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;
	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];
	strncpy(tutu, line.c_str(), 250);

	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

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