Adds Velocity penalty adjoint stabilization source term. More...

#include <parsed_velocity_source_adjoint_stab.h>

Inheritance diagram for GRINS::ParsedVelocitySourceAdjointStabilization< Viscosity >:

Collaboration diagram for GRINS::ParsedVelocitySourceAdjointStabilization< Viscosity >:

Public Member Functions
	ParsedVelocitySourceAdjointStabilization (const std::string &physics_name, const GetPot &input)

	~ParsedVelocitySourceAdjointStabilization ()

virtual void	init_context (AssemblyContext &context)
	Initialize context for added physics variables. More...

virtual void	element_time_derivative (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Time dependent part(s) of physics for element interiors. More...

virtual void	element_constraint (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Constraint part(s) of physics for element interiors. More...

virtual void	read_input_options (const GetPot &input)
	Read options from GetPot input file. More...

void	set_time_evolving_vars (libMesh::FEMSystem *system)
	Sets velocity variables to be time-evolving. More...

bool	compute_force (const libMesh::Point &point, const libMesh::Real time, const AssemblyContext &c, libMesh::NumberVectorValue &F, libMesh::NumberTensorValue *dFdU=NULL)

virtual void	init_variables (libMesh::FEMSystem *system)
	Initialization of Navier-Stokes variables. More...

virtual void	register_parameter (const std::string &param_name, libMesh::ParameterMultiPointer< libMesh::Number > &param_pointer) const
	Each subclass will register its copy of an independent. More...

virtual bool	enabled_on_elem (const libMesh::Elem *elem)
	Find if current physics is active on supplied element. More...

void	set_is_steady (bool is_steady)
	Sets whether this physics is to be solved with a steady solver or not. More...

bool	is_steady () const
	Returns whether or not this physics is being solved with a steady solver. More...

virtual void	auxiliary_init (MultiphysicsSystem &system)
	Any auxillary initialization a Physics class may need. More...

virtual void	register_postprocessing_vars (const GetPot &input, PostProcessedQuantities< libMesh::Real > &postprocessing)
	Register name of postprocessed quantity with PostProcessedQuantities. More...

virtual void	side_time_derivative (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Time dependent part(s) of physics for boundaries of elements on the domain boundary. More...

virtual void	nonlocal_time_derivative (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Time dependent part(s) of physics for scalar variables. More...

virtual void	side_constraint (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Constraint part(s) of physics for boundaries of elements on the domain boundary. More...

virtual void	nonlocal_constraint (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Constraint part(s) of physics for scalar variables. More...

virtual void	mass_residual (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Mass matrix part(s) for element interiors. All boundary terms lie within the time_derivative part. More...

virtual void	nonlocal_mass_residual (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Mass matrix part(s) for scalar variables. More...

void	init_bcs (libMesh::FEMSystem *system)

void	init_ics (libMesh::FEMSystem *system, libMesh::CompositeFunction< libMesh::Number > &all_ics)

void	attach_neumann_bound_func (GRINS::NBCContainer &neumann_bcs)

void	attach_dirichlet_bound_func (const GRINS::DBCContainer &dirichlet_bc)

virtual void	compute_element_time_derivative_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_side_time_derivative_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_nonlocal_time_derivative_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_element_constraint_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_side_constraint_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_nonlocal_constraint_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_mass_residual_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_nonlocal_mass_residual_cache (const AssemblyContext &context, CachedValues &cache)

virtual void	compute_postprocessed_quantity (unsigned int quantity_index, const AssemblyContext &context, const libMesh::Point &point, libMesh::Real &value)

BCHandlingBase *	get_bc_handler ()

ICHandlingBase *	get_ic_handler ()

virtual void	set_parameter (libMesh::Number &param_variable, const GetPot &input, const std::string &param_name, libMesh::Number param_default)
	Each subclass can simultaneously read a parameter value from. More...

Protected Attributes
Viscosity	_mu

IncompressibleNavierStokesStabilizationHelper	_stab_helper

std::string	source_function_string

libMesh::AutoPtr< libMesh::FEMFunctionBase< libMesh::Number > >	velocity_source_function

unsigned int	_dim
	Physical dimension of problem. More...

PrimitiveFlowFEVariables	_flow_vars

libMesh::Number	_rho
	Material parameters, read from input. More...

const PhysicsName	_physics_name
	Name of the physics object. Used for reading physics specific inputs. More...

GRINS::BCHandlingBase *	_bc_handler

GRINS::ICHandlingBase *	_ic_handler

std::set< libMesh::subdomain_id_type >	_enabled_subdomains
	Subdomains on which the current Physics class is enabled. More...

bool	_is_axisymmetric

Static Protected Attributes
static bool	_is_steady = false
	Caches whether or not the solver that's being used is steady or not. More...

Private Member Functions
	ParsedVelocitySourceAdjointStabilization ()

Detailed Description

template<class Viscosity>
class GRINS::ParsedVelocitySourceAdjointStabilization< Viscosity >

Adds Velocity penalty adjoint stabilization source term.

This class implements the adjoint stabilization term for the ParsedVelocitySource Physics. Intended to be used with IncompressibleNavierStokesAdjointStabilization.

Definition at line 42 of file parsed_velocity_source_adjoint_stab.h.

Constructor & Destructor Documentation

template<class Mu >

GRINS::ParsedVelocitySourceAdjointStabilization< Mu >::ParsedVelocitySourceAdjointStabilization	(	const std::string &	physics_name,
		const GetPot &	input
	)

Definition at line 42 of file parsed_velocity_source_adjoint_stab.C.

     : ParsedVelocitySourceBase<Mu>(physics_name,input),
       _mu( input ),
       _stab_helper( physics_name+"StabHelper", input )
   {
   }

template<class Mu >

GRINS::ParsedVelocitySourceAdjointStabilization< Mu >::~ParsedVelocitySourceAdjointStabilization ( )

Definition at line 50 of file parsed_velocity_source_adjoint_stab.C.

   {
     return;
   }

template<class Viscosity >

GRINS::ParsedVelocitySourceAdjointStabilization< Viscosity >::ParsedVelocitySourceAdjointStabilization ( )

private

Member Function Documentation

void GRINS::Physics::attach_dirichlet_bound_func ( const GRINS::DBCContainer & dirichlet_bc )

inherited

Definition at line 150 of file physics.C.

References GRINS::Physics::_bc_handler, and GRINS::BCHandlingBase::attach_dirichlet_bound_func().

   {
     _bc_handler->attach_dirichlet_bound_func( dirichlet_bc );
     return;
   }

void GRINS::Physics::attach_neumann_bound_func ( GRINS::NBCContainer & neumann_bcs )

inherited

Definition at line 144 of file physics.C.

References GRINS::Physics::_bc_handler, and GRINS::BCHandlingBase::attach_neumann_bound_func().

   {
     _bc_handler->attach_neumann_bound_func( neumann_bcs );
     return;
   }

void GRINS::Physics::auxiliary_init ( MultiphysicsSystem & system )

virtualinherited

Any auxillary initialization a Physics class may need.

This is called after all variables are added, so this method can safely query the MultiphysicsSystem about variable information.

Definition at line 113 of file physics.C.

   {
     return;
   }

void GRINS::Physics::compute_element_constraint_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 185 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::element_constraint().

   {
     return;
   }

void GRINS::Physics::compute_element_time_derivative_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Reimplemented in GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >, and GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >.

Definition at line 167 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::element_time_derivative().

   {
     return;
   }

template<class Mu >

bool GRINS::ParsedVelocitySourceBase< Mu >::compute_force	(	const libMesh::Point &	point,
		const libMesh::Real	time,
		const AssemblyContext &	c,
		libMesh::NumberVectorValue &	F,
		libMesh::NumberTensorValue *	dFdU = `NULL`
	)

inherited

Definition at line 78 of file parsed_velocity_source_base.C.

   {
     libmesh_assert(velocity_source_function.get());
 
     libMesh::DenseVector<libMesh::Number> output_vec(3);
 
     (*velocity_source_function)(c, point, time,
                                 output_vec);
 
     F(0) = output_vec(0);
     F(1) = output_vec(1);
     F(2) = output_vec(2);
 
     if (dFdU)
       for (unsigned int i=0; i != 3; ++i)
         for (unsigned int j=0; j != 3; ++j)
           (*dFdU)(i,j) = 0; // FIXME
 
     if (F(0) || F(1) || F(2))
       return true;
 
     return false;
   }

void GRINS::Physics::compute_mass_residual_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 203 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::mass_residual().

   {
     return;
   }

void GRINS::Physics::compute_nonlocal_constraint_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 197 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_constraint().

   {
     return;
   }

void GRINS::Physics::compute_nonlocal_mass_residual_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 209 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_mass_residual().

   {
     return;
   }

void GRINS::Physics::compute_nonlocal_time_derivative_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 179 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_time_derivative().

   {
     return;
   }

void GRINS::Physics::compute_postprocessed_quantity	(	unsigned int	quantity_index,
		const AssemblyContext &	context,
		const libMesh::Point &	point,
		libMesh::Real &	value
	)

virtualinherited

Reimplemented in GRINS::IncompressibleNavierStokes< Viscosity >, GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >, GRINS::HeatTransfer< Conductivity >, GRINS::ParsedVelocitySource< Viscosity >, GRINS::VelocityPenalty< Viscosity >, GRINS::ElasticMembrane< StressStrainLaw >, and GRINS::ElasticCable< StressStrainLaw >.

Definition at line 271 of file physics.C.

   {
     return;
   }

void GRINS::Physics::compute_side_constraint_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Definition at line 191 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::side_constraint().

   {
     return;
   }

void GRINS::Physics::compute_side_time_derivative_cache	(	const AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Reimplemented in GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >.

Definition at line 173 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::side_time_derivative().

   {
     return;
   }

template<class Mu >

void GRINS::ParsedVelocitySourceAdjointStabilization< Mu >::element_constraint	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtual

Constraint part(s) of physics for element interiors.

Reimplemented from GRINS::Physics.

Definition at line 245 of file parsed_velocity_source_adjoint_stab.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("ParsedVelocitySourceAdjointStabilization::element_constraint");
 #endif
 
     // The number of local degrees of freedom in each variable.
     const unsigned int n_p_dofs = context.get_dof_indices(this->_flow_vars.p_var()).size();
     const unsigned int n_u_dofs = context.get_dof_indices(this->_flow_vars.u_var()).size();
 
     // Element Jacobian * quadrature weights for interior integration.
     const std::vector<libMesh::Real> &JxW =
       context.get_element_fe(this->_flow_vars.u_var())->get_JxW();
 
     const std::vector<libMesh::Point>& u_qpoint = 
       context.get_element_fe(this->_flow_vars.u_var())->get_xyz();
 
     const std::vector<std::vector<libMesh::Real> >& u_phi =
       context.get_element_fe(this->_flow_vars.u_var())->get_phi();
 
     const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
       context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_flow_vars.p_var()); // R_{p}
 
     libMesh::DenseSubMatrix<libMesh::Number> &Kpu = 
       context.get_elem_jacobian(this->_flow_vars.p_var(), this->_flow_vars.u_var()); // J_{pu}
     libMesh::DenseSubMatrix<libMesh::Number> &Kpv = 
       context.get_elem_jacobian(this->_flow_vars.p_var(), this->_flow_vars.v_var()); // J_{pv}
     libMesh::DenseSubMatrix<libMesh::Number> *Kpw = NULL;
  
     if(this->_dim == 3)
       {
         Kpw = &context.get_elem_jacobian
           (this->_flow_vars.p_var(), this->_flow_vars.w_var()); // J_{pw}
       }
 
     // 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.get_element_qrule().n_points();
 
     libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u_var());
 
     for (unsigned int qp=0; qp != n_qpoints; qp++)
       {
         libMesh::RealGradient g = this->_stab_helper.compute_g( fe, context, qp );
         libMesh::RealTensor G = this->_stab_helper.compute_G( fe, context, qp );
 
         libMesh::RealGradient U( context.interior_value( this->_flow_vars.u_var(), qp ),
                                  context.interior_value( this->_flow_vars.v_var(), qp ) );
         if( this->_dim == 3 )
           {
             U(2) = context.interior_value( this->_flow_vars.w_var(), qp );
           }
 
         // Compute the viscosity at this qp
         libMesh::Real mu_qp = this->_mu(context, qp);
 
         libMesh::Real tau_M;
         libMesh::Real d_tau_M_d_rho;
         libMesh::Gradient d_tau_M_dU;
 
         if (compute_jacobian)
           this->_stab_helper.compute_tau_momentum_and_derivs
             ( context, qp, g, G, this->_rho, U, mu_qp,
               tau_M, d_tau_M_d_rho, d_tau_M_dU,
               this->_is_steady );
         else
           tau_M = this->_stab_helper.compute_tau_momentum
                     ( context, qp, g, G, this->_rho, U, mu_qp,
                       this->_is_steady );
 
         libMesh::NumberVectorValue F;
         libMesh::NumberTensorValue dFdU;
         libMesh::NumberTensorValue* dFdU_ptr =
           compute_jacobian ? &dFdU : NULL;
         if (!this->compute_force(u_qpoint[qp], context.time, context, F, dFdU_ptr))
           continue;
 
         // First, an i-loop over the velocity degrees of freedom.
         // We know that n_u_dofs == n_v_dofs so we can compute contributions
         // for both at the same time.
         for (unsigned int i=0; i != n_p_dofs; i++)
           {
             Fp(i) += -tau_M*F*p_dphi[i][qp]*JxW[qp];
 
             if (compute_jacobian)
               {
                 for (unsigned int j=0; j != n_u_dofs; ++j)
                   {
                     Kpu(i,j) += -d_tau_M_dU(0)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     Kpv(i,j) += -d_tau_M_dU(1)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     for (unsigned int d=0; d != 3; ++d)
                       {
                         Kpu(i,j) += -tau_M*dFdU(d,0)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
                         Kpv(i,j) += -tau_M*dFdU(d,1)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
                       }
                   }
                 if( this->_dim == 3 )
                   for (unsigned int j=0; j != n_u_dofs; ++j)
                     {
                       (*Kpw)(i,j) += -d_tau_M_dU(2)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
                       for (unsigned int d=0; d != 3; ++d)
                         {
                           (*Kpw)(i,j) += -tau_M*dFdU(d,2)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
                         }
                     }
               }
           }
       } // End quadrature loop
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("ParsedVelocitySourceAdjointStabilization::element_constraint");
 #endif
 
     return;
   }

template<class Mu >

void GRINS::ParsedVelocitySourceAdjointStabilization< Mu >::element_time_derivative	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtual

Time dependent part(s) of physics for element interiors.

Reimplemented from GRINS::Physics.

Definition at line 69 of file parsed_velocity_source_adjoint_stab.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("ParsedVelocitySourceAdjointStabilization::element_time_derivative");
 #endif
 
     // The number of local degrees of freedom in each variable.
     const unsigned int n_u_dofs = context.get_dof_indices(this->_flow_vars.u_var()).size();
 
     // Element Jacobian * quadrature weights for interior integration.
     const std::vector<libMesh::Real> &JxW =
       context.get_element_fe(this->_flow_vars.u_var())->get_JxW();
 
     const std::vector<libMesh::Point>& u_qpoint = 
       context.get_element_fe(this->_flow_vars.u_var())->get_xyz();
 
     const std::vector<std::vector<libMesh::Real> >& u_phi =
       context.get_element_fe(this->_flow_vars.u_var())->get_phi();
 
     const std::vector<std::vector<libMesh::RealGradient> >& u_gradphi =
       context.get_element_fe(this->_flow_vars.u_var())->get_dphi();
 
     const std::vector<std::vector<libMesh::RealTensor> >& u_hessphi =
       context.get_element_fe(this->_flow_vars.u_var())->get_d2phi();
 
     // Get residuals and jacobians
     libMesh::DenseSubVector<libMesh::Number> &Fu = context.get_elem_residual(this->_flow_vars.u_var()); // R_{u}
     libMesh::DenseSubVector<libMesh::Number> &Fv = context.get_elem_residual(this->_flow_vars.v_var()); // R_{v}
     libMesh::DenseSubVector<libMesh::Number> *Fw = NULL;
 
     libMesh::DenseSubMatrix<libMesh::Number> &Kuu = 
       context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.u_var()); // J_{uu}
     libMesh::DenseSubMatrix<libMesh::Number> &Kuv = 
       context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.v_var()); // J_{uv}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvu = 
       context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.u_var()); // J_{vu}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvv = 
       context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.v_var()); // J_{vv}
 
     libMesh::DenseSubMatrix<libMesh::Number> *Kuw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kvw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kwu = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kwv = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kww = NULL;
 
     if(this->_dim == 3)
       {
         Fw = &context.get_elem_residual(this->_flow_vars.w_var()); // R_{w}
         Kuw = &context.get_elem_jacobian
           (this->_flow_vars.u_var(), this->_flow_vars.w_var()); // J_{uw}
         Kvw = &context.get_elem_jacobian
           (this->_flow_vars.v_var(), this->_flow_vars.w_var()); // J_{vw}
         Kwu = &context.get_elem_jacobian
           (this->_flow_vars.w_var(), this->_flow_vars.u_var()); // J_{wu}
         Kwv = &context.get_elem_jacobian
           (this->_flow_vars.w_var(), this->_flow_vars.v_var()); // J_{wv}
         Kww = &context.get_elem_jacobian
           (this->_flow_vars.w_var(), this->_flow_vars.w_var()); // J_{ww}
       }
 
     // 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.get_element_qrule().n_points();
 
     libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u_var());
 
     for (unsigned int qp=0; qp != n_qpoints; qp++)
       {
         libMesh::RealGradient g = this->_stab_helper.compute_g( fe, context, qp );
         libMesh::RealTensor G = this->_stab_helper.compute_G( fe, context, qp );
 
         libMesh::RealGradient U( context.interior_value( this->_flow_vars.u_var(), qp ),
                                  context.interior_value( this->_flow_vars.v_var(), qp ) );
         if( this->_dim == 3 )
           {
             U(2) = context.interior_value( this->_flow_vars.w_var(), qp );
           }
 
         // Compute the viscosity at this qp
         libMesh::Real mu_qp = this->_mu(context, qp);
 
         libMesh::Real tau_M;
         libMesh::Real d_tau_M_d_rho;
         libMesh::Gradient d_tau_M_dU;
 
         if (compute_jacobian)
           this->_stab_helper.compute_tau_momentum_and_derivs
             ( context, qp, g, G, this->_rho, U, mu_qp,
               tau_M, d_tau_M_d_rho, d_tau_M_dU,
               this->_is_steady );
         else
           tau_M = this->_stab_helper.compute_tau_momentum
                     ( context, qp, g, G, this->_rho, U, mu_qp,
                       this->_is_steady );
 
         libMesh::NumberVectorValue F;
         libMesh::NumberTensorValue dFdU;
         libMesh::NumberTensorValue* dFdU_ptr =
           compute_jacobian ? &dFdU : NULL;
         if (!this->compute_force(u_qpoint[qp], context.time, context, F, dFdU_ptr))
           continue;
 
         for (unsigned int i=0; i != n_u_dofs; i++)
           {
             libMesh::Real test_func = this->_rho*U*u_gradphi[i][qp] + 
               mu_qp*( u_hessphi[i][qp](0,0) + u_hessphi[i][qp](1,1) + u_hessphi[i][qp](2,2) );
             Fu(i) += tau_M*F(0)*test_func*JxW[qp];
 
             Fv(i) += tau_M*F(1)*test_func*JxW[qp];
 
             if (this->_dim == 3)
               {
                 (*Fw)(i) += tau_M*F(2)*test_func*JxW[qp];
               }
 
             if (compute_jacobian)
               {
                 libMesh::Gradient d_test_func_dU = this->_rho*u_gradphi[i][qp];
 
                 for (unsigned int j=0; j != n_u_dofs; ++j)
                   {
                     Kuu(i,j) += tau_M*F(0)*d_test_func_dU(0)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     Kuu(i,j) += d_tau_M_dU(0)*u_phi[j][qp]*F(0)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kuu(i,j) += tau_M*dFdU(0,0)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kuv(i,j) += tau_M*F(0)*d_test_func_dU(1)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     Kuv(i,j) += d_tau_M_dU(1)*u_phi[j][qp]*F(0)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kuv(i,j) += tau_M*dFdU(0,1)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kvu(i,j) += tau_M*F(1)*d_test_func_dU(0)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     Kvu(i,j) += d_tau_M_dU(0)*u_phi[j][qp]*F(1)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kvu(i,j) += tau_M*dFdU(1,0)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kvv(i,j) += tau_M*F(1)*d_test_func_dU(1)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                     Kvv(i,j) += d_tau_M_dU(1)*u_phi[j][qp]*F(1)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                     Kvv(i,j) += tau_M*dFdU(1,1)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                   }
 
                 if (this->_dim == 3)
                   {
                     for (unsigned int j=0; j != n_u_dofs; ++j)
                       {
                         (*Kuw)(i,j) += tau_M*F(0)*d_test_func_dU(2)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kuw)(i,j) += d_tau_M_dU(2)*u_phi[j][qp]*F(0)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kuw)(i,j) += tau_M*dFdU(0,2)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kvw)(i,j) += tau_M*F(1)*d_test_func_dU(2)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kvw)(i,j) += d_tau_M_dU(2)*u_phi[j][qp]*F(1)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kvw)(i,j) += tau_M*dFdU(1,2)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwu)(i,j) += tau_M*F(2)*d_test_func_dU(0)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwu)(i,j) += d_tau_M_dU(0)*u_phi[j][qp]*F(2)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwu)(i,j) += tau_M*dFdU(2,0)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwv)(i,j) += tau_M*F(2)*d_test_func_dU(1)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwv)(i,j) += d_tau_M_dU(1)*u_phi[j][qp]*F(2)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kwv)(i,j) += tau_M*dFdU(2,1)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kww)(i,j) += tau_M*F(2)*d_test_func_dU(2)*u_phi[j][qp]*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kww)(i,j) += d_tau_M_dU(2)*u_phi[j][qp]*F(2)*test_func*JxW[qp]*context.get_elem_solution_derivative();
                         (*Kww)(i,j) += tau_M*dFdU(2,2)*u_phi[j][qp]*test_func*JxW[qp]*context.get_elem_solution_derivative();
                       }
                   }
 
               } // End compute_jacobian check
 
           } // End i dof loop
       } // End quadrature loop
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("BoussinesqBuoyancyAdjointStabilization::element_time_derivative");
 #endif
 
     return;
   }

bool GRINS::Physics::enabled_on_elem ( const libMesh::Elem * elem )

virtualinherited

Find if current physics is active on supplied element.

Definition at line 83 of file physics.C.

References GRINS::Physics::_enabled_subdomains.

   {
     // Check if enabled_subdomains flag has been set and if we're
     // looking at a real element (rather than a nonlocal evaluation)
     if( !elem || _enabled_subdomains.empty() ) 
       return true;
   
     // Check if current physics is enabled on elem
     if( _enabled_subdomains.find( elem->subdomain_id() ) == _enabled_subdomains.end() )
       return false;
 
     return true;
   }

BCHandlingBase * GRINS::Physics::get_bc_handler ( )

inlineinherited

Definition at line 282 of file physics.h.

References GRINS::Physics::_bc_handler.

   {
     return _bc_handler;
   }

ICHandlingBase * GRINS::Physics::get_ic_handler ( )

inlineinherited

Definition at line 288 of file physics.h.

References GRINS::Physics::_ic_handler.

   {
     return _ic_handler;
   }

void GRINS::Physics::init_bcs ( libMesh::FEMSystem * system )

inherited

Definition at line 118 of file physics.C.

References GRINS::Physics::_bc_handler, GRINS::BCHandlingBase::init_bc_data(), GRINS::BCHandlingBase::init_dirichlet_bc_func_objs(), GRINS::BCHandlingBase::init_dirichlet_bcs(), and GRINS::BCHandlingBase::init_periodic_bcs().

   {
     // Only need to init BC's if the physics actually created a handler
     if( _bc_handler )
       {
         _bc_handler->init_bc_data( *system );
         _bc_handler->init_dirichlet_bcs( system );
         _bc_handler->init_dirichlet_bc_func_objs( system );
         _bc_handler->init_periodic_bcs( system );
       }
 
     return;
   }

template<class Mu >

void GRINS::ParsedVelocitySourceAdjointStabilization< Mu >::init_context ( AssemblyContext & context )

virtual

Initialize context for added physics variables.

Reimplemented from GRINS::IncompressibleNavierStokesBase< Viscosity >.

Definition at line 56 of file parsed_velocity_source_adjoint_stab.C.

   {
     context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     context.get_element_fe(this->_flow_vars.u_var())->get_xyz();
     context.get_element_fe(this->_flow_vars.u_var())->get_phi();
     context.get_element_fe(this->_flow_vars.u_var())->get_dphi();
     context.get_element_fe(this->_flow_vars.u_var())->get_d2phi();
 
     return;
   }

void GRINS::Physics::init_ics	(	libMesh::FEMSystem *	system,
		libMesh::CompositeFunction< libMesh::Number > &	all_ics
	)

inherited

Definition at line 133 of file physics.C.

References GRINS::Physics::_ic_handler, and GRINS::ICHandlingBase::init_ic_data().

   {
     if( _ic_handler )
       {
         _ic_handler->init_ic_data( *system, all_ics );
       }
 
     return;
   }

template<class Mu >

void GRINS::IncompressibleNavierStokesBase< Mu >::init_variables ( libMesh::FEMSystem * system )

virtualinherited

Initialization of Navier-Stokes variables.

Add velocity and pressure variables to system.

Implements GRINS::Physics.

Reimplemented in GRINS::AveragedTurbineBase< Viscosity >, and GRINS::IncompressibleNavierStokesStabilizationBase< Viscosity >.

Definition at line 63 of file inc_navier_stokes_base.C.

Referenced by GRINS::IncompressibleNavierStokesStabilizationBase< Viscosity >::init_variables(), and GRINS::AveragedTurbineBase< Viscosity >::init_variables().

   {
     this->_dim = system->get_mesh().mesh_dimension();
 
     this->_flow_vars.init(system);
     
     this->_mu.init(system); 
    
     return;
   }

bool GRINS::Physics::is_steady ( ) const

inherited

Returns whether or not this physics is being solved with a steady solver.

Definition at line 103 of file physics.C.

References GRINS::Physics::_is_steady.

Referenced by GRINS::Physics::set_is_steady().

   {
     return _is_steady;
   }

void GRINS::Physics::mass_residual	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Mass matrix part(s) for element interiors. All boundary terms lie within the time_derivative part.

Reimplemented in GRINS::AxisymmetricHeatTransfer< Conductivity >, GRINS::IncompressibleNavierStokes< Viscosity >, GRINS::SpalartAllmaras< Viscosity >, GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::HeatTransfer< Conductivity >, GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >, GRINS::Stokes< Viscosity >, GRINS::BoussinesqBuoyancySPGSMStabilization< Viscosity >, GRINS::ElasticMembrane< StressStrainLaw >, GRINS::ElasticCable< StressStrainLaw >, GRINS::HeatConduction< Conductivity >, GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >, GRINS::IncompressibleNavierStokesSPGSMStabilization< Viscosity >, GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >, GRINS::HeatTransferAdjointStabilization< Conductivity >, GRINS::HeatTransferSPGSMStabilization< Conductivity >, GRINS::LowMachNavierStokesBraackStabilization< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::LowMachNavierStokesVMSStabilization< Viscosity, SpecificHeat, ThermalConductivity >, and GRINS::LowMachNavierStokesSPGSMStabilization< Viscosity, SpecificHeat, ThermalConductivity >.

Definition at line 257 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::mass_residual().

   {
     return;
   }

void GRINS::Physics::nonlocal_constraint	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Constraint part(s) of physics for scalar variables.

Reimplemented in GRINS::ScalarODE.

Definition at line 250 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_constraint().

   {
     return;
   }   

void GRINS::Physics::nonlocal_mass_residual	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Mass matrix part(s) for scalar variables.

Reimplemented in GRINS::ScalarODE, and GRINS::AveragedTurbine< Viscosity >.

Definition at line 264 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_mass_residual().

   {
     return;
   }

void GRINS::Physics::nonlocal_time_derivative	(	bool	compute_jacobian,
		AssemblyContext &	context,
		CachedValues &	cache
	)

virtualinherited

Time dependent part(s) of physics for scalar variables.

Reimplemented in GRINS::AveragedTurbine< Viscosity >, and GRINS::ScalarODE.

Definition at line 229 of file physics.C.

Referenced by GRINS::MultiphysicsSystem::nonlocal_time_derivative().

   {
     return;
   }

template<class Mu >

void GRINS::ParsedVelocitySourceBase< Mu >::read_input_options ( const GetPot & input )

virtualinherited

Read options from GetPot input file.

Reimplemented from GRINS::Physics.

Definition at line 56 of file parsed_velocity_source_base.C.

Referenced by GRINS::ParsedVelocitySourceBase< Viscosity >::ParsedVelocitySourceBase().

   {
     std::string base_physics_name = "ParsedVelocitySource";
 
     source_function_string =
       input("Physics/"+base_physics_name+"/source_function",
         std::string("0"));
 
     if (source_function_string == "0")
       std::cout << "Warning! Zero ParsedVelocitySource specified!" << std::endl;
   }

template<class Mu >

void GRINS::IncompressibleNavierStokesBase< Mu >::register_parameter	(	const std::string &	param_name,
		libMesh::ParameterMultiPointer< libMesh::Number > &	param_pointer
	)		const

virtualinherited

Each subclass will register its copy of an independent.

Reimplemented from GRINS::ParameterUser.

Definition at line 114 of file inc_navier_stokes_base.C.

References GRINS::ParameterUser::register_parameter().

   {
     ParameterUser::register_parameter(param_name, param_pointer);
     _mu.register_parameter(param_name, param_pointer);
   }

void GRINS::Physics::register_postprocessing_vars	(	const GetPot &	input,
		PostProcessedQuantities< libMesh::Real > &	postprocessing
	)

virtualinherited

Register name of postprocessed quantity with PostProcessedQuantities.

Each Physics class will need to cache an unsigned int corresponding to each postprocessed quantity. This will be used in computing the values and putting them in the CachedVariables object.

Reimplemented in GRINS::ParsedVelocitySource< Viscosity >, GRINS::VelocityPenalty< Viscosity >, GRINS::IncompressibleNavierStokes< Viscosity >, GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::HeatTransfer< Conductivity >, GRINS::ElasticCable< StressStrainLaw >, GRINS::ElasticMembrane< StressStrainLaw >, and GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >.

Definition at line 161 of file physics.C.

   {
     return;
   }

void GRINS::Physics::set_is_steady ( bool is_steady )

inherited

Sets whether this physics is to be solved with a steady solver or not.

Since the member variable is static, only needs to be called on a single physics.

Definition at line 97 of file physics.C.

References GRINS::Physics::_is_steady, and GRINS::Physics::is_steady().

   {
     _is_steady = is_steady;
     return;
   }

void GRINS::ParameterUser::set_parameter	(	libMesh::Number &	param_variable,
		const GetPot &	input,
		const std::string &	param_name,
		libMesh::Number	param_default
	)

virtualinherited

Each subclass can simultaneously read a parameter value from.

Definition at line 35 of file parameter_user.C.

References GRINS::ParameterUser::_my_name, and GRINS::ParameterUser::_my_parameters.

Referenced by GRINS::AveragedFanAdjointStabilization< Viscosity >::AveragedFanAdjointStabilization(), GRINS::AveragedTurbineAdjointStabilization< Viscosity >::AveragedTurbineAdjointStabilization(), GRINS::BoussinesqBuoyancyAdjointStabilization< Viscosity >::BoussinesqBuoyancyAdjointStabilization(), GRINS::BoussinesqBuoyancyBase::BoussinesqBuoyancyBase(), GRINS::BoussinesqBuoyancySPGSMStabilization< Viscosity >::BoussinesqBuoyancySPGSMStabilization(), GRINS::ConstantConductivity::ConstantConductivity(), GRINS::ConstantPrandtlConductivity::ConstantPrandtlConductivity(), GRINS::ConstantSourceFunction::ConstantSourceFunction(), GRINS::ConstantSourceTerm::ConstantSourceTerm(), GRINS::ConstantSpecificHeat::ConstantSpecificHeat(), GRINS::ConstantViscosity::ConstantViscosity(), GRINS::ElasticCable< StressStrainLaw >::ElasticCable(), GRINS::ElasticCableConstantGravity::ElasticCableConstantGravity(), GRINS::ElasticMembrane< StressStrainLaw >::ElasticMembrane(), GRINS::ElasticMembraneConstantPressure::ElasticMembraneConstantPressure(), GRINS::HeatConduction< Conductivity >::HeatConduction(), GRINS::HeatTransferBase< Conductivity >::HeatTransferBase(), GRINS::IncompressibleNavierStokesBase< Viscosity >::IncompressibleNavierStokesBase(), GRINS::AverageNusseltNumber::init(), GRINS::MooneyRivlin::MooneyRivlin(), GRINS::ReactingLowMachNavierStokesBase< Mixture, Evaluator >::ReactingLowMachNavierStokesBase(), GRINS::HookesLaw1D::read_input_options(), GRINS::HookesLaw::read_input_options(), GRINS::AxisymmetricBoussinesqBuoyancy::read_input_options(), and GRINS::VelocityDragAdjointStabilization< Viscosity >::VelocityDragAdjointStabilization().

   {
     param_variable = input(param_name, param_default);
 
     libmesh_assert_msg(!_my_parameters.count(param_name),
       "ERROR: " << _my_name << " double-registered parameter " <<
       param_name);
 
     _my_parameters[param_name] = &param_variable;
   }

template<class Mu >

void GRINS::ParsedVelocitySourceBase< Mu >::set_time_evolving_vars ( libMesh::FEMSystem * system )

virtualinherited

Sets velocity variables to be time-evolving.

Reimplemented from GRINS::IncompressibleNavierStokesBase< Viscosity >.

Definition at line 69 of file parsed_velocity_source_base.C.

   {
     this->velocity_source_function.reset
       (new libMesh::ParsedFEMFunction<libMesh::Number>
         (*system, this->source_function_string));
   }