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)
	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)

Public Member Functions inherited from GRINS::VelocityPenaltyBase< Viscosity >
	VelocityPenaltyBase (const std::string &physics_name, const GetPot &input)

	~VelocityPenaltyBase ()

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

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

Public Member Functions inherited from GRINS::IncompressibleNavierStokesBase< Viscosity >
	IncompressibleNavierStokesBase (const std::string &my_physics_name, const std::string &core_physics_name, const GetPot &input)

	~IncompressibleNavierStokesBase ()

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

libMesh::Real	get_viscosity_value (AssemblyContext &context, unsigned int qp) const

Public Member Functions inherited from GRINS::Physics
	Physics (const GRINS::PhysicsName &physics_name, const GetPot &input)

virtual	~Physics ()

virtual void	init_variables (libMesh::FEMSystem *)
	Initialize variables for this physics. 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	preassembly (MultiphysicsSystem &)
	Perform any necessary setup before element assembly begins. More...

virtual void	reinit (MultiphysicsSystem &)
	Any reinitialization that needs to be done. More...

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

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

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

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

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

virtual void	damping_residual (bool, AssemblyContext &)
	Damping matrix part(s) for element interiors. All boundary terms lie within the time_derivative part. More...

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

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

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

virtual void	compute_element_time_derivative_cache (AssemblyContext &)

virtual void	compute_side_time_derivative_cache (AssemblyContext &)

virtual void	compute_nonlocal_time_derivative_cache (AssemblyContext &)

virtual void	compute_element_constraint_cache (AssemblyContext &)

virtual void	compute_side_constraint_cache (AssemblyContext &)

virtual void	compute_nonlocal_constraint_cache (AssemblyContext &)

virtual void	compute_damping_residual_cache (AssemblyContext &)

virtual void	compute_mass_residual_cache (AssemblyContext &)

virtual void	compute_nonlocal_mass_residual_cache (AssemblyContext &)

ICHandlingBase *	get_ic_handler ()

Public Member Functions inherited from GRINS::ParameterUser
	ParameterUser (const std::string &user_name)

virtual	~ParameterUser ()

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	set_parameter (libMesh::ParsedFunction< libMesh::Number, libMesh::Gradient > &func, const GetPot &input, const std::string &func_param_name, const std::string &param_default)
	Each subclass can simultaneously read a parsed function from. More...

virtual void	set_parameter (libMesh::ParsedFEMFunction< libMesh::Number > &func, const GetPot &input, const std::string &func_param_name, const std::string &param_default)
	Each subclass can simultaneously read a parsed function from. More...

virtual void	move_parameter (const libMesh::Number &old_parameter, libMesh::Number &new_parameter)
	When cloning an object, we need to update parameter pointers. More...

virtual void	move_parameter (const libMesh::ParsedFunction< libMesh::Number, libMesh::Gradient > &old_func, libMesh::ParsedFunction< libMesh::Number, libMesh::Gradient > &new_func)
	When cloning an object, we need to update parameter pointers. More...

virtual void	move_parameter (const libMesh::ParsedFEMFunction< libMesh::Number > &old_func, libMesh::ParsedFEMFunction< libMesh::Number > &new_func)
	When cloning an object, we need to update parameter pointers. 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...

Additional Inherited Members
Static Public Member Functions inherited from GRINS::Physics
static void	set_is_axisymmetric (bool is_axisymmetric)
	Set whether we should treat the problem as axisymmetric. More...

static bool	is_axisymmetric ()

Static Public Attributes inherited from GRINS::ParameterUser
static std::string	zero_vector_function = std::string("{0}")
	A parseable function string with LIBMESH_DIM components, all 0. More...

Protected Member Functions inherited from GRINS::Physics
libMesh::UniquePtr< libMesh::FEGenericBase< libMesh::Real > >	build_new_fe (const libMesh::Elem elem, const libMesh::FEGenericBase< libMesh::Real > fe, const libMesh::Point p)

void	parse_enabled_subdomains (const GetPot &input, const std::string &physics_name)

void	check_var_subdomain_consistency (const FEVariablesBase &var) const
	Check that var is enabled on at least the subdomains this Physics is. More...

Protected Attributes inherited from GRINS::VelocityPenaltyBase< Viscosity >
std::string	base_physics_name

bool	_quadratic_scaling

libMesh::UniquePtr< libMesh::FEMFunctionBase< libMesh::Number > >	normal_vector_function

libMesh::UniquePtr< libMesh::FEMFunctionBase< libMesh::Number > >	base_velocity_function

Protected Attributes inherited from GRINS::IncompressibleNavierStokesBase< Viscosity >
VelocityVariable &	_flow_vars

PressureFEVariable &	_press_var

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

Viscosity	_mu
	Viscosity object. More...

Protected Attributes inherited from GRINS::Physics
const PhysicsName	_physics_name
	Name of the physics object. Used for reading physics specific inputs. More...

GRINS::ICHandlingBase *	_ic_handler

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

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

static bool	_is_axisymmetric = false
	Caches whether we are solving an axisymmetric problem or not. 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

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 231 of file velocity_penalty.C.

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

template<class Mu >

void GRINS::VelocityPenalty< Mu >::element_time_derivative	(	bool	,
		AssemblyContext &
	)

virtual

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

Reimplemented from GRINS::Physics.

Definition at line 127 of file velocity_penalty.C.

   {
     // Element Jacobian * quadrature weights for interior integration
     const std::vector<libMesh::Real> &JxW =
       context.get_element_fe(this->_flow_vars.u())->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())->get_phi();
 
     const std::vector<libMesh::Point>& u_qpoint =
       context.get_element_fe(this->_flow_vars.u())->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()).size();
 
     // The subvectors and submatrices we need to fill:
     libMesh::DenseSubMatrix<libMesh::Number> &Kuu = context.get_elem_jacobian(this->_flow_vars.u(), this->_flow_vars.u()); // R_{u},{u}
     libMesh::DenseSubMatrix<libMesh::Number> &Kuv = context.get_elem_jacobian(this->_flow_vars.u(), this->_flow_vars.v()); // R_{u},{v}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvu = context.get_elem_jacobian(this->_flow_vars.v(), this->_flow_vars.u()); // R_{v},{u}
     libMesh::DenseSubMatrix<libMesh::Number> &Kvv = context.get_elem_jacobian(this->_flow_vars.v(), this->_flow_vars.v()); // 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()); // R_{u}
     libMesh::DenseSubVector<libMesh::Number> &Fv = context.get_elem_residual(this->_flow_vars.v()); // R_{v}
     libMesh::DenseSubVector<libMesh::Number>* Fw = NULL;
 
     if( this->_flow_vars.dim() == 3 )
       {
         Kuw = &context.get_elem_jacobian(this->_flow_vars.u(), this->_flow_vars.w()); // R_{u},{w}
         Kvw = &context.get_elem_jacobian(this->_flow_vars.v(), this->_flow_vars.w()); // R_{v},{w}
 
         Kwu = &context.get_elem_jacobian(this->_flow_vars.w(), this->_flow_vars.u()); // R_{w},{u}
         Kwv = &context.get_elem_jacobian(this->_flow_vars.w(), this->_flow_vars.v()); // R_{w},{v}
         Kww = &context.get_elem_jacobian(this->_flow_vars.w(), this->_flow_vars.w()); // R_{w},{w}
         Fw  = &context.get_elem_residual(this->_flow_vars.w()); // 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(), qp);
         v = context.interior_value(this->_flow_vars.v(), qp);
 
         libMesh::NumberVectorValue U(u,v);
         if (this->_flow_vars.dim() == 3)
           U(2) = context.interior_value(this->_flow_vars.w(), qp); // w
 
         libMesh::NumberVectorValue F;
         libMesh::NumberTensorValue dFdU;
         libMesh::NumberTensorValue* dFdU_ptr =
           compute_jacobian ? &dFdU : NULL;
         if (!this->compute_force(u_qpoint[qp], context, 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->_flow_vars.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->_flow_vars.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);
                       }
                   }
               }
           }
       }
   }

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

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;
   }