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41 #include "gromacs/utility/futil.h"
42 #include "gromacs/math/vec.h"
43 #include "gromacs/utility/smalloc.h"
45 #include "types/commrec.h"
47 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/fileio/confio.h"
51 #include "gromacs/pbcutil/pbc.h"
53 #include "gmx_ga2la.h"
55 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
56 t_mdatoms *md, rvec *x,
65 if (!ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
75 if (a >= 0 && a < md->homenr)
77 copy_rvec(x[a], x_pbc);
86 copy_rvec(x[pgrp->pbcatom], x_pbc);
90 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
91 t_mdatoms *md, rvec *x,
97 for (g = 0; g < pull->ngroup; g++)
99 if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
101 clear_rvec(x_pbc[g]);
105 pull_set_pbcatom(cr, &pull->group[g], md, x, x_pbc[g]);
106 for (m = 0; m < DIM; m++)
108 if (pull->dim[m] == 0)
117 if (cr && PAR(cr) && n > 0)
119 /* Sum over the nodes to get x_pbc from the home node of pbcatom */
120 gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
124 /* switch function, x between r and w */
125 static real get_weight(real x, real r1, real r0)
139 weight = (r0 - x)/(r0 - r1);
145 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
146 t_pbc *pbc, double t, rvec *x, rvec *xp)
148 int c, i, ii, m, start, end;
150 double r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
152 t_pull_group *pref, *pgrp, *pdyna;
153 gmx_ga2la_t ga2la = NULL;
155 if (pull->dbuf_cyl == NULL)
157 snew(pull->dbuf_cyl, pull->ncoord*4);
160 if (cr && DOMAINDECOMP(cr))
162 ga2la = cr->dd->ga2la;
168 r0_2 = dsqr(pull->cyl_r0);
170 /* loop over all groups to make a reference group for each*/
171 for (c = 0; c < pull->ncoord; c++)
173 pcrd = &pull->coord[c];
175 /* pref will be the same group for all pull coordinates */
176 pref = &pull->group[pcrd->group[0]];
177 pgrp = &pull->group[pcrd->group[1]];
178 pdyna = &pull->dyna[c];
179 copy_rvec(pcrd->vec, dir);
186 for (m = 0; m < DIM; m++)
188 g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
191 /* loop over all atoms in the main ref group */
192 for (i = 0; i < pref->nat; i++)
197 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
202 if (ii >= start && ii < end)
204 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
205 inp = iprod(dir, dx);
207 for (m = 0; m < DIM; m++)
209 dr2 += dsqr(dx[m] - inp*dir[m]);
214 /* add to index, to sum of COM, to weight array */
215 if (pdyna->nat_loc >= pdyna->nalloc_loc)
217 pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
218 srenew(pdyna->ind_loc, pdyna->nalloc_loc);
219 srenew(pdyna->weight_loc, pdyna->nalloc_loc);
221 pdyna->ind_loc[pdyna->nat_loc] = ii;
222 mass = md->massT[ii];
223 weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
224 pdyna->weight_loc[pdyna->nat_loc] = weight;
225 sum_a += mass*weight*inp;
228 pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
229 inp = iprod(dir, dx);
230 sum_ap += mass*weight*inp;
232 wmass += mass*weight;
233 wwmass += mass*sqr(weight);
238 pull->dbuf_cyl[c*4+0] = wmass;
239 pull->dbuf_cyl[c*4+1] = wwmass;
240 pull->dbuf_cyl[c*4+2] = sum_a;
241 pull->dbuf_cyl[c*4+3] = sum_ap;
246 /* Sum the contributions over the nodes */
247 gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
250 for (c = 0; c < pull->ncoord; c++)
252 pcrd = &pull->coord[c];
254 pdyna = &pull->dyna[c];
255 pgrp = &pull->group[pcrd->group[1]];
257 wmass = pull->dbuf_cyl[c*4+0];
258 wwmass = pull->dbuf_cyl[c*4+1];
259 pdyna->wscale = wmass/wwmass;
260 pdyna->invtm = 1.0/(pdyna->wscale*wmass);
262 for (m = 0; m < DIM; m++)
264 g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
265 pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
268 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
274 fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
275 c, pdyna->x[0], pdyna->x[1],
276 pdyna->x[2], 1.0/pdyna->invtm);
281 static double atan2_0_2pi(double y, double x)
293 /* calculates center of mass of selection index from all coordinates x */
294 void pull_calc_coms(t_commrec *cr,
295 t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
299 real mass, w, wm, twopi_box = 0;
300 double wmass, wwmass, invwmass;
302 double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
303 rvec *xx[2], x_pbc = {0, 0, 0}, dx;
306 if (pull->rbuf == NULL)
308 snew(pull->rbuf, pull->ngroup);
310 if (pull->dbuf == NULL)
312 snew(pull->dbuf, 3*pull->ngroup);
317 pull_set_pbcatoms(cr, pull, md, x, pull->rbuf);
320 if (pull->cosdim >= 0)
322 for (m = pull->cosdim+1; m < pull->npbcdim; m++)
324 if (pbc->box[m][pull->cosdim] != 0)
326 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
329 twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
332 for (g = 0; g < pull->ngroup; g++)
334 pgrp = &pull->group[g];
346 if (!(g == 0 && PULL_CYL(pull)))
348 if (pgrp->epgrppbc == epgrppbcREFAT)
350 /* Set the pbc atom */
351 copy_rvec(pull->rbuf[g], x_pbc);
354 for (i = 0; i < pgrp->nat_loc; i++)
356 ii = pgrp->ind_loc[i];
357 mass = md->massT[ii];
358 if (pgrp->epgrppbc != epgrppbcCOS)
360 if (pgrp->weight_loc)
362 w = pgrp->weight_loc[i];
367 if (pgrp->epgrppbc == epgrppbcNONE)
369 /* Plain COM: sum the coordinates */
370 for (m = 0; m < DIM; m++)
372 com[m] += wm*x[ii][m];
376 for (m = 0; m < DIM; m++)
378 comp[m] += wm*xp[ii][m];
384 /* Sum the difference with the reference atom */
385 pbc_dx(pbc, x[ii], x_pbc, dx);
386 for (m = 0; m < DIM; m++)
392 /* For xp add the difference between xp and x to dx,
393 * such that we use the same periodic image,
394 * also when xp has a large displacement.
396 for (m = 0; m < DIM; m++)
398 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
405 /* Determine cos and sin sums */
406 csw = cos(x[ii][pull->cosdim]*twopi_box);
407 snw = sin(x[ii][pull->cosdim]*twopi_box);
416 csw = cos(xp[ii][pull->cosdim]*twopi_box);
417 snw = sin(xp[ii][pull->cosdim]*twopi_box);
425 /* Copy local sums to a buffer for global summing */
426 switch (pgrp->epgrppbc)
430 copy_dvec(com, pull->dbuf[g*3]);
431 copy_dvec(comp, pull->dbuf[g*3+1]);
432 pull->dbuf[g*3+2][0] = wmass;
433 pull->dbuf[g*3+2][1] = wwmass;
434 pull->dbuf[g*3+2][2] = 0;
437 pull->dbuf[g*3 ][0] = cm;
438 pull->dbuf[g*3 ][1] = sm;
439 pull->dbuf[g*3 ][2] = 0;
440 pull->dbuf[g*3+1][0] = ccm;
441 pull->dbuf[g*3+1][1] = csm;
442 pull->dbuf[g*3+1][2] = ssm;
443 pull->dbuf[g*3+2][0] = cmp;
444 pull->dbuf[g*3+2][1] = smp;
445 pull->dbuf[g*3+2][2] = 0;
452 /* Sum the contributions over the nodes */
453 gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
456 for (g = 0; g < pull->ngroup; g++)
458 pgrp = &pull->group[g];
459 if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
461 if (pgrp->epgrppbc != epgrppbcCOS)
463 /* Determine the inverse mass */
464 wmass = pull->dbuf[g*3+2][0];
465 wwmass = pull->dbuf[g*3+2][1];
467 /* invtm==0 signals a frozen group, so then we should keep it zero */
470 pgrp->wscale = wmass/wwmass;
471 pgrp->invtm = 1.0/(pgrp->wscale*wmass);
473 /* Divide by the total mass */
474 for (m = 0; m < DIM; m++)
476 pgrp->x[m] = pull->dbuf[g*3 ][m]*invwmass;
479 pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
481 if (pgrp->epgrppbc == epgrppbcREFAT)
483 pgrp->x[m] += pull->rbuf[g][m];
486 pgrp->xp[m] += pull->rbuf[g][m];
493 /* Determine the optimal location of the cosine weight */
494 csw = pull->dbuf[g*3][0];
495 snw = pull->dbuf[g*3][1];
496 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
497 /* Set the weights for the local atoms */
498 wmass = sqrt(csw*csw + snw*snw);
499 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
500 pull->dbuf[g*3+1][1]*csw*snw +
501 pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
502 pgrp->wscale = wmass/wwmass;
503 pgrp->invtm = 1.0/(pgrp->wscale*wmass);
504 /* Set the weights for the local atoms */
507 for (i = 0; i < pgrp->nat_loc; i++)
509 ii = pgrp->ind_loc[i];
510 pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
511 snw*sin(twopi_box*x[ii][pull->cosdim]);
515 csw = pull->dbuf[g*3+2][0];
516 snw = pull->dbuf[g*3+2][1];
517 pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
522 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
523 g, wmass, wwmass, pgrp->invtm);
530 /* Calculate the COMs for the cyclinder reference groups */
531 make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);