*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017,2018,2019, 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.
#define MIN(a, b) (((a) < (b)) ? (a) : (b))
-
/* 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()
*/
-void
-dd_make_local_group_indices(const 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? */
+void dd_make_local_group_indices(const 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? */
{
GMX_ASSERT(ga2la, "We need a valid ga2la object");
int localnr = 0;
for (int i = 0; i < nr; i++)
{
- if (const int *ii = ga2la->findHome(anrs[i]))
+ if (const int* ii = ga2la->findHome(anrs[i]))
{
/* The atom with this index is a home atom */
if (localnr >= *nalloc_loc) /* Check whether memory suffices */
{
- *nalloc_loc = over_alloc_dd(localnr+1);
+ *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);
}
-static void get_shifts_group(
- int npbcdim,
- const matrix box,
- rvec *xcoll, /* IN: Collective set of positions [0..nr] */
- 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 */
+static void get_shifts_group(int npbcdim,
+ const matrix box,
+ rvec* xcoll, /* IN: Collective set of positions [0..nr] */
+ 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;
rvec dx;
/* If this is more than just a bit, it has changed its home pbc box */
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])
+ while (dx[m] < -0.5 * box[m][m])
{
for (d = 0; d < DIM; d++)
{
}
shifts[i][m]++;
}
- while (dx[m] >= 0.5*box[m][m])
+ while (dx[m] >= 0.5 * box[m][m])
{
for (d = 0; d < DIM; d++)
{
}
-static void shift_positions_group(
- const matrix box,
- rvec x[], /* The positions [0..nr] */
- ivec *is, /* The shifts [0..nr] */
- int nr) /* The number of positions and shifts */
+static void shift_positions_group(const 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 */
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
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]
* 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 */
+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;
if (PAR(cr))
{
/* Add the arrays from all nodes together */
- gmx_sum(nr*3, xcoll[0], cr);
+ gmx_sum(nr * 3, xcoll[0], cr);
}
/* Now we have all the positions of the group in the xcoll array present on all
* nodes.
}
else
{
- denom = nr; /* Divide by the number of atoms */
-
+ denom = nr; /* Divide by the number of atoms */
}
- dsvmul(1.0/denom, dcenter, dcenter);
+ dsvmul(1.0 / denom, dcenter, dcenter);
rcenter[XX] = dcenter[XX];
rcenter[YY] = dcenter[YY];
/* Get the center from local positions that already have the correct
* PBC representation */
-extern void get_center_comm(
- const 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 */
+extern void get_center_comm(const 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 */
{
double weight_sum, denom;
dvec dsumvec;
if (weight_loc != nullptr)
{
- denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
+ 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 */
-
+ 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;
+ center[XX] = dsumvec[XX] * denom;
+ center[YY] = dsumvec[YY] * denom;
+ center[ZZ] = dsumvec[ZZ] * denom;
}
x[i][j] = 0;
for (k = 0; k < 3; k++)
{
- x[i][j] += rmat[k][j]*x_old[k];
+ x[i][j] += rmat[k][j] * x_old[k];
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff