/* Assemble the positions of the group such that every node has all of them.
* The atom indices are retrieved from anrs_loc[0..nr_loc]
* Note that coll_ind[i] = i is needed in the serial case */
extern void communicate_group_positions(
t_commrec *cr,
rvec *xcoll, /* OUT: Collective array of positions */
ivec *shifts, /* IN+OUT: Collective array of shifts for xcoll */
ivec *extra_shifts, /* BUF: Extra shifts since last time step */
const gmx_bool bNS, /* IN: NS step, the shifts have changed */
rvec *x_loc, /* IN: Local positions on this node */
const int nr, /* IN: Total number of atoms in the group */
const int nr_loc, /* IN: Local number of atoms in the group */
int *anrs_loc, /* IN: Local atom numbers */
int *coll_ind, /* IN: Collective index */
rvec *xcoll_old, /* IN+OUT: Positions from the last time step, used to make group whole */
matrix box)
{
int i;
/* Zero out the groups' global position array */
clear_rvecs(nr, xcoll);
/* Put the local positions that this node has into the right place of
* the collective array. Note that in the serial case, coll_ind[i] = i */
for (i=0; i<nr_loc; i++)
copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
if (PAR(cr))
{
/* Add the arrays from all nodes together */
gmx_sum(nr*3, xcoll[0], cr);
}
/* To make the group whole, start with a whole group and each
* step move the assembled positions at closest distance to the positions
* from the last step. First shift the positions with the saved shift
* vectors (these are 0 when this routine is called for the first time!) */
shift_positions_group(box, xcoll, shifts, nr);
/* Now check if some shifts changed since the last step.
* This only needs to be done when the shifts are expected to have changed,
* i.e. after neighboursearching */
if (bNS)
{
get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
/* Shift with the additional shifts such that we get a whole group now */
shift_positions_group(box, xcoll, extra_shifts, nr);
/* Add the shift vectors together for the next time step */
for (i=0; i<nr; i++)
{
shifts[i][XX] += extra_shifts[i][XX];
shifts[i][YY] += extra_shifts[i][YY];
shifts[i][ZZ] += extra_shifts[i][ZZ];
}
/* Store current correctly-shifted positions for comparison in the next NS time step */
for (i=0; i<nr; i++)
copy_rvec(xcoll[i],xcoll_old[i]);
}
}
/* Assemble the positions of the group such that every node has all of them.
* The atom indices are retrieved from anrs_loc[0..nr_loc]
* Note that coll_ind[i] = i is needed in the serial case */
extern void communicate_group_positions(
const t_commrec *cr, /* Pointer to MPI communication data */
rvec *xcoll, /* Collective array of positions */
ivec *shifts, /* Collective array of shifts for xcoll (can be NULL) */
ivec *extra_shifts, /* (optional) Extra shifts since last time step */
const gmx_bool bNS, /* (optional) NS step, the shifts have changed */
const rvec *x_loc, /* Local positions on this node */
const int nr, /* Total number of atoms in the group */
const int nr_loc, /* Local number of atoms in the group */
const int *anrs_loc, /* Local atom numbers */
const int *coll_ind, /* Collective index */
rvec *xcoll_old, /* (optional) Positions from the last time step,
used to make group whole */
const matrix box) /* (optional) The box */
{
int i;
/* Zero out the groups' global position array */
clear_rvecs(nr, xcoll);
/* Put the local positions that this node has into the right place of
* the collective array. Note that in the serial case, coll_ind[i] = i */
for (i = 0; i < nr_loc; i++)
{
copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
}
if (PAR(cr))
{
/* Add the arrays from all nodes together */
gmx_sum(nr*3, xcoll[0], cr);
}
/* Now we have all the positions of the group in the xcoll array present on all
* nodes.
*
* The rest of the code is for making the group whole again in case atoms changed
* their PBC representation / crossed a box boundary. We only do that if the
* shifts array is allocated. */
if (nullptr != shifts)
{
/* To make the group whole, start with a whole group and each
* step move the assembled positions at closest distance to the positions
* from the last step. First shift the positions with the saved shift
* vectors (these are 0 when this routine is called for the first time!) */
shift_positions_group(box, xcoll, shifts, nr);
/* Now check if some shifts changed since the last step.
* This only needs to be done when the shifts are expected to have changed,
* i.e. after neighbor searching */
if (bNS)
{
get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
/* Shift with the additional shifts such that we get a whole group now */
shift_positions_group(box, xcoll, extra_shifts, nr);
/* Add the shift vectors together for the next time step */
for (i = 0; i < nr; i++)
{
shifts[i][XX] += extra_shifts[i][XX];
shifts[i][YY] += extra_shifts[i][YY];
shifts[i][ZZ] += extra_shifts[i][ZZ];
}
/* Store current correctly-shifted positions for comparison in the next NS time step */
for (i = 0; i < nr; i++)
{
copy_rvec(xcoll[i], xcoll_old[i]);
}
}
}
}