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44 #include "gromacs/gmxlib/network.h"
45 #include "gromacs/linearalgebra/nrjac.h"
46 #include "gromacs/math/do_fit.h"
47 #include "gromacs/math/functions.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/mdtypes/commrec.h"
50 #include "gromacs/mdtypes/fcdata.h"
51 #include "gromacs/mdtypes/inputrec.h"
52 #include "gromacs/mdtypes/mdatom.h"
53 #include "gromacs/mdtypes/state.h"
54 #include "gromacs/pbcutil/ishift.h"
55 #include "gromacs/pbcutil/mshift.h"
56 #include "gromacs/pbcutil/pbc.h"
57 #include "gromacs/topology/ifunc.h"
58 #include "gromacs/topology/mtop_util.h"
59 #include "gromacs/topology/topology.h"
60 #include "gromacs/utility/fatalerror.h"
61 #include "gromacs/utility/pleasecite.h"
62 #include "gromacs/utility/smalloc.h"
64 // TODO This implementation of ensemble orientation restraints is nasty because
65 // a user can't just do multi-sim with single-sim orientation restraints.
67 void init_orires(FILE *fplog,
68 const gmx_mtop_t *mtop,
71 const gmx_multisim_t *ms,
75 od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
78 /* Not doing orientation restraints */
82 const int numFitParams = 5;
83 if (od->nr <= numFitParams)
85 gmx_fatal(FARGS, "The system has %d orientation restraints, but at least %d are required, since there are %d fitting parameters.",
86 od->nr, numFitParams + 1, numFitParams);
89 if (ir->bPeriodicMols)
91 /* Since we apply fitting, we need to make molecules whole and this
92 * can not be done when periodic molecules are present.
94 gmx_fatal(FARGS, "Orientation restraints can not be applied when periodic molecules are present in the system");
99 gmx_fatal(FARGS, "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, if possible.");
102 GMX_RELEASE_ASSERT(globalState != nullptr, "We need a valid global state in init_orires");
104 od->fc = ir->orires_fc;
111 int *nr_ex = nullptr;
112 int typeMin = INT_MAX;
114 gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
116 while (const InteractionLists *il = gmx_mtop_ilistloop_next(iloop, &nmol))
120 gmx_fatal(FARGS, "Found %d copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun.", nmol);
123 for (int i = 0; i < (*il)[F_ORIRES].size(); i += 3)
125 int type = (*il)[F_ORIRES].iatoms[i];
126 int ex = mtop->ffparams.iparams[type].orires.ex;
130 for (int j = od->nex; j < ex+1; j++)
136 GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
139 typeMin = std::min(typeMin, type);
140 typeMax = std::max(typeMax, type);
143 /* With domain decomposition we use the type index for indexing in global arrays */
144 GMX_RELEASE_ASSERT(typeMax - typeMin + 1 == od->nr, "All orientation restraint parameter entries in the topology should be consecutive");
145 /* Store typeMin so we can index array with the type offset */
146 od->typeMin = typeMin;
148 snew(od->S, od->nex);
149 /* When not doing time averaging, the instaneous and time averaged data
150 * are indentical and the pointers can point to the same memory.
152 snew(od->Dinsl, od->nr);
156 snew(od->Dins, od->nr);
160 od->Dins = od->Dinsl;
163 if (ir->orires_tau == 0)
171 snew(od->Dtav, od->nr);
172 od->edt = std::exp(-ir->delta_t/ir->orires_tau);
173 od->edt_1 = 1.0 - od->edt;
175 /* Extend the state with the orires history */
176 globalState->flags |= (1<<estORIRE_INITF);
177 globalState->hist.orire_initf = 1;
178 globalState->flags |= (1<<estORIRE_DTAV);
179 globalState->hist.norire_Dtav = od->nr*5;
180 snew(globalState->hist.orire_Dtav, globalState->hist.norire_Dtav);
183 snew(od->oinsl, od->nr);
186 snew(od->oins, od->nr);
190 od->oins = od->oinsl;
192 if (ir->orires_tau == 0)
198 snew(od->otav, od->nr);
200 snew(od->tmpEq, od->nex);
203 for (int i = 0; i < mtop->natoms; i++)
205 if (getGroupType(mtop->groups, SimulationAtomGroupType::OrientationRestraintsFit, i) == 0)
210 snew(od->mref, od->nref);
211 snew(od->xref, od->nref);
212 snew(od->xtmp, od->nref);
214 snew(od->eig, od->nex*12);
216 /* Determine the reference structure on the master node.
217 * Copy it to the other nodes after checking multi compatibility,
218 * so we are sure the subsystems match before copying.
220 auto x = makeArrayRef(globalState->x);
221 rvec com = { 0, 0, 0 };
224 for (const AtomProxy atomP : AtomRange(*mtop))
226 const t_atom &local = atomP.atom();
227 int i = atomP.globalAtomNumber();
228 if (mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit].empty() ||
229 mtop->groups.groupNumbers[SimulationAtomGroupType::OrientationRestraintsFit][i] == 0)
231 /* Not correct for free-energy with changing masses */
232 od->mref[j] = local.m;
233 // Note that only one rank per sim is supported.
236 copy_rvec(x[i], od->xref[j]);
237 for (int d = 0; d < DIM; d++)
239 com[d] += od->mref[j]*x[i][d];
246 svmul(1.0/mtot, com, com);
249 for (int j = 0; j < od->nref; j++)
251 rvec_dec(od->xref[j], com);
255 fprintf(fplog, "Found %d orientation experiments\n", od->nex);
256 for (int i = 0; i < od->nex; i++)
258 fprintf(fplog, " experiment %d has %d restraints\n", i+1, nr_ex[i]);
263 fprintf(fplog, " the fit group consists of %d atoms and has total mass %g\n",
268 fprintf(fplog, " the orientation restraints are ensemble averaged over %d systems\n", ms->nsim);
270 check_multi_int(fplog, ms, od->nr,
271 "the number of orientation restraints",
273 check_multi_int(fplog, ms, od->nref,
274 "the number of fit atoms for orientation restraining",
276 check_multi_int(fplog, ms, ir->nsteps, "nsteps", FALSE);
277 /* Copy the reference coordinates from the master to the other nodes */
278 gmx_sum_sim(DIM*od->nref, od->xref[0], ms);
281 please_cite(fplog, "Hess2003");
284 void diagonalize_orires_tensors(t_oriresdata *od)
286 if (od->M == nullptr)
289 for (int i = 0; i < DIM; i++)
293 snew(od->eig_diag, DIM);
295 for (int i = 0; i < DIM; i++)
301 for (int ex = 0; ex < od->nex; ex++)
303 /* Rotate the S tensor back to the reference frame */
305 mmul(od->R, od->S[ex], TMP);
306 mtmul(TMP, od->R, S);
307 for (int i = 0; i < DIM; i++)
309 for (int j = 0; j < DIM; j++)
311 od->M[i][j] = S[i][j];
316 jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
319 for (int i = 0; i < DIM; i++)
323 for (int i = 0; i < DIM; i++)
325 for (int j = i+1; j < DIM; j++)
327 if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
336 for (int i = 0; i < DIM; i++)
338 od->eig[ex*12 + i] = od->eig_diag[ord[i]];
340 for (int i = 0; i < DIM; i++)
342 for (int j = 0; j < DIM; j++)
344 od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
350 void print_orires_log(FILE *log, t_oriresdata *od)
354 diagonalize_orires_tensors(od);
356 for (int ex = 0; ex < od->nex; ex++)
358 eig = od->eig + ex*12;
359 fprintf(log, " Orientation experiment %d:\n", ex+1);
360 fprintf(log, " order parameter: %g\n", eig[0]);
361 for (int i = 0; i < DIM; i++)
363 fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n",
364 (eig[0] != 0) ? eig[i]/eig[0] : eig[i],
373 real calc_orires_dev(const gmx_multisim_t *ms,
374 int nfa, const t_iatom forceatoms[], const t_iparams ip[],
375 const t_mdatoms *md, const rvec x[], const t_pbc *pbc,
376 t_fcdata *fcd, history_t *hist)
379 real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
383 rvec *xref, *xtmp, com, r_unrot, r;
386 const real two_thr = 2.0/3.0;
392 /* This means that this is not the master node */
393 gmx_fatal(FARGS, "Orientation restraints are only supported on the master rank, use fewer ranks");
396 bTAV = (od->edt != 0);
407 od->exp_min_t_tau = hist->orire_initf*edt;
409 /* Correction factor to correct for the lack of history
412 corrfac = 1.0/(1.0 - od->exp_min_t_tau);
431 for (int i = 0; i < md->nr; i++)
433 if (md->cORF[i] == 0)
435 copy_rvec(x[i], xtmp[j]);
436 mref[j] = md->massT[i];
437 for (int d = 0; d < DIM; d++)
439 com[d] += mref[j]*xtmp[j][d];
445 svmul(1.0/mtot, com, com);
446 for (int j = 0; j < nref; j++)
448 rvec_dec(xtmp[j], com);
450 /* Calculate the rotation matrix to rotate x to the reference orientation */
451 calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
453 for (int fa = 0; fa < nfa; fa += 3)
455 const int type = forceatoms[fa];
456 const int restraintIndex = type - od->typeMin;
459 pbc_dx_aiuc(pbc, x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
463 rvec_sub(x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
465 mvmul(od->R, r_unrot, r);
467 invr = gmx::invsqrt(r2);
468 /* Calculate the prefactor for the D tensor, this includes the factor 3! */
469 pfac = ip[type].orires.c*invr*invr*3;
470 for (int i = 0; i < ip[type].orires.power; i++)
474 rvec5 &Dinsl = od->Dinsl[restraintIndex];
475 Dinsl[0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
476 Dinsl[1] = pfac*(2*r[0]*r[1]);
477 Dinsl[2] = pfac*(2*r[0]*r[2]);
478 Dinsl[3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
479 Dinsl[4] = pfac*(2*r[1]*r[2]);
483 for (int i = 0; i < 5; i++)
485 od->Dins[restraintIndex][i] = Dinsl[i]*invn;
492 gmx_sum_sim(5*od->nr, od->Dins[0], ms);
495 /* Calculate the order tensor S for each experiment via optimization */
496 for (int ex = 0; ex < od->nex; ex++)
498 for (int i = 0; i < 5; i++)
500 matEq[ex].rhs[i] = 0;
501 for (int j = 0; j <= i; j++)
503 matEq[ex].mat[i][j] = 0;
508 for (int fa = 0; fa < nfa; fa += 3)
510 const int type = forceatoms[fa];
511 const int restraintIndex = type - od->typeMin;
512 rvec5 &Dtav = od->Dtav[restraintIndex];
515 /* Here we update Dtav in t_fcdata using the data in history_t.
516 * Thus the results stay correct when this routine
517 * is called multiple times.
519 for (int i = 0; i < 5; i++)
522 edt*hist->orire_Dtav[restraintIndex*5 + i] +
523 edt_1*od->Dins[restraintIndex][i];
527 int ex = ip[type].orires.ex;
528 real weight = ip[type].orires.kfac;
529 /* Calculate the vector rhs and half the matrix T for the 5 equations */
530 for (int i = 0; i < 5; i++)
532 matEq[ex].rhs[i] += Dtav[i]*ip[type].orires.obs*weight;
533 for (int j = 0; j <= i; j++)
535 matEq[ex].mat[i][j] += Dtav[i]*Dtav[j]*weight;
539 /* Now we have all the data we can calculate S */
540 for (int ex = 0; ex < od->nex; ex++)
542 OriresMatEq &eq = matEq[ex];
543 /* Correct corrfac and copy one half of T to the other half */
544 for (int i = 0; i < 5; i++)
546 eq.rhs[i] *= corrfac;
547 eq.mat[i][i] *= gmx::square(corrfac);
548 for (int j = 0; j < i; j++)
550 eq.mat[i][j] *= gmx::square(corrfac);
551 eq.mat[j][i] = eq.mat[i][j];
554 m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
555 /* Calculate the orientation tensor S for this experiment */
556 matrix &S = od->S[ex];
562 for (int i = 0; i < 5; i++)
564 S[0][0] += 1.5*eq.mat[0][i]*eq.rhs[i];
565 S[0][1] += 1.5*eq.mat[1][i]*eq.rhs[i];
566 S[0][2] += 1.5*eq.mat[2][i]*eq.rhs[i];
567 S[1][1] += 1.5*eq.mat[3][i]*eq.rhs[i];
568 S[1][2] += 1.5*eq.mat[4][i]*eq.rhs[i];
573 S[2][2] = -S[0][0] - S[1][1];
576 const matrix *S = od->S;
581 for (int fa = 0; fa < nfa; fa += 3)
583 const int type = forceatoms[fa];
584 const int restraintIndex = type - od->typeMin;
585 const int ex = ip[type].orires.ex;
587 const rvec5 &Dtav = od->Dtav[restraintIndex];
588 od->otav[restraintIndex] = two_thr*
589 corrfac*(S[ex][0][0]*Dtav[0] + S[ex][0][1]*Dtav[1] +
590 S[ex][0][2]*Dtav[2] + S[ex][1][1]*Dtav[3] +
591 S[ex][1][2]*Dtav[4]);
594 const rvec5 &Dins = od->Dins[restraintIndex];
595 od->oins[restraintIndex] = two_thr*
596 (S[ex][0][0]*Dins[0] + S[ex][0][1]*Dins[1] +
597 S[ex][0][2]*Dins[2] + S[ex][1][1]*Dins[3] +
598 S[ex][1][2]*Dins[4]);
602 /* When ensemble averaging is used recalculate the local orientation
603 * for output to the energy file.
605 const rvec5 &Dinsl = od->Dinsl[restraintIndex];
606 od->oinsl[restraintIndex] = two_thr*
607 (S[ex][0][0]*Dinsl[0] + S[ex][0][1]*Dinsl[1] +
608 S[ex][0][2]*Dinsl[2] + S[ex][1][1]*Dinsl[3] +
609 S[ex][1][2]*Dinsl[4]);
612 dev = od->otav[restraintIndex] - ip[type].orires.obs;
614 wsv2 += ip[type].orires.kfac*gmx::square(dev);
615 sw += ip[type].orires.kfac;
617 od->rmsdev = std::sqrt(wsv2/sw);
619 /* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
620 for (int ex = 0; ex < od->nex; ex++)
623 tmmul(od->R, od->S[ex], RS);
624 mmul(RS, od->R, od->S[ex]);
629 /* Approx. 120*nfa/3 flops */
632 real orires(int nfa, const t_iatom forceatoms[], const t_iparams ip[],
633 const rvec x[], rvec4 f[], rvec fshift[],
634 const t_pbc *pbc, const t_graph *g,
635 real gmx_unused lambda, real gmx_unused *dvdlambda,
636 const t_mdatoms gmx_unused *md, t_fcdata *fcd,
637 int gmx_unused *global_atom_index)
639 int ex, power, ki = CENTRAL;
641 real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
644 const t_oriresdata *od;
652 bTAV = (od->edt != 0);
657 /* Smoothly switch on the restraining when time averaging is used */
658 smooth_fc *= (1.0 - od->exp_min_t_tau);
661 for (int fa = 0; fa < nfa; fa += 3)
663 const int type = forceatoms[fa];
664 const int ai = forceatoms[fa + 1];
665 const int aj = forceatoms[fa + 2];
666 const int restraintIndex = type - od->typeMin;
669 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
673 rvec_sub(x[ai], x[aj], r);
676 invr = gmx::invsqrt(r2);
678 ex = ip[type].orires.ex;
679 power = ip[type].orires.power;
680 fc = smooth_fc*ip[type].orires.kfac;
681 dev = od->otav[restraintIndex] - ip[type].orires.obs;
684 * there is no real potential when time averaging is applied
686 vtot += 0.5*fc*gmx::square(dev);
690 /* Calculate the force as the sqrt of tav times instantaneous */
691 devins = od->oins[restraintIndex] - ip[type].orires.obs;
698 dev = std::sqrt(dev*devins);
706 pfac = fc*ip[type].orires.c*invr2;
707 for (int i = 0; i < power; i++)
711 mvmul(od->S[ex], r, Sr);
712 for (int i = 0; i < DIM; i++)
715 -pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr, r)*r[i]);
720 ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
724 for (int i = 0; i < DIM; i++)
728 fshift[ki][i] += fij[i];
729 fshift[CENTRAL][i] -= fij[i];
736 /* Approx. 80*nfa/3 flops */
739 void update_orires_history(const t_fcdata *fcd, history_t *hist)
741 const t_oriresdata *od = &(fcd->orires);
745 /* Copy the new time averages that have been calculated
746 * in calc_orires_dev.
748 hist->orire_initf = od->exp_min_t_tau;
749 for (int pair = 0; pair < od->nr; pair++)
751 for (int i = 0; i < 5; i++)
753 hist->orire_Dtav[pair*5+i] = od->Dtav[pair][i];