Physics class for arbitrary scalar-valued ODEs. More...

#include <scalar_ode.h>

Inheritance diagram for GRINS::ScalarODE:

Collaboration diagram for GRINS::ScalarODE:

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

	~ScalarODE ()

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

virtual void	set_time_evolving_vars (libMesh::FEMSystem *system)
	Sets scalar variable(s) to be time-evolving. More...

virtual void	init_context (AssemblyContext &context)
	Prepare the context for evaluations. 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	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...

VariableIndex	scalar_ode_var () 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	register_postprocessing_vars (const GetPot &input, PostProcessedQuantities< libMesh::Real > &postprocessing)
	Register name of postprocessed quantity with PostProcessedQuantities. 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	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	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	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...

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)

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

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...

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...

Private Member Functions
	ScalarODE ()

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

Private Attributes
libMesh::UniquePtr< libMesh::FEMFunctionBase< libMesh::Number > >	time_deriv_function

libMesh::UniquePtr< libMesh::FEMFunctionBase< libMesh::Number > >	constraint_function

libMesh::UniquePtr< libMesh::FEMFunctionBase< libMesh::Number > >	mass_residual_function

libMesh::Number	_order

libMesh::Number	_epsilon

VariableIndex	_scalar_ode_var

std::string	_scalar_ode_var_name

const GetPot &	_input

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::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

Physics class for arbitrary scalar-valued ODEs.

Definition at line 50 of file scalar_ode.h.

Constructor & Destructor Documentation

GRINS::ScalarODE::ScalarODE	(	const std::string &	physics_name,
		const GetPot &	input
	)

Definition at line 40 of file scalar_ode.C.

References GRINS::Physics::_ic_handler, and read_input_options().

     : Physics(physics_name, input),
       _order(1),
       _epsilon(1e-6),
       _input(input)
   {
     this->read_input_options(input);
 
     this->_ic_handler = new GenericICHandler( physics_name, input );
   }

GRINS::ScalarODE::~ScalarODE ( )

inline

Definition at line 56 of file scalar_ode.h.

56 {};

GRINS::ScalarODE::ScalarODE ( )

private

Member Function Documentation

void GRINS::ScalarODE::init_context ( AssemblyContext & context )

virtual

Prepare the context for evaluations.

Reimplemented from GRINS::Physics.

Definition at line 109 of file scalar_ode.C.

References constraint_function, mass_residual_function, and time_deriv_function.

   {
     mass_residual_function->init_context(context);
     time_deriv_function->init_context(context);
     constraint_function->init_context(context);
   }

void GRINS::ScalarODE::init_variables ( libMesh::FEMSystem * system )

virtual

Initialization of variables.

Add scalar variable(s) to system.

Implements GRINS::Physics.

Definition at line 51 of file scalar_ode.C.

References _order, _scalar_ode_var, and _scalar_ode_var_name.

   {
     this->_scalar_ode_var = system->add_variable(_scalar_ode_var_name,
                                                  libMesh::Order(this->_order),
                                                  libMesh::SCALAR);
   }

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

virtual

Constraint part(s) of physics for scalar variables.

Reimplemented from GRINS::Physics.

Definition at line 209 of file scalar_ode.C.

References _epsilon, and _scalar_ode_var.

   {
     libMesh::DenseSubMatrix<libMesh::Number> &Kss =
             context.get_elem_jacobian(_scalar_ode_var, _scalar_ode_var); // R_{s},{s}
 
     libMesh::DenseSubVector<libMesh::Number> &Fs =
             context.get_elem_residual(_scalar_ode_var); // R_{s}
 
     const libMesh::Number constraint =
       (*constraint_function)(context, libMesh::Point(0),
                              context.get_time());
 
     Fs(0) += constraint;
 
     if (compute_jacobian)
       {
         // FIXME: we should replace this hacky FDM with a hook to the
         // AD fparser stuff
         libMesh::DenseSubVector<libMesh::Number> &Us =
           const_cast<libMesh::DenseSubVector<libMesh::Number>&>
             (context.get_elem_solution(_scalar_ode_var)); // U_{s}
 
         const libMesh::Number s = Us(0);
         Us(0) = s + this->_epsilon;
         libMesh::Number constraint_jacobian =
           (*constraint_function)(context, libMesh::Point(0),
                                  context.get_time());
 
         Us(0) = s - this->_epsilon;
         constraint_jacobian -=
           (*constraint_function)(context, libMesh::Point(0),
                                  context.get_time());
 
         Us(0) = s;
         constraint_jacobian /= (2*this->_epsilon);
 
         Kss(0,0) += constraint_jacobian *
           context.get_elem_solution_derivative();
       }
 
     return;
   }

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

virtual

Mass matrix part(s) for scalar variables.

Reimplemented from GRINS::Physics.

Definition at line 163 of file scalar_ode.C.

References _epsilon, and _scalar_ode_var.

   {
     libMesh::DenseSubMatrix<libMesh::Number> &Kss =
             context.get_elem_jacobian(_scalar_ode_var, _scalar_ode_var); // R_{s},{s}
 
     libMesh::DenseSubVector<libMesh::Number> &Fs =
             context.get_elem_residual(_scalar_ode_var); // R_{s}
 
     const libMesh::Number mass_res =
       (*mass_residual_function)(context, libMesh::Point(0),
                                 context.get_time());
 
     Fs(0) -= mass_res;
 
     if (compute_jacobian)
       {
         // FIXME: we should replace this hacky FDM with a hook to the
         // AD fparser stuff
         libMesh::DenseSubVector<libMesh::Number> &Us =
           const_cast<libMesh::DenseSubVector<libMesh::Number>&>
             (context.get_elem_solution_rate(_scalar_ode_var)); // U_{s}
 
         const libMesh::Number s = Us(0);
         Us(0) = s + this->_epsilon;
         libMesh::Number mass_residual_jacobian =
           (*mass_residual_function)(context, libMesh::Point(0),
                                     context.get_time());
 
         Us(0) = s - this->_epsilon;
         mass_residual_jacobian -=
           (*mass_residual_function)(context, libMesh::Point(0),
                                     context.get_time());
 
         Us(0) = s;
         mass_residual_jacobian /= (2*this->_epsilon);
 
         Kss(0,0) -= mass_residual_jacobian *
           context.get_elem_solution_rate_derivative();
       }
 
     return;
   }

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

virtual

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

Reimplemented from GRINS::Physics.

Definition at line 117 of file scalar_ode.C.

References _epsilon, and _scalar_ode_var.

   {
     libMesh::DenseSubMatrix<libMesh::Number> &Kss =
             context.get_elem_jacobian(_scalar_ode_var, _scalar_ode_var); // R_{s},{s}
 
     libMesh::DenseSubVector<libMesh::Number> &Fs =
             context.get_elem_residual(_scalar_ode_var); // R_{s}
 
     const libMesh::Number time_deriv =
       (*time_deriv_function)(context, libMesh::Point(0),
                              context.get_time());
 
     Fs(0) += time_deriv;
 
     if (compute_jacobian)
       {
         // FIXME: we should replace this hacky FDM with a hook to the
         // AD fparser stuff
         libMesh::DenseSubVector<libMesh::Number> &Us =
           const_cast<libMesh::DenseSubVector<libMesh::Number>&>
             (context.get_elem_solution(_scalar_ode_var)); // U_{s}
 
         const libMesh::Number s = Us(0);
         Us(0) = s + this->_epsilon;
         libMesh::Number time_deriv_jacobian =
           (*time_deriv_function)(context, libMesh::Point(0),
                                  context.get_time());
 
         Us(0) = s - this->_epsilon;
         time_deriv_jacobian -=
           (*time_deriv_function)(context, libMesh::Point(0),
                                  context.get_time());
 
         Us(0) = s;
         time_deriv_jacobian /= (2*this->_epsilon);
 
         Kss(0,0) += time_deriv_jacobian *
           context.get_elem_solution_derivative();
       }
 
     return;
   }

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

private

Read options from GetPot input file.

Definition at line 98 of file scalar_ode.C.

References _epsilon, _order, _scalar_ode_var_name, GRINS::PhysicsNaming::scalar_ode(), and GRINS::scalar_ode_var_name_default.

Referenced by ScalarODE().

   {
     this->_epsilon = input("Physics/"+PhysicsNaming::scalar_ode()+"/epsilon", 1e-6);
 
     this->_order = input("Physics/"+PhysicsNaming::scalar_ode()+"/order", 1);
 
     _scalar_ode_var_name = input("Physics/VariableNames/scalar_ode",
                                  scalar_ode_var_name_default);
   }

VariableIndex GRINS::ScalarODE::scalar_ode_var ( ) const

inline

Definition at line 87 of file scalar_ode.h.

References _scalar_ode_var.

Referenced by set_time_evolving_vars().

87 { return _scalar_ode_var; }

GRINS::ScalarODE::_scalar_ode_var

VariableIndex _scalar_ode_var

Definition: scalar_ode.h:105

void GRINS::ScalarODE::set_time_evolving_vars ( libMesh::FEMSystem * system )

virtual

Sets scalar variable(s) to be time-evolving.

Reimplemented from GRINS::Physics.

Definition at line 58 of file scalar_ode.C.

References _input, constraint_function, mass_residual_function, GRINS::PhysicsNaming::scalar_ode(), scalar_ode_var(), GRINS::ParameterUser::set_parameter(), and time_deriv_function.

   {
     system->time_evolving(this->scalar_ode_var());
 
     // FIXME: this doesn't fit here at all, but it's the only time
     // we've clearly got a System to grab hold of with all it's
     // variables initialized.
 
     libMesh::ParsedFEMFunction<libMesh::Number> *tdf
       (new libMesh::ParsedFEMFunction<libMesh::Number> (*system, ""));
     this->time_deriv_function.reset(tdf);
 
     if (tdf->expression() == "0")
       std::cout << "Warning! Zero time_deriv function specified!" << std::endl;
 
     this->set_parameter(*tdf, _input,
                         "Physics/"+PhysicsNaming::scalar_ode()+"/time_deriv",
                         std::string("0"));
 
     libMesh::ParsedFEMFunction<libMesh::Number> *mrf
       (new libMesh::ParsedFEMFunction<libMesh::Number> (*system, ""));
     this->mass_residual_function.reset(mrf);
 
     if (mrf->expression() == "0")
       std::cout << "Warning! Zero mass_residual function specified!" << std::endl;
 
     this->set_parameter(*mrf, _input,
                         "Physics/"+PhysicsNaming::scalar_ode()+"/mass_residual",
                         std::string("0"));
 
     libMesh::ParsedFEMFunction<libMesh::Number> *cf
       (new libMesh::ParsedFEMFunction<libMesh::Number> (*system, ""));
     this->constraint_function.reset(cf);
 
     this->set_parameter(*cf, _input,
                         "Physics/"+PhysicsNaming::scalar_ode()+"/constraint",
                         std::string("0"));
   }