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39 * \brief Defines SHAKE code.
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \author Berk Hess <hess@kth.se>
43 * \author Mark Abraham <mark.j.abraham@gmail.com>
44 * \ingroup module_mdlib
55 #include "gromacs/gmxlib/nrnb.h"
56 #include "gromacs/math/functions.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/constr.h"
59 #include "gromacs/mdlib/splitter.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/md_enums.h"
62 #include "gromacs/pbcutil/pbc.h"
63 #include "gromacs/topology/invblock.h"
64 #include "gromacs/utility/arrayref.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/smalloc.h"
77 //! Compares sort blocks.
78 static int pcomp(const void* p1, const void* p2)
81 int min1, min2, max1, max2;
82 const t_sortblock* a1 = reinterpret_cast<const t_sortblock*>(p1);
83 const t_sortblock* a2 = reinterpret_cast<const t_sortblock*>(p2);
85 db = a1->blocknr - a2->blocknr;
92 min1 = std::min(a1->iatom[1], a1->iatom[2]);
93 max1 = std::max(a1->iatom[1], a1->iatom[2]);
94 min2 = std::min(a2->iatom[1], a2->iatom[2]);
95 max2 = std::max(a2->iatom[1], a2->iatom[2]);
107 //! Prints sortblocks
108 static void pr_sortblock(FILE* fp, const char* title, int nsb, t_sortblock sb[])
112 fprintf(fp, "%s\n", title);
113 for (i = 0; (i < nsb); i++)
116 "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n",
125 //! Reallocates a vector.
126 static void resizeLagrangianData(shakedata* shaked, int ncons)
128 shaked->scaled_lagrange_multiplier.resize(ncons);
131 void make_shake_sblock_serial(shakedata* shaked, InteractionDefinitions* idef, const int numAtoms)
139 /* Since we are processing the local topology,
140 * the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
142 ncons = idef->il[F_CONSTR].size() / 3;
144 init_blocka(&sblocks);
145 sfree(sblocks.index); // To solve memory leak
146 gen_sblocks(nullptr, numAtoms, *idef, &sblocks, FALSE);
149 bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
150 nblocks=blocks->multinr[idef->nodeid] - bstart;
155 fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n", ncons, bstart, sblocks.nr);
158 /* Calculate block number for each atom */
159 inv_sblock = make_invblocka(&sblocks, numAtoms);
161 done_blocka(&sblocks);
163 /* Store the block number in temp array and
164 * sort the constraints in order of the sblock number
165 * and the atom numbers, really sorting a segment of the array!
167 int* iatom = idef->il[F_CONSTR].iatoms.data();
169 for (i = 0; (i < ncons); i++, iatom += 3)
171 for (m = 0; (m < 3); m++)
173 sb[i].iatom[m] = iatom[m];
175 sb[i].blocknr = inv_sblock[iatom[1]];
178 /* Now sort the blocks */
181 pr_sortblock(debug, "Before sorting", ncons, sb);
182 fprintf(debug, "Going to sort constraints\n");
185 std::qsort(sb, ncons, sizeof(*sb), pcomp);
189 pr_sortblock(debug, "After sorting", ncons, sb);
192 iatom = idef->il[F_CONSTR].iatoms.data();
193 for (i = 0; (i < ncons); i++, iatom += 3)
195 for (m = 0; (m < 3); m++)
197 iatom[m] = sb[i].iatom[m];
201 shaked->sblock.clear();
203 for (i = 0; (i < ncons); i++)
205 if (sb[i].blocknr != bnr)
208 shaked->sblock.push_back(3 * i);
212 shaked->sblock.push_back(3 * ncons);
216 resizeLagrangianData(shaked, ncons);
219 void make_shake_sblock_dd(shakedata* shaked, const InteractionList& ilcon)
223 ncons = ilcon.size() / 3;
224 const int* iatom = ilcon.iatoms.data();
225 shaked->sblock.clear();
227 for (c = 0; c < ncons; c++)
229 if (c == 0 || iatom[1] >= cg + 1)
231 shaked->sblock.push_back(3 * c);
232 while (iatom[1] >= cg + 1)
239 shaked->sblock.push_back(3 * ncons);
240 resizeLagrangianData(shaked, ncons);
243 /*! \brief Inner kernel for SHAKE constraints
245 * Original implementation from R.C. van Schaik and W.F. van Gunsteren
246 * (ETH Zuerich, June 1992), adapted for GROMACS by David van der
247 * Spoel November 1992.
249 * The algorithm here is based section five of Ryckaert, Ciccotti and
250 * Berendsen, J Comp Phys, 23, 327, 1977.
252 * \param[in] iatom Mini-topology of triplets of constraint type (unused
253 * in this function) and indices of two atoms involved
254 * \param[in] ncon Number of constraints
255 * \param[out] nnit Number of iterations performed
256 * \param[in] maxnit Maximum number of iterations permitted
257 * \param[in] constraint_distance_squared The objective value for each constraint
258 * \param[inout] positions The initial (and final) values of the positions
260 * \param[in] pbc PBC information
261 * \param[in] initial_displacements The initial displacements of each constraint
262 * \param[in] half_of_reduced_mass Half of the reduced mass for each constraint
263 * \param[in] omega SHAKE over-relaxation factor (set non-1.0 by
264 * using shake-sor=yes in the .mdp,
265 * but there is no documentation anywhere)
266 * \param[in] invmass Inverse mass of each atom
267 * \param[in] distance_squared_tolerance Multiplicative tolerance on the difference in the
268 * square of the constrained distance (see code)
269 * \param[out] scaled_lagrange_multiplier Scaled Lagrange multiplier for each constraint
270 * (-2 * eta from p. 336 of the paper, divided by
271 * the constraint distance)
272 * \param[out] nerror Zero upon success, returns one more than the index of
273 * the problematic constraint if the input was malformed
275 * \todo Make SHAKE use better data structures, in particular for iatom. */
276 void cshake(const int iatom[],
280 ArrayRef<const real> constraint_distance_squared,
281 ArrayRef<RVec> positions,
283 ArrayRef<const RVec> initial_displacements,
284 ArrayRef<const real> half_of_reduced_mass,
286 ArrayRef<const real> invmass,
287 ArrayRef<const real> distance_squared_tolerance,
288 ArrayRef<real> scaled_lagrange_multiplier,
291 /* default should be increased! MRS 8/4/2009 */
292 const real mytol = 1e-10;
294 // TODO nconv is used solely as a boolean, so we should write the
299 for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
302 for (int ll = 0; (ll < ncon) && (error == 0); ll++)
304 const int l3 = 3 * ll;
305 const real rijx = initial_displacements[ll][XX];
306 const real rijy = initial_displacements[ll][YY];
307 const real rijz = initial_displacements[ll][ZZ];
308 const int i = iatom[l3 + 1];
309 const int j = iatom[l3 + 2];
311 /* Compute r prime between atoms i and j, which is the
312 displacement *before* this update stage */
316 pbc_dx(pbc, positions[i], positions[j], r_prime);
320 rvec_sub(positions[i], positions[j], r_prime);
322 const real r_prime_squared = norm2(r_prime);
323 const real constraint_distance_squared_ll = constraint_distance_squared[ll];
324 const real diff = constraint_distance_squared_ll - r_prime_squared;
326 /* iconvf is less than 1 when the error is smaller than a bound */
327 const real iconvf = std::abs(diff) * distance_squared_tolerance[ll];
329 if (iconvf > 1.0_real)
331 nconv = static_cast<int>(iconvf);
332 const real r_dot_r_prime =
333 (rijx * r_prime[XX] + rijy * r_prime[YY] + rijz * r_prime[ZZ]);
335 if (r_dot_r_prime < constraint_distance_squared_ll * mytol)
341 /* The next line solves equation 5.6 (neglecting
342 the term in g^2), for g */
343 real scaled_lagrange_multiplier_ll =
344 omega * diff * half_of_reduced_mass[ll] / r_dot_r_prime;
345 scaled_lagrange_multiplier[ll] += scaled_lagrange_multiplier_ll;
346 const real xh = rijx * scaled_lagrange_multiplier_ll;
347 const real yh = rijy * scaled_lagrange_multiplier_ll;
348 const real zh = rijz * scaled_lagrange_multiplier_ll;
349 const real im = invmass[i];
350 const real jm = invmass[j];
351 positions[i][XX] += xh * im;
352 positions[i][YY] += yh * im;
353 positions[i][ZZ] += zh * im;
354 positions[j][XX] -= xh * jm;
355 positions[j][YY] -= yh * jm;
356 positions[j][ZZ] -= zh * jm;
365 //! Implements RATTLE (ie. SHAKE for velocity verlet integrators)
366 static void crattle(const int iatom[],
370 ArrayRef<const real> constraint_distance_squared,
372 ArrayRef<const RVec> rij,
373 ArrayRef<const real> m2,
375 ArrayRef<const real> invmass,
376 ArrayRef<const real> distance_squared_tolerance,
377 ArrayRef<real> scaled_lagrange_multiplier,
382 * r.c. van schaik and w.f. van gunsteren
385 * Adapted for use with Gromacs by David van der Spoel november 92 and later.
386 * rattle added by M.R. Shirts, April 2004, from code written by Jay Ponder in TINKER
387 * second part of rattle algorithm
390 // TODO nconv is used solely as a boolean, so we should write the
395 for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
398 for (int ll = 0; (ll < ncon) && (error == 0); ll++)
400 const int l3 = 3 * ll;
401 const real rijx = rij[ll][XX];
402 const real rijy = rij[ll][YY];
403 const real rijz = rij[ll][ZZ];
404 const int i = iatom[l3 + 1];
405 const int j = iatom[l3 + 2];
407 rvec_sub(vp[i], vp[j], v);
409 const real vpijd = v[XX] * rijx + v[YY] * rijy + v[ZZ] * rijz;
410 const real constraint_distance_squared_ll = constraint_distance_squared[ll];
412 /* iconv is zero when the error is smaller than a bound */
413 const real iconvf = fabs(vpijd) * (distance_squared_tolerance[ll] / invdt);
415 if (iconvf > 1.0_real)
417 nconv = static_cast<int>(iconvf);
418 const real fac = omega * 2.0_real * m2[ll] / constraint_distance_squared_ll;
419 const real acor = -fac * vpijd;
420 scaled_lagrange_multiplier[ll] += acor;
421 const real xh = rijx * acor;
422 const real yh = rijy * acor;
423 const real zh = rijz * acor;
425 const real im = invmass[i];
426 const real jm = invmass[j];
428 vp[i][XX] += xh * im;
429 vp[i][YY] += yh * im;
430 vp[i][ZZ] += zh * im;
431 vp[j][XX] -= xh * jm;
432 vp[j][YY] -= yh * jm;
433 vp[j][ZZ] -= zh * jm;
442 static int vec_shakef(FILE* fplog,
444 ArrayRef<const real> invmass,
446 ArrayRef<const t_iparams> ip,
449 ArrayRef<const RVec> x,
450 ArrayRef<RVec> prime,
455 ArrayRef<real> scaled_lagrange_multiplier,
460 ConstraintVariable econq)
463 int nit = 0, ll, i, j, d, d2, type;
466 real constraint_distance;
468 shaked->rij.resize(ncon);
469 shaked->half_of_reduced_mass.resize(ncon);
470 shaked->distance_squared_tolerance.resize(ncon);
471 shaked->constraint_distance_squared.resize(ncon);
473 ArrayRef<RVec> rij = shaked->rij;
474 ArrayRef<real> half_of_reduced_mass = shaked->half_of_reduced_mass;
475 ArrayRef<real> distance_squared_tolerance = shaked->distance_squared_tolerance;
476 ArrayRef<real> constraint_distance_squared = shaked->constraint_distance_squared;
478 L1 = 1.0_real - lambda;
479 const int* ia = iatom;
480 for (ll = 0; (ll < ncon); ll++, ia += 3)
488 pbc_dx(pbc, x[i], x[j], rij[ll]);
492 rvec_sub(x[i], x[j], rij[ll]);
494 const real mm = 2.0_real * (invmass[i] + invmass[j]);
495 half_of_reduced_mass[ll] = 1.0_real / mm;
498 constraint_distance = L1 * ip[type].constr.dA + lambda * ip[type].constr.dB;
502 constraint_distance = ip[type].constr.dA;
504 constraint_distance_squared[ll] = gmx::square(constraint_distance);
505 distance_squared_tolerance[ll] = 0.5 / (constraint_distance_squared[ll] * tol);
510 case ConstraintVariable::Positions:
515 constraint_distance_squared,
519 half_of_reduced_mass,
522 distance_squared_tolerance,
523 scaled_lagrange_multiplier,
526 case ConstraintVariable::Velocities:
531 constraint_distance_squared,
534 half_of_reduced_mass,
537 distance_squared_tolerance,
538 scaled_lagrange_multiplier,
542 default: gmx_incons("Unknown constraint quantity for SHAKE");
549 fprintf(fplog, "Shake did not converge in %d steps\n", maxnit);
551 fprintf(stderr, "Shake did not converge in %d steps\n", maxnit);
559 "Inner product between old and new vector <= 0.0!\n"
560 "constraint #%d atoms %d and %d\n",
562 iatom[3 * (error - 1) + 1] + 1,
563 iatom[3 * (error - 1) + 2] + 1);
566 "Inner product between old and new vector <= 0.0!\n"
567 "constraint #%d atoms %d and %d\n",
569 iatom[3 * (error - 1) + 1] + 1,
570 iatom[3 * (error - 1) + 2] + 1);
574 /* Constraint virial and correct the Lagrange multipliers for the length */
578 for (ll = 0; (ll < ncon); ll++, ia += 3)
584 if ((econq == ConstraintVariable::Positions) && !v.empty())
586 /* Correct the velocities */
587 real mm = scaled_lagrange_multiplier[ll] * invmass[i] * invdt;
588 for (d = 0; d < DIM; d++)
590 v[ia[1]][d] += mm * rij[ll][d];
592 mm = scaled_lagrange_multiplier[ll] * invmass[j] * invdt;
593 for (d = 0; d < DIM; d++)
595 v[ia[2]][d] -= mm * rij[ll][d];
600 /* constraint virial */
603 const real mm = scaled_lagrange_multiplier[ll];
604 for (d = 0; d < DIM; d++)
606 const real tmp = mm * rij[ll][d];
607 for (d2 = 0; d2 < DIM; d2++)
609 vir_r_m_dr[d][d2] -= tmp * rij[ll][d2];
615 /* cshake and crattle produce Lagrange multipliers scaled by
616 the reciprocal of the constraint length, so fix that */
619 constraint_distance = L1 * ip[type].constr.dA + lambda * ip[type].constr.dB;
623 constraint_distance = ip[type].constr.dA;
625 scaled_lagrange_multiplier[ll] *= constraint_distance;
631 //! Check that constraints are satisfied.
632 static void check_cons(FILE* log,
634 ArrayRef<const RVec> x,
635 ArrayRef<const RVec> prime,
636 ArrayRef<const RVec> v,
638 ArrayRef<const t_iparams> ip,
640 ArrayRef<const real> invmass,
641 ConstraintVariable econq)
648 GMX_ASSERT(!v.empty(), "Input has to be non-null");
649 fprintf(log, " i mi j mj before after should be\n");
650 const int* ia = iatom;
651 for (i = 0; (i < nc); i++, ia += 3)
655 rvec_sub(x[ai], x[aj], dx);
660 case ConstraintVariable::Positions:
663 pbc_dx(pbc, prime[ai], prime[aj], dx);
667 rvec_sub(prime[ai], prime[aj], dx);
671 "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
678 ip[ia[0]].constr.dA);
680 case ConstraintVariable::Velocities:
681 rvec_sub(v[ai], v[aj], dv);
683 rvec_sub(prime[ai], prime[aj], dv);
686 "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
695 default: gmx_incons("Unknown constraint quantity for SHAKE");
701 static bool bshakef(FILE* log,
703 ArrayRef<const real> invmass,
704 const InteractionDefinitions& idef,
705 const t_inputrec& ir,
706 ArrayRef<const RVec> x_s,
707 ArrayRef<RVec> prime,
717 ConstraintVariable econq)
720 int i, n0, ncon, blen, type, ll;
721 int tnit = 0, trij = 0;
723 ncon = idef.il[F_CONSTR].size() / 3;
725 for (ll = 0; ll < ncon; ll++)
727 shaked->scaled_lagrange_multiplier[ll] = 0;
730 // TODO Rewrite this block so that it is obvious that i, iatoms
731 // and lam are all iteration variables. Is this easier if the
732 // sblock data structure is organized differently?
733 const int* iatoms = &(idef.il[F_CONSTR].iatoms[shaked->sblock[0]]);
734 ArrayRef<real> lam = shaked->scaled_lagrange_multiplier;
735 for (i = 0; (i < shaked->numShakeBlocks());)
737 blen = (shaked->sblock[i + 1] - shaked->sblock[i]);
750 ir.efep != FreeEnergyPerturbationType::No,
761 if (bDumpOnError && log)
764 check_cons(log, blen, x_s, prime, v, pbc, idef.iparams, iatoms, invmass, econq);
771 iatoms += 3 * blen; /* Increment pointer! */
772 lam = lam.subArray(blen, lam.ssize() - blen);
775 /* only for position part? */
776 if (econq == ConstraintVariable::Positions)
778 if (ir.efep != FreeEnergyPerturbationType::No)
780 ArrayRef<const t_iparams> iparams = idef.iparams;
782 /* TODO This should probably use invdt, so that sd integrator scaling works properly */
783 dt_2 = 1 / gmx::square(ir.delta_t);
785 for (ll = 0; ll < ncon; ll++)
787 type = idef.il[F_CONSTR].iatoms[3 * ll];
789 /* Per equations in the manual, dv/dl = -2 \sum_ll lagrangian_ll * r_ll * (d_B - d_A) */
790 /* The vector scaled_lagrange_multiplier[ll] contains the value -2 r_ll eta_ll
791 (eta_ll is the estimate of the Langrangian, definition on page 336 of Ryckaert et
792 al 1977), so the pre-factors are already present. */
793 const real bondA = iparams[type].constr.dA;
794 const real bondB = iparams[type].constr.dB;
795 dvdl += shaked->scaled_lagrange_multiplier[ll] * dt_2 * (bondB - bondA);
802 if (tnit > shaked->gamma)
804 shaked->delta *= -0.5;
806 shaked->omega += shaked->delta;
807 shaked->gamma = tnit;
809 inc_nrnb(nrnb, eNR_SHAKE, tnit);
810 inc_nrnb(nrnb, eNR_SHAKE_RIJ, trij);
813 inc_nrnb(nrnb, eNR_CONSTR_V, trij * 2);
817 inc_nrnb(nrnb, eNR_CONSTR_VIR, trij);
823 bool constrain_shake(FILE* log,
825 ArrayRef<const real> invmass,
826 const InteractionDefinitions& idef,
827 const t_inputrec& ir,
828 ArrayRef<const RVec> x_s,
829 ArrayRef<RVec> xprime,
830 ArrayRef<RVec> vprime,
840 ConstraintVariable econq)
842 if (shaked->numShakeBlocks() == 0)
849 case (ConstraintVariable::Positions):
851 log, shaked, invmass, idef, ir, x_s, xprime, pbc, nrnb, lambda, dvdlambda, invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
853 case (ConstraintVariable::Velocities):
874 "Internal error, SHAKE called for constraining something else than "