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mesh_io_diana.cc
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			/**
			* @file mesh_io_diana.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
			*
			* @date creation: Sat Mar 26 2011
			* @date last modification: Tue Feb 20 2018
			*
			* @brief handles diana meshes
			*
			* @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/>.
			*
			*/

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

			/* -------------------------------------------------------------------------- */
			#include <fstream>
			#include <iostream>

			/* -------------------------------------------------------------------------- */
			#include "element_group.hh"
			#include "mesh_io_diana.hh"
			#include "mesh_utils.hh"
			/* -------------------------------------------------------------------------- */
			#include <string.h>
			/* -------------------------------------------------------------------------- */
			#include <stdio.h>

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			/* Methods Implentations */
			/* -------------------------------------------------------------------------- */

			MeshIODiana::MeshIODiana() {
			canReadSurface = true;
			canReadExtendedData = true;
			_diana_to_akantu_element_types["T9TM"] = _triangle_3;
			_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
			_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
			_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
			_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
			_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
			_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
			_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
			_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
			_diana_to_akantu_mat_prop["YOUNG"] = "E";
			_diana_to_akantu_mat_prop["DENSIT"] = "rho";
			_diana_to_akantu_mat_prop["POISON"] = "nu";

			std::map<std::string, ElementType>::iterator it;
			for (it = _diana_to_akantu_element_types.begin();
			it != _diana_to_akantu_element_types.end(); ++it) {
			UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);

			auto * tmp = new UInt[nb_nodes];
			for (UInt i = 0; i < nb_nodes; ++i) {
			tmp[i] = i;
			}

			switch (it->second) {
			case _tetrahedron_10:
			tmp[8] = 9;
			tmp[9] = 8;
			break;
			case _pentahedron_15:
			tmp[0] = 2;
			tmp[1] = 8;
			tmp[2] = 0;
			tmp[3] = 6;
			tmp[4] = 1;
			tmp[5] = 7;
			tmp[6] = 11;
			tmp[7] = 9;
			tmp[8] = 10;
			tmp[9] = 5;
			tmp[10] = 14;
			tmp[11] = 3;
			tmp[12] = 12;
			tmp[13] = 4;
			tmp[14] = 13;
			break;
			case _hexahedron_20:
			tmp[0] = 5;
			tmp[1] = 16;
			tmp[2] = 4;
			tmp[3] = 19;
			tmp[4] = 7;
			tmp[5] = 18;
			tmp[6] = 6;
			tmp[7] = 17;
			tmp[8] = 13;
			tmp[9] = 12;
			tmp[10] = 15;
			tmp[11] = 14;
			tmp[12] = 1;
			tmp[13] = 8;
			tmp[14] = 0;
			tmp[15] = 11;
			tmp[16] = 3;
			tmp[17] = 10;
			tmp[18] = 2;
			tmp[19] = 9;
			break;
			default:
			// nothing to change
			break;
			}
			_read_order[it->second] = tmp;
			}
			}

			/* -------------------------------------------------------------------------- */
			MeshIODiana::~MeshIODiana() = default;

			/* -------------------------------------------------------------------------- */
			inline void my_getline(std::ifstream & infile, std::string & line) {
			std::getline(infile, line); // read the line
			size_t pos = line.find('\r'); /// remove the extra \r if needed
			line = line.substr(0, pos);
			}

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

			MeshAccessor mesh_accessor(mesh);

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

			std::string line;
			UInt first_node_number = std::numeric_limits<UInt>::max();
			diana_element_number_to_elements.clear();

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

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

			/// read all nodes
			if (line == "'COORDINATES'") {
			line = readCoordinates(infile, mesh, first_node_number);
			}

			/// read all elements
			if (line == "'ELEMENTS'") {
			line = readElements(infile, mesh, first_node_number);
			}

			/// read the material properties and write a .dat file
			if (line == "'MATERIALS'") {
			line = readMaterial(infile, filename);
			}

			/// read the material properties and write a .dat file
			if (line == "'GROUPS'") {
			line = readGroups(infile, mesh, first_node_number);
			}
			}
			infile.close();

			mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());

			MeshUtils::fillElementToSubElementsData(mesh);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
			__attribute__((unused)) const Mesh & mesh) {
			AKANTU_TO_IMPLEMENT();
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readCoordinates(std::ifstream & infile, Mesh & mesh,
			UInt & first_node_number) {
			AKANTU_DEBUG_IN();

			MeshAccessor mesh_accessor(mesh);

			Array<Real> & nodes = mesh_accessor.getNodes();

			std::string line;

			UInt index;
			Vector<Real> coord(3);

			do {
			my_getline(infile, line);
			if ("'ELEMENTS'" == line)
			break;

			std::stringstream sstr_node(line);
			sstr_node >> index >> coord(0) >> coord(1) >> coord(2);

			first_node_number = first_node_number < index ? first_node_number : index;

			nodes.push_back(coord);
			} while (true);

			AKANTU_DEBUG_OUT();
			return line;
			}

			/* -------------------------------------------------------------------------- */
			UInt MeshIODiana::readInterval(std::stringstream & line,
			std::set<UInt> & interval) {
			UInt first;
			line >> first;
			if (line.fail()) {
			return 0;
			}
			interval.insert(first);

			UInt second;
			int dash;
			dash = line.get();
			if (dash == '-') {
			line >> second;
			interval.insert(second);
			return 2;
			}

			if (line.fail())
			line.clear(std::ios::eofbit); // in case of get at end of the line
			else
			line.unget();
			return 1;
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
			UInt first_node_number) {
			AKANTU_DEBUG_IN();

			std::string line;
			my_getline(infile, line);

			bool reading_nodes_group = false;

			while (line != "'SUPPORTS'") {
			if (line == "NODES") {
			reading_nodes_group = true;
			my_getline(infile, line);
			}

			if (line == "ELEMEN") {
			reading_nodes_group = false;
			my_getline(infile, line);
			}

			auto * str = new std::stringstream(line);

			UInt id;
			std::string name;
			char c;
			*str >> id >> name >> c;

			auto * list_ids = new Array<UInt>(0, 1, name);

			UInt s = 1;
			bool end = false;
			while (!end) {
			while (!str->eof() && s != 0) {
			std::set<UInt> interval;
			s = readInterval(*str, interval);
			auto it = interval.begin();
			if (s == 1)
			list_ids->push_back(*it);
			if (s == 2) {
			UInt first = *it;
			++it;
			UInt second = *it;
			for (UInt i = first; i <= second; ++i) {
			list_ids->push_back(i);
			}
			}
			}
			if (str->fail())
			end = true;
			else {
			my_getline(infile, line);
			delete str;
			str = new std::stringstream(line);
			}
			}

			delete str;

			if (reading_nodes_group) {
			NodeGroup & ng = mesh.createNodeGroup(name);
			for (UInt i = 0; i < list_ids->size(); ++i) {
			UInt node = (*list_ids)(i)-first_node_number;
			ng.add(node, false);
			}
			delete list_ids;

			} else {
			ElementGroup & eg = mesh.createElementGroup(name);
			for (UInt i = 0; i < list_ids->size(); ++i) {
			Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
			if (elem.type != _not_defined)
			eg.add(elem, false, false);
			}

			eg.optimize();
			delete list_ids;
			}

			my_getline(infile, line);
			}

			AKANTU_DEBUG_OUT();
			return line;
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
			UInt first_node_number) {
			AKANTU_DEBUG_IN();

			std::string line;
			my_getline(infile, line);

			if ("CONNECTIVITY" == line) {
			line = readConnectivity(infile, mesh, first_node_number);
			}

			/// read the line corresponding to the materials
			if ("MATERIALS" == line) {
			line = readMaterialElement(infile, mesh);
			}

			AKANTU_DEBUG_OUT();
			return line;
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
			UInt first_node_number) {
			AKANTU_DEBUG_IN();

			MeshAccessor mesh_accessor(mesh);
			Int index;
			std::string lline;

			std::string diana_type;
			ElementType akantu_type, akantu_type_old = _not_defined;
			Array<UInt> * connectivity = nullptr;
			UInt node_per_element = 0;
			Element elem;
			UInt * read_order = nullptr;

			while (true) {
			my_getline(infile, lline);
			// std::cerr << lline << std::endl;
			std::stringstream sstr_elem(lline);
			if (lline == "MATERIALS")
			break;

			/// traiter les coordonnees
			sstr_elem >> index;
			sstr_elem >> diana_type;

			akantu_type = _diana_to_akantu_element_types[diana_type];

			if (akantu_type == _not_defined)
			continue;

			if (akantu_type != akantu_type_old) {
			connectivity = &(mesh_accessor.getConnectivity(akantu_type));

			node_per_element = connectivity->getNbComponent();
			akantu_type_old = akantu_type;
			read_order = _read_order[akantu_type];
			}

			Vector<UInt> local_connect(node_per_element);

			// used if element is written on two lines
			UInt j_last = 0;

			for (UInt j = 0; j < node_per_element; ++j) {
			UInt node_index;
			sstr_elem >> node_index;

			// check s'il y a pas plus rien après un certain point

			if (sstr_elem.fail()) {
			sstr_elem.clear();
			sstr_elem.ignore();
			break;
			}

			node_index -= first_node_number;
			local_connect(read_order[j]) = node_index;
			j_last = j;
			}

			// check if element is written in two lines
			if (j_last != (node_per_element - 1)) {

			// if this is the case, read on more line
			my_getline(infile, lline);
			std::stringstream sstr_elem(lline);

			for (UInt j = (j_last + 1); j < node_per_element; ++j) {

			UInt node_index;
			sstr_elem >> node_index;

			node_index -= first_node_number;
			local_connect(read_order[j]) = node_index;
			}
			}

			connectivity->push_back(local_connect);

			elem.type = akantu_type;
			elem.element = connectivity->size() - 1;

			diana_element_number_to_elements[index] = elem;
			akantu_number_to_diana_number[elem] = index;
			}

			AKANTU_DEBUG_OUT();
			return lline;
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
			Mesh & mesh) {
			AKANTU_DEBUG_IN();

			std::string line;

			for (auto type : mesh.elementTypes()) {
			UInt nb_element = mesh.getNbElement(type);
			mesh.getDataPointer<UInt>("material", type, _not_ghost, 1)
			.resize(nb_element);
			}

			my_getline(infile, line);
			while (line != "'MATERIALS'") {
			line =
			line.substr(line.find('/') + 1,
			std::string::npos); // erase the first slash / of the line
			char tutu[250] = {'\0'};
			strncpy(tutu, line.c_str(), 249);

			AKANTU_DEBUG_WARNING("reading line " << line);
			Array<UInt> temp_id(0, 2);
			UInt mat;
			while (true) {
			std::stringstream sstr_intervals_elements(line);
			Vector<UInt> id(2);
			char temp;
			while (sstr_intervals_elements.good()) {
			sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
			if (!sstr_intervals_elements.fail())
			temp_id.push_back(id);
			}
			if (sstr_intervals_elements.fail()) {
			sstr_intervals_elements.clear();
			sstr_intervals_elements.ignore();
			sstr_intervals_elements >> mat;
			break;
			}
			my_getline(infile, line);
			}

			// loop over elements
			// UInt * temp_id_val = temp_id.storage();
			for (UInt i = 0; i < temp_id.size(); ++i)
			for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
			Element & element = diana_element_number_to_elements[j];
			if (element.type == _not_defined)
			continue;
			UInt elem = element.element;
			ElementType type = element.type;
			Array<UInt> & data =
			mesh.getDataPointer<UInt>("material", type, _not_ghost);
			data(elem) = mat;
			}

			my_getline(infile, line);
			}

			AKANTU_DEBUG_OUT();
			return line;
			}

			/* -------------------------------------------------------------------------- */
			std::string MeshIODiana::readMaterial(std::ifstream & infile,
			const std::string & filename) {
			AKANTU_DEBUG_IN();

			std::stringstream mat_file_name;

			mat_file_name << "material_" << filename;

			std::ofstream material_file;
			material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());

			UInt mat_index;
			std::string line;

			bool first_mat = true;
			bool end = false;

			UInt mat_id = 0;

			using MatProp = std::map<std::string, Real>;
			MatProp mat_prop;
			do {
			my_getline(infile, line);
			std::stringstream sstr_material(line);
			if (("'GROUPS'" == line) \|\| ("'END'" == line)) {
			if (!mat_prop.empty()) {
			material_file << "material elastic [" << std::endl;
			material_file << "\tname = material" << ++mat_id << std::endl;
			for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
			material_file << "\t" << it->first << " = " << it->second
			<< std::endl;
			material_file << "]" << std::endl;
			mat_prop.clear();
			}
			end = true;
			} else {
			/// traiter les caractéristiques des matériaux
			sstr_material >> mat_index;

			if (!sstr_material.fail()) {
			if (!first_mat) {
			if (!mat_prop.empty()) {
			material_file << "material elastic [" << std::endl;
			material_file << "\tname = material" << ++mat_id << std::endl;
			for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
			material_file << "\t" << it->first << " = " << it->second
			<< std::endl;
			material_file << "]" << std::endl;
			mat_prop.clear();
			}
			}
			first_mat = false;
			} else {
			sstr_material.clear();
			}

			std::string prop_name;
			sstr_material >> prop_name;

			std::map<std::string, std::string>::iterator it;
			it = _diana_to_akantu_mat_prop.find(prop_name);

			if (it != _diana_to_akantu_mat_prop.end()) {
			Real value;
			sstr_material >> value;
			mat_prop[it->second] = value;
			} else {
			AKANTU_DEBUG_INFO("In material reader, property " << prop_name
			<< "not recognized");
			}
			}
			} while (!end);

			AKANTU_DEBUG_OUT();
			return line;
			}

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

			} // namespace akantu

rAKA/src/io/mesh_io/mesh_io_diana.cc6b6d5ac0192cfeatures/9-generate-a…

mesh_io_diana.ccView Options

rAKA/src/io/mesh_io/mesh_io_diana.cc
6b6d5ac0192cfeatures/9-generate-a…

mesh_io_diana.cc
View Options