#phase_field_model.cc#
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#phase_field_model.cc#
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	/**
	* @file phase_field_model.cc
	*
	* @author Mohit Pundir <mohit.pundir@epfl.ch>
	*
	* @date creation: Wed Aug 01 2018
	* @date last modification: Wed Aug 01 2018
	*
	* @brief Implementation of PhaseFieldModel class
	*
	* @section LICENSE
	*
	* Copyright (©) 2010-2018 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 "phase_field_model.hh"
	#include "dumpable_inline_impl.hh"
	#include "element_synchronizer.hh"
	#include "fe_engine_template.hh"
	#include "group_manager_inline_impl.cc"
	#include "integrator_gauss.hh"
	#include "mesh.hh"
	#include "parser.hh"
	#include "shape_lagrange.hh"

	#ifdef AKANTU_USE_IOHELPER
	#include "dumper_element_partition.hh"
	#include "dumper_elemental_field.hh"
	#include "dumper_internal_material_field.hh"
	#include "dumper_iohelper_paraview.hh"
	#endif

	/* -------------------------------------------------------------------------- */
	namespace akantu {

	// functor can be created

	}


	/* -------------------------------------------------------------------------- */
	PhaseFieldModel::PhaseFieldModel(Mesh & mesh, UInt dim, const ID & id,
	const MemoryID & memory_id)
	: Model(mesh, ModelType::_phase_field_model, dim, id, memory_id),
	damage_gradient("damage_gradient", id),
	damage_on_qpoints("damage_on_qpoints", id),
	strain_history_on_qpoints("strain_history_on_qpoints", id),
	displacement_on_qpoints("displacement_on_qpoints", id){

	AKANTU_DEBUG_IN();

	this->initDOFManager();

	this->registerDataAccessor(*this);

	if (this->mesh.isDistributed()) {
	auto & synchronizer = this->mesh.getElementSynchronizer();
	this->registerSynchronizer(synchronizer, _gst_pfm_damage);
	this->registerSynchronizer(synchronizer, _gst_pfm_gradient_damage);
	}

	registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);

	#ifdef AKANTU_USE_IOHELPER
	this->mesh.registerDumper<DumperParaview>("phase_field", id, true);
	this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
	#endif // AKANTU_USE_IOHELPER

	this->registerParam("l0", l_0, 0., _pat_parsmod, "length scale");
	this->registerParam("gc", g_c, _pat_parsmod, "critical local fracture energy density");
	this->registerParam("lambda", lame_lambda, _pat_parsmod, "lame parameter lambda");
	this->registerParam("mu", lame_mu, _pat_parsmod, "lame paramter mu");


	AKANTU_DEBUG_OUT();
	}


	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::initModel() {
	auto & fem = this->getFEEngine();
	fem.initShapeFunctions(_not_ghost);
	fem.initShapeFunctions(_ghost);

	damage_on_qpoints.initialize(fem, _nb_component = 1);
	damage_gradient.initialize(fem, _nb_component = spatial_dimension);
	displacement_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
	strain_history_on_qpoints.initialize(fem, _nb_component = 1);

	}


	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::assembleMatrix(const ID & matrix_id) {
	if (matrix_id == "K") {
	this->assembleDamageMatrix();
	} else if (matrix_id == "M" and need_to_reassemble_capacity) {
	this->assembleDamageGradMatrix();
	}
	}


	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::initSolver(TimeStepSolverType time_step_solver_type,
	NonLinearSolverType) {
	DOFManager & dof_manager = this->getDOFManager();

	this->allocNodalField(this->damage, "damage");
	this->allocNodalField(this->external_force, "external_force");
	this->allocNodalField(this->internal_force, "internal_force");
	this->allocNodalField(this->blocked_dofs, "blocked_dofs");

	if (!dof_manager.hasDOFs("damage")) {
	dof_manager.registerDOFs("damage", *this->damage, _dst_nodal);
	dof_manager.registerBlockedDOFs("damage", *this->blocked_dofs);
	}

	/*if (time_step_solver_type == _tsst_dynamic \|\|
	time_step_solver_type == _tsst_dynamic_lumped) {
	this->allocNodalField(this->damage_rate, "damage_rate");

	if (!dof_manager.hasDOFsDerivatives("damage", 1)) {
	dof_manager.registerDOFsDerivative("damage", 1,
	*this->damage_rate);
	}
	}*/
	}



	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::assembleDamageMatrix() {
	AKANTU_DEBUG_IN();

	AKANTU_DEBUG_INFO("Assemble the new damage matrix");

	this->computeStrainHistoryOnQuadPoints(_not_ghost);

	if (!this->getDOFManager().hasMatrix("K")) {
	this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
	}
	this->getDOFManager().clearMatrix("K");

	switch (mesh.getSpatialDimension()) {
	case 1:
	this->assembleDamageMatrix<1>(_not_ghost);
	break;
	case 2:
	this->assembleDamageMatrix<2>(_not_ghost);
	break;
	case 3:
	this->assembleDamageMatrix<3>(_not_ghost);
	break;
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::assembleDamageGradMatrix() {
	AKANTU_DEBUG_IN();

	AKANTU_DEBUG_INFO("Assemble the new damage gradient matrix");

	if (!this->getDOFManager().hasMatrix("K")) {
	this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
	}
	this->getDOFManager().clearMatrix("K");

	switch (mesh.getSpatialDimension()) {
	case 1:
	this->assembleDamageGradMatrix<1>(_not_ghost);
	break;
	case 2:
	this->assembleDamageGradMatrix<2>(_not_ghost);
	break;
	case 3:
	this->assembleDamageGradMatrix<3>(_not_ghost);
	break;
	}

	AKANTU_DEBUG_OUT();
	}


	/* -------------------------------------------------------------------------- */
	std::tuple<ID, TimeStepSolverType>
	PhaseFieldModel::getDefaultSolverID(const AnalysisMethod & method) {
	switch (method) {
	case _explicit_lumped_mass: {
	return std::make_tuple("explicit_lumped", _tsst_dynamic_lumped);
	}
	case _static: {
	return std::make_tuple("static", _tsst_static);
	}
	case _implicit_dynamic: {
	return std::make_tuple("implicit", _tsst_dynamic);
	}
	default:
	return std::make_tuple("unknown", _tsst_not_defined);
	}
	}

	/* -------------------------------------------------------------------------- */
	ModelSolverOptions PhaseFieldModel::getDefaultSolverOptions(
	const TimeStepSolverType & type) const {
	ModelSolverOptions options;

	switch (type) {
	case _tsst_dynamic_lumped: {
	options.non_linear_solver_type = _nls_lumped;
	options.integration_scheme_type["damage"] = _ist_forward_euler;
	options.solution_type["damage"] = IntegrationScheme::_temperature_rate;
	break;
	}
	case _tsst_static: {
	options.non_linear_solver_type = _nls_newton_raphson;
	options.integration_scheme_type["damage"] = _ist_pseudo_time;
	options.solution_type["damage"] = IntegrationScheme::_not_defined;
	break;
	}
	case _tsst_dynamic: {
	if (this->method == _explicit_consistent_mass) {
	options.non_linear_solver_type = _nls_newton_raphson;
	options.integration_scheme_type["damage"] = _ist_forward_euler;
	options.solution_type["damage"] =
	IntegrationScheme::_temperature_rate;
	} else {
	options.non_linear_solver_type = _nls_newton_raphson;
	options.integration_scheme_type["damage"] = _ist_backward_euler;
	options.solution_type["damage"] = IntegrationScheme::_temperature;
	}
	break;
	}
	default:
	AKANTU_EXCEPTION(type << " is not a valid time step solver type");
	}

	return options;
	}


	/* -------------------------------------------------------------------------- */
	template<UInt dim>
	void PhaseFieldModel::assembleDamageMatrix(const GhostType & ghost_type) {

	AKANTU_DEBUG_IN();


	auto & fem = this->getFEEngine();

	for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
	auto nb_element = mesh.getNbElement(type, ghost_type);
	auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);

	auto nt_d_n = std::make_unique<Array<Real>>(
	nb_element * nb_quadrature_points,
	nb_nodes_per_element * nb_nodes_per_element, "N^tDN");

	// conductivity_on_qpoints = gc/l0 + 2*strain_history + eta/tau = scalar
	fem.computeNtDN(conductivity_on_qpoints(type, ghost_type), *nt_d_n, type,
	ghost_type);

	/// compute @f$ K_d = \int_e \mathbf{N}^t * \mathbf{D} *
	/// \mathbf{N}@f$
	auto K_d = std::make_unique<Array<Real>>(
	nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_d");

	fem.integrate(nt_d_n, K_d, nb_nodes_per_element * nb_nodes_per_element,
	type, ghost_type);

	this->getDOFManager().assembleElementalMatricesToMatrix(
	"K", "phasefield", *K_d, type, ghost_type, _symmetric);
	}

	AKANTU_DEBUG_OUT();
	}


	/* -------------------------------------------------------------------------- */
	template<UInt dim>
	void PhaseFieldModel::assembleDamageGradMatrix(const GhostType & ghost_type) {

	AKANTU_DEBUG_IN();


	auto & fem = this->getFEEngine();

	for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
	auto nb_element = mesh.getNbElement(type, ghost_type);
	auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
	auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);

	auto bt_d_b = std::make_unique<Array<Real>>(
	nb_element * nb_quadrature_points,
	nb_nodes_per_element * nb_nodes_per_element, "B^tDB");

	// conductivity_on_qpoints = gc*l0 = scalar
	fem.computeBtDB(conductivity_on_qpoints(type, ghost_type), *bt_d_b, type,
	ghost_type);

	/// compute @f$ K_{\grad d} = \int_e \mathbf{B}^t * \mathbf{W} *
	/// \mathbf{B}@f$
	auto K_b = std::make_unique<Array<Real>>(
	nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_b");

	fem.integrate(bt_d_b, K_b, nb_nodes_per_element * nb_nodes_per_element,
	type, ghost_type);

	this->getDOFManager().assembleElementalMatricesToMatrix(
	"K", "phasefield", *K_b, type, ghost_type, _symmetric);
	}

	AKANTU_DEBUG_OUT();
	}


	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::computeStrainHistoryOnQuadPoints(
	const GhostType & ghost_type) {

	for (auto & type : mesh.elementType(spatial_dimension, ghost_type)) {
	auto & displacement_interpolated = displacement_on_qpoints(type, ghost_type);

	// compute the strain on quadrature points
	this->getFEEngine().interpolateOnIntegrationPoints(
	*displacement, displacement_interpolated, , type, ghost_type);

	auto & strain_history = strain_history_on_qpoints(type, ghost_type);
	for (auto && tuple :
	zip(make_view(strain_history, spatial_dimension, spatial_dimension),
	displacement_interpolated)) {

	// compute strain on quad from displacement_interpolated
	// commpute matrix sigma_plus and sigma_minus using
	// lame_lambda and lame_mu

	// compute phi_plus
	// updated strain_history


	}
	}

	}

	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::assembleResidual() {

	AKANTU_DEBUG_IN();

	this->assembleInternalForces();

	this->getDOFManager().assembleToResidual("damage",
	*this->external_force, 1);
	this->getDOFManager().assembleToResidual("damage",
	*this->internal_force, 1);


	AKANTU_DEBUG_OUT();
	}



	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::assembleInternalForces() {
	AKANTU_DEBUG_IN();

	this->internal_force->clear();

	this->synchronize(_gst_pfm_damage);
	auto & fem = this->getFFEngine();

	for (auto ghost_type: ghost_types) {

	for (auto type: mesh.elementTypes(spatial_dimension, ghost_type)) {
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

	auto & strain_history_on_qpoints_vect = strain_history_on_qpoints(type, ghost_type);

	UInt nb_quad_points = strain_history_on_qpoints_vect.size();
	Array<Real> nt_strain_history(nb_quad_points, nb_nodes_per_element);
	fem.computeNtb(strain_history_on_qpoints_vect, nt_strain_history, type, ghost_type);

	UInt nb_elements = mesh.getNbElement(type, ghost_type);
	Array<Real> int_nt_srain_history(nb_elements, nb_nodes_per_element);

	fem.integrate(nt_strain_history, int_nt_srain_history, nb_nodes_per_element, type,
	ghost_type);

	this->getDOFManager().assembleElementalArrayLocalArray(
	int_nt_srain_history, *this->internal_force, type, ghost_type, -1);
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::readMaterials() {
	auto sect = this->getParserSection();

	if (not std::get<1>(sect)) {
	const auto & section = std::get<0>(sect);
	this->parseSection(section);
	}

	gc_on_qpoints.set(g_c);
	}

	/* -------------------------------------------------------------------------- */
	void PhaseFieldModel::initFullImpl(const ModelOptions & options) {
	Model::initFullImpl(options);

	readMaterials();
	}


	}

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