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40 #include "types/commrec.h"
45 #include "gromacs/pbcutil/pbc.h"
46 #include "gromacs/topology/mtop_util.h"
48 #include "gromacs/linearalgebra/nrjac.h"
49 #include "gromacs/math/do_fit.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/pbcutil/ishift.h"
52 #include "gromacs/pbcutil/mshift.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/smalloc.h"
56 void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
59 const t_commrec *cr, t_oriresdata *od,
62 int i, j, d, ex, nmol, *nr_ex;
65 gmx_mtop_ilistloop_t iloop;
67 gmx_mtop_atomloop_all_t aloop;
69 const gmx_multisim_t *ms;
71 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
74 /* Not doing orientation restraints */
80 gmx_fatal(FARGS, "Orientation restraints do not work with more than one domain (ie. MPI rank).");
82 /* Orientation restraints */
90 od->fc = ir->orires_fc;
99 iloop = gmx_mtop_ilistloop_init(mtop);
100 while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
102 for (i = 0; i < il[F_ORIRES].nr; i += 3)
104 ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
108 for (j = od->nex; j < ex+1; j++)
117 snew(od->S, od->nex);
118 /* When not doing time averaging, the instaneous and time averaged data
119 * are indentical and the pointers can point to the same memory.
121 snew(od->Dinsl, od->nr);
124 snew(od->Dins, od->nr);
128 od->Dins = od->Dinsl;
131 if (ir->orires_tau == 0)
139 snew(od->Dtav, od->nr);
140 od->edt = exp(-ir->delta_t/ir->orires_tau);
141 od->edt_1 = 1.0 - od->edt;
143 /* Extend the state with the orires history */
144 state->flags |= (1<<estORIRE_INITF);
145 state->hist.orire_initf = 1;
146 state->flags |= (1<<estORIRE_DTAV);
147 state->hist.norire_Dtav = od->nr*5;
148 snew(state->hist.orire_Dtav, state->hist.norire_Dtav);
151 snew(od->oinsl, od->nr);
154 snew(od->oins, od->nr);
158 od->oins = od->oinsl;
160 if (ir->orires_tau == 0)
166 snew(od->otav, od->nr);
168 snew(od->tmp, od->nex);
169 snew(od->TMP, od->nex);
170 for (ex = 0; ex < od->nex; ex++)
172 snew(od->TMP[ex], 5);
173 for (i = 0; i < 5; i++)
175 snew(od->TMP[ex][i], 5);
180 for (i = 0; i < mtop->natoms; i++)
182 if (ggrpnr(&mtop->groups, egcORFIT, i) == 0)
187 snew(od->mref, od->nref);
188 snew(od->xref, od->nref);
189 snew(od->xtmp, od->nref);
191 snew(od->eig, od->nex*12);
193 /* Determine the reference structure on the master node.
194 * Copy it to the other nodes after checking multi compatibility,
195 * so we are sure the subsystems match before copying.
200 aloop = gmx_mtop_atomloop_all_init(mtop);
201 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
203 if (mtop->groups.grpnr[egcORFIT] == NULL ||
204 mtop->groups.grpnr[egcORFIT][i] == 0)
206 /* Not correct for free-energy with changing masses */
207 od->mref[j] = atom->m;
208 if (ms == NULL || MASTERSIM(ms))
210 copy_rvec(xref[i], od->xref[j]);
211 for (d = 0; d < DIM; d++)
213 com[d] += od->mref[j]*xref[i][d];
220 svmul(1.0/mtot, com, com);
221 if (ms == NULL || MASTERSIM(ms))
223 for (j = 0; j < od->nref; j++)
225 rvec_dec(od->xref[j], com);
229 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
230 for (i = 0; i < od->nex; i++)
232 fprintf(fplog, " experiment %d has %d restraints\n", i+1, nr_ex[i]);
237 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n",
242 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->nsim);
244 check_multi_int(fplog, ms, od->nr,
245 "the number of orientation restraints",
247 check_multi_int(fplog, ms, od->nref,
248 "the number of fit atoms for orientation restraining",
250 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
251 /* Copy the reference coordinates from the master to the other nodes */
252 gmx_sum_sim(DIM*od->nref, od->xref[0], ms);
255 please_cite(fplog, "Hess2003");
258 void diagonalize_orires_tensors(t_oriresdata *od)
260 int ex, i, j, nrot, ord[DIM], t;
266 for (i = 0; i < DIM; i++)
270 snew(od->eig_diag, DIM);
272 for (i = 0; i < DIM; i++)
278 for (ex = 0; ex < od->nex; ex++)
280 /* Rotate the S tensor back to the reference frame */
281 mmul(od->R, od->S[ex], TMP);
282 mtmul(TMP, od->R, S);
283 for (i = 0; i < DIM; i++)
285 for (j = 0; j < DIM; j++)
287 od->M[i][j] = S[i][j];
291 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
293 for (i = 0; i < DIM; i++)
297 for (i = 0; i < DIM; i++)
299 for (j = i+1; j < DIM; j++)
301 if (sqr(od->eig_diag[ord[j]]) > sqr(od->eig_diag[ord[i]]))
310 for (i = 0; i < DIM; i++)
312 od->eig[ex*12 + i] = od->eig_diag[ord[i]];
314 for (i = 0; i < DIM; i++)
316 for (j = 0; j < DIM; j++)
318 od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
324 void print_orires_log(FILE *log, t_oriresdata *od)
329 diagonalize_orires_tensors(od);
331 for (ex = 0; ex < od->nex; ex++)
333 eig = od->eig + ex*12;
334 fprintf(log, " Orientation experiment %d:\n", ex+1);
335 fprintf(log, " order parameter: %g\n", eig[0]);
336 for (i = 0; i < DIM; i++)
338 fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n",
339 (eig[0] != 0) ? eig[i]/eig[0] : eig[i],
348 real calc_orires_dev(const gmx_multisim_t *ms,
349 int nfa, const t_iatom forceatoms[], const t_iparams ip[],
350 const t_mdatoms *md, const rvec x[], const t_pbc *pbc,
351 t_fcdata *fcd, history_t *hist)
353 int fa, d, i, j, type, ex, nref;
354 real edt, edt_1, invn, pfac, r2, invr, corrfac, weight, wsv2, sw, dev;
356 rvec5 *Dinsl, *Dins, *Dtav, *rhs;
359 rvec *xref, *xtmp, com, r_unrot, r;
362 const real two_thr = 2.0/3.0;
368 /* This means that this is not the master node */
369 gmx_fatal(FARGS, "Orientation restraints are only supported on the master rank, use fewer ranks");
372 bTAV = (od->edt != 0);
388 od->exp_min_t_tau = hist->orire_initf*edt;
390 /* Correction factor to correct for the lack of history
393 corrfac = 1.0/(1.0 - od->exp_min_t_tau);
412 for (i = 0; i < md->nr; i++)
414 if (md->cORF[i] == 0)
416 copy_rvec(x[i], xtmp[j]);
417 mref[j] = md->massT[i];
418 for (d = 0; d < DIM; d++)
420 com[d] += mref[j]*xref[j][d];
426 svmul(1.0/mtot, com, com);
427 for (j = 0; j < nref; j++)
429 rvec_dec(xtmp[j], com);
431 /* Calculate the rotation matrix to rotate x to the reference orientation */
432 calc_fit_R(DIM, nref, mref, xref, xtmp, R);
436 for (fa = 0; fa < nfa; fa += 3)
438 type = forceatoms[fa];
441 pbc_dx_aiuc(pbc, x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
445 rvec_sub(x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
447 mvmul(R, r_unrot, r);
449 invr = gmx_invsqrt(r2);
450 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
451 pfac = ip[type].orires.c*invr*invr*3;
452 for (i = 0; i < ip[type].orires.power; i++)
456 Dinsl[d][0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
457 Dinsl[d][1] = pfac*(2*r[0]*r[1]);
458 Dinsl[d][2] = pfac*(2*r[0]*r[2]);
459 Dinsl[d][3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
460 Dinsl[d][4] = pfac*(2*r[1]*r[2]);
464 for (i = 0; i < 5; i++)
466 Dins[d][i] = Dinsl[d][i]*invn;
475 gmx_sum_sim(5*od->nr, Dins[0], ms);
478 /* Calculate the order tensor S for each experiment via optimization */
479 for (ex = 0; ex < od->nex; ex++)
481 for (i = 0; i < 5; i++)
484 for (j = 0; j <= i; j++)
491 for (fa = 0; fa < nfa; fa += 3)
495 /* Here we update Dtav in t_fcdata using the data in history_t.
496 * Thus the results stay correct when this routine
497 * is called multiple times.
499 for (i = 0; i < 5; i++)
501 Dtav[d][i] = edt*hist->orire_Dtav[d*5+i] + edt_1*Dins[d][i];
505 type = forceatoms[fa];
506 ex = ip[type].orires.ex;
507 weight = ip[type].orires.kfac;
508 /* Calculate the vector rhs and half the matrix T for the 5 equations */
509 for (i = 0; i < 5; i++)
511 rhs[ex][i] += Dtav[d][i]*ip[type].orires.obs*weight;
512 for (j = 0; j <= i; j++)
514 T[ex][i][j] += Dtav[d][i]*Dtav[d][j]*weight;
519 /* Now we have all the data we can calculate S */
520 for (ex = 0; ex < od->nex; ex++)
522 /* Correct corrfac and copy one half of T to the other half */
523 for (i = 0; i < 5; i++)
525 rhs[ex][i] *= corrfac;
526 T[ex][i][i] *= sqr(corrfac);
527 for (j = 0; j < i; j++)
529 T[ex][i][j] *= sqr(corrfac);
530 T[ex][j][i] = T[ex][i][j];
533 m_inv_gen(T[ex], 5, T[ex]);
534 /* Calculate the orientation tensor S for this experiment */
540 for (i = 0; i < 5; i++)
542 S[ex][0][0] += 1.5*T[ex][0][i]*rhs[ex][i];
543 S[ex][0][1] += 1.5*T[ex][1][i]*rhs[ex][i];
544 S[ex][0][2] += 1.5*T[ex][2][i]*rhs[ex][i];
545 S[ex][1][1] += 1.5*T[ex][3][i]*rhs[ex][i];
546 S[ex][1][2] += 1.5*T[ex][4][i]*rhs[ex][i];
548 S[ex][1][0] = S[ex][0][1];
549 S[ex][2][0] = S[ex][0][2];
550 S[ex][2][1] = S[ex][1][2];
551 S[ex][2][2] = -S[ex][0][0] - S[ex][1][1];
558 for (fa = 0; fa < nfa; fa += 3)
560 type = forceatoms[fa];
561 ex = ip[type].orires.ex;
563 od->otav[d] = two_thr*
564 corrfac*(S[ex][0][0]*Dtav[d][0] + S[ex][0][1]*Dtav[d][1] +
565 S[ex][0][2]*Dtav[d][2] + S[ex][1][1]*Dtav[d][3] +
566 S[ex][1][2]*Dtav[d][4]);
569 od->oins[d] = two_thr*(S[ex][0][0]*Dins[d][0] + S[ex][0][1]*Dins[d][1] +
570 S[ex][0][2]*Dins[d][2] + S[ex][1][1]*Dins[d][3] +
571 S[ex][1][2]*Dins[d][4]);
575 /* When ensemble averaging is used recalculate the local orientation
576 * for output to the energy file.
578 od->oinsl[d] = two_thr*
579 (S[ex][0][0]*Dinsl[d][0] + S[ex][0][1]*Dinsl[d][1] +
580 S[ex][0][2]*Dinsl[d][2] + S[ex][1][1]*Dinsl[d][3] +
581 S[ex][1][2]*Dinsl[d][4]);
584 dev = od->otav[d] - ip[type].orires.obs;
586 wsv2 += ip[type].orires.kfac*sqr(dev);
587 sw += ip[type].orires.kfac;
591 od->rmsdev = sqrt(wsv2/sw);
593 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
594 for (ex = 0; ex < od->nex; ex++)
596 tmmul(R, S[ex], TMP);
602 /* Approx. 120*nfa/3 flops */
605 real orires(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
606 const rvec x[], rvec f[], rvec fshift[],
607 const t_pbc *pbc, const t_graph *g,
608 real gmx_unused lambda, real gmx_unused *dvdlambda,
609 const t_mdatoms gmx_unused *md, t_fcdata *fcd,
610 int gmx_unused *global_atom_index)
613 int fa, d, i, type, ex, power, ki = CENTRAL;
615 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
618 const t_oriresdata *od;
626 bTAV = (od->edt != 0);
631 /* Smoothly switch on the restraining when time averaging is used */
632 smooth_fc *= (1.0 - od->exp_min_t_tau);
636 for (fa = 0; fa < nfa; fa += 3)
638 type = forceatoms[fa];
639 ai = forceatoms[fa+1];
640 aj = forceatoms[fa+2];
643 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
647 rvec_sub(x[ai], x[aj], r);
650 invr = gmx_invsqrt(r2);
652 ex = ip[type].orires.ex;
653 power = ip[type].orires.power;
654 fc = smooth_fc*ip[type].orires.kfac;
655 dev = od->otav[d] - ip[type].orires.obs;
658 * there is no real potential when time averaging is applied
660 vtot += 0.5*fc*sqr(dev);
664 /* Calculate the force as the sqrt of tav times instantaneous */
665 devins = od->oins[d] - ip[type].orires.obs;
672 dev = sqrt(dev*devins);
680 pfac = fc*ip[type].orires.c*invr2;
681 for (i = 0; i < power; i++)
685 mvmul(od->S[ex], r, Sr);
686 for (i = 0; i < DIM; i++)
689 -pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr, r)*r[i]);
694 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
698 for (i = 0; i < DIM; i++)
702 fshift[ki][i] += fij[i];
703 fshift[CENTRAL][i] -= fij[i];
711 /* Approx. 80*nfa/3 flops */
714 void update_orires_history(t_fcdata *fcd, history_t *hist)
722 /* Copy the new time averages that have been calculated
723 * in calc_orires_dev.
725 hist->orire_initf = od->exp_min_t_tau;
726 for (pair = 0; pair < od->nr; pair++)
728 for (i = 0; i < 5; i++)
730 hist->orire_Dtav[pair*5+i] = od->Dtav[pair][i];