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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"
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			// The boost spirit is a work on the way it does not compile so I kept the
			// current code. The current code does not handle files generated on Windows
			// <CRLF>

			// #include <boost/config/warning_disable.hpp>
			// #include <boost/spirit/include/qi.hpp>
			// #include <boost/spirit/include/phoenix_core.hpp>
			// #include <boost/spirit/include/phoenix_fusion.hpp>
			// #include <boost/spirit/include/phoenix_object.hpp>
			// #include <boost/spirit/include/phoenix_container.hpp>
			// #include <boost/spirit/include/phoenix_operator.hpp>
			// #include <boost/spirit/include/phoenix_bind.hpp>
			// #include <boost/spirit/include/phoenix_stl.hpp>
			/* -------------------------------------------------------------------------- */

			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;

			/* -------------------------------------------------------------------------- */
			/* Spirit stuff */
			/* -------------------------------------------------------------------------- */
			// namespace _parser {
			// namespace spirit = ::boost::spirit;
			// namespace qi = ::boost::spirit::qi;
			// namespace ascii = ::boost::spirit::ascii;
			// namespace lbs = ::boost::spirit::qi::labels;
			// namespace phx = ::boost::phoenix;

			// /* ------------------------------------------------------------------------
			// */
			// /* Lazy functors */
			// /* ------------------------------------------------------------------------
			// */
			// struct _Element {
			// int index;
			// std::vector<int> tags;
			// std::vector<int> connectivity;
			// ElementType type;
			// };

			// /* ------------------------------------------------------------------------
			// */
			// struct lazy_get_nb_nodes_ {
			// template <class elem_type> struct result { typedef int type; };
			// template <class elem_type> bool operator()(elem_type et) {
			// return MeshIOMSH::_msh_nodes_per_elem[et];
			// }
			// };

			// /* ------------------------------------------------------------------------
			// */
			// struct lazy_element_ {
			// template <class id_t, class tags_t, class elem_type, class conn_t>
			// struct result {
			// typedef _Element type;
			// };
			// template <class id_t, class tags_t, class elem_type, class conn_t>
			// _Element operator()(id_t id, const elem_type & et, const tags_t & t,
			// const conn_t & c) {
			// _Element tmp_el;
			// tmp_el.index = id;
			// tmp_el.tags = t;
			// tmp_el.connectivity = c;
			// tmp_el.type = et;
			// return tmp_el;
			// }
			// };

			// /* ------------------------------------------------------------------------
			// */
			// struct lazy_check_value_ {
			// template <class T> struct result { typedef void type; };
			// template <class T> void operator()(T v1, T v2) {
			// if (v1 != v2) {
			// AKANTU_EXCEPTION("The msh parser expected a "
			// << v2 << " in the header bug got a " << v1);
			// }
			// }
			// };

			// /* ------------------------------------------------------------------------
			// */
			// struct lazy_node_read_ {
			// template <class Mesh, class ID, class V, class size, class Map>
			// struct result {
			// typedef bool type;
			// };
			// template <class Mesh, class ID, class V, class size, class Map>
			// bool operator()(Mesh & mesh, const ID & id, const V & pos, size max,
			// Map & nodes_mapping) const {
			// Vector<Real> tmp_pos(mesh.getSpatialDimension());
			// UInt i = 0;
			// for (typename V::const_iterator it = pos.begin();
			// it != pos.end() \|\| i < mesh.getSpatialDimension(); ++it)
			// tmp_pos[i++] = *it;

			// nodes_mapping[id] = mesh.getNbNodes();
			// mesh.getNodes().push_back(tmp_pos);
			// return (mesh.getNbNodes() < UInt(max));
			// }
			// };

			// /* ------------------------------------------------------------------------
			// */
			// struct lazy_element_read_ {
			// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
			// struct result {
			// typedef bool type;
			// };

			// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
			// bool operator()(Mesh & mesh, const EL & element, size max,
			// const NodeMap & nodes_mapping,
			// ElemMap & elements_mapping) const {
			// Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(element.type));

			// AKANTU_DEBUG_ASSERT(element.connectivity.size() == tmp_conn.size(),
			// "The element "
			// << element.index
			// << "in the MSH file has too many nodes.");

			// mesh.addConnectivityType(element.type);
			// Array<UInt> & connectivity = mesh.getConnectivity(element.type);

			// UInt i = 0;
			// for (std::vector<int>::const_iterator it =
			// element.connectivity.begin();
			// it != element.connectivity.end(); ++it) {
			// typename NodeMap::const_iterator nit = nodes_mapping.find(*it);
			// AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
			// "There is an unknown node in the connectivity.");
			// tmp_conn[i++] = nit->second;
			// }

			// ::akantu::Element el(element.type, connectivity.size());
			// elements_mapping[element.index] = el;

			// connectivity.push_back(tmp_conn);

			// for (UInt i = 0; i < element.tags.size(); ++i) {
			// std::stringstream tag_sstr;
			// tag_sstr << "tag_" << i;
			// Array<UInt> * data =
			// mesh.template getDataPointer<UInt>(tag_sstr.str(), element.type,
			// _not_ghost);
			// data->push_back(element.tags[i]);
			// }

			// return (mesh.getNbElement() < UInt(max));
			// }
			// };

			// /* ------------------------------------------------------------------------
			// */
			// template <class Iterator, typename Skipper = ascii::space_type>
			// struct MshMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
			// public:
			// MshMeshGrammar(Mesh & mesh)
			// : MshMeshGrammar::base_type(start, "msh_mesh_reader"), mesh(mesh) {
			// phx::function<lazy_element_> lazy_element;
			// phx::function<lazy_get_nb_nodes_> lazy_get_nb_nodes;
			// phx::function<lazy_check_value_> lazy_check_value;
			// phx::function<lazy_node_read_> lazy_node_read;
			// phx::function<lazy_element_read_> lazy_element_read;

			// clang-format off

			// start
			// = *( known_section \| unknown_section
			// )
			// ;

			// known_section
			// = qi::char_("$")
			// >> sections [ lbs::_a = lbs::_1 ]
			// >> qi::lazy(*lbs::_a)
			// >> qi::lit("$End")
			// //>> qi::lit(phx::ref(lbs::_a))
			// ;

			// unknown_section
			// = qi::char_("$")
			// >> qi::char_("") [ lbs::_a = lbs::_1 ]
			// >> ignore_section
			// >> qi::lit("$End")
			// >> qi::lit(phx::val(lbs::_a))
			// ;

			// mesh_format // version followed by 0 or 1 for ascii or binary
			// = version >> (
			// ( qi::char_("0")
			// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
			// )
			// \| ( qi::char_("1")
			// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
			// >> qi::dword [ lazy_check_value(lbs::_1, 1) ]
			// )
			// )
			// ;

			// nodes
			// = nodes_
			// ;

			// nodes_
			// = qi::int_ [ lbs::_a = lbs::_1 ]
			// > *(
			// ( qi::int_ >> position ) [ lazy_node_read(phx::ref(mesh),
			// lbs::_1,
			// phx::cref(lbs::_2),
			// lbs::_a,
			// phx::ref(this->msh_nodes_to_akantu)) ]
			// )
			// ;

			// element
			// = elements_
			// ;

			// elements_
			// = qi::int_ [ lbs::_a = lbs::_1 ]
			// > qi::repeat(phx::ref(lbs::_a))[ element [ lazy_element_read(phx::ref(mesh),
			// lbs::_1,
			// phx::cref(lbs::_a),
			// phx::cref(this->msh_nodes_to_akantu),
			// phx::ref(this->msh_elemt_to_akantu)) ]]
			// ;

			// ignore_section
			// = *(qi::char_ - qi::char_('$'))
			// ;

			// interpolation_scheme = ignore_section;
			// element_data = ignore_section;
			// node_data = ignore_section;

			// version
			// = qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ]
			// >> *( qi::char_(".") >> qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ] )
			// ;

			// position
			// = real [ phx::push_back(lbs::_val, lbs::_1) ]
			// > real [ phx::push_back(lbs::_val, lbs::_1) ]
			// > real [ phx::push_back(lbs::_val, lbs::_1) ]
			// ;

			// tags
			// = qi::int_ [ lbs::_a = lbs::_1 ]
			// > qi::repeat(phx::val(lbs::_a))[ qi::int_ [ phx::push_back(lbs::_val,
			// lbs::_1) ] ]
			// ;

			// element
			// = ( qi::int_ [ lbs::_a = lbs::_1 ]
			// > msh_element_type [ lbs::_b = lazy_get_nb_nodes(lbs::_1) ]
			// > tags [ lbs::_c = lbs::_1 ]
			// > connectivity(lbs::_a) [ lbs::_d = lbs::_1 ]
			// ) [ lbs::_val = lazy_element(lbs::_a,
			// phx::cref(lbs::_b),
			// phx::cref(lbs::_c),
			// phx::cref(lbs::_d)) ]
			// ;
			// connectivity
			// = qi::repeat(lbs::_r1)[ qi::int_ [ phx::push_back(lbs::_val,
			// lbs::_1) ] ]
			// ;

			// sections.add
			// ("MeshFormat", &mesh_format)
			// ("Nodes", &nodes)
			// ("Elements", &elements)
			// ("PhysicalNames", &physical_names)
			// ("InterpolationScheme", &interpolation_scheme)
			// ("ElementData", &element_data)
			// ("NodeData", &node_data);

			// msh_element_type.add
			// ("0" , _not_defined )
			// ("1" , _segment_2 )
			// ("2" , _triangle_3 )
			// ("3" , _quadrangle_4 )
			// ("4" , _tetrahedron_4 )
			// ("5" , _hexahedron_8 )
			// ("6" , _pentahedron_6 )
			// ("7" , _not_defined )
			// ("8" , _segment_3 )
			// ("9" , _triangle_6 )
			// ("10", _not_defined )
			// ("11", _tetrahedron_10)
			// ("12", _not_defined )
			// ("13", _not_defined )
			// ("14", _hexahedron_20 )
			// ("15", _pentahedron_15)
			// ("16", _not_defined )
			// ("17", _point_1 )
			// ("18", _quadrangle_8 );

			// mesh_format .name("MeshFormat" );
			// nodes .name("Nodes" );
			// elements .name("Elements" );
			// physical_names .name("PhysicalNames" );
			// interpolation_scheme.name("InterpolationScheme");
			// element_data .name("ElementData" );
			// node_data .name("NodeData" );

			// clang-format on
			// }

			// /* ----------------------------------------------------------------------
			// */
			// /* Rules */
			// /* ----------------------------------------------------------------------
			// */
			// private:
			// qi::symbols<char, ElementType> msh_element_type;
			// qi::symbols<char, qi::rule<Iterator, void(), Skipper> *> sections;
			// qi::rule<Iterator, void(), Skipper> start;
			// qi::rule<Iterator, void(), Skipper, qi::locals<std::string> >
			// unknown_section;
			// qi::rule<Iterator, void(), Skipper, qi::locals<qi::rule<Iterator,
			// Skipper> *> > known_section;
			// qi::rule<Iterator, void(), Skipper> mesh_format, nodes, elements,
			// physical_names, ignore_section,
			// interpolation_scheme, element_data, node_data, any_line;
			// qi::rule<Iterator, void(), Skipper, qi::locals<int> > nodes_;
			// qi::rule<Iterator, void(), Skipper, qi::locals< int, int, vector<int>,
			// vector<int> > > elements_;

			// qi::rule<Iterator, std::vector<int>(), Skipper> version;
			// qi::rule<Iterator, _Element(), Skipper, qi::locals<ElementType> >
			// element;
			// qi::rule<Iterator, std::vector<int>(), Skipper, qi::locals<int> > tags;
			// qi::rule<Iterator, std::vector<int>(int), Skipper> connectivity;
			// qi::rule<Iterator, std::vector<Real>(), Skipper> position;

			// qi::real_parser<Real, qi::real_policies<Real> > real;

			// /* ----------------------------------------------------------------------
			// */
			// /* Members */
			// /* ----------------------------------------------------------------------
			// */
			// private:
			// /// reference to the mesh to read
			// Mesh & mesh;

			// /// correspondance between the numbering of nodes in the abaqus file and
			// in
			// /// the akantu mesh
			// std::map<UInt, UInt> msh_nodes_to_akantu;

			// /// correspondance between the element number in the abaqus file and the
			// /// Element in the akantu mesh
			// std::map<UInt, Element> msh_elemt_to_akantu;
			// };
			// }

			// /* --------------------------------------------------------------------------
			// */
			// void MeshIOAbaqus::read(const std::string& filename, Mesh& mesh) {
			// namespace qi = boost::spirit::qi;
			// namespace ascii = boost::spirit::ascii;

			// std::ifstream infile;
			// infile.open(filename.c_str());

			// if(!infile.good()) {
			// AKANTU_ERROR("Cannot open file " << filename);
			// }

			// std::string storage; // We will read the contents here.
			// infile.unsetf(std::ios::skipws); // No white space skipping!
			// std::copy(std::istream_iterator<char>(infile),
			// std::istream_iterator<char>(),
			// std::back_inserter(storage));

			// typedef std::string::const_iterator iterator_t;
			// typedef ascii::space_type skipper;
			// typedef _parser::MshMeshGrammar<iterator_t, skipper> grammar;

			// grammar g(mesh);
			// skipper ws;

			// iterator_t iter = storage.begin();
			// iterator_t end = storage.end();

			// qi::phrase_parse(iter, end, g, ws);

			// this->setNbGlobalNodes(mesh, mesh.getNodes().size());
			// MeshUtils::fillElementToSubElementsData(mesh);
			// }

			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);
			}

			while (infile.good()) {
			my_getline(infile, line);
			current_line++;

			/// read the header
			if (line == "$MeshFormat") {
			my_getline(infile, line); /// the format line
			std::stringstream sstr(line);
			std::string version;
			sstr >> version;
			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;
			}

			/// read the physical names
			if (line == "$PhysicalNames") {
			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;
			}
			}

			/// read all nodes
			if (line == "$Nodes" \|\| line == "$NOD") {
			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
			}

			/// read all elements
			if (line == "$Elements" \|\| line == "$ELM") {
			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
			}

			if (line == "$Periodic") {
			UInt nb_periodic_entities;
			my_getline(infile, line);

			std::stringstream sstr(line);
			sstr >> nb_periodic_entities;

			for(UInt p = 0; p < nb_periodic_entities; ++p) {
			// dimension slave-tag master-tag
			my_getline(infile, line);

			// 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);
			}
			}

			my_getline(infile, line);
			}

			if ((line[0] == '$') && (line.find("End") == std::string::npos)) {
			AKANTU_DEBUG_WARNING("Unsuported block_kind " << line << " at line "
			<< current_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 << "$MeshFormat" << std::endl;
			outfile << "2.1 0 8" << std::endl;
			outfile << "$EndMeshFormat" << std::endl;

			outfile << std::setprecision(std::numeric_limits<Real>::digits10);
			outfile << "$Nodes" << std::endl;

			outfile << nodes.size() << std::endl;

			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 << std::endl;
			;
			}
			outfile << std::nouppercase;
			outfile << "$EndNodes" << std::endl;
			;

			outfile << "$Elements" << std::endl;
			;

			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 << std::endl;

			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 << std::endl;
			element_idx++;
			}
			}

			outfile << "$EndElements" << std::endl;
			;

			outfile.close();
			}

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

			} // namespace akantu

rAKA/src/io/mesh_io/mesh_io_msh.cc11d8a4d1b2c5bugfixes/39-the-python…

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rAKA/src/io/mesh_io/mesh_io_msh.cc
11d8a4d1b2c5bugfixes/39-the-python…

mesh_io_msh.cc
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