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33 * Groningen Machine for Chemical Simulation
40 #include "groupcoord.h"
45 #include "gmx_ga2la.h"
47 #define MIN(a, b) (((a) < (b)) ? (a) : (b))
51 /* Select the indices of the group's atoms which are local and store them in
52 * anrs_loc[0..nr_loc]. The indices are saved in coll_ind[] for later reduction
53 * in communicate_group_positions()
55 extern void dd_make_local_group_indices(
57 const int nr, /* IN: Total number of atoms in the group */
58 int anrs[], /* IN: Global atom numbers of the groups atoms */
59 int *nr_loc, /* OUT: Number of group atoms found locally */
60 int *anrs_loc[], /* OUT: Local atom numbers of the group */
61 int *nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
62 int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
68 /* Loop over all the atom indices of the group to check
69 * which ones are on the local node */
71 for (i = 0; i < nr; i++)
73 if (ga2la_get_home(ga2la, anrs[i], &ii))
75 /* The atom with this index is a home atom */
76 if (localnr >= *nalloc_loc) /* Check whether memory suffices */
78 *nalloc_loc = over_alloc_dd(localnr+1);
79 /* We never need more memory than the number of atoms in the group */
80 *nalloc_loc = MIN(*nalloc_loc, nr);
81 srenew(*anrs_loc, *nalloc_loc);
83 /* Save the atoms index in the local atom numbers array */
84 (*anrs_loc)[localnr] = ii;
88 /* Keep track of where this local atom belongs in the collective index array.
89 * This is needed when reducing the local arrays to a collective/global array
90 * in communicate_group_positions */
91 coll_ind[localnr] = i;
94 /* add one to the local atom count */
99 /* Return the number of local atoms that were found */
104 static void get_shifts_group(
107 rvec *xcoll, /* IN: Collective set of positions [0..nr] */
108 int nr, /* IN: Total number of atoms in the group */
109 rvec *xcoll_old, /* IN: Positions from the last time step [0...nr] */
110 ivec *shifts) /* OUT: Shifts for xcoll */
116 /* Get the shifts such that each atom is within closest
117 * distance to its position at the last NS time step after shifting.
118 * If we start with a whole group, and always keep track of
119 * shift changes, the group will stay whole this way */
120 for (i = 0; i < nr; i++)
122 clear_ivec(shifts[i]);
125 for (i = 0; i < nr; i++)
127 /* The distance this atom moved since the last time step */
128 /* If this is more than just a bit, it has changed its home pbc box */
129 rvec_sub(xcoll[i], xcoll_old[i], dx);
131 for (m = npbcdim-1; m >= 0; m--)
133 while (dx[m] < -0.5*box[m][m])
135 for (d = 0; d < DIM; d++)
141 while (dx[m] >= 0.5*box[m][m])
143 for (d = 0; d < DIM; d++)
154 static void shift_positions_group(
156 rvec x[], /* The positions [0..nr] */
157 ivec *is, /* The shifts [0..nr] */
158 int nr) /* The number of positions and shifts */
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];
179 for (i = 0; i < nr; i++)
185 x[i][XX] = x[i][XX]+tx*box[XX][XX];
186 x[i][YY] = x[i][YY]+ty*box[YY][YY];
187 x[i][ZZ] = x[i][ZZ]+tz*box[ZZ][ZZ];
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 /* Zero out the groups' global position array */
214 clear_rvecs(nr, xcoll);
216 /* Put the local positions that this node has into the right place of
217 * the collective array. Note that in the serial case, coll_ind[i] = i */
218 for (i = 0; i < nr_loc; i++)
220 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 */
245 for (i = 0; i < nr; i++)
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 */
253 for (i = 0; i < nr; i++)
255 copy_rvec(xcoll[i], xcoll_old[i]);
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);
308 denom = weight_sum; /* Divide by the sum of weight */
312 denom = nr; /* Divide by the number of atoms */
315 dsvmul(1.0/denom, dcenter, dcenter);
317 rcenter[XX] = dcenter[XX];
318 rcenter[YY] = dcenter[YY];
319 rcenter[ZZ] = dcenter[ZZ];
323 /* Get the center from local positions that already have the correct
324 * PBC representation */
325 extern void get_center_comm(
327 rvec x_loc[], /* Local positions */
328 real weight_loc[], /* Local masses or other weights */
329 int nr_loc, /* Local number of atoms */
330 int nr_group, /* Total number of atoms of the group */
331 rvec center) /* Weighted center */
333 double weight_sum, denom;
338 weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
340 /* Add the local contributions from all nodes. Put the sum vector and the
341 * weight in a buffer array so that we get along with a single communication
345 buf[0] = dsumvec[XX];
346 buf[1] = dsumvec[YY];
347 buf[2] = dsumvec[ZZ];
350 /* Communicate buffer */
351 gmx_sumd(4, buf, cr);
353 dsumvec[XX] = buf[0];
354 dsumvec[YY] = buf[1];
355 dsumvec[ZZ] = buf[2];
359 if (weight_loc != NULL)
361 denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
365 denom = 1.0/nr_group; /* Divide by the number of atoms to get the geometrical center */
368 center[XX] = dsumvec[XX]*denom;
369 center[YY] = dsumvec[YY]*denom;
370 center[ZZ] = dsumvec[ZZ]*denom;
374 /* Translate x with transvec */
375 extern void translate_x(rvec x[], const int nr, const rvec transvec)
380 for (i = 0; i < nr; i++)
382 rvec_inc(x[i], transvec);
387 extern void rotate_x(rvec x[], const int nr, matrix rmat)
393 /* Apply the rotation matrix */
394 for (i = 0; i < nr; i++)
396 for (j = 0; j < 3; j++)
400 for (j = 0; j < 3; j++)
403 for (k = 0; k < 3; k++)
405 x[i][j] += rmat[k][j]*x_old[k];