variables_sub.hpp
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variables_sub.hpp
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	/*-------------------------------------------------------------------------------

	Copyright (c) 2015 F. Georget <fabieng@princeton.edu>, Princeton University
	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.

	-----------------------------------------------------------------------------*/

	//! \file unsaturated/variables_sub.hpp
	//! \brief base structures for the variables

	#ifndef SPECMICP_REACTMICP_UNSATURATED_VARIABLESSUB_HPP
	#define SPECMICP_REACTMICP_UNSATURATED_VARIABLESSUB_HPP

	#include "../../../types.hpp"
	#include "../../../specmicp/adimensional/adimensional_system_solution.hpp"

	#include "../../../utils/compat.hpp"

	#include "../../../physics/constants.hpp"
	#include "../../../physics/units.hpp"

	#include <vector>
	#include <memory>

	namespace specmicp {
	namespace reactmicp {
	namespace systems {
	namespace unsaturated {

	//! \brief A simple variable
	struct BaseVariable
	{

	Vector variable; //!< The variable

	//! \brief Return value of the variable
	scalar_t& operator() (index_t node) {
	return variable(node);
	}

	//! \brief Return value of the variable
	scalar_t operator() (index_t node) const {
	return variable(node);
	}

	//! \brief Return the size of the vector
	index_t size() const {
	return variable.rows();
	}

	//! \brief The variables are all set to 'value'
	void set_constant(scalar_t value) {
	variable.setConstant(value);
	}

	//! \brief Set the variables to zero
	void set_zero() {
	variable.setZero();
	}

	//! \brief Build a variable of size 'size'
	//!
	//! The varaibles are initialized to zero
	BaseVariable(index_t size):
	variable(Vector::Zero(size))
	{}
	};

	//! \brief A transient variable
	//!
	//! These type of variable store the rate of change of the variable (velocity)
	//! and the value at the beginning of the timestep (predictor)
	struct BaseTransientVariable:
	public BaseVariable
	{
	Vector velocity; //!< Rate of change of the variable
	Vector predictor; //!< Predictor, value before first iteration

	BaseTransientVariable(index_t size):
	BaseVariable(size),
	velocity(Vector::Zero(size)),
	predictor(Vector::Zero(size))
	{}

	//! \brief Update the variable
	void update(scalar_t dt) {
	variable = predictor + dt*velocity;
	}
	};

	//! \brief A main variable, used to solve the governing equations
	//!
	//! These variables also store the chemistry and transport rates for the
	//! coupling
	struct MainVariable:
	public BaseTransientVariable
	{
	//! \brief Transport fluxes of the corresponding governing equations
	Vector transport_fluxes;
	//! \brief Chemical exchange rate
	Vector chemistry_rate;

	MainVariable(index_t size):
	BaseTransientVariable(size),
	transport_fluxes(Vector::Zero(size)),
	chemistry_rate(Vector::Zero(size))
	{}

	//! \brief Reset the variables
	//!
	//! This function is called if the solver failed and must be restarted
	void reset() {
	transport_fluxes.setZero();
	chemistry_rate.setZero();
	velocity.setZero();
	variable = predictor;
	}
	};

	//! \brief List of main variables
	struct ListMainVariable
	{
	// Variables are stored as pointer so we can skip components
	// that do not exist
	// But still access their variables through their index
	using value_type = std::unique_ptr<MainVariable>;
	using vector_type = std::vector<value_type>;
	using iterator = vector_type::iterator;
	using const_iterator = vector_type::const_iterator;

	vector_type variables;

	MainVariable& water() {
	return *variables[0];
	}

	MainVariable& aqueous_component(index_t aq_component) {
	specmicp_assert(variables[aq_component] != nullptr);
	return *variables[aq_component];
	}

	MainVariable& component(index_t component) {
	specmicp_assert(variables[component] != nullptr);
	return *variables[component];
	}

	MainVariable* operator() (index_t component) {
	return variables[component].get();
	}

	// Implementations of the following methods
	// is in variables.cpp

	//! \brief Initialize the variables
	ListMainVariable(index_t nb_vars, index_t nb_nodes);
	//! \brief Initialize some variables
	//!
	//! Only initialize values given by 'to_init'
	ListMainVariable(index_t nb_vars, index_t nb_nodes, std::vector<bool> to_init);

	//! \brief Reset the variables
	void reset();

	//! \brief Hard reset, erase all info for a component;
	void hard_reset(index_t component, index_t nb_nodes);
	};

	//! \brief A secondary variable
	struct SecondaryVariable:
	public BaseVariable
	{
	SecondaryVariable(index_t size):
	BaseVariable(size)
	{}

	};

	//! \brief A secondary transient variable
	//!
	//! e.g. the porosity
	struct SecondaryTransientVariable:
	public BaseTransientVariable
	{
	SecondaryTransientVariable(index_t size):
	BaseTransientVariable(size)
	{}
	};

	//! \brief The chemistry solutions
	struct ChemistrySolutions
	{
	std::vector<AdimensionalSystemSolution> solutions;

	ChemistrySolutions(index_t size):
	solutions(size)
	{}

	//! \brief Return a solution
	AdimensionalSystemSolution& solution(index_t node) {
	return solutions[node];
	}

	//! \brief Return a const solution
	const AdimensionalSystemSolution& solution(index_t node) const {
	return solutions[node];
	}

	//! \brief Set a solution
	void update_solution(
	index_t node,
	const AdimensionalSystemSolution& new_solution
	) {
	solutions[node] = new_solution;
	}
	};

	//! \brief List of constants used in the problems
	struct ConstantBox
	{
	//! \brief R*T
	//!
	//! R : ideal gas constant
	//! T : temperature
	scalar_t rt {constants::gas_constant*units::celsius(25.0)};
	//! \brief Viscosity of liquid water
	scalar_t viscosity_liquid_water {constants::water_viscosity};
	//! \brief Total pressure
	scalar_t total_pressure {1.01325e5};

	//! \brief Scale the constants
	void scale(units::LengthUnit length_unit);
	};




	} //end namespace unsaturated
	} //end namespace systems
	} //end namespace reactmicp
	} //end namespace specmicp

	#endif // SPECMICP_REACTMICP_UNSATURATED_VARIABLESSUB_HPP

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