void Corr3::
deposit (const std::vector<std::vector<ValueType> > & coord,
const VectorType & box,
const CellList & clist)
{
int xiter = rup / clist.getCellSize().x;
if (xiter * clist.getCellSize().x < rup) xiter ++;
int yiter = rup / clist.getCellSize().y;
if (yiter * clist.getCellSize().y < rup) yiter ++;
int ziter = rup / clist.getCellSize().z;
if (ziter * clist.getCellSize().z < rup) ziter ++;
IntVectorType nCell = clist.getNumCell();
ValueType myNatom = 0.;
printf ("\n");
for (unsigned iCellIndex = 0; iCellIndex < unsigned(nCell.x * nCell.y * nCell.z); ++iCellIndex){
// myNatom += clist.getList()[iCellIndex].size();
printf ("## calculating cell %d in %d \r",
iCellIndex, unsigned(nCell.x * nCell.y * nCell.z));
fflush (stdout);
std::vector<unsigned > neighborCellIndex =
clist.neighboringCellIndex (iCellIndex, IntVectorType (xiter, yiter, ziter));
for (unsigned iNeighborCellIndex = 0; iNeighborCellIndex < neighborCellIndex.size(); ++iNeighborCellIndex){
unsigned jCellIndex = neighborCellIndex[iNeighborCellIndex];
for (unsigned ii = 0; ii < clist.getList()[iCellIndex].size(); ++ii){
VectorType icoord;
icoord.x = coord[clist.getList()[iCellIndex][ii]][0];
if (x1 != 0. && (!(icoord.x >= x0 && icoord.x < x1))) continue;
if (iNeighborCellIndex == 0) myNatom += 1.;
icoord.y = coord[clist.getList()[iCellIndex][ii]][1];
icoord.z = coord[clist.getList()[iCellIndex][ii]][2];
bool sameCell (iCellIndex == jCellIndex);
for (unsigned jj = 0; jj < clist.getList()[jCellIndex].size(); ++jj){
if (sameCell && ii == jj) continue;
VectorType jcoord;
jcoord.x = coord[clist.getList()[jCellIndex][jj]][0];
jcoord.y = coord[clist.getList()[jCellIndex][jj]][1];
jcoord.z = coord[clist.getList()[jCellIndex][jj]][2];
VectorType diff;
diff.x = - icoord.x + jcoord.x;
diff.y = - icoord.y + jcoord.y;
diff.z = - icoord.z + jcoord.z;
if (diff.x < -.5 * box.x) diff.x += box.x;
else if (diff.x >= .5 * box.x) diff.x -= box.x;
if (diff.y < -.5 * box.y) diff.y += box.y;
else if (diff.y >= .5 * box.y) diff.y -= box.y;
if (diff.z < -.5 * box.z) diff.z += box.z;
else if (diff.z >= .5 * box.z) diff.z -= box.z;
ValueType dr = diff.x * diff.x + diff.y * diff.y + diff.z * diff.z;
dr = sqrt (dr);
unsigned index = (dr + offset) / binSize;
if (dr < rup){
if (index >= unsigned(nbins)){
// printf ("# dr: %f, index: %d, rup: %f, nbins: %d\n",
// dr, index, rup, nbins);
index = nbins - 1;
}
hist[index] += 1.;
double tmpx = h1extend + rup;
// if (tmpx < rup) tmpx = rup;
double body3range = sqrt(tmpx * tmpx + h2extend * h2extend);
int body3xiter = body3range / clist.getCellSize().x;
if (body3xiter * clist.getCellSize().x < body3range) body3xiter ++;
int body3yiter = body3range / clist.getCellSize().y;
if (body3yiter * clist.getCellSize().y < body3range) body3yiter ++;
int body3ziter = body3range / clist.getCellSize().z;
if (body3ziter * clist.getCellSize().z < body3range) body3ziter ++;
std::vector<unsigned > body3NeighborCellIndex =
clist.neighboringCellIndex (iCellIndex, IntVectorType (body3xiter, body3yiter, body3ziter));
for (unsigned ibody3Cell = 0; ibody3Cell < body3NeighborCellIndex.size(); ++ibody3Cell){
unsigned kCellIndex = body3NeighborCellIndex[ibody3Cell];
for (unsigned kk = 0; kk < clist.getList()[kCellIndex].size(); ++kk){
if (clist.getList()[iCellIndex][ii] == clist.getList()[kCellIndex][kk] ||
clist.getList()[jCellIndex][jj] == clist.getList()[kCellIndex][kk] ) continue;
VectorType kcoord;
kcoord.x = coord[clist.getList()[kCellIndex][kk]][0];
kcoord.y = coord[clist.getList()[kCellIndex][kk]][1];
kcoord.z = coord[clist.getList()[kCellIndex][kk]][2];
VectorType diff2;
diff2.x = - icoord.x + kcoord.x;
diff2.y = - icoord.y + kcoord.y;
diff2.z = - icoord.z + kcoord.z;
if (diff2.x < -.5 * box.x) diff2.x += box.x;
else if (diff2.x >= .5 * box.x) diff2.x -= box.x;
if (diff2.y < -.5 * box.y) diff2.y += box.y;
else if (diff2.y >= .5 * box.y) diff2.y -= box.y;
if (diff2.z < -.5 * box.z) diff2.z += box.z;
else if (diff2.z >= .5 * box.z) diff2.z -= box.z;
double h1 = (diff.x * diff2.x +
diff.y * diff2.y +
diff.z * diff2.z ) / dr;
if (h1 <= h1low || h1 >= h1up) continue;
double dr22 = (diff2.x * diff2.x + diff2.y * diff2.y + diff2.z * diff2.z);
double h2 = sqrt(dr22 - h1 * h1);
if (h2 >= h2extend) continue;
dists[index].deposit (h1, h2);
}
}
}
}
}
}
}
printf ("\n");
nframe ++;
if (x1 == x0){
rho += myNatom / (box.x * box.y * box.z);
}
else {
rho += myNatom / ((x1 - x0) * box.y * box.z);
}
natom += myNatom;
}
