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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: Tue Sep 16 2014
			*
			* @brief Model of Solid Mechanics
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014 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/>.
			*
			*/

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

			#ifndef __AKANTU_SOLID_MECHANICS_MODEL_HH__
			#define __AKANTU_SOLID_MECHANICS_MODEL_HH__


			/* -------------------------------------------------------------------------- */
			#include <fstream>
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			#include "aka_common.hh"
			#include "aka_types.hh"
			#include "model.hh"
			#include "data_accessor.hh"
			#include "mesh.hh"
			#include "dumpable.hh"
			#include "boundary_condition.hh"
			#include "integrator_gauss.hh"
			#include "shape_lagrange.hh"
			#include "integration_scheme_2nd_order.hh"
			#include "solver.hh"
			#include "material_selector.hh"
			#include "solid_mechanics_model_event_handler.hh"
			/* -------------------------------------------------------------------------- */
			namespace akantu {
			class Material;
			class IntegrationScheme2ndOrder;
			class SparseMatrix;
			class DumperIOHelper;
			}
			/* -------------------------------------------------------------------------- */


			__BEGIN_AKANTU__

			struct SolidMechanicsModelOptions : public ModelOptions {
			SolidMechanicsModelOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
			bool no_init_materials = false) :
			analysis_method(analysis_method),
			no_init_materials(no_init_materials) { }
			AnalysisMethod analysis_method;
			bool no_init_materials;
			};

			extern const SolidMechanicsModelOptions default_solid_mechanics_model_options;


			class SolidMechanicsModel : public Model,
			public DataAccessor,
			public MeshEventHandler,
			public BoundaryCondition<SolidMechanicsModel>,
			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;
			};

			typedef FEEngineTemplate <IntegratorGauss, ShapeLagrange> MyFEEngineType;

			protected:
			typedef EventHandlerManager <SolidMechanicsModelEventHandler> EventManager;

			public:
			SolidMechanicsModel(Mesh & mesh,
			UInt spatial_dimension = _all_dimensions,
			const ID & id = "solid_mechanics_model",
			const MemoryID & memory_id = 0);

			virtual ~SolidMechanicsModel();

			/* ------------------------------------------------------------------------ */
			/* Methods */
			/* ------------------------------------------------------------------------ */
			public:
			/// initialize completely the model
			virtual void initFull(const ModelOptions & options = default_solid_mechanics_model_options);

			/// initialize the fem object needed for boundary conditions
			void initFEEngineBoundary();

			/// register the tags associated with the parallel synchronizer
			void initParallel(MeshPartition partition, DataAccessor data_accessor = NULL);

			/// allocate all vectors
			void initArrays();

			/// allocate all vectors
			void initArraysPreviousDisplacment();

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

			/// initialize the model
			virtual void initModel();

			/// init PBC synchronizer
			void initPBC();

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

			/// re-initialize model to set fields to 0
			void reInitialize();

			/* ------------------------------------------------------------------------ */
			/* PBC */
			/* ------------------------------------------------------------------------ */
			public:
			/// change the equation number for proper assembly when using PBC
			// void changeEquationNumberforPBC(std::map <UInt, UInt> & pbc_pair);

			/// synchronize Residual for output
			void synchronizeResidual();

			protected:
			/// register PBC synchronizer
			void registerPBCSynchronizer();

			/* ------------------------------------------------------------------------ */
			/* Explicit */
			/* ------------------------------------------------------------------------ */
			public:
			/// initialize the stuff for the explicit scheme
			void initExplicit(AnalysisMethod analysis_method = _explicit_lumped_mass);

			bool isExplicit() {
			return method == _explicit_lumped_mass \|\| method == _explicit_consistent_mass;
			}

			/// initialize the array needed by updateResidual (residual, current_position)
			void initializeUpdateResidualData();

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

			/// assemble the residual for the explicit scheme
			virtual void updateResidual(bool need_initialize = true);

			/**
			* \brief compute the acceleration from the residual
			* this function is the explicit equivalent to solveDynamic in implicit
			* In the case of lumped mass just divide the residual by the mass
			* In the case of not lumped mass call solveDynamic<_acceleration_corrector>
			*/
			void updateAcceleration();

			void updateIncrement();
			void updatePreviousDisplacement();
			void saveStressAndStrainBeforeDamage();
			void updateEnergiesAfterDamage();

			/// Solve the system @f[ A x = \alpha b @f] with A a lumped matrix
			void solveLumped(Array <Real> & x,
			const Array <Real> & A,
			const Array <Real> & b,
			const Array <bool> & blocked_dofs,
			Real alpha);

			/// explicit integration predictor
			void explicitPred();

			/// explicit integration corrector
			void explicitCorr();

			public:
			void solveStep();

			/* ------------------------------------------------------------------------ */
			/* Implicit */
			/* ------------------------------------------------------------------------ */
			public:
			/// initialize the solver and the jacobian_matrix (called by initImplicit)
			void initSolver(SolverOptions & options = _solver_no_options);

			/// initialize the stuff for the implicit solver
			void initImplicit(bool dynamic = false,
			SolverOptions & solver_options = _solver_no_options);

			/// solve Ma = f to get the initial acceleration
			void initialAcceleration();

			/// assemble the stiffness matrix
			void assembleStiffnessMatrix();

			public:
			/**
			* solve a step (predictor + convergence loop + corrector) using the
			* the given convergence method (see akantu::SolveConvergenceMethod)
			* and the given convergence criteria (see
			* akantu::SolveConvergenceCriteria)
			**/
			template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
			bool solveStep(Real tolerance, UInt max_iteration = 100);

			template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
			bool solveStep(Real tolerance,
			Real & error,
			UInt max_iteration = 100,
			bool do_not_factorize = false);

			public:
			/**
			* solve Ku = f using the the given convergence method (see
			* akantu::SolveConvergenceMethod) and the given convergence
			* criteria (see akantu::SolveConvergenceCriteria)
			**/
			template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
			bool solveStatic(Real tolerance, UInt max_iteration,
			bool do_not_factorize = false);

			/// test if the system is converged
			template <SolveConvergenceCriteria criteria>
			bool testConvergence(Real tolerance, Real & error);

			/// test the convergence (norm of increment)
			bool testConvergenceIncrement(Real tolerance) __attribute__((deprecated));
			bool testConvergenceIncrement(Real tolerance, Real & error) __attribute__((deprecated));

			/// test the convergence (norm of residual)
			bool testConvergenceResidual(Real tolerance) __attribute__((deprecated));
			bool testConvergenceResidual(Real tolerance, Real & error) __attribute__((deprecated));

			/// create and return the velocity damping matrix
			SparseMatrix & initVelocityDampingMatrix();

			/// implicit time integration predictor
			void implicitPred();

			/// implicit time integration corrector
			void implicitCorr();

			/// compute the Cauchy stress on user demand.
			void computeCauchyStresses();

			protected:
			/// finish the computation of residual to solve in increment
			void updateResidualInternal();

			/// compute the support reaction and store it in force
			void updateSupportReaction();


			public:

			//protected: Daniel changed it just for a test
			/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
			template <NewmarkBeta::IntegrationSchemeCorrectorType type>
			void solve(Array<Real> &increment, Real block_val = 1.,
			bool need_factorize = true, bool has_profile_changed = false);

			private:
			/// re-initialize the J matrix (to use if the profile of K changed)
			void initJacobianMatrix();

			/* ------------------------------------------------------------------------ */
			/* Explicit/Implicit */
			/* ------------------------------------------------------------------------ */

			public:
			/// Update the stresses for the computation of the residual of the Stiffness
			/// matrix in the case of finite deformation
			void computeStresses();

			/// synchronize the ghost element boundaries values
			void synchronizeBoundaries();

			/* ------------------------------------------------------------------------ */
			/* Materials (solid_mechanics_model_material.cc) */
			/* ------------------------------------------------------------------------ */
			public:
			/// registers all the custom materials of a given type present in the input file
			template <typename M>
			void registerNewCustomMaterials(const ID & mat_type);

			/// register an empty material of a given type
			template <typename M>
			Material & registerNewEmptyMaterial(const std::string & name);

			// /// Use a UIntData in the mesh to specify the material to use per element
			// void setMaterialIDsFromIntData(const std::string & data_name);

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

			protected:
			/// register a material in the dynamic database
			template <typename M>
			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
			void assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = NULL);

			/* ------------------------------------------------------------------------ */
			/* 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);


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

			inline virtual void packElementData(CommunicationBuffer & buffer,
			const Array <Element> & elements,
			SynchronizationTag tag) const;

			inline virtual void unpackElementData(CommunicationBuffer & buffer,
			const Array <Element> & elements,
			SynchronizationTag tag);

			inline virtual UInt getNbDataToPack(SynchronizationTag tag) const;
			inline virtual UInt getNbDataToUnpack(SynchronizationTag tag) const;

			inline virtual void packData(CommunicationBuffer & buffer,
			const UInt index,
			SynchronizationTag tag) const;

			inline virtual void unpackData(CommunicationBuffer & buffer,
			const UInt index,
			SynchronizationTag tag);

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

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

			/* ------------------------------------------------------------------------ */
			/* 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, const ElementKind & element_kind);
			#ifndef SWIG
			//! give the amount of data per element
			virtual ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
			const ElementKind & kind);

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

			virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag);

			virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag);


			virtual dumper::Field * createElementalField(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag,
			const UInt & spatial_dimension,
			const ElementKind & kind);



			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);

			virtual void dump();

			virtual void dump(UInt step);

			virtual void dump(Real time, UInt step);

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

			/// get the current value of the time step
			AKANTU_GET_MACRO(TimeStep, time_step, Real);
			/// set the value of the time step
			void setTimeStep(Real time_step);

			/// return the of iterations done in the last solveStep
			AKANTU_GET_MACRO(NumberIter, n_iter, UInt);

			/// 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 vector
			AKANTU_GET_MACRO(Displacement, *displacement, Array <Real> &);

			/// get the SolidMechanicsModel::previous_displacement vector
			AKANTU_GET_MACRO(PreviousDisplacement, *previous_displacement, Array <Real> &);

			/// get the SolidMechanicsModel::current_position vector \warn only consistent
			/// after a call to SolidMechanicsModel::updateCurrentPosition
			AKANTU_GET_MACRO(CurrentPosition, *current_position, const Array <Real> &);

			/// get the SolidMechanicsModel::increment vector \warn only consistent if
			/// SolidMechanicsModel::setIncrementFlagOn has been called before
			AKANTU_GET_MACRO(Increment, *increment, Array <Real> &);

			/// get the lumped SolidMechanicsModel::mass vector
			AKANTU_GET_MACRO(Mass, *mass, Array <Real> &);

			/// get the SolidMechanicsModel::velocity vector
			AKANTU_GET_MACRO(Velocity, *velocity, Array <Real> &);

			/// get the SolidMechanicsModel::acceleration vector, updated by
			/// SolidMechanicsModel::updateAcceleration
			AKANTU_GET_MACRO(Acceleration, *acceleration, Array <Real> &);

			/// get the SolidMechanicsModel::force vector (boundary forces)
			AKANTU_GET_MACRO(Force, *force, Array <Real> &);

			/// get the SolidMechanicsModel::residual vector, computed by
			/// SolidMechanicsModel::updateResidual
			AKANTU_GET_MACRO(Residual, *residual, Array <Real> &);

			/// get the SolidMechanicsModel::blocked_dofs vector
			AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array <bool> &);

			/// get the SolidMechnicsModel::incrementAcceleration vector
			AKANTU_GET_MACRO(IncrementAcceleration, *increment_acceleration, Array <Real> &);

			/// get the value of the SolidMechanicsModel::increment_flag
			AKANTU_GET_MACRO(IncrementFlag, increment_flag, bool);

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

			/// get a particular material (by 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();
			}

			inline void setMaterialSelector(MaterialSelector & selector);

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

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

			/// compute the potential energy
			Real getPotentialEnergy();

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

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

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

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

			/**
			* @brief set the SolidMechanicsModel::increment_flag to on, the activate the
			* update of the SolidMechanicsModel::increment vector
			*/
			void setIncrementFlagOn();

			/// get the stiffness matrix
			AKANTU_GET_MACRO(StiffnessMatrix, *stiffness_matrix, SparseMatrix &);

			/// get the global jacobian matrix of the system
			AKANTU_GET_MACRO(GlobalJacobianMatrix, *jacobian_matrix, const SparseMatrix &);

			/// get the mass matrix
			AKANTU_GET_MACRO(MassMatrix, *mass_matrix, SparseMatrix &);

			/// get the velocity damping matrix
			AKANTU_GET_MACRO(VelocityDampingMatrix, *velocity_damping_matrix, SparseMatrix &);

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

			/// get integrator
			AKANTU_GET_MACRO(Integrator, *integrator, const IntegrationScheme2ndOrder &);

			/// get access to the internal solver
			AKANTU_GET_MACRO(Solver, *solver, Solver &);

			/// get synchronizer
			AKANTU_GET_MACRO(Synchronizer, *synch_parallel, const DistributedSynchronizer &);

			AKANTU_GET_MACRO(MaterialByElement, material_index, 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);

			/// Get the type of analysis method used
			AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);

			template <int dim, class model_type>
			friend struct ContactData;

			template <int Dim, AnalysisMethod s, ContactResolutionMethod r>
			friend class ContactResolution;

			protected:
			friend class Material;

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

			/* ------------------------------------------------------------------------ */
			/* Class Members */
			/* ------------------------------------------------------------------------ */
			protected:
			/// number of iterations
			UInt n_iter;

			/// time step
			Real time_step;

			/// conversion coefficient form force/mass to acceleration
			Real f_m2a;

			/// displacements array
			Array <Real> *displacement;

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

			/// lumped mass array
			Array <Real> *mass;

			/// velocities array
			Array <Real> *velocity;

			/// accelerations array
			Array <Real> *acceleration;

			/// accelerations array
			Array <Real> *increment_acceleration;

			/// forces array
			Array <Real> *force;

			/// residuals array
			Array <Real> *residual;

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

			/// array of current position used during update residual
			Array <Real> *current_position;

			/// mass matrix
			SparseMatrix *mass_matrix;

			/// velocity damping matrix
			SparseMatrix *velocity_damping_matrix;

			/// stiffness matrix
			SparseMatrix *stiffness_matrix;

			/// jacobian matrix @f[A = cM + dD + K@f] with @f[c = \frac{1}{\beta \Delta
			/// t^2}, d = \frac{\gamma}{\beta \Delta t} @f]
			SparseMatrix *jacobian_matrix;

			/// 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 <Material *> materials;

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

			/// class defining of to choose a material
			MaterialSelector *material_selector;

			/// define if it is the default selector or not
			bool is_default_material_selector;

			/// integration scheme of second order used
			IntegrationScheme2ndOrder *integrator;

			/// increment of displacement
			Array <Real> *increment;

			/// flag defining if the increment must be computed or not
			bool increment_flag;

			/// solver for implicit
			Solver *solver;

			/// analysis method check the list in akantu::AnalysisMethod
			AnalysisMethod method;

			/// internal synchronizer for parallel computations
			DistributedSynchronizer *synch_parallel;

			/// tells if the material are instantiated
			bool are_materials_instantiated;

			/// map a registered internals to be flattened for dump purposes
			std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *> registered_internals;
			};


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

			__END_AKANTU__

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

			__BEGIN_AKANTU__

			#include "solid_mechanics_model_tmpl.hh"

			#if defined (AKANTU_INCLUDE_INLINE_IMPL)
			# include "solid_mechanics_model_inline_impl.cc"
			#endif

			/// standard output stream operator
			inline std::ostream & operator << (std::ostream & stream, const SolidMechanicsModel &_this) {
			_this.printself(stream);
			return stream;
			}

			__END_AKANTU__


			#include "material_selector_tmpl.hh"

			#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */

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rAKA/src/model/solid_mechanics/solid_mechanics_model.hh
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solid_mechanics_model.hh
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