t_edpar *edi,
gmx_large_int_t step,
matrix box,
- t_commrec *cr)
+ t_commrec *cr,
+ gmx_bool bNS) /* Are we in a neighbor searching step? */
{
int i;
matrix rotmat; /* rotation matrix */
buf=edi->buf->do_edsam;
+
/* Broadcast the positions of the AVERAGE structure such that they are known on
* every processor. Each node contributes its local positions x and stores them in
* the collective ED array buf->xcoll */
- communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, buf->bUpdateShifts, x,
+ communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, bNS, x,
edi->sav.nr, edi->sav.nr_loc, edi->sav.anrs_loc, edi->sav.c_ind, edi->sav.x_old, box);
/* Only assembly REFERENCE positions if their indices differ from the average ones */
if (!edi->bRefEqAv)
- communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, buf->bUpdateShifts, x,
+ communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, bNS, x,
edi->sref.nr, edi->sref.nr_loc, edi->sref.anrs_loc, edi->sref.c_ind, edi->sref.x_old, box);
/* If bUpdateShifts was TRUE, the shifts have just been updated in get_positions.
rvec force[], /* forcefield forces, to these the flooding forces are added */
gmx_edsam_t ed, /* ed data structure contains all ED and flooding datasets */
matrix box, /* the box */
- gmx_large_int_t step) /* The relative time step since ir->init_step is already subtracted */
+ gmx_large_int_t step, /* The relative time step since ir->init_step is already subtracted */
+ gmx_bool bNS) /* Are we in a neighbor searching step? */
{
t_edpar *edi;
{
/* Call flooding for one matrix */
if (edi->flood.vecs.neig)
- do_single_flood(ed->edo,x,force,edi,step,box,cr);
+ do_single_flood(ed->edo,x,force,edi,step,box,cr,bNS);
edi = edi->next_edi;
}
}
/* allocate space for reference positions and read them */
snew(edi->sref.anrs,edi->sref.nr);
snew(edi->sref.x ,edi->sref.nr);
- if (PAR(cr))
- snew(edi->sref.x_old,edi->sref.nr);
+ snew(edi->sref.x_old,edi->sref.nr);
edi->sref.sqrtm =NULL;
read_edx(in,edi->sref.nr,edi->sref.anrs,edi->sref.x);
edi->sav.nr=read_checked_edint(in,"NAV");
snew(edi->sav.anrs,edi->sav.nr);
snew(edi->sav.x ,edi->sav.nr);
- if (PAR(cr))
- snew(edi->sav.x_old,edi->sav.nr);
+ snew(edi->sav.x_old,edi->sav.nr);
read_edx(in,edi->sav.nr,edi->sav.anrs,edi->sav.x);
/* Check if the same atom indices are used for reference and average positions */
{
copy_rvec(x_pbc[edi->sref.anrs[i]], xfit[i]);
- /* Save the sref positions such that in the next time step the molecule can
- * be made whole again (in the parallel case) */
- if (PAR(cr))
- copy_rvec(xfit[i], edi->sref.x_old[i]);
+ /* Save the sref positions such that in the next time step we can make the ED group whole
+ * in case any of the atoms do not have the correct PBC representation */
+ copy_rvec(xfit[i], edi->sref.x_old[i]);
}
/* Extract the positions of the atoms subject to ED sampling */
{
copy_rvec(x_pbc[edi->sav.anrs[i]], xstart[i]);
- /* Save the sav positions such that in the next time step the molecule can
- * be made whole again (in the parallel case) */
- if (PAR(cr))
- copy_rvec(xstart[i], edi->sav.x_old[i]);
+ /* Save the sav positions such that in the next time step we can make the ED group whole
+ * in case any of the atoms do not have the correct PBC representation */
+ copy_rvec(xstart[i], edi->sav.x_old[i]);
}
/* Make the fit to the REFERENCE structure, get translation and rotation */
/* calculate initial projections */
project(xstart, edi);
+ /* For the target and origin structure both a reference (fit) and an
+ * average structure can be provided in make_edi. If both structures
+ * are the same, make_edi only stores one of them in the .edi file.
+ * If they differ, first the fit and then the average structure is stored
+ * in star (or sor), thus the number of entries in star/sor is
+ * (n_fit + n_av) with n_fit the size of the fitting group and n_av
+ * the size of the average group. */
+
/* process target structure, if required */
if (edi->star.nr > 0)
{
* the collective buf->xcoll array. Note that for edinr > 1
* xs could already have been modified by an earlier ED */
- communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, buf->bUpdateShifts, xs,
+ communicate_group_positions(cr, buf->xcoll, buf->shifts_xcoll, buf->extra_shifts_xcoll, PAR(cr) ? buf->bUpdateShifts : TRUE, xs,
edi->sav.nr, edi->sav.nr_loc, edi->sav.anrs_loc, edi->sav.c_ind, edi->sav.x_old, box);
#ifdef DEBUG_ED
#endif
/* Only assembly reference positions if their indices differ from the average ones */
if (!edi->bRefEqAv)
- communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, buf->bUpdateShifts, xs,
+ communicate_group_positions(cr, buf->xc_ref, buf->shifts_xc_ref, buf->extra_shifts_xc_ref, PAR(cr) ? buf->bUpdateShifts : TRUE, xs,
edi->sref.nr, edi->sref.nr_loc, edi->sref.anrs_loc, edi->sref.c_ind, edi->sref.x_old, box);
- /* If bUpdateShifts was TRUE then the shifts have just been updated in get_positions.
- * We do not need to uptdate the shifts until the next NS step */
+ /* If bUpdateShifts was TRUE then the shifts have just been updated in communicate_group_positions.
+ * We do not need to update the shifts until the next NS step. Note that dd_make_local_ed_indices
+ * set bUpdateShifts=TRUE in the parallel case. */
buf->bUpdateShifts = FALSE;
/* Now all nodes have all of the ED positions in edi->sav->xcoll,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff