material.hh
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material.hh
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	/**
	* @file material.hh
	*
	* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	*
	* @date creation: Fri Jun 18 2010
	* @date last modification: Wed Nov 25 2015
	*
	* @brief Mother class for all materials
	*
	* @section LICENSE
	*
	* Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
	* Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
	* Solides)
	*
	* Akantu is free software: you can redistribute it and/or modify it under the
	* terms of the GNU Lesser General Public License as published by the Free
	* Software Foundation, either version 3 of the License, or (at your option) any
	* later version.
	*
	* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
	* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
	* details.
	*
	* You should have received a copy of the GNU Lesser General Public License
	* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
	*
	*/

	/* -------------------------------------------------------------------------- */
	#include "aka_factory.hh"
	#include "aka_voigthelper.hh"
	#include "data_accessor.hh"
	#include "integration_point.hh"
	#include "parsable.hh"
	#include "parser.hh"
	/* -------------------------------------------------------------------------- */
	#include "internal_field.hh"
	#include "random_internal_field.hh"
	/* -------------------------------------------------------------------------- */
	#include "mesh_events.hh"
	#include "solid_mechanics_model_event_handler.hh"
	/* -------------------------------------------------------------------------- */

	#ifndef __AKANTU_MATERIAL_HH__
	#define __AKANTU_MATERIAL_HH__

	/* -------------------------------------------------------------------------- */
	namespace akantu {
	class Model;
	class SolidMechanicsModel;
	} // namespace akantu

	namespace akantu {

	/**
	* Interface of all materials
	* Prerequisites for a new material
	* - inherit from this class
	* - implement the following methods:
	* \code
	* virtual Real getStableTimeStep(Real h, const Element & element =
	* ElementNull);
	*
	* virtual void computeStress(ElementType el_type,
	* GhostType ghost_type = _not_ghost);
	*
	* virtual void computeTangentStiffness(const ElementType & el_type,
	* Array<Real> & tangent_matrix,
	* GhostType ghost_type = _not_ghost);
	* \endcode
	*
	*/

	class Material : public Memory,
	public DataAccessor<Element>,
	public Parsable,
	public MeshEventHandler,
	protected SolidMechanicsModelEventHandler {
	/* ------------------------------------------------------------------------ */
	/* Constructors/Destructors */
	/* ------------------------------------------------------------------------ */
	public:
	#if __cplusplus > 199711L
	Material(const Material & mat) = delete;
	Material & operator=(const Material & mat) = delete;
	#endif

	/// Initialize material with defaults
	Material(SolidMechanicsModel & model, const ID & id = "");

	/// Initialize material with custom mesh & fe_engine
	Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
	FEEngine & fe_engine, const ID & id = "");

	/// Destructor
	~Material() override;

	protected:
	void initialize();

	/* ------------------------------------------------------------------------ */
	/* Function that materials can/should reimplement */
	/* ------------------------------------------------------------------------ */
	protected:
	/// constitutive law
	virtual void computeStress(__attribute__((unused)) ElementType el_type,
	__attribute__((unused))
	GhostType ghost_type = _not_ghost) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	/// compute the tangent stiffness matrix
	virtual void computeTangentModuli(__attribute__((unused))
	const ElementType & el_type,
	__attribute__((unused))
	Array<Real> & tangent_matrix,
	__attribute__((unused))
	GhostType ghost_type = _not_ghost) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	/// compute the potential energy
	virtual void computePotentialEnergy(ElementType el_type,
	GhostType ghost_type = _not_ghost);

	/// compute the potential energy for an element
	virtual void
	computePotentialEnergyByElement(__attribute__((unused)) ElementType type,
	__attribute__((unused)) UInt index,
	__attribute__((unused))
	Vector<Real> & epot_on_quad_points) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	virtual void updateEnergies(__attribute__((unused)) ElementType el_type,
	__attribute__((unused))
	GhostType ghost_type = _not_ghost) {}

	virtual void updateEnergiesAfterDamage(__attribute__((unused))
	ElementType el_type,
	__attribute__((unused))
	GhostType ghost_type = _not_ghost) {}

	/// set the material to steady state (to be implemented for materials that
	/// need it)
	virtual void setToSteadyState(__attribute__((unused)) ElementType el_type,
	__attribute__((unused))
	GhostType ghost_type = _not_ghost) {}

	/// function called to update the internal parameters when the modifiable
	/// parameters are modified
	virtual void updateInternalParameters() {}

	public:
	/// extrapolate internal values
	virtual void extrapolateInternal(const ID & id, const Element & element,
	const Matrix<Real> & points,
	Matrix<Real> & extrapolated);

	/// compute the p-wave speed in the material
	virtual Real getPushWaveSpeed(__attribute__((unused))
	const Element & element) const {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	/// compute the s-wave speed in the material
	virtual Real getShearWaveSpeed(__attribute__((unused))
	const Element & element) const {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	/// get a material celerity to compute the stable time step (default: is the
	/// push wave speed)
	virtual Real getCelerity(const Element & element) const {
	return getPushWaveSpeed(element);
	}

	/* ------------------------------------------------------------------------ */
	/* Methods */
	/* ------------------------------------------------------------------------ */
	public:
	template <typename T>
	void registerInternal(__attribute__((unused)) InternalField<T> & vect) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	template <typename T>
	void unregisterInternal(__attribute__((unused)) InternalField<T> & vect) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	}

	/// initialize the material computed parameter
	virtual void initMaterial();

	/// compute the residual for this material
	// virtual void updateResidual(GhostType ghost_type = _not_ghost);

	/// assemble the residual for this material
	virtual void assembleInternalForces(GhostType ghost_type);

	/// save the stress in the previous_stress if needed
	virtual void savePreviousState();

	/// compute the stresses for this material
	virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
	virtual void
	computeAllStressesFromTangentModuli(GhostType ghost_type = _not_ghost);
	virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost);

	/// set material to steady state
	void setToSteadyState(GhostType ghost_type = _not_ghost);

	/// compute the stiffness matrix
	virtual void assembleStiffnessMatrix(GhostType ghost_type);

	/// add an element to the local mesh filter
	inline UInt addElement(const ElementType & type, UInt element,
	const GhostType & ghost_type);
	inline UInt addElement(const Element & element);

	/// add many elements at once
	void addElements(const Array<Element> & elements_to_add);

	/// remove many element at once
	void removeElements(const Array<Element> & elements_to_remove);

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

	/**
	* interpolate stress on given positions for each element by means
	* of a geometrical interpolation on quadrature points
	*/
	void interpolateStress(ElementTypeMapArray<Real> & result,
	const GhostType ghost_type = _not_ghost);

	/**
	* interpolate stress on given positions for each element by means
	* of a geometrical interpolation on quadrature points and store the
	* results per facet
	*/
	void interpolateStressOnFacets(ElementTypeMapArray<Real> & result,
	ElementTypeMapArray<Real> & by_elem_result,
	const GhostType ghost_type = _not_ghost);

	/**
	* function to initialize the elemental field interpolation
	* function by inverting the quadrature points' coordinates
	*/
	void initElementalFieldInterpolation(
	const ElementTypeMapArray<Real> & interpolation_points_coordinates);

	/* ------------------------------------------------------------------------ */
	/* Common part */
	/* ------------------------------------------------------------------------ */
	protected:
	/* ------------------------------------------------------------------------ */
	inline UInt getTangentStiffnessVoigtSize(UInt spatial_dimension) const;

	/// compute the potential energy by element
	void computePotentialEnergyByElements();

	/// resize the intenals arrays
	virtual void resizeInternals();

	/* ------------------------------------------------------------------------ */
	/* Finite deformation functions */
	/* This functions area implementing what is described in the paper of Bathe */
	/* et al, in IJNME, Finite Element Formulations For Large Deformation */
	/* Dynamic Analysis, Vol 9, 353-386, 1975 */
	/* ------------------------------------------------------------------------ */
	protected:
	/// assemble the residual
	template <UInt dim> void assembleInternalForces(GhostType ghost_type);

	/// Computation of Cauchy stress tensor in the case of finite deformation from
	/// the 2nd Piola-Kirchhoff for a given element type
	template <UInt dim>
	void computeCauchyStress(ElementType el_type,
	GhostType ghost_type = _not_ghost);

	/// Computation the Cauchy stress the 2nd Piola-Kirchhoff and the deformation
	/// gradient
	template <UInt dim>
	inline void computeCauchyStressOnQuad(const Matrix<Real> & F,
	const Matrix<Real> & S,
	Matrix<Real> & cauchy,
	const Real & C33 = 1.0) const;

	template <UInt dim>
	void computeAllStressesFromTangentModuli(const ElementType & type,
	GhostType ghost_type);

	template <UInt dim>
	void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);

	/// assembling in finite deformation
	template <UInt dim>
	void assembleStiffnessMatrixNL(const ElementType & type,
	GhostType ghost_type);

	template <UInt dim>
	void assembleStiffnessMatrixL2(const ElementType & type,
	GhostType ghost_type);

	/// Size of the Stress matrix for the case of finite deformation see: Bathe et
	/// al, IJNME, Vol 9, 353-386, 1975
	inline UInt getCauchyStressMatrixSize(UInt spatial_dimension) const;

	/// Sets the stress matrix according to Bathe et al, IJNME, Vol 9, 353-386,
	/// 1975
	template <UInt dim>
	inline void setCauchyStressMatrix(const Matrix<Real> & S_t,
	Matrix<Real> & sigma);

	/// write the stress tensor in the Voigt notation.
	template <UInt dim>
	inline void setCauchyStressArray(const Matrix<Real> & S_t,
	Matrix<Real> & sigma_voight);

	/* ------------------------------------------------------------------------ */
	/* Conversion functions */
	/* ------------------------------------------------------------------------ */
	public:
	template <UInt dim>
	static inline void gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F);
	static inline void rightCauchy(const Matrix<Real> & F, Matrix<Real> & C);
	static inline void leftCauchy(const Matrix<Real> & F, Matrix<Real> & B);

	template <UInt dim>
	static inline void gradUToEpsilon(const Matrix<Real> & grad_u,
	Matrix<Real> & epsilon);
	template <UInt dim>
	static inline void gradUToGreenStrain(const Matrix<Real> & grad_u,
	Matrix<Real> & epsilon);

	static inline Real stressToVonMises(const Matrix<Real> & stress);

	protected:
	/// converts global element to local element
	inline Element convertToLocalElement(const Element & global_element) const;
	/// converts local element to global element
	inline Element convertToGlobalElement(const Element & local_element) const;

	/// converts global quadrature point to local quadrature point
	inline IntegrationPoint
	convertToLocalPoint(const IntegrationPoint & global_point) const;
	/// converts local quadrature point to global quadrature point
	inline IntegrationPoint
	convertToGlobalPoint(const IntegrationPoint & local_point) const;

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

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

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

	template <typename T>
	inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
	CommunicationBuffer & buffer,
	const Array<Element> & elements,
	const ID & fem_id = ID()) const;

	template <typename T>
	inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
	CommunicationBuffer & buffer,
	const Array<Element> & elements,
	const ID & fem_id = ID());

	/* ------------------------------------------------------------------------ */
	/* MeshEventHandler inherited members */
	/* ------------------------------------------------------------------------ */
	public:
	/* ------------------------------------------------------------------------ */
	void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override{};
	void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
	const RemovedNodesEvent &) 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> &, const Array<Element> &,
	const ElementTypeMapArray<UInt> &,
	const ChangedElementsEvent &) override{};

	/* ------------------------------------------------------------------------ */
	/* SolidMechanicsModelEventHandler inherited members */
	/* ------------------------------------------------------------------------ */
	public:
	virtual void beforeSolveStep();
	virtual void afterSolveStep();

	void onDamageIteration() override;
	void onDamageUpdate() override;
	void onDump() override;

	/* ------------------------------------------------------------------------ */
	/* Accessors */
	/* ------------------------------------------------------------------------ */
	public:
	AKANTU_GET_MACRO(Name, name, const std::string &);

	AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &)

	AKANTU_GET_MACRO(ID, Memory::getID(), const ID &);
	AKANTU_GET_MACRO(Rho, rho, Real);
	AKANTU_SET_MACRO(Rho, rho, Real);

	AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);

	/// return the potential energy for the subset of elements contained by the
	/// material
	Real getPotentialEnergy();
	/// return the potential energy for the provided element
	Real getPotentialEnergy(ElementType & type, UInt index);

	/// return the energy (identified by id) for the subset of elements contained
	/// by the material
	virtual Real getEnergy(const std::string & energy_id);
	/// return the energy (identified by id) for the provided element
	virtual Real getEnergy(const std::string & energy_id, ElementType type, UInt index);

	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(GradU, gradu, Real);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
	AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PotentialEnergy, potential_energy,
	Real);
	AKANTU_GET_MACRO(GradU, gradu, const ElementTypeMapArray<Real> &);
	AKANTU_GET_MACRO(Stress, stress, const ElementTypeMapArray<Real> &);
	AKANTU_GET_MACRO(ElementFilter, element_filter,
	const ElementTypeMapArray<UInt> &);
	AKANTU_GET_MACRO(FEEngine, fem, FEEngine &);

	bool isNonLocal() const { return is_non_local; }

	template <typename T>
	const Array<T> & getArray(const ID & id, const ElementType & type,
	const GhostType & ghost_type = _not_ghost) const;
	template <typename T>
	Array<T> & getArray(const ID & id, const ElementType & type,
	const GhostType & ghost_type = _not_ghost);

	template <typename T>
	const InternalField<T> & getInternal(const ID & id) const;
	template <typename T> InternalField<T> & getInternal(const ID & id);

	template <typename T>
	inline bool isInternal(const ID & id, const ElementKind & element_kind) const;

	template <typename T>
	ElementTypeMap<UInt>
	getInternalDataPerElem(const ID & id, const ElementKind & element_kind) const;

	bool isFiniteDeformation() const { return finite_deformation; }
	bool isInelasticDeformation() const { return inelastic_deformation; }

	template <typename T> inline void setParam(const ID & param, T value);
	inline const Parameter & getParam(const ID & param) const;

	template <typename T>
	void flattenInternal(const std::string & field_id,
	ElementTypeMapArray<T> & internal_flat,
	const GhostType ghost_type = _not_ghost,
	ElementKind element_kind = _ek_not_defined) const;

	/// apply a constant eigengrad_u everywhere in the material
	virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
	const GhostType = _not_ghost);

	/// specify if the matrix need to be recomputed for this material
	virtual bool hasStiffnessMatrixChanged() { return true; }

	protected:
	bool isInit() const { return is_init; }

	/* ------------------------------------------------------------------------ */
	/* Class Members */
	/* ------------------------------------------------------------------------ */
	protected:
	/// boolean to know if the material has been initialized
	bool is_init;

	std::map<ID, InternalField<Real> *> internal_vectors_real;
	std::map<ID, InternalField<UInt> *> internal_vectors_uint;
	std::map<ID, InternalField<bool> *> internal_vectors_bool;

	protected:
	/// Link to the fem object in the model
	FEEngine & fem;

	/// Finite deformation
	bool finite_deformation;

	/// Finite deformation
	bool inelastic_deformation;

	/// material name
	std::string name;

	/// The model to witch the material belong
	SolidMechanicsModel & model;

	/// density : rho
	Real rho;

	/// spatial dimension
	UInt spatial_dimension;

	/// list of element handled by the material
	ElementTypeMapArray<UInt> element_filter;

	/// stresses arrays ordered by element types
	InternalField<Real> stress;

	/// eigengrad_u arrays ordered by element types
	InternalField<Real> eigengradu;

	/// grad_u arrays ordered by element types
	InternalField<Real> gradu;

	/// Green Lagrange strain (Finite deformation)
	InternalField<Real> green_strain;

	/// Second Piola-Kirchhoff stress tensor arrays ordered by element types
	/// (Finite deformation)
	InternalField<Real> piola_kirchhoff_2;

	/// potential energy by element
	InternalField<Real> potential_energy;

	/// tell if using in non local mode or not
	bool is_non_local;

	/// tell if the material need the previous stress state
	bool use_previous_stress;

	/// tell if the material need the previous strain state
	bool use_previous_gradu;

	/// elemental field interpolation coordinates
	InternalField<Real> interpolation_inverse_coordinates;

	/// elemental field interpolation points
	InternalField<Real> interpolation_points_matrices;

	/// vector that contains the names of all the internals that need to
	/// be transferred when material interfaces move
	std::vector<ID> internals_to_transfer;
	};

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

	} // namespace akantu

	#include "material_inline_impl.cc"

	#include "internal_field_tmpl.hh"
	#include "random_internal_field_tmpl.hh"

	/* -------------------------------------------------------------------------- */
	/* Auto loop */
	/* -------------------------------------------------------------------------- */
	/// This can be used to automatically write the loop on quadrature points in
	/// functions such as computeStress. This macro in addition to write the loop
	/// provides two tensors (matrices) sigma and grad_u
	#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
	Array<Real>::matrix_iterator gradu_it = \
	this->gradu(el_type, ghost_type) \
	.begin(this->spatial_dimension, this->spatial_dimension); \
	Array<Real>::matrix_iterator gradu_end = \
	this->gradu(el_type, ghost_type) \
	.end(this->spatial_dimension, this->spatial_dimension); \
	\
	this->stress(el_type, ghost_type) \
	.resize(this->gradu(el_type, ghost_type).size()); \
	\
	Array<Real>::iterator<Matrix<Real>> stress_it = \
	this->stress(el_type, ghost_type) \
	.begin(this->spatial_dimension, this->spatial_dimension); \
	\
	if (this->isFiniteDeformation()) { \
	this->piola_kirchhoff_2(el_type, ghost_type) \
	.resize(this->gradu(el_type, ghost_type).size()); \
	stress_it = this->piola_kirchhoff_2(el_type, ghost_type) \
	.begin(this->spatial_dimension, this->spatial_dimension); \
	} \
	\
	for (; gradu_it != gradu_end; ++gradu_it, ++stress_it) { \
	Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
	Matrix<Real> & __attribute__((unused)) sigma = *stress_it

	#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END }

	/// This can be used to automatically write the loop on quadrature points in
	/// functions such as computeTangentModuli. This macro in addition to write the
	/// loop provides two tensors (matrices) sigma_tensor, grad_u, and a matrix
	/// where the elemental tangent moduli should be stored in Voigt Notation
	#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
	Array<Real>::matrix_iterator gradu_it = \
	this->gradu(el_type, ghost_type) \
	.begin(this->spatial_dimension, this->spatial_dimension); \
	Array<Real>::matrix_iterator gradu_end = \
	this->gradu(el_type, ghost_type) \
	.end(this->spatial_dimension, this->spatial_dimension); \
	Array<Real>::matrix_iterator sigma_it = \
	this->stress(el_type, ghost_type) \
	.begin(this->spatial_dimension, this->spatial_dimension); \
	\
	tangent_mat.resize(this->gradu(el_type, ghost_type).size()); \
	\
	UInt tangent_size = \
	this->getTangentStiffnessVoigtSize(this->spatial_dimension); \
	Array<Real>::matrix_iterator tangent_it = \
	tangent_mat.begin(tangent_size, tangent_size); \
	\
	for (; gradu_it != gradu_end; ++gradu_it, ++sigma_it, ++tangent_it) { \
	Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
	Matrix<Real> & __attribute__((unused)) sigma_tensor = *sigma_it; \
	Matrix<Real> & tangent = *tangent_it

	#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END }

	/* -------------------------------------------------------------------------- */
	namespace akantu {
	using MaterialFactory =
	Factory<Material, UInt, const ID &, SolidMechanicsModel &, const ID &>;
	} // namespace akantu

	#define INSTANTIATE_MATERIAL_ONLY(mat_name) \
	template class mat_name<1>; \
	template class mat_name<2>; \
	template class mat_name<3>

	#define MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name) \
	[](UInt dim, const ID &, SolidMechanicsModel & model, \
	const ID & id) -> std::unique_ptr<Material> { \
	switch (dim) { \
	case 1: \
	return std::make_unique<mat_name<1>>(model, id); \
	case 2: \
	return std::make_unique<mat_name<2>>(model, id); \
	case 3: \
	return std::make_unique<mat_name<3>>(model, id); \
	default: \
	AKANTU_EXCEPTION("The dimension " \
	<< dim << "is not a valid dimension for the material " \
	<< #id); \
	} \
	}

	#define INSTANTIATE_MATERIAL(id, mat_name) \
	INSTANTIATE_MATERIAL_ONLY(mat_name); \
	static bool material_is_alocated_##id = \
	MaterialFactory::getInstance().registerAllocator( \
	#id, MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name))

	#endif /* __AKANTU_MATERIAL_HH__ */

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