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aka_common.hh
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			/**
			* @file aka_common.hh
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Mon Jun 14 2010
			* @date last modification: Mon Feb 12 2018
			*
			* @brief common type descriptions for akantu
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2018 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/>.
			*
			* @section DESCRIPTION
			*
			* All common things to be included in the projects files
			*
			*/

			/* -------------------------------------------------------------------------- */

			#ifndef __AKANTU_COMMON_HH__
			#define __AKANTU_COMMON_HH__

			#include "aka_compatibilty_with_cpp_standard.hh"

			/* -------------------------------------------------------------------------- */
			#define __BEGIN_AKANTU_DUMPER__ namespace dumper {
			#define __END_AKANTU_DUMPER__ }
			/* -------------------------------------------------------------------------- */
			#if defined(WIN32)
			#define __attribute__(x)
			#endif

			/* -------------------------------------------------------------------------- */
			#include "aka_config.hh"
			#include "aka_error.hh"
			#include "aka_safe_enum.hh"
			/* -------------------------------------------------------------------------- */
			#include <boost/preprocessor.hpp>
			#include <limits>
			#include <list>
			#include <string>
			#include <type_traits>
			#include <unordered_map>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			/* Common types */
			/* -------------------------------------------------------------------------- */
			using ID = std::string;

			#ifdef AKANTU_NDEBUG
			static const Real REAL_INIT_VALUE = Real(0.);
			#else
			static const Real REAL_INIT_VALUE = std::numeric_limits<Real>::quiet_NaN();
			#endif

			/* -------------------------------------------------------------------------- */
			/* Memory types */
			/* -------------------------------------------------------------------------- */

			using MemoryID = UInt;

			// using Surface = std::string;
			// using SurfacePair= std::pair<Surface, Surface>;
			// using SurfacePairList = std::list<SurfacePair>;

			/* -------------------------------------------------------------------------- */
			extern const UInt _all_dimensions;

			#define AKANTU_PP_ENUM(s, data, i, elem) \
			BOOST_PP_TUPLE_REM() \
			elem BOOST_PP_COMMA_IF(BOOST_PP_NOT_EQUAL(i, BOOST_PP_DEC(data)))
			} // namespace akantu

			#if (defined(__GNUC__) \|\| defined(__GNUG__))
			#define AKA_GCC_VERSION \
			(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
			#if AKA_GCC_VERSION < 60000
			#define AKANTU_ENUM_HASH(type_name) \
			namespace std { \
			template <> struct hash<::akantu::type_name> { \
			using argument_type = ::akantu::type_name; \
			size_t operator()(const argument_type & e) const noexcept { \
			auto ue = underlying_type_t<argument_type>(e); \
			return uh(ue); \
			} \
			\
			private: \
			const hash<underlying_type_t<argument_type>> uh{}; \
			}; \
			}
			#else
			#define AKANTU_ENUM_HASH(type_name)
			#endif // AKA_GCC_VERSION
			#endif // GNU

			#include "aka_element_classes_info.hh"

			namespace akantu {

			#define AKANTU_PP_CAT(s, data, elem) BOOST_PP_CAT(data, elem)

			#define AKANTU_PP_TYPE_TO_STR(s, data, elem) \
			({BOOST_PP_CAT(data::_, elem), BOOST_PP_STRINGIZE(elem)})

			#define AKANTU_PP_STR_TO_TYPE(s, data, elem) \
			({BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(data::_, elem)})

			#define AKANTU_ENUM_DECLARE(type_name, list) \
			enum class type_name { \
			BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_CAT, _, list)) \
			};

			#define AKANTU_ENUM_OUTPUT_STREAM(type_name, list) \
			} \
			AKANTU_ENUM_HASH(type_name) \
			namespace aka { \
			inline std::string to_string(const ::akantu::type_name & type) { \
			static std::unordered_map<::akantu::type_name, std::string> convert{ \
			BOOST_PP_SEQ_FOR_EACH_I( \
			AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
			BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_TYPE_TO_STR, \
			::akantu::type_name, list))}; \
			return convert.at(type); \
			} \
			} \
			namespace akantu { \
			inline std::ostream & operator<<(std::ostream & stream, \
			const type_name & type) { \
			stream << aka::to_string(type); \
			return stream; \
			}

			#define AKANTU_ENUM_INPUT_STREAM(type_name, list) \
			inline std::istream & operator>>(std::istream & stream, type_name & type) { \
			std::string str; \
			stream >> str; \
			static std::unordered_map<std::string, type_name> convert{ \
			BOOST_PP_SEQ_FOR_EACH_I( \
			AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
			BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_TYPE, type_name, list))}; \
			type = convert.at(str); \
			return stream; \
			}

			/* -------------------------------------------------------------------------- */
			/* Mesh/FEM/Model types */
			/* -------------------------------------------------------------------------- */

			/// small help to use names for directions
			enum SpatialDirection { _x = 0, _y = 1, _z = 2 };

			/// enum MeshIOType type of mesh reader/writer
			enum MeshIOType {
			_miot_auto, ///< Auto guess of the reader to use based on the extension
			_miot_gmsh, ///< Gmsh files
			_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has
			/// structures elements
			_miot_diana, ///< TNO Diana mesh format
			_miot_abaqus ///< Abaqus mesh format
			};

			/// enum MeshEventHandlerPriority defines relative order of execution of events
			enum EventHandlerPriority {
			_ehp_highest = 0,
			_ehp_mesh = 5,
			_ehp_fe_engine = 9,
			_ehp_synchronizer = 10,
			_ehp_dof_manager = 20,
			_ehp_model = 94,
			_ehp_non_local_manager = 100,
			_ehp_lowest = 100
			};

			#ifndef SWIG
			// clang-format off
			#define AKANTU_MODEL_TYPES \
			(model) \
			(solid_mechanics_model) \
			(solid_mechanics_model_cohesive) \
			(heat_transfer_model) \
			(structural_mechanics_model) \
			(embedded_model) \
			(contact_mechanics_model)
			// clang-format on

			/// enum ModelType defines which type of physics is solved
			AKANTU_ENUM_DECLARE(ModelType, AKANTU_MODEL_TYPES)
			AKANTU_ENUM_OUTPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
			AKANTU_ENUM_INPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
			#else
			enum class ModelType {
			_model,
			_solid_mechanics_model,
			_solid_mechanics_model_cohesive,
			_heat_transfer_model,
			_structural_mechanics_model,
			_embedded_model,
			_contact_mechanics_model
			};
			#endif

			/// enum AnalysisMethod type of solving method used to solve the equation of
			/// motion
			enum AnalysisMethod {
			_static = 0,
			_implicit_dynamic = 1,
			_explicit_lumped_mass = 2,
			_explicit_lumped_capacity = 2,
			_explicit_consistent_mass = 3,
			_explicit_contact = 4,
			_implicit_contact = 5
			};

			/// enum DOFSupportType defines which kind of dof that can exists
			enum DOFSupportType { _dst_nodal, _dst_generic };

			/// Type of non linear resolution available in akantu
			enum NonLinearSolverType {
			_nls_linear, ///< No non linear convergence loop
			_nls_newton_raphson, ///< Regular Newton-Raphson
			_nls_newton_raphson_modified, ///< Newton-Raphson with initial tangent
			_nls_lumped, ///< Case of lumped mass or equivalent matrix
			_nls_auto ///< This will take a default value that make sense in case of
			/// model::getNewSolver
			};

			/// Type of time stepping solver
			enum TimeStepSolverType {
			_tsst_static, ///< Static solution
			_tsst_dynamic, ///< Dynamic solver
			_tsst_dynamic_lumped, ///< Dynamic solver with lumped mass
			_tsst_not_defined, ///< For not defined cases
			};

			/// Type of integration scheme
			enum IntegrationSchemeType {
			_ist_pseudo_time, ///< Pseudo Time
			_ist_forward_euler, ///< GeneralizedTrapezoidal(0)
			_ist_trapezoidal_rule_1, ///< GeneralizedTrapezoidal(1/2)
			_ist_backward_euler, ///< GeneralizedTrapezoidal(1)
			_ist_central_difference, ///< NewmarkBeta(0, 1/2)
			_ist_fox_goodwin, ///< NewmarkBeta(1/6, 1/2)
			_ist_trapezoidal_rule_2, ///< NewmarkBeta(1/2, 1/2)
			_ist_linear_acceleration, ///< NewmarkBeta(1/3, 1/2)
			_ist_newmark_beta, ///< generic NewmarkBeta with user defined
			/// alpha and beta
			_ist_generalized_trapezoidal ///< generic GeneralizedTrapezoidal with user
			/// defined alpha
			};

			/// enum SolveConvergenceCriteria different convergence criteria
			enum SolveConvergenceCriteria {
			_scc_residual, ///< Use residual to test the convergence
			_scc_solution, ///< Use solution to test the convergence
			_scc_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to testb
			};

			/// enum CohesiveMethod type of insertion of cohesive elements
			enum CohesiveMethod { _intrinsic, _extrinsic };

			/// @enum SparseMatrixType type of sparse matrix used
			enum MatrixType { _unsymmetric, _symmetric, _mt_not_defined };

			/* -------------------------------------------------------------------------- */
			/* Ghosts handling */
			/* -------------------------------------------------------------------------- */
			/// @enum CommunicatorType type of communication method to use
			enum CommunicatorType { _communicator_mpi, _communicator_dummy };

			/// @enum SynchronizationTag type of synchronizations
			enum SynchronizationTag {
			//--- Generic tags ---
			_gst_whatever,
			_gst_update,
			_gst_ask_nodes,
			_gst_size,

			//--- SolidMechanicsModel tags ---
			_gst_smm_mass, ///< synchronization of the SolidMechanicsModel.mass
			_gst_smm_for_gradu, ///< synchronization of the
			/// SolidMechanicsModel.displacement
			_gst_smm_boundary, ///< synchronization of the boundary, forces, velocities
			/// and displacement
			_gst_smm_uv, ///< synchronization of the nodal velocities and displacement
			_gst_smm_res, ///< synchronization of the nodal residual
			_gst_smm_init_mat, ///< synchronization of the data to initialize materials
			_gst_smm_stress, ///< synchronization of the stresses to compute the internal
			/// forces
			_gst_smmc_facets, ///< synchronization of facet data to setup facet synch
			_gst_smmc_facets_conn, ///< synchronization of facet global connectivity
			_gst_smmc_facets_stress, ///< synchronization of facets' stress to setup facet
			/// synch
			_gst_smmc_damage, ///< synchronization of damage

			// --- GlobalIdsUpdater tags ---
			_gst_giu_global_conn, ///< synchronization of global connectivities

			// --- CohesiveElementInserter tags ---
			_gst_ce_groups, ///< synchronization of cohesive element insertion depending
			/// on facet groups

			// --- GroupManager tags ---
			_gst_gm_clusters, ///< synchronization of clusters

			// --- HeatTransfer tags ---
			_gst_htm_temperature, ///< synchronization of the nodal temperature
			_gst_htm_gradient_temperature, ///< synchronization of the element gradient
			/// temperature
			// --- LevelSet tags ---
			_gst_htm_phi, ///< synchronization of the nodal level set value phi
			_gst_htm_gradient_phi, ///< synchronization of the element gradient phi

			//--- Material non local ---
			_gst_mnl_for_average, ///< synchronization of data to average in non local
			/// material
			_gst_mnl_weight, ///< synchronization of data for the weight computations

			// --- NeighborhoodSynchronization tags ---
			_gst_nh_criterion,

			// --- General tags ---
			_gst_test, ///< Test tag
			_gst_user_1, ///< tag for user simulations
			_gst_user_2, ///< tag for user simulations
			_gst_material_id, ///< synchronization of the material ids
			_gst_for_dump, ///< everything that needs to be synch before dump

			// --- Contact & Friction ---
			_gst_cf_nodal, ///< synchronization of disp, velo, and current position
			_gst_cf_incr, ///< synchronization of increment

			// --- Solver tags ---
			_gst_solver_solution ///< synchronization of the solution obained with the
			/// PETSc solver
			};

			/// standard output stream operator for SynchronizationTag
			inline std::ostream & operator<<(std::ostream & stream,
			SynchronizationTag type);

			/// @enum GhostType type of ghost
			enum GhostType {
			_not_ghost = 0,
			_ghost = 1,
			_casper // not used but a real cute ghost
			};

			/// @enum ContactElementType type of contact element
			enum class ContactElementType {
			_node_to_node,
			_node_to_segment
			};

			/// @enum ContactDetectorType type of contact detection
			enum class ContactDetectorType {
			extrinsic,
			intrinsic
			};


			/// Define the flag that can be set to a node
			enum class NodeFlag : std::uint8_t {
			_normal = 0x00,
			_distributed = 0x01,
			_master = 0x03,
			_slave = 0x05,
			_pure_ghost = 0x09,
			_shared_mask = 0x0F,
			_periodic = 0x10,
			_periodic_master = 0x30,
			_periodic_slave = 0x50,
			_periodic_mask = 0xF0,
			_local_master_mask = 0xCC, // ~(_master & _periodic_mask)
			};

			inline NodeFlag operator&(const NodeFlag & a, const NodeFlag & b) {
			using under = std::underlying_type_t<NodeFlag>;
			return NodeFlag(under(a) & under(b));
			}

			inline NodeFlag operator\|(const NodeFlag & a, const NodeFlag & b) {
			using under = std::underlying_type_t<NodeFlag>;
			return NodeFlag(under(a) \| under(b));
			}

			inline NodeFlag & operator\|=(NodeFlag & a, const NodeFlag & b) {
			a = a \| b;
			return a;
			}

			inline NodeFlag & operator&=(NodeFlag & a, const NodeFlag & b) {
			a = a & b;
			return a;
			}

			inline NodeFlag operator~(const NodeFlag & a) {
			using under = std::underlying_type_t<NodeFlag>;
			return NodeFlag(~under(a));
			}

			inline std::ostream & operator<<(std::ostream & stream, const NodeFlag & flag) {
			using under = std::underlying_type_t<NodeFlag>;
			stream << under(flag);
			return stream;
			}

			} // namespace akantu

			#ifndef SWIG
			AKANTU_ENUM_HASH(GhostType)
			#endif

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			struct GhostType_def {
			using type = GhostType;
			static const type _begin_ = _not_ghost;
			static const type _end_ = _casper;
			};

			using ghost_type_t = safe_enum<GhostType_def>;
			extern ghost_type_t ghost_types;

			/// standard output stream operator for GhostType
			inline std::ostream & operator<<(std::ostream & stream, GhostType type);

			/* -------------------------------------------------------------------------- */
			/* Global defines */
			/* -------------------------------------------------------------------------- */
			#define AKANTU_MIN_ALLOCATION 2000

			#define AKANTU_INDENT " "
			#define AKANTU_INCLUDE_INLINE_IMPL

			/* -------------------------------------------------------------------------- */
			/* Type traits */
			/* -------------------------------------------------------------------------- */
			struct TensorTrait {};
			/* -------------------------------------------------------------------------- */
			template <typename T> using is_tensor = std::is_base_of<TensorTrait, T>;
			/* -------------------------------------------------------------------------- */
			template <typename T> using is_scalar = std::is_arithmetic<T>;
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			#define AKANTU_SET_MACRO(name, variable, type) \
			inline void set##name(type variable) { this->variable = variable; }

			#define AKANTU_GET_MACRO(name, variable, type) \
			inline type get##name() const { return variable; }

			#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
			inline type get##name() { return variable; }

			#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, support, con) \
			inline con Array<type> & get##name( \
			const support & el_type, const GhostType & ghost_type = _not_ghost) \
			con { \
			return variable(el_type, ghost_type); \
			}

			#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
			AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, )
			#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
			AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)

			#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
			AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, )
			#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
			AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)

			/* -------------------------------------------------------------------------- */
			/// initialize the static part of akantu
			void initialize(int & argc, char **& argv);
			/// initialize the static part of akantu and read the global input_file
			void initialize(const std::string & input_file, int & argc, char **& argv);
			/* -------------------------------------------------------------------------- */
			/// finilize correctly akantu and clean the memory
			void finalize();
			/* -------------------------------------------------------------------------- */
			/// Read an new input file
			void readInputFile(const std::string & input_file);
			/* -------------------------------------------------------------------------- */

			/*
			* For intel compiler annoying remark
			*/
			// #if defined(__INTEL_COMPILER)
			// /// remark #981: operands are evaluated in unspecified order
			// #pragma warning(disable : 981)
			// /// remark #383: value copied to temporary, reference to temporary used
			// #pragma warning(disable : 383)
			// #endif // defined(__INTEL_COMPILER)

			/* -------------------------------------------------------------------------- */
			/* string manipulation */
			/* -------------------------------------------------------------------------- */
			inline std::string to_lower(const std::string & str);
			/* -------------------------------------------------------------------------- */
			inline std::string trim(const std::string & to_trim);
			inline std::string trim(const std::string & to_trim, char c);
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			/// give a string representation of the a human readable size in bit
			template <typename T> std::string printMemorySize(UInt size);
			/* -------------------------------------------------------------------------- */

			} // namespace akantu

			#include "aka_fwd.hh"

			namespace akantu {

			/// get access to the internal argument parser
			cppargparse::ArgumentParser & getStaticArgumentParser();

			/// get access to the internal input file parser
			Parser & getStaticParser();

			/// get access to the user part of the internal input file parser
			const ParserSection & getUserParser();

			} // namespace akantu

			#include "aka_common_inline_impl.cc"

			/* -------------------------------------------------------------------------- */

			#if AKANTU_INTEGER_SIZE == 4
			#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b9
			#elif AKANTU_INTEGER_SIZE == 8
			#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b97f4a7c13LL
			#endif

			namespace std {
			/**
			* Hashing function for pairs based on hash_combine from boost The magic number
			* is coming from the golden number @f[\phi = \frac{1 + \sqrt5}{2}@f]
			* @f[\frac{2^32}{\phi} = 0x9e3779b9@f]
			* http://stackoverflow.com/questions/4948780/magic-number-in-boosthash-combine
			* http://burtleburtle.net/bob/hash/doobs.html
			*/
			template <typename a, typename b> struct hash<std::pair<a, b>> {
			hash() = default;
			size_t operator()(const std::pair<a, b> & p) const {
			size_t seed = ah(p.first);
			return bh(p.second) + AKANTU_HASH_COMBINE_MAGIC_NUMBER + (seed << 6) +
			(seed >> 2);
			}

			private:
			const hash<a> ah{};
			const hash<b> bh{};
			};

			} // namespace std

			#endif /* __AKANTU_COMMON_HH__ */

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rAKA/src/common/aka_common.hh
c50dec22606dbugfixes/init…

aka_common.hh
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