newmen/versatile-diamond

#include "finder.h"
#include "handbook.h"

#include "species/base/bridge.h"
#include "species/base/methyl_on_dimer.h"
#include "species/base/bridge_with_dimer.h"
#include "species/base/two_bridges.h"
#include "species/sidepiece/dimer.h"
#include "species/specific/cross_bridge_on_bridges.h"
#include "reactions/ubiquitous/surface_activation.h"
#include "reactions/ubiquitous/surface_deactivation.h"

void Finder::initFind(Atom **atoms, uint n)
{
    uint index = 0;
    Atom **dup = new Atom *[n];
    for (uint i = 0; i < n; ++i)
    {
        Atom *atom = atoms[i];
        if (!atom) continue;
        if (atom->lattice() && atom->lattice()->coords().z == 0) continue;

        dup[index++] = atom;
    }

    findAll(dup, index);

    delete [] dup;
}

void Finder::findAll(Atom **atoms, uint n)
{
#ifdef PRINT
    debugPrint([&](IndentStream &os) {
        os << " ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n";
        os << "Finder::findAll by " << n << " atoms";
        for (uint i = 0; i < n; ++i)
        {
            os << " [" << atoms[i] << "]";
        }
    });
#endif // PRINT

#ifndef NDEBUG
    for (uint i = 0; i < n; ++i)
    {
        assert(atoms[i]);
    }
#endif // NDEBUG

    for (uint i = 0; i < n; ++i)
    {
        atoms[i]->setUnvisited();
    }

    for (uint i = 0; i < n; ++i)
    {
        atoms[i]->removeUnsupportedSpecies();
    }

    for (uint i = 0; i < n; ++i)
    {
        atoms[i]->setSpecsUnvisited();
    }

#ifdef PRINT
    debugPrint([&](IndentStream &os) {
        os << "Finder::findAll preparations complete";
    });
#endif // PRINT

    // ---------------------------------------------------------------------------------------------------------- //

    for (uint i = 0; i < n; ++i)
    {
        Bridge::find(atoms[i]);
    }

    for (uint i = 0; i < n; ++i)
    {
        Dimer::find(atoms[i]);
    }

    for (uint i = 0; i < n; ++i)
    {
        MethylOnDimer::find(atoms[i]);
    }

    for (uint i = 0; i < n; ++i)
    {
        TwoBridges::find(atoms[i]);
    }

    for (uint i = 0; i < n; ++i)
    {
        BridgeWithDimer::find(atoms[i]);
    }

    for (uint i = 0; i < n; ++i)
    {
        CrossBridgeOnBridges::find(atoms[i]);
    }

    // ---------------------------------------------------------------------------------------------------------- //

    for (uint i = 0; i < n; ++i)
    {
        atoms[i]->findUnvisitedChildren();
    }

    for (uint i = 0; i < n; ++i)
    {
        SurfaceActivation::find(atoms[i]);
        SurfaceDeactivation::find(atoms[i]);
    }

    // order is important
    Handbook::specificKeeper().find();
    Handbook::lateralKeeper().find();

    for (uint i = 0; i < n; ++i)
    {
        atoms[i]->setVisited();
    }

    finalize();
}

void Finder::removeAll(Atom **atoms, uint n)
{
    for (uint i = 0; i < n; ++i)
    {
        Atom *atom = atoms[i];
        if (!atom) continue;
        atom->prepareToRemove();
    }

    initFind(atoms, n);
}

void Finder::finalize()
{
    Handbook::specificKeeper().clear();
    Handbook::lateralKeeper().clear();

    Handbook::scavenger().clear();
}