void grid_last(t_grid *grid, int cg0, int cg1, int ncg)
{
int CG0[2], CG1[2];
int i, m;
int ci, not_used, ind, ncells;
int *cell_index = grid->cell_index;
int *nra = grid->nra;
int *index = grid->index;
int *a = grid->a;
ncells = grid->ncells;
if (ncells <= 0)
{
gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
}
not_used = ci_not_used(grid->n);
calc_bor(cg0, cg1, ncg, CG0, CG1);
for (m = 0; (m < 2); m++)
{
for (i = CG0[m]; (i < CG1[m]); i++)
{
ci = cell_index[i];
if (ci != not_used)
{
range_check_mesg(ci, 0, ncells, range_warn);
ind = index[ci]+nra[ci]++;
range_check_mesg(ind, 0, grid->nr, range_warn);
a[ind] = i;
}
}
}
}
void calc_ptrs(t_grid *grid)
{
int *index = grid->index;
int *nra = grid->nra;
int ix, iy, iz, ci, nr;
int nnra, ncells;
ncells = grid->ncells;
if (ncells <= 0)
{
gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
}
ci = nr = 0;
for (ix = 0; (ix < grid->n[XX]); ix++)
{
for (iy = 0; (iy < grid->n[YY]); iy++)
{
for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
{
range_check_mesg(ci, 0, ncells, range_warn);
index[ci] = nr;
nnra = nra[ci];
nr += nnra;
nra[ci] = 0;
}
}
}
}
void ci2xyz(t_grid *grid, int i, int *x, int *y, int *z)
/* Return x,y and z from the cell index */
{
int ci;
range_check_mesg(i, 0, grid->nr, range_warn);
ci = grid->cell_index[i];
*x = ci / (grid->n[YY]*grid->n[ZZ]);
ci -= (*x)*grid->n[YY]*grid->n[ZZ];
*y = ci / grid->n[ZZ];
ci -= (*y)*grid->n[ZZ];
*z = ci;
}
void check_grid(t_grid *grid)
{
int ix, iy, iz, ci, cci, nra;
if (grid->ncells <= 0)
{
gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
}
ci = 0;
cci = 0;
for (ix = 0; (ix < grid->n[XX]); ix++)
{
for (iy = 0; (iy < grid->n[YY]); iy++)
{
for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
{
if (ci > 0)
{
nra = grid->index[ci]-grid->index[cci];
if (nra != grid->nra[cci])
{
gmx_fatal(FARGS, "nra=%d, grid->nra=%d, cci=%d",
nra, grid->nra[cci], cci);
}
}
cci = xyz2ci(grid->n[YY], grid->n[ZZ], ix, iy, iz);
range_check_mesg(cci, 0, grid->ncells, range_warn);
if (cci != ci)
{
gmx_fatal(FARGS, "ci = %d, cci = %d", ci, cci);
}
}
}
}
}
int pbc_dx_aiuc(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx)
{
int i, j, is;
rvec dx_start, trial;
real d2min, d2trial;
ivec ishift, ishift_start;
rvec_sub(x1, x2, dx);
clear_ivec(ishift);
switch (pbc->ePBCDX)
{
case epbcdxRECTANGULAR:
for (i = 0; i < DIM; i++)
{
if (dx[i] > pbc->hbox_diag[i])
{
dx[i] -= pbc->fbox_diag[i];
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
dx[i] += pbc->fbox_diag[i];
ishift[i]++;
}
}
break;
case epbcdxTRICLINIC:
/* For triclinic boxes the performance difference between
* if/else and two while loops is negligible.
* However, the while version can cause extreme delays
* before a simulation crashes due to large forces which
* can cause unlimited displacements.
* Also allowing multiple shifts would index fshift beyond bounds.
*/
for (i = DIM-1; i >= 1; i--)
{
if (dx[i] > pbc->hbox_diag[i])
{
for (j = i; j >= 0; j--)
{
dx[j] -= pbc->box[i][j];
}
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
for (j = i; j >= 0; j--)
{
dx[j] += pbc->box[i][j];
}
ishift[i]++;
}
}
/* Allow 2 shifts in x */
if (dx[XX] > pbc->hbox_diag[XX])
{
dx[XX] -= pbc->fbox_diag[XX];
ishift[XX]--;
if (dx[XX] > pbc->hbox_diag[XX])
{
dx[XX] -= pbc->fbox_diag[XX];
ishift[XX]--;
}
}
else if (dx[XX] <= pbc->mhbox_diag[XX])
{
dx[XX] += pbc->fbox_diag[XX];
ishift[XX]++;
if (dx[XX] <= pbc->mhbox_diag[XX])
{
dx[XX] += pbc->fbox_diag[XX];
ishift[XX]++;
}
}
/* dx is the distance in a rectangular box */
d2min = norm2(dx);
if (d2min > pbc->max_cutoff2)
{
copy_rvec(dx, dx_start);
copy_ivec(ishift, ishift_start);
d2min = norm2(dx);
/* Now try all possible shifts, when the distance is within max_cutoff
* it must be the shortest possible distance.
*/
i = 0;
while ((d2min > pbc->max_cutoff2) && (i < pbc->ntric_vec))
{
rvec_add(dx_start, pbc->tric_vec[i], trial);
d2trial = norm2(trial);
if (d2trial < d2min)
{
copy_rvec(trial, dx);
ivec_add(ishift_start, pbc->tric_shift[i], ishift);
d2min = d2trial;
}
i++;
}
}
break;
case epbcdx2D_RECT:
for (i = 0; i < DIM; i++)
{
if (i != pbc->dim)
{
if (dx[i] > pbc->hbox_diag[i])
{
dx[i] -= pbc->fbox_diag[i];
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
dx[i] += pbc->fbox_diag[i];
ishift[i]++;
}
}
}
break;
case epbcdx2D_TRIC:
d2min = 0;
for (i = DIM-1; i >= 1; i--)
{
if (i != pbc->dim)
{
if (dx[i] > pbc->hbox_diag[i])
{
for (j = i; j >= 0; j--)
{
dx[j] -= pbc->box[i][j];
}
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
for (j = i; j >= 0; j--)
{
dx[j] += pbc->box[i][j];
}
ishift[i]++;
}
d2min += dx[i]*dx[i];
}
}
if (pbc->dim != XX)
{
/* Allow 2 shifts in x */
if (dx[XX] > pbc->hbox_diag[XX])
{
dx[XX] -= pbc->fbox_diag[XX];
ishift[XX]--;
if (dx[XX] > pbc->hbox_diag[XX])
{
dx[XX] -= pbc->fbox_diag[XX];
ishift[XX]--;
}
}
else if (dx[XX] <= pbc->mhbox_diag[XX])
{
dx[XX] += pbc->fbox_diag[XX];
ishift[XX]++;
if (dx[XX] <= pbc->mhbox_diag[XX])
{
dx[XX] += pbc->fbox_diag[XX];
ishift[XX]++;
}
}
d2min += dx[XX]*dx[XX];
}
if (d2min > pbc->max_cutoff2)
{
copy_rvec(dx, dx_start);
copy_ivec(ishift, ishift_start);
/* Now try all possible shifts, when the distance is within max_cutoff
* it must be the shortest possible distance.
*/
i = 0;
while ((d2min > pbc->max_cutoff2) && (i < pbc->ntric_vec))
{
rvec_add(dx_start, pbc->tric_vec[i], trial);
d2trial = 0;
for (j = 0; j < DIM; j++)
{
if (j != pbc->dim)
{
d2trial += trial[j]*trial[j];
}
}
if (d2trial < d2min)
{
copy_rvec(trial, dx);
ivec_add(ishift_start, pbc->tric_shift[i], ishift);
d2min = d2trial;
}
i++;
}
}
break;
case epbcdx1D_RECT:
i = pbc->dim;
if (dx[i] > pbc->hbox_diag[i])
{
dx[i] -= pbc->fbox_diag[i];
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
dx[i] += pbc->fbox_diag[i];
ishift[i]++;
}
break;
case epbcdx1D_TRIC:
i = pbc->dim;
if (dx[i] > pbc->hbox_diag[i])
{
rvec_dec(dx, pbc->box[i]);
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
rvec_inc(dx, pbc->box[i]);
ishift[i]++;
}
break;
case epbcdxSCREW_RECT:
/* The shift definition requires x first */
if (dx[XX] > pbc->hbox_diag[XX])
{
dx[XX] -= pbc->fbox_diag[XX];
ishift[XX]--;
}
else if (dx[XX] <= pbc->mhbox_diag[XX])
{
dx[XX] += pbc->fbox_diag[XX];
ishift[XX]++;
}
if (ishift[XX] == 1 || ishift[XX] == -1)
{
/* Rotate around the x-axis in the middle of the box */
dx[YY] = pbc->box[YY][YY] - x1[YY] - x2[YY];
dx[ZZ] = pbc->box[ZZ][ZZ] - x1[ZZ] - x2[ZZ];
}
/* Normal pbc for y and z */
for (i = YY; i <= ZZ; i++)
{
if (dx[i] > pbc->hbox_diag[i])
{
dx[i] -= pbc->fbox_diag[i];
ishift[i]--;
}
else if (dx[i] <= pbc->mhbox_diag[i])
{
dx[i] += pbc->fbox_diag[i];
ishift[i]++;
}
}
break;
case epbcdxNOPBC:
case epbcdxUNSUPPORTED:
break;
default:
gmx_fatal(FARGS, "Internal error in pbc_dx_aiuc, set_pbc_dd or set_pbc has not been called");
break;
}
is = IVEC2IS(ishift);
if (debug)
{
range_check_mesg(is, 0, SHIFTS, "PBC shift vector index range check.");
}
return is;
}
