material.cc
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material.cc
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	/**
	* @file material.cc
	*
	* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
	* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	*
	* @date creation: Tue Jul 27 2010
	* @date last modification: Tue Nov 24 2015
	*
	* @brief Implementation of the common part of the material class
	*
	* @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 "material.hh"
	#include "solid_mechanics_model.hh"
	#include "sparse_matrix.hh"
	#include "dof_synchronizer.hh"
	/* -------------------------------------------------------------------------- */

	__BEGIN_AKANTU__

	/* -------------------------------------------------------------------------- */
	Material::Material(SolidMechanicsModel & model, const ID & id)
	: Memory(id, model.getMemoryID()), Parsable(_st_material, id),
	is_init(false), fem(&(model.getFEEngine())), finite_deformation(false),
	name(""), model(&model),
	spatial_dimension(this->model->getSpatialDimension()),
	element_filter("element_filter", id, this->memory_id),
	stress("stress", this), eigengradu("eigen_grad_u", this),
	gradu("grad_u", this), green_strain("green_strain", this),
	piola_kirchhoff_2("piola_kirchhoff_2", *this),
	potential_energy("potential_energy", *this), is_non_local(false),
	use_previous_stress(false), use_previous_gradu(false),
	interpolation_inverse_coordinates("interpolation inverse coordinates",
	*this),
	interpolation_points_matrices("interpolation points matrices", *this) {
	AKANTU_DEBUG_IN();

	/// for each connectivity types allocate the element filer array of the
	/// material
	model.getMesh().initElementTypeMapArray(element_filter, 1, spatial_dimension,
	false, _ek_regular);

	this->initialize();
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	Material::Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
	FEEngine & fe_engine, const ID & id)
	: Memory(id, model.getMemoryID()), Parsable(_st_material, id),
	is_init(false), fem(&(model.getFEEngine())), finite_deformation(false),
	name(""), model(&model), spatial_dimension(dim),
	element_filter("element_filter", id, this->memory_id),
	stress("stress", *this, dim, fe_engine, this->element_filter),
	eigengradu("eigen_grad_u", *this, dim, fe_engine, this->element_filter),
	gradu("gradu", *this, dim, fe_engine, this->element_filter),
	green_strain("green_strain", *this, dim, fe_engine, this->element_filter),
	piola_kirchhoff_2("poila_kirchhoff_2", *this, dim, fe_engine,
	this->element_filter),
	potential_energy("potential_energy", *this, dim, fe_engine,
	this->element_filter),
	is_non_local(false), use_previous_stress(false),
	use_previous_gradu(false),
	interpolation_inverse_coordinates("interpolation inverse_coordinates",
	*this, dim, fe_engine,
	this->element_filter),
	interpolation_points_matrices("interpolation points matrices", *this, dim,
	fe_engine, this->element_filter) {

	AKANTU_DEBUG_IN();
	mesh.initElementTypeMapArray(element_filter, 1, spatial_dimension, false,
	_ek_regular);

	this->initialize();
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	Material::~Material() {
	AKANTU_DEBUG_IN();

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::initialize() {
	registerParam("rho", rho, Real(0.), _pat_parsable \| _pat_modifiable,
	"Density");
	registerParam("name", name, std::string(), _pat_parsable \| _pat_readable);
	registerParam("finite_deformation", finite_deformation, false,
	_pat_parsable \| _pat_readable, "Is finite deformation");
	registerParam("inelastic_deformation", inelastic_deformation, false,
	_pat_internal, "Is inelastic deformation");

	/// allocate gradu stress for local elements
	eigengradu.initialize(spatial_dimension * spatial_dimension);
	gradu.initialize(spatial_dimension * spatial_dimension);
	stress.initialize(spatial_dimension * spatial_dimension);

	potential_energy.initialize(1);

	this->model->registerEventHandler(*this);
	}

	/* -------------------------------------------------------------------------- */
	void Material::initMaterial() {
	AKANTU_DEBUG_IN();

	if (finite_deformation) {
	this->piola_kirchhoff_2.initialize(spatial_dimension * spatial_dimension);
	if (use_previous_stress)
	this->piola_kirchhoff_2.initializeHistory();
	this->green_strain.initialize(spatial_dimension * spatial_dimension);
	}

	if (use_previous_stress)
	this->stress.initializeHistory();
	if (use_previous_gradu)
	this->gradu.initializeHistory();

	for (std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.begin();
	it != internal_vectors_real.end(); ++it)
	it->second->resize();

	for (std::map<ID, InternalField<UInt> *>::iterator it =
	internal_vectors_uint.begin();
	it != internal_vectors_uint.end(); ++it)
	it->second->resize();

	for (std::map<ID, InternalField<bool> *>::iterator it =
	internal_vectors_bool.begin();
	it != internal_vectors_bool.end(); ++it)
	it->second->resize();

	is_init = true;

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::savePreviousState() {
	AKANTU_DEBUG_IN();

	for (std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.begin();
	it != internal_vectors_real.end(); ++it) {
	if (it->second->hasHistory())
	it->second->saveCurrentValues();
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	/**
	* Compute the residual by assembling @f$\int_{e} \sigma_e \frac{\partial
	* \varphi}{\partial X} dX @f$
	*
	* @param[in] displacements nodes displacements
	* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
	*/
	// void Material::updateResidual(GhostType ghost_type) {
	// AKANTU_DEBUG_IN();

	// computeAllStresses(ghost_type);
	// assembleResidual(ghost_type);

	// AKANTU_DEBUG_OUT();
	// }

	/* -------------------------------------------------------------------------- */
	void Material::assembleInternalForces(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	UInt spatial_dimension = model->getSpatialDimension();

	if (!finite_deformation) {

	Array<Real> & internal_force = const_cast<Array<Real> &>(model->getInternalForce());

	Mesh & mesh = fem->getMesh();
	Mesh::type_iterator it =
	element_filter.firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	element_filter.lastType(spatial_dimension, ghost_type);
	for (; it != last_type; ++it) {
	Array<UInt> & elem_filter = element_filter(*it, ghost_type);
	UInt nb_element = elem_filter.getSize();
	if (nb_element) {
	const Array<Real> & shapes_derivatives =
	fem->getShapesDerivatives(*it, ghost_type);

	UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
	UInt nb_quadrature_points =
	fem->getNbIntegrationPoints(*it, ghost_type);

	/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by
	/// @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
	Array<Real> * sigma_dphi_dx =
	new Array<Real>(nb_element * nb_quadrature_points,
	size_of_shapes_derivatives, "sigma_x_dphi_/_dX");

	Array<Real> * shapesd_filtered =
	new Array<Real>(0, size_of_shapes_derivatives, "filtered shapesd");

	FEEngine::filterElementalData(mesh, shapes_derivatives,
	shapesd_filtered, it, ghost_type,
	elem_filter);

	Array<Real> & stress_vect = this->stress(*it, ghost_type);

	Array<Real>::matrix_iterator sigma =
	stress_vect.begin(spatial_dimension, spatial_dimension);
	Array<Real>::matrix_iterator B =
	shapesd_filtered->begin(spatial_dimension, nb_nodes_per_element);
	Array<Real>::matrix_iterator Bt_sigma_it =
	sigma_dphi_dx->begin(spatial_dimension, nb_nodes_per_element);

	for (UInt q = 0; q < nb_element * nb_quadrature_points;
	++q, ++sigma, ++B, ++Bt_sigma_it)
	Bt_sigma_it->mul<false, false>(sigma, B);

	delete shapesd_filtered;

	/**
	* compute @f$\int \sigma * \frac{\partial \varphi}{\partial X}dX@f$ by
	* @f$ \sum_q \mathbf{B}^t
	* \mathbf{\sigma}_q \overline w_q J_q@f$
	*/
	Array<Real> * int_sigma_dphi_dx = new Array<Real>(
	nb_element, nb_nodes_per_element * spatial_dimension,
	"int_sigma_x_dphi_/_dX");

	fem->integrate(sigma_dphi_dx, int_sigma_dphi_dx,
	size_of_shapes_derivatives, *it, ghost_type,
	elem_filter);
	delete sigma_dphi_dx;

	/// assemble
	model->getDOFManager().assembleElementalArrayLocalArray(*int_sigma_dphi_dx, internal_force,
	*it, ghost_type, 1, elem_filter);
	delete int_sigma_dphi_dx;
	}
	}
	} else {
	switch (spatial_dimension) {
	case 1:
	this->assembleInternalForces<1>(ghost_type);
	break;
	case 2:
	this->assembleInternalForces<2>(ghost_type);
	break;
	case 3:
	this->assembleInternalForces<3>(ghost_type);
	break;
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	/**
	* Compute the stress from the gradu
	*
	* @param[in] current_position nodes postition + displacements
	* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
	*/
	void Material::computeAllStresses(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	UInt spatial_dimension = model->getSpatialDimension();

	Mesh::type_iterator it =
	fem->getMesh().firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	fem->getMesh().lastType(spatial_dimension, ghost_type);

	for (; it != last_type; ++it) {
	Array<UInt> & elem_filter = element_filter(*it, ghost_type);
	if (elem_filter.getSize() == 0)
	continue;
	Array<Real> & gradu_vect = gradu(*it, ghost_type);

	/// compute @f$\nabla u@f$
	fem->gradientOnIntegrationPoints(model->getDisplacement(), gradu_vect,
	spatial_dimension, *it, ghost_type,
	elem_filter);

	gradu_vect -= eigengradu(*it, ghost_type);

	/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
	computeStress(*it, ghost_type);
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::computeAllCauchyStresses(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	AKANTU_DEBUG_ASSERT(finite_deformation, "The Cauchy stress can only be "
	"computed if you are working in "
	"finite deformation.");

	// resizeInternalArray(stress);

	Mesh::type_iterator it =
	fem->getMesh().firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	fem->getMesh().lastType(spatial_dimension, ghost_type);

	for (; it != last_type; ++it)
	switch (spatial_dimension) {
	case 1:
	this->computeCauchyStress<1>(*it, ghost_type);
	break;
	case 2:
	this->computeCauchyStress<2>(*it, ghost_type);
	break;
	case 3:
	this->computeCauchyStress<3>(*it, ghost_type);
	break;
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim>
	void Material::computeCauchyStress(ElementType el_type, GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	Array<Real>::matrix_iterator gradu_it =
	this->gradu(el_type, ghost_type).begin(dim, dim);

	Array<Real>::matrix_iterator gradu_end =
	this->gradu(el_type, ghost_type).end(dim, dim);

	Array<Real>::matrix_iterator piola_it =
	this->piola_kirchhoff_2(el_type, ghost_type).begin(dim, dim);

	Array<Real>::matrix_iterator stress_it =
	this->stress(el_type, ghost_type).begin(dim, dim);

	Matrix<Real> F_tensor(dim, dim);

	for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it) {
	Matrix<Real> & grad_u = *gradu_it;
	Matrix<Real> & piola = *piola_it;
	Matrix<Real> & sigma = *stress_it;

	gradUToF<dim>(grad_u, F_tensor);
	this->computeCauchyStressOnQuad<dim>(F_tensor, piola, sigma);
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::setToSteadyState(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	const Array<Real> & displacement = model->getDisplacement();

	// resizeInternalArray(gradu);

	UInt spatial_dimension = model->getSpatialDimension();

	Mesh::type_iterator it =
	fem->getMesh().firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	fem->getMesh().lastType(spatial_dimension, ghost_type);

	for (; it != last_type; ++it) {
	Array<UInt> & elem_filter = element_filter(*it, ghost_type);
	Array<Real> & gradu_vect = gradu(*it, ghost_type);

	/// compute @f$\nabla u@f$
	fem->gradientOnIntegrationPoints(displacement, gradu_vect,
	spatial_dimension, *it, ghost_type,
	elem_filter);

	setToSteadyState(*it, ghost_type);
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	/**
	* Compute the stiffness matrix by assembling @f$\int_{\omega} B^t \times D
	* \times B d\omega @f$
	*
	* @param[in] current_position nodes postition + displacements
	* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
	*/
	void Material::assembleStiffnessMatrix(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	UInt spatial_dimension = model->getSpatialDimension();

	Mesh::type_iterator it =
	element_filter.firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	element_filter.lastType(spatial_dimension, ghost_type);
	for (; it != last_type; ++it) {
	if (finite_deformation) {
	switch (spatial_dimension) {
	case 1: {
	assembleStiffnessMatrixNL<1>(*it, ghost_type);
	assembleStiffnessMatrixL2<1>(*it, ghost_type);
	break;
	}
	case 2: {
	assembleStiffnessMatrixNL<2>(*it, ghost_type);
	assembleStiffnessMatrixL2<2>(*it, ghost_type);
	break;
	}
	case 3: {
	assembleStiffnessMatrixNL<3>(*it, ghost_type);
	assembleStiffnessMatrixL2<3>(*it, ghost_type);
	break;
	}
	}
	} else {
	switch (spatial_dimension) {
	case 1: {
	assembleStiffnessMatrix<1>(*it, ghost_type);
	break;
	}
	case 2: {
	assembleStiffnessMatrix<2>(*it, ghost_type);
	break;
	}
	case 3: {
	assembleStiffnessMatrix<3>(*it, ghost_type);
	break;
	}
	}
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim>
	void Material::assembleStiffnessMatrix(const ElementType & type,
	GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	Array<UInt> & elem_filter = element_filter(type, ghost_type);
	if (elem_filter.getSize()) {

	const Array<Real> & shapes_derivatives = fem->getShapesDerivatives(type,
	ghost_type);

	Array<Real> & gradu_vect = gradu(type, ghost_type);

	UInt nb_element = elem_filter.getSize();
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	UInt nb_quadrature_points = fem->getNbIntegrationPoints(type, ghost_type);

	gradu_vect.resize(nb_quadrature_points * nb_element);

	fem->gradientOnIntegrationPoints(model->getDisplacement(), gradu_vect, dim,
	type, ghost_type, elem_filter);

	UInt tangent_size = getTangentStiffnessVoigtSize(dim);

	Array<Real> * tangent_stiffness_matrix = new Array<Real>(
	nb_element * nb_quadrature_points, tangent_size * tangent_size,
	"tangent_stiffness_matrix");

	tangent_stiffness_matrix->clear();

	computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);

	Array<Real> * shapesd_filtered =
	new Array<Real>(nb_element, dim * nb_nodes_per_element, "filtered shapesd");

	FEEngine::filterElementalData(fem->getMesh(), shapes_derivatives,
	*shapesd_filtered, type, ghost_type,
	elem_filter);

	/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	UInt bt_d_b_size = dim * nb_nodes_per_element;

	Array<Real> * bt_d_b =
	new Array<Real>(nb_element * nb_quadrature_points,
	bt_d_b_size * bt_d_b_size, "B^tDB");

	Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
	Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);

	Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
	shapesd_filtered->begin(dim, nb_nodes_per_element);

	Array<Real>::matrix_iterator Bt_D_B_it =
	bt_d_b->begin(dim * nb_nodes_per_element, dim * nb_nodes_per_element);

	Array<Real>::matrix_iterator D_it =
	tangent_stiffness_matrix->begin(tangent_size, tangent_size);

	Array<Real>::matrix_iterator D_end =
	tangent_stiffness_matrix->end(tangent_size, tangent_size);

	for (; D_it != D_end;
	++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it) {
	Matrix<Real> & D = *D_it;
	Matrix<Real> & Bt_D_B = *Bt_D_B_it;

	VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
	*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
	Bt_D.mul<true, false>(B, D);
	Bt_D_B.mul<false, false>(Bt_D, B);
	}

	delete tangent_stiffness_matrix;
	delete shapesd_filtered;

	/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	Array<Real> * K_e =
	new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");

	fem->integrate(bt_d_b, K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
	elem_filter);

	delete bt_d_b;

	model->getDOFManager().assembleElementalMatricesToMatrix("K", "displacement", *K_e,
	type, ghost_type, _symmetric,
	elem_filter);
	delete K_e;
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim>
	void Material::assembleStiffnessMatrixNL(const ElementType & type,
	GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	const Array<Real> & shapes_derivatives = fem->getShapesDerivatives(type, ghost_type);

	Array<UInt> & elem_filter = element_filter(type, ghost_type);
	// Array<Real> & gradu_vect = delta_gradu(type, ghost_type);

	UInt nb_element = elem_filter.getSize();
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	UInt nb_quadrature_points = fem->getNbIntegrationPoints(type, ghost_type);

	// gradu_vect.resize(nb_quadrature_points * nb_element);

	// fem->gradientOnIntegrationPoints(model->getIncrement(), gradu_vect,
	// dim, type, ghost_type, &elem_filter);

	Array<Real> * shapes_derivatives_filtered = new Array<Real>(
	nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
	"shapes derivatives filtered");

	Array<Real>::const_matrix_iterator shapes_derivatives_it =
	shapes_derivatives.begin(spatial_dimension, nb_nodes_per_element);

	Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
	shapes_derivatives_filtered->begin(spatial_dimension,
	nb_nodes_per_element);
	UInt * elem_filter_val = elem_filter.storage();
	for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
	for (UInt q = 0; q < nb_quadrature_points;
	++q, ++shapes_derivatives_filtered_it)
	*shapes_derivatives_filtered_it =
	shapes_derivatives_it[elem_filter_val nb_quadrature_points + q];

	/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	UInt bt_s_b_size = dim * nb_nodes_per_element;

	Array<Real> * bt_s_b = new Array<Real>(nb_element * nb_quadrature_points,
	bt_s_b_size * bt_s_b_size, "B^tDB");

	UInt piola_matrix_size = getCauchyStressMatrixSize(dim);

	Matrix<Real> B(piola_matrix_size, bt_s_b_size);
	Matrix<Real> Bt_S(bt_s_b_size, piola_matrix_size);
	Matrix<Real> S(piola_matrix_size, piola_matrix_size);

	shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
	spatial_dimension, nb_nodes_per_element);

	Array<Real>::matrix_iterator Bt_S_B_it =
	bt_s_b->begin(bt_s_b_size, bt_s_b_size);
	Array<Real>::matrix_iterator Bt_S_B_end =
	bt_s_b->end(bt_s_b_size, bt_s_b_size);

	Array<Real>::matrix_iterator piola_it =
	piola_kirchhoff_2(type, ghost_type).begin(dim, dim);

	for (; Bt_S_B_it != Bt_S_B_end;
	++Bt_S_B_it, ++shapes_derivatives_filtered_it, ++piola_it) {
	Matrix<Real> & Bt_S_B = *Bt_S_B_it;
	Matrix<Real> & Piola_kirchhoff_matrix = *piola_it;

	setCauchyStressMatrix<dim>(Piola_kirchhoff_matrix, S);
	VoigtHelper<dim>::transferBMatrixToBNL(*shapes_derivatives_filtered_it, B,
	nb_nodes_per_element);
	Bt_S.mul<true, false>(B, S);
	Bt_S_B.mul<false, false>(Bt_S, B);
	}

	delete shapes_derivatives_filtered;

	/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	Array<Real> * K_e = new Array<Real > (nb_element,
	bt_s_b_size * bt_s_b_size,
	"K_e");

	fem->integrate(bt_s_b, K_e,
	bt_s_b_size * bt_s_b_size,
	type, ghost_type,
	elem_filter);

	delete bt_s_b;

	model->getDOFManager().assembleElementalMatricesToMatrix("K", "displacement", *K_e,
	type, ghost_type, _symmetric,
	elem_filter);

	delete K_e;

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim>
	void Material::assembleStiffnessMatrixL2(const ElementType & type,
	GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	const Array<Real> & shapes_derivatives = fem->getShapesDerivatives(type, ghost_type);

	Array<UInt> & elem_filter = element_filter(type, ghost_type);
	Array<Real> & gradu_vect = gradu(type, ghost_type);

	UInt nb_element = elem_filter.getSize();
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	UInt nb_quadrature_points = fem->getNbIntegrationPoints(type, ghost_type);

	gradu_vect.resize(nb_quadrature_points * nb_element);

	fem->gradientOnIntegrationPoints(model->getDisplacement(), gradu_vect, dim,
	type, ghost_type, elem_filter);

	UInt tangent_size = getTangentStiffnessVoigtSize(dim);

	Array<Real> * tangent_stiffness_matrix =
	new Array<Real>(nb_element * nb_quadrature_points,
	tangent_size * tangent_size, "tangent_stiffness_matrix");

	tangent_stiffness_matrix->clear();

	computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);

	Array<Real> * shapes_derivatives_filtered = new Array<Real>(
	nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
	"shapes derivatives filtered");

	Array<Real>::const_matrix_iterator shapes_derivatives_it =
	shapes_derivatives.begin(spatial_dimension, nb_nodes_per_element);

	Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
	shapes_derivatives_filtered->begin(spatial_dimension,
	nb_nodes_per_element);
	UInt * elem_filter_val = elem_filter.storage();
	for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
	for (UInt q = 0; q < nb_quadrature_points;
	++q, ++shapes_derivatives_filtered_it)
	*shapes_derivatives_filtered_it =
	shapes_derivatives_it[elem_filter_val nb_quadrature_points + q];

	/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	UInt bt_d_b_size = dim * nb_nodes_per_element;

	Array<Real> * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
	bt_d_b_size * bt_d_b_size, "B^tDB");

	Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
	Matrix<Real> B2(tangent_size, dim * nb_nodes_per_element);
	Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);

	shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
	spatial_dimension, nb_nodes_per_element);

	Array<Real>::matrix_iterator Bt_D_B_it =
	bt_d_b->begin(dim * nb_nodes_per_element, dim * nb_nodes_per_element);

	Array<Real>::matrix_iterator grad_u_it = gradu_vect.begin(dim, dim);

	Array<Real>::matrix_iterator D_it =
	tangent_stiffness_matrix->begin(tangent_size, tangent_size);
	Array<Real>::matrix_iterator D_end =
	tangent_stiffness_matrix->end(tangent_size, tangent_size);

	for (; D_it != D_end;
	++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it, ++grad_u_it) {
	Matrix<Real> & grad_u = *grad_u_it;
	Matrix<Real> & D = *D_it;
	Matrix<Real> & Bt_D_B = *Bt_D_B_it;

	// transferBMatrixToBL1<dim > (*shapes_derivatives_filtered_it, B,
	// nb_nodes_per_element);
	VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
	*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
	VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
	grad_u, B2, nb_nodes_per_element);
	B += B2;
	Bt_D.mul<true, false>(B, D);
	Bt_D_B.mul<false, false>(Bt_D, B);
	}

	delete tangent_stiffness_matrix;
	delete shapes_derivatives_filtered;

	/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	Array<Real> * K_e =
	new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");

	fem->integrate(bt_d_b, K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
	elem_filter);

	delete bt_d_b;

	model->getDOFManager().assembleElementalMatricesToMatrix("K", "displacement", *K_e,
	type, ghost_type, _symmetric,
	elem_filter);
	delete K_e;

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim> void Material::assembleInternalForces(GhostType ghost_type) {

	AKANTU_DEBUG_IN();

	Array<Real> & internal_force = model->getInternalForce();

	Mesh & mesh = fem->getMesh();
	Mesh::type_iterator it = element_filter.firstType(dim, ghost_type);
	Mesh::type_iterator last_type = element_filter.lastType(dim, ghost_type);
	for (; it != last_type; ++it) {
	const Array<Real> & shapes_derivatives =
	fem->getShapesDerivatives(*it, ghost_type);

	Array<UInt> & elem_filter = element_filter(*it, ghost_type);
	if (elem_filter.getSize() == 0)
	continue;
	UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
	UInt nb_element = elem_filter.getSize();
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
	UInt nb_quadrature_points = fem->getNbIntegrationPoints(*it, ghost_type);

	Array<Real> * shapesd_filtered =
	new Array<Real>(nb_element, size_of_shapes_derivatives, "filtered shapesd");

	FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
	*it, ghost_type, elem_filter);

	Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
	shapesd_filtered->begin(dim, nb_nodes_per_element);

	// Set stress vectors

	UInt stress_size = getTangentStiffnessVoigtSize(dim);

	// Set matrices B and BNL*
	UInt bt_s_size = dim * nb_nodes_per_element;

	Array<Real> * bt_s =
	new Array<Real>(nb_element * nb_quadrature_points, bt_s_size, "B^t*S");

	Array<Real>::matrix_iterator grad_u_it =
	this->gradu(*it, ghost_type).begin(dim, dim);

	Array<Real>::matrix_iterator grad_u_end =
	this->gradu(*it, ghost_type).end(dim, dim);

	Array<Real>::matrix_iterator stress_it =
	this->piola_kirchhoff_2(*it, ghost_type).begin(dim, dim);

	shapes_derivatives_filtered_it =
	shapesd_filtered->begin(dim, nb_nodes_per_element);

	Array<Real>::matrix_iterator bt_s_it = bt_s->begin(bt_s_size, 1);

	Matrix<Real> S_vect(stress_size, 1);
	Matrix<Real> B_tensor(stress_size, bt_s_size);
	Matrix<Real> B2_tensor(stress_size, bt_s_size);

	for (; grad_u_it != grad_u_end; ++grad_u_it, ++stress_it,
	++shapes_derivatives_filtered_it,
	++bt_s_it) {
	Matrix<Real> & grad_u = *grad_u_it;
	Matrix<Real> & r_it = *bt_s_it;
	Matrix<Real> & S_it = *stress_it;

	setCauchyStressArray<dim>(S_it, S_vect);
	VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
	*shapes_derivatives_filtered_it, B_tensor, nb_nodes_per_element);
	VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
	grad_u, B2_tensor,
	nb_nodes_per_element);

	B_tensor += B2_tensor;

	r_it.mul<true, false>(B_tensor, S_vect);
	}

	delete shapesd_filtered;

	/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
	Array<Real> * r_e = new Array<Real>(nb_element, bt_s_size, "r_e");

	fem->integrate(bt_s, r_e, bt_s_size, *it, ghost_type, elem_filter);

	delete bt_s;

	model->getDOFManager().assembleElementalArrayLocalArray(*r_e, internal_force,
	*it, ghost_type, 1, elem_filter);
	delete r_e;
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::computeAllStressesFromTangentModuli(GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	UInt spatial_dimension = model->getSpatialDimension();

	Mesh::type_iterator it =
	element_filter.firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last_type =
	element_filter.lastType(spatial_dimension, ghost_type);
	for (; it != last_type; ++it) {
	switch (spatial_dimension) {
	case 1: {
	computeAllStressesFromTangentModuli<1>(*it, ghost_type);
	break;
	}
	case 2: {
	computeAllStressesFromTangentModuli<2>(*it, ghost_type);
	break;
	}
	case 3: {
	computeAllStressesFromTangentModuli<3>(*it, ghost_type);
	break;
	}
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	template <UInt dim>
	void Material::computeAllStressesFromTangentModuli(const ElementType & type,
	GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	const Array<Real> & shapes_derivatives =
	fem->getShapesDerivatives(type, ghost_type);
	Array<UInt> & elem_filter = element_filter(type, ghost_type);
	Array<Real> & gradu_vect = gradu(type, ghost_type);

	UInt nb_element = elem_filter.getSize();
	if (nb_element) {
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	UInt nb_quadrature_points = fem->getNbIntegrationPoints(type, ghost_type);

	gradu_vect.resize(nb_quadrature_points * nb_element);

	Array<Real> & disp = model->getDisplacement();

	fem->gradientOnIntegrationPoints(disp, gradu_vect, dim, type, ghost_type,
	elem_filter);

	UInt tangent_moduli_size = getTangentStiffnessVoigtSize(dim);

	Array<Real> * tangent_moduli_tensors = new Array<Real>(
	nb_element * nb_quadrature_points,
	tangent_moduli_size * tangent_moduli_size, "tangent_moduli_tensors");

	tangent_moduli_tensors->clear();
	computeTangentModuli(type, *tangent_moduli_tensors, ghost_type);

	Array<Real> * shapesd_filtered =
	new Array<Real>(nb_element, dim * nb_nodes_per_element, "filtered shapesd");

	FEEngine::filterElementalData(fem->getMesh(), shapes_derivatives,
	*shapesd_filtered, type, ghost_type,
	elem_filter);

	Array<Real> filtered_u(nb_element,
	nb_nodes_per_element * spatial_dimension);

	FEEngine::extractNodalToElementField(fem->getMesh(), disp, filtered_u, type,
	ghost_type, elem_filter);

	/// compute @f$\mathbf{D} \mathbf{B} \mathbf{u}@f$
	Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
	shapesd_filtered->begin(dim, nb_nodes_per_element);

	Array<Real>::matrix_iterator D_it =
	tangent_moduli_tensors->begin(tangent_moduli_size, tangent_moduli_size);
	Array<Real>::matrix_iterator sigma_it =
	stress(type, ghost_type).begin(spatial_dimension, spatial_dimension);
	Array<Real>::vector_iterator u_it =
	filtered_u.begin(spatial_dimension * nb_nodes_per_element);

	Matrix<Real> B(tangent_moduli_size,
	spatial_dimension * nb_nodes_per_element);
	Vector<Real> Bu(tangent_moduli_size);
	Vector<Real> DBu(tangent_moduli_size);

	for (UInt e = 0; e < nb_element; ++e, ++u_it) {
	for (UInt q = 0; q < nb_quadrature_points;
	++q, ++D_it, ++shapes_derivatives_filtered_it, ++sigma_it) {
	Vector<Real> & u = *u_it;
	Matrix<Real> & sigma = *sigma_it;
	Matrix<Real> & D = *D_it;

	VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
	*shapes_derivatives_filtered_it, B, nb_nodes_per_element);

	Bu.mul<false>(B, u);
	DBu.mul<false>(D, Bu);

	// Voigt notation to full symmetric tensor
	for (UInt i = 0; i < dim; ++i)
	sigma(i, i) = DBu(i);
	if (dim == 2) {
	sigma(0, 1) = sigma(1, 0) = DBu(2);
	} else if (dim == 3) {
	sigma(1, 2) = sigma(2, 1) = DBu(3);
	sigma(0, 2) = sigma(2, 0) = DBu(4);
	sigma(0, 1) = sigma(1, 0) = DBu(5);
	}
	}
	}
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::computePotentialEnergyByElements() {
	AKANTU_DEBUG_IN();

	Mesh::type_iterator it = element_filter.firstType(spatial_dimension);
	Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension);
	for (; it != last_type; ++it) {
	computePotentialEnergy(*it);
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::computePotentialEnergy(__attribute__((unused))
	ElementType el_type,
	__attribute__((unused))
	GhostType ghost_type) {
	AKANTU_DEBUG_IN();

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	Real Material::getPotentialEnergy() {
	AKANTU_DEBUG_IN();
	Real epot = 0.;

	computePotentialEnergyByElements();

	/// integrate the potential energy for each type of elements
	Mesh::type_iterator it = element_filter.firstType(spatial_dimension);
	Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension);
	for (; it != last_type; ++it) {

	epot += fem->integrate(potential_energy(it, _not_ghost), it, _not_ghost,
	element_filter(*it, _not_ghost));
	}

	AKANTU_DEBUG_OUT();
	return epot;
	}

	/* -------------------------------------------------------------------------- */
	Real Material::getPotentialEnergy(ElementType & type, UInt index) {
	AKANTU_DEBUG_IN();
	Real epot = 0.;

	Vector<Real> epot_on_quad_points(fem->getNbIntegrationPoints(type));

	computePotentialEnergyByElement(type, index, epot_on_quad_points);

	epot = fem->integrate(epot_on_quad_points, type, element_filter(type)(index));

	AKANTU_DEBUG_OUT();
	return epot;
	}

	/* -------------------------------------------------------------------------- */
	Real Material::getEnergy(std::string type) {
	AKANTU_DEBUG_IN();
	if (type == "potential")
	return getPotentialEnergy();
	AKANTU_DEBUG_OUT();
	return 0.;
	}

	/* -------------------------------------------------------------------------- */
	Real Material::getEnergy(std::string energy_id, ElementType type, UInt index) {
	AKANTU_DEBUG_IN();
	if (energy_id == "potential")
	return getPotentialEnergy(type, index);
	AKANTU_DEBUG_OUT();
	return 0.;
	}

	/* -------------------------------------------------------------------------- */
	void Material::initElementalFieldInterpolation(
	const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
	AKANTU_DEBUG_IN();

	this->fem->initElementalFieldInterpolationFromIntegrationPoints(
	interpolation_points_coordinates, this->interpolation_points_matrices,
	this->interpolation_inverse_coordinates, &(this->element_filter));
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::interpolateStress(ElementTypeMapArray<Real> & result,
	const GhostType ghost_type) {

	this->fem->interpolateElementalFieldFromIntegrationPoints(
	this->stress, this->interpolation_points_matrices,
	this->interpolation_inverse_coordinates, result, ghost_type,
	&(this->element_filter));
	}

	/* -------------------------------------------------------------------------- */
	void Material::interpolateStressOnFacets(
	ElementTypeMapArray<Real> & result,
	ElementTypeMapArray<Real> & by_elem_result, const GhostType ghost_type) {

	interpolateStress(by_elem_result, ghost_type);

	UInt stress_size = this->stress.getNbComponent();

	const Mesh & mesh = this->model->getMesh();
	const Mesh & mesh_facets = mesh.getMeshFacets();

	Mesh::type_iterator it =
	this->element_filter.firstType(spatial_dimension, ghost_type);
	Mesh::type_iterator last =
	this->element_filter.lastType(spatial_dimension, ghost_type);

	for (; it != last; ++it) {

	ElementType type = *it;
	Array<UInt> & elem_fil = element_filter(type, ghost_type);
	Array<Real> & by_elem_res = by_elem_result(type, ghost_type);
	UInt nb_element = elem_fil.getSize();
	UInt nb_element_full =
	this->model->getMesh().getNbElement(type, ghost_type);
	UInt nb_interpolation_points_per_elem =
	by_elem_res.getSize() / nb_element_full;

	const Array<Element> & facet_to_element =
	mesh_facets.getSubelementToElement(type, ghost_type);
	ElementType type_facet = Mesh::getFacetType(type);
	UInt nb_facet_per_elem = facet_to_element.getNbComponent();
	UInt nb_quad_per_facet =
	nb_interpolation_points_per_elem / nb_facet_per_elem;
	Element element_for_comparison(type, 0, ghost_type);
	const Array<std::vector<Element> > * element_to_facet = NULL;
	GhostType current_ghost_type = _casper;
	Array<Real> * result_vec = NULL;

	Array<Real>::const_matrix_iterator result_it =
	by_elem_res.begin_reinterpret(
	stress_size, nb_interpolation_points_per_elem, nb_element_full);

	for (UInt el = 0; el < nb_element; ++el) {
	UInt global_el = elem_fil(el);
	element_for_comparison.element = global_el;
	for (UInt f = 0; f < nb_facet_per_elem; ++f) {

	Element facet_elem = facet_to_element(global_el, f);
	UInt global_facet = facet_elem.element;
	if (facet_elem.ghost_type != current_ghost_type) {
	current_ghost_type = facet_elem.ghost_type;
	element_to_facet = &mesh_facets.getElementToSubelement(
	type_facet, current_ghost_type);
	result_vec = &result(type_facet, current_ghost_type);
	}

	bool is_second_element =
	(*element_to_facet)(global_facet)[0] != element_for_comparison;

	for (UInt q = 0; q < nb_quad_per_facet; ++q) {
	Vector<Real> result_local(result_vec->storage() +
	(global_facet * nb_quad_per_facet + q) *
	result_vec->getNbComponent() +
	is_second_element * stress_size,
	stress_size);

	const Matrix<Real> & result_tmp(result_it[global_el]);
	result_local = result_tmp(f * nb_quad_per_facet + q);
	}
	}
	}
	}
	}

	/* -------------------------------------------------------------------------- */
	template <typename T>
	const Array<T> & Material::getArray(const ID & vect_id,
	const ElementType & type,
	const GhostType & ghost_type) const {
	AKANTU_DEBUG_TO_IMPLEMENT();
	return NULL;
	}

	/* -------------------------------------------------------------------------- */
	template <typename T>
	Array<T> & Material::getArray(const ID & vect_id, const ElementType & type,
	const GhostType & ghost_type) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	return NULL;
	}

	/* -------------------------------------------------------------------------- */
	template <>
	const Array<Real> & Material::getArray(const ID & vect_id,
	const ElementType & type,
	const GhostType & ghost_type) const {
	std::stringstream sstr;
	std::string ghost_id = "";
	if (ghost_type == _ghost)
	ghost_id = ":ghost";
	sstr << getID() << ":" << vect_id << ":" << type << ghost_id;

	ID fvect_id = sstr.str();
	try {
	return Memory::getArray<Real>(fvect_id);
	} catch (debug::Exception & e) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain a vector "
	<< vect_id << "(" << fvect_id
	<< ") [" << e << "]");
	}
	}

	/* -------------------------------------------------------------------------- */
	template <>
	Array<Real> & Material::getArray(const ID & vect_id, const ElementType & type,
	const GhostType & ghost_type) {
	std::stringstream sstr;
	std::string ghost_id = "";
	if (ghost_type == _ghost)
	ghost_id = ":ghost";
	sstr << getID() << ":" << vect_id << ":" << type << ghost_id;

	ID fvect_id = sstr.str();
	try {
	return Memory::getArray<Real>(fvect_id);
	} catch (debug::Exception & e) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain a vector "
	<< vect_id << "(" << fvect_id
	<< ") [" << e << "]");
	}
	}

	/* -------------------------------------------------------------------------- */
	template <>
	const Array<UInt> & Material::getArray(const ID & vect_id,
	const ElementType & type,
	const GhostType & ghost_type) const {
	std::stringstream sstr;
	std::string ghost_id = "";
	if (ghost_type == _ghost)
	ghost_id = ":ghost";
	sstr << getID() << ":" << vect_id << ":" << type << ghost_id;

	ID fvect_id = sstr.str();
	try {
	return Memory::getArray<UInt>(fvect_id);
	} catch (debug::Exception & e) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain a vector "
	<< vect_id << "(" << fvect_id
	<< ") [" << e << "]");
	}
	}

	/* -------------------------------------------------------------------------- */
	template <>
	Array<UInt> & Material::getArray(const ID & vect_id, const ElementType & type,
	const GhostType & ghost_type) {
	std::stringstream sstr;
	std::string ghost_id = "";
	if (ghost_type == _ghost)
	ghost_id = ":ghost";
	sstr << getID() << ":" << vect_id << ":" << type << ghost_id;

	ID fvect_id = sstr.str();
	try {
	return Memory::getArray<UInt>(fvect_id);
	} catch (debug::Exception & e) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain a vector "
	<< vect_id << "(" << fvect_id
	<< ") [" << e << "]");
	}
	}

	/* -------------------------------------------------------------------------- */
	template <typename T>
	const InternalField<T> & Material::getInternal(__attribute__((unused))
	const ID & int_id) const {
	AKANTU_DEBUG_TO_IMPLEMENT();
	return NULL;
	}

	/* -------------------------------------------------------------------------- */
	template <typename T>
	InternalField<T> & Material::getInternal(__attribute__((unused))
	const ID & int_id) {
	AKANTU_DEBUG_TO_IMPLEMENT();
	return NULL;
	}

	/* -------------------------------------------------------------------------- */
	template <>
	const InternalField<Real> & Material::getInternal(const ID & int_id) const {
	std::map<ID, InternalField<Real> *>::const_iterator it =
	internal_vectors_real.find(getID() + ":" + int_id);
	if (it == internal_vectors_real.end()) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain an internal "
	<< int_id << " ("
	<< (getID() + ":" + int_id) << ")");
	}
	return *it->second;
	}

	/* -------------------------------------------------------------------------- */
	template <> InternalField<Real> & Material::getInternal(const ID & int_id) {
	std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.find(getID() + ":" + int_id);
	if (it == internal_vectors_real.end()) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain an internal "
	<< int_id << " ("
	<< (getID() + ":" + int_id) << ")");
	}
	return *it->second;
	}

	/* -------------------------------------------------------------------------- */
	template <>
	const InternalField<UInt> & Material::getInternal(const ID & int_id) const {
	std::map<ID, InternalField<UInt> *>::const_iterator it =
	internal_vectors_uint.find(getID() + ":" + int_id);
	if (it == internal_vectors_uint.end()) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain an internal "
	<< int_id << " ("
	<< (getID() + ":" + int_id) << ")");
	}
	return *it->second;
	}

	/* -------------------------------------------------------------------------- */
	template <> InternalField<UInt> & Material::getInternal(const ID & int_id) {
	std::map<ID, InternalField<UInt> *>::iterator it =
	internal_vectors_uint.find(getID() + ":" + int_id);
	if (it == internal_vectors_uint.end()) {
	AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
	<< ") does not contain an internal "
	<< int_id << " ("
	<< (getID() + ":" + int_id) << ")");
	}
	return *it->second;
	}

	/* -------------------------------------------------------------------------- */
	void Material::addElements(const Array<Element> & elements_to_add) {
	AKANTU_DEBUG_IN();
	UInt mat_id = model->getInternalIndexFromID(getID());
	Array<Element>::const_iterator<Element> el_begin = elements_to_add.begin();
	Array<Element>::const_iterator<Element> el_end = elements_to_add.end();
	for (; el_begin != el_end; ++el_begin) {
	const Element & element = *el_begin;
	Array<UInt> & mat_indexes =
	model->getMaterialByElement(element.type, element.ghost_type);
	Array<UInt> & mat_loc_num =
	model->getMaterialLocalNumbering(element.type, element.ghost_type);

	UInt index =
	this->addElement(element.type, element.element, element.ghost_type);
	mat_indexes(element.element) = mat_id;
	mat_loc_num(element.element) = index;
	}

	this->resizeInternals();

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::removeElements(const Array<Element> & elements_to_remove) {
	AKANTU_DEBUG_IN();

	Array<Element>::const_iterator<Element> el_begin = elements_to_remove.begin();
	Array<Element>::const_iterator<Element> el_end = elements_to_remove.end();

	if (el_begin == el_end)
	return;

	ElementTypeMapArray<UInt> material_local_new_numbering("remove mat filter elem", getID(), getMemoryID());

	Element element;
	for (ghost_type_t::iterator gt = ghost_type_t::begin();
	gt != ghost_type_t::end(); ++gt) {
	GhostType ghost_type = *gt;
	element.ghost_type = ghost_type;

	ElementTypeMapArray<UInt>::type_iterator it =
	element_filter.firstType(_all_dimensions, ghost_type, _ek_not_defined);
	ElementTypeMapArray<UInt>::type_iterator end =
	element_filter.lastType(_all_dimensions, ghost_type, _ek_not_defined);

	for (; it != end; ++it) {
	ElementType type = *it;
	element.type = type;

	Array<UInt> & elem_filter = this->element_filter(type, ghost_type);
	Array<UInt> & mat_loc_num =
	this->model->getMaterialLocalNumbering(type, ghost_type);

	if (!material_local_new_numbering.exists(type, ghost_type))
	material_local_new_numbering.alloc(elem_filter.getSize(), 1, type,
	ghost_type);
	Array<UInt> & mat_renumbering =
	material_local_new_numbering(type, ghost_type);

	UInt nb_element = elem_filter.getSize();
	element.kind = (*el_begin).kind;
	Array<UInt> elem_filter_tmp;

	UInt new_id = 0;
	for (UInt el = 0; el < nb_element; ++el) {
	element.element = elem_filter(el);

	if (std::find(el_begin, el_end, element) == el_end) {
	elem_filter_tmp.push_back(element.element);

	mat_renumbering(el) = new_id;
	mat_loc_num(element.element) = new_id;
	++new_id;
	} else {
	mat_renumbering(el) = UInt(-1);
	}
	}

	elem_filter.resize(elem_filter_tmp.getSize());
	elem_filter.copy(elem_filter_tmp);
	}
	}

	for (std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.begin();
	it != internal_vectors_real.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);

	for (std::map<ID, InternalField<UInt> *>::iterator it =
	internal_vectors_uint.begin();
	it != internal_vectors_uint.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);

	for (std::map<ID, InternalField<bool> *>::iterator it =
	internal_vectors_bool.begin();
	it != internal_vectors_bool.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::resizeInternals() {
	AKANTU_DEBUG_IN();
	for (std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.begin();
	it != internal_vectors_real.end(); ++it)
	it->second->resize();

	for (std::map<ID, InternalField<UInt> *>::iterator it =
	internal_vectors_uint.begin();
	it != internal_vectors_uint.end(); ++it)
	it->second->resize();

	for (std::map<ID, InternalField<bool> *>::iterator it =
	internal_vectors_bool.begin();
	it != internal_vectors_bool.end(); ++it)
	it->second->resize();
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void Material::onElementsAdded(__attribute__((unused))
	const Array<Element> & element_list,
	__attribute__((unused))
	const NewElementsEvent & event) {
	this->resizeInternals();
	}

	/* -------------------------------------------------------------------------- */
	void Material::onElementsRemoved(
	const Array<Element> & element_list,
	const ElementTypeMapArray<UInt> & new_numbering,
	__attribute__((unused)) const RemovedElementsEvent & event) {
	UInt my_num = model->getInternalIndexFromID(getID());

	ElementTypeMapArray<UInt> material_local_new_numbering("remove mat filter elem", getID(), getMemoryID());

	Array<Element>::const_iterator<Element> el_begin = element_list.begin();
	Array<Element>::const_iterator<Element> el_end = element_list.end();

	for (ghost_type_t::iterator g = ghost_type_t::begin();
	g != ghost_type_t::end(); ++g) {
	GhostType gt = *g;

	ElementTypeMapArray<UInt>::type_iterator it =
	new_numbering.firstType(_all_dimensions, gt, _ek_not_defined);
	ElementTypeMapArray<UInt>::type_iterator end =
	new_numbering.lastType(_all_dimensions, gt, _ek_not_defined);
	for (; it != end; ++it) {
	ElementType type = *it;
	if (element_filter.exists(type, gt) &&
	element_filter(type, gt).getSize()) {
	Array<UInt> & elem_filter = element_filter(type, gt);

	Array<UInt> & mat_indexes = this->model->getMaterialByElement(*it, gt);
	Array<UInt> & mat_loc_num =
	this->model->getMaterialLocalNumbering(*it, gt);
	UInt nb_element = this->model->getMesh().getNbElement(type, gt);

	// all materials will resize of the same size...
	mat_indexes.resize(nb_element);
	mat_loc_num.resize(nb_element);

	if (!material_local_new_numbering.exists(type, gt))
	material_local_new_numbering.alloc(elem_filter.getSize(), 1, type,
	gt);

	Array<UInt> & mat_renumbering = material_local_new_numbering(type, gt);
	const Array<UInt> & renumbering = new_numbering(type, gt);
	Array<UInt> elem_filter_tmp;
	UInt ni = 0;
	Element el;
	el.type = type;
	el.ghost_type = gt;
	el.kind = Mesh::getKind(type);
	for (UInt i = 0; i < elem_filter.getSize(); ++i) {
	el.element = elem_filter(i);
	if (std::find(el_begin, el_end, el) == el_end) {
	UInt new_el = renumbering(el.element);
	AKANTU_DEBUG_ASSERT(
	new_el != UInt(-1),
	"A not removed element as been badly renumbered");
	elem_filter_tmp.push_back(new_el);
	mat_renumbering(i) = ni;

	mat_indexes(new_el) = my_num;
	mat_loc_num(new_el) = ni;
	++ni;
	} else {
	mat_renumbering(i) = UInt(-1);
	}
	}

	elem_filter.resize(elem_filter_tmp.getSize());
	elem_filter.copy(elem_filter_tmp);
	}
	}
	}

	for (std::map<ID, InternalField<Real> *>::iterator it =
	internal_vectors_real.begin();
	it != internal_vectors_real.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);

	for (std::map<ID, InternalField<UInt> *>::iterator it =
	internal_vectors_uint.begin();
	it != internal_vectors_uint.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);

	for (std::map<ID, InternalField<bool> *>::iterator it =
	internal_vectors_bool.begin();
	it != internal_vectors_bool.end(); ++it)
	it->second->removeIntegrationPoints(material_local_new_numbering);
	}

	/* -------------------------------------------------------------------------- */
	void Material::onBeginningSolveStep(__attribute__((unused))
	const AnalysisMethod & method) {
	this->savePreviousState();
	}

	/* -------------------------------------------------------------------------- */
	void Material::onEndSolveStep(__attribute__((unused))
	const AnalysisMethod & method) {
	ElementTypeMapArray<UInt>::type_iterator it = this->element_filter.firstType(
	_all_dimensions, _not_ghost, _ek_not_defined);
	ElementTypeMapArray<UInt>::type_iterator end =
	element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);

	for (; it != end; ++it) {
	this->updateEnergies(*it, _not_ghost);
	}
	}
	/* -------------------------------------------------------------------------- */
	void Material::onDamageIteration() { this->savePreviousState(); }

	/* -------------------------------------------------------------------------- */
	void Material::onDamageUpdate() {
	ElementTypeMapArray<UInt>::type_iterator it = this->element_filter.firstType(
	_all_dimensions, _not_ghost, _ek_not_defined);
	ElementTypeMapArray<UInt>::type_iterator end =
	element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);

	for (; it != end; ++it) {
	this->updateEnergiesAfterDamage(*it, _not_ghost);
	}
	}

	/* -------------------------------------------------------------------------- */
	void Material::onDump() {
	if (this->isFiniteDeformation())
	this->computeAllCauchyStresses(_not_ghost);
	}

	/* -------------------------------------------------------------------------- */
	void Material::printself(std::ostream & stream, int indent) const {
	std::string space;
	for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
	;

	std::string type = getID().substr(getID().find_last_of(":") + 1);

	stream << space << "Material " << type << " [" << std::endl;
	Parsable::printself(stream, indent);
	stream << space << "]" << std::endl;
	}

	/* -------------------------------------------------------------------------- */
	/// extrapolate internal values
	void Material::extrapolateInternal(const ID & id, const Element & element,
	__attribute__((unused))
	const Matrix<Real> & point,
	Matrix<Real> & extrapolated) {
	if (this->isInternal<Real>(id, element.kind)) {
	UInt nb_element =
	this->element_filter(element.type, element.ghost_type).getSize();
	const ID name = this->getID() + ":" + id;
	UInt nb_quads =
	this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
	element.type, element.ghost_type);
	const Array<Real> & internal =
	this->getArray<Real>(id, element.type, element.ghost_type);
	UInt nb_component = internal.getNbComponent();
	Array<Real>::const_matrix_iterator internal_it =
	internal.begin_reinterpret(nb_component, nb_quads, nb_element);
	Element local_element = this->convertToLocalElement(element);

	/// instead of really extrapolating, here the value of the first GP
	/// is copied into the result vector. This works only for linear
	/// elements
	/// @todo extrapolate!!!!
	AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");

	const Matrix<Real> & values = internal_it[local_element.element];
	UInt index = 0;
	Vector<Real> tmp(nb_component);
	for (UInt j = 0; j < values.cols(); ++j) {
	tmp = values(j);
	if (tmp.norm() > 0) {
	index = j;
	break;
	}
	}

	for (UInt i = 0; i < extrapolated.size(); ++i) {
	extrapolated(i) = values(index);
	}
	} else {
	Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
	extrapolated = default_values;
	}
	}

	/* -------------------------------------------------------------------------- */
	void Material::applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
	const GhostType ghost_type) {

	ElementTypeMapArray<UInt>::type_iterator it = this->element_filter.firstType(
	_all_dimensions, _not_ghost, _ek_not_defined);
	ElementTypeMapArray<UInt>::type_iterator end =
	element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);

	for (; it != end; ++it) {
	ElementType type = *it;
	if (!element_filter(type, ghost_type).getSize())
	continue;
	Array<Real>::matrix_iterator eigen_it =
	this->eigengradu(type, ghost_type)
	.begin(spatial_dimension, spatial_dimension);
	Array<Real>::matrix_iterator eigen_end =
	this->eigengradu(type, ghost_type)
	.end(spatial_dimension, spatial_dimension);
	for (; eigen_it != eigen_end; ++eigen_it) {
	Matrix<Real> & current_eigengradu = *eigen_it;
	current_eigengradu = prescribed_eigen_grad_u;
	}
	}
	}

	__END_AKANTU__

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