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50 #include "gromacs/domdec/dlbtiming.h"
51 #include "gromacs/domdec/domdec.h"
52 #include "gromacs/domdec/domdec_struct.h"
53 #include "gromacs/domdec/mdsetup.h"
54 #include "gromacs/gmxlib/network.h"
55 #include "gromacs/math/functions.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/math/vecdump.h"
59 #include "gromacs/mdlib/constr.h"
60 #include "gromacs/mdlib/enerdata_utils.h"
61 #include "gromacs/mdlib/force.h"
62 #include "gromacs/mdlib/force_flags.h"
63 #include "gromacs/mdlib/gmx_omp_nthreads.h"
64 #include "gromacs/mdlib/mdatoms.h"
65 #include "gromacs/mdlib/vsite.h"
66 #include "gromacs/mdtypes/commrec.h"
67 #include "gromacs/mdtypes/enerdata.h"
68 #include "gromacs/mdtypes/forcerec.h"
69 #include "gromacs/mdtypes/inputrec.h"
70 #include "gromacs/mdtypes/md_enums.h"
71 #include "gromacs/mdtypes/state.h"
72 #include "gromacs/pbcutil/mshift.h"
73 #include "gromacs/pbcutil/pbc.h"
74 #include "gromacs/topology/ifunc.h"
75 #include "gromacs/topology/mtop_lookup.h"
76 #include "gromacs/topology/mtop_util.h"
77 #include "gromacs/utility/arrayref.h"
78 #include "gromacs/utility/arraysize.h"
79 #include "gromacs/utility/cstringutil.h"
80 #include "gromacs/utility/fatalerror.h"
81 #include "gromacs/utility/gmxassert.h"
82 #include "gromacs/utility/smalloc.h"
87 int shell; /* The shell id */
88 int nucl1, nucl2, nucl3; /* The nuclei connected to the shell */
89 /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
90 real k; /* force constant */
91 real k_1; /* 1 over force constant */
99 /* Shell counts, indices, parameters and working data */
100 int nshell_gl; /* The number of shells in the system */
101 t_shell* shell_gl; /* All the shells (for DD only) */
102 int* shell_index_gl; /* Global shell index (for DD only) */
103 gmx_bool bInterCG; /* Are there inter charge-group shells? */
104 int nshell; /* The number of local shells */
105 t_shell* shell; /* The local shells */
106 int shell_nalloc; /* The allocation size of shell */
107 gmx_bool bPredict; /* Predict shell positions */
108 gmx_bool bRequireInit; /* Require initialization of shell positions */
109 int nflexcon; /* The number of flexible constraints */
111 /* Temporary arrays, should be fixed size 2 when fully converted to C++ */
112 PaddedHostVector<gmx::RVec>* x; /* Array for iterative minimization */
113 PaddedHostVector<gmx::RVec>* f; /* Array for iterative minimization */
115 /* Flexible constraint working data */
116 rvec* acc_dir; /* Acceleration direction for flexcon */
117 rvec* x_old; /* Old coordinates for flexcon */
118 int flex_nalloc; /* The allocation size of acc_dir and x_old */
119 rvec* adir_xnold; /* Work space for init_adir */
120 rvec* adir_xnew; /* Work space for init_adir */
121 int adir_nalloc; /* Work space for init_adir */
122 std::int64_t numForceEvaluations; /* Total number of force evaluations */
123 int numConvergedIterations; /* Total number of iterations that converged */
127 static void pr_shell(FILE* fplog, int ns, t_shell s[])
131 fprintf(fplog, "SHELL DATA\n");
132 fprintf(fplog, "%5s %8s %5s %5s %5s\n", "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
133 for (i = 0; (i < ns); i++)
135 fprintf(fplog, "%5d %8.3f %5d", s[i].shell, 1.0 / s[i].k_1, s[i].nucl1);
138 fprintf(fplog, " %5d\n", s[i].nucl2);
140 else if (s[i].nnucl == 3)
142 fprintf(fplog, " %5d %5d\n", s[i].nucl2, s[i].nucl3);
146 fprintf(fplog, "\n");
151 /* TODO The remain call of this function passes non-NULL mass and NULL
152 * mtop, so this routine can be simplified.
154 * The other code path supported doing prediction before the MD loop
155 * started, but even when called, the prediction was always
156 * over-written by a subsequent call in the MD loop, so has been
158 static void predict_shells(FILE* fplog,
168 int i, m, s1, n1, n2, n3;
169 real dt_1, fudge, tm, m1, m2, m3;
172 GMX_RELEASE_ASSERT(mass || mtop, "Must have masses or a way to look them up");
174 /* We introduce a fudge factor for performance reasons: with this choice
175 * the initial force on the shells is about a factor of two lower than
184 fprintf(fplog, "RELAX: Using prediction for initial shell placement\n");
196 for (i = 0; (i < ns); i++)
207 for (m = 0; (m < DIM); m++)
209 x[s1][m] += ptr[n1][m] * dt_1;
222 /* Not the correct masses with FE, but it is just a prediction... */
223 m1 = mtopGetAtomMass(mtop, n1, &molb);
224 m2 = mtopGetAtomMass(mtop, n2, &molb);
226 tm = dt_1 / (m1 + m2);
227 for (m = 0; (m < DIM); m++)
229 x[s1][m] += (m1 * ptr[n1][m] + m2 * ptr[n2][m]) * tm;
244 /* Not the correct masses with FE, but it is just a prediction... */
245 m1 = mtopGetAtomMass(mtop, n1, &molb);
246 m2 = mtopGetAtomMass(mtop, n2, &molb);
247 m3 = mtopGetAtomMass(mtop, n3, &molb);
249 tm = dt_1 / (m1 + m2 + m3);
250 for (m = 0; (m < DIM); m++)
252 x[s1][m] += (m1 * ptr[n1][m] + m2 * ptr[n2][m] + m3 * ptr[n3][m]) * tm;
255 default: gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
260 /*! \brief Count the different particle types in a system
262 * Routine prints a warning to stderr in case an unknown particle type
264 * \param[in] fplog Print what we have found if not NULL
265 * \param[in] mtop Molecular topology.
266 * \returns Array holding the number of particles of a type
268 std::array<int, eptNR> countPtypes(FILE* fplog, const gmx_mtop_t* mtop)
270 std::array<int, eptNR> nptype = { { 0 } };
271 /* Count number of shells, and find their indices */
272 for (int i = 0; (i < eptNR); i++)
277 gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
280 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
286 case eptShell: nptype[atom->ptype] += nmol; break;
288 fprintf(stderr, "Warning unsupported particle type %d in countPtypes",
289 static_cast<int>(atom->ptype));
294 /* Print the number of each particle type */
296 for (const auto& i : nptype)
300 fprintf(fplog, "There are: %d %ss\n", i, ptype_str[n]);
308 gmx_shellfc_t* init_shell_flexcon(FILE* fplog, const gmx_mtop_t* mtop, int nflexcon, int nstcalcenergy, bool usingDomainDecomposition)
312 int* shell_index = nullptr;
315 int i, j, type, a_offset, mol, ftype, nra;
317 int aS, aN = 0; /* Shell and nucleus */
318 int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
319 #define NBT asize(bondtypes)
320 const gmx_ffparams_t* ffparams;
322 std::array<int, eptNR> n = countPtypes(fplog, mtop);
323 nshell = n[eptShell];
325 if (nshell == 0 && nflexcon == 0)
327 /* We're not doing shells or flexible constraints */
332 shfc->x = new PaddedHostVector<gmx::RVec>[2] {};
333 shfc->f = new PaddedHostVector<gmx::RVec>[2] {};
334 shfc->nflexcon = nflexcon;
338 /* Only flexible constraints, no shells.
339 * Note that make_local_shells() does not need to be called.
342 shfc->bPredict = FALSE;
347 if (nstcalcenergy != 1)
350 "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is "
351 "not supported in combination with shell particles.\nPlease make a new tpr file.",
354 if (usingDomainDecomposition)
358 "Shell particles are not implemented with domain decomposition, use a single rank");
361 /* We have shells: fill the shell data structure */
363 /* Global system sized array, this should be avoided */
364 snew(shell_index, mtop->natoms);
367 for (const AtomProxy atomP : AtomRange(*mtop))
369 const t_atom& local = atomP.atom();
370 int i = atomP.globalAtomNumber();
371 if (local.ptype == eptShell)
373 shell_index[i] = nshell++;
379 /* Initiate the shell structures */
380 for (i = 0; (i < nshell); i++)
387 /* shell[i].bInterCG=FALSE; */
392 ffparams = &mtop->ffparams;
394 /* Now fill the structures */
395 /* TODO: See if we can use update groups that cover shell constructions */
396 shfc->bInterCG = FALSE;
399 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
401 const gmx_molblock_t* molb = &mtop->molblock[mb];
402 const gmx_moltype_t* molt = &mtop->moltype[molb->type];
404 const t_atom* atom = molt->atoms.atom;
405 for (mol = 0; mol < molb->nmol; mol++)
407 for (j = 0; (j < NBT); j++)
409 const int* ia = molt->ilist[bondtypes[j]].iatoms.data();
410 for (i = 0; (i < molt->ilist[bondtypes[j]].size());)
413 ftype = ffparams->functype[type];
414 nra = interaction_function[ftype].nratoms;
416 /* Check whether we have a bond with a shell */
419 switch (bondtypes[j])
426 if (atom[ia[1]].ptype == eptShell)
431 else if (atom[ia[2]].ptype == eptShell)
438 aN = ia[4]; /* Dummy */
439 aS = ia[5]; /* Shell */
441 default: gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
448 /* Check whether one of the particles is a shell... */
449 nsi = shell_index[a_offset + aS];
450 if ((nsi < 0) || (nsi >= nshell))
452 gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d", nsi, nshell, aS);
454 if (shell[nsi].shell == -1)
456 shell[nsi].shell = a_offset + aS;
459 else if (shell[nsi].shell != a_offset + aS)
461 gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
464 if (shell[nsi].nucl1 == -1)
466 shell[nsi].nucl1 = a_offset + aN;
468 else if (shell[nsi].nucl2 == -1)
470 shell[nsi].nucl2 = a_offset + aN;
472 else if (shell[nsi].nucl3 == -1)
474 shell[nsi].nucl3 = a_offset + aN;
480 pr_shell(fplog, ns, shell);
482 gmx_fatal(FARGS, "Can not handle more than three bonds per shell\n");
486 /* shell[nsi].bInterCG = TRUE; */
487 shfc->bInterCG = TRUE;
490 switch (bondtypes[j])
494 shell[nsi].k += ffparams->iparams[type].harmonic.krA;
497 shell[nsi].k += ffparams->iparams[type].cubic.kb;
501 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS * 10))
504 "polarize can not be used with qA(%e) != qB(%e) for "
505 "atom %d of molecule block %zu",
506 qS, atom[aS].qB, aS + 1, mb + 1);
508 shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0
509 / ffparams->iparams[type].polarize.alpha;
512 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS * 10))
515 "water_pol can not be used with qA(%e) != qB(%e) for "
516 "atom %d of molecule block %zu",
517 qS, atom[aS].qB, aS + 1, mb + 1);
519 alpha = (ffparams->iparams[type].wpol.al_x
520 + ffparams->iparams[type].wpol.al_y
521 + ffparams->iparams[type].wpol.al_z)
523 shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0 / alpha;
525 default: gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
533 a_offset += molt->atoms.nr;
535 /* Done with this molecule type */
538 /* Verify whether it's all correct */
541 gmx_fatal(FARGS, "Something weird with shells. They may not be bonded to something");
544 for (i = 0; (i < ns); i++)
546 shell[i].k_1 = 1.0 / shell[i].k;
551 pr_shell(debug, ns, shell);
555 shfc->nshell_gl = ns;
556 shfc->shell_gl = shell;
557 shfc->shell_index_gl = shell_index;
559 shfc->bPredict = (getenv("GMX_NOPREDICT") == nullptr);
560 shfc->bRequireInit = FALSE;
565 fprintf(fplog, "\nWill never predict shell positions\n");
570 shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != nullptr);
571 if (shfc->bRequireInit && fplog)
573 fprintf(fplog, "\nWill always initiate shell positions\n");
584 "\nNOTE: in the current version shell prediction during the crun is "
587 /* Prediction improves performance, so we should implement either:
588 * 1. communication for the atoms needed for prediction
589 * 2. prediction using the velocities of shells; currently the
590 * shell velocities are zeroed, it's a bit tricky to keep
591 * track of the shell displacements and thus the velocity.
593 shfc->bPredict = FALSE;
600 void make_local_shells(const t_commrec* cr, const t_mdatoms* md, gmx_shellfc_t* shfc)
603 int a0, a1, *ind, nshell, i;
604 gmx_domdec_t* dd = nullptr;
606 if (DOMAINDECOMP(cr))
610 a1 = dd_numHomeAtoms(*dd);
614 /* Single node: we need all shells, just copy the pointer */
615 shfc->nshell = shfc->nshell_gl;
616 shfc->shell = shfc->shell_gl;
621 ind = shfc->shell_index_gl;
625 for (i = a0; i < a1; i++)
627 if (md->ptype[i] == eptShell)
629 if (nshell + 1 > shfc->shell_nalloc)
631 shfc->shell_nalloc = over_alloc_dd(nshell + 1);
632 srenew(shell, shfc->shell_nalloc);
636 shell[nshell] = shfc->shell_gl[ind[dd->globalAtomIndices[i]]];
640 shell[nshell] = shfc->shell_gl[ind[i]];
643 /* With inter-cg shells we can no do shell prediction,
644 * so we do not need the nuclei numbers.
648 shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
649 if (shell[nshell].nnucl > 1)
651 shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
653 if (shell[nshell].nnucl > 2)
655 shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
658 shell[nshell].shell = i;
663 shfc->nshell = nshell;
667 static void do_1pos(rvec xnew, const rvec xold, const rvec f, real step)
685 static void do_1pos3(rvec xnew, const rvec xold, const rvec f, const rvec step)
694 dx = f[XX] * step[XX];
695 dy = f[YY] * step[YY];
696 dz = f[ZZ] * step[ZZ];
703 static void directional_sd(gmx::ArrayRef<const gmx::RVec> xold,
704 gmx::ArrayRef<gmx::RVec> xnew,
705 const rvec acc_dir[],
709 const rvec* xo = as_rvec_array(xold.data());
710 rvec* xn = as_rvec_array(xnew.data());
712 for (int i = 0; i < homenr; i++)
714 do_1pos(xn[i], xo[i], acc_dir[i], step);
718 static void shell_pos_sd(gmx::ArrayRef<const gmx::RVec> xcur,
719 gmx::ArrayRef<gmx::RVec> xnew,
720 gmx::ArrayRef<const gmx::RVec> f,
725 const real step_scale_min = 0.8, step_scale_increment = 0.2, step_scale_max = 1.2,
726 step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
731 real step_min, step_max;
736 for (i = 0; (i < ns); i++)
741 for (d = 0; d < DIM; d++)
743 s[i].step[d] = s[i].k_1;
745 step_min = std::min(step_min, s[i].step[d]);
746 step_max = std::max(step_max, s[i].step[d]);
752 for (d = 0; d < DIM; d++)
754 dx = xcur[shell][d] - s[i].xold[d];
755 df = f[shell][d] - s[i].fold[d];
756 /* -dx/df gets used to generate an interpolated value, but would
757 * cause a NaN if df were binary-equal to zero. Values close to
758 * zero won't cause problems (because of the min() and max()), so
759 * just testing for binary inequality is OK. */
763 /* Scale the step size by a factor interpolated from
764 * step_scale_min to step_scale_max, as k_est goes from 0 to
765 * step_scale_multiple * s[i].step[d] */
766 s[i].step[d] = step_scale_min * s[i].step[d]
767 + step_scale_increment
768 * std::min(step_scale_multiple * s[i].step[d],
769 std::max(k_est, zero));
774 if (gmx_numzero(dx)) /* 0 == dx */
776 /* Likely this will never happen, but if it does just
777 * don't scale the step. */
781 s[i].step[d] *= step_scale_max;
785 step_min = std::min(step_min, s[i].step[d]);
786 step_max = std::max(step_max, s[i].step[d]);
790 copy_rvec(xcur[shell], s[i].xold);
791 copy_rvec(f[shell], s[i].fold);
793 do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
797 fprintf(debug, "shell[%d] = %d\n", i, shell);
798 pr_rvec(debug, 0, "fshell", f[shell], DIM, TRUE);
799 pr_rvec(debug, 0, "xold", xcur[shell], DIM, TRUE);
800 pr_rvec(debug, 0, "step", s[i].step, DIM, TRUE);
801 pr_rvec(debug, 0, "xnew", xnew[shell], DIM, TRUE);
805 printf("step %.3e %.3e\n", step_min, step_max);
809 static void decrease_step_size(int nshell, t_shell s[])
813 for (i = 0; i < nshell; i++)
815 svmul(0.8, s[i].step, s[i].step);
819 static void print_epot(FILE* fp, int64_t mdstep, int count, real epot, real df, int ndir, real sf_dir)
823 fprintf(fp, "MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e", gmx_step_str(mdstep, buf), count, epot, df);
826 fprintf(fp, ", dir. rmsF: %6.2e\n", std::sqrt(sf_dir / ndir));
835 static real rms_force(const t_commrec* cr,
836 gmx::ArrayRef<const gmx::RVec> force,
844 const rvec* f = as_rvec_array(force.data());
847 for (int i = 0; i < ns; i++)
849 int shell = s[i].shell;
850 buf[0] += norm2(f[shell]);
859 gmx_sumd(4, buf, cr);
860 ntot = gmx::roundToInt(buf[1]);
866 return (ntot ? std::sqrt(buf[0] / ntot) : 0);
869 static void dump_shells(FILE* fp, gmx::ArrayRef<gmx::RVec> f, real ftol, int ns, t_shell s[])
874 ft2 = gmx::square(ftol);
876 for (i = 0; (i < ns); i++)
879 ff2 = iprod(f[shell], f[shell]);
882 fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n", shell,
883 f[shell][XX], f[shell][YY], f[shell][ZZ], std::sqrt(ff2));
888 static void init_adir(gmx_shellfc_t* shfc,
889 gmx::Constraints* constr,
890 const t_inputrec* ir,
902 gmx::ArrayRef<const real> lambda,
908 unsigned short* ptype;
910 if (DOMAINDECOMP(cr))
918 if (n > shfc->adir_nalloc)
920 shfc->adir_nalloc = over_alloc_dd(n);
921 srenew(shfc->adir_xnold, shfc->adir_nalloc);
922 srenew(shfc->adir_xnew, shfc->adir_nalloc);
924 xnold = shfc->adir_xnold;
925 xnew = shfc->adir_xnew;
931 /* Does NOT work with freeze or acceleration groups (yet) */
932 for (n = 0; n < end; n++)
934 w_dt = md->invmass[n] * dt;
936 for (d = 0; d < DIM; d++)
938 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
940 xnold[n][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
941 xnew[n][d] = 2 * x[n][d] - x_old[n][d] + f[n][d] * w_dt * dt;
945 xnold[n][d] = x[n][d];
946 xnew[n][d] = x[n][d];
950 constr->apply(FALSE, FALSE, step, 0, 1.0, x, xnold, nullptr, box, lambda[efptBONDED],
951 &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Positions);
952 constr->apply(FALSE, FALSE, step, 0, 1.0, x, xnew, nullptr, box, lambda[efptBONDED],
953 &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Positions);
955 for (n = 0; n < end; n++)
957 for (d = 0; d < DIM; d++)
959 xnew[n][d] = -(2 * x[n][d] - xnold[n][d] - xnew[n][d]) / gmx::square(dt)
960 - f[n][d] * md->invmass[n];
962 clear_rvec(acc_dir[n]);
965 /* Project the acceleration on the old bond directions */
966 constr->apply(FALSE, FALSE, step, 0, 1.0, x_old, xnew, acc_dir, box, lambda[efptBONDED],
967 &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
970 void relax_shell_flexcon(FILE* fplog,
972 const gmx_multisim_t* ms,
974 gmx_enfrot* enforcedRotation,
976 const t_inputrec* inputrec,
977 gmx::ImdSession* imdSession,
981 const gmx_localtop_t* top,
982 gmx::Constraints* constr,
983 gmx_enerdata_t* enerd,
986 gmx::ArrayRefWithPadding<gmx::RVec> x,
987 gmx::ArrayRefWithPadding<gmx::RVec> v,
989 gmx::ArrayRef<real> lambda,
991 gmx::ArrayRefWithPadding<gmx::RVec> f,
995 gmx_wallcycle_t wcycle,
999 gmx::MdrunScheduleWorkload* runScheduleWork,
1002 const gmx_vsite_t* vsite,
1003 const DDBalanceRegionHandler& ddBalanceRegionHandler)
1005 auto xRvec = as_rvec_array(x.paddedArrayRef().data());
1006 auto vRvec = as_rvec_array(v.paddedArrayRef().data());
1011 rvec * acc_dir = nullptr, *x_old = nullptr;
1012 real Epot[2], df[2];
1016 gmx_bool bCont, bInit, bConverged;
1017 int nat, dd_ac0, dd_ac1 = 0, i;
1018 int homenr = md->homenr, end = homenr;
1019 int nflexcon, number_steps, d, Min = 0, count = 0;
1020 #define Try (1 - Min) /* At start Try = 1 */
1022 bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
1023 bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
1024 ftol = inputrec->em_tol;
1025 number_steps = inputrec->niter;
1026 nshell = shfc->nshell;
1027 shell = shfc->shell;
1028 nflexcon = shfc->nflexcon;
1032 if (DOMAINDECOMP(cr))
1034 nat = dd_natoms_vsite(cr->dd);
1037 dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
1038 nat = std::max(nat, dd_ac1);
1046 for (i = 0; (i < 2); i++)
1048 shfc->x[i].resizeWithPadding(nat);
1049 shfc->f[i].resizeWithPadding(nat);
1052 /* Create views that we can swap */
1053 gmx::ArrayRefWithPadding<gmx::RVec> posWithPadding[2];
1054 gmx::ArrayRefWithPadding<gmx::RVec> forceWithPadding[2];
1055 gmx::ArrayRef<gmx::RVec> pos[2];
1056 gmx::ArrayRef<gmx::RVec> force[2];
1057 for (i = 0; (i < 2); i++)
1059 posWithPadding[i] = shfc->x[i].arrayRefWithPadding();
1060 pos[i] = posWithPadding[i].paddedArrayRef();
1061 forceWithPadding[i] = shfc->f[i].arrayRefWithPadding();
1062 force[i] = forceWithPadding[i].paddedArrayRef();
1065 if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
1067 /* This is the only time where the coordinates are used
1068 * before do_force is called, which normally puts all
1069 * charge groups in the box.
1071 auto xRef = x.paddedArrayRef();
1072 put_atoms_in_box_omp(fr->ePBC, box, xRef.subArray(0, md->homenr),
1073 gmx_omp_nthreads_get(emntDefault));
1077 mk_mshift(fplog, graph, fr->ePBC, box, xRvec);
1081 /* After this all coordinate arrays will contain whole charge groups */
1084 shift_self(graph, box, xRvec);
1089 if (nat > shfc->flex_nalloc)
1091 shfc->flex_nalloc = over_alloc_dd(nat);
1092 srenew(shfc->acc_dir, shfc->flex_nalloc);
1093 srenew(shfc->x_old, shfc->flex_nalloc);
1095 acc_dir = shfc->acc_dir;
1096 x_old = shfc->x_old;
1097 auto xArrayRef = x.paddedArrayRef();
1098 auto vArrayRef = v.paddedArrayRef();
1099 for (i = 0; i < homenr; i++)
1101 for (d = 0; d < DIM; d++)
1103 shfc->x_old[i][d] = xArrayRef[i][d] - vArrayRef[i][d] * inputrec->delta_t;
1108 /* Do a prediction of the shell positions, when appropriate.
1109 * Without velocities (EM, NM, BD) we only do initial prediction.
1111 if (shfc->bPredict && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
1113 predict_shells(fplog, xRvec, vRvec, inputrec->delta_t, nshell, shell, md->massT, nullptr, bInit);
1116 /* do_force expected the charge groups to be in the box */
1119 unshift_self(graph, box, xRvec);
1122 /* Calculate the forces first time around */
1125 pr_rvecs(debug, 0, "x b4 do_force", xRvec, homenr);
1127 int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
1128 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
1129 nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
1130 lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
1131 (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
1136 init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old, xRvec, xRvec,
1137 as_rvec_array(force[Min].data()), shfc->acc_dir, box, lambda, &dum);
1139 for (i = 0; i < end; i++)
1141 sf_dir += md->massT[i] * norm2(shfc->acc_dir[i]);
1144 sum_epot(&(enerd->grpp), enerd->term);
1145 Epot[Min] = enerd->term[F_EPOT];
1147 df[Min] = rms_force(cr, forceWithPadding[Min].paddedArrayRef(), nshell, shell, nflexcon,
1148 &sf_dir, &Epot[Min]);
1152 fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
1157 pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min].data()), md->nr);
1160 if (nshell + nflexcon > 0)
1162 /* Copy x to pos[Min] & pos[Try]: during minimization only the
1163 * shell positions are updated, therefore the other particles must
1164 * be set here, in advance.
1166 std::copy(x.paddedArrayRef().begin(), x.paddedArrayRef().end(),
1167 posWithPadding[Min].paddedArrayRef().begin());
1168 std::copy(x.paddedArrayRef().begin(), x.paddedArrayRef().end(),
1169 posWithPadding[Try].paddedArrayRef().begin());
1172 if (bVerbose && MASTER(cr))
1174 print_epot(stdout, mdstep, 0, Epot[Min], df[Min], nflexcon, sf_dir);
1179 fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EKIN].longname, enerd->term[F_EKIN]);
1180 fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EPOT].longname, enerd->term[F_EPOT]);
1181 fprintf(debug, "%17s: %14.10e\n", interaction_function[F_ETOT].longname, enerd->term[F_ETOT]);
1182 fprintf(debug, "SHELLSTEP %s\n", gmx_step_str(mdstep, sbuf));
1185 /* First check whether we should do shells, or whether the force is
1186 * low enough even without minimization.
1188 bConverged = (df[Min] < ftol);
1190 for (count = 1; (!(bConverged) && (count < number_steps)); count++)
1194 construct_vsites(vsite, as_rvec_array(pos[Min].data()), inputrec->delta_t, vRvec,
1195 idef->iparams, idef->il, fr->ePBC, fr->bMolPBC, cr, box);
1200 init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, x_old, xRvec,
1201 as_rvec_array(pos[Min].data()), as_rvec_array(force[Min].data()), acc_dir,
1204 directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
1207 /* New positions, Steepest descent */
1208 shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
1210 /* do_force expected the charge groups to be in the box */
1213 unshift_self(graph, box, as_rvec_array(pos[Try].data()));
1218 pr_rvecs(debug, 0, "RELAX: pos[Min] ", as_rvec_array(pos[Min].data()), homenr);
1219 pr_rvecs(debug, 0, "RELAX: pos[Try] ", as_rvec_array(pos[Try].data()), homenr);
1221 /* Try the new positions */
1222 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
1223 wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
1224 enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
1225 shellfc_flags, ddBalanceRegionHandler);
1226 sum_epot(&(enerd->grpp), enerd->term);
1229 pr_rvecs(debug, 0, "RELAX: force[Min]", as_rvec_array(force[Min].data()), homenr);
1230 pr_rvecs(debug, 0, "RELAX: force[Try]", as_rvec_array(force[Try].data()), homenr);
1235 init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, x_old, xRvec,
1236 as_rvec_array(pos[Try].data()), as_rvec_array(force[Try].data()), acc_dir,
1239 for (i = 0; i < end; i++)
1241 sf_dir += md->massT[i] * norm2(acc_dir[i]);
1245 Epot[Try] = enerd->term[F_EPOT];
1247 df[Try] = rms_force(cr, force[Try], nshell, shell, nflexcon, &sf_dir, &Epot[Try]);
1251 fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
1258 pr_rvecs(debug, 0, "F na do_force", as_rvec_array(force[Try].data()), homenr);
1262 fprintf(debug, "SHELL ITER %d\n", count);
1263 dump_shells(debug, force[Try], ftol, nshell, shell);
1267 if (bVerbose && MASTER(cr))
1269 print_epot(stdout, mdstep, count, Epot[Try], df[Try], nflexcon, sf_dir);
1272 bConverged = (df[Try] < ftol);
1274 if ((df[Try] < df[Min]))
1278 fprintf(debug, "Swapping Min and Try\n");
1282 /* Correct the velocities for the flexible constraints */
1283 invdt = 1 / inputrec->delta_t;
1284 auto vArrayRef = v.paddedArrayRef();
1285 for (i = 0; i < end; i++)
1287 for (d = 0; d < DIM; d++)
1289 vArrayRef[i][d] += (pos[Try][i][d] - pos[Min][i][d]) * invdt;
1297 decrease_step_size(nshell, shell);
1300 shfc->numForceEvaluations += count;
1303 shfc->numConvergedIterations++;
1305 if (MASTER(cr) && !(bConverged))
1307 /* Note that the energies and virial are incorrect when not converged */
1310 fprintf(fplog, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
1311 gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
1313 fprintf(stderr, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
1314 gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
1317 /* Copy back the coordinates and the forces */
1318 std::copy(pos[Min].begin(), pos[Min].end(), x.paddedArrayRef().data());
1319 std::copy(force[Min].begin(), force[Min].end(), f.unpaddedArrayRef().begin());
1322 void done_shellfc(FILE* fplog, gmx_shellfc_t* shfc, int64_t numSteps)
1324 if (shfc && fplog && numSteps > 0)
1326 double numStepsAsDouble = static_cast<double>(numSteps);
1327 fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
1328 (shfc->numConvergedIterations * 100.0) / numStepsAsDouble);
1329 fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
1330 shfc->numForceEvaluations / numStepsAsDouble);
1333 // TODO Deallocate memory in shfc