sorption.cc

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#include <boost/foreach.hpp>

#include "reaction/isotherm.hh"
#include "reaction/sorption.hh"
//#include "system/system.hh"
#include "system/sys_profiler.hh"

#include "mesh/mesh.h"

using namespace std;


IT::Record SorptionSimple::input_type
    = IT::Record("Sorption", "Information about all the limited solubility affected adsorptions.")
    .derive_from( ReactionTerm::input_type )
    .copy_keys(SorptionBase::input_type)
    .declare_key("output_fields", IT::Array(make_output_selection("conc_solid", "Sorption_Output")),
            IT::Default("conc_solid"), "List of fields to write to output stream.");



SorptionSimple::SorptionSimple(Mesh &init_mesh, Input::Record in_rec)//
  : SorptionBase(init_mesh, in_rec)
{
  //DBGMSG("SorptionSimple constructor.\n");
    data_ = new EqData("conc_solid");
    output_selection = make_output_selection("conc_solid", "SorptionSimple_Output");
}

SorptionSimple::~SorptionSimple(void)
{
}

void SorptionSimple::isotherm_reinit(std::vector<Isotherm> &isotherms_vec, const ElementAccessor<3> &elem)
{
    START_TIMER("SorptionSimple::isotherm_reinit");

    double rock_density = data_->rock_density.value(elem.centre(),elem);
    double por_m = data_->porosity.value(elem.centre(),elem);

    // List of types of isotherms in particular regions
    arma::uvec adsorption_type = data_->sorption_type.value(elem.centre(),elem);
    arma::Col<double> mult_coef_vec = data_->isotherm_mult.value(elem.centre(),elem);
    arma::Col<double> second_coef_vec = data_->isotherm_other.value(elem.centre(),elem);

    for(int i_subst = 0; i_subst < n_substances_; i_subst++)
    {
        double mult_coef = mult_coef_vec[i_subst];
        double second_coef = second_coef_vec[i_subst];
        Isotherm & isotherm = isotherms_vec[i_subst];

        //scales are different for the case of sorption in mobile and immobile pores
        double scale_aqua = por_m, 
                       scale_sorbed = (1 - por_m) * rock_density * molar_masses[i_subst];

                //DBGMSG("molar_masses[%d %d]: %f\n",i_subst, substance_id[i_subst], molar_masses[i_subst]);
        if ( scale_sorbed == 0.0)
            xprintf(UsrErr, "Sorption::init_from_input() failed. Parameter scale_sorbed (phi * (1 - por_m - por_imm) * rock_density * molar_masses[i_subst]) is equal to zero.");
        bool limited_solubility_on = false;
        double table_limit;
        if (solubility_vec_[i_subst] <= 0.0) {
            limited_solubility_on = false;
            table_limit=table_limit_[i_subst];
        } else {
            limited_solubility_on = true;
            table_limit=solubility_vec_[i_subst];
        }
        isotherm.reinit(Isotherm::SorptionType(adsorption_type[i_subst]), limited_solubility_on,
                    solvent_density, scale_aqua, scale_sorbed, table_limit, mult_coef, second_coef);

    }

    END_TIMER("SorptionSimple::isotherm_reinit");
}