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specmicp/src/reactmicp/systems/secondary_variables/secondary.hpp
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/*-------------------------------------------------------
- Module : reactmicp/systems/diffusion
- File : diffusion_secondary.hpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien 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:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* 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.
* Neither the name of the Princeton University 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 OWNER 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_REACTMICP_SECONDARY_VARIABLES_SECONDARY_HPP
#define SPECMICP_REACTMICP_SECONDARY_VARIABLES_SECONDARY_HPP
#include "common.hpp"
#include "database.hpp"
namespace specmicp {
namespace reactmicp {
//! \brief handle secondary variables for the diffusion system
template <class Derived>
class SecondaryVariables
{
public:
SecondaryVariables(int nb_nodes,
RawDatabasePtr thedatabase
):
m_data(thedatabase),
m_ionic_strength(nb_nodes),
m_secondary_variables(thedatabase->nb_component+thedatabase->nb_aqueous, nb_nodes),
m_secondary_concentration(thedatabase->nb_aqueous, nb_nodes)
{
m_secondary_variables.setZero();
m_secondary_concentration.setZero();
}
Derived* derived() {return static_cast<Derived*>(this);}
// Access to primary variables
// ===========================
scalar_t component_concentration(index_t node, index_t component) {
return derived()->component_concentration(node, component);
}
scalar_t log_component_concentration(index_t node, index_t component) {
return derived()->log_component_concentration(node, component);
}
// Secondary variables
// ===================
// Algorithms
// ----------
//! \brief Set secondary concentrations
void compute_secondary_concentrations();
//! \brief Set secondary concentrations for node 'node'
void nodal_secondary_concentrations(index_t node);
//! \brief Solve for secondary variables
int solve_secondary_variables();
//! \brief Solve for secondary variables in one node
int nodal_solve_secondary_variables(index_t node);
//! \brief Compute secondary variables
void compute_secondary_variables();
//! \brief Compute the secondary variables at node 'node'
void nodal_secondary_variables(index_t node);
//! \brief compute the ionic strengths
void compute_ionic_strength();
//! \brief compute the ionic strength for node 'node'
void nodal_ionic_strength(index_t node);
//! \brief compute the activity coefficients
void compute_log_gamma();
//! \brief compute the logarithm of the activity coefficients for node 'node'
void nodal_log_gamma(index_t node);
//! \brief compute the activity coefficient for the components of node 'node'
void nodal_log_gamma_component(index_t node);
//! \brief compute the activity coefficient for the aqueous species of node 'node'
void nodal_log_gamma_aqueous(index_t node);
// Getters and setters
// -------------------
//! \brief Secondary species concentration
scalar_t& secondary_concentration(index_t node, index_t aqueous) {
specmicp_assert(aqueous >= 0 and aqueous < m_data->nb_aqueous);
return m_secondary_concentration.coeffRef(aqueous, node);
}
//! \brief Secondary species concentration
scalar_t secondary_concentration(index_t node, index_t aqueous) const {
specmicp_assert(aqueous >= 0 and aqueous < m_data->nb_aqueous);
return m_secondary_concentration.coeff(aqueous, node);
}
//! \brief Return the loggamma of a component
scalar_t& log_gamma_component(index_t node, index_t component) {
specmicp_assert(component >= 1 and component < m_data->nb_component);
return m_secondary_variables.coeffRef(component, node);
}
//! \brief Return the loggamma of a component
scalar_t log_gamma_component(index_t node, index_t component) const {
specmicp_assert(component >= 1 and component < m_data->nb_component);
return m_secondary_variables.coeff(component, node);
}
//! \brief Return the loggamma of a secondary species
scalar_t& log_gamma_secondary(index_t node, index_t aqueous) {
specmicp_assert(aqueous >= 0 and aqueous < m_data->nb_aqueous);
return m_secondary_variables.coeffRef(m_data->nb_component + aqueous, node);
}
//! \brief Return the loggamma of a secondary species
scalar_t log_gamma_secondary(index_t node, index_t aqueous) const {
specmicp_assert(aqueous >= 0 and aqueous < m_data->nb_aqueous);
return m_secondary_variables.coeff(m_data->nb_component + aqueous, node);
}
//! \brief Return ionic strength
scalar_t& ionic_strength(index_t node) {
return m_ionic_strength.coeffRef(node);
}
//! \brief Return ionic strength
scalar_t ionic_strength(index_t node) const {
return m_ionic_strength.coeff(node);
}
//! \brief Return norm of the loggamma
scalar_t log_gamma_norm() const {
return m_secondary_variables.norm();
}
private:
// Return the norm used to check the convergence of the fixed-point iterations
scalar_t norm_secondary_variables();
scalar_t nodal_norm_secondary_variables(index_t node);
RawDatabasePtr m_data;
protected:
Vector m_ionic_strength;
Matrix m_secondary_variables;
Matrix m_secondary_concentration;
};
} // end namespace reactmicp
} // end namespace specmicp
// =================================== //
// //
// Implementation //
// //
// =================================== //
#include "secondary.inl"
#endif // SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_SECONDARY_HPP
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