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perf-test-akantu/no_abaqus.patch
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no_abaqus.patch
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diff --git a/packages/core.cmake b/packages/core.cmake
index 70e2c03fa..731f926b3 100644
--- a/packages/core.cmake
+++ b/packages/core.cmake
@@ -119,8 +119,6 @@ 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/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index 3e38ff859..f09db88c3 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -151,7 +151,7 @@ public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
- stream << "Rand48Generator [seed=" << seed << "]";
+ stream << "Rand48Generator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index 97694ab27..f3e3f4af4 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -62,7 +62,6 @@ MeshIO * MeshIO::getMeshIO(const std::string & filename, const MeshIOType & type
if(ext == "msh") { 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 <<"). "
<< "Please provide the MeshIOType to the read function");
@@ -74,7 +73,6 @@ MeshIO * MeshIO::getMeshIO(const std::string & filename, const MeshIOType & type
case _miot_gmsh_struct : return new MeshIOMSHStruct();
#endif
case _miot_diana : return new MeshIODiana();
- case _miot_abaqus : return new MeshIOAbaqus();
default:
return NULL;
}
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index 6420037c3..2dc7663d3 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -118,7 +118,6 @@ __END_AKANTU__
#include "mesh_io_msh.hh"
#include "mesh_io_diana.hh"
-#include "mesh_io_abaqus.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
# include "mesh_io_msh_struct.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 7fdb2735a..000000000
--- a/src/io/mesh_io/mesh_io_abaqus.cc
+++ /dev/null
@@ -1,481 +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_io_abaqus.hh"
-#include "mesh.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/qi.hpp>
-#include <boost/spirit/include/phoenix.hpp>
-/* -------------------------------------------------------------------------- */
-
-__BEGIN_AKANTU__
-
-/* -------------------------------------------------------------------------- */
-MeshIOAbaqus::MeshIOAbaqus() {}
-
-/* -------------------------------------------------------------------------- */
-MeshIOAbaqus::~MeshIOAbaqus() {}
-
-/* -------------------------------------------------------------------------- */
-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 (std::vector<Int>::const_iterator it = conn.begin(); it != conn.end(); ++it) {
- std::map<UInt, UInt>::const_iterator 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.getSize());
- 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 (std::vector<Real>::const_iterator 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) {
- std::map<UInt, Element>::const_iterator 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) {
- Mesh::element_group_iterator 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) {
- Mesh::node_group_iterator 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) {
- std::map<UInt, UInt>::const_iterator 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));
-
- typedef std::string::const_iterator iterator_t;
- typedef AbaqusSkipper<iterator_t> skipper;
- 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);
-
- std::vector<std::string>::const_iterator mnit = g.getMaterialNames().begin();
- std::vector<std::string>::const_iterator mnend = g.getMaterialNames().end();
-
- for (; mnit != mnend; ++mnit) {
- Mesh::element_group_iterator eg_it = mesh.element_group_find(*mnit);
- ElementGroup & eg = *eg_it->second;
- if (eg_it != mesh.element_group_end()) {
- ElementGroup::type_iterator tit = eg.firstType();
- ElementGroup::type_iterator tend = eg.lastType();
-
- for (; tit != tend; ++tit) {
- Array<std::string> & abaqus_material =
- this->getData<std::string>(mesh, "abaqus_material", *tit);
-
- ElementGroup::const_element_iterator eit = eg.element_begin(*tit);
- ElementGroup::const_element_iterator eend = eg.element_end(*tit);
- for (; eit != eend; ++eit) {
- abaqus_material(*eit) = *mnit;
- }
- }
- }
- }
-
- this->setNbGlobalNodes(mesh, mesh.getNodes().getSize());
- MeshUtils::fillElementToSubElementsData(mesh);
-}
-
-__END_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 3cd861fec..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__
-
-__BEGIN_AKANTU__
-
-/* -------------------------------------------------------------------------- */
-class MeshIOAbaqus : public MeshIO, private MeshAccessor {
-public:
- MeshIOAbaqus();
- virtual ~MeshIOAbaqus();
-
- /// read a mesh from the file
- virtual void read(const std::string & filename, Mesh & mesh);
-
- /// 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;
-};
-
-__END_AKANTU__
-
-#endif /* __AKANTU_MESH_IO_ABAQUS_HH__ */
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