mesh_io_msh.cc
No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Mon, Jun 3, 19:54

mesh_io_msh.cc
View Options

	/**
	* @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.registerNodalData<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) {
	if (mesh.getTypeCode(tag, MeshDataType::_nodal) != _tc_real)
	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

mesh_io_msh.ccNo OneTemporaryActions

File Metadata

mesh_io_msh.ccView Options

Event Timeline

mesh_io_msh.cc
No OneTemporary
Actions

mesh_io_msh.cc
View Options