System Class Reference

#include <system.h>

Inheritance diagram for System:

[legend]

List of all members.

Classes
class	BuildProjectionList
class	ProjectSolution
class	ProjectVector
class	Variable
Public Types
typedef System	sys_type
typedef std::map< std::string, NumericVector< Number > * >::iterator	vectors_iterator
typedef std::map< std::string, NumericVector< Number > * >::const_iterator	const_vectors_iterator
Public Member Functions
virtual	~System ()
sys_type &	system ()
virtual void	clear ()
void	init ()
virtual void	reinit ()
virtual void	update ()
virtual void	assemble ()
virtual void	assemble_qoi (const QoISet &qoi_indices=QoISet())
virtual void	assemble_qoi_derivative (const QoISet &qoi_indices=QoISet())
virtual void	assemble_residual_derivatives (const ParameterVector &parameters)
virtual void	solve ()=0
virtual std::pair< unsigned int, Real >	sensitivity_solve (const ParameterVector &parameters)
virtual std::pair< unsigned int, Real >	weighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights)
virtual std::pair< unsigned int, Real >	adjoint_solve (const QoISet &qoi_indices=QoISet())
virtual std::pair< unsigned int, Real >	weighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet())
virtual void	qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
virtual void	adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
virtual void	forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
virtual void	qoi_parameter_hessian_vector_product (const QoISet &qoi_indices, const ParameterVector &parameters, const ParameterVector &vector, SensitivityData &product)
virtual bool	compare (const System &other_system, const Real threshold, const bool verbose) const
const std::string &	name () const
virtual std::string	system_type () const
void	project_solution (Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Parameters &parameters) const
void	project_vector (Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Parameters &parameters, NumericVector< Number > &new_vector) const
unsigned int	number () const
void	update_global_solution (std::vector< Number > &global_soln) const
void	update_global_solution (std::vector< Number > &global_soln, const unsigned int dest_proc) const
const MeshBase &	get_mesh () const
MeshBase &	get_mesh ()
const DofMap &	get_dof_map () const
DofMap &	get_dof_map ()
const EquationSystems &	get_equation_systems () const
EquationSystems &	get_equation_systems ()
bool	active () const
void	activate ()
void	deactivate ()
vectors_iterator	vectors_begin ()
const_vectors_iterator	vectors_begin () const
vectors_iterator	vectors_end ()
const_vectors_iterator	vectors_end () const
NumericVector< Number > &	add_vector (const std::string &vec_name, const bool projections=true)
bool &	project_solution_on_reinit (void)
bool	have_vector (const std::string &vec_name) const
const NumericVector< Number > *	request_vector (const std::string &vec_name) const
NumericVector< Number > *	request_vector (const std::string &vec_name)
const NumericVector< Number > *	request_vector (const unsigned int vec_num) const
NumericVector< Number > *	request_vector (const unsigned int vec_num)
const NumericVector< Number > &	get_vector (const std::string &vec_name) const
NumericVector< Number > &	get_vector (const std::string &vec_name)
const NumericVector< Number > &	get_vector (const unsigned int vec_num) const
NumericVector< Number > &	get_vector (const unsigned int vec_num)
const std::string &	vector_name (const unsigned int vec_num)
NumericVector< Number > &	add_adjoint_solution (unsigned int i=0)
NumericVector< Number > &	get_adjoint_solution (unsigned int i=0)
const NumericVector< Number > &	get_adjoint_solution (unsigned int i=0) const
NumericVector< Number > &	add_sensitivity_solution (unsigned int i=0)
NumericVector< Number > &	get_sensitivity_solution (unsigned int i=0)
const NumericVector< Number > &	get_sensitivity_solution (unsigned int i=0) const
NumericVector< Number > &	add_weighted_sensitivity_adjoint_solution (unsigned int i=0)
NumericVector< Number > &	get_weighted_sensitivity_adjoint_solution (unsigned int i=0)
const NumericVector< Number > &	get_weighted_sensitivity_adjoint_solution (unsigned int i=0) const
NumericVector< Number > &	add_weighted_sensitivity_solution ()
NumericVector< Number > &	get_weighted_sensitivity_solution ()
const NumericVector< Number > &	get_weighted_sensitivity_solution () const
NumericVector< Number > &	add_adjoint_rhs (unsigned int i=0)
NumericVector< Number > &	get_adjoint_rhs (unsigned int i=0)
const NumericVector< Number > &	get_adjoint_rhs (unsigned int i=0) const
NumericVector< Number > &	add_sensitivity_rhs (unsigned int i=0)
NumericVector< Number > &	get_sensitivity_rhs (unsigned int i=0)
const NumericVector< Number > &	get_sensitivity_rhs (unsigned int i=0) const
unsigned int	n_vectors () const
unsigned int	n_vars () const
unsigned int	n_dofs () const
unsigned int	n_active_dofs () const
unsigned int	n_constrained_dofs () const
unsigned int	n_local_dofs () const
unsigned int	add_variable (const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=NULL)
unsigned int	add_variable (const std::string &var, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=NULL)
const Variable &	variable (unsigned int var) const
bool	has_variable (const std::string &var) const
const std::string &	variable_name (const unsigned int i) const
unsigned short int	variable_number (const std::string &var) const
const FEType &	variable_type (const unsigned int i) const
const FEType &	variable_type (const std::string &var) const
Real	calculate_norm (NumericVector< Number > &v, unsigned int var=0, FEMNormType norm_type=L2) const
Real	calculate_norm (NumericVector< Number > &v, const SystemNorm &norm) const
void	read_header (Xdr &io, const std::string &version, const bool read_header=true, const bool read_additional_data=true, const bool read_legacy_format=false)
void	read_legacy_data (Xdr &io, const bool read_additional_data=true)
void	read_serialized_data (Xdr &io, const bool read_additional_data=true)
void	read_parallel_data (Xdr &io, const bool read_additional_data)
void	write_header (Xdr &io, const std::string &version, const bool write_additional_data) const
void	write_serialized_data (Xdr &io, const bool write_additional_data=true) const
void	write_parallel_data (Xdr &io, const bool write_additional_data) const
std::string	get_info () const
void	attach_init_function (void fptr(EquationSystems &es, const std::string &name))
void	attach_assemble_function (void fptr(EquationSystems &es, const std::string &name))
void	attach_constraint_function (void fptr(EquationSystems &es, const std::string &name))
void	attach_QOI_function (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices))
void	attach_QOI_derivative (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices))
virtual void	user_initialization ()
virtual void	user_assembly ()
virtual void	user_constrain ()
virtual void	user_QOI (const QoISet &qoi_indices)
virtual void	user_QOI_derivative (const QoISet &qoi_indices)
virtual void	re_update ()
virtual void	restrict_vectors ()
virtual void	prolong_vectors ()
Number	current_solution (const unsigned int global_dof_number) const
void	local_dof_indices (const unsigned int var, std::set< unsigned int > &var_indices) const
void	zero_variable (NumericVector< Number > &v, unsigned int var_num) const
Static Public Member Functions
static std::string	get_info ()
static void	print_info ()
static unsigned int	n_objects ()
Public Attributes
bool	assemble_before_solve
AutoPtr< NumericVector< Number > >	solution
AutoPtr< NumericVector< Number > >	current_local_solution
std::vector< Number >	qoi
Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
Protected Member Functions
	System (EquationSystems &es, const std::string &name, const unsigned int number)
virtual void	init_data ()
void	project_vector (NumericVector< Number > &) const
void	project_vector (const NumericVector< Number > &, NumericVector< Number > &) const
void	increment_constructor_count (const std::string &name)
void	increment_destructor_count (const std::string &name)
Static Protected Attributes
static Counts	_counts
static Threads::atomic < unsigned int >	_n_objects
static Threads::spin_mutex	_mutex
Private Member Functions
Real	discrete_var_norm (NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
template<typename iterator_type >
unsigned int	read_serialized_blocked_dof_objects (const unsigned int var, const unsigned int n_objects, const iterator_type begin, const iterator_type end, Xdr &io, NumericVector< Number > &vec) const
void	read_serialized_vector (Xdr &io, NumericVector< Number > &vec)
template<typename iterator_type >
unsigned int	write_serialized_blocked_dof_objects (const NumericVector< Number > &vec, const unsigned int var, const unsigned int n_objects, const iterator_type begin, const iterator_type end, Xdr &io) const
void	write_serialized_vector (Xdr &io, const NumericVector< Number > &vec) const
Private Attributes
void(*	_init_system )(EquationSystems &es, const std::string &name)
void(*	_assemble_system )(EquationSystems &es, const std::string &name)
void(*	_constrain_system )(EquationSystems &es, const std::string &name)
void(*	_qoi_evaluate )(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
void(*	_qoi_evaluate_derivative )(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
AutoPtr< DofMap >	_dof_map
EquationSystems &	_equation_systems
MeshBase &	_mesh
const std::string	_sys_name
const unsigned int	_sys_number
std::vector< System::Variable >	_variables
std::map< std::string, unsigned short int >	_variable_numbers
bool	_active
std::map< std::string, NumericVector< Number > * >	_vectors
std::map< std::string, bool >	_vector_projections
bool	_solution_projection
bool	_can_add_vectors
bool	_additional_data_written

---

Detailed Description

This is the base class for classes which contain information related to any physical process that might be simulated. Such information may range from the actual solution values to algorithmic flags that may be used to control the numerical methods employed. In general, use an EqnSystems<T_sys> object to handle one or more of the children of this class. Note that templating EqnSystems relaxes the use of virtual members.

Author:

Benjamin S. Kirk, 2003-2004.

Definition at line 68 of file system.h.

---

Member Typedef Documentation

typedef std::map<std::string, NumericVector<Number>* >::const_iterator System::const_vectors_iterator

Definition at line 405 of file system.h.

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > ReferenceCounter::Counts [protected, inherited]

Data structure to log the information. The log is identified by the class name.

Definition at line 105 of file reference_counter.h.

typedef System System::sys_type

The type of system.

Reimplemented in ContinuationSystem, DifferentiableSystem, EigenSystem, ExplicitSystem, FEMSystem, ImplicitSystem, LinearImplicitSystem, NewmarkSystem, and NonlinearImplicitSystem.

Definition at line 92 of file system.h.

typedef std::map<std::string, NumericVector<Number>* >::iterator System::vectors_iterator

Vector iterator typedefs.

Definition at line 404 of file system.h.

---

Constructor & Destructor Documentation

System::System	(	EquationSystems &	es,
		const std::string &	name,
		const unsigned int	number
	)			[protected]

Constructor. Optionally initializes required data structures. Protected so that this base class cannot be explicitly instantiated.

Definition at line 48 of file system.C.

                                           :

  assemble_before_solve    (true),
  solution                 (NumericVector<Number>::build()),
  current_local_solution   (NumericVector<Number>::build()),
  qoi                      (0),
  _init_system             (NULL),
  _assemble_system         (NULL),
  _constrain_system        (NULL),
  _dof_map                 (new DofMap(number)),
  _equation_systems        (es),
  _mesh                    (es.get_mesh()),
  _sys_name                (name),
  _sys_number              (number),
  _active                  (true),
  _solution_projection     (true),
  _can_add_vectors         (true),
  _additional_data_written (false)
{
}

System::~System

(

)

[virtual]

Destructor.

Definition at line 73 of file system.C.

References _assemble_system, _init_system, clear(), and libMesh::closed().

{
  // Null-out the function pointers.  Since this
  // class is getting destructed it is pointless,
  // but a good habit.
  _init_system = _assemble_system = NULL;

  // Clear data
  this->clear ();

  libmesh_assert (!libMesh::closed());
}

---

Member Function Documentation

void System::activate

(

)

[inline]

Activates the system. Only active systems are solved.

Definition at line 1374 of file system.h.

References _active.

{
  _active = true;
}

bool System::active

(

)

const [inline]

Returns:

true if the system is active, false otherwise. An active system will be solved.

Definition at line 1366 of file system.h.

References _active.

{
  return _active;  
}

NumericVector< Number > & System::add_adjoint_rhs

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 824 of file system.C.

References add_vector().

Referenced by FEMSystem::assemble_qoi_derivative(), and ExplicitSystem::assemble_qoi_derivative().

{
  OStringStream adjoint_rhs_name;
  adjoint_rhs_name << "adjoint_rhs" << i;

  return this->add_vector(adjoint_rhs_name.str());
}

NumericVector< Number > & System::add_adjoint_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 764 of file system.C.

References add_vector().

Referenced by ImplicitSystem::adjoint_solve().

{
  OStringStream adjoint_name;
  adjoint_name << "adjoint_solution" << i;

  return this->add_vector(adjoint_name.str());
}

NumericVector< Number > & System::add_sensitivity_rhs

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter. Creates the vector if it doesn't already exist.

Definition at line 854 of file system.C.

References add_vector().

Referenced by ImplicitSystem::assemble_residual_derivatives().

{
  OStringStream sensitivity_rhs_name;
  sensitivity_rhs_name << "sensitivity_rhs" << i;

  return this->add_vector(sensitivity_rhs_name.str());
}

NumericVector< Number > & System::add_sensitivity_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter. Creates the vector if it doesn't already exist.

Definition at line 714 of file system.C.

References add_vector().

{
  OStringStream sensitivity_name;
  sensitivity_name << "sensitivity_solution" << i;

  return this->add_vector(sensitivity_name.str());
}

unsigned int System::add_variable	(	const std::string &	var,
		const Order	order = FIRST,
		const FEFamily	family = LAGRANGE,
		const std::set< subdomain_id_type > *const	active_subdomains = NULL
	)

Adds the variable var to the list of variables for this system. Same as before, but assumes LAGRANGE as default value for FEType.family.

Definition at line 923 of file system.C.

References add_variable().

{
  return this->add_variable(var, 
                            FEType(order, family), 
                            active_subdomains);
}

unsigned int System::add_variable	(	const std::string &	var,
		const FEType &	type,
		const std::set< subdomain_id_type > *const	active_subdomains = NULL
	)

Adds the variable var to the list of variables for this system. Returns the index number for the new variable.

Definition at line 884 of file system.C.

References _dof_map, _variable_numbers, _variables, n_vars(), number(), variable_name(), and variable_type().

Referenced by add_variable(), ErrorVector::plot_error(), and read_header().

{  
  // Make sure the variable isn't there already
  // or if it is, that it's the type we want
  for (unsigned int v=0; v<this->n_vars(); v++)
    if (this->variable_name(v) == var)
      {
        if (this->variable_type(v) == type)
          return _variables[v].number();

        std::cerr << "ERROR: incompatible variable "
                  << var
                  << " has already been added for this system!"
                  << std::endl;
        libmesh_error();
      }

  const unsigned int curr_n_vars = this->n_vars();                                              

  // Add the variable to the list
  _variables.push_back((active_subdomains == NULL) ?
                       Variable(var, curr_n_vars, type) :
                       Variable(var, curr_n_vars, type, *active_subdomains));

  libmesh_assert ((curr_n_vars+1) == this->n_vars());

  _variable_numbers[var] = curr_n_vars;

  // Add the variable to the _dof_map
  _dof_map->add_variable (_variables.back());

  // Return the number of the new variable
  return curr_n_vars;
}

NumericVector< Number > & System::add_vector	(	const std::string &	vec_name,
		const bool	projections = true
	)

Adds the additional vector vec_name to this system. Only allowed prior to init(). All the additional vectors are similarly distributed, like the solution, and inititialized to zero.

By default vectors added by add_vector are projected to changed grids by reinit(). To zero them instead (more efficient), pass "false" as the second argument

Definition at line 549 of file system.C.

References _can_add_vectors, _vector_projections, _vectors, have_vector(), NumericVector< T >::init(), n_dofs(), n_local_dofs(), and libMeshEnums::PARALLEL.

Referenced by add_adjoint_rhs(), add_adjoint_solution(), add_sensitivity_rhs(), add_sensitivity_solution(), ExplicitSystem::add_system_rhs(), add_weighted_sensitivity_solution(), UnsteadySolver::init(), ContinuationSystem::init_data(), NewmarkSystem::NewmarkSystem(), read_header(), FrequencySystem::set_frequencies(), FrequencySystem::set_frequencies_by_range(), and FrequencySystem::set_frequencies_by_steps().

{
  // Return the vector if it is already there.
  if (this->have_vector(vec_name))
    return *(_vectors[vec_name]);

  // Otherwise build the vector
  NumericVector<Number>* buf = NumericVector<Number>::build().release();
  _vectors.insert (std::make_pair (vec_name, buf));
  _vector_projections.insert (std::make_pair (vec_name, projections));

  // Initialize it if necessary
  if (!_can_add_vectors)
    buf->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);

  return *buf;
}

NumericVector< Number > & System::add_weighted_sensitivity_adjoint_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 794 of file system.C.

References get_vector().

Referenced by ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
  OStringStream adjoint_name;
  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;

  return this->get_vector(adjoint_name.str());
}

NumericVector< Number > & System::add_weighted_sensitivity_solution

(

)

Returns:

a reference to the solution of the last weighted sensitivity solve Creates the vector if it doesn't already exist.

Definition at line 743 of file system.C.

References add_vector().

Referenced by ImplicitSystem::weighted_sensitivity_solve().

{
  return this->add_vector("weighted_sensitivity_solution");
}

virtual void System::adjoint_qoi_parameter_sensitivity	(	const QoISet &	qoi_indices,
		const ParameterVector &	parameters,
		SensitivityData &	sensitivities
	)			[inline, virtual]

Solves for parameter sensitivities using the adjoint method.

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 254 of file system.h.

    { libmesh_not_implemented(); }

virtual std::pair<unsigned int, Real> System::adjoint_solve

(

const QoISet &

qoi_indices = QoISet()

)

[inline, virtual]

Solves the adjoint system, for the specified qoi indices, or for every qoi if qoi_indices is NULL. Must be overloaded in derived systems.

Returns a pair with the total number of linear iterations performed and the (sum of the) final residual norms

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 205 of file system.h.

Referenced by AdjointResidualErrorEstimator::estimate_error().

      { libmesh_not_implemented(); }

void System::assemble

(

)

[virtual]

Prepares matrix and _dof_map for matrix assembly. Does not actually assemble anything. For matrix assembly, use the assemble() in derived classes. Should be overloaded in derived classes.

Reimplemented in DifferentiableSystem, EigenSystem, FrequencySystem, ImplicitSystem, LinearImplicitSystem, and NewmarkSystem.

Definition at line 340 of file system.C.

References user_assembly().

Referenced by ImplicitSystem::assemble(), EigenSystem::assemble(), and ExplicitSystem::solve().

{
  // Log how long the user's matrix assembly code takes
  START_LOG("assemble()", "System");
  
  // Call the user-specified assembly function
  this->user_assembly();

  // Stop logging the user code
  STOP_LOG("assemble()", "System");
}

void System::assemble_qoi

(

const QoISet &

qoi_indices = QoISet()

)

[virtual]

Calls user qoi function. Can be overloaded in derived classes.

Reimplemented in ExplicitSystem, and FEMSystem.

Definition at line 354 of file system.C.

References user_QOI().

Referenced by ExplicitSystem::assemble_qoi().

{
  // Log how long the user's matrix assembly code takes
  START_LOG("assemble_qoi()", "System");
  
  // Call the user-specified quantity of interest function
  this->user_QOI(qoi_indices);

  // Stop logging the user code
  STOP_LOG("assemble_qoi()", "System");
}

void System::assemble_qoi_derivative

(

const QoISet &

qoi_indices = QoISet()

)

[virtual]

Calls user qoi derivative function. Can be overloaded in derived classes.

Reimplemented in ExplicitSystem, and FEMSystem.

Definition at line 368 of file system.C.

References user_QOI_derivative().

Referenced by ExplicitSystem::assemble_qoi_derivative().

{
  // Log how long the user's matrix assembly code takes
  START_LOG("assemble_qoi_derivative()", "System");
  
  // Call the user-specified quantity of interest function
  this->user_QOI_derivative(qoi_indices);

  // Stop logging the user code
  STOP_LOG("assemble_qoi_derivative()", "System");
}

virtual void System::assemble_residual_derivatives

(

const ParameterVector &

parameters

)

[inline, virtual]

Calls residual parameter derivative function.

Library subclasses use finite differences by default.

This should assemble the sensitivity rhs vectors to hold -(partial R / partial p_i), making them ready to solve the forward sensitivity equation.

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 158 of file system.h.

    { libmesh_not_implemented(); }

void System::attach_assemble_function

(

void

fptrEquationSystems &es,const std::string &name

)

Register a user function to use in assembling the system matrix and RHS.

Definition at line 1316 of file system.C.

References _assemble_system.

{
  libmesh_assert (fptr != NULL);
  
  _assemble_system = fptr;  
}

void System::attach_constraint_function

(

void

fptrEquationSystems &es,const std::string &name

)

Register a user function for imposing constraints.

Definition at line 1326 of file system.C.

References _constrain_system.

{
  libmesh_assert (fptr != NULL);
  
  _constrain_system = fptr;  
}

void System::attach_init_function

(

void

fptrEquationSystems &es,const std::string &name

)

Register a user function to use in initializing the system.

Definition at line 1306 of file system.C.

References _init_system.

{
  libmesh_assert (fptr != NULL);
  
  _init_system = fptr;
}

void System::attach_QOI_derivative

(

void

fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices

)

Register a user function for evaluating derivatives of a quantity of interest with respect to test functions, whose values should be placed in System::rhs

void System::attach_QOI_function

(

void

fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices

)

Register a user function for evaluating the quantities of interest, whose values should be placed in System::qoi

Real System::calculate_norm	(	NumericVector< Number > &	v,
		const SystemNorm &	norm
	)			const

Returns:

a norm of the vector v, using component_norm and component_scale to choose and weight the norms of each variable.

Definition at line 1077 of file system.C.

References _dof_map, MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), TypeTensor< T >::add_scaled(), TypeVector< T >::add_scaled(), FEBase::build(), FEType::default_quadrature_rule(), dim, libMeshEnums::DISCRETE_L1, libMeshEnums::DISCRETE_L2, libMeshEnums::DISCRETE_L_INF, discrete_var_norm(), DofMap::dof_indices(), AutoPtr< Tp >::get(), get_dof_map(), get_mesh(), libMeshEnums::H1, libMeshEnums::H1_SEMINORM, libMeshEnums::H2, libMeshEnums::H2_SEMINORM, SystemNorm::is_discrete(), NumericVector< T >::l1_norm(), libMeshEnums::L2, NumericVector< T >::l2_norm(), libmesh_norm(), NumericVector< T >::linfty_norm(), NumericVector< T >::localize(), MeshBase::mesh_dimension(), n_vars(), libMeshEnums::SERIAL, NumericVector< T >::size(), TypeTensor< T >::size_sq(), TypeVector< T >::size_sq(), SystemNorm::type(), DofMap::variable_type(), SystemNorm::weight(), and SystemNorm::weight_sq().

{
  // This function must be run on all processors at once
  parallel_only();

  START_LOG ("calculate_norm()", "System");

  // Zero the norm before summation
  Real v_norm = 0.;

  if (norm.is_discrete())
    {
      STOP_LOG ("calculate_norm()", "System");
      //Check to see if all weights are 1.0
      unsigned int check_var = 0;
      for (; check_var != this->n_vars(); ++check_var)
        if(norm.weight(check_var) != 1.0)
          break;

      //All weights were 1.0 so just do the full vector discrete norm
      if(check_var == this->n_vars())
        {
          FEMNormType norm_type = norm.type(0);
          
          if(norm_type == DISCRETE_L1)
            return v.l1_norm();
          if(norm_type == DISCRETE_L2)
            return v.l2_norm();
          if(norm_type == DISCRETE_L_INF)
            return v.linfty_norm();
          else
            libmesh_error();
        }

      for (unsigned int var=0; var != this->n_vars(); ++var)
        {
          // Skip any variables we don't need to integrate
          if (norm.weight(var) == 0.0)
            continue;

          v_norm += norm.weight(var) * discrete_var_norm(v, var, norm.type(var));
        }

      return v_norm;
    }

  // Localize the potentially parallel vector
  AutoPtr<NumericVector<Number> > local_v = NumericVector<Number>::build();
  local_v->init(v.size(), true, SERIAL);
  v.localize (*local_v, _dof_map->get_send_list()); 

  unsigned int dim = this->get_mesh().mesh_dimension();

  // Loop over all variables
  for (unsigned int var=0; var != this->n_vars(); ++var)
    {
      // Skip any variables we don't need to integrate
      if (norm.weight(var) == 0.0)
        continue;

      const FEType& fe_type = this->get_dof_map().variable_type(var);
      AutoPtr<QBase> qrule =
        fe_type.default_quadrature_rule (dim);
      AutoPtr<FEBase> fe
        (FEBase::build(dim, fe_type));
      fe->attach_quadrature_rule (qrule.get());

      const std::vector<Real>&               JxW = fe->get_JxW();
      const std::vector<std::vector<Real> >* phi = NULL;
      if (norm.type(var) == H1 ||
          norm.type(var) == H2 ||
          norm.type(var) == L2)
        phi = &(fe->get_phi());

      const std::vector<std::vector<RealGradient> >* dphi = NULL;
      if (norm.type(var) == H1 ||
          norm.type(var) == H2 ||
          norm.type(var) == H1_SEMINORM)
        dphi = &(fe->get_dphi());
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
      const std::vector<std::vector<RealTensor> >*   d2phi = NULL;
      if (norm.type(var) == H2 ||
          norm.type(var) == H2_SEMINORM)
        d2phi = &(fe->get_d2phi());
#endif

      std::vector<unsigned int> dof_indices;

      // Begin the loop over the elements
      MeshBase::const_element_iterator       el     =
        this->get_mesh().active_local_elements_begin();
      const MeshBase::const_element_iterator end_el =
        this->get_mesh().active_local_elements_end();

      for ( ; el != end_el; ++el)
        {
          const Elem* elem = *el;

          fe->reinit (elem);

          this->get_dof_map().dof_indices (elem, dof_indices, var);

          const unsigned int n_qp = qrule->n_points();

          const unsigned int n_sf = dof_indices.size();

          // Begin the loop over the Quadrature points.
          for (unsigned int qp=0; qp<n_qp; qp++)
            {
              if (norm.type(var) == H1 ||
                  norm.type(var) == H2 ||
                  norm.type(var) == L2)
                {
                  Number u_h = 0.;
                  for (unsigned int i=0; i != n_sf; ++i)
                    u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
                  v_norm += norm.weight_sq(var) *
                            JxW[qp] * libmesh_norm(u_h);
                }

              if (norm.type(var) == H1 ||
                  norm.type(var) == H2 ||
                  norm.type(var) == H1_SEMINORM)
                {
                  Gradient grad_u_h;
                  for (unsigned int i=0; i != n_sf; ++i)
                    grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
                  v_norm += norm.weight_sq(var) *
                            JxW[qp] * grad_u_h.size_sq();
                }

#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
              if (norm.type(var) == H2 ||
                  norm.type(var) == H2_SEMINORM)
                {
                  Tensor hess_u_h;
                  for (unsigned int i=0; i != n_sf; ++i)
                    hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
                  v_norm += norm.weight_sq(var) *
                            JxW[qp] * hess_u_h.size_sq();
                }
#endif
            }
        }
    }

  Parallel::sum(v_norm);

  STOP_LOG ("calculate_norm()", "System");

  return std::sqrt(v_norm);
}

Real System::calculate_norm	(	NumericVector< Number > &	v,
		unsigned int	var = 0,
		FEMNormType	norm_type = L2
	)			const

Returns:

a norm of variable var in the vector v, in the specified norm (e.g. L2, H0, H1)

Definition at line 1056 of file system.C.

References libMeshEnums::DISCRETE_L1, libMeshEnums::DISCRETE_L2, libMeshEnums::DISCRETE_L_INF, discrete_var_norm(), libMeshEnums::L2, and n_vars().

Referenced by AdaptiveTimeSolver::calculate_norm(), and UnsteadySolver::du().

{
  //short circuit to save time
  if(norm_type == DISCRETE_L1 ||
     norm_type == DISCRETE_L2 ||
     norm_type == DISCRETE_L_INF)
    return discrete_var_norm(v,var,norm_type);

  // Not a discrete norm
  std::vector<FEMNormType> norms(this->n_vars(), L2);
  std::vector<Real> weights(this->n_vars(), 0.0);
  norms[var] = norm_type;
  weights[var] = 1.0;
  Real val = this->calculate_norm(v, SystemNorm(norms, weights));
  return val;
}

void System::clear

(

)

[virtual]

Clear all the data structures associated with the system.

Reimplemented in ContinuationSystem, DifferentiableSystem, EigenSystem, ExplicitSystem, FEMSystem, FrequencySystem, ImplicitSystem, LinearImplicitSystem, NewmarkSystem, and NonlinearImplicitSystem.

Definition at line 128 of file system.C.

References _can_add_vectors, _dof_map, _variable_numbers, _variables, _vector_projections, _vectors, current_local_solution, and solution.

Referenced by ExplicitSystem::clear(), EigenSystem::clear(), read_header(), and ~System().

{
  _variables.clear();
  
  _variable_numbers.clear();

  _dof_map->clear ();
  
  solution->clear ();

  current_local_solution->clear ();
  
  // clear any user-added vectors
  {
    for (vectors_iterator pos = _vectors.begin(); pos != _vectors.end(); ++pos)
      {
        pos->second->clear ();
        delete pos->second;
        pos->second = NULL;
      }
    
    _vectors.clear();
    _vector_projections.clear();
    _can_add_vectors = true;
  }

}

bool System::compare	(	const System &	other_system,
		const Real	threshold,
		const bool	verbose
	)			const [virtual]

Returns:

true when the other system contains identical data, up to the given threshold. Outputs some diagnostic info when verbose is set.

Definition at line 399 of file system.C.

References _can_add_vectors, _sys_name, _vectors, get_vector(), n_vectors(), name(), and solution.

Referenced by EquationSystems::compare().

{
  // we do not care for matrices, but for vectors
  libmesh_assert (!_can_add_vectors);
  libmesh_assert (!other_system._can_add_vectors);

  if (verbose)
    {
      std::cout << "  Systems \"" << _sys_name << "\"" << std::endl;
      std::cout << "   comparing matrices not supported." << std::endl;
      std::cout << "   comparing names...";
    }

  // compare the name: 0 means identical
  const int name_result = _sys_name.compare(other_system.name());
  if (verbose)
    {
      if (name_result == 0)
        std::cout << " identical." << std::endl;
      else
        std::cout << "  names not identical." << std::endl;
      std::cout << "   comparing solution vector...";
    }


  // compare the solution: -1 means identical
  const int solu_result = solution->compare (*other_system.solution.get(),
                                             threshold);

  if (verbose)
    {
      if (solu_result == -1)
        std::cout << " identical up to threshold." << std::endl;
      else
        std::cout << "  first difference occured at index = " 
                  << solu_result << "." << std::endl;
    }


  // safety check, whether we handle at least the same number
  // of vectors
  std::vector<int> ov_result;

  if (this->n_vectors() != other_system.n_vectors())
    {
      if (verbose)
        {
          std::cout << "   Fatal difference. This system handles " 
                    << this->n_vectors() << " add'l vectors," << std::endl
                    << "   while the other system handles "
                    << other_system.n_vectors() 
                    << " add'l vectors." << std::endl
                    << "   Aborting comparison." << std::endl;
        }
      return false;
    }
  else if (this->n_vectors() == 0)
    {
      // there are no additional vectors...
      ov_result.clear ();
    }
  else
    {
      // compare other vectors
      for (const_vectors_iterator pos = _vectors.begin();
           pos != _vectors.end(); ++pos)
        {
          if (verbose)
              std::cout << "   comparing vector \""
                        << pos->first << "\" ...";

          // assume they have the same name
          const NumericVector<Number>& other_system_vector = 
              other_system.get_vector(pos->first);

          ov_result.push_back(pos->second->compare (other_system_vector,
                                                    threshold));

          if (verbose)
            {
              if (ov_result[ov_result.size()-1] == -1)
                std::cout << " identical up to threshold." << std::endl;
              else
                std::cout << " first difference occured at" << std::endl
                          << "   index = " << ov_result[ov_result.size()-1] << "." << std::endl;
            }

        }

    } // finished comparing additional vectors


  bool overall_result;
       
  // sum up the results
  if ((name_result==0) && (solu_result==-1))
    {
      if (ov_result.size()==0)
        overall_result = true;
      else
        {
          bool ov_identical;
          unsigned int n    = 0;
          do
            {
              ov_identical = (ov_result[n]==-1);
              n++;
            }
          while (ov_identical && n<ov_result.size());
          overall_result = ov_identical;
        }
    }
  else
    overall_result = false;

  if (verbose)
    {
      std::cout << "   finished comparisons, ";
      if (overall_result)
        std::cout << "found no differences." << std::endl << std::endl;
      else 
        std::cout << "found differences." << std::endl << std::endl;
    }
          
  return overall_result;
}

Number System::current_solution

(

const unsigned int

global_dof_number

)

const

Returns:

the current solution for the specified global DOF.

Definition at line 117 of file system.C.

References current_local_solution, and n_dofs().

Referenced by ExactSolution::_compute_error(), HPCoarsenTest::add_projection(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), FEMSystem::eulerian_residual(), PatchRecoveryErrorEstimator::EstimateError::operator()(), FEMContext::reinit(), HPCoarsenTest::select_refinement(), VTKIO::solution_to_vtk(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().

{
  // Check the sizes
  libmesh_assert (global_dof_number < _dof_map->n_dofs());
  libmesh_assert (global_dof_number < current_local_solution->size());
   
  return (*current_local_solution)(global_dof_number);
}

void System::deactivate

(

)

[inline]

Deactivates the system. Only active systems are solved.

Definition at line 1382 of file system.h.

References _active.

{
  _active = false;
}

Real System::discrete_var_norm	(	NumericVector< Number > &	v,
		unsigned int	var,
		FEMNormType	norm_type
	)			const [private]

Finds the discrete norm for the entries in the vector corresponding to Dofs associated with var.

Definition at line 1039 of file system.C.

References libMeshEnums::DISCRETE_L1, libMeshEnums::DISCRETE_L2, libMeshEnums::DISCRETE_L_INF, local_dof_indices(), NumericVector< T >::subset_l1_norm(), NumericVector< T >::subset_l2_norm(), and NumericVector< T >::subset_linfty_norm().

Referenced by calculate_norm().

{
  std::set<unsigned int> var_indices;
  local_dof_indices(var, var_indices);

  if(norm_type == DISCRETE_L1)
    return v.subset_l1_norm(var_indices);
  if(norm_type == DISCRETE_L2)
    return v.subset_l2_norm(var_indices);
  if(norm_type == DISCRETE_L_INF)
    return v.subset_linfty_norm(var_indices);
  else
    libmesh_error();
}

virtual void System::forward_qoi_parameter_sensitivity	(	const QoISet &	qoi_indices,
		const ParameterVector &	parameters,
		SensitivityData &	sensitivities
	)			[inline, virtual]

Solves for parameter sensitivities using the forward method.

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 264 of file system.h.

    { libmesh_not_implemented(); }

const NumericVector< Number > & System::get_adjoint_rhs

(

unsigned int

i = 0

)

const

Returns:

a reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi.

Definition at line 844 of file system.C.

References get_vector().

{
  OStringStream adjoint_rhs_name;
  adjoint_rhs_name << "adjoint_rhs" << i;

  return this->get_vector(adjoint_rhs_name.str());
}

NumericVector< Number > & System::get_adjoint_rhs

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. This what the user's QoI derivative code should assemble when setting up an adjoint problem

Definition at line 834 of file system.C.

References get_vector().

Referenced by ImplicitSystem::adjoint_solve(), FEMSystem::assemble_qoi_derivative(), and ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
  OStringStream adjoint_rhs_name;
  adjoint_rhs_name << "adjoint_rhs" << i;

  return this->get_vector(adjoint_rhs_name.str());
}

const NumericVector< Number > & System::get_adjoint_solution

(

unsigned int

i = 0

)

const

Returns:

a reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 784 of file system.C.

References get_vector().

{
  OStringStream adjoint_name;
  adjoint_name << "adjoint_solution" << i;

  return this->get_vector(adjoint_name.str());
}

NumericVector< Number > & System::get_adjoint_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 774 of file system.C.

References get_vector().

Referenced by ImplicitSystem::adjoint_solve(), AdjointResidualErrorEstimator::estimate_error(), and ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
  OStringStream adjoint_name;
  adjoint_name << "adjoint_solution" << i;

  return this->get_vector(adjoint_name.str());
}

DofMap & System::get_dof_map

(

)

[inline]

Returns:

a writeable reference to this system's _dof_map.

Definition at line 1358 of file system.h.

References _dof_map.

{
  return *_dof_map;
}

const DofMap & System::get_dof_map

(

)

const [inline]

Returns:

a constant reference to this system's _dof_map.

Definition at line 1350 of file system.h.

References _dof_map.

Referenced by __libmesh_petsc_diff_solver_jacobian(), __libmesh_petsc_diff_solver_residual(), ExactSolution::_compute_error(), HPCoarsenTest::add_projection(), ImplicitSystem::adjoint_solve(), FEMSystem::assemble_qoi_derivative(), FEMSystem::assembly(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), calculate_norm(), DofMap::enforce_constraints_exactly(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), get_info(), EigenSystem::init_data(), ImplicitSystem::init_matrices(), local_dof_indices(), DofMap::max_constraint_error(), FEMSystem::mesh_position_get(), UnsteadySolver::old_nonlinear_solution(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), ErrorVector::plot_error(), project_vector(), FEMContext::reinit(), EquationSystems::reinit(), HPCoarsenTest::select_refinement(), ImplicitSystem::sensitivity_solve(), UnsteadySolver::solve(), PetscDiffSolver::solve(), NewtonSolver::solve(), ImplicitSystem::weighted_sensitivity_adjoint_solve(), ImplicitSystem::weighted_sensitivity_solve(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().

{
  return *_dof_map;
}

EquationSystems& System::get_equation_systems

(

)

[inline]

Returns:

a reference to this system's parent EquationSystems object.

Definition at line 383 of file system.h.

References _equation_systems.

{ return _equation_systems; }

const EquationSystems& System::get_equation_systems

(

)

const [inline]

Returns:

a constant reference to this system's parent EquationSystems object.

Definition at line 378 of file system.h.

References _equation_systems.

Referenced by NewmarkSystem::clear(), FrequencySystem::clear_all(), ExactErrorEstimator::find_squared_element_error(), ImplicitSystem::get_linear_solve_parameters(), FrequencySystem::init_data(), FrequencySystem::n_frequencies(), FrequencySystem::set_current_frequency(), FrequencySystem::set_frequencies(), FrequencySystem::set_frequencies_by_range(), FrequencySystem::set_frequencies_by_steps(), NewmarkSystem::set_newmark_parameters(), NonlinearImplicitSystem::set_solver_parameters(), LinearImplicitSystem::solve(), FrequencySystem::solve(), and EigenSystem::solve().

{ return _equation_systems; }

std::string ReferenceCounter::get_info

(

)

[static, inherited]

Gets a string containing the reference information.

Definition at line 45 of file reference_counter.C.

References ReferenceCounter::_counts, and QuadratureRules::name().

Referenced by ReferenceCounter::print_info().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)

  std::ostringstream out;
  
  out << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";
  
  for (Counts::iterator it = _counts.begin();
       it != _counts.end(); ++it)
    {
      const std::string name(it->first);
      const unsigned int creations    = it->second.first;
      const unsigned int destructions = it->second.second;

      out << "| " << name << " reference count information:\n"
          << "|  Creations:    " << creations    << '\n'
          << "|  Destructions: " << destructions << '\n';
    }
  
  out << " ---------------------------------------------------------------------------- \n";

  return out.str();

#else

  return "";
  
#endif
}

std::string System::get_info

(

)

const

Returns:

a string containing information about the system.

Definition at line 1233 of file system.C.

References Utility::enum_to_string< FEFamily >(), Utility::enum_to_string< InfMapType >(), Utility::enum_to_string< Order >(), FEType::family, get_dof_map(), FEType::inf_map, n_constrained_dofs(), n_dofs(), n_local_dofs(), n_vars(), n_vectors(), name(), FEType::order, FEType::radial_family, FEType::radial_order, system_type(), variable_name(), and DofMap::variable_type().

{
  std::ostringstream out;

  
  const std::string& sys_name = this->name();
      
  out << "   System \"" << sys_name << "\"\n"
      << "    Type \""  << this->system_type() << "\"\n"
      << "    Variables=";
  
  for (unsigned int vn=0; vn<this->n_vars(); vn++)
      out << "\"" << this->variable_name(vn) << "\" ";
     
  out << '\n';

  out << "    Finite Element Types=";
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
  for (unsigned int vn=0; vn<this->n_vars(); vn++)
    out << "\""
        << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).family)
        << "\" ";  
#else
  for (unsigned int vn=0; vn<this->n_vars(); vn++)
    {
      out << "\""
          << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).family)
          << "\", \""
          << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).radial_family)
          << "\" ";
    }

  out << '\n' << "    Infinite Element Mapping=";
  for (unsigned int vn=0; vn<this->n_vars(); vn++)
    out << "\""
        << Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_type(vn).inf_map)
        << "\" ";
#endif      

  out << '\n';
      
  out << "    Approximation Orders=";
  for (unsigned int vn=0; vn<this->n_vars(); vn++)
    {
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
      out << "\""
          << Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).order)
          << "\" ";
#else
      out << "\""
          << Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).order)
          << "\", \""
          << Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).radial_order)
          << "\" ";
#endif
    }

  out << '\n';
      
  out << "    n_dofs()="             << this->n_dofs()             << '\n';
  out << "    n_local_dofs()="       << this->n_local_dofs()       << '\n';
#ifdef LIBMESH_ENABLE_AMR
  out << "    n_constrained_dofs()=" << this->n_constrained_dofs() << '\n';
#endif

  out << "    " << "n_vectors()="  << this->n_vectors()  << '\n';
//   out << "    " << "n_additional_matrices()=" << this->n_additional_matrices() << '\n';
  
  return out.str();
}

MeshBase & System::get_mesh

(

)

[inline]

Returns:

a reference to this systems's _mesh.

Definition at line 1342 of file system.h.

References _mesh.

{
  return _mesh;
}

const MeshBase & System::get_mesh

(

)

const [inline]

Returns:

a constant reference to this systems's _mesh.

Definition at line 1334 of file system.h.

References _mesh.

Referenced by ExactSolution::_compute_error(), HPCoarsenTest::add_projection(), FEMSystem::assemble_qoi(), FEMSystem::assemble_qoi_derivative(), FEMSystem::assembly(), calculate_norm(), PatchRecoveryErrorEstimator::estimate_error(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), AdjointResidualErrorEstimator::estimate_error(), init_data(), EigenSystem::init_data(), ImplicitSystem::init_matrices(), local_dof_indices(), DofMap::max_constraint_error(), FEMSystem::mesh_position_get(), FEMSystem::mesh_position_set(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), FEMSystem::postprocess(), project_vector(), read_header(), read_legacy_data(), read_parallel_data(), read_serialized_vector(), HPSingularity::select_refinement(), HPCoarsenTest::select_refinement(), write_header(), write_parallel_data(), write_serialized_vector(), and zero_variable().

{
  return _mesh;
}

const NumericVector< Number > & System::get_sensitivity_rhs

(

unsigned int

i = 0

)

const

Returns:

a reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter.

Definition at line 874 of file system.C.

References get_vector().

{
  OStringStream sensitivity_rhs_name;
  sensitivity_rhs_name << "sensitivity_rhs" << i;

  return this->get_vector(sensitivity_rhs_name.str());
}

NumericVector< Number > & System::get_sensitivity_rhs

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter. By default these vectors are built by the library, using finite differences, when assemble_residual_derivatives() is called.

When assembled, this vector should hold -(partial R / partial p_i)

Definition at line 864 of file system.C.

References get_vector().

Referenced by ImplicitSystem::sensitivity_solve().

{
  OStringStream sensitivity_rhs_name;
  sensitivity_rhs_name << "sensitivity_rhs" << i;

  return this->get_vector(sensitivity_rhs_name.str());
}

const NumericVector< Number > & System::get_sensitivity_solution

(

unsigned int

i = 0

)

const

Returns:

a reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter.

Definition at line 733 of file system.C.

References get_vector().

{
  OStringStream sensitivity_name;
  sensitivity_name << "sensitivity_solution" << i;

  return this->get_vector(sensitivity_name.str());
}

NumericVector< Number > & System::get_sensitivity_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter.

Definition at line 723 of file system.C.

References get_vector().

Referenced by ImplicitSystem::sensitivity_solve().

{
  OStringStream sensitivity_name;
  sensitivity_name << "sensitivity_solution" << i;

  return this->get_vector(sensitivity_name.str());
}

NumericVector< Number > & System::get_vector

(

const unsigned int

vec_num

)

Returns:

a writeable reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 682 of file system.C.

References vectors_begin(), and vectors_end().

{
  vectors_iterator v = vectors_begin();
  vectors_iterator v_end = vectors_end();
  unsigned int num = 0;
  while((num<vec_num) && (v!=v_end))
    {
      num++;
      ++v;
    }
  libmesh_assert(v!=v_end);
  return *(v->second);
}

const NumericVector< Number > & System::get_vector

(

const unsigned int

vec_num

)

const

Returns:

a const reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 666 of file system.C.

References vectors_begin(), and vectors_end().

{
  const_vectors_iterator v = vectors_begin();
  const_vectors_iterator v_end = vectors_end();
  unsigned int num = 0;
  while((num<vec_num) && (v!=v_end))
    {
      num++;
      ++v;
    }
  libmesh_assert(v!=v_end);
  return *(v->second);
}

NumericVector< Number > & System::get_vector

(

const std::string &

vec_name

)

Returns:

a writeable reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

Definition at line 647 of file system.C.

References _vectors.

{
  // Make sure the vector exists
  vectors_iterator pos = _vectors.find(vec_name);
  
  if (pos == _vectors.end())
    {
      std::cerr << "ERROR: vector "
                << vec_name
                << " does not exist in this system!"
                << std::endl;      
      libmesh_error();
    }
  
  return *(pos->second);
}

const NumericVector< Number > & System::get_vector

(

const std::string &

vec_name

)

const

Returns:

a const reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

Definition at line 628 of file system.C.

References _vectors.

Referenced by add_weighted_sensitivity_adjoint_solution(), UnsteadySolver::advance_timestep(), AdaptiveTimeSolver::advance_timestep(), compare(), UnsteadySolver::du(), get_adjoint_rhs(), get_adjoint_solution(), get_sensitivity_rhs(), get_sensitivity_solution(), get_weighted_sensitivity_adjoint_solution(), get_weighted_sensitivity_solution(), NewmarkSystem::initial_conditions(), UnsteadySolver::solve(), TwostepTimeSolver::solve(), FrequencySystem::solve(), NewmarkSystem::update_rhs(), and NewmarkSystem::update_u_v_a().

{
  // Make sure the vector exists
  const_vectors_iterator pos = _vectors.find(vec_name);
  
  if (pos == _vectors.end())
    {
      std::cerr << "ERROR: vector "
                << vec_name
                << " does not exist in this system!"
                << std::endl;      
      libmesh_error();
    }
  
  return *(pos->second);
}

const NumericVector< Number > & System::get_weighted_sensitivity_adjoint_solution

(

unsigned int

i = 0

)

const

Returns:

a reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 814 of file system.C.

References get_vector().

{
  OStringStream adjoint_name;
  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;

  return this->get_vector(adjoint_name.str());
}

NumericVector< Number > & System::get_weighted_sensitivity_adjoint_solution

(

unsigned int

i = 0

)

Returns:

a reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 804 of file system.C.

References get_vector().

Referenced by ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
  OStringStream adjoint_name;
  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;

  return this->get_vector(adjoint_name.str());
}

const NumericVector< Number > & System::get_weighted_sensitivity_solution

(

)

const

Returns:

a reference to the solution of the last weighted sensitivity solve

Definition at line 757 of file system.C.

References get_vector().

{
  return this->get_vector("weighted_sensitivity_solution");
}

NumericVector< Number > & System::get_weighted_sensitivity_solution

(

)

Returns:

a reference to the solution of the last weighted sensitivity solve

Definition at line 750 of file system.C.

References get_vector().

Referenced by ImplicitSystem::weighted_sensitivity_solve().

{
  return this->get_vector("weighted_sensitivity_solution");
}

bool System::has_variable

(

const std::string &

var

)

const

Returns:

true if a variable named var exists in this System

Definition at line 935 of file system.C.

References _variable_numbers.

Referenced by GMVIO::copy_nodal_solution().

{
  return _variable_numbers.count(var);
}

bool System::have_vector

(

const std::string &

vec_name

)

const [inline]

Returns:

true if this System has a vector associated with the given name, false otherwise.

Definition at line 1444 of file system.h.

References _vectors.

Referenced by add_vector().

{
  return (_vectors.count(vec_name));
}

void ReferenceCounter::increment_constructor_count

(

const std::string &

name

)

[inline, protected, inherited]

Increments the construction counter. Should be called in the constructor of any derived class that will be reference counted.

Definition at line 149 of file reference_counter.h.

References ReferenceCounter::_counts, and Threads::spin_mtx.

Referenced by ReferenceCountedObject< SparseMatrix< T > >::ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int>& p = _counts[name];

  p.first++;
}

void ReferenceCounter::increment_destructor_count

(

const std::string &

name

)

[inline, protected, inherited]

Increments the destruction counter. Should be called in the destructor of any derived class that will be reference counted.

Definition at line 167 of file reference_counter.h.

References ReferenceCounter::_counts, and Threads::spin_mtx.

Referenced by ReferenceCountedObject< SparseMatrix< T > >::~ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int>& p = _counts[name];

  p.second++;
}

void System::init

(

)

Initializes degrees of freedom on the current mesh. Sets the

Definition at line 158 of file system.C.

References init_data(), n_vars(), and user_initialization().

{ 
  // First initialize any required data
  this->init_data();
  
  //If no variables have been added to this system
  //don't do anything
  if(!this->n_vars())
    return;
 
  // Then call the user-provided intialization function
  this->user_initialization();
}

void System::init_data

(

)

[protected, virtual]

Initializes the data for the system. Note that this is called before any user-supplied intitialization function so that all required storage will be available.

Reimplemented in ContinuationSystem, DifferentiableSystem, EigenSystem, ExplicitSystem, FEMSystem, FrequencySystem, and ImplicitSystem.

Definition at line 174 of file system.C.

References _can_add_vectors, _dof_map, _vectors, current_local_solution, get_mesh(), libMeshEnums::GHOSTED, mesh, n_dofs(), n_local_dofs(), libMeshEnums::PARALLEL, libMeshEnums::SERIAL, solution, and user_constrain().

Referenced by init(), ExplicitSystem::init_data(), and EigenSystem::init_data().

{
  MeshBase &mesh = this->get_mesh();

  // Distribute the degrees of freedom on the mesh
  _dof_map->distribute_dofs (mesh);

#ifdef LIBMESH_ENABLE_AMR

  // Recreate any hanging node constraints
  _dof_map->create_dof_constraints(mesh);

  // Apply any user-defined constraints
  this->user_constrain();

  // Expand any recursive constraints
  _dof_map->process_constraints();

  // And clean up the send_list before we first use it
  _dof_map->prepare_send_list();

#endif
  
  // Resize the solution conformal to the current mesh
  solution->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);

  // Resize the current_local_solution for the current mesh
#ifdef LIBMESH_ENABLE_GHOSTED
  current_local_solution->init (this->n_dofs(), this->n_local_dofs(),
                                _dof_map->get_send_list(), false,
                                GHOSTED);
#else
  current_local_solution->init (this->n_dofs(), false, SERIAL);
#endif

  // from now on, no chance to add additional vectors
  _can_add_vectors = false;

  // initialize & zero other vectors, if necessary
  for (vectors_iterator pos = _vectors.begin(); pos != _vectors.end(); ++pos)
      pos->second->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
}

void System::local_dof_indices	(	const unsigned int	var,
		std::set< unsigned int > &	var_indices
	)			const

Fills the std::set with the degrees of freedom on the local processor corresponding the the variable number passed in.

Definition at line 962 of file system.C.

References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), DofMap::dof_indices(), DofMap::end_dof(), DofMap::first_dof(), get_dof_map(), and get_mesh().

Referenced by discrete_var_norm().

{
  // Make sure the set is clear
  var_indices.clear();

  std::vector<unsigned int> dof_indices;
  
  // Begin the loop over the elements
  MeshBase::const_element_iterator       el     =
    this->get_mesh().active_local_elements_begin();
  const MeshBase::const_element_iterator end_el =
    this->get_mesh().active_local_elements_end();

  const unsigned int 
    first_local = this->get_dof_map().first_dof(),
    end_local   = this->get_dof_map().end_dof();

  for ( ; el != end_el; ++el)
    {
      const Elem* elem = *el;      
      this->get_dof_map().dof_indices (elem, dof_indices, var);

      for(unsigned int i=0; i<dof_indices.size(); i++)
        {
          unsigned int dof = dof_indices[i];

          //If the dof is owned by the local processor
          if(first_local <= dof && dof < end_local)
            var_indices.insert(dof_indices[i]);
        }
    }
}

unsigned int System::n_active_dofs

(

)

const [inline]

Returns the number of active degrees of freedom for this System.

Definition at line 1436 of file system.h.

References n_constrained_dofs(), and n_dofs().

{
  return this->n_dofs() - this->n_constrained_dofs();
}

unsigned int System::n_constrained_dofs

(

)

const

Returns:

the number of constrained degrees of freedom in the system.

Definition at line 95 of file system.C.

References _dof_map.

Referenced by get_info(), and n_active_dofs().

{
#ifdef LIBMESH_ENABLE_AMR

  return _dof_map->n_constrained_dofs();

#else

  return 0;

#endif
}

unsigned int System::n_dofs

(

)

const

Returns:

the number of degrees of freedom in the system

Definition at line 88 of file system.C.

References _dof_map.

Referenced by add_vector(), current_solution(), get_info(), init_data(), FEMSystem::mass_residual(), n_active_dofs(), System::ProjectVector::operator()(), project_vector(), read_legacy_data(), reinit(), restrict_vectors(), and UnsteadySolver::solve().

{
  return _dof_map->n_dofs();
}

unsigned int System::n_local_dofs

(

)

const

Returns:

the number of degrees of freedom local to this processor

Definition at line 110 of file system.C.

References _dof_map, and libMesh::processor_id().

Referenced by add_vector(), get_info(), init_data(), project_vector(), read_serialized_blocked_dof_objects(), reinit(), restrict_vectors(), and UnsteadySolver::solve().

{
  return _dof_map->n_dofs_on_processor (libMesh::processor_id());
}

static unsigned int ReferenceCounter::n_objects

(

)

[inline, static, inherited]

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 76 of file reference_counter.h.

References ReferenceCounter::_n_objects.

  { return _n_objects; }

unsigned int System::n_vars

(

)

const [inline]

Returns:

the number of variables in the system

Definition at line 1390 of file system.h.

References _variables.

Referenced by add_variable(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), calculate_norm(), DiffContext::DiffContext(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), ErrorEstimator::estimate_errors(), FEMSystem::eulerian_residual(), ExactSolution::ExactSolution(), FEMContext::FEMContext(), get_info(), init(), FEMSystem::init_context(), DifferentiableSystem::init_data(), FEMSystem::mass_residual(), FEMSystem::mesh_position_get(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), project_vector(), re_update(), read_header(), read_legacy_data(), read_parallel_data(), read_serialized_vector(), reinit(), FEMContext::reinit(), EquationSystems::reinit(), HPCoarsenTest::select_refinement(), VTKIO::solution_to_vtk(), write_header(), write_parallel_data(), write_serialized_vector(), and zero_variable().

{
  return _variables.size();
}

unsigned int System::n_vectors

(

)

const [inline]

Returns:

the number of vectors (in addition to the solution) handled by this system This is the size of the _vectors map

Definition at line 1452 of file system.h.

References _vectors.

Referenced by ExplicitSystem::add_system_rhs(), compare(), get_info(), read_header(), and write_header().

{
  return _vectors.size(); 
}

const std::string & System::name

(

)

const [inline]

Returns:

the system name.

Definition at line 1318 of file system.h.

References _sys_name.

Referenced by compare(), ExactErrorEstimator::estimate_error(), ExactSolution::ExactSolution(), ExactErrorEstimator::find_squared_element_error(), get_info(), System::ProjectVector::operator()(), project_vector(), FrequencySystem::solve(), user_assembly(), user_constrain(), user_initialization(), user_QOI(), user_QOI_derivative(), write_header(), write_parallel_data(), and write_serialized_data().

{
  return _sys_name;
}

unsigned int System::number

(

)

const [inline]

Returns:

the system number.

Definition at line 1326 of file system.h.

References _sys_number.

Referenced by add_variable(), FEMSystem::eulerian_residual(), FEMSystem::mesh_position_get(), FEMSystem::mesh_position_set(), FEMSystem::mesh_x_position(), FEMSystem::mesh_y_position(), FEMSystem::mesh_z_position(), FEMSystem::numerical_jacobian(), read_legacy_data(), read_parallel_data(), read_serialized_blocked_dof_objects(), HPCoarsenTest::select_refinement(), write_parallel_data(), write_serialized_blocked_dof_objects(), and zero_variable().

{
  return _sys_number;
}

void ReferenceCounter::print_info

(

)

[static, inherited]

Prints the reference information to std::cout.

Definition at line 83 of file reference_counter.C.

References ReferenceCounter::get_info().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
  
  std::cout << ReferenceCounter::get_info();
  
#endif
}

void System::project_solution	(	Number	fptrconst Point &p,const Parameters &parameters,const std::string &sys_name,const std::string &unknown_name,
		Gradient	gptrconst Point &p,const Parameters &parameters,const std::string &sys_name,const std::string &unknown_name,
		Parameters &	parameters
	)			const

Projects the continuous functions onto the current solution.

This method projects an analytic function onto the solution via L2 projections and nodal interpolations on each element.

Definition at line 237 of file system_projection.C.

References current_local_solution, project_vector(), and solution.

{
  this->project_vector(fptr, gptr, parameters, *solution);

  solution->localize(*current_local_solution);
}

bool& System::project_solution_on_reinit

(

void

)

[inline]

Tells the System whether or not to project the solution vector onto new grids when the system is reinitialized. The solution will be projected unless project_solution_on_reinit() = false is called.

Definition at line 445 of file system.h.

References _solution_projection.

    { return _solution_projection; }

void System::project_vector	(	const NumericVector< Number > &	old_v,
		NumericVector< Number > &	new_v
	)			const [protected]

Projects the vector defined on the old mesh onto the new mesh. The original vector is unchanged and the new vector is passed through the second argument.

This method projects the vector via L2 projections or nodal interpolations on each element.

This method projects a solution from an old mesh to a current, refined mesh. The input vector old_v gives the solution on the old mesh, while the new_v gives the solution (to be computed) on the new mesh.

Definition at line 60 of file system_projection.C.

References NumericVector< T >::clear(), NumericVector< T >::close(), DofMap::enforce_constraints_exactly(), FEType::family, AutoPtr< Tp >::get(), get_dof_map(), get_mesh(), libMeshEnums::GHOSTED, NumericVector< T >::init(), NumericVector< T >::local_size(), NumericVector< T >::localize(), n_dofs(), n_local_dofs(), libMesh::n_processors(), n_vars(), libMeshEnums::PARALLEL, Threads::parallel_for(), Threads::parallel_reduce(), libMesh::processor_id(), libMeshEnums::SCALAR, DofMap::SCALAR_dof_indices(), System::BuildProjectionList::send_list, libMeshEnums::SERIAL, NumericVector< T >::set(), NumericVector< T >::size(), System::Variable::type(), NumericVector< T >::type(), System::BuildProjectionList::unique(), and variable().

{
  START_LOG ("project_vector()", "System");

  new_v.clear();

#ifdef LIBMESH_ENABLE_AMR

  // Resize the new vector and get a serial version.
  NumericVector<Number> *new_vector_ptr = NULL;
  AutoPtr<NumericVector<Number> > new_vector_built;
  NumericVector<Number> *local_old_vector;
  AutoPtr<NumericVector<Number> > local_old_vector_built;
  const NumericVector<Number> *old_vector_ptr = NULL;

  ConstElemRange active_local_elem_range 
    (this->get_mesh().active_local_elements_begin(),
     this->get_mesh().active_local_elements_end());

  // If the old vector was uniprocessor, make the new
  // vector uniprocessor
  if (old_v.type() == SERIAL)
    {
      new_v.init (this->n_dofs(), false, SERIAL);
      new_vector_ptr = &new_v;
      old_vector_ptr = &old_v;
    }

  // Otherwise it is a parallel, distributed vector, which
  // we need to localize.
  else if (old_v.type() == PARALLEL)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range, 
                                projection_list);

      // Create a sorted, unique send_list
      projection_list.unique();

      new_v.init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      new_vector_built = NumericVector<Number>::build();
      local_old_vector_built = NumericVector<Number>::build();
      new_vector_ptr = new_vector_built.get();
      local_old_vector = local_old_vector_built.get();
      new_vector_ptr->init(this->n_dofs(), false, SERIAL);
      local_old_vector->init(old_v.size(), false, SERIAL);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else if (old_v.type() == GHOSTED)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range, 
                                projection_list);

      // Create a sorted, unique send_list
      projection_list.unique();

      new_v.init (this->n_dofs(), this->n_local_dofs(),
                  this->get_dof_map().get_send_list(), false, GHOSTED);

      local_old_vector_built = NumericVector<Number>::build();
      new_vector_ptr = &new_v;
      local_old_vector = local_old_vector_built.get();
      local_old_vector->init(old_v.size(), old_v.local_size(),
                             projection_list.send_list, false, GHOSTED);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else // unknown old_v.type()
    {
      std::cerr << "ERROR: Unknown old_v.type() == " << old_v.type() 
                << std::endl;
      libmesh_error();
    }
  
  // Note that the above will have zeroed the new_vector.
  // Just to be sure, assert that new_vector_ptr and old_vector_ptr
  // were successfully set before trying to deref them.
  libmesh_assert(new_vector_ptr);
  libmesh_assert(old_vector_ptr);

  NumericVector<Number> &new_vector = *new_vector_ptr;
  const NumericVector<Number> &old_vector = *old_vector_ptr;
    
  Threads::parallel_for (active_local_elem_range,
                         ProjectVector(*this,
                                       old_vector,
                                       new_vector)
                         );

  // Copy the SCALAR dofs from old_vector to new_vector
  // Note: We assume that all SCALAR dofs are on the
  // processor with highest ID
  if(libMesh::processor_id() == (libMesh::n_processors()-1))
  {
    const DofMap& dof_map = this->get_dof_map();
    for (unsigned int var=0; var<this->n_vars(); var++)
      if(this->variable(var).type().family == SCALAR)
        {
          // We can just map SCALAR dofs directly across
          std::vector<unsigned int> new_SCALAR_indices, old_SCALAR_indices;
          dof_map.SCALAR_dof_indices (new_SCALAR_indices, var, false);
          dof_map.SCALAR_dof_indices (old_SCALAR_indices, var, true);
          const unsigned int new_n_dofs = new_SCALAR_indices.size();

          for (unsigned int i=0; i<new_n_dofs; i++)
          {
            new_vector.set( new_SCALAR_indices[i], old_vector(old_SCALAR_indices[i]) );
          }
        }
  }

  new_vector.close();

  // If the old vector was serial, we probably need to send our values
  // to other processors
  //
  // FIXME: I'm not sure how to make a NumericVector do that without
  // creating a temporary parallel vector to use localize! - RHS
  if (old_v.type() == SERIAL)
    {
      AutoPtr<NumericVector<Number> > dist_v = NumericVector<Number>::build();
      dist_v->init(this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      dist_v->close();
    
      for (unsigned int i=0; i!=dist_v->size(); i++)
        if (new_vector(i) != 0.0)
          dist_v->set(i, new_vector(i));

      dist_v->close();

      dist_v->localize (new_v, this->get_dof_map().get_send_list());
      new_v.close();
    }
  // If the old vector was parallel, we need to update it
  // and free the localized copies
  else if (old_v.type() == PARALLEL)
    {
      // We may have to set dof values that this processor doesn't
      // own in certain special cases, like LAGRANGE FIRST or
      // HERMITE THIRD elements on second-order meshes
      for (unsigned int i=0; i!=new_v.size(); i++)
        if (new_vector(i) != 0.0)
          new_v.set(i, new_vector(i));
      new_v.close();
    }

  this->get_dof_map().enforce_constraints_exactly(*this, &new_v);

#else

  // AMR is disabled: simply copy the vector
  new_v = old_v;
  
#endif // #ifdef LIBMESH_ENABLE_AMR

  STOP_LOG("project_vector()", "System");
}

void System::project_vector

(

NumericVector< Number > &

vector

)

const [protected]

Projects the vector defined on the old mesh onto the new mesh.

Definition at line 43 of file system_projection.C.

References NumericVector< T >::clone(), and project_vector().

{
  // Create a copy of the vector, which currently
  // contains the old data.
  AutoPtr<NumericVector<Number> >
    old_vector (vector.clone());

  // Project the old vector to the new vector
  this->project_vector (*old_vector, vector);
}

void System::project_vector	(	Number	fptrconst Point &p,const Parameters &parameters,const std::string &sys_name,const std::string &unknown_name,
		Gradient	gptrconst Point &p,const Parameters &parameters,const std::string &sys_name,const std::string &unknown_name,
		Parameters &	parameters,
		NumericVector< Number > &	new_vector
	)			const

Projects the continuous functions onto the current mesh.

This method projects an analytic function via L2 projections and nodal interpolations on each element.

Definition at line 258 of file system_projection.C.

References NumericVector< T >::close(), DofMap::enforce_constraints_exactly(), FEType::family, get_dof_map(), get_mesh(), libMesh::n_processors(), n_vars(), name(), Threads::parallel_for(), libMesh::processor_id(), libMeshEnums::SCALAR, DofMap::SCALAR_dof_indices(), NumericVector< T >::set(), System::Variable::type(), variable(), and variable_name().

Referenced by project_solution(), project_vector(), and restrict_vectors().

{
  START_LOG ("project_vector()", "System");

  Threads::parallel_for (ConstElemRange (this->get_mesh().active_local_elements_begin(),
                                         this->get_mesh().active_local_elements_end(),
                                         1000),
                         ProjectSolution(*this,
                                         fptr,
                                         gptr,
                                         parameters,
                                         new_vector)
                         );

  // Also, load values into the SCALAR dofs
  // Note: We assume that all SCALAR dofs are on the
  // processor with highest ID
  if(libMesh::processor_id() == (libMesh::n_processors()-1))
  {
    const DofMap& dof_map = this->get_dof_map();
    for (unsigned int var=0; var<this->n_vars(); var++)
      if(this->variable(var).type().family == SCALAR)
        {
          std::vector<unsigned int> SCALAR_indices;
          dof_map.SCALAR_dof_indices (SCALAR_indices, var);
          const unsigned int n_SCALAR_dofs = SCALAR_indices.size();

          for (unsigned int i=0; i<n_SCALAR_dofs; i++)
          {
            const unsigned int index = SCALAR_indices[i];

            // We pass the point (i,0,0) to the fptr to distinguish
            // the different scalars within the SCALAR variable
            Point p_i(i,0,0);
            new_vector.set( index, fptr(p_i,
                                        parameters,
                                        this->name(),
                                        this->variable_name(var))
                          );
          }
        }
  }

  new_vector.close();

#ifdef LIBMESH_ENABLE_AMR
  this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
#endif

  STOP_LOG("project_vector()", "System");
}

void System::prolong_vectors

(

)

[virtual]

Prolong vectors after the mesh has refined

Definition at line 255 of file system.C.

References restrict_vectors().

Referenced by EquationSystems::reinit().

{
#ifdef LIBMESH_ENABLE_AMR
  // Currently project_vector handles both restriction and prolongation
  this->restrict_vectors();
#endif
}

virtual void System::qoi_parameter_hessian_vector_product	(	const QoISet &	qoi_indices,
		const ParameterVector &	parameters,
		const ParameterVector &	vector,
		SensitivityData &	product
	)			[inline, virtual]

For each of the system's quantities of interest q in qoi[qoi_indices], and for a vector of parameters p, the parameter sensitivity Hessian H_ij is defined as H_ij = (d^2 q)/(d p_i d p_j) The Hessian-vector product, for a vector v_k in parameter space, is S_j = H_jk v_k This product is the output of this method, where for each q_i, S_j is stored in sensitivities[i][j].

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 281 of file system.h.

    { libmesh_not_implemented(); }

void System::qoi_parameter_sensitivity	(	const QoISet &	qoi_indices,
		const ParameterVector &	parameters,
		SensitivityData &	sensitivities
	)			[virtual]

Solves for the derivative of each of the system's quantities of interest q in qoi[qoi_indices] with respect to each parameter in parameters, placing the result for qoi i and parameter j into sensitivities[i][j].

Note that parameters is a const vector, not a vector-of-const; parameter values in this vector need to be mutable for finite differencing to work.

Automatically chooses the forward method for problems with more quantities of interest than parameters, or the adjoint method otherwise.

This method is only usable in derived classes which overload an implementation.

Definition at line 383 of file system.C.

References ParameterVector::size(), and QoISet::size().

{
  // Forward sensitivities are more efficient for Nq > Np
  if (qoi_indices.size(*this) > parameters.size())
    forward_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
  // Adjoint sensitivities are more efficient for Np > Nq,
  // and an adjoint may be more reusable than a forward 
  // solution sensitivity in the Np == Nq case.
  else
    adjoint_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
}

void System::re_update

(

)

[virtual]

Re-update the local values when the mesh has changed. This method takes the data updated by update() and makes it up-to-date on the current mesh.

Definition at line 314 of file system.C.

References current_local_solution, Utility::iota(), n_vars(), and solution.

{
  //const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();

  // If this system is empty... don't do anything!
  if(!this->n_vars())
    return;

  // Explicitly build a send_list
  std::vector<unsigned int> send_list(solution->size());
  Utility::iota (send_list.begin(), send_list.end(), 0);
  
  // Check sizes
  libmesh_assert (current_local_solution->size()       == solution->size());
  // Not true with ghosted vectors
  // libmesh_assert (current_local_solution->local_size() == solution->size());
  libmesh_assert (!send_list.empty());
  libmesh_assert (send_list.size() <= solution->size());

  // Create current_local_solution from solution.  This will
  // put a local copy of solution into current_local_solution.
  solution->localize (*current_local_solution, send_list);
}

void System::read_header	(	Xdr &	io,
		const std::string &	version,
		const bool	read_header = true,
		const bool	read_additional_data = true,
		const bool	read_legacy_format = false
	)

Reads the basic data header for this System.

Definition at line 78 of file system_io.C.

References _additional_data_written, _can_add_vectors, add_variable(), add_vector(), clear(), Xdr::data(), FEType::family, get_mesh(), FEType::inf_map, MeshBase::mesh_dimension(), libMeshEnums::MONOMIAL, n_vars(), n_vectors(), libMesh::on_command_line(), FEType::order, libMesh::processor_id(), FEType::radial_family, FEType::radial_order, Xdr::reading(), type, and libMeshEnums::XYZ.

Referenced by EquationSystems::_read_impl().

{
  // This method implements the input of a
  // System object, embedded in the output of
  // an EquationSystems<T_sys>.  This warrants some 
  // documentation.  The output file essentially
  // consists of 5 sections:
  //
  // for this system
  //
  //   5.) The number of variables in the system (unsigned int)
  //
  //   for each variable in the system
  //     
  //     6.) The name of the variable (string)
  //     
  //     7.) Combined in an FEType:
  //         - The approximation order(s) of the variable 
  //           (Order Enum, cast to int/s)
  //         - The finite element family/ies of the variable 
  //           (FEFamily Enum, cast to int/s)
  // 
  //   end variable loop
  //
  //   8.) The number of additional vectors (unsigned int),      
  //
  //     for each additional vector in the system object
  // 
  //     9.) the name of the additional vector  (string)
  //
  // end system
  libmesh_assert (io.reading());
  
  // Possibly clear data structures and start from scratch.
  if (read_header)
    this->clear ();

  // Figure out if we need to read infinite element information.
  // This will be true if the version string contains " with infinite elements"
  const bool read_ifem_info =
    (version.rfind(" with infinite elements") < version.size()) ||
    libMesh::on_command_line ("--read_ifem_systems");
  
  
  {
    // 5.) 
    // Read the number of variables in the system
    unsigned int n_vars=0;
    if (libMesh::processor_id() == 0) io.data (n_vars);
    Parallel::broadcast(n_vars);
      
    for (unsigned int var=0; var<n_vars; var++)
      {             
        // 6.)
        // Read the name of the var-th variable
        std::string var_name;     
        if (libMesh::processor_id() == 0) io.data (var_name);
        Parallel::broadcast(var_name);
                
        // 7.)
        // Read the approximation order(s) of the var-th variable 
        int order=0;      
        if (libMesh::processor_id() == 0) io.data (order);
        Parallel::broadcast(order);
        
        
        // do the same for infinite element radial_order 
        int rad_order=0;
        if (read_ifem_info)
          {
            if (libMesh::processor_id() == 0) io.data(rad_order);
            Parallel::broadcast(rad_order);
          }


        // Read the finite element type of the var-th variable 
        int fam=0;
        if (libMesh::processor_id() == 0) io.data (fam);
        Parallel::broadcast(fam);
        FEType type;
        type.order  = static_cast<Order>(order);
        type.family = static_cast<FEFamily>(fam);

        // Check for incompatibilities.  The shape function indexing was
        // changed for the monomial and xyz finite element families to 
        // simplify extension to arbitrary p.  The consequence is that 
        // old restart files will not be read correctly.  This is expected
        // to be an unlikely occurance, but catch it anyway.
        if (read_legacy_format)
          if ((type.family == MONOMIAL || type.family == XYZ) && 
              ((type.order > 2 && this->get_mesh().mesh_dimension() == 2) ||
               (type.order > 1 && this->get_mesh().mesh_dimension() == 3)))
            {
              libmesh_here();
              std::cout << "*****************************************************************\n"
                        << "* WARNING: reading a potentially incompatible restart file!!!   *\n"
                        << "*  contact libmesh-users@lists.sourceforge.net for more details *\n"
                        << "*****************************************************************"
                        << std::endl;
            }
                        
        // Read additional information for infinite elements    
        int radial_fam=0;
        int i_map=0;
        if (read_ifem_info)
          {
            if (libMesh::processor_id() == 0) io.data (radial_fam);
            Parallel::broadcast(radial_fam);
            if (libMesh::processor_id() == 0) io.data (i_map);
            Parallel::broadcast(i_map);
          }
        
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
        
        type.radial_order  = static_cast<Order>(rad_order);
        type.radial_family = static_cast<FEFamily>(radial_fam);
        type.inf_map       = static_cast<InfMapType>(i_map);      

#endif

        if (read_header) 
          this->add_variable (var_name, type);
      }
  }

  // 8.)  
  // Read the number of additional vectors.  
  unsigned int n_vectors=0;  
  if (libMesh::processor_id() == 0) io.data (n_vectors);
  Parallel::broadcast(n_vectors);
  
  // If n_vectors > 0, this means that write_additional_data
  // was true when this file was written.  We will need to
  // make use of this fact later.
  if (n_vectors > 0)
    this->_additional_data_written = true;  
  
  for (unsigned int vec=0; vec<n_vectors; vec++)
    {
      // 9.)
      // Read the name of the vec-th additional vector
      std::string vec_name;      
      if (libMesh::processor_id() == 0) io.data (vec_name);
      Parallel::broadcast(vec_name);
      
      if (read_additional_data)
        {
          // sanity checks
          libmesh_assert(this->_can_add_vectors);
          // Some systems may have added their own vectors already
//        libmesh_assert(this->_vectors.count(vec_name) == 0);

          this->add_vector(vec_name);
        }
    }
}

void System::read_legacy_data	(	Xdr &	io,
		const bool	read_additional_data = true
	)

Reads additional data, namely vectors, for this System.

Definition at line 241 of file system_io.C.

References _additional_data_written, _vectors, MeshBase::active_elements_begin(), MeshBase::active_elements_end(), Xdr::data(), get_mesh(), DofObject::invalid_id, n_dofs(), n_vars(), MeshBase::nodes_begin(), MeshBase::nodes_end(), number(), libMesh::processor_id(), Xdr::reading(), solution, and libMesh::zero.

{
  libmesh_deprecated();
  
  // This method implements the output of the vectors
  // contained in this System object, embedded in the 
  // output of an EquationSystems<T_sys>. 
  //
  //   10.) The global solution vector, re-ordered to be node-major 
  //       (More on this later.)                                    
  //                                                                
  //      for each additional vector in the object          
  //                                                                
  //      11.) The global additional vector, re-ordered to be       
  //           node-major (More on this later.)
  libmesh_assert (io.reading());

  // read and reordering buffers
  std::vector<Number> global_vector;
  std::vector<Number> reordered_vector;

  // 10.)
  // Read and set the solution vector
  {     
    if (libMesh::processor_id() == 0) io.data (global_vector);    
    Parallel::broadcast(global_vector);
    
    // Remember that the stored vector is node-major.
    // We need to put it into whatever application-specific
    // ordering we may have using the dof_map.
    reordered_vector.resize(global_vector.size());

    //std::cout << "global_vector.size()=" << global_vector.size() << std::endl;
    //std::cout << "this->n_dofs()=" << this->n_dofs() << std::endl;
    
    libmesh_assert (global_vector.size() == this->n_dofs());
        
    unsigned int cnt=0;

    const unsigned int sys     = this->number();
    const unsigned int n_vars  = this->n_vars();

    for (unsigned int var=0; var<n_vars; var++)
      { 
        // First reorder the nodal DOF values
        {
          MeshBase::node_iterator
            it  = this->get_mesh().nodes_begin(),
            end = this->get_mesh().nodes_end();
        
          for (; it != end; ++it)
            for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
              {
                libmesh_assert ((*it)->dof_number(sys, var, index) !=
                        DofObject::invalid_id);
                
                libmesh_assert (cnt < global_vector.size());
                
                reordered_vector[(*it)->dof_number(sys, var, index)] =
                  global_vector[cnt++]; 
              }
        }
        
        // Then reorder the element DOF values
        {
          MeshBase::element_iterator
            it  = this->get_mesh().active_elements_begin(),
            end = this->get_mesh().active_elements_end();

          for (; it != end; ++it)
            for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
              {  
                libmesh_assert ((*it)->dof_number(sys, var, index) !=
                        DofObject::invalid_id);
                
                libmesh_assert (cnt < global_vector.size());
                
                reordered_vector[(*it)->dof_number(sys, var, index)] =
                  global_vector[cnt++]; 
              }
        }
      }
            
    *(this->solution) = reordered_vector;
  }

  // For each additional vector, simply go through the list.
  // ONLY attempt to do this IF additional data was actually
  // written to the file for this system (controlled by the
  // _additional_data_written flag).  
  if (this->_additional_data_written)
    {
      std::map<std::string, NumericVector<Number>* >::iterator
        pos = this->_vectors.begin();
  
      for (; pos != this->_vectors.end(); ++pos)
        {
          // 11.)          
          // Read the values of the vec-th additional vector.
          // Prior do _not_ clear, but fill with zero, since the
          // additional vectors _have_ to have the same size
          // as the solution vector
          std::fill (global_vector.begin(), global_vector.end(), libMesh::zero);

          if (libMesh::processor_id() == 0) io.data (global_vector);
          Parallel::broadcast(global_vector);

          // If read_additional_data==true, then we will keep this vector, otherwise
          // we are going to throw it away.
          if (read_additional_data)
            {
              // Remember that the stored vector is node-major.
              // We need to put it into whatever application-specific
              // ordering we may have using the dof_map.
              std::fill (reordered_vector.begin(),
                         reordered_vector.end(),
                         libMesh::zero);
        
              reordered_vector.resize(global_vector.size());    

              libmesh_assert (global_vector.size() == this->n_dofs());
        
              unsigned int cnt=0;

              const unsigned int sys     = this->number();
              const unsigned int n_vars  = this->n_vars();
        
              for (unsigned int var=0; var<n_vars; var++)
                {
                  // First reorder the nodal DOF values
                  {
                    MeshBase::node_iterator
                      it  = this->get_mesh().nodes_begin(),
                      end = this->get_mesh().nodes_end();

                    for (; it!=end; ++it)
                      for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
                        {
                          libmesh_assert ((*it)->dof_number(sys, var, index) !=
                                  DofObject::invalid_id);
                          
                          libmesh_assert (cnt < global_vector.size());
                          
                          reordered_vector[(*it)->dof_number(sys, var, index)] =
                            global_vector[cnt++]; 
                        }
                  }

                  // Then reorder the element DOF values
                  {
                    MeshBase::element_iterator
                      it  = this->get_mesh().active_elements_begin(),
                      end = this->get_mesh().active_elements_end();

                    for (; it!=end; ++it)
                      for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
                        {  
                          libmesh_assert ((*it)->dof_number(sys, var, index) !=
                                  DofObject::invalid_id);
                          
                          libmesh_assert (cnt < global_vector.size());
                          
                          reordered_vector[(*it)->dof_number(sys, var, index)] =
                            global_vector[cnt++]; 
                        }
                  }
                }
            
              // use the overloaded operator=(std::vector) to assign the values
              *(pos->second) = reordered_vector;
            }
        }
    } // end if (_additional_data_written)    
}

void System::read_parallel_data	(	Xdr &	io,
		const bool	read_additional_data
	)

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh. This method will read an individual file for each processor in the simulation where the local solution components for that processor are stored.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

Definition at line 419 of file system_io.C.

References _vectors, Xdr::data(), get_mesh(), DofObject::invalid_id, Xdr::is_open(), n_vars(), number(), Xdr::reading(), and solution.

{
  libmesh_assert (io.reading());
  libmesh_assert (io.is_open());

  // build the ordered nodes and element maps.
  // when writing/reading parallel files we need to iterate
  // over our nodes/elements in order of increasing global id().
  // however, this is not guaranteed to be ordering we obtain
  // by using the node_iterators/element_iterators directly.
  // so build a set, sorted by id(), that provides the ordering.
  // further, for memory economy build the set but then transfer
  // its contents to vectors, which will be sorted.
  std::vector<const DofObject*> ordered_nodes, ordered_elements;
  {    
    std::set<const DofObject*, CompareDofObjectsByID>
      ordered_nodes_set (this->get_mesh().local_nodes_begin(),
                         this->get_mesh().local_nodes_end());
      
      ordered_nodes.insert(ordered_nodes.end(),
                           ordered_nodes_set.begin(),
                           ordered_nodes_set.end());
  }
  {
    std::set<const DofObject*, CompareDofObjectsByID>
      ordered_elements_set (this->get_mesh().local_elements_begin(),
                            this->get_mesh().local_elements_end());
      
      ordered_elements.insert(ordered_elements.end(),
                              ordered_elements_set.begin(),
                              ordered_elements_set.end());
  }
  
  std::vector<Number> io_buffer;
  
  // 9.)
  //
  // Actually read the solution components
  // for the ith system to disk
  io.data(io_buffer);
  
  const unsigned int sys_num = this->number();
  const unsigned int n_vars  = this->n_vars();

  unsigned int cnt=0;
  
  // Loop over each variable and each node, and read out the value.
  for (unsigned int var=0; var<n_vars; var++)
    {
      // First read the node DOF values
      for (std::vector<const DofObject*>::const_iterator
             it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
        for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
          {
            libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                    DofObject::invalid_id);
            libmesh_assert (cnt < io_buffer.size());
            this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
          }

      // Then read the element DOF values
      for (std::vector<const DofObject*>::const_iterator
             it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
        for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
          {
            libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                    DofObject::invalid_id);
            libmesh_assert (cnt < io_buffer.size());
            this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
          }      
    }
  
  // Only read additional vectors if wanted  
  if (read_additional_data)
    {     
      std::map<std::string, NumericVector<Number>* >::const_iterator
        pos = _vectors.begin();
  
      for(; pos != this->_vectors.end(); ++pos)
        {
          cnt=0;
          io_buffer.clear();
          
          // 10.)
          //
          // Actually read the additional vector components
          // for the ith system to disk
          io.data(io_buffer);
          
          // Loop over each variable and each node, and read out the value.
          for (unsigned int var=0; var<n_vars; var++)
            {
              // First read the node DOF values
              for (std::vector<const DofObject*>::const_iterator
                     it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
                for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
                  {
                    libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                            DofObject::invalid_id);
                    libmesh_assert (cnt < io_buffer.size());
                    this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
                  }          
              
              // Then read the element DOF values
              for (std::vector<const DofObject*>::const_iterator
                     it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
                for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
                  {
                    libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                            DofObject::invalid_id);
                    libmesh_assert (cnt < io_buffer.size());
                    this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
                  }           
            }
        }
    }
}

template<typename iterator_type >

unsigned int System::read_serialized_blocked_dof_objects	(	const unsigned int	var,
		const unsigned int	n_objects,
		const iterator_type	begin,
		const iterator_type	end,
		Xdr &	io,
		NumericVector< Number > &	vec
	)			const [inline, private]

Reads an input vector from the stream io and assigns the values to a set of DofObjects. This method uses blocked input and is safe to call on a distributed memory-mesh.

Definition at line 608 of file system_io.C.

References Xdr::data_stream(), NumericVector< T >::first_local_index(), MeshTools::Generation::Private::idx(), libMesh::invalid_uint, io_blksize, NumericVector< T >::last_local_index(), std::min(), n_local_dofs(), libMesh::n_processors(), number(), libMesh::processor_id(), and NumericVector< T >::set().

Referenced by read_serialized_vector().

{
  const unsigned int sys_num = this->number();
  
  std::vector<Number> input_buffer;        // buffer to hold the input block read from io.               
  std::vector<Number> local_values;
  std::vector<std::vector<unsigned int> >  // The IDs from each processor which map to the objects
    recv_ids(libMesh::n_processors());     //  read in the current block
  std::vector<unsigned int> idx_map;       // Reordering map to traverse entry-wise rather than processor-wise
  unsigned int n_assigned_vals = 0;        // the number of values assigned, this will be returned.
  
  //-----------------------------------
  // Collect the values for all objects
  unsigned int first_object=0, last_object=0;

  for (unsigned int blk=0; last_object<n_objects; blk++)
    {
      //std::cout << "Reading object block " << blk << std::endl;
      
      // Each processor should build up its transfer buffers for its
      // local objects in [first_object,last_object).
      first_object = blk*io_blksize;
      last_object  = std::min((blk+1)*io_blksize,n_objects);
      
      // Clear the transfer buffers for this block.
      recv_ids[libMesh::processor_id()].clear();
      unsigned int n_local_dofs=0;
      for (iterator_type it=begin; it!=end; ++it)
        if (((*it)->id() >= first_object) && // object in [first_object,last_object)
            ((*it)->id() <   last_object) &&
            (*it)->n_comp(sys_num,var))      // var has a nonzero # of components on this object
          {
            recv_ids[libMesh::processor_id()].push_back((*it)->id());
            recv_ids[libMesh::processor_id()].push_back((*it)->n_comp(sys_num, var));
            recv_ids[libMesh::processor_id()].push_back(n_local_dofs);
            n_local_dofs += (*it)->n_comp(sys_num, var);            
          }
      
      // Get the recv_ids for all other processors.
      {
        const unsigned int curr_vec_size = recv_ids[libMesh::processor_id()].size();
        std::vector<unsigned int> recv_id_sizes(libMesh::n_processors());
        Parallel::allgather(curr_vec_size, recv_id_sizes);
        for (unsigned int pid=0; pid<libMesh::n_processors(); pid++)
          {
            recv_ids[pid].resize(recv_id_sizes[pid]);
            Parallel::broadcast(recv_ids[pid], pid);
          }
      }

      // create the idx map for all processors -- this will match the ordering
      // in the input buffer chunk which we are about to read.
      idx_map.resize(3*io_blksize); std::fill (idx_map.begin(), idx_map.end(), libMesh::invalid_uint);
      unsigned int tot_n_comp=0;
      for (unsigned int pid=0; pid<libMesh::n_processors(); pid++)
        for (unsigned int idx=0; idx<recv_ids[pid].size(); idx+=3)
          {
            const unsigned int local_idx = recv_ids[pid][idx+0]-first_object;
            libmesh_assert (local_idx < std::min(io_blksize,n_objects));
            const unsigned int n_comp    = recv_ids[pid][idx+1];
            const unsigned int start_pos = recv_ids[pid][idx+2];
            
            idx_map[3*local_idx+0] = pid;
            idx_map[3*local_idx+1] = n_comp;
            idx_map[3*local_idx+2] = start_pos; // this tells us where the values
                                                // for this object will live in the local_values buffer
            tot_n_comp += n_comp;
          }
      
      // Processor 0 will read the block from the buffer stream and send it to all other processors
      input_buffer.resize (tot_n_comp);
      if (libMesh::processor_id() == 0) io.data_stream(input_buffer.empty() ? NULL : &input_buffer[0], tot_n_comp);
      Parallel::broadcast(input_buffer);

      // Extract the values corresponding to the local objects from the input_buffer
      // and place them into the local_values temporary buffer.
      {
        unsigned int processed_size=0;
        std::vector<Number>::const_iterator next_value = input_buffer.begin();
        local_values.clear(); local_values.resize(n_local_dofs);

        for (unsigned int idx=0; idx<idx_map.size(); idx+=3)
          if (idx_map[idx] != libMesh::invalid_uint) // this could happen when an object
            {                                        // has no components for the current variable
              const unsigned int pid       = idx_map[idx+0];
              const unsigned int n_comp    = idx_map[idx+1];
              const unsigned int start_pos = idx_map[idx+2];
              
              for (unsigned int comp=0; comp<n_comp; comp++)
                {
                  libmesh_assert (next_value != input_buffer.end());
                  if (pid == libMesh::processor_id())
                    {
                      libmesh_assert ((start_pos+comp) < local_values.size());
                      local_values[start_pos+comp] = *next_value;
                    }
                  ++next_value;
                  ++processed_size;                             
                }
            }
        libmesh_assert (processed_size == input_buffer.size());
      }
      
      // A subset of the components (potentially null set) will match our objects in
      // [first_object,last_object), and we will assign the corresponding values from
      // the local_values buffer.
      for (iterator_type it=begin; it!=end; ++it)
        if (((*it)->id() >= first_object) && // object in [first_object,last_object)
            ((*it)->id() <   last_object) &&
            (*it)->n_comp(sys_num,var))      // var has a nonzero # of components on this object
          {
            const unsigned int local_idx = (*it)->id()-first_object;
            libmesh_assert (local_idx < std::min(io_blksize,n_objects));

#ifndef NDEBUG
            // We only need to check the pid when asserts are active
            const unsigned int pid       = idx_map[3*local_idx+0];
#endif
            libmesh_assert (pid == libMesh::processor_id());
            
            const unsigned int n_comp    = idx_map[3*local_idx+1];
            const unsigned int start_pos = idx_map[3*local_idx+2];
            
            libmesh_assert (n_comp == (*it)->n_comp(sys_num, var));
            
            for (unsigned int comp=0; comp<n_comp; comp++)
              {
                libmesh_assert ((start_pos+comp) < local_values.size());
                const Number &value = local_values[start_pos+comp];                             
                const unsigned int dof_index = (*it)->dof_number (sys_num, var, comp);
                libmesh_assert (dof_index >= vec.first_local_index());
                libmesh_assert (dof_index <  vec.last_local_index());
                //std::cout << "di=" << dof_index << ", val=" << value << std::endl;
                vec.set (dof_index, value);
                ++n_assigned_vals;
              }
          }
    }
      
  return n_assigned_vals;
}

void System::read_serialized_data	(	Xdr &	io,
		const bool	read_additional_data = true
	)

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh.

Definition at line 559 of file system_io.C.

References _vectors, Xdr::comment(), libMesh::processor_id(), read_serialized_vector(), and solution.

{
  // This method implements the input of the vectors
  // contained in this System object, embedded in the 
  // output of an EquationSystems<T_sys>. 
  //
  //   10.) The global solution vector, re-ordered to be node-major 
  //       (More on this later.)                                    
  //                                                                
  //      for each additional vector in the object          
  //                                                                
  //      11.) The global additional vector, re-ordered to be       
  //          node-major (More on this later.)
  parallel_only();
  std::string comment;

  // 10.)
  // Read the global solution vector
  {
    this->read_serialized_vector(io, *this->solution); 

    // get the comment
    if (libMesh::processor_id() == 0)
      io.comment (comment);  
  }
  
  // 11.)
  // Only read additional vectors if wanted  
  if (read_additional_data)
    {     
      std::map<std::string, NumericVector<Number>* >::const_iterator
        pos = _vectors.begin();
  
      for(; pos != this->_vectors.end(); ++pos)
        {
          this->read_serialized_vector(io, *pos->second);

          // get the comment
          if (libMesh::processor_id() == 0)
            io.comment (comment);         
            
        }
    }
}

void System::read_serialized_vector	(	Xdr &	io,
		NumericVector< Number > &	vec
	)			[private]

Reads a vector for this System. This method may safely be called on a distributed-memory mesh.

Definition at line 757 of file system_io.C.

References NumericVector< T >::close(), Xdr::data(), get_mesh(), io_blksize, MeshTools::n_elem(), n_nodes, libMesh::n_processors(), n_vars(), libMeshEnums::PARALLEL, libMesh::processor_id(), read_serialized_blocked_dof_objects(), Xdr::reading(), and NumericVector< T >::type().

Referenced by read_serialized_data().

{
  parallel_only();

#ifndef NDEBUG
  // In parallel we better be reading a parallel vector -- if not
  // we will not set all of its components below!!
  if (libMesh::n_processors() > 1)
    libmesh_assert (vec.type() == PARALLEL);
   
  // If this is not the same on all processors we're in trouble!
  Parallel::verify(io_blksize);
#endif
  
  libmesh_assert (io.reading());

  // vector length
  unsigned int vector_length=0, n_assigned_vals=0;

  // Get the buffer size
  if (libMesh::processor_id() == 0) io.data(vector_length, "# vector length");
  Parallel::broadcast(vector_length);
  
  // Loop over each variable in the system, and then each node/element in the mesh.
  for (unsigned int var=0; var<this->n_vars(); var++)
    {      
      //---------------------------------
      // Collect the values for all nodes
      n_assigned_vals +=
        this->read_serialized_blocked_dof_objects (var,
                                                   this->get_mesh().n_nodes(),
                                                   this->get_mesh().local_nodes_begin(),
                                                   this->get_mesh().local_nodes_end(),
                                                   io,
                                                   vec);
      
      
      //------------------------------------
      // Collect the values for all elements
      n_assigned_vals +=
        this->read_serialized_blocked_dof_objects (var,
                                                   this->get_mesh().n_elem(),
                                                   this->get_mesh().local_elements_begin(),
                                                   this->get_mesh().local_elements_end(),
                                                   io,
                                                   vec);
    } // end variable loop

  vec.close();

#ifndef NDEBUG
  Parallel::sum (n_assigned_vals);
  libmesh_assert (n_assigned_vals == vector_length);
#endif
}

void System::reinit

(

)

[virtual]

Reinitializes degrees of freedom and other required data on the current mesh. Note that the matrix is not initialized at this time since it may not be required for all applications. Should be overloaded in derived classes.

Reimplemented in DifferentiableSystem, EigenSystem, ExplicitSystem, ImplicitSystem, LinearImplicitSystem, NewmarkSystem, and NonlinearImplicitSystem.

Definition at line 265 of file system.C.

References current_local_solution, n_dofs(), n_local_dofs(), n_vars(), libMeshEnums::PARALLEL, and solution.

Referenced by ExplicitSystem::reinit(), and EigenSystem::reinit().

{
#ifdef LIBMESH_ENABLE_AMR
  //If no variables have been added to this system
  //don't do anything
  if(!this->n_vars())
    return;

  // Constraints get handled in EquationSystems::reinit now
//  _dof_map->create_dof_constraints(this->get_mesh());

  // Update the solution based on the projected
  // current_local_solution.
  solution->init (this->n_dofs(), this->n_local_dofs(), true, PARALLEL);
        
  libmesh_assert (solution->size() == current_local_solution->size());
  // Not true with ghosted vectors
  // libmesh_assert (solution->size() == current_local_solution->local_size());

  const unsigned int first_local_dof = solution->first_local_index();
  const unsigned int local_size      = solution->local_size();
      
  for (unsigned int i=0; i<local_size; i++)
    solution->set(i+first_local_dof,
                  (*current_local_solution)(i+first_local_dof));
#endif
}

NumericVector< Number > * System::request_vector

(

const unsigned int

vec_num

)

Returns:

a writeable pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or returns NULL if the system has no such vector.

Definition at line 611 of file system.C.

References vectors_begin(), and vectors_end().

{
  vectors_iterator v = vectors_begin();
  vectors_iterator v_end = vectors_end();
  unsigned int num = 0;
  while((num<vec_num) && (v!=v_end))
    {
      num++;
      ++v;
    }
  if (v==v_end)
    return NULL;
  return v->second;
}

const NumericVector< Number > * System::request_vector

(

const unsigned int

vec_num

)

const

Returns:

a const pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or returns NULL if the system has no such vector.

Definition at line 594 of file system.C.

References vectors_begin(), and vectors_end().

{
  const_vectors_iterator v = vectors_begin();
  const_vectors_iterator v_end = vectors_end();
  unsigned int num = 0;
  while((num<vec_num) && (v!=v_end))
    {
      num++;
      ++v;
    }
  if (v==v_end)
    return NULL;
  return v->second;
}

NumericVector< Number > * System::request_vector

(

const std::string &

vec_name

)

Returns:

a pointer to the vector if this System has a vector associated with the given name, NULL otherwise.

Definition at line 582 of file system.C.

References _vectors.

{
  vectors_iterator pos = _vectors.find(vec_name);
  
  if (pos == _vectors.end())
    return NULL;
  
  return pos->second;
}

const NumericVector< Number > * System::request_vector

(

const std::string &

vec_name

)

const

Returns:

a const pointer to the vector if this System has a vector associated with the given name, NULL otherwise.

Definition at line 570 of file system.C.

References _vectors.

{
  const_vectors_iterator pos = _vectors.find(vec_name);
  
  if (pos == _vectors.end())
    return NULL;
  
  return pos->second;
}

void System::restrict_vectors

(

)

[virtual]

Restrict vectors after the mesh has coarsened

Definition at line 219 of file system.C.

References _dof_map, _solution_projection, _vector_projections, _vectors, current_local_solution, libMeshEnums::GHOSTED, NumericVector< T >::init(), n_dofs(), n_local_dofs(), libMeshEnums::PARALLEL, project_vector(), and solution.

Referenced by prolong_vectors(), and EquationSystems::reinit().

{
#ifdef LIBMESH_ENABLE_AMR
  // Restrict the _vectors on the coarsened cells
  for (vectors_iterator pos = _vectors.begin(); pos != _vectors.end(); ++pos)
    {
      NumericVector<Number>* v = pos->second;
      
      if (_vector_projections[pos->first])
        this->project_vector (*v);
      else
        v->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
    }

  const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();

  // Restrict the solution on the coarsened cells
  if (_solution_projection)
    this->project_vector (*solution);

#ifdef LIBMESH_ENABLE_GHOSTED
  current_local_solution->init(this->n_dofs(),
                               this->n_local_dofs(), send_list, 
                               false, GHOSTED);
#else
  current_local_solution->init(this->n_dofs());
#endif

  if (_solution_projection)
    solution->localize (*current_local_solution, send_list); 

#endif // LIBMESH_ENABLE_AMR
}

virtual std::pair<unsigned int, Real> System::sensitivity_solve

(

const ParameterVector &

parameters

)

[inline, virtual]

Solves the sensitivity system, for the provided parameters. Must be overloaded in derived systems.

Returns a pair with the total number of linear iterations performed and the (sum of the) final residual norms

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 176 of file system.h.

      { libmesh_not_implemented(); }

virtual void System::solve

(

)

[pure virtual]

Solves the system. Must be overloaded in derived systems.

Implemented in ContinuationSystem, DifferentiableSystem, EigenSystem, ExplicitSystem, FEMSystem, FrequencySystem, LinearImplicitSystem, and NonlinearImplicitSystem.

sys_type& System::system

(

)

[inline]

Returns:

a clever pointer to the system.

Reimplemented in EigenSystem, ExplicitSystem, ImplicitSystem, LinearImplicitSystem, and NonlinearImplicitSystem.

Definition at line 97 of file system.h.

{ return *this; }

virtual std::string System::system_type

(

)

const [inline, virtual]

Returns:

the type of system, helpful in identifying which system type to use when reading equation system data from file. Should be overloaded in derived classes.

Reimplemented in EigenSystem, ExplicitSystem, FrequencySystem, ImplicitSystem, LinearImplicitSystem, NewmarkSystem, and NonlinearImplicitSystem.

Definition at line 306 of file system.h.

Referenced by get_info().

{ return "BasicSystem"; }

void System::update

(

)

[virtual]

Update the local values to reflect the solution on neighboring processors.

Definition at line 295 of file system.C.

References _dof_map, current_local_solution, and solution.

Referenced by __libmesh_petsc_diff_solver_jacobian(), __libmesh_petsc_diff_solver_residual(), FEMSystem::assemble_qoi(), FEMSystem::assemble_qoi_derivative(), FEMSystem::assembly(), Problem_Interface::computeF(), GMVIO::copy_nodal_solution(), FEMSystem::mesh_position_get(), FEMSystem::postprocess(), NonlinearImplicitSystem::solve(), NewtonSolver::solve(), LinearImplicitSystem::solve(), and ExplicitSystem::solve().

{
  const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();

  // Check sizes
  libmesh_assert (current_local_solution->size() == solution->size());
// More processors than elements => empty send_list
//  libmesh_assert (!send_list.empty());
  libmesh_assert (send_list.size() <= solution->size());

  // Create current_local_solution from solution.  This will
  // put a local copy of solution into current_local_solution.
  // Only the necessary values (specified by the send_list)
  // are copied to minimize communication
  solution->localize (*current_local_solution, send_list); 
}

void System::update_global_solution	(	std::vector< Number > &	global_soln,
		const unsigned int	dest_proc
	)			const

Fill the input vector global_soln so that it contains the global solution on processor dest_proc. Requires communication with all other processors.

Definition at line 539 of file system.C.

References solution.

{
  global_soln.resize        (solution->size());

  solution->localize_to_one (global_soln, dest_proc);
}

void System::update_global_solution

(

std::vector< Number > &

global_soln

)

const

Fill the input vector global_soln so that it contains the global solution on all processors. Requires communication with all other processors.

Definition at line 530 of file system.C.

References solution.

Referenced by ExactSolution::_compute_error(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), and ExactErrorEstimator::estimate_error().

{
  global_soln.resize (solution->size());

  solution->localize (global_soln);
}

void System::user_assembly

(

)

[virtual]

Calls user's attached assembly function, or is overloaded by the user in derived classes.

Definition at line 1367 of file system.C.

References _assemble_system, _equation_systems, and name().

Referenced by assemble().

{
  // Call the user-provided assembly function,
  // if it was provided
  if (_assemble_system != NULL)
    this->_assemble_system (_equation_systems, this->name());
}

void System::user_constrain

(

)

[virtual]

Calls user's attached constraint function, or is overloaded by the user in derived classes.

Definition at line 1377 of file system.C.

References _constrain_system, _equation_systems, and name().

Referenced by init_data(), and EquationSystems::reinit().

{
  // Call the user-provided constraint function, 
  // if it was provided
  if(_constrain_system!= NULL)
    this->_constrain_system(_equation_systems, this->name());
}

void System::user_initialization

(

)

[virtual]

Calls user's attached initialization function, or is overloaded by the user in derived classes.

Definition at line 1358 of file system.C.

References _equation_systems, _init_system, and name().

Referenced by init(), and NewmarkSystem::initial_conditions().

{
  // Call the user-provided intialization function,
  // if it was provided
  if (_init_system != NULL)
    this->_init_system (_equation_systems, this->name());
}

void System::user_QOI

(

const QoISet &

qoi_indices

)

[virtual]

Calls user's attached quantity of interest function, or is overloaded by the user in derived classes.

Definition at line 1387 of file system.C.

References _equation_systems, _qoi_evaluate, and name().

Referenced by assemble_qoi().

{
  // Call the user-provided quantity of interest function, 
  // if it was provided
  if(_qoi_evaluate != NULL)
    this->_qoi_evaluate(_equation_systems, this->name(), qoi_indices);
}

void System::user_QOI_derivative

(

const QoISet &

qoi_indices

)

[virtual]

Calls user's attached quantity of interest derivative function, or is overloaded by the user in derived classes.

Definition at line 1397 of file system.C.

References _equation_systems, _qoi_evaluate_derivative, and name().

Referenced by assemble_qoi_derivative().

{
  // Call the user-provided quantity of interest derivative, 
  // if it was provided
  if(_qoi_evaluate_derivative != NULL)
    this->_qoi_evaluate_derivative(_equation_systems, this->name(), qoi_indices);
}

const System::Variable & System::variable

(

unsigned int

var

)

const [inline]

Return a constant reference to Variable var.

Definition at line 1398 of file system.h.

References _variables.

Referenced by EquationSystems::build_solution_vector(), and project_vector().

{
  libmesh_assert (i < _variables.size());

  return _variables[i];
}

const std::string & System::variable_name

(

const unsigned int

i

)

const [inline]

Returns:

the name of variable i.

Definition at line 1408 of file system.h.

References _variables.

Referenced by add_variable(), KellyErrorEstimator::boundary_side_integration(), DiscontinuityMeasure::boundary_side_integration(), ExactErrorEstimator::estimate_error(), ExactSolution::ExactSolution(), get_info(), System::ProjectVector::operator()(), project_vector(), VTKIO::solution_to_vtk(), and write_header().

{
  libmesh_assert (i < _variables.size());

  return _variables[i].name();
}

unsigned short int System::variable_number

(

const std::string &

var

)

const

Returns:

the variable number assoicated with the user-specified variable named var.

Definition at line 942 of file system.C.

References _variable_numbers, and _variables.

Referenced by ExactSolution::_compute_error(), GMVIO::copy_nodal_solution(), ExactErrorEstimator::estimate_error(), ExactErrorEstimator::find_squared_element_error(), variable_type(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().

{
  // Make sure the variable exists
  std::map<std::string, unsigned short int>::const_iterator
    pos = _variable_numbers.find(var);
  
  if (pos == _variable_numbers.end())
    {
      std::cerr << "ERROR: variable "
                << var
                << " does not exist in this system!"
                << std::endl;      
      libmesh_error();
    }
  libmesh_assert (_variables[pos->second].name() == var);

  return pos->second;
}

const FEType & System::variable_type

(

const std::string &

var

)

const [inline]

Returns:

the finite element type for variable var.

Definition at line 1428 of file system.h.

References _variables, and variable_number().

{
  return _variables[this->variable_number(var)].type();
}

const FEType & System::variable_type

(

const unsigned int

i

)

const [inline]

Returns:

the finite element type variable number i.

Definition at line 1418 of file system.h.

References _variables.

Referenced by add_variable(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), GMVIO::copy_nodal_solution(), FEMContext::FEMContext(), write_header(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().

{
  libmesh_assert (i < _variables.size());
  
  return _variables[i].type();
}

const std::string & System::vector_name

(

const unsigned int

vec_num

)

Returns:

the name of this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 698 of file system.C.

References vectors_begin(), and vectors_end().

{
  const_vectors_iterator v = vectors_begin();
  const_vectors_iterator v_end = vectors_end();
  unsigned int num = 0;
  while((num<vec_num) && (v!=v_end))
    {
      num++;
      ++v;
    }
  libmesh_assert(v!=v_end);
  return v->first;
}

System::const_vectors_iterator System::vectors_begin

(

)

const [inline]

Beginning of vectors container

Definition at line 1464 of file system.h.

References _vectors.

{
  return _vectors.begin();
}

System::vectors_iterator System::vectors_begin

(

)

[inline]

Beginning of vectors container

Definition at line 1458 of file system.h.

References _vectors.

Referenced by get_vector(), request_vector(), VTKIO::system_vectors_to_vtk(), and vector_name().

{
  return _vectors.begin();
}

System::const_vectors_iterator System::vectors_end

(

)

const [inline]

End of vectors container

Definition at line 1476 of file system.h.

References _vectors.

{
  return _vectors.end();
}

System::vectors_iterator System::vectors_end

(

)

[inline]

End of vectors container

Definition at line 1470 of file system.h.

References _vectors.

Referenced by get_vector(), request_vector(), VTKIO::system_vectors_to_vtk(), and vector_name().

{
  return _vectors.end();
}

virtual std::pair<unsigned int, Real> System::weighted_sensitivity_adjoint_solve	(	const ParameterVector &	parameters,
		const ParameterVector &	weights,
		const QoISet &	qoi_indices = QoISet()
	)			[inline, virtual]

Assembles & solves the linear system(s) (dR/du)^T*z_w = sum(w_p*(d^2q/dudp - d^2R/dudp*z)), for those parameters p contained within parameters, weighted by the values w_p found within weights.

Assumes that adjoint_solve has already calculated z for each qoi in qoi_indices.

Returns a pair with the total number of linear iterations performed and the (sum of the) final residual norms

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 223 of file system.h.

      { libmesh_not_implemented(); }

virtual std::pair<unsigned int, Real> System::weighted_sensitivity_solve	(	const ParameterVector &	parameters,
		const ParameterVector &	weights
	)			[inline, virtual]

Assembles & solves the linear system(s) (dR/du)*u_w = sum(w_p*-dR/dp), for those parameters p contained within parameters weighted by the values w_p found within weights.

Returns a pair with the total number of linear iterations performed and the (sum of the) final residual norms

This method is only implemented in some derived classes.

Reimplemented in ImplicitSystem.

Definition at line 190 of file system.h.

      { libmesh_not_implemented(); }

void System::write_header	(	Xdr &	io,
		const std::string &	version,
		const bool	write_additional_data
	)			const

Writes the basic data header for this System.

This method implements the output of a System object, embedded in the output of an EquationSystems<T_sys>. This warrants some documentation. The output of this part consists of 5 sections:

for this system

5.) The number of variables in the system (unsigned int)

for each variable in the system

6.) The name of the variable (string)

7.) Combined in an FEType:

• The approximation order(s) of the variable (Order Enum, cast to int/s)
• The finite element family/ies of the variable (FEFamily Enum, cast to int/s)

end variable loop

8.) The number of additional vectors (unsigned int),

for each additional vector in the system object

9.) the name of the additional vector (string)

end system

Definition at line 815 of file system_io.C.

References _vectors, Xdr::data(), FEType::family, get_mesh(), FEType::inf_map, n_vars(), n_vectors(), name(), FEType::order, MeshBase::processor_id(), FEType::radial_family, FEType::radial_order, type, variable_name(), variable_type(), and Xdr::writing().

{
  libmesh_assert (io.writing());


  // Only write the header information
  // if we are processor 0.
  if (this->get_mesh().processor_id() != 0)
    return;
  
  std::string comment;
  char buf[80];

  // 5.) 
  // Write the number of variables in the system

  {
    // set up the comment
    comment = "# No. of Variables in System \"";
    comment += this->name();
    comment += "\"";    
          
    unsigned int n_vars = this->n_vars();   
    io.data (n_vars, comment.c_str());
  }


  for (unsigned int var=0; var<this->n_vars(); var++)
    {
      // 6.)
      // Write the name of the var-th variable
      {
        // set up the comment
        comment  = "#   Name, Variable No. ";
        std::sprintf(buf, "%d", var);
        comment += buf;
        comment += ", System \"";
        comment += this->name();
        comment += "\"";
              
        std::string var_name = this->variable_name(var);             
        io.data (var_name, comment.c_str());
      }
      
      // 7.)
      // Write the approximation order of the var-th variable 
      // in this system
      {
        // set up the comment
        comment = "#     Approximation Order, Variable \"";
        std::sprintf(buf, "%s", this->variable_name(var).c_str());
        comment += buf;
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";
              
        int order = static_cast<int>(this->variable_type(var).order);         
        io.data (order, comment.c_str());
      }


#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
      
      // do the same for radial_order
      {
        comment = "#     Radial Approximation Order, Variable \"";
        std::sprintf(buf, "%s", this->variable_name(var).c_str());
        comment += buf;
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";
      
        int rad_order = static_cast<int>(this->variable_type(var).radial_order);              
        io.data (rad_order, comment.c_str());
      }

#endif
      
      // Write the Finite Element type of the var-th variable 
      // in this System
      {
        // set up the comment
        comment = "#     FE Family, Variable \"";
        std::sprintf(buf, "%s", this->variable_name(var).c_str());
        comment += buf;
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";
      
        const FEType& type = this->variable_type(var);        
        int fam = static_cast<int>(type.family);              
        io.data (fam, comment.c_str());

#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
        
        comment = "#     Radial FE Family, Variable \"";
        std::sprintf(buf, "%s", this->variable_name(var).c_str());
        comment += buf;
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";
      
        int radial_fam = static_cast<int>(type.radial_family);
        io.data (radial_fam, comment.c_str());  
        
        comment = "#     Infinite Mapping Type, Variable \"";
        std::sprintf(buf, "%s", this->variable_name(var).c_str());
        comment += buf;
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        int i_map = static_cast<int>(type.inf_map);           
        io.data (i_map, comment.c_str());
#endif
      }
    } // end of the variable loop
 
  // 8.) 
  // Write the number of additional vectors in the System.
  // If write_additional_data==false, then write zero for
  // the number of additional vectors.
  {       
    {
      // set up the comment
      comment = "# No. of Additional Vectors, System \"";
      comment += this->name();
      comment += "\"";
    
      unsigned int n_vectors = write_additional_data ? this->n_vectors () : 0;
      io.data (n_vectors, comment.c_str());
    }  
      
    if (write_additional_data)
      {
        std::map<std::string, NumericVector<Number>* >::const_iterator
          vec_pos = this->_vectors.begin();
        unsigned int cnt=0;
        
        for (; vec_pos != this->_vectors.end(); ++vec_pos)
          {
            // 9.)
            // write the name of the cnt-th additional vector
            comment =  "# Name of ";
            std::sprintf(buf, "%d", cnt++);
            comment += buf;
            comment += "th vector";
            std::string vec_name = vec_pos->first;
            
            io.data (vec_name, comment.c_str());
          }
      }
  }
}

void System::write_parallel_data	(	Xdr &	io,
		const bool	write_additional_data
	)			const

Writes additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh. This method will create an individual file for each processor in the simulation where the local solution components for that processor will be stored.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

Definition at line 1213 of file system_io.C.

References _vectors, Xdr::data(), get_mesh(), DofObject::invalid_id, n_vars(), name(), number(), solution, and Xdr::writing().

{
  std::string comment;
  
  libmesh_assert (io.writing());

  std::vector<Number> io_buffer; io_buffer.reserve(this->solution->local_size());

  // build the ordered nodes and element maps.
  // when writing/reading parallel files we need to iterate
  // over our nodes/elements in order of increasing global id().
  // however, this is not guaranteed to be ordering we obtain
  // by using the node_iterators/element_iterators directly.
  // so build a set, sorted by id(), that provides the ordering.
  // further, for memory economy build the set but then transfer
  // its contents to vectors, which will be sorted.
  std::vector<const DofObject*> ordered_nodes, ordered_elements;
  {    
    std::set<const DofObject*, CompareDofObjectsByID>
      ordered_nodes_set (this->get_mesh().local_nodes_begin(),
                         this->get_mesh().local_nodes_end());
      
      ordered_nodes.insert(ordered_nodes.end(),
                           ordered_nodes_set.begin(),
                           ordered_nodes_set.end());
  }
  {
    std::set<const DofObject*, CompareDofObjectsByID>
      ordered_elements_set (this->get_mesh().local_elements_begin(),
                            this->get_mesh().local_elements_end());
      
      ordered_elements.insert(ordered_elements.end(),
                              ordered_elements_set.begin(),
                              ordered_elements_set.end());
  }
  
  const unsigned int sys_num = this->number();
  const unsigned int n_vars  = this->n_vars();
  
  // Loop over each variable and each node, and write out the value.
  for (unsigned int var=0; var<n_vars; var++)
    {
      // First write the node DOF values
      for (std::vector<const DofObject*>::const_iterator
             it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)      
        for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
          {
            //std::cout << "(*it)->id()=" << (*it)->id() << std::endl;
            libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                    DofObject::invalid_id);
            
            io_buffer.push_back((*this->solution)((*it)->dof_number(sys_num, var, comp)));
          }

      // Then write the element DOF values
      for (std::vector<const DofObject*>::const_iterator
             it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
        for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
          {
            libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
                    DofObject::invalid_id);
              
            io_buffer.push_back((*this->solution)((*it)->dof_number(sys_num, var, comp)));    
          }
    }