atom.h

#ifndef ATOM_H
#define ATOM_H

#include "vector3.h"

#include <vector>
#include <unordered_set>

constexpr double dt = 1e-6;

class Atom;

struct Bond {
    Atom* partner;
    int order;           // Single bond: 1, triple bond: 3
};

struct LonePair {
	Vector3 relativePos; // s.t. AtomPos + relativePos = ElectronPos
};

class Atom {
public:
    // Assigned system values
    int atomID;
    int moleculeID;

    int AtomicNumber;

    Vector3 pos;
    Vector3 vel;
    Vector3 force;

    double charge;
    double velocityloss_pertick;

    std::vector<Bond> bonds;            // Useful for iterating through
    std::unordered_set<Atom*> bondsSet; // Same as bonds, but useful for faster lookup times

    double mass;
    double covalentRadius;
    double vdw_radius;       // Van der Waals radius
    double electronegativity;
    int maxbonds;
    int valency;

    int valenceVacancies;

    LonePair lonePairs[4];	// Any atom can only have, at most, 8 valence electrons, therefore 4 is the maximum no. lone pairs
    int numLonePairs;		// Number of lone pairs present

    int brownianNoiseIndex;

    Atom(
        int AtomicNumber,
        Vector3 pos,	// Position
        Vector3 vel,	// Velocity
        double charge,
        double velocityloss_pertick
    );

    void update();

    void bondWith(Atom* atom);
    void breakWith(Atom* atom);

    void spawnLonePairs();

    std::vector<double> getLPPositions() const;

    bool isBondedWith(Atom* atom) const;
};

#endif