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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/mshift.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "gromacs/topology/ifunc.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/topology.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/pleasecite.h"
64 #include "gromacs/utility/smalloc.h"
66 // TODO This implementation of ensemble orientation restraints is nasty because
67 // a user can't just do multi-sim with single-sim orientation restraints.
69 void init_orires(FILE* fplog,
70 const gmx_mtop_t* mtop,
73 const gmx_multisim_t* ms,
77 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
80 /* Not doing orientation restraints */
84 const int numFitParams = 5;
85 if (od->nr <= numFitParams)
88 "The system has %d orientation restraints, but at least %d are required, since "
89 "there are %d fitting parameters.",
90 od->nr, numFitParams + 1, numFitParams);
93 if (ir->bPeriodicMols)
95 /* Since we apply fitting, we need to make molecules whole and this
96 * can not be done when periodic molecules are present.
99 "Orientation restraints can not be applied when periodic molecules are present "
106 "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, "
110 GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");
112 od->fc = ir->orires_fc;
119 int* nr_ex = nullptr;
120 int typeMin = INT_MAX;
122 gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
124 while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
126 if (nmol > 1 && (*il)[F_ORIRES].size() > 0)
129 "Found %d copies of a molecule with orientation restrains while the current "
130 "code only supports a single copy. If you want to ensemble average, run "
131 "multiple copies of the system using the multi-sim feature of mdrun.",
135 for (int i = 0; i < (*il)[F_ORIRES].size(); i += 3)
137 int type = (*il)[F_ORIRES].iatoms[i];
138 int ex = mtop->ffparams.iparams[type].orires.ex;
141 srenew(nr_ex, ex + 1);
142 for (int j = od->nex; j < ex + 1; j++)
148 GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
151 typeMin = std::min(typeMin, type);
152 typeMax = std::max(typeMax, type);
155 /* With domain decomposition we use the type index for indexing in global arrays */
157 typeMax - typeMin + 1 == od->nr,
158 "All orientation restraint parameter entries in the topology should be consecutive");
159 /* Store typeMin so we can index array with the type offset */
160 od->typeMin = typeMin;
162 snew(od->S, od->nex);
163 /* When not doing time averaging, the instaneous and time averaged data
164 * are indentical and the pointers can point to the same memory.
166 snew(od->Dinsl, od->nr);
170 snew(od->Dins, od->nr);
174 od->Dins = od->Dinsl;
177 if (ir->orires_tau == 0)
185 snew(od->Dtav, od->nr);
186 od->edt = std::exp(-ir->delta_t / ir->orires_tau);
187 od->edt_1 = 1.0 - od->edt;
189 /* Extend the state with the orires history */
190 globalState->flags |= (1 << estORIRE_INITF);
191 globalState->hist.orire_initf = 1;
192 globalState->flags |= (1 << estORIRE_DTAV);
193 globalState->hist.norire_Dtav = od->nr * 5;
194 snew(globalState->hist.orire_Dtav, globalState->hist.norire_Dtav);
197 snew(od->oinsl, od->nr);
200 snew(od->oins, od->nr);
204 od->oins = od->oinsl;
206 if (ir->orires_tau == 0)
212 snew(od->otav, od->nr);
214 snew(od->tmpEq, od->nex);
217 for (int i = 0; i < mtop->natoms; i++)
219 if (getGroupType(mtop->groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
224 snew(od->mref, od->nref);
225 snew(od->xref, od->nref);
226 snew(od->xtmp, od->nref);
228 snew(od->eig, od->nex * 12);
230 /* Determine the reference structure on the master node.
231 * Copy it to the other nodes after checking multi compatibility,
232 * so we are sure the subsystems match before copying.
234 auto x = makeArrayRef(globalState->x);
235 rvec com = { 0, 0, 0 };
238 for (const AtomProxy atomP : AtomRange(*mtop))
240 const t_atom& local = atomP.atom();
241 int i = atomP.globalAtomNumber();
242 if (mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty()
243 || mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
245 /* Not correct for free-energy with changing masses */
246 od->mref[j] = local.m;
247 // Note that only one rank per sim is supported.
250 copy_rvec(x[i], od->xref[j]);
251 for (int d = 0; d < DIM; d++)
253 com[d] += od->mref[j] * x[i][d];
260 svmul(1.0 / mtot, com, com);
263 for (int j = 0; j < od->nref; j++)
265 rvec_dec(od->xref[j], com);
269 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
270 for (int i = 0; i < od->nex; i++)
272 fprintf(fplog, " experiment %d has %d restraints\n", i + 1, nr_ex[i]);
277 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n", od->nref, mtot);
281 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->nsim);
283 check_multi_int(fplog, ms, od->nr, "the number of orientation restraints", FALSE);
284 check_multi_int(fplog, ms, od->nref, "the number of fit atoms for orientation restraining", FALSE);
285 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
286 /* Copy the reference coordinates from the master to the other nodes */
287 gmx_sum_sim(DIM * od->nref, od->xref[0], ms);
290 please_cite(fplog, "Hess2003");
293 void diagonalize_orires_tensors(t_oriresdata* od)
295 if (od->M == nullptr)
298 for (int i = 0; i < DIM; i++)
302 snew(od->eig_diag, DIM);
304 for (int i = 0; i < DIM; i++)
310 for (int ex = 0; ex < od->nex; ex++)
312 /* Rotate the S tensor back to the reference frame */
314 mmul(od->R, od->S[ex], TMP);
315 mtmul(TMP, od->R, S);
316 for (int i = 0; i < DIM; i++)
318 for (int j = 0; j < DIM; j++)
320 od->M[i][j] = S[i][j];
325 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
328 for (int i = 0; i < DIM; i++)
332 for (int i = 0; i < DIM; i++)
334 for (int j = i + 1; j < DIM; j++)
336 if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
345 for (int i = 0; i < DIM; i++)
347 od->eig[ex * 12 + i] = od->eig_diag[ord[i]];
349 for (int i = 0; i < DIM; i++)
351 for (int j = 0; j < DIM; j++)
353 od->eig[ex * 12 + 3 + 3 * i + j] = od->v[j][ord[i]];
359 void print_orires_log(FILE* log, t_oriresdata* od)
363 diagonalize_orires_tensors(od);
365 for (int ex = 0; ex < od->nex; ex++)
367 eig = od->eig + ex * 12;
368 fprintf(log, " Orientation experiment %d:\n", ex + 1);
369 fprintf(log, " order parameter: %g\n", eig[0]);
370 for (int i = 0; i < DIM; i++)
372 fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n", (eig[0] != 0) ? eig[i] / eig[0] : eig[i],
373 eig[DIM + i * DIM + XX], eig[DIM + i * DIM + YY], eig[DIM + i * DIM + ZZ]);
379 real calc_orires_dev(const gmx_multisim_t* ms,
381 const t_iatom forceatoms[],
382 const t_iparams ip[],
390 real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
394 rvec * xref, *xtmp, com, r_unrot, r;
397 const real two_thr = 2.0 / 3.0;
403 /* This means that this is not the master node */
405 "Orientation restraints are only supported on the master rank, use fewer ranks");
408 bTAV = (od->edt != 0);
419 od->exp_min_t_tau = hist->orire_initf * edt;
421 /* Correction factor to correct for the lack of history
424 corrfac = 1.0 / (1.0 - od->exp_min_t_tau);
433 invn = 1.0 / ms->nsim;
443 for (int i = 0; i < md->nr; i++)
445 if (md->cORF[i] == 0)
447 copy_rvec(x[i], xtmp[j]);
448 mref[j] = md->massT[i];
449 for (int d = 0; d < DIM; d++)
451 com[d] += mref[j] * xtmp[j][d];
457 svmul(1.0 / mtot, com, com);
458 for (int j = 0; j < nref; j++)
460 rvec_dec(xtmp[j], com);
462 /* Calculate the rotation matrix to rotate x to the reference orientation */
463 calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
465 for (int fa = 0; fa < nfa; fa += 3)
467 const int type = forceatoms[fa];
468 const int restraintIndex = type - od->typeMin;
471 pbc_dx_aiuc(pbc, x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
475 rvec_sub(x[forceatoms[fa + 1]], x[forceatoms[fa + 2]], r_unrot);
477 mvmul(od->R, r_unrot, r);
479 invr = gmx::invsqrt(r2);
480 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
481 pfac = ip[type].orires.c * invr * invr * 3;
482 for (int i = 0; i < ip[type].orires.power; i++)
486 rvec5& Dinsl = od->Dinsl[restraintIndex];
487 Dinsl[0] = pfac * (2 * r[0] * r[0] + r[1] * r[1] - r2);
488 Dinsl[1] = pfac * (2 * r[0] * r[1]);
489 Dinsl[2] = pfac * (2 * r[0] * r[2]);
490 Dinsl[3] = pfac * (2 * r[1] * r[1] + r[0] * r[0] - r2);
491 Dinsl[4] = pfac * (2 * r[1] * r[2]);
495 for (int i = 0; i < 5; i++)
497 od->Dins[restraintIndex][i] = Dinsl[i] * invn;
504 gmx_sum_sim(5 * od->nr, od->Dins[0], ms);
507 /* Calculate the order tensor S for each experiment via optimization */
508 for (int ex = 0; ex < od->nex; ex++)
510 for (int i = 0; i < 5; i++)
512 matEq[ex].rhs[i] = 0;
513 for (int j = 0; j <= i; j++)
515 matEq[ex].mat[i][j] = 0;
520 for (int fa = 0; fa < nfa; fa += 3)
522 const int type = forceatoms[fa];
523 const int restraintIndex = type - od->typeMin;
524 rvec5& Dtav = od->Dtav[restraintIndex];
527 /* Here we update Dtav in t_fcdata using the data in history_t.
528 * Thus the results stay correct when this routine
529 * is called multiple times.
531 for (int i = 0; i < 5; i++)
533 Dtav[i] = edt * hist->orire_Dtav[restraintIndex * 5 + i]
534 + edt_1 * od->Dins[restraintIndex][i];
538 int ex = ip[type].orires.ex;
539 real weight = ip[type].orires.kfac;
540 /* Calculate the vector rhs and half the matrix T for the 5 equations */
541 for (int i = 0; i < 5; i++)
543 matEq[ex].rhs[i] += Dtav[i] * ip[type].orires.obs * weight;
544 for (int j = 0; j <= i; j++)
546 matEq[ex].mat[i][j] += Dtav[i] * Dtav[j] * weight;
550 /* Now we have all the data we can calculate S */
551 for (int ex = 0; ex < od->nex; ex++)
553 OriresMatEq& eq = matEq[ex];
554 /* Correct corrfac and copy one half of T to the other half */
555 for (int i = 0; i < 5; i++)
557 eq.rhs[i] *= corrfac;
558 eq.mat[i][i] *= gmx::square(corrfac);
559 for (int j = 0; j < i; j++)
561 eq.mat[i][j] *= gmx::square(corrfac);
562 eq.mat[j][i] = eq.mat[i][j];
565 m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
566 /* Calculate the orientation tensor S for this experiment */
567 matrix& S = od->S[ex];
573 for (int i = 0; i < 5; i++)
575 S[0][0] += 1.5 * eq.mat[0][i] * eq.rhs[i];
576 S[0][1] += 1.5 * eq.mat[1][i] * eq.rhs[i];
577 S[0][2] += 1.5 * eq.mat[2][i] * eq.rhs[i];
578 S[1][1] += 1.5 * eq.mat[3][i] * eq.rhs[i];
579 S[1][2] += 1.5 * eq.mat[4][i] * eq.rhs[i];
584 S[2][2] = -S[0][0] - S[1][1];
587 const matrix* S = od->S;
592 for (int fa = 0; fa < nfa; fa += 3)
594 const int type = forceatoms[fa];
595 const int restraintIndex = type - od->typeMin;
596 const int ex = ip[type].orires.ex;
598 const rvec5& Dtav = od->Dtav[restraintIndex];
599 od->otav[restraintIndex] =
601 * (S[ex][0][0] * Dtav[0] + S[ex][0][1] * Dtav[1] + S[ex][0][2] * Dtav[2]
602 + S[ex][1][1] * Dtav[3] + S[ex][1][2] * Dtav[4]);
605 const rvec5& Dins = od->Dins[restraintIndex];
606 od->oins[restraintIndex] =
608 * (S[ex][0][0] * Dins[0] + S[ex][0][1] * Dins[1] + S[ex][0][2] * Dins[2]
609 + S[ex][1][1] * Dins[3] + S[ex][1][2] * Dins[4]);
613 /* When ensemble averaging is used recalculate the local orientation
614 * for output to the energy file.
616 const rvec5& Dinsl = od->Dinsl[restraintIndex];
617 od->oinsl[restraintIndex] =
619 * (S[ex][0][0] * Dinsl[0] + S[ex][0][1] * Dinsl[1] + S[ex][0][2] * Dinsl[2]
620 + S[ex][1][1] * Dinsl[3] + S[ex][1][2] * Dinsl[4]);
623 dev = od->otav[restraintIndex] - ip[type].orires.obs;
625 wsv2 += ip[type].orires.kfac * gmx::square(dev);
626 sw += ip[type].orires.kfac;
628 od->rmsdev = std::sqrt(wsv2 / sw);
630 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
631 for (int ex = 0; ex < od->nex; ex++)
634 tmmul(od->R, od->S[ex], RS);
635 mmul(RS, od->R, od->S[ex]);
640 /* Approx. 120*nfa/3 flops */
644 const t_iatom forceatoms[],
645 const t_iparams ip[],
651 real gmx_unused lambda,
652 real gmx_unused* dvdlambda,
653 const t_mdatoms gmx_unused* md,
655 int gmx_unused* global_atom_index)
657 int ex, power, ki = CENTRAL;
659 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
662 const t_oriresdata* od;
670 bTAV = (od->edt != 0);
675 /* Smoothly switch on the restraining when time averaging is used */
676 smooth_fc *= (1.0 - od->exp_min_t_tau);
679 for (int fa = 0; fa < nfa; fa += 3)
681 const int type = forceatoms[fa];
682 const int ai = forceatoms[fa + 1];
683 const int aj = forceatoms[fa + 2];
684 const int restraintIndex = type - od->typeMin;
687 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
691 rvec_sub(x[ai], x[aj], r);
694 invr = gmx::invsqrt(r2);
696 ex = ip[type].orires.ex;
697 power = ip[type].orires.power;
698 fc = smooth_fc * ip[type].orires.kfac;
699 dev = od->otav[restraintIndex] - ip[type].orires.obs;
702 * there is no real potential when time averaging is applied
704 vtot += 0.5 * fc * gmx::square(dev);
708 /* Calculate the force as the sqrt of tav times instantaneous */
709 devins = od->oins[restraintIndex] - ip[type].orires.obs;
710 if (dev * devins <= 0)
716 dev = std::sqrt(dev * devins);
724 pfac = fc * ip[type].orires.c * invr2;
725 for (int i = 0; i < power; i++)
729 mvmul(od->S[ex], r, Sr);
730 for (int i = 0; i < DIM; i++)
732 fij[i] = -pfac * dev * (4 * Sr[i] - 2 * (2 + power) * invr2 * iprod(Sr, r) * r[i]);
737 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
741 for (int i = 0; i < DIM; i++)
747 fshift[ki][i] += fij[i];
748 fshift[CENTRAL][i] -= fij[i];
756 /* Approx. 80*nfa/3 flops */
759 void update_orires_history(const t_fcdata* fcd, history_t* hist)
761 const t_oriresdata* od = &(fcd->orires);
765 /* Copy the new time averages that have been calculated
766 * in calc_orires_dev.
768 hist->orire_initf = od->exp_min_t_tau;
769 for (int pair = 0; pair < od->nr; pair++)
771 for (int i = 0; i < 5; i++)
773 hist->orire_Dtav[pair * 5 + i] = od->Dtav[pair][i];