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mesh_io_diana.cc
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			/**
			* @file mesh_io_diana.cc
			*
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Sat Mar 26 2011
			* @date last modification: Thu Mar 27 2014
			*
			* @brief handles diana meshes
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014 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 "mesh_io_diana.hh"
			#include "mesh_utils.hh"
			#include "element_group.hh"
			/* -------------------------------------------------------------------------- */
			#include <string.h>
			/* -------------------------------------------------------------------------- */
			#include <stdio.h>

			__BEGIN_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";
			}

			/* -------------------------------------------------------------------------- */
			MeshIODiana::~MeshIODiana() {
			std::map<std::string, Array<UInt> *>::iterator ng_it;
			std::map<std::string, std::vector<Element> *>::iterator eg_it;

			for (ng_it = node_groups.begin(); ng_it != node_groups.end(); ++ng_it) {
			delete ng_it->second;
			}

			for (eg_it = element_groups.begin(); eg_it != element_groups.end(); ++eg_it) {
			delete eg_it->second;
			}

			}

			/* -------------------------------------------------------------------------- */
			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();

			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_DEBUG_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, first_node_number);
			}

			}
			infile.close();

			mesh.nb_global_nodes = mesh.nodes->getSize();

			createGroupsInMesh(mesh);

			MeshUtils::fillElementToSubElementsData(mesh);

			AKANTU_DEBUG_OUT();
			}

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

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

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

			std::string line;

			UInt index;
			Real coord[3];

			do {
			my_getline(infile, line);
			if("'ELEMENTS'" == line)
			break;
			//end = true;
			//else {
			/// for each node, read the coordinates

			std::stringstream sstr_node(line);

			sstr_node >> index >> coord[0] >> coord[1] >> coord[2];

			//if (!sstr_node.fail())
			//break;

			first_node_number = first_node_number < index ? first_node_number : index;

			nodes.push_back(coord);
			// }
			} while(true);//!end);

			AKANTU_DEBUG_OUT();
			return line;
			}

			/* -------------------------------------------------------------------------- */
			UInt MeshIODiana::readInterval(std::stringstream & line,
			std::set<UInt> & interval) {

			int space;
			space = line.get();
			while (space == ' '){
			space = line.get();
			if(line.fail()) {
			line.clear(std::ios::eofbit);
			return 0;
			}
			}
			if(!line.fail()) line.unget();
			else {
			line.clear(std::ios::eofbit);
			return 0;
			}

			UInt first;
			line >> first;
			if(line.fail()) { return 0; }
			interval.insert(first);

			// std::cerr << "first: " << first << std::endl;

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

			// std::cerr << "second: " << second << std::endl;

			int bracket;
			UInt unknown_stuff;
			bracket = line.get();
			if(bracket == '('){
			line >> unknown_stuff;
			bracket = line.get();
			}
			else{
			if(line.fail()) line.clear(std::ios::eofbit);
			else line.unget();
			}
			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,
			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);
			}

			// std::cerr << line << std::endl;
			std::stringstream *str = new std::stringstream(line);

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

			// std::cerr << "AAAA " << id << " " << name << " " << c << std::endl;

			Array<UInt> * 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);
			std::set<UInt>::iterator 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);
			s = 1;
			}
			}

			delete str;

			if(reading_nodes_group) {

			// reading a node group

			for (UInt i = 0; i < list_ids->getSize(); ++i) {
			(*list_ids)(i) -= first_node_number;
			}
			node_groups[name] = list_ids;
			} else {

			// reading an element group

			std::vector<Element> * elem = new std::vector<Element>;
			elem->reserve(list_ids->getSize());
			for (UInt i = 0; i < list_ids->getSize(); ++i) {
			Element & e = diana_element_number_to_elements[(*list_ids)(i)];
			if(e.type != _not_defined)
			elem->push_back(e);
			}

			element_groups[name] = elem;
			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();

			Int index;
			std::string lline;

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

			while (1) {
			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.getConnectivityPointer(akantu_type);

			node_per_element = connectivity->getNbComponent();
			akantu_type_old = akantu_type;
			}

			UInt local_connect[node_per_element];

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

			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[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[j] = node_index;
			}
			}

			// Exceptions
			UInt local_connect_non_modified[node_per_element];

			// Create a new unmodified vector
			for(UInt k = 0; k < node_per_element; ++k) {
			local_connect_non_modified[k] = local_connect[k];
			}

			switch(akantu_type){

			case _pentahedron_15:
			local_connect[0] = local_connect_non_modified[2];
			local_connect[1] = local_connect_non_modified[4];
			local_connect[2] = local_connect_non_modified[0];
			local_connect[3] = local_connect_non_modified[11];
			local_connect[4] = local_connect_non_modified[13];
			local_connect[5] = local_connect_non_modified[9];
			local_connect[6] = local_connect_non_modified[3];
			local_connect[7] = local_connect_non_modified[5];
			local_connect[8] = local_connect_non_modified[1];
			local_connect[9] = local_connect_non_modified[7];
			local_connect[10] =local_connect_non_modified[8];
			local_connect[11] =local_connect_non_modified[6];
			local_connect[12] =local_connect_non_modified[12];
			local_connect[13] =local_connect_non_modified[14];
			local_connect[14] =local_connect_non_modified[10];
			break;

			case _hexahedron_20:
			local_connect[0] = local_connect_non_modified[14];
			local_connect[8] = local_connect_non_modified[13];
			local_connect[1] = local_connect_non_modified[12];
			local_connect[9] = local_connect_non_modified[19];
			local_connect[2] = local_connect_non_modified[18];
			local_connect[10] = local_connect_non_modified[17];
			local_connect[3] = local_connect_non_modified[16];
			local_connect[11] = local_connect_non_modified[15];
			local_connect[12] = local_connect_non_modified[9];
			local_connect[13] = local_connect_non_modified[8];
			local_connect[14] = local_connect_non_modified[11];
			local_connect[15] = local_connect_non_modified[10];
			local_connect[4] = local_connect_non_modified[2];
			local_connect[16] = local_connect_non_modified[1];
			local_connect[5] = local_connect_non_modified[0];
			local_connect[17] = local_connect_non_modified[7];
			local_connect[6] = local_connect_non_modified[6];
			local_connect[18] = local_connect_non_modified[5];
			local_connect[7] = local_connect_non_modified[4];
			local_connect[19] = local_connect_non_modified[3];
			break;

			default:
			//nothing to change
			break;
			}

			connectivity->push_back(local_connect);

			elem.type = akantu_type;
			elem.element = connectivity->getSize() - 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;
			std::stringstream sstr_tag_name; sstr_tag_name << "tag_" << 0;

			Mesh::type_iterator it = mesh.firstType();
			Mesh::type_iterator end = mesh.lastType();
			for(; it != end; ++it) {
			UInt nb_element = mesh.getNbElement(*it);
			mesh.getDataPointer<UInt>("material", *it, _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];
			strcpy(tutu, line.c_str());

			// AKANTU_DEBUG_WARNING("reading line " << line);
			Array<UInt> temp_id(0, 2);
			UInt mat;
			while(true){
			std::stringstream sstr_intervals_elements(line);
			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.getSize(); ++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;

			typedef std::map<std::string, Real> MatProp;
			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(MatProp::iterator 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(MatProp::iterator 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;
			}

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

			void MeshIODiana::createGroupsInMesh(Mesh & mesh) {

			/* ------------------------------------------------------------------------ */
			// create the element groups
			/* ------------------------------------------------------------------------ */

			{
			std::map<std::string, std::vector<Element> *>::iterator git
			= element_groups.begin();
			std::map<std::string, std::vector<Element> *>::iterator gend
			= element_groups.end();

			for (;git != gend; ++git) {
			std::string group_name = git->first;
			std::vector<Element> & element_group = *git->second;

			if (element_group.size() == 0) continue;

			std::cerr << "adding group " << group_name << std::endl;
			Element & first_element = element_group[0];

			UInt group_dim = mesh.getSpatialDimension(first_element.type);
			mesh.createElementGroup(group_name, group_dim);
			ElementGroup & group = mesh.getElementGroup(git->first);

			std::vector<Element>::iterator it = element_group.begin();
			std::vector<Element>::iterator end = element_group.end();

			for(; it != end; ++it){
			std::cerr << "adding element " << it->element << "(" << it->type << ") : ";
			Array<UInt> & connectivity = *mesh.getConnectivityPointer(it->type);
			UInt node_per_element = connectivity.getNbComponent();
			for (UInt n = 0 ; n < node_per_element; ++n)
			std::cerr << connectivity(it->element,n) << " ";
			std::cerr << std::endl;
			group.add(*it,true,false);
			}

			}
			}

			/* ------------------------------------------------------------------------ */
			// create the node groups
			/* ------------------------------------------------------------------------ */

			{
			std::map<std::string, Array<UInt> *>::iterator git
			= node_groups.begin();
			std::map<std::string, Array<UInt> *>::iterator gend
			= node_groups.end();

			for (;git != gend; ++git) {
			std::string group_name = git->first;
			Array<UInt> & node_group = *git->second;

			if (node_group.getSize() == 0) continue;
			// Element & first_element = element_group[0];

			UInt group_dim = 1;//mesh.getSpatialDimension(first_element.type);
			mesh.createNodeGroup(group_name, group_dim);
			NodeGroup & group = mesh.getNodeGroup(git->first);

			Array<UInt>::iterator<UInt> it = node_group.begin();
			Array<UInt>::iterator<UInt> end = node_group.end();

			for(; it != end; ++it){
			group.add(*it);
			}

			}
			}
			}


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

			void MeshIODiana::printself(std::ostream & stream,int indent) const {

			MeshIO::printself(stream,indent);

			std::string space;
			for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);

			if (node_groups.size()){
			stream << space << "Read node groups: ";
			std::map<std::string, Array<UInt> *>::const_iterator it = node_groups.begin();
			std::map<std::string, Array<UInt> *>::const_iterator end = node_groups.end();

			for (;it != end; ++it) {
			stream << "'" << it->first << "' ";
			}
			stream << std::endl;
			}

			if (element_groups.size()){
			stream << space << "Read element groups: ";
			std::map<std::string, std::vector<Element> *>::const_iterator it = element_groups.begin();
			std::map<std::string, std::vector<Element> *>::const_iterator end = element_groups.end();

			for (;it != end; ++it) {
			stream << "'" << it->first << "' ";
			}
			stream << std::endl;
			}
			}


			__END_AKANTU__

rAKA/src/io/mesh_io/mesh_io_diana.cc4453a52c8f8ebugfixes/bug-fix-in…

mesh_io_diana.ccView Options

rAKA/src/io/mesh_io/mesh_io_diana.cc
4453a52c8f8ebugfixes/bug-fix-in…

mesh_io_diana.cc
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