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45 #include "gromacs/gmxlib/network.h"
46 #include "gromacs/linearalgebra/nrjac.h"
47 #include "gromacs/math/do_fit.h"
48 #include "gromacs/math/functions.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/mdrunutility/multisim.h"
51 #include "gromacs/mdtypes/commrec.h"
52 #include "gromacs/mdtypes/fcdata.h"
53 #include "gromacs/mdtypes/inputrec.h"
54 #include "gromacs/mdtypes/mdatom.h"
55 #include "gromacs/mdtypes/state.h"
56 #include "gromacs/pbcutil/ishift.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/ifunc.h"
59 #include "gromacs/topology/mtop_util.h"
60 #include "gromacs/topology/topology.h"
61 #include "gromacs/utility/arrayref.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/pleasecite.h"
64 #include "gromacs/utility/smalloc.h"
69 // TODO This implementation of ensemble orientation restraints is nasty because
70 // a user can't just do multi-sim with single-sim orientation restraints.
72 void init_orires(FILE* fplog,
73 const gmx_mtop_t& mtop,
76 const gmx_multisim_t* ms,
80 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
83 /* Not doing orientation restraints */
87 const int numFitParams = 5;
88 if (od->nr <= numFitParams)
91 "The system has %d orientation restraints, but at least %d are required, since "
92 "there are %d fitting parameters.",
98 if (ir->bPeriodicMols)
100 /* Since we apply fitting, we need to make molecules whole and this
101 * can not be done when periodic molecules are present.
104 "Orientation restraints can not be applied when periodic molecules are present "
111 "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, "
115 GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");
117 od->fc = ir->orires_fc;
124 int* nr_ex = nullptr;
125 int typeMin = INT_MAX;
127 for (const auto il : IListRange(mtop))
129 const int numOrires = il.list()[F_ORIRES].size();
130 if (il.nmol() > 1 && numOrires > 0)
133 "Found %d copies of a molecule with orientation restrains while the current "
134 "code only supports a single copy. If you want to ensemble average, run "
135 "multiple copies of the system using the multi-sim feature of mdrun.",
139 for (int i = 0; i < numOrires; i += 3)
141 int type = il.list()[F_ORIRES].iatoms[i];
142 int ex = mtop.ffparams.iparams[type].orires.ex;
145 srenew(nr_ex, ex + 1);
146 for (int j = od->nex; j < ex + 1; j++)
152 GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
155 typeMin = std::min(typeMin, type);
156 typeMax = std::max(typeMax, type);
159 /* With domain decomposition we use the type index for indexing in global arrays */
161 typeMax - typeMin + 1 == od->nr,
162 "All orientation restraint parameter entries in the topology should be consecutive");
163 /* Store typeMin so we can index array with the type offset */
164 od->typeMin = typeMin;
166 snew(od->S, od->nex);
167 /* When not doing time averaging, the instaneous and time averaged data
168 * are indentical and the pointers can point to the same memory.
170 snew(od->Dinsl, od->nr);
174 snew(od->Dins, od->nr);
178 od->Dins = od->Dinsl;
181 if (ir->orires_tau == 0)
189 snew(od->Dtav, od->nr);
190 od->edt = std::exp(-ir->delta_t / ir->orires_tau);
191 od->edt_1 = 1.0 - od->edt;
193 /* Extend the state with the orires history */
194 globalState->flags |= enumValueToBitMask(StateEntry::OrireInitF);
195 globalState->hist.orire_initf = 1;
196 globalState->flags |= enumValueToBitMask(StateEntry::OrireDtav);
197 globalState->hist.orire_Dtav.resize(od->nr * 5);
200 snew(od->oinsl, od->nr);
203 snew(od->oins, od->nr);
207 od->oins = od->oinsl;
209 if (ir->orires_tau == 0)
215 snew(od->otav, od->nr);
217 snew(od->tmpEq, od->nex);
220 for (int i = 0; i < mtop.natoms; i++)
222 if (getGroupType(mtop.groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
227 snew(od->mref, od->nref);
228 snew(od->xref, od->nref);
229 snew(od->xtmp, od->nref);
231 snew(od->eig, od->nex * 12);
233 /* Determine the reference structure on the master node.
234 * Copy it to the other nodes after checking multi compatibility,
235 * so we are sure the subsystems match before copying.
237 auto x = makeArrayRef(globalState->x);
238 rvec com = { 0, 0, 0 };
241 for (const AtomProxy atomP : AtomRange(mtop))
243 const t_atom& local = atomP.atom();
244 int i = atomP.globalAtomNumber();
245 if (mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty()
246 || mtop.groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
248 /* Not correct for free-energy with changing masses */
249 od->mref[j] = local.m;
250 // Note that only one rank per sim is supported.
253 copy_rvec(x[i], od->xref[j]);
254 for (int d = 0; d < DIM; d++)
256 com[d] += od->mref[j] * x[i][d];
263 svmul(1.0 / mtot, com, com);
266 for (int j = 0; j < od->nref; j++)
268 rvec_dec(od->xref[j], com);
272 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
273 for (int i = 0; i < od->nex; i++)
275 fprintf(fplog, " experiment %d has %d restraints\n", i + 1, nr_ex[i]);
280 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n", od->nref, mtot);
284 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->numSimulations_);
286 check_multi_int(fplog, ms, od->nr, "the number of orientation restraints", FALSE);
287 check_multi_int(fplog, ms, od->nref, "the number of fit atoms for orientation restraining", FALSE);
288 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
289 /* Copy the reference coordinates from the master to the other nodes */
290 gmx_sum_sim(DIM * od->nref, od->xref[0], ms);
293 please_cite(fplog, "Hess2003");
296 void diagonalize_orires_tensors(t_oriresdata* od)
298 if (od->M == nullptr)
301 for (int i = 0; i < DIM; i++)
305 snew(od->eig_diag, DIM);
307 for (int i = 0; i < DIM; i++)
313 for (int ex = 0; ex < od->nex; ex++)
315 /* Rotate the S tensor back to the reference frame */
317 mmul(od->R, od->S[ex], TMP);
318 mtmul(TMP, od->R, S);
319 for (int i = 0; i < DIM; i++)
321 for (int j = 0; j < DIM; j++)
323 od->M[i][j] = S[i][j];
328 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
331 for (int i = 0; i < DIM; i++)
335 for (int i = 0; i < DIM; i++)
337 for (int j = i + 1; j < DIM; j++)
339 if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
348 for (int i = 0; i < DIM; i++)
350 od->eig[ex * 12 + i] = od->eig_diag[ord[i]];
352 for (int i = 0; i < DIM; i++)
354 for (int j = 0; j < DIM; j++)
356 od->eig[ex * 12 + 3 + 3 * i + j] = od->v[j][ord[i]];
362 void print_orires_log(FILE* log, t_oriresdata* od)
366 diagonalize_orires_tensors(od);
368 for (int ex = 0; ex < od->nex; ex++)
370 eig = od->eig + ex * 12;
371 fprintf(log, " Orientation experiment %d:\n", ex + 1);
372 fprintf(log, " order parameter: %g\n", eig[0]);
373 for (int i = 0; i < DIM; i++)
376 " eig: %6.3f %6.3f %6.3f %6.3f\n",
377 (eig[0] != 0) ? eig[i] / eig[0] : eig[i],
378 eig[DIM + i * DIM + XX],
379 eig[DIM + i * DIM + YY],
380 eig[DIM + i * DIM + ZZ]);
386 real calc_orires_dev(const gmx_multisim_t* ms,
388 const t_iatom forceatoms[],
389 const t_iparams ip[],
391 ArrayRef<const RVec> xWholeMolecules,
395 const history_t* hist)
398 real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
402 rvec * xref, *xtmp, com, r_unrot, r;
404 const real two_thr = 2.0 / 3.0;
408 /* This means that this is not the master node */
410 "Orientation restraints are only supported on the master rank, use fewer ranks");
413 bTAV = (od->edt != 0);
424 od->exp_min_t_tau = hist->orire_initf * edt;
426 /* Correction factor to correct for the lack of history
429 corrfac = 1.0 / (1.0 - od->exp_min_t_tau);
438 invn = 1.0 / ms->numSimulations_;
448 auto* massT = md->massT;
449 auto* cORF = md->cORF;
450 for (int i = 0; i < md->nr; i++)
454 copy_rvec(xWholeMolecules[i], xtmp[j]);
456 for (int d = 0; d < DIM; d++)
458 com[d] += mref[j] * xtmp[j][d];
464 svmul(1.0 / mtot, com, com);
465 for (int j = 0; j < nref; j++)
467 rvec_dec(xtmp[j], com);
469 /* Calculate the rotation matrix to rotate x to the reference orientation */
470 calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
472 for (int fa = 0; fa < nfa; fa += 3)
474 const int type = forceatoms[fa];
475 const int restraintIndex = type - od->typeMin;
478 pbc_dx_aiuc(pbc, x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
482 rvec_sub(x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
484 mvmul(od->R, r_unrot, r);
486 invr = gmx::invsqrt(r2);
487 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
488 pfac = ip[type].orires.c * invr * invr * 3;
489 for (int i = 0; i < ip[type].orires.power; i++)
493 rvec5& Dinsl = od->Dinsl[restraintIndex];
494 Dinsl[0] = pfac * (2 * r[0] * r[0] + r[1] * r[1] - r2);
495 Dinsl[1] = pfac * (2 * r[0] * r[1]);
496 Dinsl[2] = pfac * (2 * r[0] * r[2]);
497 Dinsl[3] = pfac * (2 * r[1] * r[1] + r[0] * r[0] - r2);
498 Dinsl[4] = pfac * (2 * r[1] * r[2]);
502 for (int i = 0; i < 5; i++)
504 od->Dins[restraintIndex][i] = Dinsl[i] * invn;
511 gmx_sum_sim(5 * od->nr, od->Dins[0], ms);
514 /* Calculate the order tensor S for each experiment via optimization */
515 for (int ex = 0; ex < od->nex; ex++)
517 for (int i = 0; i < 5; i++)
519 matEq[ex].rhs[i] = 0;
520 for (int j = 0; j <= i; j++)
522 matEq[ex].mat[i][j] = 0;
527 for (int fa = 0; fa < nfa; fa += 3)
529 const int type = forceatoms[fa];
530 const int restraintIndex = type - od->typeMin;
531 rvec5& Dtav = od->Dtav[restraintIndex];
534 /* Here we update Dtav in t_fcdata using the data in history_t.
535 * Thus the results stay correct when this routine
536 * is called multiple times.
538 for (int i = 0; i < 5; i++)
540 Dtav[i] = edt * hist->orire_Dtav[restraintIndex * 5 + i]
541 + edt_1 * od->Dins[restraintIndex][i];
545 int ex = ip[type].orires.ex;
546 real weight = ip[type].orires.kfac;
547 /* Calculate the vector rhs and half the matrix T for the 5 equations */
548 for (int i = 0; i < 5; i++)
550 matEq[ex].rhs[i] += Dtav[i] * ip[type].orires.obs * weight;
551 for (int j = 0; j <= i; j++)
553 matEq[ex].mat[i][j] += Dtav[i] * Dtav[j] * weight;
557 /* Now we have all the data we can calculate S */
558 for (int ex = 0; ex < od->nex; ex++)
560 OriresMatEq& eq = matEq[ex];
561 /* Correct corrfac and copy one half of T to the other half */
562 for (int i = 0; i < 5; i++)
564 eq.rhs[i] *= corrfac;
565 eq.mat[i][i] *= gmx::square(corrfac);
566 for (int j = 0; j < i; j++)
568 eq.mat[i][j] *= gmx::square(corrfac);
569 eq.mat[j][i] = eq.mat[i][j];
572 m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
573 /* Calculate the orientation tensor S for this experiment */
574 matrix& S = od->S[ex];
580 for (int i = 0; i < 5; i++)
582 S[0][0] += 1.5 * eq.mat[0][i] * eq.rhs[i];
583 S[0][1] += 1.5 * eq.mat[1][i] * eq.rhs[i];
584 S[0][2] += 1.5 * eq.mat[2][i] * eq.rhs[i];
585 S[1][1] += 1.5 * eq.mat[3][i] * eq.rhs[i];
586 S[1][2] += 1.5 * eq.mat[4][i] * eq.rhs[i];
591 S[2][2] = -S[0][0] - S[1][1];
594 const matrix* S = od->S;
599 for (int fa = 0; fa < nfa; fa += 3)
601 const int type = forceatoms[fa];
602 const int restraintIndex = type - od->typeMin;
603 const int ex = ip[type].orires.ex;
605 const rvec5& Dtav = od->Dtav[restraintIndex];
606 od->otav[restraintIndex] =
608 * (S[ex][0][0] * Dtav[0] + S[ex][0][1] * Dtav[1] + S[ex][0][2] * Dtav[2]
609 + S[ex][1][1] * Dtav[3] + S[ex][1][2] * Dtav[4]);
612 const rvec5& Dins = od->Dins[restraintIndex];
613 od->oins[restraintIndex] =
615 * (S[ex][0][0] * Dins[0] + S[ex][0][1] * Dins[1] + S[ex][0][2] * Dins[2]
616 + S[ex][1][1] * Dins[3] + S[ex][1][2] * Dins[4]);
620 /* When ensemble averaging is used recalculate the local orientation
621 * for output to the energy file.
623 const rvec5& Dinsl = od->Dinsl[restraintIndex];
624 od->oinsl[restraintIndex] =
626 * (S[ex][0][0] * Dinsl[0] + S[ex][0][1] * Dinsl[1] + S[ex][0][2] * Dinsl[2]
627 + S[ex][1][1] * Dinsl[3] + S[ex][1][2] * Dinsl[4]);
630 dev = od->otav[restraintIndex] - ip[type].orires.obs;
632 wsv2 += ip[type].orires.kfac * gmx::square(dev);
633 sw += ip[type].orires.kfac;
635 od->rmsdev = std::sqrt(wsv2 / sw);
637 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
638 for (int ex = 0; ex < od->nex; ex++)
641 tmmul(od->R, od->S[ex], RS);
642 mmul(RS, od->R, od->S[ex]);
647 /* Approx. 120*nfa/3 flops */
651 const t_iatom forceatoms[],
652 const t_iparams ip[],
657 real gmx_unused lambda,
658 real gmx_unused* dvdlambda,
659 gmx::ArrayRef<const real> /*charge*/,
660 t_fcdata gmx_unused* fcd,
661 t_disresdata gmx_unused* disresdata,
662 t_oriresdata* oriresdata,
663 int gmx_unused* global_atom_index)
665 int ex, power, ki = gmx::c_centralShiftIndex;
666 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
673 if (oriresdata->fc != 0)
675 bTAV = (oriresdata->edt != 0);
677 smooth_fc = oriresdata->fc;
680 /* Smoothly switch on the restraining when time averaging is used */
681 smooth_fc *= (1.0 - oriresdata->exp_min_t_tau);
684 for (int fa = 0; fa < nfa; fa += 3)
686 const int type = forceatoms[fa];
687 const int ai = forceatoms[fa + 1];
688 const int aj = forceatoms[fa + 2];
689 const int restraintIndex = type - oriresdata->typeMin;
692 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
696 rvec_sub(x[ai], x[aj], r);
699 invr = gmx::invsqrt(r2);
701 ex = ip[type].orires.ex;
702 power = ip[type].orires.power;
703 fc = smooth_fc * ip[type].orires.kfac;
704 dev = oriresdata->otav[restraintIndex] - ip[type].orires.obs;
707 * there is no real potential when time averaging is applied
709 vtot += 0.5 * fc * gmx::square(dev);
713 /* Calculate the force as the sqrt of tav times instantaneous */
714 devins = oriresdata->oins[restraintIndex] - ip[type].orires.obs;
715 if (dev * devins <= 0)
721 dev = std::sqrt(dev * devins);
729 pfac = fc * ip[type].orires.c * invr2;
730 for (int i = 0; i < power; i++)
734 mvmul(oriresdata->S[ex], r, Sr);
735 for (int i = 0; i < DIM; i++)
737 fij[i] = -pfac * dev * (4 * Sr[i] - 2 * (2 + power) * invr2 * iprod(Sr, r) * r[i]);
740 for (int i = 0; i < DIM; i++)
746 fshift[ki][i] += fij[i];
747 fshift[gmx::c_centralShiftIndex][i] -= fij[i];
755 /* Approx. 80*nfa/3 flops */
758 void update_orires_history(const t_oriresdata& od, history_t* hist)
762 /* Copy the new time averages that have been calculated
763 * in calc_orires_dev.
765 hist->orire_initf = od.exp_min_t_tau;
766 for (int pair = 0; pair < od.nr; pair++)
768 for (int i = 0; i < 5; i++)
770 hist->orire_Dtav[pair * 5 + i] = od.Dtav[pair][i];