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perf-test-akantu/no_abaqus_1.patch
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no_abaqus_1.patch
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diff --git a/packages/core.cmake b/packages/core.cmake
index 5cba49858..ce40de373 100644
--- a/packages/core.cmake
+++ b/packages/core.cmake
@@ -136,8 +136,6 @@ package_declare_sources(core
io/mesh_io.cc
io/mesh_io.hh
- io/mesh_io/mesh_io_abaqus.cc
- io/mesh_io/mesh_io_abaqus.hh
io/mesh_io/mesh_io_diana.cc
io/mesh_io/mesh_io_diana.hh
io/mesh_io/mesh_io_msh.cc
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index cdc56a716..1954973c6 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -62,8 +62,6 @@ std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
- } else if (ext == "inp") {
- t = _miot_abaqus;
} else
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
@@ -79,8 +77,6 @@ std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
#endif
case _miot_diana:
return std::make_unique<MeshIODiana>();
- case _miot_abaqus:
- return std::make_unique<MeshIOAbaqus>();
default:
return nullptr;
}
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index 5e4860613..cff5e88ee 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -107,7 +107,6 @@ inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
} // namespace akantu
-#include "mesh_io_abaqus.hh"
#include "mesh_io_diana.hh"
#include "mesh_io_msh.hh"
diff --git a/src/io/mesh_io/mesh_io_abaqus.cc b/src/io/mesh_io/mesh_io_abaqus.cc
deleted file mode 100644
index 658ba77f7..000000000
--- a/src/io/mesh_io/mesh_io_abaqus.cc
+++ /dev/null
@@ -1,475 +0,0 @@
-/**
- * @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: Fri Dec 11 2015
- *
- * @brief read a mesh from an abaqus input file
- *
- * @section LICENSE
- *
- * Copyright (©) 2014, 2015 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_DEBUG_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>;
- typedef AbaqusMeshGrammar<iterator_t, skipper> grammar;
-
- 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
diff --git a/src/io/mesh_io/mesh_io_abaqus.hh b/src/io/mesh_io/mesh_io_abaqus.hh
deleted file mode 100644
index 0f6beec0a..000000000
--- a/src/io/mesh_io/mesh_io_abaqus.hh
+++ /dev/null
@@ -1,60 +0,0 @@
-/**
- * @file mesh_io_abaqus.hh
- *
- * @author Nicolas Richart <nicolas.richart@epfl.ch>
- *
- * @date creation: Sun Sep 26 2010
- * @date last modification: Tue Jun 30 2015
- *
- * @brief read a mesh from an abaqus input file
- *
- * @section LICENSE
- *
- * Copyright (©) 2010-2012, 2014, 2015 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 "mesh_io.hh"
-#include "mesh_accessor.hh"
-
-#ifndef __AKANTU_MESH_IO_ABAQUS_HH__
-#define __AKANTU_MESH_IO_ABAQUS_HH__
-
-namespace akantu {
-
-/* -------------------------------------------------------------------------- */
-class MeshIOAbaqus : public MeshIO {
-public:
- MeshIOAbaqus();
- ~MeshIOAbaqus() override;
-
- /// read a mesh from the file
- void read(const std::string & filename, Mesh & mesh) override;
-
- /// write a mesh to a file
- // virtual void write(const std::string & filename, const Mesh & mesh);
-
-private:
- /// correspondence between msh element types and akantu element types
- std::map<std::string, ElementType> _abaqus_to_akantu_element_types;
-};
-
-} // akantu
-
-#endif /* __AKANTU_MESH_IO_ABAQUS_HH__ */
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