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solid_mechanics_model.cc
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			/**
			* @file solid_mechanics_model.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@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: Fri Sep 19 2014
			*
			* @brief Implementation of the SolidMechanicsModel class
			*
			* @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/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			#include "aka_math.hh"
			#include "aka_common.hh"
			#include "solid_mechanics_model.hh"
			#include "group_manager_inline_impl.cc"
			#include "dumpable_inline_impl.hh"
			#include "integration_scheme_2nd_order.hh"
			#include "element_group.hh"

			#include "static_communicator.hh"

			#include "dof_synchronizer.hh"
			#include "element_group.hh"

			#include <cmath>

			#ifdef AKANTU_USE_MUMPS
			#include "solver_mumps.hh"
			#endif

			#ifdef AKANTU_USE_PETSC
			#include "solver_petsc.hh"
			#include "petsc_matrix.hh"
			#endif

			#ifdef AKANTU_USE_IOHELPER
			# include "dumper_field.hh"
			# include "dumper_paraview.hh"
			# include "dumper_homogenizing_field.hh"
			# include "dumper_internal_material_field.hh"
			# include "dumper_elemental_field.hh"
			# include "dumper_material_padders.hh"
			# include "dumper_element_partition.hh"
			# include "dumper_iohelper.hh"
			#endif

			#ifdef AKANTU_DAMAGE_NON_LOCAL
			# include "non_local_manager.hh"
			#endif

			/* -------------------------------------------------------------------------- */
			__BEGIN_AKANTU__

			const SolidMechanicsModelOptions default_solid_mechanics_model_options(_explicit_lumped_mass, false);

			/* -------------------------------------------------------------------------- */
			/**
			* A solid mechanics model need a mesh and a dimension to be created. the model
			* by it self can not do a lot, the good init functions should be called in
			* order to configure the model depending on what we want to do.
			*
			* @param mesh mesh representing the model we want to simulate
			* @param dim spatial dimension of the problem, if dim = 0 (default value) the
			* dimension of the problem is assumed to be the on of the mesh
			* @param id an id to identify the model
			*/
			SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh,
			UInt dim,
			const ID & id,
			const MemoryID & memory_id) :
			Model(mesh, dim, id, memory_id),
			BoundaryCondition<SolidMechanicsModel>(),
			time_step(NAN), f_m2a(1.0),
			mass_matrix(NULL),
			velocity_damping_matrix(NULL),
			stiffness_matrix(NULL),
			jacobian_matrix(NULL),
			material_index("material index", id),
			material_local_numbering("material local numbering", id),
			material_selector(new DefaultMaterialSelector(material_index)),
			is_default_material_selector(true),
			integrator(NULL),
			increment_flag(false), solver(NULL),
			synch_parallel(NULL),
			are_materials_instantiated(false),
			non_local_manager(NULL) {

			AKANTU_DEBUG_IN();

			createSynchronizerRegistry(this);

			registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh, spatial_dimension);

			this->displacement = NULL;
			this->mass = NULL;
			this->velocity = NULL;
			this->acceleration = NULL;
			this->force = NULL;
			this->residual = NULL;
			this->blocked_dofs = NULL;

			this->increment = NULL;
			this->increment_acceleration = NULL;

			this->dof_synchronizer = NULL;

			this->previous_displacement = NULL;

			materials.clear();

			mesh.registerEventHandler(*this);

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
			this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
			#endif
			AKANTU_DEBUG_OUT();
			}



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

			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			delete *mat_it;
			}

			materials.clear();

			delete integrator;

			delete solver;
			delete mass_matrix;
			delete velocity_damping_matrix;

			if(stiffness_matrix && stiffness_matrix != jacobian_matrix)
			delete stiffness_matrix;

			delete jacobian_matrix;

			delete synch_parallel;

			if(is_default_material_selector) {
			delete material_selector;
			material_selector = NULL;
			}

			#ifdef AKANTU_DAMAGE_NON_LOCAL
			delete non_local_manager;
			non_local_manager = NULL;
			#endif

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::setTimeStep(Real time_step) {
			this->time_step = time_step;

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.getDumper().setTimeStep(time_step);
			#endif
			}

			/* -------------------------------------------------------------------------- */
			/* Initialisation */
			/* -------------------------------------------------------------------------- */
			/**
			* This function groups many of the initialization in on function. For most of
			* basics case the function should be enough. The functions initialize the
			* model, the internal vectors, set them to 0, and depending on the parameters
			* it also initialize the explicit or implicit solver.
			*
			* @param material_file the file containing the materials to use
			* @param method the analysis method wanted. See the akantu::AnalysisMethod for
			* the different possibilities
			*/
			void SolidMechanicsModel::initFull(const ModelOptions & options) {
			Model::initFull(options);

			const SolidMechanicsModelOptions & smm_options =
			dynamic_cast<const SolidMechanicsModelOptions &>(options);

			this->method = smm_options.analysis_method;

			// initialize the vectors
			this->initArrays();

			// set the initial condition to 0
			this->force->clear();
			this->velocity->clear();
			this->acceleration->clear();
			this->displacement->clear();

			// initialize pbc
			if(this->pbc_pair.size()!=0)
			this->initPBC();

			// initialize the time integration schemes
			switch(this->method) {
			case _explicit_lumped_mass:
			this->initExplicit();
			break;
			case _explicit_consistent_mass:
			this->initSolver();
			this->initExplicit();
			break;
			case _implicit_dynamic:
			this->initImplicit(true);
			break;
			case _static:
			this->initImplicit(false);
			this->initArraysPreviousDisplacment();
			break;
			default:
			AKANTU_EXCEPTION("analysis method not recognised by SolidMechanicsModel");
			break;
			}

			#ifdef AKANTU_DAMAGE_NON_LOCAL
			/// create the non-local manager object for non-local damage computations
			this->non_local_manager = new NonLocalManager(*this);
			#endif

			// initialize the materials
			if(this->parser->getLastParsedFile() != "") {
			this->instantiateMaterials();
			}

			if(!smm_options.no_init_materials) {
			this->initMaterials();
			}

			if(this->increment_flag)
			this->initBC(this, this->displacement, this->increment, this->force);
			else
			this->initBC(this, this->displacement, *this->force);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initParallel(MeshPartition * partition,
			DataAccessor * data_accessor) {
			AKANTU_DEBUG_IN();

			if (data_accessor == NULL) data_accessor = this;
			synch_parallel = &createParallelSynch(partition,data_accessor);

			synch_registry->registerSynchronizer(*synch_parallel, _gst_material_id);
			synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_mass);
			synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_stress);
			synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_boundary);
			synch_registry->registerSynchronizer(*synch_parallel, _gst_for_dump);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initFEEngineBoundary() {
			FEEngine & fem_boundary = getFEEngineBoundary();
			fem_boundary.initShapeFunctions(_not_ghost);
			fem_boundary.initShapeFunctions(_ghost);

			fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
			fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
			}


			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initExplicit(AnalysisMethod analysis_method) {
			AKANTU_DEBUG_IN();

			//in case of switch from implicit to explicit
			if(!this->isExplicit())
			method = analysis_method;

			if (integrator) delete integrator;
			integrator = new CentralDifference();

			UInt nb_nodes = acceleration->getSize();
			UInt nb_degree_of_freedom = acceleration->getNbComponent();

			std::stringstream sstr; sstr << id << ":increment_acceleration";
			increment_acceleration = &(alloc<Real>(sstr.str(), nb_nodes, nb_degree_of_freedom, Real()));

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initArraysPreviousDisplacment() {
			AKANTU_DEBUG_IN();

			this->setIncrementFlagOn();
			if(not this->previous_displacement) {
			UInt nb_nodes = this->mesh.getNbNodes();
			std::stringstream sstr_disp_t;
			sstr_disp_t << this->id << ":previous_displacement";

			this->previous_displacement = &(this->alloc<Real > (sstr_disp_t.str(), nb_nodes, this->spatial_dimension, 0.));
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Allocate all the needed vectors. By default their are not necessarily set to
			* 0
			*
			*/
			void SolidMechanicsModel::initArrays() {
			AKANTU_DEBUG_IN();

			UInt nb_nodes = mesh.getNbNodes();
			std::stringstream sstr_disp; sstr_disp << id << ":displacement";
			// std::stringstream sstr_mass; sstr_mass << id << ":mass";
			std::stringstream sstr_velo; sstr_velo << id << ":velocity";
			std::stringstream sstr_acce; sstr_acce << id << ":acceleration";
			std::stringstream sstr_forc; sstr_forc << id << ":force";
			std::stringstream sstr_resi; sstr_resi << id << ":residual";
			std::stringstream sstr_boun; sstr_boun << id << ":blocked_dofs";

			displacement = &(alloc<Real>(sstr_disp.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
			// mass = &(alloc<Real>(sstr_mass.str(), nb_nodes, spatial_dimension, 0));
			velocity = &(alloc<Real>(sstr_velo.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
			acceleration = &(alloc<Real>(sstr_acce.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
			force = &(alloc<Real>(sstr_forc.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
			residual = &(alloc<Real>(sstr_resi.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
			blocked_dofs = &(alloc<bool>(sstr_boun.str(), nb_nodes, spatial_dimension, false));

			std::stringstream sstr_curp; sstr_curp << id << ":current_position";
			current_position = &(alloc<Real>(sstr_curp.str(), 0, spatial_dimension, REAL_INIT_VALUE));

			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, _ek_not_defined);
			Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, _ek_not_defined);
			for(; it != end; ++it) {
			UInt nb_element = mesh.getNbElement(*it, gt);
			material_index.alloc(nb_element, 1, *it, gt);
			material_local_numbering.alloc(nb_element, 1, *it, gt);
			}
			}

			dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
			dof_synchronizer->initLocalDOFEquationNumbers();
			dof_synchronizer->initGlobalDOFEquationNumbers();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the model,basically it pre-compute the shapes, shapes derivatives
			* and jacobian
			*
			*/
			void SolidMechanicsModel::initModel() {
			/// \todo add the current position as a parameter to initShapeFunctions for
			/// large deformation
			getFEEngine().initShapeFunctions(_not_ghost);
			getFEEngine().initShapeFunctions(_ghost);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initPBC() {
			Model::initPBC();
			registerPBCSynchronizer();

			// as long as there are ones on the diagonal of the matrix, we can put boudandary true for slaves
			std::map<UInt, UInt>::iterator it = pbc_pair.begin();
			std::map<UInt, UInt>::iterator end = pbc_pair.end();
			UInt dim = mesh.getSpatialDimension();
			while(it != end) {
			for (UInt i=0; i<dim; ++i)
			(blocked_dofs)((it).first,i) = true;
			++it;
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::registerPBCSynchronizer(){
			PBCSynchronizer * synch = new PBCSynchronizer(pbc_pair);
			synch_registry->registerSynchronizer(*synch, _gst_smm_uv);
			synch_registry->registerSynchronizer(*synch, _gst_smm_mass);
			synch_registry->registerSynchronizer(*synch, _gst_smm_res);
			synch_registry->registerSynchronizer(*synch, _gst_for_dump);
			changeLocalEquationNumberForPBC(pbc_pair, mesh.getSpatialDimension());
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateCurrentPosition() {
			AKANTU_DEBUG_IN();
			UInt nb_nodes = mesh.getNbNodes();

			current_position->resize(nb_nodes);
			Real * current_position_val = current_position->storage();
			Real * position_val = mesh.getNodes().storage();
			Real * displacement_val = displacement->storage();

			/// compute current_position = initial_position + displacement
			memcpy(current_position_val, position_val, nb_nodesspatial_dimensionsizeof(Real));
			for (UInt n = 0; n < nb_nodes*spatial_dimension; ++n) {
			current_position_val++ += displacement_val++;
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initializeUpdateResidualData() {
			AKANTU_DEBUG_IN();
			UInt nb_nodes = mesh.getNbNodes();
			residual->resize(nb_nodes);

			/// copy the forces in residual for boundary conditions
			memcpy(residual->storage(), force->storage(), nb_nodesspatial_dimensionsizeof(Real));

			// start synchronization
			synch_registry->asynchronousSynchronize(_gst_smm_uv);
			synch_registry->waitEndSynchronize(_gst_smm_uv);

			updateCurrentPosition();

			AKANTU_DEBUG_OUT();
			}

			/----------------------------------------------------------------------------/
			void SolidMechanicsModel::reInitialize()
			{

			}


			/* -------------------------------------------------------------------------- */
			/* Explicit scheme */
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			/**
			* This function compute the second member of the motion equation. That is to
			* say the sum of forces @f$ r = F_{ext} - F_{int} @f$. @f$ F_{ext} @f$ is given
			* by the user in the force vector, and @f$ F_{int} @f$ is computed as @f$
			* F_{int} = \int_{\Omega} N \sigma d\Omega@f$
			*
			*/
			void SolidMechanicsModel::updateResidual(bool need_initialize) {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the internal forces");
			// f = f_ext - f_int

			// f = f_ext
			if(need_initialize) initializeUpdateResidualData();

			AKANTU_DEBUG_INFO("Compute local stresses");

			std::vector<Material *>::iterator mat_it;
			for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			mat.computeAllStresses(_not_ghost);
			}

			#ifdef AKANTU_DAMAGE_NON_LOCAL
			/* ------------------------------------------------------------------------ */
			/* Computation of the non local part */
			this->non_local_manager->computeAllNonLocalStresses();
			#endif

			/* ------------------------------------------------------------------------ */
			/* assembling the forces internal */
			// communicate the stress
			AKANTU_DEBUG_INFO("Send data for residual assembly");
			synch_registry->asynchronousSynchronize(_gst_smm_stress);

			AKANTU_DEBUG_INFO("Assemble residual for local elements");
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			mat.assembleResidual(_not_ghost);
			}


			AKANTU_DEBUG_INFO("Wait distant stresses");
			// finalize communications
			synch_registry->waitEndSynchronize(_gst_smm_stress);

			AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			mat.assembleResidual(_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::computeStresses() {
			if (isExplicit()) {
			// start synchronization
			synch_registry->asynchronousSynchronize(_gst_smm_uv);
			synch_registry->waitEndSynchronize(_gst_smm_uv);

			// compute stresses on all local elements for each materials
			std::vector<Material *>::iterator mat_it;
			for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			mat.computeAllStresses(_not_ghost);
			}

			/* ------------------------------------------------------------------------ */
			#ifdef AKANTU_DAMAGE_NON_LOCAL
			/* Computation of the non local part */
			this->non_local_manager->computeAllNonLocalStresses();
			#endif
			} else {
			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			mat.computeAllStressesFromTangentModuli(_not_ghost);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateResidualInternal() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Update the residual");
			// f = f_ext - f_int - Ma - Cv = r - Ma - Cv;

			if(method != _static) {
			// f -= Ma
			if(mass_matrix) {
			// if full mass_matrix
			Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
			Ma = *mass_matrix;
			/// \todo check unit conversion for implicit dynamics
			// *Ma /= f_m2a
			residual -= Ma;
			delete Ma;
			} else if (mass) {

			// else lumped mass
			UInt nb_nodes = acceleration->getSize();
			UInt nb_degree_of_freedom = acceleration->getNbComponent();

			Real * mass_val = mass->storage();
			Real * accel_val = acceleration->storage();
			Real * res_val = residual->storage();
			bool * blocked_dofs_val = blocked_dofs->storage();

			for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
			if(!(*blocked_dofs_val)) {
			res_val -= accel_val * *mass_val /f_m2a;
			}
			blocked_dofs_val++;
			res_val++;
			mass_val++;
			accel_val++;
			}
			} else {
			AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
			}

			// f -= Cv
			if(velocity_damping_matrix) {
			Array<Real> * Cv = new Array<Real>(*velocity);
			Cv = *velocity_damping_matrix;
			residual -= Cv;
			delete Cv;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateAcceleration() {
			AKANTU_DEBUG_IN();

			updateResidualInternal();

			if(method == _explicit_lumped_mass) {
			/* residual = residual_{n+1} - M * acceleration_n therefore
			solution = increment acceleration not acceleration */
			solveLumped(*increment_acceleration,
			*mass,
			*residual,
			*blocked_dofs,
			f_m2a);
			} else if (method == _explicit_consistent_mass) {
			solve<NewmarkBeta::_acceleration_corrector>(*increment_acceleration);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::solveLumped(Array<Real> & x,
			const Array<Real> & A,
			const Array<Real> & b,
			const Array<bool> & blocked_dofs,
			Real alpha) {

			Real * A_val = A.storage();
			Real * b_val = b.storage();
			Real * x_val = x.storage();
			bool * blocked_dofs_val = blocked_dofs.storage();

			UInt nb_degrees_of_freedom = x.getSize() * x.getNbComponent();

			for (UInt n = 0; n < nb_degrees_of_freedom; ++n) {
			if(!(*blocked_dofs_val)) {
			x_val = alpha (b_val / A_val);
			}
			x_val++;
			A_val++;
			b_val++;
			blocked_dofs_val++;
			}
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::explicitPred() {
			AKANTU_DEBUG_IN();

			if(increment_flag) {
			if(previous_displacement) increment->copy(*previous_displacement);
			else increment->copy(*displacement);
			}

			AKANTU_DEBUG_ASSERT(integrator,"itegrator should have been allocated: "
			<< "have called initExplicit ? "
			<< "or initImplicit ?");

			integrator->integrationSchemePred(time_step,
			*displacement,
			*velocity,
			*acceleration,
			*blocked_dofs);

			if(increment_flag) {
			Real * inc_val = increment->storage();
			Real * dis_val = displacement->storage();
			UInt nb_degree_of_freedom = displacement->getSize() * displacement->getNbComponent();

			for (UInt n = 0; n < nb_degree_of_freedom; ++n) {
			inc_val = dis_val - *inc_val;
			inc_val++;
			dis_val++;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::explicitCorr() {
			AKANTU_DEBUG_IN();

			integrator->integrationSchemeCorrAccel(time_step,
			*displacement,
			*velocity,
			*acceleration,
			*blocked_dofs,
			*increment_acceleration);

			if(previous_displacement) previous_displacement->copy(*displacement);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::solveStep() {
			AKANTU_DEBUG_IN();

			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));

			this->explicitPred();
			this->updateResidual();
			this->updateAcceleration();
			this->explicitCorr();

			EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			/* Implicit scheme */
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the solver and create the sparse matrices needed.
			*
			*/
			void SolidMechanicsModel::initSolver(__attribute__((unused)) SolverOptions & options) {
			#if !defined(AKANTU_USE_MUMPS) && !defined(AKANTU_USE_PETSC)// or other solver in the future \todo add AKANTU_HAS_SOLVER in CMake
			AKANTU_DEBUG_ERROR("You should at least activate one solver.");
			#else
			UInt nb_global_nodes = mesh.getNbGlobalNodes();

			delete jacobian_matrix;
			std::stringstream sstr; sstr << id << ":jacobian_matrix";

			#ifdef AKANTU_USE_PETSC
			jacobian_matrix = new PETScMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
			#else
			jacobian_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
			#endif //AKANTU_USE PETSC
			jacobian_matrix->buildProfile(mesh, *dof_synchronizer, spatial_dimension);

			if (!isExplicit()) {
			delete stiffness_matrix;
			std::stringstream sstr_sti; sstr_sti << id << ":stiffness_matrix";
			#ifdef AKANTU_USE_PETSC
			stiffness_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
			stiffness_matrix->buildProfile(mesh, *dof_synchronizer, spatial_dimension);
			#else
			stiffness_matrix = new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
			#endif //AKANTU_USE_PETSC
			}

			delete solver;
			std::stringstream sstr_solv; sstr_solv << id << ":solver";
			#ifdef AKANTU_USE_PETSC
			solver = new SolverPETSc(*jacobian_matrix, sstr_solv.str());
			#elif defined(AKANTU_USE_MUMPS)
			solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
			dof_synchronizer->initScatterGatherCommunicationScheme();
			#else
			AKANTU_DEBUG_ERROR("You should at least activate one solver.");
			#endif //AKANTU_USE_MUMPS

			if(solver)
			solver->initialize(options);
			#endif //AKANTU_HAS_SOLVER
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initJacobianMatrix() {
			#if defined(AKANTU_USE_MUMPS) && !defined(AKANTU_USE_PETSC)

			// @todo make it more flexible: this is an ugly patch to treat the case of non
			// fix profile of the K matrix
			delete jacobian_matrix;
			std::stringstream sstr_sti; sstr_sti << id << ":jacobian_matrix";
			jacobian_matrix = new SparseMatrix(*stiffness_matrix, sstr_sti.str(), memory_id);

			std::stringstream sstr_solv; sstr_solv << id << ":solver";
			delete solver;
			solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
			if(solver)
			solver->initialize(_solver_no_options);
			#else
			AKANTU_DEBUG_ERROR("You need to activate the solver mumps.");
			#endif
			}

			/* -------------------------------------------------------------------------- */
			/**
			* Initialize the implicit solver, either for dynamic or static cases,
			*
			* @param dynamic
			*/
			void SolidMechanicsModel::initImplicit(bool dynamic, SolverOptions & solver_options) {
			AKANTU_DEBUG_IN();

			method = dynamic ? _implicit_dynamic : _static;

			if (!increment) setIncrementFlagOn();

			initSolver(solver_options);

			if(method == _implicit_dynamic) {
			if(integrator) delete integrator;
			integrator = new TrapezoidalRule2();
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::initialAcceleration() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Solving Ma = f");

			Solver * acc_solver = NULL;

			std::stringstream sstr; sstr << id << ":tmp_mass_matrix";
			SparseMatrix * tmp_mass = new SparseMatrix(*mass_matrix, sstr.str(), memory_id);

			#ifdef AKANTU_USE_MUMPS
			std::stringstream sstr_solver; sstr << id << ":solver_mass_matrix";
			acc_solver = new SolverMumps(*mass_matrix, sstr_solver.str());

			dof_synchronizer->initScatterGatherCommunicationScheme();
			#else
			AKANTU_DEBUG_ERROR("You should at least activate one solver.");
			#endif //AKANTU_USE_MUMPS

			acc_solver->initialize();

			tmp_mass->applyBoundary(*blocked_dofs);

			acc_solver->setRHS(*residual);
			acc_solver->solve(*acceleration);

			delete acc_solver;
			delete tmp_mass;

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::assembleStiffnessMatrix() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");

			stiffness_matrix->clear();

			// call compute stiffness matrix on each local elements
			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			(*mat_it)->assembleStiffnessMatrix(_not_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			SparseMatrix & SolidMechanicsModel::initVelocityDampingMatrix() {
			if(!velocity_damping_matrix)
			velocity_damping_matrix =
			new SparseMatrix(*jacobian_matrix, id + ":velocity_damping_matrix", memory_id);

			return *velocity_damping_matrix;
			}

			/* -------------------------------------------------------------------------- */
			template<>
			bool SolidMechanicsModel::testConvergence<_scc_increment>(Real tolerance, Real & error){
			AKANTU_DEBUG_IN();

			UInt nb_nodes = displacement->getSize();
			UInt nb_degree_of_freedom = displacement->getNbComponent();

			error = 0;
			Real norm[2] = {0., 0.};
			Real * increment_val = increment->storage();
			bool * blocked_dofs_val = blocked_dofs->storage();
			Real * displacement_val = displacement->storage();

			for (UInt n = 0; n < nb_nodes; ++n) {
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
			if(!(*blocked_dofs_val) && is_local_node) {
			norm[0] += increment_val *increment_val;
			norm[1] += displacement_val *displacement_val;
			}
			blocked_dofs_val++;
			increment_val++;
			displacement_val++;
			}
			}

			StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);

			norm[0] = sqrt(norm[0]);
			norm[1] = sqrt(norm[1]);

			AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]), "Something goes wrong in the solve phase");

			if (norm[1] < Math::getTolerance()) {
			error = norm[0];
			AKANTU_DEBUG_OUT();
			// cout<<"Error 1: "<<error<<endl;
			return error < tolerance;
			}


			AKANTU_DEBUG_OUT();
			if(norm[1] > Math::getTolerance())
			error = norm[0] / norm[1];
			else
			error = norm[0]; //In case the total displacement is zero!

			// cout<<"Error 2: "<<error<<endl;

			return (error < tolerance);
			}


			/* -------------------------------------------------------------------------- */
			template<>
			bool SolidMechanicsModel::testConvergence<_scc_residual>(Real tolerance, Real & norm) {
			AKANTU_DEBUG_IN();

			UInt nb_nodes = residual->getSize();
			UInt nb_degree_of_freedom = displacement->getNbComponent();

			norm = 0;
			Real * residual_val = residual->storage();
			bool * blocked_dofs_val = blocked_dofs->storage();

			for (UInt n = 0; n < nb_nodes; ++n) {
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			if(is_local_node) {
			for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
			if(!(*blocked_dofs_val)) {
			norm += residual_val *residual_val;
			}
			blocked_dofs_val++;
			residual_val++;
			}
			} else {
			blocked_dofs_val += spatial_dimension;
			residual_val += spatial_dimension;
			}
			}

			StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);

			norm = sqrt(norm);

			AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");

			AKANTU_DEBUG_OUT();
			return (norm < tolerance);
			}

			/* -------------------------------------------------------------------------- */
			template<>
			bool SolidMechanicsModel::testConvergence<_scc_residual_mass_wgh>(Real tolerance,
			Real & norm) {
			AKANTU_DEBUG_IN();



			UInt nb_nodes = residual->getSize();

			norm = 0;
			Real * residual_val = residual->storage();
			Real * mass_val = this->mass->storage();
			bool * blocked_dofs_val = blocked_dofs->storage();

			for (UInt n = 0; n < nb_nodes; ++n) {
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			if(is_local_node) {
			for (UInt d = 0; d < spatial_dimension; ++d) {
			if(!(*blocked_dofs_val)) {
			norm += residual_val residual_val/(mass_val * *mass_val);
			}
			blocked_dofs_val++;
			residual_val++;
			mass_val++;
			}
			} else {
			blocked_dofs_val += spatial_dimension;
			residual_val += spatial_dimension;
			mass_val += spatial_dimension;
			}
			}

			StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);

			norm = sqrt(norm);

			AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");

			AKANTU_DEBUG_OUT();
			return (norm < tolerance);
			}

			/* -------------------------------------------------------------------------- */
			bool SolidMechanicsModel::testConvergenceResidual(Real tolerance){
			AKANTU_DEBUG_IN();

			Real error=0;
			bool res = this->testConvergence<_scc_residual>(tolerance, error);
			AKANTU_DEBUG_OUT();
			return res;
			}

			/* -------------------------------------------------------------------------- */
			bool SolidMechanicsModel::testConvergenceResidual(Real tolerance, Real & error){
			AKANTU_DEBUG_IN();

			bool res = this->testConvergence<_scc_residual>(tolerance, error);

			AKANTU_DEBUG_OUT();
			return res;
			}

			/* -------------------------------------------------------------------------- */
			bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance){
			AKANTU_DEBUG_IN();

			Real error=0;
			bool res = this->testConvergence<_scc_increment>(tolerance, error);

			AKANTU_DEBUG_OUT();
			return res;
			}

			/* -------------------------------------------------------------------------- */
			bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance, Real & error){
			AKANTU_DEBUG_IN();

			bool res = this->testConvergence<_scc_increment>(tolerance, error);

			AKANTU_DEBUG_OUT();
			return res;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::implicitPred() {
			AKANTU_DEBUG_IN();

			if(method == _implicit_dynamic)
			integrator->integrationSchemePred(time_step,
			*displacement,
			*velocity,
			*acceleration,
			*blocked_dofs);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::implicitCorr() {
			AKANTU_DEBUG_IN();

			if(method == _implicit_dynamic) {
			integrator->integrationSchemeCorrDispl(time_step,
			*displacement,
			*velocity,
			*acceleration,
			*blocked_dofs,
			*increment);
			} else {
			UInt nb_nodes = displacement->getSize();
			UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;

			Real * incr_val = increment->storage();
			Real * disp_val = displacement->storage();
			bool * boun_val = blocked_dofs->storage();

			for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++boun_val){
			incr_val = (1. - *boun_val);
			disp_val += incr_val;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateIncrement() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
			<< " Are you working with Finite or Ineslactic deformations?");

			UInt nb_nodes = displacement->getSize();
			UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;

			Real * incr_val = increment->storage();
			Real * disp_val = displacement->storage();
			Real * prev_disp_val = previous_displacement->storage();

			for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++prev_disp_val)
			incr_val = (disp_val - *prev_disp_val);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updatePreviousDisplacement() {
			AKANTU_DEBUG_IN();

			AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
			<< " Are you working with Finite or Ineslactic deformations?");

			previous_displacement->copy(*displacement);

			AKANTU_DEBUG_OUT();
			}
			/* -------------------------------------------------------------------------- */
			/* Information */
			/* -------------------------------------------------------------------------- */

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::synchronizeBoundaries() {
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
			<< " Did you call initParallel?");
			synch_registry->synchronize(_gst_smm_boundary);
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::synchronizeResidual() {
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
			<< " Did you call initPBC?");
			synch_registry->synchronize(_gst_smm_res);
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::setIncrementFlagOn() {
			AKANTU_DEBUG_IN();

			if(!increment) {
			UInt nb_nodes = mesh.getNbNodes();
			std::stringstream sstr_inc; sstr_inc << id << ":increment";
			increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, spatial_dimension, 0.));
			}

			increment_flag = true;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getStableTimeStep() {
			AKANTU_DEBUG_IN();

			Real min_dt = getStableTimeStep(_not_ghost);

			/// reduction min over all processors
			StaticCommunicator::getStaticCommunicator().allReduce(&min_dt, 1, _so_min);

			AKANTU_DEBUG_OUT();
			return min_dt;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			Material ** mat_val = &(materials.at(0));
			Real min_dt = std::numeric_limits<Real>::max();

			updateCurrentPosition();

			Element elem;
			elem.ghost_type = ghost_type;
			elem.kind = _ek_regular;

			Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type, _ek_regular);
			Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type, _ek_regular);
			for(; it != end; ++it) {
			elem.type = *it;
			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
			UInt nb_element = mesh.getNbElement(*it);

			Array<UInt>::const_scalar_iterator mat_indexes = material_index(*it, ghost_type).begin();
			Array<UInt>::const_scalar_iterator mat_loc_num = material_local_numbering(*it, ghost_type).begin();

			Array<Real> X(0, nb_nodes_per_element*spatial_dimension);
			FEEngine::extractNodalToElementField(mesh, *current_position,
			X, *it, _not_ghost);

			Array<Real>::matrix_iterator X_el =
			X.begin(spatial_dimension, nb_nodes_per_element);

			for (UInt el = 0; el < nb_element; ++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
			elem.element = *mat_loc_num;
			Real el_h = getFEEngine().getElementInradius(X_el, it);
			Real el_c = mat_val[*mat_indexes]->getCelerity(elem);
			Real el_dt = el_h / el_c;

			min_dt = std::min(min_dt, el_dt);
			}
			}

			AKANTU_DEBUG_OUT();
			return min_dt;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getKineticEnergy() {
			AKANTU_DEBUG_IN();

			if (!mass && !mass_matrix)
			AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");


			Real ekin = 0.;

			UInt nb_nodes = mesh.getNbNodes();

			Real * vel_val = velocity->storage();
			Real * mass_val = mass->storage();

			for (UInt n = 0; n < nb_nodes; ++n) {
			Real mv2 = 0;
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
			bool count_node = is_local_node && is_not_pbc_slave_node;
			for (UInt i = 0; i < spatial_dimension; ++i) {
			if (count_node)
			mv2 += vel_val vel_val *mass_val;

			vel_val++;
			mass_val++;
			}
			ekin += mv2;
			}

			StaticCommunicator::getStaticCommunicator().allReduce(&ekin, 1, _so_sum);

			AKANTU_DEBUG_OUT();
			return ekin * .5;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getKineticEnergy(const ElementType & type, UInt index) {
			AKANTU_DEBUG_IN();

			UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);

			Array<Real> vel_on_quad(nb_quadrature_points, spatial_dimension);
			Array<UInt> filter_element(1, 1, index);

			getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
			spatial_dimension,
			type, _not_ghost,
			filter_element);

			Array<Real>::vector_iterator vit = vel_on_quad.begin(spatial_dimension);
			Array<Real>::vector_iterator vend = vel_on_quad.end(spatial_dimension);

			Vector<Real> rho_v2(nb_quadrature_points);

			Real rho = materials[material_index(type)(index)]->getRho();

			for (UInt q = 0; vit != vend; ++vit, ++q) {
			rho_v2(q) = rho * vit->dot(*vit);
			}

			AKANTU_DEBUG_OUT();

			return .5*getFEEngine().integrate(rho_v2, type, index);
			}


			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getExternalWork() {
			AKANTU_DEBUG_IN();

			Real * incr_or_velo = NULL;
			if(this->method == _static){
			incr_or_velo = this->increment->storage();
			}
			else
			incr_or_velo = this->velocity->storage();
			Real * forc = this->force->storage();
			Real * resi = this->residual->storage();
			bool * boun = this->blocked_dofs->storage();

			Real work = 0.;

			UInt nb_nodes = this->mesh.getNbNodes();

			for (UInt n = 0; n < nb_nodes; ++n) {
			bool is_local_node = this->mesh.isLocalOrMasterNode(n);
			bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
			bool count_node = is_local_node && is_not_pbc_slave_node;

			for (UInt i = 0; i < this->spatial_dimension; ++i) {
			if (count_node) {
			if(*boun)
			work -= resi *incr_or_velo;
			else
			work += forc *incr_or_velo;
			}

			++incr_or_velo;
			++forc;
			++resi;
			++boun;
			}
			}

			StaticCommunicator::getStaticCommunicator().allReduce(&work, 1, _so_sum);

			if(this->method != _static)
			work *= this->time_step;
			AKANTU_DEBUG_OUT();
			return work;
			}

			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
			AKANTU_DEBUG_IN();

			if (energy_id == "kinetic") {
			return getKineticEnergy();
			} else if (energy_id == "external work"){
			return getExternalWork();
			}

			Real energy = 0.;
			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			energy += (*mat_it)->getEnergy(energy_id);
			}

			/// reduction sum over all processors
			StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);

			AKANTU_DEBUG_OUT();
			return energy;
			}
			/* -------------------------------------------------------------------------- */
			Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
			const ElementType & type,
			UInt index) {
			AKANTU_DEBUG_IN();

			if (energy_id == "kinetic") {
			return getKineticEnergy(type, index);
			}

			std::vector<Material *>::iterator mat_it;
			UInt mat_index = this->material_index(type, _not_ghost)(index);
			UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
			Real energy = this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);

			AKANTU_DEBUG_OUT();
			return energy;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
			const NewElementsEvent & event) {
			AKANTU_DEBUG_IN();

			this->getFEEngine().initShapeFunctions(_not_ghost);
			this->getFEEngine().initShapeFunctions(_ghost);

			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			Mesh::type_iterator it = this->mesh.firstType(spatial_dimension, gt, _ek_not_defined);
			Mesh::type_iterator end = this->mesh.lastType(spatial_dimension, gt, _ek_not_defined);
			for(; it != end; ++it) {
			UInt nb_element = this->mesh.getNbElement(*it, gt);
			if(!material_index.exists(*it, gt)) {
			this->material_index .alloc(nb_element, 1, *it, gt);
			this->material_local_numbering.alloc(nb_element, 1, *it, gt);
			} else {
			this->material_index (*it, gt).resize(nb_element);
			this->material_local_numbering(*it, gt).resize(nb_element);
			}
			}
			}

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

			ElementTypeMapArray<UInt> filter("new_element_filter", this->getID());

			for (UInt el = 0; it != end; ++it, ++el) {
			const Element & elem = *it;

			if(!filter.exists(elem.type, elem.ghost_type))
			filter.alloc(0, 1, elem.type, elem.ghost_type);

			filter(elem.type, elem.ghost_type).push_back(elem.element);
			}

			this->assignMaterialToElements(&filter);

			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			(*mat_it)->onElementsAdded(element_list, event);
			}

			if(method == _explicit_lumped_mass) this->assembleMassLumped();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onElementsRemoved(__attribute__((unused)) const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			const RemovedElementsEvent & event) {
			this->getFEEngine().initShapeFunctions(_not_ghost);
			this->getFEEngine().initShapeFunctions(_ghost);

			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			(*mat_it)->onElementsRemoved(element_list, new_numbering, event);
			}

			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
			__attribute__((unused)) const NewNodesEvent & event) {
			AKANTU_DEBUG_IN();
			UInt nb_nodes = mesh.getNbNodes();

			if(displacement) displacement->resize(nb_nodes);
			if(mass ) mass ->resize(nb_nodes);
			if(velocity ) velocity ->resize(nb_nodes);
			if(acceleration) acceleration->resize(nb_nodes);
			if(force ) force ->resize(nb_nodes);
			if(residual ) residual ->resize(nb_nodes);
			if(blocked_dofs) blocked_dofs->resize(nb_nodes);

			if(previous_displacement) previous_displacement->resize(nb_nodes);
			if(increment_acceleration) increment_acceleration->resize(nb_nodes);
			if(increment) increment->resize(nb_nodes);

			if(current_position) current_position->resize(nb_nodes);

			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			(*mat_it)->onNodesAdded(nodes_list, event);
			}

			delete dof_synchronizer;
			dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
			dof_synchronizer->initLocalDOFEquationNumbers();
			dof_synchronizer->initGlobalDOFEquationNumbers();

			if (method != _explicit_lumped_mass) {
			this->initSolver();
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::onNodesRemoved(__attribute__((unused)) const Array<UInt> & element_list,
			const Array<UInt> & new_numbering,
			__attribute__((unused)) const RemovedNodesEvent & event) {
			if(displacement) mesh.removeNodesFromArray(*displacement, new_numbering);
			if(mass ) mesh.removeNodesFromArray(*mass , new_numbering);
			if(velocity ) mesh.removeNodesFromArray(*velocity , new_numbering);
			if(acceleration) mesh.removeNodesFromArray(*acceleration, new_numbering);
			if(force ) mesh.removeNodesFromArray(*force , new_numbering);
			if(residual ) mesh.removeNodesFromArray(*residual , new_numbering);
			if(blocked_dofs) mesh.removeNodesFromArray(*blocked_dofs, new_numbering);

			if(increment_acceleration) mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
			if(increment) mesh.removeNodesFromArray(*increment , new_numbering);

			delete dof_synchronizer;
			dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
			dof_synchronizer->initLocalDOFEquationNumbers();
			dof_synchronizer->initGlobalDOFEquationNumbers();

			if (method != _explicit_lumped_mass) {
			this->initSolver();
			}

			}

			/* -------------------------------------------------------------------------- */
			bool SolidMechanicsModel::isInternal(const std::string & field_name,
			const ElementKind & element_kind) {

			bool is_internal = false;

			/// check if at least one material contains field_id as an internal
			for (UInt m = 0; m < materials.size() && !is_internal; ++m) {
			is_internal \|= materials[m]->isInternal<Real>(field_name, element_kind);
			}

			return is_internal;
			}
			/* -------------------------------------------------------------------------- */
			ElementTypeMap<UInt>
			SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
			const ElementKind & element_kind) {

			if (!(this->isInternal(field_name, element_kind)))
			AKANTU_EXCEPTION("unknown internal " << field_name);

			for (UInt m = 0; m < materials.size(); ++m) {
			if (materials[m]->isInternal<Real>(field_name, element_kind))
			return materials[m]->getInternalDataPerElem<Real>(field_name, element_kind);
			}

			return ElementTypeMap<UInt>();
			}

			/* -------------------------------------------------------------------------- */
			ElementTypeMapArray<Real> &
			SolidMechanicsModel::flattenInternal(const std::string & field_name,
			const ElementKind & kind,
			const GhostType ghost_type) {
			std::pair<std::string, ElementKind> key(field_name, kind);
			if (this->registered_internals.count(key) == 0) {
			this->registered_internals[key] =
			new ElementTypeMapArray<Real>(field_name, this->id);
			}

			ElementTypeMapArray<Real> * internal_flat = this->registered_internals[key];

			typedef ElementTypeMapArray<Real>::type_iterator iterator;
			iterator tit = internal_flat->firstType(spatial_dimension, ghost_type, kind);
			iterator end = internal_flat->lastType(spatial_dimension, ghost_type, kind);

			for (; tit != end; ++tit) {
			ElementType type = *tit;
			(*internal_flat)(type, ghost_type).clear();
			}

			for (UInt m = 0; m < materials.size(); ++m) {
			if (materials[m]->isInternal<Real>(field_name, kind))
			materials[m]->flattenInternal(field_name, *internal_flat, ghost_type,
			kind);
			}

			return *internal_flat;
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::flattenAllRegisteredInternals(
			const ElementKind & kind) {

			typedef std::map<std::pair<std::string, ElementKind>,
			ElementTypeMapArray<Real> *>::iterator iterator;
			iterator it = this->registered_internals.begin();
			iterator end = this->registered_internals.end();

			while (it != end) {
			if (kind == it->first.second)
			this->flattenInternal(it->first.first, kind);
			++it;
			}
			}

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

			void SolidMechanicsModel::onDump(){
			this->flattenAllRegisteredInternals(_ek_regular);
			}
			/* -------------------------------------------------------------------------- */

			#ifdef AKANTU_USE_IOHELPER

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

			dumper::Field * field = NULL;

			if(field_name == "partitions")
			field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(mesh.getConnectivities(),group_name,spatial_dimension,kind);
			else if(field_name == "material_index")
			field = mesh.createElementalField<UInt, Vector, dumper::ElementalField >(material_index,group_name,spatial_dimension,kind);
			else {
			// this copy of field_name is used to compute derivated data such as
			// strain and von mises stress that are based on grad_u and stress
			std::string field_name_copy(field_name);

			if (field_name == "strain"
			\|\| field_name == "Green strain"
			\|\| field_name == "principal strain"
			\|\| field_name == "principal Green strain")
			field_name_copy = "grad_u";
			else if (field_name == "Von Mises stress")
			field_name_copy = "stress";

			bool is_internal = this->isInternal(field_name_copy,kind);

			if (is_internal) {
			ElementTypeMap<UInt> nb_data_per_elem = this->getInternalDataPerElem(field_name_copy, kind);
			ElementTypeMapArray<Real> & internal_flat = this->flattenInternal(field_name_copy,kind);
			field = mesh.createElementalField<Real, dumper::InternalMaterialField>(internal_flat,
			group_name,
			spatial_dimension,kind,nb_data_per_elem);
			if (field_name == "strain"){
			dumper::ComputeStrain<false> * foo = new dumper::ComputeStrain<false>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			} else if (field_name == "Von Mises stress") {
			dumper::ComputeVonMisesStress * foo = new dumper::ComputeVonMisesStress(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			} else if (field_name == "Green strain") {
			dumper::ComputeStrain<true> * foo = new dumper::ComputeStrain<true>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			} else if (field_name == "principal strain") {
			dumper::ComputePrincipalStrain<false> * foo = new dumper::ComputePrincipalStrain<false>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			} else if (field_name == "principal Green strain") {
			dumper::ComputePrincipalStrain<true> * foo = new dumper::ComputePrincipalStrain<true>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			}

			//treat the paddings
			if (padding_flag){
			if (field_name == "stress"){
			if (spatial_dimension == 2) {
			dumper::StressPadder<2> * foo = new dumper::StressPadder<2>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			}
			} else if (field_name == "strain" \|\| field_name == "Green strain"){
			if (spatial_dimension == 2) {
			dumper::StrainPadder<2> * foo = new dumper::StrainPadder<2>(*this);
			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
			}
			}
			}

			// homogenize the field
			dumper::ComputeFunctorInterface * foo =
			dumper::HomogenizerProxy::createHomogenizer(*field);

			field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);

			}
			}
			return field;
			}

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

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

			std::map<std::string,Array<Real>* > real_nodal_fields;
			real_nodal_fields["displacement" ] = displacement;
			real_nodal_fields["mass" ] = mass;
			real_nodal_fields["velocity" ] = velocity;
			real_nodal_fields["acceleration" ] = acceleration;
			real_nodal_fields["force" ] = force;
			real_nodal_fields["residual" ] = residual;
			real_nodal_fields["increment" ] = increment;

			dumper::Field * field = NULL;
			if (padding_flag)
			field = mesh.createNodalField(real_nodal_fields[field_name], group_name, 3);
			else
			field = mesh.createNodalField(real_nodal_fields[field_name], group_name);

			return field;
			}
			/* -------------------------------------------------------------------------- */

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

			std::map<std::string,Array<bool>* > uint_nodal_fields;
			uint_nodal_fields["blocked_dofs" ] = blocked_dofs;

			dumper::Field * field = NULL;
			field = mesh.createNodalField(uint_nodal_fields[field_name],group_name);
			return field;

			}
			/* -------------------------------------------------------------------------- */
			#else
			/* -------------------------------------------------------------------------- */

			dumper::Field * SolidMechanicsModel
			::createElementalField(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag,
			const UInt & spatial_dimension,
			const ElementKind & kind){
			return NULL;
			}

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

			dumper::Field * SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) {
			return NULL;
			}

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

			dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string & field_name,
			const std::string & group_name,
			bool padding_flag) {
			return NULL;
			}

			#endif
			/* -------------------------------------------------------------------------- */

			void SolidMechanicsModel::dump(const std::string & dumper_name) {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump(dumper_name);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump(dumper_name, step);
			}

			/* ------------------------------------------------------------------------- */
			void SolidMechanicsModel::dump(const std::string & dumper_name, Real time, UInt step) {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump(dumper_name, time, step);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::dump() {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::dump(UInt step) {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump(step);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::dump(Real time, UInt step) {
			this->onDump();
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
			mesh.dump(time, step);
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::computeCauchyStresses() {
			AKANTU_DEBUG_IN();

			// call compute stiffness matrix on each local elements
			std::vector<Material *>::iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			Material & mat = **mat_it;
			if(mat.isFiniteDeformation())
			mat.computeAllCauchyStresses(_not_ghost);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::saveStressAndStrainBeforeDamage() {
			EventManager::sendEvent(SolidMechanicsModelEvent::BeginningOfDamageIterationEvent());
			}

			/* -------------------------------------------------------------------------- */
			void SolidMechanicsModel::updateEnergiesAfterDamage() {
			EventManager::sendEvent(SolidMechanicsModelEvent::AfterDamageEvent());
			}

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

			stream << space << "Solid Mechanics Model [" << std::endl;
			stream << space << " + id : " << id << std::endl;
			stream << space << " + spatial dimension : " << spatial_dimension << std::endl;
			stream << space << " + fem [" << std::endl;
			getFEEngine().printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;
			stream << space << " + nodals information [" << std::endl;
			displacement->printself(stream, indent + 2);
			mass ->printself(stream, indent + 2);
			velocity ->printself(stream, indent + 2);
			acceleration->printself(stream, indent + 2);
			force ->printself(stream, indent + 2);
			residual ->printself(stream, indent + 2);
			blocked_dofs->printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << " + material information [" << std::endl;
			material_index.printself(stream, indent + 2);
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << " + materials [" << std::endl;
			std::vector<Material *>::const_iterator mat_it;
			for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
			const Material & mat = (mat_it);
			mat.printself(stream, indent + 1);
			}
			stream << space << AKANTU_INDENT << "]" << std::endl;

			stream << space << "]" << std::endl;
			}

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

			__END_AKANTU__

rAKA/src/model/solid_mechanics/solid_mechanics_model.cc495126944c1ffeatures/22-problem-in…

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rAKA/src/model/solid_mechanics/solid_mechanics_model.cc
495126944c1ffeatures/22-problem-in…

solid_mechanics_model.cc
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