-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- * 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.
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
* 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.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Groningen Machine for Chemical Simulation
+ * 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))
+#define MIN(a, b) (((a) < (b)) ? (a) : (b))
-/* Select the indices of the group's atoms which are local and store them in
+/* Select the indices of the group's atoms which are local and store them in
* anrs_loc[0..nr_loc]. The indices are saved in coll_ind[] for later reduction
* in communicate_group_positions()
*/
extern void dd_make_local_group_indices(
- gmx_ga2la_t ga2la,
- const int nr, /* IN: Total number of atoms in the group */
- int anrs[], /* IN: Global atom numbers of the groups atoms */
+ gmx_ga2la_t ga2la,
+ const int nr, /* IN: Total number of atoms in the group */
+ int anrs[], /* IN: Global atom numbers of the groups atoms */
int *nr_loc, /* OUT: Number of group atoms found locally */
int *anrs_loc[], /* OUT: Local atom numbers of the group */
int *nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
- int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
+ int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
{
- int i,ii;
- int localnr;
+ int i, ii;
+ int localnr;
+
-
/* Loop over all the atom indices of the group to check
* which ones are on the local node */
localnr = 0;
- for(i=0; i<nr; i++)
+ for (i = 0; i < nr; i++)
{
- if (ga2la_get_home(ga2la,anrs[i],&ii))
+ if (ga2la_get_home(ga2la, anrs[i], &ii))
{
/* The atom with this index is a home atom */
if (localnr >= *nalloc_loc) /* Check whether memory suffices */
*nalloc_loc = over_alloc_dd(localnr+1);
/* We never need more memory than the number of atoms in the group */
*nalloc_loc = MIN(*nalloc_loc, nr);
- srenew(*anrs_loc,*nalloc_loc);
+ srenew(*anrs_loc, *nalloc_loc);
}
/* Save the atoms index in the local atom numbers array */
(*anrs_loc)[localnr] = ii;
localnr++;
}
}
-
+
/* Return the number of local atoms that were found */
*nr_loc = localnr;
}
static void get_shifts_group(
- int npbcdim,
- matrix box,
+ int npbcdim,
+ matrix box,
rvec *xcoll, /* IN: Collective set of positions [0..nr] */
- int nr, /* IN: Total number of atoms in the group */
+ int nr, /* IN: Total number of atoms in the group */
rvec *xcoll_old, /* IN: Positions from the last time step [0...nr] */
ivec *shifts) /* OUT: Shifts for xcoll */
{
- int i,m,d;
+ int i, m, d;
rvec dx;
/* Get the shifts such that each atom is within closest
* distance to its position at the last NS time step after shifting.
- * If we start with a whole group, and always keep track of
+ * If we start with a whole group, and always keep track of
* shift changes, the group will stay whole this way */
- for (i=0; i < nr; i++)
+ for (i = 0; i < nr; i++)
+ {
clear_ivec(shifts[i]);
+ }
- for (i=0; i<nr; i++)
+ for (i = 0; i < nr; i++)
{
/* The distance this atom moved since the last time step */
/* If this is more than just a bit, it has changed its home pbc box */
- rvec_sub(xcoll[i],xcoll_old[i],dx);
+ rvec_sub(xcoll[i], xcoll_old[i], dx);
- for(m=npbcdim-1; m>=0; m--)
+ for (m = npbcdim-1; m >= 0; m--)
{
while (dx[m] < -0.5*box[m][m])
{
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
+ {
dx[d] += box[m][d];
+ }
shifts[i][m]++;
}
while (dx[m] >= 0.5*box[m][m])
{
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
+ {
dx[d] -= box[m][d];
+ }
shifts[i][m]--;
}
}
static void shift_positions_group(
- matrix box,
- rvec x[], /* The positions [0..nr] */
- ivec *is, /* The shifts [0..nr] */
- int nr) /* The number of positions and shifts */
+ matrix box,
+ rvec x[], /* The positions [0..nr] */
+ ivec *is, /* The shifts [0..nr] */
+ int nr) /* The number of positions and shifts */
{
- int i,tx,ty,tz;
+ int i, tx, ty, tz;
/* Loop over the group's atoms */
- if(TRICLINIC(box))
+ if (TRICLINIC(box))
{
- for (i=0; i < nr; i++)
+ for (i = 0; i < nr; i++)
{
- tx=is[i][XX];
- ty=is[i][YY];
- tz=is[i][ZZ];
+ tx = is[i][XX];
+ ty = is[i][YY];
+ tz = is[i][ZZ];
- x[i][XX]=x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
- x[i][YY]=x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
- x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
+ x[i][XX] = x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
+ x[i][YY] = x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
+ x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
}
- } else
+ }
+ else
{
- for (i=0; i < nr; i++)
+ for (i = 0; i < nr; i++)
{
- tx=is[i][XX];
- ty=is[i][YY];
- tz=is[i][ZZ];
+ tx = is[i][XX];
+ ty = is[i][YY];
+ tz = is[i][ZZ];
- x[i][XX]=x[i][XX]+tx*box[XX][XX];
- x[i][YY]=x[i][YY]+ty*box[YY][YY];
- x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
+ x[i][XX] = x[i][XX]+tx*box[XX][XX];
+ x[i][YY] = x[i][YY]+ty*box[YY][YY];
+ x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
}
- }
+ }
}
-/* 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]
+/* 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)
+ 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;
/* Zero out the groups' global position array */
clear_rvecs(nr, xcoll);
- /* Put the local positions that this node has into the right place of
+ /* 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++)
+ 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)
+ /* 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]);
+ }
+ }
}
}
/* Determine the (weighted) sum vector from positions x */
extern double get_sum_of_positions(rvec x[], real weight[], const int nat, dvec dsumvec)
{
- int i;
- rvec x_weighted;
+ int i;
+ rvec x_weighted;
double weight_sum = 0.0;
/* Loop over all atoms and add their weighted position vectors */
if (weight != NULL)
{
- for (i=0; i<nat; i++)
+ for (i = 0; i < nat; i++)
{
weight_sum += weight[i];
svmul(weight[i], x[i], x_weighted);
}
else
{
- for (i=0; i<nat; i++)
+ for (i = 0; i < nat; i++)
{
dsumvec[XX] += x[i][XX];
dsumvec[YY] += x[i][YY];
dvec dcenter;
double weight_sum, denom;
-
+
weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
-
+
if (weight != NULL)
+ {
denom = weight_sum; /* Divide by the sum of weight */
+ }
else
+ {
denom = nr; /* Divide by the number of atoms */
-
+
+ }
dsvmul(1.0/denom, dcenter, dcenter);
-
+
rcenter[XX] = dcenter[XX];
rcenter[YY] = dcenter[YY];
rcenter[ZZ] = dcenter[ZZ];
* PBC representation */
extern void get_center_comm(
t_commrec *cr,
- rvec x_loc[], /* Local positions */
- real weight_loc[], /* Local masses or other weights */
- int nr_loc, /* Local number of atoms */
- int nr_group, /* Total number of atoms of the group */
- rvec center) /* Weighted center */
+ rvec x_loc[], /* Local positions */
+ real weight_loc[], /* Local masses or other weights */
+ int nr_loc, /* Local number of atoms */
+ int nr_group, /* Total number of atoms of the group */
+ rvec center) /* Weighted center */
{
double weight_sum, denom;
dvec dsumvec;
- double buf[4];
-
-
+ double buf[4];
+
+
weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
-
- /* Add the local contributions from all nodes. Put the sum vector and the
+
+ /* Add the local contributions from all nodes. Put the sum vector and the
* weight in a buffer array so that we get along with a single communication
* call. */
if (PAR(cr))
buf[1] = dsumvec[YY];
buf[2] = dsumvec[ZZ];
buf[3] = weight_sum;
-
+
/* Communicate buffer */
gmx_sumd(4, buf, cr);
-
+
dsumvec[XX] = buf[0];
dsumvec[YY] = buf[1];
dsumvec[ZZ] = buf[2];
weight_sum = buf[3];
}
-
+
if (weight_loc != NULL)
+ {
denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
+ }
else
+ {
denom = 1.0/nr_group; /* Divide by the number of atoms to get the geometrical center */
-
+
+ }
center[XX] = dsumvec[XX]*denom;
center[YY] = dsumvec[YY]*denom;
center[ZZ] = dsumvec[ZZ]*denom;
extern void translate_x(rvec x[], const int nr, const rvec transvec)
{
int i;
-
-
- for (i=0; i<nr; i++)
+
+
+ for (i = 0; i < nr; i++)
+ {
rvec_inc(x[i], transvec);
+ }
}
extern void rotate_x(rvec x[], const int nr, matrix rmat)
{
- int i,j,k;
+ int i, j, k;
rvec x_old;
-
+
/* Apply the rotation matrix */
- for (i=0; i<nr; i++)
+ for (i = 0; i < nr; i++)
{
- for (j=0; j<3; j++)
+ for (j = 0; j < 3; j++)
+ {
x_old[j] = x[i][j];
- for (j=0; j<3; j++)
+ }
+ for (j = 0; j < 3; j++)
{
x[i][j] = 0;
- for (k=0; k<3; k++)
+ for (k = 0; k < 3; k++)
+ {
x[i][j] += rmat[k][j]*x_old[k];
+ }
}
}
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff