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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
			*
			*
			* 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 "element_group.hh"
			#include "mesh_io.hh"
			#include "mesh_utils.hh"
			#include "node_group.hh"
			/* -------------------------------------------------------------------------- */
			#include <fstream>
			/* -------------------------------------------------------------------------- */

			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;

			/* -------------------------------------------------------------------------- */
			namespace {
			struct File {
			std::string filename;
			std::ifstream infile;
			std::string line;
			size_t current_line{0};

			size_t first_node_number{std::numeric_limits<UInt>::max()},
			last_node_number{0};
			bool has_physical_names{false};

			std::unordered_map<size_t, size_t> node_tags;
			std::unordered_map<size_t, Element> element_tags;
			double version{0};
			int size_of_size_t{0};
			Mesh & mesh;
			MeshAccessor mesh_accessor;

			std::multimap<std::pair<int, int>, int> entity_tag_to_physical_tags;

			File(const std::string & filename, Mesh & mesh)
			: filename(filename), mesh(mesh), mesh_accessor(mesh) {
			infile.open(filename.c_str());
			if (not infile.good()) {
			AKANTU_EXCEPTION("Cannot open file " << filename);
			}
			}

			~File() { infile.close(); }

			auto good() { return infile.good(); }

			std::stringstream get_line() {
			std::string tmp_str;
			if (infile.eof()) {
			AKANTU_EXCEPTION("Reached the end of the file " << filename);
			}
			std::getline(infile, tmp_str);
			line = trim(tmp_str);
			++current_line;

			return std::stringstream(line);
			}

			template <typename... Ts> void read_line(Ts &&... ts) {
			auto && sstr = get_line();
			(void)std::initializer_list<int>{
			(sstr >> std::forward<decltype(ts)>(ts), 0)...};
			}
			};
			} // namespace

			/* -------------------------------------------------------------------------- */
			template <typename File, typename Readers>
			void MeshIOMSH::populateReaders2(File & file, Readers & readers) {
			readers["$NOD"] = readers["$Nodes"] = [&](const std::string & /unused/) {
			UInt nb_nodes;
			file.read_line(nb_nodes);

			Array<Real> & nodes = file.mesh_accessor.getNodes();
			nodes.resize(nb_nodes);
			file.mesh_accessor.setNbGlobalNodes(nb_nodes);

			size_t index;
			Vector<double> coord(3);

			/// for each node, read the coordinates
			for (auto && data : enumerate(make_view(nodes, nodes.getNbComponent()))) {
			file.read_line(index, coord(0), coord(1), coord(2));

			if (index > std::numeric_limits<UInt>::max()) {
			AKANTU_EXCEPTION(
			"There are more nodes in this files than the index type of akantu "
			"can handle, consider recompiling with a bigger index type");
			}

			file.first_node_number = std::min(file.first_node_number, index);
			file.last_node_number = std::max(file.last_node_number, index);

			for (auto && coord_data : zip(std::get<1>(data), coord)) {
			std::get<0>(coord_data) = std::get<1>(coord_data);
			}
			file.node_tags[index] = std::get<0>(data);
			}
			};

			readers["$ELM"] = readers["$Elements"] = [&](const std::string & /unused/) {
			UInt nb_elements;
			file.read_line(nb_elements);

			Int index;
			UInt msh_type;
			ElementType akantu_type;

			for (UInt i = 0; i < nb_elements; ++i) {
			auto && sstr_elem = file.get_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 " << file.current_line);
			continue;
			}

			Element elem{akantu_type, 0, _not_ghost};

			auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
			auto node_per_element = connectivity.getNbComponent();
			auto & read_order = this->_read_order[akantu_type];

			/// read tags informations
			if (file.version < 2) {
			Int tag0;
			Int tag1;
			Int nb_nodes; // reg-phys, reg-elem, number-of-nodes
			sstr_elem >> tag0 >> tag1 >> nb_nodes;

			auto & data0 =
			file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
			data0.push_back(tag0);

			auto & data1 =
			file.mesh_accessor.template getData<UInt>("tag_1", akantu_type);
			data1.push_back(tag1);
			} else if (file.version < 4) {
			UInt nb_tags;
			sstr_elem >> nb_tags;
			for (UInt j = 0; j < nb_tags; ++j) {
			Int tag;
			sstr_elem >> tag;

			auto & data = file.mesh_accessor.template getData<UInt>(
			"tag_" + std::to_string(j), akantu_type);
			data.push_back(tag);
			}
			}

			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 <= file.last_node_number,
			"Node number not in range : line "
			<< file.current_line);

			local_connect(read_order[j]) = file.node_tags[node_index];
			}

			connectivity.push_back(local_connect);
			elem.element = connectivity.size() - 1;
			file.element_tags[index] = elem;
			}
			};

			readers["$Periodic"] = [&](const std::string & /unused/) {
			UInt nb_periodic_entities;
			file.read_line(nb_periodic_entities);

			file.mesh_accessor.getNodesFlags().resize(file.mesh.getNbNodes(),
			NodeFlag::_normal);

			for (UInt p = 0; p < nb_periodic_entities; ++p) {
			// dimension slave-tag master-tag
			UInt dimension;
			file.read_line(dimension);

			// transformation
			file.get_line();

			// nb nodes
			UInt nb_nodes;
			file.read_line(nb_nodes);

			for (UInt n = 0; n < nb_nodes; ++n) {
			// slave master
			auto && sstr = file.get_line();

			// The info in the mesh seem inconsistent so they are ignored for now.
			continue;

			if (dimension == file.mesh.getSpatialDimension() - 1) {
			UInt slave;
			UInt master;

			sstr >> slave;
			sstr >> master;
			file.mesh_accessor.addPeriodicSlave(file.node_tags[slave],
			file.node_tags[master]);
			}
			}
			}

			// mesh_accessor.markMeshPeriodic();
			};
			}

			/* -------------------------------------------------------------------------- */
			template <typename File, typename Readers>
			void MeshIOMSH::populateReaders4(File & file, Readers & readers) {
			static std::map<int, std::string> entity_type{
			{0, "points"},
			{1, "curve"},
			{2, "surface"},
			{3, "volume"},
			};

			readers["$Entities"] = [&](const std::string & /unused/) {
			size_t num_entity[4];
			file.read_line(num_entity[0], num_entity[1], num_entity[2], num_entity[3]);

			for (auto entity_dim : arange(4)) {
			for (auto _ [[gnu::unused]] : arange(num_entity[entity_dim])) {
			auto && sstr = file.get_line();

			int tag;
			double min_x;
			double min_y;
			double min_z;
			double max_x;
			double max_y;
			double max_z;
			size_t num_physical_tags;
			sstr >> tag >> min_x >> min_y >> min_z;

			if (entity_dim > 0 or file.version < 4.1) {
			sstr >> max_x >> max_y >> max_z;
			}

			sstr >> num_physical_tags;

			for (auto _ [[gnu::unused]] : arange(num_physical_tags)) {
			int phys_tag;
			sstr >> phys_tag;

			std::string physical_name;
			if (this->physical_names.find(phys_tag) ==
			this->physical_names.end()) {
			physical_name = "msh_block_" + std::to_string(phys_tag);
			} else {
			physical_name = this->physical_names[phys_tag];
			}

			if (not file.mesh.elementGroupExists(physical_name)) {
			file.mesh.createElementGroup(physical_name, entity_dim);
			} else {
			file.mesh.getElementGroup(physical_name).addDimension(entity_dim);
			}
			file.entity_tag_to_physical_tags.insert(
			std::make_pair(std::make_pair(tag, entity_dim), phys_tag));
			}
			}
			}
			};

			readers["$Nodes"] = [&](const std::string & /unused/) {
			size_t num_blocks;
			size_t num_nodes;
			if (file.version >= 4.1) {
			file.read_line(num_blocks, num_nodes, file.first_node_number,
			file.last_node_number);
			} else {
			file.read_line(num_blocks, num_nodes);
			}
			auto & nodes = file.mesh_accessor.getNodes();
			nodes.reserve(num_nodes);
			file.mesh_accessor.setNbGlobalNodes(num_nodes);

			if (num_nodes > std::numeric_limits<UInt>::max()) {
			AKANTU_EXCEPTION(
			"There are more nodes in this files than the index type of akantu "
			"can handle, consider recompiling with a bigger index type");
			}

			size_t node_id{0};

			for (auto block [[gnu::unused]] : arange(num_blocks)) {
			int entity_dim;
			int entity_tag;
			int parametric;
			size_t num_nodes_in_block;
			Vector<double> pos(3);
			Vector<double> real_pos(nodes.getNbComponent());

			if (file.version >= 4.1) {
			file.read_line(entity_dim, entity_tag, parametric, num_nodes_in_block);
			if (parametric) {
			AKANTU_EXCEPTION(
			"Akantu does not support parametric nodes in msh files");
			}
			for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
			size_t tag;
			file.read_line(tag);
			file.node_tags[tag] = node_id;
			++node_id;
			}

			for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
			file.read_line(pos(_x), pos(_y), pos(_z));
			for (auto && data : zip(real_pos, pos)) {
			std::get<0>(data) = std::get<1>(data);
			}

			nodes.push_back(real_pos);
			}
			} else {
			file.read_line(entity_tag, entity_dim, parametric, num_nodes_in_block);

			for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
			size_t tag;
			file.read_line(tag, pos(_x), pos(_y), pos(_z));

			if (file.version < 4.1) {
			file.first_node_number = std::min(file.first_node_number, tag);
			file.last_node_number = std::max(file.last_node_number, tag);
			}

			for (auto && data : zip(real_pos, pos)) {
			std::get<0>(data) = std::get<1>(data);
			}

			nodes.push_back(real_pos);
			file.node_tags[tag] = node_id;
			++node_id;
			}
			}
			}
			};

			readers["$Elements"] = [&](const std::string & /unused/) {
			size_t num_blocks;
			size_t num_elements;
			file.read_line(num_blocks, num_elements);

			for (auto block [[gnu::unused]] : arange(num_blocks)) {
			int entity_dim;
			int entity_tag;
			int element_type;
			size_t num_elements_in_block;

			if (file.version >= 4.1) {
			file.read_line(entity_dim, entity_tag, element_type,
			num_elements_in_block);
			} else {
			file.read_line(entity_tag, entity_dim, element_type,
			num_elements_in_block);
			}

			/// get the connectivity vector depending on the element type
			auto && akantu_type =
			this->_msh_to_akantu_element_types[(MSHElementType)element_type];

			if (akantu_type == _not_defined) {
			AKANTU_DEBUG_WARNING("Unsuported element kind " << element_type
			<< " at line "
			<< file.current_line);
			continue;
			}

			Element elem{akantu_type, 0, _not_ghost};

			auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
			Vector<UInt> local_connect(connectivity.getNbComponent());
			auto && read_order = this->_read_order[akantu_type];

			auto & data0 =
			file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
			data0.resize(data0.size() + num_elements_in_block, 0);

			auto & physical_data = file.mesh_accessor.template getData<std::string>(
			"physical_names", akantu_type);
			physical_data.resize(physical_data.size() + num_elements_in_block, "");

			for (auto _ [[gnu::unused]] : arange(num_elements_in_block)) {
			auto && sstr_elem = file.get_line();
			size_t elem_tag;
			sstr_elem >> elem_tag;
			for (auto && c : arange(connectivity.getNbComponent())) {
			size_t node_tag;
			sstr_elem >> node_tag;

			AKANTU_DEBUG_ASSERT(node_tag <= file.last_node_number,
			"Node number not in range : line "
			<< file.current_line);

			node_tag = file.node_tags[node_tag];
			local_connect(read_order[c]) = node_tag;
			}
			connectivity.push_back(local_connect);
			elem.element = connectivity.size() - 1;
			file.element_tags[elem_tag] = elem;

			auto range = file.entity_tag_to_physical_tags.equal_range(
			std::make_pair(entity_tag, entity_dim));
			bool first = true;
			for (auto it = range.first; it != range.second; ++it) {
			auto phys_it = this->physical_names.find(it->second);
			if (first) {
			data0(elem.element) =
			it->second; // for compatibility with version 2
			if (phys_it != this->physical_names.end()) {
			physical_data(elem.element) = phys_it->second;
			}
			first = false;
			}
			if (phys_it != this->physical_names.end()) {
			file.mesh.getElementGroup(phys_it->second).add(elem, true, false);
			}
			}
			}
			}

			for (auto && element_group : file.mesh.iterateElementGroups()) {
			element_group.getNodeGroup().optimize();
			}
			};
			}

			/* -------------------------------------------------------------------------- */
			void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {

			File file(filename, mesh);

			std::map<std::string, std::function<void(const std::string &)>> readers;

			readers["$MeshFormat"] = [&](const std::string & /unused/) {
			auto && sstr = file.get_line();

			int format;
			sstr >> file.version >> format;

			if (format != 0) {
			AKANTU_ERROR("This reader can only read ASCII files.");
			}

			if (file.version > 2) {
			sstr >> file.size_of_size_t;
			if (file.size_of_size_t > int(sizeof(UInt))) {
			AKANTU_DEBUG_INFO("The size of the indexes in akantu might be to small "
			"to read this file (akantu "
			<< sizeof(UInt) << " vs. msh file "
			<< file.size_of_size_t << ")");
			}
			}

			if (file.version < 4) {
			this->populateReaders2(file, readers);
			} else {
			this->populateReaders4(file, readers);
			}
			};

			auto && read_data = [&](auto && entity_tags, auto && get_data,
			auto && read_data) {
			auto read_data_tags = [&](auto x) {
			UInt number_of_tags{0};
			file.read_line(number_of_tags);
			std::vector<decltype(x)> tags(number_of_tags);

			for (auto && tag : tags) {
			file.read_line(tag);
			}
			return tags;
			};

			auto && string_tags = read_data_tags(std::string{});
			auto && real_tags [[gnu::unused]] = read_data_tags(double{});
			auto && int_tags = read_data_tags(int{});

			for (auto & s : string_tags) {
			s = trim(s, '"');
			}

			auto id = string_tags[0];
			auto size = int_tags[2];
			auto nb_component = int_tags[1];
			auto & data = get_data(id, size, nb_component);

			for (auto n [[gnu::unused]] : arange(size)) {
			auto && sstr = file.get_line();

			size_t tag;
			sstr >> tag;
			const auto & entity = entity_tags[tag];
			read_data(entity, sstr, data, nb_component);
			}
			};

			readers["$NodeData"] = [&](const std::string & /unused/) {
			/* $NodeData
			numStringTags(ASCII int)
			stringTag(string) ...
			numRealTags(ASCII int)
			realTag(ASCII double) ...
			numIntegerTags(ASCII int)
			integerTag(ASCII int) ...
			nodeTag(size_t) value(double) ...
			...
			$EndNodeData */
			read_data(
			file.node_tags,
			[&](auto && id, auto && size [[gnu::unused]],
			auto && nb_component [[gnu::unused]]) -> Array<double> & {
			auto & data =
			file.mesh.template getNodalData<double>(id, nb_component);
			data.resize(size);
			return data;
			},
			[&](auto && node, auto && sstr, auto && data,
			auto && nb_component [[gnu::unused]]) {
			for (auto c : arange(nb_component)) {
			sstr >> data(node, c);
			}
			});
			};

			readers["$ElementData"] = [&](const std::string & /unused/) {
			/* $ElementData
			numStringTags(ASCII int)
			stringTag(string) ...
			numRealTags(ASCII int)
			realTag(ASCII double) ...
			numIntegerTags(ASCII int)
			integerTag(ASCII int) ...
			elementTag(size_t) value(double) ...
			...
			$EndElementData
			*/
			read_data(
			file.element_tags,
			[&](auto && id, auto && size [[gnu::unused]],
			auto && nb_component
			[[gnu::unused]]) -> ElementTypeMapArray<double> & {
			file.mesh.template getElementalData<double>(id);
			return file.mesh.template getElementalData<double>(id);
			},
			[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
			if (not data.exists(element.type)) {
			data.alloc(mesh.getNbElement(element.type), nb_component,
			element.type, element.ghost_type);
			}
			auto & data_array = data(element.type);
			for (auto c : arange(nb_component)) {
			sstr >> data_array(element.element, c);
			}
			});
			};

			readers["$ElementNodeData"] = [&](const std::string & /unused/) {
			/* $ElementNodeData
			numStringTags(ASCII int)
			stringTag(string) ...
			numRealTags(ASCII int)
			realTag(ASCII double) ...
			numIntegerTags(ASCII int)
			integerTag(ASCII int) ...
			elementTag(size_t) value(double) ...
			...
			$EndElementNodeData
			*/
			read_data(
			file.element_tags,
			[&](auto && id, auto && size [[gnu::unused]],
			auto && nb_component
			[[gnu::unused]]) -> ElementTypeMapArray<double> & {
			file.mesh.template getElementalData<double>(id);
			auto & data = file.mesh.template getElementalData<double>(id);
			data.isNodal(true);
			return data;
			},
			[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
			int nb_nodes_per_element;
			sstr >> nb_nodes_per_element;
			if (not data.exists(element.type)) {
			data.alloc(mesh.getNbElement(element.type),
			nb_component * nb_nodes_per_element, element.type,
			element.ghost_type);
			}
			auto & data_array = data(element.type);
			for (auto c : arange(nb_component)) {
			sstr >> data_array(element.element, c);
			}
			});
			};

			readers["$PhysicalNames"] = [&](const std::string & /unused/) {
			file.has_physical_names = true;
			int num_of_phys_names;
			file.read_line(num_of_phys_names); /// the format line

			for (auto k [[gnu::unused]] : arange(num_of_phys_names)) {
			int phys_name_id;
			int phys_dim;
			std::string phys_name;
			file.read_line(phys_dim, phys_name_id, std::quoted(phys_name));

			this->physical_names[phys_name_id] = phys_name;
			}
			};

			readers["Unsupported"] = [&](const std::string & _block) {
			std::string block = _block.substr(1);
			AKANTU_DEBUG_WARNING("Unsupported block_kind " << block << " at line "
			<< file.current_line);
			auto && end_block = "$End" + block;
			while (file.line != end_block) {
			file.get_line();
			}
			};

			while (file.good()) {
			std::string block;
			file.read_line(block);

			auto && it = readers.find(block);

			if (it != readers.end()) {
			it->second(block);

			std::string end_block;
			file.read_line(end_block);
			block = block.substr(1);

			if (end_block != "$End" + block) {
			AKANTU_EXCEPTION("The reader failed to properly read the block "
			<< block << ". Expected a $End" << block << " at line "
			<< file.current_line);
			}
			} else if (not block.empty()) {
			readers["Unsupported"](block);
			}
			}

			// mesh.updateTypesOffsets(_not_ghost);
			if (file.version < 4) {
			this->constructPhysicalNames("tag_0", mesh);
			if (file.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 << "$MeshFormat"
			<< "\n";
			outfile << "2.2 0 8"
			<< "\n";
			outfile << "$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";

			std::map<Element, size_t> element_to_msh_element;

			UInt element_idx = 1;
			auto element = ElementNull;
			for (auto && type :
			mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
			const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
			element.type = type;

			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 (auto && data :
			enumerate(make_view(connectivity, connectivity.getNbComponent()))) {
			element.element = std::get<0>(data);
			const auto & conn = std::get<1>(data);
			element_to_msh_element.insert(std::make_pair(element, element_idx));

			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] != nullptr) {
			outfile << " " << tag[t][element.element];
			} else {
			outfile << " 0";
			}
			}

			for (auto && c : conn) {
			outfile << " " << c + 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";
			}
			}

			if (mesh.hasData(MeshDataType::_elemental)) {
			auto && tags = mesh.getTagNames();
			for (auto && tag : tags) {
			auto && data = mesh.getElementalData<double>(tag);
			auto type = mesh.getTypeCode(tag, MeshDataType::_elemental);
			if (type != MeshDataTypeCode::_real) {
			AKANTU_DEBUG_WARNING(
			"The field "
			<< tag << " is ignored by the MSH writer, msh files do not support "
			<< type << " data");
			continue;
			}
			if (data.isNodal()) {
			continue;
			}

			auto size = data.size();
			if (size == 0) {
			continue;
			}
			auto && nb_components = data.getNbComponents();
			auto nb_component = nb_components(*(data.elementTypes().begin()));

			outfile << "$ElementData"
			<< "\n";
			outfile << "1"
			<< "\n";
			outfile << "\"" << tag << "\"\n";
			outfile << "1\n0.0"
			<< "\n";
			outfile << "3\n0"
			<< "\n";
			outfile << nb_component << "\n";
			outfile << size << "\n";

			Element element;
			for (auto type : data.elementTypes()) {
			element.type = type;
			for (auto && _ :
			enumerate(make_view(data(type), nb_components(type)))) {
			element.element = std::get<0>(_);
			outfile << element_to_msh_element[element];
			for (auto && v : std::get<1>(_)) {
			outfile << " " << v;
			}
			outfile << "\n";
			}
			}
			outfile << "$EndElementData"
			<< "\n";
			}
			}

			outfile.close();
			}

			/* --------------------------------------------------------------------------
			*/

			} // namespace akantu

rAKA/src/io/mesh_io/mesh_io_msh.cc1a7b1e2153f4bugfixes/bug-fix-in…

mesh_io_msh.ccView Options

rAKA/src/io/mesh_io/mesh_io_msh.cc
1a7b1e2153f4bugfixes/bug-fix-in…

mesh_io_msh.cc
View Options