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7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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39 * \brief This file defines integrators for energy minimization
41 * \author Berk Hess <hess@kth.se>
42 * \author Erik Lindahl <erik@kth.se>
43 * \ingroup module_mdlib
58 #include "gromacs/commandline/filenm.h"
59 #include "gromacs/domdec/domdec.h"
60 #include "gromacs/domdec/domdec_struct.h"
61 #include "gromacs/ewald/pme.h"
62 #include "gromacs/fileio/confio.h"
63 #include "gromacs/fileio/mtxio.h"
64 #include "gromacs/gmxlib/network.h"
65 #include "gromacs/gmxlib/nrnb.h"
66 #include "gromacs/imd/imd.h"
67 #include "gromacs/linearalgebra/sparsematrix.h"
68 #include "gromacs/listed-forces/manage-threading.h"
69 #include "gromacs/math/functions.h"
70 #include "gromacs/math/vec.h"
71 #include "gromacs/mdlib/constr.h"
72 #include "gromacs/mdlib/force.h"
73 #include "gromacs/mdlib/forcerec.h"
74 #include "gromacs/mdlib/gmx_omp_nthreads.h"
75 #include "gromacs/mdlib/md_support.h"
76 #include "gromacs/mdlib/mdatoms.h"
77 #include "gromacs/mdlib/mdebin.h"
78 #include "gromacs/mdlib/mdrun.h"
79 #include "gromacs/mdlib/mdsetup.h"
80 #include "gromacs/mdlib/ns.h"
81 #include "gromacs/mdlib/shellfc.h"
82 #include "gromacs/mdlib/sim_util.h"
83 #include "gromacs/mdlib/tgroup.h"
84 #include "gromacs/mdlib/trajectory_writing.h"
85 #include "gromacs/mdlib/update.h"
86 #include "gromacs/mdlib/vsite.h"
87 #include "gromacs/mdtypes/commrec.h"
88 #include "gromacs/mdtypes/inputrec.h"
89 #include "gromacs/mdtypes/md_enums.h"
90 #include "gromacs/mdtypes/state.h"
91 #include "gromacs/pbcutil/mshift.h"
92 #include "gromacs/pbcutil/pbc.h"
93 #include "gromacs/timing/wallcycle.h"
94 #include "gromacs/timing/walltime_accounting.h"
95 #include "gromacs/topology/mtop_util.h"
96 #include "gromacs/topology/topology.h"
97 #include "gromacs/utility/cstringutil.h"
98 #include "gromacs/utility/exceptions.h"
99 #include "gromacs/utility/fatalerror.h"
100 #include "gromacs/utility/logger.h"
101 #include "gromacs/utility/smalloc.h"
103 //! Utility structure for manipulating states during EM
105 //! Copy of the global state
111 //! Norm of the force
119 //! Print the EM starting conditions
120 static void print_em_start(FILE *fplog
,
122 gmx_walltime_accounting_t walltime_accounting
,
123 gmx_wallcycle_t wcycle
,
126 walltime_accounting_start(walltime_accounting
);
127 wallcycle_start(wcycle
, ewcRUN
);
128 print_start(fplog
, cr
, walltime_accounting
, name
);
131 //! Stop counting time for EM
132 static void em_time_end(gmx_walltime_accounting_t walltime_accounting
,
133 gmx_wallcycle_t wcycle
)
135 wallcycle_stop(wcycle
, ewcRUN
);
137 walltime_accounting_end(walltime_accounting
);
140 //! Printing a log file and console header
141 static void sp_header(FILE *out
, const char *minimizer
, real ftol
, int nsteps
)
144 fprintf(out
, "%s:\n", minimizer
);
145 fprintf(out
, " Tolerance (Fmax) = %12.5e\n", ftol
);
146 fprintf(out
, " Number of steps = %12d\n", nsteps
);
149 //! Print warning message
150 static void warn_step(FILE *fp
, real ftol
, gmx_bool bLastStep
, gmx_bool bConstrain
)
156 "\nEnergy minimization reached the maximum number "
157 "of steps before the forces reached the requested "
158 "precision Fmax < %g.\n", ftol
);
163 "\nEnergy minimization has stopped, but the forces have "
164 "not converged to the requested precision Fmax < %g (which "
165 "may not be possible for your system). It stopped "
166 "because the algorithm tried to make a new step whose size "
167 "was too small, or there was no change in the energy since "
168 "last step. Either way, we regard the minimization as "
169 "converged to within the available machine precision, "
170 "given your starting configuration and EM parameters.\n%s%s",
172 sizeof(real
) < sizeof(double) ?
173 "\nDouble precision normally gives you higher accuracy, but "
174 "this is often not needed for preparing to run molecular "
178 "You might need to increase your constraint accuracy, or turn\n"
179 "off constraints altogether (set constraints = none in mdp file)\n" :
182 fputs(wrap_lines(buffer
, 78, 0, FALSE
), fp
);
185 //! Print message about convergence of the EM
186 static void print_converged(FILE *fp
, const char *alg
, real ftol
,
187 gmx_int64_t count
, gmx_bool bDone
, gmx_int64_t nsteps
,
188 const em_state_t
*ems
, double sqrtNumAtoms
)
190 char buf
[STEPSTRSIZE
];
194 fprintf(fp
, "\n%s converged to Fmax < %g in %s steps\n",
195 alg
, ftol
, gmx_step_str(count
, buf
));
197 else if (count
< nsteps
)
199 fprintf(fp
, "\n%s converged to machine precision in %s steps,\n"
200 "but did not reach the requested Fmax < %g.\n",
201 alg
, gmx_step_str(count
, buf
), ftol
);
205 fprintf(fp
, "\n%s did not converge to Fmax < %g in %s steps.\n",
206 alg
, ftol
, gmx_step_str(count
, buf
));
210 fprintf(fp
, "Potential Energy = %21.14e\n", ems
->epot
);
211 fprintf(fp
, "Maximum force = %21.14e on atom %d\n", ems
->fmax
, ems
->a_fmax
+ 1);
212 fprintf(fp
, "Norm of force = %21.14e\n", ems
->fnorm
/sqrtNumAtoms
);
214 fprintf(fp
, "Potential Energy = %14.7e\n", ems
->epot
);
215 fprintf(fp
, "Maximum force = %14.7e on atom %d\n", ems
->fmax
, ems
->a_fmax
+ 1);
216 fprintf(fp
, "Norm of force = %14.7e\n", ems
->fnorm
/sqrtNumAtoms
);
220 //! Compute the norm and max of the force array in parallel
221 static void get_f_norm_max(t_commrec
*cr
,
222 t_grpopts
*opts
, t_mdatoms
*mdatoms
, const rvec
*f
,
223 real
*fnorm
, real
*fmax
, int *a_fmax
)
227 int la_max
, a_max
, start
, end
, i
, m
, gf
;
229 /* This routine finds the largest force and returns it.
230 * On parallel machines the global max is taken.
236 end
= mdatoms
->homenr
;
237 if (mdatoms
->cFREEZE
)
239 for (i
= start
; i
< end
; i
++)
241 gf
= mdatoms
->cFREEZE
[i
];
243 for (m
= 0; m
< DIM
; m
++)
245 if (!opts
->nFreeze
[gf
][m
])
247 fam
+= gmx::square(f
[i
][m
]);
260 for (i
= start
; i
< end
; i
++)
272 if (la_max
>= 0 && DOMAINDECOMP(cr
))
274 a_max
= cr
->dd
->gatindex
[la_max
];
282 snew(sum
, 2*cr
->nnodes
+1);
283 sum
[2*cr
->nodeid
] = fmax2
;
284 sum
[2*cr
->nodeid
+1] = a_max
;
285 sum
[2*cr
->nnodes
] = fnorm2
;
286 gmx_sumd(2*cr
->nnodes
+1, sum
, cr
);
287 fnorm2
= sum
[2*cr
->nnodes
];
288 /* Determine the global maximum */
289 for (i
= 0; i
< cr
->nnodes
; i
++)
291 if (sum
[2*i
] > fmax2
)
294 a_max
= (int)(sum
[2*i
+1] + 0.5);
302 *fnorm
= sqrt(fnorm2
);
314 //! Compute the norm of the force
315 static void get_state_f_norm_max(t_commrec
*cr
,
316 t_grpopts
*opts
, t_mdatoms
*mdatoms
,
319 get_f_norm_max(cr
, opts
, mdatoms
, as_rvec_array(ems
->f
.data()),
320 &ems
->fnorm
, &ems
->fmax
, &ems
->a_fmax
);
323 //! Initialize the energy minimization
324 static void init_em(FILE *fplog
, const char *title
,
325 t_commrec
*cr
, gmx::IMDOutputProvider
*outputProvider
,
327 t_state
*state_global
, gmx_mtop_t
*top_global
,
328 em_state_t
*ems
, gmx_localtop_t
**top
,
329 t_nrnb
*nrnb
, rvec mu_tot
,
330 t_forcerec
*fr
, gmx_enerdata_t
**enerd
,
331 t_graph
**graph
, t_mdatoms
*mdatoms
, gmx_global_stat_t
*gstat
,
332 gmx_vsite_t
*vsite
, gmx_constr_t constr
, gmx_shellfc_t
**shellfc
,
333 int nfile
, const t_filenm fnm
[],
334 gmx_mdoutf_t
*outf
, t_mdebin
**mdebin
,
335 int imdport
, unsigned long gmx_unused Flags
,
336 gmx_wallcycle_t wcycle
)
342 fprintf(fplog
, "Initiating %s\n", title
);
345 state_global
->ngtc
= 0;
347 /* Initialize lambda variables */
348 initialize_lambdas(fplog
, ir
, &(state_global
->fep_state
), state_global
->lambda
, nullptr);
352 /* Interactive molecular dynamics */
353 init_IMD(ir
, cr
, top_global
, fplog
, 1, as_rvec_array(state_global
->x
.data()),
354 nfile
, fnm
, nullptr, imdport
, Flags
);
358 GMX_ASSERT(shellfc
!= NULL
, "With NM we always support shells");
360 *shellfc
= init_shell_flexcon(stdout
,
362 n_flexible_constraints(constr
),
368 GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir
->eI
), "This else currently only handles energy minimizers, consider if your algorithm needs shell/flexible-constraint support");
370 /* With energy minimization, shells and flexible constraints are
371 * automatically minimized when treated like normal DOFS.
373 if (shellfc
!= nullptr)
379 if (DOMAINDECOMP(cr
))
381 *top
= dd_init_local_top(top_global
);
383 dd_init_local_state(cr
->dd
, state_global
, &ems
->s
);
385 /* Distribute the charge groups over the nodes from the master node */
386 dd_partition_system(fplog
, ir
->init_step
, cr
, TRUE
, 1,
387 state_global
, top_global
, ir
,
388 &ems
->s
, &ems
->f
, mdatoms
, *top
,
390 nrnb
, nullptr, FALSE
);
391 dd_store_state(cr
->dd
, &ems
->s
);
397 state_change_natoms(state_global
, state_global
->natoms
);
398 /* Just copy the state */
399 ems
->s
= *state_global
;
400 state_change_natoms(&ems
->s
, ems
->s
.natoms
);
401 /* We need to allocate one element extra, since we might use
402 * (unaligned) 4-wide SIMD loads to access rvec entries.
404 ems
->f
.resize(ems
->s
.natoms
+ 1);
407 mdAlgorithmsSetupAtomData(cr
, ir
, top_global
, *top
, fr
,
409 vsite
, shellfc
? *shellfc
: nullptr);
413 set_vsite_top(vsite
, *top
, mdatoms
, cr
);
417 update_mdatoms(mdatoms
, state_global
->lambda
[efptMASS
]);
421 if (ir
->eConstrAlg
== econtSHAKE
&&
422 gmx_mtop_ftype_count(top_global
, F_CONSTR
) > 0)
424 gmx_fatal(FARGS
, "Can not do energy minimization with %s, use %s\n",
425 econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
428 if (!DOMAINDECOMP(cr
))
430 set_constraints(constr
, *top
, ir
, mdatoms
, cr
);
433 if (!ir
->bContinuation
)
435 /* Constrain the starting coordinates */
437 constrain(PAR(cr
) ? nullptr : fplog
, TRUE
, TRUE
, constr
, &(*top
)->idef
,
438 ir
, cr
, -1, 0, 1.0, mdatoms
,
439 as_rvec_array(ems
->s
.x
.data()),
440 as_rvec_array(ems
->s
.x
.data()),
442 fr
->bMolPBC
, ems
->s
.box
,
443 ems
->s
.lambda
[efptFEP
], &dvdl_constr
,
444 nullptr, nullptr, nrnb
, econqCoord
);
450 *gstat
= global_stat_init(ir
);
457 *outf
= init_mdoutf(fplog
, nfile
, fnm
, 0, cr
, outputProvider
, ir
, top_global
, nullptr, wcycle
);
460 init_enerdata(top_global
->groups
.grps
[egcENER
].nr
, ir
->fepvals
->n_lambda
,
463 if (mdebin
!= nullptr)
465 /* Init bin for energy stuff */
466 *mdebin
= init_mdebin(mdoutf_get_fp_ene(*outf
), top_global
, ir
, nullptr);
470 calc_shifts(ems
->s
.box
, fr
->shift_vec
);
473 //! Finalize the minimization
474 static void finish_em(t_commrec
*cr
, gmx_mdoutf_t outf
,
475 gmx_walltime_accounting_t walltime_accounting
,
476 gmx_wallcycle_t wcycle
)
478 if (!(cr
->duty
& DUTY_PME
))
480 /* Tell the PME only node to finish */
481 gmx_pme_send_finish(cr
);
486 em_time_end(walltime_accounting
, wcycle
);
489 //! Swap two different EM states during minimization
490 static void swap_em_state(em_state_t
**ems1
, em_state_t
**ems2
)
499 //! Save the EM trajectory
500 static void write_em_traj(FILE *fplog
, t_commrec
*cr
,
502 gmx_bool bX
, gmx_bool bF
, const char *confout
,
503 gmx_mtop_t
*top_global
,
504 t_inputrec
*ir
, gmx_int64_t step
,
506 t_state
*state_global
,
507 ObservablesHistory
*observablesHistory
)
513 mdof_flags
|= MDOF_X
;
517 mdof_flags
|= MDOF_F
;
520 /* If we want IMD output, set appropriate MDOF flag */
523 mdof_flags
|= MDOF_IMD
;
526 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
527 top_global
, step
, (double)step
,
528 &state
->s
, state_global
, observablesHistory
,
531 if (confout
!= nullptr && MASTER(cr
))
533 GMX_RELEASE_ASSERT(bX
, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
534 /* With domain decomposition the call above collected the state->s.x
535 * into state_global->x. Without DD we copy the local state pointer.
537 if (!DOMAINDECOMP(cr
))
539 state_global
= &state
->s
;
542 if (ir
->ePBC
!= epbcNONE
&& !ir
->bPeriodicMols
&& DOMAINDECOMP(cr
))
544 /* Make molecules whole only for confout writing */
545 do_pbc_mtop(fplog
, ir
->ePBC
, state
->s
.box
, top_global
,
546 as_rvec_array(state_global
->x
.data()));
549 write_sto_conf_mtop(confout
,
550 *top_global
->name
, top_global
,
551 as_rvec_array(state_global
->x
.data()), nullptr, ir
->ePBC
, state
->s
.box
);
555 //! \brief Do one minimization step
557 // \returns true when the step succeeded, false when a constraint error occurred
558 static bool do_em_step(t_commrec
*cr
, t_inputrec
*ir
, t_mdatoms
*md
,
560 em_state_t
*ems1
, real a
, const PaddedRVecVector
*force
,
562 gmx_constr_t constr
, gmx_localtop_t
*top
,
563 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
570 int nthreads gmx_unused
;
572 bool validStep
= true;
577 if (DOMAINDECOMP(cr
) && s1
->ddp_count
!= cr
->dd
->ddp_count
)
579 gmx_incons("state mismatch in do_em_step");
582 s2
->flags
= s1
->flags
;
584 if (s2
->natoms
!= s1
->natoms
)
586 state_change_natoms(s2
, s1
->natoms
);
587 /* We need to allocate one element extra, since we might use
588 * (unaligned) 4-wide SIMD loads to access rvec entries.
590 ems2
->f
.resize(s2
->natoms
+ 1);
592 if (DOMAINDECOMP(cr
) && s2
->cg_gl
.size() != s1
->cg_gl
.size())
594 s2
->cg_gl
.resize(s1
->cg_gl
.size());
597 copy_mat(s1
->box
, s2
->box
);
598 /* Copy free energy state */
599 s2
->lambda
= s1
->lambda
;
600 copy_mat(s1
->box
, s2
->box
);
605 // cppcheck-suppress unreadVariable
606 nthreads
= gmx_omp_nthreads_get(emntUpdate
);
607 #pragma omp parallel num_threads(nthreads)
609 const rvec
*x1
= as_rvec_array(s1
->x
.data());
610 rvec
*x2
= as_rvec_array(s2
->x
.data());
611 const rvec
*f
= as_rvec_array(force
->data());
614 #pragma omp for schedule(static) nowait
615 for (int i
= start
; i
< end
; i
++)
623 for (int m
= 0; m
< DIM
; m
++)
625 if (ir
->opts
.nFreeze
[gf
][m
])
631 x2
[i
][m
] = x1
[i
][m
] + a
*f
[i
][m
];
635 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
638 if (s2
->flags
& (1<<estCGP
))
640 /* Copy the CG p vector */
641 const rvec
*p1
= as_rvec_array(s1
->cg_p
.data());
642 rvec
*p2
= as_rvec_array(s2
->cg_p
.data());
643 #pragma omp for schedule(static) nowait
644 for (int i
= start
; i
< end
; i
++)
646 // Trivial OpenMP block that does not throw
647 copy_rvec(p1
[i
], p2
[i
]);
651 if (DOMAINDECOMP(cr
))
653 s2
->ddp_count
= s1
->ddp_count
;
655 /* OpenMP does not supported unsigned loop variables */
656 #pragma omp for schedule(static) nowait
657 for (int i
= 0; i
< static_cast<int>(s2
->cg_gl
.size()); i
++)
659 s2
->cg_gl
[i
] = s1
->cg_gl
[i
];
661 s2
->ddp_count_cg_gl
= s1
->ddp_count_cg_gl
;
667 wallcycle_start(wcycle
, ewcCONSTR
);
670 constrain(nullptr, TRUE
, TRUE
, constr
, &top
->idef
,
671 ir
, cr
, count
, 0, 1.0, md
,
672 as_rvec_array(s1
->x
.data()), as_rvec_array(s2
->x
.data()),
673 nullptr, bMolPBC
, s2
->box
,
674 s2
->lambda
[efptBONDED
], &dvdl_constr
,
675 nullptr, nullptr, nrnb
, econqCoord
);
676 wallcycle_stop(wcycle
, ewcCONSTR
);
678 // We should move this check to the different minimizers
679 if (!validStep
&& ir
->eI
!= eiSteep
)
681 gmx_fatal(FARGS
, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
682 EI(ir
->eI
), EI(eiSteep
), EI(ir
->eI
));
689 //! Prepare EM for using domain decomposition parallellization
690 static void em_dd_partition_system(FILE *fplog
, int step
, t_commrec
*cr
,
691 gmx_mtop_t
*top_global
, t_inputrec
*ir
,
692 em_state_t
*ems
, gmx_localtop_t
*top
,
693 t_mdatoms
*mdatoms
, t_forcerec
*fr
,
694 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
695 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
)
697 /* Repartition the domain decomposition */
698 dd_partition_system(fplog
, step
, cr
, FALSE
, 1,
699 nullptr, top_global
, ir
,
701 mdatoms
, top
, fr
, vsite
, constr
,
702 nrnb
, wcycle
, FALSE
);
703 dd_store_state(cr
->dd
, &ems
->s
);
706 //! De one energy evaluation
707 static void evaluate_energy(FILE *fplog
, t_commrec
*cr
,
708 gmx_mtop_t
*top_global
,
709 em_state_t
*ems
, gmx_localtop_t
*top
,
710 t_inputrec
*inputrec
,
711 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
712 gmx_global_stat_t gstat
,
713 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
715 t_graph
*graph
, t_mdatoms
*mdatoms
,
716 t_forcerec
*fr
, rvec mu_tot
,
717 gmx_enerdata_t
*enerd
, tensor vir
, tensor pres
,
718 gmx_int64_t count
, gmx_bool bFirst
)
722 tensor force_vir
, shake_vir
, ekin
;
723 real dvdl_constr
, prescorr
, enercorr
, dvdlcorr
;
726 /* Set the time to the initial time, the time does not change during EM */
727 t
= inputrec
->init_t
;
730 (DOMAINDECOMP(cr
) && ems
->s
.ddp_count
< cr
->dd
->ddp_count
))
732 /* This is the first state or an old state used before the last ns */
738 if (inputrec
->nstlist
> 0)
746 construct_vsites(vsite
, as_rvec_array(ems
->s
.x
.data()), 1, nullptr,
747 top
->idef
.iparams
, top
->idef
.il
,
748 fr
->ePBC
, fr
->bMolPBC
, cr
, ems
->s
.box
);
751 if (DOMAINDECOMP(cr
) && bNS
)
753 /* Repartition the domain decomposition */
754 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
755 ems
, top
, mdatoms
, fr
, vsite
, constr
,
759 /* Calc force & energy on new trial position */
760 /* do_force always puts the charge groups in the box and shifts again
761 * We do not unshift, so molecules are always whole in congrad.c
763 do_force(fplog
, cr
, inputrec
,
764 count
, nrnb
, wcycle
, top
, &top_global
->groups
,
765 ems
->s
.box
, &ems
->s
.x
, &ems
->s
.hist
,
766 &ems
->f
, force_vir
, mdatoms
, enerd
, fcd
,
767 ems
->s
.lambda
, graph
, fr
, vsite
, mu_tot
, t
, nullptr, TRUE
,
768 GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
|
769 GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
|
770 (bNS
? GMX_FORCE_NS
: 0));
772 /* Clear the unused shake virial and pressure */
773 clear_mat(shake_vir
);
776 /* Communicate stuff when parallel */
777 if (PAR(cr
) && inputrec
->eI
!= eiNM
)
779 wallcycle_start(wcycle
, ewcMoveE
);
781 global_stat(gstat
, cr
, enerd
, force_vir
, shake_vir
, mu_tot
,
782 inputrec
, nullptr, nullptr, nullptr, 1, &terminate
,
788 wallcycle_stop(wcycle
, ewcMoveE
);
791 /* Calculate long range corrections to pressure and energy */
792 calc_dispcorr(inputrec
, fr
, ems
->s
.box
, ems
->s
.lambda
[efptVDW
],
793 pres
, force_vir
, &prescorr
, &enercorr
, &dvdlcorr
);
794 enerd
->term
[F_DISPCORR
] = enercorr
;
795 enerd
->term
[F_EPOT
] += enercorr
;
796 enerd
->term
[F_PRES
] += prescorr
;
797 enerd
->term
[F_DVDL
] += dvdlcorr
;
799 ems
->epot
= enerd
->term
[F_EPOT
];
803 /* Project out the constraint components of the force */
804 wallcycle_start(wcycle
, ewcCONSTR
);
806 rvec
*f_rvec
= as_rvec_array(ems
->f
.data());
807 constrain(nullptr, FALSE
, FALSE
, constr
, &top
->idef
,
808 inputrec
, cr
, count
, 0, 1.0, mdatoms
,
809 as_rvec_array(ems
->s
.x
.data()), f_rvec
, f_rvec
,
810 fr
->bMolPBC
, ems
->s
.box
,
811 ems
->s
.lambda
[efptBONDED
], &dvdl_constr
,
812 nullptr, &shake_vir
, nrnb
, econqForceDispl
);
813 enerd
->term
[F_DVDL_CONSTR
] += dvdl_constr
;
814 m_add(force_vir
, shake_vir
, vir
);
815 wallcycle_stop(wcycle
, ewcCONSTR
);
819 copy_mat(force_vir
, vir
);
823 enerd
->term
[F_PRES
] =
824 calc_pres(fr
->ePBC
, inputrec
->nwall
, ems
->s
.box
, ekin
, vir
, pres
);
826 sum_dhdl(enerd
, ems
->s
.lambda
, inputrec
->fepvals
);
828 if (EI_ENERGY_MINIMIZATION(inputrec
->eI
))
830 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, ems
);
834 //! Parallel utility summing energies and forces
835 static double reorder_partsum(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
836 gmx_mtop_t
*top_global
,
837 em_state_t
*s_min
, em_state_t
*s_b
)
840 int ncg
, *cg_gl
, *index
, c
, cg
, i
, a0
, a1
, a
, gf
, m
;
842 unsigned char *grpnrFREEZE
;
846 fprintf(debug
, "Doing reorder_partsum\n");
849 const rvec
*fm
= as_rvec_array(s_min
->f
.data());
850 const rvec
*fb
= as_rvec_array(s_b
->f
.data());
852 cgs_gl
= dd_charge_groups_global(cr
->dd
);
853 index
= cgs_gl
->index
;
855 /* Collect fm in a global vector fmg.
856 * This conflicts with the spirit of domain decomposition,
857 * but to fully optimize this a much more complicated algorithm is required.
860 snew(fmg
, top_global
->natoms
);
862 ncg
= s_min
->s
.cg_gl
.size();
863 cg_gl
= s_min
->s
.cg_gl
.data();
865 for (c
= 0; c
< ncg
; c
++)
870 for (a
= a0
; a
< a1
; a
++)
872 copy_rvec(fm
[i
], fmg
[a
]);
876 gmx_sum(top_global
->natoms
*3, fmg
[0], cr
);
878 /* Now we will determine the part of the sum for the cgs in state s_b */
879 ncg
= s_b
->s
.cg_gl
.size();
880 cg_gl
= s_b
->s
.cg_gl
.data();
884 grpnrFREEZE
= top_global
->groups
.grpnr
[egcFREEZE
];
885 for (c
= 0; c
< ncg
; c
++)
890 for (a
= a0
; a
< a1
; a
++)
892 if (mdatoms
->cFREEZE
&& grpnrFREEZE
)
896 for (m
= 0; m
< DIM
; m
++)
898 if (!opts
->nFreeze
[gf
][m
])
900 partsum
+= (fb
[i
][m
] - fmg
[a
][m
])*fb
[i
][m
];
912 //! Print some stuff, like beta, whatever that means.
913 static real
pr_beta(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
914 gmx_mtop_t
*top_global
,
915 em_state_t
*s_min
, em_state_t
*s_b
)
919 /* This is just the classical Polak-Ribiere calculation of beta;
920 * it looks a bit complicated since we take freeze groups into account,
921 * and might have to sum it in parallel runs.
924 if (!DOMAINDECOMP(cr
) ||
925 (s_min
->s
.ddp_count
== cr
->dd
->ddp_count
&&
926 s_b
->s
.ddp_count
== cr
->dd
->ddp_count
))
928 const rvec
*fm
= as_rvec_array(s_min
->f
.data());
929 const rvec
*fb
= as_rvec_array(s_b
->f
.data());
932 /* This part of code can be incorrect with DD,
933 * since the atom ordering in s_b and s_min might differ.
935 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
937 if (mdatoms
->cFREEZE
)
939 gf
= mdatoms
->cFREEZE
[i
];
941 for (int m
= 0; m
< DIM
; m
++)
943 if (!opts
->nFreeze
[gf
][m
])
945 sum
+= (fb
[i
][m
] - fm
[i
][m
])*fb
[i
][m
];
952 /* We need to reorder cgs while summing */
953 sum
= reorder_partsum(cr
, opts
, mdatoms
, top_global
, s_min
, s_b
);
957 gmx_sumd(1, &sum
, cr
);
960 return sum
/gmx::square(s_min
->fnorm
);
966 /*! \brief Do conjugate gradients minimization
967 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
968 int nfile, const t_filenm fnm[],
969 const gmx_output_env_t *oenv, gmx_bool bVerbose,
971 gmx_vsite_t *vsite, gmx_constr_t constr,
973 gmx::IMDOutputProvider *outputProvider,
974 t_inputrec *inputrec,
975 gmx_mtop_t *top_global, t_fcdata *fcd,
976 t_state *state_global,
978 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
981 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
982 gmx_membed_t gmx_unused *membed,
983 real cpt_period, real max_hours,
986 gmx_walltime_accounting_t walltime_accounting)
988 double do_cg(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
989 int nfile
, const t_filenm fnm
[],
990 const gmx_output_env_t gmx_unused
*oenv
, gmx_bool bVerbose
,
991 int gmx_unused nstglobalcomm
,
992 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
993 int gmx_unused stepout
,
994 gmx::IMDOutputProvider
*outputProvider
,
995 t_inputrec
*inputrec
,
996 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
997 t_state
*state_global
,
998 ObservablesHistory
*observablesHistory
,
1000 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1001 gmx_edsam_t gmx_unused ed
,
1003 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
1004 gmx_membed_t gmx_unused
*membed
,
1005 real gmx_unused cpt_period
, real gmx_unused max_hours
,
1007 unsigned long gmx_unused Flags
,
1008 gmx_walltime_accounting_t walltime_accounting
)
1010 const char *CG
= "Polak-Ribiere Conjugate Gradients";
1012 gmx_localtop_t
*top
;
1013 gmx_enerdata_t
*enerd
;
1014 gmx_global_stat_t gstat
;
1016 double tmp
, minstep
;
1018 real a
, b
, c
, beta
= 0.0;
1022 gmx_bool converged
, foundlower
;
1024 gmx_bool do_log
= FALSE
, do_ene
= FALSE
, do_x
, do_f
;
1026 int number_steps
, neval
= 0, nstcg
= inputrec
->nstcgsteep
;
1028 int m
, step
, nminstep
;
1032 // Ensure the extra per-atom state array gets allocated
1033 state_global
->flags
|= (1<<estCGP
);
1035 /* Create 4 states on the stack and extract pointers that we will swap */
1036 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1037 em_state_t
*s_min
= &s0
;
1038 em_state_t
*s_a
= &s1
;
1039 em_state_t
*s_b
= &s2
;
1040 em_state_t
*s_c
= &s3
;
1042 /* Init em and store the local state in s_min */
1043 init_em(fplog
, CG
, cr
, outputProvider
, inputrec
,
1044 state_global
, top_global
, s_min
, &top
,
1045 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
,
1046 vsite
, constr
, nullptr,
1047 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
1049 /* Print to log file */
1050 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, CG
);
1052 /* Max number of steps */
1053 number_steps
= inputrec
->nsteps
;
1057 sp_header(stderr
, CG
, inputrec
->em_tol
, number_steps
);
1061 sp_header(fplog
, CG
, inputrec
->em_tol
, number_steps
);
1064 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1065 /* do_force always puts the charge groups in the box and shifts again
1066 * We do not unshift, so molecules are always whole in congrad.c
1068 evaluate_energy(fplog
, cr
,
1069 top_global
, s_min
, top
,
1070 inputrec
, nrnb
, wcycle
, gstat
,
1071 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1072 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1077 /* Copy stuff to the energy bin for easy printing etc. */
1078 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1079 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1080 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1082 print_ebin_header(fplog
, step
, step
);
1083 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1084 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1088 /* Estimate/guess the initial stepsize */
1089 stepsize
= inputrec
->em_stepsize
/s_min
->fnorm
;
1093 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1094 fprintf(stderr
, " F-max = %12.5e on atom %d\n",
1095 s_min
->fmax
, s_min
->a_fmax
+1);
1096 fprintf(stderr
, " F-Norm = %12.5e\n",
1097 s_min
->fnorm
/sqrtNumAtoms
);
1098 fprintf(stderr
, "\n");
1099 /* and copy to the log file too... */
1100 fprintf(fplog
, " F-max = %12.5e on atom %d\n",
1101 s_min
->fmax
, s_min
->a_fmax
+1);
1102 fprintf(fplog
, " F-Norm = %12.5e\n",
1103 s_min
->fnorm
/sqrtNumAtoms
);
1104 fprintf(fplog
, "\n");
1106 /* Start the loop over CG steps.
1107 * Each successful step is counted, and we continue until
1108 * we either converge or reach the max number of steps.
1111 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1114 /* start taking steps in a new direction
1115 * First time we enter the routine, beta=0, and the direction is
1116 * simply the negative gradient.
1119 /* Calculate the new direction in p, and the gradient in this direction, gpa */
1120 rvec
*pm
= as_rvec_array(s_min
->s
.cg_p
.data());
1121 const rvec
*sfm
= as_rvec_array(s_min
->f
.data());
1124 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1126 if (mdatoms
->cFREEZE
)
1128 gf
= mdatoms
->cFREEZE
[i
];
1130 for (m
= 0; m
< DIM
; m
++)
1132 if (!inputrec
->opts
.nFreeze
[gf
][m
])
1134 pm
[i
][m
] = sfm
[i
][m
] + beta
*pm
[i
][m
];
1135 gpa
-= pm
[i
][m
]*sfm
[i
][m
];
1136 /* f is negative gradient, thus the sign */
1145 /* Sum the gradient along the line across CPUs */
1148 gmx_sumd(1, &gpa
, cr
);
1151 /* Calculate the norm of the search vector */
1152 get_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, pm
, &pnorm
, nullptr, nullptr);
1154 /* Just in case stepsize reaches zero due to numerical precision... */
1157 stepsize
= inputrec
->em_stepsize
/pnorm
;
1161 * Double check the value of the derivative in the search direction.
1162 * If it is positive it must be due to the old information in the
1163 * CG formula, so just remove that and start over with beta=0.
1164 * This corresponds to a steepest descent step.
1169 step
--; /* Don't count this step since we are restarting */
1170 continue; /* Go back to the beginning of the big for-loop */
1173 /* Calculate minimum allowed stepsize, before the average (norm)
1174 * relative change in coordinate is smaller than precision
1177 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1179 for (m
= 0; m
< DIM
; m
++)
1181 tmp
= fabs(s_min
->s
.x
[i
][m
]);
1190 /* Add up from all CPUs */
1193 gmx_sumd(1, &minstep
, cr
);
1196 minstep
= GMX_REAL_EPS
/sqrt(minstep
/(3*state_global
->natoms
));
1198 if (stepsize
< minstep
)
1204 /* Write coordinates if necessary */
1205 do_x
= do_per_step(step
, inputrec
->nstxout
);
1206 do_f
= do_per_step(step
, inputrec
->nstfout
);
1208 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr,
1209 top_global
, inputrec
, step
,
1210 s_min
, state_global
, observablesHistory
);
1212 /* Take a step downhill.
1213 * In theory, we should minimize the function along this direction.
1214 * That is quite possible, but it turns out to take 5-10 function evaluations
1215 * for each line. However, we dont really need to find the exact minimum -
1216 * it is much better to start a new CG step in a modified direction as soon
1217 * as we are close to it. This will save a lot of energy evaluations.
1219 * In practice, we just try to take a single step.
1220 * If it worked (i.e. lowered the energy), we increase the stepsize but
1221 * the continue straight to the next CG step without trying to find any minimum.
1222 * If it didn't work (higher energy), there must be a minimum somewhere between
1223 * the old position and the new one.
1225 * Due to the finite numerical accuracy, it turns out that it is a good idea
1226 * to even accept a SMALL increase in energy, if the derivative is still downhill.
1227 * This leads to lower final energies in the tests I've done. / Erik
1229 s_a
->epot
= s_min
->epot
;
1231 c
= a
+ stepsize
; /* reference position along line is zero */
1233 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
< cr
->dd
->ddp_count
)
1235 em_dd_partition_system(fplog
, step
, cr
, top_global
, inputrec
,
1236 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
1240 /* Take a trial step (new coords in s_c) */
1241 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, c
, &s_min
->s
.cg_p
, s_c
,
1242 constr
, top
, nrnb
, wcycle
, -1);
1245 /* Calculate energy for the trial step */
1246 evaluate_energy(fplog
, cr
,
1247 top_global
, s_c
, top
,
1248 inputrec
, nrnb
, wcycle
, gstat
,
1249 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1250 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1252 /* Calc derivative along line */
1253 const rvec
*pc
= as_rvec_array(s_c
->s
.cg_p
.data());
1254 const rvec
*sfc
= as_rvec_array(s_c
->f
.data());
1256 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1258 for (m
= 0; m
< DIM
; m
++)
1260 gpc
-= pc
[i
][m
]*sfc
[i
][m
]; /* f is negative gradient, thus the sign */
1263 /* Sum the gradient along the line across CPUs */
1266 gmx_sumd(1, &gpc
, cr
);
1269 /* This is the max amount of increase in energy we tolerate */
1270 tmp
= sqrt(GMX_REAL_EPS
)*fabs(s_a
->epot
);
1272 /* Accept the step if the energy is lower, or if it is not significantly higher
1273 * and the line derivative is still negative.
1275 if (s_c
->epot
< s_a
->epot
|| (gpc
< 0 && s_c
->epot
< (s_a
->epot
+ tmp
)))
1278 /* Great, we found a better energy. Increase step for next iteration
1279 * if we are still going down, decrease it otherwise
1283 stepsize
*= 1.618034; /* The golden section */
1287 stepsize
*= 0.618034; /* 1/golden section */
1292 /* New energy is the same or higher. We will have to do some work
1293 * to find a smaller value in the interval. Take smaller step next time!
1296 stepsize
*= 0.618034;
1302 /* OK, if we didn't find a lower value we will have to locate one now - there must
1303 * be one in the interval [a=0,c].
1304 * The same thing is valid here, though: Don't spend dozens of iterations to find
1305 * the line minimum. We try to interpolate based on the derivative at the endpoints,
1306 * and only continue until we find a lower value. In most cases this means 1-2 iterations.
1308 * I also have a safeguard for potentially really pathological functions so we never
1309 * take more than 20 steps before we give up ...
1311 * If we already found a lower value we just skip this step and continue to the update.
1320 /* Select a new trial point.
1321 * If the derivatives at points a & c have different sign we interpolate to zero,
1322 * otherwise just do a bisection.
1324 if (gpa
< 0 && gpc
> 0)
1326 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
1333 /* safeguard if interpolation close to machine accuracy causes errors:
1334 * never go outside the interval
1336 if (b
<= a
|| b
>= c
)
1341 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
1343 /* Reload the old state */
1344 em_dd_partition_system(fplog
, -1, cr
, top_global
, inputrec
,
1345 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
1349 /* Take a trial step to this new point - new coords in s_b */
1350 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, b
, &s_min
->s
.cg_p
, s_b
,
1351 constr
, top
, nrnb
, wcycle
, -1);
1354 /* Calculate energy for the trial step */
1355 evaluate_energy(fplog
, cr
,
1356 top_global
, s_b
, top
,
1357 inputrec
, nrnb
, wcycle
, gstat
,
1358 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1359 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1361 /* p does not change within a step, but since the domain decomposition
1362 * might change, we have to use cg_p of s_b here.
1364 const rvec
*pb
= as_rvec_array(s_b
->s
.cg_p
.data());
1365 const rvec
*sfb
= as_rvec_array(s_b
->f
.data());
1367 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1369 for (m
= 0; m
< DIM
; m
++)
1371 gpb
-= pb
[i
][m
]*sfb
[i
][m
]; /* f is negative gradient, thus the sign */
1374 /* Sum the gradient along the line across CPUs */
1377 gmx_sumd(1, &gpb
, cr
);
1382 fprintf(debug
, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
1383 s_a
->epot
, s_b
->epot
, s_c
->epot
, gpb
);
1386 epot_repl
= s_b
->epot
;
1388 /* Keep one of the intervals based on the value of the derivative at the new point */
1391 /* Replace c endpoint with b */
1392 swap_em_state(&s_b
, &s_c
);
1398 /* Replace a endpoint with b */
1399 swap_em_state(&s_b
, &s_a
);
1405 * Stop search as soon as we find a value smaller than the endpoints.
1406 * Never run more than 20 steps, no matter what.
1410 while ((epot_repl
> s_a
->epot
|| epot_repl
> s_c
->epot
) &&
1413 if (fabs(epot_repl
- s_min
->epot
) < fabs(s_min
->epot
)*GMX_REAL_EPS
||
1416 /* OK. We couldn't find a significantly lower energy.
1417 * If beta==0 this was steepest descent, and then we give up.
1418 * If not, set beta=0 and restart with steepest descent before quitting.
1428 /* Reset memory before giving up */
1434 /* Select min energy state of A & C, put the best in B.
1436 if (s_c
->epot
< s_a
->epot
)
1440 fprintf(debug
, "CGE: C (%f) is lower than A (%f), moving C to B\n",
1441 s_c
->epot
, s_a
->epot
);
1443 swap_em_state(&s_b
, &s_c
);
1450 fprintf(debug
, "CGE: A (%f) is lower than C (%f), moving A to B\n",
1451 s_a
->epot
, s_c
->epot
);
1453 swap_em_state(&s_b
, &s_a
);
1462 fprintf(debug
, "CGE: Found a lower energy %f, moving C to B\n",
1465 swap_em_state(&s_b
, &s_c
);
1469 /* new search direction */
1470 /* beta = 0 means forget all memory and restart with steepest descents. */
1471 if (nstcg
&& ((step
% nstcg
) == 0))
1477 /* s_min->fnorm cannot be zero, because then we would have converged
1481 /* Polak-Ribiere update.
1482 * Change to fnorm2/fnorm2_old for Fletcher-Reeves
1484 beta
= pr_beta(cr
, &inputrec
->opts
, mdatoms
, top_global
, s_min
, s_b
);
1486 /* Limit beta to prevent oscillations */
1487 if (fabs(beta
) > 5.0)
1493 /* update positions */
1494 swap_em_state(&s_min
, &s_b
);
1497 /* Print it if necessary */
1502 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1503 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
1504 step
, s_min
->epot
, s_min
->fnorm
/sqrtNumAtoms
,
1505 s_min
->fmax
, s_min
->a_fmax
+1);
1508 /* Store the new (lower) energies */
1509 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1510 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1511 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1513 do_log
= do_per_step(step
, inputrec
->nstlog
);
1514 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
1516 /* Prepare IMD energy record, if bIMD is TRUE. */
1517 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, step
, TRUE
);
1521 print_ebin_header(fplog
, step
, step
);
1523 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
1524 do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
1525 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1528 /* Send energies and positions to the IMD client if bIMD is TRUE. */
1529 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state_global
->box
, as_rvec_array(state_global
->x
.data()), inputrec
, 0, wcycle
) && MASTER(cr
))
1531 IMD_send_positions(inputrec
->imd
);
1534 /* Stop when the maximum force lies below tolerance.
1535 * If we have reached machine precision, converged is already set to true.
1537 converged
= converged
|| (s_min
->fmax
< inputrec
->em_tol
);
1539 } /* End of the loop */
1541 /* IMD cleanup, if bIMD is TRUE. */
1542 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
1546 step
--; /* we never took that last step in this case */
1549 if (s_min
->fmax
> inputrec
->em_tol
)
1553 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1554 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1561 /* If we printed energy and/or logfile last step (which was the last step)
1562 * we don't have to do it again, but otherwise print the final values.
1566 /* Write final value to log since we didn't do anything the last step */
1567 print_ebin_header(fplog
, step
, step
);
1569 if (!do_ene
|| !do_log
)
1571 /* Write final energy file entries */
1572 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
1573 !do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
1574 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1578 /* Print some stuff... */
1581 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
1585 * For accurate normal mode calculation it is imperative that we
1586 * store the last conformation into the full precision binary trajectory.
1588 * However, we should only do it if we did NOT already write this step
1589 * above (which we did if do_x or do_f was true).
1591 do_x
= !do_per_step(step
, inputrec
->nstxout
);
1592 do_f
= (inputrec
->nstfout
> 0 && !do_per_step(step
, inputrec
->nstfout
));
1594 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
1595 top_global
, inputrec
, step
,
1596 s_min
, state_global
, observablesHistory
);
1601 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1602 print_converged(stderr
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1603 s_min
, sqrtNumAtoms
);
1604 print_converged(fplog
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1605 s_min
, sqrtNumAtoms
);
1607 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
1610 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
1612 /* To print the actual number of steps we needed somewhere */
1613 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
1616 } /* That's all folks */
1619 /*! \brief Do L-BFGS conjugate gradients minimization
1620 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
1621 int nfile, const t_filenm fnm[],
1622 const gmx_output_env_t *oenv, gmx_bool bVerbose,
1624 gmx_vsite_t *vsite, gmx_constr_t constr,
1626 gmx::IMDOutputProvider *outputProvider,
1627 t_inputrec *inputrec,
1628 gmx_mtop_t *top_global, t_fcdata *fcd,
1629 t_state *state_global,
1631 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
1634 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
1635 gmx_membed_t gmx_unused *membed,
1636 real cpt_period, real max_hours,
1638 unsigned long Flags,
1639 gmx_walltime_accounting_t walltime_accounting)
1641 double do_lbfgs(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
1642 int nfile
, const t_filenm fnm
[],
1643 const gmx_output_env_t gmx_unused
*oenv
, gmx_bool bVerbose
,
1644 int gmx_unused nstglobalcomm
,
1645 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
1646 int gmx_unused stepout
,
1647 gmx::IMDOutputProvider
*outputProvider
,
1648 t_inputrec
*inputrec
,
1649 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
1650 t_state
*state_global
,
1651 ObservablesHistory
*observablesHistory
,
1653 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1654 gmx_edsam_t gmx_unused ed
,
1656 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
1657 gmx_membed_t gmx_unused
*membed
,
1658 real gmx_unused cpt_period
, real gmx_unused max_hours
,
1660 unsigned long gmx_unused Flags
,
1661 gmx_walltime_accounting_t walltime_accounting
)
1663 static const char *LBFGS
= "Low-Memory BFGS Minimizer";
1665 gmx_localtop_t
*top
;
1666 gmx_enerdata_t
*enerd
;
1667 gmx_global_stat_t gstat
;
1669 int ncorr
, nmaxcorr
, point
, cp
, neval
, nminstep
;
1670 double stepsize
, step_taken
, gpa
, gpb
, gpc
, tmp
, minstep
;
1671 real
*rho
, *alpha
, *p
, *s
, **dx
, **dg
;
1672 real a
, b
, c
, maxdelta
, delta
;
1674 real dgdx
, dgdg
, sq
, yr
, beta
;
1678 gmx_bool do_log
, do_ene
, do_x
, do_f
, foundlower
, *frozen
;
1680 int start
, end
, number_steps
;
1682 int i
, k
, m
, n
, gf
, step
;
1687 gmx_fatal(FARGS
, "Cannot do parallel L-BFGS Minimization - yet.\n");
1690 if (nullptr != constr
)
1692 gmx_fatal(FARGS
, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
1695 n
= 3*state_global
->natoms
;
1696 nmaxcorr
= inputrec
->nbfgscorr
;
1701 snew(rho
, nmaxcorr
);
1702 snew(alpha
, nmaxcorr
);
1705 for (i
= 0; i
< nmaxcorr
; i
++)
1711 for (i
= 0; i
< nmaxcorr
; i
++)
1720 init_em(fplog
, LBFGS
, cr
, outputProvider
, inputrec
,
1721 state_global
, top_global
, &ems
, &top
,
1722 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
,
1723 vsite
, constr
, nullptr,
1724 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
1727 end
= mdatoms
->homenr
;
1729 /* We need 4 working states */
1730 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1731 em_state_t
*sa
= &s0
;
1732 em_state_t
*sb
= &s1
;
1733 em_state_t
*sc
= &s2
;
1734 em_state_t
*last
= &s3
;
1735 /* Initialize by copying the state from ems (we could skip x and f here) */
1740 /* Print to log file */
1741 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, LBFGS
);
1743 do_log
= do_ene
= do_x
= do_f
= TRUE
;
1745 /* Max number of steps */
1746 number_steps
= inputrec
->nsteps
;
1748 /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
1750 for (i
= start
; i
< end
; i
++)
1752 if (mdatoms
->cFREEZE
)
1754 gf
= mdatoms
->cFREEZE
[i
];
1756 for (m
= 0; m
< DIM
; m
++)
1758 frozen
[3*i
+m
] = inputrec
->opts
.nFreeze
[gf
][m
];
1763 sp_header(stderr
, LBFGS
, inputrec
->em_tol
, number_steps
);
1767 sp_header(fplog
, LBFGS
, inputrec
->em_tol
, number_steps
);
1772 construct_vsites(vsite
, as_rvec_array(state_global
->x
.data()), 1, nullptr,
1773 top
->idef
.iparams
, top
->idef
.il
,
1774 fr
->ePBC
, fr
->bMolPBC
, cr
, state_global
->box
);
1777 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1778 /* do_force always puts the charge groups in the box and shifts again
1779 * We do not unshift, so molecules are always whole
1782 evaluate_energy(fplog
, cr
,
1783 top_global
, &ems
, top
,
1784 inputrec
, nrnb
, wcycle
, gstat
,
1785 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1786 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1791 /* Copy stuff to the energy bin for easy printing etc. */
1792 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1793 mdatoms
->tmass
, enerd
, state_global
, inputrec
->fepvals
, inputrec
->expandedvals
, state_global
->box
,
1794 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1796 print_ebin_header(fplog
, step
, step
);
1797 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1798 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1802 /* Set the initial step.
1803 * since it will be multiplied by the non-normalized search direction
1804 * vector (force vector the first time), we scale it by the
1805 * norm of the force.
1810 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1811 fprintf(stderr
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1812 fprintf(stderr
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1813 fprintf(stderr
, " F-Norm = %12.5e\n", ems
.fnorm
/sqrtNumAtoms
);
1814 fprintf(stderr
, "\n");
1815 /* and copy to the log file too... */
1816 fprintf(fplog
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1817 fprintf(fplog
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1818 fprintf(fplog
, " F-Norm = %12.5e\n", ems
.fnorm
/sqrtNumAtoms
);
1819 fprintf(fplog
, "\n");
1822 // Point is an index to the memory of search directions, where 0 is the first one.
1825 // Set initial search direction to the force (-gradient), or 0 for frozen particles.
1826 real
*fInit
= static_cast<real
*>(as_rvec_array(ems
.f
.data())[0]);
1827 for (i
= 0; i
< n
; i
++)
1831 dx
[point
][i
] = fInit
[i
]; /* Initial search direction */
1839 // Stepsize will be modified during the search, and actually it is not critical
1840 // (the main efficiency in the algorithm comes from changing directions), but
1841 // we still need an initial value, so estimate it as the inverse of the norm
1842 // so we take small steps where the potential fluctuates a lot.
1843 stepsize
= 1.0/ems
.fnorm
;
1845 /* Start the loop over BFGS steps.
1846 * Each successful step is counted, and we continue until
1847 * we either converge or reach the max number of steps.
1852 /* Set the gradient from the force */
1854 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1857 /* Write coordinates if necessary */
1858 do_x
= do_per_step(step
, inputrec
->nstxout
);
1859 do_f
= do_per_step(step
, inputrec
->nstfout
);
1864 mdof_flags
|= MDOF_X
;
1869 mdof_flags
|= MDOF_F
;
1874 mdof_flags
|= MDOF_IMD
;
1877 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
1878 top_global
, step
, (real
)step
, &ems
.s
, state_global
, observablesHistory
, &ems
.f
);
1880 /* Do the linesearching in the direction dx[point][0..(n-1)] */
1882 /* make s a pointer to current search direction - point=0 first time we get here */
1885 real
*xx
= static_cast<real
*>(as_rvec_array(ems
.s
.x
.data())[0]);
1886 real
*ff
= static_cast<real
*>(as_rvec_array(ems
.f
.data())[0]);
1888 // calculate line gradient in position A
1889 for (gpa
= 0, i
= 0; i
< n
; i
++)
1894 /* Calculate minimum allowed stepsize along the line, before the average (norm)
1895 * relative change in coordinate is smaller than precision
1897 for (minstep
= 0, i
= 0; i
< n
; i
++)
1907 minstep
= GMX_REAL_EPS
/sqrt(minstep
/n
);
1909 if (stepsize
< minstep
)
1915 // Before taking any steps along the line, store the old position
1917 real
*lastx
= static_cast<real
*>(as_rvec_array(last
->s
.x
.data())[0]);
1918 real
*lastf
= static_cast<real
*>(as_rvec_array(last
->f
.data())[0]);
1923 /* Take a step downhill.
1924 * In theory, we should find the actual minimum of the function in this
1925 * direction, somewhere along the line.
1926 * That is quite possible, but it turns out to take 5-10 function evaluations
1927 * for each line. However, we dont really need to find the exact minimum -
1928 * it is much better to start a new BFGS step in a modified direction as soon
1929 * as we are close to it. This will save a lot of energy evaluations.
1931 * In practice, we just try to take a single step.
1932 * If it worked (i.e. lowered the energy), we increase the stepsize but
1933 * continue straight to the next BFGS step without trying to find any minimum,
1934 * i.e. we change the search direction too. If the line was smooth, it is
1935 * likely we are in a smooth region, and then it makes sense to take longer
1936 * steps in the modified search direction too.
1938 * If it didn't work (higher energy), there must be a minimum somewhere between
1939 * the old position and the new one. Then we need to start by finding a lower
1940 * value before we change search direction. Since the energy was apparently
1941 * quite rough, we need to decrease the step size.
1943 * Due to the finite numerical accuracy, it turns out that it is a good idea
1944 * to accept a SMALL increase in energy, if the derivative is still downhill.
1945 * This leads to lower final energies in the tests I've done. / Erik
1948 // State "A" is the first position along the line.
1949 // reference position along line is initially zero
1952 // Check stepsize first. We do not allow displacements
1953 // larger than emstep.
1957 // Pick a new position C by adding stepsize to A.
1960 // Calculate what the largest change in any individual coordinate
1961 // would be (translation along line * gradient along line)
1963 for (i
= 0; i
< n
; i
++)
1966 if (delta
> maxdelta
)
1971 // If any displacement is larger than the stepsize limit, reduce the step
1972 if (maxdelta
> inputrec
->em_stepsize
)
1977 while (maxdelta
> inputrec
->em_stepsize
);
1979 // Take a trial step and move the coordinate array xc[] to position C
1980 real
*xc
= static_cast<real
*>(as_rvec_array(sc
->s
.x
.data())[0]);
1981 for (i
= 0; i
< n
; i
++)
1983 xc
[i
] = lastx
[i
] + c
*s
[i
];
1987 // Calculate energy for the trial step in position C
1988 evaluate_energy(fplog
, cr
,
1989 top_global
, sc
, top
,
1990 inputrec
, nrnb
, wcycle
, gstat
,
1991 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1992 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
1994 // Calc line gradient in position C
1995 real
*fc
= static_cast<real
*>(as_rvec_array(sc
->f
.data())[0]);
1996 for (gpc
= 0, i
= 0; i
< n
; i
++)
1998 gpc
-= s
[i
]*fc
[i
]; /* f is negative gradient, thus the sign */
2000 /* Sum the gradient along the line across CPUs */
2003 gmx_sumd(1, &gpc
, cr
);
2006 // This is the max amount of increase in energy we tolerate.
2007 // By allowing VERY small changes (close to numerical precision) we
2008 // frequently find even better (lower) final energies.
2009 tmp
= sqrt(GMX_REAL_EPS
)*fabs(sa
->epot
);
2011 // Accept the step if the energy is lower in the new position C (compared to A),
2012 // or if it is not significantly higher and the line derivative is still negative.
2013 if (sc
->epot
< sa
->epot
|| (gpc
< 0 && sc
->epot
< (sa
->epot
+ tmp
)))
2015 // Great, we found a better energy. We no longer try to alter the
2016 // stepsize, but simply accept this new better position. The we select a new
2017 // search direction instead, which will be much more efficient than continuing
2018 // to take smaller steps along a line. Set fnorm based on the new C position,
2019 // which will be used to update the stepsize to 1/fnorm further down.
2024 // If we got here, the energy is NOT lower in point C, i.e. it will be the same
2025 // or higher than in point A. In this case it is pointless to move to point C,
2026 // so we will have to do more iterations along the same line to find a smaller
2027 // value in the interval [A=0.0,C].
2028 // Here, A is still 0.0, but that will change when we do a search in the interval
2029 // [0.0,C] below. That search we will do by interpolation or bisection rather
2030 // than with the stepsize, so no need to modify it. For the next search direction
2031 // it will be reset to 1/fnorm anyway.
2037 // OK, if we didn't find a lower value we will have to locate one now - there must
2038 // be one in the interval [a,c].
2039 // The same thing is valid here, though: Don't spend dozens of iterations to find
2040 // the line minimum. We try to interpolate based on the derivative at the endpoints,
2041 // and only continue until we find a lower value. In most cases this means 1-2 iterations.
2042 // I also have a safeguard for potentially really pathological functions so we never
2043 // take more than 20 steps before we give up.
2044 // If we already found a lower value we just skip this step and continue to the update.
2049 // Select a new trial point B in the interval [A,C].
2050 // If the derivatives at points a & c have different sign we interpolate to zero,
2051 // otherwise just do a bisection since there might be multiple minima/maxima
2052 // inside the interval.
2053 if (gpa
< 0 && gpc
> 0)
2055 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
2062 /* safeguard if interpolation close to machine accuracy causes errors:
2063 * never go outside the interval
2065 if (b
<= a
|| b
>= c
)
2070 // Take a trial step to point B
2071 real
*xb
= static_cast<real
*>(as_rvec_array(sb
->s
.x
.data())[0]);
2072 for (i
= 0; i
< n
; i
++)
2074 xb
[i
] = lastx
[i
] + b
*s
[i
];
2078 // Calculate energy for the trial step in point B
2079 evaluate_energy(fplog
, cr
,
2080 top_global
, sb
, top
,
2081 inputrec
, nrnb
, wcycle
, gstat
,
2082 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2083 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
2086 // Calculate gradient in point B
2087 real
*fb
= static_cast<real
*>(as_rvec_array(sb
->f
.data())[0]);
2088 for (gpb
= 0, i
= 0; i
< n
; i
++)
2090 gpb
-= s
[i
]*fb
[i
]; /* f is negative gradient, thus the sign */
2093 /* Sum the gradient along the line across CPUs */
2096 gmx_sumd(1, &gpb
, cr
);
2099 // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
2100 // at the new point B, and rename the endpoints of this new interval A and C.
2103 /* Replace c endpoint with b */
2105 /* swap states b and c */
2106 swap_em_state(&sb
, &sc
);
2110 /* Replace a endpoint with b */
2112 /* swap states a and b */
2113 swap_em_state(&sa
, &sb
);
2117 * Stop search as soon as we find a value smaller than the endpoints,
2118 * or if the tolerance is below machine precision.
2119 * Never run more than 20 steps, no matter what.
2123 while ((sb
->epot
> sa
->epot
|| sb
->epot
> sc
->epot
) && (nminstep
< 20));
2125 if (fabs(sb
->epot
- Epot0
) < GMX_REAL_EPS
|| nminstep
>= 20)
2127 /* OK. We couldn't find a significantly lower energy.
2128 * If ncorr==0 this was steepest descent, and then we give up.
2129 * If not, reset memory to restart as steepest descent before quitting.
2141 /* Search in gradient direction */
2142 for (i
= 0; i
< n
; i
++)
2144 dx
[point
][i
] = ff
[i
];
2146 /* Reset stepsize */
2147 stepsize
= 1.0/fnorm
;
2152 /* Select min energy state of A & C, put the best in xx/ff/Epot
2154 if (sc
->epot
< sa
->epot
)
2176 /* Update the memory information, and calculate a new
2177 * approximation of the inverse hessian
2180 /* Have new data in Epot, xx, ff */
2181 if (ncorr
< nmaxcorr
)
2186 for (i
= 0; i
< n
; i
++)
2188 dg
[point
][i
] = lastf
[i
]-ff
[i
];
2189 dx
[point
][i
] *= step_taken
;
2194 for (i
= 0; i
< n
; i
++)
2196 dgdg
+= dg
[point
][i
]*dg
[point
][i
];
2197 dgdx
+= dg
[point
][i
]*dx
[point
][i
];
2202 rho
[point
] = 1.0/dgdx
;
2205 if (point
>= nmaxcorr
)
2211 for (i
= 0; i
< n
; i
++)
2218 /* Recursive update. First go back over the memory points */
2219 for (k
= 0; k
< ncorr
; k
++)
2228 for (i
= 0; i
< n
; i
++)
2230 sq
+= dx
[cp
][i
]*p
[i
];
2233 alpha
[cp
] = rho
[cp
]*sq
;
2235 for (i
= 0; i
< n
; i
++)
2237 p
[i
] -= alpha
[cp
]*dg
[cp
][i
];
2241 for (i
= 0; i
< n
; i
++)
2246 /* And then go forward again */
2247 for (k
= 0; k
< ncorr
; k
++)
2250 for (i
= 0; i
< n
; i
++)
2252 yr
+= p
[i
]*dg
[cp
][i
];
2256 beta
= alpha
[cp
]-beta
;
2258 for (i
= 0; i
< n
; i
++)
2260 p
[i
] += beta
*dx
[cp
][i
];
2270 for (i
= 0; i
< n
; i
++)
2274 dx
[point
][i
] = p
[i
];
2282 /* Print it if necessary */
2287 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2288 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
2289 step
, ems
.epot
, ems
.fnorm
/sqrtNumAtoms
, ems
.fmax
, ems
.a_fmax
+ 1);
2292 /* Store the new (lower) energies */
2293 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
2294 mdatoms
->tmass
, enerd
, state_global
, inputrec
->fepvals
, inputrec
->expandedvals
, state_global
->box
,
2295 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2296 do_log
= do_per_step(step
, inputrec
->nstlog
);
2297 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
2300 print_ebin_header(fplog
, step
, step
);
2302 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
2303 do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
2304 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2307 /* Send x and E to IMD client, if bIMD is TRUE. */
2308 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state_global
->box
, as_rvec_array(state_global
->x
.data()), inputrec
, 0, wcycle
) && MASTER(cr
))
2310 IMD_send_positions(inputrec
->imd
);
2313 // Reset stepsize in we are doing more iterations
2314 stepsize
= 1.0/ems
.fnorm
;
2316 /* Stop when the maximum force lies below tolerance.
2317 * If we have reached machine precision, converged is already set to true.
2319 converged
= converged
|| (ems
.fmax
< inputrec
->em_tol
);
2321 } /* End of the loop */
2323 /* IMD cleanup, if bIMD is TRUE. */
2324 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2328 step
--; /* we never took that last step in this case */
2331 if (ems
.fmax
> inputrec
->em_tol
)
2335 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2336 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2341 /* If we printed energy and/or logfile last step (which was the last step)
2342 * we don't have to do it again, but otherwise print the final values.
2344 if (!do_log
) /* Write final value to log since we didn't do anythin last step */
2346 print_ebin_header(fplog
, step
, step
);
2348 if (!do_ene
|| !do_log
) /* Write final energy file entries */
2350 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
2351 !do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
2352 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2355 /* Print some stuff... */
2358 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2362 * For accurate normal mode calculation it is imperative that we
2363 * store the last conformation into the full precision binary trajectory.
2365 * However, we should only do it if we did NOT already write this step
2366 * above (which we did if do_x or do_f was true).
2368 do_x
= !do_per_step(step
, inputrec
->nstxout
);
2369 do_f
= !do_per_step(step
, inputrec
->nstfout
);
2370 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
2371 top_global
, inputrec
, step
,
2372 &ems
, state_global
, observablesHistory
);
2376 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2377 print_converged(stderr
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2378 number_steps
, &ems
, sqrtNumAtoms
);
2379 print_converged(fplog
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2380 number_steps
, &ems
, sqrtNumAtoms
);
2382 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
2385 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2387 /* To print the actual number of steps we needed somewhere */
2388 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
2391 } /* That's all folks */
2393 /*! \brief Do steepest descents minimization
2394 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
2395 int nfile, const t_filenm fnm[],
2396 const gmx_output_env_t *oenv, gmx_bool bVerbose,
2398 gmx_vsite_t *vsite, gmx_constr_t constr,
2400 gmx::IMDOutputProvider *outputProvider,
2401 t_inputrec *inputrec,
2402 gmx_mtop_t *top_global, t_fcdata *fcd,
2403 t_state *state_global,
2405 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2408 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
2409 real cpt_period, real max_hours,
2411 unsigned long Flags,
2412 gmx_walltime_accounting_t walltime_accounting)
2414 double do_steep(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
2415 int nfile
, const t_filenm fnm
[],
2416 const gmx_output_env_t gmx_unused
*oenv
, gmx_bool bVerbose
,
2417 int gmx_unused nstglobalcomm
,
2418 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2419 int gmx_unused stepout
,
2420 gmx::IMDOutputProvider
*outputProvider
,
2421 t_inputrec
*inputrec
,
2422 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2423 t_state
*state_global
,
2424 ObservablesHistory
*observablesHistory
,
2426 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2427 gmx_edsam_t gmx_unused ed
,
2429 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
2430 gmx_membed_t gmx_unused
*membed
,
2431 real gmx_unused cpt_period
, real gmx_unused max_hours
,
2433 unsigned long gmx_unused Flags
,
2434 gmx_walltime_accounting_t walltime_accounting
)
2436 const char *SD
= "Steepest Descents";
2437 gmx_localtop_t
*top
;
2438 gmx_enerdata_t
*enerd
;
2439 gmx_global_stat_t gstat
;
2445 gmx_bool bDone
, bAbort
, do_x
, do_f
;
2450 int steps_accepted
= 0;
2452 /* Create 2 states on the stack and extract pointers that we will swap */
2453 em_state_t s0
{}, s1
{};
2454 em_state_t
*s_min
= &s0
;
2455 em_state_t
*s_try
= &s1
;
2457 /* Init em and store the local state in s_try */
2458 init_em(fplog
, SD
, cr
, outputProvider
, inputrec
,
2459 state_global
, top_global
, s_try
, &top
,
2460 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
,
2461 vsite
, constr
, nullptr,
2462 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
2464 /* Print to log file */
2465 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, SD
);
2467 /* Set variables for stepsize (in nm). This is the largest
2468 * step that we are going to make in any direction.
2470 ustep
= inputrec
->em_stepsize
;
2473 /* Max number of steps */
2474 nsteps
= inputrec
->nsteps
;
2478 /* Print to the screen */
2479 sp_header(stderr
, SD
, inputrec
->em_tol
, nsteps
);
2483 sp_header(fplog
, SD
, inputrec
->em_tol
, nsteps
);
2486 /**** HERE STARTS THE LOOP ****
2487 * count is the counter for the number of steps
2488 * bDone will be TRUE when the minimization has converged
2489 * bAbort will be TRUE when nsteps steps have been performed or when
2490 * the stepsize becomes smaller than is reasonable for machine precision
2495 while (!bDone
&& !bAbort
)
2497 bAbort
= (nsteps
>= 0) && (count
== nsteps
);
2499 /* set new coordinates, except for first step */
2500 bool validStep
= true;
2504 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
,
2505 s_min
, stepsize
, &s_min
->f
, s_try
,
2506 constr
, top
, nrnb
, wcycle
, count
);
2511 evaluate_energy(fplog
, cr
,
2512 top_global
, s_try
, top
,
2513 inputrec
, nrnb
, wcycle
, gstat
,
2514 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2515 mu_tot
, enerd
, vir
, pres
, count
, count
== 0);
2519 // Signal constraint error during stepping with energy=inf
2520 s_try
->epot
= std::numeric_limits
<real
>::infinity();
2525 print_ebin_header(fplog
, count
, count
);
2530 s_min
->epot
= s_try
->epot
;
2533 /* Print it if necessary */
2538 fprintf(stderr
, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
2539 count
, ustep
, s_try
->epot
, s_try
->fmax
, s_try
->a_fmax
+1,
2540 ( (count
== 0) || (s_try
->epot
< s_min
->epot
) ) ? '\n' : '\r');
2544 if ( (count
== 0) || (s_try
->epot
< s_min
->epot
) )
2546 /* Store the new (lower) energies */
2547 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)count
,
2548 mdatoms
->tmass
, enerd
, &s_try
->s
, inputrec
->fepvals
, inputrec
->expandedvals
,
2549 s_try
->s
.box
, nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2551 /* Prepare IMD energy record, if bIMD is TRUE. */
2552 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, count
, TRUE
);
2554 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
,
2555 do_per_step(steps_accepted
, inputrec
->nstdisreout
),
2556 do_per_step(steps_accepted
, inputrec
->nstorireout
),
2557 fplog
, count
, count
, eprNORMAL
,
2558 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2563 /* Now if the new energy is smaller than the previous...
2564 * or if this is the first step!
2565 * or if we did random steps!
2568 if ( (count
== 0) || (s_try
->epot
< s_min
->epot
) )
2572 /* Test whether the convergence criterion is met... */
2573 bDone
= (s_try
->fmax
< inputrec
->em_tol
);
2575 /* Copy the arrays for force, positions and energy */
2576 /* The 'Min' array always holds the coords and forces of the minimal
2578 swap_em_state(&s_min
, &s_try
);
2584 /* Write to trn, if necessary */
2585 do_x
= do_per_step(steps_accepted
, inputrec
->nstxout
);
2586 do_f
= do_per_step(steps_accepted
, inputrec
->nstfout
);
2587 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr,
2588 top_global
, inputrec
, count
,
2589 s_min
, state_global
, observablesHistory
);
2593 /* If energy is not smaller make the step smaller... */
2596 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
2598 /* Reload the old state */
2599 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
2600 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
2605 /* Determine new step */
2606 stepsize
= ustep
/s_min
->fmax
;
2608 /* Check if stepsize is too small, with 1 nm as a characteristic length */
2610 if (count
== nsteps
|| ustep
< 1e-12)
2612 if (count
== nsteps
|| ustep
< 1e-6)
2617 warn_step(stderr
, inputrec
->em_tol
, count
== nsteps
, constr
!= nullptr);
2618 warn_step(fplog
, inputrec
->em_tol
, count
== nsteps
, constr
!= nullptr);
2623 /* Send IMD energies and positions, if bIMD is TRUE. */
2624 if (do_IMD(inputrec
->bIMD
, count
, cr
, TRUE
, state_global
->box
, as_rvec_array(state_global
->x
.data()), inputrec
, 0, wcycle
) && MASTER(cr
))
2626 IMD_send_positions(inputrec
->imd
);
2630 } /* End of the loop */
2632 /* IMD cleanup, if bIMD is TRUE. */
2633 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2635 /* Print some data... */
2638 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2640 write_em_traj(fplog
, cr
, outf
, TRUE
, inputrec
->nstfout
, ftp2fn(efSTO
, nfile
, fnm
),
2641 top_global
, inputrec
, count
,
2642 s_min
, state_global
, observablesHistory
);
2646 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2648 print_converged(stderr
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2649 s_min
, sqrtNumAtoms
);
2650 print_converged(fplog
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2651 s_min
, sqrtNumAtoms
);
2654 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2656 /* To print the actual number of steps we needed somewhere */
2657 inputrec
->nsteps
= count
;
2659 walltime_accounting_set_nsteps_done(walltime_accounting
, count
);
2662 } /* That's all folks */
2664 /*! \brief Do normal modes analysis
2665 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
2666 int nfile, const t_filenm fnm[],
2667 const gmx_output_env_t *oenv, gmx_bool bVerbose,
2669 gmx_vsite_t *vsite, gmx_constr_t constr,
2671 gmx::IMDOutputProvider *outputProvider,
2672 t_inputrec *inputrec,
2673 gmx_mtop_t *top_global, t_fcdata *fcd,
2674 t_state *state_global,
2676 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2679 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
2680 real cpt_period, real max_hours,
2682 unsigned long Flags,
2683 gmx_walltime_accounting_t walltime_accounting)
2685 double do_nm(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger
&mdlog
,
2686 int nfile
, const t_filenm fnm
[],
2687 const gmx_output_env_t gmx_unused
*oenv
, gmx_bool bVerbose
,
2688 int gmx_unused nstglobalcomm
,
2689 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2690 int gmx_unused stepout
,
2691 gmx::IMDOutputProvider
*outputProvider
,
2692 t_inputrec
*inputrec
,
2693 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2694 t_state
*state_global
,
2695 ObservablesHistory gmx_unused
*observablesHistory
,
2697 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2698 gmx_edsam_t gmx_unused ed
,
2700 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
2701 gmx_membed_t gmx_unused
*membed
,
2702 real gmx_unused cpt_period
, real gmx_unused max_hours
,
2704 unsigned long gmx_unused Flags
,
2705 gmx_walltime_accounting_t walltime_accounting
)
2707 const char *NM
= "Normal Mode Analysis";
2710 gmx_localtop_t
*top
;
2711 gmx_enerdata_t
*enerd
;
2712 gmx_global_stat_t gstat
;
2717 gmx_bool bSparse
; /* use sparse matrix storage format */
2719 gmx_sparsematrix_t
* sparse_matrix
= nullptr;
2720 real
* full_matrix
= nullptr;
2722 /* added with respect to mdrun */
2724 real der_range
= 10.0*sqrt(GMX_REAL_EPS
);
2726 bool bIsMaster
= MASTER(cr
);
2728 if (constr
!= nullptr)
2730 gmx_fatal(FARGS
, "Constraints present with Normal Mode Analysis, this combination is not supported");
2733 gmx_shellfc_t
*shellfc
;
2735 em_state_t state_work
{};
2737 /* Init em and store the local state in state_minimum */
2738 init_em(fplog
, NM
, cr
, outputProvider
, inputrec
,
2739 state_global
, top_global
, &state_work
, &top
,
2740 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
,
2741 vsite
, constr
, &shellfc
,
2742 nfile
, fnm
, &outf
, nullptr, imdport
, Flags
, wcycle
);
2744 std::vector
<size_t> atom_index
= get_atom_index(top_global
);
2745 snew(fneg
, atom_index
.size());
2746 snew(dfdx
, atom_index
.size());
2752 "NOTE: This version of GROMACS has been compiled in single precision,\n"
2753 " which MIGHT not be accurate enough for normal mode analysis.\n"
2754 " GROMACS now uses sparse matrix storage, so the memory requirements\n"
2755 " are fairly modest even if you recompile in double precision.\n\n");
2759 /* Check if we can/should use sparse storage format.
2761 * Sparse format is only useful when the Hessian itself is sparse, which it
2762 * will be when we use a cutoff.
2763 * For small systems (n<1000) it is easier to always use full matrix format, though.
2765 if (EEL_FULL(fr
->eeltype
) || fr
->rlist
== 0.0)
2767 GMX_LOG(mdlog
.warning
).appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
2770 else if (atom_index
.size() < 1000)
2772 GMX_LOG(mdlog
.warning
).appendTextFormatted("Small system size (N=%d), using full Hessian format.",
2778 GMX_LOG(mdlog
.warning
).appendText("Using compressed symmetric sparse Hessian format.");
2782 /* Number of dimensions, based on real atoms, that is not vsites or shell */
2783 sz
= DIM
*atom_index
.size();
2785 fprintf(stderr
, "Allocating Hessian memory...\n\n");
2789 sparse_matrix
= gmx_sparsematrix_init(sz
);
2790 sparse_matrix
->compressed_symmetric
= TRUE
;
2794 snew(full_matrix
, sz
*sz
);
2801 /* Write start time and temperature */
2802 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, NM
);
2804 /* fudge nr of steps to nr of atoms */
2805 inputrec
->nsteps
= atom_index
.size()*2;
2809 fprintf(stderr
, "starting normal mode calculation '%s'\n%d steps.\n\n",
2810 *(top_global
->name
), (int)inputrec
->nsteps
);
2813 nnodes
= cr
->nnodes
;
2815 /* Make evaluate_energy do a single node force calculation */
2817 evaluate_energy(fplog
, cr
,
2818 top_global
, &state_work
, top
,
2819 inputrec
, nrnb
, wcycle
, gstat
,
2820 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2821 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
2822 cr
->nnodes
= nnodes
;
2824 /* if forces are not small, warn user */
2825 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, &state_work
);
2827 GMX_LOG(mdlog
.warning
).appendTextFormatted("Maximum force:%12.5e", state_work
.fmax
);
2828 if (state_work
.fmax
> 1.0e-3)
2830 GMX_LOG(mdlog
.warning
).appendText(
2831 "The force is probably not small enough to "
2832 "ensure that you are at a minimum.\n"
2833 "Be aware that negative eigenvalues may occur\n"
2834 "when the resulting matrix is diagonalized.");
2837 /***********************************************************
2839 * Loop over all pairs in matrix
2841 * do_force called twice. Once with positive and
2842 * once with negative displacement
2844 ************************************************************/
2846 /* Steps are divided one by one over the nodes */
2848 for (unsigned int aid
= cr
->nodeid
; aid
< atom_index
.size(); aid
+= nnodes
)
2850 size_t atom
= atom_index
[aid
];
2851 for (size_t d
= 0; d
< DIM
; d
++)
2853 gmx_bool bBornRadii
= FALSE
;
2854 gmx_int64_t step
= 0;
2855 int force_flags
= GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
;
2858 x_min
= state_work
.s
.x
[atom
][d
];
2860 for (unsigned int dx
= 0; (dx
< 2); dx
++)
2864 state_work
.s
.x
[atom
][d
] = x_min
- der_range
;
2868 state_work
.s
.x
[atom
][d
] = x_min
+ der_range
;
2871 /* Make evaluate_energy do a single node force calculation */
2875 /* Now is the time to relax the shells */
2876 (void) relax_shell_flexcon(fplog
, cr
, bVerbose
, step
,
2877 inputrec
, bNS
, force_flags
,
2880 &state_work
.s
, &state_work
.f
, vir
, mdatoms
,
2881 nrnb
, wcycle
, graph
, &top_global
->groups
,
2882 shellfc
, fr
, bBornRadii
, t
, mu_tot
,
2889 evaluate_energy(fplog
, cr
,
2890 top_global
, &state_work
, top
,
2891 inputrec
, nrnb
, wcycle
, gstat
,
2892 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2893 mu_tot
, enerd
, vir
, pres
, atom
*2+dx
, FALSE
);
2896 cr
->nnodes
= nnodes
;
2900 for (size_t i
= 0; i
< atom_index
.size(); i
++)
2902 copy_rvec(state_work
.f
[atom_index
[i
]], fneg
[i
]);
2907 /* x is restored to original */
2908 state_work
.s
.x
[atom
][d
] = x_min
;
2910 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2912 for (size_t k
= 0; (k
< DIM
); k
++)
2915 -(state_work
.f
[atom_index
[j
]][k
] - fneg
[j
][k
])/(2*der_range
);
2922 #define mpi_type GMX_MPI_REAL
2923 MPI_Send(dfdx
[0], atom_index
.size()*DIM
, mpi_type
, MASTER(cr
),
2924 cr
->nodeid
, cr
->mpi_comm_mygroup
);
2929 for (node
= 0; (node
< nnodes
&& atom
+node
< atom_index
.size()); node
++)
2935 MPI_Recv(dfdx
[0], atom_index
.size()*DIM
, mpi_type
, node
, node
,
2936 cr
->mpi_comm_mygroup
, &stat
);
2941 row
= (atom
+ node
)*DIM
+ d
;
2943 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2945 for (size_t k
= 0; k
< DIM
; k
++)
2951 if (col
>= row
&& dfdx
[j
][k
] != 0.0)
2953 gmx_sparsematrix_increment_value(sparse_matrix
,
2954 row
, col
, dfdx
[j
][k
]);
2959 full_matrix
[row
*sz
+col
] = dfdx
[j
][k
];
2966 if (bVerbose
&& fplog
)
2971 /* write progress */
2972 if (bIsMaster
&& bVerbose
)
2974 fprintf(stderr
, "\rFinished step %d out of %d",
2975 static_cast<int>(std::min(atom
+nnodes
, atom_index
.size())),
2976 static_cast<int>(atom_index
.size()));
2983 fprintf(stderr
, "\n\nWriting Hessian...\n");
2984 gmx_mtxio_write(ftp2fn(efMTX
, nfile
, fnm
), sz
, sz
, full_matrix
, sparse_matrix
);
2987 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2989 walltime_accounting_set_nsteps_done(walltime_accounting
, atom_index
.size()*2);