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specmicp/src/specmicp/equilibrium_data.cpp
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equilibrium_data.cpp
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/*-------------------------------------------------------
- Module : specmicp
- File : equilibrium_data.cpp
- 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.
---------------------------------------------------------*/
#include "equilibrium_data.hpp"
#include "database/module.hpp"
#include "physics/constants.hpp"
#define POW10(m) std::pow(10.0, m)
namespace specmicp {
scalar_t EquilibriumState::logIAP(index_t m) const
{
scalar_t logiap = 0.0;
for (index_t i=1; i<m_data->nb_component; ++i) logiap += m_main_variables(i)*m_data->nu_mineral(m, i);
return logiap;
}
scalar_t EquilibriumState::logIAP(const std::string& label_mineral) const
{
database::DatabaseModule namer(m_data);
index_t idm = namer.safe_label_to_id(label_mineral, m_data->labels_minerals);
return logIAP(idm);
}
scalar_t EquilibriumState::saturation_index(const std::string& label_mineral) const
{
database::DatabaseModule namer(m_data);
index_t idm = namer.safe_label_to_id(label_mineral, m_data->labels_minerals);
return logIAP(idm) - m_data->logk_mineral(idm);
}
scalar_t EquilibriumState::logIAP_kinetic(index_t m) const
{
scalar_t logiap = 0.0;
for (index_t i=1; i<m_data->nb_component; ++i) logiap += m_main_variables(i)*m_data->nu_mineral_kinetic(m, i);
return logiap;
}
scalar_t EquilibriumState::logIAP_kinetic(const std::string& label_mineral) const
{
database::DatabaseModule namer(m_data);
int idm = namer.safe_label_to_id(label_mineral, m_data->labels_minerals_kinetic);
return logIAP_kinetic(idm);
}
scalar_t EquilibriumState::saturation_index_kinetic(const std::string& label_mineral) const
{
database::DatabaseModule namer(m_data);
index_t idm = namer.safe_label_to_id(label_mineral, m_data->labels_minerals);
return logIAP_kinetic(idm) - m_data->logk_mineral_kinetic(idm);
}
scalar_t EquilibriumState::total_aqueous_concentration_component(index_t i) const
{
scalar_t totconc;
if (i > 0) totconc = molality_component(i); // aqueous component
else totconc = 1.0/m_data->molar_mass_basis_si(0); // water
totconc += m_data->nu_aqueous.col(i).dot(m_concentration_secondary);
return totconc;
}
void EquilibriumState::total_aqueous_concentrations(Eigen::VectorXd& totconc) const
{
assert(totconc.rows() == m_data->nb_component);
for (index_t i: m_data->range_component())
totconc(i) = total_aqueous_concentration_component(i);
}
void EquilibriumState::total_concentrations(Vector& total_conc) const
{
total_conc.resize(m_data->nb_component);
total_conc.setZero();
// Aqueous concentration : m_w * B_i
total_aqueous_concentrations(total_conc);
total_conc = mass_water()*total_conc;
// Minerals : nu_{mi} n_m
for (index_t mineral: m_data->range_mineral())
{
if (moles_mineral(mineral) == 0.0) continue;
for (index_t component: m_data->range_component())
{
total_conc(component) += m_data->nu_mineral(mineral, component)*moles_mineral(mineral);
}
}
}
scalar_t EquilibriumState::pH() const
{
// search where the information about "H[+]" is stored
// (i.e. was the component H[+] or HO[-] ?)
database::DatabaseModule namer(m_data);
scalar_t id = namer.component_label_to_id("H[+]");
if (id != no_species) return -std::log10(activity_component(id));
else
{
id = namer.aqueous_label_to_id("H[+]");
assert(id != no_species);
return -std::log10(activity_secondary(id));
}
}
scalar_t EquilibriumState::mass_mineral(index_t m) const
{
return m_data->molar_mass_mineral(m)*m_main_variables(m_data->nb_component+m);
}
scalar_t EquilibriumState::condensed_phase_volume() const
{
scalar_t volume = mass_water()/constants::water_density_25;
for (index_t m=0; m<m_data->nb_mineral; ++m)
{
volume += moles_mineral(m)*m_data->molar_volume_mineral(m);
}
return volume;
}
scalar_t EquilibriumState::gas_phase_volume() const
{
assert(is_fixed_volume());
return (get_volume() - condensed_phase_volume());
}
//! \brief Return the volume of all minerals
scalar_t EquilibriumState::moles_minerals() const
{
return m_main_variables.segment(m_data->nb_component, m_data->nb_mineral).sum();
}
scalar_t EquilibriumState::volume_minerals() const
{
scalar_t volume = 0;
for (index_t m=0; m<m_data->nb_mineral; ++m)
{
volume += moles_mineral(m)*m_data->molar_volume_mineral(m);
}
return volume;
}
void EquilibriumState::scale_condensed(scalar_t scale)
{
m_main_variables(0) *= scale;
m_main_variables.segment(m_data->nb_component, m_data->nb_mineral) *= scale;
}
} // end namespace specmicp
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