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rAKA/src/io/mesh_io/mesh_io_diana.cc
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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();
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 _triangle_6:
local_connect[0] = local_connect_non_modified[0];
local_connect[1] = local_connect_non_modified[2];
local_connect[2] = local_connect_non_modified[4];
local_connect[3] = local_connect_non_modified[1];
local_connect[4] = local_connect_non_modified[3];
local_connect[5] = local_connect_non_modified[5];
break;
case _quadrangle_8:
local_connect[0] = local_connect_non_modified[0];
local_connect[1] = local_connect_non_modified[2];
local_connect[2] = local_connect_non_modified[4];
local_connect[3] = local_connect_non_modified[6];
local_connect[4] = local_connect_non_modified[1];
local_connect[5] = local_connect_non_modified[3];
local_connect[6] = local_connect_non_modified[5];
local_connect[7] = local_connect_non_modified[7];
break;
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::createElementGroupInMesh(Mesh & mesh, const std::string & group_name) {
std::map<std::string, std::vector<Element> *>::iterator git
= element_groups.find(group_name);
if (git == element_groups.end()) {
AKANTU_EXCEPTION("group '" << group_name
<< "' not found in data loaded from Diana");
}
std::vector<Element> & element_group = *git->second;
if (element_group.size() == 0) return;
// 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){
group.add(*it,true,false);
}
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::createNodeGroupInMesh(Mesh & mesh, const std::string & group_name) {
std::map<std::string, Array<UInt> *>::iterator git
= node_groups.find(group_name);
if (git == node_groups.end()) {
AKANTU_EXCEPTION("group '" << group_name
<< "' not found in data loaded from Diana");
}
Array<UInt> & node_group = *git->second;
mesh.createNodeGroup(group_name);
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;
}
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) {
std::map<std::string, Array<UInt> *>::iterator it = node_groups.begin();
std::map<std::string, Array<UInt> *>::iterator end = node_groups.end();
for (; it != end; ++it) {
Array<UInt> & group = *(it->second);
Array<UInt>::iterator<> git = group.begin();
Array<UInt>::iterator<> gend = group.end();
for (; git != gend; ++git) {
UInt new_id = new_numbering(*git);
AKANTU_DEBUG_ASSERT(new_id != UInt(-1), "Argh " << *git << " was suppressed!");
*git = new_id;
}
}
}
__END_AKANTU__
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