Adds VMS-based stabilization to LowMachNavierStokes physics class. More...

#include <inc_navier_stokes_adjoint_stab.h>

Inheritance diagram for GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >:

Collaboration diagram for GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >:

Public Member Functions
	IncompressibleNavierStokesAdjointStabilization (const GRINS::PhysicsName &physics_name, const GetPot &input)

virtual	~IncompressibleNavierStokesAdjointStabilization ()

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

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

virtual void	set_time_evolving_vars (libMesh::FEMSystem *system)
	Sets velocity variables to be time-evolving. 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 void	read_input_options (const GetPot &input)
	Read options from GetPot input file. By default, nothing is read. 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	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
IncompressibleNavierStokesStabilizationHelper	_stab_helper

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

PrimitiveFlowFEVariables	_flow_vars

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

Viscosity	_mu
	Viscosity object. 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
	IncompressibleNavierStokesAdjointStabilization ()

Detailed Description

template<class Viscosity>
class GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >

Adds VMS-based stabilization to LowMachNavierStokes physics class.

Definition at line 35 of file inc_navier_stokes_adjoint_stab.h.

Constructor & Destructor Documentation

template<class Mu >

GRINS::IncompressibleNavierStokesAdjointStabilization< Mu >::IncompressibleNavierStokesAdjointStabilization	(	const GRINS::PhysicsName &	physics_name,
		const GetPot &	input
	)

Definition at line 40 of file inc_navier_stokes_adjoint_stab.C.

References GRINS::Physics::read_input_options().

     : IncompressibleNavierStokesStabilizationBase<Mu>(physics_name,input)
   {
     this->read_input_options(input);
 
     return;
   }

template<class Mu >

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

virtual

Definition at line 50 of file inc_navier_stokes_adjoint_stab.C.

   {
     return;
   }

template<class Viscosity >

GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >::IncompressibleNavierStokesAdjointStabilization ( )

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;
   }

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::IncompressibleNavierStokesAdjointStabilization< 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 386 of file inc_navier_stokes_adjoint_stab.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("IncompressibleNavierStokesAdjointStabilization::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();
 
     // The pressure shape functions at interior quadrature points.
     const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
       context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     // The velocity shape functions at interior quadrature points.
     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_dphi =
       context.get_element_fe(this->_flow_vars.u_var())->get_dphi();
 
     const std::vector<std::vector<libMesh::RealTensor> >& u_d2phi =
       context.get_element_fe(this->_flow_vars.u_var())->get_d2phi();
 
     libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_flow_vars.p_var()); // R_{p}
 
     libMesh::DenseSubMatrix<libMesh::Number> &Kpp = 
       context.get_elem_jacobian(this->_flow_vars.p_var(), this->_flow_vars.p_var()); // J_{pp}
     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}
       }
 
     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 );
           }
 
         libMesh::Real tau_M;
         libMesh::Real d_tau_M_d_rho;
         libMesh::Gradient d_tau_M_dU;
         libMesh::Gradient RM_s, d_RM_s_uvw_dgraduvw;
         libMesh::Tensor d_RM_s_dgradp, d_RM_s_dU, d_RM_s_uvw_dhessuvw;
         
         // Compute the viscosity at this qp
         libMesh::Real _mu_qp = this->_mu(context, qp);  
 
         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 );
             this->_stab_helper.compute_res_momentum_steady_and_derivs
               ( context, qp, this->_rho, _mu_qp,
                 RM_s, d_RM_s_dgradp, d_RM_s_dU, d_RM_s_uvw_dgraduvw,
                 d_RM_s_uvw_dhessuvw);
           }
         else
           {
             tau_M = this->_stab_helper.compute_tau_momentum( context, qp, g, G, this->_rho, U, _mu_qp, this->_is_steady );
             RM_s = this->_stab_helper.compute_res_momentum_steady( context, qp, this->_rho, _mu_qp );
           }
 
         // Now a loop over the pressure degrees of freedom.  This
         // computes the contributions of the continuity equation.
         for (unsigned int i=0; i != n_p_dofs; i++)
           {
             Fp(i) += tau_M*(RM_s*p_dphi[i][qp])*JxW[qp];
 
             if (compute_jacobian)
               {
                 const libMesh::Real fixed_deriv =
                   context.get_fixed_solution_derivative();
 
                 const libMesh::TypeVector<libMesh::Number>
                   p_dphiiT_d_RM_s_dgradp = 
                   d_RM_s_dgradp.transpose() * p_dphi[i][qp];
 
                 for (unsigned int j=0; j != n_p_dofs; j++)
                   {
                     Kpp(i,j) += tau_M*(p_dphiiT_d_RM_s_dgradp*p_dphi[j][qp])*JxW[qp];
                   }
 
                 for (unsigned int j=0; j != n_u_dofs; j++)
                   {
                     Kpu(i,j) += (
                                   d_tau_M_dU(0)*u_phi[j][qp]*(RM_s*p_dphi[i][qp])
                                   + tau_M*
                                   (
                                     d_RM_s_dU(0,0)*u_phi[j][qp]*p_dphi[i][qp](0) +
                                     d_RM_s_dU(1,0)*u_phi[j][qp]*p_dphi[i][qp](1) +
                                     d_RM_s_dU(2,0)*u_phi[j][qp]*p_dphi[i][qp](2) +
                                     d_RM_s_uvw_dgraduvw*u_dphi[j][qp]*p_dphi[i][qp](0) +
                                     d_RM_s_uvw_dhessuvw.contract(u_d2phi[j][qp])*p_dphi[i][qp](0)
                                   )*fixed_deriv
                                 )*JxW[qp];
                     Kpv(i,j) += (
                                   d_tau_M_dU(1)*u_phi[j][qp]*(RM_s*p_dphi[i][qp])
                                   + tau_M*
                                   (
                                     d_RM_s_dU(0,1)*u_phi[j][qp]*p_dphi[i][qp](0) +
                                     d_RM_s_dU(1,1)*u_phi[j][qp]*p_dphi[i][qp](1) +
                                     d_RM_s_dU(2,1)*u_phi[j][qp]*p_dphi[i][qp](2) +
                                     d_RM_s_uvw_dgraduvw*u_dphi[j][qp]*p_dphi[i][qp](1) +
                                     d_RM_s_uvw_dhessuvw.contract(u_d2phi[j][qp])*p_dphi[i][qp](0)
                                   )*fixed_deriv
                                 )*JxW[qp];
                   }
 
                 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]*(RM_s*p_dphi[i][qp])
                                          + tau_M*
                                          (
                                            d_RM_s_dU(0,2)*u_phi[j][qp]*p_dphi[i][qp](0) +
                                            d_RM_s_dU(1,2)*u_phi[j][qp]*p_dphi[i][qp](1) +
                                            d_RM_s_dU(2,2)*u_phi[j][qp]*p_dphi[i][qp](2) +
                                            d_RM_s_uvw_dgraduvw*u_dphi[j][qp]*p_dphi[i][qp](2) +
                                            d_RM_s_uvw_dhessuvw.contract(u_d2phi[j][qp])*p_dphi[i][qp](0)
                                          )*fixed_deriv
                                        )*JxW[qp];
                       }
                   }
               }
           }
       }
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("IncompressibleNavierStokesAdjointStabilization::element_constraint");
 #endif
 
     return;
   }

template<class Mu >

void GRINS::IncompressibleNavierStokesAdjointStabilization< 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 56 of file inc_navier_stokes_adjoint_stab.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("IncompressibleNavierStokesAdjointStabilization::element_time_derivative");
 #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<std::vector<libMesh::RealGradient> >& p_gradphi =
       context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     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();
 
     libMesh::DenseSubVector<libMesh::Number> &Fu = context.get_elem_residual(this->_flow_vars.u_var()); // R_{p}
     libMesh::DenseSubVector<libMesh::Number> &Fv = context.get_elem_residual(this->_flow_vars.v_var()); // R_{p}
     libMesh::DenseSubMatrix<libMesh::Number> &Kup = 
       context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.p_var()); // J_{up}
     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> &Kvp = 
       context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.p_var()); // J_{vp}
     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::DenseSubVector<libMesh::Number> *Fw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kuw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kvw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number> *Kwp = 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}
         Kwp = &context.get_elem_jacobian
           (this->_flow_vars.w_var(), this->_flow_vars.p_var()); // J_{wp}
         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}
       }
 
     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 );
           }
       
         /*
           libMesh::Gradient grad_u, grad_v, grad_w;
           grad_u = context.interior_gradient(this->_flow_vars.u_var(), qp);
           grad_v = context.interior_gradient(this->_flow_vars.v_var(), qp);
           if (_dim == 3)
           grad_w = context.interior_gradient(this->_flow_vars.w_var(), qp);
         */
 
         libMesh::Real tau_M, tau_C;
         libMesh::Real d_tau_M_d_rho, d_tau_C_d_rho;
         libMesh::Gradient d_tau_M_dU, d_tau_C_dU;
         libMesh::Gradient RM_s, d_RM_s_uvw_dgraduvw;
         libMesh::Real RC;
         libMesh::Tensor d_RC_dgradU,
           d_RM_s_dgradp, d_RM_s_dU, d_RM_s_uvw_dhessuvw;
 
         // Compute the viscosity at this qp
         libMesh::Real _mu_qp = this->_mu(context, qp);
 
         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 );
             this->_stab_helper.compute_tau_continuity_and_derivs
               ( tau_M, d_tau_M_d_rho, d_tau_M_dU,
                 g,
                 tau_C, d_tau_C_d_rho, d_tau_C_dU );
             this->_stab_helper.compute_res_momentum_steady_and_derivs
               ( context, qp, this->_rho, _mu_qp,
                 RM_s, d_RM_s_dgradp, d_RM_s_dU, d_RM_s_uvw_dgraduvw,
                 d_RM_s_uvw_dhessuvw);
             this->_stab_helper.compute_res_continuity_and_derivs
               ( context, qp, RC, d_RC_dgradU );
           }
         else
           {
             tau_M = this->_stab_helper.compute_tau_momentum( context, qp, g, G, this->_rho, U, _mu_qp, this->_is_steady );
             tau_C = this->_stab_helper.compute_tau_continuity( tau_M, g );
             RM_s = this->_stab_helper.compute_res_momentum_steady( context, qp, this->_rho, _mu_qp );
             RC = this->_stab_helper.compute_res_continuity( context, qp );
           }
 
         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) );
             libMesh::Gradient d_test_func_dU = this->_rho*u_gradphi[i][qp];
 
             //libMesh::RealGradient zeroth_order_term = - this->_rho*u_phi[i][qp]*(grad_u + grad_v + grad_w);
 
             Fu(i) += ( -tau_M*RM_s(0)*test_func - tau_C*RC*u_gradphi[i][qp](0) )*JxW[qp];
 
             Fv(i) += ( -tau_M*RM_s(1)*test_func - tau_C*RC*u_gradphi[i][qp](1) )*JxW[qp];
 
             if(this->_dim == 3)
               {
                 (*Fw)(i) += ( -tau_M*RM_s(2)*test_func - tau_C*RC*u_gradphi[i][qp](2) )*JxW[qp];
               }
 
             if (compute_jacobian)
               {
                 const libMesh::Real fixed_deriv =
                   context.get_fixed_solution_derivative();
                 for (unsigned int j=0; j != n_p_dofs; j++)
                   {
                     Kup(i,j) += ( -tau_M*
                                   ( d_RM_s_dgradp(0,0) *
                                     p_gradphi[j][qp](0) +
                                     d_RM_s_dgradp(0,1) *
                                     p_gradphi[j][qp](1) +
                                     d_RM_s_dgradp(0,2) *
                                     p_gradphi[j][qp](2)
                                   )*test_func)*fixed_deriv*JxW[qp];
                     Kvp(i,j) += ( -tau_M*
                                   ( d_RM_s_dgradp(1,0) *
                                     p_gradphi[j][qp](0) +
                                     d_RM_s_dgradp(1,1) *
                                     p_gradphi[j][qp](1) +
                                     d_RM_s_dgradp(1,2) *
                                     p_gradphi[j][qp](2)
                                   )*test_func)*fixed_deriv*JxW[qp];
                   }
                 for (unsigned int j=0; j != n_u_dofs; j++)
                   {
                     Kuu(i,j) += ( -d_tau_M_dU(0)*RM_s(0)*test_func
                                   -tau_M*d_RM_s_dU(0,0)*test_func
                                   - d_tau_C_dU(0)*RC*u_gradphi[i][qp](0)
                                 )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                     Kuu(i,j) += ( -tau_M*RM_s(0)*d_test_func_dU(0)
                                 )*u_phi[j][qp]*JxW[qp];
                     Kuu(i,j) += ( - tau_C*
                                   (
                                     d_RC_dgradU(0,0)*u_gradphi[j][qp](0) +
                                     d_RC_dgradU(0,1)*u_gradphi[j][qp](1) +
                                     d_RC_dgradU(0,2)*u_gradphi[j][qp](2)
                                   )
                                     *fixed_deriv*u_gradphi[i][qp](0)
                                 )*JxW[qp];
                     Kuu(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dgraduvw*u_gradphi[j][qp])
                                 )*fixed_deriv*JxW[qp];
                     Kuu(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dhessuvw.contract(u_hessphi[j][qp]))
                                 )*fixed_deriv*JxW[qp];
                     Kuv(i,j) += ( -d_tau_M_dU(1)*RM_s(0)*test_func
                                   -tau_M*d_RM_s_dU(0,1)*test_func
                                 )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                     Kuv(i,j) += ( -tau_M*RM_s(0)*d_test_func_dU(1)
                                 )*u_phi[j][qp]*JxW[qp];
                     Kuv(i,j) += ( - tau_C*
                                   (
                                     d_RC_dgradU(1,0)*u_gradphi[j][qp](0) +
                                     d_RC_dgradU(1,1)*u_gradphi[j][qp](1) +
                                     d_RC_dgradU(1,2)*u_gradphi[j][qp](2)
                                   )
                                     *fixed_deriv*u_gradphi[i][qp](0)
                                 )*JxW[qp];
                     Kvu(i,j) += ( -d_tau_M_dU(0)*RM_s(1)*test_func
                                   -tau_M*d_RM_s_dU(1,0)*test_func
                                 )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                     Kvu(i,j) += ( -tau_M*RM_s(1)*d_test_func_dU(0)
                                 )*u_phi[j][qp]*JxW[qp];
                     Kvu(i,j) += ( - tau_C*
                                   (
                                     d_RC_dgradU(0,0)*u_gradphi[j][qp](0) +
                                     d_RC_dgradU(0,1)*u_gradphi[j][qp](1) +
                                     d_RC_dgradU(0,2)*u_gradphi[j][qp](2)
                                   )
                                     *fixed_deriv*u_gradphi[i][qp](1)
                                 )*JxW[qp];
                     Kvv(i,j) += ( -d_tau_M_dU(1)*RM_s(1)*test_func
                                   -tau_M*d_RM_s_dU(1,1)*test_func
                                 )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                     Kvv(i,j) += ( -tau_M*RM_s(1)*d_test_func_dU(1)
                                 )*u_phi[j][qp]*JxW[qp];
                     Kvv(i,j) += ( - tau_C*
                                   (
                                     d_RC_dgradU(1,0)*u_gradphi[j][qp](0) +
                                     d_RC_dgradU(1,1)*u_gradphi[j][qp](1) +
                                     d_RC_dgradU(1,2)*u_gradphi[j][qp](2)
                                   )
                                     *fixed_deriv*u_gradphi[i][qp](1)
                                 )*JxW[qp];
                     Kvv(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dgraduvw*u_gradphi[j][qp])
                                 )*fixed_deriv*JxW[qp];
                     Kvv(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dhessuvw.contract(u_hessphi[j][qp]))
                                 )*fixed_deriv*JxW[qp];
                   }
                 if(this->_dim == 3)
                   {
                     for (unsigned int j=0; j != n_p_dofs; j++)
                       {
                         (*Kwp)(i,j) += ( -tau_M*
                                          ( d_RM_s_dgradp(2,0) *
                                            p_gradphi[j][qp](0) +
                                            d_RM_s_dgradp(2,1) *
                                            p_gradphi[j][qp](1) +
                                            d_RM_s_dgradp(2,2) *
                                            p_gradphi[j][qp](2)
                                          )*test_func)*fixed_deriv*JxW[qp];
                       }
                     for (unsigned int j=0; j != n_u_dofs; j++)
                       {
                         (*Kuw)(i,j) += ( -d_tau_M_dU(2)*RM_s(0)*test_func
                                          -tau_M*d_RM_s_dU(0,2)*test_func
                                        )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                         (*Kuw)(i,j) += ( -tau_M*RM_s(0)*d_test_func_dU(2)
                                        )*u_phi[j][qp]*JxW[qp];
                         (*Kuw)(i,j) += ( - tau_C*
                                          (
                                            d_RC_dgradU(2,0)*u_gradphi[j][qp](0) +
                                            d_RC_dgradU(2,1)*u_gradphi[j][qp](1) +
                                            d_RC_dgradU(2,2)*u_gradphi[j][qp](2)
                                          )
                                          *fixed_deriv* u_gradphi[i][qp](0)
                                        )*JxW[qp];
                         (*Kvw)(i,j) += ( -d_tau_M_dU(2)*RM_s(1)*test_func
                                          -tau_M*d_RM_s_dU(1,2)*test_func
                                        )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                         (*Kvw)(i,j) += ( -tau_M*RM_s(1)*d_test_func_dU(2)
                                        )*u_phi[j][qp]*JxW[qp];
                         (*Kvw)(i,j) += ( - tau_C*
                                          (
                                            d_RC_dgradU(2,0)*u_gradphi[j][qp](0) +
                                            d_RC_dgradU(2,1)*u_gradphi[j][qp](1) +
                                            d_RC_dgradU(2,2)*u_gradphi[j][qp](2)
                                          )
                                          *fixed_deriv* u_gradphi[i][qp](1)
                                        )*JxW[qp];
                         (*Kwu)(i,j) += ( -d_tau_M_dU(0)*RM_s(2)*test_func
                                          -tau_M*d_RM_s_dU(2,0)*test_func
                                        )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                         (*Kwu)(i,j) += ( -tau_M*RM_s(2)*d_test_func_dU(0)
                                        )*u_phi[j][qp]*JxW[qp];
                         (*Kwu)(i,j) += ( - tau_C*
                                          (
                                            d_RC_dgradU(0,0)*u_gradphi[j][qp](0) +
                                            d_RC_dgradU(0,1)*u_gradphi[j][qp](1) +
                                            d_RC_dgradU(0,2)*u_gradphi[j][qp](2)
                                          )
                                          *fixed_deriv* u_gradphi[i][qp](2)
                                        )*JxW[qp];
                         (*Kwv)(i,j) += ( -d_tau_M_dU(1)*RM_s(2)*test_func
                                          -tau_M*d_RM_s_dU(2,1)*test_func
                                        )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                         (*Kwv)(i,j) += ( -tau_M*RM_s(2)*d_test_func_dU(1)
                                        )*u_phi[j][qp]*JxW[qp];
                         (*Kwv)(i,j) += ( - tau_C*
                                          (
                                            d_RC_dgradU(1,0)*u_gradphi[j][qp](0) +
                                            d_RC_dgradU(1,1)*u_gradphi[j][qp](1) +
                                            d_RC_dgradU(1,2)*u_gradphi[j][qp](2)
                                          )
                                          *fixed_deriv* u_gradphi[i][qp](2)
                                        )*JxW[qp];
                         (*Kww)(i,j) += ( -d_tau_M_dU(2)*RM_s(2)*test_func
                                          -tau_M*d_RM_s_dU(2,2)*test_func
                                        )*fixed_deriv*u_phi[j][qp]*JxW[qp];
                         (*Kww)(i,j) += ( -tau_M*RM_s(2)*d_test_func_dU(2)
                                        )*u_phi[j][qp]*JxW[qp];
                         (*Kww)(i,j) += ( - tau_C*
                                          (
                                            d_RC_dgradU(2,0)*u_gradphi[j][qp](0) +
                                            d_RC_dgradU(2,1)*u_gradphi[j][qp](1) +
                                            d_RC_dgradU(2,2)*u_gradphi[j][qp](2)
                                          )
                                          *fixed_deriv* u_gradphi[i][qp](2)
                                        )*JxW[qp];
                         (*Kww)(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dgraduvw*u_gradphi[j][qp])
                                        )*fixed_deriv*JxW[qp];
                         (*Kww)(i,j) += ( -tau_M*test_func*(d_RM_s_uvw_dhessuvw.contract(u_hessphi[j][qp]))
                                        )*fixed_deriv*JxW[qp];
 
                       }
                   }
               }
           }
       }
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("IncompressibleNavierStokesAdjointStabilization::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::IncompressibleNavierStokesStabilizationBase< Mu >::init_context ( AssemblyContext & context )

virtualinherited

Initialize context for added physics variables.

Reimplemented from GRINS::IncompressibleNavierStokesBase< Viscosity >.

Definition at line 54 of file inc_navier_stokes_stab_base.C.

References GRINS::IncompressibleNavierStokesBase< Viscosity >::init_context().

   {
     // First call base class
     IncompressibleNavierStokesBase<Mu>::init_context(context);
   
     // We need pressure derivatives
     context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     // We also need second derivatives, so initialize those.
     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::IncompressibleNavierStokesStabilizationBase< Mu >::init_variables ( libMesh::FEMSystem * system )

virtualinherited

Initialization of Navier-Stokes variables.

Add velocity and pressure variables to system.

Reimplemented from GRINS::IncompressibleNavierStokesBase< Viscosity >.

Definition at line 69 of file inc_navier_stokes_stab_base.C.

References GRINS::IncompressibleNavierStokesBase< Viscosity >::init_variables().

   {
     // First call base class
     IncompressibleNavierStokesBase<Mu>::init_variables(system);
 
     _stab_helper.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;
   }

template<class Mu >

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

virtual

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

Reimplemented from GRINS::Physics.

Definition at line 549 of file inc_navier_stokes_adjoint_stab.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("IncompressibleNavierStokesAdjointStabilization::mass_residual");
 #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();
 
     // The pressure shape functions at interior quadrature points.
     const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
       context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
 
     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();
 
     libMesh::DenseSubVector<libMesh::Number> &Fu = context.get_elem_residual(this->_flow_vars.u_var()); // R_{p}
     libMesh::DenseSubVector<libMesh::Number> &Fv = context.get_elem_residual(this->_flow_vars.v_var()); // R_{p}
     libMesh::DenseSubVector<libMesh::Number> *Fw = NULL;
 
     libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_flow_vars.p_var()); // R_{p}
 
     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;
 
     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)
       {
         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}
 
         Kpw = &context.get_elem_jacobian
           (this->_flow_vars.p_var(), this->_flow_vars.w_var()); // J_{pw}
       }
 
     unsigned int n_qpoints = context.get_element_qrule().n_points();
 
     for (unsigned int qp=0; qp != n_qpoints; qp++)
       {
         libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u_var());
 
         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.fixed_interior_value( this->_flow_vars.u_var(), qp ),
                                  context.fixed_interior_value( this->_flow_vars.v_var(), qp ) );
         if( this->_dim == 3 )
           {
             U(2) = context.fixed_interior_value( this->_flow_vars.w_var(), qp );
           }
 
         /*
           libMesh::Gradient grad_u, grad_v, grad_w;
           grad_u = context.interior_gradient(this->_flow_vars.u_var(), qp);
           grad_v = context.interior_gradient(this->_flow_vars.v_var(), qp);
           if (_dim == 3)
           grad_w = context.interior_gradient(this->_flow_vars.w_var(), qp);
         */
 
         libMesh::Real tau_M;
 
         libMesh::Real d_tau_M_d_rho;
 
         libMesh::Gradient d_tau_M_dU;
 
         libMesh::RealGradient RM_t;
 
         libMesh::Real d_RM_t_uvw_duvw;
 
         // Compute the viscosity at this qp
         libMesh::Real _mu_qp = this->_mu(context, qp);
 
         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,
                 false );
             this->_stab_helper.compute_res_momentum_transient_and_derivs
               ( context, qp, this->_rho,
                 RM_t, d_RM_t_uvw_duvw );
           }
         else
           {
             tau_M = this->_stab_helper.compute_tau_momentum( context, qp, g, G, this->_rho, U, _mu_qp, false );
             RM_t = this->_stab_helper.compute_res_momentum_transient( context, qp, this->_rho );
           }
 
 
         // Now a loop over the pressure degrees of freedom.  This
         // computes the contributions of the continuity equation.
         for (unsigned int i=0; i != n_p_dofs; i++)
           {
             Fp(i) -= tau_M*RM_t*p_dphi[i][qp]*JxW[qp];
 
             if (compute_jacobian)
               {
                 const libMesh::Real fixed_deriv =
                   context.get_fixed_solution_derivative();
 
                 for (unsigned int j=0; j != n_u_dofs; j++)
                   {
                     Kpu(i,j) -= d_tau_M_dU(0)*u_phi[j][qp]*RM_t*p_dphi[i][qp]*fixed_deriv*JxW[qp];
                     Kpu(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*p_dphi[i][qp](0)*fixed_deriv*JxW[qp];
 
                     Kpv(i,j) -= d_tau_M_dU(1)*u_phi[j][qp]*RM_t*p_dphi[i][qp]*fixed_deriv*JxW[qp];
                     Kpv(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*p_dphi[i][qp](1)*fixed_deriv*JxW[qp];
                   }
 
                 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]*RM_t*p_dphi[i][qp]*fixed_deriv*JxW[qp];
                         (*Kpw)(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*p_dphi[i][qp](2)*fixed_deriv*JxW[qp];
                       }
                   }
               }
           }
 
         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) );
             libMesh::Gradient d_test_func_dU = this->_rho*u_gradphi[i][qp];
 
             //libMesh::RealGradient zeroth_order_term = - this->_rho*u_phi[i][qp]*(grad_u + grad_v + grad_w);
 
             Fu(i) -= tau_M*RM_t(0)*test_func*JxW[qp];
 
             Fv(i) -= tau_M*RM_t(1)*test_func*JxW[qp];
 
             if(this->_dim == 3)
               {
                 (*Fw)(i) -= tau_M*RM_t(2)*test_func*JxW[qp];
               }
 
             if (compute_jacobian)
               {
                 const libMesh::Real fixed_deriv =
                   context.get_fixed_solution_derivative();
 
                 for (unsigned int j=0; j != n_u_dofs; j++)
                   {
                     Kuu(i,j) -= d_tau_M_dU(0)*u_phi[j][qp]*RM_t(0)*test_func*fixed_deriv*JxW[qp];
                     Kuu(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*test_func*fixed_deriv*JxW[qp];
                     Kuu(i,j) -= tau_M*RM_t(0)*d_test_func_dU(0)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                     Kuv(i,j) -= d_tau_M_dU(1)*u_phi[j][qp]*RM_t(0)*test_func*fixed_deriv*JxW[qp];
                     Kuv(i,j) -= tau_M*RM_t(0)*d_test_func_dU(1)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                     Kvu(i,j) -= d_tau_M_dU(0)*u_phi[j][qp]*RM_t(1)*test_func*fixed_deriv*JxW[qp];
                     Kvu(i,j) -= tau_M*RM_t(1)*d_test_func_dU(0)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                     Kvv(i,j) -= d_tau_M_dU(1)*u_phi[j][qp]*RM_t(1)*test_func*fixed_deriv*JxW[qp];
                     Kvv(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*test_func*fixed_deriv*JxW[qp];
                     Kvv(i,j) -= tau_M*RM_t(1)*d_test_func_dU(1)*u_phi[j][qp]*fixed_deriv*JxW[qp];
                   }
                 if(this->_dim == 3)
                   {
                     for (unsigned int j=0; j != n_u_dofs; j++)
                       {
                         (*Kuw)(i,j) -= d_tau_M_dU(2)*u_phi[j][qp]*RM_t(0)*test_func*fixed_deriv*JxW[qp];
                         (*Kuw)(i,j) -= tau_M*RM_t(0)*d_test_func_dU(2)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                         (*Kvw)(i,j) -= d_tau_M_dU(2)*u_phi[j][qp]*RM_t(1)*test_func*fixed_deriv*JxW[qp];
                         (*Kvw)(i,j) -= tau_M*RM_t(1)*d_test_func_dU(2)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                         (*Kwu)(i,j) -= d_tau_M_dU(0)*u_phi[j][qp]*RM_t(2)*test_func*fixed_deriv*JxW[qp];
                         (*Kwu)(i,j) -= tau_M*RM_t(2)*d_test_func_dU(0)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                         (*Kwv)(i,j) -= d_tau_M_dU(1)*u_phi[j][qp]*RM_t(2)*test_func*fixed_deriv*JxW[qp];
                         (*Kwv)(i,j) -= tau_M*RM_t(2)*d_test_func_dU(1)*u_phi[j][qp]*fixed_deriv*JxW[qp];
 
                         (*Kww)(i,j) -= d_tau_M_dU(2)*u_phi[j][qp]*RM_t(2)*test_func*fixed_deriv*JxW[qp];
                         (*Kww)(i,j) -= tau_M*d_RM_t_uvw_duvw*u_phi[j][qp]*test_func*fixed_deriv*JxW[qp];
                         (*Kww)(i,j) -= tau_M*RM_t(2)*d_test_func_dU(2)*u_phi[j][qp]*fixed_deriv*JxW[qp];
                       }
                   }
               }
           }
 
       }
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("IncompressibleNavierStokesAdjointStabilization::mass_residual");
 #endif
     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;
   }

void GRINS::Physics::read_input_options ( const GetPot & input )

virtualinherited

Read options from GetPot input file. By default, nothing is read.

Reimplemented in GRINS::ScalarODE, GRINS::AveragedTurbineBase< Viscosity >, GRINS::AxisymmetricBoussinesqBuoyancy, GRINS::LowMachNavierStokesBase< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::AxisymmetricHeatTransfer< Conductivity >, GRINS::AveragedFanBase< Viscosity >, GRINS::ParsedVelocitySourceBase< Viscosity >, GRINS::VelocityDragBase< Viscosity >, GRINS::VelocityPenaltyBase< Viscosity >, GRINS::IncompressibleNavierStokes< Viscosity >, GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::HeatTransfer< Conductivity >, GRINS::ReactingLowMachNavierStokesBase< Mixture, Evaluator >, and GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >.

Definition at line 70 of file physics.C.

References GRINS::Physics::_enabled_subdomains, and GRINS::Physics::_physics_name.

Referenced by GRINS::HeatTransferBase< Conductivity >::HeatTransferBase(), GRINS::HeatTransferStabilizationBase< Conductivity >::HeatTransferStabilizationBase(), GRINS::IncompressibleNavierStokesAdjointStabilization< Viscosity >::IncompressibleNavierStokesAdjointStabilization(), GRINS::IncompressibleNavierStokesSPGSMStabilization< Viscosity >::IncompressibleNavierStokesSPGSMStabilization(), GRINS::Physics::Physics(), and GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >::SpalartAllmarasSPGSMStabilization().

   {
     int num_ids = input.vector_variable_size( "Physics/"+this->_physics_name+"/enabled_subdomains" );
 
     for( int i = 0; i < num_ids; i++ )
       {
         libMesh::subdomain_id_type dumvar = input( "Physics/"+this->_physics_name+"/enabled_subdomains", -1, i );
         _enabled_subdomains.insert( dumvar );
       }
 
     return;
   }

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::IncompressibleNavierStokesBase< Mu >::set_time_evolving_vars ( libMesh::FEMSystem * system )

virtualinherited

Sets velocity variables to be time-evolving.

Reimplemented from GRINS::Physics.

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

Definition at line 75 of file inc_navier_stokes_base.C.

Referenced by GRINS::AveragedTurbineBase< Viscosity >::set_time_evolving_vars().

   {
     const unsigned int dim = system->get_mesh().mesh_dimension();
 
     // Tell the system to march velocity forward in time, but
     // leave p as a constraint only
     system->time_evolving(_flow_vars.u_var());
     system->time_evolving(_flow_vars.v_var());
 
     if (dim == 3)
       system->time_evolving(_flow_vars.w_var());
 
     return;
   }