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39 #include "groupcoord.h"
41 #include "gromacs/domdec/ga2la.h"
42 #include "gromacs/gmxlib/network.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/mdtypes/commrec.h"
45 #include "gromacs/pbcutil/pbc.h"
46 #include "gromacs/utility/smalloc.h"
48 #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 void dd_make_local_group_indices(const gmx_ga2la_t* ga2la,
56 const int nr, /* IN: Total number of atoms in the group */
57 int anrs[], /* IN: Global atom numbers of the groups atoms */
58 int* nr_loc, /* OUT: Number of group atoms found locally */
59 int* anrs_loc[], /* OUT: Local atom numbers of the group */
60 int* nalloc_loc, /* IN+OUT: Allocation size of anrs_loc */
61 int coll_ind[]) /* OUT (opt): Where is this position found in the collective array? */
63 GMX_ASSERT(ga2la, "We need a valid ga2la object");
65 /* Loop over all the atom indices of the group to check
66 * which ones are on the local node */
68 for (int i = 0; i < nr; i++)
70 if (const int* ii = ga2la->findHome(anrs[i]))
72 /* The atom with this index is a home atom */
73 if (localnr >= *nalloc_loc) /* Check whether memory suffices */
75 *nalloc_loc = over_alloc_dd(localnr + 1);
76 /* We never need more memory than the number of atoms in the group */
77 *nalloc_loc = MIN(*nalloc_loc, nr);
78 srenew(*anrs_loc, *nalloc_loc);
80 /* Save the atoms index in the local atom numbers array */
81 (*anrs_loc)[localnr] = *ii;
83 if (coll_ind != nullptr)
85 /* Keep track of where this local atom belongs in the collective index array.
86 * This is needed when reducing the local arrays to a collective/global array
87 * in communicate_group_positions */
88 coll_ind[localnr] = i;
91 /* add one to the local atom count */
96 /* Return the number of local atoms that were found */
101 static void get_shifts_group(int npbcdim,
103 rvec* xcoll, /* IN: Collective set of positions [0..nr] */
104 int nr, /* IN: Total number of atoms in the group */
105 rvec* xcoll_old, /* IN: Positions from the last time step [0...nr] */
106 ivec* shifts) /* OUT: Shifts for xcoll */
112 /* Get the shifts such that each atom is within closest
113 * distance to its position at the last NS time step after shifting.
114 * If we start with a whole group, and always keep track of
115 * shift changes, the group will stay whole this way */
116 for (i = 0; i < nr; i++)
118 clear_ivec(shifts[i]);
121 for (i = 0; i < nr; i++)
123 /* The distance this atom moved since the last time step */
124 /* If this is more than just a bit, it has changed its home pbc box */
125 rvec_sub(xcoll[i], xcoll_old[i], dx);
127 for (m = npbcdim - 1; m >= 0; m--)
129 while (dx[m] < -0.5 * box[m][m])
131 for (d = 0; d < DIM; d++)
137 while (dx[m] >= 0.5 * box[m][m])
139 for (d = 0; d < DIM; d++)
150 static void shift_positions_group(const matrix box,
151 rvec x[], /* The positions [0..nr] */
152 ivec* is, /* The shifts [0..nr] */
153 int nr) /* The number of positions and shifts */
158 /* Loop over the group's atoms */
161 for (i = 0; i < nr; i++)
167 x[i][XX] = x[i][XX] + tx * box[XX][XX] + ty * box[YY][XX] + tz * box[ZZ][XX];
168 x[i][YY] = x[i][YY] + ty * box[YY][YY] + tz * box[ZZ][YY];
169 x[i][ZZ] = x[i][ZZ] + tz * box[ZZ][ZZ];
174 for (i = 0; i < nr; i++)
180 x[i][XX] = x[i][XX] + tx * box[XX][XX];
181 x[i][YY] = x[i][YY] + ty * box[YY][YY];
182 x[i][ZZ] = x[i][ZZ] + tz * box[ZZ][ZZ];
188 /* Assemble the positions of the group such that every node has all of them.
189 * The atom indices are retrieved from anrs_loc[0..nr_loc]
190 * Note that coll_ind[i] = i is needed in the serial case */
191 extern void communicate_group_positions(const t_commrec* cr, /* Pointer to MPI communication data */
192 rvec* xcoll, /* Collective array of positions */
193 ivec* shifts, /* Collective array of shifts for xcoll (can be NULL) */
194 ivec* extra_shifts, /* (optional) Extra shifts since last time step */
195 const gmx_bool bNS, /* (optional) NS step, the shifts have changed */
196 const rvec* x_loc, /* Local positions on this node */
197 const int nr, /* Total number of atoms in the group */
198 const int nr_loc, /* Local number of atoms in the group */
199 const int* anrs_loc, /* Local atom numbers */
200 const int* coll_ind, /* Collective index */
201 rvec* xcoll_old, /* (optional) Positions from the last time
202 step, used to make group whole */
203 const matrix box) /* (optional) The box */
208 /* Zero out the groups' global position array */
209 clear_rvecs(nr, xcoll);
211 /* Put the local positions that this node has into the right place of
212 * the collective array. Note that in the serial case, coll_ind[i] = i */
213 for (i = 0; i < nr_loc; i++)
215 copy_rvec(x_loc[anrs_loc[i]], xcoll[coll_ind[i]]);
220 /* Add the arrays from all nodes together */
221 gmx_sum(nr * 3, xcoll[0], cr);
223 /* Now we have all the positions of the group in the xcoll array present on all
226 * The rest of the code is for making the group whole again in case atoms changed
227 * their PBC representation / crossed a box boundary. We only do that if the
228 * shifts array is allocated. */
229 if (nullptr != shifts)
231 /* To make the group whole, start with a whole group and each
232 * step move the assembled positions at closest distance to the positions
233 * from the last step. First shift the positions with the saved shift
234 * vectors (these are 0 when this routine is called for the first time!) */
235 shift_positions_group(box, xcoll, shifts, nr);
237 /* Now check if some shifts changed since the last step.
238 * This only needs to be done when the shifts are expected to have changed,
239 * i.e. after neighbor searching */
242 get_shifts_group(3, box, xcoll, nr, xcoll_old, extra_shifts);
244 /* Shift with the additional shifts such that we get a whole group now */
245 shift_positions_group(box, xcoll, extra_shifts, nr);
247 /* Add the shift vectors together for the next time step */
248 for (i = 0; i < nr; i++)
250 shifts[i][XX] += extra_shifts[i][XX];
251 shifts[i][YY] += extra_shifts[i][YY];
252 shifts[i][ZZ] += extra_shifts[i][ZZ];
255 /* Store current correctly-shifted positions for comparison in the next NS time step */
256 for (i = 0; i < nr; i++)
258 copy_rvec(xcoll[i], xcoll_old[i]);
265 /* Determine the (weighted) sum vector from positions x */
266 extern double get_sum_of_positions(rvec x[], real weight[], const int nat, dvec dsumvec)
270 double weight_sum = 0.0;
273 /* Zero out the center */
276 /* Loop over all atoms and add their weighted position vectors */
277 if (weight != nullptr)
279 for (i = 0; i < nat; i++)
281 weight_sum += weight[i];
282 svmul(weight[i], x[i], x_weighted);
283 dsumvec[XX] += x_weighted[XX];
284 dsumvec[YY] += x_weighted[YY];
285 dsumvec[ZZ] += x_weighted[ZZ];
290 for (i = 0; i < nat; i++)
292 dsumvec[XX] += x[i][XX];
293 dsumvec[YY] += x[i][YY];
294 dsumvec[ZZ] += x[i][ZZ];
301 /* Determine center of structure from collective positions x */
302 extern void get_center(rvec x[], real weight[], const int nr, rvec rcenter)
305 double weight_sum, denom;
308 weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
310 if (weight != nullptr)
312 denom = weight_sum; /* Divide by the sum of weight */
316 denom = nr; /* Divide by the number of atoms */
318 dsvmul(1.0 / denom, dcenter, dcenter);
320 rcenter[XX] = dcenter[XX];
321 rcenter[YY] = dcenter[YY];
322 rcenter[ZZ] = dcenter[ZZ];
326 /* Get the center from local positions that already have the correct
327 * PBC representation */
328 extern void get_center_comm(const t_commrec* cr,
329 rvec x_loc[], /* Local positions */
330 real weight_loc[], /* Local masses or other weights */
331 int nr_loc, /* Local number of atoms */
332 int nr_group, /* Total number of atoms of the group */
333 rvec center) /* Weighted center */
335 double weight_sum, denom;
340 weight_sum = get_sum_of_positions(x_loc, weight_loc, nr_loc, dsumvec);
342 /* Add the local contributions from all nodes. Put the sum vector and the
343 * weight in a buffer array so that we get along with a single communication
347 buf[0] = dsumvec[XX];
348 buf[1] = dsumvec[YY];
349 buf[2] = dsumvec[ZZ];
352 /* Communicate buffer */
353 gmx_sumd(4, buf, cr);
355 dsumvec[XX] = buf[0];
356 dsumvec[YY] = buf[1];
357 dsumvec[ZZ] = buf[2];
361 if (weight_loc != nullptr)
363 denom = 1.0 / weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
367 denom = 1.0 / nr_group; /* Divide by the number of atoms to get the geometrical center */
369 center[XX] = dsumvec[XX] * denom;
370 center[YY] = dsumvec[YY] * denom;
371 center[ZZ] = dsumvec[ZZ] * denom;
375 /* Translate x with transvec */
376 extern void translate_x(rvec x[], const int nr, const rvec transvec)
381 for (i = 0; i < nr; i++)
383 rvec_inc(x[i], transvec);
388 extern void rotate_x(rvec x[], const int nr, matrix rmat)
394 /* Apply the rotation matrix */
395 for (i = 0; i < nr; i++)
397 for (j = 0; j < 3; j++)
401 for (j = 0; j < 3; j++)
404 for (k = 0; k < 3; k++)
406 x[i][j] += rmat[k][j] * x_old[k];