EquationSystems Class Reference

#include <equation_systems.h>

Inheritance diagram for EquationSystems:

[legend]

List of all members.

Public Types
enum	ReadFlags {   READ_HEADER = 1, READ_DATA = 2, READ_ADDITIONAL_DATA = 4, READ_LEGACY_FORMAT = 8,   TRY_READ_IFEMS = 16 }
enum	WriteFlags { WRITE_DATA = 1, WRITE_ADDITIONAL_DATA = 2, WRITE_PARALLEL_FILES = 4 }
Public Member Functions
	EquationSystems (MeshBase &mesh, MeshData *mesh_data=NULL)
virtual	~EquationSystems ()
virtual void	clear ()
virtual void	init ()
virtual void	reinit ()
void	update ()
unsigned int	n_systems () const
bool	has_system (const std::string &name) const
template<typename T_sys >
const T_sys &	get_system (const std::string &name) const
template<typename T_sys >
T_sys &	get_system (const std::string &name)
template<typename T_sys >
const T_sys &	get_system (const unsigned int num) const
template<typename T_sys >
T_sys &	get_system (const unsigned int num)
const System &	get_system (const std::string &name) const
System &	get_system (const std::string &name)
const System &	get_system (const unsigned int num) const
System &	get_system (const unsigned int num)
virtual System &	add_system (const std::string &system_type, const std::string &name)
template<typename T_sys >
T_sys &	add_system (const std::string &name)
void	delete_system (const std::string &name)
unsigned int	n_vars () const
unsigned int	n_dofs () const
unsigned int	n_active_dofs () const
virtual void	solve ()
virtual void	adjoint_solve (const QoISet &qoi_indices=QoISet())
virtual void	sensitivity_solve (const ParameterVector &parameters)
void	build_variable_names (std::vector< std::string > &var_names) const
void	build_solution_vector (std::vector< Number > &soln, const std::string &system_name, const std::string &variable_name="all_vars") const
void	build_solution_vector (std::vector< Number > &soln) const
void	build_discontinuous_solution_vector (std::vector< Number > &soln) const
void	read (const std::string &name, const libMeshEnums::XdrMODE, const unsigned int read_flags=(READ_HEADER|READ_DATA))
void	read (const std::string &name, const unsigned int read_flags=(READ_HEADER|READ_DATA))
void	write (const std::string &name, const libMeshEnums::XdrMODE, const unsigned int write_flags=(WRITE_DATA)) const
void	write (const std::string &name, const unsigned int write_flags=(WRITE_DATA)) const
virtual bool	compare (const EquationSystems &other_es, const Real threshold, const bool verbose) const
virtual std::string	get_info () const
void	print_info (std::ostream &os=libMesh::out) const
const MeshBase &	get_mesh () const
MeshBase &	get_mesh ()
bool	has_mesh_data () const
const MeshData &	get_mesh_data () const
MeshData &	get_mesh_data ()
void	allgather ()
Static Public Member Functions
static std::string	get_info ()
static void	print_info (std::ostream &out=std::cout)
static unsigned int	n_objects ()
Public Attributes
Parameters	parameters
Protected Types
typedef std::map< std::string, System * >::iterator	system_iterator
typedef std::map< std::string, System * >::const_iterator	const_system_iterator
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
Protected Member Functions
void	increment_constructor_count (const std::string &name)
void	increment_destructor_count (const std::string &name)
Protected Attributes
MeshBase &	_mesh
MeshData *	_mesh_data
std::map< std::string, System * >	_systems
Static Protected Attributes
static Counts	_counts
static Threads::atomic < unsigned int >	_n_objects
static Threads::spin_mutex	_mutex
Private Member Functions
void	_read_impl (const std::string &name, const libMeshEnums::XdrMODE, const unsigned int read_flags)
void	_add_system_to_nodes_and_elems ()
Friends
std::ostream &	operator<< (std::ostream &os, const EquationSystems &es)

---

Detailed Description

This is the EquationSystems class. It is in charge of handling all the various equation systems defined for a MeshBase. It may have multiple systems, which may be active or inactive, so that at different solution stages only a sub-set may be solved for. Also, through the templated access, different types of systems may be handled. Also other features, like flags, parameters, I/O etc are provided.

Author:

Benjamin S. Kirk, 2002-2007

Definition at line 65 of file equation_systems.h.

---

Member Typedef Documentation

typedef std::map<std::string, System*>::const_iterator EquationSystems::const_system_iterator [protected]

Typedef for constatnt system iterators

Definition at line 419 of file equation_systems.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 106 of file reference_counter.h.

typedef std::map<std::string, System*>::iterator EquationSystems::system_iterator [protected]

Typedef for system iterators

Definition at line 414 of file equation_systems.h.

---

Member Enumeration Documentation

enum EquationSystems::ReadFlags

Define enumeration to set properties in EquationSystems::read()

Enumerator:

READ_HEADER
READ_DATA
READ_ADDITIONAL_DATA
READ_LEGACY_FORMAT
TRY_READ_IFEMS

Definition at line 72 of file equation_systems.h.

                 { READ_HEADER           = 1,
                   READ_DATA             = 2,
                   READ_ADDITIONAL_DATA  = 4,
                   READ_LEGACY_FORMAT    = 8,
                   TRY_READ_IFEMS        = 16 };

enum EquationSystems::WriteFlags

Define enumeration to set properties in EquationSystems::write()

Enumerator:

WRITE_DATA
WRITE_ADDITIONAL_DATA
WRITE_PARALLEL_FILES

Definition at line 81 of file equation_systems.h.

                  { WRITE_DATA             = 1,
                    WRITE_ADDITIONAL_DATA  = 2,
                    WRITE_PARALLEL_FILES   = 4 };

---

Constructor & Destructor Documentation

EquationSystems::EquationSystems	(	MeshBase &	mesh,
		MeshData *	mesh_data = NULL
	)

Constructor.

Definition at line 50 of file equation_systems.C.

References parameters, and Parameters::set().

00051                                                                   :
00052   _mesh      (m),
00053   _mesh_data (mesh_data)
00054 {
00055   // Set default parameters
00056   this->parameters.set<Real>        ("linear solver tolerance") = TOLERANCE * TOLERANCE;
00057   this->parameters.set<unsigned int>("linear solver maximum iterations") = 5000;  
}

EquationSystems::~EquationSystems

(

)

[virtual]

Destructor. Should be virtual, since the user may want to derive subclasses of EquationSystems.

Definition at line 61 of file equation_systems.C.

References clear().

{
  this->clear ();
}

---

Member Function Documentation

void EquationSystems::_add_system_to_nodes_and_elems

(

)

[private]

This function is used in the implementation of add_system, it loops over the nodes and elements of the Mesh, adding the system to each one. The main reason to separate this part is to avoid coupling this header file to mesh.h, and elem.h.

Definition at line 921 of file equation_systems.C.

References _mesh, MeshBase::elements_begin(), MeshBase::elements_end(), MeshBase::nodes_begin(), and MeshBase::nodes_end().

Referenced by add_system().

{
  // All the nodes
  MeshBase::node_iterator       node_it  = _mesh.nodes_begin();
  const MeshBase::node_iterator node_end = _mesh.nodes_end();
 
  for ( ; node_it != node_end; ++node_it)
    (*node_it)->add_system();
 
  // All the elements
  MeshBase::element_iterator       elem_it  = _mesh.elements_begin();
  const MeshBase::element_iterator elem_end = _mesh.elements_end();
 
  for ( ; elem_it != elem_end; ++elem_it)
    (*elem_it)->add_system();
}

void EquationSystems::_read_impl	(	const std::string &	name,
		const libMeshEnums::XdrMODE	mode,
		const unsigned int	read_flags
	)			[private]

Actual read implementation. This can be called repeatedly inside a try-catch block in an attempt to read broken files.

This program implements the output of an EquationSystems object. This warrants some documentation. The output file essentially consists of 11 sections:

     1.) A version header (for non-'legacy' formats, libMesh-0.7.0 and greater). 
     2.) The number of individual equation systems (unsigned int)
     
       for each system
                                                          
        3.)  The name of the system (string)
        4.)  The type of the system (string)
    
        handled through System::read():
    
     +-------------------------------------------------------------+
     |  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 equation system object |
     |                                                             |
     |    9.) the name of the additional vector  (string)          |
     +-------------------------------------------------------------+
    
     end system loop
    
    
       for each system, handled through System::read_{serialized,parallel}_data():
       
     +--------------------------------------------------------------+
     | 10.) The global solution vector, re-ordered to be node-major |
     |     (More on this later.)                                    |
     |                                                              |
     |    for each additional vector in the equation system object  |
     |                                                              |
     |    11.) The global additional vector, re-ordered to be       |
     |         node-major (More on this later.)                     |
     +--------------------------------------------------------------+
    
     end system loop
   

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 134 of file equation_systems_io.C.

References _mesh, _systems, add_system(), Parallel::broadcast(), Xdr::close(), Xdr::data(), libMesh::err, MeshTools::Private::fix_broken_node_and_element_numbering(), get_mesh(), get_system(), MeshTools::Private::globally_renumber_nodes_and_elements(), init(), libMesh::processor_id(), read(), READ_ADDITIONAL_DATA, READ_DATA, System::read_header(), READ_HEADER, READ_LEGACY_FORMAT, Xdr::reading(), TRY_READ_IFEMS, and update().

Referenced by read().

{
   // Set booleans from the read_flags argument
   const bool read_header          = read_flags & EquationSystems::READ_HEADER;
   const bool read_data            = read_flags & EquationSystems::READ_DATA;
   const bool read_additional_data = read_flags & EquationSystems::READ_ADDITIONAL_DATA;
   const bool read_legacy_format   = read_flags & EquationSystems::READ_LEGACY_FORMAT;
   const bool try_read_ifems       = read_flags & EquationSystems::TRY_READ_IFEMS;
         bool read_parallel_files  = false;
         
  // This will unzip a file with .bz2 as the extension, otherwise it
  // simply returns the name if the file need not be unzipped.
  Xdr io ((libMesh::processor_id() == 0) ? name : "", mode);
  libmesh_assert (io.reading());
          
  {
    // 1.)
    // Read the version header.
    std::string version = "legacy";
    if (!read_legacy_format)
      {
        if (libMesh::processor_id() == 0) io.data(version);     
        Parallel::broadcast(version);
        
        // All processors have the version header, if it does not contain
        // "libMesh" something then it is a legacy file.
        if (!(version.find("libMesh") < version.size()))
          {
            io.close();
            
            // Recursively call this read() function but with the 
            // EquationSystems::READ_LEGACY_FORMAT bit set.
            this->read (name, mode, (read_flags | EquationSystems::READ_LEGACY_FORMAT));
            return;
          }

        read_parallel_files = (version.rfind(" parallel") < version.size());

        // If requested that we try to read infinite element information,
        // and the string " with infinite elements" is not in the version,
        // then tack it on.  This is for compatibility reading ifem
        // files written prior to 11/10/2008 - BSK
        if (try_read_ifems)
          if (!(version.rfind(" with infinite elements") < version.size()))
            version += " with infinite elements";
        
      }
    else
      libmesh_deprecated();

  START_LOG("read()","EquationSystems");
      
    // 2.)  
    // Read the number of equation systems
    unsigned int n_sys=0;
    if (libMesh::processor_id() == 0) io.data (n_sys);
    Parallel::broadcast(n_sys);

    for (unsigned int sys=0; sys<n_sys; sys++)
      {
        // 3.)
        // Read the name of the sys-th equation system
        std::string sys_name;      
        if (libMesh::processor_id() == 0) io.data (sys_name);
        Parallel::broadcast(sys_name);
        
        // 4.)
        // Read the type of the sys-th equation system
        std::string sys_type;   
        if (libMesh::processor_id() == 0) io.data (sys_type);
        Parallel::broadcast(sys_type);
        
        if (read_header)
          this->add_system (sys_type, sys_name);

        // 5.) - 9.)
        // Let System::read_header() do the job
        System& new_system = this->get_system(sys_name);          
        new_system.read_header (io,
                                version,
                                read_header,
                                read_additional_data,
                                read_legacy_format);
      }
  }
      


  // Now we are ready to initialize the underlying data
  // structures. This will initialize the vectors for 
  // storage, the dof_map, etc...
  if (read_header) 
    this->init();

  // 10.) & 11.)
  // Read and set the numeric vector values
  if (read_data)
    {
      // the EquationSystems::read() method should look constant from the mesh
      // perspective, but we need to assign a temporary numbering to the nodes
      // and elements in the mesh, which requires that we abuse const_cast
      if (!read_legacy_format)
        {
          MeshBase &mesh = const_cast<MeshBase&>(this->get_mesh());
          MeshTools::Private::globally_renumber_nodes_and_elements(mesh);
        }

      Xdr local_io (read_parallel_files ? local_file_name(name) : "", mode);
   
      std::map<std::string, System*>::iterator
        pos = _systems.begin();
      
      for (; pos != _systems.end(); ++pos)
        if (read_legacy_format)
          {
            libmesh_deprecated();
            pos->second->read_legacy_data (io, read_additional_data);
          }
        else
          if (read_parallel_files)
            pos->second->read_parallel_data   (local_io, read_additional_data);
          else
            pos->second->read_serialized_data (io, read_additional_data);

      
      // Undo the temporary numbering.
      if (!read_legacy_format)
        {
          if (dynamic_cast<ParallelMesh*>(const_cast<MeshBase*>(&_mesh)))
            {
              ParallelMesh *mesh = dynamic_cast<ParallelMesh*>(const_cast<MeshBase*>(&_mesh));    
              MeshTools::Private::fix_broken_node_and_element_numbering(*mesh);
            }
          else if (dynamic_cast<SerialMesh*>(const_cast<MeshBase*>(&_mesh)))
            {
              SerialMesh *mesh = dynamic_cast<SerialMesh*>(const_cast<MeshBase*>(&_mesh));    
              MeshTools::Private::fix_broken_node_and_element_numbering(*mesh);
            }
          else
            {
              libMesh::err << "ERROR:  dynamic_cast<> to ParallelMesh and SerialMesh failed!"
                            << std::endl;
              libmesh_error();
            }     
        }
    }  

  STOP_LOG("read()","EquationSystems");
  
  // Localize each system's data
  this->update();
}

template<typename T_sys >

T_sys & EquationSystems::add_system

(

const std::string &

name

)

[inline]

Add the system named name to the systems array.

Definition at line 492 of file equation_systems.h.

References _add_system_to_nodes_and_elems(), _systems, and n_systems().

{
  T_sys* ptr = NULL;
  
  if (!_systems.count(name))
    {
      ptr = new T_sys(*this, name, this->n_systems());

      _systems.insert (std::make_pair(name, ptr));   

      // Tell all the \p DofObject entities to add a system.
      this->_add_system_to_nodes_and_elems();
    }
  else
    {
      // We now allow redundant add_system calls, to make it
      // easier to load data from files for user-derived system
      // subclasses
//      libMesh::err << "ERROR: There was already a system"
//              << " named " << name
//              << std::endl;

//      libmesh_error();

      ptr = &(this->get_system<T_sys>(name));
    }

  // Return a dynamically casted reference to the newly added System.
  return *ptr;
}

System & EquationSystems::add_system	(	const std::string &	system_type,
		const std::string &	name
	)			[virtual]

Add the system of type system_type named name to the systems array.

Definition at line 304 of file equation_systems.C.

References _systems, libMesh::err, and get_system().

Referenced by _read_impl(), and ErrorVector::plot_error().

{
  // If the user already built a system with this name, we'll
  // trust them and we'll use it.  That way they can pre-add
  // non-standard derived system classes, and if their restart file
  // has some non-standard sys_type we won't throw an error.
  if (_systems.count(name))
    {
      return this->get_system(name);
    }
  // Build a Newmark system
  else if (sys_type == "Newmark")
    this->add_system<NewmarkSystem> (name);

  // Build an Explicit system
  else if ((sys_type == "Explicit"))
    this->add_system<ExplicitSystem> (name);

  // Build an Implicit system
  else if ((sys_type == "Implicit") ||
           (sys_type == "Steady"  ))
    this->add_system<ImplicitSystem> (name);

  // build a transient implicit linear system
  else if ((sys_type == "Transient") ||
           (sys_type == "TransientImplicit") ||
           (sys_type == "TransientLinearImplicit"))
    this->add_system<TransientLinearImplicitSystem> (name);

  // build a transient implicit nonlinear system
  else if (sys_type == "TransientNonlinearImplicit")
    this->add_system<TransientNonlinearImplicitSystem> (name);

  // build a transient explicit system
  else if (sys_type == "TransientExplicit")
    this->add_system<TransientExplicitSystem> (name);

  // build a linear implicit system
  else if (sys_type == "LinearImplicit")
    this->add_system<LinearImplicitSystem> (name);

  // build a nonlinear implicit system
  else if (sys_type == "NonlinearImplicit")
    this->add_system<NonlinearImplicitSystem> (name);

#if defined(LIBMESH_USE_COMPLEX_NUMBERS)
  // build a frequency system
  else if (sys_type == "Frequency")
    this->add_system<FrequencySystem> (name);
#endif

  else
    {
      libMesh::err << "ERROR: Unknown system type: "
                    << sys_type
                    << std::endl;
      libmesh_error();
    }

  // Return a reference to the new system
  //return (*this)(name);
  return this->get_system(name);
}

void EquationSystems::adjoint_solve

(

const QoISet &

qoi_indices = QoISet()

)

[virtual]

Call adjoint_solve on all the individual equation systems.

By default this function solves each system's adjoint once, in the reverse order from that in which they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.

Definition at line 413 of file equation_systems.C.

References get_system(), and n_systems().

Referenced by AdjointRefinementEstimator::estimate_error().

{
  libmesh_assert (this->n_systems());

  for (unsigned int i=this->n_systems(); i != 0; --i)
    this->get_system(i-1).adjoint_solve(qoi_indices);
}

void EquationSystems::allgather

(

)

Serializes a distributed mesh and its associated degree of freedom numbering for all systems

Definition at line 254 of file equation_systems.C.

References _mesh, MeshBase::allgather(), MeshBase::elements_begin(), MeshBase::elements_end(), get_system(), MeshBase::is_serial(), n_systems(), MeshBase::nodes_begin(), and MeshBase::nodes_end().

{
  // A serial mesh means nothing needs to be done
  if (_mesh.is_serial())
    return;

  const unsigned int n_sys = this->n_systems();

  libmesh_assert (n_sys != 0);

  // Gather the mesh
  _mesh.allgather();
  
  // Tell all the \p DofObject entities how many systems
  // there are.
  {
    MeshBase::node_iterator       node_it  = _mesh.nodes_begin();
    const MeshBase::node_iterator node_end = _mesh.nodes_end();

    for ( ; node_it != node_end; ++node_it)
      (*node_it)->set_n_systems(n_sys);
    
    MeshBase::element_iterator       elem_it  = _mesh.elements_begin();
    const MeshBase::element_iterator elem_end = _mesh.elements_end();
    
    for ( ; elem_it != elem_end; ++elem_it)
      (*elem_it)->set_n_systems(n_sys);
  }

  // And distribute each system's dofs
  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).get_dof_map().distribute_dofs(_mesh);
}

void EquationSystems::build_discontinuous_solution_vector

(

std::vector< Number > &

soln

)

const

Fill the input vector soln with solution values. The entries will be in variable-major format (corresponding to the names from build_variable_names()).

Definition at line 664 of file equation_systems.C.

References _mesh, _systems, MeshBase::active_elements_begin(), MeshBase::active_elements_end(), DofMap::dof_indices(), System::get_dof_map(), Elem::infinite(), MeshBase::mesh_dimension(), Elem::n_nodes(), n_systems(), System::n_vars(), n_vars(), FEInterface::nodal_soln(), MeshBase::processor_id(), System::update_global_solution(), and System::variable_type().

Referenced by ExodusII_IO::write_discontinuous_exodusII(), and GMVIO::write_discontinuous_gmv().

{
  libmesh_assert (this->n_systems());

  const unsigned int dim = _mesh.mesh_dimension();
  const unsigned int nv  = this->n_vars();
  unsigned int tw=0;

  // get the total weight
  {
    MeshBase::element_iterator       it  = _mesh.active_elements_begin();
    const MeshBase::element_iterator end = _mesh.active_elements_end(); 

    for ( ; it != end; ++it)
      tw += (*it)->n_nodes();
  }
  

  // Only if we are on processor zero, allocate the storage
  // to hold (number_of_nodes)*(number_of_variables) entries.
  if (_mesh.processor_id() == 0)
    soln.resize(tw*nv);

  std::vector<Number> sys_soln; 

  
  unsigned int var_num=0;

  // For each system in this EquationSystems object,
  // update the global solution and if we are on processor 0,
  // loop over the elements and build the nodal solution
  // from the element solution.  Then insert this nodal solution
  // into the vector passed to build_solution_vector.
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    {  
      const System& system  = *(pos->second);
      const unsigned int nv_sys = system.n_vars();
      
      system.update_global_solution (sys_soln, 0);
      
      if (_mesh.processor_id() == 0)
        {
          std::vector<Number>       elem_soln;   // The finite element solution
          std::vector<Number>       nodal_soln;  // The FE solution interpolated to the nodes
          std::vector<unsigned int> dof_indices; // The DOF indices for the finite element 
              
          for (unsigned int var=0; var<nv_sys; var++)
            {
              const FEType& fe_type    = system.variable_type(var);

              MeshBase::element_iterator       it  = _mesh.active_elements_begin();
              const MeshBase::element_iterator end = _mesh.active_elements_end(); 

              unsigned int nn=0;
              
              for ( ; it != end; ++it)
                {
                  const Elem* elem = *it;
                  system.get_dof_map().dof_indices (elem, dof_indices, var);
                  
                  elem_soln.resize(dof_indices.size());
                  
                  for (unsigned int i=0; i<dof_indices.size(); i++)
                    elem_soln[i] = sys_soln[dof_indices[i]];
                  
                  FEInterface::nodal_soln (dim,
                                           fe_type,
                                           elem,
                                           elem_soln,
                                           nodal_soln);

#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
                  // infinite elements should be skipped...
                  if (!elem->infinite())
#endif
                    { 
                      libmesh_assert (nodal_soln.size() == elem->n_nodes());
                  
                      for (unsigned int n=0; n<elem->n_nodes(); n++)
                        {
                          soln[nv*(nn++) + (var + var_num)] +=
                            nodal_soln[n];
                        }
                    }
                }
            }    
        }

      var_num += nv_sys;
    }
}

void EquationSystems::build_solution_vector

(

std::vector< Number > &

soln

)

const

Fill the input vector soln with solution values. The entries will be in variable-major format (corresponding to the names from build_variable_names()).

Definition at line 528 of file equation_systems.C.

References _mesh, _systems, MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), System::Variable::active_on_subdomain(), DofMap::dof_indices(), System::get_dof_map(), System::Variable::implicitly_active(), Elem::infinite(), std::max(), MeshBase::max_node_id(), MeshBase::mesh_dimension(), Elem::n_nodes(), MeshBase::n_nodes(), n_systems(), System::n_vars(), n_vars(), FEInterface::nodal_soln(), Elem::node(), Parallel::sum(), System::update_global_solution(), System::variable(), System::variable_type(), and libMesh::zero.

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

  libmesh_assert (this->n_systems());

  const unsigned int dim = _mesh.mesh_dimension();
  const unsigned int nn  = _mesh.n_nodes();
  const unsigned int nv  = this->n_vars();
  const unsigned short int one = 1;

  // We'd better have a contiguous node numbering
  libmesh_assert (nn == _mesh.max_node_id());

  // allocate storage to hold
  // (number_of_nodes)*(number_of_variables) entries.
  soln.resize(nn*nv);
  
  // Zero out the soln vector
  std::fill (soln.begin(), soln.end(), libMesh::zero);

  std::vector<Number>  sys_soln;

  // (Note that we use an unsigned short int here even though an
  // unsigned char would be more that sufficient.  The MPI 1.1
  // standard does not require that MPI_SUM, MPI_PROD etc... be
  // implemented for char data types. 12/23/2003 - BSK)  
  std::vector<unsigned short int> node_conn(nn), repeat_count(nn);

  // Get the number of elements that share each node.  We will
  // compute the average value at each node.  This is particularly
  // useful for plotting discontinuous data.
  MeshBase::element_iterator       e_it  = _mesh.active_local_elements_begin();
  const MeshBase::element_iterator e_end = _mesh.active_local_elements_end(); 

  for ( ; e_it != e_end; ++e_it)
    for (unsigned int n=0; n<(*e_it)->n_nodes(); n++)
      node_conn[(*e_it)->node(n)]++;

  // Gather the distributed node_conn arrays in the case of
  // multiple processors.
  Parallel::sum(node_conn);

  unsigned int var_num=0;

  // For each system in this EquationSystems object,
  // update the global solution and if we are on processor 0,
  // loop over the elements and build the nodal solution
  // from the element solution.  Then insert this nodal solution
  // into the vector passed to build_solution_vector.
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();
  
  for (; pos != end; ++pos)
    {  
      const System& system  = *(pos->second);
      const unsigned int nv_sys = system.n_vars();
      
      system.update_global_solution (sys_soln);
      
      std::vector<Number>       elem_soln;   // The finite element solution
      std::vector<Number>       nodal_soln;  // The FE solution interpolated to the nodes
      std::vector<unsigned int> dof_indices; // The DOF indices for the finite element 
      
      for (unsigned int var=0; var<nv_sys; var++)
        {
          const FEType& fe_type                   = system.variable_type(var);
          const System::Variable &var_description = system.variable(var);
          const DofMap &dof_map                   = system.get_dof_map();

          std::fill (repeat_count.begin(), repeat_count.end(), 0);

          MeshBase::element_iterator       it  = _mesh.active_local_elements_begin();
          const MeshBase::element_iterator end = _mesh.active_local_elements_end(); 

          for ( ; it != end; ++it)
            if (var_description.active_on_subdomain((*it)->subdomain_id()))
              {
                const Elem* elem = *it;      

                dof_map.dof_indices (elem, dof_indices, var);
              
                elem_soln.resize(dof_indices.size());
              
                for (unsigned int i=0; i<dof_indices.size(); i++)
                  elem_soln[i] = sys_soln[dof_indices[i]];
                  
                FEInterface::nodal_soln (dim,
                                         fe_type,
                                         elem,
                                         elem_soln,
                                         nodal_soln);

#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
                // infinite elements should be skipped...
                if (!elem->infinite())
#endif
                  { 
                    libmesh_assert (nodal_soln.size() == elem->n_nodes());
                  
                    for (unsigned int n=0; n<elem->n_nodes(); n++)
                      {
                        repeat_count[elem->node(n)]++;
                        soln[nv*(elem->node(n)) + (var + var_num)] += nodal_soln[n];
                      }
                  }
              } // end loop over elements        

          // when a variable is active everywhere the repeat_count
          // and node_conn arrays should be identical, so let's
          // use that information to avoid unnecessary communication
          if (var_description.implicitly_active())
            repeat_count = node_conn;
            
          else
            Parallel::sum (repeat_count);

          for (unsigned int n=0; n<nn; n++)
            soln[nv*n + (var + var_num)] /= 
              static_cast<Real>(std::max (repeat_count[n], one));
          
      
        } // end loop on variables in this system
  
      var_num += nv_sys;
    } // end loop over systems

  // Now each processor has computed contriburions to the
  // soln vector.  Gather them all up.
  Parallel::sum(soln);
}

void EquationSystems::build_solution_vector	(	std::vector< Number > &	soln,
		const std::string &	system_name,
		const std::string &	variable_name = "all_vars"
	)			const

Fill the input vector soln with the solution values for the system named name. Note that the input vector soln will only be assembled on processor 0, so this method is only applicable to outputting plot files from processor 0.

Definition at line 441 of file equation_systems.C.

Referenced by MeshOutput< MT >::_build_variable_names_and_solution_vector().

{
  //TODO:[BSK] re-implement this from the method below
  libmesh_error();

//   // Get a reference to the named system
//   const System& system = this->get_system(system_name);

//   // Get the number associated with the variable_name we are passed
//   const unsigned short int variable_num = system.variable_number(variable_name);

//   // Get the dimension of the current mesh
//   const unsigned int dim = _mesh.mesh_dimension();

//   // If we're on processor 0, allocate enough memory to hold the solution.
//   // Since we're only looking at one variable, there will be one solution value
//   // for each node in the mesh.
//   if (_mesh.processor_id() == 0)
//     soln.resize(_mesh.n_nodes());

//   // Vector to hold the global solution from all processors
//   std::vector<Number> sys_soln;
  
//   // Update the global solution from all processors
//   system.update_global_solution (sys_soln, 0);
  
//   // Temporary vector to store the solution on an individual element.
//   std::vector<Number>       elem_soln;   

//   // The FE solution interpolated to the nodes
//   std::vector<Number>       nodal_soln;  

//   // The DOF indices for the element
//   std::vector<unsigned int> dof_indices; 

//   // Determine the finite/infinite element type used in this system 
//   const FEType& fe_type    = system.variable_type(variable_num);

//   // Define iterators to iterate over all the elements of the mesh
//   const_active_elem_iterator       it (_mesh.elements_begin());
//   const const_active_elem_iterator end(_mesh.elements_end());

//   // Loop over elements
//   for ( ; it != end; ++it)
//     {
//       // Convenient shortcut to the element pointer
//       const Elem* elem = *it;

//       // Fill the dof_indices vector for this variable
//       system.get_dof_map().dof_indices(elem,
//                                     dof_indices,
//                                     variable_num);

//       // Resize the element solution vector to fit the
//       // dof_indices for this element.
//       elem_soln.resize(dof_indices.size());

//       // Transfer the system solution to the element
//       // solution by mapping it through the dof_indices vector.
//       for (unsigned int i=0; i<dof_indices.size(); i++)
//      elem_soln[i] = sys_soln[dof_indices[i]];

//       // Using the FE interface, compute the nodal_soln
//       // for the current elemnt type given the elem_soln
//       FEInterface::nodal_soln (dim,
//                             fe_type,
//                             elem,
//                             elem_soln,
//                             nodal_soln);

//       // Sanity check -- make sure that there are the same number
//       // of entries in the nodal_soln as there are nodes in the
//       // element!
//       libmesh_assert (nodal_soln.size() == elem->n_nodes());

//       // Copy the nodal solution over into the correct place in
//       // the global soln vector which will be returned to the user.
//       for (unsigned int n=0; n<elem->n_nodes(); n++)
//      soln[elem->node(n)] = nodal_soln[n];
//     }
}

void EquationSystems::build_variable_names

(

std::vector< std::string > &

var_names

)

const

Fill the input vector var_names with the names of the variables for each system.

Definition at line 423 of file equation_systems.C.

References _systems, n_systems(), and n_vars().

Referenced by MeshOutput< MT >::_build_variable_names_and_solution_vector(), ExodusII_IO::write_discontinuous_exodusII(), and GMVIO::write_discontinuous_gmv().

{
  libmesh_assert (this->n_systems());
  
  var_names.resize (this->n_vars());

  unsigned int var_num=0;
  
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    for (unsigned int vn=0; vn<pos->second->n_vars(); vn++)
      var_names[var_num++] = pos->second->variable_name(vn);       
}

void EquationSystems::clear

(

)

[virtual]

Returns tha data structure to a pristine state.

Definition at line 68 of file equation_systems.C.

References _systems, Parameters::clear(), and parameters.

Referenced by ~EquationSystems().

{
  // Clear any additional parameters
  parameters.clear ();

  // clear the systems.  We must delete them
  // since we newed them!
  while (!_systems.empty())
    {
      system_iterator pos = _systems.begin();
      
      System *sys = pos->second;
      delete sys;
      sys = NULL;
      
      _systems.erase (pos);
    }
}

bool EquationSystems::compare	(	const EquationSystems &	other_es,
		const Real	threshold,
		const bool	verbose
	)			const [virtual]

Returns:

true when this equation system contains identical data, up to the given threshold. Delegates most of the comparisons to perform to the responsible systems

Definition at line 761 of file equation_systems.C.

References _systems, System::compare(), get_system(), n_systems(), and libMesh::out.

{
  // safety check, whether we handle at least the same number
  // of systems
  std::vector<bool> os_result;

  if (this->n_systems() != other_es.n_systems())
    {
      if (verbose)
        {
          libMesh::out << "  Fatal difference. This system handles " 
                        << this->n_systems() << " systems," << std::endl
                        << "  while the other system handles "
                        << other_es.n_systems() 
                        << " systems." << std::endl
                        << "  Aborting comparison." << std::endl;
        }
      return false;
    }
  else
    {
      // start comparing each system      
      const_system_iterator       pos = _systems.begin();
      const const_system_iterator end = _systems.end();

      for (; pos != end; ++pos)
        {
          const std::string& sys_name = pos->first;
          const System&  system        = *(pos->second);
      
          // get the other system
          const System& other_system   = other_es.get_system (sys_name);

          os_result.push_back (system.compare (other_system, threshold, verbose));

        }

    }
  

  // sum up the results
  if (os_result.size()==0)
    return true;
  else
    {
      bool os_identical;
      unsigned int n = 0;
          do
            {
              os_identical = os_result[n];
              n++;
            }
          while (os_identical && n<os_result.size());
          return os_identical;
        }
}

void EquationSystems::delete_system

(

const std::string &

name

)

Remove the system named name from the systems array. This function is now deprecated - write the libmesh-devel mailing list if you need it reimplemented.

Definition at line 374 of file equation_systems.C.

References _systems, and libMesh::err.

{
  libmesh_deprecated();

  if (!_systems.count(name))
    {
      libMesh::err << "ERROR: no system named "
                    << name  << std::endl;

      libmesh_error();
    }
  
  delete _systems[name];
  
  _systems.erase (name);
}

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, Quality::name(), and libMesh::out.

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 EquationSystems::get_info

(

)

const [virtual]

Returns:

a string containing information about the systems, flags, and parameters.

Definition at line 822 of file equation_systems.C.

References _systems, n_systems(), and libMesh::out.

Referenced by print_info().

{
  std::ostringstream out;
  
  out << " EquationSystems\n"
      << "  n_systems()=" << this->n_systems() << '\n';

  // Print the info for the individual systems
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    out << pos->second->get_info();

  
//   // Possibly print the parameters  
//   if (!this->parameters.empty())
//     {  
//       out << "  n_parameters()=" << this->n_parameters() << '\n';
//       out << "   Parameters:\n";
      
//       for (std::map<std::string, Real>::const_iterator
//           param = _parameters.begin(); param != _parameters.end();
//         ++param)
//      out << "    "
//          << "\""
//          << param->first
//          << "\""
//          << "="
//          << param->second
//          << '\n';
//     }
  
  return out.str();
}

MeshBase & EquationSystems::get_mesh

(

)

[inline]

Returns:

a reference to the mesh

Definition at line 453 of file equation_systems.h.

References _mesh.

{
  return _mesh;
}

const MeshBase & EquationSystems::get_mesh

(

)

const [inline]

Returns:

a constant reference to the mesh

Definition at line 445 of file equation_systems.h.

References _mesh.

Referenced by _read_impl(), AdjointRefinementEstimator::estimate_error(), MeshFunction::gradient(), MeshFunction::hessian(), MeshFunction::init(), MeshFunction::operator()(), reinit(), VTKIO::solution_to_vtk(), VTKIO::system_vectors_to_vtk(), write(), and VTKIO::write_equation_systems().

{
  return _mesh;
}

MeshData & EquationSystems::get_mesh_data

(

)

[inline]

Returns:

a reference to the mesh_data

Definition at line 468 of file equation_systems.h.

References _mesh_data.

{
  libmesh_assert (_mesh_data != NULL);
  return *_mesh_data;
}

const MeshData & EquationSystems::get_mesh_data

(

)

const [inline]

Returns:

a constant reference to the mesh_data

Definition at line 460 of file equation_systems.h.

References _mesh_data.

{
  libmesh_assert (_mesh_data != NULL);
  return *_mesh_data;
}

System& EquationSystems::get_system

(

const unsigned int

num

)

Returns:

a writeable referene to the system number num.

const System& EquationSystems::get_system

(

const unsigned int

num

)

const

Returns:

a constant reference to system number num.

System& EquationSystems::get_system

(

const std::string &

name

)

Returns:

a writeable referene to the system named name.

const System& EquationSystems::get_system

(

const std::string &

name

)

const

Returns:

a constant reference to the system named name.

template<typename T_sys >

System & EquationSystems::get_system

(

const unsigned int

num

)

[inline]

Returns:

a writeable referene to the system number num. The template argument defines the return type. For example, const SteadySystem& sys = eq.get_system<SteadySystem> (0); is an example of how the method might be used

Definition at line 578 of file equation_systems.h.

References _systems, libMesh::err, and n_systems().

{
  libmesh_assert (num < this->n_systems());
  
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    if (pos->second->number() == num)
      break;

  // Check for errors
  if (pos == end)
    {
      libMesh::err << "ERROR: no system number " << num << " found!"
                    << std::endl;
      libmesh_error();
    }

  // Attempt dynamic cast
  T_sys* ptr = dynamic_cast<T_sys*>(pos->second);

  // Check for failure of dynamic cast
  if (ptr == NULL)
    {
      LIBMESH_THROW(libMesh::DynamicCastFailure());
    }

  return *ptr; 
}

template<typename T_sys >

const System & EquationSystems::get_system

(

const unsigned int

num

)

const [inline]

Returns:

a constant reference to system number num. The template argument defines the return type. For example, const SteadySystem& sys = eq.get_system<SteadySystem> (0); is an example of how the method might be used

Definition at line 538 of file equation_systems.h.

References _systems, libMesh::err, and n_systems().

{
  libmesh_assert (num < this->n_systems());


  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    if (pos->second->number() == num)
      break;

  // Check for errors
  if (pos == end)
    {
      libMesh::err << "ERROR: no system number " << num << " found!"
                    << std::endl;
      libmesh_error();
    }

  // Attempt dynamic cast
  T_sys* ptr = dynamic_cast<T_sys*>(pos->second);

  // Check for failure of dynamic cast
  if (ptr == NULL)
    {
      libMesh::err << "ERROR: cannot convert system "
                    << num << " to requested type!"
                    << std::endl;
      libmesh_error();
    }
  
  return *ptr;
}

template<typename T_sys >

System & EquationSystems::get_system

(

const std::string &

name

)

[inline]

Returns:

a writeable referene to the system named name. The template argument defines the return type. For example, const SteadySystem& sys = eq.get_system<SteadySystem> ("sys"); is an example of how the method might be used

Definition at line 647 of file equation_systems.h.

References _systems, and libMesh::err.

{
  system_iterator pos = _systems.find(name);

  // Check for errors
  if (pos == _systems.end())
    {
      libMesh::err << "ERROR: no system named " << name << " found!"
                    << std::endl;
      libmesh_error();
    }

  // Attempt dynamic cast
  T_sys* ptr = dynamic_cast<T_sys*>(pos->second);

  // Check for failure of dynamic cast
  if (ptr == NULL)
    {
      std::cerr << "ERROR: cannot convert system \""
                << name << "\" to requested type!"
                << std::endl;
      libmesh_error();
    }

  return *ptr; 
}

template<typename T_sys >

const System & EquationSystems::get_system

(

const std::string &

name

)

const [inline]

Returns:

a constant reference to the system named name. The template argument defines the return type. For example, const SteadySystem& sys = eq.get_system<SteadySystem> ("sys"); is an example of how the method might be used

Definition at line 616 of file equation_systems.h.

References _systems, and libMesh::err.

Referenced by ExactSolution::_compute_error(), _read_impl(), EnsightIO::add_scalar(), add_system(), EnsightIO::add_vector(), adjoint_solve(), allgather(), compare(), GMVIO::copy_nodal_solution(), ErrorEstimator::estimate_errors(), ExactSolution::ExactSolution(), init(), reinit(), sensitivity_solve(), VTKIO::solution_to_vtk(), solve(), VTKIO::system_vectors_to_vtk(), update(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().

{
  const_system_iterator pos = _systems.find(name);

  // Check for errors
  if (pos == _systems.end())
    {
      libMesh::err << "ERROR: no system named \"" << name << "\" found!"
                    << std::endl;
      libmesh_error();
    }

  // Attempt dynamic cast
  T_sys* ptr = dynamic_cast<T_sys*>(pos->second);

  // Check for failure of dynamic cast
  if (ptr == NULL)
    {
      LIBMESH_THROW(libMesh::DynamicCastFailure());
    }

  return *ptr; 
}

bool EquationSystems::has_mesh_data

(

)

const [inline]

Returns:

true when the _mesh_data pointer is not NULL. This is needed because get_mesh_data will fail if it is NULL

Definition at line 475 of file equation_systems.h.

References _mesh_data.

{
  return (_mesh_data!=NULL);
}

bool EquationSystems::has_system

(

const std::string &

name

)

const [inline]

Returns:

true if the system named name exists within this EquationSystems object.

Definition at line 526 of file equation_systems.h.

References _systems.

Referenced by EnsightIO::add_scalar(), and EnsightIO::add_vector().

{
  if (_systems.find(name) == _systems.end())
    return false;
  return true;
}

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 150 of file reference_counter.h.

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

Referenced by ReferenceCountedObject< Value >::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 168 of file reference_counter.h.

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

Referenced by ReferenceCountedObject< Value >::~ReferenceCountedObject().

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

  p.second++;
}

void EquationSystems::init

(

)

[virtual]

Initialize all the systems

Definition at line 89 of file equation_systems.C.

References _mesh, MeshBase::delete_remote_elements(), MeshBase::elements_begin(), MeshBase::elements_end(), get_system(), libMesh::n_processors(), n_systems(), MeshBase::nodes_begin(), and MeshBase::nodes_end().

Referenced by _read_impl(), Solver::init(), and ErrorVector::plot_error().

{
  const unsigned int n_sys = this->n_systems();

  libmesh_assert (n_sys != 0);

  // Distribute the mesh if possible
  if (libMesh::n_processors() > 1)
    _mesh.delete_remote_elements();
  
  // Tell all the \p DofObject entities how many systems
  // there are.
  {
    MeshBase::node_iterator       node_it  = _mesh.nodes_begin();
    const MeshBase::node_iterator node_end = _mesh.nodes_end();

    for ( ; node_it != node_end; ++node_it)
      (*node_it)->set_n_systems(n_sys);
    
    MeshBase::element_iterator       elem_it  = _mesh.elements_begin();
    const MeshBase::element_iterator elem_end = _mesh.elements_end();
    
    for ( ; elem_it != elem_end; ++elem_it)
      (*elem_it)->set_n_systems(n_sys);
  }

  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).init();
}

unsigned int EquationSystems::n_active_dofs

(

)

const

Returns the number of active degrees of freedom for the EquationSystems object.

Definition at line 907 of file equation_systems.C.

References _systems.

{
  unsigned int tot=0;

  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    tot += pos->second->n_active_dofs();

  return tot;      
}

unsigned int EquationSystems::n_dofs

(

)

const

Returns:

the total number of degrees of freedom in all systems.

Definition at line 891 of file equation_systems.C.

References _systems.

{
  unsigned int tot=0;

  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    tot += pos->second->n_dofs();

  return tot;      
}

static unsigned int ReferenceCounter::n_objects

(

)

[inline, static, inherited]

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

Definition at line 77 of file reference_counter.h.

References ReferenceCounter::_n_objects.

  { return _n_objects; }

unsigned int EquationSystems::n_systems

(

)

const [inline]

Returns:

the number of equation systems.

Definition at line 482 of file equation_systems.h.

References _systems.

Referenced by add_system(), adjoint_solve(), allgather(), build_discontinuous_solution_vector(), build_solution_vector(), build_variable_names(), compare(), GMVIO::copy_nodal_solution(), AdjointRefinementEstimator::estimate_error(), ErrorEstimator::estimate_errors(), ExactSolution::ExactSolution(), get_info(), get_system(), init(), reinit(), sensitivity_solve(), VTKIO::solution_to_vtk(), solve(), VTKIO::system_vectors_to_vtk(), update(), write(), and VTKIO::write_equation_systems().

{
  return _systems.size();
}

unsigned int EquationSystems::n_vars

(

)

const

Returns:

the total number of variables in all systems.

Definition at line 876 of file equation_systems.C.

References _systems.

Referenced by build_discontinuous_solution_vector(), build_solution_vector(), and build_variable_names().

{
  unsigned int tot=0;
  
  const_system_iterator       pos = _systems.begin();
  const const_system_iterator end = _systems.end();

  for (; pos != end; ++pos)
    tot += pos->second->n_vars();

  return tot;
}

void ReferenceCounter::print_info

(

std::ostream &

out = std::cout

)

[static, inherited]

Prints the reference information, by default to std::cout.

Definition at line 86 of file reference_counter.C.

References ReferenceCounter::get_info().

{
  
  out_stream << ReferenceCounter::get_info();
  
}

void EquationSystems::print_info

(

std::ostream &

os = libMesh::out

)

const

Prints information about the equation systems, by default to libMesh::out.

Definition at line 860 of file equation_systems.C.

References get_info().

Referenced by operator<<().

{
  os << this->get_info()
     << std::endl;
}

void EquationSystems::read	(	const std::string &	name,
		const unsigned int	read_flags = (READ_HEADER | READ_DATA)
	)

Definition at line 68 of file equation_systems_io.C.

References libMeshEnums::DECODE, read(), and libMeshEnums::READ.

{
  libMeshEnums::XdrMODE mode = READ;
  if (name.find(".xdr") != std::string::npos)
    mode = DECODE;
  this->read(name, mode, read_flags);
}

void EquationSystems::read	(	const std::string &	name,
		const libMeshEnums::XdrMODE	mode,
		const unsigned int	read_flags = (READ_HEADER | READ_DATA)
	)

Read & initialize the systems from disk using the XDR data format. This format allows for machine-independent binary output.

Set which sections of the file to read by bitwise OR'ing the EquationSystems::ReadFlags enumeration together. For example, to read all sections of the file, set read_flags to: (READ_HEADER | READ_DATA | READ_ADDITIONAL_DATA)

Note that the equation system can be defined without initializing the data vectors to any solution values. This can be done by omitting READ_DATA in the read_flags parameter.

If XdrMODE is omitted, it will be inferred as READ for filenames containing .xda or as DECODE for filenames containing .xdr

Definition at line 79 of file equation_systems_io.C.

References _read_impl(), libMesh::out, and TRY_READ_IFEMS.

Referenced by _read_impl(), and read().

{
#ifdef LIBMESH_ENABLE_EXCEPTIONS

  // If we have exceptions enabled we can be considerate and try
  // to read old restart files which contain infinite element
  // information but do not have the " with infinite elements"
  // string in the version information.
  
  // First try the read the user requested
  try
    {
      this->_read_impl (name, mode, read_flags);
    }

  // If that fails, try it again but explicitly request we look for infinite element info      
  catch (...)
    {
      libMesh::out << "\n*********************************************************************\n"
                    << "READING THE FILE \"" << name << "\" FAILED.\n"
                    << "It is possible this file contains infinite element information,\n"
                    << "but the version string does not contain \" with infinite elements\"\n"
                    << "Let's try this again, but looking for infinite element information...\n"
                    << "*********************************************************************\n"
                    << std::endl;

      try
        {
          this->_read_impl (name, mode, read_flags | EquationSystems::TRY_READ_IFEMS);
        }

      // If all that failed, we are out of ideas here...
      catch (...)
        {
          libMesh::out << "\n*********************************************************************\n"
                        << "Well, at least we tried!\n"
                        << "Good Luck!!\n"
                        << "*********************************************************************\n"
                        << std::endl;
          throw;
        }
    }

#else

  // no exceptions - cross your fingers...
  this->_read_impl (name, mode, read_flags);
  
#endif // #ifdef LIBMESH_ENABLE_EXCEPTIONS
}

void EquationSystems::reinit

(

)

[virtual]

Reinitialize all the systems

Definition at line 121 of file equation_systems.C.

References _mesh, MeshRefinement::coarsen_elements(), MeshBase::contract(), DofMap::create_dof_constraints(), DofMap::distribute_dofs(), MeshBase::elements_begin(), MeshBase::elements_end(), MeshRefinement::face_level_mismatch_limit(), System::get_dof_map(), get_mesh(), get_system(), n_systems(), System::n_vars(), MeshBase::nodes_begin(), MeshBase::nodes_end(), DofMap::prepare_send_list(), DofMap::process_constraints(), System::prolong_vectors(), MeshRefinement::refine_elements(), System::restrict_vectors(), and System::user_constrain().

Referenced by AdjointRefinementEstimator::estimate_error().

{
  libmesh_assert (this->n_systems() != 0);
  
#ifdef DEBUG
  // Make sure all the \p DofObject entities know how many systems
  // there are.
  {
    // All the nodes
    MeshBase::node_iterator       node_it  = _mesh.nodes_begin();
    const MeshBase::node_iterator node_end = _mesh.nodes_end();

    for ( ; node_it != node_end; ++node_it)
      libmesh_assert((*node_it)->n_systems() == this->n_systems());
    
    // All the elements
    MeshBase::element_iterator       elem_it  = _mesh.elements_begin();
    const MeshBase::element_iterator elem_end = _mesh.elements_end();
    
    for ( ; elem_it != elem_end; ++elem_it)
      libmesh_assert((*elem_it)->n_systems() == this->n_systems());
  }
#endif

  // Localize each system's vectors
  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).re_update();

#ifdef LIBMESH_ENABLE_AMR

  bool dof_constraints_created = false;
  bool mesh_changed = false;

  // FIXME: For backwards compatibility, assume
  // refine_and_coarsen_elements or refine_uniformly have already
  // been called
  {
    for (unsigned int i=0; i != this->n_systems(); ++i)
      {
        System &sys = this->get_system(i);

        // Don't do anything if the system doesn't have any variables in it
        if(!sys.n_vars())
          continue;
        
        sys.get_dof_map().distribute_dofs(_mesh);

        // Recreate any hanging node constraints
        sys.get_dof_map().create_dof_constraints(_mesh);

        // Apply any user-defined constraints
        sys.user_constrain();

        // Expand any recursive constraints
        sys.get_dof_map().process_constraints();

        // And clean up the send_list before we use it again
        sys.get_dof_map().prepare_send_list();

        sys.prolong_vectors();
      }
    mesh_changed = true;
    dof_constraints_created = true;
  }
  
  // FIXME: Where should the user set maintain_level_one now??
  // Don't override previous settings, for now

  MeshRefinement mesh_refine(_mesh);

  mesh_refine.face_level_mismatch_limit() = false;

  // Try to coarsen the mesh, then restrict each system's vectors
  // if necessary
  if (mesh_refine.coarsen_elements())
    {
      for (unsigned int i=0; i != this->n_systems(); ++i)
        {
          System &sys = this->get_system(i);
          if (!dof_constraints_created)
            {
              sys.get_dof_map().distribute_dofs(_mesh);
              sys.get_dof_map().create_dof_constraints(_mesh);
              sys.user_constrain();
              sys.get_dof_map().process_constraints();
              sys.get_dof_map().prepare_send_list();

            }
          sys.restrict_vectors();
        }
      mesh_changed = true;
      dof_constraints_created = true;
    }

  // Once vectors are all restricted, we can delete
  // children of coarsened elements
  if (mesh_changed)
    this->get_mesh().contract();
  
  // Try to refine the mesh, then prolong each system's vectors
  // if necessary
  if (mesh_refine.refine_elements())
    {
      for (unsigned int i=0; i != this->n_systems(); ++i)
        {
          System &sys = this->get_system(i);
          if (!dof_constraints_created)
            {
              sys.get_dof_map().distribute_dofs(_mesh);
              sys.get_dof_map().create_dof_constraints(_mesh);
              sys.user_constrain();
              sys.get_dof_map().process_constraints();
              sys.get_dof_map().prepare_send_list();

            }
          sys.prolong_vectors();
        }
      mesh_changed = true;
      dof_constraints_created = true;
    }

  // If the mesh has changed, systems will need to create new dof
  // constraints and update their global solution vectors
  if (mesh_changed)
    {
      for (unsigned int i=0; i != this->n_systems(); ++i)
        this->get_system(i).reinit();
    }
#endif // #ifdef LIBMESH_ENABLE_AMR
}

void EquationSystems::sensitivity_solve

(

const ParameterVector &

parameters

)

[virtual]

Call sensitivity_solve on all the individual equation systems.

By default this function solves each sensitivity system once, in the order in which in which they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.

Definition at line 403 of file equation_systems.C.

References get_system(), and n_systems().

{
  libmesh_assert (this->n_systems());

  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).sensitivity_solve(parameters);
}

void EquationSystems::solve

(

)

[virtual]

Call solve on all the individual equation systems.

By default this function solves each equation system once, in the order they were added. For more sophisticated decoupled problems the user may with to override this behavior in a derived class.

Definition at line 393 of file equation_systems.C.

References get_system(), and n_systems().

Referenced by AdjointRefinementEstimator::estimate_error(), and Solver::solve().

{
  libmesh_assert (this->n_systems());

  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).solve();
}

void EquationSystems::update

(

)

Updates local values for all the systems

Definition at line 291 of file equation_systems.C.

References get_system(), and n_systems().

Referenced by _read_impl().

{
  START_LOG("update()","EquationSystems");
  
  // Localize each system's vectors
  for (unsigned int i=0; i != this->n_systems(); ++i)
    this->get_system(i).update();
  
  STOP_LOG("update()","EquationSystems");
}

void EquationSystems::write	(	const std::string &	name,
		const unsigned int	write_flags = (WRITE_DATA)
	)			const

Definition at line 354 of file equation_systems_io.C.

References libMeshEnums::ENCODE, write(), and libMeshEnums::WRITE.

{
  libMeshEnums::XdrMODE mode = WRITE;
  if (name.find(".xdr") != std::string::npos)
    mode = ENCODE;
  this->write(name, mode, write_flags);
}

void EquationSystems::write	(	const std::string &	name,
		const libMeshEnums::XdrMODE	mode,
		const unsigned int	write_flags = (WRITE_DATA)
	)			const

Write the systems to disk using the XDR data format. This format allows for machine-independent binary output.

Set the writing properties using the EquationSystems::WriteFlags enumeration. Set which sections to write out by bitwise OR'ing the enumeration values. Write everything by setting write_flags to: (WRITE_DATA | WRITE_ADDITIONAL_DATA)

Note that the solution data can be omitted by calling this routine with WRITE_DATA omitted in the write_flags argument.

If XdrMODE is omitted, it will be inferred as WRITE for filenames containing .xda or as ENCODE for filenames containing .xdr

This program implements the output of an EquationSystems object. This warrants some documentation. The output file essentially consists of 11 sections:

     1.) The version header.
     2.) The number of individual equation systems (unsigned int)
     
       for each system
                                                          
        3.)  The name of the system (string)            
        4.)  The type of the system (string)            
   
        handled through System::read():
   
     +-------------------------------------------------------------+
     |  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 equation system object |
     |                                                             |
     |    9.) the name of the additional vector  (string)          |
     +-------------------------------------------------------------+
   
    end system loop
   
   
    for each system, handled through System::write_{serialized,parallel}_data():
       
     +--------------------------------------------------------------+
     | 10.) The global solution vector, re-ordered to be node-major |
     |     (More on this later.)                                    |
     |                                                              |
     |    for each additional vector in the equation system object  |
     |                                                              |
     |    11.) The global additional vector, re-ordered to be       |
     |         node-major (More on this later.)                     |
     +--------------------------------------------------------------+

    end system loop
   

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 write XDR or ASCII files with no changes.

Definition at line 365 of file equation_systems_io.C.

References _mesh, _systems, Xdr::data(), libMesh::err, MeshTools::Private::fix_broken_node_and_element_numbering(), get_mesh(), MeshTools::Private::globally_renumber_nodes_and_elements(), n_systems(), libMesh::processor_id(), WRITE_ADDITIONAL_DATA, WRITE_DATA, WRITE_PARALLEL_FILES, and Xdr::writing().

Referenced by write().

{
  // the EquationSystems::write() method should look constant,
  // but we need to assign a temporary numbering to the nodes
  // and elements in the mesh, which requires that we abuse const_cast
  {
    MeshBase &mesh = const_cast<MeshBase&>(this->get_mesh());
    MeshTools::Private::globally_renumber_nodes_and_elements(mesh);
  }
  
   // set booleans from write_flags argument
   const bool write_data            = write_flags & EquationSystems::WRITE_DATA;
   const bool write_parallel_files  = write_flags & EquationSystems::WRITE_PARALLEL_FILES;
   const bool write_additional_data = write_flags & EquationSystems::WRITE_ADDITIONAL_DATA;

  // New scope so that io will close before we try to zip the file
  {
    Xdr io((libMesh::processor_id()==0) ? name : "", mode);    
    libmesh_assert (io.writing());
    
    START_LOG("write()","EquationSystems");

    const unsigned int proc_id = libMesh::processor_id();
    unsigned int n_sys         = this->n_systems();
    
    std::map<std::string, System*>::const_iterator
      pos = _systems.begin();
    
    std::string comment;
    char buf[256];
    
    // Only write the header information
    // if we are processor 0.
    if (proc_id == 0) 
      {
        // 1.)
        // Write the version header
        std::string version = "libMesh-0.7.0+";
        if (write_parallel_files) version += " parallel";
        
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
        version += " with infinite elements";
#endif
        io.data (version, "# File Format Identifier");
        
        // 2.)  
        // Write the number of equation systems
        io.data (n_sys, "# No. of Equation Systems");
        
        while (pos != _systems.end())
          {
            // 3.)
            // Write the name of the sys_num-th system
            {
              const unsigned int sys_num = pos->second->number();
              std::string sys_name       = pos->first;
              
              comment =  "# Name, System No. ";
              std::sprintf(buf, "%d", sys_num);
              comment += buf;
          
              io.data (sys_name, comment.c_str());
            }
          
            // 4.)
            // Write the type of system handled
            {
              const unsigned int sys_num = pos->second->number();
              std::string sys_type       = pos->second->system_type();

              comment =  "# Type, System No. ";
              std::sprintf(buf, "%d", sys_num);
              comment += buf;
          
              io.data (sys_type, comment.c_str());
            }
        
            // 5.) - 9.)
            // Let System::write_header() do the job
            pos->second->write_header (io, version, write_additional_data);
            
            ++pos;
          }
      }

    // Start from the first system, again,
    // to write vectors to disk, if wanted
    if (write_data)
      {
        // open a parallel buffer if warranted.
        Xdr local_io (write_parallel_files ? local_file_name(name) : "", mode);
        
        for (pos = _systems.begin(); pos != _systems.end(); ++pos) 
          {
            // 10.) + 11.)
            if (write_parallel_files)
              pos->second->write_parallel_data (local_io,write_additional_data);
            else
              pos->second->write_serialized_data (io,write_additional_data);
          }
      }
        
    STOP_LOG("write()","EquationSystems");
  }
 
  // the EquationSystems::write() method should look constant,
  // but we need to undo the temporary numbering of the nodes
  // and elements in the mesh, which requires that we abuse const_cast
  if (dynamic_cast<ParallelMesh*>(const_cast<MeshBase*>(&_mesh)))
    {
      ParallelMesh *mesh = dynamic_cast<ParallelMesh*>(const_cast<MeshBase*>(&_mesh));    
      MeshTools::Private::fix_broken_node_and_element_numbering(*mesh);
    }
  else if (dynamic_cast<SerialMesh*>(const_cast<MeshBase*>(&_mesh)))
    {
      SerialMesh *mesh = dynamic_cast<SerialMesh*>(const_cast<MeshBase*>(&_mesh));    
      MeshTools::Private::fix_broken_node_and_element_numbering(*mesh);
    }
  else
    {
      libMesh::err << "ERROR:  dynamic_cast<> to ParallelMesh and SerialMesh failed!"
                    << std::endl;
      libmesh_error();
    }
}

---

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const EquationSystems &	es
	)			[friend]

Same as above, but allows you to also use stream syntax.

Definition at line 868 of file equation_systems.C.

{
  es.print_info(os);
  return os;
}

---

Member Data Documentation

ReferenceCounter::Counts ReferenceCounter::_counts [static, protected, inherited]

Actually holds the data.

Definition at line 111 of file reference_counter.h.

Referenced by ReferenceCounter::get_info(), ReferenceCounter::increment_constructor_count(), and ReferenceCounter::increment_destructor_count().

MeshBase& EquationSystems::_mesh [protected]

The mesh data structure

Definition at line 398 of file equation_systems.h.

Referenced by _add_system_to_nodes_and_elems(), _read_impl(), allgather(), build_discontinuous_solution_vector(), build_solution_vector(), get_mesh(), init(), reinit(), and write().

MeshData* EquationSystems::_mesh_data [protected]

A pointer to the MeshData object you would like to use. Can be NULL.

Definition at line 404 of file equation_systems.h.

Referenced by get_mesh_data(), and has_mesh_data().

Threads::spin_mutex ReferenceCounter::_mutex [static, protected, inherited]

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 124 of file reference_counter.h.

Threads::atomic< unsigned int > ReferenceCounter::_n_objects [static, protected, inherited]

The number of objects. Print the reference count information when the number returns to 0.

Definition at line 119 of file reference_counter.h.

Referenced by ReferenceCounter::n_objects(), ReferenceCounter::ReferenceCounter(), and ReferenceCounter::~ReferenceCounter().

std::map<std::string, System*> EquationSystems::_systems [protected]

Data structure holding the systems.

Definition at line 409 of file equation_systems.h.

Referenced by _read_impl(), add_system(), build_discontinuous_solution_vector(), build_solution_vector(), build_variable_names(), clear(), compare(), delete_system(), get_info(), get_system(), has_system(), n_active_dofs(), n_dofs(), n_systems(), n_vars(), and write().

Parameters EquationSystems::parameters

Data structure holding arbitrary parameters.

Definition at line 389 of file equation_systems.h.

Referenced by ExactSolution::_compute_error(), NewmarkSystem::clear(), clear(), FrequencySystem::clear_all(), EquationSystems(), ExactErrorEstimator::find_squared_element_error(), FEComputeData::init(), FrequencySystem::init_data(), FrequencySystem::n_frequencies(), NewmarkSystem::NewmarkSystem(), NonlinearImplicitSystem::NonlinearImplicitSystem(), 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().

---

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

• equation_systems.h
• equation_systems.C
• equation_systems_io.C