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dof_manager.hh
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			/**
			* @file dof_manager.hh
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Tue Aug 18 2015
			* @date last modification: Fri Jul 24 2020
			*
			* @brief Class handling the different types of dofs
			*
			*
			* @section LICENSE
			*
			* Copyright (©) 2015-2021 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/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "aka_factory.hh"
			#include "mesh.hh"
			/* -------------------------------------------------------------------------- */
			#include <map>
			#include <set>
			/* -------------------------------------------------------------------------- */

			#ifndef AKANTU_DOF_MANAGER_HH_
			#define AKANTU_DOF_MANAGER_HH_

			namespace akantu {
			class TermsToAssemble;
			class NonLinearSolver;
			class TimeStepSolver;
			class SparseMatrix;
			class SolverVector;
			class SolverCallback;
			} // namespace akantu

			namespace akantu {

			class DOFManager : protected MeshEventHandler {
			/* ------------------------------------------------------------------------ */
			/* Constructors/Destructors */
			/* ------------------------------------------------------------------------ */
			protected:
			struct DOFData;

			public:
			DOFManager(const ID & id = "dof_manager");
			DOFManager(Mesh & mesh, const ID & id = "dof_manager");
			~DOFManager() override;

			/* ------------------------------------------------------------------------ */
			/* Methods */
			/* ------------------------------------------------------------------------ */
			public:
			/// register an array of degree of freedom
			virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
			const DOFSupportType & support_type);

			/// the dof as an implied type of _dst_nodal and is defined only on a subset
			/// of nodes
			virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
			const ID & support_group);

			/// register an array of previous values of the degree of freedom
			virtual void registerDOFsPrevious(const ID & dof_id,
			Array<Real> & dofs_array);

			/// register an array of increment of degree of freedom
			virtual void registerDOFsIncrement(const ID & dof_id,
			Array<Real> & dofs_array);

			/// register an array of derivatives for a particular dof array
			virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
			Array<Real> & dofs_derivative);

			/// register array representing the blocked degree of freedoms
			virtual void registerBlockedDOFs(const ID & dof_id,
			Array<bool> & blocked_dofs);

			/// Assemble an array to the global residual array
			virtual void assembleToResidual(const ID & dof_id,
			Array<Real> & array_to_assemble,
			Real scale_factor = 1.);

			/// Assemble an array to the global lumped matrix array
			virtual void assembleToLumpedMatrix(const ID & dof_id,
			Array<Real> & array_to_assemble,
			const ID & lumped_mtx,
			Real scale_factor = 1.);

			/**
			* Assemble elementary values to a local array of the size nb_nodes *
			* nb_dof_per_node. The dof number is implicitly considered as
			* conn(el, n) * nb_nodes_per_element + d.
			* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
			**/
			virtual void assembleElementalArrayLocalArray(
			const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
			ElementType type, GhostType ghost_type,
			Real scale_factor = 1.,
			const Array<UInt> & filter_elements = empty_filter);

			/**
			* Assemble elementary values to the global residual array. The dof number is
			* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
			* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
			**/
			virtual void assembleElementalArrayToResidual(
			const ID & dof_id, const Array<Real> & elementary_vect,
			ElementType type, GhostType ghost_type,
			Real scale_factor = 1.,
			const Array<UInt> & filter_elements = empty_filter);

			/**
			* Assemble elementary values to a global array corresponding to a lumped
			* matrix
			*/
			virtual void assembleElementalArrayToLumpedMatrix(
			const ID & dof_id, const Array<Real> & elementary_vect,
			const ID & lumped_mtx, ElementType type,
			GhostType ghost_type, Real scale_factor = 1.,
			const Array<UInt> & filter_elements = empty_filter);

			/**
			* Assemble elementary values to the global residual array. The dof number is
			* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
			* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
			**/
			virtual void assembleElementalMatricesToMatrix(
			const ID & matrix_id, const ID & dof_id,
			const Array<Real> & elementary_mat, ElementType type,
			GhostType ghost_type = _not_ghost,
			const MatrixType & elemental_matrix_type = _symmetric,
			const Array<UInt> & filter_elements = empty_filter) = 0;

			/// multiply a vector by a matrix and assemble the result to the residual
			virtual void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
			const Array<Real> & x,
			Array<Real> & array,
			Real scale_factor = 1) = 0;

			/// multiply a vector by a lumped matrix and assemble the result to the
			/// residual
			virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
			const ID & A_id,
			const Array<Real> & x,
			Real scale_factor = 1) = 0;

			/// assemble coupling terms between to dofs
			virtual void assemblePreassembledMatrix(const ID & dof_id_m,
			const ID & dof_id_n,
			const ID & matrix_id,
			const TermsToAssemble & terms) = 0;

			/// multiply a vector by a matrix and assemble the result to the residual
			virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
			const Array<Real> & x,
			Real scale_factor = 1);

			/// multiply the dofs by a matrix and assemble the result to the residual
			virtual void assembleMatMulDOFsToResidual(const ID & A_id,
			Real scale_factor = 1);

			/// updates the global blocked_dofs array
			virtual void updateGlobalBlockedDofs();

			/// sets the residual to 0
			virtual void zeroResidual();
			/// sets the matrix to 0
			virtual void zeroMatrix(const ID & mtx);
			/// sets the lumped matrix to 0
			virtual void zeroLumpedMatrix(const ID & mtx);

			virtual void applyBoundary(const ID & matrix_id = "J");
			// virtual void applyBoundaryLumped(const ID & matrix_id = "J");

			/// extract a lumped matrix part corresponding to a given dof
			virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
			Array<Real> & lumped);

			/// splits the solution storage from a global view to the per dof storages
			void splitSolutionPerDOFs();

			private:
			/// dispatch the creation of the dof data and register it
			DOFData & getNewDOFDataInternal(const ID & dof_id);

			protected:
			/// common function to help registering dofs the return values are the add new
			/// numbers of local dofs, pure local dofs, and system size
			virtual std::tuple<UInt, UInt, UInt>
			registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);

			/// minimum functionality to implement per derived version of the DOFManager
			/// to allow the splitSolutionPerDOFs function to work
			virtual void getSolutionPerDOFs(const ID & dof_id,
			Array<Real> & solution_array);

			/// fill a Vector with the equation numbers corresponding to the given
			/// connectivity
			static inline void extractElementEquationNumber(
			const Array<Int> & equation_numbers, const Vector<UInt> & connectivity,
			UInt nb_degree_of_freedom, Vector<Int> & element_equation_number);

			/// Assemble a array to a global one
			void assembleMatMulVectToGlobalArray(const ID & dof_id, const ID & A_id,
			const Array<Real> & x,
			SolverVector & array,
			Real scale_factor = 1.);

			/// common function that can be called by derived class with proper matrice
			/// types
			template <typename Mat>
			void assemblePreassembledMatrix_(Mat & A, const ID & dof_id_m,
			const ID & dof_id_n,
			const TermsToAssemble & terms);

			template <typename Mat>
			void assembleElementalMatricesToMatrix_(
			Mat & A, const ID & dof_id, const Array<Real> & elementary_mat,
			ElementType type, GhostType ghost_type,
			const MatrixType & elemental_matrix_type,
			const Array<UInt> & filter_elements);

			template <typename Vec>
			void assembleMatMulVectToArray_(const ID & dof_id, const ID & A_id,
			const Array<Real> & x, Array<Real> & array,
			Real scale_factor);

			/* ------------------------------------------------------------------------ */
			/* Accessors */
			/* ------------------------------------------------------------------------ */
			public:
			/// Get the location type of a given dof
			inline bool isLocalOrMasterDOF(UInt local_dof_num);

			/// Answer to the question is a dof a slave dof ?
			inline bool isSlaveDOF(UInt local_dof_num);

			/// Answer to the question is a dof a slave dof ?
			inline bool isPureGhostDOF(UInt local_dof_num);

			/// tells if the dof manager knows about a global dof
			bool hasGlobalEquationNumber(Int global) const;

			/// return the local index of the global equation number
			inline Int globalToLocalEquationNumber(Int global) const;

			/// converts local equation numbers to global equation numbers;
			inline Int localToGlobalEquationNumber(Int local) const;

			/// get the array of dof types (use only if you know what you do...)
			inline NodeFlag getDOFFlag(Int local_id) const;

			/// defines if the boundary changed
			bool hasBlockedDOFsChanged() {
			return this->global_blocked_dofs_release !=
			this->previous_global_blocked_dofs_release;
			}

			/// Global number of dofs
			AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);

			/// Local number of dofs
			AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);

			/// Pure local number of dofs
			AKANTU_GET_MACRO(PureLocalSystemSize, this->pure_local_system_size, UInt);

			/// Retrieve all the registered DOFs
			std::vector<ID> getDOFIDs() const;

			/* ------------------------------------------------------------------------ */
			/* DOFs and derivatives accessors */
			/* ------------------------------------------------------------------------ */
			/// Get a reference to the registered dof array for a given id
			inline Array<Real> & getDOFs(const ID & dofs_id);

			/// Get the support type of a given dof
			inline DOFSupportType getSupportType(const ID & dofs_id) const;

			/// are the dofs registered
			inline bool hasDOFs(const ID & dof_id) const;

			/// Get a reference to the registered dof derivatives array for a given id
			inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);

			/// Does the dof has derivatives
			inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;

			/// Get a reference to the blocked dofs array registered for the given id
			inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;

			/// Does the dof has a blocked array
			inline bool hasBlockedDOFs(const ID & dofs_id) const;

			/// Get a reference to the registered dof increment array for a given id
			inline Array<Real> & getDOFsIncrement(const ID & dofs_id);

			/// Does the dof has a increment array
			inline bool hasDOFsIncrement(const ID & dofs_id) const;

			/// Does the dof has a previous array
			inline Array<Real> & getPreviousDOFs(const ID & dofs_id);

			/// Get a reference to the registered dof array for previous step values a
			/// given id
			inline bool hasPreviousDOFs(const ID & dofs_id) const;

			/// saves the values from dofs to previous dofs
			virtual void savePreviousDOFs(const ID & dofs_id);

			/// Get a reference to the solution array registered for the given id
			inline const Array<Real> & getSolution(const ID & dofs_id) const;

			/// Get a reference to the solution array registered for the given id
			inline Array<Real> & getSolution(const ID & dofs_id);

			/// Get the blocked dofs array
			AKANTU_GET_MACRO(GlobalBlockedDOFs, global_blocked_dofs, const Array<Int> &);
			/// Get the blocked dofs array
			AKANTU_GET_MACRO(PreviousGlobalBlockedDOFs, previous_global_blocked_dofs,
			const Array<Int> &);

			/* ------------------------------------------------------------------------ */
			/* Matrices accessors */
			/* ------------------------------------------------------------------------ */
			/// Get an instance of a new SparseMatrix
			virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
			const MatrixType & matrix_type) = 0;

			/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
			/// matrix_to_copy_id
			virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
			const ID & matrix_to_copy_id) = 0;

			/// Get the equation numbers corresponding to a dof_id. This might be used to
			/// access the matrix.
			inline const Array<Int> & getLocalEquationsNumbers(const ID & dof_id) const;

			protected:
			/// get the array of dof types (use only if you know what you do...)
			inline const Array<UInt> & getDOFsAssociatedNodes(const ID & dof_id) const;

			protected:
			/* ------------------------------------------------------------------------ */
			/// register a matrix
			SparseMatrix & registerSparseMatrix(const ID & matrix_id,
			std::unique_ptr<SparseMatrix> & matrix);

			/// register a lumped matrix (aka a Vector)
			SolverVector & registerLumpedMatrix(const ID & matrix_id,
			std::unique_ptr<SolverVector> & matrix);

			/// register a non linear solver instantiated by a derived class
			NonLinearSolver &
			registerNonLinearSolver(const ID & non_linear_solver_id,
			std::unique_ptr<NonLinearSolver> & non_linear_solver);

			/// register a time step solver instantiated by a derived class
			TimeStepSolver &
			registerTimeStepSolver(const ID & time_step_solver_id,
			std::unique_ptr<TimeStepSolver> & time_step_solver);

			template <class NLSType, class DMType>
			NonLinearSolver & registerNonLinearSolver(DMType & dm, const ID & id,
			const NonLinearSolverType & type) {
			ID non_linear_solver_id = this->id + ":nls:" + id;
			std::unique_ptr<NonLinearSolver> nls = std::make_unique<NLSType>(
			dm, type, non_linear_solver_id);
			return this->registerNonLinearSolver(non_linear_solver_id, nls);
			}

			template <class TSSType, class DMType>
			TimeStepSolver & registerTimeStepSolver(DMType & dm, const ID & id,
			const TimeStepSolverType & type,
			NonLinearSolver & non_linear_solver,
			SolverCallback & solver_callback) {
			ID time_step_solver_id = this->id + ":tss:" + id;
			std::unique_ptr<TimeStepSolver> tss =
			std::make_unique<TSSType>(dm, type, non_linear_solver, solver_callback,
			time_step_solver_id);
			return this->registerTimeStepSolver(time_step_solver_id, tss);
			}

			template <class MatType, class DMType>
			SparseMatrix & registerSparseMatrix(DMType & dm, const ID & id,
			const MatrixType & matrix_type) {
			ID matrix_id = this->id + ":mtx:" + id;
			std::unique_ptr<SparseMatrix> sm =
			std::make_unique<MatType>(dm, matrix_type, matrix_id);
			return this->registerSparseMatrix(matrix_id, sm);
			}

			template <class MatType>
			SparseMatrix & registerSparseMatrix(const ID & id,
			const ID & matrix_to_copy_id) {
			ID matrix_id = this->id + ":mtx:" + id;
			auto & sm_to_copy =
			aka::as_type<MatType>(this->getMatrix(matrix_to_copy_id));
			std::unique_ptr<SparseMatrix> sm =
			std::make_unique<MatType>(sm_to_copy, matrix_id);
			return this->registerSparseMatrix(matrix_id, sm);
			}

			template <class MatType, class DMType>
			SolverVector & registerLumpedMatrix(DMType & dm, const ID & id) {
			ID matrix_id = this->id + ":lumped_mtx:" + id;
			std::unique_ptr<SolverVector> sm = std::make_unique<MatType>(dm, matrix_id);
			return this->registerLumpedMatrix(matrix_id, sm);
			}

			protected:
			virtual void makeConsistentForPeriodicity(const ID & dof_id,
			SolverVector & array) = 0;

			virtual void assembleToGlobalArray(const ID & dof_id,
			const Array<Real> & array_to_assemble,
			SolverVector & global_array,
			Real scale_factor) = 0;

			public:
			/// extract degrees of freedom (identified by ID) from a global solver array
			virtual void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
			Array<Real> & local) = 0;

			/// Get the reference of an existing matrix
			SparseMatrix & getMatrix(const ID & matrix_id);

			/// check if the given matrix exists
			bool hasMatrix(const ID & matrix_id) const;

			/// Get an instance of a new lumped matrix
			virtual SolverVector & getNewLumpedMatrix(const ID & matrix_id) = 0;
			/// Get the lumped version of a given matrix
			const SolverVector & getLumpedMatrix(const ID & matrix_id) const;
			/// Get the lumped version of a given matrix
			SolverVector & getLumpedMatrix(const ID & matrix_id);

			/// check if the given matrix exists
			bool hasLumpedMatrix(const ID & matrix_id) const;

			/* ------------------------------------------------------------------------ */
			/* Non linear system solver */
			/* ------------------------------------------------------------------------ */
			/// Get instance of a non linear solver
			virtual NonLinearSolver & getNewNonLinearSolver(
			const ID & nls_solver_id,
			const NonLinearSolverType & _non_linear_solver_type) = 0;

			/// get instance of a non linear solver
			virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);

			/// check if the given solver exists
			bool hasNonLinearSolver(const ID & solver_id) const;

			/* ------------------------------------------------------------------------ */
			/* Time-Step Solver */
			/* ------------------------------------------------------------------------ */
			/// Get instance of a time step solver
			virtual TimeStepSolver &
			getNewTimeStepSolver(const ID & time_step_solver_id,
			const TimeStepSolverType & type,
			NonLinearSolver & non_linear_solver,
			SolverCallback & solver_callback) = 0;

			/// get instance of a time step solver
			virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);

			/// check if the given solver exists
			bool hasTimeStepSolver(const ID & solver_id) const;

			/* ------------------------------------------------------------------------ */
			const Mesh & getMesh() {
			if (mesh != nullptr) {
			return *mesh;
			}
			AKANTU_EXCEPTION("No mesh registered in this dof manager");
			}

			/* ------------------------------------------------------------------------ */
			AKANTU_GET_MACRO(Communicator, communicator, const auto &);
			AKANTU_GET_MACRO_NOT_CONST(Communicator, communicator, auto &);

			/* ------------------------------------------------------------------------ */
			AKANTU_GET_MACRO(Solution, *(solution.get()), const auto &);
			AKANTU_GET_MACRO_NOT_CONST(Solution, *(solution.get()), auto &);

			AKANTU_GET_MACRO(Residual, *(residual.get()), const auto &);
			AKANTU_GET_MACRO_NOT_CONST(Residual, *(residual.get()), auto &);

			/* ------------------------------------------------------------------------ */
			/* MeshEventHandler interface */
			/* ------------------------------------------------------------------------ */
			protected:
			friend class GlobalDOFInfoDataAccessor;
			/// helper function for the DOFManager::onNodesAdded method
			virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
			const Array<UInt> & nodes_list);

			template <typename Func>
			auto countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
			Func && getNode);

			void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
			UInt nb_new_pure_local, UInt nb_nodes,
			const std::function<UInt(UInt)> & getNode);

			void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
			UInt nb_new_pure_local);

			auto computeFirstDOFIDs(UInt nb_new_local_dofs, UInt nb_new_pure_local);

			/// resize all the global information and takes the needed measure like
			/// cleaning matrices profiles
			virtual void resizeGlobalArrays();

			public:
			/// function to implement to react on akantu::NewNodesEvent
			void onNodesAdded(const Array<UInt> & nodes_list,
			const NewNodesEvent & event) override;
			/// function to implement to react on akantu::RemovedNodesEvent
			void onNodesRemoved(const Array<UInt> & nodes_list,
			const Array<UInt> & new_numbering,
			const RemovedNodesEvent & event) override;
			/// function to implement to react on akantu::NewElementsEvent
			void onElementsAdded(const Array<Element> & elements_list,
			const NewElementsEvent & event) override;
			/// function to implement to react on akantu::RemovedElementsEvent
			void onElementsRemoved(const Array<Element> & elements_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) override;
			/// function to implement to react on akantu::ChangedElementsEvent
			void onElementsChanged(const Array<Element> & old_elements_list,
			const Array<Element> & new_elements_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const ChangedElementsEvent & event) override;

			protected:
			inline DOFData & getDOFData(const ID & dof_id);
			inline const DOFData & getDOFData(const ID & dof_id) const;
			template <class DOFData_>
			inline DOFData_ & getDOFDataTyped(const ID & dof_id);
			template <class DOFData_>
			inline const DOFData_ & getDOFDataTyped(const ID & dof_id) const;

			virtual std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) = 0;

			/* ------------------------------------------------------------------------ */
			/* Class Members */
			/* ------------------------------------------------------------------------ */
			protected:
			/// dof representations in the dof manager
			struct DOFData {
			DOFData() = delete;
			explicit DOFData(const ID & dof_id);
			virtual ~DOFData();

			/// DOF support type (nodal, general) this is needed to determine how the
			/// dof are shared among processors
			DOFSupportType support_type;

			ID group_support;

			/// Degree of freedom array
			Array<Real> * dof{nullptr};

			/// Blocked degree of freedoms array
			Array<bool> * blocked_dofs{nullptr};

			/// Degree of freedoms increment
			Array<Real> * increment{nullptr};

			/// Degree of freedoms at previous step
			Array<Real> * previous{nullptr};

			/// Solution associated to the dof
			Array<Real> solution;

			/* ---------------------------------------------------------------------- */
			/* data for dynamic simulations */
			/* ---------------------------------------------------------------------- */
			/// Degree of freedom derivatives arrays
			std::vector<Array<Real> *> dof_derivatives;

			/* ---------------------------------------------------------------------- */
			/// number of dofs to consider locally for this dof id
			UInt local_nb_dofs{0};

			/// Number of purely local dofs
			UInt pure_local_nb_dofs{0};

			/// number of ghost dofs
			UInt ghosts_nb_dofs{0};

			/// local numbering equation numbers
			Array<Int> local_equation_number;

			/// associated node for _dst_nodal dofs only
			Array<UInt> associated_nodes;

			virtual Array<Int> & getLocalEquationsNumbers() {
			return local_equation_number;
			}
			};

			/// type to store dofs information
			using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;

			/// type to store all the matrices
			using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;

			/// type to store all the lumped matrices
			using LumpedMatricesMap = std::map<ID, std::unique_ptr<SolverVector>>;

			/// type to store all the non linear solver
			using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;

			/// type to store all the time step solver
			using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;

			ID id;

			/// store a reference to the dof arrays
			DOFStorage dofs;

			/// list of sparse matrices that where created
			SparseMatricesMap matrices;

			/// list of lumped matrices
			LumpedMatricesMap lumped_matrices;

			/// non linear solvers storage
			NonLinearSolversMap non_linear_solvers;

			/// time step solvers storage
			TimeStepSolversMap time_step_solvers;

			/// reference to the underlying mesh
			Mesh * mesh{nullptr};

			/// Total number of degrees of freedom (size with the ghosts)
			UInt local_system_size{0};

			/// Number of purely local dofs (size without the ghosts)
			UInt pure_local_system_size{0};

			/// Total number of degrees of freedom
			UInt system_size{0};

			/// rhs to the system of equation corresponding to the residual linked to the
			/// different dofs
			std::unique_ptr<SolverVector> residual;

			/// solution of the system of equation corresponding to the different dofs
			std::unique_ptr<SolverVector> solution;

			/// a vector that helps internally to perform some tasks
			std::unique_ptr<SolverVector> data_cache;

			/// define the dofs type, local, shared, ghost
			Array<NodeFlag> dofs_flag;

			/// equation number in global numbering
			Array<Int> global_equation_number;

			using equation_numbers_map = std::unordered_map<Int, Int>;

			/// dual information of global_equation_number
			equation_numbers_map global_to_local_mapping;

			/// Communicator used for this manager, should be the same as in the mesh if a
			/// mesh is registered
			Communicator & communicator;

			/// accumulator to know what would be the next global id to use
			UInt first_global_dof_id{0};

			/// Release at last apply boundary on jacobian
			UInt jacobian_release{0};

			/// blocked degree of freedom in the system equation corresponding to the
			/// different dofs
			Array<Int> global_blocked_dofs;

			UInt global_blocked_dofs_release{0};

			/// blocked degree of freedom in the system equation corresponding to the
			/// different dofs
			Array<Int> previous_global_blocked_dofs;

			UInt previous_global_blocked_dofs_release{0};

			private:
			/// This is for unit testing
			friend class DOFManagerTester;
			};

			using DefaultDOFManagerFactory =
			Factory<DOFManager, ID, const ID &>;
			using DOFManagerFactory =
			Factory<DOFManager, ID, Mesh &, const ID &>;

			} // namespace akantu

			#include "dof_manager_inline_impl.hh"

			#endif /* AKANTU_DOF_MANAGER_HH_ */

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rAKA/src/model/common/dof_manager/dof_manager.hh
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dof_manager.hh
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