#include "linkedcell.hpp"
#include "molecules.hpp"

/** Constructor for class LinkedCell.
 */
LinkedCell::LinkedCell()
{
	LC = NULL;
	for(int i=0;i<NDIM;i++)
		N[i] = 0;
	index = -1;
	RADIUS = 0.;
	max.Zero();
	min.Zero();
};

/** Puts all atoms in \a *mol into a linked cell list with cell's lengths of \a RADIUS
 * \param *mol molecule structure with all Atom's
 * \param RADIUS edge length of cells
 */
LinkedCell::LinkedCell(molecule *mol, double radius)
{
	atom *Walker = NULL;

	RADIUS = radius;
	LC = NULL;
	for(int i=0;i<NDIM;i++)
		N[i] = 0;
	index = -1;
	max.Zero();
	min.Zero();
	cout << Verbose(1) << "Begin of LinkedCell" << endl;
	if (mol->start->next == mol->end) {
		cerr << "ERROR: molecule contains no atoms!" << endl;
		return;
	}
	// 1. find max and min per axis of atoms
	Walker = mol->start->next;
	for (int i=0;i<NDIM;i++) {
		max.x[i] = Walker->x.x[i];
		min.x[i] = Walker->x.x[i];
	}
	while (Walker != mol->end) {
		for (int i=0;i<NDIM;i++) {
			if (max.x[i] < Walker->x.x[i])
				max.x[i] = Walker->x.x[i];
			if (min.x[i] > Walker->x.x[i])
				min.x[i] = Walker->x.x[i];
		}
		Walker = Walker->next;
	}
	cout << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl;

	// 2. find then umber of cells per axis
	for (int i=0;i<NDIM;i++) {
		N[i] = (int)floor((max.x[i] - min.x[i])/RADIUS)+1;
	}
	cout << Verbose(2) << "Number of cells per axis are " << N[0] << ", " << N[1] << " and " << N[2] << "." << endl;

	// 3. allocate the lists
	cout << Verbose(2) << "Allocating cells ... " << endl;
	if (LC != NULL) {
		cout << Verbose(1) << "ERROR: Linked Cell list is already allocated, I do nothing." << endl;
		return;
	}
	LC = new LinkedAtoms[N[0]*N[1]*N[2]];
	for (index=0;index<N[0]*N[1]*N[2];index++) {
		LC [index].clear();
	}

	// 4. put each atom into its respective cell
	Walker = mol->start;
	while (Walker->next != mol->end) {
		Walker = Walker->next;
		for (int i=0;i<NDIM;i++) {
			n[i] = (int)floor((Walker->x.x[i] - min.x[i])/RADIUS);
		}
		index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
		LC[index].push_back(Walker);
		cout << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
	}
	cout << Verbose(1) << "End of LinkedCell" << endl;
};

/** Destructor for class LinkedCell.
 */
LinkedCell::~LinkedCell()
{
	if (LC != NULL)
	for (index=0;index<N[0]*N[1]*N[2];index++)
		LC[index].clear();
	delete[](LC);
	for(int i=0;i<NDIM;i++)
		N[i] = 0;
	index = -1;
	max.Zero();
	min.Zero();
};

/** Checks whether LinkedCell::n[] is each within [0,N[]].
 * \return if all in intervals - true, else -false
 */
bool LinkedCell::CheckBounds()
{
	bool status = true;
	for(int i=0;i<NDIM;i++)
		status = status && ((n[i] >=0) && (n[i] < N[i]));
	if (!status)
	cerr << "ERROR: indices are out of bounds!" << endl;
	return status;
};


/** Returns a pointer to the current cell.
 * \return LinkedAtoms pointer to current cell, NULL if LinkedCell::n[] are out of bounds.
 */
LinkedAtoms* LinkedCell::GetCurrentCell()
{
	if (CheckBounds()) {
		index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
		return (&(LC[index]));
	} else {
		return NULL;
	}
};

/** Calculates the index for a given atom *Walker.
 * \param *Walker atom to set index to
 * \return if the atom is also found in this cell - true, else - false
 */
bool LinkedCell::SetIndexToAtom(atom *Walker)
{
	bool status = false;
	for (int i=0;i<NDIM;i++) {
		n[i] = (int)floor((Walker->x.x[i] - min.x[i])/RADIUS);
	}
	index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
	if (CheckBounds()) {
		for (LinkedAtoms::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
			status = status || ((*Runner) == Walker);
		return status;
	} else {
		cerr << Verbose(1) << "ERROR: Atom "<< *Walker << " at " << Walker->x << " is out of bounds." << endl;
		return false;
	}
};

/** Calculates the index for a given Vector *x.
 * \param *x Vector with coordinates
 * \return Vector is inside bounding box - true, else - false
 */
bool LinkedCell::SetIndexToVector(Vector *x)
{
	bool status = true;
	for (int i=0;i<NDIM;i++) {
		n[i] = (int)floor((x->x[i] - min.x[i])/RADIUS);
		if (max.x[i] < x->x[i])
			status = false;
		if (min.x[i] > x->x[i])
			status = false;
	}
	return status;
};