using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
-
void nbnxn_atomdata_t::resizeCoordinateBuffer(int numAtoms)
{
numAtoms_ = numAtoms;
static int numAtomsFromGrids(const nbnxn_search &nbs)
{
- const nbnxn_grid_t &lastGrid = nbs.grid.back();
-
- return (lastGrid.cell0 + lastGrid.nc)*lastGrid.na_sc;
+ return nbs.grid.back().atomIndexEnd();
}
/* Sets the atom type in nbnxn_atomdata_t */
{
params->type.resize(numAtomsFromGrids(*nbs));
- for (const nbnxn_grid_t &grid : nbs->grid)
+ for (const Nbnxm::Grid &grid : nbs->grid)
{
/* Loop over all columns and copy and fill */
- for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
+ for (int i = 0; i < grid.numColumns(); i++)
{
- int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
- int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
+ const int numAtoms = grid.paddedNumAtomsInColumn(i);
+ const int atomOffset = grid.firstAtomInColumn(i);
- copy_int_to_nbat_int(nbs->a.data() + ash, grid.cxy_na[i], ncz*grid.na_sc,
- type, params->numTypes - 1, params->type.data() + ash);
+ copy_int_to_nbat_int(nbs->a.data() + atomOffset, grid.numAtomsInColumn(i), numAtoms,
+ type, params->numTypes - 1, params->type.data() + atomOffset);
}
}
}
if (params->comb_rule != ljcrNONE)
{
- for (const nbnxn_grid_t &grid : nbs->grid)
+ for (const Nbnxm::Grid &grid : nbs->grid)
{
/* Loop over all columns and copy and fill */
- for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
+ for (int i = 0; i < grid.numColumns(); i++)
{
- int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
- int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
+ const int numAtoms = grid.paddedNumAtomsInColumn(i);
+ const int atomOffset = grid.firstAtomInColumn(i);
if (XFormat == nbatX4)
{
copy_lj_to_nbat_lj_comb<c_packX4>(params->nbfp_comb,
- params->type.data() + ash,
- ncz*grid.na_sc,
- params->lj_comb.data() + ash*2);
+ params->type.data() + atomOffset,
+ numAtoms,
+ params->lj_comb.data() + atomOffset*2);
}
else if (XFormat == nbatX8)
{
copy_lj_to_nbat_lj_comb<c_packX8>(params->nbfp_comb,
- params->type.data() + ash,
- ncz*grid.na_sc,
- params->lj_comb.data() + ash*2);
+ params->type.data() + atomOffset,
+ numAtoms,
+ params->lj_comb.data() + atomOffset*2);
}
else if (XFormat == nbatXYZQ)
{
copy_lj_to_nbat_lj_comb<1>(params->nbfp_comb,
- params->type.data() + ash,
- ncz*grid.na_sc,
- params->lj_comb.data() + ash*2);
+ params->type.data() + atomOffset,
+ numAtoms,
+ params->lj_comb.data() + atomOffset*2);
}
}
}
nbat->paramsDeprecated().q.resize(nbat->numAtoms());
}
- for (const nbnxn_grid_t &grid : nbs->grid)
+ for (const Nbnxm::Grid &grid : nbs->grid)
{
/* Loop over all columns and copy and fill */
- for (int cxy = 0; cxy < grid.numCells[XX]*grid.numCells[YY]; cxy++)
+ for (int cxy = 0; cxy < grid.numColumns(); cxy++)
{
- int ash = (grid.cell0 + grid.cxy_ind[cxy])*grid.na_sc;
- int na = grid.cxy_na[cxy];
- int na_round = (grid.cxy_ind[cxy+1] - grid.cxy_ind[cxy])*grid.na_sc;
+ const int atomOffset = grid.firstAtomInColumn(cxy);
+ const int numAtoms = grid.numAtomsInColumn(cxy);
+ const int paddedNumAtoms = grid.paddedNumAtomsInColumn(cxy);
if (nbat->XFormat == nbatXYZQ)
{
- real *q = nbat->x().data() + ash*STRIDE_XYZQ + ZZ + 1;
+ real *q = nbat->x().data() + atomOffset*STRIDE_XYZQ + ZZ + 1;
int i;
- for (i = 0; i < na; i++)
+ for (i = 0; i < numAtoms; i++)
{
- *q = charge[nbs->a[ash+i]];
+ *q = charge[nbs->a[atomOffset + i]];
q += STRIDE_XYZQ;
}
/* Complete the partially filled last cell with zeros */
- for (; i < na_round; i++)
+ for (; i < paddedNumAtoms; i++)
{
*q = 0;
q += STRIDE_XYZQ;
}
else
{
- real *q = nbat->paramsDeprecated().q.data() + ash;
+ real *q = nbat->paramsDeprecated().q.data() + atomOffset;
int i;
- for (i = 0; i < na; i++)
+ for (i = 0; i < numAtoms; i++)
{
- *q = charge[nbs->a[ash+i]];
+ *q = charge[nbs->a[atomOffset + i]];
q++;
}
/* Complete the partially filled last cell with zeros */
- for (; i < na_round; i++)
+ for (; i < paddedNumAtoms; i++)
{
*q = 0;
q++;
stride_q = 1;
}
- for (const nbnxn_grid_t &grid : nbs->grid)
+ for (const Nbnxm::Grid &grid : nbs->grid)
{
int nsubc;
- if (grid.bSimple)
+ if (grid.geometry().isSimple)
{
nsubc = 1;
}
nsubc = c_gpuNumClusterPerCell;
}
- int c_offset = grid.cell0*grid.na_sc;
+ int c_offset = grid.firstAtomInColumn(0);
/* Loop over all columns and copy and fill */
- for (int c = 0; c < grid.nc*nsubc; c++)
+ for (int c = 0; c < grid.numCells()*nsubc; c++)
{
/* Does this cluster contain perturbed particles? */
- if (grid.fep[c] != 0)
+ if (grid.clusterIsPerturbed(c))
{
- for (int i = 0; i < grid.na_c; i++)
+ const int numAtomsPerCluster = grid.geometry().numAtomsICluster;
+ for (int i = 0; i < numAtomsPerCluster; i++)
{
/* Is this a perturbed particle? */
- if (grid.fep[c] & (1 << i))
+ if (grid.atomIsPerturbed(c, i))
{
- int ind = c_offset + c*grid.na_c + i;
+ int ind = c_offset + c*numAtomsPerCluster + i;
/* Set atom type and charge to non-interacting */
params.type[ind] = params.numTypes - 1;
q[ind*stride_q] = 0;
params->energrp.resize(numAtomsFromGrids(*nbs));
- for (const nbnxn_grid_t &grid : nbs->grid)
+ for (const Nbnxm::Grid &grid : nbs->grid)
{
/* Loop over all columns and copy and fill */
- for (int i = 0; i < grid.numCells[XX]*grid.numCells[YY]; i++)
+ for (int i = 0; i < grid.numColumns(); i++)
{
- int ncz = grid.cxy_ind[i+1] - grid.cxy_ind[i];
- int ash = (grid.cell0 + grid.cxy_ind[i])*grid.na_sc;
+ const int numAtoms = grid.paddedNumAtomsInColumn(i);
+ const int atomOffset = grid.firstAtomInColumn(i);
- copy_egp_to_nbat_egps(nbs->a.data() + ash, grid.cxy_na[i], ncz*grid.na_sc,
+ copy_egp_to_nbat_egps(nbs->a.data() + atomOffset, grid.numAtomsInColumn(i), numAtoms,
c_nbnxnCpuIClusterSize, params->neg_2log,
atinfo,
- params->energrp.data() + (ash >> grid.na_c_2log));
+ params->energrp.data() + grid.atomToCluster(atomOffset));
}
}
}
if (FillLocal)
{
- nbat->natoms_local = nbs->grid[0].nc*nbs->grid[0].na_sc;
+ nbat->natoms_local = nbs->grid[0].atomIndexEnd();
}
nth = gmx_omp_nthreads_get(emntPairsearch);
{
for (int g = g0; g < g1; g++)
{
- const nbnxn_grid_t &grid = nbs->grid[g];
- const int numCellsXY = grid.numCells[XX]*grid.numCells[YY];
+ const Nbnxm::Grid &grid = nbs->grid[g];
+ const int numCellsXY = grid.numColumns();
const int cxy0 = (numCellsXY* th + nth - 1)/nth;
const int cxy1 = (numCellsXY*(th + 1) + nth - 1)/nth;
for (int cxy = cxy0; cxy < cxy1; cxy++)
{
- int na, ash, na_fill;
-
- na = grid.cxy_na[cxy];
- ash = (grid.cell0 + grid.cxy_ind[cxy])*grid.na_sc;
+ const int na = grid.numAtomsInColumn(cxy);
+ const int ash = grid.firstAtomInColumn(cxy);
+ int na_fill;
if (g == 0 && FillLocal)
{
- na_fill =
- (grid.cxy_ind[cxy+1] - grid.cxy_ind[cxy])*grid.na_sc;
+ na_fill = grid.paddedNumAtomsInColumn(cxy);
}
else
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff