-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 4.5
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * Groningen Machine for Chemical Simulation
+ * 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