NeighborList.h

//
//  Copyright (C) 2017, Alexander Stukowski and Paul Erhart
//
//  This file is part of atomicrex.
//
//  Atomicrex is free software; you can redistribute it and/or modify
//  it under the terms of the GNU General Public License as published by
//  the Free Software Foundation; either version 3 of the License, or
//  (at your option) any later version.
//
//  Atomicrex 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.
//
//  You should have received a copy of the GNU General Public License
//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
//

#pragma once

#include "../Atomicrex.h"

namespace atomicrex {

class AtomicStructure;
class Potential;

struct NeighborListEntry
{
    Vector3 delta;              // delta = x[j] - x[i]
    double r;                   // r = |delta|
    int index;                  // Index of second atom of the neighbor bond (this may be a local or a ghost atom).
    int localIndex;             // Index of second local atom (this is always the corresponding local atom).

    // Pointer to additional memory for the potential routines to store pair-wise information.
    void* bondDataPtr;

    template<typename T>
    T& bondData() {
        BOOST_ASSERT(bondDataPtr != nullptr);
        return *static_cast<T*>(bondDataPtr);
    }

    template<typename T>
    const T& bondData() const {
        BOOST_ASSERT(bondDataPtr != nullptr);
        return *static_cast<const T*>(bondDataPtr);
    }
};

class NeighborList
{
public:

    NeighborList() : _numAtoms(0) {}

    int numAtoms() const { return _numAtoms; }

    int atomIndex(int i) const { return _ilist[i]; }

    int numNeighborsHalf(int atomIndex) const { return _numNeighborsHalf[atomIndex]; }

    int numNeighborsFull(int atomIndex) const { return _numNeighborsFull[atomIndex]; }

    NeighborListEntry* neighborList(int atomIndex) {
        BOOST_ASSERT(atomIndex >= 0 && atomIndex < _firstNeighbor.size());
        return &_neighborList[_firstNeighbor[atomIndex]];
    }

    const NeighborListEntry* neighborList(int atomIndex) const {
        BOOST_ASSERT(atomIndex >= 0 && atomIndex < _firstNeighbor.size());
        return &_neighborList[_firstNeighbor[atomIndex]];
    }

    void build(const AtomicStructure& structure, const Potential& potential, double cutoffRange);

    void update(const AtomicStructure& structure);

private:

    int _numAtoms;
    std::vector<int> _ilist;
    std::vector<int> _numNeighborsHalf;
    std::vector<int> _numNeighborsFull;
    std::vector<int> _firstNeighbor;
    std::vector<NeighborListEntry> _neighborList;
    std::vector<unsigned char> _perBondPotentialData;
};

} // End of namespace