gistfile1.js

        updateShortRangeForces = function () {
          // Fast path if Lennard Jones interaction is disabled.
          if (!useLennardJonesInteraction) return;

          var rows = cellList.getRowsNum(),
              cols = cellList.getColsNum(),
              i, j, temp, cellIdx, cell1, cell2,
              a, b, atom1Idx, cell1Len, cell2Len,
              n, nLen, cellNeighbors;

          for (i = 0; i < rows; i++) {
            temp = i * cols;
            for (j = 0; j < cols; j++) {
              cellIdx = temp + j;

              cell1 = cellList.getCell(cellIdx);
              cellNeighbors = cellList.getNeighboringCells(i, j);

              for (a = 0, cell1Len = cell1.length; a < cell1Len; a++) {
                atom1Idx = cell1[a];

                // Interactions inside the cell.
                for (b = 0; b < a; b++) {
                  calculateLJInteraction(atom1Idx, cell1[b]);
                }
                // Interactions between neighboring cells.
                for (n = 0, nLen = cellNeighbors.length; n < nLen; n++) {
                  cell2 = cellNeighbors[n];
                  for (b = 0, cell2Len = cell2.length; b < cell2Len; b++) {
                    calculateLJInteraction(atom1Idx, cell2[b]);
                  }
                }
              }
            }
          }
        },