libMesh::MatlabIO Class Reference

This class implements reading meshes in the Matlab PDE toolkit in a proprietary format. More...

#include <matlab_io.h>

Inheritance diagram for libMesh::MatlabIO:

Public Member Functions
	MatlabIO (MeshBase &)
	Constructor. More...
virtual void	read (const std::string &name) override
	Reads in a matlab data file based on the string you pass it. More...
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...

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...

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

Private Member Functions
void	read_stream (std::istream &in)
	Implementation of the read() function. More...

Detailed Description

This class implements reading meshes in the Matlab PDE toolkit in a proprietary format.

A VALID INPUT FILE for this type of mesh should be generated in Matlab with the following steps: 1.) Draw the domain and triangulate it in the GUI 2.) Export the mesh to matlab using Mesh->Export Mesh 3.) Create a file with this script:

fid = fopen('filename', 'w');
fprintf(fid, '%d %d \n', length(p), length(t));
fprintf(fid, '%f %f \n', p);
fprintf(fid, '%d %d %d %d \n', t);
fclose(fid);

What's going on here? There is no standard for exporting PDE toolkit meshes to files in Matlab. When you choose "export mesh" in the GUI, it returns three matrices that it likes to call p, e, and t. All meshes (as far as I can tell) that come from the PDE toolkit are 2D triangle meshes.

p is the point matrix... Row 1: x coordinate Row 2: y coordinate

e is the edge matrix ... Row 1: starting point number (dummy) Row 2: ending point number (dummy) Row 3: starting parameter value (?) (dummy) Row 4: ending parameter value (?) (dummy) Row 5: boundary segment number (?) (dummy) Row 6: left-hand subdomain number (dummy) Row 7: right-hand subdomain number (dummy)

t is the triangle matrix ... Row 1: Node number 1 Row 2: Node number 2 Row 3: Node number 3 Row 4: subdomain number (dummy)

There are some important things to notice here: o The implied ordering of the p matrix is 1..N o The e matrix is entirely irrelevant in this code o All of the matrices are row based

Author

John W. Peterson

Date

2004

Definition at line 85 of file matlab_io.h.

Constructor & Destructor Documentation

MatlabIO()

libMesh::MatlabIO::MatlabIO ( MeshBase &  mesh_in )

inlineexplicit

Constructor.

Takes a non-const Mesh reference which it will fill up with elements.

Definition at line 114 of file matlab_io.h.

                                      :
  MeshInput<MeshBase>  (mesh_in)
{}

Member Function Documentation

is_parallel_format()

bool libMesh::MeshInput< MeshBase >::is_parallel_format ( ) const

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.

{ return this->_is_parallel_format; }

mesh()

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

inlineprotectedinherited

Returns

The object as a writable reference.

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(), 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().

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

read()

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

overridevirtual

Reads in a matlab data file based on the string you pass it.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 33 of file matlab_io.C.

References libMesh::Quality::name(), and read_stream().

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

{
  std::ifstream in (name.c_str());

  this->read_stream(in);
}

read_stream()

void libMesh::MatlabIO::read_stream ( std::istream &  in )

private

Implementation of the read() function.

This function is called by the public interface function and implements reading the file.

Definition at line 41 of file matlab_io.C.

References libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::Elem::build_with_id(), libMesh::MeshBase::clear(), libMesh::libmesh_assert(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshBase::node_ptr(), libMesh::Real, libMesh::MeshBase::set_mesh_dimension(), libMesh::Elem::set_node(), and libMesh::TRI3.

Referenced by read().

{
  // This is a serial-only process for now;
  // the Mesh should be read on processor 0 and
  // broadcast later
  libmesh_assert_equal_to (this->mesh().processor_id(), 0);

  // Get a reference to the mesh
  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();

  // Clear any existing mesh data
  the_mesh.clear();

  // PDE toolkit only works in 2D
  the_mesh.set_mesh_dimension(2);

#if LIBMESH_DIM < 2
  libmesh_error_msg("Cannot open dimension 2 mesh file when configured without 2D support.");
#endif

  // Check the input buffer
  libmesh_assert (in.good());

  unsigned int nNodes=0, nElem=0;

  in >> nNodes   // Read the number of nodes
     >> nElem;   // Read the number of elements

  // Sort of check that it worked
  libmesh_assert_greater (nNodes, 0);
  libmesh_assert_greater (nElem, 0);

  // Read the nodal coordinates
  {
    Real x=0., y=0., z=0.;

    for (unsigned int i=0; i<nNodes; i++)
      {
        in >> x   // x-coordinate value
           >> y;  // y-coordinate value

        the_mesh.add_point ( Point(x,y,z), i);
      }
  }

  // Read the elements (elements)
  {
    unsigned int node=0, dummy=0;

    for (unsigned int i=0; i<nElem; i++)
      {
        // Always build a triangle
        Elem * elem = the_mesh.add_elem(Elem::build_with_id(TRI3, i));

        for (unsigned int n=0; n<3; n++)  // Always read three 3 nodes
          {
            in >> node;
            elem->set_node(n) = the_mesh.node_ptr(node-1);  // Assign the node number
          }

        // There is an additional subdomain number here,
        // so we read it and get rid of it!
        in >> dummy;
      }
  }

}

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 101 of file mesh_input.h.

References libMesh::MeshInput< MT >::mesh().

Referenced by libMesh::Nemesis_IO::read(), and libMesh::XdrIO::read_header().

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

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 187 of file mesh_input.h.

Referenced by libMesh::TetGenIO::read(), and libMesh::UCDIO::read_implementation().

{
  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);
}

Member Data Documentation

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 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().

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

• include/mesh/matlab_io.h
• src/mesh/matlab_io.C