reinit();
}
/* Optimization since we expect this function to be called many times with
the same point. _prev_point initialized to something absurd so this should
always be false the first time. */
if( _prev_point != p )
{
_prev_point = p;
std::vector<libMesh::Point> point_vec(1,p);
this->_cache.clear();
_multiphysics_sys->compute_element_cache( *(this->_multiphysics_context), point_vec, this->_cache );
}
return this->compute_quantities( component );
}
void PostProcessedQuantities<NumericType>::init_context( const libMesh::FEMContext& context )
{
// Make sure we prepare shape functions for our output variables.
/*! \todo I believe this is redundant because it's done in the project_vector call. Double check. */
for( typename std::map<VariableIndex,unsigned int>::const_iterator it = _quantity_var_map.begin();
it != _quantity_var_map.end(); it++ )
{
libMesh::FEBase* elem_fe = NULL;
context.get_element_fe( it->first, elem_fe );
elem_fe->get_phi();
elem_fe->get_dphi();
elem_fe->get_JxW();
elem_fe->get_xyz();
libMesh::FEBase* side_fe = NULL;
context.get_side_fe( it->first, side_fe );
side_fe->get_phi();
side_fe->get_dphi();
side_fe->get_JxW();
side_fe->get_xyz();
}
// Create the context we'll be using to compute MultiphysicsSystem quantities
_multiphysics_context.reset( new AssemblyContext( *_multiphysics_sys ) );
_multiphysics_sys->init_context(*_multiphysics_context);
return;
}
void BoundaryConditions::pin_value( libMesh::FEMContext& context,
const CachedValues& /*cache*/,
const bool request_jacobian,
const VariableIndex var,
const double pin_value,
const libMesh::Point& pin_location,
const double penalty )
{
if (context.elem->contains_point(pin_location))
{
libMesh::DenseSubVector<libMesh::Number> &F_var = *context.elem_subresiduals[var]; // residual
libMesh::DenseSubMatrix<libMesh::Number> &K_var = *context.elem_subjacobians[var][var]; // jacobian
// The number of local degrees of freedom in p variable.
const unsigned int n_var_dofs = context.dof_indices_var[var].size();
libMesh::Number var_value = context.point_value(var, pin_location);
libMesh::FEType fe_type = context.element_fe_var[var]->get_fe_type();
libMesh::Point point_loc_in_masterelem =
libMesh::FEInterface::inverse_map(context.dim, fe_type, context.elem, pin_location);
std::vector<libMesh::Real> phi(n_var_dofs);
for (unsigned int i=0; i != n_var_dofs; i++)
phi[i] = libMesh::FEInterface::shape( context.dim, fe_type, context.elem, i,
point_loc_in_masterelem );
for (unsigned int i=0; i != n_var_dofs; i++)
{
F_var(i) += penalty*(var_value - pin_value)*phi[i];
/** \todo What the hell is the context.elem_solution_derivative all about? */
if (request_jacobian && context.elem_solution_derivative)
{
libmesh_assert (context.elem_solution_derivative == 1.0);
for (unsigned int j=0; j != n_var_dofs; j++)
K_var(i,j) += penalty*phi[i]*phi[j];
} // End if request_jacobian
} // End i loop
} // End if pin_location
return;
}
void HeatTransfer::side_time_derivative( bool compute_jacobian,
libMesh::FEMContext& context,
CachedValues& cache )
{
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->BeginTimer("HeatTransfer::side_time_derivative");
#endif
std::vector<BoundaryID> ids = context.side_boundary_ids();
for( std::vector<BoundaryID>::const_iterator it = ids.begin();
it != ids.end(); it++ )
{
libmesh_assert (*it != libMesh::BoundaryInfo::invalid_id);
_bc_handler->apply_neumann_bcs( context, cache, compute_jacobian, *it );
}
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->EndTimer("HeatTransfer::side_time_derivative");
#endif
return;
}
NumericType PostProcessedQuantities<NumericType>::component( const libMesh::FEMContext& context,
unsigned int component,
const libMesh::Point& p,
libMesh::Real /*time*/ )
{
// Check if the Elem is the same between the incoming context and the cached one.
// If not, reinit the cached MultiphysicsSystem context
if(context.has_elem() && _multiphysics_context->has_elem())
{
if( &(context.get_elem()) != &(_multiphysics_context->get_elem()) )
{
_multiphysics_context->pre_fe_reinit(*_multiphysics_sys,&context.get_elem());
_multiphysics_context->elem_fe_reinit();
}
}
else if( !context.has_elem() && _multiphysics_context->has_elem() )
{
// Incoming context has NULL elem ==> SCALAR variables
_multiphysics_context->pre_fe_reinit(*_multiphysics_sys,NULL);
_multiphysics_context->elem_fe_reinit();
}
else if( context.has_elem() && !_multiphysics_context->has_elem() )
{
_multiphysics_context->pre_fe_reinit(*_multiphysics_sys,&context.get_elem());
_multiphysics_context->elem_fe_reinit();
}
//else
/* If has_elem() is false for both contexts, we're still dealing with SCALAR variables
and therefore don't need to reinit. */
libMesh::Real value = 0.0;
// Quantity we want had better be there.
libmesh_assert(_quantity_index_var_map.find(component) != _quantity_index_var_map.end());
unsigned int quantity_index = _quantity_index_var_map.find(component)->second;
_multiphysics_sys->compute_postprocessed_quantity( quantity_index,
*(this->_multiphysics_context),
p, value );
return value;
}
void HeatTransfer::element_time_derivative( bool compute_jacobian,
libMesh::FEMContext& context,
CachedValues& /*cache*/ )
{
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->BeginTimer("HeatTransfer::element_time_derivative");
#endif
// The number of local degrees of freedom in each variable.
const unsigned int n_T_dofs = context.dof_indices_var[_T_var].size();
const unsigned int n_u_dofs = context.dof_indices_var[_u_var].size();
//TODO: check n_T_dofs is same as n_u_dofs, n_v_dofs, n_w_dofs
// We get some references to cell-specific data that
// will be used to assemble the linear system.
// Element Jacobian * quadrature weights for interior integration.
const std::vector<libMesh::Real> &JxW =
context.element_fe_var[_T_var]->get_JxW();
// The temperature shape functions at interior quadrature points.
const std::vector<std::vector<libMesh::Real> >& T_phi =
context.element_fe_var[_T_var]->get_phi();
// The velocity shape functions at interior quadrature points.
const std::vector<std::vector<libMesh::Real> >& vel_phi =
context.element_fe_var[_u_var]->get_phi();
// The temperature shape function gradients (in global coords.)
// at interior quadrature points.
const std::vector<std::vector<libMesh::RealGradient> >& T_gradphi =
context.element_fe_var[_T_var]->get_dphi();
const std::vector<libMesh::Point>& u_qpoint =
context.element_fe_var[this->_u_var]->get_xyz();
// We do this in the incompressible Navier-Stokes class and need to do it here too
// since _w_var won't have been defined in the global map.
if (_dim != 3)
_w_var = _u_var; // for convenience
libMesh::DenseSubMatrix<libMesh::Number> &KTT = *context.elem_subjacobians[_T_var][_T_var]; // R_{T},{T}
libMesh::DenseSubMatrix<libMesh::Number> &KTu = *context.elem_subjacobians[_T_var][_u_var]; // R_{T},{u}
libMesh::DenseSubMatrix<libMesh::Number> &KTv = *context.elem_subjacobians[_T_var][_v_var]; // R_{T},{v}
libMesh::DenseSubMatrix<libMesh::Number> &KTw = *context.elem_subjacobians[_T_var][_w_var]; // R_{T},{w}
libMesh::DenseSubVector<libMesh::Number> &FT = *context.elem_subresiduals[_T_var]; // R_{T}
// Now we will build the element Jacobian and residual.
// Constructing the residual requires the solution and its
// gradient from the previous timestep. This must be
// calculated at each quadrature point by summing the
// solution degree-of-freedom values by the appropriate
// weight functions.
unsigned int n_qpoints = context.element_qrule->n_points();
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
// Compute the solution & its gradient at the old Newton iterate.
libMesh::Number u, v, w;
u = context.interior_value(_u_var, qp);
v = context.interior_value(_v_var, qp);
if (_dim == 3)
w = context.interior_value(_w_var, qp);
libMesh::Gradient grad_T;
grad_T = context.interior_gradient(_T_var, qp);
libMesh::NumberVectorValue U (u,v);
if (_dim == 3)
U(2) = w;
const libMesh::Number r = u_qpoint[qp](0);
libMesh::Real jac = JxW[qp];
if( _is_axisymmetric )
{
jac *= r;
}
// First, an i-loop over the degrees of freedom.
for (unsigned int i=0; i != n_T_dofs; i++)
{
FT(i) += jac *
(-_rho*_Cp*T_phi[i][qp]*(U*grad_T) // convection term
-_k*(T_gradphi[i][qp]*grad_T) ); // diffusion term
if (compute_jacobian)
{
for (unsigned int j=0; j != n_T_dofs; j++)
{
// TODO: precompute some terms like:
// _rho*_Cp*T_phi[i][qp]*(vel_phi[j][qp]*T_grad_phi[j][qp])
KTT(i,j) += jac *
(-_rho*_Cp*T_phi[i][qp]*(U*T_gradphi[j][qp]) // convection term
-_k*(T_gradphi[i][qp]*T_gradphi[j][qp])); // diffusion term
} // end of the inner dof (j) loop
// Matrix contributions for the Tu, Tv and Tw couplings (n_T_dofs same as n_u_dofs, n_v_dofs and n_w_dofs)
for (unsigned int j=0; j != n_u_dofs; j++)
{
KTu(i,j) += jac*(-_rho*_Cp*T_phi[i][qp]*(vel_phi[j][qp]*grad_T(0)));
KTv(i,j) += jac*(-_rho*_Cp*T_phi[i][qp]*(vel_phi[j][qp]*grad_T(1)));
if (_dim == 3)
KTw(i,j) += jac*(-_rho*_Cp*T_phi[i][qp]*(vel_phi[j][qp]*grad_T(2)));
} // end of the inner dof (j) loop
} // end - if (compute_jacobian && context.elem_solution_derivative)
} // end of the outer dof (i) loop
} // end of the quadrature point (qp) loop
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->EndTimer("HeatTransfer::element_time_derivative");
#endif
return;
}
void HeatTransfer::mass_residual( bool compute_jacobian,
libMesh::FEMContext& context,
CachedValues& /*cache*/ )
{
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->BeginTimer("HeatTransfer::mass_residual");
#endif
// First we get some references to cell-specific data that
// will be used to assemble the linear system.
// Element Jacobian * quadrature weights for interior integration
const std::vector<libMesh::Real> &JxW =
context.element_fe_var[_T_var]->get_JxW();
// The shape functions at interior quadrature points.
const std::vector<std::vector<libMesh::Real> >& phi =
context.element_fe_var[_T_var]->get_phi();
const std::vector<libMesh::Point>& u_qpoint =
context.element_fe_var[this->_u_var]->get_xyz();
// The number of local degrees of freedom in each variable
const unsigned int n_T_dofs = context.dof_indices_var[_T_var].size();
// The subvectors and submatrices we need to fill:
libMesh::DenseSubVector<libMesh::Real> &F = *context.elem_subresiduals[_T_var];
libMesh::DenseSubMatrix<libMesh::Real> &M = *context.elem_subjacobians[_T_var][_T_var];
unsigned int n_qpoints = context.element_qrule->n_points();
for (unsigned int qp = 0; qp != n_qpoints; ++qp)
{
// For the mass residual, we need to be a little careful.
// The time integrator is handling the time-discretization
// for us so we need to supply M(u_fixed)*u for the residual.
// u_fixed will be given by the fixed_interior_* functions
// while u will be given by the interior_* functions.
libMesh::Real T_dot = context.interior_value(_T_var, qp);
const libMesh::Number r = u_qpoint[qp](0);
libMesh::Real jac = JxW[qp];
if( _is_axisymmetric )
{
jac *= r;
}
for (unsigned int i = 0; i != n_T_dofs; ++i)
{
F(i) += _rho*_Cp*T_dot*phi[i][qp]*jac;
if( compute_jacobian )
{
for (unsigned int j=0; j != n_T_dofs; j++)
{
// We're assuming rho, cp are constant w.r.t. T here.
M(i,j) += _rho*_Cp*phi[j][qp]*phi[i][qp]*jac;
}
}// End of check on Jacobian
} // End of element dof loop
} // End of the quadrature point loop
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->EndTimer("HeatTransfer::mass_residual");
#endif
return;
}