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solid_mechanics_model_inline_impl.cc
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			/**
			* @file solid_mechanics_model_inline_impl.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Wed Aug 04 2010
			* @date last modification: Wed Nov 18 2015
			*
			* @brief Implementation of the inline functions of the SolidMechanicsModel 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/>.
			*
			*/

			/* -------------------------------------------------------------------------- */
			inline Material & SolidMechanicsModel::getMaterial(UInt mat_index) {
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
			"The model " << id << " has no material no "<< mat_index);
			AKANTU_DEBUG_OUT();
			return *materials[mat_index];
			}

			/* -------------------------------------------------------------------------- */
			inline const Material & SolidMechanicsModel::getMaterial(UInt mat_index) const {
			AKANTU_DEBUG_IN();
			AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
			"The model " << id << " has no material no "<< mat_index);
			AKANTU_DEBUG_OUT();
			return *materials[mat_index];
			}

			/* -------------------------------------------------------------------------- */
			inline Material & SolidMechanicsModel::getMaterial(const std::string & name) {
			AKANTU_DEBUG_IN();
			std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
			AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
			"The model " << id << " has no material named "<< name);
			AKANTU_DEBUG_OUT();
			return *materials[it->second];
			}

			/* -------------------------------------------------------------------------- */
			inline UInt SolidMechanicsModel::getMaterialIndex(const std::string & name) const {
			AKANTU_DEBUG_IN();
			std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
			AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
			"The model " << id << " has no material named "<< name);
			AKANTU_DEBUG_OUT();
			return it->second;
			}

			/* -------------------------------------------------------------------------- */
			inline const Material & SolidMechanicsModel::getMaterial(const std::string & name) const {
			AKANTU_DEBUG_IN();
			std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
			AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
			"The model " << id << " has no material named "<< name);
			AKANTU_DEBUG_OUT();
			return *materials[it->second];
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::setMaterialSelector(MaterialSelector & selector) {
			if(is_default_material_selector) delete material_selector;
			material_selector = &selector;
			is_default_material_selector = false;
			}

			/* -------------------------------------------------------------------------- */
			inline FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
			return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<MyFEEngineType>(name));
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::splitElementByMaterial(const Array<Element> & elements,
			Array<Element> * elements_per_mat) const {
			ElementType current_element_type = _not_defined;
			GhostType current_ghost_type = _casper;
			const Array<UInt> * mat_indexes = NULL;
			const Array<UInt> * mat_loc_num = NULL;

			Array<Element>::const_iterator<Element> it = elements.begin();
			Array<Element>::const_iterator<Element> end = elements.end();
			for (; it != end; ++it) {
			Element el = *it;

			if(el.type != current_element_type \|\| el.ghost_type != current_ghost_type) {
			current_element_type = el.type;
			current_ghost_type = el.ghost_type;
			mat_indexes = &(this->material_index(el.type, el.ghost_type));
			mat_loc_num = &(this->material_local_numbering(el.type, el.ghost_type));
			}

			UInt old_id = el.element;
			el.element = (*mat_loc_num)(old_id);
			elements_per_mat[(*mat_indexes)(old_id)].push_back(el);
			}
			}

			/* -------------------------------------------------------------------------- */
			inline UInt SolidMechanicsModel::getNbDataForElements(const Array<Element> & elements,
			SynchronizationTag tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			UInt nb_nodes_per_element = 0;

			Array<Element>::const_iterator<Element> it = elements.begin();
			Array<Element>::const_iterator<Element> end = elements.end();
			for (; it != end; ++it) {
			const Element & el = *it;
			nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
			}

			switch(tag) {
			case _gst_material_id: {
			size += elements.getSize() * sizeof(UInt);
			break;
			}
			case _gst_smm_mass: {
			size += nb_nodes_per_element * sizeof(Real) * spatial_dimension; // mass vector
			break;
			}
			case _gst_smm_for_gradu: {
			size += nb_nodes_per_element * spatial_dimension * sizeof(Real); // displacement
			break;
			}
			case _gst_smm_boundary: {
			// force, displacement, boundary
			size += nb_nodes_per_element * spatial_dimension * (2 * sizeof(Real) + sizeof(bool));
			break;
			}
			case _gst_for_dump: {
			// displacement, velocity, acceleration, residual, force
			size += nb_nodes_per_element * spatial_dimension * sizeof(Real) * 5;
			break;
			}
			default: { }
			}

			if(tag != _gst_material_id) {
			Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
			this->splitElementByMaterial(elements, elements_per_mat);

			for (UInt i = 0; i < materials.size(); ++i) {
			size += materials[i]->getNbDataForElements(elements_per_mat[i], tag);
			}
			delete [] elements_per_mat;
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::packElementData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			SynchronizationTag tag) const {
			AKANTU_DEBUG_IN();

			switch(tag) {
			case _gst_material_id: {
			packElementalDataHelper(material_index, buffer, elements, false, getFEEngine());
			break;
			}
			case _gst_smm_mass: {
			packNodalDataHelper(*mass, buffer, elements, mesh);
			break;
			}
			case _gst_smm_for_gradu: {
			packNodalDataHelper(*displacement, buffer, elements, mesh);
			break;
			}
			case _gst_for_dump: {
			packNodalDataHelper(*displacement, buffer, elements, mesh);
			packNodalDataHelper(*velocity, buffer, elements, mesh);
			packNodalDataHelper(*acceleration, buffer, elements, mesh);
			packNodalDataHelper(*residual, buffer, elements, mesh);
			packNodalDataHelper(*force, buffer, elements, mesh);
			break;
			}
			case _gst_smm_boundary: {
			packNodalDataHelper(*force, buffer, elements, mesh);
			packNodalDataHelper(*velocity, buffer, elements, mesh);
			packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
			break;
			}
			default: {
			}
			}

			if(tag != _gst_material_id) {
			Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
			splitElementByMaterial(elements, elements_per_mat);

			for (UInt i = 0; i < materials.size(); ++i) {
			materials[i]->packElementData(buffer, elements_per_mat[i], tag);
			}

			delete [] elements_per_mat;
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::unpackElementData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			SynchronizationTag tag) {
			AKANTU_DEBUG_IN();

			switch(tag) {
			case _gst_material_id: {
			unpackElementalDataHelper(material_index, buffer, elements,
			false, getFEEngine());
			break;
			}
			case _gst_smm_mass: {
			unpackNodalDataHelper(*mass, buffer, elements, mesh);
			break;
			}
			case _gst_smm_for_gradu: {
			unpackNodalDataHelper(*displacement, buffer, elements, mesh);
			break;
			}
			case _gst_for_dump: {
			unpackNodalDataHelper(*displacement, buffer, elements, mesh);
			unpackNodalDataHelper(*velocity, buffer, elements, mesh);
			unpackNodalDataHelper(*acceleration, buffer, elements, mesh);
			unpackNodalDataHelper(*residual, buffer, elements, mesh);
			unpackNodalDataHelper(*force, buffer, elements, mesh);
			break;
			}
			case _gst_smm_boundary: {
			unpackNodalDataHelper(*force, buffer, elements, mesh);
			unpackNodalDataHelper(*velocity, buffer, elements, mesh);
			unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
			break;
			}
			default: {
			}
			}

			if(tag != _gst_material_id) {
			Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
			splitElementByMaterial(elements, elements_per_mat);

			for (UInt i = 0; i < materials.size(); ++i) {
			materials[i]->unpackElementData(buffer, elements_per_mat[i], tag);
			}

			delete [] elements_per_mat;
			}

			AKANTU_DEBUG_OUT();
			}


			/* -------------------------------------------------------------------------- */
			inline UInt SolidMechanicsModel::getNbDataToPack(SynchronizationTag tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			// UInt nb_nodes = mesh.getNbNodes();

			switch(tag) {
			case _gst_smm_uv: {
			size += sizeof(Real) * spatial_dimension * 2;
			break;
			}
			case _gst_smm_res: {
			size += sizeof(Real) * spatial_dimension;
			break;
			}
			case _gst_smm_mass: {
			size += sizeof(Real) * spatial_dimension;
			break;
			}
			case _gst_for_dump: {
			size += sizeof(Real) * spatial_dimension * 5;
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline UInt SolidMechanicsModel::getNbDataToUnpack(SynchronizationTag tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			// UInt nb_nodes = mesh.getNbNodes();

			switch(tag) {
			case _gst_smm_uv: {
			size += sizeof(Real) * spatial_dimension * 2;
			break;
			}
			case _gst_smm_res: {
			size += sizeof(Real) * spatial_dimension;
			break;
			}
			case _gst_smm_mass: {
			size += sizeof(Real) * spatial_dimension;
			break;
			}
			case _gst_for_dump: {
			size += sizeof(Real) * spatial_dimension * 5;
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
			const UInt index,
			SynchronizationTag tag) const {
			AKANTU_DEBUG_IN();

			switch(tag) {
			case _gst_smm_uv: {
			Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
			Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
			Vector<Real> disp(it_disp[index]); buffer << disp;
			Vector<Real> velo(it_velo[index]); buffer << velo;
			break;
			}
			case _gst_smm_res: {
			Array<Real>::const_vector_iterator it_res = residual->begin(spatial_dimension);
			Vector<Real> resi(it_res[index]); buffer << resi;
			break;
			}
			case _gst_smm_mass: {
			AKANTU_DEBUG_INFO("pack mass of node " << index << " which is " << (*mass)(index,0));
			Array<Real>::const_vector_iterator it_mass = mass->begin(spatial_dimension);
			Vector<Real> mass(it_mass[index]); buffer << mass;
			break;
			}
			case _gst_for_dump: {
			Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
			Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
			Array<Real>::const_vector_iterator it_acce = acceleration->begin(spatial_dimension);
			Array<Real>::const_vector_iterator it_resi = residual->begin(spatial_dimension);
			Array<Real>::const_vector_iterator it_forc = force->begin(spatial_dimension);
			Vector<Real> disp(it_disp[index]); buffer << disp;
			Vector<Real> velo(it_velo[index]); buffer << velo;
			Vector<Real> acce(it_acce[index]); buffer << acce;
			Vector<Real> resi(it_resi[index]); buffer << resi;
			Vector<Real> forc(it_forc[index]); buffer << forc;
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			inline void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
			const UInt index,
			SynchronizationTag tag) {
			AKANTU_DEBUG_IN();

			switch(tag) {
			case _gst_smm_uv: {
			Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
			Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
			Vector<Real> disp(it_disp[index]); buffer >> disp;
			Vector<Real> velo(it_velo[index]); buffer >> velo;
			break;
			}
			case _gst_smm_res: {
			Array<Real>::vector_iterator it_res = residual->begin(spatial_dimension);
			Vector<Real> res(it_res[index]); buffer >> res;
			break;
			}
			case _gst_smm_mass: {
			AKANTU_DEBUG_INFO("mass of node " << index << " was " << (*mass)(index,0));
			Array<Real>::vector_iterator it_mass = mass->begin(spatial_dimension);
			Vector<Real> mass_v(it_mass[index]); buffer >> mass_v;
			AKANTU_DEBUG_INFO("mass of node " << index << " is now " << (*mass)(index,0));
			break;
			}
			case _gst_for_dump: {
			Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
			Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
			Array<Real>::vector_iterator it_acce = acceleration->begin(spatial_dimension);
			Array<Real>::vector_iterator it_resi = residual->begin(spatial_dimension);
			Array<Real>::vector_iterator it_forc = force->begin(spatial_dimension);
			Vector<Real> disp(it_disp[index]); buffer >> disp;
			Vector<Real> velo(it_velo[index]); buffer >> velo;
			Vector<Real> acce(it_acce[index]); buffer >> acce;
			Vector<Real> resi(it_resi[index]); buffer >> resi;
			Vector<Real> forc(it_forc[index]); buffer >> forc;
			break;
			}
			default: {
			AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			__END_AKANTU__

			#include "sparse_matrix.hh"
			#include "solver.hh"

			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			template <NewmarkBeta::IntegrationSchemeCorrectorType type>
			void SolidMechanicsModel::solve(Array<Real> &increment, Real block_val,
			bool need_factorize, bool has_profile_changed) {

			if(has_profile_changed) {
			this->initJacobianMatrix();
			need_factorize = true;
			}

			updateResidualInternal(); //doesn't do anything for static

			if(need_factorize) {
			Real c = 0.,d = 0.,e = 0.;

			if(method == _static) {
			AKANTU_DEBUG_INFO("Solving K inc = r");
			e = 1.;
			} else {
			AKANTU_DEBUG_INFO("Solving (c M + d C + e K) inc = r");

			NewmarkBeta * nmb_int = dynamic_cast<NewmarkBeta *>(integrator);
			c = nmb_int->getAccelerationCoefficient<type>(time_step);
			d = nmb_int->getVelocityCoefficient<type>(time_step);
			e = nmb_int->getDisplacementCoefficient<type>(time_step);
			}


			jacobian_matrix->clear();
			// J = c M + d C + e K
			if(stiffness_matrix)
			jacobian_matrix->add(*stiffness_matrix, e);

			if(mass_matrix)
			jacobian_matrix->add(*mass_matrix, c);

			#if !defined(AKANTU_NDEBUG)
			if(mass_matrix && AKANTU_DEBUG_TEST(dblDump)) {
			UInt prank = StaticCommunicator::getStaticCommunicator().whoAmI();
			std::stringstream sstr; sstr << "M" << prank << ".mtx";
			mass_matrix->saveMatrix(sstr.str());
			}
			#endif

			if(velocity_damping_matrix)
			jacobian_matrix->add(*velocity_damping_matrix, d);

			jacobian_matrix->applyBoundary(*blocked_dofs, block_val);

			#if !defined(AKANTU_NDEBUG)
			if(AKANTU_DEBUG_TEST(dblDump)) {
			UInt prank = StaticCommunicator::getStaticCommunicator().whoAmI();
			std::stringstream sstr; sstr << "J" << prank << ".mtx";
			jacobian_matrix->saveMatrix(sstr.str());
			}
			#endif

			solver->factorize();
			}

			// if (rhs.getSize() != 0)
			// solver->setRHS(rhs);
			// else

			solver->setOperators();

			solver->setRHS(*residual);

			// solve @f[ J \delta w = r @f]
			solver->solve(increment);

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

			bool * blocked_dofs_val = blocked_dofs->storage();
			Real * increment_val = increment.storage();

			for (UInt j = 0; j < nb_degree_of_freedom;
			++j,++increment_val, ++blocked_dofs_val) {
			if ((*blocked_dofs_val))
			*increment_val = 0.0;
			}

			}


			/* -------------------------------------------------------------------------- */
			template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
			bool SolidMechanicsModel::solveStatic(Real tolerance, UInt max_iteration,
			bool do_not_factorize,
			StaticCommunicator & comm) {

			AKANTU_DEBUG_INFO("Solving Ku = f");
			AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
			"You should first initialize the implicit solver and assemble the stiffness matrix by calling initImplicit");

			AnalysisMethod analysis_method=method;
			Real error = 0.;
			method=_static;
			bool converged = this->template solveStep<cmethod, criteria>(tolerance, error, max_iteration, do_not_factorize, comm);
			method=analysis_method;
			return converged;

			}

			/* -------------------------------------------------------------------------- */
			template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
			bool SolidMechanicsModel::solveStep(Real tolerance,
			UInt max_iteration) {
			Real error = 0.;
			return this->template solveStep<cmethod,criteria>(tolerance,
			error,
			max_iteration);
			}

			/* -------------------------------------------------------------------------- */
			template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
			bool SolidMechanicsModel::solveStep(Real tolerance, Real & error, UInt max_iteration,
			bool do_not_factorize,
			StaticCommunicator & comm) {
			EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
			this->implicitPred();
			this->updateResidual();

			AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
			"You should first initialize the implicit solver and assemble the stiffness matrix");

			bool need_factorize = !do_not_factorize;

			if (method==_implicit_dynamic) {
			AKANTU_DEBUG_ASSERT(mass_matrix != NULL,
			"You should first initialize the implicit solver and assemble the mass matrix");
			}

			switch (cmethod) {
			case _scm_newton_raphson_tangent:
			case _scm_newton_raphson_tangent_not_computed:
			break;
			case _scm_newton_raphson_tangent_modified:
			this->assembleStiffnessMatrix();
			break;
			default:
			AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
			}

			this->n_iter = 0;
			bool converged = false;
			error = 0.;
			if(criteria == _scc_residual) {
			converged = this->testConvergence<criteria> (tolerance, error, comm);
			if (converged) {
			EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));

			if(increment_flag && previous_displacement) {
			this->updateIncrement();
			}

			if(previous_displacement) previous_displacement->copy(*displacement);
			return converged;
			}
			}

			do {
			if (cmethod == _scm_newton_raphson_tangent)
			this->assembleStiffnessMatrix();

			solve<NewmarkBeta::_displacement_corrector> (*increment, 1., need_factorize);

			this->implicitCorr();

			if(criteria == _scc_residual) this->updateResidual();

			converged = this->testConvergence<criteria> (tolerance, error, comm);

			if(criteria == _scc_increment && !converged) this->updateResidual();
			//this->dump();

			this->n_iter++;
			AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
			<< std::setw(std::log10(max_iteration)) << this->n_iter
			<< ": error " << error << (converged ? " < " : " > ") << tolerance);

			switch (cmethod) {
			case _scm_newton_raphson_tangent:
			need_factorize = true;
			break;
			case _scm_newton_raphson_tangent_not_computed:
			case _scm_newton_raphson_tangent_modified:
			need_factorize = false;
			break;
			default:
			AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
			}


			} while (!converged && this->n_iter < max_iteration);

			// this makes sure that you have correct strains and stresses after the solveStep function (e.g., for dumping)
			if(criteria == _scc_increment) this->updateResidual();

			if (converged) {
			EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));

			if(increment_flag && previous_displacement) {
			this->updateIncrement();
			}

			if(previous_displacement) previous_displacement->copy(*displacement);
			} else if(this->n_iter == max_iteration) {
			AKANTU_DEBUG_WARNING("[" << criteria << "] Convergence not reached after "
			<< std::setw(std::log10(max_iteration)) << this->n_iter <<
			" iteration" << (this->n_iter == 1 ? "" : "s") << "!" << std::endl);
			}

			return converged;
			}

rAKA/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc8b0311418f95bugfixes/heat_virtual_d…

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rAKA/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
8b0311418f95bugfixes/heat_virtual_d…

solid_mechanics_model_inline_impl.cc
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