コード例 #1
0
ファイル: haloExchange.c プロジェクト: jmohdyusof/CoMD
/// Make a list of link cells that need to be sent across the specified
/// face.  For each face, the list must include all cells, local and
/// halo, in the first two planes of link cells.  Halo cells must be
/// included in the list of link cells to send since local atoms may
/// have moved from local cells into halo cells on this time step.
/// (Actual remote atoms should have been deleted, so the halo cells
/// should contain only these few atoms that have just crossed.)
/// Sending these atoms will allow them to be reassigned to the task
/// that covers the spatial domain they have moved into.
///
/// Note that link cell grid coordinates range from -1 to gridSize[iAxis].
/// \see initLinkCells for an explanation link cell grid coordinates.
///
/// \param [in] boxes  Link cell information.
/// \param [in] iFace  Index of the face data will be sent across.
/// \param [in] nCells Number of cells to send.  This is used for a
///                    consistency check.
/// \return The list of cells to send.  Caller is responsible to free
/// the list.
int* mkAtomCellList(LinkCell* boxes, enum HaloFaceOrder iFace, const int nCells)
{
   int* list = comdMalloc(nCells*sizeof(int));
   int xBegin = -1;
   int xEnd   = boxes->gridSize[0]+1;
   int yBegin = -1;
   int yEnd   = boxes->gridSize[1]+1;
   int zBegin = -1;
   int zEnd   = boxes->gridSize[2]+1;

   if (iFace == HALO_X_MINUS) xEnd = xBegin+2;
   if (iFace == HALO_X_PLUS)  xBegin = xEnd-2;
   if (iFace == HALO_Y_MINUS) yEnd = yBegin+2;
   if (iFace == HALO_Y_PLUS)  yBegin = yEnd-2;
   if (iFace == HALO_Z_MINUS) zEnd = zBegin+2;
   if (iFace == HALO_Z_PLUS)  zBegin = zEnd-2;

   int count = 0;
   for (int ix=xBegin; ix<xEnd; ++ix)
      for (int iy=yBegin; iy<yEnd; ++iy)
         for (int iz=zBegin; iz<zEnd; ++iz)
            list[count++] = getBoxFromTuple(boxes, ix, iy, iz);
   assert(count == nCells);
   return list;
}
コード例 #2
0
ファイル: linkCells.cpp プロジェクト: kempj/CoMD-tasking
/// Get the index of the link cell that contains the specified
/// coordinate.  This can be either a halo or a local link cell.
///
/// Because the rank ownership of an atom is strictly determined by the
/// atom's position, we need to take care that all ranks will agree which
/// rank owns an atom.  The conditionals at the end of this function are
/// special care to ensure that all ranks make compatible link cell
/// assignments for atoms that are near a link cell boundaries.  If no
/// ranks claim an atom in a local cell it will be lost.  If multiple
/// ranks claim an atom it will be duplicated.
int getBoxFromCoord(LinkCell* boxes, real_t rr[3])
{
    const real_t* localMin = boxes->localMin; // alias
    const real_t* localMax = boxes->localMax; // alias
    const int*    gridSize = boxes->gridSize; // alias
    int ix = (int)(floor((rr[0] - localMin[0])*boxes->invBoxSize[0]));
    int iy = (int)(floor((rr[1] - localMin[1])*boxes->invBoxSize[1]));
    int iz = (int)(floor((rr[2] - localMin[2])*boxes->invBoxSize[2]));

    // For each axis, if we are inside the local domain, make sure we get
    // a local link cell.  Otherwise, make sure we get a halo link cell.
    if(rr[0] < localMax[0]) {
        if (ix == gridSize[0]) {
            ix = gridSize[0] - 1;
        }
    } else {
        ix = gridSize[0]; // assign to halo cell
    }
    if(rr[1] < localMax[1]) {
        if (iy == gridSize[1]) {
            iy = gridSize[1] - 1;
        }
    } else {
        iy = gridSize[1];
    }
    if(rr[2] < localMax[2]) {
        if (iz == gridSize[2]) {
            iz = gridSize[2] - 1;
        }
    } else {
        iz = gridSize[2];
    }

    return getBoxFromTuple(boxes, ix, iy, iz);
}
コード例 #3
0
ファイル: linkCells.cpp プロジェクト: kempj/CoMD-tasking
//for shared memory only, takes a box ID for a halo cell and returns the local cell that it corresponds to.
int getLocalHaloTuple(LinkCell *boxes, int iBox) {
    int x,y,z;
    getTuple(boxes, iBox, &x, &y, &z);

    haloToLocalCell(&x, &y, &z, boxes->gridSize);

    return getBoxFromTuple(boxes, x, y, z);
}
コード例 #4
0
/// \details
/// Populates the nbrBoxes array with the 27 boxes that are adjacent to
/// iBox.  The count is 27 instead of 26 because iBox is included in the
/// list (as neighbor 13).  Caller is responsible to alloc and free
/// nbrBoxes.
/// \return The number of nbr boxes (always 27 in this implementation).
int getNeighborBoxes(LinkCell* boxes, int iBox, int* nbrBoxes)
{
   int ix, iy, iz;
   getTuple(boxes, iBox, &ix, &iy, &iz);
   
   int count = 0;
   for (int i=ix-1; i<=ix+1; i++)
      for (int j=iy-1; j<=iy+1; j++)
         for (int k=iz-1; k<=iz+1; k++)
            nbrBoxes[count++] = getBoxFromTuple(boxes,i,j,k);
   
   return count;
}
コード例 #5
0
ファイル: haloExchange.c プロジェクト: jmohdyusof/CoMD
/// Make a list of link cells that need to receive data across the
/// specified face.  Note that this list must be compatible with the
/// corresponding send list to ensure that the data goes to the correct
/// atoms.
///
/// \see initLinkCells for information about the conventions for grid
/// coordinates of link cells.
int* mkForceRecvCellList(LinkCell* boxes, int face, int nCells)
{
   int* list = comdMalloc(nCells*sizeof(int));
   int xBegin, xEnd, yBegin, yEnd, zBegin, zEnd;

   int nx = boxes->gridSize[0];
   int ny = boxes->gridSize[1];
   int nz = boxes->gridSize[2];
   switch(face)
   {
     case HALO_X_MINUS:
      xBegin=-1; xEnd=0;    yBegin=0;  yEnd=ny;   zBegin=0;  zEnd=nz;
      break;
     case HALO_X_PLUS:
      xBegin=nx; xEnd=nx+1; yBegin=0;  yEnd=ny;   zBegin=0;  zEnd=nz;
      break;
     case HALO_Y_MINUS:
      xBegin=-1; xEnd=nx+1; yBegin=-1; yEnd=0;    zBegin=0;  zEnd=nz;
      break;
     case HALO_Y_PLUS:
      xBegin=-1; xEnd=nx+1; yBegin=ny; yEnd=ny+1; zBegin=0;  zEnd=nz;
      break;
     case HALO_Z_MINUS:
      xBegin=-1; xEnd=nx+1; yBegin=-1; yEnd=ny+1; zBegin=-1; zEnd=0;
      break;
     case HALO_Z_PLUS:
      xBegin=-1; xEnd=nx+1; yBegin=-1; yEnd=ny+1; zBegin=nz; zEnd=nz+1;
      break;
     default:
      assert(1==0);
   }
   
   int count = 0;
   for (int ix=xBegin; ix<xEnd; ++ix)
      for (int iy=yBegin; iy<yEnd; ++iy)
         for (int iz=zBegin; iz<zEnd; ++iz)
            list[count++] = getBoxFromTuple(boxes, ix, iy, iz);
   
   assert(count == nCells);
   return list;
}