solid_mechanics_model_RVE.cc
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solid_mechanics_model_RVE.cc
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	/**
	* @file solid_mechanics_model_RVE.cc
	* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
	* @date Wed Jan 13 15:32:35 2016
	*
	* @brief Implementation of SolidMechanicsModelRVE
	*
	* @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 "solid_mechanics_model_RVE.hh"
	#include "element_group.hh"
	#include "material_damage_iterative.hh"
	#include "node_group.hh"
	#include "non_linear_solver.hh"
	#include "non_local_manager.hh"
	#include "parser.hh"
	#include "sparse_matrix.hh"
	/* -------------------------------------------------------------------------- */
	#include <string>
	/* -------------------------------------------------------------------------- */

	namespace akantu {

	/* -------------------------------------------------------------------------- */
	SolidMechanicsModelRVE::SolidMechanicsModelRVE(Mesh & mesh,
	bool use_RVE_mat_selector,
	UInt nb_gel_pockets, UInt dim,
	const ID & id,
	const MemoryID & memory_id)
	: SolidMechanicsModel(mesh, dim, id, memory_id), volume(0.),
	use_RVE_mat_selector(use_RVE_mat_selector),
	nb_gel_pockets(nb_gel_pockets), nb_dumps(0) {
	AKANTU_DEBUG_IN();
	/// find the four corner nodes of the RVE
	findCornerNodes();

	/// remove the corner nodes from the surface node groups:
	/// This most be done because corner nodes a not periodic
	mesh.getElementGroup("top").removeNode(corner_nodes(2));
	mesh.getElementGroup("top").removeNode(corner_nodes(3));
	mesh.getElementGroup("left").removeNode(corner_nodes(3));
	mesh.getElementGroup("left").removeNode(corner_nodes(0));
	mesh.getElementGroup("bottom").removeNode(corner_nodes(1));
	mesh.getElementGroup("bottom").removeNode(corner_nodes(0));
	mesh.getElementGroup("right").removeNode(corner_nodes(2));
	mesh.getElementGroup("right").removeNode(corner_nodes(1));

	const auto & bottom = mesh.getElementGroup("bottom").getNodeGroup();
	bottom_nodes.insert(bottom.begin(), bottom.end());

	const auto & left = mesh.getElementGroup("left").getNodeGroup();
	left_nodes.insert(left.begin(), left.end());

	// /// enforce periodicity on the displacement fluctuations
	// auto surface_pair_1 = std::make_pair("top", "bottom");
	// auto surface_pair_2 = std::make_pair("right", "left");
	// SurfacePairList surface_pairs_list;
	// surface_pairs_list.push_back(surface_pair_1);
	// surface_pairs_list.push_back(surface_pair_2);
	// TODO: To Nicolas correct the PBCs
	// this->setPBC(surface_pairs_list);

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	SolidMechanicsModelRVE::~SolidMechanicsModelRVE() = default;

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::initFullImpl(const ModelOptions & options) {
	AKANTU_DEBUG_IN();

	auto options_cp(options);
	options_cp.analysis_method = AnalysisMethod::_static;

	SolidMechanicsModel::initFullImpl(options_cp);

	// this->initMaterials();
	auto & fem = this->getFEEngine("SolidMechanicsFEEngine");

	/// compute the volume of the RVE
	GhostType gt = _not_ghost;
	for (auto element_type :
	this->mesh.elementTypes(spatial_dimension, gt, _ek_not_defined)) {
	Array<Real> Volume(this->mesh.getNbElement(element_type) *
	fem.getNbIntegrationPoints(element_type),
	1, 1.);
	this->volume = fem.integrate(Volume, element_type);
	}

	std::cout << "The volume of the RVE is " << this->volume << std::endl;

	/// dumping
	std::stringstream base_name;
	base_name << this->id; // << this->memory_id - 1;
	this->setBaseName(base_name.str());
	this->addDumpFieldVector("displacement");
	this->addDumpField("stress");
	this->addDumpField("grad_u");
	this->addDumpField("eigen_grad_u");
	this->addDumpField("blocked_dofs");
	this->addDumpField("material_index");
	this->addDumpField("damage");
	this->addDumpField("Sc");
	this->addDumpField("external_force");
	this->addDumpField("equivalent_stress");
	this->addDumpField("internal_force");
	this->addDumpField("delta_T");

	this->dump();
	this->nb_dumps += 1;
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::applyBoundaryConditions(
	const Matrix<Real> & displacement_gradient) {
	AKANTU_DEBUG_IN();
	/// get the position of the nodes
	const Array<Real> & pos = mesh.getNodes();
	/// storage for the coordinates of a given node and the displacement that will
	/// be applied
	Vector<Real> x(spatial_dimension);
	Vector<Real> appl_disp(spatial_dimension);

	/// fix top right node
	UInt node = this->corner_nodes(2);
	x(0) = pos(node, 0);
	x(1) = pos(node, 1);
	appl_disp.mul<false>(displacement_gradient, x);
	(*this->blocked_dofs)(node, 0) = true;
	(*this->displacement)(node, 0) = appl_disp(0);
	(*this->blocked_dofs)(node, 1) = true;
	(*this->displacement)(node, 1) = appl_disp(1);
	// (this->blocked_dofs)(node,0) = true; (this->displacement)(node,0) = 0.;
	// (this->blocked_dofs)(node,1) = true; (this->displacement)(node,1) = 0.;

	/// apply Hx at all the other corner nodes; H: displ. gradient
	node = this->corner_nodes(0);
	x(0) = pos(node, 0);
	x(1) = pos(node, 1);
	appl_disp.mul<false>(displacement_gradient, x);
	(*this->blocked_dofs)(node, 0) = true;
	(*this->displacement)(node, 0) = appl_disp(0);
	(*this->blocked_dofs)(node, 1) = true;
	(*this->displacement)(node, 1) = appl_disp(1);

	node = this->corner_nodes(1);
	x(0) = pos(node, 0);
	x(1) = pos(node, 1);
	appl_disp.mul<false>(displacement_gradient, x);
	(*this->blocked_dofs)(node, 0) = true;
	(*this->displacement)(node, 0) = appl_disp(0);
	(*this->blocked_dofs)(node, 1) = true;
	(*this->displacement)(node, 1) = appl_disp(1);

	node = this->corner_nodes(3);
	x(0) = pos(node, 0);
	x(1) = pos(node, 1);
	appl_disp.mul<false>(displacement_gradient, x);
	(*this->blocked_dofs)(node, 0) = true;
	(*this->displacement)(node, 0) = appl_disp(0);
	(*this->blocked_dofs)(node, 1) = true;
	(*this->displacement)(node, 1) = appl_disp(1);
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::applyHomogeneousTemperature(
	const Real & temperature) {

	for (UInt m = 0; m < this->getNbMaterials(); ++m) {
	Material & mat = this->getMaterial(m);

	const ElementTypeMapArray<UInt> & filter_map = mat.getElementFilter();

	// Loop over all element types
	for (auto && type : filter_map.elementTypes(spatial_dimension)) {
	const Array<UInt> & filter = filter_map(type);
	if (filter.size() == 0)
	continue;

	Array<Real> & delta_T = mat.getArray<Real>("delta_T", type);
	Array<Real>::scalar_iterator delta_T_it = delta_T.begin();
	Array<Real>::scalar_iterator delta_T_end = delta_T.end();

	for (; delta_T_it != delta_T_end; ++delta_T_it) {
	*delta_T_it = temperature;
	}
	}
	}
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::findCornerNodes() {
	AKANTU_DEBUG_IN();

	// find corner nodes
	const auto & position = mesh.getNodes();
	const auto & lower_bounds = mesh.getLowerBounds();
	const auto & upper_bounds = mesh.getUpperBounds();

	AKANTU_DEBUG_ASSERT(spatial_dimension == 2, "This is 2D only!");
	corner_nodes.resize(4);
	corner_nodes.set(UInt(-1));

	for (auto && data : enumerate(make_view(position, spatial_dimension))) {
	auto node = std::get<0>(data);
	const auto & X = std::get<1>(data);

	auto distance = X.distance(lower_bounds);
	// node 1
	if (Math::are_float_equal(distance, 0)) {
	corner_nodes(0) = node;
	}
	// node 2
	else if (Math::are_float_equal(X(_x), upper_bounds(_x)) &&
	Math::are_float_equal(X(_y), lower_bounds(_y))) {
	corner_nodes(1) = node;
	}
	// node 3
	else if (Math::are_float_equal(X(_x), upper_bounds(_x)) &&
	Math::are_float_equal(X(_y), upper_bounds(_y))) {
	corner_nodes(2) = node;
	}
	// node 4
	else if (Math::are_float_equal(X(_x), lower_bounds(_x)) &&
	Math::are_float_equal(X(_y), upper_bounds(_y))) {
	corner_nodes(3) = node;
	}
	}

	for (UInt i = 0; i < corner_nodes.size(); ++i) {
	if (corner_nodes(i) == UInt(-1))
	AKANTU_ERROR("The corner node " << i + 1 << " wasn't found");
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::advanceASR(const Matrix<Real> & prestrain) {
	AKANTU_DEBUG_IN();
	AKANTU_DEBUG_ASSERT(spatial_dimension == 2, "This is 2D only!");

	/// apply the new eigenstrain
	for (auto element_type :
	mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
	Array<Real> & prestrain_vect =
	const_cast<Array<Real> &>(this->getMaterial("gel").getInternal<Real>(
	"eigen_grad_u")(element_type));
	auto prestrain_it =
	prestrain_vect.begin(spatial_dimension, spatial_dimension);
	auto prestrain_end =
	prestrain_vect.end(spatial_dimension, spatial_dimension);

	for (; prestrain_it != prestrain_end; ++prestrain_it)
	(*prestrain_it) = prestrain;
	}

	/// advance the damage
	MaterialDamageIterative<2> & mat_paste =
	dynamic_cast<MaterialDamageIterative<2> &>(*this->materials[1]);
	MaterialDamageIterative<2> & mat_aggregate =
	dynamic_cast<MaterialDamageIterative<2> &>(*this->materials[0]);
	UInt nb_damaged_elements = 0;
	Real max_eq_stress_aggregate = 0;
	Real max_eq_stress_paste = 0;

	auto & solver = this->getNonLinearSolver();
	solver.set("max_iterations", 2);
	solver.set("threshold", 1e-6);
	solver.set("convergence_type", SolveConvergenceCriteria::_solution);

	do {
	this->solveStep();

	/// compute damage
	max_eq_stress_aggregate = mat_aggregate.getNormMaxEquivalentStress();
	max_eq_stress_paste = mat_paste.getNormMaxEquivalentStress();

	nb_damaged_elements = 0;
	if (max_eq_stress_aggregate > max_eq_stress_paste)
	nb_damaged_elements = mat_aggregate.updateDamage();
	else if (max_eq_stress_aggregate < max_eq_stress_paste)
	nb_damaged_elements = mat_paste.updateDamage();
	else
	nb_damaged_elements =
	(mat_paste.updateDamage() + mat_aggregate.updateDamage());

	std::cout << "the number of damaged elements is " << nb_damaged_elements
	<< std::endl;
	} while (nb_damaged_elements);

	if (this->nb_dumps % 10 == 0) {
	this->dump();
	}
	this->nb_dumps += 1;

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	Real SolidMechanicsModelRVE::averageTensorField(UInt row_index, UInt col_index,
	const ID & field_type) {
	AKANTU_DEBUG_IN();
	auto & fem = this->getFEEngine("SolidMechanicsFEEngine");
	Real average = 0;

	GhostType gt = _not_ghost;
	for (auto element_type :
	mesh.elementTypes(spatial_dimension, gt, _ek_not_defined)) {
	if (field_type == "stress") {
	for (UInt m = 0; m < this->materials.size(); ++m) {
	const auto & stress_vec = this->materials[m]->getStress(element_type);
	const auto & elem_filter =
	this->materials[m]->getElementFilter(element_type);
	Array<Real> int_stress_vec(elem_filter.size(),
	spatial_dimension * spatial_dimension,
	"int_of_stress");

	fem.integrate(stress_vec, int_stress_vec,
	spatial_dimension * spatial_dimension, element_type,
	_not_ghost, elem_filter);

	for (UInt k = 0; k < elem_filter.size(); ++k)
	average += int_stress_vec(k, row_index * spatial_dimension +
	col_index); // 3 is the value
	// for the yy (in
	// 3D, the value is
	// 4)
	}
	} else if (field_type == "strain") {
	for (UInt m = 0; m < this->materials.size(); ++m) {
	const auto & gradu_vec = this->materials[m]->getGradU(element_type);
	const auto & elem_filter =
	this->materials[m]->getElementFilter(element_type);
	Array<Real> int_gradu_vec(elem_filter.size(),
	spatial_dimension * spatial_dimension,
	"int_of_gradu");

	fem.integrate(gradu_vec, int_gradu_vec,
	spatial_dimension * spatial_dimension, element_type,
	_not_ghost, elem_filter);

	for (UInt k = 0; k < elem_filter.size(); ++k)
	/// averaging is done only for normal components, so stress and strain
	/// are equal
	average +=
	0.5 *
	(int_gradu_vec(k, row_index * spatial_dimension + col_index) +
	int_gradu_vec(k, col_index * spatial_dimension + row_index));
	}
	} else if (field_type == "eigen_grad_u") {
	for (UInt m = 0; m < this->materials.size(); ++m) {
	const auto & eigen_gradu_vec =
	this->materials[m]->getInternal<Real>("eigen_grad_u")(element_type);
	const auto & elem_filter =
	this->materials[m]->getElementFilter(element_type);
	Array<Real> int_eigen_gradu_vec(elem_filter.size(),
	spatial_dimension * spatial_dimension,
	"int_of_gradu");

	fem.integrate(eigen_gradu_vec, int_eigen_gradu_vec,
	spatial_dimension * spatial_dimension, element_type,
	_not_ghost, elem_filter);

	for (UInt k = 0; k < elem_filter.size(); ++k)
	/// averaging is done only for normal components, so stress and strain
	/// are equal
	average +=
	int_eigen_gradu_vec(k, row_index * spatial_dimension + col_index);
	}
	} else {
	AKANTU_ERROR("Averaging not implemented for this field!!!");
	}
	}

	return average / this->volume;

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::homogenizeStiffness(Matrix<Real> & C_macro) {
	AKANTU_DEBUG_IN();
	const UInt dim = 2;
	AKANTU_DEBUG_ASSERT(this->spatial_dimension == dim,
	"Is only implemented for 2D!!!");

	/// apply three independent loading states to determine C
	/// 1. eps_el = (1;0;0) 2. eps_el = (0,1,0) 3. eps_el = (0,0,0.5)

	/// clear the eigenstrain
	Matrix<Real> zero_eigengradu(dim, dim, 0.);
	GhostType gt = _not_ghost;
	for (auto element_type : mesh.elementTypes(dim, gt, _ek_not_defined)) {
	auto & prestrain_vect =
	const_cast<Array<Real> &>(this->getMaterial("gel").getInternal<Real>(
	"eigen_grad_u")(element_type));
	auto prestrain_it =
	prestrain_vect.begin(spatial_dimension, spatial_dimension);
	auto prestrain_end =
	prestrain_vect.end(spatial_dimension, spatial_dimension);

	for (; prestrain_it != prestrain_end; ++prestrain_it)
	(*prestrain_it) = zero_eigengradu;
	}

	/// storage for results of 3 different loading states
	UInt voigt_size = VoigtHelper<dim>::size;
	Matrix<Real> stresses(voigt_size, voigt_size, 0.);
	Matrix<Real> strains(voigt_size, voigt_size, 0.);
	Matrix<Real> H(dim, dim, 0.);

	/// save the damage state before filling up cracks
	// ElementTypeMapReal saved_damage("saved_damage");
	// saved_damage.initialize(getFEEngine(), _nb_component = 1, _default_value =
	// 0);
	// this->fillCracks(saved_damage);

	/// virtual test 1:
	H(0, 0) = 0.01;
	this->performVirtualTesting(H, stresses, strains, 0);

	/// virtual test 2:
	H.clear();
	H(1, 1) = 0.01;
	this->performVirtualTesting(H, stresses, strains, 1);

	/// virtual test 3:
	H.clear();
	H(0, 1) = 0.01;
	this->performVirtualTesting(H, stresses, strains, 2);

	/// drain cracks
	// this->drainCracks(saved_damage);
	/// compute effective stiffness
	Matrix<Real> eps_inverse(voigt_size, voigt_size);
	eps_inverse.inverse(strains);
	C_macro.mul<false, false>(stresses, eps_inverse);
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::performVirtualTesting(const Matrix<Real> & H,
	Matrix<Real> & eff_stresses,
	Matrix<Real> & eff_strains,
	const UInt test_no) {
	AKANTU_DEBUG_IN();
	this->applyBoundaryConditions(H);

	auto & solver = this->getNonLinearSolver();
	solver.set("max_iterations", 2);
	solver.set("threshold", 1e-6);
	solver.set("convergence_type", SolveConvergenceCriteria::_solution);
	this->solveStep();

	/// get average stress and strain
	eff_stresses(0, test_no) = this->averageTensorField(0, 0, "stress");
	eff_strains(0, test_no) = this->averageTensorField(0, 0, "strain");
	eff_stresses(1, test_no) = this->averageTensorField(1, 1, "stress");
	eff_strains(1, test_no) = this->averageTensorField(1, 1, "strain");
	eff_stresses(2, test_no) = this->averageTensorField(1, 0, "stress");
	eff_strains(2, test_no) = 2. * this->averageTensorField(1, 0, "strain");
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::homogenizeEigenGradU(
	Matrix<Real> & eigen_gradu_macro) {
	AKANTU_DEBUG_IN();
	eigen_gradu_macro(0, 0) = this->averageTensorField(0, 0, "eigen_grad_u");
	eigen_gradu_macro(1, 1) = this->averageTensorField(1, 1, "eigen_grad_u");
	eigen_gradu_macro(0, 1) = this->averageTensorField(0, 1, "eigen_grad_u");
	eigen_gradu_macro(1, 0) = this->averageTensorField(1, 0, "eigen_grad_u");
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::initMaterials() {
	AKANTU_DEBUG_IN();

	// make sure the material are instantiated
	if (!are_materials_instantiated)
	instantiateMaterials();

	if (use_RVE_mat_selector) {
	const Vector<Real> & lowerBounds = mesh.getLowerBounds();
	const Vector<Real> & upperBounds = mesh.getUpperBounds();
	Real bottom = lowerBounds(1);
	Real top = upperBounds(1);
	Real box_size = std::abs(top - bottom);
	Real eps = box_size * 1e-6;

	auto tmp = std::make_shared<GelMaterialSelector>(*this, box_size, "gel",
	this->nb_gel_pockets, eps);
	tmp->setFallback(material_selector);
	material_selector = tmp;
	}

	this->assignMaterialToElements();
	// synchronize the element material arrays
	this->synchronize(SynchronizationTag::_material_id);

	for (auto & material : materials) {
	/// init internals properties
	const auto type = material->getID();
	if (type.find("material_FE2") != std::string::npos)
	continue;
	material->initMaterial();
	}

	this->synchronize(SynchronizationTag::_smm_init_mat);

	if (this->non_local_manager) {
	this->non_local_manager->initialize();
	}
	// SolidMechanicsModel::initMaterials();

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::fillCracks(ElementTypeMapReal & saved_damage) {
	const auto & mat_gel = this->getMaterial("gel");
	Real E_gel = mat_gel.get("E");
	Real E_homogenized = 0.;

	for (auto && mat : materials) {
	if (mat->getName() == "gel" \|\| mat->getName() == "FE2_mat")
	continue;

	Real E = mat->get("E");
	auto & damage = mat->getInternal<Real>("damage");

	for (auto && type : damage.elementTypes()) {
	const auto & elem_filter = mat->getElementFilter(type);
	auto nb_integration_point = getFEEngine().getNbIntegrationPoints(type);

	auto sav_dam_it =
	make_view(saved_damage(type), nb_integration_point).begin();
	for (auto && data :
	zip(elem_filter, make_view(damage(type), nb_integration_point))) {
	auto el = std::get<0>(data);
	auto & dam = std::get<1>(data);
	Vector<Real> sav_dam = sav_dam_it[el];

	sav_dam = dam;

	for (auto q : arange(dam.size())) {
	E_homogenized = (E_gel - E) * dam(q) + E;
	dam(q) = 1. - (E_homogenized / E);
	}
	}
	}
	}
	}

	/* -------------------------------------------------------------------------- */
	void SolidMechanicsModelRVE::drainCracks(
	const ElementTypeMapReal & saved_damage) {
	for (auto && mat : materials) {
	if (mat->getName() == "gel" \|\| mat->getName() == "FE2_mat")
	continue;
	auto & damage = mat->getInternal<Real>("damage");

	for (auto && type : damage.elementTypes()) {
	const auto & elem_filter = mat->getElementFilter(type);
	auto nb_integration_point = getFEEngine().getNbIntegrationPoints(type);

	auto sav_dam_it =
	make_view(saved_damage(type), nb_integration_point).begin();
	for (auto && data :
	zip(elem_filter, make_view(damage(type), nb_integration_point))) {
	auto el = std::get<0>(data);
	auto & dam = std::get<1>(data);
	Vector<Real> sav_dam = sav_dam_it[el];

	dam = sav_dam;
	}
	}
	}
	}

	} // namespace akantu

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