source: src/linkedcell.cpp@ 0dbddc

#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 ... ";
  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();
  }
  cout << "done."  << endl;

  // 4. put each atom into its respective cell
  cout << Verbose(2) << "Filling cells ... ";
  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 << "done."  << 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(const 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 interval bounds of the linked cell grid.
 * \param *lower lower bounds
 * \param *upper upper bounds
 */
void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM])
{
  for (int i=0;i<NDIM;i++) {
    lower[i] = ((n[i]-1) >= 0) ? n[i]-1 : 0;
    upper[i] = ((n[i]+1) < N[i]) ? n[i]+1 : N[i]-1;
    //cout << " [" << Nlower[i] << "," << Nupper[i] << "] ";
    // check for this axis whether the point is outside of our grid
    if (n[i] < 0)
      upper[i] = lower[i];
    if (n[i] > N[i])
      lower[i] = upper[i];

    //cout << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
  }
};

/** 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(const 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;
};