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)
 

Protected Member Functions

MeshBasemesh ()
 
void skip_comment_lines (std::istream &in, const char comment_start)
 

Protected Attributes

std::vector< bool > elems_of_dimension
 

Private Member Functions

virtual 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

Author
John W. Peterson, 2004

Definition at line 89 of file matlab_io.h.

Constructor & Destructor Documentation

libMesh::MatlabIO::MatlabIO ( MeshBase mesh_in)
inlineexplicit

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

Definition at line 118 of file matlab_io.h.

118  :
119  MeshInput<MeshBase> (mesh_in)
120 {}

Member Function Documentation

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

Returns the object as a writeable reference.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::VTKIO::cells_to_vtk(), libMesh::TetGenIO::element_in(), libMesh::UNVIO::element_in(), libMesh::UNVIO::element_out(), libMesh::TetGenIO::node_in(), libMesh::UNVIO::node_in(), libMesh::UNVIO::node_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::ExodusII_IO::read(), libMesh::Nemesis_IO::read(), libMesh::GMVIO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::VTKIO::read(), libMesh::LegacyXdrIO::read_ascii(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::UCDIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::CheckpointIO::read_nodes(), libMesh::CheckpointIO::read_nodesets(), libMesh::XdrIO::read_serialized_bcs(), 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::TetGenIO::write(), libMesh::ExodusII_IO::write(), libMesh::Nemesis_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::CheckpointIO::write_connectivity(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::UCDIO::write_implementation(), libMesh::UNVIO::write_implementation(), libMesh::GmshIO::write_mesh(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::Nemesis_IO::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_nodes(), libMesh::CheckpointIO::write_nodesets(), libMesh::XdrIO::write_parallel(), libMesh::GmshIO::write_post(), libMesh::XdrIO::write_serialized_bcs(), 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)
virtual

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::UnstructuredMesh::read().

34 {
35  std::ifstream in (name.c_str());
36 
37  this->read_stream(in);
38 }
void libMesh::MatlabIO::read_stream ( std::istream &  in)
privatevirtual

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::err, libMesh::libmesh_assert(), libMesh::libmesh_assert_greater(), 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(), and libMesh::Elem::set_node().

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);
47 
48  // Get a reference to the mesh
49  MeshBase& the_mesh = MeshInput<MeshBase>::mesh();
50 
51  // Clear any existing mesh data
52  the_mesh.clear();
53 
54  // PDE toolkit only works in 2D
55  the_mesh.set_mesh_dimension(2);
56 
57 #if LIBMESH_DIM < 2
58  libMesh::err << "Cannot open dimension 2 mesh file when configured without 2D support." <<
59  std::endl;
60  libmesh_error();
61 #endif
62 
63  // Check the input buffer
64  libmesh_assert (in.good());
65 
66  unsigned int nNodes=0, nElem=0;
67 
68  in >> nNodes // Read the number of nodes
69  >> nElem; // Read the number of elements
70 
71  // Sort of check that it worked
72  libmesh_assert_greater (nNodes, 0);
73  libmesh_assert_greater (nElem, 0);
74 
75  // Read the nodal coordinates
76  {
77  Real x=0., y=0., z=0.;
78 
79  for (unsigned int i=0; i<nNodes; i++)
80  {
81  in >> x // x-coordinate value
82  >> y; // y-coordinate value
83 
84  the_mesh.add_point ( Point(x,y,z), i);
85  }
86  }
87 
88  // Read the elements (elements)
89  {
90  unsigned int node=0, dummy=0;
91 
92  for (unsigned int i=0; i<nElem; i++)
93  {
94  Elem* elem = new Tri3; // Always build a triangle
95  elem->set_id(i);
96  the_mesh.add_elem (elem);
97 
98  for (unsigned int n=0; n<3; n++) // Always read three 3 nodes
99  {
100  in >> node;
101  elem->set_node(n) = the_mesh.node_ptr(node-1); // Assign the node number
102  }
103 
104  // There is an additional subdomain number here,
105  // so we read it and get rid of it!
106  in >> dummy;
107  }
108  }
109 
110 }
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.

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

Member Data Documentation


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

Site Created By: libMesh Developers
Last modified: February 07 2014 16:58:01 UTC

Hosted By:
SourceForge.net Logo