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rAKA/mesh_utils/mesh_io/mesh_io_msh.cc
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/**
* @file mesh_io_msh.cc
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @date Fri Jun 18 11:36:35 2010
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
/* Constant arrays initialisation */
/* -------------------------------------------------------------------------- */
UInt MeshIOMSH::_read_order[_max_element_type][MAX_NUMBER_OF_NODE_PER_ELEMENT] = {
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, // _not_defined
{ 0, 1, 0, 0, 0, 0, 0, 0, 0, 0 }, // _line1
{ 0, 1, 2, 0, 0, 0, 0, 0, 0, 0 }, // _line2
{ 0, 1, 2, 0, 0, 0, 0, 0, 0, 0 }, // _triangle_3
{ 0, 1, 2, 3, 4, 5, 6, 0, 0, 0 }, // _triangle_6
{ 0, 1, 2, 3, 4, 0, 0, 0, 0, 0 }, // _tetrahedron_4
{ 0, 1, 2, 3, 4, 5, 6, 7, 9, 8 }, // _tetrahedron_10
{ 0, 1, 2, 3, 0, 0, 0, 0, 0, 0 }, // _quadrangle_4
{ 0, 1, 2, 3, 4, 5, 6, 7, 0, 0 } // _hexahedron_8
};
UInt MeshIOMSH::_msh_nodes_per_elem[16] =
{ 0, // element types began at 1
2, 3, 4, 4, 8, 6, 5, // 1st order
3, 6, 9, 10, 27, 18, 14, // 2st order
1
};
ElementType MeshIOMSH::_msh_to_akantu_element_types[16] =
{ _not_defined, // element types began at 1
_segment_2, _triangle_3, _quadrangle_4, _tetrahedron_4, // 1st order
_hexahedron_8, _not_defined, _not_defined,
_segment_3, _triangle_6, _not_defined, _tetrahedron_10, // 2nd order
_not_defined, _not_defined, _not_defined,
_not_defined
};
MeshIOMSH::MSHElementType MeshIOMSH::_akantu_to_msh_element_types[_max_element_type] =
{
_msh_not_defined, // _not_defined
_msh_segment_2, // _segment_2
_msh_segment_3, // _segment_3
_msh_triangle_3, // _triangle_3
_msh_triangle_6, // _triangle_6
_msh_tetrahedron_4, // _tetrahedron_4
_msh_tetrahedron_10,// _tetrahedron_10
_msh_quadrangle_1, // _quadrangle_4
_msh_hexahedron_8 // _hexahedron_8
};
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() {
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max(), last_node_number = 0,
file_format = 1, current_line = 0;
if(!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
while(infile.good()) {
std::getline(infile, line);
current_line++;
/// read the header
if(line == "$MeshFormat") {
std::getline(infile, line); /// the format line
std::stringstream sstr(line);
std::string version; sstr >> version;
Int format; sstr >> format;
if(format != 0) AKANTU_DEBUG_ERROR("This reader can only read ASCII files.");
std::getline(infile, line); /// the end of block line
current_line += 2;
file_format = 2;
}
/// read all nodes
if(line == "$Nodes" || line == "$NOD") {
UInt nb_nodes;
std::getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_nodes;
current_line++;
Vector<Real> & nodes = const_cast<Vector<Real> &>(mesh.getNodes());
nodes.resize(nb_nodes);
mesh.nb_global_nodes = nb_nodes;
UInt index;
Real coord[3];
UInt spatial_dimension = nodes.getNbComponent();
/// for each node, read the coordinates
for(UInt i = 0; i < nb_nodes; ++i) {
UInt offset = i * spatial_dimension;
std::getline(infile, line);
std::stringstream sstr_node(line);
sstr_node >> index >> coord[0] >> coord[1] >> coord[2];
current_line++;
first_node_number = std::min(first_node_number,index);
last_node_number = std::max(last_node_number, index);
/// read the coordinates
for(UInt j = 0; j < spatial_dimension; ++j)
nodes.values[offset + j] = coord[j];
}
std::getline(infile, line); /// the end of block line
}
/// read all elements
if(line == "$Elements" || line == "$ELM") {
UInt nb_elements;
std::getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_elements;
current_line++;
Int index;
UInt msh_type;
ElementType akantu_type, akantu_type_old = _not_defined;
Vector<UInt> *connectivity = NULL;
UInt node_per_element = 0;
for(UInt i = 0; i < nb_elements; ++i) {
std::getline(infile, line);
std::stringstream sstr_elem(line);
current_line++;
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type = _msh_to_akantu_element_types[msh_type];
if(akantu_type == _not_defined) continue;
if(akantu_type != akantu_type_old) {
connectivity = mesh.getConnectivityPointer(akantu_type);
connectivity->resize(0);
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
}
/// read tags informations
if(file_format == 2) {
UInt nb_tags;
sstr_elem >> nb_tags;
for(UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
std::stringstream sstr_tag_name; sstr_tag_name << "tag_" << j;
Vector<UInt> * data = mesh.getUIntDataPointer(akantu_type, sstr_tag_name.str());
data->push_back(tag);
}
} else if (file_format == 1) {
Int tag;
sstr_elem >> tag; //reg-phys
std::string tag_name = "tag_0";
Vector<UInt> * data = mesh.getUIntDataPointer(akantu_type, tag_name);
data->push_back(tag);
sstr_elem >> tag; //reg-elem
tag_name = "tag_1";
data = mesh.getUIntDataPointer(akantu_type, tag_name);
data->push_back(tag);
sstr_elem >> tag; //number-of-nodes
}
UInt local_connect[node_per_element];
for(UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= last_node_number,
"Node number not in range : line " << current_line);
node_index -= first_node_number;
local_connect[_read_order[akantu_type][j]] = node_index;
}
connectivity->push_back(local_connect);
}
std::getline(infile, line); /// the end of block line
}
if((line[0] == '$') && (line.find("End") == std::string::npos)) {
AKANTU_DEBUG_WARNING("Unsuported block_kind " << line
<< " at line " << current_line);
}
}
infile.close();
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Vector<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat" << std::endl;
outfile << "2.1 0 8" << std::endl;;
outfile << "$EndMeshFormat" << std::endl;;
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes" << std::endl;;
outfile << nodes.getSize() << std::endl;;
outfile << std::uppercase;
for(UInt i = 0; i < nodes.getSize(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i+1;
for(UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.values[offset + j];
}
if(nodes.getNbComponent() == 2)
outfile << " " << 0.;
outfile << std::endl;;
}
outfile << std::nouppercase;
outfile << "$EndNodes" << std::endl;;
outfile << "$Elements" << std::endl;;
const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
Mesh::ConnectivityTypeList::const_iterator it;
Int nb_elements = 0;
for(it = type_list.begin(); it != type_list.end(); ++it) {
const Vector<UInt> & connectivity = mesh.getConnectivity(*it);
nb_elements += connectivity.getSize();
}
outfile << nb_elements << std::endl;
UInt element_idx = 1;
for(it = type_list.begin(); it != type_list.end(); ++it) {
ElementType type = *it;
const Vector<UInt> & connectivity = mesh.getConnectivity(type);
for(UInt i = 0; i < connectivity.getSize(); ++i) {
UInt offset = i * connectivity.getNbComponent();
outfile << element_idx << " " << _akantu_to_msh_element_types[type] << " 3 1 1 0"; /// \todo write the real data in the file
for(UInt j = 0; j < connectivity.getNbComponent(); ++j) {
outfile << " " << connectivity.values[offset + j] + 1;
}
outfile << std::endl;
element_idx++;
}
}
outfile << "$EndElements" << std::endl;;
outfile.close();
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
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