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42 #include "groupcoord.h"
47 #include "gmx_ga2la.h"
49 #define MIN(a, b) (((a) < (b)) ? (a) : (b))
53 /* Select the indices of the group's atoms which are local and store them in
54 * anrs_loc[0..nr_loc]. The indices are saved in coll_ind[] for later reduction
55 * in communicate_group_positions()
57 extern void dd_make_local_group_indices(
59 const int nr, /* IN: Total number of atoms in the group */
60 int anrs[], /* IN: Global atom numbers of the groups atoms */
61 int *nr_loc, /* OUT: Number of group atoms found locally */
62 int *anrs_loc[], /* OUT: Local atom numbers of the group */
63 int *nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
64 int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
70 /* Loop over all the atom indices of the group to check
71 * which ones are on the local node */
73 for (i = 0; i < nr; i++)
75 if (ga2la_get_home(ga2la, anrs[i], &ii))
77 /* The atom with this index is a home atom */
78 if (localnr >= *nalloc_loc) /* Check whether memory suffices */
80 *nalloc_loc = over_alloc_dd(localnr+1);
81 /* We never need more memory than the number of atoms in the group */
82 *nalloc_loc = MIN(*nalloc_loc, nr);
83 srenew(*anrs_loc, *nalloc_loc);
85 /* Save the atoms index in the local atom numbers array */
86 (*anrs_loc)[localnr] = ii;
90 /* Keep track of where this local atom belongs in the collective index array.
91 * This is needed when reducing the local arrays to a collective/global array
92 * in communicate_group_positions */
93 coll_ind[localnr] = i;
96 /* add one to the local atom count */
101 /* Return the number of local atoms that were found */
106 static void get_shifts_group(
109 rvec *xcoll, /* IN: Collective set of positions [0..nr] */
110 int nr, /* IN: Total number of atoms in the group */
111 rvec *xcoll_old, /* IN: Positions from the last time step [0...nr] */
112 ivec *shifts) /* OUT: Shifts for xcoll */
118 /* Get the shifts such that each atom is within closest
119 * distance to its position at the last NS time step after shifting.
120 * If we start with a whole group, and always keep track of
121 * shift changes, the group will stay whole this way */
122 for (i = 0; i < nr; i++)
124 clear_ivec(shifts[i]);
127 for (i = 0; i < nr; 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])
137 for (d = 0; d < DIM; d++)
143 while (dx[m] >= 0.5*box[m][m])
145 for (d = 0; d < DIM; d++)
156 static void shift_positions_group(
158 rvec x[], /* The positions [0..nr] */
159 ivec *is, /* The shifts [0..nr] */
160 int nr) /* The number of positions and shifts */
165 /* Loop over the group's atoms */
168 for (i = 0; i < nr; i++)
174 x[i][XX] = x[i][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
175 x[i][YY] = x[i][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
176 x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
181 for (i = 0; i < nr; i++)
187 x[i][XX] = x[i][XX]+tx*box[XX][XX];
188 x[i][YY] = x[i][YY]+ty*box[YY][YY];
189 x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
195 /* Assemble the positions of the group such that every node has all of them.
196 * The atom indices are retrieved from anrs_loc[0..nr_loc]
197 * Note that coll_ind[i] = i is needed in the serial case */
198 extern void communicate_group_positions(
199 t_commrec *cr, /* Pointer to MPI communication data */
200 rvec *xcoll, /* Collective array of positions */
201 ivec *shifts, /* Collective array of shifts for xcoll (can be NULL) */
202 ivec *extra_shifts, /* (optional) Extra shifts since last time step */
203 const gmx_bool bNS, /* (optional) NS step, the shifts have changed */
204 rvec *x_loc, /* Local positions on this node */
205 const int nr, /* Total number of atoms in the group */
206 const int nr_loc, /* Local number of atoms in the group */
207 int *anrs_loc, /* Local atom numbers */
208 int *coll_ind, /* Collective index */
209 rvec *xcoll_old, /* (optional) Positions from the last time step,
210 used to make group whole */
211 matrix box) /* (optional) The box */
216 /* Zero out the groups' global position array */
217 clear_rvecs(nr, xcoll);
219 /* Put the local positions that this node has into the right place of
220 * the collective array. Note that in the serial case, coll_ind[i] = i */
221 for (i = 0; i < nr_loc; i++)
223 copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
228 /* Add the arrays from all nodes together */
229 gmx_sum(nr*3, xcoll[0], cr);
231 /* Now we have all the positions of the group in the xcoll array present on all
234 * The rest of the code is for making the group whole again in case atoms changed
235 * their PBC representation / crossed a box boundary. We only do that if the
236 * shifts array is allocated. */
239 /* To make the group whole, start with a whole group and each
240 * step move the assembled positions at closest distance to the positions
241 * from the last step. First shift the positions with the saved shift
242 * vectors (these are 0 when this routine is called for the first time!) */
243 shift_positions_group(box, xcoll, shifts, nr);
245 /* Now check if some shifts changed since the last step.
246 * This only needs to be done when the shifts are expected to have changed,
247 * i.e. after neighbor searching */
250 get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
252 /* Shift with the additional shifts such that we get a whole group now */
253 shift_positions_group(box, xcoll, extra_shifts, nr);
255 /* Add the shift vectors together for the next time step */
256 for (i = 0; i < nr; i++)
258 shifts[i][XX] += extra_shifts[i][XX];
259 shifts[i][YY] += extra_shifts[i][YY];
260 shifts[i][ZZ] += extra_shifts[i][ZZ];
263 /* Store current correctly-shifted positions for comparison in the next NS time step */
264 for (i = 0; i < nr; i++)
266 copy_rvec(xcoll[i], xcoll_old[i]);
273 /* Determine the (weighted) sum vector from positions x */
274 extern double get_sum_of_positions(rvec x[], real weight[], const int nat, dvec dsumvec)
278 double weight_sum = 0.0;
281 /* Zero out the center */
284 /* Loop over all atoms and add their weighted position vectors */
287 for (i = 0; i < nat; i++)
289 weight_sum += weight[i];
290 svmul(weight[i], x[i], x_weighted);
291 dsumvec[XX] += x_weighted[XX];
292 dsumvec[YY] += x_weighted[YY];
293 dsumvec[ZZ] += x_weighted[ZZ];
298 for (i = 0; i < nat; i++)
300 dsumvec[XX] += x[i][XX];
301 dsumvec[YY] += x[i][YY];
302 dsumvec[ZZ] += x[i][ZZ];
309 /* Determine center of structure from collective positions x */
310 extern void get_center(rvec x[], real weight[], const int nr, rvec rcenter)
313 double weight_sum, denom;
316 weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
320 denom = weight_sum; /* Divide by the sum of weight */
324 denom = nr; /* Divide by the number of atoms */
327 dsvmul(1.0/denom, dcenter, dcenter);
329 rcenter[XX] = dcenter[XX];
330 rcenter[YY] = dcenter[YY];
331 rcenter[ZZ] = dcenter[ZZ];
335 /* Get the center from local positions that already have the correct
336 * PBC representation */
337 extern void get_center_comm(
339 rvec x_loc[], /* Local positions */
340 real weight_loc[], /* Local masses or other weights */
341 int nr_loc, /* Local number of atoms */
342 int nr_group, /* Total number of atoms of the group */
343 rvec center) /* Weighted center */
345 double weight_sum, denom;
350 weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
352 /* Add the local contributions from all nodes. Put the sum vector and the
353 * weight in a buffer array so that we get along with a single communication
357 buf[0] = dsumvec[XX];
358 buf[1] = dsumvec[YY];
359 buf[2] = dsumvec[ZZ];
362 /* Communicate buffer */
363 gmx_sumd(4, buf, cr);
365 dsumvec[XX] = buf[0];
366 dsumvec[YY] = buf[1];
367 dsumvec[ZZ] = buf[2];
371 if (weight_loc != NULL)
373 denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
377 denom = 1.0/nr_group; /* Divide by the number of atoms to get the geometrical center */
380 center[XX] = dsumvec[XX]*denom;
381 center[YY] = dsumvec[YY]*denom;
382 center[ZZ] = dsumvec[ZZ]*denom;
386 /* Translate x with transvec */
387 extern void translate_x(rvec x[], const int nr, const rvec transvec)
392 for (i = 0; i < nr; i++)
394 rvec_inc(x[i], transvec);
399 extern void rotate_x(rvec x[], const int nr, matrix rmat)
405 /* Apply the rotation matrix */
406 for (i = 0; i < nr; i++)
408 for (j = 0; j < 3; j++)
412 for (j = 0; j < 3; j++)
415 for (k = 0; k < 3; k++)
417 x[i][j] += rmat[k][j]*x_old[k];