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51 #include "mtop_util.h"
53 void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
56 const gmx_multisim_t *ms, t_oriresdata *od,
59 int i, j, d, ex, nmol, nr, *nr_ex;
62 gmx_mtop_ilistloop_t iloop;
64 gmx_mtop_atomloop_all_t aloop;
67 od->fc = ir->orires_fc;
75 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
83 iloop = gmx_mtop_ilistloop_init(mtop);
84 while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
86 for (i = 0; i < il[F_ORIRES].nr; i += 3)
88 ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
92 for (j = od->nex; j < ex+1; j++)
101 snew(od->S, od->nex);
102 /* When not doing time averaging, the instaneous and time averaged data
103 * are indentical and the pointers can point to the same memory.
105 snew(od->Dinsl, od->nr);
108 snew(od->Dins, od->nr);
112 od->Dins = od->Dinsl;
115 if (ir->orires_tau == 0)
123 snew(od->Dtav, od->nr);
124 od->edt = exp(-ir->delta_t/ir->orires_tau);
125 od->edt_1 = 1.0 - od->edt;
127 /* Extend the state with the orires history */
128 state->flags |= (1<<estORIRE_INITF);
129 state->hist.orire_initf = 1;
130 state->flags |= (1<<estORIRE_DTAV);
131 state->hist.norire_Dtav = od->nr*5;
132 snew(state->hist.orire_Dtav, state->hist.norire_Dtav);
135 snew(od->oinsl, od->nr);
138 snew(od->oins, od->nr);
142 od->oins = od->oinsl;
144 if (ir->orires_tau == 0)
150 snew(od->otav, od->nr);
152 snew(od->tmp, od->nex);
153 snew(od->TMP, od->nex);
154 for (ex = 0; ex < od->nex; ex++)
156 snew(od->TMP[ex], 5);
157 for (i = 0; i < 5; i++)
159 snew(od->TMP[ex][i], 5);
164 for (i = 0; i < mtop->natoms; i++)
166 if (ggrpnr(&mtop->groups, egcORFIT, i) == 0)
171 snew(od->mref, od->nref);
172 snew(od->xref, od->nref);
173 snew(od->xtmp, od->nref);
175 snew(od->eig, od->nex*12);
177 /* Determine the reference structure on the master node.
178 * Copy it to the other nodes after checking multi compatibility,
179 * so we are sure the subsystems match before copying.
184 aloop = gmx_mtop_atomloop_all_init(mtop);
185 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
187 if (mtop->groups.grpnr[egcORFIT] == NULL ||
188 mtop->groups.grpnr[egcORFIT][i] == 0)
190 /* Not correct for free-energy with changing masses */
191 od->mref[j] = atom->m;
192 if (ms == NULL || MASTERSIM(ms))
194 copy_rvec(xref[i], od->xref[j]);
195 for (d = 0; d < DIM; d++)
197 com[d] += od->mref[j]*xref[i][d];
204 svmul(1.0/mtot, com, com);
205 if (ms == NULL || MASTERSIM(ms))
207 for (j = 0; j < od->nref; j++)
209 rvec_dec(od->xref[j], com);
213 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
214 for (i = 0; i < od->nex; i++)
216 fprintf(fplog, " experiment %d has %d restraints\n", i+1, nr_ex[i]);
221 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n",
226 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->nsim);
228 check_multi_int(fplog, ms, od->nr,
229 "the number of orientation restraints",
231 check_multi_int(fplog, ms, od->nref,
232 "the number of fit atoms for orientation restraining",
234 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
235 /* Copy the reference coordinates from the master to the other nodes */
236 gmx_sum_sim(DIM*od->nref, od->xref[0], ms);
239 please_cite(fplog, "Hess2003");
242 void diagonalize_orires_tensors(t_oriresdata *od)
244 int ex, i, j, nrot, ord[DIM], t;
250 for (i = 0; i < DIM; i++)
254 snew(od->eig_diag, DIM);
256 for (i = 0; i < DIM; i++)
262 for (ex = 0; ex < od->nex; ex++)
264 /* Rotate the S tensor back to the reference frame */
265 mmul(od->R, od->S[ex], TMP);
266 mtmul(TMP, od->R, S);
267 for (i = 0; i < DIM; i++)
269 for (j = 0; j < DIM; j++)
271 od->M[i][j] = S[i][j];
275 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
277 for (i = 0; i < DIM; i++)
281 for (i = 0; i < DIM; i++)
283 for (j = i+1; j < DIM; j++)
285 if (sqr(od->eig_diag[ord[j]]) > sqr(od->eig_diag[ord[i]]))
294 for (i = 0; i < DIM; i++)
296 od->eig[ex*12 + i] = od->eig_diag[ord[i]];
298 for (i = 0; i < DIM; i++)
300 for (j = 0; j < DIM; j++)
302 od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
308 void print_orires_log(FILE *log, t_oriresdata *od)
313 diagonalize_orires_tensors(od);
315 for (ex = 0; ex < od->nex; ex++)
317 eig = od->eig + ex*12;
318 fprintf(log, " Orientation experiment %d:\n", ex+1);
319 fprintf(log, " order parameter: %g\n", eig[0]);
320 for (i = 0; i < DIM; i++)
322 fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n",
323 (eig[0] != 0) ? eig[i]/eig[0] : eig[i],
332 real calc_orires_dev(const gmx_multisim_t *ms,
333 int nfa, const t_iatom forceatoms[], const t_iparams ip[],
334 const t_mdatoms *md, const rvec x[], const t_pbc *pbc,
335 t_fcdata *fcd, history_t *hist)
337 int fa, d, i, j, type, ex, nref;
338 real edt, edt_1, invn, pfac, r2, invr, corrfac, weight, wsv2, sw, dev;
340 rvec5 *Dinsl, *Dins, *Dtav, *rhs;
343 rvec *xref, *xtmp, com, r_unrot, r;
346 const real two_thr = 2.0/3.0;
352 /* This means that this is not the master node */
353 gmx_fatal(FARGS, "Orientation restraints are only supported on the master node, use less processors");
356 bTAV = (od->edt != 0);
372 od->exp_min_t_tau = hist->orire_initf*edt;
374 /* Correction factor to correct for the lack of history
377 corrfac = 1.0/(1.0 - od->exp_min_t_tau);
396 for (i = 0; i < md->nr; i++)
398 if (md->cORF[i] == 0)
400 copy_rvec(x[i], xtmp[j]);
401 mref[j] = md->massT[i];
402 for (d = 0; d < DIM; d++)
404 com[d] += mref[j]*xref[j][d];
410 svmul(1.0/mtot, com, com);
411 for (j = 0; j < nref; j++)
413 rvec_dec(xtmp[j], com);
415 /* Calculate the rotation matrix to rotate x to the reference orientation */
416 calc_fit_R(DIM, nref, mref, xref, xtmp, R);
420 for (fa = 0; fa < nfa; fa += 3)
422 type = forceatoms[fa];
425 pbc_dx_aiuc(pbc, x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
429 rvec_sub(x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
431 mvmul(R, r_unrot, r);
433 invr = gmx_invsqrt(r2);
434 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
435 pfac = ip[type].orires.c*invr*invr*3;
436 for (i = 0; i < ip[type].orires.power; i++)
440 Dinsl[d][0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
441 Dinsl[d][1] = pfac*(2*r[0]*r[1]);
442 Dinsl[d][2] = pfac*(2*r[0]*r[2]);
443 Dinsl[d][3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
444 Dinsl[d][4] = pfac*(2*r[1]*r[2]);
448 for (i = 0; i < 5; i++)
450 Dins[d][i] = Dinsl[d][i]*invn;
459 gmx_sum_sim(5*od->nr, Dins[0], ms);
462 /* Calculate the order tensor S for each experiment via optimization */
463 for (ex = 0; ex < od->nex; ex++)
465 for (i = 0; i < 5; i++)
468 for (j = 0; j <= i; j++)
475 for (fa = 0; fa < nfa; fa += 3)
479 /* Here we update Dtav in t_fcdata using the data in history_t.
480 * Thus the results stay correct when this routine
481 * is called multiple times.
483 for (i = 0; i < 5; i++)
485 Dtav[d][i] = edt*hist->orire_Dtav[d*5+i] + edt_1*Dins[d][i];
489 type = forceatoms[fa];
490 ex = ip[type].orires.ex;
491 weight = ip[type].orires.kfac;
492 /* Calculate the vector rhs and half the matrix T for the 5 equations */
493 for (i = 0; i < 5; i++)
495 rhs[ex][i] += Dtav[d][i]*ip[type].orires.obs*weight;
496 for (j = 0; j <= i; j++)
498 T[ex][i][j] += Dtav[d][i]*Dtav[d][j]*weight;
503 /* Now we have all the data we can calculate S */
504 for (ex = 0; ex < od->nex; ex++)
506 /* Correct corrfac and copy one half of T to the other half */
507 for (i = 0; i < 5; i++)
509 rhs[ex][i] *= corrfac;
510 T[ex][i][i] *= sqr(corrfac);
511 for (j = 0; j < i; j++)
513 T[ex][i][j] *= sqr(corrfac);
514 T[ex][j][i] = T[ex][i][j];
517 m_inv_gen(T[ex], 5, T[ex]);
518 /* Calculate the orientation tensor S for this experiment */
524 for (i = 0; i < 5; i++)
526 S[ex][0][0] += 1.5*T[ex][0][i]*rhs[ex][i];
527 S[ex][0][1] += 1.5*T[ex][1][i]*rhs[ex][i];
528 S[ex][0][2] += 1.5*T[ex][2][i]*rhs[ex][i];
529 S[ex][1][1] += 1.5*T[ex][3][i]*rhs[ex][i];
530 S[ex][1][2] += 1.5*T[ex][4][i]*rhs[ex][i];
532 S[ex][1][0] = S[ex][0][1];
533 S[ex][2][0] = S[ex][0][2];
534 S[ex][2][1] = S[ex][1][2];
535 S[ex][2][2] = -S[ex][0][0] - S[ex][1][1];
542 for (fa = 0; fa < nfa; fa += 3)
544 type = forceatoms[fa];
545 ex = ip[type].orires.ex;
547 od->otav[d] = two_thr*
548 corrfac*(S[ex][0][0]*Dtav[d][0] + S[ex][0][1]*Dtav[d][1] +
549 S[ex][0][2]*Dtav[d][2] + S[ex][1][1]*Dtav[d][3] +
550 S[ex][1][2]*Dtav[d][4]);
553 od->oins[d] = two_thr*(S[ex][0][0]*Dins[d][0] + S[ex][0][1]*Dins[d][1] +
554 S[ex][0][2]*Dins[d][2] + S[ex][1][1]*Dins[d][3] +
555 S[ex][1][2]*Dins[d][4]);
559 /* When ensemble averaging is used recalculate the local orientation
560 * for output to the energy file.
562 od->oinsl[d] = two_thr*
563 (S[ex][0][0]*Dinsl[d][0] + S[ex][0][1]*Dinsl[d][1] +
564 S[ex][0][2]*Dinsl[d][2] + S[ex][1][1]*Dinsl[d][3] +
565 S[ex][1][2]*Dinsl[d][4]);
568 dev = od->otav[d] - ip[type].orires.obs;
570 wsv2 += ip[type].orires.kfac*sqr(dev);
571 sw += ip[type].orires.kfac;
575 od->rmsdev = sqrt(wsv2/sw);
577 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
578 for (ex = 0; ex < od->nex; ex++)
580 tmmul(R, S[ex], TMP);
586 /* Approx. 120*nfa/3 flops */
589 real orires(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
590 const rvec x[], rvec f[], rvec fshift[],
591 const t_pbc *pbc, const t_graph *g,
592 real gmx_unused lambda, real gmx_unused *dvdlambda,
593 const t_mdatoms gmx_unused *md, t_fcdata *fcd,
594 int gmx_unused *global_atom_index)
597 int fa, d, i, type, ex, power, ki = CENTRAL;
599 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
602 const t_oriresdata *od;
610 bTAV = (od->edt != 0);
615 /* Smoothly switch on the restraining when time averaging is used */
616 smooth_fc *= (1.0 - od->exp_min_t_tau);
620 for (fa = 0; fa < nfa; fa += 3)
622 type = forceatoms[fa];
623 ai = forceatoms[fa+1];
624 aj = forceatoms[fa+2];
627 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
631 rvec_sub(x[ai], x[aj], r);
634 invr = gmx_invsqrt(r2);
636 ex = ip[type].orires.ex;
637 power = ip[type].orires.power;
638 fc = smooth_fc*ip[type].orires.kfac;
639 dev = od->otav[d] - ip[type].orires.obs;
642 * there is no real potential when time averaging is applied
644 vtot += 0.5*fc*sqr(dev);
648 /* Calculate the force as the sqrt of tav times instantaneous */
649 devins = od->oins[d] - ip[type].orires.obs;
656 dev = sqrt(dev*devins);
664 pfac = fc*ip[type].orires.c*invr2;
665 for (i = 0; i < power; i++)
669 mvmul(od->S[ex], r, Sr);
670 for (i = 0; i < DIM; i++)
673 -pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr, r)*r[i]);
678 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
682 for (i = 0; i < DIM; i++)
686 fshift[ki][i] += fij[i];
687 fshift[CENTRAL][i] -= fij[i];
695 /* Approx. 80*nfa/3 flops */
698 void update_orires_history(t_fcdata *fcd, history_t *hist)
706 /* Copy the new time averages that have been calculated
707 * in calc_orires_dev.
709 hist->orire_initf = od->exp_min_t_tau;
710 for (pair = 0; pair < od->nr; pair++)
712 for (i = 0; i < 5; i++)
714 hist->orire_Dtav[pair*5+i] = od->Dtav[pair][i];