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specmicp/src/specmicp/adimensional/adimensional_system_solution_extractor.cpp
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adimensional_system_solution_extractor.cpp
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/*-------------------------------------------------------
Copyright (c) 2014,2015 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 "adimensional_system_solution_extractor.hpp"
#include "physics/laws.hpp"
#include "database/database.hpp"
namespace specmicp {
scalar_t AdimensionalSystemSolutionExtractor::density_water() const
{
return laws::density_water(units::celsius(25.0), length_unit(), mass_unit());
}
scalar_t AdimensionalSystemSolutionExtractor::mass_concentration_water() const
{
return density_water()*total_saturation_water();
}
scalar_t AdimensionalSystemSolutionExtractor::pH() const
{
// find species responsible for pH
index_t id = m_data->get_id_component("HO[-]");
if (id != no_species)
{
return 14+log_activity_component(id);
}
else
{
id = m_data->get_id_component("H[+]");
if (id != no_species)
return -log_activity_component(id);
throw std::runtime_error("No component corresponding to the dissociation of water !");
}
}
scalar_t AdimensionalSystemSolutionExtractor::total_saturation_minerals() const
{
return m_solution.main_variables.segment(offset_minerals(), m_data->nb_mineral()).sum();
}
scalar_t AdimensionalSystemSolutionExtractor::mole_concentration_mineral(index_t mineral) const
{
return total_saturation_mineral(mineral)/m_data->molar_volume_mineral(mineral, length_unit());
}
scalar_t AdimensionalSystemSolutionExtractor::mass_concentration_mineral(index_t mineral) const
{
return mole_concentration_mineral(mineral)*m_data->molar_mass_mineral(mineral, mass_unit());
}
//! \brief Return the total aqueous concentration
scalar_t AdimensionalSystemSolutionExtractor::total_aqueous_concentration(index_t component) const
{
scalar_t conc = molality_component(component);
for (index_t aqueous: m_data->range_aqueous())
{
if (m_data->nu_aqueous(aqueous, component) != 0.0)
{
conc += m_data->nu_aqueous(aqueous, component)*molality_aqueous(aqueous);
}
}
return conc;
}
//! \brief Return the total solid concentration
scalar_t AdimensionalSystemSolutionExtractor::total_solid_concentration(index_t component) const
{
scalar_t conc= 0;
for (index_t mineral: m_data->range_mineral())
{
if (m_data->nu_mineral(mineral, component) != 0.0)
{
conc += m_data->nu_mineral(mineral, component)
* total_saturation_mineral(mineral)
/ m_data->molar_volume_mineral(mineral, length_unit());
}
}
return conc;
}
//! \brief Return the total immobile concentration
scalar_t AdimensionalSystemSolutionExtractor::total_immobile_concentration(index_t component) const
{
scalar_t conc= total_solid_concentration(component);
const scalar_t conc_w = density_water()*volume_fraction_water();
for (index_t sorbed: m_data->range_sorbed())
{
if (m_data->nu_sorbed(sorbed, component) != 0.0)
{
conc += conc_w*m_data->nu_sorbed(sorbed, component)
* sorbed_species_molalities(sorbed);
}
}
return conc;
}
//! Return the saturation index for 'mineral'
scalar_t AdimensionalSystemSolutionExtractor::saturation_index(index_t mineral) const
{
scalar_t saturation_index = - m_data->logk_mineral(mineral);
for (index_t component: m_data->range_aqueous_component())
{
saturation_index += m_data->nu_mineral(mineral, component) *
log_activity_component(component);
}
return saturation_index;
}
//! Return the saturation index for 'mineral_kinetic'
scalar_t AdimensionalSystemSolutionExtractor::saturation_index_kinetic(index_t mineral_kinetic) const
{
scalar_t saturation_index = - m_data->logk_mineral_kinetic(mineral_kinetic);
for (index_t component: m_data->range_aqueous_component())
{
saturation_index += m_data->nu_mineral_kinetic(mineral_kinetic, component) *
log_activity_component(component);
}
return saturation_index;
}
// ########################### //
// //
// Modificator //
// //
// ########################### //
void AdimensionalSystemSolutionModificator::scale_total_concentration(
index_t component,
scalar_t new_value)
{
const scalar_t old_value = total_solid_concentration(component);
const scalar_t factor = new_value/old_value;
m_nonconst_solution.main_variables.segment(dof_mineral(0), m_data->nb_mineral()) *= factor;
}
void AdimensionalSystemSolutionModificator::remove_solids()
{
m_nonconst_solution.main_variables.segment(dof_mineral(0), m_data->nb_mineral()).setZero();
}
Vector AdimensionalSystemSolutionModificator::set_minerals_kinetics(std::vector<index_t>& list_species)
{
index_t nb_kinetics = list_species.size();
index_t nb_new_mineral = m_data->nb_mineral() - nb_kinetics;
std::vector<index_t> minerals_to_keep;
minerals_to_keep.reserve(nb_new_mineral);
std::vector<index_t> new_kinetics_index(nb_kinetics, no_species);
Vector saturation_kinetics(nb_kinetics);
index_t new_ind_eq = m_data->nb_component();
index_t new_ind_kin = 0;
index_t tot_ind_kin = m_data->nb_mineral_kinetic();
// ###TODO optimize
for (index_t mineral: m_data->range_mineral())
{
auto is_kin = std::find(list_species.begin(), list_species.end(), mineral);
// If mineral is still at equilibrium
if (is_kin == list_species.end())
{
minerals_to_keep.push_back(mineral);
m_nonconst_solution.main_variables(new_ind_eq) = total_saturation_mineral(mineral);
++new_ind_eq;
}
// If mineral is governed by kinetics
else
{
saturation_kinetics(new_ind_kin) = total_saturation_mineral(mineral);
++new_ind_kin;
// save the new index (index in the kinetics vector)
// The order is conserved !
new_kinetics_index[is_kin - list_species.begin()] = tot_ind_kin;
++tot_ind_kin;
}
}
specmicp_assert(new_ind_eq == m_data->nb_component()+nb_new_mineral);
// change the database
database::Database dbhandler(m_data);
dbhandler.minerals_keep_only(minerals_to_keep);
// update the list of species
list_species.swap(new_kinetics_index);
// resize
m_nonconst_solution.main_variables.conservativeResize(m_data->nb_component()+nb_new_mineral);
return saturation_kinetics;
}
} // end namespace specmicp
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