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43 #include "groupcoord.h"
44 #include "mpelogging.h"
49 #include "gmx_ga2la.h"
51 #define MIN(a,b) (((a)<(b))?(a):(b))
55 /* Select the indices of the group's atoms which are local and store them in
56 * anrs_loc[0..nr_loc]. The indices are saved in coll_ind[] for later reduction
57 * in communicate_group_positions()
59 extern void dd_make_local_group_indices(
61 const int nr, /* IN: Total number of atoms in the group */
62 int anrs[], /* IN: Global atom numbers of the groups atoms */
63 int *nr_loc, /* OUT: Number of group atoms found locally */
64 int *anrs_loc[], /* OUT: Local atom numbers of the group */
65 int *nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
66 int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
72 /* Loop over all the atom indices of the group to check
73 * which ones are on the local node */
77 if (ga2la_get_home(ga2la,anrs[i],&ii))
79 /* The atom with this index is a home atom */
80 if (localnr >= *nalloc_loc) /* Check whether memory suffices */
82 *nalloc_loc = over_alloc_dd(localnr+1);
83 /* We never need more memory than the number of atoms in the group */
84 *nalloc_loc = MIN(*nalloc_loc, nr);
85 srenew(*anrs_loc,*nalloc_loc);
87 /* Save the atoms index in the local atom numbers array */
88 (*anrs_loc)[localnr] = ii;
92 /* Keep track of where this local atom belongs in the collective index array.
93 * This is needed when reducing the local arrays to a collective/global array
94 * in communicate_group_positions */
95 coll_ind[localnr] = i;
98 /* add one to the local atom count */
103 /* Return the number of local atoms that were found */
108 static void get_shifts_group(
111 rvec *xcoll, /* IN: Collective set of positions [0..nr] */
112 int nr, /* IN: Total number of atoms in the group */
113 rvec *xcoll_old, /* IN: Positions from the last time step [0...nr] */
114 ivec *shifts) /* OUT: Shifts for xcoll */
120 /* Get the shifts such that each atom is within closest
121 * distance to its position at the last NS time step after shifting.
122 * If we start with a whole group, and always keep track of
123 * shift changes, the group will stay whole this way */
124 for (i=0; i < nr; i++)
125 clear_ivec(shifts[i]);
129 /* The distance this atom moved since the last time step */
130 /* If this is more than just a bit, it has changed its home pbc box */
131 rvec_sub(xcoll[i],xcoll_old[i],dx);
133 for(m=npbcdim-1; m>=0; m--)
135 while (dx[m] < -0.5*box[m][m])
141 while (dx[m] >= 0.5*box[m][m])
152 static void shift_positions_group(
154 rvec x[], /* The positions [0..nr] */
155 ivec *is, /* The shifts [0..nr] */
156 int nr) /* The number of positions and shifts */
161 GMX_MPE_LOG(ev_shift_start);
163 /* Loop over the group's atoms */
166 for (i=0; i < nr; i++)
172 x[i][XX]=x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
173 x[i][YY]=x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
174 x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
178 for (i=0; i < nr; i++)
184 x[i][XX]=x[i][XX]+tx*box[XX][XX];
185 x[i][YY]=x[i][YY]+ty*box[YY][YY];
186 x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
189 GMX_MPE_LOG(ev_shift_finish);
193 /* Assemble the positions of the group such that every node has all of them.
194 * The atom indices are retrieved from anrs_loc[0..nr_loc]
195 * Note that coll_ind[i] = i is needed in the serial case */
196 extern void communicate_group_positions(
198 rvec *xcoll, /* OUT: Collective array of positions */
199 ivec *shifts, /* IN+OUT: Collective array of shifts for xcoll */
200 ivec *extra_shifts, /* BUF: Extra shifts since last time step */
201 const gmx_bool bNS, /* IN: NS step, the shifts have changed */
202 rvec *x_loc, /* IN: Local positions on this node */
203 const int nr, /* IN: Total number of atoms in the group */
204 const int nr_loc, /* IN: Local number of atoms in the group */
205 int *anrs_loc, /* IN: Local atom numbers */
206 int *coll_ind, /* IN: Collective index */
207 rvec *xcoll_old, /* IN+OUT: Positions from the last time step, used to make group whole */
213 GMX_MPE_LOG(ev_get_group_x_start);
215 /* Zero out the groups' global position array */
216 clear_rvecs(nr, xcoll);
218 /* Put the local positions that this node has into the right place of
219 * the collective array. Note that in the serial case, coll_ind[i] = i */
220 for (i=0; i<nr_loc; i++)
221 copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
225 /* Add the arrays from all nodes together */
226 gmx_sum(nr*3, xcoll[0], cr);
228 /* To make the group whole, start with a whole group and each
229 * step move the assembled positions at closest distance to the positions
230 * from the last step. First shift the positions with the saved shift
231 * vectors (these are 0 when this routine is called for the first time!) */
232 shift_positions_group(box, xcoll, shifts, nr);
234 /* Now check if some shifts changed since the last step.
235 * This only needs to be done when the shifts are expected to have changed,
236 * i.e. after neighboursearching */
239 get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
241 /* Shift with the additional shifts such that we get a whole group now */
242 shift_positions_group(box, xcoll, extra_shifts, nr);
244 /* Add the shift vectors together for the next time step */
247 shifts[i][XX] += extra_shifts[i][XX];
248 shifts[i][YY] += extra_shifts[i][YY];
249 shifts[i][ZZ] += extra_shifts[i][ZZ];
252 /* Store current correctly-shifted positions for comparison in the next NS time step */
254 copy_rvec(xcoll[i],xcoll_old[i]);
257 GMX_MPE_LOG(ev_get_group_x_finish);
261 /* Determine the (weighted) sum vector from positions x */
262 extern double get_sum_of_positions(rvec x[], real weight[], const int nat, dvec dsumvec)
266 double weight_sum = 0.0;
269 /* Zero out the center */
272 /* Loop over all atoms and add their weighted position vectors */
275 for (i=0; i<nat; i++)
277 weight_sum += weight[i];
278 svmul(weight[i], x[i], x_weighted);
279 dsumvec[XX] += x_weighted[XX];
280 dsumvec[YY] += x_weighted[YY];
281 dsumvec[ZZ] += x_weighted[ZZ];
286 for (i=0; i<nat; i++)
288 dsumvec[XX] += x[i][XX];
289 dsumvec[YY] += x[i][YY];
290 dsumvec[ZZ] += x[i][ZZ];
297 /* Determine center of structure from collective positions x */
298 extern void get_center(rvec x[], real weight[], const int nr, rvec rcenter)
301 double weight_sum, denom;
304 weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
307 denom = weight_sum; /* Divide by the sum of weight */
309 denom = nr; /* Divide by the number of atoms */
311 dsvmul(1.0/denom, dcenter, dcenter);
313 rcenter[XX] = dcenter[XX];
314 rcenter[YY] = dcenter[YY];
315 rcenter[ZZ] = dcenter[ZZ];
319 /* Get the center from local positions that already have the correct
320 * PBC representation */
321 extern void get_center_comm(
323 rvec x_loc[], /* Local positions */
324 real weight_loc[], /* Local masses or other weights */
325 int nr_loc, /* Local number of atoms */
326 int nr_group, /* Total number of atoms of the group */
327 rvec center) /* Weighted center */
329 double weight_sum, denom;
334 weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
336 /* Add the local contributions from all nodes. Put the sum vector and the
337 * weight in a buffer array so that we get along with a single communication
341 buf[0] = dsumvec[XX];
342 buf[1] = dsumvec[YY];
343 buf[2] = dsumvec[ZZ];
346 /* Communicate buffer */
347 gmx_sumd(4, buf, cr);
349 dsumvec[XX] = buf[0];
350 dsumvec[YY] = buf[1];
351 dsumvec[ZZ] = buf[2];
355 if (weight_loc != NULL)
356 denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
358 denom = 1.0/nr_group; /* Divide by the number of atoms to get the geometrical center */
360 center[XX] = dsumvec[XX]*denom;
361 center[YY] = dsumvec[YY]*denom;
362 center[ZZ] = dsumvec[ZZ]*denom;
366 /* Translate x with transvec */
367 extern void translate_x(rvec x[], const int nr, const rvec transvec)
373 rvec_inc(x[i], transvec);
377 extern void rotate_x(rvec x[], const int nr, matrix rmat)
383 /* Apply the rotation matrix */
392 x[i][j] += rmat[k][j]*x_old[k];