importKinetics.cpp

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/**
 *  @file importKinetics.cpp
 *     Declarations of global routines for the importing
 *     of kinetics data from XML files (see \ref inputfiles).
 *
 *     This file contains routines which are global routines, that is,
 *     not part of any object. These routine take as input, ctml
 *     pointers to data, and pointers to %Cantera objects. The purpose
 *     of these routines is to initialize the %Cantera objects with data
 *     from the ctml tree structures.
 */
 
// This file is part of Cantera. See License.txt in the top-level directory or
// at https://cantera.org/license.txt for license and copyright information.
 
#include "cantera/kinetics/importKinetics.h"
#include "cantera/thermo/ThermoFactory.h"
#include "cantera/kinetics/Reaction.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/ctml.h"
#include "cantera/base/yaml.h"
 
#include <cstring>
 
using namespace std;
 
namespace Cantera
{
 
bool installReactionArrays(const XML_Node& p, Kinetics& kin,
                           std::string default_phase, bool check_for_duplicates)
{
    int itot = 0;
 
    // Search the children of the phase element for the XML element named
    // reactionArray. If we can't find it, then return signaling having not
    // found any reactions. Apparently, we allow multiple reactionArray elements
    // here Each one will be processed sequentially, with the end result being
    // purely additive.
    vector<XML_Node*> rarrays = p.getChildren("reactionArray");
    if (rarrays.empty()) {
        return false;
    }
    for (size_t n = 0; n < rarrays.size(); n++) {
        // Go get a reference to the current XML element, reactionArray. We will
        // process this element now.
        const XML_Node& rxns = *rarrays[n];
 
        // The reactionArray element has an attribute called, datasrc. The value
        // of the attribute is the XML element comprising the top of the tree of
        // reactions for the phase. Find this datasrc element starting with the
        // root of the current XML node.
        const XML_Node* rdata = get_XML_Node(rxns["datasrc"], &rxns.root());
 
        // If the reactionArray element has a child element named "skip", and if
        // the attribute of skip called "species" has a value of "undeclared",
        // we will set rxnrule.skipUndeclaredSpecies to 'true'. rxnrule is
        // passed to the routine that parses each individual reaction so that
        // the parser will skip all reactions containing an undefined species
        // without throwing an error.
        //
        // Similarly, an attribute named "third_bodies" with the value of
        // "undeclared" will skip undeclared third body efficiencies (while
        // retaining the reaction and any other efficiencies).
        if (rxns.hasChild("skip")) {
            const XML_Node& sk = rxns.child("skip");
            if (sk["species"] == "undeclared") {
                kin.skipUndeclaredSpecies(true);
            }
            if (sk["third_bodies"] == "undeclared") {
                kin.skipUndeclaredThirdBodies(true);
            }
        }
 
        // Search for child elements called include. We only include a reaction
        // if it's tagged by one of the include fields. Or, we include all
        // reactions if there are no include fields.
        vector<XML_Node*> incl = rxns.getChildren("include");
        vector<XML_Node*> allrxns = rdata->getChildren("reaction");
        // if no 'include' directive, then include all reactions
        if (incl.empty()) {
            for (size_t i = 0; i < allrxns.size(); i++) {
                checkElectrochemReaction(p,kin,*allrxns[i]);
                kin.addReaction(newReaction(*allrxns[i]), false);
                ++itot;
            }
        } else {
            for (size_t nii = 0; nii < incl.size(); nii++) {
                const XML_Node& ii = *incl[nii];
                string imin = ii["min"];
                string imax = ii["max"];
 
                string::size_type iwild = string::npos;
                if (imax == imin) {
                    iwild = imin.find("*");
                    if (iwild != string::npos) {
                        imin = imin.substr(0,iwild);
                        imax = imin;
                    }
                }
 
                for (size_t i = 0; i < allrxns.size(); i++) {
                    const XML_Node* r = allrxns[i];
                    string rxid;
                    if (r) {
                        rxid = r->attrib("id");
                        if (iwild != string::npos) {
                            rxid = rxid.substr(0,iwild);
                        }
 
                        // To decide whether the reaction is included or not we
                        // do a lexical min max and operation. This sometimes
                        // has surprising results.
                        if ((rxid >= imin) && (rxid <= imax)) {
                            checkElectrochemReaction(p,kin,*r);
                            kin.addReaction(newReaction(*r), false);
                            ++itot;
                        }
                    }
                }
            }
        }
    }
 
    if (check_for_duplicates) {
        kin.checkDuplicates();
    }
 
    kin.resizeReactions();
 
    return true;
}
 
bool importKinetics(const XML_Node& phase, std::vector<ThermoPhase*> th,
                    Kinetics* k)
{
    if (k == 0) {
        return false;
    }
 
    // This phase will be the owning phase for the kinetics operator
    // For interfaces, it is the surface phase between two volumes.
    // For homogeneous kinetics, it's the current volumetric phase.
    string owning_phase = phase["id"];
 
    bool check_for_duplicates = false;
    if (phase.parent() && phase.parent()->hasChild("validate")) {
        const XML_Node& d = phase.parent()->child("validate");
        if (d["reactions"] == "yes") {
            check_for_duplicates = true;
        }
    }
 
    // If other phases are involved in the reaction mechanism, they must be
    // listed in a 'phaseArray' child element. Homogeneous mechanisms do not
    // need to include a phaseArray element.
    vector<string> phase_ids;
    if (phase.hasChild("phaseArray")) {
        const XML_Node& pa = phase.child("phaseArray");
        getStringArray(pa, phase_ids);
    }
    phase_ids.push_back(owning_phase);
 
    // for each referenced phase, attempt to find its id among those
    // phases specified.
    string msg = "";
    for (size_t n = 0; n < phase_ids.size(); n++) {
        string phase_id = phase_ids[n];
        bool phase_ok = false;
        // loop over the supplied 'ThermoPhase' objects representing
        // phases, to find an object with the same id.
        for (size_t m = 0; m < th.size(); m++) {
            if (th[m]->name() == phase_id) {
                phase_ok = true;
                // if no phase with this id has been added to
                //the kinetics manager yet, then add this one
                if (k->phaseIndex(phase_id) == npos) {
                    k->addPhase(*th[m]);
                }
            }
            msg += " "+th[m]->name();
        }
        if (!phase_ok) {
            throw CanteraError("importKinetics",
                               "phase "+phase_id+" not found. Supplied phases are:"+msg);
        }
    }
 
    // allocates arrays, etc. Must be called after the phases have been added to
    // 'kin', so that the number of species in each phase is known.
    k->init();
 
    // Install the reactions.
    return installReactionArrays(phase, *k, owning_phase, check_for_duplicates);
}
 
bool buildSolutionFromXML(XML_Node& root, const std::string& id,
                          const std::string& nm, ThermoPhase* th, Kinetics* kin)
{
    XML_Node* x = get_XML_NameID(nm, string("#")+id, &root);
    if (!x) {
        return false;
    }
 
    // Fill in the ThermoPhase object by querying the const XML_Node tree
    // located at x.
    importPhase(*x, th);
 
    // Create a vector of ThermoPhase pointers of length 1 having the current th
    // ThermoPhase as the entry.
    std::vector<ThermoPhase*> phases{th};
 
    // Fill in the kinetics object k, by querying the const XML_Node tree
    // located by x. The source terms and eventually the source term vector will
    // be constructed from the list of ThermoPhases in the vector, phases.
    importKinetics(*x, phases, kin);
    return true;
}
 
bool checkElectrochemReaction(const XML_Node& p, Kinetics& kin, const XML_Node& r)
{
    // If other phases are involved in the reaction mechanism, they must be
    // listed in a 'phaseArray' child element. Homogeneous mechanisms do not
    // need to include a phaseArray element.
    vector<string> phase_ids;
    if (p.hasChild("phaseArray")) {
        const XML_Node& pa = p.child("phaseArray");
        getStringArray(pa, phase_ids);
    }
    phase_ids.push_back(p["id"]);
 
    // Get reaction product and reactant information
    Composition reactants = parseCompString(r.child("reactants").value());
    Composition products = parseCompString(r.child("products").value());
 
 
    // If the reaction has undeclared species don't perform electrochemical check
    for (const auto& sp : reactants) {
        if (kin.kineticsSpeciesIndex(sp.first) == npos) {
            return true;
        }
    }
 
    for (const auto& sp : products) {
        if (kin.kineticsSpeciesIndex(sp.first) == npos) {
            return true;
        }
    }
 
    // Initialize the electron counter for each phase
    std::vector<double> e_counter(phase_ids.size(), 0.0);
 
    // Find the amount of electrons in the products for each phase
    for (const auto& sp : products) {
        const ThermoPhase& ph = kin.speciesPhase(sp.first);
        size_t k = ph.speciesIndex(sp.first);
        double stoich = sp.second;
        for (size_t m = 0; m < phase_ids.size(); m++) {
            if (phase_ids[m] == ph.name()) {
                e_counter[m] += stoich * ph.charge(k);
                break;
            }
        }
    }
 
    // Subtract the amount of electrons in the reactants for each phase
    for (const auto& sp : reactants) {
        const ThermoPhase& ph = kin.speciesPhase(sp.first);
        size_t k = ph.speciesIndex(sp.first);
        double stoich = sp.second;
        for (size_t m = 0; m < phase_ids.size(); m++) {
            if (phase_ids[m] == ph.name()) {
                e_counter[m] -= stoich * ph.charge(k);
                break;
            }
        }
    }
 
    // If the electrons change phases then the reaction is electrochemical
    bool echemical = false;
    for(size_t m = 0; m < phase_ids.size(); m++) {
        if (fabs(e_counter[m]) > 1e-4) {
            echemical = true;
            break;
        }
    }
 
    // If the reaction is electrochemical, ensure the reaction is identified as
    // electrochemical. If not already specified beta is assumed to be 0.5
    std::string type = toLowerCopy(r["type"]);
    if (!r.child("rateCoeff").hasChild("electrochem")) {
        if ((type != "butlervolmer_noactivitycoeffs" &&
             type != "butlervolmer" &&
             type != "surfaceaffinity") &&
             echemical) {
            XML_Node& f = r.child("rateCoeff").addChild("electrochem","");
            f.addAttribute("beta",0.5);
        }
    }
    return true;
}
 
}