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solid_mechanics_model.hh
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			/**
			* @file solid_mechanics_model.hh
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Tue Jul 27 2010
			* @date last modification: Wed Feb 21 2018
			*
			* @brief Model of Solid Mechanics
			*
			*
			* 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/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "boundary_condition.hh"
			#include "data_accessor.hh"
			#include "fe_engine.hh"
			#include "model.hh"
			#include "non_local_manager_callback.hh"
			#include "solid_mechanics_model_event_handler.hh"
			/* -------------------------------------------------------------------------- */

			#ifndef AKANTU_SOLID_MECHANICS_MODEL_HH_
			#define AKANTU_SOLID_MECHANICS_MODEL_HH_

			namespace akantu {
			class Material;
			class MaterialSelector;
			class DumperIOHelper;
			class NonLocalManager;
			template <ElementKind kind, class IntegrationOrderFunctor>
			class IntegratorGauss;
			template <ElementKind kind> class ShapeLagrange;
			} // namespace akantu

			/* -------------------------------------------------------------------------- */
			namespace akantu {

			/* -------------------------------------------------------------------------- */
			class SolidMechanicsModel
			: public Model,
			public DataAccessor<Element>,
			public DataAccessor<UInt>,
			public BoundaryCondition<SolidMechanicsModel>,
			public NonLocalManagerCallback,
			public EventHandlerManager<SolidMechanicsModelEventHandler> {

			/* ------------------------------------------------------------------------ */
			/* Constructors/Destructors */
			/* ------------------------------------------------------------------------ */
			public:
			class NewMaterialElementsEvent : public NewElementsEvent {
			public:
			AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array<UInt> &);
			AKANTU_GET_MACRO(MaterialList, material, const Array<UInt> &);

			protected:
			Array<UInt> material;
			};

			using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;

			protected:
			using EventManager = EventHandlerManager<SolidMechanicsModelEventHandler>;

			public:
			SolidMechanicsModel(Mesh & mesh, UInt dim = _all_dimensions,
			const ID & id = "solid_mechanics_model",
			ModelType model_type = ModelType::_solid_mechanics_model);

			~SolidMechanicsModel() override;

			/* ------------------------------------------------------------------------ */
			/* Methods */
			/* ------------------------------------------------------------------------ */
			protected:
			/// initialize completely the model
			void initFullImpl(
			const ModelOptions & options = SolidMechanicsModelOptions()) override;

			public:
			/// initialize all internal arrays for materials
			virtual void initMaterials();

			protected:
			/// initialize the model
			void initModel() override;

			/// function to print the containt of the class
			void printself(std::ostream & stream, int indent = 0) const override;

			/// get some default values for derived classes
			std::tuple<ID, TimeStepSolverType>
			getDefaultSolverID(const AnalysisMethod & method) override;

			/* ------------------------------------------------------------------------ */
			/* Solver interface */
			/* ------------------------------------------------------------------------ */
			public:
			/// assembles the stiffness matrix,
			virtual void assembleStiffnessMatrix();
			/// assembles the internal forces in the array internal_forces
			virtual void assembleInternalForces();

			protected:
			/// callback for the solver, this adds f_{ext} - f_{int} to the residual
			void assembleResidual() override;

			/// callback for the solver, this adds f_{ext} or f_{int} to the residual
			void assembleResidual(const ID & residual_part) override;
			bool canSplitResidual() override { return true; }

			/// get the type of matrix needed
			MatrixType getMatrixType(const ID & matrix_id) override;

			/// callback for the solver, this assembles different matrices
			void assembleMatrix(const ID & matrix_id) override;

			/// callback for the solver, this assembles the stiffness matrix
			void assembleLumpedMatrix(const ID & matrix_id) override;

			/// callback for the solver, this is called at beginning of solve
			void predictor() override;
			/// callback for the solver, this is called at end of solve
			void corrector() override;

			/// callback for the solver, this is called at beginning of solve
			void beforeSolveStep() override;
			/// callback for the solver, this is called at end of solve
			void afterSolveStep(bool converged = true) override;

			/// Callback for the model to instantiate the matricees when needed
			void initSolver(TimeStepSolverType time_step_solver_type,
			NonLinearSolverType non_linear_solver_type) override;

			protected:
			/* ------------------------------------------------------------------------ */
			TimeStepSolverType getDefaultSolverType() const override;
			/* ------------------------------------------------------------------------ */
			ModelSolverOptions
			getDefaultSolverOptions(const TimeStepSolverType & type) const override;

			public:
			bool isDefaultSolverExplicit() {
			return method == _explicit_lumped_mass \|\|
			method == _explicit_consistent_mass;
			}

			protected:
			/// update the current position vector
			void updateCurrentPosition();

			/* ------------------------------------------------------------------------ */
			/* Materials (solid_mechanics_model_material.cc) */
			/* ------------------------------------------------------------------------ */
			public:
			/// register an empty material of a given type
			Material & registerNewMaterial(const ID & mat_name, const ID & mat_type,
			const ID & opt_param);

			/// reassigns materials depending on the material selector
			virtual void reassignMaterial();

			/// apply a constant eigen_grad_u on all quadrature points of a given material
			virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
			const ID & material_name,
			GhostType ghost_type = _not_ghost);

			protected:
			/// register a material in the dynamic database
			Material & registerNewMaterial(const ParserSection & mat_section);

			/// read the material files to instantiate all the materials
			void instantiateMaterials();

			/// set the element_id_by_material and add the elements to the good materials
			virtual void
			assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = nullptr);

			/* ------------------------------------------------------------------------ */
			/* Mass (solid_mechanics_model_mass.cc) */
			/* ------------------------------------------------------------------------ */
			public:
			/// assemble the lumped mass matrix
			void assembleMassLumped();

			/// assemble the mass matrix for consistent mass resolutions
			void assembleMass();

			protected:
			/// assemble the lumped mass matrix for local and ghost elements
			void assembleMassLumped(GhostType ghost_type);

			/// assemble the mass matrix for either _ghost or _not_ghost elements
			void assembleMass(GhostType ghost_type);

			/// fill a vector of rho
			void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);

			/// compute the kinetic energy
			Real getKineticEnergy();
			Real getKineticEnergy(ElementType type, UInt index);

			/// compute the external work (for impose displacement, the velocity should be
			/// given too)
			Real getExternalWork();

			/* ------------------------------------------------------------------------ */
			/* NonLocalManager inherited members */
			/* ------------------------------------------------------------------------ */
			protected:
			void initializeNonLocal() override;

			void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;

			void computeNonLocalStresses(GhostType ghost_type) override;

			void insertIntegrationPointsInNeighborhoods(GhostType ghost_type) override;

			/// update the values of the non local internal
			void updateLocalInternal(ElementTypeMapReal & internal_flat,
			GhostType ghost_type, ElementKind kind) override;

			/// copy the results of the averaging in the materials
			void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
			GhostType ghost_type, ElementKind kind) override;

			/* ------------------------------------------------------------------------ */
			/* Data Accessor inherited members */
			/* ------------------------------------------------------------------------ */
			public:
			UInt getNbData(const Array<Element> & elements,
			const SynchronizationTag & tag) const override;

			void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) const override;

			void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) override;

			UInt getNbData(const Array<UInt> & dofs,
			const SynchronizationTag & tag) const override;

			void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
			const SynchronizationTag & tag) const override;

			void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
			const SynchronizationTag & tag) override;

			protected:
			void
			splitElementByMaterial(const Array<Element> & elements,
			std::vector<Array<Element>> & elements_per_mat) const;

			template <typename Operation>
			void splitByMaterial(const Array<Element> & elements, Operation && op) const;

			/* ------------------------------------------------------------------------ */
			/* Mesh Event Handler inherited members */
			/* ------------------------------------------------------------------------ */
			protected:
			void onNodesAdded(const Array<UInt> & nodes_list,
			const NewNodesEvent & event) override;
			void onNodesRemoved(const Array<UInt> & element_list,
			const Array<UInt> & new_numbering,
			const RemovedNodesEvent & event) override;
			void onElementsAdded(const Array<Element> & element_list,
			const NewElementsEvent & event) override;
			void onElementsRemoved(const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) override;
			void onElementsChanged(const Array<Element> & /unused/,
			const Array<Element> & /unused/,
			const ElementTypeMapArray<UInt> & /unused/,
			const ChangedElementsEvent & /unused/) override{};

			/* ------------------------------------------------------------------------ */
			/* Dumpable interface (kept for convenience) and dumper relative functions */
			/* ------------------------------------------------------------------------ */
			public:
			virtual void onDump();

			//! decide wether a field is a material internal or not
			bool isInternal(const std::string & field_name, ElementKind element_kind);
			//! give the amount of data per element
			virtual ElementTypeMap<UInt>
			getInternalDataPerElem(const std::string & field_name, ElementKind kind);

			//! flatten a given material internal field
			ElementTypeMapArray<Real> &
			flattenInternal(const std::string & field_name, ElementKind kind,
			GhostType ghost_type = _not_ghost);
			//! flatten all the registered material internals
			void flattenAllRegisteredInternals(ElementKind kind);

			std::shared_ptr<dumpers::Field>
			createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) override;

			std::shared_ptr<dumpers::Field>
			createNodalFieldBool(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) override;

			std::shared_ptr<dumpers::Field>
			createElementalField(const std::string & field_name,
			const std::string & group_name, bool padding_flag,
			UInt spatial_dimension, ElementKind kind) override;

			virtual void dump(const std::string & dumper_name);
			virtual void dump(const std::string & dumper_name, UInt step);
			virtual void dump(const std::string & dumper_name, Real time, UInt step);

			void dump() override;
			void dump(UInt step) override;
			void dump(Real time, UInt step) override;

			/* ------------------------------------------------------------------------ */
			/* Accessors */
			/* ------------------------------------------------------------------------ */
			public:
			/// return the dimension of the system space
			AKANTU_GET_MACRO(SpatialDimension, Model::spatial_dimension, UInt);

			/// set the value of the time step
			void setTimeStep(Real time_step, const ID & solver_id = "") override;

			/// get the value of the conversion from forces/ mass to acceleration
			AKANTU_GET_MACRO(F_M2A, f_m2a, Real);

			/// set the value of the conversion from forces/ mass to acceleration
			AKANTU_SET_MACRO(F_M2A, f_m2a, Real);

			/// get the SolidMechanicsModel::displacement array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Displacement, displacement);
			/// get the SolidMechanicsModel::displacement array
			AKANTU_GET_MACRO_DEREF_PTR(Displacement, displacement);

			/// get the SolidMechanicsModel::previous_displacement array
			AKANTU_GET_MACRO_DEREF_PTR(PreviousDisplacement, previous_displacement);

			/// get the SolidMechanicsModel::current_position array
			const Array<Real> & getCurrentPosition();

			/// get the SolidMechanicsModel::displacement_increment array
			AKANTU_GET_MACRO_DEREF_PTR(Increment, displacement_increment);
			/// get the SolidMechanicsModel::displacement_increment array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Increment, displacement_increment);

			/// get the lumped SolidMechanicsModel::mass array
			AKANTU_GET_MACRO_DEREF_PTR(Mass, mass);

			/// get the SolidMechanicsModel::velocity array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Velocity, velocity);
			/// get the SolidMechanicsModel::velocity array
			AKANTU_GET_MACRO_DEREF_PTR(Velocity, velocity);

			/// get the SolidMechanicsModel::acceleration array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Acceleration, acceleration);
			/// get the SolidMechanicsModel::acceleration array
			AKANTU_GET_MACRO_DEREF_PTR(Acceleration, acceleration);

			/// get the SolidMechanicsModel::external_force array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(ExternalForce, external_force);
			/// get the SolidMechanicsModel::external_force array
			AKANTU_GET_MACRO_DEREF_PTR(ExternalForce, external_force);

			/// get the SolidMechanicsModel::force array (external forces)
			[[deprecated("Use getExternalForce instead of this function")]] Array<Real> &
			getForce() {
			return getExternalForce();
			}

			/// get the SolidMechanicsModel::internal_force array (internal forces)
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(InternalForce, internal_force);
			/// get the SolidMechanicsModel::internal_force array (internal forces)
			AKANTU_GET_MACRO_DEREF_PTR(InternalForce, internal_force);

			/// get the SolidMechanicsModel::blocked_dofs array
			AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(BlockedDOFs, blocked_dofs);
			/// get the SolidMechanicsModel::blocked_dofs array
			AKANTU_GET_MACRO_DEREF_PTR(BlockedDOFs, blocked_dofs);

			/// get an iterable on the materials
			inline decltype(auto) getMaterials();

			/// get an iterable on the materials
			inline decltype(auto) getMaterials() const;

			/// get a particular material (by numerical material index)
			inline Material & getMaterial(UInt mat_index);

			/// get a particular material (by numerical material index)
			inline const Material & getMaterial(UInt mat_index) const;

			/// get a particular material (by material name)
			inline Material & getMaterial(const std::string & name);

			/// get a particular material (by material name)
			inline const Material & getMaterial(const std::string & name) const;

			/// get a particular material id from is name
			inline UInt getMaterialIndex(const std::string & name) const;

			/// give the number of materials
			inline UInt getNbMaterials() const { return materials.size(); }

			/// give the material internal index from its id
			Int getInternalIndexFromID(const ID & id) const;

			/// compute the stable time step
			Real getStableTimeStep();

			/// get the energies
			Real getEnergy(const std::string & energy_id);

			/// compute the energy for an element
			Real getEnergy(const std::string & energy_id, ElementType type, UInt index);

			/// compute the energy for an element
			Real getEnergy(const std::string & energy_id, const Element & element) {
			return getEnergy(energy_id, element.type, element.element);
			}

			/// compute the energy for an element group
			Real getEnergy(const ID & energy_id, const ID & group_id);

			AKANTU_GET_MACRO(MaterialByElement, material_index,
			const ElementTypeMapArray<UInt> &);
			AKANTU_GET_MACRO(MaterialLocalNumbering, material_local_numbering,
			const ElementTypeMapArray<UInt> &);

			/// vectors containing local material element index for each global element
			/// index
			AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialByElement, material_index,
			UInt);
			// AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialByElement, material_index, UInt);
			AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialLocalNumbering,
			material_local_numbering, UInt);
			// AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialLocalNumbering,
			// material_local_numbering, UInt);

			AKANTU_GET_MACRO_NOT_CONST(MaterialSelector, *material_selector,
			MaterialSelector &);
			void
			setMaterialSelector(std::shared_ptr<MaterialSelector> material_selector) {
			this->material_selector = std::move(material_selector);
			}

			/// Access the non_local_manager interface
			AKANTU_GET_MACRO(NonLocalManager, *non_local_manager, NonLocalManager &);

			/// get the FEEngine object to integrate or interpolate on the boundary
			FEEngine & getFEEngineBoundary(const ID & name = "") override;

			protected:
			/// compute the stable time step
			Real getStableTimeStep(GhostType ghost_type);

			/* ------------------------------------------------------------------------ */
			/* Class Members */
			/* ------------------------------------------------------------------------ */
			private:
			/// release version of the displacement array
			UInt displacement_release{0};

			/// release version of the current_position array
			UInt current_position_release{0};

			/// Check if materials need to recompute the mass array
			bool need_to_reassemble_lumped_mass{true};
			/// Check if materials need to recompute the mass matrix
			bool need_to_reassemble_mass{true};

			/// mapping between material name and material internal id
			std::map<std::string, UInt> materials_names_to_id;

			protected:
			/// conversion coefficient form force/mass to acceleration
			Real f_m2a{1.0};

			/// displacements array
			std::unique_ptr<Array<Real>> displacement;

			/// displacements array at the previous time step (used in finite deformation)
			std::unique_ptr<Array<Real>> previous_displacement;

			/// increment of displacement
			std::unique_ptr<Array<Real>> displacement_increment;

			/// lumped mass array
			std::unique_ptr<Array<Real>> mass;

			/// velocities array
			std::unique_ptr<Array<Real>> velocity;

			/// accelerations array
			std::unique_ptr<Array<Real>> acceleration;

			/// external forces array
			std::unique_ptr<Array<Real>> external_force;

			/// internal forces array
			std::unique_ptr<Array<Real>> internal_force;

			/// array specifing if a degree of freedom is blocked or not
			std::unique_ptr<Array<bool>> blocked_dofs;

			/// array of current position used during update residual
			std::unique_ptr<Array<Real>> current_position;

			/// Arrays containing the material index for each element
			ElementTypeMapArray<UInt> material_index;

			/// Arrays containing the position in the element filter of the material
			/// (material's local numbering)
			ElementTypeMapArray<UInt> material_local_numbering;

			/// list of used materials
			std::vector<std::unique_ptr<Material>> materials;

			/// class defining of to choose a material
			std::shared_ptr<MaterialSelector> material_selector;

			using flatten_internal_map =
			std::map<std::pair<std::string, ElementKind>,
			std::unique_ptr<ElementTypeMapArray<Real>>>;

			/// map a registered internals to be flattened for dump purposes
			flatten_internal_map registered_internals;

			/// non local manager
			std::unique_ptr<NonLocalManager> non_local_manager;

			/// tells if the material are instantiated
			bool are_materials_instantiated{false};

			friend class Material;
			};

			/* -------------------------------------------------------------------------- */
			namespace BC {
			namespace Neumann {
			using FromStress = FromHigherDim;
			using FromTraction = FromSameDim;
			} // namespace Neumann
			} // namespace BC

			} // namespace akantu

			/* -------------------------------------------------------------------------- */
			/* inline functions */
			/* -------------------------------------------------------------------------- */
			#include "material.hh"
			#include "parser.hh"

			#include "solid_mechanics_model_inline_impl.hh"
			#include "solid_mechanics_model_tmpl.hh"
			/* -------------------------------------------------------------------------- */

			#endif /* AKANTU_SOLID_MECHANICS_MODEL_HH_ */

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rAKA/src/model/solid_mechanics/solid_mechanics_model.hh
9cb01e0c3a12bugfixes/python_interfa…

solid_mechanics_model.hh
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