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7 * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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40 * \brief This file defines integrators for energy minimization
42 * \author Berk Hess <hess@kth.se>
43 * \author Erik Lindahl <erik@kth.se>
44 * \ingroup module_mdrun
57 #include "gromacs/commandline/filenm.h"
58 #include "gromacs/domdec/collect.h"
59 #include "gromacs/domdec/dlbtiming.h"
60 #include "gromacs/domdec/domdec.h"
61 #include "gromacs/domdec/domdec_struct.h"
62 #include "gromacs/domdec/mdsetup.h"
63 #include "gromacs/domdec/partition.h"
64 #include "gromacs/ewald/pme.h"
65 #include "gromacs/fileio/confio.h"
66 #include "gromacs/fileio/mtxio.h"
67 #include "gromacs/gmxlib/network.h"
68 #include "gromacs/gmxlib/nrnb.h"
69 #include "gromacs/imd/imd.h"
70 #include "gromacs/linearalgebra/sparsematrix.h"
71 #include "gromacs/listed_forces/manage_threading.h"
72 #include "gromacs/math/functions.h"
73 #include "gromacs/math/vec.h"
74 #include "gromacs/mdlib/constr.h"
75 #include "gromacs/mdlib/dispersioncorrection.h"
76 #include "gromacs/mdlib/ebin.h"
77 #include "gromacs/mdlib/enerdata_utils.h"
78 #include "gromacs/mdlib/energyoutput.h"
79 #include "gromacs/mdlib/force.h"
80 #include "gromacs/mdlib/forcerec.h"
81 #include "gromacs/mdlib/gmx_omp_nthreads.h"
82 #include "gromacs/mdlib/md_support.h"
83 #include "gromacs/mdlib/mdatoms.h"
84 #include "gromacs/mdlib/stat.h"
85 #include "gromacs/mdlib/tgroup.h"
86 #include "gromacs/mdlib/trajectory_writing.h"
87 #include "gromacs/mdlib/update.h"
88 #include "gromacs/mdlib/vsite.h"
89 #include "gromacs/mdrunutility/handlerestart.h"
90 #include "gromacs/mdrunutility/printtime.h"
91 #include "gromacs/mdtypes/commrec.h"
92 #include "gromacs/mdtypes/inputrec.h"
93 #include "gromacs/mdtypes/md_enums.h"
94 #include "gromacs/mdtypes/mdrunoptions.h"
95 #include "gromacs/mdtypes/state.h"
96 #include "gromacs/pbcutil/mshift.h"
97 #include "gromacs/pbcutil/pbc.h"
98 #include "gromacs/timing/wallcycle.h"
99 #include "gromacs/timing/walltime_accounting.h"
100 #include "gromacs/topology/mtop_util.h"
101 #include "gromacs/topology/topology.h"
102 #include "gromacs/utility/cstringutil.h"
103 #include "gromacs/utility/exceptions.h"
104 #include "gromacs/utility/fatalerror.h"
105 #include "gromacs/utility/logger.h"
106 #include "gromacs/utility/smalloc.h"
108 #include "legacysimulator.h"
111 using gmx::MdrunScheduleWorkload
;
113 //! Utility structure for manipulating states during EM
116 //! Copy of the global state
119 PaddedHostVector
<gmx::RVec
> f
;
122 //! Norm of the force
130 //! Print the EM starting conditions
131 static void print_em_start(FILE* fplog
,
133 gmx_walltime_accounting_t walltime_accounting
,
134 gmx_wallcycle_t wcycle
,
137 walltime_accounting_start_time(walltime_accounting
);
138 wallcycle_start(wcycle
, ewcRUN
);
139 print_start(fplog
, cr
, walltime_accounting
, name
);
142 //! Stop counting time for EM
143 static void em_time_end(gmx_walltime_accounting_t walltime_accounting
, gmx_wallcycle_t wcycle
)
145 wallcycle_stop(wcycle
, ewcRUN
);
147 walltime_accounting_end_time(walltime_accounting
);
150 //! Printing a log file and console header
151 static void sp_header(FILE* out
, const char* minimizer
, real ftol
, int nsteps
)
154 fprintf(out
, "%s:\n", minimizer
);
155 fprintf(out
, " Tolerance (Fmax) = %12.5e\n", ftol
);
156 fprintf(out
, " Number of steps = %12d\n", nsteps
);
159 //! Print warning message
160 static void warn_step(FILE* fp
, real ftol
, real fmax
, gmx_bool bLastStep
, gmx_bool bConstrain
)
162 constexpr bool realIsDouble
= GMX_DOUBLE
;
165 if (!std::isfinite(fmax
))
168 "\nEnergy minimization has stopped because the force "
169 "on at least one atom is not finite. This usually means "
170 "atoms are overlapping. Modify the input coordinates to "
171 "remove atom overlap or use soft-core potentials with "
172 "the free energy code to avoid infinite forces.\n%s",
173 !realIsDouble
? "You could also be lucky that switching to double precision "
174 "is sufficient to obtain finite forces.\n"
180 "\nEnergy minimization reached the maximum number "
181 "of steps before the forces reached the requested "
182 "precision Fmax < %g.\n",
188 "\nEnergy minimization has stopped, but the forces have "
189 "not converged to the requested precision Fmax < %g (which "
190 "may not be possible for your system). It stopped "
191 "because the algorithm tried to make a new step whose size "
192 "was too small, or there was no change in the energy since "
193 "last step. Either way, we regard the minimization as "
194 "converged to within the available machine precision, "
195 "given your starting configuration and EM parameters.\n%s%s",
197 !realIsDouble
? "\nDouble precision normally gives you higher accuracy, but "
198 "this is often not needed for preparing to run molecular "
201 bConstrain
? "You might need to increase your constraint accuracy, or turn\n"
202 "off constraints altogether (set constraints = none in mdp file)\n"
206 fputs(wrap_lines(buffer
, 78, 0, FALSE
), stderr
);
207 fputs(wrap_lines(buffer
, 78, 0, FALSE
), fp
);
210 //! Print message about convergence of the EM
211 static void print_converged(FILE* fp
,
217 const em_state_t
* ems
,
220 char buf
[STEPSTRSIZE
];
224 fprintf(fp
, "\n%s converged to Fmax < %g in %s steps\n", alg
, ftol
, gmx_step_str(count
, buf
));
226 else if (count
< nsteps
)
229 "\n%s converged to machine precision in %s steps,\n"
230 "but did not reach the requested Fmax < %g.\n",
231 alg
, gmx_step_str(count
, buf
), ftol
);
235 fprintf(fp
, "\n%s did not converge to Fmax < %g in %s steps.\n", alg
, ftol
,
236 gmx_step_str(count
, buf
));
240 fprintf(fp
, "Potential Energy = %21.14e\n", ems
->epot
);
241 fprintf(fp
, "Maximum force = %21.14e on atom %d\n", ems
->fmax
, ems
->a_fmax
+ 1);
242 fprintf(fp
, "Norm of force = %21.14e\n", ems
->fnorm
/ sqrtNumAtoms
);
244 fprintf(fp
, "Potential Energy = %14.7e\n", ems
->epot
);
245 fprintf(fp
, "Maximum force = %14.7e on atom %d\n", ems
->fmax
, ems
->a_fmax
+ 1);
246 fprintf(fp
, "Norm of force = %14.7e\n", ems
->fnorm
/ sqrtNumAtoms
);
250 //! Compute the norm and max of the force array in parallel
251 static void get_f_norm_max(const t_commrec
* cr
,
261 int la_max
, a_max
, start
, end
, i
, m
, gf
;
263 /* This routine finds the largest force and returns it.
264 * On parallel machines the global max is taken.
270 end
= mdatoms
->homenr
;
271 if (mdatoms
->cFREEZE
)
273 for (i
= start
; i
< end
; i
++)
275 gf
= mdatoms
->cFREEZE
[i
];
277 for (m
= 0; m
< DIM
; m
++)
279 if (!opts
->nFreeze
[gf
][m
])
281 fam
+= gmx::square(f
[i
][m
]);
294 for (i
= start
; i
< end
; i
++)
306 if (la_max
>= 0 && DOMAINDECOMP(cr
))
308 a_max
= cr
->dd
->globalAtomIndices
[la_max
];
316 snew(sum
, 2 * cr
->nnodes
+ 1);
317 sum
[2 * cr
->nodeid
] = fmax2
;
318 sum
[2 * cr
->nodeid
+ 1] = a_max
;
319 sum
[2 * cr
->nnodes
] = fnorm2
;
320 gmx_sumd(2 * cr
->nnodes
+ 1, sum
, cr
);
321 fnorm2
= sum
[2 * cr
->nnodes
];
322 /* Determine the global maximum */
323 for (i
= 0; i
< cr
->nnodes
; i
++)
325 if (sum
[2 * i
] > fmax2
)
328 a_max
= gmx::roundToInt(sum
[2 * i
+ 1]);
336 *fnorm
= sqrt(fnorm2
);
348 //! Compute the norm of the force
349 static void get_state_f_norm_max(const t_commrec
* cr
, t_grpopts
* opts
, t_mdatoms
* mdatoms
, em_state_t
* ems
)
351 get_f_norm_max(cr
, opts
, mdatoms
, ems
->f
.rvec_array(), &ems
->fnorm
, &ems
->fmax
, &ems
->a_fmax
);
354 //! Initialize the energy minimization
355 static void init_em(FILE* fplog
,
356 const gmx::MDLogger
& mdlog
,
360 gmx::ImdSession
* imdSession
,
362 t_state
* state_global
,
363 gmx_mtop_t
* top_global
,
369 gmx::MDAtoms
* mdAtoms
,
370 gmx_global_stat_t
* gstat
,
372 gmx::Constraints
* constr
,
373 gmx_shellfc_t
** shellfc
)
379 fprintf(fplog
, "Initiating %s\n", title
);
384 state_global
->ngtc
= 0;
386 initialize_lambdas(fplog
, *ir
, MASTER(cr
), &(state_global
->fep_state
), state_global
->lambda
, nullptr);
390 GMX_ASSERT(shellfc
!= nullptr, "With NM we always support shells");
392 *shellfc
= init_shell_flexcon(stdout
, top_global
, constr
? constr
->numFlexibleConstraints() : 0,
393 ir
->nstcalcenergy
, DOMAINDECOMP(cr
));
397 GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir
->eI
),
398 "This else currently only handles energy minimizers, consider if your algorithm "
399 "needs shell/flexible-constraint support");
401 /* With energy minimization, shells and flexible constraints are
402 * automatically minimized when treated like normal DOFS.
404 if (shellfc
!= nullptr)
410 auto mdatoms
= mdAtoms
->mdatoms();
411 if (DOMAINDECOMP(cr
))
413 top
->useInDomainDecomp_
= true;
414 dd_init_local_top(*top_global
, top
);
416 dd_init_local_state(cr
->dd
, state_global
, &ems
->s
);
418 /* Distribute the charge groups over the nodes from the master node */
419 dd_partition_system(fplog
, mdlog
, ir
->init_step
, cr
, TRUE
, 1, state_global
, *top_global
, ir
,
420 imdSession
, pull_work
, &ems
->s
, &ems
->f
, mdAtoms
, top
, fr
, vsite
,
421 constr
, nrnb
, nullptr, FALSE
);
422 dd_store_state(cr
->dd
, &ems
->s
);
428 state_change_natoms(state_global
, state_global
->natoms
);
429 /* Just copy the state */
430 ems
->s
= *state_global
;
431 state_change_natoms(&ems
->s
, ems
->s
.natoms
);
432 ems
->f
.resizeWithPadding(ems
->s
.natoms
);
434 mdAlgorithmsSetupAtomData(cr
, ir
, *top_global
, top
, fr
, graph
, mdAtoms
, constr
, vsite
,
435 shellfc
? *shellfc
: nullptr);
439 set_vsite_top(vsite
, top
, mdatoms
);
443 update_mdatoms(mdAtoms
->mdatoms(), ems
->s
.lambda
[efptMASS
]);
447 // TODO how should this cross-module support dependency be managed?
448 if (ir
->eConstrAlg
== econtSHAKE
&& gmx_mtop_ftype_count(top_global
, F_CONSTR
) > 0)
450 gmx_fatal(FARGS
, "Can not do energy minimization with %s, use %s\n",
451 econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
454 if (!ir
->bContinuation
)
456 /* Constrain the starting coordinates */
458 constr
->apply(TRUE
, TRUE
, -1, 0, 1.0, ems
->s
.x
.rvec_array(), ems
->s
.x
.rvec_array(),
459 nullptr, ems
->s
.box
, ems
->s
.lambda
[efptFEP
], &dvdl_constr
, nullptr,
460 nullptr, gmx::ConstraintVariable::Positions
);
466 *gstat
= global_stat_init(ir
);
473 calc_shifts(ems
->s
.box
, fr
->shift_vec
);
476 //! Finalize the minimization
477 static void finish_em(const t_commrec
* cr
,
479 gmx_walltime_accounting_t walltime_accounting
,
480 gmx_wallcycle_t wcycle
)
482 if (!thisRankHasDuty(cr
, DUTY_PME
))
484 /* Tell the PME only node to finish */
485 gmx_pme_send_finish(cr
);
490 em_time_end(walltime_accounting
, wcycle
);
493 //! Swap two different EM states during minimization
494 static void swap_em_state(em_state_t
** ems1
, em_state_t
** ems2
)
503 //! Save the EM trajectory
504 static void write_em_traj(FILE* fplog
,
510 gmx_mtop_t
* top_global
,
514 t_state
* state_global
,
515 ObservablesHistory
* observablesHistory
)
521 mdof_flags
|= MDOF_X
;
525 mdof_flags
|= MDOF_F
;
528 /* If we want IMD output, set appropriate MDOF flag */
531 mdof_flags
|= MDOF_IMD
;
534 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
, top_global
->natoms
, step
,
535 static_cast<double>(step
), &state
->s
, state_global
,
536 observablesHistory
, state
->f
);
538 if (confout
!= nullptr)
540 if (DOMAINDECOMP(cr
))
542 /* If bX=true, x was collected to state_global in the call above */
545 auto globalXRef
= MASTER(cr
) ? state_global
->x
: gmx::ArrayRef
<gmx::RVec
>();
546 dd_collect_vec(cr
->dd
, &state
->s
, state
->s
.x
, globalXRef
);
551 /* Copy the local state pointer */
552 state_global
= &state
->s
;
557 if (ir
->ePBC
!= epbcNONE
&& !ir
->bPeriodicMols
&& DOMAINDECOMP(cr
))
559 /* Make molecules whole only for confout writing */
560 do_pbc_mtop(ir
->ePBC
, state
->s
.box
, top_global
, state_global
->x
.rvec_array());
563 write_sto_conf_mtop(confout
, *top_global
->name
, top_global
,
564 state_global
->x
.rvec_array(), nullptr, ir
->ePBC
, state
->s
.box
);
569 //! \brief Do one minimization step
571 // \returns true when the step succeeded, false when a constraint error occurred
572 static bool do_em_step(const t_commrec
* cr
,
577 const PaddedHostVector
<gmx::RVec
>* force
,
579 gmx::Constraints
* constr
,
586 int nthreads gmx_unused
;
588 bool validStep
= true;
593 if (DOMAINDECOMP(cr
) && s1
->ddp_count
!= cr
->dd
->ddp_count
)
595 gmx_incons("state mismatch in do_em_step");
598 s2
->flags
= s1
->flags
;
600 if (s2
->natoms
!= s1
->natoms
)
602 state_change_natoms(s2
, s1
->natoms
);
603 ems2
->f
.resizeWithPadding(s2
->natoms
);
605 if (DOMAINDECOMP(cr
) && s2
->cg_gl
.size() != s1
->cg_gl
.size())
607 s2
->cg_gl
.resize(s1
->cg_gl
.size());
610 copy_mat(s1
->box
, s2
->box
);
611 /* Copy free energy state */
612 s2
->lambda
= s1
->lambda
;
613 copy_mat(s1
->box
, s2
->box
);
618 nthreads
= gmx_omp_nthreads_get(emntUpdate
);
619 #pragma omp parallel num_threads(nthreads)
621 const rvec
* x1
= s1
->x
.rvec_array();
622 rvec
* x2
= s2
->x
.rvec_array();
623 const rvec
* f
= force
->rvec_array();
626 #pragma omp for schedule(static) nowait
627 for (int i
= start
; i
< end
; i
++)
635 for (int m
= 0; m
< DIM
; m
++)
637 if (ir
->opts
.nFreeze
[gf
][m
])
643 x2
[i
][m
] = x1
[i
][m
] + a
* f
[i
][m
];
647 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
650 if (s2
->flags
& (1 << estCGP
))
652 /* Copy the CG p vector */
653 const rvec
* p1
= s1
->cg_p
.rvec_array();
654 rvec
* p2
= s2
->cg_p
.rvec_array();
655 #pragma omp for schedule(static) nowait
656 for (int i
= start
; i
< end
; i
++)
658 // Trivial OpenMP block that does not throw
659 copy_rvec(p1
[i
], p2
[i
]);
663 if (DOMAINDECOMP(cr
))
665 /* OpenMP does not supported unsigned loop variables */
666 #pragma omp for schedule(static) nowait
667 for (gmx::index i
= 0; i
< gmx::ssize(s2
->cg_gl
); i
++)
669 s2
->cg_gl
[i
] = s1
->cg_gl
[i
];
674 if (DOMAINDECOMP(cr
))
676 s2
->ddp_count
= s1
->ddp_count
;
677 s2
->ddp_count_cg_gl
= s1
->ddp_count_cg_gl
;
683 validStep
= constr
->apply(TRUE
, TRUE
, count
, 0, 1.0, s1
->x
.rvec_array(), s2
->x
.rvec_array(),
684 nullptr, s2
->box
, s2
->lambda
[efptBONDED
], &dvdl_constr
, nullptr,
685 nullptr, gmx::ConstraintVariable::Positions
);
689 /* This global reduction will affect performance at high
690 * parallelization, but we can not really avoid it.
691 * But usually EM is not run at high parallelization.
693 int reductionBuffer
= static_cast<int>(!validStep
);
694 gmx_sumi(1, &reductionBuffer
, cr
);
695 validStep
= (reductionBuffer
== 0);
698 // We should move this check to the different minimizers
699 if (!validStep
&& ir
->eI
!= eiSteep
)
702 "The coordinates could not be constrained. Minimizer '%s' can not handle "
703 "constraint failures, use minimizer '%s' before using '%s'.",
704 EI(ir
->eI
), EI(eiSteep
), EI(ir
->eI
));
711 //! Prepare EM for using domain decomposition parallellization
712 static void em_dd_partition_system(FILE* fplog
,
713 const gmx::MDLogger
& mdlog
,
716 gmx_mtop_t
* top_global
,
718 gmx::ImdSession
* imdSession
,
722 gmx::MDAtoms
* mdAtoms
,
725 gmx::Constraints
* constr
,
727 gmx_wallcycle_t wcycle
)
729 /* Repartition the domain decomposition */
730 dd_partition_system(fplog
, mdlog
, step
, cr
, FALSE
, 1, nullptr, *top_global
, ir
, imdSession
, pull_work
,
731 &ems
->s
, &ems
->f
, mdAtoms
, top
, fr
, vsite
, constr
, nrnb
, wcycle
, FALSE
);
732 dd_store_state(cr
->dd
, &ems
->s
);
738 /*! \brief Class to handle the work of setting and doing an energy evaluation.
740 * This class is a mere aggregate of parameters to pass to evaluate an
741 * energy, so that future changes to names and types of them consume
742 * less time when refactoring other code.
744 * Aggregate initialization is used, for which the chief risk is that
745 * if a member is added at the end and not all initializer lists are
746 * updated, then the member will be value initialized, which will
747 * typically mean initialization to zero.
749 * Use a braced initializer list to construct one of these. */
750 class EnergyEvaluator
753 /*! \brief Evaluates an energy on the state in \c ems.
755 * \todo In practice, the same objects mu_tot, vir, and pres
756 * are always passed to this function, so we would rather have
757 * them as data members. However, their C-array types are
758 * unsuited for aggregate initialization. When the types
759 * improve, the call signature of this method can be reduced.
761 void run(em_state_t
* ems
, rvec mu_tot
, tensor vir
, tensor pres
, int64_t count
, gmx_bool bFirst
);
762 //! Handles logging (deprecated).
765 const gmx::MDLogger
& mdlog
;
766 //! Handles communication.
768 //! Coordinates multi-simulations.
769 const gmx_multisim_t
* ms
;
770 //! Holds the simulation topology.
771 gmx_mtop_t
* top_global
;
772 //! Holds the domain topology.
774 //! User input options.
775 t_inputrec
* inputrec
;
776 //! The Interactive Molecular Dynamics session.
777 gmx::ImdSession
* imdSession
;
778 //! The pull work object.
780 //! Manages flop accounting.
782 //! Manages wall cycle accounting.
783 gmx_wallcycle_t wcycle
;
784 //! Coordinates global reduction.
785 gmx_global_stat_t gstat
;
786 //! Handles virtual sites.
788 //! Handles constraints.
789 gmx::Constraints
* constr
;
790 //! Handles strange things.
792 //! Molecular graph for SHAKE.
794 //! Per-atom data for this domain.
795 gmx::MDAtoms
* mdAtoms
;
796 //! Handles how to calculate the forces.
798 //! Schedule of force-calculation work each step for this task.
799 MdrunScheduleWorkload
* runScheduleWork
;
800 //! Stores the computed energies.
801 gmx_enerdata_t
* enerd
;
804 void EnergyEvaluator::run(em_state_t
* ems
, rvec mu_tot
, tensor vir
, tensor pres
, int64_t count
, gmx_bool bFirst
)
808 tensor force_vir
, shake_vir
, ekin
;
812 /* Set the time to the initial time, the time does not change during EM */
813 t
= inputrec
->init_t
;
815 if (bFirst
|| (DOMAINDECOMP(cr
) && ems
->s
.ddp_count
< cr
->dd
->ddp_count
))
817 /* This is the first state or an old state used before the last ns */
823 if (inputrec
->nstlist
> 0)
831 construct_vsites(vsite
, ems
->s
.x
.rvec_array(), 1, nullptr, top
->idef
.iparams
, top
->idef
.il
,
832 fr
->ePBC
, fr
->bMolPBC
, cr
, ems
->s
.box
);
835 if (DOMAINDECOMP(cr
) && bNS
)
837 /* Repartition the domain decomposition */
838 em_dd_partition_system(fplog
, mdlog
, count
, cr
, top_global
, inputrec
, imdSession
, pull_work
,
839 ems
, top
, mdAtoms
, fr
, vsite
, constr
, nrnb
, wcycle
);
842 /* Calc force & energy on new trial position */
843 /* do_force always puts the charge groups in the box and shifts again
844 * We do not unshift, so molecules are always whole in congrad.c
846 do_force(fplog
, cr
, ms
, inputrec
, nullptr, nullptr, imdSession
, pull_work
, count
, nrnb
, wcycle
,
847 top
, ems
->s
.box
, ems
->s
.x
.arrayRefWithPadding(), &ems
->s
.hist
,
848 ems
->f
.arrayRefWithPadding(), force_vir
, mdAtoms
->mdatoms(), enerd
, fcd
, ems
->s
.lambda
,
849 graph
, fr
, runScheduleWork
, vsite
, mu_tot
, t
, nullptr,
850 GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
| GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
851 | (bNS
? GMX_FORCE_NS
: 0),
852 DDBalanceRegionHandler(cr
));
854 /* Clear the unused shake virial and pressure */
855 clear_mat(shake_vir
);
858 /* Communicate stuff when parallel */
859 if (PAR(cr
) && inputrec
->eI
!= eiNM
)
861 wallcycle_start(wcycle
, ewcMoveE
);
863 global_stat(gstat
, cr
, enerd
, force_vir
, shake_vir
, mu_tot
, inputrec
, nullptr, nullptr, nullptr,
864 1, &terminate
, nullptr, FALSE
, CGLO_ENERGY
| CGLO_PRESSURE
| CGLO_CONSTRAINT
);
866 wallcycle_stop(wcycle
, ewcMoveE
);
869 if (fr
->dispersionCorrection
)
871 /* Calculate long range corrections to pressure and energy */
872 const DispersionCorrection::Correction correction
=
873 fr
->dispersionCorrection
->calculate(ems
->s
.box
, ems
->s
.lambda
[efptVDW
]);
875 enerd
->term
[F_DISPCORR
] = correction
.energy
;
876 enerd
->term
[F_EPOT
] += correction
.energy
;
877 enerd
->term
[F_PRES
] += correction
.pressure
;
878 enerd
->term
[F_DVDL
] += correction
.dvdl
;
882 enerd
->term
[F_DISPCORR
] = 0;
885 ems
->epot
= enerd
->term
[F_EPOT
];
889 /* Project out the constraint components of the force */
891 rvec
* f_rvec
= ems
->f
.rvec_array();
892 constr
->apply(FALSE
, FALSE
, count
, 0, 1.0, ems
->s
.x
.rvec_array(), f_rvec
, f_rvec
,
893 ems
->s
.box
, ems
->s
.lambda
[efptBONDED
], &dvdl_constr
, nullptr, &shake_vir
,
894 gmx::ConstraintVariable::ForceDispl
);
895 enerd
->term
[F_DVDL_CONSTR
] += dvdl_constr
;
896 m_add(force_vir
, shake_vir
, vir
);
900 copy_mat(force_vir
, vir
);
904 enerd
->term
[F_PRES
] = calc_pres(fr
->ePBC
, inputrec
->nwall
, ems
->s
.box
, ekin
, vir
, pres
);
906 sum_dhdl(enerd
, ems
->s
.lambda
, *inputrec
->fepvals
);
908 if (EI_ENERGY_MINIMIZATION(inputrec
->eI
))
910 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdAtoms
->mdatoms(), ems
);
916 //! Parallel utility summing energies and forces
917 static double reorder_partsum(const t_commrec
* cr
,
919 gmx_mtop_t
* top_global
,
925 fprintf(debug
, "Doing reorder_partsum\n");
928 const rvec
* fm
= s_min
->f
.rvec_array();
929 const rvec
* fb
= s_b
->f
.rvec_array();
931 /* Collect fm in a global vector fmg.
932 * This conflicts with the spirit of domain decomposition,
933 * but to fully optimize this a much more complicated algorithm is required.
935 const int natoms
= top_global
->natoms
;
939 gmx::ArrayRef
<const int> indicesMin
= s_min
->s
.cg_gl
;
941 for (int a
: indicesMin
)
943 copy_rvec(fm
[i
], fmg
[a
]);
946 gmx_sum(top_global
->natoms
* 3, fmg
[0], cr
);
948 /* Now we will determine the part of the sum for the cgs in state s_b */
949 gmx::ArrayRef
<const int> indicesB
= s_b
->s
.cg_gl
;
954 gmx::ArrayRef
<unsigned char> grpnrFREEZE
=
955 top_global
->groups
.groupNumbers
[SimulationAtomGroupType::Freeze
];
956 for (int a
: indicesB
)
958 if (!grpnrFREEZE
.empty())
962 for (int m
= 0; m
< DIM
; m
++)
964 if (!opts
->nFreeze
[gf
][m
])
966 partsum
+= (fb
[i
][m
] - fmg
[a
][m
]) * fb
[i
][m
];
977 //! Print some stuff, like beta, whatever that means.
978 static real
pr_beta(const t_commrec
* cr
,
981 gmx_mtop_t
* top_global
,
987 /* This is just the classical Polak-Ribiere calculation of beta;
988 * it looks a bit complicated since we take freeze groups into account,
989 * and might have to sum it in parallel runs.
992 if (!DOMAINDECOMP(cr
)
993 || (s_min
->s
.ddp_count
== cr
->dd
->ddp_count
&& s_b
->s
.ddp_count
== cr
->dd
->ddp_count
))
995 const rvec
* fm
= s_min
->f
.rvec_array();
996 const rvec
* fb
= s_b
->f
.rvec_array();
999 /* This part of code can be incorrect with DD,
1000 * since the atom ordering in s_b and s_min might differ.
1002 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1004 if (mdatoms
->cFREEZE
)
1006 gf
= mdatoms
->cFREEZE
[i
];
1008 for (int m
= 0; m
< DIM
; m
++)
1010 if (!opts
->nFreeze
[gf
][m
])
1012 sum
+= (fb
[i
][m
] - fm
[i
][m
]) * fb
[i
][m
];
1019 /* We need to reorder cgs while summing */
1020 sum
= reorder_partsum(cr
, opts
, top_global
, s_min
, s_b
);
1024 gmx_sumd(1, &sum
, cr
);
1027 return sum
/ gmx::square(s_min
->fnorm
);
1033 void LegacySimulator::do_cg()
1035 const char* CG
= "Polak-Ribiere Conjugate Gradients";
1038 gmx_global_stat_t gstat
;
1040 double tmp
, minstep
;
1042 real a
, b
, c
, beta
= 0.0;
1045 gmx_bool converged
, foundlower
;
1046 rvec mu_tot
= { 0 };
1047 gmx_bool do_log
= FALSE
, do_ene
= FALSE
, do_x
, do_f
;
1049 int number_steps
, neval
= 0, nstcg
= inputrec
->nstcgsteep
;
1050 int m
, step
, nminstep
;
1051 auto mdatoms
= mdAtoms
->mdatoms();
1056 "Note that activating conjugate gradient energy minimization via the "
1057 "integrator .mdp option and the command gmx mdrun may "
1058 "be available in a different form in a future version of GROMACS, "
1059 "e.g. gmx minimize and an .mdp option.");
1065 // In CG, the state is extended with a search direction
1066 state_global
->flags
|= (1 << estCGP
);
1068 // Ensure the extra per-atom state array gets allocated
1069 state_change_natoms(state_global
, state_global
->natoms
);
1071 // Initialize the search direction to zero
1072 for (RVec
& cg_p
: state_global
->cg_p
)
1078 /* Create 4 states on the stack and extract pointers that we will swap */
1079 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1080 em_state_t
* s_min
= &s0
;
1081 em_state_t
* s_a
= &s1
;
1082 em_state_t
* s_b
= &s2
;
1083 em_state_t
* s_c
= &s3
;
1085 /* Init em and store the local state in s_min */
1086 init_em(fplog
, mdlog
, CG
, cr
, inputrec
, imdSession
, pull_work
, state_global
, top_global
, s_min
,
1087 &top
, nrnb
, fr
, &graph
, mdAtoms
, &gstat
, vsite
, constr
, nullptr);
1089 init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, mdModulesNotifier
,
1090 inputrec
, top_global
, nullptr, wcycle
, StartingBehavior::NewSimulation
);
1091 gmx::EnergyOutput
energyOutput(mdoutf_get_fp_ene(outf
), top_global
, inputrec
, pull_work
, nullptr,
1092 false, StartingBehavior::NewSimulation
, mdModulesNotifier
);
1094 /* Print to log file */
1095 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, CG
);
1097 /* Max number of steps */
1098 number_steps
= inputrec
->nsteps
;
1102 sp_header(stderr
, CG
, inputrec
->em_tol
, number_steps
);
1106 sp_header(fplog
, CG
, inputrec
->em_tol
, number_steps
);
1109 EnergyEvaluator energyEvaluator
{
1110 fplog
, mdlog
, cr
, ms
, top_global
, &top
, inputrec
,
1111 imdSession
, pull_work
, nrnb
, wcycle
, gstat
, vsite
, constr
,
1112 fcd
, graph
, mdAtoms
, fr
, runScheduleWork
, enerd
1114 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1115 /* do_force always puts the charge groups in the box and shifts again
1116 * We do not unshift, so molecules are always whole in congrad.c
1118 energyEvaluator
.run(s_min
, mu_tot
, vir
, pres
, -1, TRUE
);
1122 /* Copy stuff to the energy bin for easy printing etc. */
1123 matrix nullBox
= {};
1124 energyOutput
.addDataAtEnergyStep(false, false, static_cast<double>(step
), mdatoms
->tmass
,
1125 enerd
, nullptr, nullptr, nullptr, nullBox
, nullptr,
1126 nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1128 energyOutput
.printHeader(fplog
, step
, step
);
1129 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
,
1130 step
, fcd
, nullptr);
1133 /* Estimate/guess the initial stepsize */
1134 stepsize
= inputrec
->em_stepsize
/ s_min
->fnorm
;
1138 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1139 fprintf(stderr
, " F-max = %12.5e on atom %d\n", s_min
->fmax
, s_min
->a_fmax
+ 1);
1140 fprintf(stderr
, " F-Norm = %12.5e\n", s_min
->fnorm
/ sqrtNumAtoms
);
1141 fprintf(stderr
, "\n");
1142 /* and copy to the log file too... */
1143 fprintf(fplog
, " F-max = %12.5e on atom %d\n", s_min
->fmax
, s_min
->a_fmax
+ 1);
1144 fprintf(fplog
, " F-Norm = %12.5e\n", s_min
->fnorm
/ sqrtNumAtoms
);
1145 fprintf(fplog
, "\n");
1147 /* Start the loop over CG steps.
1148 * Each successful step is counted, and we continue until
1149 * we either converge or reach the max number of steps.
1152 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1155 /* start taking steps in a new direction
1156 * First time we enter the routine, beta=0, and the direction is
1157 * simply the negative gradient.
1160 /* Calculate the new direction in p, and the gradient in this direction, gpa */
1161 rvec
* pm
= s_min
->s
.cg_p
.rvec_array();
1162 const rvec
* sfm
= s_min
->f
.rvec_array();
1165 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1167 if (mdatoms
->cFREEZE
)
1169 gf
= mdatoms
->cFREEZE
[i
];
1171 for (m
= 0; m
< DIM
; m
++)
1173 if (!inputrec
->opts
.nFreeze
[gf
][m
])
1175 pm
[i
][m
] = sfm
[i
][m
] + beta
* pm
[i
][m
];
1176 gpa
-= pm
[i
][m
] * sfm
[i
][m
];
1177 /* f is negative gradient, thus the sign */
1186 /* Sum the gradient along the line across CPUs */
1189 gmx_sumd(1, &gpa
, cr
);
1192 /* Calculate the norm of the search vector */
1193 get_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, pm
, &pnorm
, nullptr, nullptr);
1195 /* Just in case stepsize reaches zero due to numerical precision... */
1198 stepsize
= inputrec
->em_stepsize
/ pnorm
;
1202 * Double check the value of the derivative in the search direction.
1203 * If it is positive it must be due to the old information in the
1204 * CG formula, so just remove that and start over with beta=0.
1205 * This corresponds to a steepest descent step.
1210 step
--; /* Don't count this step since we are restarting */
1211 continue; /* Go back to the beginning of the big for-loop */
1214 /* Calculate minimum allowed stepsize, before the average (norm)
1215 * relative change in coordinate is smaller than precision
1218 auto s_min_x
= makeArrayRef(s_min
->s
.x
);
1219 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1221 for (m
= 0; m
< DIM
; m
++)
1223 tmp
= fabs(s_min_x
[i
][m
]);
1228 tmp
= pm
[i
][m
] / tmp
;
1229 minstep
+= tmp
* tmp
;
1232 /* Add up from all CPUs */
1235 gmx_sumd(1, &minstep
, cr
);
1238 minstep
= GMX_REAL_EPS
/ sqrt(minstep
/ (3 * top_global
->natoms
));
1240 if (stepsize
< minstep
)
1246 /* Write coordinates if necessary */
1247 do_x
= do_per_step(step
, inputrec
->nstxout
);
1248 do_f
= do_per_step(step
, inputrec
->nstfout
);
1250 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr, top_global
, inputrec
, step
, s_min
,
1251 state_global
, observablesHistory
);
1253 /* Take a step downhill.
1254 * In theory, we should minimize the function along this direction.
1255 * That is quite possible, but it turns out to take 5-10 function evaluations
1256 * for each line. However, we dont really need to find the exact minimum -
1257 * it is much better to start a new CG step in a modified direction as soon
1258 * as we are close to it. This will save a lot of energy evaluations.
1260 * In practice, we just try to take a single step.
1261 * If it worked (i.e. lowered the energy), we increase the stepsize but
1262 * the continue straight to the next CG step without trying to find any minimum.
1263 * If it didn't work (higher energy), there must be a minimum somewhere between
1264 * the old position and the new one.
1266 * Due to the finite numerical accuracy, it turns out that it is a good idea
1267 * to even accept a SMALL increase in energy, if the derivative is still downhill.
1268 * This leads to lower final energies in the tests I've done. / Erik
1270 s_a
->epot
= s_min
->epot
;
1272 c
= a
+ stepsize
; /* reference position along line is zero */
1274 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
< cr
->dd
->ddp_count
)
1276 em_dd_partition_system(fplog
, mdlog
, step
, cr
, top_global
, inputrec
, imdSession
,
1277 pull_work
, s_min
, &top
, mdAtoms
, fr
, vsite
, constr
, nrnb
, wcycle
);
1280 /* Take a trial step (new coords in s_c) */
1281 do_em_step(cr
, inputrec
, mdatoms
, s_min
, c
, &s_min
->s
.cg_p
, s_c
, constr
, -1);
1284 /* Calculate energy for the trial step */
1285 energyEvaluator
.run(s_c
, mu_tot
, vir
, pres
, -1, FALSE
);
1287 /* Calc derivative along line */
1288 const rvec
* pc
= s_c
->s
.cg_p
.rvec_array();
1289 const rvec
* sfc
= s_c
->f
.rvec_array();
1291 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1293 for (m
= 0; m
< DIM
; m
++)
1295 gpc
-= pc
[i
][m
] * sfc
[i
][m
]; /* f is negative gradient, thus the sign */
1298 /* Sum the gradient along the line across CPUs */
1301 gmx_sumd(1, &gpc
, cr
);
1304 /* This is the max amount of increase in energy we tolerate */
1305 tmp
= std::sqrt(GMX_REAL_EPS
) * fabs(s_a
->epot
);
1307 /* Accept the step if the energy is lower, or if it is not significantly higher
1308 * and the line derivative is still negative.
1310 if (s_c
->epot
< s_a
->epot
|| (gpc
< 0 && s_c
->epot
< (s_a
->epot
+ tmp
)))
1313 /* Great, we found a better energy. Increase step for next iteration
1314 * if we are still going down, decrease it otherwise
1318 stepsize
*= 1.618034; /* The golden section */
1322 stepsize
*= 0.618034; /* 1/golden section */
1327 /* New energy is the same or higher. We will have to do some work
1328 * to find a smaller value in the interval. Take smaller step next time!
1331 stepsize
*= 0.618034;
1335 /* OK, if we didn't find a lower value we will have to locate one now - there must
1336 * be one in the interval [a=0,c].
1337 * The same thing is valid here, though: Don't spend dozens of iterations to find
1338 * the line minimum. We try to interpolate based on the derivative at the endpoints,
1339 * and only continue until we find a lower value. In most cases this means 1-2 iterations.
1341 * I also have a safeguard for potentially really pathological functions so we never
1342 * take more than 20 steps before we give up ...
1344 * If we already found a lower value we just skip this step and continue to the update.
1353 /* Select a new trial point.
1354 * If the derivatives at points a & c have different sign we interpolate to zero,
1355 * otherwise just do a bisection.
1357 if (gpa
< 0 && gpc
> 0)
1359 b
= a
+ gpa
* (a
- c
) / (gpc
- gpa
);
1366 /* safeguard if interpolation close to machine accuracy causes errors:
1367 * never go outside the interval
1369 if (b
<= a
|| b
>= c
)
1374 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
1376 /* Reload the old state */
1377 em_dd_partition_system(fplog
, mdlog
, -1, cr
, top_global
, inputrec
, imdSession
, pull_work
,
1378 s_min
, &top
, mdAtoms
, fr
, vsite
, constr
, nrnb
, wcycle
);
1381 /* Take a trial step to this new point - new coords in s_b */
1382 do_em_step(cr
, inputrec
, mdatoms
, s_min
, b
, &s_min
->s
.cg_p
, s_b
, constr
, -1);
1385 /* Calculate energy for the trial step */
1386 energyEvaluator
.run(s_b
, mu_tot
, vir
, pres
, -1, FALSE
);
1388 /* p does not change within a step, but since the domain decomposition
1389 * might change, we have to use cg_p of s_b here.
1391 const rvec
* pb
= s_b
->s
.cg_p
.rvec_array();
1392 const rvec
* sfb
= s_b
->f
.rvec_array();
1394 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1396 for (m
= 0; m
< DIM
; m
++)
1398 gpb
-= pb
[i
][m
] * sfb
[i
][m
]; /* f is negative gradient, thus the sign */
1401 /* Sum the gradient along the line across CPUs */
1404 gmx_sumd(1, &gpb
, cr
);
1409 fprintf(debug
, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n", s_a
->epot
, s_b
->epot
,
1413 epot_repl
= s_b
->epot
;
1415 /* Keep one of the intervals based on the value of the derivative at the new point */
1418 /* Replace c endpoint with b */
1419 swap_em_state(&s_b
, &s_c
);
1425 /* Replace a endpoint with b */
1426 swap_em_state(&s_b
, &s_a
);
1432 * Stop search as soon as we find a value smaller than the endpoints.
1433 * Never run more than 20 steps, no matter what.
1436 } while ((epot_repl
> s_a
->epot
|| epot_repl
> s_c
->epot
) && (nminstep
< 20));
1438 if (std::fabs(epot_repl
- s_min
->epot
) < fabs(s_min
->epot
) * GMX_REAL_EPS
|| nminstep
>= 20)
1440 /* OK. We couldn't find a significantly lower energy.
1441 * If beta==0 this was steepest descent, and then we give up.
1442 * If not, set beta=0 and restart with steepest descent before quitting.
1452 /* Reset memory before giving up */
1458 /* Select min energy state of A & C, put the best in B.
1460 if (s_c
->epot
< s_a
->epot
)
1464 fprintf(debug
, "CGE: C (%f) is lower than A (%f), moving C to B\n", s_c
->epot
,
1467 swap_em_state(&s_b
, &s_c
);
1474 fprintf(debug
, "CGE: A (%f) is lower than C (%f), moving A to B\n", s_a
->epot
,
1477 swap_em_state(&s_b
, &s_a
);
1485 fprintf(debug
, "CGE: Found a lower energy %f, moving C to B\n", s_c
->epot
);
1487 swap_em_state(&s_b
, &s_c
);
1491 /* new search direction */
1492 /* beta = 0 means forget all memory and restart with steepest descents. */
1493 if (nstcg
&& ((step
% nstcg
) == 0))
1499 /* s_min->fnorm cannot be zero, because then we would have converged
1503 /* Polak-Ribiere update.
1504 * Change to fnorm2/fnorm2_old for Fletcher-Reeves
1506 beta
= pr_beta(cr
, &inputrec
->opts
, mdatoms
, top_global
, s_min
, s_b
);
1508 /* Limit beta to prevent oscillations */
1509 if (fabs(beta
) > 5.0)
1515 /* update positions */
1516 swap_em_state(&s_min
, &s_b
);
1519 /* Print it if necessary */
1522 if (mdrunOptions
.verbose
)
1524 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1525 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n", step
,
1526 s_min
->epot
, s_min
->fnorm
/ sqrtNumAtoms
, s_min
->fmax
, s_min
->a_fmax
+ 1);
1529 /* Store the new (lower) energies */
1530 matrix nullBox
= {};
1531 energyOutput
.addDataAtEnergyStep(false, false, static_cast<double>(step
), mdatoms
->tmass
,
1532 enerd
, nullptr, nullptr, nullptr, nullBox
, nullptr,
1533 nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1535 do_log
= do_per_step(step
, inputrec
->nstlog
);
1536 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
1538 imdSession
->fillEnergyRecord(step
, TRUE
);
1542 energyOutput
.printHeader(fplog
, step
, step
);
1544 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
1545 do_log
? fplog
: nullptr, step
, step
, fcd
, nullptr);
1548 /* Send energies and positions to the IMD client if bIMD is TRUE. */
1549 if (MASTER(cr
) && imdSession
->run(step
, TRUE
, state_global
->box
, state_global
->x
.rvec_array(), 0))
1551 imdSession
->sendPositionsAndEnergies();
1554 /* Stop when the maximum force lies below tolerance.
1555 * If we have reached machine precision, converged is already set to true.
1557 converged
= converged
|| (s_min
->fmax
< inputrec
->em_tol
);
1559 } /* End of the loop */
1563 step
--; /* we never took that last step in this case */
1565 if (s_min
->fmax
> inputrec
->em_tol
)
1569 warn_step(fplog
, inputrec
->em_tol
, s_min
->fmax
, step
- 1 == number_steps
, FALSE
);
1576 /* If we printed energy and/or logfile last step (which was the last step)
1577 * we don't have to do it again, but otherwise print the final values.
1581 /* Write final value to log since we didn't do anything the last step */
1582 energyOutput
.printHeader(fplog
, step
, step
);
1584 if (!do_ene
|| !do_log
)
1586 /* Write final energy file entries */
1587 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
1588 !do_log
? fplog
: nullptr, step
, step
, fcd
, nullptr);
1592 /* Print some stuff... */
1595 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
1599 * For accurate normal mode calculation it is imperative that we
1600 * store the last conformation into the full precision binary trajectory.
1602 * However, we should only do it if we did NOT already write this step
1603 * above (which we did if do_x or do_f was true).
1605 /* Note that with 0 < nstfout != nstxout we can end up with two frames
1606 * in the trajectory with the same step number.
1608 do_x
= !do_per_step(step
, inputrec
->nstxout
);
1609 do_f
= (inputrec
->nstfout
> 0 && !do_per_step(step
, inputrec
->nstfout
));
1611 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
), top_global
, inputrec
,
1612 step
, s_min
, state_global
, observablesHistory
);
1617 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1618 print_converged(stderr
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
, s_min
, sqrtNumAtoms
);
1619 print_converged(fplog
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
, s_min
, sqrtNumAtoms
);
1621 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
1624 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
1626 /* To print the actual number of steps we needed somewhere */
1627 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
1631 void LegacySimulator::do_lbfgs()
1633 static const char* LBFGS
= "Low-Memory BFGS Minimizer";
1636 gmx_global_stat_t gstat
;
1638 int ncorr
, nmaxcorr
, point
, cp
, neval
, nminstep
;
1639 double stepsize
, step_taken
, gpa
, gpb
, gpc
, tmp
, minstep
;
1640 real
* rho
, *alpha
, *p
, *s
, **dx
, **dg
;
1641 real a
, b
, c
, maxdelta
, delta
;
1643 real dgdx
, dgdg
, sq
, yr
, beta
;
1645 rvec mu_tot
= { 0 };
1646 gmx_bool do_log
, do_ene
, do_x
, do_f
, foundlower
, *frozen
;
1648 int start
, end
, number_steps
;
1649 int i
, k
, m
, n
, gf
, step
;
1651 auto mdatoms
= mdAtoms
->mdatoms();
1656 "Note that activating L-BFGS energy minimization via the "
1657 "integrator .mdp option and the command gmx mdrun may "
1658 "be available in a different form in a future version of GROMACS, "
1659 "e.g. gmx minimize and an .mdp option.");
1663 gmx_fatal(FARGS
, "L-BFGS minimization only supports a single rank");
1666 if (nullptr != constr
)
1670 "The combination of constraints and L-BFGS minimization is not implemented. Either "
1671 "do not use constraints, or use another minimizer (e.g. steepest descent).");
1674 n
= 3 * state_global
->natoms
;
1675 nmaxcorr
= inputrec
->nbfgscorr
;
1680 snew(rho
, nmaxcorr
);
1681 snew(alpha
, nmaxcorr
);
1684 for (i
= 0; i
< nmaxcorr
; i
++)
1690 for (i
= 0; i
< nmaxcorr
; i
++)
1699 init_em(fplog
, mdlog
, LBFGS
, cr
, inputrec
, imdSession
, pull_work
, state_global
, top_global
,
1700 &ems
, &top
, nrnb
, fr
, &graph
, mdAtoms
, &gstat
, vsite
, constr
, nullptr);
1702 init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, mdModulesNotifier
,
1703 inputrec
, top_global
, nullptr, wcycle
, StartingBehavior::NewSimulation
);
1704 gmx::EnergyOutput
energyOutput(mdoutf_get_fp_ene(outf
), top_global
, inputrec
, pull_work
, nullptr,
1705 false, StartingBehavior::NewSimulation
, mdModulesNotifier
);
1708 end
= mdatoms
->homenr
;
1710 /* We need 4 working states */
1711 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1712 em_state_t
* sa
= &s0
;
1713 em_state_t
* sb
= &s1
;
1714 em_state_t
* sc
= &s2
;
1715 em_state_t
* last
= &s3
;
1716 /* Initialize by copying the state from ems (we could skip x and f here) */
1721 /* Print to log file */
1722 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, LBFGS
);
1724 do_log
= do_ene
= do_x
= do_f
= TRUE
;
1726 /* Max number of steps */
1727 number_steps
= inputrec
->nsteps
;
1729 /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
1731 for (i
= start
; i
< end
; i
++)
1733 if (mdatoms
->cFREEZE
)
1735 gf
= mdatoms
->cFREEZE
[i
];
1737 for (m
= 0; m
< DIM
; m
++)
1739 frozen
[3 * i
+ m
] = (inputrec
->opts
.nFreeze
[gf
][m
] != 0);
1744 sp_header(stderr
, LBFGS
, inputrec
->em_tol
, number_steps
);
1748 sp_header(fplog
, LBFGS
, inputrec
->em_tol
, number_steps
);
1753 construct_vsites(vsite
, state_global
->x
.rvec_array(), 1, nullptr, top
.idef
.iparams
,
1754 top
.idef
.il
, fr
->ePBC
, fr
->bMolPBC
, cr
, state_global
->box
);
1757 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1758 /* do_force always puts the charge groups in the box and shifts again
1759 * We do not unshift, so molecules are always whole
1762 EnergyEvaluator energyEvaluator
{
1763 fplog
, mdlog
, cr
, ms
, top_global
, &top
, inputrec
,
1764 imdSession
, pull_work
, nrnb
, wcycle
, gstat
, vsite
, constr
,
1765 fcd
, graph
, mdAtoms
, fr
, runScheduleWork
, enerd
1767 energyEvaluator
.run(&ems
, mu_tot
, vir
, pres
, -1, TRUE
);
1771 /* Copy stuff to the energy bin for easy printing etc. */
1772 matrix nullBox
= {};
1773 energyOutput
.addDataAtEnergyStep(false, false, static_cast<double>(step
), mdatoms
->tmass
,
1774 enerd
, nullptr, nullptr, nullptr, nullBox
, nullptr,
1775 nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1777 energyOutput
.printHeader(fplog
, step
, step
);
1778 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
,
1779 step
, fcd
, nullptr);
1782 /* Set the initial step.
1783 * since it will be multiplied by the non-normalized search direction
1784 * vector (force vector the first time), we scale it by the
1785 * norm of the force.
1790 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1791 fprintf(stderr
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1792 fprintf(stderr
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1793 fprintf(stderr
, " F-Norm = %12.5e\n", ems
.fnorm
/ sqrtNumAtoms
);
1794 fprintf(stderr
, "\n");
1795 /* and copy to the log file too... */
1796 fprintf(fplog
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1797 fprintf(fplog
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1798 fprintf(fplog
, " F-Norm = %12.5e\n", ems
.fnorm
/ sqrtNumAtoms
);
1799 fprintf(fplog
, "\n");
1802 // Point is an index to the memory of search directions, where 0 is the first one.
1805 // Set initial search direction to the force (-gradient), or 0 for frozen particles.
1806 real
* fInit
= static_cast<real
*>(ems
.f
.rvec_array()[0]);
1807 for (i
= 0; i
< n
; i
++)
1811 dx
[point
][i
] = fInit
[i
]; /* Initial search direction */
1819 // Stepsize will be modified during the search, and actually it is not critical
1820 // (the main efficiency in the algorithm comes from changing directions), but
1821 // we still need an initial value, so estimate it as the inverse of the norm
1822 // so we take small steps where the potential fluctuates a lot.
1823 stepsize
= 1.0 / ems
.fnorm
;
1825 /* Start the loop over BFGS steps.
1826 * Each successful step is counted, and we continue until
1827 * we either converge or reach the max number of steps.
1832 /* Set the gradient from the force */
1834 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1837 /* Write coordinates if necessary */
1838 do_x
= do_per_step(step
, inputrec
->nstxout
);
1839 do_f
= do_per_step(step
, inputrec
->nstfout
);
1844 mdof_flags
|= MDOF_X
;
1849 mdof_flags
|= MDOF_F
;
1854 mdof_flags
|= MDOF_IMD
;
1857 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
, top_global
->natoms
, step
,
1858 static_cast<real
>(step
), &ems
.s
, state_global
,
1859 observablesHistory
, ems
.f
);
1861 /* Do the linesearching in the direction dx[point][0..(n-1)] */
1863 /* make s a pointer to current search direction - point=0 first time we get here */
1866 real
* xx
= static_cast<real
*>(ems
.s
.x
.rvec_array()[0]);
1867 real
* ff
= static_cast<real
*>(ems
.f
.rvec_array()[0]);
1869 // calculate line gradient in position A
1870 for (gpa
= 0, i
= 0; i
< n
; i
++)
1872 gpa
-= s
[i
] * ff
[i
];
1875 /* Calculate minimum allowed stepsize along the line, before the average (norm)
1876 * relative change in coordinate is smaller than precision
1878 for (minstep
= 0, i
= 0; i
< n
; i
++)
1886 minstep
+= tmp
* tmp
;
1888 minstep
= GMX_REAL_EPS
/ sqrt(minstep
/ n
);
1890 if (stepsize
< minstep
)
1896 // Before taking any steps along the line, store the old position
1898 real
* lastx
= static_cast<real
*>(last
->s
.x
.data()[0]);
1899 real
* lastf
= static_cast<real
*>(last
->f
.data()[0]);
1904 /* Take a step downhill.
1905 * In theory, we should find the actual minimum of the function in this
1906 * direction, somewhere along the line.
1907 * That is quite possible, but it turns out to take 5-10 function evaluations
1908 * for each line. However, we dont really need to find the exact minimum -
1909 * it is much better to start a new BFGS step in a modified direction as soon
1910 * as we are close to it. This will save a lot of energy evaluations.
1912 * In practice, we just try to take a single step.
1913 * If it worked (i.e. lowered the energy), we increase the stepsize but
1914 * continue straight to the next BFGS step without trying to find any minimum,
1915 * i.e. we change the search direction too. If the line was smooth, it is
1916 * likely we are in a smooth region, and then it makes sense to take longer
1917 * steps in the modified search direction too.
1919 * If it didn't work (higher energy), there must be a minimum somewhere between
1920 * the old position and the new one. Then we need to start by finding a lower
1921 * value before we change search direction. Since the energy was apparently
1922 * quite rough, we need to decrease the step size.
1924 * Due to the finite numerical accuracy, it turns out that it is a good idea
1925 * to accept a SMALL increase in energy, if the derivative is still downhill.
1926 * This leads to lower final energies in the tests I've done. / Erik
1929 // State "A" is the first position along the line.
1930 // reference position along line is initially zero
1933 // Check stepsize first. We do not allow displacements
1934 // larger than emstep.
1938 // Pick a new position C by adding stepsize to A.
1941 // Calculate what the largest change in any individual coordinate
1942 // would be (translation along line * gradient along line)
1944 for (i
= 0; i
< n
; i
++)
1947 if (delta
> maxdelta
)
1952 // If any displacement is larger than the stepsize limit, reduce the step
1953 if (maxdelta
> inputrec
->em_stepsize
)
1957 } while (maxdelta
> inputrec
->em_stepsize
);
1959 // Take a trial step and move the coordinate array xc[] to position C
1960 real
* xc
= static_cast<real
*>(sc
->s
.x
.rvec_array()[0]);
1961 for (i
= 0; i
< n
; i
++)
1963 xc
[i
] = lastx
[i
] + c
* s
[i
];
1967 // Calculate energy for the trial step in position C
1968 energyEvaluator
.run(sc
, mu_tot
, vir
, pres
, step
, FALSE
);
1970 // Calc line gradient in position C
1971 real
* fc
= static_cast<real
*>(sc
->f
.rvec_array()[0]);
1972 for (gpc
= 0, i
= 0; i
< n
; i
++)
1974 gpc
-= s
[i
] * fc
[i
]; /* f is negative gradient, thus the sign */
1976 /* Sum the gradient along the line across CPUs */
1979 gmx_sumd(1, &gpc
, cr
);
1982 // This is the max amount of increase in energy we tolerate.
1983 // By allowing VERY small changes (close to numerical precision) we
1984 // frequently find even better (lower) final energies.
1985 tmp
= std::sqrt(GMX_REAL_EPS
) * fabs(sa
->epot
);
1987 // Accept the step if the energy is lower in the new position C (compared to A),
1988 // or if it is not significantly higher and the line derivative is still negative.
1989 foundlower
= sc
->epot
< sa
->epot
|| (gpc
< 0 && sc
->epot
< (sa
->epot
+ tmp
));
1990 // If true, great, we found a better energy. We no longer try to alter the
1991 // stepsize, but simply accept this new better position. The we select a new
1992 // search direction instead, which will be much more efficient than continuing
1993 // to take smaller steps along a line. Set fnorm based on the new C position,
1994 // which will be used to update the stepsize to 1/fnorm further down.
1996 // If false, the energy is NOT lower in point C, i.e. it will be the same
1997 // or higher than in point A. In this case it is pointless to move to point C,
1998 // so we will have to do more iterations along the same line to find a smaller
1999 // value in the interval [A=0.0,C].
2000 // Here, A is still 0.0, but that will change when we do a search in the interval
2001 // [0.0,C] below. That search we will do by interpolation or bisection rather
2002 // than with the stepsize, so no need to modify it. For the next search direction
2003 // it will be reset to 1/fnorm anyway.
2007 // OK, if we didn't find a lower value we will have to locate one now - there must
2008 // be one in the interval [a,c].
2009 // The same thing is valid here, though: Don't spend dozens of iterations to find
2010 // the line minimum. We try to interpolate based on the derivative at the endpoints,
2011 // and only continue until we find a lower value. In most cases this means 1-2 iterations.
2012 // I also have a safeguard for potentially really pathological functions so we never
2013 // take more than 20 steps before we give up.
2014 // If we already found a lower value we just skip this step and continue to the update.
2019 // Select a new trial point B in the interval [A,C].
2020 // If the derivatives at points a & c have different sign we interpolate to zero,
2021 // otherwise just do a bisection since there might be multiple minima/maxima
2022 // inside the interval.
2023 if (gpa
< 0 && gpc
> 0)
2025 b
= a
+ gpa
* (a
- c
) / (gpc
- gpa
);
2032 /* safeguard if interpolation close to machine accuracy causes errors:
2033 * never go outside the interval
2035 if (b
<= a
|| b
>= c
)
2040 // Take a trial step to point B
2041 real
* xb
= static_cast<real
*>(sb
->s
.x
.rvec_array()[0]);
2042 for (i
= 0; i
< n
; i
++)
2044 xb
[i
] = lastx
[i
] + b
* s
[i
];
2048 // Calculate energy for the trial step in point B
2049 energyEvaluator
.run(sb
, mu_tot
, vir
, pres
, step
, FALSE
);
2052 // Calculate gradient in point B
2053 real
* fb
= static_cast<real
*>(sb
->f
.rvec_array()[0]);
2054 for (gpb
= 0, i
= 0; i
< n
; i
++)
2056 gpb
-= s
[i
] * fb
[i
]; /* f is negative gradient, thus the sign */
2058 /* Sum the gradient along the line across CPUs */
2061 gmx_sumd(1, &gpb
, cr
);
2064 // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
2065 // at the new point B, and rename the endpoints of this new interval A and C.
2068 /* Replace c endpoint with b */
2070 /* copy state b to c */
2075 /* Replace a endpoint with b */
2077 /* copy state b to a */
2082 * Stop search as soon as we find a value smaller than the endpoints,
2083 * or if the tolerance is below machine precision.
2084 * Never run more than 20 steps, no matter what.
2087 } while ((sb
->epot
> sa
->epot
|| sb
->epot
> sc
->epot
) && (nminstep
< 20));
2089 if (std::fabs(sb
->epot
- Epot0
) < GMX_REAL_EPS
|| nminstep
>= 20)
2091 /* OK. We couldn't find a significantly lower energy.
2092 * If ncorr==0 this was steepest descent, and then we give up.
2093 * If not, reset memory to restart as steepest descent before quitting.
2105 /* Search in gradient direction */
2106 for (i
= 0; i
< n
; i
++)
2108 dx
[point
][i
] = ff
[i
];
2110 /* Reset stepsize */
2111 stepsize
= 1.0 / fnorm
;
2116 /* Select min energy state of A & C, put the best in xx/ff/Epot
2118 if (sc
->epot
< sa
->epot
)
2139 /* Update the memory information, and calculate a new
2140 * approximation of the inverse hessian
2143 /* Have new data in Epot, xx, ff */
2144 if (ncorr
< nmaxcorr
)
2149 for (i
= 0; i
< n
; i
++)
2151 dg
[point
][i
] = lastf
[i
] - ff
[i
];
2152 dx
[point
][i
] *= step_taken
;
2157 for (i
= 0; i
< n
; i
++)
2159 dgdg
+= dg
[point
][i
] * dg
[point
][i
];
2160 dgdx
+= dg
[point
][i
] * dx
[point
][i
];
2165 rho
[point
] = 1.0 / dgdx
;
2168 if (point
>= nmaxcorr
)
2174 for (i
= 0; i
< n
; i
++)
2181 /* Recursive update. First go back over the memory points */
2182 for (k
= 0; k
< ncorr
; k
++)
2191 for (i
= 0; i
< n
; i
++)
2193 sq
+= dx
[cp
][i
] * p
[i
];
2196 alpha
[cp
] = rho
[cp
] * sq
;
2198 for (i
= 0; i
< n
; i
++)
2200 p
[i
] -= alpha
[cp
] * dg
[cp
][i
];
2204 for (i
= 0; i
< n
; i
++)
2209 /* And then go forward again */
2210 for (k
= 0; k
< ncorr
; k
++)
2213 for (i
= 0; i
< n
; i
++)
2215 yr
+= p
[i
] * dg
[cp
][i
];
2218 beta
= rho
[cp
] * yr
;
2219 beta
= alpha
[cp
] - beta
;
2221 for (i
= 0; i
< n
; i
++)
2223 p
[i
] += beta
* dx
[cp
][i
];
2233 for (i
= 0; i
< n
; i
++)
2237 dx
[point
][i
] = p
[i
];
2245 /* Print it if necessary */
2248 if (mdrunOptions
.verbose
)
2250 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2251 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n", step
,
2252 ems
.epot
, ems
.fnorm
/ sqrtNumAtoms
, ems
.fmax
, ems
.a_fmax
+ 1);
2255 /* Store the new (lower) energies */
2256 matrix nullBox
= {};
2257 energyOutput
.addDataAtEnergyStep(false, false, static_cast<double>(step
), mdatoms
->tmass
,
2258 enerd
, nullptr, nullptr, nullptr, nullBox
, nullptr,
2259 nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2261 do_log
= do_per_step(step
, inputrec
->nstlog
);
2262 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
2264 imdSession
->fillEnergyRecord(step
, TRUE
);
2268 energyOutput
.printHeader(fplog
, step
, step
);
2270 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
2271 do_log
? fplog
: nullptr, step
, step
, fcd
, nullptr);
2274 /* Send x and E to IMD client, if bIMD is TRUE. */
2275 if (imdSession
->run(step
, TRUE
, state_global
->box
, state_global
->x
.rvec_array(), 0) && MASTER(cr
))
2277 imdSession
->sendPositionsAndEnergies();
2280 // Reset stepsize in we are doing more iterations
2283 /* Stop when the maximum force lies below tolerance.
2284 * If we have reached machine precision, converged is already set to true.
2286 converged
= converged
|| (ems
.fmax
< inputrec
->em_tol
);
2288 } /* End of the loop */
2292 step
--; /* we never took that last step in this case */
2294 if (ems
.fmax
> inputrec
->em_tol
)
2298 warn_step(fplog
, inputrec
->em_tol
, ems
.fmax
, step
- 1 == number_steps
, FALSE
);
2303 /* If we printed energy and/or logfile last step (which was the last step)
2304 * we don't have to do it again, but otherwise print the final values.
2306 if (!do_log
) /* Write final value to log since we didn't do anythin last step */
2308 energyOutput
.printHeader(fplog
, step
, step
);
2310 if (!do_ene
|| !do_log
) /* Write final energy file entries */
2312 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
2313 !do_log
? fplog
: nullptr, step
, step
, fcd
, nullptr);
2316 /* Print some stuff... */
2319 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2323 * For accurate normal mode calculation it is imperative that we
2324 * store the last conformation into the full precision binary trajectory.
2326 * However, we should only do it if we did NOT already write this step
2327 * above (which we did if do_x or do_f was true).
2329 do_x
= !do_per_step(step
, inputrec
->nstxout
);
2330 do_f
= !do_per_step(step
, inputrec
->nstfout
);
2331 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
), top_global
, inputrec
,
2332 step
, &ems
, state_global
, observablesHistory
);
2336 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2337 print_converged(stderr
, LBFGS
, inputrec
->em_tol
, step
, converged
, number_steps
, &ems
, sqrtNumAtoms
);
2338 print_converged(fplog
, LBFGS
, inputrec
->em_tol
, step
, converged
, number_steps
, &ems
, sqrtNumAtoms
);
2340 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
2343 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2345 /* To print the actual number of steps we needed somewhere */
2346 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
2349 void LegacySimulator::do_steep()
2351 const char* SD
= "Steepest Descents";
2353 gmx_global_stat_t gstat
;
2357 gmx_bool bDone
, bAbort
, do_x
, do_f
;
2359 rvec mu_tot
= { 0 };
2362 int steps_accepted
= 0;
2363 auto mdatoms
= mdAtoms
->mdatoms();
2368 "Note that activating steepest-descent energy minimization via the "
2369 "integrator .mdp option and the command gmx mdrun may "
2370 "be available in a different form in a future version of GROMACS, "
2371 "e.g. gmx minimize and an .mdp option.");
2373 /* Create 2 states on the stack and extract pointers that we will swap */
2374 em_state_t s0
{}, s1
{};
2375 em_state_t
* s_min
= &s0
;
2376 em_state_t
* s_try
= &s1
;
2378 /* Init em and store the local state in s_try */
2379 init_em(fplog
, mdlog
, SD
, cr
, inputrec
, imdSession
, pull_work
, state_global
, top_global
, s_try
,
2380 &top
, nrnb
, fr
, &graph
, mdAtoms
, &gstat
, vsite
, constr
, nullptr);
2382 init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, mdModulesNotifier
,
2383 inputrec
, top_global
, nullptr, wcycle
, StartingBehavior::NewSimulation
);
2384 gmx::EnergyOutput
energyOutput(mdoutf_get_fp_ene(outf
), top_global
, inputrec
, pull_work
, nullptr,
2385 false, StartingBehavior::NewSimulation
, mdModulesNotifier
);
2387 /* Print to log file */
2388 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, SD
);
2390 /* Set variables for stepsize (in nm). This is the largest
2391 * step that we are going to make in any direction.
2393 ustep
= inputrec
->em_stepsize
;
2396 /* Max number of steps */
2397 nsteps
= inputrec
->nsteps
;
2401 /* Print to the screen */
2402 sp_header(stderr
, SD
, inputrec
->em_tol
, nsteps
);
2406 sp_header(fplog
, SD
, inputrec
->em_tol
, nsteps
);
2408 EnergyEvaluator energyEvaluator
{
2409 fplog
, mdlog
, cr
, ms
, top_global
, &top
, inputrec
,
2410 imdSession
, pull_work
, nrnb
, wcycle
, gstat
, vsite
, constr
,
2411 fcd
, graph
, mdAtoms
, fr
, runScheduleWork
, enerd
2414 /**** HERE STARTS THE LOOP ****
2415 * count is the counter for the number of steps
2416 * bDone will be TRUE when the minimization has converged
2417 * bAbort will be TRUE when nsteps steps have been performed or when
2418 * the stepsize becomes smaller than is reasonable for machine precision
2423 while (!bDone
&& !bAbort
)
2425 bAbort
= (nsteps
>= 0) && (count
== nsteps
);
2427 /* set new coordinates, except for first step */
2428 bool validStep
= true;
2431 validStep
= do_em_step(cr
, inputrec
, mdatoms
, s_min
, stepsize
, &s_min
->f
, s_try
, constr
, count
);
2436 energyEvaluator
.run(s_try
, mu_tot
, vir
, pres
, count
, count
== 0);
2440 // Signal constraint error during stepping with energy=inf
2441 s_try
->epot
= std::numeric_limits
<real
>::infinity();
2446 energyOutput
.printHeader(fplog
, count
, count
);
2451 s_min
->epot
= s_try
->epot
;
2454 /* Print it if necessary */
2457 if (mdrunOptions
.verbose
)
2459 fprintf(stderr
, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
2460 count
, ustep
, s_try
->epot
, s_try
->fmax
, s_try
->a_fmax
+ 1,
2461 ((count
== 0) || (s_try
->epot
< s_min
->epot
)) ? '\n' : '\r');
2465 if ((count
== 0) || (s_try
->epot
< s_min
->epot
))
2467 /* Store the new (lower) energies */
2468 matrix nullBox
= {};
2469 energyOutput
.addDataAtEnergyStep(false, false, static_cast<double>(count
), mdatoms
->tmass
,
2470 enerd
, nullptr, nullptr, nullptr, nullBox
, nullptr,
2471 nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2473 imdSession
->fillEnergyRecord(count
, TRUE
);
2475 const bool do_dr
= do_per_step(steps_accepted
, inputrec
->nstdisreout
);
2476 const bool do_or
= do_per_step(steps_accepted
, inputrec
->nstorireout
);
2477 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), TRUE
, do_dr
, do_or
,
2478 fplog
, count
, count
, fcd
, nullptr);
2483 /* Now if the new energy is smaller than the previous...
2484 * or if this is the first step!
2485 * or if we did random steps!
2488 if ((count
== 0) || (s_try
->epot
< s_min
->epot
))
2492 /* Test whether the convergence criterion is met... */
2493 bDone
= (s_try
->fmax
< inputrec
->em_tol
);
2495 /* Copy the arrays for force, positions and energy */
2496 /* The 'Min' array always holds the coords and forces of the minimal
2498 swap_em_state(&s_min
, &s_try
);
2504 /* Write to trn, if necessary */
2505 do_x
= do_per_step(steps_accepted
, inputrec
->nstxout
);
2506 do_f
= do_per_step(steps_accepted
, inputrec
->nstfout
);
2507 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr, top_global
, inputrec
, count
, s_min
,
2508 state_global
, observablesHistory
);
2512 /* If energy is not smaller make the step smaller... */
2515 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
2517 /* Reload the old state */
2518 em_dd_partition_system(fplog
, mdlog
, count
, cr
, top_global
, inputrec
, imdSession
,
2519 pull_work
, s_min
, &top
, mdAtoms
, fr
, vsite
, constr
, nrnb
, wcycle
);
2523 // If the force is very small after finishing minimization,
2524 // we risk dividing by zero when calculating the step size.
2525 // So we check first if the minimization has stopped before
2526 // trying to obtain a new step size.
2529 /* Determine new step */
2530 stepsize
= ustep
/ s_min
->fmax
;
2533 /* Check if stepsize is too small, with 1 nm as a characteristic length */
2535 if (count
== nsteps
|| ustep
< 1e-12)
2537 if (count
== nsteps
|| ustep
< 1e-6)
2542 warn_step(fplog
, inputrec
->em_tol
, s_min
->fmax
, count
== nsteps
, constr
!= nullptr);
2547 /* Send IMD energies and positions, if bIMD is TRUE. */
2548 if (imdSession
->run(count
, TRUE
, state_global
->box
,
2549 MASTER(cr
) ? state_global
->x
.rvec_array() : nullptr, 0)
2552 imdSession
->sendPositionsAndEnergies();
2556 } /* End of the loop */
2558 /* Print some data... */
2561 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2563 write_em_traj(fplog
, cr
, outf
, TRUE
, inputrec
->nstfout
!= 0, ftp2fn(efSTO
, nfile
, fnm
),
2564 top_global
, inputrec
, count
, s_min
, state_global
, observablesHistory
);
2568 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2570 print_converged(stderr
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
, s_min
, sqrtNumAtoms
);
2571 print_converged(fplog
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
, s_min
, sqrtNumAtoms
);
2574 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2576 /* To print the actual number of steps we needed somewhere */
2577 inputrec
->nsteps
= count
;
2579 walltime_accounting_set_nsteps_done(walltime_accounting
, count
);
2582 void LegacySimulator::do_nm()
2584 const char* NM
= "Normal Mode Analysis";
2587 gmx_global_stat_t gstat
;
2590 rvec mu_tot
= { 0 };
2592 gmx_bool bSparse
; /* use sparse matrix storage format */
2594 gmx_sparsematrix_t
* sparse_matrix
= nullptr;
2595 real
* full_matrix
= nullptr;
2597 /* added with respect to mdrun */
2599 real der_range
= 10.0 * std::sqrt(GMX_REAL_EPS
);
2601 bool bIsMaster
= MASTER(cr
);
2602 auto mdatoms
= mdAtoms
->mdatoms();
2607 "Note that activating normal-mode analysis via the integrator "
2608 ".mdp option and the command gmx mdrun may "
2609 "be available in a different form in a future version of GROMACS, "
2610 "e.g. gmx normal-modes.");
2612 if (constr
!= nullptr)
2616 "Constraints present with Normal Mode Analysis, this combination is not supported");
2619 gmx_shellfc_t
* shellfc
;
2621 em_state_t state_work
{};
2623 /* Init em and store the local state in state_minimum */
2624 init_em(fplog
, mdlog
, NM
, cr
, inputrec
, imdSession
, pull_work
, state_global
, top_global
,
2625 &state_work
, &top
, nrnb
, fr
, &graph
, mdAtoms
, &gstat
, vsite
, constr
, &shellfc
);
2627 init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, mdModulesNotifier
,
2628 inputrec
, top_global
, nullptr, wcycle
, StartingBehavior::NewSimulation
);
2630 std::vector
<int> atom_index
= get_atom_index(top_global
);
2631 std::vector
<gmx::RVec
> fneg(atom_index
.size(), { 0, 0, 0 });
2632 snew(dfdx
, atom_index
.size());
2638 "NOTE: This version of GROMACS has been compiled in single precision,\n"
2639 " which MIGHT not be accurate enough for normal mode analysis.\n"
2640 " GROMACS now uses sparse matrix storage, so the memory requirements\n"
2641 " are fairly modest even if you recompile in double precision.\n\n");
2645 /* Check if we can/should use sparse storage format.
2647 * Sparse format is only useful when the Hessian itself is sparse, which it
2648 * will be when we use a cutoff.
2649 * For small systems (n<1000) it is easier to always use full matrix format, though.
2651 if (EEL_FULL(fr
->ic
->eeltype
) || fr
->rlist
== 0.0)
2653 GMX_LOG(mdlog
.warning
)
2654 .appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
2657 else if (atom_index
.size() < 1000)
2659 GMX_LOG(mdlog
.warning
)
2660 .appendTextFormatted("Small system size (N=%zu), using full Hessian format.",
2666 GMX_LOG(mdlog
.warning
).appendText("Using compressed symmetric sparse Hessian format.");
2670 /* Number of dimensions, based on real atoms, that is not vsites or shell */
2671 sz
= DIM
* atom_index
.size();
2673 fprintf(stderr
, "Allocating Hessian memory...\n\n");
2677 sparse_matrix
= gmx_sparsematrix_init(sz
);
2678 sparse_matrix
->compressed_symmetric
= TRUE
;
2682 snew(full_matrix
, sz
* sz
);
2685 /* Write start time and temperature */
2686 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, NM
);
2688 /* fudge nr of steps to nr of atoms */
2689 inputrec
->nsteps
= atom_index
.size() * 2;
2693 fprintf(stderr
, "starting normal mode calculation '%s'\n%" PRId64
" steps.\n\n",
2694 *(top_global
->name
), inputrec
->nsteps
);
2697 nnodes
= cr
->nnodes
;
2699 /* Make evaluate_energy do a single node force calculation */
2701 EnergyEvaluator energyEvaluator
{
2702 fplog
, mdlog
, cr
, ms
, top_global
, &top
, inputrec
,
2703 imdSession
, pull_work
, nrnb
, wcycle
, gstat
, vsite
, constr
,
2704 fcd
, graph
, mdAtoms
, fr
, runScheduleWork
, enerd
2706 energyEvaluator
.run(&state_work
, mu_tot
, vir
, pres
, -1, TRUE
);
2707 cr
->nnodes
= nnodes
;
2709 /* if forces are not small, warn user */
2710 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, &state_work
);
2712 GMX_LOG(mdlog
.warning
).appendTextFormatted("Maximum force:%12.5e", state_work
.fmax
);
2713 if (state_work
.fmax
> 1.0e-3)
2715 GMX_LOG(mdlog
.warning
)
2717 "The force is probably not small enough to "
2718 "ensure that you are at a minimum.\n"
2719 "Be aware that negative eigenvalues may occur\n"
2720 "when the resulting matrix is diagonalized.");
2723 /***********************************************************
2725 * Loop over all pairs in matrix
2727 * do_force called twice. Once with positive and
2728 * once with negative displacement
2730 ************************************************************/
2732 /* Steps are divided one by one over the nodes */
2734 auto state_work_x
= makeArrayRef(state_work
.s
.x
);
2735 auto state_work_f
= makeArrayRef(state_work
.f
);
2736 for (index aid
= cr
->nodeid
; aid
< ssize(atom_index
); aid
+= nnodes
)
2738 size_t atom
= atom_index
[aid
];
2739 for (size_t d
= 0; d
< DIM
; d
++)
2742 int force_flags
= GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
;
2745 x_min
= state_work_x
[atom
][d
];
2747 for (unsigned int dx
= 0; (dx
< 2); dx
++)
2751 state_work_x
[atom
][d
] = x_min
- der_range
;
2755 state_work_x
[atom
][d
] = x_min
+ der_range
;
2758 /* Make evaluate_energy do a single node force calculation */
2762 /* Now is the time to relax the shells */
2763 relax_shell_flexcon(fplog
, cr
, ms
, mdrunOptions
.verbose
, nullptr, step
, inputrec
,
2764 imdSession
, pull_work
, bNS
, force_flags
, &top
, constr
, enerd
,
2765 fcd
, state_work
.s
.natoms
, state_work
.s
.x
.arrayRefWithPadding(),
2766 state_work
.s
.v
.arrayRefWithPadding(), state_work
.s
.box
,
2767 state_work
.s
.lambda
, &state_work
.s
.hist
,
2768 state_work
.f
.arrayRefWithPadding(), vir
, mdatoms
, nrnb
,
2769 wcycle
, graph
, shellfc
, fr
, runScheduleWork
, t
, mu_tot
,
2770 vsite
, DDBalanceRegionHandler(nullptr));
2776 energyEvaluator
.run(&state_work
, mu_tot
, vir
, pres
, aid
* 2 + dx
, FALSE
);
2779 cr
->nnodes
= nnodes
;
2783 std::copy(state_work_f
.begin(), state_work_f
.begin() + atom_index
.size(),
2788 /* x is restored to original */
2789 state_work_x
[atom
][d
] = x_min
;
2791 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2793 for (size_t k
= 0; (k
< DIM
); k
++)
2795 dfdx
[j
][k
] = -(state_work_f
[atom_index
[j
]][k
] - fneg
[j
][k
]) / (2 * der_range
);
2802 # define mpi_type GMX_MPI_REAL
2803 MPI_Send(dfdx
[0], atom_index
.size() * DIM
, mpi_type
, MASTER(cr
), cr
->nodeid
,
2804 cr
->mpi_comm_mygroup
);
2809 for (index node
= 0; (node
< nnodes
&& aid
+ node
< ssize(atom_index
)); node
++)
2815 MPI_Recv(dfdx
[0], atom_index
.size() * DIM
, mpi_type
, node
, node
,
2816 cr
->mpi_comm_mygroup
, &stat
);
2821 row
= (aid
+ node
) * DIM
+ d
;
2823 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2825 for (size_t k
= 0; k
< DIM
; k
++)
2831 if (col
>= row
&& dfdx
[j
][k
] != 0.0)
2833 gmx_sparsematrix_increment_value(sparse_matrix
, row
, col
, dfdx
[j
][k
]);
2838 full_matrix
[row
* sz
+ col
] = dfdx
[j
][k
];
2845 if (mdrunOptions
.verbose
&& fplog
)
2850 /* write progress */
2851 if (bIsMaster
&& mdrunOptions
.verbose
)
2853 fprintf(stderr
, "\rFinished step %d out of %td",
2854 std::min
<int>(atom
+ nnodes
, atom_index
.size()), ssize(atom_index
));
2861 fprintf(stderr
, "\n\nWriting Hessian...\n");
2862 gmx_mtxio_write(ftp2fn(efMTX
, nfile
, fnm
), sz
, sz
, full_matrix
, sparse_matrix
);
2865 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2867 walltime_accounting_set_nsteps_done(walltime_accounting
, atom_index
.size() * 2);