The ExodusII_IO class implements reading meshes in the ExodusII file format from Sandia National Labs. More...

#include <exodusII_io.h>

Inheritance diagram for libMesh::ExodusII_IO:

Public Member Functions
	ExodusII_IO (MeshBase &mesh, bool single_precision=false)
	Constructor. More...

virtual	~ExodusII_IO ()
	Destructor. More...

virtual void	read (const std::string &name) override
	This method implements reading a mesh from a specified file. More...

virtual void	write (const std::string &fname) override
	This method implements writing a mesh to a specified file. More...

void	verbose (bool set_verbosity)
	Set the flag indicating if we should be verbose. More...

const std::vector< Real > &	get_time_steps ()

int	get_num_time_steps ()

void	copy_nodal_solution (System &system, std::string var_name, unsigned int timestep=1)
	Backward compatibility version of function that takes a single variable name. More...

void	copy_nodal_solution (System &system, std::string system_var_name, std::string exodus_var_name, unsigned int timestep=1)
	If we read in a nodal solution while reading in a mesh, we can attempt to copy that nodal solution into an EquationSystems object. More...

void	copy_elemental_solution (System &system, std::string system_var_name, std::string exodus_var_name, unsigned int timestep=1)
	If we read in a elemental solution while reading in a mesh, we can attempt to copy that elemental solution into an EquationSystems object. More...

void	copy_scalar_solution (System &system, std::vector< std::string > system_var_names, std::vector< std::string > exodus_var_names, unsigned int timestep=1)
	Copy global variables into scalar variables of a System object. More...

void	read_elemental_variable (std::string elemental_var_name, unsigned int timestep, std::map< unsigned int, Real > &unique_id_to_value_map)
	Given an elemental variable and a time step, returns a mapping from the elements (top parent) unique IDs to the value of the elemental variable at the corresponding time step index. More...

void	read_global_variable (std::vector< std::string > global_var_names, unsigned int timestep, std::vector< Real > &global_values)
	Given a vector of global variables and a time step, returns the values of the global variable at the corresponding time step index. More...

void	write_discontinuous_exodusII (const std::string &name, const EquationSystems &es, const std::set< std::string > *system_names=nullptr)
	Writes a exodusII file with discontinuous data. More...

void	write_timestep_discontinuous (const std::string &fname, const EquationSystems &es, const int timestep, const Real time, const std::set< std::string > *system_names=nullptr)
	Writes a discontinuous solution at a specific timestep. More...

void	write_element_data (const EquationSystems &es)
	Write out element solution. More...

void	write_element_data_from_discontinuous_nodal_data (const EquationSystems &es, const std::set< std::string > *system_names=nullptr, const std::string &var_suffix="_elem_node_")
	Similar to the function above, but instead of only handling (CONSTANT, MONOMIAL) data, writes out a general discontinuous solution field, e.g. More...

virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	Write out a nodal solution. More...

void	write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	Write out a discontinuous nodal solution. More...

void	write_global_data (const std::vector< Number > &, const std::vector< std::string > &)
	Write out global variables. More...

void	write_information_records (const std::vector< std::string > &)
	Write out information records. More...

void	write_timestep (const std::string &fname, const EquationSystems &es, const int timestep, const Real time, const std::set< std::string > *system_names=nullptr)
	Writes out the solution at a specific timestep. More...

void	write_sideset_data (int timestep, const std::vector< std::string > &var_names, const std::vector< std::set< boundary_id_type >> &side_ids, const std::vector< std::map< BoundaryInfo::BCTuple, Real >> &bc_vals)
	The Exodus format can also store values on sidesets. More...

void	read_sideset_data (int timestep, std::vector< std::string > &var_names, std::vector< std::set< boundary_id_type >> &side_ids, std::vector< std::map< BoundaryInfo::BCTuple, Real >> &bc_vals)
	Similar to write_sideset_data(), this function is used to read the data at a particular timestep. More...

void	set_output_variables (const std::vector< std::string > &output_variables, bool allow_empty=true)
	Sets the list of variable names to be included in the output. More...

void	use_mesh_dimension_instead_of_spatial_dimension (bool val)
	In the general case, meshes containing 2D elements can be manifolds living in 3D space, thus by default we write all meshes with the Exodus dimension set to LIBMESH_DIM = mesh.spatial_dimension(). More...

void	write_as_dimension (unsigned dim)
	Directly control the num_dim which is written to the Exodus file. More...

void	set_coordinate_offset (Point p)
	Allows you to set a vector that is added to the coordinates of all of the nodes. More...

void	append (bool val)
	If true, this flag will cause the ExodusII_IO object to attempt to open an existing file for writing, rather than creating a new file. More...

const std::vector< std::string > &	get_elem_var_names ()
	Return list of the elemental variable names. More...

const std::vector< std::string > &	get_nodal_var_names ()
	Return list of the nodal variable names. More...

const std::vector< std::string > &	get_global_var_names ()
	Return list of the global variable names. More...

ExodusII_IO_Helper &	get_exio_helper ()
	Return a reference to the ExodusII_IO_Helper object. More...

void	write_nodal_data_common (std::string fname, const std::vector< std::string > &names, bool continuous=true)
	This function factors out a bunch of code which is common to the write_nodal_data() and write_nodal_data_discontinuous() functions. More...

virtual void	write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with data to a specified file where the data is taken from the `EquationSystems` object. More...

virtual void	write_discontinuous_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the `EquationSystems` object. More...

virtual void	write_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
	This method may be overridden by "parallel" output formats for writing nodal data. More...

virtual void	write_nodal_data (const std::string &, const EquationSystems &, const std::set< std::string > *)
	This method should be overridden by "parallel" output formats for writing nodal data. More...

unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files. More...

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Protected Member Functions
MeshBase &	mesh ()

void	set_n_partitions (unsigned int n_parts)
	Sets the number of partitions in the mesh. More...

void	skip_comment_lines (std::istream &in, const char comment_start)
	Reads input from `in`, skipping all the lines that start with the character `comment_start`. More...

const MeshBase &	mesh () const

Protected Attributes
std::vector< bool >	elems_of_dimension
	A vector of bools describing what dimension elements have been encountered when reading a mesh. More...

const bool	_is_parallel_format
	Flag specifying whether this format is parallel-capable. More...

const bool	_serial_only_needed_on_proc_0
	Flag specifying whether this format can be written by only serializing the mesh to processor zero. More...

const Parallel::Communicator &	_communicator

Private Attributes
std::unique_ptr< ExodusII_IO_Helper >	exio_helper
	Only attempt to instantiate an ExodusII helper class if the Exodus API is defined. More...

int	_timestep
	Stores the current value of the timestep when calling ExodusII_IO::write_timestep(). More...

bool	_verbose
	should we be verbose? More...

bool	_append
	Default false. More...

std::vector< std::string >	_output_variables
	The names of the variables to be output. More...

bool	_allow_empty_variables
	If true, _output_variables is allowed to remain empty. More...

MeshBase *	_obj
	A pointer to a non-const object object. More...

const bool	_is_parallel_format
	Flag specifying whether this format is parallel-capable. More...

unsigned int	_ascii_precision
	Precision to use when writing ASCII files. More...

Detailed Description

The ExodusII_IO class implements reading meshes in the ExodusII file format from Sandia National Labs.

By default, LibMesh expects ExodusII files to have a ".exd" or ".e" file extension.

Author: Benjamin Kirk; John Peterson

Date: 2004

Handles reading and writing of Exodus binary files.

Definition at line 51 of file exodusII_io.h.

Constructor & Destructor Documentation

◆ ExodusII_IO()

libMesh::ExodusII_IO::ExodusII_IO	(	MeshBase &	mesh,
		bool	single_precision = `false`
	)

explicit

Constructor.

Takes a writable reference to a mesh object. This is the constructor required to read a mesh.

Definition at line 49 of file exodusII_io.C.

                             :
   MeshInput<MeshBase> (mesh),
   MeshOutput<MeshBase> (mesh,
                         /* is_parallel_format = */ false,
                         /* serial_only_needed_on_proc_0 = */ true),
   ParallelObject(mesh),
 #ifdef LIBMESH_HAVE_EXODUS_API
   exio_helper(libmesh_make_unique<ExodusII_IO_Helper>(*this, false, true, single_precision)),
   _timestep(1),
   _verbose(false),
   _append(false),
 #endif
   _allow_empty_variables(false)
 {
 }

◆ ~ExodusII_IO()

libMesh::ExodusII_IO::~ExodusII_IO ( )

virtual

Destructor.

Definition at line 136 of file exodusII_io.C.

 {
   exio_helper->close();
 }

References exio_helper.

Member Function Documentation

◆ append()

void libMesh::ExodusII_IO::append ( bool val )

If true, this flag will cause the ExodusII_IO object to attempt to open an existing file for writing, rather than creating a new file.

Obviously this will only work if the file already exists.

Definition at line 466 of file exodusII_io.C.

 {
   _append = val;
 }

References _append.

Referenced by main().

◆ ascii_precision()

unsigned int & libMesh::MeshOutput< MeshBase >::ascii_precision ( )

inlineinherited

Return/set the precision to use when writing ASCII files.

By default we use numeric_limits<Real>::max_digits10, which should be enough to write out to ASCII and get the exact same Real back when reading in.

Definition at line 257 of file mesh_output.h.

 {
   return _ascii_precision;
 }

◆ 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.

◆ copy_elemental_solution()

void libMesh::ExodusII_IO::copy_elemental_solution	(	System &	system,
		std::string	system_var_name,
		std::string	exodus_var_name,
		unsigned int	timestep = `1`
	)

If we read in a elemental solution while reading in a mesh, we can attempt to copy that elemental solution into an EquationSystems object.

Definition at line 529 of file exodusII_io.C.

 {
   if (system.comm().rank() == 0)
     {
       if (!exio_helper->opened_for_reading)
         libmesh_error_msg("ERROR, ExodusII file must be opened for reading before copying an elemental solution!");
  
       // Map from element ID to elemental variable value.  We need to use
       // a map here rather than a vector (e.g. elem_var_values) since the
       // libmesh element numbering can contain "holes".  This is the case
       // if we are reading elemental var values from an adaptively refined
       // mesh that has not been sequentially renumbered.
       std::map<dof_id_type, Real> elem_var_value_map;
       exio_helper->read_elemental_var_values(exodus_var_name, timestep, elem_var_value_map);
  
       const unsigned int var_num = system.variable_number(system_var_name);
       if (system.variable_type(var_num) != FEType(CONSTANT, MONOMIAL))
         libmesh_error_msg("Error! Trying to copy elemental solution into a variable that is not of CONSTANT MONOMIAL type.");
  
       std::map<dof_id_type, Real>::iterator
         it = elem_var_value_map.begin(),
         end = elem_var_value_map.end();
  
       for (; it!=end; ++it)
         {
           const Elem * elem = MeshInput<MeshBase>::mesh().query_elem_ptr(it->first);
  
           if (elem && elem->n_comp(system.number(), var_num) > 0)
             {
               dof_id_type dof_index = elem->dof_number(system.number(), var_num, 0);
               system.solution->set (dof_index, it->second);
             }
         }
     }
  
   system.solution->close();
   system.update();
 }

References libMesh::ParallelObject::comm(), libMesh::CONSTANT, libMesh::DofObject::dof_number(), end, exio_helper, libMesh::MeshInput< MT >::mesh(), libMesh::MONOMIAL, libMesh::DofObject::n_comp(), libMesh::System::number(), libMesh::System::solution, libMesh::System::update(), libMesh::System::variable_number(), and libMesh::System::variable_type().

Referenced by MeshInputTest::testExodusCopyElementSolution(), and MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData().

◆ copy_nodal_solution() [1/2]

void libMesh::ExodusII_IO::copy_nodal_solution	(	System &	system,
		std::string	system_var_name,
		std::string	exodus_var_name,
		unsigned int	timestep = `1`
	)

If we read in a nodal solution while reading in a mesh, we can attempt to copy that nodal solution into an EquationSystems object.

Definition at line 495 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_reading)
     libmesh_error_msg("ERROR, ExodusII file must be opened for reading before copying a nodal solution!");
  
   exio_helper->read_nodal_var_values(exodus_var_name, timestep);
  
   const unsigned int var_num = system.variable_number(system_var_name);
  
   for (dof_id_type i=0,
        n_nodal = cast_int<dof_id_type>(exio_helper->nodal_var_values.size());
        i != n_nodal; ++i)
     {
       const Node * node = MeshInput<MeshBase>::mesh().query_node_ptr(i);
  
       if (node && node->n_comp(system.number(), var_num) > 0)
         {
           dof_id_type dof_index = node->dof_number(system.number(), var_num, 0);
  
           // If the dof_index is local to this processor, set the value
           if ((dof_index >= system.solution->first_local_index()) && (dof_index < system.solution->last_local_index()))
             system.solution->set (dof_index, exio_helper->nodal_var_values[i]);
         }
     }
  
   system.solution->close();
   system.update();
 }

References libMesh::DofObject::dof_number(), exio_helper, libMesh::MeshInput< MT >::mesh(), libMesh::DofObject::n_comp(), libMesh::System::number(), libMesh::System::solution, libMesh::System::update(), and libMesh::System::variable_number().

◆ copy_nodal_solution() [2/2]

void libMesh::ExodusII_IO::copy_nodal_solution	(	System &	system,
		std::string	var_name,
		unsigned int	timestep = `1`
	)

Backward compatibility version of function that takes a single variable name.

Definition at line 82 of file exodusII_io.C.

 {
   libmesh_deprecated();
   copy_nodal_solution(system, var_name, var_name, timestep);
 }

Referenced by WriteVecAndScalar::testWrite().

◆ copy_scalar_solution()

void libMesh::ExodusII_IO::copy_scalar_solution	(	System &	system,
		std::vector< std::string >	system_var_names,
		std::vector< std::string >	exodus_var_names,
		unsigned int	timestep = `1`
	)

Copy global variables into scalar variables of a System object.

Definition at line 571 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_reading)
     libmesh_error_msg("ERROR, ExodusII file must be opened for reading before copying a scalar solution!");
  
   if (system_var_names.size() != exodus_var_names.size())
     libmesh_error_msg("ERROR, the number of system_var_names must match exodus_var_names.");
  
   std::vector<Real> values_from_exodus;
   read_global_variable(exodus_var_names, timestep, values_from_exodus);
  
 #ifdef LIBMESH_HAVE_MPI
   if (this->n_processors() > 1)
   {
     const Parallel::MessageTag tag(1);
     if (this->processor_id() == this->n_processors()-1)
       this->comm().receive(0, values_from_exodus, tag);
     if (this->processor_id() == 0)
       this->comm().send(this->n_processors()-1, values_from_exodus, tag);
   }
 #endif
  
   if (system.processor_id() == (system.n_processors()-1))
   {
     const DofMap & dof_map = system.get_dof_map();
  
     for (auto i : index_range(system_var_names))
     {
       const unsigned int var_num = system.variable_scalar_number(system_var_names[i], 0);
  
       std::vector<dof_id_type> SCALAR_dofs;
       dof_map.SCALAR_dof_indices(SCALAR_dofs, var_num);
  
       system.solution->set (SCALAR_dofs[0], values_from_exodus[i]);
     }
   }
  
   system.solution->close();
   system.update();
 }

References libMesh::ParallelObject::comm(), exio_helper, libMesh::System::get_dof_map(), libMesh::index_range(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), read_global_variable(), libMesh::DofMap::SCALAR_dof_indices(), libMesh::System::solution, libMesh::System::update(), and libMesh::System::variable_scalar_number().

◆ get_elem_var_names()

const std::vector< std::string > & libMesh::ExodusII_IO::get_elem_var_names ( )

Return list of the elemental variable names.

Definition at line 1487 of file exodusII_io.C.

 {
   exio_helper->read_var_names(ExodusII_IO_Helper::ELEMENTAL);
   return exio_helper->elem_var_names;
 }

References libMesh::ExodusII_IO_Helper::ELEMENTAL, and exio_helper.

◆ get_exio_helper()

ExodusII_IO_Helper & libMesh::ExodusII_IO::get_exio_helper ( )

Return a reference to the ExodusII_IO_Helper object.

Definition at line 1499 of file exodusII_io.C.

 {
   // Provide a warning when accessing the helper object
   // since it is a non-public API and is likely to see
   // future API changes
   libmesh_experimental();
  
   return *exio_helper;
 }

References exio_helper.

◆ get_global_var_names()

const std::vector< std::string > & libMesh::ExodusII_IO::get_global_var_names ( )

Return list of the global variable names.

Definition at line 1493 of file exodusII_io.C.

 {
   exio_helper->read_var_names(ExodusII_IO_Helper::GLOBAL);
   return exio_helper->global_var_names;
 }

References exio_helper, and libMesh::ExodusII_IO_Helper::GLOBAL.

◆ get_nodal_var_names()

const std::vector< std::string > & libMesh::ExodusII_IO::get_nodal_var_names ( )

Return list of the nodal variable names.

Definition at line 1481 of file exodusII_io.C.

 {
   exio_helper->read_var_names(ExodusII_IO_Helper::NODAL);
   return exio_helper->nodal_var_names;
 }

References exio_helper, and libMesh::ExodusII_IO_Helper::NODAL.

Referenced by WriteVecAndScalar::testWrite().

◆ get_num_time_steps()

int libMesh::ExodusII_IO::get_num_time_steps ( )

Returns: The number of timesteps currently stored in the Exodus file.

Knowing the number of time steps currently stored in the file is sometimes necessary when appending, so we can know where to start writing new data. Throws an error if the file is not currently open for reading or writing.

Definition at line 484 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_reading && !exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be opened for reading or writing before calling ExodusII_IO::get_num_time_steps()!");
  
   exio_helper->read_num_time_steps();
   return exio_helper->num_time_steps;
 }

References exio_helper.

◆ get_time_steps()

const std::vector< Real > & libMesh::ExodusII_IO::get_time_steps ( )

Returns: An array containing the timesteps in the file.

Definition at line 473 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_reading)
     libmesh_error_msg("ERROR, ExodusII file must be opened for reading before calling ExodusII_IO::get_time_steps()!");
  
   exio_helper->read_time_steps();
   return exio_helper->time_steps;
 }

References exio_helper.

◆ mesh() [1/2]

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )

inlineprotectedinherited

Returns: The object as a writable reference.

Definition at line 169 of file mesh_input.h.

 {
   if (_obj == nullptr)
     libmesh_error_msg("ERROR: _obj should not be nullptr!");
   return *_obj;
 }

◆ mesh() [2/2]

const MeshBase & libMesh::MeshOutput< MeshBase >::mesh ( ) const

inlineprotectedinherited

Returns: The object as a read-only reference.

Definition at line 247 of file mesh_output.h.

 {
   libmesh_assert(_obj);
   return *_obj;
 }

◆ 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.

◆ 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()

void libMesh::ExodusII_IO::read ( const std::string & name )

overridevirtual

This method implements reading a mesh from a specified file.

Open the file named name and read the mesh in Sandia National Lab's ExodusII format. This is the method to use for reading in meshes generated by cubit. Works in 2D for TRIs, TRI6s, QUAD s, and QUAD9s. Works in 3D for TET4s, TET10s, HEX8s, and HEX27s.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 143 of file exodusII_io.C.

 {
   // Get a reference to the mesh we are reading
   MeshBase & mesh = MeshInput<MeshBase>::mesh();
  
   // Clear any existing mesh data
   mesh.clear();
  
   // Keep track of what kinds of elements this file contains
   elems_of_dimension.clear();
   elems_of_dimension.resize(4, false);
  
   // Open the exodus file in EX_READ mode
   exio_helper->open(fname.c_str(), /*read_only=*/true);
  
   // Get header information from exodus file
   exio_helper->read_header();
  
   // Read the QA records
   exio_helper->read_qa_records();
  
   // Print header information
   exio_helper->print_header();
  
   // Read nodes from the exodus file
   exio_helper->read_nodes();
  
   // Reserve space for the nodes.
   mesh.reserve_nodes(exio_helper->num_nodes);
  
   // Read the node number map from the Exodus file.  This is
   // required if we want to preserve the numbering of nodes as it
   // exists in the Exodus file.  If the Exodus file does not contain
   // a node_num_map, the identity map is returned by this call.
   exio_helper->read_node_num_map();
  
   // Loop over the nodes, create Nodes with local processor_id 0.
   for (int i=0; i<exio_helper->num_nodes; i++)
     {
       // Use the node_num_map to get the correct ID for Exodus
       int exodus_id = exio_helper->node_num_map[i];
  
       // Catch the node that was added to the mesh
       Node * added_node = mesh.add_point (Point(exio_helper->x[i], exio_helper->y[i], exio_helper->z[i]), exodus_id-1);
  
       // If the Mesh assigned an ID different from what is in the
       // Exodus file, we should probably error.
       if (added_node->id() != static_cast<unsigned>(exodus_id-1))
         libmesh_error_msg("Error!  Mesh assigned node ID "    \
                           << added_node->id()                         \
                           << " which is different from the (zero-based) Exodus ID " \
                           << exodus_id-1                              \
                           << "!");
     }
  
   // This assert is no longer valid if the nodes are not numbered
   // sequentially starting from 1 in the Exodus file.
   // libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->num_nodes), mesh.n_nodes());
  
   // Get information about all the element and edge blocks
   exio_helper->read_block_info();
  
   // Reserve space for the elements
   mesh.reserve_elem(exio_helper->num_elem);
  
   // Read the element number map from the Exodus file.  This is
   // required if we want to preserve the numbering of elements as it
   // exists in the Exodus file.  If the Exodus file does not contain
   // an elem_num_map, the identity map is returned by this call.
   exio_helper->read_elem_num_map();
  
   // Read in the element connectivity for each block.
   int nelem_last_block = 0;
  
   // Loop over all the element blocks
   for (int i=0; i<exio_helper->num_elem_blk; i++)
     {
       // Read the information for block i
       exio_helper->read_elem_in_block (i);
       int subdomain_id = exio_helper->get_block_id(i);
  
       // populate the map of names
       std::string subdomain_name = exio_helper->get_block_name(i);
       if (!subdomain_name.empty())
         mesh.subdomain_name(static_cast<subdomain_id_type>(subdomain_id)) = subdomain_name;
  
       // Set any relevant node/edge maps for this element
       const std::string type_str (exio_helper->get_elem_type());
       const auto & conv = exio_helper->get_conversion(type_str);
  
       // Loop over all the faces in this block
       int jmax = nelem_last_block+exio_helper->num_elem_this_blk;
       for (int j=nelem_last_block; j<jmax; j++)
         {
           Elem * elem = Elem::build (conv.libmesh_elem_type()).release();
           libmesh_assert (elem);
           elem->subdomain_id() = static_cast<subdomain_id_type>(subdomain_id) ;
  
           // Use the elem_num_map to obtain the ID of this element in the Exodus file
           int exodus_id = exio_helper->elem_num_map[j];
  
           // Assign this element the same ID it had in the Exodus
           // file, but make it zero-based by subtracting 1.  Note:
           // some day we could use 1-based numbering in libmesh and
           // thus match the Exodus numbering exactly, but at the
           // moment libmesh is zero-based.
           elem->set_id(exodus_id-1);
  
           // Record that we have seen an element of dimension elem->dim()
           elems_of_dimension[elem->dim()] = true;
  
           // Catch the Elem pointer that the Mesh throws back
           elem = mesh.add_elem (elem);
  
           // If the Mesh assigned an ID different from what is in the
           // Exodus file, we should probably error.
           if (elem->id() != static_cast<unsigned>(exodus_id-1))
             libmesh_error_msg("Error!  Mesh assigned ID "       \
                               << elem->id()                             \
                               << " which is different from the (zero-based) Exodus ID " \
                               << exodus_id-1                            \
                               << "!");
  
           // Set all the nodes for this element
           for (int k=0; k<exio_helper->num_nodes_per_elem; k++)
             {
               // global index
               int gi = (j-nelem_last_block)*exio_helper->num_nodes_per_elem + conv.get_node_map(k);
  
               // The entries in 'connect' are actually (1-based)
               // indices into the node_num_map, so to get the right
               // node ID we:
               // 1.) Subtract 1 from connect[gi]
               // 2.) Pass it through node_num_map to get the corresponding Exodus ID
               // 3.) Subtract 1 from that, since libmesh node numbering is "zero"-based,
               //     even when the Exodus node numbering doesn't start with 1.
               int libmesh_node_id = exio_helper->node_num_map[exio_helper->connect[gi] - 1] - 1;
  
               // Set the node pointer in the Elem
               elem->set_node(k) = mesh.node_ptr(libmesh_node_id);
             }
         }
  
       // running sum of # of elements per block,
       // (should equal total number of elements in the end)
       nelem_last_block += exio_helper->num_elem_this_blk;
     }
  
   // Read in edge blocks, storing information in the BoundaryInfo object.
   // Edge blocks are treated as BCs.
   exio_helper->read_edge_blocks(mesh);
  
   // Set the mesh dimension to the largest encountered for an element
   for (unsigned char i=0; i!=4; ++i)
     if (elems_of_dimension[i])
       mesh.set_mesh_dimension(i);
  
   // Read in sideset information -- this is useful for applying boundary conditions
   {
     // Get basic information about all sidesets
     exio_helper->read_sideset_info();
     int offset=0;
     for (int i=0; i<exio_helper->num_side_sets; i++)
       {
         // Compute new offset
         offset += (i > 0 ? exio_helper->num_sides_per_set[i-1] : 0);
         exio_helper->read_sideset (i, offset);
  
         std::string sideset_name = exio_helper->get_side_set_name(i);
         if (!sideset_name.empty())
           mesh.get_boundary_info().sideset_name
             (cast_int<boundary_id_type>(exio_helper->get_side_set_id(i)))
             = sideset_name;
       }
  
     for (auto e : index_range(exio_helper->elem_list))
       {
         // The numbers in the Exodus file sidesets should be thought
         // of as (1-based) indices into the elem_num_map array.  So,
         // to get the right element ID we have to:
         // 1.) Subtract 1 from elem_list[e] (to get a zero-based index)
         // 2.) Pass it through elem_num_map (to get the corresponding Exodus ID)
         // 3.) Subtract 1 from that, since libmesh is "zero"-based,
         //     even when the Exodus numbering doesn't start with 1.
         dof_id_type libmesh_elem_id =
           cast_int<dof_id_type>(exio_helper->elem_num_map[exio_helper->elem_list[e] - 1] - 1);
  
         // Set any relevant node/edge maps for this element
         Elem & elem = mesh.elem_ref(libmesh_elem_id);
  
         const auto & conv = exio_helper->get_conversion(elem.type());
  
         // Map the zero-based Exodus side numbering to the libmesh side numbering
         unsigned int raw_side_index = exio_helper->side_list[e]-1;
         std::size_t side_index_offset = conv.get_shellface_index_offset();
  
         if (raw_side_index < side_index_offset)
           {
             // We assume this is a "shell face"
             int mapped_shellface = raw_side_index;
  
             // Check for errors
             if (mapped_shellface == ExodusII_IO_Helper::Conversion::invalid_id)
               libmesh_error_msg("Invalid 1-based side id: "                 \
                                 << mapped_shellface                         \
                                 << " detected for "                         \
                                 << Utility::enum_to_string(elem.type()));
  
             // Add this (elem,shellface,id) triplet to the BoundaryInfo object.
             mesh.get_boundary_info().add_shellface (libmesh_elem_id,
                                                     cast_int<unsigned short>(mapped_shellface),
                                                     cast_int<boundary_id_type>(exio_helper->id_list[e]));
           }
         else
           {
             unsigned int side_index = static_cast<unsigned int>(raw_side_index - side_index_offset);
             int mapped_side = conv.get_side_map(side_index);
  
             // Check for errors
             if (mapped_side == ExodusII_IO_Helper::Conversion::invalid_id)
               libmesh_error_msg("Invalid 1-based side id: "                 \
                                 << side_index                               \
                                 << " detected for "                         \
                                 << Utility::enum_to_string(elem.type()));
  
             // Add this (elem,side,id) triplet to the BoundaryInfo object.
             mesh.get_boundary_info().add_side (libmesh_elem_id,
                                                cast_int<unsigned short>(mapped_side),
                                                cast_int<boundary_id_type>(exio_helper->id_list[e]));
           }
       } // end for (elem_list)
   } // end read sideset info
  
   // Read nodeset info
   {
     // This fills in the following fields of the helper for later use:
     // nodeset_ids
     // num_nodes_per_set
     // num_node_df_per_set
     // node_sets_node_index
     // node_sets_dist_index
     // node_sets_node_list
     // node_sets_dist_fact
     exio_helper->read_all_nodesets();
  
     for (int nodeset=0; nodeset<exio_helper->num_node_sets; nodeset++)
       {
         boundary_id_type nodeset_id =
           cast_int<boundary_id_type>(exio_helper->nodeset_ids[nodeset]);
  
         std::string nodeset_name = exio_helper->get_node_set_name(nodeset);
         if (!nodeset_name.empty())
           mesh.get_boundary_info().nodeset_name(nodeset_id) = nodeset_name;
  
         // Get starting index of node ids for current nodeset.
         unsigned int offset = exio_helper->node_sets_node_index[nodeset];
  
         for (int i=0; i<exio_helper->num_nodes_per_set[nodeset]; ++i)
           {
             int exodus_id = exio_helper->node_sets_node_list[i + offset];
  
             // It's possible for nodesets to have invalid ids in them
             // by accident.  Instead of possibly accessing past the
             // end of node_num_map, let's make sure we have that many
             // entries.
             if (static_cast<std::size_t>(exodus_id - 1) >= exio_helper->node_num_map.size())
               libmesh_error_msg("Invalid Exodus node id " << exodus_id
                                 << " found in nodeset " << nodeset_id);
  
             // As before, the entries in 'node_list' are 1-based
             // indices into the node_num_map array, so we have to map
             // them.  See comment above.
             int libmesh_node_id = exio_helper->node_num_map[exodus_id - 1] - 1;
             mesh.get_boundary_info().add_node(cast_int<dof_id_type>(libmesh_node_id),
                                               nodeset_id);
           }
       }
   }
  
 #if LIBMESH_DIM < 3
   if (mesh.mesh_dimension() > LIBMESH_DIM)
     libmesh_error_msg("Cannot open dimension "        \
                       << mesh.mesh_dimension()            \
                       << " mesh file when configured without "        \
                       << mesh.mesh_dimension()                        \
                       << "D support.");
 #endif
 }

Referenced by libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), WriteEdgesetData::testWrite(), WriteSidesetData::testWrite(), and WriteVecAndScalar::testWrite().

◆ read_elemental_variable()

void libMesh::ExodusII_IO::read_elemental_variable	(	std::string	elemental_var_name,
		unsigned int	timestep,
		std::map< unsigned int, Real > &	unique_id_to_value_map
	)

Given an elemental variable and a time step, returns a mapping from the elements (top parent) unique IDs to the value of the elemental variable at the corresponding time step index.

Note that this function MUST only be called before renumbering! This function is essentially a wrapper for read_elemental_var_values from the exodus helper (which is not accessible outside this class).

Parameters

elemental_var_name	Name of an elemental variable
timestep	The corresponding time step index
unique_id_to_value_map	The map to be filled

Definition at line 615 of file exodusII_io.C.

 {
   // Note that this function MUST be called before renumbering
   std::map<dof_id_type, Real> elem_var_value_map;
  
   exio_helper->read_elemental_var_values(elemental_var_name, timestep, elem_var_value_map);
   for (auto & pr : elem_var_value_map)
     {
       const Elem * elem = MeshInput<MeshBase>::mesh().query_elem_ptr(pr.first);
       unique_id_to_value_map.insert(std::make_pair(elem->top_parent()->unique_id(), pr.second));
     }
 }

References exio_helper, libMesh::MeshInput< MT >::mesh(), libMesh::Elem::top_parent(), and libMesh::DofObject::unique_id().

◆ read_global_variable()

void libMesh::ExodusII_IO::read_global_variable	(	std::vector< std::string >	global_var_names,
		unsigned int	timestep,
		std::vector< Real > &	global_values
	)

Given a vector of global variables and a time step, returns the values of the global variable at the corresponding time step index.

Parameters

global_var_names	Vector of names of global variables
timestep	The corresponding time step index
global_values	The vector to be filled

Definition at line 630 of file exodusII_io.C.

 {
   std::size_t size = global_var_names.size();
   if (size == 0)
     libmesh_error_msg("ERROR, empty list of global variables to read from the Exodus file.");
  
   // read the values for all global variables
   std::vector<Real> values_from_exodus;
   exio_helper->read_var_names(ExodusII_IO_Helper::GLOBAL);
   exio_helper->read_global_values(values_from_exodus, timestep);
   std::vector<std::string> global_var_names_exodus = exio_helper->global_var_names;
  
   if (values_from_exodus.size() == 0)
     return;   // This will happen in parallel on procs that are not 0
  
   global_values.clear();
   for (std::size_t i = 0; i != size; ++i)
     {
       // for each global variable in global_var_names, look the corresponding one in global_var_names_from_exodus
       // and fill global_values accordingly
       auto it = find(global_var_names_exodus.begin(), global_var_names_exodus.end(), global_var_names[i]);
       if (it != global_var_names_exodus.end())
         global_values.push_back(values_from_exodus[it - global_var_names_exodus.begin()]);
       else
         libmesh_error_msg("ERROR, Global variable " << global_var_names[i] << \
                           " not found in Exodus file.");
     }
  
 }

References exio_helper, and libMesh::ExodusII_IO_Helper::GLOBAL.

Referenced by copy_scalar_solution().

◆ read_sideset_data()

void libMesh::ExodusII_IO::read_sideset_data	(	int	timestep,
		std::vector< std::string > &	var_names,
		std::vector< std::set< boundary_id_type >> &	side_ids,
		std::vector< std::map< BoundaryInfo::BCTuple, Real >> &	bc_vals
	)

Similar to write_sideset_data(), this function is used to read the data at a particular timestep.

TODO: currently all the sideset variables are read, but we might want to change this to only read the requested ones.

Definition at line 1322 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_reading)
     libmesh_error_msg("ERROR, ExodusII file must be opened for reading "
                       "before calling ExodusII_IO::read_sideset_data()!");
  
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
   exio_helper->read_sideset_data(mesh, timestep, var_names, side_ids, bc_vals);
 }

References exio_helper, libMesh::MeshInput< MeshBase >::mesh(), and libMesh::MeshOutput< MT >::mesh().

Referenced by WriteSidesetData::testWrite().

◆ set_coordinate_offset()

void libMesh::ExodusII_IO::set_coordinate_offset ( Point p )

Allows you to set a vector that is added to the coordinates of all of the nodes.

Effectively, this "moves" the mesh to a particular position.

Definition at line 458 of file exodusII_io.C.

 {
   libmesh_warning("This method may be deprecated in the future");
   exio_helper->set_coordinate_offset(p);
 }

References exio_helper.

◆ set_n_partitions()

void libMesh::MeshInput< MeshBase >::set_n_partitions ( unsigned int n_parts )

inlineprotectedinherited

Sets the number of partitions in the mesh.

Typically this gets done by the partitioner, but some parallel file formats begin "pre-partitioned".

Definition at line 91 of file mesh_input.h.

91 { this->mesh().set_n_partitions() = n_parts; }

◆ set_output_variables()

void libMesh::ExodusII_IO::set_output_variables	(	const std::vector< std::string > &	output_variables,
		bool	allow_empty = `true`
	)

Sets the list of variable names to be included in the output.

This is optional. If this is never called then all variables will be present. If this is called and an empty vector is supplied no variables will be output. Setting the allow_empty = false will result in empty vectors supplied here to also be populated with all variables.

Definition at line 72 of file exodusII_io.C.

 {
   _output_variables = output_variables;
   _allow_empty_variables = allow_empty;
 }

References _allow_empty_variables, and _output_variables.

◆ skip_comment_lines()

void libMesh::MeshInput< MeshBase >::skip_comment_lines	(	std::istream &	in,
		const char	comment_start
	)

protectedinherited

Reads input from in, skipping all the lines that start with the character comment_start.

Definition at line 179 of file mesh_input.h.

 {
   char c, line[256];
  
   while (in.get(c), c==comment_start)
     in.getline (line, 255);
  
   // put back first character of
   // first non-comment line
   in.putback (c);
 }

◆ use_mesh_dimension_instead_of_spatial_dimension()

void libMesh::ExodusII_IO::use_mesh_dimension_instead_of_spatial_dimension ( bool val )

In the general case, meshes containing 2D elements can be manifolds living in 3D space, thus by default we write all meshes with the Exodus dimension set to LIBMESH_DIM = mesh.spatial_dimension().

In certain cases, however, the user may know his 2D mesh actually lives in the z=0 plane, and therefore wants to write a truly 2D Exodus mesh. In such a case, he should call this function with val=true.

Definition at line 444 of file exodusII_io.C.

 {
   exio_helper->use_mesh_dimension_instead_of_spatial_dimension(val);
 }

References exio_helper.

◆ verbose()

void libMesh::ExodusII_IO::verbose ( bool set_verbosity )

Set the flag indicating if we should be verbose.

Definition at line 434 of file exodusII_io.C.

 {
   _verbose = set_verbosity;
  
   // Set the verbose flag in the helper object as well.
   exio_helper->verbose = _verbose;
 }

References _verbose, and exio_helper.

◆ write()

void libMesh::ExodusII_IO::write ( const std::string & fname )

overridevirtual

This method implements writing a mesh to a specified file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 1338 of file exodusII_io.C.

 {
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
  
   // We may need to gather a DistributedMesh to output it, making that
   // const qualifier in our constructor a dirty lie
   // The "true" specifies that we only need the mesh serialized to processor 0
   MeshSerializer serialize(MeshInput<MeshBase>::mesh(), !MeshOutput<MeshBase>::_is_parallel_format, true);
  
   libmesh_assert( !exio_helper->opened_for_writing );
  
   // If the user has set the append flag here, it doesn't really make
   // sense: the intent of this function is to write a Mesh with no
   // data, while "appending" is really intended to add data to an
   // existing file.  If we're verbose, print a message to this effect.
   if (_append && _verbose)
     libmesh_warning("Warning: Appending in ExodusII_IO::write() does not make sense.\n"
                     "Creating a new file instead!");
  
   exio_helper->create(fname);
   exio_helper->initialize(fname,mesh);
   exio_helper->write_nodal_coordinates(mesh);
   exio_helper->write_elements(mesh);
   exio_helper->write_sidesets(mesh);
   exio_helper->write_nodesets(mesh);
  
   if ((mesh.get_boundary_info().n_edge_conds() > 0) && _verbose)
     libmesh_warning("Warning: Mesh contains edge boundary IDs, but these "
                     "are not supported by the ExodusII format.");
 }

References _append, _verbose, exio_helper, libMesh::MeshBase::get_boundary_info(), libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), and libMesh::BoundaryInfo::n_edge_conds().

Referenced by main(), libMesh::ErrorVector::plot_error(), WriteEdgesetData::testWrite(), WriteSidesetData::testWrite(), and libMesh::NameBasedIO::write().

◆ write_as_dimension()

void libMesh::ExodusII_IO::write_as_dimension ( unsigned dim )

Directly control the num_dim which is written to the Exodus file.

If non-zero, this value supersedes all other dimensions, including: 1.) MeshBase::spatial_dimension() 2.) MeshBase::mesh_dimension() 3.) Any value passed to use_mesh_dimension_instead_of_spatial_dimension() This is useful/necessary for working around a bug in Paraview which prevents the "Plot Over Line" filter from working on 1D meshes.

Definition at line 451 of file exodusII_io.C.

 {
   exio_helper->write_as_dimension(dim);
 }

References dim, and exio_helper.

◆ write_discontinuous_equation_systems()

void libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems	(	const std::string &	fname,
		const EquationSystems &	es,
		const std::set< std::string > *	system_names = `nullptr`
	)

virtualinherited

This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the EquationSystems object.

Definition at line 87 of file mesh_output.C.

 {
   LOG_SCOPE("write_discontinuous_equation_systems()", "MeshOutput");
  
   // We may need to gather and/or renumber a DistributedMesh to output
   // it, making that const qualifier in our constructor a dirty lie
   MT & my_mesh = const_cast<MT &>(*_obj);
  
   // If we're asked to write data that's associated with a different
   // mesh, output files full of garbage are the result.
   libmesh_assert_equal_to(&es.get_mesh(), _obj);
  
   // A non-renumbered mesh may not have a contiguous numbering, and
   // that needs to be fixed before we can build a solution vector.
   if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
       my_mesh.max_node_id() != my_mesh.n_nodes())
     {
       // If we were allowed to renumber then we should have already
       // been properly renumbered...
       libmesh_assert(!my_mesh.allow_renumbering());
  
       libmesh_do_once(libMesh::out <<
                       "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                       << std::endl;);
  
       my_mesh.allow_renumbering(true);
  
       my_mesh.renumber_nodes_and_elements();
  
       // Not sure what good going back to false will do here, the
       // renumbering horses have already left the barn...
       my_mesh.allow_renumbering(false);
     }
  
   MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
  
   // Build the list of variable names that will be written.
   std::vector<std::string> names;
   es.build_variable_names  (names, nullptr, system_names);
  
   if (!_is_parallel_format)
     {
       // Build the nodal solution values & get the variable
       // names from the EquationSystems object
       std::vector<Number> soln;
       es.build_discontinuous_solution_vector (soln, system_names);
  
       this->write_nodal_data_discontinuous (fname, soln, names);
     }
   else // _is_parallel_format
     {
       libmesh_not_implemented();
     }
 }

◆ write_discontinuous_exodusII()

void libMesh::ExodusII_IO::write_discontinuous_exodusII	(	const std::string &	name,
		const EquationSystems &	es,
		const std::set< std::string > *	system_names = `nullptr`
	)

Writes a exodusII file with discontinuous data.

Definition at line 93 of file exodusII_io.C.

 {
   std::vector<std::string> solution_names;
   std::vector<Number>      v;
  
   es.build_variable_names  (solution_names, nullptr, system_names);
   es.build_discontinuous_solution_vector (v, system_names);
   this->write_nodal_data_discontinuous(name, v, solution_names);
 }

References libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_variable_names(), and write_nodal_data_discontinuous().

Referenced by main().

◆ write_element_data()

void libMesh::ExodusII_IO::write_element_data ( const EquationSystems & es )

Write out element solution.

Definition at line 662 of file exodusII_io.C.

 {
   // Be sure the file has been opened for writing!
   if (MeshOutput<MeshBase>::mesh().processor_id() == 0 && !exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting element variables.");
  
   // This function currently only works on serialized meshes. We rely
   // on having a reference to a non-const MeshBase object from our
   // MeshInput parent class to construct a MeshSerializer object,
   // similar to what is done in ExodusII_IO::write().  Note that
   // calling ExodusII_IO::write_timestep() followed by
   // ExodusII_IO::write_element_data() when the underlying Mesh is a
   // DistributedMesh will result in an unnecessary additional
   // serialization/re-parallelization step.
   // The "true" specifies that we only need the mesh serialized to processor 0
   MeshSerializer serialize(MeshInput<MeshBase>::mesh(), !MeshOutput<MeshBase>::_is_parallel_format, true);
  
   // To be (possibly) filled with a filtered list of variable names to output.
   std::vector<std::string> names;
  
   // If _output_variables is populated, only output the monomials which are
   // also in the _output_variables vector.
   if (_output_variables.size() > 0)
     {
       std::vector<std::string> monomials;
       const FEType type(CONSTANT, MONOMIAL);
  
       // Create a list of monomial variable names
       es.build_variable_names(monomials, &type);
  
       // Filter that list against the _output_variables list.  Note: if names is still empty after
       // all this filtering, all the monomial variables will be gathered
       for (const auto & var : monomials)
         if (std::find(_output_variables.begin(), _output_variables.end(), var) != _output_variables.end())
           names.push_back(var);
     }
  
   // If we pass in a list of names to "build_elemental_solution_vector()"
   // it'll filter the variables coming back.
   std::vector<Number> soln;
   es.build_elemental_solution_vector(soln, names);
  
   // Also, store the list of subdomains on which each variable is active
   std::vector<std::set<subdomain_id_type>> vars_active_subdomains;
   es.get_vars_active_subdomains(names, vars_active_subdomains);
  
   if (soln.empty()) // If there is nothing to write just return
     return;
  
   // The data must ultimately be written block by block.  This means that this data
   // must be sorted appropriately.
   if (MeshOutput<MeshBase>::mesh().processor_id())
     return;
  
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
  
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
  
   std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
  
   std::vector<std::set<subdomain_id_type>> complex_vars_active_subdomains =
     exio_helper->get_complex_vars_active_subdomains(vars_active_subdomains);
   exio_helper->initialize_element_variables(complex_names, complex_vars_active_subdomains);
  
   unsigned int num_values = soln.size();
   unsigned int num_vars = names.size();
   unsigned int num_elems = num_values / num_vars;
  
   // This will contain the real and imaginary parts and the magnitude
   // of the values in soln
   std::vector<Real> complex_soln(3*num_values);
  
   for (unsigned i=0; i<num_vars; ++i)
     {
  
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + j] = value.real();
         }
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + num_elems +j] = value.imag();
         }
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + 2*num_elems + j] = std::abs(value);
         }
     }
  
   exio_helper->write_element_values(mesh, complex_soln, _timestep, complex_vars_active_subdomains);
  
 #else
   exio_helper->initialize_element_variables(names, vars_active_subdomains);
   exio_helper->write_element_values(mesh, soln, _timestep, vars_active_subdomains);
 #endif
 }

References _output_variables, _timestep, std::abs(), libMesh::EquationSystems::build_elemental_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::CONSTANT, exio_helper, libMesh::EquationSystems::get_vars_active_subdomains(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MONOMIAL, libMesh::ParallelObject::processor_id(), and value.

Referenced by libMesh::ErrorVector::plot_error(), and MeshInputTest::testExodusCopyElementSolution().

◆ write_element_data_from_discontinuous_nodal_data()

void libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data	(	const EquationSystems &	es,
		const std::set< std::string > *	system_names = `nullptr`,
		const std::string &	var_suffix = `"_elem_node_"`
	)

Similar to the function above, but instead of only handling (CONSTANT, MONOMIAL) data, writes out a general discontinuous solution field, e.g.

(FIRST, L2_LAGRANGE) or (SECOND, MONOMIAL) as a number of elemental fields equal to the number of vertices in each element. For example, if you have a (FIRST, L2_LAGRANGE) variable "u" defined on HEX8 elements, calling this function would by default write 8 elemental fields named u_elem_node_0, u_elem_node_1, u_elem_node_2, etc.

This may be useful if you have a viz tool which is capable of interpreting this element data as a discontinuous solution field. Note that (CONSTANT, MONOMIAL) data is still written as a single value per element, as it makes no sense to write n_vertices copies of the same value.

The 'var_suffix' parameter, which defaults to "_elem_node_", is used to generate the elemental variable names, and is inserted between the base variable name and the node id which the variable applies to, e.g. "u_elem_node_0", "u_elem_node_1", etc.

Definition at line 766 of file exodusII_io.C.

 {
   // Be sure that some other function has already opened the file and prepared it
   // for writing. This is the same behavior as the write_element_data() function
   // which we are trying to mimic.
   if (MeshOutput<MeshBase>::mesh().processor_id() == 0 && !exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting element variables.");
  
   // This function currently only works on serialized meshes.  The
   // "true" flag specifies that we only need the mesh serialized to
   // processor 0
   MeshSerializer serialize(MeshInput<MeshBase>::mesh(),
                            !MeshOutput<MeshBase>::_is_parallel_format,
                            true);
  
   // Note: in general we want to respect the contents of
   // _output_variables, only building a solution vector with values
   // from the requested variables. First build a list of all variable
   // names, then throw out ones that aren't in _output_variables, if
   // any.
   std::vector<std::string> var_names;
   es.build_variable_names (var_names, /*fetype=*/nullptr, system_names);
  
   // Get a subset of all variable names that are CONSTANT,
   // MONOMIALs. We treat those slightly differently since they can
   // truly only have a single value per Elem.
   std::vector<std::string> monomial_var_names;
   const FEType fe_type(CONSTANT, MONOMIAL);
   es.build_variable_names(monomial_var_names, &fe_type);
  
   // Remove all names from var_names that are not in _output_variables.
   // Note: This approach avoids errors when the user provides invalid
   // variable names in _output_variables, as the code will not try to
   // write a variable that doesn't exist.
   if (!_output_variables.empty())
     {
       var_names.erase
         (std::remove_if
          (var_names.begin(),
           var_names.end(),
           [this](const std::string & name)
           {return !std::count(_output_variables.begin(),
                               _output_variables.end(),
                               name);}),
          var_names.end());
  
       // Also filter the monomial variable names.
       monomial_var_names.erase
         (std::remove_if
          (monomial_var_names.begin(),
           monomial_var_names.end(),
           [this](const std::string & name)
           {return !std::count(_output_variables.begin(),
                               _output_variables.end(),
                               name);}),
          monomial_var_names.end());
     }
  
   // Build a solution vector, limiting the results to the variables in
   // var_names and the Systems in system_names, and only computing values
   // at the vertices.
   std::vector<Number> v;
   es.build_discontinuous_solution_vector
     (v, system_names, &var_names, /*vertices_only=*/true);
  
   // Get active subdomains for each variable in var_names.
   std::vector<std::set<subdomain_id_type>> vars_active_subdomains;
   es.get_vars_active_subdomains(var_names, vars_active_subdomains);
  
   // Determine names of variables to write based on the number of
   // nodes/vertices the elements in different subdomains have.
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
   std::map<subdomain_id_type, unsigned int> subdomain_id_to_vertices_per_elem;
   for (const auto & elem : mesh.active_element_ptr_range())
     {
       // Try to insert key/value pair into the map. If this returns
       // false, check the returned iterator's value to make sure it
       // matches. It shouldn't actually be possible for this to fail
       // (since if the Mesh was like this it would have already
       // failed) but it doesn't hurt to be on the safe side.
       auto pr2 = subdomain_id_to_vertices_per_elem.insert
         (std::make_pair(elem->subdomain_id(), elem->n_vertices()));
       if (!pr2.second && pr2.first->second != elem->n_vertices())
         libmesh_error_msg("Elem with different number of vertices found.");
     }
  
   // Determine "derived" variable names. These names are created by
   // starting with the base variable name and appending the user's
   // variable_suffix (default: "_elem_node_") followed by a node id.
   //
   // Not every derived variable will be active on every subdomain,
   // even if the original variable _is_ active.  Subdomains can have
   // different geometric element types (with differing numbers of
   // nodes), so some of the derived variable names will be inactive on
   // those subdomains.
   //
   // Since we would otherwise generate the same name once per
   // subdomain, we keep the list of names unique as we are creating
   // it. We can't use a std::set for this because we don't want the
   // variables names to be in a different order from the order
   // they were written in the call to: build_discontinuous_solution_vector()
   //
   // The list of derived variable names includes one for each vertex,
   // for higher-order elements we currently only write out vertex
   // values, but this could be changed in the future without too much
   // trouble.
   std::vector<std::string> derived_var_names;
  
   // Keep track of mapping from derived_name to (orig_name, node_id)
   // pair. We will use this later to determine whether a given
   // variable is active on a given subdomain.
   std::map<std::string, std::pair<std::string, unsigned int>>
     derived_name_to_orig_name_and_node_id;
  
   for (const auto & pr : subdomain_id_to_vertices_per_elem)
     {
       const subdomain_id_type sbd_id = pr.first;
       const unsigned int vertices_per_elem =
         subdomain_id_to_vertices_per_elem[sbd_id];
  
       std::ostringstream oss;
       for (unsigned int n=0; n<vertices_per_elem; ++n)
         for (const auto & orig_var_name : var_names)
           {
             oss.str("");
             oss.clear();
             oss << orig_var_name << var_suffix << n;
             std::string derived_name = oss.str();
  
             // Only add this var name if it's not already in the list.
             if (!std::count(derived_var_names.begin(), derived_var_names.end(), derived_name))
               {
                 derived_var_names.push_back(derived_name);
                 // Add entry for derived_name -> (orig_name, node_id) mapping.
                 derived_name_to_orig_name_and_node_id[derived_name] =
                   std::make_pair(orig_var_name, n);
               }
           }
     }
  
   // For each derived variable name, determine whether it is active
   // based on how many nodes/vertices the elements in a given subdomain have,
   // and whether they were active on the subdomain to begin with.
   std::vector<std::set<subdomain_id_type>>
     derived_vars_active_subdomains(derived_var_names.size());
  
   // A new data structure for keeping track of a list of variable names
   // that are in the discontinous solution vector on each subdomain. Used
   // for indexing. Note: if a variable was inactive at the System level,
   // an entry for it will still be in the discontinuous solution vector,
   // but it will just have a value of zero. On the other hand, when we
   // create the derived variable names some of them are "inactive" on
   // different subdomains in the sense that they don't exist at all, i.e.
   // there is no zero padding for them. We need to be able to distinguish
   // between these two types in order to do the indexing into this vector
   // correctly.
   std::map<subdomain_id_type, std::vector<std::string>>
     subdomain_to_var_names;
  
   for (auto derived_var_id : index_range(derived_var_names))
     {
       const auto & derived_name = derived_var_names[derived_var_id];
       const auto & name_and_id =
         libmesh_map_find (derived_name_to_orig_name_and_node_id,
                   derived_name);
  
       // Convenience variables for the map entry's contents.
       const std::string & orig_name = name_and_id.first;
       const unsigned int node_id = name_and_id.second;
  
       // For each subdomain, determine whether the current variable
       // should be active on that subdomain.
       for (const auto & pr : subdomain_id_to_vertices_per_elem)
         {
           // Convenience variables for the current subdomain and the
           // number of nodes elements in this subdomain have.
           subdomain_id_type sbd_id = pr.first;
           unsigned int vertices_per_elem_this_sbd =
             subdomain_id_to_vertices_per_elem[sbd_id];
  
           // Check whether variable orig_name was active on this
           // subdomain to begin with by looking in the
           // vars_active_subdomains container. We assume that the
           // location of orig_name in the var_names vector matches its
           // index in the vars_active_subdomains container.
           auto var_loc = std::find(var_names.begin(), var_names.end(), orig_name);
           if (var_loc == var_names.end())
             libmesh_error_msg("Variable " << orig_name << " somehow not found in var_names array.");
           auto var_id = std::distance(var_names.begin(), var_loc);
  
           // The derived_var will only be active if this subdomain has
           // enough vertices for that to be the case.
           if (node_id < vertices_per_elem_this_sbd)
             {
               // Regardless of whether the original variable was not active on this subdomain,
               // the discontinuous solution vector will have zero padding for it, and
               // we will need to account for it. Therefore it should still be added to
               // the subdomain_to_var_names data structure!
               subdomain_to_var_names[sbd_id].push_back(derived_name);
  
               // If the original variable was not active on the
               // current subdomain, it should not be added to the
               // derived_vars_active_subdomains data structure, since
               // it will not be written to the Exodus file.
  
               // Determine if the original variable was active on the
               // current subdomain.
               bool orig_var_active =
                 (vars_active_subdomains[var_id].empty() ||
                  vars_active_subdomains[var_id].count(sbd_id));
  
               // And only if it was, add it to the
               // derived_vars_active_subdomains data structure.
               if (orig_var_active)
                 derived_vars_active_subdomains[derived_var_id].insert(sbd_id);
             }
         } // end loop over subdomain_id_to_vertices_per_elem
     } // end loop over derived_var_names
  
   // At this point we've built the "true" list of derived names, but
   // if there are any CONSTANT MONOMIALS in this list, we now want to
   // remove all but one copy of them from the derived_var_names list,
   // and rename them in (but not remove them from) the
   // subdomain_to_var_names list, and then update the
   // derived_vars_active_subdomains containers before finally calling
   // the Exodus helper functions.
   for (auto & derived_var_name : derived_var_names)
     {
       // Get the original name associated with this derived name.
       const auto & name_and_id =
         libmesh_map_find (derived_name_to_orig_name_and_node_id,
                   derived_var_name);
  
       // Convenience variables for the map entry's contents.
       const std::string & orig_name = name_and_id.first;
  
       // Was the original name a constant monomial?
       if (std::count(monomial_var_names.begin(),
                      monomial_var_names.end(),
                      orig_name))
         {
           // Rename this variable in the subdomain_to_var_names vectors.
           for (auto & pr : subdomain_to_var_names)
             {
               // Reference to ordered list of variable names on this subdomain.
               auto & name_vec = pr.second;
  
               auto name_vec_it =
                 std::find(name_vec.begin(),
                           name_vec.end(),
                           derived_var_name);
  
               if (name_vec_it != name_vec.end())
                 {
                   // Actually rename it back to the orig_name, dropping
                   // the "_elem_corner_" stuff.
                   *name_vec_it = orig_name;
                 }
             }
  
           // Finally, rename the variable in the derived_var_names vector itself.
           derived_var_name = orig_name;
         } // if (monomial)
     } // end loop over derived names
  
   // Now remove duplicate entries from derived_var_names after the first.
   // Also update the derived_vars_active_subdomains container in a consistent way.
   {
     std::vector<std::string> derived_var_names_edited;
     std::vector<std::set<subdomain_id_type>> derived_vars_active_subdomains_edited;
     std::vector<unsigned int> found_first(monomial_var_names.size());
  
     for (auto i : index_range(derived_var_names))
       {
         const auto & derived_var_name = derived_var_names[i];
         const auto & active_set = derived_vars_active_subdomains[i];
  
         // Determine whether we will keep this derived variable name in
         // the final container.
         bool keep = true;
         for (auto j : index_range(monomial_var_names))
           if (derived_var_name == monomial_var_names[j])
             {
               if (!found_first[j])
                 found_first[j] = 1;
  
               else
                 keep = false;
             }
  
         // We also don't keep variables that are not active on any subdomains.
         // Contrary to other uses of the var_active_subdomains container where
         // the empty set means "all" subdomains, here it really means "none".
         if (active_set.empty())
           keep = false;
  
         if (keep)
           {
             derived_var_names_edited.push_back(derived_var_name);
             derived_vars_active_subdomains_edited.push_back(active_set);
           }
       }
  
     // We built the filtered ranges, now swap them with the originals.
     derived_var_names.swap(derived_var_names_edited);
     derived_vars_active_subdomains.swap(derived_vars_active_subdomains_edited);
   }
  
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
   // Build complex variable names "r_foo", "i_foo", "a_foo" and the lists of
   // subdomains on which they are active.
   auto complex_var_names =
     exio_helper->get_complex_names(derived_var_names);
   auto complex_vars_active_subdomains =
     exio_helper->get_complex_vars_active_subdomains(derived_vars_active_subdomains);
   auto complex_subdomain_to_var_names =
     exio_helper->get_complex_subdomain_to_var_names(subdomain_to_var_names);
  
   // Make expanded version of vector "v" in which each entry in the
   // original expands to an ("r_", "i_", "a_") triple.
   std::vector<Real> complex_v;
   complex_v.reserve(3 * v.size());
   for (const auto & val : v)
     {
       complex_v.push_back(val.real());
       complex_v.push_back(val.imag());
       complex_v.push_back(std::abs(val));
     }
  
   // Finally, initialize storage for the variables and write them to file.
   exio_helper->initialize_element_variables
     (complex_var_names, complex_vars_active_subdomains);
   exio_helper->write_element_values_element_major
     (mesh, complex_v, _timestep,
      complex_vars_active_subdomains,
      complex_var_names,
      complex_subdomain_to_var_names);
 #else
  
   // Call function which writes the derived variable names to the
   // Exodus file.
   exio_helper->initialize_element_variables(derived_var_names, derived_vars_active_subdomains);
  
   // ES::build_discontinuous_solution_vector() creates a vector with
   // an element-major ordering, so call Helper::write_element_values()
   // passing false for the last argument.
   exio_helper->write_element_values_element_major
     (mesh, v, _timestep,
      derived_vars_active_subdomains,
      derived_var_names,
      subdomain_to_var_names);
 #endif
 }

References std::abs(), libMesh::MeshBase::active_element_ptr_range(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::CONSTANT, distance(), libMesh::EquationSystems::get_vars_active_subdomains(), libMesh::index_range(), libMesh::MeshOutput< MT >::mesh(), mesh, libMesh::MONOMIAL, and libMesh::Quality::name().

Referenced by MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData().

◆ write_equation_systems()

void libMesh::MeshOutput< MeshBase >::write_equation_systems	(	const std::string &	fname,
		const EquationSystems &	es,
		const std::set< std::string > *	system_names = `nullptr`
	)

virtualinherited

This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems object.

Reimplemented in libMesh::NameBasedIO.

Definition at line 31 of file mesh_output.C.

 {
   LOG_SCOPE("write_equation_systems()", "MeshOutput");
  
   // We may need to gather and/or renumber a DistributedMesh to output
   // it, making that const qualifier in our constructor a dirty lie
   MT & my_mesh = const_cast<MT &>(*_obj);
  
   // If we're asked to write data that's associated with a different
   // mesh, output files full of garbage are the result.
   libmesh_assert_equal_to(&es.get_mesh(), _obj);
  
   // A non-renumbered mesh may not have a contiguous numbering, and
   // that needs to be fixed before we can build a solution vector.
   if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
       my_mesh.max_node_id() != my_mesh.n_nodes())
     {
       // If we were allowed to renumber then we should have already
       // been properly renumbered...
       libmesh_assert(!my_mesh.allow_renumbering());
  
       libmesh_do_once(libMesh::out <<
                       "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                       << std::endl;);
  
       my_mesh.allow_renumbering(true);
  
       my_mesh.renumber_nodes_and_elements();
  
       // Not sure what good going back to false will do here, the
       // renumbering horses have already left the barn...
       my_mesh.allow_renumbering(false);
     }
  
   if (!_is_parallel_format)
     {
       MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
  
       // Build the list of variable names that will be written.
       std::vector<std::string> names;
       es.build_variable_names  (names, nullptr, system_names);
  
       // Build the nodal solution values & get the variable
       // names from the EquationSystems object
       std::vector<Number> soln;
       es.build_solution_vector (soln, system_names);
  
       this->write_nodal_data (fname, soln, names);
     }
   else // _is_parallel_format
     this->write_nodal_data (fname, es, system_names);
 }

◆ write_global_data()

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

Write out global variables.

Definition at line 1233 of file exodusII_io.C.

 {
   if (MeshOutput<MeshBase>::mesh().processor_id())
     return;
  
   if (!exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting global variables.");
  
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
  
   std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
  
   exio_helper->initialize_global_variables(complex_names);
  
   unsigned int num_values = soln.size();
   unsigned int num_vars = names.size();
   unsigned int num_elems = num_values / num_vars;
  
   // This will contain the real and imaginary parts and the magnitude
   // of the values in soln
   std::vector<Real> complex_soln(3*num_values);
  
   for (unsigned i=0; i<num_vars; ++i)
     {
  
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + j] = value.real();
         }
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + num_elems +j] = value.imag();
         }
       for (unsigned int j=0; j<num_elems; ++j)
         {
           Number value = soln[i*num_vars + j];
           complex_soln[3*i*num_elems + 2*num_elems + j] = std::abs(value);
         }
     }
  
   exio_helper->write_global_values(complex_soln, _timestep);
  
 #else
   exio_helper->initialize_global_variables(names);
   exio_helper->write_global_values(soln, _timestep);
 #endif
 }

References _timestep, std::abs(), exio_helper, libMesh::ParallelObject::processor_id(), and value.

◆ write_information_records()

void libMesh::ExodusII_IO::write_information_records ( const std::vector< std::string > & records )

Write out information records.

Definition at line 1220 of file exodusII_io.C.

 {
   if (MeshOutput<MeshBase>::mesh().processor_id())
     return;
  
   if (!exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be initialized before outputting information records.");
  
   exio_helper->write_information_records(records);
 }

References exio_helper, and libMesh::ParallelObject::processor_id().

◆ write_nodal_data() [1/3]

void libMesh::MeshOutput< MeshBase >::write_nodal_data	(	const std::string &	fname,
		const EquationSystems &	es,
		const std::set< std::string > *	system_names
	)

virtualinherited

This method should be overridden by "parallel" output formats for writing nodal data.

Instead of getting a localized copy of the nodal solution vector, it directly uses EquationSystems current_local_solution vectors to look up nodal values.

If not implemented, reorders the solutions into a nodal-only NumericVector and calls the above version of this function.

Reimplemented in libMesh::Nemesis_IO.

Definition at line 158 of file mesh_output.C.

 {
   std::vector<std::string> names;
   es.build_variable_names  (names, nullptr, system_names);
  
   std::unique_ptr<NumericVector<Number>> parallel_soln =
     es.build_parallel_solution_vector(system_names);
  
   this->write_nodal_data (fname, *parallel_soln, names);
 }

◆ write_nodal_data() [2/3]

void libMesh::MeshOutput< MeshBase >::write_nodal_data	(	const std::string &	fname,
		const NumericVector< Number > &	parallel_soln,
		const std::vector< std::string > &	names
	)

virtualinherited

This method may be overridden by "parallel" output formats for writing nodal data.

Instead of getting a localized copy of the nodal solution vector, it is passed a NumericVector of type=PARALLEL which is in node-major order i.e. (u0,v0,w0, u1,v1,w1, u2,v2,w2, u3,v3,w3, ...) and contains n_nodes*n_vars total entries. Then, it is up to the individual I/O class to extract the required solution values from this vector and write them in parallel.

If not implemented, localizes the parallel vector into a std::vector and calls the other version of this function.

Reimplemented in libMesh::Nemesis_IO.

Definition at line 145 of file mesh_output.C.

 {
   // This is the fallback implementation for parallel I/O formats that
   // do not yet implement proper writing in parallel, and instead rely
   // on the full solution vector being available on all processors.
   std::vector<Number> soln;
   parallel_soln.localize(soln);
   this->write_nodal_data(fname, soln, names);
 }

◆ write_nodal_data() [3/3]

void libMesh::ExodusII_IO::write_nodal_data	(	const std::string &	fname,
		const std::vector< Number > &	soln,
		const std::vector< std::string > &	names
	)

overridevirtual

Write out a nodal solution.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 1124 of file exodusII_io.C.

 {
   LOG_SCOPE("write_nodal_data()", "ExodusII_IO");
  
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
  
   int num_vars = cast_int<int>(names.size());
   dof_id_type num_nodes = mesh.n_nodes();
  
   // The names of the variables to be output
   std::vector<std::string> output_names;
  
   if (_allow_empty_variables || !_output_variables.empty())
     output_names = _output_variables;
   else
     output_names = names;
  
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
  
   std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
  
   // Call helper function for opening/initializing data, giving it the
   // complex variable names
   this->write_nodal_data_common(fname, complex_names, /*continuous=*/true);
 #else
   // Call helper function for opening/initializing data
   this->write_nodal_data_common(fname, output_names, /*continuous=*/true);
 #endif
  
   if (mesh.processor_id())
     return;
  
   // This will count the number of variables actually output
   for (int c=0; c<num_vars; c++)
     {
       std::stringstream name_to_find;
  
       std::vector<std::string>::iterator pos =
         std::find(output_names.begin(), output_names.end(), names[c]);
       if (pos == output_names.end())
         continue;
  
       unsigned int variable_name_position =
         cast_int<unsigned int>(pos - output_names.begin());
  
       // Set up temporary vectors to be passed to Exodus to write the
       // nodal values for a single variable at a time.
 #ifdef LIBMESH_USE_REAL_NUMBERS
       std::vector<Number> cur_soln;
  
       // num_nodes is either exactly how much space we will need for
       // each vector, or a safe upper bound for the amount of memory
       // we will require when there are gaps in the numbering.
       cur_soln.reserve(num_nodes);
 #else
       std::vector<Real> real_parts;
       std::vector<Real> imag_parts;
       std::vector<Real> magnitudes;
       real_parts.reserve(num_nodes);
       imag_parts.reserve(num_nodes);
       magnitudes.reserve(num_nodes);
 #endif
  
       // There could be gaps in "soln", but it will always be in the
       // order of [num_vars * node_id + var_id]. We now copy the
       // proper solution values contiguously into "cur_soln",
       // removing the gaps.
       for (const auto & node : mesh.node_ptr_range())
         {
           dof_id_type idx = node->id()*num_vars + c;
 #ifdef LIBMESH_USE_REAL_NUMBERS
           cur_soln.push_back(soln[idx]);
 #else
           real_parts.push_back(soln[idx].real());
           imag_parts.push_back(soln[idx].imag());
           magnitudes.push_back(std::abs(soln[idx]));
 #endif
         }
  
       // Finally, actually call the Exodus API to write to file.
 #ifdef LIBMESH_USE_REAL_NUMBERS
       exio_helper->write_nodal_values(variable_name_position+1, cur_soln, _timestep);
 #else
       exio_helper->write_nodal_values(3*variable_name_position+1, real_parts, _timestep);
       exio_helper->write_nodal_values(3*variable_name_position+2, imag_parts, _timestep);
       exio_helper->write_nodal_values(3*variable_name_position+3, magnitudes, _timestep);
 #endif
  
     }
 }

References _allow_empty_variables, _output_variables, _timestep, std::abs(), exio_helper, libMesh::MeshTools::Generation::Private::idx(), std::imag(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::node_ptr_range(), libMesh::ParallelObject::processor_id(), std::real(), and write_nodal_data_common().

Referenced by libMesh::NameBasedIO::write_nodal_data().

◆ write_nodal_data_common()

void libMesh::ExodusII_IO::write_nodal_data_common	(	std::string	fname,
		const std::vector< std::string > &	names,
		bool	continuous = `true`
	)

This function factors out a bunch of code which is common to the write_nodal_data() and write_nodal_data_discontinuous() functions.

Definition at line 1429 of file exodusII_io.C.

 {
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
  
   // This function can be called multiple times, we only want to open
   // the ExodusII file the first time it's called.
   if (!exio_helper->opened_for_writing)
     {
       // If we're appending, open() the file with read_only=false,
       // otherwise create() it and write the contents of the mesh to
       // it.
       if (_append)
         {
           exio_helper->open(fname.c_str(), /*read_only=*/false);
           // If we're appending, it's not valid to call exio_helper->initialize()
           // or exio_helper->initialize_nodal_variables(), but we do need to set up
           // certain aspects of the Helper object itself, such as the number of nodes
           // and elements.  We do that by reading the header...
           exio_helper->read_header();
  
           // ...and reading the block info
           exio_helper->read_block_info();
         }
       else
         {
           exio_helper->create(fname);
  
           exio_helper->initialize(fname, mesh, !continuous);
           exio_helper->write_nodal_coordinates(mesh, !continuous);
           exio_helper->write_elements(mesh, !continuous);
  
           exio_helper->write_sidesets(mesh);
           exio_helper->write_nodesets(mesh);
  
           exio_helper->initialize_nodal_variables(names);
         }
     }
   else
     {
       // We are already open for writing, so check that the filename
       // passed to this function matches the filename currently in use
       // by the helper.
       if (fname != exio_helper->current_filename)
         libmesh_error_msg("Error! This ExodusII_IO object is already associated with file: " \
                           << exio_helper->current_filename              \
                           << ", cannot use it with requested file: "    \
                           << fname);
     }
 }

References _append, exio_helper, libMesh::MeshInput< MeshBase >::mesh(), and libMesh::MeshOutput< MT >::mesh().

Referenced by write_nodal_data(), and write_nodal_data_discontinuous().

◆ write_nodal_data_discontinuous()

void libMesh::ExodusII_IO::write_nodal_data_discontinuous	(	const std::string &	fname,
		const std::vector< Number > &	soln,
		const std::vector< std::string > &	names
	)

overridevirtual

Write out a discontinuous nodal solution.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 1371 of file exodusII_io.C.

 {
   LOG_SCOPE("write_nodal_data_discontinuous()", "ExodusII_IO");
  
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
  
   int num_vars = cast_int<int>(names.size());
   int num_nodes = 0;
   for (const auto & elem : mesh.active_element_ptr_range())
     num_nodes += elem->n_nodes();
  
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
  
   std::vector<std::string> complex_names = exio_helper->get_complex_names(names);
  
   // Call helper function for opening/initializing data, giving it the
   // complex variable names
   this->write_nodal_data_common(fname, complex_names, /*continuous=*/false);
 #else
   // Call helper function for opening/initializing data
   this->write_nodal_data_common(fname, names, /*continuous=*/false);
 #endif
  
   if (mesh.processor_id())
     return;
  
   for (int c=0; c<num_vars; c++)
     {
 #ifdef LIBMESH_USE_COMPLEX_NUMBERS
       std::vector<Real> real_parts(num_nodes);
       std::vector<Real> imag_parts(num_nodes);
       std::vector<Real> magnitudes(num_nodes);
  
       for (int i=0; i<num_nodes; ++i)
         {
           real_parts[i] = soln[i*num_vars + c].real();
           imag_parts[i] = soln[i*num_vars + c].imag();
           magnitudes[i] = std::abs(soln[i*num_vars + c]);
         }
       exio_helper->write_nodal_values(3*c+1,real_parts,_timestep);
       exio_helper->write_nodal_values(3*c+2,imag_parts,_timestep);
       exio_helper->write_nodal_values(3*c+3,magnitudes,_timestep);
 #else
       // Copy out this variable's solution
       std::vector<Number> cur_soln(num_nodes);
  
       for (int i=0; i<num_nodes; i++)
         cur_soln[i] = soln[i*num_vars + c];
  
       exio_helper->write_nodal_values(c+1,cur_soln,_timestep);
 #endif
     }
 }

References _timestep, std::abs(), libMesh::MeshBase::active_element_ptr_range(), exio_helper, libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::ParallelObject::processor_id(), and write_nodal_data_common().

Referenced by write_discontinuous_exodusII().

◆ write_sideset_data()

void libMesh::ExodusII_IO::write_sideset_data	(	int	timestep,
		const std::vector< std::string > &	var_names,
		const std::vector< std::set< boundary_id_type >> &	side_ids,
		const std::vector< std::map< BoundaryInfo::BCTuple, Real >> &	bc_vals
	)

The Exodus format can also store values on sidesets.

This can be thought of as an alternative to defining an elemental variable field on lower-dimensional elements making up a part of the boundary. The inputs to the function are: .) var_names[i] is the name of the ith sideset variable to be written to file. .) side_ids[i] is a set of side_ids where var_names[i] is active. .) bc_vals[i] is a map from (elem,side,id) BCTuple objects to the corresponding real-valued data.

Note: You must have already written the mesh by calling e.g. write() before calling this function, because it uses the existing ordering of the Exodus sidesets.

Definition at line 1305 of file exodusII_io.C.

 {
   if (!exio_helper->opened_for_writing)
     libmesh_error_msg("ERROR, ExodusII file must be opened for writing "
                       "before calling ExodusII_IO::write_sideset_data()!");
  
   const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
   exio_helper->write_sideset_data(mesh, timestep, var_names, side_ids, bc_vals);
 }

References exio_helper, libMesh::MeshInput< MeshBase >::mesh(), and libMesh::MeshOutput< MT >::mesh().

Referenced by WriteSidesetData::testWrite().

◆ write_timestep()

void libMesh::ExodusII_IO::write_timestep	(	const std::string &	fname,
		const EquationSystems &	es,
		const int	timestep,
		const Real	time,
		const std::set< std::string > *	system_names = `nullptr`
	)

Writes out the solution at a specific timestep.

Parameters

fname	Name of the file to write to
es	EquationSystems object which contains the solution vector.
timestep	The timestep to write out, should be 1 indexed.
time	The current simulation time.
system_names	Optional list of systems to write solutions for.

Definition at line 1286 of file exodusII_io.C.

 {
   _timestep = timestep;
   write_equation_systems(fname,es,system_names);
  
   if (MeshOutput<MeshBase>::mesh().processor_id())
     return;
  
   exio_helper->write_timestep(timestep, time);
 }

References _timestep, exio_helper, libMesh::ParallelObject::processor_id(), and libMesh::MeshOutput< MeshBase >::write_equation_systems().

Referenced by main(), and write_output().

◆ write_timestep_discontinuous()

void libMesh::ExodusII_IO::write_timestep_discontinuous	(	const std::string &	fname,
		const EquationSystems &	es,
		const int	timestep,
		const Real	time,
		const std::set< std::string > *	system_names = `nullptr`
	)

Writes a discontinuous solution at a specific timestep.

Parameters

fname	Name of the file to be written
es	EquationSystems object which contains the solution vector
timestep	The timestep to write out. (should be 1 indexed)
time	The current simulation time
system_names	Optional list of systems to write solutions for.

Definition at line 107 of file exodusII_io.C.

 {
   _timestep = timestep;
   write_discontinuous_equation_systems (fname,es,system_names);
  
   if (MeshOutput<MeshBase>::mesh().processor_id())
     return;
  
   exio_helper->write_timestep(timestep, time);
 }

References _timestep, exio_helper, libMesh::ParallelObject::processor_id(), and libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems().

Member Data Documentation

◆ _allow_empty_variables

bool libMesh::ExodusII_IO::_allow_empty_variables

private

If true, _output_variables is allowed to remain empty.

If false, if _output_variables is empty it will be populated with a complete list of all variables By default, calling set_output_variables() sets this flag to true, but it provides an override.

Definition at line 425 of file exodusII_io.h.

Referenced by set_output_variables(), and write_nodal_data().

◆ _append

bool libMesh::ExodusII_IO::_append

private

Default false.

If true, files will be opened with EX_WRITE rather than created from scratch when writing.

Definition at line 411 of file exodusII_io.h.

Referenced by append(), write(), and write_nodal_data_common().

◆ _ascii_precision

unsigned int libMesh::MeshOutput< MeshBase >::_ascii_precision

privateinherited

Precision to use when writing ASCII files.

Definition at line 195 of file mesh_output.h.

◆ _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().

◆ _is_parallel_format [1/2]

const bool libMesh::MeshInput< MeshBase >::_is_parallel_format

privateinherited

Flag specifying whether this format is parallel-capable.

If this is false (default) I/O is only permitted when the mesh has been serialized.

Definition at line 121 of file mesh_input.h.

◆ _is_parallel_format [2/2]

const bool libMesh::MeshOutput< MeshBase >::_is_parallel_format

protectedinherited

Flag specifying whether this format is parallel-capable.

If this is false (default) I/O is only permitted when the mesh has been serialized.

Definition at line 172 of file mesh_output.h.

◆ _obj

MeshBase * libMesh::MeshInput< MeshBase >::_obj

privateinherited

A pointer to a non-const object object.

This allows us to read the object from file.

Definition at line 114 of file mesh_input.h.

◆ _output_variables

std::vector<std::string> libMesh::ExodusII_IO::_output_variables

private

The names of the variables to be output.

If this is empty then all variables are output.

Definition at line 418 of file exodusII_io.h.

Referenced by set_output_variables(), write_element_data(), and write_nodal_data().

◆ _serial_only_needed_on_proc_0

const bool libMesh::MeshOutput< MeshBase >::_serial_only_needed_on_proc_0

protectedinherited

Flag specifying whether this format can be written by only serializing the mesh to processor zero.

If this is false (default) the mesh will be serialized to all processors

Definition at line 181 of file mesh_output.h.

◆ _timestep

int libMesh::ExodusII_IO::_timestep

private

Stores the current value of the timestep when calling ExodusII_IO::write_timestep().

Definition at line 400 of file exodusII_io.h.

Referenced by write_element_data(), write_global_data(), write_nodal_data(), write_nodal_data_discontinuous(), write_timestep(), and write_timestep_discontinuous().

◆ _verbose

bool libMesh::ExodusII_IO::_verbose

private

should we be verbose?

Definition at line 405 of file exodusII_io.h.

Referenced by verbose(), and write().

◆ elems_of_dimension

std::vector<bool> libMesh::MeshInput< MeshBase >::elems_of_dimension

protectedinherited

A vector of bools describing what dimension elements have been encountered when reading a mesh.

Definition at line 97 of file mesh_input.h.

◆ exio_helper

std::unique_ptr<ExodusII_IO_Helper> libMesh::ExodusII_IO::exio_helper

private

Only attempt to instantiate an ExodusII helper class if the Exodus API is defined.

This class will have no functionality when LIBMESH_HAVE_EXODUS_API is not defined.

Definition at line 394 of file exodusII_io.h.

Referenced by copy_elemental_solution(), copy_nodal_solution(), copy_scalar_solution(), get_elem_var_names(), get_exio_helper(), get_global_var_names(), get_nodal_var_names(), get_num_time_steps(), get_time_steps(), read(), read_elemental_variable(), read_global_variable(), read_sideset_data(), set_coordinate_offset(), use_mesh_dimension_instead_of_spatial_dimension(), verbose(), write(), write_as_dimension(), write_element_data(), write_global_data(), write_information_records(), write_nodal_data(), write_nodal_data_common(), write_nodal_data_discontinuous(), write_sideset_data(), write_timestep(), write_timestep_discontinuous(), and ~ExodusII_IO().

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

include/mesh/exodusII_io.h
src/mesh/exodusII_io.C

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ExodusII_IO()

◆ ~ExodusII_IO()

Member Function Documentation

◆ append()

◆ ascii_precision()

◆ comm()

◆ copy_elemental_solution()

◆ copy_nodal_solution() [1/2]

◆ copy_nodal_solution() [2/2]

◆ copy_scalar_solution()

◆ get_elem_var_names()

◆ get_exio_helper()

◆ get_global_var_names()

◆ get_nodal_var_names()

◆ get_num_time_steps()

◆ get_time_steps()

◆ mesh() [1/2]

◆ mesh() [2/2]

◆ n_processors()

◆ processor_id()

◆ read()

◆ read_elemental_variable()

◆ read_global_variable()

◆ read_sideset_data()

◆ set_coordinate_offset()

◆ set_n_partitions()

◆ set_output_variables()

◆ skip_comment_lines()

◆ use_mesh_dimension_instead_of_spatial_dimension()

◆ verbose()

◆ write()

◆ write_as_dimension()

◆ write_discontinuous_equation_systems()

◆ write_discontinuous_exodusII()

◆ write_element_data()

◆ write_element_data_from_discontinuous_nodal_data()

◆ write_equation_systems()

◆ write_global_data()

◆ write_information_records()

◆ write_nodal_data() [1/3]

◆ write_nodal_data() [2/3]

◆ write_nodal_data() [3/3]

◆ write_nodal_data_common()

◆ write_nodal_data_discontinuous()

◆ write_sideset_data()

◆ write_timestep()

◆ write_timestep_discontinuous()

Member Data Documentation

◆ _allow_empty_variables

◆ _append

◆ _ascii_precision

◆ _communicator

◆ _is_parallel_format [1/2]

◆ _is_parallel_format [2/2]

◆ _obj

◆ _output_variables

◆ _serial_only_needed_on_proc_0

◆ _timestep

◆ _verbose

◆ elems_of_dimension

◆ exio_helper