Physics class for Velocity Penalty. More...

#include <velocity_penalty.h>

Inheritance diagram for GRINS::VelocityPenalty< Viscosity >:

Collaboration diagram for GRINS::VelocityPenalty< Viscosity >:

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

	~VelocityPenalty ()

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

virtual void	register_postprocessing_vars (const GetPot &input, PostProcessedQuantities< libMesh::Real > &postprocessing)
	Register postprocessing variables for VelocityPenalty. More...

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

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

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

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

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

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

void	init_bcs (libMesh::FEMSystem *system)

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

void	attach_neumann_bound_func (GRINS::NBCContainer &neumann_bcs)

void	attach_dirichlet_bound_func (const GRINS::DBCContainer &dirichlet_bc)

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

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

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

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

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

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

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

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

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
bool	_quadratic_scaling

libMesh::AutoPtr< libMesh::FunctionBase< libMesh::Number > >	normal_vector_function

libMesh::AutoPtr< libMesh::FunctionBase< libMesh::Number > >	base_velocity_function

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
	VelocityPenalty ()

Private Attributes
unsigned int	_velocity_penalty_x_index
	Index from registering this quantity. More...

unsigned int	_velocity_penalty_y_index
	Index from registering this quantity. More...

unsigned int	_velocity_penalty_z_index
	Index from registering this quantity. More...

unsigned int	_velocity_penalty_base_x_index
	Index from registering this quantity. More...

unsigned int	_velocity_penalty_base_y_index
	Index from registering this quantity. More...

unsigned int	_velocity_penalty_base_z_index
	Index from registering this quantity. More...

Detailed Description

template<class Viscosity>
class GRINS::VelocityPenalty< Viscosity >

Physics class for Velocity Penalty.

Definition at line 50 of file velocity_penalty.h.

Constructor & Destructor Documentation

template<class Mu >

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

Definition at line 41 of file velocity_penalty.C.

     : VelocityPenaltyBase<Mu>(physics_name, input),
     _velocity_penalty_x_index(0),
     _velocity_penalty_y_index(0),
     _velocity_penalty_z_index(0),
     _velocity_penalty_base_x_index(0),
     _velocity_penalty_base_y_index(0),
     _velocity_penalty_base_z_index(0)
   {
     return;
   }

template<class Mu >

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

Definition at line 54 of file velocity_penalty.C.

   {
     return;
   }

template<class Viscosity >

GRINS::VelocityPenalty< Viscosity >::VelocityPenalty ( )

private

Member Function Documentation

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

inherited

Definition at line 150 of file physics.C.

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

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

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

inherited

Definition at line 144 of file physics.C.

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

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

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

virtualinherited

Any auxillary initialization a Physics class may need.

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

Definition at line 113 of file physics.C.

   {
     return;
   }

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

virtualinherited

Definition at line 185 of file physics.C.

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

   {
     return;
   }

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

virtualinherited

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

Definition at line 167 of file physics.C.

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

   {
     return;
   }

template<class Mu >

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

inherited

Definition at line 100 of file velocity_penalty_base.C.

   {
     // Velocity discrepancy (current velocity minus base velocity)
     // normal to constraint plane, scaled by constraint penalty
     // value
     libmesh_assert(normal_vector_function.get());
     libmesh_assert(base_velocity_function.get());
 
     libMesh::DenseVector<libMesh::Number> output_vec(3);
 
     (*normal_vector_function)(point, time,
                               output_vec);
 
     libMesh::NumberVectorValue U_N(output_vec(0),
                                    output_vec(1),
                                    output_vec(2));
 
     (*base_velocity_function)(point, time,
                               output_vec);
 
     const libMesh::NumberVectorValue U_B(output_vec(0),
                                          output_vec(1),
                                          output_vec(2));
 
     const libMesh::NumberVectorValue U_Rel = U-U_B;
 
     // Old code
     // const libMesh::NumberVectorValue F1 = (U_Rel*U_N)*U_N; //
 
     // With correct sign and more natural normalization
     const libMesh::Number U_N_mag = std::sqrt(U_N*U_N);
 
     if (!U_N_mag)
       return false;
 
     const libMesh::NumberVectorValue U_N_unit = U_N/U_N_mag;
 
     F = -(U_Rel*U_N)*U_N_unit;
 
     if (dFdU)
       for (unsigned int i=0; i != 3; ++i)
         for (unsigned int j=0; j != 3; ++j)
           (*dFdU)(i,j) = -(U_N(j))*U_N_unit(i);
 
     // With quadratic scaling
     if (_quadratic_scaling)
       {
         const libMesh::Number U_Rel_mag = std::sqrt(U_Rel * U_Rel);
 
         // Modify dFdU first so as to reuse the old value of F
         if (dFdU)
           {
             // dU_Rel/dU = I
             // d(U_Rel*U_Rel)/dU = 2*U_Rel
             // d|U_Rel|/dU = U_Rel/|U_Rel|
 
             const libMesh::NumberVectorValue U_Rel_unit = U_Rel/U_Rel_mag;
 
             (*dFdU) *= U_Rel_mag;
 
             if (U_Rel_mag)
               for (unsigned int i=0; i != 3; ++i)
                 for (unsigned int j=0; j != 3; ++j)
                   (*dFdU)(i,j) += F(i)*U_Rel_unit(j);
           }
 
         F *= U_Rel_mag;
       }
 
     // With correction term to avoid doing work on flow
     bool do_correction = false;
     if (do_correction)
       {
         if (dFdU)
           libmesh_not_implemented();
 
         const libMesh::Number U_Rel_mag_sq = U_Rel * U_Rel;
         if (U_Rel_mag_sq)
           {
             F -= (U_Rel*F)*U_Rel/U_Rel_mag_sq;
           }
       }
     return true;
   }

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;
   }

template<class Mu >

void GRINS::VelocityPenalty< Mu >::compute_postprocessed_quantity	(	unsigned int	quantity_index,
		const AssemblyContext &	context,
		const libMesh::Point &	point,
		libMesh::Real &	value
	)

virtual

Reimplemented from GRINS::Physics.

Definition at line 242 of file velocity_penalty.C.

   {
     libMesh::DenseVector<libMesh::Number> output_vec(3);
 
     if( quantity_index == this->_velocity_penalty_x_index )
       {
         (*this->normal_vector_function)(point, context.time, output_vec);
 
         value = output_vec(0);
       }
     else if( quantity_index == this->_velocity_penalty_y_index )
       {
         (*this->normal_vector_function)(point, context.time, output_vec);
 
         value = output_vec(1);
       }
     else if( quantity_index == this->_velocity_penalty_z_index )
       {
         (*this->normal_vector_function)(point, context.time, output_vec);
 
         value = output_vec(2);
       }
     else if( quantity_index == this->_velocity_penalty_base_x_index )
       {
         (*this->base_velocity_function)(point, context.time, output_vec);
 
         value = output_vec(0);
       }
     else if( quantity_index == this->_velocity_penalty_base_y_index )
       {
         (*this->base_velocity_function)(point, context.time, output_vec);
 
         value = output_vec(1);
       }
     else if( quantity_index == this->_velocity_penalty_base_z_index )
       {
         (*this->base_velocity_function)(point, context.time, output_vec);
 
         value = output_vec(2);
       }
 
     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::VelocityPenalty< 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 126 of file velocity_penalty.C.

   {
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->BeginTimer("VelocityPenalty::element_time_derivative");
 #endif
 
     // 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 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<libMesh::Point>& u_qpoint = 
       context.get_element_fe(this->_flow_vars.u_var())->get_xyz();
 
     // The number of local degrees of freedom in each variable
     const unsigned int n_u_dofs = context.get_dof_indices(this->_flow_vars.u_var()).size();
 
     // The subvectors and submatrices we need to fill:
     libMesh::DenseSubMatrix<libMesh::Number> &Kuu = context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.u_var()); // R_{u},{u}
     libMesh::DenseSubMatrix<libMesh::Number> &Kuv = context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.v_var()); // R_{u},{v}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvu = context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.u_var()); // R_{v},{u}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvv = context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.v_var()); // R_{v},{v}
 
     libMesh::DenseSubMatrix<libMesh::Number>* Kwu = NULL;
     libMesh::DenseSubMatrix<libMesh::Number>* Kwv = NULL;
     libMesh::DenseSubMatrix<libMesh::Number>* Kww = NULL;
     libMesh::DenseSubMatrix<libMesh::Number>* Kuw = NULL;
     libMesh::DenseSubMatrix<libMesh::Number>* Kvw = NULL;
 
     libMesh::DenseSubVector<libMesh::Number> &Fu = context.get_elem_residual(this->_flow_vars.u_var()); // R_{u}
     libMesh::DenseSubVector<libMesh::Number> &Fv = context.get_elem_residual(this->_flow_vars.v_var()); // R_{v}
     libMesh::DenseSubVector<libMesh::Number>* Fw = NULL;
 
     if( this->_dim == 3 )
       {
         Kuw = &context.get_elem_jacobian(this->_flow_vars.u_var(), this->_flow_vars.w_var()); // R_{u},{w}
         Kvw = &context.get_elem_jacobian(this->_flow_vars.v_var(), this->_flow_vars.w_var()); // R_{v},{w}
 
         Kwu = &context.get_elem_jacobian(this->_flow_vars.w_var(), this->_flow_vars.u_var()); // R_{w},{u}
         Kwv = &context.get_elem_jacobian(this->_flow_vars.w_var(), this->_flow_vars.v_var()); // R_{w},{v}
         Kww = &context.get_elem_jacobian(this->_flow_vars.w_var(), this->_flow_vars.w_var()); // R_{w},{w}
         Fw  = &context.get_elem_residual(this->_flow_vars.w_var()); // R_{w}
       }
 
     unsigned int n_qpoints = context.get_element_qrule().n_points();
 
     for (unsigned int qp=0; qp != n_qpoints; qp++)
       {
         // Compute the solution at the old Newton iterate.
         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); // w
 
         libMesh::NumberVectorValue F;
         libMesh::NumberTensorValue dFdU;
         libMesh::NumberTensorValue* dFdU_ptr =
           compute_jacobian ? &dFdU : NULL;
         if (!this->compute_force(u_qpoint[qp], context.time, U, F, dFdU_ptr))
           continue;
 
         const libMesh::Real jac = JxW[qp];
 
         for (unsigned int i=0; i != n_u_dofs; i++)
           {
             const libMesh::Number jac_i = jac * u_phi[i][qp];
 
             Fu(i) += F(0)*jac_i;
 
             Fv(i) += F(1)*jac_i;
             if( this->_dim == 3 )
               {
                 (*Fw)(i) += F(2)*jac_i;
               }
 
             if( compute_jacobian )
               {
                 for (unsigned int j=0; j != n_u_dofs; j++)
                   {
                     const libMesh::Number jac_ij = context.get_elem_solution_derivative() * jac_i * u_phi[j][qp];
                     Kuu(i,j) += jac_ij * dFdU(0,0);
                     Kuv(i,j) += jac_ij * dFdU(0,1);
                     Kvu(i,j) += jac_ij * dFdU(1,0);
                     Kvv(i,j) += jac_ij * dFdU(1,1);
 
                     if( this->_dim == 3 )
                       {
                         (*Kuw)(i,j) += jac_ij * dFdU(0,2);
                         (*Kvw)(i,j) += jac_ij * dFdU(1,2);
 
                         (*Kwu)(i,j) += jac_ij * dFdU(2,0);
                         (*Kwv)(i,j) += jac_ij * dFdU(2,1);
                         (*Kww)(i,j) += jac_ij * dFdU(2,2);
                       }
                   }
               }
           }
       }
 
 
 #ifdef GRINS_USE_GRVY_TIMERS
     this->_timer->EndTimer("VelocityPenalty::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::VelocityPenalty< Mu >::init_context ( AssemblyContext & context )

virtual

Initialize context for added physics variables.

Reimplemented from GRINS::IncompressibleNavierStokesBase< Viscosity >.

Definition at line 60 of file velocity_penalty.C.

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

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

inherited

Definition at line 133 of file physics.C.

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

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

template<class Mu >

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

virtualinherited

Initialization of Navier-Stokes variables.

Add velocity and pressure variables to system.

Implements GRINS::Physics.

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

Definition at line 63 of file inc_navier_stokes_base.C.

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

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

bool GRINS::Physics::is_steady ( ) const

inherited

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

Definition at line 103 of file physics.C.

References GRINS::Physics::_is_steady.

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

   {
     return _is_steady;
   }

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

virtualinherited

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

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

Definition at line 257 of file physics.C.

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

   {
     return;
   }

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

virtualinherited

Constraint part(s) of physics for scalar variables.

Reimplemented in GRINS::ScalarODE.

Definition at line 250 of file physics.C.

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

   {
     return;
   }   

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

virtualinherited

Mass matrix part(s) for scalar variables.

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

Definition at line 264 of file physics.C.

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

   {
     return;
   }

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

virtualinherited

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

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

Definition at line 229 of file physics.C.

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

   {
     return;
   }

template<class Mu >

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

virtualinherited

Read options from GetPot input file.

Reimplemented from GRINS::Physics.

Definition at line 58 of file velocity_penalty_base.C.

References GRINS::velocity_penalty2, GRINS::velocity_penalty2_adjoint_stab, GRINS::velocity_penalty3, and GRINS::velocity_penalty3_adjoint_stab.

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

   {
     std::string base_physics_name = "VelocityPenalty";
     if (this->_physics_name == velocity_penalty2 ||
         this->_physics_name == velocity_penalty2_adjoint_stab)
       base_physics_name.push_back('2');
 
     if (this->_physics_name == velocity_penalty3 ||
         this->_physics_name == velocity_penalty3_adjoint_stab)
       base_physics_name.push_back('3');
 
     std::string penalty_function =
       input("Physics/"+base_physics_name+"/penalty_function",
         std::string("0"));
 
     if (penalty_function == "0")
       this->normal_vector_function.reset
         (new libMesh::ZeroFunction<libMesh::Number>());
     else
       this->normal_vector_function.reset
         (new libMesh::ParsedFunction<libMesh::Number>(penalty_function));
 
     std::string base_function =
       input("Physics/"+base_physics_name+"/base_velocity",
         std::string("0"));
 
     if (penalty_function == "0" && base_function == "0")
       std::cout << "Warning! Zero VelocityPenalty specified!" << std::endl;
 
     if (base_function == "0")
       this->base_velocity_function.reset
         (new libMesh::ZeroFunction<libMesh::Number>());
     else
       this->base_velocity_function.reset
         (new libMesh::ParsedFunction<libMesh::Number>(base_function));
 
     _quadratic_scaling = 
       input("Physics/"+base_physics_name+"/quadratic_scaling", false);
   }

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);
   }

template<class Mu >

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

virtual

Register postprocessing variables for VelocityPenalty.

Reimplemented from GRINS::Physics.

Definition at line 69 of file velocity_penalty.C.

References GRINS::PostProcessedQuantities< NumericType >::register_quantity().

   {
     std::string section = "Physics/"+this->_physics_name+"/output_vars";
 
     std::string vel_penalty = "vel_penalty";
     if (this->_physics_name == "VelocityPenalty2")
       vel_penalty += '2';
 
     if (this->_physics_name == "VelocityPenalty3")
       vel_penalty += '3';
 
     if( input.have_variable(section) )
       {
         unsigned int n_vars = input.vector_variable_size(section);
 
         for( unsigned int v = 0; v < n_vars; v++ )
           {
             std::string name = input(section,"DIE!",v);
 
             if( name == std::string("velocity_penalty") )
               {
                 _velocity_penalty_x_index =
                   postprocessing.register_quantity( vel_penalty+"_x" );
 
                 _velocity_penalty_y_index =
                   postprocessing.register_quantity( vel_penalty+"_y" );
 
                 _velocity_penalty_z_index =
                   postprocessing.register_quantity( vel_penalty+"_z" );
               }
             else if( name == std::string("velocity_penalty_base") )
               {
                 _velocity_penalty_base_x_index =
                   postprocessing.register_quantity( vel_penalty+"_base_x" );
 
                 _velocity_penalty_base_y_index =
                   postprocessing.register_quantity( vel_penalty+"_base_y" );
 
                 _velocity_penalty_base_z_index =
                   postprocessing.register_quantity( vel_penalty+"_base_z" );
               }
             else
               {
                 std::cerr << "Error: Invalue output_vars value for "+this->_physics_name << std::endl
                           << "       Found " << name << std::endl
                           << "       Acceptable values are: velocity_penalty" << std::endl
                           << "                              velocity_penalty_base" << std::endl;
                 libmesh_error();
               }
           }
       }
 
     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;
   }

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

virtualinherited

Constraint part(s) of physics for boundaries of elements on the domain boundary.

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

Definition at line 243 of file physics.C.

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

   {
     return;
   }   

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

virtualinherited

Time dependent part(s) of physics for boundaries of elements on the domain boundary.

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

Definition at line 222 of file physics.C.

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

   {
     return;
   }

Member Data Documentation

GRINS::BCHandlingBase* GRINS::Physics::_bc_handler

protectedinherited

Definition at line 256 of file physics.h.

Referenced by GRINS::Physics::attach_dirichlet_bound_func(), GRINS::Physics::attach_neumann_bound_func(), GRINS::AxisymmetricHeatTransfer< Conductivity >::AxisymmetricHeatTransfer(), GRINS::ElasticCable< StressStrainLaw >::ElasticCable(), GRINS::ElasticMembrane< StressStrainLaw >::ElasticMembrane(), GRINS::Physics::get_bc_handler(), GRINS::HeatConduction< Conductivity >::HeatConduction(), GRINS::HeatTransfer< Conductivity >::HeatTransfer(), GRINS::IncompressibleNavierStokes< Viscosity >::IncompressibleNavierStokes(), GRINS::Physics::init_bcs(), GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >::LowMachNavierStokes(), GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >::ReactingLowMachNavierStokes(), GRINS::SpalartAllmaras< Viscosity >::SpalartAllmaras(), GRINS::Stokes< Viscosity >::Stokes(), and GRINS::Physics::~Physics().

template<class Viscosity >

unsigned int GRINS::IncompressibleNavierStokesBase< Viscosity >::_dim

protectedinherited

Physical dimension of problem.

Todo:: Do we really need to cache this?

Definition at line 79 of file inc_navier_stokes_base.h.

std::set<libMesh::subdomain_id_type> GRINS::Physics::_enabled_subdomains

protectedinherited

Subdomains on which the current Physics class is enabled.

Definition at line 261 of file physics.h.

Referenced by GRINS::Physics::enabled_on_elem(), and GRINS::Physics::read_input_options().

template<class Viscosity >

PrimitiveFlowFEVariables GRINS::IncompressibleNavierStokesBase< Viscosity >::_flow_vars

protectedinherited

Definition at line 81 of file inc_navier_stokes_base.h.

GRINS::ICHandlingBase* GRINS::Physics::_ic_handler

protectedinherited

Definition at line 258 of file physics.h.

Referenced by GRINS::AveragedTurbine< Viscosity >::AveragedTurbine(), GRINS::AxisymmetricHeatTransfer< Conductivity >::AxisymmetricHeatTransfer(), GRINS::ElasticCable< StressStrainLaw >::ElasticCable(), GRINS::ElasticMembrane< StressStrainLaw >::ElasticMembrane(), GRINS::Physics::get_ic_handler(), GRINS::HeatConduction< Conductivity >::HeatConduction(), GRINS::HeatTransfer< Conductivity >::HeatTransfer(), GRINS::IncompressibleNavierStokes< Viscosity >::IncompressibleNavierStokes(), GRINS::Physics::init_ics(), GRINS::LowMachNavierStokes< Viscosity, SpecificHeat, ThermalConductivity >::LowMachNavierStokes(), GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >::ReactingLowMachNavierStokes(), GRINS::ScalarODE::ScalarODE(), GRINS::SpalartAllmaras< Viscosity >::SpalartAllmaras(), GRINS::Stokes< Viscosity >::Stokes(), and GRINS::Physics::~Physics().

bool GRINS::Physics::_is_axisymmetric

protectedinherited

Definition at line 268 of file physics.h.

Referenced by GRINS::HeatTransfer< Conductivity >::HeatTransfer(), GRINS::IncompressibleNavierStokes< Viscosity >::IncompressibleNavierStokes(), GRINS::Physics::Physics(), and GRINS::ReactingLowMachNavierStokes< Mixture, Evaluator >::ReactingLowMachNavierStokes().

bool GRINS::Physics::_is_steady = false

staticprotectedinherited

Caches whether or not the solver that's being used is steady or not.

This is need, for example, in flow stabilization as the tau terms change depending on whether the solver is steady or unsteady.

Definition at line 266 of file physics.h.

Referenced by GRINS::Physics::is_steady(), and GRINS::Physics::set_is_steady().

template<class Viscosity >

Viscosity GRINS::IncompressibleNavierStokesBase< Viscosity >::_mu

protectedinherited

Viscosity object.

Definition at line 88 of file inc_navier_stokes_base.h.

const PhysicsName GRINS::Physics::_physics_name

protectedinherited

Name of the physics object. Used for reading physics specific inputs.

We use a reference because the physics names are const global objects in GRINS namespace

No, we use a copy, because otherwise as soon as the memory in std::set<std::string> requested_physics gets overwritten we get in trouble.

Definition at line 254 of file physics.h.

Referenced by GRINS::SourceTermBase::parse_var_info(), and GRINS::Physics::read_input_options().

template<class Viscosity >

bool GRINS::VelocityPenaltyBase< Viscosity >::_quadratic_scaling

protectedinherited

Definition at line 64 of file velocity_penalty_base.h.

template<class Viscosity >

libMesh::Number GRINS::IncompressibleNavierStokesBase< Viscosity >::_rho

protectedinherited

Material parameters, read from input.

Todo:: Create objects to allow for function specification

Definition at line 85 of file inc_navier_stokes_base.h.

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

template<class Viscosity >

unsigned int GRINS::VelocityPenalty< Viscosity >::_velocity_penalty_base_x_index

private