Diffusion akantu (features/fluid_diffusion) Browse

fluid_diffusion

test_model_solver_dynamic.cc
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			/**
			* @file test_dof_manager_default.cc
			*
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date Wed Feb 24 12:28:44 2016
			*
			* @brief Test default dof manager
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2011 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 "dof_manager.hh"
			#include "mesh.hh"
			#include "mesh_accessor.hh"
			#include "model_solver.hh"
			#include "non_linear_solver.hh"
			#include "sparse_matrix.hh"
			#include "static_communicator.hh"
			#include "synchronizer_registry.hh"
			#include "data_accessor.hh"
			#include "element_synchronizer.hh"
			/* -------------------------------------------------------------------------- */
			#include <fstream>
			/* -------------------------------------------------------------------------- */

			#ifndef EXPLICIT
			#define EXPLICIT true
			#endif

			using namespace akantu;

			class MyModel;
			static void genMesh(Mesh & mesh, UInt nb_nodes);

			/**
			* =\o-----o-----o-> F
			* \| \|
			* \|---- L ----\|
			*/
			class MyModel : public ModelSolver, public DataAccessor<Element> {
			public:
			MyModel(Real F, Mesh & mesh, bool lumped)
			: ModelSolver(mesh, "model_solver", 0),
			mesh(mesh), nb_dofs(mesh.getNbNodes()),
			nb_elements(mesh.getNbElement()),
			E(1.), A(1.), rho(1.), lumped(lumped),
			displacement(nb_dofs, 1, "disp"),
			velocity(nb_dofs, 1, "velo"),
			acceleration(nb_dofs, 1, "accel"),
			blocked(nb_dofs, 1, "blocked"),
			forces(nb_dofs, 1, "force_ext"),
			internal_forces(nb_dofs, 1, "force_int"),
			stresses(nb_elements, 1, "stress"),
			strains(nb_elements, 1, "strain"),
			initial_lengths(nb_elements, 1, "L0") {
			this->initDOFManager();

			this->getDOFManager().registerDOFs("disp", displacement, _dst_nodal);
			this->getDOFManager().registerDOFsDerivative("disp", 1, velocity);
			this->getDOFManager().registerDOFsDerivative("disp", 2, acceleration);

			this->getDOFManager().registerBlockedDOFs("disp", blocked);

			this->getDOFManager().getNewMatrix("K", _symmetric);
			this->getDOFManager().getNewMatrix("M", "K");
			this->getDOFManager().getNewMatrix("J", "K");

			this->getDOFManager().getNewLumpedMatrix("M");

			if (lumped) {
			this->assembleLumpedMass();
			} else {
			this->assembleMass();
			this->assembleStiffness();
			}
			this->assembleJacobian();

			displacement.set(0.);
			velocity.set(0.);
			acceleration.set(0.);

			forces.set(0.);
			blocked.set(false);

			UInt global_nb_nodes = mesh.getNbGlobalNodes();
			for(UInt n = 0; n < nb_dofs; ++n) {
			if (mesh.getGlobalNodesIds()(n) == (global_nb_nodes -1))
			forces(n, _x) = F;

			if (mesh.getGlobalNodesIds()(n) == 0)
			blocked(n, _x) = true;
			}

			auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
			auto cend = this->mesh.getConnectivity(_segment_2).end(2);
			auto L_it = this->initial_lengths.begin();

			for (; cit != cend; ++cit, ++L_it) {
			const Vector<UInt> & conn = *cit;
			UInt n1 = conn(0);
			UInt n2 = conn(1);
			Real p1 = this->mesh.getNodes()(n1, _x);
			Real p2 = this->mesh.getNodes()(n2, _x);

			*L_it = std::abs(p2 - p1);
			}

			this->registerDataAccessor(*this);
			this->registerSynchronizer(const_cast<ElementSynchronizer &>(this->mesh.getElementSynchronizer()),
			_gst_user_1);
			}

			void assembleLumpedMass() {
			Array<Real> & M = this->getDOFManager().getLumpedMatrix("M");
			M.clear();

			this->assembleLumpedMass(_not_ghost);
			if (this->mesh.getNbElement(_segment_2, _ghost) > 0)
			this->assembleLumpedMass(_ghost);
			}

			void assembleLumpedMass(const GhostType & ghost_type) {
			Array<Real> & M = this->getDOFManager().getLumpedMatrix("M");

			Array<Real> m_all_el(this->mesh.getNbElement(_segment_2, ghost_type), 2);

			Array<Real>::vector_iterator m_it = m_all_el.begin(2);

			auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
			auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);

			for (; cit != cend; ++cit, ++m_it) {
			const Vector<UInt> & conn = *cit;
			UInt n1 = conn(0);
			UInt n2 = conn(1);

			Real p1 = this->mesh.getNodes()(n1, _x);
			Real p2 = this->mesh.getNodes()(n2, _x);

			Real L = std::abs(p2 - p1);

			Real M_n = rho * A * L / 2;
			(m_it)(0) = (m_it)(1) = M_n;
			}

			this->getDOFManager().assembleElementalArrayLocalArray(
			m_all_el, M, _segment_2, ghost_type);
			}

			void assembleMass() {
			SparseMatrix & M = this->getDOFManager().getMatrix("M");
			M.clear();

			Array<Real> m_all_el(this->nb_elements, 4);
			Array<Real>::matrix_iterator m_it = m_all_el.begin(2, 2);

			auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
			auto cend = this->mesh.getConnectivity(_segment_2).end(2);

			Matrix<Real> m(2, 2);
			m(0, 0) = m(1, 1) = 2;
			m(0, 1) = m(1, 0) = 1;

			// under integrated
			// m(0, 0) = m(1, 1) = 3./2.;
			// m(0, 1) = m(1, 0) = 3./2.;

			// lumping the mass matrix
			// m(0, 0) += m(0, 1);
			// m(1, 1) += m(1, 0);
			// m(0, 1) = m(1, 0) = 0;

			for (; cit != cend; ++cit, ++m_it) {
			const Vector<UInt> & conn = *cit;
			UInt n1 = conn(0);
			UInt n2 = conn(1);

			Real p1 = this->mesh.getNodes()(n1, _x);
			Real p2 = this->mesh.getNodes()(n2, _x);

			Real L = std::abs(p2 - p1);

			Matrix<Real> & m_el = *m_it;
			m_el = m;
			m_el = rho A * L / 6.;
			}
			this->getDOFManager().assembleElementalMatricesToMatrix(
			"M", "disp", m_all_el, _segment_2);
			}

			void assembleJacobian() {}
			void assembleStiffness() {
			SparseMatrix & K = this->getDOFManager().getMatrix("K");
			K.clear();

			Matrix<Real> k(2, 2);
			k(0, 0) = k(1, 1) = 1;
			k(0, 1) = k(1, 0) = -1;

			Array<Real> k_all_el(this->nb_elements, 4);

			auto k_it = k_all_el.begin(2, 2);
			auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
			auto cend = this->mesh.getConnectivity(_segment_2).end(2);

			for (; cit != cend; ++cit, ++k_it) {
			const auto & conn = *cit;
			UInt n1 = conn(0);
			UInt n2 = conn(1);

			Real p1 = this->mesh.getNodes()(n1, _x);
			Real p2 = this->mesh.getNodes()(n2, _x);

			Real L = std::abs(p2 - p1);

			auto & k_el = *k_it;
			k_el = k;
			k_el = E A / L;
			}

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "disp", k_all_el, _segment_2);
			}

			void assembleResidual() {
			this->getDOFManager().assembleToResidual("disp", forces);
			internal_forces.clear();

			this->assembleResidual(_not_ghost);

			this->synchronize(_gst_user_1);

			this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
			}

			void assembleResidual(const GhostType & ghost_type) {
			Array<Real> forces_internal_el(
			this->mesh.getNbElement(_segment_2, ghost_type), 2);

			auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
			auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);

			auto f_it = forces_internal_el.begin(2);

			auto strain_it = this->strains.begin();
			auto stress_it = this->stresses.begin();
			auto L_it = this->initial_lengths.begin();

			for (; cit != cend; ++cit, ++f_it, ++strain_it, ++stress_it, ++L_it) {
			const auto & conn = *cit;
			UInt n1 = conn(0);
			UInt n2 = conn(1);

			Real u1 = this->displacement(n1, _x);
			Real u2 = this->displacement(n2, _x);

			strain_it = (u2 - u1) / L_it;
			stress_it = E *strain_it;
			Real f_n = A * *stress_it;
			Vector<Real> & f = *f_it;

			f(0) = -f_n;
			f(1) = f_n;
			}

			this->getDOFManager().assembleElementalArrayLocalArray(
			forces_internal_el, internal_forces, _segment_2, ghost_type);
			}

			Real getPotentialEnergy() {
			Real res = 0;

			if (!lumped) {
			res = this->mulVectMatVect(this->displacement,
			this->getDOFManager().getMatrix("K"),
			this->displacement);
			} else {
			auto strain_it = this->strains.begin();
			auto stress_it = this->stresses.begin();
			auto strain_end = this->strains.end();
			auto L_it = this->initial_lengths.begin();

			for (; strain_it != strain_end; ++strain_it, ++stress_it, ++L_it) {
			res += strain_it stress_it A * *L_it;
			}

			StaticCommunicator::getStaticCommunicator().allReduce(res, _so_sum);
			}

			return res / 2.;
			}

			Real getKineticEnergy() {
			Real res = 0;
			if (!lumped) {
			res = this->mulVectMatVect(
			this->velocity, this->getDOFManager().getMatrix("M"), this->velocity);
			} else {
			auto & m = this->getDOFManager().getLumpedMatrix("M");
			auto it = velocity.begin();
			auto end = velocity.end();
			auto m_it = m.begin();

			for (UInt node = 0; it != end; ++it, ++m_it, ++node) {
			if (mesh.isLocalOrMasterNode(node))
			res += m_it it *it;
			}

			StaticCommunicator::getStaticCommunicator().allReduce(res, _so_sum);
			}

			return res / 2.;
			}

			Real getExternalWorkIncrement() {
			Real res = 0;

			auto it = velocity.begin();
			auto end = velocity.end();
			auto if_it = internal_forces.begin();
			auto ef_it = forces.begin();
			auto b_it = blocked.begin();

			for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
			if (mesh.isLocalOrMasterNode(node))
			res += (b_it ? - if_it : ef_it) *it;
			}

			StaticCommunicator::getStaticCommunicator().allReduce(res, _so_sum);

			return res * this->getTimeStep();
			}

			Real mulVectMatVect(const Array<Real> & x, const SparseMatrix & A,
			const Array<Real> & y) {
			Array<Real> Ay(this->nb_dofs, 1, 0.);
			A.matVecMul(y, Ay);
			Real res = 0.;

			Array<Real>::const_scalar_iterator it = Ay.begin();
			Array<Real>::const_scalar_iterator end = Ay.end();
			Array<Real>::const_scalar_iterator x_it = x.begin();

			for (UInt node = 0; it != end; ++it, ++x_it, ++node) {
			if (mesh.isLocalOrMasterNode(node))
			res += x_it *it;
			}

			StaticCommunicator::getStaticCommunicator().allReduce(res, _so_sum);
			return res;
			}

			void predictor() {}
			void corrector() {}

			/* ------------------------------------------------------------------------ */
			UInt getNbData(const Array<Element> & elements, const SynchronizationTag &) const {
			return elements.getSize() * sizeof(Real);
			}

			void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			if(tag == _gst_user_1) {
			for(const auto & el : elements) {
			buffer << this->stresses(el.element);
			}
			}
			}


			void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
			const SynchronizationTag & tag) {
			if(tag == _gst_user_1) {
			auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);

			for(const auto & el : elements) {
			Real stress;
			buffer >> stress;

			Real f = A * stress;

			Vector<UInt> conn = cit[el.element];
			this->internal_forces(conn(0), _x) += -f;
			this->internal_forces(conn(1), _x) += f;
			}
			}
			}

			private:
			Mesh & mesh;
			UInt nb_dofs;
			UInt nb_elements;
			Real E, A, rho;

			bool lumped;
			public:
			Array<Real> displacement;
			Array<Real> velocity;
			Array<Real> acceleration;
			Array<bool> blocked;
			Array<Real> forces;
			Array<Real> internal_forces;

			Array<Real> stresses;
			Array<Real> strains;

			Array<Real> initial_lengths;
			};

			/* -------------------------------------------------------------------------- */
			int main(int argc, char * argv[]) {
			initialize(argc, argv);

			UInt prank = StaticCommunicator::getStaticCommunicator().whoAmI();
			UInt global_nb_nodes = 201;
			UInt max_steps = 200;
			Real time_step = 0.001;
			Mesh mesh(1);
			Real F = -9.81;
			bool _explicit = EXPLICIT;

			genMesh(mesh, global_nb_nodes);

			mesh.distribute();

			MyModel model(F, mesh, _explicit);

			if (!_explicit) {
			model.getNewSolver("dynamic", _tsst_dynamic, _nls_newton_raphson);
			model.setIntegrationScheme("dynamic", "disp", _ist_trapezoidal_rule_2,
			IntegrationScheme::_displacement);
			} else {
			model.getNewSolver("dynamic", _tsst_dynamic_lumped, _nls_lumped);
			model.setIntegrationScheme("dynamic", "disp", _ist_central_difference,
			IntegrationScheme::_acceleration);
			}

			model.setTimeStep(time_step);

			// #if EXPLICIT == true
			// std::ofstream output("output_dynamic_explicit.csv");
			// #else
			// std::ofstream output("output_dynamic_implicit.csv");
			// #endif

			if (prank == 0) {
			std::cout << std::scientific;
			std::cout << std::setw(14) << "time"
			<< "," << std::setw(14) << "wext"
			<< "," << std::setw(14) << "epot"
			<< "," << std::setw(14) << "ekin"
			<< "," << std::setw(14) << "total" << std::endl;
			}
			Real wext = 0.;

			model.assembleResidual();

			Real epot = model.getPotentialEnergy();
			Real ekin = model.getKineticEnergy();
			Real einit = ekin + epot;
			Real etot = ekin + epot - wext - einit;
			if (prank == 0) {
			std::cout << std::setw(14) << 0.
			<< "," << std::setw(14) << wext
			<< "," << std::setw(14) << epot
			<< "," << std::setw(14) << ekin
			<< "," << std::setw(14) << etot
			<< std::endl;
			}

			#if EXPLICIT == false
			NonLinearSolver & solver =
			model.getDOFManager().getNonLinearSolver("dynamic");

			solver.set("max_iterations", 2);
			#endif

			for (UInt i = 1; i < max_steps + 1; ++i) {
			model.solveStep();

			#if EXPLICIT == false
			int nb_iter = solver.get("nb_iterations");
			Real error = solver.get("error");
			bool converged = solver.get("converged");
			if(prank == 0)
			std::cerr << error << " " << nb_iter << " -> " << converged << std::endl;
			#endif

			epot = model.getPotentialEnergy();
			ekin = model.getKineticEnergy();
			wext += model.getExternalWorkIncrement();
			etot = ekin + epot - wext - einit;
			if (prank == 0) {
			std::cout << std::setw(14) << time_step * i
			<< "," << std::setw(14) << wext
			<< "," << std::setw(14) << epot
			<< "," << std::setw(14) << ekin
			<< "," << std::setw(14) << etot
			<< std::endl;
			}

			if (std::abs(etot) > 1e1) {
			AKANTU_DEBUG_ERROR("The total energy of the system is not conserved!");
			}
			}

			// output.close();
			finalize();
			return EXIT_SUCCESS;
			}

			/* -------------------------------------------------------------------------- */
			void genMesh(Mesh & mesh, UInt nb_nodes) {
			MeshAccessor mesh_accessor(mesh);
			Array<Real> & nodes = mesh_accessor.getNodes();
			Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);

			nodes.resize(nb_nodes);

			for (UInt n = 0; n < nb_nodes; ++n) {
			nodes(n, _x) = n * (1. / (nb_nodes - 1));
			}

			conn.resize(nb_nodes - 1);
			for (UInt n = 0; n < nb_nodes - 1; ++n) {
			conn(n, 0) = n;
			conn(n, 1) = n + 1;
			}
			}

rAKA/test/test_model/test_model_solver/test_model_solver_dynamic.ccfd0f85acb8fffeatures/fluid_diffusion

test_model_solver_dynamic.ccView Options

rAKA/test/test_model/test_model_solver/test_model_solver_dynamic.cc
fd0f85acb8fffeatures/fluid_diffusion

test_model_solver_dynamic.cc
View Options