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mesh_io_abaqus.cc
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/**
* @file mesh_io_abaqus.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Tue Feb 20 2018
*
* @brief read a mesh from an abaqus input file
*
* @section LICENSE
*
* Copyright (©) 2014-2018 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/>.
*
*/
/* -------------------------------------------------------------------------- */
// std library header files
#include <fstream>
// akantu header files
#include "mesh.hh"
#include "mesh_io_abaqus.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
#include "node_group.hh"
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/spirit/include/qi.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::MeshIOAbaqus() = default;
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::~MeshIOAbaqus() = default;
/* -------------------------------------------------------------------------- */
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace ascii = boost::spirit::ascii;
namespace lbs = boost::spirit::qi::labels;
namespace phx = boost::phoenix;
/* -------------------------------------------------------------------------- */
void element_read(Mesh & mesh, const ElementType & type, UInt id,
const std::vector<Int> & conn,
const std::map<UInt, UInt> & nodes_mapping,
std::map<UInt, Element> & elements_mapping) {
Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(type));
AKANTU_DEBUG_ASSERT(conn.size() == tmp_conn.size(),
"The nodes in the Abaqus file have too many coordinates"
<< " for the mesh you try to fill.");
mesh.addConnectivityType(type);
Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt i = 0;
for (auto it = conn.begin(); it != conn.end(); ++it) {
auto nit = nodes_mapping.find(*it);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the connectivity.");
tmp_conn[i++] = nit->second;
}
Element el{type, connectivity.size(), _not_ghost};
elements_mapping[id] = el;
connectivity.push_back(tmp_conn);
}
void node_read(Mesh & mesh, UInt id, const std::vector<Real> & pos,
std::map<UInt, UInt> & nodes_mapping) {
Vector<Real> tmp_pos(mesh.getSpatialDimension());
UInt i = 0;
for (auto it = pos.begin(); it != pos.end() || i < mesh.getSpatialDimension();
++it)
tmp_pos[i++] = *it;
nodes_mapping[id] = mesh.getNbNodes();
mesh.getNodes().push_back(tmp_pos);
}
/* ------------------------------------------------------------------------ */
void add_element_to_group(ElementGroup * el_grp, UInt element,
const std::map<UInt, Element> & elements_mapping) {
auto eit = elements_mapping.find(element);
AKANTU_DEBUG_ASSERT(eit != elements_mapping.end(),
"There is an unknown element ("
<< element << ") in the in the ELSET "
<< el_grp->getName() << ".");
el_grp->add(eit->second, true, false);
}
ElementGroup * element_group_create(Mesh & mesh, const ID & name) {
auto eg_it = mesh.element_group_find(name);
if (eg_it != mesh.element_group_end()) {
return eg_it->second;
} else {
return &mesh.createElementGroup(name, _all_dimensions);
}
}
NodeGroup * node_group_create(Mesh & mesh, const ID & name) {
auto ng_it = mesh.node_group_find(name);
if (ng_it != mesh.node_group_end()) {
return ng_it->second;
} else {
return &mesh.createNodeGroup(name, mesh.getSpatialDimension());
}
}
void add_node_to_group(NodeGroup * node_grp, UInt node,
const std::map<UInt, UInt> & nodes_mapping) {
auto nit = nodes_mapping.find(node);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the in the NSET "
<< node_grp->getName() << ".");
node_grp->add(nit->second, false);
}
void optimize_group(NodeGroup * grp) { grp->optimize(); }
void optimize_element_group(ElementGroup * grp) { grp->optimize(); }
/* -------------------------------------------------------------------------- */
template <class Iterator> struct AbaqusSkipper : qi::grammar<Iterator> {
AbaqusSkipper() : AbaqusSkipper::base_type(skip, "abaqus_skipper") {
/* clang-format off */
skip
= (ascii::space - spirit::eol)
| "**" >> *(qi::char_ - spirit::eol) >> spirit::eol
;
/* clang-format on */
}
qi::rule<Iterator> skip;
};
/* -------------------------------------------------------------------------- */
template <class Iterator, typename Skipper = AbaqusSkipper<Iterator>>
struct AbaqusMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
public:
AbaqusMeshGrammar(Mesh & mesh)
: AbaqusMeshGrammar::base_type(start, "abaqus_mesh_reader"), mesh(mesh) {
/* clang-format off */
start
= *(
(qi::char_('*')
> ( (qi::no_case[ qi::lit("node output") ] > any_section)
| (qi::no_case[ qi::lit("element output") ] > any_section)
| (qi::no_case[ qi::lit("node") ] > nodes)
| (qi::no_case[ qi::lit("element") ] > elements)
| (qi::no_case[ qi::lit("heading") ] > header)
| (qi::no_case[ qi::lit("elset") ] > elements_set)
| (qi::no_case[ qi::lit("nset") ] > nodes_set)
| (qi::no_case[ qi::lit("material") ] > material)
| (keyword > any_section)
)
)
| spirit::eol
)
;
header
= spirit::eol
> *any_line
;
nodes
= *(qi::char_(',') >> option)
>> spirit::eol
>> *( (qi::int_
> node_position) [ phx::bind(&node_read,
phx::ref(mesh),
lbs::_1,
lbs::_2,
phx::ref(abaqus_nodes_to_akantu)) ]
>> spirit::eol
)
;
elements
= (
( qi::char_(',') >> qi::no_case[qi::lit("type")] >> '='
>> abaqus_element_type [ lbs::_a = lbs::_1 ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> *( (qi::int_
> connectivity) [ phx::bind(&element_read,
phx::ref(mesh),
lbs::_a,
lbs::_1,
lbs::_2,
phx::cref(abaqus_nodes_to_akantu),
phx::ref(abaqus_elements_to_akantu)) ]
>> spirit::eol
)
;
elements_set
= (
(
( qi::char_(',') >> qi::no_case[ qi::lit("elset") ] >> '='
>> value [ lbs::_a = phx::bind<ElementGroup *>(&element_group_create,
phx::ref(mesh),
lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_element_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_elements_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_element_group, lbs::_a) ]
;
nodes_set
= (
(
( qi::char_(',')
>> qi::no_case[ qi::lit("nset") ] >> '='
>> value [ lbs::_a = phx::bind<NodeGroup *>(&node_group_create, phx::ref(mesh), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_node_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_nodes_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_group, lbs::_a) ]
;
material
= (
( qi::char_(',') >> qi::no_case[ qi::lit("name") ] >> '='
>> value [ phx::push_back(phx::ref(material_names), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
) >> spirit::eol;
;
node_position
= +(qi::char_(',') > real [ phx::push_back(lbs::_val, lbs::_1) ])
;
connectivity
= +(qi::char_(',') > qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ])
;
any_section
= *(qi::char_(',') >> option) > spirit::eol
> *any_line
;
any_line
= *(qi::char_ - spirit::eol - qi::char_('*')) >> spirit::eol
;
keyword
= qi::lexeme[ +(qi::char_ - (qi::char_('*') | spirit::eol)) ]
;
option
= key > -( '=' >> value );
key
= qi::char_("a-zA-Z_") >> *(qi::char_("a-zA-Z_0-9") | qi::char_('-'))
;
value
= key.alias()
;
BOOST_SPIRIT_DEBUG_NODE(start);
abaqus_element_type.add
#if defined(AKANTU_STRUCTURAL_MECHANICS)
("BE21" , _bernoulli_beam_2)
("BE31" , _bernoulli_beam_3)
#endif
("T3D2" , _segment_2) // Gmsh generates this elements
("T3D3" , _segment_3) // Gmsh generates this elements
("CPE3" , _triangle_3)
("CPS3" , _triangle_3)
("DC2D3" , _triangle_3)
("CPE6" , _triangle_6)
("CPS6" , _triangle_6)
("DC2D6" , _triangle_6)
("CPE4" , _quadrangle_4)
("CPS4" , _quadrangle_4)
("DC2D4" , _quadrangle_4)
("CPE8" , _quadrangle_8)
("CPS8" , _quadrangle_8)
("DC2D8" , _quadrangle_8)
("C3D4" , _tetrahedron_4)
("DC3D4" , _tetrahedron_4)
("C3D8" , _hexahedron_8)
("C3D8R" , _hexahedron_8)
("DC3D8" , _hexahedron_8)
("C3D10" , _tetrahedron_10)
("DC3D10", _tetrahedron_10);
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start .name("abaqus-start-rule");
connectivity .name("abaqus-connectivity");
node_position .name("abaqus-nodes-position");
nodes .name("abaqus-nodes");
any_section .name("abaqus-any_section");
header .name("abaqus-header");
material .name("abaqus-material");
elements .name("abaqus-elements");
elements_set .name("abaqus-elements-set");
nodes_set .name("abaqus-nodes-set");
key .name("abaqus-key");
value .name("abaqus-value");
option .name("abaqus-option");
keyword .name("abaqus-keyword");
any_line .name("abaqus-any-line");
abaqus_element_type.name("abaqus-element-type");
/* clang-format on */
}
public:
AKANTU_GET_MACRO(MaterialNames, material_names,
const std::vector<std::string> &);
/* ------------------------------------------------------------------------ */
/* Rules */
/* ------------------------------------------------------------------------ */
private:
qi::rule<Iterator, void(), Skipper> start;
qi::rule<Iterator, std::vector<int>(), Skipper> connectivity;
qi::rule<Iterator, std::vector<Real>(), Skipper> node_position;
qi::rule<Iterator, void(), Skipper> nodes, any_section, header, material;
qi::rule<Iterator, void(), qi::locals<ElementType>, Skipper> elements;
qi::rule<Iterator, void(), qi::locals<ElementGroup *>, Skipper> elements_set;
qi::rule<Iterator, void(), qi::locals<NodeGroup *>, Skipper> nodes_set;
qi::rule<Iterator, std::string(), Skipper> key, value, option, keyword,
any_line;
qi::real_parser<Real, qi::real_policies<Real>> real;
qi::symbols<char, ElementType> abaqus_element_type;
/* ------------------------------------------------------------------------ */
/* Mambers */
/* ------------------------------------------------------------------------ */
private:
/// reference to the mesh to read
Mesh & mesh;
/// correspondance between the numbering of nodes in the abaqus file and in
/// the akantu mesh
std::map<UInt, UInt> abaqus_nodes_to_akantu;
/// correspondance between the element number in the abaqus file and the
/// Element in the akantu mesh
std::map<UInt, Element> abaqus_elements_to_akantu;
/// list of the material names
std::vector<std::string> material_names;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void MeshIOAbaqus::read(const std::string & filename, Mesh & mesh) {
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
std::ifstream infile;
infile.open(filename.c_str());
if (!infile.good()) {
AKANTU_ERROR("Cannot open file " << filename);
}
std::string storage; // We will read the contents here.
infile.unsetf(std::ios::skipws); // No white space skipping!
std::copy(std::istream_iterator<char>(infile), std::istream_iterator<char>(),
std::back_inserter(storage));
using iterator_t = std::string::const_iterator;
using skipper = AbaqusSkipper<iterator_t>;
using grammar = AbaqusMeshGrammar<iterator_t, skipper>;
grammar g(mesh);
skipper ws;
iterator_t iter = storage.begin();
iterator_t end = storage.end();
qi::phrase_parse(iter, end, g, ws);
MeshAccessor mesh_accessor(mesh);
for (auto & mat_name : g.getMaterialNames()) {
auto eg_it = mesh.element_group_find(mat_name);
auto & eg = *eg_it->second;
if (eg_it != mesh.element_group_end()) {
for (auto & type : eg.elementTypes()) {
Array<std::string> & abaqus_material =
mesh_accessor.getData<std::string>("abaqus_material", type);
for (auto elem : eg.getElements(type)) {
abaqus_material(elem) = mat_name;
}
}
}
}
mesh_accessor.setNbGlobalNodes(mesh.getNodes().size());
MeshUtils::fillElementToSubElementsData(mesh);
}
} // namespace akantu

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