The Biharmonic class encapsulates most of the data structures necessary to calculate the biharmonic residual and Jacobian, auxiliary quantities, to take a timestep, and to output the state – biharmonic solution and vectors of auxiliary quantities. More...

#include <biharmonic.h>

Inheritance diagram for Biharmonic:

[legend]

Classes
class	JR
	Biharmonic's friend class definition. More...

Public Types
enum	InitialStateEnum { STRIP = 0, ROD = 1, BALL = 2 }

enum	FreeEnergyEnum { DOUBLE_WELL = 1, DOUBLE_OBSTACLE = 2, LOG_DOUBLE_WELL = 3, LOG_DOUBLE_OBSTACLE = 4 }

enum	ReadFlags { READ_HEADER = 1, READ_DATA = 2, READ_ADDITIONAL_DATA = 4, READ_LEGACY_FORMAT = 8, TRY_READ_IFEMS = 16, READ_BASIC_ONLY = 32 }
	Define enumeration to set properties in EquationSystems::read() More...

enum	WriteFlags { WRITE_DATA = 1, WRITE_ADDITIONAL_DATA = 2, WRITE_PARALLEL_FILES = 4, WRITE_SERIAL_FILES = 8 }
	Define enumeration to set properties in EquationSystems::write() More...

Public Member Functions
	Biharmonic (ReplicatedMesh &mesh)
	Constructor retrieves command-line options, setting defaults, if necessary. More...

	~Biharmonic ()
	Destructor. More...

bool	verbose ()

Real	dt0 ()

Real	dt ()

void	viewParameters ()

void	init ()
	Initialize all the systems. More...

void	step (const Real &dt=-1.0)

void	output (int timestep, const Real &t, Real &o_t, bool force=false)

void	run ()

virtual void	clear ()
	Restores the data structure to a pristine state. More...

virtual void	reinit ()
	Handle any mesh changes and reinitialize all the systems on the updated mesh. More...

virtual void	enable_default_ghosting (bool enable)
	Enable or disable default ghosting functors on the Mesh and on all Systems. More...

void	update ()
	Updates local values for all the systems. More...

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

template<typename T_sys >
T_sys &	add_system (const std::string &name)
	Add the system named `name` to the systems array. More...

void	delete_system (const std::string &name)
	Remove the system named `name` from the systems array. More...

unsigned int	n_vars () const

std::size_t	n_dofs () const

std::size_t	n_active_dofs () const

virtual void	solve ()
	Call `solve` on all the individual equation systems. More...

virtual void	adjoint_solve (const QoISet &qoi_indices=QoISet())
	Call `adjoint_solve` on all the individual equation systems. More...

virtual void	sensitivity_solve (const ParameterVector &parameters)
	Call `sensitivity_solve` on all the individual equation systems. More...

void	build_variable_names (std::vector< std::string > &var_names, const FEType type=nullptr, const std::set< std::string > system_names=nullptr) const
	Fill the input vector `var_names` with the names of the variables for each system. More...

void	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`. More...

void	build_solution_vector (std::vector< Number > &soln, const std::set< std::string > *system_names=nullptr) const
	Fill the input vector `soln` with solution values. More...

std::unique_ptr< NumericVector< Number > >	build_parallel_solution_vector (const std::set< std::string > *system_names=nullptr) const
	A version of build_solution_vector which is appropriate for "parallel" output formats like Nemesis. More...

void	get_vars_active_subdomains (const std::vector< std::string > &names, std::vector< std::set< subdomain_id_type >> &vars_active_subdomains) const
	Retrieve `vars_active_subdomains`, which indicates the active subdomains for each variable in `names`. More...

void	get_solution (std::vector< Number > &soln, std::vector< std::string > &names) const
	Retrieve the solution data for CONSTANT MONOMIALs. More...

void	build_elemental_solution_vector (std::vector< Number > &soln, std::vector< std::string > &names) const
	Retrieve the solution data for CONSTANT MONOMIALs. More...

std::vector< std::pair< unsigned int, unsigned int > >	find_variable_numbers (std::vector< std::string > &names, const FEType *type=nullptr) const
	Finds system and variable numbers for any variables of `type` corresponding to the entries in the input 'names' vector. More...

std::unique_ptr< NumericVector< Number > >	build_parallel_elemental_solution_vector (std::vector< std::string > &names) const
	Builds a parallel vector of CONSTANT MONOMIAL solution values corresponding to the entries in the input 'names' vector. More...

void	build_discontinuous_solution_vector (std::vector< Number > &soln, const std::set< std::string > system_names=nullptr, const std::vector< std::string > var_names=nullptr, bool vertices_only=false) const
	Fill the input vector `soln` with solution values. More...

template<typename InValType >
void	read (const std::string &name, const XdrMODE, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)
	Read & initialize the systems from disk using the XDR data format. More...

void	read (const std::string &name, const XdrMODE mode, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

template<typename InValType >
void	read (const std::string &name, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

void	read (const std::string &name, const unsigned int read_flags=(READ_HEADER\|READ_DATA), bool partition_agnostic=true)

void	write (const std::string &name, const XdrMODE, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) const
	Write the systems to disk using the XDR data format. More...

void	write (const std::string &name, const unsigned int write_flags=(WRITE_DATA), bool partition_agnostic=true) 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
	Prints information about the equation systems, by default to libMesh::out. More...

const MeshBase &	get_mesh () const

MeshBase &	get_mesh ()

void	allgather ()
	Serializes a distributed mesh and its associated degree of freedom numbering for all systems. More...

void	enable_refine_in_reinit ()
	Calls to reinit() will also do two-step coarsen-then-refine. More...

void	disable_refine_in_reinit ()
	Calls to reinit() will not try to coarsen or refine the mesh. More...

bool	refine_in_reinit_flag ()

bool	reinit_solutions ()
	Handle any mesh changes and project any solutions onto the updated mesh. More...

virtual void	reinit_systems ()
	Reinitialize all systems on the current mesh. More...

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static std::string	get_info ()
	Gets a string containing the reference information. More...

static void	print_info (std::ostream &out=libMesh::out)
	Prints the reference information, by default to `libMesh::out`. More...

static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...

static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info() More...

static void	disable_print_counter_info ()

Public Attributes
Parameters	parameters
	Data structure holding arbitrary parameters. More...

Protected Types
typedef std::map< std::string, System * >::iterator	system_iterator
	Typedef for system iterators. More...

typedef std::map< std::string, System * >::const_iterator	const_system_iterator
	Typedef for constant system iterators. More...

typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
	Data structure to log the information. More...

Protected Member Functions
void	increment_constructor_count (const std::string &name)
	Increments the construction counter. More...

void	increment_destructor_count (const std::string &name)
	Increments the destruction counter. More...

Protected Attributes
std::map< std::string, System * >	_systems
	Data structure holding the systems. More...

bool	_refine_in_reinit
	Flag for whether to call coarsen/refine in reinit(). More...

bool	_enable_default_ghosting
	Flag for whether to enable default ghosting on newly added Systems. More...

const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
	Actually holds the data. More...

static Threads::atomic< unsigned int >	_n_objects
	The number of objects. More...

static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting. More...

static bool	_enable_print_counter = true
	Flag to control whether reference count information is printed when print_info is called. More...

Private Member Functions
template<typename InValType >
void	_read_impl (const std::string &name, const XdrMODE, const unsigned int read_flags, bool partition_agnostic=true)
	Actual read implementation. More...

void	_add_system_to_nodes_and_elems ()
	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. More...

void	_remove_default_ghosting (unsigned int sys_num)
	This just calls DofMap::remove_default_ghosting() but using a shim lets us forward-declare DofMap. More...

Private Attributes
unsigned int	_dim

unsigned int	_N

Real	_kappa

Real	_theta

Real	_theta_c

Real	_tol

bool	_growth

bool	_degenerate

bool	_cahn_hillard

bool	_netforce

FreeEnergyEnum	_energy

int	_log_truncation

bool	_verbose

InitialStateEnum	_initialState

Point	_initialCenter

Real	_initialWidth

Real	_dt0

Real	_dt

Real	_t0

Real	_T

Real	_t1

Real	_cnWeight

std::string	_ofile_base

std::string	_ofile

std::unique_ptr< ExodusII_IO >	_exio

Real	_o_dt

int	_o_count

ReplicatedMesh &	_mesh

JR *	_jr

Friends
class	JR

Detailed Description

The Biharmonic class encapsulates most of the data structures necessary to calculate the biharmonic residual and Jacobian, auxiliary quantities, to take a timestep, and to output the state – biharmonic solution and vectors of auxiliary quantities.

The main reason for this design is to have a data structure that has all of the necessary data in one place, where all of the calculation subroutines can access these data. Currently these data are split up among several interdependent objects with no clear hierarchy between them: mesh, equation system, equation system bundle, residual/Jacobian calculator.

Since no object contains all others and the data are distributed among many objects, the natural control and data flow resides outside of these objects and is typically implemented in main(). We, however, would like to split the calculation into natural chunks – subroutines – while retaining these subroutines access to the common necessary data – biharmonic parameters, mesh and time interval sizes, etc. Thus, class Biharmonic. Finally, making Biharmonic inherit from EquationSystems makes it possible to include it in the most common callbacks that do not pass back a user context, but only an EquationSystems object.

Definition at line 45 of file biharmonic.h.

Member Typedef Documentation

◆ const_system_iterator

typedef std::map<std::string, System *>::const_iterator libMesh::EquationSystems::const_system_iterator

protectedinherited

Typedef for constant system iterators.

Definition at line 581 of file equation_systems.h.

◆ Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 117 of file reference_counter.h.

◆ system_iterator

typedef std::map<std::string, System *>::iterator libMesh::EquationSystems::system_iterator

protectedinherited

Typedef for system iterators.

Definition at line 576 of file equation_systems.h.

Member Enumeration Documentation

◆ FreeEnergyEnum

enum Biharmonic::FreeEnergyEnum

Enumerator
DOUBLE_WELL
DOUBLE_OBSTACLE
LOG_DOUBLE_WELL
LOG_DOUBLE_OBSTACLE

Definition at line 54 of file biharmonic.h.

                       {DOUBLE_WELL         = 1,
                        DOUBLE_OBSTACLE     = 2,
                        LOG_DOUBLE_WELL     = 3,
                        LOG_DOUBLE_OBSTACLE = 4};

◆ InitialStateEnum

enum Biharmonic::InitialStateEnum

Enumerator
STRIP
ROD
BALL

Definition at line 49 of file biharmonic.h.

                         {STRIP = 0,
                          ROD   = 1,
                          BALL  = 2};

◆ ReadFlags

enum libMesh::EquationSystems::ReadFlags

inherited

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

Enumerator
READ_HEADER
READ_DATA
READ_ADDITIONAL_DATA
READ_LEGACY_FORMAT
TRY_READ_IFEMS
READ_BASIC_ONLY

Definition at line 83 of file equation_systems.h.

                  { READ_HEADER           = 1,
                    READ_DATA             = 2,
                    READ_ADDITIONAL_DATA  = 4,
                    READ_LEGACY_FORMAT    = 8,
                    TRY_READ_IFEMS        = 16,
                    READ_BASIC_ONLY       = 32 };

◆ WriteFlags

enum libMesh::EquationSystems::WriteFlags

inherited

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

Enumerator
WRITE_DATA
WRITE_ADDITIONAL_DATA
WRITE_PARALLEL_FILES
WRITE_SERIAL_FILES

Definition at line 93 of file equation_systems.h.

                   { WRITE_DATA             = 1,
                     WRITE_ADDITIONAL_DATA  = 2,
                     WRITE_PARALLEL_FILES   = 4,
                     WRITE_SERIAL_FILES     = 8 };

Constructor & Destructor Documentation

◆ Biharmonic()

Biharmonic::Biharmonic ( ReplicatedMesh & mesh )

Constructor retrieves command-line options, setting defaults, if necessary.

It then builds the mesh using these options, then the equations systems around it, and, finally, sets up the output. We recommend that this be used through the factory Create function, which allocates the mesh. In that case don't forget to call Destroy at the end, to free the mesh up.

Definition at line 14 of file biharmonic.C.

                                             :
   EquationSystems(mesh),
   _mesh(mesh)
 {
   // Retrieve parameters and set defaults
   _verbose      = false;
   _growth       = false;
   _degenerate   = false;
   _cahn_hillard = false;
   _netforce     = false;
  
   if (on_command_line("--verbose"))
     _verbose = true;
   if (on_command_line("--growth"))
     _growth = true;
   if (on_command_line("--degenerate"))
     _degenerate = true;
   if (on_command_line("--cahn_hillard"))
     _cahn_hillard = true;
   if (on_command_line("--netforce"))
     _netforce = true;
  
   _kappa = command_line_value("kappa", 1.0);
  
   // "type of energy (double well, double obstacle, logarithmic+double well, logarithmic+double obstacle)"
   std::string energy = command_line_value("energy", std::string("double_well"));
  
   if (energy == "double_well")
     _energy = DOUBLE_WELL;
   else if (energy == "double_obstacle")
     _energy = DOUBLE_OBSTACLE;
   else if (energy == "log_double_well")
     _energy = LOG_DOUBLE_WELL;
   else if (energy == "log_double_obstacle")
     _energy = LOG_DOUBLE_OBSTACLE;
   else
     libmesh_error_msg("Unknown energy type: " << energy);
  
   _tol     = command_line_value("tol", 1.0e-8);
   _theta   = command_line_value("theta", .001);
   _theta_c = command_line_value("theta_c", 1.0);
  
   // "order of log truncation (0=none, 2=quadratic, 3=cubic)"
   _log_truncation = command_line_value("log_truncation", 2);
  
   if (!_log_truncation)
     libMesh::out << "WARNING: no truncation is being used for the logarithmic free energy term.\nWARNING: division by zero possible!\n";
  
  
   // Dimension
   _dim = command_line_value("dim", 1);
  
   libmesh_assert_msg((_dim <= 3) && (_dim > 0), "Invalid mesh dimension");
  
   // Build the mesh
   // Yes, it's better to make a coarse mesh and then refine it. We'll get to it later.
   _N = command_line_value("N", 8);
   libmesh_assert_msg(_N > 0, "Invalid mesh size");
  
   switch (_dim)
     {
     case 1:
       MeshTools::Generation::build_line(_mesh, _N, 0.0, 1.0, EDGE2);
       break;
     case 2:
       MeshTools::Generation::build_square(_mesh, _N, _N, 0.0, 1.0, 0.0, 1.0, QUAD4);
       break;
     case 3:
       MeshTools::Generation::build_cube(_mesh, _N, _N, _N, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, HEX8);
       break;
     default:
       libmesh_assert_msg((_dim <= 3) && (_dim > 0), "Invalid mesh dimension");
       break;
     }
  
   // Determine the initial timestep size
   _dt0 = command_line_value("dt", 1.0/(10*_kappa*_N*_N*_N*_N));
   libmesh_assert_msg(_dt0>=0, "Negative initial timestep");
  
   _t0 = command_line_value("min_time", 0.0);
   _t1 = command_line_value("max_time", _t0 + 50.0*_dt0);
   libmesh_assert_msg(_t1 >= _t0, "Final time less than initial time");
   _T = _t1 - _t0;
  
   _cnWeight = command_line_value("crank_nicholson_weight", 1.0);
   libmesh_assert_msg(_cnWeight <= 1 && _cnWeight >= 0, "Crank-Nicholson weight must be between 0 and 1");
  
   // Initial state
   _initialState = STRIP;
   std::string initialState = command_line_value("initial_state", std::string("strip"));
  
   if (initialState == std::string("ball"))
     _initialState = BALL;
   else if (initialState == std::string("strip"))
     _initialState = STRIP;
   else if (initialState == std::string("rod"))
     _initialState = ROD;
   else
     libmesh_error_msg("Unknown initial state: neither ball nor rod nor strip");
  
   std::vector<Real> icenter;
   command_line_vector("initial_center", icenter);
  
   // Check that the point defining the center was in the right spatial dimension
   if (icenter.size() > _dim)
     libmesh_assert_msg(icenter.size() > _dim, "Invalid dimension for the initial state center of mass");
  
   // Pad
   icenter.resize(3);
   for (std::size_t i = icenter.size(); i < _dim; ++i)
     icenter[i] = 0.5;
  
   for (unsigned int i = _dim; i < 3; ++i)
     icenter[i] = 0.0;
  
   _initialCenter = Point(icenter[0], icenter[1], icenter[2]);
   _initialWidth = command_line_value("initial_width", 0.125);
  
   // Build the main equation encapsulated in the JR (Jacobian-Residual or J(R) "jet of R") object
   _jr = &(add_system<Biharmonic::JR>(std::string("Biharmonic::JR")));
  
   // Output options
 #ifdef LIBMESH_HAVE_EXODUS_API
   if (on_command_line("output_base"))
     _ofile_base = command_line_value("output_base", std::string("bih"));
  
   else
     {
       switch(_dim)
         {
         case 1:
           _ofile_base = std::string("bih.1");
           break;
         case 2:
           _ofile_base = std::string("bih.2");
           break;
         case 3:
           _ofile_base = std::string("bih.3");
           break;
         default:
           _ofile_base = std::string("bih");
           break;
         }
     }
   _ofile = _ofile_base + ".e";
   _exio = libmesh_make_unique<ExodusII_IO>(_mesh);
   _o_dt = command_line_value("output_dt", 0.0);
 #endif // #ifdef LIBMESH_HAVE_EXODUS_API
 } // constructor

References _cahn_hillard, _cnWeight, _degenerate, _dim, _dt0, _energy, _exio, _growth, _initialCenter, _initialState, _initialWidth, _jr, _kappa, _log_truncation, _mesh, _N, _netforce, _o_dt, _ofile, _ofile_base, _T, _t0, _t1, _theta, _theta_c, _tol, _verbose, BALL, libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_line(), libMesh::MeshTools::Generation::build_square(), libMesh::command_line_value(), libMesh::command_line_vector(), DOUBLE_OBSTACLE, DOUBLE_WELL, libMesh::EDGE2, libMesh::HEX8, LOG_DOUBLE_OBSTACLE, LOG_DOUBLE_WELL, libMesh::on_command_line(), libMesh::out, libMesh::QUAD4, ROD, and STRIP.

◆ ~Biharmonic()

Biharmonic::~Biharmonic ( )

inline

Destructor.

Definition at line 72 of file biharmonic.h.

   {
     // delete _meshRefinement;
   }

Member Function Documentation

◆ _add_system_to_nodes_and_elems()

void libMesh::EquationSystems::_add_system_to_nodes_and_elems ( )

privateinherited

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 1376 of file equation_systems.C.

 {
   // All the nodes
   for (auto & node : _mesh.node_ptr_range())
     node->add_system();
  
   // All the elements
   for (auto & elem : _mesh.element_ptr_range())
     elem->add_system();
 }

References libMesh::EquationSystems::_mesh, libMesh::MeshBase::element_ptr_range(), and libMesh::MeshBase::node_ptr_range().

Referenced by libMesh::EquationSystems::add_system().

◆ _read_impl()

template<typename InValType >

template void libMesh::EquationSystems::_read_impl< Real >	(	const std::string &	name,
		const	XdrMODE,
		const unsigned int	read_flags,
		bool	partition_agnostic = `true`
	)

privateinherited

Actual read implementation.

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

Parameters

name	Name of the file to be read.
read_flags	Single flag created by bitwise-OR'ing several flags together.
partition_agnostic	If true then the mesh and degrees of freedom will be temporarily renumbered in a partition agnostic way so that files written using "n" mpi processes can be re-read on "m" mpi processes.

Note: This renumbering is not compatible with meshes that have two nodes in exactly the same position!

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 143 of file equation_systems_io.C.

 {
   // 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;
   const bool read_basic_only      = read_flags & EquationSystems::READ_BASIC_ONLY;
   bool read_parallel_files  = false;
  
   std::vector<std::pair<std::string, System *>> xda_systems;
  
   // 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 ((this->processor_id() == 0) ? name : "", mode);
   libmesh_assert (io.reading());
  
   {
     // 1.)
     // Read the version header.
     std::string version = "legacy";
     if (!read_legacy_format)
       {
         if (this->processor_id() == 0) io.data(version);
         this->comm().broadcast(version);
  
         // All processors have the version header, if it does not contain
         // the libMesh_label string then it is a legacy file.
         const std::string libMesh_label = "libMesh-";
         std::string::size_type lm_pos = version.find(libMesh_label);
         if (lm_pos==std::string::npos)
           {
             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), partition_agnostic);
             return;
           }
  
         // Figure out the libMesh version that created this file
         std::istringstream iss(version.substr(lm_pos + libMesh_label.size()));
         int ver_major = 0, ver_minor = 0, ver_patch = 0;
         char dot;
         iss >> ver_major >> dot >> ver_minor >> dot >> ver_patch;
         io.set_version(LIBMESH_VERSION_ID(ver_major, ver_minor, ver_patch));
  
  
         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 (this->processor_id() == 0) io.data (n_sys);
     this->comm().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 (this->processor_id() == 0) io.data (sys_name);
         this->comm().broadcast(sys_name);
  
         // 4.)
         // Read the type of the sys-th equation system
         std::string sys_type;
         if (this->processor_id() == 0) io.data (sys_type);
         this->comm().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);
  
         xda_systems.push_back(std::make_pair(sys_name, &new_system));
  
         // If we're only creating "basic" systems, we need to tell
         // each system that before we call init() later.
         if (read_basic_only)
           new_system.set_basic_system_only();
       }
   }
  
  
  
   // 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 && partition_agnostic)
         {
           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(this->processor_id(),name) : "", mode);
  
       for (auto & pr : xda_systems)
         if (read_legacy_format)
           {
             libmesh_deprecated();
 #ifdef LIBMESH_ENABLE_DEPRECATED
             pr.second->read_legacy_data (io, read_additional_data);
 #endif
           }
         else
           if (read_parallel_files)
             pr.second->read_parallel_data<InValType>   (local_io, read_additional_data);
           else
             pr.second->read_serialized_data<InValType> (io, read_additional_data);
  
  
       // Undo the temporary numbering.
       if (!read_legacy_format && partition_agnostic)
         _mesh.fix_broken_node_and_element_numbering();
     }
  
   STOP_LOG("read()","EquationSystems");
  
   // Localize each system's data
   this->update();
 }

◆ _remove_default_ghosting()

void libMesh::EquationSystems::_remove_default_ghosting ( unsigned int sys_num )

privateinherited

This just calls DofMap::remove_default_ghosting() but using a shim lets us forward-declare DofMap.

Definition at line 1387 of file equation_systems.C.

 {
   this->get_system(sys_num).get_dof_map().remove_default_ghosting();
 }

References libMesh::EquationSystems::get_system().

Referenced by libMesh::EquationSystems::add_system().

◆ add_system() [1/2]

template<typename T_sys >

T_sys & libMesh::EquationSystems::add_system ( const std::string & name )

inlineinherited

Add the system named name to the systems array.

Definition at line 662 of file equation_systems.h.

 {
   T_sys * ptr = nullptr;
  
   if (!_systems.count(name))
     {
       const unsigned int sys_num = this->n_systems();
       ptr = new T_sys(*this, name, sys_num);
  
       _systems.insert (std::make_pair(name, ptr));
  
       if (!_enable_default_ghosting)
         this->_remove_default_ghosting(sys_num);
  
       // 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
       ptr = &(this->get_system<T_sys>(name));
     }
  
   // Return a dynamically casted reference to the newly added System.
   return *ptr;
 }

References libMesh::EquationSystems::_add_system_to_nodes_and_elems(), libMesh::EquationSystems::_enable_default_ghosting, libMesh::EquationSystems::_remove_default_ghosting(), libMesh::EquationSystems::_systems, libMesh::EquationSystems::n_systems(), and libMesh::Quality::name().

◆ add_system() [2/2]

System & libMesh::EquationSystems::add_system	(	const std::string &	system_type,
		const std::string &	name
	)

virtualinherited

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

Definition at line 345 of file equation_systems.C.

 {
   // 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 basic System
   else if (sys_type == "Basic")
     this->add_system<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);
  
   // build a Reduced Basis Construction system
   else if (sys_type == "RBConstruction")
     this->add_system<RBConstruction> (name);
  
   // build a transient Reduced Basis Construction system
   else if (sys_type == "TransientRBConstruction")
     this->add_system<TransientRBConstruction> (name);
  
 #ifdef LIBMESH_HAVE_SLEPC
   // build an eigen system
   else if (sys_type == "Eigen")
     this->add_system<EigenSystem> (name);
   else if (sys_type == "TransientEigenSystem")
     this->add_system<TransientEigenSystem> (name);
 #endif
  
 #if defined(LIBMESH_USE_COMPLEX_NUMBERS)
   // build a frequency system
   else if (sys_type == "Frequency")
     this->add_system<FrequencySystem> (name);
 #endif
  
   else
     libmesh_error_msg("ERROR: Unknown system type: " << sys_type);
  
   // Return a reference to the new system
   //return (*this)(name);
   return this->get_system(name);
 }

References libMesh::EquationSystems::_systems, libMesh::EquationSystems::get_system(), and libMesh::Quality::name().

◆ adjoint_solve()

void libMesh::EquationSystems::adjoint_solve ( const QoISet & qoi_indices = QoISet() )

virtualinherited

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 466 of file equation_systems.C.

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

References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), and libMesh::EquationSystems::n_systems().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error().

◆ allgather()

void libMesh::EquationSystems::allgather ( )

inherited

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

Definition at line 274 of file equation_systems.C.

 {
   // A serial mesh means nothing needs to be done
   if (_mesh.is_serial())
     return;
  
   const unsigned int n_sys = this->n_systems();
  
   libmesh_assert_not_equal_to (n_sys, 0);
  
   // Gather the mesh
   _mesh.allgather();
  
   // Tell all the \p DofObject entities how many systems
   // there are.
   for (auto & node : _mesh.node_ptr_range())
     node->set_n_systems(n_sys);
  
   for (auto & elem : _mesh.element_ptr_range())
     elem->set_n_systems(n_sys);
  
   // And distribute each system's dofs
   for (unsigned int i=0; i != this->n_systems(); ++i)
     {
       System & sys = this->get_system(i);
       DofMap & dof_map = sys.get_dof_map();
       dof_map.distribute_dofs(_mesh);
  
       // The user probably won't need constraint equations or the
       // send_list after an allgather, but let's keep it in consistent
       // shape just in case.
       sys.reinit_constraints();
       dof_map.prepare_send_list();
     }
 }

References libMesh::EquationSystems::_mesh, libMesh::MeshBase::allgather(), libMesh::DofMap::distribute_dofs(), libMesh::MeshBase::element_ptr_range(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_system(), libMesh::MeshBase::is_serial(), libMesh::EquationSystems::n_systems(), libMesh::MeshBase::node_ptr_range(), libMesh::DofMap::prepare_send_list(), and libMesh::System::reinit_constraints().

◆ build_discontinuous_solution_vector()

void libMesh::EquationSystems::build_discontinuous_solution_vector	(	std::vector< Number > &	soln,
		const std::set< std::string > *	system_names = `nullptr`,
		const std::vector< std::string > *	var_names = `nullptr`,
		bool	vertices_only = `false`
	)		const

inherited

Fill the input vector soln with solution values.

The entries will be in variable-major format (corresponding to the names from build_variable_names()). If systems_names!=nullptr, only include data from the specified systems. If vertices_only == true, then for higher-order elements only the solution at the vertices is computed. This can be useful when plotting discontinous solutions on higher-order elements and only a lower-order representation is required.

Definition at line 1049 of file equation_systems.C.

 {
   LOG_SCOPE("build_discontinuous_solution_vector()", "EquationSystems");
  
   libmesh_assert (this->n_systems());
  
   const unsigned int dim = _mesh.mesh_dimension();
  
   // Get the number of variables (nv) by counting the number of variables
   // in each system listed in system_names
   unsigned int nv = 0;
  
   for (const auto & pr : _systems)
     {
       // Check current system is listed in system_names, and skip pos if not
       bool use_current_system = (system_names == nullptr);
       if (!use_current_system)
         use_current_system = system_names->count(pr.first);
       if (!use_current_system || pr.second->hide_output())
         continue;
  
       const System * system  = pr.second;
  
       // Loop over all variables in this System and check whether we
       // are supposed to use each one.
       for (auto var_id : IntRange<unsigned int>(0, system->n_vars()))
         {
           bool use_current_var = (var_names == nullptr);
           if (!use_current_var)
             use_current_var = std::count(var_names->begin(),
                                          var_names->end(),
                                          system->variable_name(var_id));
  
           // Only increment the total number of vars if we are
           // supposed to use this one.
           if (use_current_var)
             nv++;
         }
     }
  
   // get the total weight
   unsigned int tw=0;
   for (const auto & elem : _mesh.active_element_ptr_range())
     tw += vertices_only ? elem->n_vertices() : elem->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;
  
   // Keep track of the variable "offset". This is used for indexing
   // into the global solution vector.
   unsigned int var_offset = 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.
   for (const auto & pr : _systems)
     {
       // Check current system is listed in system_names, and skip pos if not
       bool use_current_system = (system_names == nullptr);
       if (!use_current_system)
         use_current_system = system_names->count(pr.first);
       if (!use_current_system || pr.second->hide_output())
         continue;
  
       const System * system  = pr.second;
       const unsigned int nv_sys = system->n_vars();
  
       system->update_global_solution (sys_soln, 0);
  
       // Keep track of the number of vars actually written.
       unsigned int n_vars_written_current_system = 0;
  
       if (_mesh.processor_id() == 0)
         {
           std::vector<Number>       soln_coeffs; // The finite element solution coeffs
           std::vector<Number>       nodal_soln;  // The FE solution interpolated to the nodes
           std::vector<dof_id_type>  dof_indices; // The DOF indices for the finite element
  
           // For each variable, determine if we are supposed to
           // write it, then loop over the active elements, compute
           // the nodal_soln and store it to the "soln" vector. We
           // store zeros for subdomain-restricted variables on
           // elements where they are not active.
           for (unsigned int var=0; var<nv_sys; var++)
             {
               bool use_current_var = (var_names == nullptr);
               if (!use_current_var)
                 use_current_var = std::count(var_names->begin(),
                                              var_names->end(),
                                              system->variable_name(var));
  
               // If we aren't supposed to write this var, go to the
               // next loop iteration.
               if (!use_current_var)
                 continue;
  
               const FEType & fe_type = system->variable_type(var);
               const Variable & var_description = system->variable(var);
  
               unsigned int nn=0;
  
               for (auto & elem : _mesh.active_element_ptr_range())
                 {
                   if (var_description.active_on_subdomain(elem->subdomain_id()))
                     {
                       system->get_dof_map().dof_indices (elem, dof_indices, var);
  
                       soln_coeffs.resize(dof_indices.size());
  
                       for (auto i : index_range(dof_indices))
                         soln_coeffs[i] = sys_soln[dof_indices[i]];
  
                       // Compute the FE solution at all the nodes, but
                       // only use the first n_vertices() entries if
                       // vertices_only == true.
                       FEInterface::nodal_soln (dim,
                                                fe_type,
                                                elem,
                                                soln_coeffs,
                                                nodal_soln);
  
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
                       // infinite elements should be skipped...
                       if (!elem->infinite())
 #endif
                         {
                           libmesh_assert_equal_to (nodal_soln.size(), elem->n_nodes());
  
                           const unsigned int n_vals =
                             vertices_only ? elem->n_vertices() : elem->n_nodes();
  
                           for (unsigned int n=0; n<n_vals; n++)
                             {
                               // Compute index into global solution vector.
                               std::size_t index =
                                 nv * (nn++) + (n_vars_written_current_system + var_offset);
  
                               soln[index] += nodal_soln[n];
                             }
                         }
                     }
                   else
                     nn += vertices_only ? elem->n_vertices() : elem->n_nodes();
                 } // end loop over active elements
  
               // If we made it here, we actually wrote a variable, so increment
               // the number of variables actually written for the current system.
               n_vars_written_current_system++;
  
             } // end loop over vars
         } // end if proc 0
  
       // Update offset for next loop iteration.
       var_offset += n_vars_written_current_system;
     } // end loop over systems
 }

References libMesh::Variable::active_on_subdomain(), dim, libMesh::DofMap::dof_indices(), libMesh::System::get_dof_map(), libMesh::index_range(), libMesh::libmesh_assert(), libMesh::System::n_vars(), libMesh::FEInterface::nodal_soln(), libMesh::System::update_global_solution(), libMesh::System::variable(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::ExodusII_IO::write_discontinuous_exodusII(), libMesh::GMVIO::write_discontinuous_gmv(), and libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data().

◆ build_elemental_solution_vector()

void libMesh::EquationSystems::build_elemental_solution_vector	(	std::vector< Number > &	soln,
		std::vector< std::string > &	names
	)		const

inherited

Retrieve the solution data for CONSTANT MONOMIALs.

If names is populated, only the variables corresponding to those names will be retrieved. This can be used to filter which variables are retrieved.

This is the more appropriately-named replacement for the get_solution() function defined above.

Definition at line 883 of file equation_systems.C.

 {
   // Call the parallel version of this function
   std::unique_ptr<NumericVector<Number>> parallel_soln =
     this->build_parallel_elemental_solution_vector(names);
  
   // Localize into 'soln', provided that parallel_soln is not empty.
   // Note: parallel_soln will be empty in the event that none of the
   // input names were CONSTANT, MONOMIAL variables or there were
   // simply no CONSTANT, MONOMIAL variables in the EquationSystems
   // object.
   soln.clear();
   if (parallel_soln)
     parallel_soln->localize_to_one(soln);
 }

References libMesh::EquationSystems::build_parallel_elemental_solution_vector().

Referenced by libMesh::EquationSystems::get_solution(), and libMesh::ExodusII_IO::write_element_data().

◆ build_parallel_elemental_solution_vector()

std::unique_ptr< NumericVector< Number > > libMesh::EquationSystems::build_parallel_elemental_solution_vector ( std::vector< std::string > & names ) const

inherited

Builds a parallel vector of CONSTANT MONOMIAL solution values corresponding to the entries in the input 'names' vector.

This vector is approximately uniformly distributed across all of the available processors.

The related function build_elemental_solution_vector() is implemented by calling this function and then calling localize_to_one() on the resulting vector.

Returns: A nullptr (if no CONSTANT, MONOMIAL variables exist on the system) or a std::unique_ptr to a var-major numeric vector of total length n_elem * n_vars ordered according to: [u0, u1, ... uN, v0, v1, ... vN, w0, w1, ... wN] for constant monomial variables (u, v, w) on a mesh with N elements.

Definition at line 957 of file equation_systems.C.

 {
   FEType type(CONSTANT, MONOMIAL);
   std::vector<std::pair<unsigned int, unsigned int>> var_nums =
     this->find_variable_numbers(names, &type);
  
   const std::size_t nv = var_nums.size();
   const dof_id_type ne = _mesh.n_elem();
   libmesh_assert_equal_to (ne, _mesh.max_elem_id());
  
   // If there are no variables to write out don't do anything...
   if (!nv)
     return std::unique_ptr<NumericVector<Number>>(nullptr);
  
   // We can handle the case where there are nullptrs in the Elem vector
   // by just having extra zeros in the solution vector.
   numeric_index_type parallel_soln_global_size = ne*nv;
  
   numeric_index_type div = parallel_soln_global_size / this->n_processors();
   numeric_index_type mod = parallel_soln_global_size % this->n_processors();
  
   // Initialize all processors to the average size.
   numeric_index_type parallel_soln_local_size = div;
  
   // The first "mod" processors get an extra entry.
   if (this->processor_id() < mod)
     parallel_soln_local_size = div+1;
  
   // Create a NumericVector to hold the parallel solution
   std::unique_ptr<NumericVector<Number>> parallel_soln_ptr = NumericVector<Number>::build(_communicator);
   NumericVector<Number> & parallel_soln = *parallel_soln_ptr;
   parallel_soln.init(parallel_soln_global_size,
                      parallel_soln_local_size,
                      /*fast=*/false,
                      /*ParallelType=*/PARALLEL);
  
   unsigned int sys_ctr = 0;
  
   // For each system in this EquationSystems object,
   // update the global solution and collect the
   // CONSTANT MONOMIALs.  The entries are in variable-major
   // format.
   for (auto i : index_range(var_nums))
     {
       std::pair<unsigned int, unsigned int> var_num = var_nums[i];
       const System & system  = this->get_system(var_num.first);
  
       // Update the current_local_solution if necessary
       if (sys_ctr != var_num.first)
         {
           System & non_const_sys = const_cast<System &>(system);
           // We used to simply call non_const_sys.solution->close()
           // here, but that is not allowed when the solution vector is
           // locked read-only, for example when printing the solution
           // during during the middle of a solve...  So try to be a bit
           // more careful about calling close() unnecessarily.
           libmesh_assert(this->comm().verify(non_const_sys.solution->closed()));
           if (!non_const_sys.solution->closed())
             non_const_sys.solution->close();
           non_const_sys.update();
           sys_ctr = var_num.first;
         }
  
       NumericVector<Number> & sys_soln(*system.current_local_solution);
  
       // The DOF indices for the finite element
       std::vector<dof_id_type> dof_indices;
  
       const unsigned int var = var_num.second;
  
       const Variable & variable = system.variable(var);
       const DofMap & dof_map = system.get_dof_map();
  
       for (const auto & elem : _mesh.active_local_element_ptr_range())
         if (variable.active_on_subdomain(elem->subdomain_id()))
           {
             dof_map.dof_indices (elem, dof_indices, var);
  
             libmesh_assert_equal_to (1, dof_indices.size());
  
             parallel_soln.set((ne*i)+elem->id(), sys_soln(dof_indices[0]));
           }
     } // end loop over var_nums
  
   parallel_soln.close();
   return std::unique_ptr<NumericVector<Number>>(parallel_soln_ptr.release());
 }

References libMesh::ParallelObject::_communicator, libMesh::EquationSystems::_mesh, libMesh::MeshBase::active_local_element_ptr_range(), libMesh::Variable::active_on_subdomain(), libMesh::NumericVector< T >::build(), libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::CONSTANT, libMesh::System::current_local_solution, libMesh::DofMap::dof_indices(), libMesh::EquationSystems::find_variable_numbers(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_system(), libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::libmesh_assert(), libMesh::MeshBase::max_elem_id(), libMesh::MONOMIAL, libMesh::MeshBase::n_elem(), libMesh::ParallelObject::n_processors(), libMesh::PARALLEL, libMesh::ParallelObject::processor_id(), libMesh::NumericVector< T >::set(), libMesh::System::solution, libMesh::System::update(), and libMesh::System::variable().

Referenced by libMesh::EquationSystems::build_elemental_solution_vector().

◆ build_parallel_solution_vector()

std::unique_ptr< NumericVector< Number > > libMesh::EquationSystems::build_parallel_solution_vector ( const std::set< std::string > * system_names = nullptr ) const

inherited

A version of build_solution_vector which is appropriate for "parallel" output formats like Nemesis.

Returns: A std::unique_ptr to a node-major NumericVector of total length n_nodes*n_vars that various I/O classes can then use to get the local values they need to write on each processor.

Definition at line 590 of file equation_systems.C.

 {
   LOG_SCOPE("build_parallel_solution_vector()", "EquationSystems");
  
   // This function must be run on all processors at once
   parallel_object_only();
  
   const unsigned int dim = _mesh.mesh_dimension();
   const dof_id_type max_nn   = _mesh.max_node_id();
  
   // allocate vector storage to hold
   // (max_node_id)*(number_of_variables) entries.
   //
   // If node renumbering is disabled and adaptive coarsening has
   // created gaps between node numbers, then this vector will be
   // sparse.
   //
   // We have to differentiate between between scalar and vector
   // variables. We intercept vector variables and treat each
   // component as a scalar variable (consistently with build_solution_names).
  
   unsigned int nv = 0;
  
   //Could this be replaced by a/some convenience methods?[PB]
   {
     unsigned int n_scalar_vars = 0;
     unsigned int n_vector_vars = 0;
     const_system_iterator       pos = _systems.begin();
     const const_system_iterator end = _systems.end();
  
     for (; pos != end; ++pos)
       {
         // Check current system is listed in system_names, and skip pos if not
         bool use_current_system = (system_names == nullptr);
         if (!use_current_system)
           use_current_system = system_names->count(pos->first);
         if (!use_current_system || pos->second->hide_output())
           continue;
  
         for (auto vn : IntRange<unsigned int>(0, pos->second->n_vars()))
           {
             if (FEInterface::field_type(pos->second->variable_type(vn)) == TYPE_VECTOR)
               n_vector_vars++;
             else
               n_scalar_vars++;
           }
       }
     // Here, we're assuming the number of vector components is the same
     // as the mesh dimension. Will break for mixed dimension meshes.
     nv = n_scalar_vars + dim*n_vector_vars;
   }
  
   // Get the number of nodes to store locally.
   dof_id_type n_local_nodes = cast_int<dof_id_type>
     (std::distance(_mesh.local_nodes_begin(),
                    _mesh.local_nodes_end()));
  
   // If node renumbering has been disabled, nodes may not be numbered
   // contiguously, and the number of nodes might not match the
   // max_node_id.  In this case we just do our best.
   dof_id_type n_total_nodes = n_local_nodes;
   _mesh.comm().sum(n_total_nodes);
  
   const dof_id_type n_gaps = max_nn - n_total_nodes;
   const dof_id_type gaps_per_processor = n_gaps / _mesh.comm().size();
   const dof_id_type remainder_gaps = n_gaps % _mesh.comm().size();
  
   n_local_nodes = n_local_nodes +      // Actual nodes
                   gaps_per_processor + // Our even share of gaps
                   (_mesh.comm().rank() < remainder_gaps); // Leftovers
  
   // Create a NumericVector to hold the parallel solution
   std::unique_ptr<NumericVector<Number>> parallel_soln_ptr = NumericVector<Number>::build(_communicator);
   NumericVector<Number> & parallel_soln = *parallel_soln_ptr;
   parallel_soln.init(max_nn*nv, n_local_nodes*nv, false, PARALLEL);
  
   // Create a NumericVector to hold the "repeat_count" for each node - this is essentially
   // the number of elements contributing to that node's value
   std::unique_ptr<NumericVector<Number>> repeat_count_ptr = NumericVector<Number>::build(_communicator);
   NumericVector<Number> & repeat_count = *repeat_count_ptr;
   repeat_count.init(max_nn*nv, n_local_nodes*nv, false, PARALLEL);
  
   repeat_count.close();
  
   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)
     {
       // Check current system is listed in system_names, and skip pos if not
       bool use_current_system = (system_names == nullptr);
       if (!use_current_system)
         use_current_system = system_names->count(pos->first);
       if (!use_current_system || pos->second->hide_output())
         continue;
  
       const System & system  = *(pos->second);
       const unsigned int nv_sys = system.n_vars();
       const unsigned int sys_num = system.number();
  
       //Could this be replaced by a/some convenience methods?[PB]
       unsigned int n_scalar_vars = 0;
       unsigned int n_vector_vars = 0;
       for (auto vn : IntRange<unsigned int>(0, pos->second->n_vars()))
         {
           if (FEInterface::field_type(pos->second->variable_type(vn)) == TYPE_VECTOR)
             n_vector_vars++;
           else
             n_scalar_vars++;
         }
  
       // Here, we're assuming the number of vector components is the same
       // as the mesh dimension. Will break for mixed dimension meshes.
       unsigned int nv_sys_split = n_scalar_vars + dim*n_vector_vars;
  
       // Update the current_local_solution
       {
         System & non_const_sys = const_cast<System &>(system);
         // We used to simply call non_const_sys.solution->close()
         // here, but that is not allowed when the solution vector is
         // locked read-only, for example when printing the solution
         // during the middle of a solve...  So try to be a bit
         // more careful about calling close() unnecessarily.
         libmesh_assert(this->comm().verify(non_const_sys.solution->closed()));
         if (!non_const_sys.solution->closed())
           non_const_sys.solution->close();
         non_const_sys.update();
       }
  
       NumericVector<Number> & sys_soln(*system.current_local_solution);
  
       std::vector<Number>      elem_soln;   // The finite element solution
       std::vector<Number>      nodal_soln;  // The FE solution interpolated to the nodes
       std::vector<dof_id_type> dof_indices; // The DOF indices for the finite element
  
       unsigned var_inc = 0;
       for (unsigned int var=0; var<nv_sys; var++)
         {
           const FEType & fe_type           = system.variable_type(var);
           const Variable & var_description = system.variable(var);
           const DofMap & dof_map           = system.get_dof_map();
  
           unsigned int n_vec_dim = FEInterface::n_vec_dim( pos->second->get_mesh(), fe_type );
  
           for (const auto & elem : _mesh.active_local_element_ptr_range())
             {
               if (var_description.active_on_subdomain(elem->subdomain_id()))
                 {
                   dof_map.dof_indices (elem, dof_indices, var);
  
                   elem_soln.resize(dof_indices.size());
  
                   for (auto i : index_range(dof_indices))
                     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_equal_to (nodal_soln.size(), n_vec_dim*elem->n_nodes());
  
                       for (auto n : elem->node_index_range())
                         {
                           for (unsigned int d=0; d < n_vec_dim; d++)
                             {
                               // For vector-valued elements, all components are in nodal_soln. For each
                               // node, the components are stored in order, i.e. node_0 -> s0_x, s0_y, s0_z
                               parallel_soln.add(nv*(elem->node_id(n)) + (var_inc+d + var_num), nodal_soln[n_vec_dim*n+d]);
  
                               // Increment the repeat count for this position
                               repeat_count.add(nv*(elem->node_id(n)) + (var_inc+d + var_num), 1);
                             }
                         }
                     }
                 }
               else // If this variable doesn't exist on this subdomain we have to still increment repeat_count so that we won't divide by 0 later:
                 for (const Node & node : elem->node_ref_range())
                   // Only do this if this variable has NO DoFs at this node... it might have some from an adjoining element...
                   if (!node.n_dofs(sys_num, var))
                     for (unsigned int d=0; d < n_vec_dim; d++)
                       repeat_count.add(nv*node.id() + (var_inc+d + var_num), 1);
  
             } // end loop over elements
           var_inc += n_vec_dim;
         } // end loop on variables in this system
  
       var_num += nv_sys_split;
     } // end loop over systems
  
   // Sum the nodal solution values and repeat counts.
   parallel_soln.close();
   repeat_count.close();
  
   // If there were gaps in the node numbering, there will be
   // corresponding zeros in the parallel_soln and repeat_count
   // vectors.  We need to set those repeat_count entries to 1
   // in order to avoid dividing by zero.
   if (n_gaps)
     {
       for (numeric_index_type i=repeat_count.first_local_index();
            i<repeat_count.last_local_index(); ++i)
         {
           // repeat_count entries are integral values but let's avoid a
           // direct floating point comparison with 0 just in case some
           // roundoff noise crept in during vector assembly?
           if (std::abs(repeat_count(i)) < TOLERANCE)
             repeat_count.set(i, 1.);
         }
  
       // Make sure the repeat_count vector is up-to-date on all
       // processors.
       repeat_count.close();
     }
  
   // Divide to get the average value at the nodes
   parallel_soln /= repeat_count;
  
   return std::unique_ptr<NumericVector<Number>>(parallel_soln_ptr.release());
 }

References libMesh::ParallelObject::_communicator, libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_systems, std::abs(), libMesh::MeshBase::active_local_element_ptr_range(), libMesh::Variable::active_on_subdomain(), libMesh::NumericVector< T >::add(), libMesh::NumericVector< T >::build(), libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::System::current_local_solution, dim, distance(), libMesh::DofMap::dof_indices(), end, libMesh::FEInterface::field_type(), libMesh::NumericVector< T >::first_local_index(), libMesh::System::get_dof_map(), libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::NumericVector< T >::last_local_index(), libMesh::libmesh_assert(), libMesh::MeshBase::local_nodes_begin(), libMesh::MeshBase::local_nodes_end(), libMesh::MeshBase::max_node_id(), libMesh::MeshBase::mesh_dimension(), libMesh::System::n_vars(), libMesh::FEInterface::n_vec_dim(), libMesh::FEInterface::nodal_soln(), libMesh::System::number(), libMesh::PARALLEL, libMesh::NumericVector< T >::set(), libMesh::System::solution, libMesh::TOLERANCE, libMesh::TYPE_VECTOR, libMesh::System::update(), libMesh::System::variable(), and libMesh::System::variable_type().

Referenced by libMesh::EquationSystems::build_solution_vector(), and libMesh::MeshOutput< MeshBase >::write_nodal_data().

◆ build_solution_vector() [1/2]

void libMesh::EquationSystems::build_solution_vector	(	std::vector< Number > &	soln,
		const std::set< std::string > *	system_names = `nullptr`
	)		const

inherited

Fill the input vector soln with solution values.

The entries will be in variable-major format (corresponding to the names from build_variable_names()). If systems_names!=nullptr, only include data from the specified systems.

Definition at line 826 of file equation_systems.C.

 {
   LOG_SCOPE("build_solution_vector()", "EquationSystems");
  
   // Call the parallel implementation
   std::unique_ptr<NumericVector<Number>> parallel_soln =
     this->build_parallel_solution_vector(system_names);
  
   // Localize the NumericVector into the provided std::vector.
   parallel_soln->localize_to_one(soln);
 }

References libMesh::EquationSystems::build_parallel_solution_vector().

◆ build_solution_vector() [2/2]

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

inherited

Fill the input vector soln with the solution values for the system named name.

Note: 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 578 of file equation_systems.C.

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

Referenced by libMesh::MeshOutput< MeshBase >::write_equation_systems().

◆ build_variable_names()

void libMesh::EquationSystems::build_variable_names	(	std::vector< std::string > &	var_names,
		const FEType *	type = `nullptr`,
		const std::set< std::string > *	system_names = `nullptr`
	)		const

inherited

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

If type is passed, only variables of the specified type will be populated. If systems_names!=nullptr, only include names from the specified systems.

Definition at line 476 of file equation_systems.C.

 {
   unsigned int var_num=0;
  
   const_system_iterator       pos = _systems.begin();
   const const_system_iterator end = _systems.end();
  
   // Need to size var_names by scalar variables plus all the
   // vector components for all the vector variables
   //Could this be replaced by a/some convenience methods?[PB]
   {
     unsigned int n_scalar_vars = 0;
     unsigned int n_vector_vars = 0;
  
     for (; pos != end; ++pos)
       {
         // Check current system is listed in system_names, and skip pos if not
         bool use_current_system = (system_names == nullptr);
         if (!use_current_system)
           use_current_system = system_names->count(pos->first);
         if (!use_current_system || pos->second->hide_output())
           continue;
  
         for (auto vn : IntRange<unsigned int>(0, pos->second->n_vars()))
           {
             if (FEInterface::field_type(pos->second->variable_type(vn)) == TYPE_VECTOR)
               n_vector_vars++;
             else
               n_scalar_vars++;
           }
       }
  
     // Here, we're assuming the number of vector components is the same
     // as the mesh dimension. Will break for mixed dimension meshes.
     unsigned int dim = this->get_mesh().mesh_dimension();
     unsigned int nv = n_scalar_vars + dim*n_vector_vars;
  
     // We'd better not have more than dim*his->n_vars() (all vector variables)
     libmesh_assert_less_equal ( nv, dim*this->n_vars() );
  
     // Here, we're assuming the number of vector components is the same
     // as the mesh dimension. Will break for mixed dimension meshes.
  
     var_names.resize( nv );
   }
  
   // reset
   pos = _systems.begin();
  
   for (; pos != end; ++pos)
     {
       // Check current system is listed in system_names, and skip pos if not
       bool use_current_system = (system_names == nullptr);
       if (!use_current_system)
         use_current_system = system_names->count(pos->first);
       if (!use_current_system || pos->second->hide_output())
         continue;
  
       for (auto vn : IntRange<unsigned int>(0, pos->second->n_vars()))
         {
           const std::string & var_name = pos->second->variable_name(vn);
           const FEType & fe_type = pos->second->variable_type(vn);
  
           unsigned int n_vec_dim = FEInterface::n_vec_dim( pos->second->get_mesh(), fe_type);
  
           // Filter on the type if requested
           if (type == nullptr || (type && *type == fe_type))
             {
               if (FEInterface::field_type(fe_type) == TYPE_VECTOR)
                 {
                   switch(n_vec_dim)
                     {
                     case 0:
                     case 1:
                       var_names[var_num++] = var_name;
                       break;
                     case 2:
                       var_names[var_num++] = var_name+"_x";
                       var_names[var_num++] = var_name+"_y";
                       break;
                     case 3:
                       var_names[var_num++] = var_name+"_x";
                       var_names[var_num++] = var_name+"_y";
                       var_names[var_num++] = var_name+"_z";
                       break;
                     default:
                       libmesh_error_msg("Invalid dim in build_variable_names");
                     }
                 }
               else
                 var_names[var_num++] = var_name;
             }
         }
     }
   // Now resize again in case we filtered any names
   var_names.resize(var_num);
 }

References libMesh::EquationSystems::_systems, dim, end, libMesh::FEInterface::field_type(), libMesh::EquationSystems::get_mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::EquationSystems::n_vars(), libMesh::FEInterface::n_vec_dim(), and libMesh::TYPE_VECTOR.

Referenced by libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::ExodusII_IO::write_discontinuous_exodusII(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data(), libMesh::MeshOutput< MeshBase >::write_equation_systems(), libMesh::Nemesis_IO::write_nodal_data(), and libMesh::MeshOutput< MeshBase >::write_nodal_data().

◆ clear()

void libMesh::EquationSystems::clear ( )

virtualinherited

Restores the data structure to a pristine state.

Definition at line 75 of file equation_systems.C.

 {
   // 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 = nullptr;
  
       _systems.erase (pos);
     }
 }

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

Referenced by main(), and libMesh::EquationSystems::~EquationSystems().

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inlineinherited

Returns: A reference to the Parallel::Communicator object used by this mesh.

Definition at line 94 of file parallel_object.h.

95 { return _communicator; }

References libMesh::ParallelObject::_communicator.

◆ compare()

bool libMesh::EquationSystems::compare	(	const EquationSystems &	other_es,
		const Real	threshold,
		const bool	verbose
	)		const

virtualinherited

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 1217 of file equation_systems.C.

 {
   // 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;
     }
 }

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

Referenced by do_compare().

◆ delete_system()

void libMesh::EquationSystems::delete_system ( const std::string & name )

inherited

Remove the system named name from the systems array.

Definition at line 431 of file equation_systems.C.

 {
   libmesh_deprecated();
  
   if (!_systems.count(name))
     libmesh_error_msg("ERROR: no system named " << name);
  
   delete _systems[name];
  
   _systems.erase (name);
 }

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

◆ disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 106 of file reference_counter.C.

 {
   _enable_print_counter = false;
   return;
 }

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::LibMeshInit::LibMeshInit().

◆ disable_refine_in_reinit()

void libMesh::EquationSystems::disable_refine_in_reinit ( )

inlineinherited

Calls to reinit() will not try to coarsen or refine the mesh.

Definition at line 534 of file equation_systems.h.

534 { this->_refine_in_reinit = false; }

References libMesh::EquationSystems::_refine_in_reinit.

Referenced by EquationSystemsTest::testRefineThenReinitPreserveFlags().

◆ dt()

Real Biharmonic::dt ( )

inline

Definition at line 81 of file biharmonic.h.

81 { return _dt; }

References _dt.

◆ dt0()

Real Biharmonic::dt0 ( )

inline

Definition at line 80 of file biharmonic.h.

80 { return _dt0; }

References _dt0.

◆ enable_default_ghosting()

void libMesh::EquationSystems::enable_default_ghosting ( bool enable )

virtualinherited

Enable or disable default ghosting functors on the Mesh and on all Systems.

Standard ghosting is enabled by default. If disabled, default ghosting will also be disabled on any later added systems.

Unless other equivalent ghosting functors have been added, removing the default coupling functor is only safe for explicit solves, and removing the default algebraic ghosting functor is only safe for codes where no evaluations on neighbor cells (e.g. no jump error estimators) are done.

Definition at line 312 of file equation_systems.C.

 {
   _enable_default_ghosting = enable;
   MeshBase &mesh = this->get_mesh();
  
   if (enable)
     mesh.add_ghosting_functor(mesh.default_ghosting());
   else
     mesh.remove_ghosting_functor(mesh.default_ghosting());
  
   for (unsigned int i=0; i != this->n_systems(); ++i)
     {
       DofMap & dof_map = this->get_system(i).get_dof_map();
       if (enable)
         dof_map.add_default_ghosting();
       else
         dof_map.remove_default_ghosting();
     }
 }

References libMesh::EquationSystems::_enable_default_ghosting, libMesh::DofMap::add_default_ghosting(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), mesh, libMesh::EquationSystems::n_systems(), and libMesh::DofMap::remove_default_ghosting().

Referenced by EquationSystemsTest::testDisableDefaultGhosting().

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

Methods to enable/disable the reference counter output from print_info()

Definition at line 100 of file reference_counter.C.

 {
   _enable_print_counter = true;
   return;
 }

References libMesh::ReferenceCounter::_enable_print_counter.

◆ enable_refine_in_reinit()

void libMesh::EquationSystems::enable_refine_in_reinit ( )

inlineinherited

Calls to reinit() will also do two-step coarsen-then-refine.

Definition at line 529 of file equation_systems.h.

529 { this->_refine_in_reinit = true; }

References libMesh::EquationSystems::_refine_in_reinit.

◆ find_variable_numbers()

std::vector< std::pair< unsigned int, unsigned int > > libMesh::EquationSystems::find_variable_numbers	(	std::vector< std::string > &	names,
		const FEType *	type = `nullptr`
	)		const

inherited

Finds system and variable numbers for any variables of type corresponding to the entries in the input 'names' vector.

Definition at line 904 of file equation_systems.C.

 {
   // This function must be run on all processors at once
   parallel_object_only();
  
   libmesh_assert (this->n_systems());
  
   // If the names vector has entries, we will only populate the soln vector
   // with names included in that list.  Note: The names vector may be
   // reordered upon exiting this function
   std::vector<std::pair<unsigned int, unsigned int>> var_nums;
   std::vector<std::string> filter_names = names;
   bool is_filter_names = !filter_names.empty();
  
   names.clear();
  
   const_system_iterator       pos = _systems.begin();
   const const_system_iterator end = _systems.end();
   unsigned sys_ctr = 0;
  
   for (; pos != end; ++pos, ++sys_ctr)
     {
       const System & system = *(pos->second);
       const unsigned int nv_sys = system.n_vars();
  
       for (unsigned int var=0; var < nv_sys; ++var)
         {
           const std::string & name = system.variable_name(var);
           if ((type && system.variable_type(var) != *type) ||
               (is_filter_names && std::find(filter_names.begin(), filter_names.end(), name) == filter_names.end()))
             continue;
  
           // Otherwise, this variable should be output
           var_nums.push_back
             (std::make_pair(system.number(), var));
         }
     }
  
   std::sort(var_nums.begin(), var_nums.end());
  
   for (const auto & var_num : var_nums)
     {
       const std::string & name =
         this->get_system(var_num.first).variable_name(var_num.second);
       if (names.empty() || names.back() != name)
         names.push_back(name);
     }
  
   return var_nums;
 }

References end, libMesh::libmesh_assert(), libMesh::System::n_vars(), libMesh::Quality::name(), libMesh::System::number(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::Nemesis_IO::write_element_data(), and libMesh::Nemesis_IO::write_nodal_data().

◆ get_info() [1/2]

std::string libMesh::ReferenceCounter::get_info ( )

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

 {
 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
  
   std::ostringstream oss;
  
   oss << '\n'
       << " ---------------------------------------------------------------------------- \n"
       << "| Reference count information                                                |\n"
       << " ---------------------------------------------------------------------------- \n";
  
   for (const auto & pr : _counts)
     {
       const std::string name(pr.first);
       const unsigned int creations    = pr.second.first;
       const unsigned int destructions = pr.second.second;
  
       oss << "| " << name << " reference count information:\n"
           << "|  Creations:    " << creations    << '\n'
           << "|  Destructions: " << destructions << '\n';
     }
  
   oss << " ---------------------------------------------------------------------------- \n";
  
   return oss.str();
  
 #else
  
   return "";
  
 #endif
 }

References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().

Referenced by libMesh::ReferenceCounter::print_info().

◆ get_info() [2/2]

std::string libMesh::EquationSystems::get_info ( ) const

virtualinherited

Returns: A string containing information about the systems, flags, and parameters.

Definition at line 1278 of file equation_systems.C.

 {
   std::ostringstream oss;
  
   oss << " 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)
     oss << pos->second->get_info();
  
  
   //   // Possibly print the parameters
   //   if (!this->parameters.empty())
   //     {
   //       oss << "  n_parameters()=" << this->n_parameters() << '\n';
   //       oss << "   Parameters:\n";
  
   //       for (const auto & pr : _parameters)
   //         oss << "    "
   //             << "\""
   //             << pr.first
   //             << "\""
   //             << "="
   //             << pr.second
   //             << '\n';
   //     }
  
   return oss.str();
 }

References libMesh::EquationSystems::_systems, end, and libMesh::EquationSystems::n_systems().

Referenced by libMesh::EquationSystems::print_info().

◆ get_mesh() [1/2]

MeshBase & libMesh::EquationSystems::get_mesh ( )

inlineinherited

Returns: A reference to the mesh

Definition at line 645 of file equation_systems.h.

 {
   return _mesh;
 }

References libMesh::EquationSystems::_mesh.

◆ get_mesh() [2/2]

const MeshBase & libMesh::EquationSystems::get_mesh ( ) const

inlineinherited

Returns: A constant reference to the mesh

Definition at line 637 of file equation_systems.h.

 {
   return _mesh;
 }

References libMesh::EquationSystems::_mesh.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::EquationSystems::_read_impl(), assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_cd(), assemble_elasticity(), assemble_ellipticdg(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), assembly_with_dg_fem_context(), libMesh::EquationSystems::build_variable_names(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::EquationSystems::enable_default_ghosting(), libMesh::AdjointRefinementEstimator::estimate_error(), fill_dirichlet_bc(), libMesh::MeshFunction::init(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), libMesh::EquationSystems::reinit_solutions(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), run_timestepping(), scale_mesh_and_plot(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), libMesh::DTKSolutionTransfer::transfer(), transform_mesh_and_plot(), libMesh::EquationSystems::write(), libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems(), libMesh::MeshOutput< MeshBase >::write_equation_systems(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), write_output(), and write_output_solvedata().

◆ get_solution()

void libMesh::EquationSystems::get_solution	(	std::vector< Number > &	soln,
		std::vector< std::string > &	names
	)		const

inherited

Retrieve the solution data for CONSTANT MONOMIALs.

If names is populated, only the variables corresponding to those names will be retrieved. This can be used to filter which variables are retrieved.

Definition at line 873 of file equation_systems.C.

 {
   libmesh_deprecated();
   this->build_elemental_solution_vector(soln, names);
 }

References libMesh::EquationSystems::build_elemental_solution_vector().

◆ get_system() [1/8]

template<typename T_sys >

T_sys & libMesh::EquationSystems::get_system ( const std::string & name )

inlineinherited

Returns: A writable 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 776 of file equation_systems.h.

 {
   system_iterator pos = _systems.find(name);
  
   // Check for errors
   if (pos == _systems.end())
     libmesh_error_msg("ERROR: no system named " << name << " found!");
  
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

◆ get_system() [2/8]

System & libMesh::EquationSystems::get_system ( const std::string & name )

inlineinherited

Returns: A writable reference to the system named name.

Definition at line 803 of file equation_systems.h.

 {
   return this->get_system<System>(name);
 }

References libMesh::Quality::name().

◆ get_system() [3/8]

template<typename T_sys >

const T_sys & libMesh::EquationSystems::get_system ( const std::string & name ) const

inlineinherited

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 757 of file equation_systems.h.

 {
   const_system_iterator pos = _systems.find(name);
  
   // Check for errors
   if (pos == _systems.end())
     libmesh_error_msg("ERROR: no system named \"" << name << "\" found!");
  
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

◆ get_system() [4/8]

const System & libMesh::EquationSystems::get_system ( const std::string & name ) const

inlineinherited

Returns: A constant reference to the system named name.

Definition at line 795 of file equation_systems.h.

 {
   return this->get_system<System>(name);
 }

References libMesh::Quality::name().

◆ get_system() [5/8]

template<typename T_sys >

T_sys & libMesh::EquationSystems::get_system ( const unsigned int num )

inlineinherited

Returns: A writable reference 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 731 of file equation_systems.h.

 {
   libmesh_assert_less (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_error_msg("ERROR: no system number " << num << " found!");
  
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

References libMesh::EquationSystems::_systems, end, and libMesh::EquationSystems::n_systems().

◆ get_system() [6/8]

System & libMesh::EquationSystems::get_system ( const unsigned int num )

inlineinherited

Returns: A writable reference to the system number num.

Definition at line 819 of file equation_systems.h.

 {
   return this->get_system<System>(num);
 }

◆ get_system() [7/8]

template<typename T_sys >

const T_sys & libMesh::EquationSystems::get_system ( const unsigned int num ) const

inlineinherited

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 706 of file equation_systems.h.

 {
   libmesh_assert_less (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_error_msg("ERROR: no system number " << num << " found!");
  
   // Attempt dynamic cast
   return *cast_ptr<T_sys *>(pos->second);
 }

References libMesh::EquationSystems::_systems, end, and libMesh::EquationSystems::n_systems().

◆ get_system() [8/8]

const System & libMesh::EquationSystems::get_system ( const unsigned int num ) const

inlineinherited

Returns: A constant reference to system number num.

Definition at line 811 of file equation_systems.h.

 {
   return this->get_system<System>(num);
 }

◆ get_vars_active_subdomains()

void libMesh::EquationSystems::get_vars_active_subdomains	(	const std::vector< std::string > &	names,
		std::vector< std::set< subdomain_id_type >> &	vars_active_subdomains
	)		const

inherited

Retrieve vars_active_subdomains, which indicates the active subdomains for each variable in names.

Definition at line 841 of file equation_systems.C.

 {
   unsigned int var_num=0;
  
   vars_active_subdomains.clear();
   vars_active_subdomains.resize(names.size());
  
   const_system_iterator       pos = _systems.begin();
   const const_system_iterator end = _systems.end();
  
   for (; pos != end; ++pos)
     {
       for (auto vn : IntRange<unsigned int>(0, pos->second->n_vars()))
         {
           const std::string & var_name = pos->second->variable_name(vn);
  
           auto names_it = std::find(names.begin(), names.end(), var_name);
           if(names_it != names.end())
             {
               const Variable & variable = pos->second->variable(vn);
               const std::set<subdomain_id_type> & active_subdomains = variable.active_subdomains();
               vars_active_subdomains[var_num++] = active_subdomains;
             }
         }
     }
  
   libmesh_assert_equal_to(var_num, names.size());
 }

References libMesh::EquationSystems::_systems, libMesh::Variable::active_subdomains(), and end.

Referenced by libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), and libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data().

◆ has_system()

bool libMesh::EquationSystems::has_system ( const std::string & name ) const

inlineinherited

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

Definition at line 694 of file equation_systems.h.

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

References libMesh::EquationSystems::_systems, and libMesh::Quality::name().

Referenced by libMesh::EnsightIO::add_scalar(), libMesh::EnsightIO::add_vector(), libMesh::ExactSolution::compute_error(), libMesh::ExactSolution::error_norm(), and main().

◆ increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string & name )

inlineprotectedinherited

Increments the construction counter.

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

Definition at line 181 of file reference_counter.h.

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

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

◆ increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string & name )

inlineprotectedinherited

Increments the destruction counter.

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

Definition at line 194 of file reference_counter.h.

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

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

◆ init()

void Biharmonic::init ( )

virtual

Initialize all the systems.

Reimplemented from libMesh::EquationSystems.

Definition at line 213 of file biharmonic.C.

 {
   if (_verbose)
     libMesh::out << ">>> Initializing Biharmonic\n";
  
   _dt  =  0;
   _o_count = 0;
   EquationSystems::init();
  
   if (_verbose)
     libMesh::out << "<<< Initializing Biharmonic\n";
 }

References _dt, _o_count, _verbose, libMesh::TriangleWrapper::init(), and libMesh::out.

◆ n_active_dofs()

std::size_t libMesh::EquationSystems::n_active_dofs ( ) const

inherited

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

Definition at line 1362 of file equation_systems.C.

 {
   std::size_t 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;
 }

References libMesh::EquationSystems::_systems, and end.

Referenced by main(), and write_output_solvedata().

◆ n_dofs()

std::size_t libMesh::EquationSystems::n_dofs ( ) const

inherited

Returns: The total number of degrees of freedom in all systems.

Definition at line 1346 of file equation_systems.C.

 {
   std::size_t 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;
 }

References libMesh::EquationSystems::_systems, and end.

Referenced by Biharmonic::JR::bounds(), and Biharmonic::JR::residual_and_jacobian().

◆ n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

inlinestaticinherited

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

Definition at line 83 of file reference_counter.h.

84 { return _n_objects; }

References libMesh::ReferenceCounter::_n_objects.

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns: The number of processors in the group.

Definition at line 100 of file parallel_object.h.

101 { return cast_int<processor_id_type>(_communicator.size()); }

References libMesh::ParallelObject::_communicator.

◆ n_systems()

unsigned int libMesh::EquationSystems::n_systems ( ) const

inlineinherited

Returns: The number of equation systems.

Definition at line 652 of file equation_systems.h.

 {
   return cast_int<unsigned int>(_systems.size());
 }

References libMesh::EquationSystems::_systems.

◆ n_vars()

unsigned int libMesh::EquationSystems::n_vars ( ) const

inherited

Returns: The total number of variables in all systems.

Definition at line 1331 of file equation_systems.C.

 {
   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;
 }

References libMesh::EquationSystems::_systems, and end.

Referenced by libMesh::EquationSystems::build_variable_names().

◆ output()

void Biharmonic::output	(	int	timestep,
		const Real &	t,
		Real &	o_t,
		bool	force = `false`
	)

Definition at line 251 of file biharmonic.C.

 {
   if (!force && t - o_t < _o_dt)
     return;
  
   ++_o_count;
  
   if (_verbose)
     libMesh::out << "Writing state "
                  << timestep
                  << " at time "
                  << t
                  << " to file "
                  << _ofile
                  << "; output a total of "
                  << _o_count
                  << " states so far\n";
  
   _exio->write_timestep(_ofile, *this, timestep, t);
  
   if (!force)
     o_t = t;
 }

References _exio, _o_count, _o_dt, _ofile, _verbose, and libMesh::out.

Referenced by run().

◆ print_info() [1/2]

void libMesh::EquationSystems::print_info ( std::ostream & os = libMesh::out ) const

inherited

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

Definition at line 1314 of file equation_systems.C.

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

References libMesh::EquationSystems::get_info().

Referenced by assemble_and_solve(), do_compare(), main(), and libMesh::operator<<().

◆ print_info() [2/2]

void libMesh::ReferenceCounter::print_info ( std::ostream & out = libMesh::out )

staticinherited

Prints the reference information, by default to libMesh::out.

Definition at line 87 of file reference_counter.C.

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

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns: The rank of this processor in the group.

Definition at line 106 of file parallel_object.h.

107 { return cast_int<processor_id_type>(_communicator.rank()); }

References libMesh::ParallelObject::_communicator.

◆ read() [1/4]

template<typename InValType >

void libMesh::EquationSystems::read	(	const std::string &	name,
		const unsigned int	read_flags = `(READ_HEADER \| READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inherited

Definition at line 72 of file equation_systems_io.C.

 {
   XdrMODE mode = READ;
   if (name.find(".xdr") != std::string::npos)
     mode = DECODE;
   this->read(name, mode, read_flags, partition_agnostic);
  
 #ifdef LIBMESH_ENABLE_AMR
   MeshRefinement mesh_refine(_mesh);
   mesh_refine.clean_refinement_flags();
 #endif
 }

References libMesh::EquationSystems::_mesh, libMesh::MeshRefinement::clean_refinement_flags(), libMesh::DECODE, libMesh::Quality::name(), libMesh::READ, and libMesh::EquationSystems::read().

◆ read() [2/4]

template void libMesh::EquationSystems::read< Real >	(	const std::string &	name,
		const unsigned int	read_flags = `(READ_HEADER\|READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inlineinherited

Definition at line 443 of file equation_systems.h.

446 { read<Number>(name, read_flags, partition_agnostic); }

References libMesh::Quality::name().

◆ read() [3/4]

template void libMesh::EquationSystems::read< Real >	(	const std::string &	name,
		const XdrMODE	mode,
		const unsigned int	read_flags = `(READ_HEADER\|READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inlineinherited

Definition at line 432 of file equation_systems.h.

436 { read<Number>(name, mode, read_flags, partition_agnostic); }

References libMesh::Quality::name().

◆ read() [4/4]

template<typename InValType >

void libMesh::EquationSystems::read	(	const std::string &	name,
		const XdrMODE	mode,
		const unsigned int	read_flags = `(READ_HEADER \| READ_DATA)`,
		bool	partition_agnostic = `true`
	)

inherited

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: 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

Parameters

name	Name of the file to be read.
read_flags	Single flag created by bitwise-OR'ing several flags together.
mode	Controls whether reading is done in binary or ascii mode.
partition_agnostic	If true then the mesh and degrees of freedom will be temporarily renumbered in a partition agnostic way so that files written using "n" mpi processes can be re-read on "m" mpi processes. This renumbering is not compatible with meshes that have two nodes in exactly the same position!

Definition at line 90 of file equation_systems_io.C.

 {
   // 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
   libmesh_try
     {
       this->_read_impl<InValType> (name, mode, read_flags, partition_agnostic);
     }
  
   // If that fails, try it again but explicitly request we look for infinite element info
   libmesh_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;
  
       libmesh_try
         {
           this->_read_impl<InValType> (name, mode, read_flags | EquationSystems::TRY_READ_IFEMS, partition_agnostic);
         }
  
       // If all that failed, we are out of ideas here...
       libmesh_catch (...)
         {
           libMesh::out << "\n*********************************************************************\n"
                        << "Well, at least we tried!\n"
                        << "Good Luck!!\n"
                        << "*********************************************************************\n"
                        << std::endl;
           LIBMESH_THROW();
         }
     }
  
 #ifdef LIBMESH_ENABLE_AMR
   MeshRefinement mesh_refine(_mesh);
   mesh_refine.clean_refinement_flags();
 #endif
 }

References libMesh::EquationSystems::_mesh, libMesh::MeshRefinement::clean_refinement_flags(), libMesh::Quality::name(), libMesh::out, and libMesh::EquationSystems::TRY_READ_IFEMS.

Referenced by libMesh::EquationSystems::_read_impl(), main(), libMesh::EquationSystems::read(), and SlitMeshRefinedSystemTest::testRestart().

◆ refine_in_reinit_flag()

bool libMesh::EquationSystems::refine_in_reinit_flag ( )

inlineinherited

Returns: Whether or not calls to reinit() will try to coarsen/refine the mesh

Definition at line 539 of file equation_systems.h.

539 { return this->_refine_in_reinit; }

References libMesh::EquationSystems::_refine_in_reinit.

◆ reinit()

void libMesh::EquationSystems::reinit ( )

virtualinherited

Handle any mesh changes and reinitialize all the systems on the updated mesh.

Definition at line 121 of file equation_systems.C.

 {
   const bool mesh_changed = this->reinit_solutions();
  
   // If the mesh has changed, systems will need to reinitialize their
   // own data on the new mesh.
   if (mesh_changed)
     this->reinit_systems();
 }

References libMesh::EquationSystems::reinit_solutions(), and libMesh::EquationSystems::reinit_systems().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), assemble_and_solve(), libMesh::AdjointRefinementEstimator::estimate_error(), main(), run_timestepping(), SlitMeshRefinedSystemTest::setUp(), EquationSystemsTest::testPostInitAddElem(), EquationSystemsTest::testPostInitAddRealSystem(), EquationSystemsTest::testPostInitAddSystem(), SystemsTest::testProjectCube(), SystemsTest::testProjectLine(), SystemsTest::testProjectSquare(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testReinitWithNodeElem(), and EquationSystemsTest::testRepartitionThenReinit().

◆ reinit_solutions()

bool libMesh::EquationSystems::reinit_solutions ( )

inherited

Handle any mesh changes and project any solutions onto the updated mesh.

Returns: Whether or not the mesh may have changed.

Definition at line 133 of file equation_systems.C.

 {
   parallel_object_only();
  
   const unsigned int n_sys = this->n_systems();
   libmesh_assert_not_equal_to (n_sys, 0);
  
   // We may have added new systems since our last
   // EquationSystems::(re)init call
   bool _added_new_systems = false;
   for (unsigned int i=0; i != n_sys; ++i)
     if (!this->get_system(i).is_initialized())
       _added_new_systems = true;
  
   if (_added_new_systems)
     {
       // Our DofObjects will need space for the additional systems
       for (auto & node : _mesh.node_ptr_range())
         node->set_n_systems(n_sys);
  
       for (auto & elem : _mesh.element_ptr_range())
         elem->set_n_systems(n_sys);
  
       // And any new systems will need initialization
       for (unsigned int i=0; i != n_sys; ++i)
         if (!this->get_system(i).is_initialized())
           this->get_system(i).init();
     }
  
  
   // We used to assert that all nodes and elements *already* had
   // n_systems() properly set; however this is false in the case where
   // user code has manually added nodes and/or elements to an
   // already-initialized system.
  
   // Make sure all the \p DofObject entities know how many systems
   // there are.
   {
     // All the nodes
     for (auto & node : _mesh.node_ptr_range())
       node->set_n_systems(this->n_systems());
  
     // All the elements
     for (auto & elem : _mesh.element_ptr_range())
       elem->set_n_systems(this->n_systems());
   }
  
   // 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 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);
  
         // Even if the system doesn't have any variables in it we want
         // consistent behavior; e.g. distribute_dofs should have the
         // opportunity to count up zero dofs on each processor.
         //
         // Who's been adding zero-var systems anyway, outside of my
         // unit tests? - RHS
         // if (!sys.n_vars())
         // continue;
  
         sys.get_dof_map().distribute_dofs(_mesh);
  
         // Recreate any user or internal constraints
         sys.reinit_constraints();
  
         sys.prolong_vectors();
       }
     mesh_changed = true;
   }
  
   if (this->_refine_in_reinit)
     {
       // Don't override any user refinement settings
       MeshRefinement mesh_refine(_mesh);
       mesh_refine.face_level_mismatch_limit() = 0; // unlimited
       mesh_refine.overrefined_boundary_limit() = -1; // unlimited
       mesh_refine.underrefined_boundary_limit() = -1; // unlimited
  
       // 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);
               sys.get_dof_map().distribute_dofs(_mesh);
               sys.reinit_constraints();
               sys.restrict_vectors();
             }
           mesh_changed = 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);
               sys.get_dof_map().distribute_dofs(_mesh);
               sys.reinit_constraints();
               sys.prolong_vectors();
             }
           mesh_changed = true;
         }
     }
  
   return mesh_changed;
  
 #endif // #ifdef LIBMESH_ENABLE_AMR
  
   return false;
 }

References libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_refine_in_reinit, libMesh::MeshRefinement::coarsen_elements(), libMesh::MeshBase::contract(), libMesh::DofMap::distribute_dofs(), libMesh::MeshBase::element_ptr_range(), libMesh::MeshRefinement::face_level_mismatch_limit(), libMesh::System::get_dof_map(), libMesh::EquationSystems::get_mesh(), libMesh::EquationSystems::get_system(), libMesh::EquationSystems::n_systems(), libMesh::MeshBase::node_ptr_range(), libMesh::MeshRefinement::overrefined_boundary_limit(), libMesh::System::prolong_vectors(), libMesh::MeshRefinement::refine_elements(), libMesh::System::reinit_constraints(), libMesh::System::restrict_vectors(), and libMesh::MeshRefinement::underrefined_boundary_limit().

Referenced by libMesh::EquationSystems::reinit().

◆ reinit_systems()

void libMesh::EquationSystems::reinit_systems ( )

virtualinherited

Reinitialize all systems on the current mesh.

Definition at line 266 of file equation_systems.C.

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

References libMesh::EquationSystems::get_system(), and libMesh::EquationSystems::n_systems().

Referenced by libMesh::EquationSystems::reinit().

◆ run()

void Biharmonic::run ( )

Definition at line 287 of file biharmonic.C.

 {
   Real t = _t0, o_t = 0.0;
   int timestep = 1;
  
   // Force-write the initial timestep
   output(timestep, t, o_t, true);
  
   while (t < _t1)
     {
       ++timestep;
  
       // A pretty update message
       if (_verbose)
         libMesh::out << "Solving for state " << timestep << ", time " << t << "\n";
  
       // Move biharmonic one timestep forward
       step();
  
       // Keep track of time and timestep
       t += _dt;
  
       // Output
       output(timestep, t, o_t);
     } // while(t < _t1)
  
   // Force-write the final timestep
   output(timestep, t, o_t, true);
 }

References _dt, _t0, _t1, _verbose, libMesh::out, output(), libMesh::Real, and step().

◆ sensitivity_solve()

void libMesh::EquationSystems::sensitivity_solve ( const ParameterVector & parameters )

virtualinherited

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 456 of file equation_systems.C.

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

References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), and libMesh::EquationSystems::n_systems().

◆ solve()

void libMesh::EquationSystems::solve ( )

virtualinherited

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 446 of file equation_systems.C.

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

References libMesh::EquationSystems::get_system(), libMesh::libmesh_assert(), and libMesh::EquationSystems::n_systems().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error().

◆ step()

void Biharmonic::step ( const Real & dt = -1.0 )

Definition at line 230 of file biharmonic.C.

 {
   // We need to update the old solution vector.
   // The old solution vector will be the current solution vector from the
   // previous time step. We use vector assignment.  Only TransientSystems
   // (and systems derived from them) contain old solutions.
   if (dt_in < 0)
     _dt = _dt0;
   else
     _dt = dt_in;
  
   *(_jr->old_local_solution) = *(_jr->current_local_solution);
  
   // this will localize the current solution, resulting in a
   // current_local_solution with correct ghost values
   _jr->solve();
 }

References _dt, _dt0, and _jr.

Referenced by run().

◆ update()

void libMesh::EquationSystems::update ( )

inherited

Updates local values for all the systems.

Definition at line 334 of file equation_systems.C.

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

References libMesh::EquationSystems::get_system(), and libMesh::EquationSystems::n_systems().

Referenced by libMesh::EquationSystems::_read_impl(), and main().

◆ verbose()

bool Biharmonic::verbose ( )

inline

Definition at line 79 of file biharmonic.h.

79 { return _verbose; }

References _verbose.

◆ viewParameters()

void Biharmonic::viewParameters ( )

Definition at line 166 of file biharmonic.C.

 {
   libMesh::out << "Biharmonic parameters:\n";
  
   // Print verbosity status
   if (_verbose)
     libMesh::out << "verbose mode is on\n";
   else
     libMesh::out << "verbose mode is off\n";
  
   // Print parameters
   libMesh::out << "mesh dimension           = " << _dim <<               "\n";
   libMesh::out << "initial linear mesh size = " << _N   <<               "\n";
   libMesh::out << "kappa                    = " << _kappa <<             "\n";
   libMesh::out << "growth                   = " << (int)_growth <<       "\n";
   libMesh::out << "degenerate               = " << (int)_degenerate <<   "\n";
   libMesh::out << "Cahn-Hillard             = " << (int)_cahn_hillard << "\n";
   libMesh::out << "netforce                 = " << (int)_netforce <<     "\n";
   libMesh::out << "energy                   = " << _energy        <<     "\n";
   libMesh::out << "tol                      = " << _tol           <<     "\n";
   libMesh::out << "theta                    = " << _theta         <<     "\n";
   libMesh::out << "theta_c                  = " << _theta_c       <<     "\n";
   libMesh::out << "log truncation           = " << _log_truncation <<    "\n";
   libMesh::out << "initial timestep size    = " << _dt0            <<    "\n";
  
   if (_initialState == STRIP)
     libMesh::out << "initial state:             strip\n";
  
   if (_initialState == ROD)
     libMesh::out << "initial state:             rod\n";
  
   if (_initialState == BALL)
     libMesh::out << "initial state:             ball\n";
  
   libMesh::out << "initial state center     = " << _initialCenter(0) << "\n";
   libMesh::out << "initial state width      = " << _initialWidth << "\n";
   libMesh::out << "initial time (min_time)  = " << _t0 << "\n";
   libMesh::out << "integration time         = " << _T  << "\n";
   libMesh::out << "final time   (max_time)  = " << _t1 << "\n";
   libMesh::out << "Crank-Nicholson weight   = " << _cnWeight << "\n";
   libMesh::out << "Output timestep          = " << _o_dt << "\n";
   libMesh::out << "Output filename base:      " <<  _ofile_base << "\n";
 }

References _cahn_hillard, _cnWeight, _degenerate, _dim, _dt0, _energy, _growth, _initialCenter, _initialState, _initialWidth, _kappa, _log_truncation, _N, _netforce, _o_dt, _ofile_base, _T, _t0, _t1, _theta, _theta_c, _tol, _verbose, BALL, int, libMesh::out, ROD, and STRIP.

◆ write() [1/2]

void libMesh::EquationSystems::write	(	const std::string &	name,
		const unsigned int	write_flags = `(WRITE_DATA)`,
		bool	partition_agnostic = `true`
	)		const

inherited

Definition at line 366 of file equation_systems_io.C.

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

References libMesh::ENCODE, libMesh::Quality::name(), libMesh::WRITE, and libMesh::EquationSystems::write().

◆ write() [2/2]

void libMesh::EquationSystems::write	(	const std::string &	name,
		const XdrMODE	mode,
		const unsigned int	write_flags = `(WRITE_DATA)`,
		bool	partition_agnostic = `true`
	)		const

inherited

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: 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

Parameters

name	Name of the file to be read.
write_flags	Single flag created by bitwise-OR'ing several flags together.
mode	Controls whether reading is done in binary or ascii mode.
partition_agnostic	If true then the mesh and degrees of freedom will be temporarily renumbered in a partition agnostic way so that files written using "n" mpi processes can be re-read on "m" mpi processes. This renumbering is not compatible with meshes that have two nodes in exactly the same position!

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 378 of file equation_systems_io.C.

 {
   // 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
   if (partition_agnostic)
     {
       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_additional_data = write_flags & EquationSystems::WRITE_ADDITIONAL_DATA;
  
   // always write parallel files if we're instructed to write in
   // parallel
   const bool write_parallel_files  =
     (write_flags & EquationSystems::WRITE_PARALLEL_FILES)
     // Even if we're on a distributed mesh, we may or may not have a
     // consistent way of reconstructing the same mesh partitioning
     // later, but we need the same mesh partitioning if we want to
     // reread the parallel solution safely, so let's write a serial file
     // unless specifically requested not to.
     // ||
     // // but also write parallel files if we haven't been instructed to
     // // write in serial and we're on a distributed mesh
     // (!(write_flags & EquationSystems::WRITE_SERIAL_FILES) &&
     // !this->get_mesh().is_serial())
     ;
  
   // New scope so that io will close before we try to zip the file
   {
     Xdr io((this->processor_id()==0) ? name : "", mode);
     libmesh_assert (io.writing());
  
     LOG_SCOPE("write()", "EquationSystems");
  
     const unsigned int proc_id = this->processor_id();
  
     unsigned int n_sys = 0;
     for (auto & pr : _systems)
       if (!pr.second->hide_output())
         n_sys++;
  
     // set the version number in the Xdr object
     io.set_version(LIBMESH_VERSION_ID(LIBMESH_MAJOR_VERSION,
                                       LIBMESH_MINOR_VERSION,
                                       LIBMESH_MICRO_VERSION));
  
     // Only write the header information
     // if we are processor 0.
     if (proc_id == 0)
       {
         std::string comment;
         char buf[256];
  
         // 1.)
         // Write the version header
         std::string version("libMesh-" + libMesh::get_io_compatibility_version());
         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");
  
         for (auto & pr : _systems)
           {
             // Ignore this system if it has been marked as hidden
             if (pr.second->hide_output()) continue;
  
             // 3.)
             // Write the name of the sys_num-th system
             {
               const unsigned int sys_num = pr.second->number();
               std::string sys_name       = pr.first;
  
               comment =  "# Name, System No. ";
               std::sprintf(buf, "%u", sys_num);
               comment += buf;
  
               io.data (sys_name, comment.c_str());
             }
  
             // 4.)
             // Write the type of system handled
             {
               const unsigned int sys_num = pr.second->number();
               std::string sys_type       = pr.second->system_type();
  
               comment =  "# Type, System No. ";
               std::sprintf(buf, "%u", sys_num);
               comment += buf;
  
               io.data (sys_type, comment.c_str());
             }
  
             // 5.) - 9.)
             // Let System::write_header() do the job
             pr.second->write_header (io, version, write_additional_data);
           }
       }
  
     // 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(this->processor_id(),name) : "", mode);
  
         for (auto & pr : _systems)
           {
             // Ignore this system if it has been marked as hidden
             if (pr.second->hide_output()) continue;
  
             // 10.) + 11.)
             if (write_parallel_files)
               pr.second->write_parallel_data (local_io,write_additional_data);
             else
               pr.second->write_serialized_data (io,write_additional_data);
           }
       }
   }
  
   // 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 (partition_agnostic)
     const_cast<MeshBase &>(_mesh).fix_broken_node_and_element_numbering();
 }

References libMesh::EquationSystems::_mesh, libMesh::EquationSystems::_systems, libMesh::Xdr::data(), libMesh::get_io_compatibility_version(), libMesh::EquationSystems::get_mesh(), libMesh::MeshTools::Private::globally_renumber_nodes_and_elements(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::processor_id(), libMesh::Xdr::set_version(), libMesh::EquationSystems::WRITE_ADDITIONAL_DATA, libMesh::EquationSystems::WRITE_DATA, libMesh::EquationSystems::WRITE_PARALLEL_FILES, and libMesh::Xdr::writing().

Referenced by main(), libMesh::ErrorVector::plot_error(), SlitMeshRefinedSystemTest::testRestart(), libMesh::EquationSystems::write(), libMesh::NameBasedIO::write_equation_systems(), and write_output().

Friends And Related Function Documentation

◆ JR

friend class JR

friend

Definition at line 110 of file biharmonic.h.

Member Data Documentation

◆ _cahn_hillard

bool Biharmonic::_cahn_hillard

private

Definition at line 95 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _cnWeight

Real Biharmonic::_cnWeight

private

Definition at line 103 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 112 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

◆ _counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

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

◆ _degenerate

bool Biharmonic::_degenerate

private

Definition at line 95 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _dim

unsigned int Biharmonic::_dim

private

Definition at line 92 of file biharmonic.h.

Referenced by Biharmonic(), Biharmonic::JR::JR(), and viewParameters().

◆ _dt

Real Biharmonic::_dt

private

Definition at line 102 of file biharmonic.h.

Referenced by dt(), init(), run(), and step().

◆ _dt0

Real Biharmonic::_dt0

private

Definition at line 102 of file biharmonic.h.

Referenced by Biharmonic(), dt0(), step(), and viewParameters().

◆ _enable_default_ghosting

bool libMesh::EquationSystems::_enable_default_ghosting

protectedinherited

Flag for whether to enable default ghosting on newly added Systems.

Default value: true

Definition at line 593 of file equation_systems.h.

Referenced by libMesh::EquationSystems::add_system(), and libMesh::EquationSystems::enable_default_ghosting().

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 141 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

◆ _energy

FreeEnergyEnum Biharmonic::_energy

private

Definition at line 96 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _exio

std::unique_ptr<ExodusII_IO> Biharmonic::_exio

private

Definition at line 106 of file biharmonic.h.

Referenced by Biharmonic(), and output().

◆ _growth

bool Biharmonic::_growth

private

Definition at line 95 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _initialCenter

Point Biharmonic::_initialCenter

private

Definition at line 100 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _initialState

InitialStateEnum Biharmonic::_initialState

private

Definition at line 99 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _initialWidth

Real Biharmonic::_initialWidth

private

Definition at line 101 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _jr

JR* Biharmonic::_jr

private

Definition at line 113 of file biharmonic.h.

Referenced by Biharmonic(), and step().

◆ _kappa

Real Biharmonic::_kappa

private

Definition at line 93 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _log_truncation

int Biharmonic::_log_truncation

private

Definition at line 97 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _mesh

ReplicatedMesh& Biharmonic::_mesh

private

Definition at line 111 of file biharmonic.h.

Referenced by Biharmonic().

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

◆ _N

unsigned int Biharmonic::_N

private

Definition at line 92 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 130 of file reference_counter.h.

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

◆ _netforce

bool Biharmonic::_netforce

private

Definition at line 95 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _o_count

int Biharmonic::_o_count

private

Definition at line 108 of file biharmonic.h.

Referenced by init(), and output().

◆ _o_dt

Real Biharmonic::_o_dt

private

Definition at line 107 of file biharmonic.h.

Referenced by Biharmonic(), output(), and viewParameters().

◆ _ofile

std::string Biharmonic::_ofile

private

Definition at line 105 of file biharmonic.h.

Referenced by Biharmonic(), and output().

◆ _ofile_base

std::string Biharmonic::_ofile_base

private

Definition at line 105 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _refine_in_reinit

bool libMesh::EquationSystems::_refine_in_reinit

protectedinherited

Flag for whether to call coarsen/refine in reinit().

Default value: true

Definition at line 587 of file equation_systems.h.

Referenced by libMesh::EquationSystems::disable_refine_in_reinit(), libMesh::EquationSystems::enable_refine_in_reinit(), libMesh::EquationSystems::refine_in_reinit_flag(), and libMesh::EquationSystems::reinit_solutions().

◆ _systems

std::map<std::string, System *> libMesh::EquationSystems::_systems

protectedinherited

Data structure holding the systems.

Definition at line 571 of file equation_systems.h.

◆ _T

Real Biharmonic::_T

private

Definition at line 102 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _t0

Real Biharmonic::_t0

private

Definition at line 102 of file biharmonic.h.

Referenced by Biharmonic(), run(), and viewParameters().

◆ _t1

Real Biharmonic::_t1

private

Definition at line 102 of file biharmonic.h.

Referenced by Biharmonic(), run(), and viewParameters().

◆ _theta

Real Biharmonic::_theta

private

Definition at line 93 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _theta_c

Real Biharmonic::_theta_c

private

Definition at line 93 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _tol

Real Biharmonic::_tol

private

Definition at line 94 of file biharmonic.h.

Referenced by Biharmonic(), and viewParameters().

◆ _verbose

bool Biharmonic::_verbose

private

Definition at line 98 of file biharmonic.h.

Referenced by Biharmonic(), init(), output(), run(), verbose(), and viewParameters().

◆ parameters

Parameters libMesh::EquationSystems::parameters

inherited

Data structure holding arbitrary parameters.

Definition at line 557 of file equation_systems.h.

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

examples/miscellaneous/miscellaneous_ex7/biharmonic.h
examples/miscellaneous/miscellaneous_ex7/biharmonic.C

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ const_system_iterator

◆ Counts

◆ system_iterator

Member Enumeration Documentation

◆ FreeEnergyEnum

◆ InitialStateEnum

◆ ReadFlags

◆ WriteFlags

Constructor & Destructor Documentation

◆ Biharmonic()

◆ ~Biharmonic()

Member Function Documentation

◆ _add_system_to_nodes_and_elems()

◆ _read_impl()

◆ _remove_default_ghosting()

◆ add_system() [1/2]

◆ add_system() [2/2]

◆ adjoint_solve()

◆ allgather()

◆ build_discontinuous_solution_vector()

◆ build_elemental_solution_vector()

◆ build_parallel_elemental_solution_vector()

◆ build_parallel_solution_vector()

◆ build_solution_vector() [1/2]

◆ build_solution_vector() [2/2]

◆ build_variable_names()

◆ clear()

◆ comm()

◆ compare()

◆ delete_system()

◆ disable_print_counter_info()

◆ disable_refine_in_reinit()

◆ dt()

◆ dt0()

◆ enable_default_ghosting()

◆ enable_print_counter_info()

◆ enable_refine_in_reinit()

◆ find_variable_numbers()

◆ get_info() [1/2]

◆ get_info() [2/2]

◆ get_mesh() [1/2]

◆ get_mesh() [2/2]

◆ get_solution()

◆ get_system() [1/8]

◆ get_system() [2/8]

◆ get_system() [3/8]

◆ get_system() [4/8]

◆ get_system() [5/8]

◆ get_system() [6/8]

◆ get_system() [7/8]

◆ get_system() [8/8]

◆ get_vars_active_subdomains()

◆ has_system()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init()

◆ n_active_dofs()

◆ n_dofs()

◆ n_objects()

◆ n_processors()

◆ n_systems()

◆ n_vars()

◆ output()

◆ print_info() [1/2]

◆ print_info() [2/2]

◆ processor_id()