libMesh::MatlabIO Class Reference

#include <matlab_io.h>

Inheritance diagram for libMesh::MatlabIO:

Public Member Functions

 MatlabIO (MeshBase &)
virtual void read (const std::string &name) libmesh_override

Protected Member Functions

MeshBasemesh ()
void set_n_partitions (unsigned int n_parts)
void skip_comment_lines (std::istream &in, const char comment_start)

Protected Attributes

std::vector< bool > elems_of_dimension

Private Member Functions

void read_stream (std::istream &in)

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
', length(p), length(t)); fprintf(fid, 'f f
', p); fprintf(fid, 'd d d d
', 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

John W. Peterson

Definition at line 83 of file matlab_io.h.

Constructor & Destructor Documentation

libMesh::MatlabIO::MatlabIO ( MeshBase mesh_in)

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

Definition at line 112 of file matlab_io.h.

112  :
113  MeshInput<MeshBase> (mesh_in)
114 {}

Member Function Documentation

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )
The object as a writable reference.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::TetGenIO::element_in(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::elements_out(), libMesh::UNVIO::groups_in(), libMesh::TetGenIO::node_in(), libMesh::UNVIO::nodes_in(), libMesh::UNVIO::nodes_out(), libMesh::GMVIO::read(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::CheckpointIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::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::OFFIO::read_stream(), read_stream(), libMesh::CheckpointIO::read_subdomain_names(), libMesh::UCDIO::UCDIO(), libMesh::VTKIO::VTKIO(), libMesh::TetGenIO::write(), libMesh::ExodusII_IO::write(), libMesh::CheckpointIO::write(), libMesh::XdrIO::write(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::CheckpointIO::write_bcs(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::UCDIO::write_implementation(), libMesh::GmshIO::write_mesh(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), 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(), and libMesh::CheckpointIO::write_subdomain_names().

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

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 read_stream().

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

34 {
35  std::ifstream in (name.c_str());
37  this->read_stream(in);
38 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:39
void read_stream(std::istream &in)
Definition: matlab_io.C:41
void libMesh::MatlabIO::read_stream ( std::istream &  in)

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::MeshBase::clear(), libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::node_ptr(), libMesh::processor_id(), libMesh::Real, libMesh::DofObject::set_id(), libMesh::MeshBase::set_mesh_dimension(), libMesh::Elem::set_node(), and libMesh::x.

Referenced by read().

42 {
43  // This is a serial-only process for now;
44  // the Mesh should be read on processor 0 and
45  // broadcast later
46  libmesh_assert_equal_to (this->mesh().processor_id(), 0);
48  // Get a reference to the mesh
49  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
51  // Clear any existing mesh data
52  the_mesh.clear();
54  // PDE toolkit only works in 2D
55  the_mesh.set_mesh_dimension(2);
57 #if LIBMESH_DIM < 2
58  libmesh_error_msg("Cannot open dimension 2 mesh file when configured without 2D support.");
59 #endif
61  // Check the input buffer
62  libmesh_assert (in.good());
64  unsigned int nNodes=0, nElem=0;
66  in >> nNodes // Read the number of nodes
67  >> nElem; // Read the number of elements
69  // Sort of check that it worked
70  libmesh_assert_greater (nNodes, 0);
71  libmesh_assert_greater (nElem, 0);
73  // Read the nodal coordinates
74  {
75  Real x=0., y=0., z=0.;
77  for (unsigned int i=0; i<nNodes; i++)
78  {
79  in >> x // x-coordinate value
80  >> y; // y-coordinate value
82  the_mesh.add_point ( Point(x,y,z), i);
83  }
84  }
86  // Read the elements (elements)
87  {
88  unsigned int node=0, dummy=0;
90  for (unsigned int i=0; i<nElem; i++)
91  {
92  Elem * elem = new Tri3; // Always build a triangle
93  elem->set_id(i);
94  the_mesh.add_elem (elem);
96  for (unsigned int n=0; n<3; n++) // Always read three 3 nodes
97  {
98  in >> node;
99  elem->set_node(n) = the_mesh.node_ptr(node-1); // Assign the node number
100  }
102  // There is an additional subdomain number here,
103  // so we read it and get rid of it!
104  in >> dummy;
105  }
106  }
108 }
PetscErrorCode Vec x
processor_id_type processor_id()
Definition: libmesh_base.h:96
void libMesh::MeshInput< MeshBase >::set_n_partitions ( unsigned int  n_parts)

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.

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

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

91 { this->mesh().set_n_partitions() = n_parts; }
unsigned int & set_n_partitions()
Definition: mesh_base.h:1302
void libMesh::MeshInput< MeshBase >::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.

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

Member Data Documentation

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