adimensional_system_solution_extractor.hpp
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adimensional_system_solution_extractor.hpp
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	/*-------------------------------------------------------------------------------

	Copyright (c) 2014,2015 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.

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

	#ifndef SPECMICP_SPECMICP_ADIMENSIONALSYSTEMSOLUTIONEXTRACTOR_HPP
	#define SPECMICP_SPECMICP_ADIMENSIONALSYSTEMSOLUTIONEXTRACTOR_HPP

	#include "../../types.hpp"
	#include "../../database.hpp"
	#include "adimensional_system_solution.hpp"
	#include "../../physics/units.hpp"
	#include "../../physics/constants.hpp"
	#include "adimensional_system_numbering.hpp"

	//! \file adimensional_system_solution_extractor.hpp Obtain data from AdimensionalSystemSolution

	namespace specmicp {

	//! \class AdimensionalSystemSolutionextractor
	//! \brief Obtain physical variables from AdimensionalSystemSolution
	//!
	//! This class can't modify the solution, use specmicp::AdimensionalSystemSolutionModificator for this.
	//!
	//! \ingroup specmicp_api
	//! \sa specmicp::AdimensionalSystemSolutionModificator
	class SPECMICP_DLL_PUBLIC AdimensionalSystemSolutionExtractor:
	public AdimemsionalSystemNumbering,
	public units::UnitBaseClass

	{
	public:
	// public members
	// ###############

	//! \brief Constructor
	//!
	//! \param solution Reference to a solution from the AdimensionalSystemSolution
	//! \param thedatabase shared_ptr to the database
	//! \param units_set Units used by the solver
	AdimensionalSystemSolutionExtractor(
	const AdimensionalSystemSolution& solution,
	RawDatabasePtr thedatabase,
	units::UnitsSet units_set):
	AdimemsionalSystemNumbering(thedatabase),
	units::UnitBaseClass(units_set),
	m_solution(solution)
	{}

	// Primary variables
	// =================

	// water
	// ------

	//! \brief Return the total saturation of water
	//!
	//! \deprecated, use the correct name : volume fraction
	scalar_t total_saturation_water() const
	SPECMICP_DEPRECATED("Use volume_fraction_water instead") {
	return m_solution.main_variables(dof_water());}
	//! \brief Return the volume fraction of water
	scalar_t volume_fraction_water() const {
	return m_solution.main_variables(dof_water());}

	//! \brief Return the density of water
	scalar_t density_water() const;

	// electron
	// ---------

	//! \brief Return the log of the activity electron
	scalar_t log_activity_electron() const {
	return m_solution.main_variables(dof_electron());
	}
	//! \brief Return the activity of the electron
	scalar_t activity_electron() const {
	return pow10(log_activity_electron());
	}
	//! \brief Return the pE
	scalar_t pE() const {
	return -log_activity_electron();
	}
	scalar_t Eh() const {
	return std::log(10.0)constants::gas_constantunits::celsius(25.0)/constants::faraday_constant*pE();
	}


	// component
	// ---------

	//! \brief Return the log_10 of the molality of 'component'
	scalar_t log_molality_component(index_t component) const {
	if (component == m_data->water_index())
	return std::log10(1.0/m_data->molar_mass_basis(component, mass_unit()));
	else if (component == m_data->electron_index())
	return -HUGE_VAL;
	return m_solution.main_variables(dof_component(component));}

	//! \brief Return the molality of 'component'
	scalar_t molality_component(index_t component) const {
	if (component == m_data->water_index())
	return 1.0/m_data->molar_mass_basis(component, mass_unit());
	else if (component == m_data->electron_index())
	return 0.0;
	return pow10(log_molality_component(component));
	}

	// solid phases
	// ------------

	//! \brief Return the total saturation of 'mineral'
	//!
	//! \deprecated, use the volume fraction instead
	scalar_t total_saturation_mineral(index_t mineral) const
	SPECMICP_DEPRECATED("Use volume_fraction_mineral instead")
	{
	return m_solution.main_variables(dof_mineral(mineral));
	}
	//! \brief Return the volume fraction of 'mineral'
	scalar_t volume_fraction_mineral(index_t mineral) const {
	return m_solution.main_variables(dof_mineral(mineral));
	}

	// surface
	// -------

	//! \brief Return the concentration of free surface
	scalar_t log_free_surface_concentration() const {
	return m_solution.main_variables(dof_surface());
	}
	//! \brief Return the concentration of free surface
	scalar_t free_surface_concentration() const {
	return pow10(m_solution.main_variables(dof_surface()));
	}

	// Secondary variables
	// ===================

	//! \brief Return the ionic strength of the solution
	scalar_t ionic_strength() const {return m_solution.ionic_strength;}

	// component
	// ---------

	//! \brief Return the log_10 of the activity coefficient of 'component'
	scalar_t log_activity_coefficient_component(index_t component) const {
	return m_solution.log_gamma(dof_component_gamma(component));
	}
	//! \brief Return the activity coefficient of 'component'
	scalar_t activity_coefficient_component(index_t component) const {
	return pow10(log_activity_coefficient_component(component));
	}
	//! \brief Return the log_10 of the activity of 'component
	scalar_t log_activity_component(index_t component) const {
	return log_molality_component(component) + log_activity_coefficient_component(component);
	}
	//! \brief Return the activity of 'component'
	scalar_t activity_component(index_t component) const {
	return pow10(log_activity_component(component));
	}

	// aqueous species
	// ---------------
	//! \brief Return the molality of secondary specis 'aqueous'
	scalar_t molality_aqueous(index_t aqueous) const {
	return m_solution.secondary_molalities(dof_aqueous(aqueous));}
	//! \brief Return the log10 of the activity ocefficient of secondary species 'aqueous'
	scalar_t log_activity_coefficient_aqueous(index_t aqueous) const {
	return m_solution.log_gamma(dof_aqueous_gamma(aqueous));
	}
	//! \brief Return the activity coefficient of secondary species 'aqueous'
	scalar_t activity_coefficient_aqueous(index_t aqueous) const {
	return pow10(log_activity_coefficient_aqueous(aqueous));
	}
	//! \brief Return the activity of secondary species 'aqueous'
	scalar_t activity_aqueous(index_t aqueous) const {
	return activity_coefficient_aqueous(aqueous)*molality_aqueous(aqueous);
	}

	// gas fugacity
	// -------------
	//! \brief Return fugacity for 'gas'
	scalar_t fugacity_gas(index_t gas) const {
	return m_solution.gas_fugacities(gas);
	}

	// Sorbed species
	// --------------
	//! \brief Return sorbed species molalities for 'sorbed'
	scalar_t molality_sorbed_species(index_t sorbed) const {
	return m_solution.sorbed_molalities(sorbed);
	}

	// Tertiary variables
	// ==================

	// Water
	// -----

	//! \brief Return the saturation of water
	scalar_t saturation_water() const {return volume_fraction_water()/porosity();}

	//! \brief Return the mass concentration of water
	scalar_t mass_concentration_water() const;

	//! \brief Return the pH of the solution
	scalar_t pH() const;

	// Component
	// ---------

	//! \brief Return the total aqueous concentration
	scalar_t total_aqueous_concentration(index_t component) const;
	//! \brief Return the total solid concentration
	scalar_t total_solid_concentration(index_t component) const;
	//! \brief Return the total immobile concentration
	scalar_t total_immobile_concentration(index_t component) const;

	// Gas phase
	// ---------

	//! \brief Return the saturation of the gas phase
	scalar_t saturation_gas_phase() const {return 1-saturation_water();}

	//! \brief Return the total saturation of the gas phase
	//! Depreacated, use volume fraction instead
	scalar_t total_saturation_gas_phase() const {return porosity() - saturation_water();}
	//! \brief Return the volume fraction occupied by the gas phase
	scalar_t volume_fraction_gas_phase() const {return porosity() - saturation_water();}

	// Component
	// ---------

	// Solid phases
	// ------------

	//! \brief Return the concentration of 'mineral'
	//!
	//! \param mineral Index of the mineral (in the database)
	scalar_t mole_concentration_mineral(index_t mineral) const;

	//! \brief Return the mass concentration of 'mineral'
	//!
	//! \param mineral Index of the mineral (in the database)
	scalar_t mass_concentration_mineral(index_t mineral) const;

	//! \brief Return the total saturation of all minerals
	//! Deprecated, use the volume fraction function instead
	scalar_t total_saturation_minerals() const;
	//! \brief Return the volume fraction occupied by the minerals
	scalar_t volume_fraction_minerals() const {return total_saturation_minerals();}

	//! \brief Return the inert volume fraction
	scalar_t volume_fraction_inert() const {return m_solution.inert_volume_fraction;}

	//! \brief Return the porosity
	scalar_t porosity() const {return 1 - total_saturation_minerals() - volume_fraction_inert();}

	//! \brief Return the saturation index for 'mineral'
	//!
	//! \param mineral Index of the mineral (in the database)
	scalar_t saturation_index(index_t mineral) const;

	//! \brief Return the saturation index for 'mineral_kinetic'
	//!
	//! \param mineral_kinetic Index of the mineral governed by the kinetic (in the database)
	scalar_t saturation_index_kinetic(index_t mineral_kinetic) const;

	//! \brief Return the vector of main variables, can be used to initialize the solver
	Vector get_main_variables() const {return m_solution.main_variables;}

	protected:
	// private attributes
	// ##################
	const AdimensionalSystemSolution& m_solution;
	};

	//! \class AdimensionalSystemSolutionModificator
	//! \brief Special class to modify (scale) the solution
	//!
	//! The set of modification are limited to straightforward modification that does not modify the equilibrium
	//!
	//! \sa AdimensionalSystemExtractor
	//! \ingroup specmicp_api
	class SPECMICP_DLL_PUBLIC AdimensionalSystemSolutionModificator: public AdimensionalSystemSolutionExtractor
	{
	public:
	AdimensionalSystemSolutionModificator(
	AdimensionalSystemSolution& solution,
	RawDatabasePtr thedatabase,
	units::UnitsSet units_set):
	AdimensionalSystemSolutionExtractor(solution, thedatabase, units_set),
	m_nonconst_solution(solution)
	{}

	//! \brief Scale the solid phases with respect to the total solid concentration of a component
	//!
	//! \param component Index of the component (in the database)
	//! \param new_value New value of the total solid concentration
	void scale_total_concentration(index_t component, scalar_t new_value);

	//! \brief Remove the solid phases
	void remove_solids();

	//! \brief Set some species to be considered as governed by kinetics
	//!
	//! \param[in,out] list_species list of minerals to flag as kinetics,
	//! The list will contain the new indexes of the corresponding solid phases;
	//! \return the vector of saturation
	//!
	//! This function modify the databse
	Vector set_minerals_kinetics(std::vector<index_t>& list_species);

	private:
	AdimensionalSystemSolution& m_nonconst_solution;
	};

	} // end namespace specmicp

	#endif // SPECMICP_SPECMICP_ADIMENSIONALSYSTEMSOLUTIONEXTRACTOR_HPP

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