libMesh
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This class supports simple reads and writes in any libMesh-supported format, by dispatching to one of the other I/O classes based on filename. More...
#include <namebased_io.h>
Public Member Functions | |
NameBasedIO (const MeshBase &) | |
Constructor. More... | |
NameBasedIO (MeshBase &) | |
Constructor. More... | |
virtual void | read (const std::string &mesh_file) override |
This method implements reading a mesh from a specified file. More... | |
virtual void | write (const std::string &mesh_file) override |
This method implements writing a mesh to a specified file. More... | |
virtual void | write_equation_systems (const std::string &filename, const EquationSystems &es, const std::set< std::string > *system_names=nullptr) override |
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_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override |
This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided. More... | |
bool | is_parallel_file_format (std::string_view filename) |
bool | is_parallel_format () const |
Returns true iff this mesh file format and input class are parallelized, so that all processors can read their share of the data at once. 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... | |
virtual void | write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) |
This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided. More... | |
unsigned int & | ascii_precision () |
Return/set the precision to use when writing ASCII files. More... | |
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 |
virtual bool | get_add_sides () |
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... | |
This class supports simple reads and writes in any libMesh-supported format, by dispatching to one of the other I/O classes based on filename.
Other I/O classes may have more advanced features that are not accessible via this interface.
Definition at line 44 of file namebased_io.h.
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inlineexplicit |
Constructor.
Takes a reference to a constant mesh object. This constructor will only allow us to write the mesh.
Definition at line 110 of file namebased_io.h.
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inlineexplicit |
Constructor.
Takes a writable reference to a mesh object. This constructor is required to let us read in a mesh.
Definition at line 116 of file namebased_io.h.
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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 269 of file mesh_output.h.
Referenced by libMesh::UNVIO::nodes_out(), libMesh::FroIO::write(), libMesh::MEDITIO::write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().
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inlineprotectedvirtualinherited |
Reimplemented in libMesh::ExodusII_IO.
Definition at line 176 of file mesh_output.h.
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inline |
Definition at line 124 of file namebased_io.h.
References libMesh::Quality::name().
Referenced by read(), and write().
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inlineinherited |
Returns true iff this mesh file format and input class are parallelized, so that all processors can read their share of the data at once.
Definition at line 87 of file mesh_input.h.
References libMesh::MeshInput< MT >::_is_parallel_format.
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inlineprotectedinherited |
Definition at line 178 of file mesh_input.h.
Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::VTKIO::cells_to_vtk(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::TetGenIO::element_in(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::elements_out(), libMesh::VTKIO::get_local_node_values(), libMesh::ExodusII_IO::get_sideset_data_indices(), libMesh::UNVIO::groups_in(), libMesh::TetGenIO::node_in(), libMesh::UNVIO::nodes_in(), libMesh::UNVIO::nodes_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::GMVIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::DynaIO::read_mesh(), libMesh::CheckpointIO::read_nodes(), libMesh::CheckpointIO::read_nodesets(), libMesh::CheckpointIO::read_remote_elem(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::ExodusII_IO::read_sideset_data(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::CheckpointIO::read_subdomain_names(), libMesh::TetGenIO::write(), libMesh::Nemesis_IO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::ExodusII_IO::write(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO::write_elemsets(), libMesh::UCDIO::write_header(), libMesh::UCDIO::write_implementation(), libMesh::UCDIO::write_interior_elems(), libMesh::GmshIO::write_mesh(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::UCDIO::write_nodes(), libMesh::CheckpointIO::write_nodesets(), libMesh::XdrIO::write_parallel(), libMesh::GmshIO::write_post(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::ExodusII_IO::write_sideset_data(), libMesh::UCDIO::write_soln(), and libMesh::CheckpointIO::write_subdomain_names().
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inlineprotectedinherited |
Definition at line 259 of file mesh_output.h.
References libMesh::libmesh_assert().
Referenced by libMesh::FroIO::write(), libMesh::TecplotIO::write(), libMesh::MEDITIO::write(), libMesh::PostscriptIO::write(), libMesh::EnsightIO::write(), libMesh::TecplotIO::write_ascii(), libMesh::TecplotIO::write_binary(), libMesh::TecplotIO::write_nodal_data(), libMesh::MEDITIO::write_nodal_data(), and libMesh::GnuPlotIO::write_solution().
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overridevirtual |
This method implements reading a mesh from a specified file.
Implements libMesh::MeshInput< MeshBase >.
Definition at line 80 of file namebased_io.C.
References libMesh::MeshBase::allow_renumbering(), libMesh::XdrIO::binary(), libMesh::MeshCommunication::broadcast(), is_parallel_file_format(), libMesh::XdrIO::legacy(), libMesh::MeshInput< MT >::mesh(), libMesh::ParallelObject::n_processors(), libMesh::Quality::name(), libMesh::ParallelObject::processor_id(), libMesh::OFFIO::read(), libMesh::AbaqusIO::read(), libMesh::TetGenIO::read(), libMesh::UCDIO::read(), libMesh::GMVIO::read(), libMesh::Nemesis_IO::read(), libMesh::UNVIO::read(), libMesh::GmshIO::read(), libMesh::DynaIO::read(), libMesh::XdrIO::read(), libMesh::ExodusII_IO::read(), libMesh::MatlabIO::read(), libMesh::CheckpointIO::read(), and libMesh::VTKIO::read().
Referenced by libMesh::UnstructuredMesh::read().
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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 101 of file mesh_input.h.
References libMesh::MeshInput< MT >::mesh().
Referenced by libMesh::Nemesis_IO::read(), and libMesh::XdrIO::read_header().
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protectedinherited |
Reads input from in
, skipping all the lines that start with the character comment_start
.
Definition at line 187 of file mesh_input.h.
Referenced by libMesh::TetGenIO::read(), and libMesh::UCDIO::read_implementation().
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overridevirtual |
This method implements writing a mesh to a specified file.
Implements libMesh::MeshOutput< MeshBase >.
Definition at line 310 of file namebased_io.C.
References TIMPI::Communicator::barrier(), TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::err, is_parallel_file_format(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::n_partitions(), libMesh::Quality::name(), libMesh::GMVIO::partitioning(), libMesh::ParallelObject::processor_id(), libMesh::FroIO::write(), libMesh::TecplotIO::write(), libMesh::MEDITIO::write(), libMesh::GMVIO::write(), libMesh::TetGenIO::write(), libMesh::UCDIO::write(), libMesh::Nemesis_IO::write(), libMesh::UNVIO::write(), libMesh::GmshIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write(), libMesh::CheckpointIO::write(), and libMesh::ExodusII_IO::write().
Referenced by libMesh::UnstructuredMesh::find_neighbors(), and libMesh::UnstructuredMesh::write().
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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 89 of file mesh_output.C.
References libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::get_mesh(), libMesh::libmesh_assert(), and libMesh::out.
Referenced by libMesh::ExodusII_IO::write_timestep_discontinuous().
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overridevirtual |
This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems
object.
We override the default MeshOutput::write_equation_systems because it only outputs nodal data by default, whereas we want to output a proper restart file if the requested filename is an XDA or XDR type.
Reimplemented from libMesh::MeshOutput< MeshBase >.
Definition at line 533 of file namebased_io.C.
References libMesh::ENCODE, libMesh::WRITE, libMesh::EquationSystems::write(), libMesh::EquationSystems::WRITE_ADDITIONAL_DATA, libMesh::EquationSystems::WRITE_DATA, and libMesh::MeshOutput< MT >::write_equation_systems().
Referenced by main().
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overridevirtual |
This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided.
Reimplemented from libMesh::MeshOutput< MeshBase >.
Definition at line 467 of file namebased_io.C.
References libMesh::err, libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::n_subdomains(), libMesh::Quality::name(), libMesh::GMVIO::partitioning(), libMesh::TecplotIO::write_nodal_data(), libMesh::MEDITIO::write_nodal_data(), libMesh::GMVIO::write_nodal_data(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::GmshIO::write_nodal_data(), libMesh::Nemesis_IO::write_nodal_data(), and libMesh::ExodusII_IO::write_nodal_data().
Referenced by libMesh::UnstructuredMesh::write().
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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 149 of file mesh_output.C.
References libMesh::NumericVector< T >::localize().
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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 162 of file mesh_output.C.
References libMesh::EquationSystems::build_parallel_solution_vector(), and libMesh::EquationSystems::build_variable_names().
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inlinevirtualinherited |
This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided.
Reimplemented in libMesh::ExodusII_IO.
Definition at line 118 of file mesh_output.h.
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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 184 of file mesh_output.h.
Referenced by libMesh::FroIO::write(), libMesh::PostscriptIO::write(), and libMesh::EnsightIO::write().
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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 193 of file mesh_output.h.
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protectedinherited |
A vector of bools describing what dimension elements have been encountered when reading a mesh.
Definition at line 107 of file mesh_input.h.
Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::max_elem_dimension_seen(), libMesh::AbaqusIO::max_elem_dimension_seen(), libMesh::AbaqusIO::read(), libMesh::GMVIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::AbaqusIO::read_elements(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), and libMesh::XdrIO::read_serialized_connectivity().