2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
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 const MdrunOptions
&mdrunOptions
,
328 t_state
*state_global
, gmx_mtop_t
*top_global
,
329 em_state_t
*ems
, gmx_localtop_t
**top
,
330 t_nrnb
*nrnb
, rvec mu_tot
,
331 t_forcerec
*fr
, gmx_enerdata_t
**enerd
,
332 t_graph
**graph
, gmx::MDAtoms
*mdAtoms
, gmx_global_stat_t
*gstat
,
333 gmx_vsite_t
*vsite
, gmx_constr_t constr
, gmx_shellfc_t
**shellfc
,
334 int nfile
, const t_filenm fnm
[],
335 gmx_mdoutf_t
*outf
, t_mdebin
**mdebin
,
336 gmx_wallcycle_t wcycle
)
342 fprintf(fplog
, "Initiating %s\n", title
);
347 state_global
->ngtc
= 0;
349 /* Initialize lambda variables */
350 initialize_lambdas(fplog
, ir
, &(state_global
->fep_state
), state_global
->lambda
, nullptr);
355 /* Interactive molecular dynamics */
356 init_IMD(ir
, cr
, top_global
, fplog
, 1,
357 MASTER(cr
) ? as_rvec_array(state_global
->x
.data()) : nullptr,
358 nfile
, fnm
, nullptr, mdrunOptions
);
362 GMX_ASSERT(shellfc
!= NULL
, "With NM we always support shells");
364 *shellfc
= init_shell_flexcon(stdout
,
366 n_flexible_constraints(constr
),
372 GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir
->eI
), "This else currently only handles energy minimizers, consider if your algorithm needs shell/flexible-constraint support");
374 /* With energy minimization, shells and flexible constraints are
375 * automatically minimized when treated like normal DOFS.
377 if (shellfc
!= nullptr)
383 auto mdatoms
= mdAtoms
->mdatoms();
384 if (DOMAINDECOMP(cr
))
386 *top
= dd_init_local_top(top_global
);
388 dd_init_local_state(cr
->dd
, state_global
, &ems
->s
);
390 /* Distribute the charge groups over the nodes from the master node */
391 dd_partition_system(fplog
, ir
->init_step
, cr
, TRUE
, 1,
392 state_global
, top_global
, ir
,
393 &ems
->s
, &ems
->f
, mdAtoms
, *top
,
395 nrnb
, nullptr, FALSE
);
396 dd_store_state(cr
->dd
, &ems
->s
);
402 state_change_natoms(state_global
, state_global
->natoms
);
403 /* Just copy the state */
404 ems
->s
= *state_global
;
405 state_change_natoms(&ems
->s
, ems
->s
.natoms
);
406 /* We need to allocate one element extra, since we might use
407 * (unaligned) 4-wide SIMD loads to access rvec entries.
409 ems
->f
.resize(gmx::paddedRVecVectorSize(ems
->s
.natoms
));
412 mdAlgorithmsSetupAtomData(cr
, ir
, top_global
, *top
, fr
,
414 vsite
, shellfc
? *shellfc
: nullptr);
418 set_vsite_top(vsite
, *top
, mdatoms
);
422 update_mdatoms(mdAtoms
->mdatoms(), ems
->s
.lambda
[efptMASS
]);
426 if (ir
->eConstrAlg
== econtSHAKE
&&
427 gmx_mtop_ftype_count(top_global
, F_CONSTR
) > 0)
429 gmx_fatal(FARGS
, "Can not do energy minimization with %s, use %s\n",
430 econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
433 if (!DOMAINDECOMP(cr
))
435 set_constraints(constr
, *top
, ir
, mdatoms
, cr
);
438 if (!ir
->bContinuation
)
440 /* Constrain the starting coordinates */
442 constrain(PAR(cr
) ? nullptr : fplog
, TRUE
, TRUE
, constr
, &(*top
)->idef
,
443 ir
, cr
, -1, 0, 1.0, mdatoms
,
444 as_rvec_array(ems
->s
.x
.data()),
445 as_rvec_array(ems
->s
.x
.data()),
447 fr
->bMolPBC
, ems
->s
.box
,
448 ems
->s
.lambda
[efptFEP
], &dvdl_constr
,
449 nullptr, nullptr, nrnb
, econqCoord
);
455 *gstat
= global_stat_init(ir
);
462 *outf
= init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, ir
, top_global
, nullptr, wcycle
);
465 init_enerdata(top_global
->groups
.grps
[egcENER
].nr
, ir
->fepvals
->n_lambda
,
468 if (mdebin
!= nullptr)
470 /* Init bin for energy stuff */
471 *mdebin
= init_mdebin(mdoutf_get_fp_ene(*outf
), top_global
, ir
, nullptr);
475 calc_shifts(ems
->s
.box
, fr
->shift_vec
);
478 //! Finalize the minimization
479 static void finish_em(t_commrec
*cr
, gmx_mdoutf_t outf
,
480 gmx_walltime_accounting_t walltime_accounting
,
481 gmx_wallcycle_t wcycle
)
483 if (!thisRankHasDuty(cr
, DUTY_PME
))
485 /* Tell the PME only node to finish */
486 gmx_pme_send_finish(cr
);
491 em_time_end(walltime_accounting
, wcycle
);
494 //! Swap two different EM states during minimization
495 static void swap_em_state(em_state_t
**ems1
, em_state_t
**ems2
)
504 //! Save the EM trajectory
505 static void write_em_traj(FILE *fplog
, t_commrec
*cr
,
507 gmx_bool bX
, gmx_bool bF
, const char *confout
,
508 gmx_mtop_t
*top_global
,
509 t_inputrec
*ir
, gmx_int64_t step
,
511 t_state
*state_global
,
512 ObservablesHistory
*observablesHistory
)
518 mdof_flags
|= MDOF_X
;
522 mdof_flags
|= MDOF_F
;
525 /* If we want IMD output, set appropriate MDOF flag */
528 mdof_flags
|= MDOF_IMD
;
531 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
532 top_global
, step
, (double)step
,
533 &state
->s
, state_global
, observablesHistory
,
536 if (confout
!= nullptr && MASTER(cr
))
538 GMX_RELEASE_ASSERT(bX
, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
539 /* With domain decomposition the call above collected the state->s.x
540 * into state_global->x. Without DD we copy the local state pointer.
542 if (!DOMAINDECOMP(cr
))
544 state_global
= &state
->s
;
547 if (ir
->ePBC
!= epbcNONE
&& !ir
->bPeriodicMols
&& DOMAINDECOMP(cr
))
549 /* Make molecules whole only for confout writing */
550 do_pbc_mtop(fplog
, ir
->ePBC
, state
->s
.box
, top_global
,
551 as_rvec_array(state_global
->x
.data()));
554 write_sto_conf_mtop(confout
,
555 *top_global
->name
, top_global
,
556 as_rvec_array(state_global
->x
.data()), nullptr, ir
->ePBC
, state
->s
.box
);
560 //! \brief Do one minimization step
562 // \returns true when the step succeeded, false when a constraint error occurred
563 static bool do_em_step(t_commrec
*cr
, t_inputrec
*ir
, t_mdatoms
*md
,
565 em_state_t
*ems1
, real a
, const PaddedRVecVector
*force
,
567 gmx_constr_t constr
, gmx_localtop_t
*top
,
568 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
575 int nthreads gmx_unused
;
577 bool validStep
= true;
582 if (DOMAINDECOMP(cr
) && s1
->ddp_count
!= cr
->dd
->ddp_count
)
584 gmx_incons("state mismatch in do_em_step");
587 s2
->flags
= s1
->flags
;
589 if (s2
->natoms
!= s1
->natoms
)
591 state_change_natoms(s2
, s1
->natoms
);
592 /* We need to allocate one element extra, since we might use
593 * (unaligned) 4-wide SIMD loads to access rvec entries.
595 ems2
->f
.resize(gmx::paddedRVecVectorSize(s2
->natoms
));
597 if (DOMAINDECOMP(cr
) && s2
->cg_gl
.size() != s1
->cg_gl
.size())
599 s2
->cg_gl
.resize(s1
->cg_gl
.size());
602 copy_mat(s1
->box
, s2
->box
);
603 /* Copy free energy state */
604 s2
->lambda
= s1
->lambda
;
605 copy_mat(s1
->box
, s2
->box
);
610 // cppcheck-suppress unreadVariable
611 nthreads
= gmx_omp_nthreads_get(emntUpdate
);
612 #pragma omp parallel num_threads(nthreads)
614 const rvec
*x1
= as_rvec_array(s1
->x
.data());
615 rvec
*x2
= as_rvec_array(s2
->x
.data());
616 const rvec
*f
= as_rvec_array(force
->data());
619 #pragma omp for schedule(static) nowait
620 for (int i
= start
; i
< end
; i
++)
628 for (int m
= 0; m
< DIM
; m
++)
630 if (ir
->opts
.nFreeze
[gf
][m
])
636 x2
[i
][m
] = x1
[i
][m
] + a
*f
[i
][m
];
640 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
;
643 if (s2
->flags
& (1<<estCGP
))
645 /* Copy the CG p vector */
646 const rvec
*p1
= as_rvec_array(s1
->cg_p
.data());
647 rvec
*p2
= as_rvec_array(s2
->cg_p
.data());
648 #pragma omp for schedule(static) nowait
649 for (int i
= start
; i
< end
; i
++)
651 // Trivial OpenMP block that does not throw
652 copy_rvec(p1
[i
], p2
[i
]);
656 if (DOMAINDECOMP(cr
))
658 s2
->ddp_count
= s1
->ddp_count
;
660 /* OpenMP does not supported unsigned loop variables */
661 #pragma omp for schedule(static) nowait
662 for (int i
= 0; i
< static_cast<int>(s2
->cg_gl
.size()); i
++)
664 s2
->cg_gl
[i
] = s1
->cg_gl
[i
];
666 s2
->ddp_count_cg_gl
= s1
->ddp_count_cg_gl
;
672 wallcycle_start(wcycle
, ewcCONSTR
);
675 constrain(nullptr, TRUE
, TRUE
, constr
, &top
->idef
,
676 ir
, cr
, count
, 0, 1.0, md
,
677 as_rvec_array(s1
->x
.data()), as_rvec_array(s2
->x
.data()),
678 nullptr, bMolPBC
, s2
->box
,
679 s2
->lambda
[efptBONDED
], &dvdl_constr
,
680 nullptr, nullptr, nrnb
, econqCoord
);
681 wallcycle_stop(wcycle
, ewcCONSTR
);
683 // We should move this check to the different minimizers
684 if (!validStep
&& ir
->eI
!= eiSteep
)
686 gmx_fatal(FARGS
, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
687 EI(ir
->eI
), EI(eiSteep
), EI(ir
->eI
));
694 //! Prepare EM for using domain decomposition parallellization
695 static void em_dd_partition_system(FILE *fplog
, int step
, t_commrec
*cr
,
696 gmx_mtop_t
*top_global
, t_inputrec
*ir
,
697 em_state_t
*ems
, gmx_localtop_t
*top
,
698 gmx::MDAtoms
*mdAtoms
, t_forcerec
*fr
,
699 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
700 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
)
702 /* Repartition the domain decomposition */
703 dd_partition_system(fplog
, step
, cr
, FALSE
, 1,
704 nullptr, top_global
, ir
,
706 mdAtoms
, top
, fr
, vsite
, constr
,
707 nrnb
, wcycle
, FALSE
);
708 dd_store_state(cr
->dd
, &ems
->s
);
711 //! De one energy evaluation
712 static void evaluate_energy(FILE *fplog
, t_commrec
*cr
,
713 gmx_mtop_t
*top_global
,
714 em_state_t
*ems
, gmx_localtop_t
*top
,
715 t_inputrec
*inputrec
,
716 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
717 gmx_global_stat_t gstat
,
718 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
720 t_graph
*graph
, gmx::MDAtoms
*mdAtoms
,
721 t_forcerec
*fr
, rvec mu_tot
,
722 gmx_enerdata_t
*enerd
, tensor vir
, tensor pres
,
723 gmx_int64_t count
, gmx_bool bFirst
)
727 tensor force_vir
, shake_vir
, ekin
;
728 real dvdl_constr
, prescorr
, enercorr
, dvdlcorr
;
731 /* Set the time to the initial time, the time does not change during EM */
732 t
= inputrec
->init_t
;
735 (DOMAINDECOMP(cr
) && ems
->s
.ddp_count
< cr
->dd
->ddp_count
))
737 /* This is the first state or an old state used before the last ns */
743 if (inputrec
->nstlist
> 0)
751 construct_vsites(vsite
, as_rvec_array(ems
->s
.x
.data()), 1, nullptr,
752 top
->idef
.iparams
, top
->idef
.il
,
753 fr
->ePBC
, fr
->bMolPBC
, cr
, ems
->s
.box
);
756 if (DOMAINDECOMP(cr
) && bNS
)
758 /* Repartition the domain decomposition */
759 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
760 ems
, top
, mdAtoms
, fr
, vsite
, constr
,
764 /* Calc force & energy on new trial position */
765 /* do_force always puts the charge groups in the box and shifts again
766 * We do not unshift, so molecules are always whole in congrad.c
768 do_force(fplog
, cr
, inputrec
,
769 count
, nrnb
, wcycle
, top
, &top_global
->groups
,
770 ems
->s
.box
, &ems
->s
.x
, &ems
->s
.hist
,
771 &ems
->f
, force_vir
, mdAtoms
->mdatoms(), enerd
, fcd
,
772 ems
->s
.lambda
, graph
, fr
, vsite
, mu_tot
, t
, nullptr, TRUE
,
773 GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
|
774 GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
|
775 (bNS
? GMX_FORCE_NS
: 0),
777 DdOpenBalanceRegionBeforeForceComputation::yes
:
778 DdOpenBalanceRegionBeforeForceComputation::no
,
780 DdCloseBalanceRegionAfterForceComputation::yes
:
781 DdCloseBalanceRegionAfterForceComputation::no
);
783 /* Clear the unused shake virial and pressure */
784 clear_mat(shake_vir
);
787 /* Communicate stuff when parallel */
788 if (PAR(cr
) && inputrec
->eI
!= eiNM
)
790 wallcycle_start(wcycle
, ewcMoveE
);
792 global_stat(gstat
, cr
, enerd
, force_vir
, shake_vir
, mu_tot
,
793 inputrec
, nullptr, nullptr, nullptr, 1, &terminate
,
799 wallcycle_stop(wcycle
, ewcMoveE
);
802 /* Calculate long range corrections to pressure and energy */
803 calc_dispcorr(inputrec
, fr
, ems
->s
.box
, ems
->s
.lambda
[efptVDW
],
804 pres
, force_vir
, &prescorr
, &enercorr
, &dvdlcorr
);
805 enerd
->term
[F_DISPCORR
] = enercorr
;
806 enerd
->term
[F_EPOT
] += enercorr
;
807 enerd
->term
[F_PRES
] += prescorr
;
808 enerd
->term
[F_DVDL
] += dvdlcorr
;
810 ems
->epot
= enerd
->term
[F_EPOT
];
814 /* Project out the constraint components of the force */
815 wallcycle_start(wcycle
, ewcCONSTR
);
817 rvec
*f_rvec
= as_rvec_array(ems
->f
.data());
818 constrain(nullptr, FALSE
, FALSE
, constr
, &top
->idef
,
819 inputrec
, cr
, count
, 0, 1.0, mdAtoms
->mdatoms(),
820 as_rvec_array(ems
->s
.x
.data()), f_rvec
, f_rvec
,
821 fr
->bMolPBC
, ems
->s
.box
,
822 ems
->s
.lambda
[efptBONDED
], &dvdl_constr
,
823 nullptr, &shake_vir
, nrnb
, econqForceDispl
);
824 enerd
->term
[F_DVDL_CONSTR
] += dvdl_constr
;
825 m_add(force_vir
, shake_vir
, vir
);
826 wallcycle_stop(wcycle
, ewcCONSTR
);
830 copy_mat(force_vir
, vir
);
834 enerd
->term
[F_PRES
] =
835 calc_pres(fr
->ePBC
, inputrec
->nwall
, ems
->s
.box
, ekin
, vir
, pres
);
837 sum_dhdl(enerd
, ems
->s
.lambda
, inputrec
->fepvals
);
839 if (EI_ENERGY_MINIMIZATION(inputrec
->eI
))
841 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdAtoms
->mdatoms(), ems
);
845 //! Parallel utility summing energies and forces
846 static double reorder_partsum(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
847 gmx_mtop_t
*top_global
,
848 em_state_t
*s_min
, em_state_t
*s_b
)
851 int ncg
, *cg_gl
, *index
, c
, cg
, i
, a0
, a1
, a
, gf
, m
;
853 unsigned char *grpnrFREEZE
;
857 fprintf(debug
, "Doing reorder_partsum\n");
860 const rvec
*fm
= as_rvec_array(s_min
->f
.data());
861 const rvec
*fb
= as_rvec_array(s_b
->f
.data());
863 cgs_gl
= dd_charge_groups_global(cr
->dd
);
864 index
= cgs_gl
->index
;
866 /* Collect fm in a global vector fmg.
867 * This conflicts with the spirit of domain decomposition,
868 * but to fully optimize this a much more complicated algorithm is required.
871 snew(fmg
, top_global
->natoms
);
873 ncg
= s_min
->s
.cg_gl
.size();
874 cg_gl
= s_min
->s
.cg_gl
.data();
876 for (c
= 0; c
< ncg
; c
++)
881 for (a
= a0
; a
< a1
; a
++)
883 copy_rvec(fm
[i
], fmg
[a
]);
887 gmx_sum(top_global
->natoms
*3, fmg
[0], cr
);
889 /* Now we will determine the part of the sum for the cgs in state s_b */
890 ncg
= s_b
->s
.cg_gl
.size();
891 cg_gl
= s_b
->s
.cg_gl
.data();
895 grpnrFREEZE
= top_global
->groups
.grpnr
[egcFREEZE
];
896 for (c
= 0; c
< ncg
; c
++)
901 for (a
= a0
; a
< a1
; a
++)
903 if (mdatoms
->cFREEZE
&& grpnrFREEZE
)
907 for (m
= 0; m
< DIM
; m
++)
909 if (!opts
->nFreeze
[gf
][m
])
911 partsum
+= (fb
[i
][m
] - fmg
[a
][m
])*fb
[i
][m
];
923 //! Print some stuff, like beta, whatever that means.
924 static real
pr_beta(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
925 gmx_mtop_t
*top_global
,
926 em_state_t
*s_min
, em_state_t
*s_b
)
930 /* This is just the classical Polak-Ribiere calculation of beta;
931 * it looks a bit complicated since we take freeze groups into account,
932 * and might have to sum it in parallel runs.
935 if (!DOMAINDECOMP(cr
) ||
936 (s_min
->s
.ddp_count
== cr
->dd
->ddp_count
&&
937 s_b
->s
.ddp_count
== cr
->dd
->ddp_count
))
939 const rvec
*fm
= as_rvec_array(s_min
->f
.data());
940 const rvec
*fb
= as_rvec_array(s_b
->f
.data());
943 /* This part of code can be incorrect with DD,
944 * since the atom ordering in s_b and s_min might differ.
946 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
948 if (mdatoms
->cFREEZE
)
950 gf
= mdatoms
->cFREEZE
[i
];
952 for (int m
= 0; m
< DIM
; m
++)
954 if (!opts
->nFreeze
[gf
][m
])
956 sum
+= (fb
[i
][m
] - fm
[i
][m
])*fb
[i
][m
];
963 /* We need to reorder cgs while summing */
964 sum
= reorder_partsum(cr
, opts
, mdatoms
, top_global
, s_min
, s_b
);
968 gmx_sumd(1, &sum
, cr
);
971 return sum
/gmx::square(s_min
->fnorm
);
977 /*! \brief Do conjugate gradients minimization
978 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
979 int nfile, const t_filenm fnm[],
980 const gmx_output_env_t *oenv,
981 const MdrunOptions &mdrunOptions,
982 gmx_vsite_t *vsite, gmx_constr_t constr,
983 gmx::IMDOutputProvider *outputProvider,
984 t_inputrec *inputrec,
985 gmx_mtop_t *top_global, t_fcdata *fcd,
986 t_state *state_global,
987 gmx::MDAtoms *mdAtoms,
988 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
991 const ReplicaExchangeParameters &replExParams,
992 gmx_membed_t gmx_unused *membed,
993 gmx_walltime_accounting_t walltime_accounting)
995 double do_cg(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
996 int nfile
, const t_filenm fnm
[],
997 const gmx_output_env_t gmx_unused
*oenv
,
998 const MdrunOptions
&mdrunOptions
,
999 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
1000 gmx::IMDOutputProvider
*outputProvider
,
1001 t_inputrec
*inputrec
,
1002 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
1003 t_state
*state_global
,
1004 ObservablesHistory
*observablesHistory
,
1005 gmx::MDAtoms
*mdAtoms
,
1006 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1008 const ReplicaExchangeParameters gmx_unused
&replExParams
,
1009 gmx_membed_t gmx_unused
*membed
,
1010 gmx_walltime_accounting_t walltime_accounting
)
1012 const char *CG
= "Polak-Ribiere Conjugate Gradients";
1014 gmx_localtop_t
*top
;
1015 gmx_enerdata_t
*enerd
;
1016 gmx_global_stat_t gstat
;
1018 double tmp
, minstep
;
1020 real a
, b
, c
, beta
= 0.0;
1024 gmx_bool converged
, foundlower
;
1026 gmx_bool do_log
= FALSE
, do_ene
= FALSE
, do_x
, do_f
;
1028 int number_steps
, neval
= 0, nstcg
= inputrec
->nstcgsteep
;
1030 int m
, step
, nminstep
;
1031 auto mdatoms
= mdAtoms
->mdatoms();
1035 // Ensure the extra per-atom state array gets allocated
1036 state_global
->flags
|= (1<<estCGP
);
1038 /* Create 4 states on the stack and extract pointers that we will swap */
1039 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1040 em_state_t
*s_min
= &s0
;
1041 em_state_t
*s_a
= &s1
;
1042 em_state_t
*s_b
= &s2
;
1043 em_state_t
*s_c
= &s3
;
1045 /* Init em and store the local state in s_min */
1046 init_em(fplog
, CG
, cr
, outputProvider
, inputrec
, mdrunOptions
,
1047 state_global
, top_global
, s_min
, &top
,
1048 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdAtoms
, &gstat
,
1049 vsite
, constr
, nullptr,
1050 nfile
, fnm
, &outf
, &mdebin
, wcycle
);
1052 /* Print to log file */
1053 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, CG
);
1055 /* Max number of steps */
1056 number_steps
= inputrec
->nsteps
;
1060 sp_header(stderr
, CG
, inputrec
->em_tol
, number_steps
);
1064 sp_header(fplog
, CG
, inputrec
->em_tol
, number_steps
);
1067 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1068 /* do_force always puts the charge groups in the box and shifts again
1069 * We do not unshift, so molecules are always whole in congrad.c
1071 evaluate_energy(fplog
, cr
,
1072 top_global
, s_min
, top
,
1073 inputrec
, nrnb
, wcycle
, gstat
,
1074 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
1075 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1080 /* Copy stuff to the energy bin for easy printing etc. */
1081 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1082 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1083 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1085 print_ebin_header(fplog
, step
, step
);
1086 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1087 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1091 /* Estimate/guess the initial stepsize */
1092 stepsize
= inputrec
->em_stepsize
/s_min
->fnorm
;
1096 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1097 fprintf(stderr
, " F-max = %12.5e on atom %d\n",
1098 s_min
->fmax
, s_min
->a_fmax
+1);
1099 fprintf(stderr
, " F-Norm = %12.5e\n",
1100 s_min
->fnorm
/sqrtNumAtoms
);
1101 fprintf(stderr
, "\n");
1102 /* and copy to the log file too... */
1103 fprintf(fplog
, " F-max = %12.5e on atom %d\n",
1104 s_min
->fmax
, s_min
->a_fmax
+1);
1105 fprintf(fplog
, " F-Norm = %12.5e\n",
1106 s_min
->fnorm
/sqrtNumAtoms
);
1107 fprintf(fplog
, "\n");
1109 /* Start the loop over CG steps.
1110 * Each successful step is counted, and we continue until
1111 * we either converge or reach the max number of steps.
1114 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1117 /* start taking steps in a new direction
1118 * First time we enter the routine, beta=0, and the direction is
1119 * simply the negative gradient.
1122 /* Calculate the new direction in p, and the gradient in this direction, gpa */
1123 rvec
*pm
= as_rvec_array(s_min
->s
.cg_p
.data());
1124 const rvec
*sfm
= as_rvec_array(s_min
->f
.data());
1127 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1129 if (mdatoms
->cFREEZE
)
1131 gf
= mdatoms
->cFREEZE
[i
];
1133 for (m
= 0; m
< DIM
; m
++)
1135 if (!inputrec
->opts
.nFreeze
[gf
][m
])
1137 pm
[i
][m
] = sfm
[i
][m
] + beta
*pm
[i
][m
];
1138 gpa
-= pm
[i
][m
]*sfm
[i
][m
];
1139 /* f is negative gradient, thus the sign */
1148 /* Sum the gradient along the line across CPUs */
1151 gmx_sumd(1, &gpa
, cr
);
1154 /* Calculate the norm of the search vector */
1155 get_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, pm
, &pnorm
, nullptr, nullptr);
1157 /* Just in case stepsize reaches zero due to numerical precision... */
1160 stepsize
= inputrec
->em_stepsize
/pnorm
;
1164 * Double check the value of the derivative in the search direction.
1165 * If it is positive it must be due to the old information in the
1166 * CG formula, so just remove that and start over with beta=0.
1167 * This corresponds to a steepest descent step.
1172 step
--; /* Don't count this step since we are restarting */
1173 continue; /* Go back to the beginning of the big for-loop */
1176 /* Calculate minimum allowed stepsize, before the average (norm)
1177 * relative change in coordinate is smaller than precision
1180 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1182 for (m
= 0; m
< DIM
; m
++)
1184 tmp
= fabs(s_min
->s
.x
[i
][m
]);
1193 /* Add up from all CPUs */
1196 gmx_sumd(1, &minstep
, cr
);
1199 minstep
= GMX_REAL_EPS
/sqrt(minstep
/(3*state_global
->natoms
));
1201 if (stepsize
< minstep
)
1207 /* Write coordinates if necessary */
1208 do_x
= do_per_step(step
, inputrec
->nstxout
);
1209 do_f
= do_per_step(step
, inputrec
->nstfout
);
1211 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr,
1212 top_global
, inputrec
, step
,
1213 s_min
, state_global
, observablesHistory
);
1215 /* Take a step downhill.
1216 * In theory, we should minimize the function along this direction.
1217 * That is quite possible, but it turns out to take 5-10 function evaluations
1218 * for each line. However, we dont really need to find the exact minimum -
1219 * it is much better to start a new CG step in a modified direction as soon
1220 * as we are close to it. This will save a lot of energy evaluations.
1222 * In practice, we just try to take a single step.
1223 * If it worked (i.e. lowered the energy), we increase the stepsize but
1224 * the continue straight to the next CG step without trying to find any minimum.
1225 * If it didn't work (higher energy), there must be a minimum somewhere between
1226 * the old position and the new one.
1228 * Due to the finite numerical accuracy, it turns out that it is a good idea
1229 * to even accept a SMALL increase in energy, if the derivative is still downhill.
1230 * This leads to lower final energies in the tests I've done. / Erik
1232 s_a
->epot
= s_min
->epot
;
1234 c
= a
+ stepsize
; /* reference position along line is zero */
1236 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
< cr
->dd
->ddp_count
)
1238 em_dd_partition_system(fplog
, step
, cr
, top_global
, inputrec
,
1239 s_min
, top
, mdAtoms
, fr
, vsite
, constr
,
1243 /* Take a trial step (new coords in s_c) */
1244 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, c
, &s_min
->s
.cg_p
, s_c
,
1245 constr
, top
, nrnb
, wcycle
, -1);
1248 /* Calculate energy for the trial step */
1249 evaluate_energy(fplog
, cr
,
1250 top_global
, s_c
, top
,
1251 inputrec
, nrnb
, wcycle
, gstat
,
1252 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
1253 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1255 /* Calc derivative along line */
1256 const rvec
*pc
= as_rvec_array(s_c
->s
.cg_p
.data());
1257 const rvec
*sfc
= as_rvec_array(s_c
->f
.data());
1259 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1261 for (m
= 0; m
< DIM
; m
++)
1263 gpc
-= pc
[i
][m
]*sfc
[i
][m
]; /* f is negative gradient, thus the sign */
1266 /* Sum the gradient along the line across CPUs */
1269 gmx_sumd(1, &gpc
, cr
);
1272 /* This is the max amount of increase in energy we tolerate */
1273 tmp
= sqrt(GMX_REAL_EPS
)*fabs(s_a
->epot
);
1275 /* Accept the step if the energy is lower, or if it is not significantly higher
1276 * and the line derivative is still negative.
1278 if (s_c
->epot
< s_a
->epot
|| (gpc
< 0 && s_c
->epot
< (s_a
->epot
+ tmp
)))
1281 /* Great, we found a better energy. Increase step for next iteration
1282 * if we are still going down, decrease it otherwise
1286 stepsize
*= 1.618034; /* The golden section */
1290 stepsize
*= 0.618034; /* 1/golden section */
1295 /* New energy is the same or higher. We will have to do some work
1296 * to find a smaller value in the interval. Take smaller step next time!
1299 stepsize
*= 0.618034;
1305 /* OK, if we didn't find a lower value we will have to locate one now - there must
1306 * be one in the interval [a=0,c].
1307 * The same thing is valid here, though: Don't spend dozens of iterations to find
1308 * the line minimum. We try to interpolate based on the derivative at the endpoints,
1309 * and only continue until we find a lower value. In most cases this means 1-2 iterations.
1311 * I also have a safeguard for potentially really pathological functions so we never
1312 * take more than 20 steps before we give up ...
1314 * If we already found a lower value we just skip this step and continue to the update.
1323 /* Select a new trial point.
1324 * If the derivatives at points a & c have different sign we interpolate to zero,
1325 * otherwise just do a bisection.
1327 if (gpa
< 0 && gpc
> 0)
1329 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
1336 /* safeguard if interpolation close to machine accuracy causes errors:
1337 * never go outside the interval
1339 if (b
<= a
|| b
>= c
)
1344 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
1346 /* Reload the old state */
1347 em_dd_partition_system(fplog
, -1, cr
, top_global
, inputrec
,
1348 s_min
, top
, mdAtoms
, fr
, vsite
, constr
,
1352 /* Take a trial step to this new point - new coords in s_b */
1353 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, b
, &s_min
->s
.cg_p
, s_b
,
1354 constr
, top
, nrnb
, wcycle
, -1);
1357 /* Calculate energy for the trial step */
1358 evaluate_energy(fplog
, cr
,
1359 top_global
, s_b
, top
,
1360 inputrec
, nrnb
, wcycle
, gstat
,
1361 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
1362 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1364 /* p does not change within a step, but since the domain decomposition
1365 * might change, we have to use cg_p of s_b here.
1367 const rvec
*pb
= as_rvec_array(s_b
->s
.cg_p
.data());
1368 const rvec
*sfb
= as_rvec_array(s_b
->f
.data());
1370 for (int i
= 0; i
< mdatoms
->homenr
; i
++)
1372 for (m
= 0; m
< DIM
; m
++)
1374 gpb
-= pb
[i
][m
]*sfb
[i
][m
]; /* f is negative gradient, thus the sign */
1377 /* Sum the gradient along the line across CPUs */
1380 gmx_sumd(1, &gpb
, cr
);
1385 fprintf(debug
, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
1386 s_a
->epot
, s_b
->epot
, s_c
->epot
, gpb
);
1389 epot_repl
= s_b
->epot
;
1391 /* Keep one of the intervals based on the value of the derivative at the new point */
1394 /* Replace c endpoint with b */
1395 swap_em_state(&s_b
, &s_c
);
1401 /* Replace a endpoint with b */
1402 swap_em_state(&s_b
, &s_a
);
1408 * Stop search as soon as we find a value smaller than the endpoints.
1409 * Never run more than 20 steps, no matter what.
1413 while ((epot_repl
> s_a
->epot
|| epot_repl
> s_c
->epot
) &&
1416 if (fabs(epot_repl
- s_min
->epot
) < fabs(s_min
->epot
)*GMX_REAL_EPS
||
1419 /* OK. We couldn't find a significantly lower energy.
1420 * If beta==0 this was steepest descent, and then we give up.
1421 * If not, set beta=0 and restart with steepest descent before quitting.
1431 /* Reset memory before giving up */
1437 /* Select min energy state of A & C, put the best in B.
1439 if (s_c
->epot
< s_a
->epot
)
1443 fprintf(debug
, "CGE: C (%f) is lower than A (%f), moving C to B\n",
1444 s_c
->epot
, s_a
->epot
);
1446 swap_em_state(&s_b
, &s_c
);
1453 fprintf(debug
, "CGE: A (%f) is lower than C (%f), moving A to B\n",
1454 s_a
->epot
, s_c
->epot
);
1456 swap_em_state(&s_b
, &s_a
);
1465 fprintf(debug
, "CGE: Found a lower energy %f, moving C to B\n",
1468 swap_em_state(&s_b
, &s_c
);
1472 /* new search direction */
1473 /* beta = 0 means forget all memory and restart with steepest descents. */
1474 if (nstcg
&& ((step
% nstcg
) == 0))
1480 /* s_min->fnorm cannot be zero, because then we would have converged
1484 /* Polak-Ribiere update.
1485 * Change to fnorm2/fnorm2_old for Fletcher-Reeves
1487 beta
= pr_beta(cr
, &inputrec
->opts
, mdatoms
, top_global
, s_min
, s_b
);
1489 /* Limit beta to prevent oscillations */
1490 if (fabs(beta
) > 5.0)
1496 /* update positions */
1497 swap_em_state(&s_min
, &s_b
);
1500 /* Print it if necessary */
1503 if (mdrunOptions
.verbose
)
1505 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1506 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
1507 step
, s_min
->epot
, s_min
->fnorm
/sqrtNumAtoms
,
1508 s_min
->fmax
, s_min
->a_fmax
+1);
1511 /* Store the new (lower) energies */
1512 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1513 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1514 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1516 do_log
= do_per_step(step
, inputrec
->nstlog
);
1517 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
1519 /* Prepare IMD energy record, if bIMD is TRUE. */
1520 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, step
, TRUE
);
1524 print_ebin_header(fplog
, step
, step
);
1526 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
1527 do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
1528 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1531 /* Send energies and positions to the IMD client if bIMD is TRUE. */
1532 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state_global
->box
, as_rvec_array(state_global
->x
.data()), inputrec
, 0, wcycle
) && MASTER(cr
))
1534 IMD_send_positions(inputrec
->imd
);
1537 /* Stop when the maximum force lies below tolerance.
1538 * If we have reached machine precision, converged is already set to true.
1540 converged
= converged
|| (s_min
->fmax
< inputrec
->em_tol
);
1542 } /* End of the loop */
1544 /* IMD cleanup, if bIMD is TRUE. */
1545 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
1549 step
--; /* we never took that last step in this case */
1552 if (s_min
->fmax
> inputrec
->em_tol
)
1556 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1557 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1564 /* If we printed energy and/or logfile last step (which was the last step)
1565 * we don't have to do it again, but otherwise print the final values.
1569 /* Write final value to log since we didn't do anything the last step */
1570 print_ebin_header(fplog
, step
, step
);
1572 if (!do_ene
|| !do_log
)
1574 /* Write final energy file entries */
1575 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
1576 !do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
1577 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1581 /* Print some stuff... */
1584 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
1588 * For accurate normal mode calculation it is imperative that we
1589 * store the last conformation into the full precision binary trajectory.
1591 * However, we should only do it if we did NOT already write this step
1592 * above (which we did if do_x or do_f was true).
1594 do_x
= !do_per_step(step
, inputrec
->nstxout
);
1595 do_f
= (inputrec
->nstfout
> 0 && !do_per_step(step
, inputrec
->nstfout
));
1597 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
1598 top_global
, inputrec
, step
,
1599 s_min
, state_global
, observablesHistory
);
1604 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1605 print_converged(stderr
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1606 s_min
, sqrtNumAtoms
);
1607 print_converged(fplog
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1608 s_min
, sqrtNumAtoms
);
1610 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
1613 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
1615 /* To print the actual number of steps we needed somewhere */
1616 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
1619 } /* That's all folks */
1622 /*! \brief Do L-BFGS conjugate gradients minimization
1623 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
1624 int nfile, const t_filenm fnm[],
1625 const gmx_output_env_t *oenv,
1626 const MdrunOptions &mdrunOptions,
1627 gmx_vsite_t *vsite, gmx_constr_t constr,
1628 gmx::IMDOutputProvider *outputProvider,
1629 t_inputrec *inputrec,
1630 gmx_mtop_t *top_global, t_fcdata *fcd,
1631 t_state *state_global,
1632 gmx::MDAtoms *mdAtoms,
1633 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
1636 const ReplicaExchangeParameters &replExParams,
1637 gmx_membed_t gmx_unused *membed,
1638 gmx_walltime_accounting_t walltime_accounting)
1640 double do_lbfgs(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
1641 int nfile
, const t_filenm fnm
[],
1642 const gmx_output_env_t gmx_unused
*oenv
,
1643 const MdrunOptions
&mdrunOptions
,
1644 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
1645 gmx::IMDOutputProvider
*outputProvider
,
1646 t_inputrec
*inputrec
,
1647 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
1648 t_state
*state_global
,
1649 ObservablesHistory
*observablesHistory
,
1650 gmx::MDAtoms
*mdAtoms
,
1651 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1653 const ReplicaExchangeParameters gmx_unused
&replExParams
,
1654 gmx_membed_t gmx_unused
*membed
,
1655 gmx_walltime_accounting_t walltime_accounting
)
1657 static const char *LBFGS
= "Low-Memory BFGS Minimizer";
1659 gmx_localtop_t
*top
;
1660 gmx_enerdata_t
*enerd
;
1661 gmx_global_stat_t gstat
;
1663 int ncorr
, nmaxcorr
, point
, cp
, neval
, nminstep
;
1664 double stepsize
, step_taken
, gpa
, gpb
, gpc
, tmp
, minstep
;
1665 real
*rho
, *alpha
, *p
, *s
, **dx
, **dg
;
1666 real a
, b
, c
, maxdelta
, delta
;
1668 real dgdx
, dgdg
, sq
, yr
, beta
;
1672 gmx_bool do_log
, do_ene
, do_x
, do_f
, foundlower
, *frozen
;
1674 int start
, end
, number_steps
;
1676 int i
, k
, m
, n
, gf
, step
;
1678 auto mdatoms
= mdAtoms
->mdatoms();
1682 gmx_fatal(FARGS
, "Cannot do parallel L-BFGS Minimization - yet.\n");
1685 if (nullptr != constr
)
1687 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).");
1690 n
= 3*state_global
->natoms
;
1691 nmaxcorr
= inputrec
->nbfgscorr
;
1696 snew(rho
, nmaxcorr
);
1697 snew(alpha
, nmaxcorr
);
1700 for (i
= 0; i
< nmaxcorr
; i
++)
1706 for (i
= 0; i
< nmaxcorr
; i
++)
1715 init_em(fplog
, LBFGS
, cr
, outputProvider
, inputrec
, mdrunOptions
,
1716 state_global
, top_global
, &ems
, &top
,
1717 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdAtoms
, &gstat
,
1718 vsite
, constr
, nullptr,
1719 nfile
, fnm
, &outf
, &mdebin
, wcycle
);
1722 end
= mdatoms
->homenr
;
1724 /* We need 4 working states */
1725 em_state_t s0
{}, s1
{}, s2
{}, s3
{};
1726 em_state_t
*sa
= &s0
;
1727 em_state_t
*sb
= &s1
;
1728 em_state_t
*sc
= &s2
;
1729 em_state_t
*last
= &s3
;
1730 /* Initialize by copying the state from ems (we could skip x and f here) */
1735 /* Print to log file */
1736 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, LBFGS
);
1738 do_log
= do_ene
= do_x
= do_f
= TRUE
;
1740 /* Max number of steps */
1741 number_steps
= inputrec
->nsteps
;
1743 /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
1745 for (i
= start
; i
< end
; i
++)
1747 if (mdatoms
->cFREEZE
)
1749 gf
= mdatoms
->cFREEZE
[i
];
1751 for (m
= 0; m
< DIM
; m
++)
1753 frozen
[3*i
+m
] = inputrec
->opts
.nFreeze
[gf
][m
];
1758 sp_header(stderr
, LBFGS
, inputrec
->em_tol
, number_steps
);
1762 sp_header(fplog
, LBFGS
, inputrec
->em_tol
, number_steps
);
1767 construct_vsites(vsite
, as_rvec_array(state_global
->x
.data()), 1, nullptr,
1768 top
->idef
.iparams
, top
->idef
.il
,
1769 fr
->ePBC
, fr
->bMolPBC
, cr
, state_global
->box
);
1772 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1773 /* do_force always puts the charge groups in the box and shifts again
1774 * We do not unshift, so molecules are always whole
1777 evaluate_energy(fplog
, cr
,
1778 top_global
, &ems
, top
,
1779 inputrec
, nrnb
, wcycle
, gstat
,
1780 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
1781 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1786 /* Copy stuff to the energy bin for easy printing etc. */
1787 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1788 mdatoms
->tmass
, enerd
, state_global
, inputrec
->fepvals
, inputrec
->expandedvals
, state_global
->box
,
1789 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
1791 print_ebin_header(fplog
, step
, step
);
1792 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1793 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1797 /* Set the initial step.
1798 * since it will be multiplied by the non-normalized search direction
1799 * vector (force vector the first time), we scale it by the
1800 * norm of the force.
1805 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
1806 fprintf(stderr
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1807 fprintf(stderr
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1808 fprintf(stderr
, " F-Norm = %12.5e\n", ems
.fnorm
/sqrtNumAtoms
);
1809 fprintf(stderr
, "\n");
1810 /* and copy to the log file too... */
1811 fprintf(fplog
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1812 fprintf(fplog
, " F-max = %12.5e on atom %d\n", ems
.fmax
, ems
.a_fmax
+ 1);
1813 fprintf(fplog
, " F-Norm = %12.5e\n", ems
.fnorm
/sqrtNumAtoms
);
1814 fprintf(fplog
, "\n");
1817 // Point is an index to the memory of search directions, where 0 is the first one.
1820 // Set initial search direction to the force (-gradient), or 0 for frozen particles.
1821 real
*fInit
= static_cast<real
*>(as_rvec_array(ems
.f
.data())[0]);
1822 for (i
= 0; i
< n
; i
++)
1826 dx
[point
][i
] = fInit
[i
]; /* Initial search direction */
1834 // Stepsize will be modified during the search, and actually it is not critical
1835 // (the main efficiency in the algorithm comes from changing directions), but
1836 // we still need an initial value, so estimate it as the inverse of the norm
1837 // so we take small steps where the potential fluctuates a lot.
1838 stepsize
= 1.0/ems
.fnorm
;
1840 /* Start the loop over BFGS steps.
1841 * Each successful step is counted, and we continue until
1842 * we either converge or reach the max number of steps.
1847 /* Set the gradient from the force */
1849 for (step
= 0; (number_steps
< 0 || step
<= number_steps
) && !converged
; step
++)
1852 /* Write coordinates if necessary */
1853 do_x
= do_per_step(step
, inputrec
->nstxout
);
1854 do_f
= do_per_step(step
, inputrec
->nstfout
);
1859 mdof_flags
|= MDOF_X
;
1864 mdof_flags
|= MDOF_F
;
1869 mdof_flags
|= MDOF_IMD
;
1872 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
1873 top_global
, step
, (real
)step
, &ems
.s
, state_global
, observablesHistory
, &ems
.f
);
1875 /* Do the linesearching in the direction dx[point][0..(n-1)] */
1877 /* make s a pointer to current search direction - point=0 first time we get here */
1880 real
*xx
= static_cast<real
*>(as_rvec_array(ems
.s
.x
.data())[0]);
1881 real
*ff
= static_cast<real
*>(as_rvec_array(ems
.f
.data())[0]);
1883 // calculate line gradient in position A
1884 for (gpa
= 0, i
= 0; i
< n
; i
++)
1889 /* Calculate minimum allowed stepsize along the line, before the average (norm)
1890 * relative change in coordinate is smaller than precision
1892 for (minstep
= 0, i
= 0; i
< n
; i
++)
1902 minstep
= GMX_REAL_EPS
/sqrt(minstep
/n
);
1904 if (stepsize
< minstep
)
1910 // Before taking any steps along the line, store the old position
1912 real
*lastx
= static_cast<real
*>(as_rvec_array(last
->s
.x
.data())[0]);
1913 real
*lastf
= static_cast<real
*>(as_rvec_array(last
->f
.data())[0]);
1918 /* Take a step downhill.
1919 * In theory, we should find the actual minimum of the function in this
1920 * direction, somewhere along the line.
1921 * That is quite possible, but it turns out to take 5-10 function evaluations
1922 * for each line. However, we dont really need to find the exact minimum -
1923 * it is much better to start a new BFGS step in a modified direction as soon
1924 * as we are close to it. This will save a lot of energy evaluations.
1926 * In practice, we just try to take a single step.
1927 * If it worked (i.e. lowered the energy), we increase the stepsize but
1928 * continue straight to the next BFGS step without trying to find any minimum,
1929 * i.e. we change the search direction too. If the line was smooth, it is
1930 * likely we are in a smooth region, and then it makes sense to take longer
1931 * steps in the modified search direction too.
1933 * If it didn't work (higher energy), there must be a minimum somewhere between
1934 * the old position and the new one. Then we need to start by finding a lower
1935 * value before we change search direction. Since the energy was apparently
1936 * quite rough, we need to decrease the step size.
1938 * Due to the finite numerical accuracy, it turns out that it is a good idea
1939 * to accept a SMALL increase in energy, if the derivative is still downhill.
1940 * This leads to lower final energies in the tests I've done. / Erik
1943 // State "A" is the first position along the line.
1944 // reference position along line is initially zero
1947 // Check stepsize first. We do not allow displacements
1948 // larger than emstep.
1952 // Pick a new position C by adding stepsize to A.
1955 // Calculate what the largest change in any individual coordinate
1956 // would be (translation along line * gradient along line)
1958 for (i
= 0; i
< n
; i
++)
1961 if (delta
> maxdelta
)
1966 // If any displacement is larger than the stepsize limit, reduce the step
1967 if (maxdelta
> inputrec
->em_stepsize
)
1972 while (maxdelta
> inputrec
->em_stepsize
);
1974 // Take a trial step and move the coordinate array xc[] to position C
1975 real
*xc
= static_cast<real
*>(as_rvec_array(sc
->s
.x
.data())[0]);
1976 for (i
= 0; i
< n
; i
++)
1978 xc
[i
] = lastx
[i
] + c
*s
[i
];
1982 // Calculate energy for the trial step in position C
1983 evaluate_energy(fplog
, cr
,
1984 top_global
, sc
, top
,
1985 inputrec
, nrnb
, wcycle
, gstat
,
1986 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
1987 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
1989 // Calc line gradient in position C
1990 real
*fc
= static_cast<real
*>(as_rvec_array(sc
->f
.data())[0]);
1991 for (gpc
= 0, i
= 0; i
< n
; i
++)
1993 gpc
-= s
[i
]*fc
[i
]; /* f is negative gradient, thus the sign */
1995 /* Sum the gradient along the line across CPUs */
1998 gmx_sumd(1, &gpc
, cr
);
2001 // This is the max amount of increase in energy we tolerate.
2002 // By allowing VERY small changes (close to numerical precision) we
2003 // frequently find even better (lower) final energies.
2004 tmp
= sqrt(GMX_REAL_EPS
)*fabs(sa
->epot
);
2006 // Accept the step if the energy is lower in the new position C (compared to A),
2007 // or if it is not significantly higher and the line derivative is still negative.
2008 if (sc
->epot
< sa
->epot
|| (gpc
< 0 && sc
->epot
< (sa
->epot
+ tmp
)))
2010 // Great, we found a better energy. We no longer try to alter the
2011 // stepsize, but simply accept this new better position. The we select a new
2012 // search direction instead, which will be much more efficient than continuing
2013 // to take smaller steps along a line. Set fnorm based on the new C position,
2014 // which will be used to update the stepsize to 1/fnorm further down.
2019 // If we got here, the energy is NOT lower in point C, i.e. it will be the same
2020 // or higher than in point A. In this case it is pointless to move to point C,
2021 // so we will have to do more iterations along the same line to find a smaller
2022 // value in the interval [A=0.0,C].
2023 // Here, A is still 0.0, but that will change when we do a search in the interval
2024 // [0.0,C] below. That search we will do by interpolation or bisection rather
2025 // than with the stepsize, so no need to modify it. For the next search direction
2026 // it will be reset to 1/fnorm anyway.
2032 // OK, if we didn't find a lower value we will have to locate one now - there must
2033 // be one in the interval [a,c].
2034 // The same thing is valid here, though: Don't spend dozens of iterations to find
2035 // the line minimum. We try to interpolate based on the derivative at the endpoints,
2036 // and only continue until we find a lower value. In most cases this means 1-2 iterations.
2037 // I also have a safeguard for potentially really pathological functions so we never
2038 // take more than 20 steps before we give up.
2039 // If we already found a lower value we just skip this step and continue to the update.
2044 // Select a new trial point B in the interval [A,C].
2045 // If the derivatives at points a & c have different sign we interpolate to zero,
2046 // otherwise just do a bisection since there might be multiple minima/maxima
2047 // inside the interval.
2048 if (gpa
< 0 && gpc
> 0)
2050 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
2057 /* safeguard if interpolation close to machine accuracy causes errors:
2058 * never go outside the interval
2060 if (b
<= a
|| b
>= c
)
2065 // Take a trial step to point B
2066 real
*xb
= static_cast<real
*>(as_rvec_array(sb
->s
.x
.data())[0]);
2067 for (i
= 0; i
< n
; i
++)
2069 xb
[i
] = lastx
[i
] + b
*s
[i
];
2073 // Calculate energy for the trial step in point B
2074 evaluate_energy(fplog
, cr
,
2075 top_global
, sb
, top
,
2076 inputrec
, nrnb
, wcycle
, gstat
,
2077 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
2078 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
2081 // Calculate gradient in point B
2082 real
*fb
= static_cast<real
*>(as_rvec_array(sb
->f
.data())[0]);
2083 for (gpb
= 0, i
= 0; i
< n
; i
++)
2085 gpb
-= s
[i
]*fb
[i
]; /* f is negative gradient, thus the sign */
2088 /* Sum the gradient along the line across CPUs */
2091 gmx_sumd(1, &gpb
, cr
);
2094 // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
2095 // at the new point B, and rename the endpoints of this new interval A and C.
2098 /* Replace c endpoint with b */
2100 /* swap states b and c */
2101 swap_em_state(&sb
, &sc
);
2105 /* Replace a endpoint with b */
2107 /* swap states a and b */
2108 swap_em_state(&sa
, &sb
);
2112 * Stop search as soon as we find a value smaller than the endpoints,
2113 * or if the tolerance is below machine precision.
2114 * Never run more than 20 steps, no matter what.
2118 while ((sb
->epot
> sa
->epot
|| sb
->epot
> sc
->epot
) && (nminstep
< 20));
2120 if (fabs(sb
->epot
- Epot0
) < GMX_REAL_EPS
|| nminstep
>= 20)
2122 /* OK. We couldn't find a significantly lower energy.
2123 * If ncorr==0 this was steepest descent, and then we give up.
2124 * If not, reset memory to restart as steepest descent before quitting.
2136 /* Search in gradient direction */
2137 for (i
= 0; i
< n
; i
++)
2139 dx
[point
][i
] = ff
[i
];
2141 /* Reset stepsize */
2142 stepsize
= 1.0/fnorm
;
2147 /* Select min energy state of A & C, put the best in xx/ff/Epot
2149 if (sc
->epot
< sa
->epot
)
2171 /* Update the memory information, and calculate a new
2172 * approximation of the inverse hessian
2175 /* Have new data in Epot, xx, ff */
2176 if (ncorr
< nmaxcorr
)
2181 for (i
= 0; i
< n
; i
++)
2183 dg
[point
][i
] = lastf
[i
]-ff
[i
];
2184 dx
[point
][i
] *= step_taken
;
2189 for (i
= 0; i
< n
; i
++)
2191 dgdg
+= dg
[point
][i
]*dg
[point
][i
];
2192 dgdx
+= dg
[point
][i
]*dx
[point
][i
];
2197 rho
[point
] = 1.0/dgdx
;
2200 if (point
>= nmaxcorr
)
2206 for (i
= 0; i
< n
; i
++)
2213 /* Recursive update. First go back over the memory points */
2214 for (k
= 0; k
< ncorr
; k
++)
2223 for (i
= 0; i
< n
; i
++)
2225 sq
+= dx
[cp
][i
]*p
[i
];
2228 alpha
[cp
] = rho
[cp
]*sq
;
2230 for (i
= 0; i
< n
; i
++)
2232 p
[i
] -= alpha
[cp
]*dg
[cp
][i
];
2236 for (i
= 0; i
< n
; i
++)
2241 /* And then go forward again */
2242 for (k
= 0; k
< ncorr
; k
++)
2245 for (i
= 0; i
< n
; i
++)
2247 yr
+= p
[i
]*dg
[cp
][i
];
2251 beta
= alpha
[cp
]-beta
;
2253 for (i
= 0; i
< n
; i
++)
2255 p
[i
] += beta
*dx
[cp
][i
];
2265 for (i
= 0; i
< n
; i
++)
2269 dx
[point
][i
] = p
[i
];
2277 /* Print it if necessary */
2280 if (mdrunOptions
.verbose
)
2282 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2283 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
2284 step
, ems
.epot
, ems
.fnorm
/sqrtNumAtoms
, ems
.fmax
, ems
.a_fmax
+ 1);
2287 /* Store the new (lower) energies */
2288 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
2289 mdatoms
->tmass
, enerd
, state_global
, inputrec
->fepvals
, inputrec
->expandedvals
, state_global
->box
,
2290 nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2291 do_log
= do_per_step(step
, inputrec
->nstlog
);
2292 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
2295 print_ebin_header(fplog
, step
, step
);
2297 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
2298 do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
2299 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2302 /* Send x and E to IMD client, if bIMD is TRUE. */
2303 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state_global
->box
, as_rvec_array(state_global
->x
.data()), inputrec
, 0, wcycle
) && MASTER(cr
))
2305 IMD_send_positions(inputrec
->imd
);
2308 // Reset stepsize in we are doing more iterations
2309 stepsize
= 1.0/ems
.fnorm
;
2311 /* Stop when the maximum force lies below tolerance.
2312 * If we have reached machine precision, converged is already set to true.
2314 converged
= converged
|| (ems
.fmax
< inputrec
->em_tol
);
2316 } /* End of the loop */
2318 /* IMD cleanup, if bIMD is TRUE. */
2319 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2323 step
--; /* we never took that last step in this case */
2326 if (ems
.fmax
> inputrec
->em_tol
)
2330 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2331 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2336 /* If we printed energy and/or logfile last step (which was the last step)
2337 * we don't have to do it again, but otherwise print the final values.
2339 if (!do_log
) /* Write final value to log since we didn't do anythin last step */
2341 print_ebin_header(fplog
, step
, step
);
2343 if (!do_ene
|| !do_log
) /* Write final energy file entries */
2345 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
2346 !do_log
? fplog
: nullptr, step
, step
, eprNORMAL
,
2347 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2350 /* Print some stuff... */
2353 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2357 * For accurate normal mode calculation it is imperative that we
2358 * store the last conformation into the full precision binary trajectory.
2360 * However, we should only do it if we did NOT already write this step
2361 * above (which we did if do_x or do_f was true).
2363 do_x
= !do_per_step(step
, inputrec
->nstxout
);
2364 do_f
= !do_per_step(step
, inputrec
->nstfout
);
2365 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
2366 top_global
, inputrec
, step
,
2367 &ems
, state_global
, observablesHistory
);
2371 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2372 print_converged(stderr
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2373 number_steps
, &ems
, sqrtNumAtoms
);
2374 print_converged(fplog
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2375 number_steps
, &ems
, sqrtNumAtoms
);
2377 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
2380 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2382 /* To print the actual number of steps we needed somewhere */
2383 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
2386 } /* That's all folks */
2388 /*! \brief Do steepest descents minimization
2389 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
2390 int nfile, const t_filenm fnm[],
2391 const gmx_output_env_t *oenv,
2392 const MdrunOptions &mdrunOptions,
2393 gmx_vsite_t *vsite, gmx_constr_t constr,
2394 gmx::IMDOutputProvider *outputProvider,
2395 t_inputrec *inputrec,
2396 gmx_mtop_t *top_global, t_fcdata *fcd,
2397 t_state *state_global,
2398 gmx::MDAtoms *mdAtoms,
2399 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2402 const ReplicaExchangeParameters &replExParams,
2403 gmx_walltime_accounting_t walltime_accounting)
2405 double do_steep(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger gmx_unused
&mdlog
,
2406 int nfile
, const t_filenm fnm
[],
2407 const gmx_output_env_t gmx_unused
*oenv
,
2408 const MdrunOptions
&mdrunOptions
,
2409 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2410 gmx::IMDOutputProvider
*outputProvider
,
2411 t_inputrec
*inputrec
,
2412 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2413 t_state
*state_global
,
2414 ObservablesHistory
*observablesHistory
,
2415 gmx::MDAtoms
*mdAtoms
,
2416 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2418 const ReplicaExchangeParameters gmx_unused
&replExParams
,
2419 gmx_membed_t gmx_unused
*membed
,
2420 gmx_walltime_accounting_t walltime_accounting
)
2422 const char *SD
= "Steepest Descents";
2423 gmx_localtop_t
*top
;
2424 gmx_enerdata_t
*enerd
;
2425 gmx_global_stat_t gstat
;
2431 gmx_bool bDone
, bAbort
, do_x
, do_f
;
2436 int steps_accepted
= 0;
2437 auto mdatoms
= mdAtoms
->mdatoms();
2439 /* Create 2 states on the stack and extract pointers that we will swap */
2440 em_state_t s0
{}, s1
{};
2441 em_state_t
*s_min
= &s0
;
2442 em_state_t
*s_try
= &s1
;
2444 /* Init em and store the local state in s_try */
2445 init_em(fplog
, SD
, cr
, outputProvider
, inputrec
, mdrunOptions
,
2446 state_global
, top_global
, s_try
, &top
,
2447 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdAtoms
, &gstat
,
2448 vsite
, constr
, nullptr,
2449 nfile
, fnm
, &outf
, &mdebin
, wcycle
);
2451 /* Print to log file */
2452 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, SD
);
2454 /* Set variables for stepsize (in nm). This is the largest
2455 * step that we are going to make in any direction.
2457 ustep
= inputrec
->em_stepsize
;
2460 /* Max number of steps */
2461 nsteps
= inputrec
->nsteps
;
2465 /* Print to the screen */
2466 sp_header(stderr
, SD
, inputrec
->em_tol
, nsteps
);
2470 sp_header(fplog
, SD
, inputrec
->em_tol
, nsteps
);
2473 /**** HERE STARTS THE LOOP ****
2474 * count is the counter for the number of steps
2475 * bDone will be TRUE when the minimization has converged
2476 * bAbort will be TRUE when nsteps steps have been performed or when
2477 * the stepsize becomes smaller than is reasonable for machine precision
2482 while (!bDone
&& !bAbort
)
2484 bAbort
= (nsteps
>= 0) && (count
== nsteps
);
2486 /* set new coordinates, except for first step */
2487 bool validStep
= true;
2491 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
,
2492 s_min
, stepsize
, &s_min
->f
, s_try
,
2493 constr
, top
, nrnb
, wcycle
, count
);
2498 evaluate_energy(fplog
, cr
,
2499 top_global
, s_try
, top
,
2500 inputrec
, nrnb
, wcycle
, gstat
,
2501 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
2502 mu_tot
, enerd
, vir
, pres
, count
, count
== 0);
2506 // Signal constraint error during stepping with energy=inf
2507 s_try
->epot
= std::numeric_limits
<real
>::infinity();
2512 print_ebin_header(fplog
, count
, count
);
2517 s_min
->epot
= s_try
->epot
;
2520 /* Print it if necessary */
2523 if (mdrunOptions
.verbose
)
2525 fprintf(stderr
, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
2526 count
, ustep
, s_try
->epot
, s_try
->fmax
, s_try
->a_fmax
+1,
2527 ( (count
== 0) || (s_try
->epot
< s_min
->epot
) ) ? '\n' : '\r');
2531 if ( (count
== 0) || (s_try
->epot
< s_min
->epot
) )
2533 /* Store the new (lower) energies */
2534 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)count
,
2535 mdatoms
->tmass
, enerd
, &s_try
->s
, inputrec
->fepvals
, inputrec
->expandedvals
,
2536 s_try
->s
.box
, nullptr, nullptr, vir
, pres
, nullptr, mu_tot
, constr
);
2538 /* Prepare IMD energy record, if bIMD is TRUE. */
2539 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, count
, TRUE
);
2541 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
,
2542 do_per_step(steps_accepted
, inputrec
->nstdisreout
),
2543 do_per_step(steps_accepted
, inputrec
->nstorireout
),
2544 fplog
, count
, count
, eprNORMAL
,
2545 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2550 /* Now if the new energy is smaller than the previous...
2551 * or if this is the first step!
2552 * or if we did random steps!
2555 if ( (count
== 0) || (s_try
->epot
< s_min
->epot
) )
2559 /* Test whether the convergence criterion is met... */
2560 bDone
= (s_try
->fmax
< inputrec
->em_tol
);
2562 /* Copy the arrays for force, positions and energy */
2563 /* The 'Min' array always holds the coords and forces of the minimal
2565 swap_em_state(&s_min
, &s_try
);
2571 /* Write to trn, if necessary */
2572 do_x
= do_per_step(steps_accepted
, inputrec
->nstxout
);
2573 do_f
= do_per_step(steps_accepted
, inputrec
->nstfout
);
2574 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, nullptr,
2575 top_global
, inputrec
, count
,
2576 s_min
, state_global
, observablesHistory
);
2580 /* If energy is not smaller make the step smaller... */
2583 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
2585 /* Reload the old state */
2586 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
2587 s_min
, top
, mdAtoms
, fr
, vsite
, constr
,
2592 /* Determine new step */
2593 stepsize
= ustep
/s_min
->fmax
;
2595 /* Check if stepsize is too small, with 1 nm as a characteristic length */
2597 if (count
== nsteps
|| ustep
< 1e-12)
2599 if (count
== nsteps
|| ustep
< 1e-6)
2604 warn_step(stderr
, inputrec
->em_tol
, count
== nsteps
, constr
!= nullptr);
2605 warn_step(fplog
, inputrec
->em_tol
, count
== nsteps
, constr
!= nullptr);
2610 /* Send IMD energies and positions, if bIMD is TRUE. */
2611 if (do_IMD(inputrec
->bIMD
, count
, cr
, TRUE
, state_global
->box
,
2612 MASTER(cr
) ? as_rvec_array(state_global
->x
.data()) : nullptr,
2613 inputrec
, 0, wcycle
) &&
2616 IMD_send_positions(inputrec
->imd
);
2620 } /* End of the loop */
2622 /* IMD cleanup, if bIMD is TRUE. */
2623 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2625 /* Print some data... */
2628 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2630 write_em_traj(fplog
, cr
, outf
, TRUE
, inputrec
->nstfout
, ftp2fn(efSTO
, nfile
, fnm
),
2631 top_global
, inputrec
, count
,
2632 s_min
, state_global
, observablesHistory
);
2636 double sqrtNumAtoms
= sqrt(static_cast<double>(state_global
->natoms
));
2638 print_converged(stderr
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2639 s_min
, sqrtNumAtoms
);
2640 print_converged(fplog
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2641 s_min
, sqrtNumAtoms
);
2644 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2646 /* To print the actual number of steps we needed somewhere */
2647 inputrec
->nsteps
= count
;
2649 walltime_accounting_set_nsteps_done(walltime_accounting
, count
);
2652 } /* That's all folks */
2654 /*! \brief Do normal modes analysis
2655 \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
2656 int nfile, const t_filenm fnm[],
2657 const gmx_output_env_t *oenv,
2658 const MdrunOptions &mdrunOptions,
2659 gmx_vsite_t *vsite, gmx_constr_t constr,
2660 gmx::IMDOutputProvider *outputProvider,
2661 t_inputrec *inputrec,
2662 gmx_mtop_t *top_global, t_fcdata *fcd,
2663 t_state *state_global,
2664 gmx::MDAtoms *mdAtoms,
2665 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
2668 const ReplicaExchangeParameters &replExParams,
2669 gmx_walltime_accounting_t walltime_accounting)
2671 double do_nm(FILE *fplog
, t_commrec
*cr
, const gmx::MDLogger
&mdlog
,
2672 int nfile
, const t_filenm fnm
[],
2673 const gmx_output_env_t gmx_unused
*oenv
,
2674 const MdrunOptions
&mdrunOptions
,
2675 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2676 gmx::IMDOutputProvider
*outputProvider
,
2677 t_inputrec
*inputrec
,
2678 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2679 t_state
*state_global
,
2680 ObservablesHistory gmx_unused
*observablesHistory
,
2681 gmx::MDAtoms
*mdAtoms
,
2682 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2684 const ReplicaExchangeParameters gmx_unused
&replExParams
,
2685 gmx_membed_t gmx_unused
*membed
,
2686 gmx_walltime_accounting_t walltime_accounting
)
2688 const char *NM
= "Normal Mode Analysis";
2691 gmx_localtop_t
*top
;
2692 gmx_enerdata_t
*enerd
;
2693 gmx_global_stat_t gstat
;
2698 gmx_bool bSparse
; /* use sparse matrix storage format */
2700 gmx_sparsematrix_t
* sparse_matrix
= nullptr;
2701 real
* full_matrix
= nullptr;
2703 /* added with respect to mdrun */
2705 real der_range
= 10.0*sqrt(GMX_REAL_EPS
);
2707 bool bIsMaster
= MASTER(cr
);
2708 auto mdatoms
= mdAtoms
->mdatoms();
2710 if (constr
!= nullptr)
2712 gmx_fatal(FARGS
, "Constraints present with Normal Mode Analysis, this combination is not supported");
2715 gmx_shellfc_t
*shellfc
;
2717 em_state_t state_work
{};
2719 /* Init em and store the local state in state_minimum */
2720 init_em(fplog
, NM
, cr
, outputProvider
, inputrec
, mdrunOptions
,
2721 state_global
, top_global
, &state_work
, &top
,
2722 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdAtoms
, &gstat
,
2723 vsite
, constr
, &shellfc
,
2724 nfile
, fnm
, &outf
, nullptr, wcycle
);
2726 std::vector
<size_t> atom_index
= get_atom_index(top_global
);
2727 snew(fneg
, atom_index
.size());
2728 snew(dfdx
, atom_index
.size());
2734 "NOTE: This version of GROMACS has been compiled in single precision,\n"
2735 " which MIGHT not be accurate enough for normal mode analysis.\n"
2736 " GROMACS now uses sparse matrix storage, so the memory requirements\n"
2737 " are fairly modest even if you recompile in double precision.\n\n");
2741 /* Check if we can/should use sparse storage format.
2743 * Sparse format is only useful when the Hessian itself is sparse, which it
2744 * will be when we use a cutoff.
2745 * For small systems (n<1000) it is easier to always use full matrix format, though.
2747 if (EEL_FULL(fr
->ic
->eeltype
) || fr
->rlist
== 0.0)
2749 GMX_LOG(mdlog
.warning
).appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
2752 else if (atom_index
.size() < 1000)
2754 GMX_LOG(mdlog
.warning
).appendTextFormatted("Small system size (N=%d), using full Hessian format.",
2760 GMX_LOG(mdlog
.warning
).appendText("Using compressed symmetric sparse Hessian format.");
2764 /* Number of dimensions, based on real atoms, that is not vsites or shell */
2765 sz
= DIM
*atom_index
.size();
2767 fprintf(stderr
, "Allocating Hessian memory...\n\n");
2771 sparse_matrix
= gmx_sparsematrix_init(sz
);
2772 sparse_matrix
->compressed_symmetric
= TRUE
;
2776 snew(full_matrix
, sz
*sz
);
2783 /* Write start time and temperature */
2784 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, NM
);
2786 /* fudge nr of steps to nr of atoms */
2787 inputrec
->nsteps
= atom_index
.size()*2;
2791 fprintf(stderr
, "starting normal mode calculation '%s'\n%d steps.\n\n",
2792 *(top_global
->name
), (int)inputrec
->nsteps
);
2795 nnodes
= cr
->nnodes
;
2797 /* Make evaluate_energy do a single node force calculation */
2799 evaluate_energy(fplog
, cr
,
2800 top_global
, &state_work
, top
,
2801 inputrec
, nrnb
, wcycle
, gstat
,
2802 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
2803 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
2804 cr
->nnodes
= nnodes
;
2806 /* if forces are not small, warn user */
2807 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, &state_work
);
2809 GMX_LOG(mdlog
.warning
).appendTextFormatted("Maximum force:%12.5e", state_work
.fmax
);
2810 if (state_work
.fmax
> 1.0e-3)
2812 GMX_LOG(mdlog
.warning
).appendText(
2813 "The force is probably not small enough to "
2814 "ensure that you are at a minimum.\n"
2815 "Be aware that negative eigenvalues may occur\n"
2816 "when the resulting matrix is diagonalized.");
2819 /***********************************************************
2821 * Loop over all pairs in matrix
2823 * do_force called twice. Once with positive and
2824 * once with negative displacement
2826 ************************************************************/
2828 /* Steps are divided one by one over the nodes */
2830 for (unsigned int aid
= cr
->nodeid
; aid
< atom_index
.size(); aid
+= nnodes
)
2832 size_t atom
= atom_index
[aid
];
2833 for (size_t d
= 0; d
< DIM
; d
++)
2835 gmx_bool bBornRadii
= FALSE
;
2836 gmx_int64_t step
= 0;
2837 int force_flags
= GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
;
2840 x_min
= state_work
.s
.x
[atom
][d
];
2842 for (unsigned int dx
= 0; (dx
< 2); dx
++)
2846 state_work
.s
.x
[atom
][d
] = x_min
- der_range
;
2850 state_work
.s
.x
[atom
][d
] = x_min
+ der_range
;
2853 /* Make evaluate_energy do a single node force calculation */
2857 /* Now is the time to relax the shells */
2858 (void) relax_shell_flexcon(fplog
, cr
, mdrunOptions
.verbose
, step
,
2859 inputrec
, bNS
, force_flags
,
2862 &state_work
.s
, &state_work
.f
, vir
, mdatoms
,
2863 nrnb
, wcycle
, graph
, &top_global
->groups
,
2864 shellfc
, fr
, bBornRadii
, t
, mu_tot
,
2866 DdOpenBalanceRegionBeforeForceComputation::no
,
2867 DdCloseBalanceRegionAfterForceComputation::no
);
2873 evaluate_energy(fplog
, cr
,
2874 top_global
, &state_work
, top
,
2875 inputrec
, nrnb
, wcycle
, gstat
,
2876 vsite
, constr
, fcd
, graph
, mdAtoms
, fr
,
2877 mu_tot
, enerd
, vir
, pres
, atom
*2+dx
, FALSE
);
2880 cr
->nnodes
= nnodes
;
2884 for (size_t i
= 0; i
< atom_index
.size(); i
++)
2886 copy_rvec(state_work
.f
[atom_index
[i
]], fneg
[i
]);
2891 /* x is restored to original */
2892 state_work
.s
.x
[atom
][d
] = x_min
;
2894 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2896 for (size_t k
= 0; (k
< DIM
); k
++)
2899 -(state_work
.f
[atom_index
[j
]][k
] - fneg
[j
][k
])/(2*der_range
);
2906 #define mpi_type GMX_MPI_REAL
2907 MPI_Send(dfdx
[0], atom_index
.size()*DIM
, mpi_type
, MASTER(cr
),
2908 cr
->nodeid
, cr
->mpi_comm_mygroup
);
2913 for (node
= 0; (node
< nnodes
&& atom
+node
< atom_index
.size()); node
++)
2919 MPI_Recv(dfdx
[0], atom_index
.size()*DIM
, mpi_type
, node
, node
,
2920 cr
->mpi_comm_mygroup
, &stat
);
2925 row
= (atom
+ node
)*DIM
+ d
;
2927 for (size_t j
= 0; j
< atom_index
.size(); j
++)
2929 for (size_t k
= 0; k
< DIM
; k
++)
2935 if (col
>= row
&& dfdx
[j
][k
] != 0.0)
2937 gmx_sparsematrix_increment_value(sparse_matrix
,
2938 row
, col
, dfdx
[j
][k
]);
2943 full_matrix
[row
*sz
+col
] = dfdx
[j
][k
];
2950 if (mdrunOptions
.verbose
&& fplog
)
2955 /* write progress */
2956 if (bIsMaster
&& mdrunOptions
.verbose
)
2958 fprintf(stderr
, "\rFinished step %d out of %d",
2959 static_cast<int>(std::min(atom
+nnodes
, atom_index
.size())),
2960 static_cast<int>(atom_index
.size()));
2967 fprintf(stderr
, "\n\nWriting Hessian...\n");
2968 gmx_mtxio_write(ftp2fn(efMTX
, nfile
, fnm
), sz
, sz
, full_matrix
, sparse_matrix
);
2971 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2973 walltime_accounting_set_nsteps_done(walltime_accounting
, atom_index
.size()*2);