*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
#include "groupcoord.h"
-#include "network.h"
-#include "pbc.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "gmx_ga2la.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
#define MIN(a, b) (((a) < (b)) ? (a) : (b))
* 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)
+ 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 */
+ 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 */
+ int *anrs_loc, /* Local atom numbers */
+ int *coll_ind, /* Collective index */
+ rvec *xcoll_old, /* (optional) Positions from the last time step,
+ used to make group whole */
+ matrix box) /* (optional) The box */
{
int i;
/* 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)
+ /* 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 (NULL != shifts)
{
- get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_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);
+ /* 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];
- }
+ /* 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]);
+ /* 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]);
+ }
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff