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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: Thu Oct 29 2020
*
* @brief Read/Write for MSH files generated by gmsh
*
*
* @section LICENSE
*
* Copyright (©) 2010-2021 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 "element_group.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
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;
/* -------------------------------------------------------------------------- */
namespace {
struct File {
std::string filename;
std::ifstream infile;
std::string line;
size_t current_line{0};
size_t first_node_number{std::numeric_limits<UInt>::max()},
last_node_number{0};
bool has_physical_names{false};
std::unordered_map<size_t, size_t> node_tags;
std::unordered_map<size_t, Element> element_tags;
int version{0};
int size_of_size_t{0};
Mesh & mesh;
MeshAccessor mesh_accessor;
std::multimap<std::pair<int, int>, int> entity_tag_to_physical_tags;
File(const std::string & filename, Mesh & mesh)
: filename(filename), mesh(mesh), mesh_accessor(mesh) {
infile.open(filename.c_str());
if (not infile.good()) {
AKANTU_EXCEPTION("Cannot open file " << filename);
}
}
~File() { infile.close(); }
auto good() { return infile.good(); }
std::stringstream get_line() {
std::string tmp_str;
if (infile.eof()) {
AKANTU_EXCEPTION("Reached the end of the file " << filename);
}
std::getline(infile, tmp_str);
line = trim(tmp_str);
++current_line;
return std::stringstream(line);
}
template <typename... Ts> void read_line(Ts &&... ts) {
auto && sstr = get_line();
(void)std::initializer_list<int>{
(sstr >> std::forward<decltype(ts)>(ts), 0)...};
}
};
} // namespace
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders2(File & file, Readers & readers) {
readers["$NOD"] = readers["$Nodes"] = [&](const std::string & /*unused*/) {
UInt nb_nodes;
file.read_line(nb_nodes);
Array<Real> & nodes = file.mesh_accessor.getNodes();
nodes.resize(nb_nodes);
file.mesh_accessor.setNbGlobalNodes(nb_nodes);
size_t index;
Vector<double> coord(3);
/// for each node, read the coordinates
for (auto && data : enumerate(make_view(nodes, nodes.getNbComponent()))) {
file.read_line(index, coord(0), coord(1), coord(2));
if (index > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
file.first_node_number = std::min(file.first_node_number, index);
file.last_node_number = std::max(file.last_node_number, index);
for (auto && coord_data : zip(std::get<1>(data), coord)) {
std::get<0>(coord_data) = std::get<1>(coord_data);
}
file.node_tags[index] = std::get<0>(data);
}
};
readers["$ELM"] = readers["$Elements"] = [&](const std::string & /*unused*/) {
UInt nb_elements;
file.read_line(nb_elements);
Int index;
UInt msh_type;
ElementType akantu_type;
for (UInt i = 0; i < nb_elements; ++i) {
auto && sstr_elem = file.get_line();
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type =
this->_msh_to_akantu_element_types[MSHElementType(msh_type)];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
auto node_per_element = connectivity.getNbComponent();
auto & read_order = this->_read_order[akantu_type];
/// read tags informations
if (file.version < 2000) {
Int tag0;
Int tag1;
Int nb_nodes; // reg-phys, reg-elem, number-of-nodes
sstr_elem >> tag0 >> tag1 >> nb_nodes;
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.push_back(tag0);
auto & data1 =
file.mesh_accessor.template getData<UInt>("tag_1", akantu_type);
data1.push_back(tag1);
} else if (file.version < 4000) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
auto & data = file.mesh_accessor.template getData<UInt>(
"tag_" + std::to_string(j), akantu_type);
data.push_back(tag);
}
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
local_connect(read_order[j]) = file.node_tags[node_index];
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[index] = elem;
}
};
readers["$Periodic"] = [&](const std::string & /*unused*/) {
UInt nb_periodic_entities;
file.read_line(nb_periodic_entities);
file.mesh_accessor.getNodesFlags().resize(file.mesh.getNbNodes(),
NodeFlag::_normal);
for (UInt p = 0; p < nb_periodic_entities; ++p) {
// dimension slave-tag master-tag
UInt dimension;
file.read_line(dimension);
// transformation
file.get_line();
// nb nodes
UInt nb_nodes;
file.read_line(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
// slave master
auto && sstr = file.get_line();
// The info in the mesh seem inconsistent so they are ignored for now.
continue;
if (dimension == file.mesh.getSpatialDimension() - 1) {
UInt slave;
UInt master;
sstr >> slave;
sstr >> master;
file.mesh_accessor.addPeriodicSlave(file.node_tags[slave],
file.node_tags[master]);
}
}
}
// mesh_accessor.markMeshPeriodic();
};
}
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders4(File & file, Readers & readers) {
static std::map<int, std::string> entity_type{
{0, "points"},
{1, "curve"},
{2, "surface"},
{3, "volume"},
};
readers["$Entities"] = [&](const std::string & /*unused*/) {
size_t num_entity[4];
file.read_line(num_entity[0], num_entity[1], num_entity[2], num_entity[3]);
for (auto entity_dim : arange(4)) {
for (auto _ [[gnu::unused]] : arange(num_entity[entity_dim])) {
auto && sstr = file.get_line();
int tag;
double min_x;
double min_y;
double min_z;
double max_x;
double max_y;
double max_z;
size_t num_physical_tags;
sstr >> tag >> min_x >> min_y >> min_z;
if (entity_dim > 0 or file.version < 4001) {
sstr >> max_x >> max_y >> max_z;
}
sstr >> num_physical_tags;
for (auto _ [[gnu::unused]] : arange(num_physical_tags)) {
int phys_tag;
sstr >> phys_tag;
std::string physical_name;
if (this->physical_names.find(phys_tag) ==
this->physical_names.end()) {
physical_name = "msh_block_" + std::to_string(phys_tag);
} else {
physical_name = this->physical_names[phys_tag];
}
if (not file.mesh.elementGroupExists(physical_name)) {
file.mesh.createElementGroup(physical_name, entity_dim);
} else {
file.mesh.getElementGroup(physical_name).addDimension(entity_dim);
}
file.entity_tag_to_physical_tags.insert(
std::make_pair(std::make_pair(tag, entity_dim), phys_tag));
}
}
}
};
readers["$Nodes"] = [&](const std::string & /*unused*/) {
size_t num_blocks;
size_t num_nodes;
if (file.version >= 4001) {
file.read_line(num_blocks, num_nodes, file.first_node_number,
file.last_node_number);
} else {
file.read_line(num_blocks, num_nodes);
}
auto & nodes = file.mesh_accessor.getNodes();
nodes.reserve(num_nodes);
file.mesh_accessor.setNbGlobalNodes(num_nodes);
if (num_nodes > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
size_t node_id{0};
for (auto block [[gnu::unused]] : arange(num_blocks)) {
int entity_dim;
int entity_tag;
int parametric;
size_t num_nodes_in_block;
Vector<double> pos(3);
Vector<double> real_pos(nodes.getNbComponent());
if (file.version >= 4001) {
file.read_line(entity_dim, entity_tag, parametric, num_nodes_in_block);
if (parametric) {
AKANTU_EXCEPTION(
"Akantu does not support parametric nodes in msh files");
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag);
file.node_tags[tag] = node_id;
++node_id;
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
file.read_line(pos(_x), pos(_y), pos(_z));
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
}
} else {
file.read_line(entity_tag, entity_dim, parametric, num_nodes_in_block);
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag, pos(_x), pos(_y), pos(_z));
file.first_node_number = std::min(file.first_node_number, tag);
file.last_node_number = std::max(file.last_node_number, tag);
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
file.node_tags[tag] = node_id;
++node_id;
}
}
}
};
readers["$Elements"] = [&](const std::string & /*unused*/) {
size_t num_blocks;
size_t num_elements;
file.read_line(num_blocks, num_elements);
for (auto block [[gnu::unused]] : arange(num_blocks)) {
int entity_dim;
int entity_tag;
int element_type;
size_t num_elements_in_block;
if (file.version >= 4001) {
file.read_line(entity_dim, entity_tag, element_type,
num_elements_in_block);
} else {
file.read_line(entity_tag, entity_dim, element_type,
num_elements_in_block);
}
/// get the connectivity vector depending on the element type
auto && akantu_type =
this->_msh_to_akantu_element_types[(MSHElementType)element_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind " << element_type
<< " at line "
<< file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
Vector<UInt> local_connect(connectivity.getNbComponent());
auto && read_order = this->_read_order[akantu_type];
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.resize(data0.size() + num_elements_in_block, 0);
auto range = file.entity_tag_to_physical_tags.equal_range(
std::make_pair(entity_tag, entity_dim));
auto & physical_data = file.mesh_accessor.template getData<std::string>(
"physical_names", akantu_type);
physical_data.resize(physical_data.size() + num_elements_in_block, "");
for (auto _ [[gnu::unused]] : arange(num_elements_in_block)) {
auto && sstr_elem = file.get_line();
size_t elem_tag;
sstr_elem >> elem_tag;
for (auto && c : arange(connectivity.getNbComponent())) {
size_t node_tag;
sstr_elem >> node_tag;
AKANTU_DEBUG_ASSERT(node_tag >= file.first_node_number,
"Node number not in range : line "
<< file.current_line);
AKANTU_DEBUG_ASSERT(node_tag <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
node_tag = file.node_tags[node_tag];
local_connect(read_order[c]) = node_tag;
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[elem_tag] = elem;
bool first = true;
for (auto it = range.first; it != range.second; ++it) {
auto phys_it = this->physical_names.find(it->second);
if (first) {
data0(elem.element) =
it->second; // for compatibility with version 2
if (phys_it != this->physical_names.end()) {
physical_data(elem.element) = phys_it->second;
}
first = false;
}
if (phys_it != this->physical_names.end()) {
file.mesh.getElementGroup(phys_it->second).add(elem, true, false);
}
}
}
}
for (auto && element_group : file.mesh.iterateElementGroups()) {
element_group.getNodeGroup().optimize();
}
};
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
File file(filename, mesh);
std::map<std::string, std::function<void(const std::string &)>> readers;
readers["$MeshFormat"] = [&](const std::string & /*unused*/) {
auto && sstr = file.get_line();
double version;
int format;
sstr >> version >> format;
int major = std::trunc(version);
int minor = std::round(10 * (version - major));
file.version = major * 1000 + minor;
if (format != 0) {
AKANTU_ERROR("This reader can only read ASCII files.");
}
if (file.version > 2000) {
sstr >> file.size_of_size_t;
if (file.size_of_size_t > int(sizeof(UInt))) {
AKANTU_DEBUG_INFO("The size of the indexes in akantu might be to small "
"to read this file (akantu "
<< sizeof(UInt) << " vs. msh file "
<< file.size_of_size_t << ")");
}
}
if (file.version < 4000) {
this->populateReaders2(file, readers);
} else {
this->populateReaders4(file, readers);
}
};
auto && read_data = [&](auto && entity_tags, auto && get_data,
auto && read_data) {
auto read_data_tags = [&](auto x) {
UInt number_of_tags{0};
file.read_line(number_of_tags);
std::vector<decltype(x)> tags(number_of_tags);
for (auto && tag : tags) {
file.read_line(tag);
}
return tags;
};
auto && string_tags = read_data_tags(std::string{});
auto && real_tags [[gnu::unused]] = read_data_tags(double{});
auto && int_tags = read_data_tags(int{});
for (auto & s : string_tags) {
s = trim(s, '"');
}
auto id = string_tags[0];
auto size = int_tags[2];
auto nb_component = int_tags[1];
auto & data = get_data(id, size, nb_component);
for (auto n [[gnu::unused]] : arange(size)) {
auto && sstr = file.get_line();
size_t tag;
sstr >> tag;
const auto & entity = entity_tags[tag];
read_data(entity, sstr, data, nb_component);
}
};
readers["$NodeData"] = [&](const std::string & /*unused*/) {
/* $NodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
nodeTag(size_t) value(double) ...
...
$EndNodeData */
read_data(
file.node_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component [[gnu::unused]]) -> Array<double> & {
auto & data =
file.mesh.template getNodalData<double>(id, nb_component);
data.resize(size);
return data;
},
[&](auto && node, auto && sstr, auto && data,
auto && nb_component [[gnu::unused]]) {
for (auto c : arange(nb_component)) {
sstr >> data(node, c);
}
});
};
readers["$ElementData"] = [&](const std::string & /*unused*/) {
/* $ElementData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
return file.mesh.template getElementalData<double>(id);
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type), nb_component,
element.type, element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
readers["$ElementNodeData"] = [&](const std::string & /*unused*/) {
/* $ElementNodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementNodeData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
auto & data = file.mesh.template getElementalData<double>(id);
data.isNodal(true);
return data;
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
int nb_nodes_per_element;
sstr >> nb_nodes_per_element;
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type),
nb_component * nb_nodes_per_element, element.type,
element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
readers["$PhysicalNames"] = [&](const std::string & /*unused*/) {
file.has_physical_names = true;
int num_of_phys_names;
file.read_line(num_of_phys_names); /// the format line
for (auto k [[gnu::unused]] : arange(num_of_phys_names)) {
int phys_name_id;
int phys_dim;
std::string phys_name;
file.read_line(phys_dim, phys_name_id, std::quoted(phys_name));
this->physical_names[phys_name_id] = phys_name;
}
};
readers["Unsupported"] = [&](const std::string & _block) {
std::string block = _block.substr(1);
AKANTU_DEBUG_WARNING("Unsupported block_kind " << block << " at line "
<< file.current_line);
auto && end_block = "$End" + block;
while (file.line != end_block) {
file.get_line();
}
};
while (file.good()) {
std::string block;
file.read_line(block);
auto && it = readers.find(block);
if (it != readers.end()) {
it->second(block);
std::string end_block;
file.read_line(end_block);
block = block.substr(1);
if (end_block != "$End" + block) {
AKANTU_EXCEPTION("The reader failed to properly read the block "
<< block << ". Expected a $End" << block << " at line "
<< file.current_line);
}
} else if (not block.empty()) {
readers["Unsupported"](block);
}
}
// mesh.updateTypesOffsets(_not_ghost);
if (file.version < 4000) {
this->constructPhysicalNames("tag_0", mesh);
if (file.has_physical_names) {
mesh.createGroupsFromMeshData<std::string>("physical_names");
}
}
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat"
<< "\n";
outfile << "2.2 0 8"
<< "\n";
outfile << "$EndMeshFormat"
<< "\n";
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes"
<< "\n";
outfile << nodes.size() << "\n";
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 << "\n";
;
}
outfile << std::nouppercase;
outfile << "$EndNodes"
<< "\n";
outfile << "$Elements"
<< "\n";
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 << "\n";
std::map<Element, size_t> element_to_msh_element;
UInt element_idx = 1;
auto element = ElementNull;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
element.type = type;
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 (auto && data :
enumerate(make_view(connectivity, connectivity.getNbComponent()))) {
element.element = std::get<0>(data);
const auto & conn = std::get<1>(data);
element_to_msh_element.insert(std::make_pair(element, element_idx));
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] != nullptr) {
outfile << " " << tag[t][element.element];
} else {
outfile << " 0";
}
}
for (auto && c : conn) {
outfile << " " << c + 1;
}
outfile << "\n";
element_idx++;
}
}
outfile << "$EndElements"
<< "\n";
if (mesh.hasData(MeshDataType::_nodal)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto type = mesh.getTypeCode(tag, MeshDataType::_nodal);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
auto && data = mesh.getNodalData<double>(tag);
outfile << "$NodeData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << data.getNbComponent() << "\n";
outfile << data.size() << "\n";
for (auto && d : enumerate(make_view(data, data.getNbComponent()))) {
outfile << std::get<0>(d) + 1;
for (auto && v : std::get<1>(d)) {
outfile << " " << v;
}
outfile << "\n";
}
outfile << "$EndNodeData"
<< "\n";
}
}
if (mesh.hasData(MeshDataType::_elemental)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto && data = mesh.getElementalData<double>(tag);
auto type = mesh.getTypeCode(tag, MeshDataType::_elemental);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
if (data.isNodal()) {
continue;
}
auto size = data.size();
if (size == 0) {
continue;
}
auto && nb_components = data.getNbComponents();
auto nb_component = nb_components(*(data.elementTypes().begin()));
outfile << "$ElementData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << nb_component << "\n";
outfile << size << "\n";
Element element;
for (auto type : data.elementTypes()) {
element.type = type;
for (auto && _ :
enumerate(make_view(data(type), nb_components(type)))) {
element.element = std::get<0>(_);
outfile << element_to_msh_element[element];
for (auto && v : std::get<1>(_)) {
outfile << " " << v;
}
outfile << "\n";
}
}
outfile << "$EndElementData"
<< "\n";
}
}
outfile.close();
}
/* --------------------------------------------------------------------------
*/
} // namespace akantu

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