first_order_reaction.cc

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 * 
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 * 
 * This program is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 * 
 * @file    first_order_reaction.cc
 * @brief   
 */

#include "reaction/first_order_reaction.hh"
#include "reaction/reaction_term.hh"
#include "reaction/pade_approximant.hh"

#include "system/global_defs.h"
#include "mesh/mesh.h"
#include "input/factory.hh"
#include "input/accessors.hh"

FLOW123D_FORCE_LINK_IN_CHILD(firstOrderReaction)


using namespace Input::Type;

const Record & FirstOrderReaction::get_input_type_reactant() {
    return Record("FirstOrderReactionReactant", "A record describing a reactant of a reaction.")
        .allow_auto_conversion("name")
        .declare_key("name", String(), Default::obligatory(),
                     "The name of the reactant.")
        //.declare_key("stoichiometric_coefficient", Integer(0.0), Default::optional(1.0))   //in future
        .close();
}
    
const Record & FirstOrderReaction::get_input_type_product() {
    return Record("FirstOrderReactionProduct", "A record describing a product of a reaction.")
        .allow_auto_conversion("name")
        .declare_key("name", String(), Default::obligatory(),
                     "The name of the product.")
        //.declare_key("stoichiometric_coefficient", Integer(0.0), Default::optional(1.0))   //in future
        .declare_key("branching_ratio", Double(0.0), Default("1.0"),
                     "The branching ratio of the product when there are more products.\n"
                     "The value must be positive. Further, the branching ratios of all products are normalized "
                     "in order to sum to one.\n"
                     "The default value 1.0, should only be used in the case of single product.")
        .close();
}
    
const Record & FirstOrderReaction::get_input_type_single_reaction() {
    return Record("Reaction", "Describes a single first order chemical reaction.")
        .declare_key("reactants", Array(FirstOrderReaction::get_input_type_reactant(), 1), Default::obligatory(),
                    "An array of reactants. Do not use array, reactions with only one reactant (decays) are implemented at the moment!")
        .declare_key("reaction_rate", Double(0.0), Default::obligatory(),
                    "The reaction rate coefficient of the first order reaction.")
        .declare_key("products", Array(FirstOrderReaction::get_input_type_product(), 1), Default::obligatory(),
                    "An array of products.")
        .close();
}


const Record & FirstOrderReaction::get_input_type() {
    return Record("FirstOrderReaction", "A model of first order chemical reactions (decompositions of a reactant into products).")
        .derive_from( ReactionTerm::it_abstract_term() )
        .derive_from( ReactionTerm::it_abstract_mobile_term() )
        .derive_from( ReactionTerm::it_abstract_immobile_term() )
        .derive_from( ReactionTerm::it_abstract_reaction() )
        .declare_key("reactions", Array( FirstOrderReaction::get_input_type_single_reaction()), Default::obligatory(),
                    "An array of first order chemical reactions.")
        .declare_key("ode_solver", PadeApproximant::get_input_type(), Default("{}"),
                     "Numerical solver for the system of first order ordinary differential equations coming from the model.")
        .close();
}

const int FirstOrderReaction::registrar =
        Input::register_class< FirstOrderReaction, Mesh &, Input::Record >("FirstOrderReaction") +
        FirstOrderReaction::get_input_type().size();


FirstOrderReaction::FirstOrderReaction(Mesh &init_mesh, Input::Record in_rec)
      : FirstOrderReactionBase(init_mesh, in_rec)
{
}

FirstOrderReaction::~FirstOrderReaction()
{
}

void FirstOrderReaction::assemble_ode_matrix(void )
{
    // create decay matrix
    reaction_matrix_ = arma::zeros(n_substances_, n_substances_);
    unsigned int reactant_index, product_index; //global indices of the substances
    double exponent;    //temporary variable for k
    for (unsigned int i_reaction = 0; i_reaction < reaction_rates_.size(); i_reaction++) {
        reactant_index = substance_ids_[i_reaction][0];
        exponent = reaction_rates_[i_reaction];
        reaction_matrix_(reactant_index, reactant_index) = -exponent;
        
        for (unsigned int i_product = 1; i_product < substance_ids_[i_reaction].size(); ++i_product){
            product_index = substance_ids_[i_reaction][i_product];
            reaction_matrix_(product_index, reactant_index) = exponent * bifurcation_[i_reaction][i_product-1];
        }
    }
}


void FirstOrderReaction::initialize_from_input()
{
    unsigned int idx;   //temporary variable, indexing substances

    Input::Array reactions_array = input_record_.val<Input::Array>("reactions");

    substance_ids_.resize( reactions_array.size() );
    reaction_rates_.resize( reactions_array.size() );
    bifurcation_.resize( reactions_array.size() );

    int i_reaction=0;
    for (Input::Iterator<Input::Record> react_it = reactions_array.begin<Input::Record>(); 
         react_it != reactions_array.end(); ++react_it, ++i_reaction)
    { 
        //read reaction rate
        reaction_rates_[i_reaction] = react_it->val<double>("reaction_rate");
        
        //read reactant name, product names and branching ratios
        Input::Array reactant_array = react_it->val<Input::Array>("reactants");
        Input::Array product_array = react_it->val<Input::Array>("products");

        //resize substance_ids array
        substance_ids_[i_reaction].resize( product_array.size()+1 );
        bifurcation_[i_reaction].resize(product_array.size());

        if(reactant_array.size() != 1)
            xprintf(UsrErr, "More than one reactant is not available at the moment.");
        
        //take only one reactant
        Input::Iterator<Input::Record> reactant_it = reactant_array.begin<Input::Record>();
        {
            string reactant_name = reactant_it->val<string>("name");
            idx = find_subst_name(reactant_name);
            if (idx < substances_.size())   
                substance_ids_[i_reaction][0] = idx;
            else THROW(ReactionTerm::ExcUnknownSubstance() 
                    << ReactionTerm::EI_Substance(reactant_name) 
                    << (*reactant_it).ei_address());
        }
        
        // set products
        unsigned int i_product = 0;
        for(Input::Iterator<Input::Record> product_it = product_array.begin<Input::Record>(); 
            product_it != product_array.end(); ++product_it, i_product++)
        {
            string product_name = product_it->val<string>("name");
            idx = find_subst_name(product_name);
            if (idx < substances_.size())
                substance_ids_[i_reaction][i_product+1] = idx;
            else THROW(ReactionTerm::ExcUnknownSubstance() 
                        << ReactionTerm::EI_Substance(product_name) 
                        << product_array.ei_address());
            
            bifurcation_[i_reaction][i_product] = product_it->val<double>("branching_ratio");
        }


        //Normalization of branching ratios in bifurcation vector by its norm.
        //sum:
        double sum=0;
        for(auto &b : bifurcation_[i_reaction])
            sum += b;
        //Normalization:
        for(auto &b : bifurcation_[i_reaction])
            b = b / sum;
    }
}