#include <spalart_allmaras_stab_base.h>

Inheritance diagram for GRINS::SpalartAllmarasStabilizationBase< Viscosity >:

Collaboration diagram for GRINS::SpalartAllmarasStabilizationBase< Viscosity >:

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

virtual	~SpalartAllmarasStabilizationBase ()

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

virtual void	init_variables (libMesh::FEMSystem *system)
	Initialize variables for this physics. More...

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

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

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...

Public Attributes
libMesh::AutoPtr< DistanceFunction >	distance_function

libMesh::AutoPtr< libMesh::SerialMesh >	boundary_mesh

Protected Attributes
SpalartAllmarasStabilizationHelper	_stab_helper

PrimitiveFlowFEVariables	_flow_vars

TurbulenceFEVariables	_turbulence_vars

SpalartAllmarasHelper	_spalart_allmaras_helper

SpalartAllmarasParameters	_sa_params
	Object handling the plethora of parameters. More...

std::set< libMesh::boundary_id_type >	_wall_ids

unsigned int	_no_of_walls

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

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
	SpalartAllmarasStabilizationBase ()

Detailed Description

template<class Viscosity>
class GRINS::SpalartAllmarasStabilizationBase< Viscosity >

Definition at line 36 of file spalart_allmaras_stab_base.h.

Constructor & Destructor Documentation

template<class Mu >

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

Definition at line 40 of file spalart_allmaras_stab_base.C.

     : SpalartAllmaras<Mu>(physics_name,input),
       _stab_helper( physics_name+"StabHelper", input )
   {
     return;
   }

template<class Mu >

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

virtual

Definition at line 49 of file spalart_allmaras_stab_base.C.

   {
     return;
   }

template<class Viscosity >

GRINS::SpalartAllmarasStabilizationBase< Viscosity >::SpalartAllmarasStabilizationBase ( )

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;
   }

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

virtualinherited

Constraint part(s) of physics for element interiors.

Definition at line 236 of file physics.C.

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

   {
     return;
   }

template<class Mu >

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

virtualinherited

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

Reimplemented from GRINS::Physics.

Reimplemented in GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >.

Definition at line 144 of file spalart_allmaras.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("SpalartAllmaras::element_time_derivative");
 #endif
 
     // Get a pointer to the current element, we need this for computing
     // the distance to wall for the  quadrature points
     libMesh::Elem &elem_pointer = context.get_elem();
 
     // We get some references to cell-specific data that
     // will be used to assemble the linear system.
 
     // Element Jacobian * quadrature weights for interior integration.
     const std::vector<libMesh::Real> &JxW =
       context.get_element_fe(this->_turbulence_vars.nu_var())->get_JxW();
 
     // The viscosity shape functions at interior quadrature points.
     const std::vector<std::vector<libMesh::Real> >& nu_phi =
       context.get_element_fe(this->_turbulence_vars.nu_var())->get_phi();
 
     // The viscosity shape function gradients (in global coords.)
     // at interior quadrature points.
     const std::vector<std::vector<libMesh::RealGradient> >& nu_gradphi =
       context.get_element_fe(this->_turbulence_vars.nu_var())->get_dphi();
 
     // The number of local degrees of freedom in each variable.
     const unsigned int n_nu_dofs = context.get_dof_indices(this->_turbulence_vars.nu_var()).size();
 
     // The subvectors and submatrices we need to fill:
     //
     // K_{\alpha \beta} = R_{\alpha},{\beta} = \partial{ R_{\alpha} } / \partial{ {\beta} } (where R denotes residual)
     // e.g., for \alpha = v and \beta = u we get: K{vu} = R_{v},{u}
     // Note that Kpu, Kpv, Kpw and Fp comes as constraint.
 
     //libMesh::DenseSubMatrix<libMesh::Number> &Knunu = context.get_elem_jacobian(this->_turbulence_vars.nu_var(), this->_turbulence_vars.nu_var()); // R_{nu},{nu}
 
     libMesh::DenseSubVector<libMesh::Number> &Fnu = context.get_elem_residual(this->_turbulence_vars.nu_var()); // R_{nu}
 
     // 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();
 
     // Auto pointer to distance fcn evaluated at quad points
     libMesh::AutoPtr< libMesh::DenseVector<libMesh::Real> > distance_qp;
 
     // Fill the vector of distances to quadrature points
     distance_qp = this->distance_function->interpolate(&elem_pointer, context.get_element_qrule().get_points());
 
     for (unsigned int qp=0; qp != n_qpoints; qp++)
       {
         // Compute the solution & its gradient at the old Newton iterate.
         libMesh::Number nu;
         nu = context.interior_value(this->_turbulence_vars.nu_var(), qp);
 
         libMesh::Gradient grad_nu;
         grad_nu = context.interior_gradient(this->_turbulence_vars.nu_var(), qp);
 
         libMesh::Real jac = JxW[qp];
 
         // The physical viscosity
         libMesh::Real mu_qp = this->_mu(context, qp);
 
         // The vorticity value
         libMesh::Real vorticity_value_qp = this->_spalart_allmaras_helper.vorticity(context, qp);
 
         // The flow velocity
         libMesh::Number u,v;
         u = context.interior_value(this->_flow_vars.u_var(), qp);
         v = context.interior_value(this->_flow_vars.v_var(), qp);
 
         libMesh::NumberVectorValue U(u,v);
         if (this->_dim == 3)
           U(2) = context.interior_value(this->_flow_vars.w_var(), qp);
 
         //The source term
         libMesh::Real S_tilde = this->_sa_params.source_fn(nu, mu_qp, (*distance_qp)(qp), vorticity_value_qp);
 
         // The ft2 function needed for the negative S-A model
         libMesh::Real chi = nu/mu_qp;
         libMesh::Real f_t2 = this->_sa_params.get_c_t3()*exp(-this->_sa_params.get_c_t4()*chi*chi);
 
         libMesh::Real source_term = ((*distance_qp)(qp)==0.0)?1.0:this->_sa_params.get_cb1()*(1 - f_t2)*S_tilde*nu;
         // For a negative turbulent viscosity nu < 0.0 we need to use a different production function
         if(nu < 0.0)
           {
             source_term = this->_sa_params.get_cb1()*(1 - this->_sa_params.get_c_t3())*vorticity_value_qp*nu;
           }
 
         // The wall destruction term
         libMesh::Real fw = this->_sa_params.destruction_fn(nu, (*distance_qp)(qp), S_tilde);
 
         libMesh::Real nud = nu/(*distance_qp)(qp);
         libMesh::Real nud2 = nud*nud;
         libMesh::Real kappa2 = (this->_sa_params.get_kappa())*(this->_sa_params.get_kappa());
         libMesh::Real destruction_term = ((*distance_qp)(qp)==0.0)?1.0:(this->_sa_params.get_cw1()*fw - (this->_sa_params.get_cb1()/kappa2)*f_t2)*nud2;
 
         // For a negative turbulent viscosity nu < 0.0 we need to use a different production function
         if(nu < 0.0)
           {
             destruction_term = -this->_sa_params.get_cw1()*nud2;
           }
 
         libMesh::Real fn1 = 1.0;
         // For a negative turbulent viscosity, fn1 needs to be calculated
         if(nu < 0.0)
           {
             libMesh::Real chi3 = chi*chi*chi;
             fn1 = (this->_sa_params.get_c_n1() + chi3)/(this->_sa_params.get_c_n1() - chi3);
           }
 
         // First, an i-loop over the viscosity degrees of freedom.
         for (unsigned int i=0; i != n_nu_dofs; i++)
           {
             Fnu(i) += jac *
               ( -this->_rho*(U*grad_nu)*nu_phi[i][qp]  // convection term (assumes incompressibility)
                 +source_term*nu_phi[i][qp] // source term
                 + (1./this->_sa_params.get_sigma())*(-(mu_qp+(fn1*nu))*grad_nu*nu_gradphi[i][qp] + this->_sa_params.get_cb2()*grad_nu*grad_nu*nu_phi[i][qp]) // diffusion term
                 - destruction_term*nu_phi[i][qp]); // destruction term
 
             // Compute the jacobian if not using numerical jacobians
             if (compute_jacobian)
               {
                 libmesh_not_implemented();
               } // end - if (compute_jacobian)
 
           } // end of the outer dof (i) loop
       } // end of the quadrature point (qp) loop
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("SpalartAllmaras::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::SpalartAllmarasStabilizationBase< Mu >::init_context ( AssemblyContext & context )

virtual

Initialize context for added physics variables.

Reimplemented from GRINS::SpalartAllmaras< Viscosity >.

Definition at line 55 of file spalart_allmaras_stab_base.C.

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

   {
     // First call base class
     SpalartAllmaras<Mu>::init_context(context);
       
     // We also need second derivatives, so initialize those.
     context.get_element_fe(this->_turbulence_vars.nu_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::SpalartAllmarasStabilizationBase< Mu >::init_variables ( libMesh::FEMSystem * system )

virtual

Initialize variables for this physics.

Reimplemented from GRINS::SpalartAllmaras< Viscosity >.

Reimplemented in GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >.

Definition at line 67 of file spalart_allmaras_stab_base.C.

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

Referenced by GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >::init_variables().

   {
     // First call base class
     SpalartAllmaras<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 K >

void GRINS::SpalartAllmaras< K >::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 from GRINS::Physics.

Reimplemented in GRINS::SpalartAllmarasSPGSMStabilization< Viscosity >.

Definition at line 287 of file spalart_allmaras.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("SpalartAllmaras::mass_residual");
 #endif
 
     // First we get some references to cell-specific data that
     // will be used to assemble the linear system.
 
     // Element Jacobian * quadrature weights for interior integration.
     const std::vector<libMesh::Real> &JxW =
       context.get_element_fe(this->_turbulence_vars.nu_var())->get_JxW();
 
     // The viscosity shape functions at interior quadrature points.
     const std::vector<std::vector<libMesh::Real> >& nu_phi =
       context.get_element_fe(this->_turbulence_vars.nu_var())->get_phi();
 
     // The number of local degrees of freedom in each variable.
     const unsigned int n_nu_dofs = context.get_dof_indices(this->_turbulence_vars.nu_var()).size();
 
     // The subvectors and submatrices we need to fill:
     libMesh::DenseSubVector<libMesh::Real> &F = context.get_elem_residual(this->_turbulence_vars.nu_var());
 
     //libMesh::DenseSubMatrix<libMesh::Real> &M = context.get_elem_jacobian(this->_turbulence_vars.nu_var(), this->_turbulence_vars.nu_var());
 
     unsigned int n_qpoints = context.get_element_qrule().n_points();
 
     for (unsigned int qp = 0; qp != n_qpoints; ++qp)
       {
         // For the mass residual, we need to be a little careful.
         // The time integrator is handling the time-discretization
         // for us so we need to supply M(u_fixed)*u' for the residual.
         // u_fixed will be given by the fixed_interior_value function
         // while u' will be given by the interior_rate function.
         libMesh::Real nu_dot;
         context.interior_rate(this->_turbulence_vars.nu_var(), qp, nu_dot);
 
         for (unsigned int i = 0; i != n_nu_dofs; ++i)
           {
             F(i) += -JxW[qp]*this->_rho*nu_dot*nu_phi[i][qp];
 
             if( compute_jacobian )
               {
                 libmesh_not_implemented();
               }// End of check on Jacobian
 
           } // End of element dof loop
 
       } // End of the quadrature point loop
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("SpalartAllmaras::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;
   }

void GRINS::ParameterUser::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 in GRINS::AxisymmetricHeatTransfer< Conductivity >, GRINS::LowMachNavierStokesBase< Viscosity, SpecificHeat, ThermalConductivity >, GRINS::IncompressibleNavierStokesBase< Viscosity >, GRINS::BoussinesqBuoyancySPGSMStabilization< Viscosity >, GRINS::HeatConduction< Conductivity >, GRINS::HeatTransferBase< Conductivity >, and GRINS::BoussinesqBuoyancyAdjointStabilization< Viscosity >.

Definition at line 50 of file parameter_user.C.

Referenced by GRINS::BoussinesqBuoyancyAdjointStabilization< Viscosity >::register_parameter(), GRINS::HeatTransferBase< Conductivity >::register_parameter(), GRINS::HeatConduction< Conductivity >::register_parameter(), GRINS::BoussinesqBuoyancySPGSMStabilization< Viscosity >::register_parameter(), GRINS::IncompressibleNavierStokesBase< Viscosity >::register_parameter(), GRINS::LowMachNavierStokesBase< Viscosity, SpecificHeat, ThermalConductivity >::register_parameter(), and GRINS::AxisymmetricHeatTransfer< Conductivity >::register_parameter().

   {
     std::map<std::string, libMesh::Number*>::const_iterator it =
       _my_parameters.find(param_name);
 
     if (it != _my_parameters.end())
       {
         std::cout << _my_name << " uses parameter " << param_name
                   << std::endl;
         param_pointer.push_back(it->second);
       }
   }

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

virtualinherited

Sets velocity variables to be time-evolving.

Reimplemented from GRINS::Physics.

Definition at line 134 of file spalart_allmaras.C.

   {
     // Tell the system to march velocity forward in time, but
     // leave p as a constraint only
     system->time_evolving(this->_turbulence_vars.nu_var());
 
     return;
   }