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rAKA/src/io/mesh_io/mesh_io_msh.cc
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mesh_io_msh.cc
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/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
* Copyright (©) 2010-2018 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.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() = default;
/* -------------------------------------------------------------------------- */
static void my_getline(std::ifstream & infile, std::string & str) {
std::string tmp_str;
std::getline(infile, tmp_str);
str = trim(tmp_str);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
MeshAccessor mesh_accessor(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;
bool has_physical_names = false;
if (!infile.good()) {
AKANTU_EXCEPTION("Cannot open file " << filename);
}
std::map<std::string, std::function<void(const std::string &)>> readers;
readers["$MeshFormat"] = [&](const std::string &) {
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
int version;
sstr >> version;
if (version > 2)
AKANTU_ERROR("This reader can not read version "
<< version << " of the MSH file format");
Int format;
sstr >> format;
if (format != 0)
AKANTU_ERROR("This reader can only read ASCII files.");
my_getline(infile, line); /// the end of block line
current_line += 2;
file_format = 2;
};
readers["$NOD"] = readers["$Nodes"] = [&](const std::string &) {
UInt nb_nodes;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_nodes;
current_line++;
Array<Real> & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
mesh_accessor.setNbGlobalNodes(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;
my_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.storage()[offset + j] = coord[j];
}
my_getline(infile, line); /// the end of block line
};
readers["$ELM"] = readers["$Elements"] = [&](const std::string &) {
UInt nb_elements;
std::vector<UInt> read_order;
my_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;
Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
for (UInt i = 0; i < nb_elements; ++i) {
my_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 =
this->_msh_to_akantu_element_types[(MSHElementType)msh_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << current_line);
continue;
}
if (akantu_type != akantu_type_old) {
connectivity = &mesh_accessor.getConnectivity(akantu_type);
// connectivity->resize(0);
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = this->_read_order[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;
Array<UInt> & data = mesh.getDataPointer<UInt>(
sstr_tag_name.str(), akantu_type, _not_ghost);
data.push_back(tag);
}
} else if (file_format == 1) {
Int tag;
sstr_elem >> tag; // reg-phys
std::string tag_name = "tag_0";
Array<UInt> * data =
&mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // reg-elem
tag_name = "tag_1";
data = &mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // number-of-nodes
}
Vector<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[j]) = node_index;
}
connectivity->push_back(local_connect);
}
my_getline(infile, line); /// the end of block line
};
readers["$PhysicalNames"] = [&](const std::string &) {
has_physical_names = true;
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
UInt num_of_phys_names;
sstr >> num_of_phys_names;
for (UInt k(0); k < num_of_phys_names; k++) {
my_getline(infile, line);
std::stringstream sstr_phys_name(line);
UInt phys_name_id;
UInt phys_dim;
sstr_phys_name >> phys_dim >> phys_name_id;
std::size_t b = line.find('\"');
std::size_t e = line.rfind('\"');
std::string phys_name = line.substr(b + 1, e - b - 1);
phys_name_map[phys_name_id] = phys_name;
}
my_getline(infile, line); /// the end of block line
};
readers["$Periodic"] = [&](const std::string &) {
UInt nb_periodic_entities;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_periodic_entities;
mesh_accessor.getNodesFlags().resize(mesh.getNbNodes(), NodeFlag::_normal);
for (UInt p = 0; p < nb_periodic_entities; ++p) {
// dimension slave-tag master-tag
my_getline(infile, line);
UInt dimension;
{
std::stringstream sstr(line);
sstr >> dimension;
}
// transformation
my_getline(infile, line);
// nb nodes
my_getline(infile, line);
UInt nb_nodes;
{
std::stringstream sstr(line);
sstr >> nb_nodes;
}
for (UInt n = 0; n < nb_nodes; ++n) {
// slave master
my_getline(infile, line);
// The info in the mesh seem inconsistent so they are ignored for know.
continue;
if (dimension == mesh.getSpatialDimension() - 1) {
UInt slave, master;
std::stringstream sstr(line);
sstr >> slave;
sstr >> master;
mesh_accessor.addPeriodicSlave(slave, master);
}
}
}
// mesh_accessor.markMeshPeriodic();
my_getline(infile, line);
};
readers["$NodeData"] = [&](const std::string &) {
/* $NodeData
number-of-string-tags
< "string-tag" >
…
number-of-real-tags
< real-tag >
…
number-of-integer-tags
< integer-tag >
…
node-number value …
…
$EndNodeData */
auto read_data_tags = [&](auto && tags) {
my_getline(infile, line); /// number of tags
UInt number_of_tags{0};
std::stringstream sstr(line);
sstr >> number_of_tags;
tags.resize(number_of_tags);
for (auto && tag : tags) {
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> tag;
}
return tags;
};
auto && string_tags = read_data_tags(std::vector<std::string>());
auto && real_tags[[gnu::unused]] = read_data_tags(std::vector<double>());
auto && int_tags = read_data_tags(std::vector<int>());
auto && data =
mesh.getNodalData<double>(trim(string_tags[0], '"'), int_tags[1]);
data.resize(mesh.getNbNodes(), 0.);
for (auto n[[gnu::unused]] : arange(int_tags[2])) {
my_getline(infile, line);
std::stringstream sstr(line);
int node;
double value;
sstr >> node;
for (auto c : arange(int_tags[1])) {
sstr >> value;
data(node - first_node_number, c) = value;
}
}
my_getline(infile, line);
};
readers["Unsupported"] = [&](const std::string & block) {
AKANTU_DEBUG_WARNING("Unsuported block_kind " << line << " at line "
<< current_line);
auto && end_block = "$End" + block;
while (line != end_block) {
my_getline(infile, line);
current_line++;
}
};
while (infile.good()) {
my_getline(infile, line);
current_line++;
auto && it = readers.find(line);
if (it != readers.end()) {
it->second(line);
} else if (line.size() != 0) {
readers["Unsupported"](line);
}
}
// mesh.updateTypesOffsets(_not_ghost);
infile.close();
this->constructPhysicalNames("tag_0", mesh);
if (has_physical_names)
mesh.createGroupsFromMeshData<std::string>("physical_names");
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat"
<< "\n";
outfile << "2.1 0 8"
<< "\n";
outfile << "$EndMeshFormat"
<< "\n";
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes"
<< "\n";
outfile << nodes.size() << "\n";
outfile << std::uppercase;
for (UInt i = 0; i < nodes.size(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
for (UInt p = nodes.getNbComponent(); p < 3; ++p)
outfile << " " << 0.;
outfile << "\n";
;
}
outfile << std::nouppercase;
outfile << "$EndNodes"
<< "\n";
outfile << "$Elements"
<< "\n";
Int nb_elements = 0;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
nb_elements += connectivity.size();
}
outfile << nb_elements << "\n";
UInt element_idx = 1;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
UInt * tag[2] = {nullptr, nullptr};
if (mesh.hasData<UInt>("tag_0", type, _not_ghost)) {
const auto & data_tag_0 = mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
}
if (mesh.hasData<UInt>("tag_1", type, _not_ghost)) {
const auto & data_tag_1 = mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
}
for (UInt i = 0; i < connectivity.size(); ++i) {
UInt offset = i * connectivity.getNbComponent();
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
for (UInt t = 0; t < 2; ++t)
if (tag[t])
outfile << " " << tag[t][i];
else
outfile << " 0";
for (UInt j = 0; j < connectivity.getNbComponent(); ++j) {
outfile << " " << connectivity.storage()[offset + j] + 1;
}
outfile << "\n";
element_idx++;
}
}
outfile << "$EndElements"
<< "\n";
if (mesh.hasData(MeshDataType::_nodal)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto type = mesh.getTypeCode(tag, MeshDataType::_nodal);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
auto && data = mesh.getNodalData<double>(tag);
outfile << "$NodeData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << data.getNbComponent() << "\n";
outfile << data.size() << "\n";
for (auto && d : enumerate(make_view(data, data.getNbComponent()))) {
outfile << std::get<0>(d) + 1;
for (auto && v : std::get<1>(d)) {
outfile << " " << v;
}
outfile << "\n";
}
outfile << "$EndNodeData"
<< "\n";
}
}
outfile.close();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
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