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test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
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			/**
			* @file test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
			*
			* @author Marco Vocialta <marco.vocialta@epfl.ch>
			*
			* @date creation: Wed Nov 05 2014
			* @date last modification: Wed Nov 08 2017
			*
			* @brief Displacement test for 3D cohesive elements
			*
			* @section LICENSE
			*
			* Copyright (©) 2015-2018 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 "dumper_paraview.hh"
			#include "material_cohesive_linear.hh"
			#include "solid_mechanics_model_cohesive.hh"

			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_paraview.hh"
			#endif

			/* -------------------------------------------------------------------------- */
			using namespace akantu;

			bool checkDisplacement(SolidMechanicsModelCohesive & model, ElementType type,
			std::ofstream & error_output, UInt step,
			bool barycenters);

			int main(int argc, char * argv[]) {
			initialize("material.dat", argc, argv);

			debug::setDebugLevel(dblWarning);

			const UInt max_steps = 500;
			Math::setTolerance(1.e-12);

			UInt spatial_dimension = 3;
			ElementType type = _tetrahedron_10;

			Mesh mesh(spatial_dimension);

			const auto & comm = Communicator::getStaticCommunicator();
			Int psize = comm.getNbProc();
			Int prank = comm.whoAmI();

			akantu::MeshPartition * partition = NULL;
			if (prank == 0) {
			// Read the mesh
			mesh.read("tetrahedron.msh");

			/// partition the mesh
			partition = new MeshPartitionScotch(mesh, spatial_dimension);
			// debug::setDebugLevel(dblDump);
			partition->partitionate(psize);
			// debug::setDebugLevel(dblWarning);
			}

			SolidMechanicsModelCohesive model(mesh);

			model.initParallel(partition, NULL, true);

			// debug::setDebugLevel(dblDump);
			// std::cout << mesh << std::endl;
			// debug::setDebugLevel(dblWarning);

			model.initFull(
			SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));

			/* ------------------------------------------------------------------------ */
			/* Facet part */
			/* ------------------------------------------------------------------------ */

			// Array<Real> limits(spatial_dimension, 2);
			// limits(0, 0) = -0.01;
			// limits(0, 1) = 0.01;
			// limits(1, 0) = -100;
			// limits(1, 1) = 100;
			// limits(2, 0) = -100;
			// limits(2, 1) = 100;

			// model.enableFacetsCheckOnArea(limits);

			/* ------------------------------------------------------------------------ */
			/* End of facet part */
			/* ------------------------------------------------------------------------ */

			// debug::setDebugLevel(dblDump);
			// std::cout << mesh_facets << std::endl;
			// debug::setDebugLevel(dblWarning);

			Real time_step = model.getStableTimeStep() * 0.1;
			model.setTimeStep(time_step);
			std::cout << "Time step: " << time_step << std::endl;

			model.assembleMassLumped();

			Array<Real> & position = mesh.getNodes();
			Array<Real> & velocity = model.getVelocity();
			Array<bool> & boundary = model.getBlockedDOFs();
			Array<Real> & displacement = model.getDisplacement();
			// const Array<Real> & residual = model.getResidual();

			UInt nb_nodes = mesh.getNbNodes();

			/// boundary conditions
			for (UInt n = 0; n < nb_nodes; ++n) {
			if (position(n, 0) > 0.99 \|\| position(n, 0) < -0.99) {
			for (UInt dim = 0; dim < spatial_dimension; ++dim) {
			boundary(n, dim) = true;
			}
			}

			if (position(n, 0) > 0.99 \|\| position(n, 0) < -0.99) {
			for (UInt dim = 0; dim < spatial_dimension; ++dim) {
			boundary(n, dim) = true;
			}
			}
			}

			// #if defined (AKANTU_DEBUG_TOOLS)
			// Vector<Real> facet_center(spatial_dimension);
			// facet_center(0) = 0;
			// facet_center(1) = -0.16666667;
			// facet_center(2) = 0.5;

			// debug::element_manager.setMesh(mesh);
			// debug::element_manager.addModule(debug::_dm_material_cohesive);
			// debug::element_manager.addModule(debug::_dm_debug_tools);
			// //debug::element_manager.addModule(debug::_dm_integrator);
			// #endif

			/// initial conditions
			Real loading_rate = 1;
			Real disp_update = loading_rate * time_step;
			for (UInt n = 0; n < nb_nodes; ++n) {
			velocity(n, 0) = loading_rate * position(n, 0);
			velocity(n, 1) = loading_rate * position(n, 0);
			}

			model.synchronizeBoundaries();
			model.updateResidual();

			std::stringstream paraview_output;
			paraview_output << "extrinsic_parallel_tetrahedron_" << psize;

			model.setBaseName(paraview_output.str());
			model.addDumpFieldVector("displacement");
			model.addDumpFieldVector("velocity");
			model.addDumpFieldVector("acceleration");
			model.addDumpFieldVector("residual");
			model.addDumpFieldTensor("stress");
			model.addDumpFieldTensor("grad_u");
			model.addDumpField("partitions");
			// model.getDumper().getDumper().setMode(iohelper::BASE64);
			model.dump();

			model.setBaseNameToDumper("cohesive elements",
			paraview_output.str() + "_cohesive_elements");
			model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
			model.addDumpFieldToDumper("cohesive elements", "damage");
			model.dump("cohesive elements");

			std::stringstream error_stream;
			error_stream << "error"
			<< ".csv";
			std::ofstream error_output;
			error_output.open(error_stream.str().c_str());
			error_output << "# Step, Average, Max, Min" << std::endl;

			if (checkDisplacement(model, type, error_output, 0, true)) {
			}

			/// Main loop
			for (UInt s = 1; s <= max_steps; ++s) {

			/// update displacement on extreme nodes
			for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
			if (position(n, 0) > 0.99 \|\| position(n, 0) < -0.99) {
			displacement(n, 0) += disp_update * position(n, 0);
			displacement(n, 1) += disp_update * position(n, 0);
			}
			}

			model.checkCohesiveStress();

			model.solveStep();

			if (s % 100 == 0) {
			if (prank == 0)
			std::cout << "passing step " << s << "/" << max_steps << std::endl;
			}
			}

			model.dump();
			model.dump("cohesive elements");

			if (!checkDisplacement(model, type, error_output, max_steps, false)) {
			finalize();
			return EXIT_FAILURE;
			}

			finalize();
			return EXIT_SUCCESS;
			}

			bool checkDisplacement(SolidMechanicsModelCohesive & model, ElementType type,
			std::ofstream & error_output, UInt step,
			bool barycenters) {

			Mesh & mesh = model.getMesh();
			UInt spatial_dimension = mesh.getSpatialDimension();
			const Array<UInt> & connectivity = mesh.getConnectivity(type);
			const Array<Real> & displacement = model.getDisplacement();
			UInt nb_element = mesh.getNbElement(type);
			UInt nb_nodes_per_elem = Mesh::getNbNodesPerElement(type);

			const auto & comm = Communicator::getStaticCommunicator();
			Int psize = comm.getNbProc();
			Int prank = comm.whoAmI();

			if (psize == 1) {
			std::stringstream displacement_file;
			displacement_file << "displacement/displacement_" << std::setfill('0')
			<< std::setw(6) << step;
			std::ofstream displacement_output;
			displacement_output.open(displacement_file.str().c_str());

			for (UInt el = 0; el < nb_element; ++el) {
			for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
			UInt node = connectivity(el, n);

			for (UInt dim = 0; dim < spatial_dimension; ++dim) {
			displacement_output << std::setprecision(15)
			<< displacement(node, dim) << " ";
			}
			displacement_output << std::endl;
			}
			}

			displacement_output.close();

			if (barycenters) {
			std::stringstream barycenter_file;
			barycenter_file << "displacement/barycenters";
			std::ofstream barycenter_output;
			barycenter_output.open(barycenter_file.str().c_str());

			Element element(type, 0);
			Vector<Real> bary(spatial_dimension);

			for (UInt el = 0; el < nb_element; ++el) {
			element.element = el;
			mesh.getBarycenter(element, bary);

			for (UInt dim = 0; dim < spatial_dimension; ++dim) {
			barycenter_output << std::setprecision(15) << bary(dim) << " ";
			}
			barycenter_output << std::endl;
			}

			barycenter_output.close();
			}
			} else {

			if (barycenters)
			return true;

			/// read data
			std::stringstream displacement_file;
			displacement_file << "displacement/displacement_" << std::setfill('0')
			<< std::setw(6) << step;
			std::ifstream displacement_input;
			displacement_input.open(displacement_file.str().c_str());

			Array<Real> displacement_serial(0, spatial_dimension);
			Vector<Real> disp_tmp(spatial_dimension);

			while (displacement_input.good()) {
			for (UInt i = 0; i < spatial_dimension; ++i)
			displacement_input >> disp_tmp(i);

			displacement_serial.push_back(disp_tmp);
			}

			std::stringstream barycenter_file;
			barycenter_file << "displacement/barycenters";
			std::ifstream barycenter_input;
			barycenter_input.open(barycenter_file.str().c_str());

			Array<Real> barycenter_serial(0, spatial_dimension);

			while (barycenter_input.good()) {
			for (UInt dim = 0; dim < spatial_dimension; ++dim)
			barycenter_input >> disp_tmp(dim);

			barycenter_serial.push_back(disp_tmp);
			}

			Element element(type, 0);
			Vector<Real> bary(spatial_dimension);

			Array<Real>::iterator<Vector<Real>> it;
			Array<Real>::iterator<Vector<Real>> begin =
			barycenter_serial.begin(spatial_dimension);
			Array<Real>::iterator<Vector<Real>> end =
			barycenter_serial.end(spatial_dimension);

			Array<Real>::const_iterator<Vector<Real>> disp_it;
			Array<Real>::iterator<Vector<Real>> disp_serial_it;

			Vector<Real> difference(spatial_dimension);
			Array<Real> error;

			/// compute error
			for (UInt el = 0; el < nb_element; ++el) {
			element.element = el;
			mesh.getBarycenter(element, bary);

			/// find element
			for (it = begin; it != end; ++it) {
			UInt matched_dim = 0;

			while (matched_dim < spatial_dimension &&
			Math::are_float_equal(bary(matched_dim), (*it)(matched_dim)))
			++matched_dim;

			if (matched_dim == spatial_dimension)
			break;
			}

			if (it == end) {
			std::cout << "Element barycenter not found!" << std::endl;
			return false;
			}

			UInt matched_el = it - begin;

			disp_serial_it = displacement_serial.begin(spatial_dimension) +
			matched_el * nb_nodes_per_elem;

			for (UInt n = 0; n < nb_nodes_per_elem; ++n, ++disp_serial_it) {
			UInt node = connectivity(el, n);
			if (!mesh.isLocalOrMasterNode(node))
			continue;

			disp_it = displacement.begin(spatial_dimension) + node;

			difference = *disp_it;
			difference -= *disp_serial_it;

			error.push_back(difference.norm());
			}
			}

			/// compute average error
			Real average_error = std::accumulate(error.begin(), error.end(), 0.);
			comm.allReduce(&average_error, 1, _so_sum);

			UInt error_size = error.getSize();
			comm.allReduce(&error_size, 1, _so_sum);

			average_error /= error_size;

			/// compute maximum and minimum
			Real max_error = *std::max_element(error.begin(), error.end());
			comm.allReduce(&max_error, 1, _so_max);

			Real min_error = *std::min_element(error.begin(), error.end());
			comm.allReduce(&min_error, 1, _so_min);

			/// output data
			if (prank == 0) {
			error_output << step << ", " << average_error << ", " << max_error << ", "
			<< min_error << std::endl;
			}

			if (max_error > 1.e-9) {
			std::cout << "Displacement error is too big!" << std::endl;
			return false;
			}
			}

			return true;
			}

rAKA/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc847ef2e1583cfeatures/python-doc

test_cohesive_parallel_extrinsic_tetrahedron_displacement.ccView Options

rAKA/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
847ef2e1583cfeatures/python-doc

test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
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