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33 * Groningen Machine for Chemical Simulation
40 #include "groupcoord.h"
41 #include "mpelogging.h"
46 #include "gmx_ga2la.h"
48 #define MIN(a,b) (((a)<(b))?(a):(b))
52 /* Select the indices of the group's atoms which are local and store them in
53 * anrs_loc[0..nr_loc]. The indices are saved in coll_ind[] for later reduction
54 * in communicate_group_positions()
56 extern void dd_make_local_group_indices(
58 const int nr, /* IN: Total number of atoms in the group */
59 int anrs[], /* IN: Global atom numbers of the groups atoms */
60 int *nr_loc, /* OUT: Number of group atoms found locally */
61 int *anrs_loc[], /* OUT: Local atom numbers of the group */
62 int *nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
63 int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
69 /* Loop over all the atom indices of the group to check
70 * which ones are on the local node */
74 if (ga2la_get_home(ga2la,anrs[i],&ii))
76 /* The atom with this index is a home atom */
77 if (localnr >= *nalloc_loc) /* Check whether memory suffices */
79 *nalloc_loc = over_alloc_dd(localnr+1);
80 /* We never need more memory than the number of atoms in the group */
81 *nalloc_loc = MIN(*nalloc_loc, nr);
82 srenew(*anrs_loc,*nalloc_loc);
84 /* Save the atoms index in the local atom numbers array */
85 (*anrs_loc)[localnr] = ii;
89 /* Keep track of where this local atom belongs in the collective index array.
90 * This is needed when reducing the local arrays to a collective/global array
91 * in communicate_group_positions */
92 coll_ind[localnr] = i;
95 /* add one to the local atom count */
100 /* Return the number of local atoms that were found */
105 static void get_shifts_group(
108 rvec *xcoll, /* IN: Collective set of positions [0..nr] */
109 int nr, /* IN: Total number of atoms in the group */
110 rvec *xcoll_old, /* IN: Positions from the last time step [0...nr] */
111 ivec *shifts) /* OUT: Shifts for xcoll */
117 /* Get the shifts such that each atom is within closest
118 * distance to its position at the last NS time step after shifting.
119 * If we start with a whole group, and always keep track of
120 * shift changes, the group will stay whole this way */
121 for (i=0; i < nr; i++)
122 clear_ivec(shifts[i]);
126 /* The distance this atom moved since the last time step */
127 /* If this is more than just a bit, it has changed its home pbc box */
128 rvec_sub(xcoll[i],xcoll_old[i],dx);
130 for(m=npbcdim-1; m>=0; m--)
132 while (dx[m] < -0.5*box[m][m])
138 while (dx[m] >= 0.5*box[m][m])
149 static void shift_positions_group(
151 rvec x[], /* The positions [0..nr] */
152 ivec *is, /* The shifts [0..nr] */
153 int nr) /* The number of positions and shifts */
158 GMX_MPE_LOG(ev_shift_start);
160 /* Loop over the group's atoms */
163 for (i=0; i < nr; i++)
169 x[i][XX]=x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
170 x[i][YY]=x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
171 x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
175 for (i=0; i < nr; i++)
181 x[i][XX]=x[i][XX]+tx*box[XX][XX];
182 x[i][YY]=x[i][YY]+ty*box[YY][YY];
183 x[i][ZZ]=x[i][ZZ]+tz*box[ZZ][ZZ];
186 GMX_MPE_LOG(ev_shift_finish);
190 /* Assemble the positions of the group such that every node has all of them.
191 * The atom indices are retrieved from anrs_loc[0..nr_loc]
192 * Note that coll_ind[i] = i is needed in the serial case */
193 extern void communicate_group_positions(
195 rvec *xcoll, /* OUT: Collective array of positions */
196 ivec *shifts, /* IN+OUT: Collective array of shifts for xcoll */
197 ivec *extra_shifts, /* BUF: Extra shifts since last time step */
198 const gmx_bool bNS, /* IN: NS step, the shifts have changed */
199 rvec *x_loc, /* IN: Local positions on this node */
200 const int nr, /* IN: Total number of atoms in the group */
201 const int nr_loc, /* IN: Local number of atoms in the group */
202 int *anrs_loc, /* IN: Local atom numbers */
203 int *coll_ind, /* IN: Collective index */
204 rvec *xcoll_old, /* IN+OUT: Positions from the last time step, used to make group whole */
210 GMX_MPE_LOG(ev_get_group_x_start);
212 /* Zero out the groups' global position array */
213 clear_rvecs(nr, xcoll);
215 /* Put the local positions that this node has into the right place of
216 * the collective array. Note that in the serial case, coll_ind[i] = i */
217 for (i=0; i<nr_loc; i++)
218 copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
222 /* Add the arrays from all nodes together */
223 gmx_sum(nr*3, xcoll[0], cr);
225 /* To make the group whole, start with a whole group and each
226 * step move the assembled positions at closest distance to the positions
227 * from the last step. First shift the positions with the saved shift
228 * vectors (these are 0 when this routine is called for the first time!) */
229 shift_positions_group(box, xcoll, shifts, nr);
231 /* Now check if some shifts changed since the last step.
232 * This only needs to be done when the shifts are expected to have changed,
233 * i.e. after neighboursearching */
236 get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
238 /* Shift with the additional shifts such that we get a whole group now */
239 shift_positions_group(box, xcoll, extra_shifts, nr);
241 /* Add the shift vectors together for the next time step */
244 shifts[i][XX] += extra_shifts[i][XX];
245 shifts[i][YY] += extra_shifts[i][YY];
246 shifts[i][ZZ] += extra_shifts[i][ZZ];
249 /* Store current correctly-shifted positions for comparison in the next NS time step */
251 copy_rvec(xcoll[i],xcoll_old[i]);
254 GMX_MPE_LOG(ev_get_group_x_finish);
258 /* Determine the (weighted) sum vector from positions x */
259 extern double get_sum_of_positions(rvec x[], real weight[], const int nat, dvec dsumvec)
263 double weight_sum = 0.0;
266 /* Zero out the center */
269 /* Loop over all atoms and add their weighted position vectors */
272 for (i=0; i<nat; i++)
274 weight_sum += weight[i];
275 svmul(weight[i], x[i], x_weighted);
276 dsumvec[XX] += x_weighted[XX];
277 dsumvec[YY] += x_weighted[YY];
278 dsumvec[ZZ] += x_weighted[ZZ];
283 for (i=0; i<nat; i++)
285 dsumvec[XX] += x[i][XX];
286 dsumvec[YY] += x[i][YY];
287 dsumvec[ZZ] += x[i][ZZ];
294 /* Determine center of structure from collective positions x */
295 extern void get_center(rvec x[], real weight[], const int nr, rvec rcenter)
298 double weight_sum, denom;
301 weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
304 denom = weight_sum; /* Divide by the sum of weight */
306 denom = nr; /* Divide by the number of atoms */
308 dsvmul(1.0/denom, dcenter, dcenter);
310 rcenter[XX] = dcenter[XX];
311 rcenter[YY] = dcenter[YY];
312 rcenter[ZZ] = dcenter[ZZ];
316 /* Get the center from local positions that already have the correct
317 * PBC representation */
318 extern void get_center_comm(
320 rvec x_loc[], /* Local positions */
321 real weight_loc[], /* Local masses or other weights */
322 int nr_loc, /* Local number of atoms */
323 int nr_group, /* Total number of atoms of the group */
324 rvec center) /* Weighted center */
326 double weight_sum, denom;
331 weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
333 /* Add the local contributions from all nodes. Put the sum vector and the
334 * weight in a buffer array so that we get along with a single communication
338 buf[0] = dsumvec[XX];
339 buf[1] = dsumvec[YY];
340 buf[2] = dsumvec[ZZ];
343 /* Communicate buffer */
344 gmx_sumd(4, buf, cr);
346 dsumvec[XX] = buf[0];
347 dsumvec[YY] = buf[1];
348 dsumvec[ZZ] = buf[2];
352 if (weight_loc != NULL)
353 denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
355 denom = 1.0/nr_group; /* Divide by the number of atoms to get the geometrical center */
357 center[XX] = dsumvec[XX]*denom;
358 center[YY] = dsumvec[YY]*denom;
359 center[ZZ] = dsumvec[ZZ]*denom;
363 /* Translate x with transvec */
364 extern void translate_x(rvec x[], const int nr, const rvec transvec)
370 rvec_inc(x[i], transvec);
374 extern void rotate_x(rvec x[], const int nr, matrix rmat)
380 /* Apply the rotation matrix */
389 x[i][j] += rmat[k][j]*x_old[k];