variables.hpp
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variables.hpp
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	/* =============================================================================

	Copyright (c) 2014-2017 F. Georget <fabieng@princeton.edu> Princeton University
	Copyright (c) 2017 F. Georget <fabien.georget@epfl.ch> EPFL
	All rights reserved.


	Redistribution and use in source and binary forms, with or without modification,
	are permitted provided that the following conditions are met:

	1. Redistributions of source code must retain the above copyright notice,
	this list of conditions and the following disclaimer.

	2. Redistributions in binary form must reproduce the above copyright notice,
	this list of conditions and the following disclaimer in the documentation
	and/or other materials provided with the distribution.

	3. Neither the name of the copyright holder nor the names of its
	contributors may be used to endorse or promote products derived from this
	software without specific prior written permission.

	* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
	AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
	IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
	ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
	ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *

	============================================================================= */

	#ifndef REACTMICP_CHLORIDE_VARIABLES_HPP
	#define REACTMICP_CHLORIDE_VARIABLES_HPP

	#include "specmicp_common/types.hpp"
	#include "reactmicp/solver/staggers_base/variables_base.hpp"
	#include "specmicp_database/database_holder.hpp"
	#include "specmicp/adimensional/adimensional_system_solution.hpp"
	#include "specmicp/adimensional/adimensional_system_solution_extractor.hpp"

	#include "dfpm/meshes/mesh1d.hpp"

	#include "dof_numbering.hpp"

	#include <functional>

	namespace specmicp {
	namespace reactmicp {
	namespace systems {
	//! \namespace specmicp::reactmicp::systems::chloride
	//! \brief The chloride system
	//!
	//! A system to describe saturated reactive advection diffusion with
	//! species-dependent diffusion coefficients
	namespace chloride {

	class ChlorideVariablesInit;

	//! \brief The variables for the chloride system
	//!
	//! Shared between the staggers
	class SPECMICP_DLL_PUBLIC ChlorideVariables:
	public solver::VariablesBase,
	public database::DatabaseHolder,
	public units::UnitBaseClass
	{
	public:
	ChlorideVariables(
	RawDatabasePtr adata,
	mesh::Mesh1DPtr amesh,
	const units::UnitsSet& units
	);

	// interface
	// =========

	void reset_main_variables() override;

	// numbering
	// =========
	//! \brief The total number of degree of freedom per node
	index_t ndof() const {
	return m_numbering.ndof();
	}
	//! \brief The total number of degree of freedom
	index_t tot_dof() const {
	return ndof()*m_mesh->nb_nodes();
	}
	//! \brief The number of degree of freedom per element
	index_t tot_edof() const {
	return m_mesh->nen*ndof();
	}
	//! \brief The number of degree of freedom per element
	index_t edof() const {
	return m_numbering.edof();
	}
	//! \brief The nodal degree of freedom for a total concentration
	index_t ndof_component(index_t component) const {
	return m_numbering.nodal_dof_component(component);
	}
	//! \brief The nodal degree of freedom of the potential
	index_t ndof_potential() const {
	return m_numbering.nodal_dof_psi();
	}
	//! \brief The element degree of freedom for a total concentration
	index_t edof_component(index_t enode, index_t component) const {
	return m_numbering.element_dof_component(enode, component);
	}
	//! \brief The nodal degree of freedom of the potential
	index_t edof_potential(index_t enode) const {
	return m_numbering.element_dof_psi(enode);
	}
	//! \brief The degree of freedom for a total concentration
	index_t dof_component(index_t node, index_t component) const {
	return m_numbering.dof_component(node, component);
	}
	//! \brief The degree of freedom for the potential
	index_t dof_potential(index_t node) const {
	return m_numbering.dof_psi(node);
	}
	//! \brief Return dof from nodal dof
	index_t ndof_to_dof(index_t node, index_t nod_dof) {
	return nod_dof+node*ndof();
	}
	//! \brief Return element dof from nodal dof
	index_t ndof_to_edof(index_t enode, index_t nod_dof) {
	return nod_dof+enode*ndof();
	}

	mesh::Mesh1DPtr get_mesh() {
	return m_mesh;
	}

	// Primary
	// =======

	//! \brief The vector of main variables
	Vector& main_variables() {
	return m_main_variables;
	}
	//! \brief Return a total mobile concentration
	scalar_t total_mobile_concentration(index_t node, index_t component) const {
	return m_main_variables(dof_component(node, component));
	}
	//! \brief Return the potential
	scalar_t potential(index_t node) const {
	return m_main_variables(dof_potential(node));
	}
	//! \brief The predictors of the main variables
	Vector& predictors() {
	return m_predictors;
	}
	//! \brief The rates of the main variables
	Vector& velocities() {
	return m_velocities;
	}
	//! \brief Return the vector of total immobile concentrations
	Vector& total_immobile_concentration() {
	return m_total_immobile_concs;
	}
	scalar_t total_immobile_concentration(index_t node, index_t component) const {
	return m_total_immobile_concs(dof_component(node, component));
	}
	//! \brief The fluid velocity (constant over the domain)
	scalar_t fluid_velocity() const {
	return m_fluid_vel;
	}
	//! \brief Return the values for the dofs of an element
	Vector get_element_dofs(index_t element, const Vector& values) const;
	//! \brief Return the values for the dofs of a node
	Vector get_nodal_dofs(index_t node, const Vector& values) const;

	// Secondary
	// =========

	//! \brief Return the porosities
	Vector& porosity() {
	return m_porosity;
	}
	//! \brief Return the porosity at 'node'
	scalar_t porosity(index_t node) const {
	return m_porosity(node);
	}
	//! \brief Return the time derivative of the porosity
	scalar_t velocity_porosity(index_t node) const {
	return m_velocity_porosity(node);
	}
	//! \brief Return the time derivative of the porosity
	scalar_t predictor_porosity(index_t node) const {
	return m_velocity_porosity(node);
	}
	//! \brief Return the specmicp solution for 'node'
	AdimensionalSystemSolution adim_solution(index_t node) const {
	return m_adim_solution[node];
	}
	//! \brief Return the specmicp solution for 'node'
	AdimensionalSystemSolution& adim_solution(index_t node) {
	return m_adim_solution[node];
	}
	//! \brief Set the adimensional solution
	void set_adim_solution(index_t node, AdimensionalSystemSolution&& solution) {
	m_adim_solution[node] = std::move(solution);
	}
	//! \brief Set the adimensional solution
	void set_adim_solution(index_t node, AdimensionalSystemSolution& solution) {
	m_adim_solution[node] = solution;
	}
	//! \brief Return the inert volume fraction for 'node'
	scalar_t inert_volume_fraction(index_t node) const {
	return m_inert_volume_fractions(node);
	}
	//! \brief Return the inert volume fraction for 'node'
	scalar_t& inert_volume_fraction(index_t node) {
	return m_inert_volume_fractions(node);
	}

	// Tertiary
	// ========

	Vector& resistance_factor() {
	return m_resistance_factor;
	}

	//! \brief Return the diffusion coefficient resistance factor for 'node'
	scalar_t resistance_factor(scalar_t node) const {
	return m_resistance_factor(node);
	}
	//! \brief Return the intrinsic diffusion coefficient for a component
	scalar_t intrinsic_diff_coeff_component(index_t i) const {
	return m_intrinsic_diffusion_i(i);
	}
	//! \brief Return the intrinsic diffusion coefficient for a secodnar aqueous species
	scalar_t intrinsic_diff_coeff_aqueous(index_t j) const {
	return m_intrinsic_diffusion_j(j);
	}

	//! \brief Return the water density
	scalar_t rho_w() const {
	return m_constants.rho_w;
	}
	//! \brief Return the Faraday constant
	scalar_t faraday() const {
	return m_constants.faraday;
	}
	//! \brief Return the product R*T
	scalar_t rt() const {
	return m_constants.rt;
	}

	//! \brief Return the transport rate of 'component' at 'node'
	scalar_t transport_rate(index_t node, index_t component) const {
	return m_transport_rates(dof_component(node, component));
	}
	//! \brief Return the transport rate of 'dof_c'
	//!
	//! 'dof_c' must be a valid degree of freedom for a total concentration
	scalar_t transport_rate(index_t dof_c) const {
	return m_transport_rates(dof_c);
	}
	scalar_t& transport_rate(index_t dof_c) {
	return m_transport_rates(dof_c);
	}
	Vector& transport_rates() {
	return m_transport_rates;
	}
	//! \brief Return the chemistry rate of 'component' at 'node'
	scalar_t chemistry_rate(index_t node, index_t component) const {
	return m_chemistry_rates(dof_component(node, component));
	}
	//! \brief Return the chemistry rate of 'dof_c'
	//!
	//! 'dof_c' must be a valid degree of freedom for a total concentration
	scalar_t chemistry_rate(index_t dof_c) const {
	return m_chemistry_rates(dof_c);
	}
	scalar_t& chemistry_rate(index_t dof_c) {
	return m_chemistry_rates(dof_c);
	}
	Vector& chemistry_rates() {
	return m_chemistry_rates;
	}

	Vector& current() {
	return m_current;
	}

	private:
	// data
	mesh::Mesh1DPtr m_mesh; //!< The mesh
	DofNumbering m_numbering; //!< Relation between database and dof numbering

	// primary
	Vector m_main_variables; //!< The vector of main variables (ndofx1)
	Vector m_predictors; //!< The vector of predictors (ndofx1)
	Vector m_velocities; //!< The vector of velocities (nodfx1)

	Vector m_total_immobile_concs; //!< The total immobile concentrations (ndofx1)
	Vector m_predictor_immobile; //!< Predictor for the immobile concentrations (ndofx1)
	Vector m_velocity_immobile; //!< Velocity vector for the immobile concentration (ndofx1)

	// secondary
	Vector m_porosity; //!< The porosity (nnpx1)
	Vector m_predictor_porosity; //!< Predictor for the porosity (nnpx1)
	Vector m_velocity_porosity; //!< Velocity for the porosity (nnpx1)

	Vector m_inert_volume_fractions; //!< The volume fraction of inert solid phases (nnpx1)
	std::vector<AdimensionalSystemSolution> m_adim_solution; //!< The SpecMiCP solutions

	Vector m_transport_rates; //!< The transport rates for the coupling (ndofx1)
	Vector m_chemistry_rates; //!< The chemistry rates for the coupling (ndofx1)

	// tertiary
	Vector m_intrinsic_diffusion_i; //!< Intrinsic diffusion coefficient for a component (Ncx1)
	Vector m_intrinsic_diffusion_j; //!< Intrinsic diffusion coefficient for a secondary aqueous species (Nrx1)
	Vector m_resistance_factor; //!< Diffusion coefficient resistance factor (nnpx1)

	scalar_t m_fluid_vel {0}; //!< The velocity of the liquid phase

	Vector m_current; // !< The current

	struct ConstantBox {
	scalar_t rho_w {0}; //!< density of water (scaled)
	scalar_t faraday {0}; //!< Faraday's constant (scaled)
	scalar_t rt {0}; //!< R*T constant (not scaled)

	ConstantBox(const units::UnitsSet& tunits);
	};
	ConstantBox m_constants; //!< The set of constants


	friend class ChlorideVariablesInterface;
	};

	//! \brief Shared pointer the unsaturated variables
	using ChlorideVariablesPtr = std::shared_ptr<ChlorideVariables>;

	//! \brief Cast from base variable
	inline ChlorideVariablesPtr cast_from_base(
	std::shared_ptr<solver::VariablesBase> ptr) {
	return std::static_pointer_cast<ChlorideVariables>(ptr);
	}

	//! \brief Cast from base variable
	inline ChlorideVariables* const cast_from_base(solver::VariablesBase* const ptr) {
	return static_cast<ChlorideVariables * const>(ptr);
	}

	} // namespace chloride
	} // namespace systems
	} // namespace reactmicp
	} // namespace specmicp

	#endif // REACTMICP_CHLORIDE_VARIABLES_HPP

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