GRINS::VelocityPenalty< Viscosity > Class Template Reference

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)
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	init_variables (libMesh::FEMSystem *system)
	Initialization of Navier-Stokes variables. More...
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 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	damping_residual (bool compute_jacobian, AssemblyContext &context, CachedValues &cache)
	Damping matrix part(s) for element interiors. All boundary terms lie within the time_derivative part. 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_ics (libMesh::FEMSystem *system, libMesh::CompositeFunction< libMesh::Number > &all_ics)
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_damping_residual_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)
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)
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 >
unsigned int	_dim
	Physical dimension of problem. More...
VelocityFEVariables	_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 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)(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  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())->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->_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->_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->_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;
  }

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;
  }

Member Data Documentation

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 89 of file velocity_penalty.h.

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 92 of file velocity_penalty.h.

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 95 of file velocity_penalty.h.

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 80 of file velocity_penalty.h.

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 83 of file velocity_penalty.h.

template<class Viscosity >

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

private

Index from registering this quantity.

Definition at line 86 of file velocity_penalty.h.

---

The documentation for this class was generated from the following files:

• src/physics/include/grins/velocity_penalty.h
• src/physics/src/velocity_penalty.C