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45 #include "gromacs/utility/cstringutil.h"
47 #include "gromacs/utility/smalloc.h"
53 #include "gmx_fatal.h"
64 #include "md_support.h"
69 #include "mtop_util.h"
72 #include "gmx_omp_nthreads.h"
73 #include "md_logging.h"
75 #include "gromacs/fileio/confio.h"
76 #include "gromacs/fileio/trajectory_writing.h"
77 #include "gromacs/linearalgebra/mtxio.h"
78 #include "gromacs/linearalgebra/sparsematrix.h"
79 #include "gromacs/timing/wallcycle.h"
80 #include "gromacs/timing/walltime_accounting.h"
81 #include "gromacs/imd/imd.h"
92 static em_state_t
*init_em_state()
98 /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
99 snew(ems
->s
.lambda
, efptNR
);
104 static void print_em_start(FILE *fplog
,
106 gmx_walltime_accounting_t walltime_accounting
,
107 gmx_wallcycle_t wcycle
,
110 walltime_accounting_start(walltime_accounting
);
111 wallcycle_start(wcycle
, ewcRUN
);
112 print_start(fplog
, cr
, walltime_accounting
, name
);
114 static void em_time_end(gmx_walltime_accounting_t walltime_accounting
,
115 gmx_wallcycle_t wcycle
)
117 wallcycle_stop(wcycle
, ewcRUN
);
119 walltime_accounting_end(walltime_accounting
);
122 static void sp_header(FILE *out
, const char *minimizer
, real ftol
, int nsteps
)
125 fprintf(out
, "%s:\n", minimizer
);
126 fprintf(out
, " Tolerance (Fmax) = %12.5e\n", ftol
);
127 fprintf(out
, " Number of steps = %12d\n", nsteps
);
130 static void warn_step(FILE *fp
, real ftol
, gmx_bool bLastStep
, gmx_bool bConstrain
)
136 "\nEnergy minimization reached the maximum number "
137 "of steps before the forces reached the requested "
138 "precision Fmax < %g.\n", ftol
);
143 "\nEnergy minimization has stopped, but the forces have "
144 "not converged to the requested precision Fmax < %g (which "
145 "may not be possible for your system). It stopped "
146 "because the algorithm tried to make a new step whose size "
147 "was too small, or there was no change in the energy since "
148 "last step. Either way, we regard the minimization as "
149 "converged to within the available machine precision, "
150 "given your starting configuration and EM parameters.\n%s%s",
152 sizeof(real
) < sizeof(double) ?
153 "\nDouble precision normally gives you higher accuracy, but "
154 "this is often not needed for preparing to run molecular "
158 "You might need to increase your constraint accuracy, or turn\n"
159 "off constraints altogether (set constraints = none in mdp file)\n" :
162 fputs(wrap_lines(buffer
, 78, 0, FALSE
), fp
);
167 static void print_converged(FILE *fp
, const char *alg
, real ftol
,
168 gmx_int64_t count
, gmx_bool bDone
, gmx_int64_t nsteps
,
169 real epot
, real fmax
, int nfmax
, real fnorm
)
171 char buf
[STEPSTRSIZE
];
175 fprintf(fp
, "\n%s converged to Fmax < %g in %s steps\n",
176 alg
, ftol
, gmx_step_str(count
, buf
));
178 else if (count
< nsteps
)
180 fprintf(fp
, "\n%s converged to machine precision in %s steps,\n"
181 "but did not reach the requested Fmax < %g.\n",
182 alg
, gmx_step_str(count
, buf
), ftol
);
186 fprintf(fp
, "\n%s did not converge to Fmax < %g in %s steps.\n",
187 alg
, ftol
, gmx_step_str(count
, buf
));
191 fprintf(fp
, "Potential Energy = %21.14e\n", epot
);
192 fprintf(fp
, "Maximum force = %21.14e on atom %d\n", fmax
, nfmax
+1);
193 fprintf(fp
, "Norm of force = %21.14e\n", fnorm
);
195 fprintf(fp
, "Potential Energy = %14.7e\n", epot
);
196 fprintf(fp
, "Maximum force = %14.7e on atom %d\n", fmax
, nfmax
+1);
197 fprintf(fp
, "Norm of force = %14.7e\n", fnorm
);
201 static void get_f_norm_max(t_commrec
*cr
,
202 t_grpopts
*opts
, t_mdatoms
*mdatoms
, rvec
*f
,
203 real
*fnorm
, real
*fmax
, int *a_fmax
)
206 real fmax2
, fmax2_0
, fam
;
207 int la_max
, a_max
, start
, end
, i
, m
, gf
;
209 /* This routine finds the largest force and returns it.
210 * On parallel machines the global max is taken.
217 end
= mdatoms
->homenr
;
218 if (mdatoms
->cFREEZE
)
220 for (i
= start
; i
< end
; i
++)
222 gf
= mdatoms
->cFREEZE
[i
];
224 for (m
= 0; m
< DIM
; m
++)
226 if (!opts
->nFreeze
[gf
][m
])
241 for (i
= start
; i
< end
; i
++)
253 if (la_max
>= 0 && DOMAINDECOMP(cr
))
255 a_max
= cr
->dd
->gatindex
[la_max
];
263 snew(sum
, 2*cr
->nnodes
+1);
264 sum
[2*cr
->nodeid
] = fmax2
;
265 sum
[2*cr
->nodeid
+1] = a_max
;
266 sum
[2*cr
->nnodes
] = fnorm2
;
267 gmx_sumd(2*cr
->nnodes
+1, sum
, cr
);
268 fnorm2
= sum
[2*cr
->nnodes
];
269 /* Determine the global maximum */
270 for (i
= 0; i
< cr
->nnodes
; i
++)
272 if (sum
[2*i
] > fmax2
)
275 a_max
= (int)(sum
[2*i
+1] + 0.5);
283 *fnorm
= sqrt(fnorm2
);
295 static void get_state_f_norm_max(t_commrec
*cr
,
296 t_grpopts
*opts
, t_mdatoms
*mdatoms
,
299 get_f_norm_max(cr
, opts
, mdatoms
, ems
->f
, &ems
->fnorm
, &ems
->fmax
, &ems
->a_fmax
);
302 void init_em(FILE *fplog
, const char *title
,
303 t_commrec
*cr
, t_inputrec
*ir
,
304 t_state
*state_global
, gmx_mtop_t
*top_global
,
305 em_state_t
*ems
, gmx_localtop_t
**top
,
306 rvec
**f
, rvec
**f_global
,
307 t_nrnb
*nrnb
, rvec mu_tot
,
308 t_forcerec
*fr
, gmx_enerdata_t
**enerd
,
309 t_graph
**graph
, t_mdatoms
*mdatoms
, gmx_global_stat_t
*gstat
,
310 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
311 int nfile
, const t_filenm fnm
[],
312 gmx_mdoutf_t
*outf
, t_mdebin
**mdebin
,
313 int imdport
, unsigned long gmx_unused Flags
,
314 gmx_wallcycle_t wcycle
)
321 fprintf(fplog
, "Initiating %s\n", title
);
324 state_global
->ngtc
= 0;
326 /* Initialize lambda variables */
327 initialize_lambdas(fplog
, ir
, &(state_global
->fep_state
), state_global
->lambda
, NULL
);
331 /* Interactive molecular dynamics */
332 init_IMD(ir
, cr
, top_global
, fplog
, 1, state_global
->x
,
333 nfile
, fnm
, NULL
, imdport
, Flags
);
335 if (DOMAINDECOMP(cr
))
337 *top
= dd_init_local_top(top_global
);
339 dd_init_local_state(cr
->dd
, state_global
, &ems
->s
);
343 /* Distribute the charge groups over the nodes from the master node */
344 dd_partition_system(fplog
, ir
->init_step
, cr
, TRUE
, 1,
345 state_global
, top_global
, ir
,
346 &ems
->s
, &ems
->f
, mdatoms
, *top
,
347 fr
, vsite
, NULL
, constr
,
349 dd_store_state(cr
->dd
, &ems
->s
);
353 snew(*f_global
, top_global
->natoms
);
363 snew(*f
, top_global
->natoms
);
365 /* Just copy the state */
366 ems
->s
= *state_global
;
367 snew(ems
->s
.x
, ems
->s
.nalloc
);
368 snew(ems
->f
, ems
->s
.nalloc
);
369 for (i
= 0; i
< state_global
->natoms
; i
++)
371 copy_rvec(state_global
->x
[i
], ems
->s
.x
[i
]);
373 copy_mat(state_global
->box
, ems
->s
.box
);
375 *top
= gmx_mtop_generate_local_top(top_global
, ir
);
378 forcerec_set_excl_load(fr
, *top
);
380 setup_bonded_threading(fr
, &(*top
)->idef
);
382 if (ir
->ePBC
!= epbcNONE
&& !fr
->bMolPBC
)
384 *graph
= mk_graph(fplog
, &((*top
)->idef
), 0, top_global
->natoms
, FALSE
, FALSE
);
391 atoms2md(top_global
, ir
, 0, NULL
, top_global
->natoms
, mdatoms
);
392 update_mdatoms(mdatoms
, state_global
->lambda
[efptFEP
]);
396 set_vsite_top(vsite
, *top
, mdatoms
, cr
);
402 if (ir
->eConstrAlg
== econtSHAKE
&&
403 gmx_mtop_ftype_count(top_global
, F_CONSTR
) > 0)
405 gmx_fatal(FARGS
, "Can not do energy minimization with %s, use %s\n",
406 econstr_names
[econtSHAKE
], econstr_names
[econtLINCS
]);
409 if (!DOMAINDECOMP(cr
))
411 set_constraints(constr
, *top
, ir
, mdatoms
, cr
);
414 if (!ir
->bContinuation
)
416 /* Constrain the starting coordinates */
418 constrain(PAR(cr
) ? NULL
: fplog
, TRUE
, TRUE
, constr
, &(*top
)->idef
,
419 ir
, NULL
, cr
, -1, 0, 1.0, mdatoms
,
420 ems
->s
.x
, ems
->s
.x
, NULL
, fr
->bMolPBC
, ems
->s
.box
,
421 ems
->s
.lambda
[efptFEP
], &dvdl_constr
,
422 NULL
, NULL
, nrnb
, econqCoord
, FALSE
, 0, 0);
428 *gstat
= global_stat_init(ir
);
431 *outf
= init_mdoutf(fplog
, nfile
, fnm
, 0, cr
, ir
, top_global
, NULL
, wcycle
);
434 init_enerdata(top_global
->groups
.grps
[egcENER
].nr
, ir
->fepvals
->n_lambda
,
439 /* Init bin for energy stuff */
440 *mdebin
= init_mdebin(mdoutf_get_fp_ene(*outf
), top_global
, ir
, NULL
);
444 calc_shifts(ems
->s
.box
, fr
->shift_vec
);
447 static void finish_em(t_commrec
*cr
, gmx_mdoutf_t outf
,
448 gmx_walltime_accounting_t walltime_accounting
,
449 gmx_wallcycle_t wcycle
)
451 if (!(cr
->duty
& DUTY_PME
))
453 /* Tell the PME only node to finish */
454 gmx_pme_send_finish(cr
);
459 em_time_end(walltime_accounting
, wcycle
);
462 static void swap_em_state(em_state_t
*ems1
, em_state_t
*ems2
)
471 static void copy_em_coords(em_state_t
*ems
, t_state
*state
)
475 for (i
= 0; (i
< state
->natoms
); i
++)
477 copy_rvec(ems
->s
.x
[i
], state
->x
[i
]);
481 static void write_em_traj(FILE *fplog
, t_commrec
*cr
,
483 gmx_bool bX
, gmx_bool bF
, const char *confout
,
484 gmx_mtop_t
*top_global
,
485 t_inputrec
*ir
, gmx_int64_t step
,
487 t_state
*state_global
, rvec
*f_global
)
490 gmx_bool bIMDout
= FALSE
;
493 /* Shall we do IMD output? */
496 bIMDout
= do_per_step(step
, IMD_get_step(ir
->imd
->setup
));
499 if ((bX
|| bF
|| bIMDout
|| confout
!= NULL
) && !DOMAINDECOMP(cr
))
501 copy_em_coords(state
, state_global
);
508 mdof_flags
|= MDOF_X
;
512 mdof_flags
|= MDOF_F
;
515 /* If we want IMD output, set appropriate MDOF flag */
518 mdof_flags
|= MDOF_IMD
;
521 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
522 top_global
, step
, (double)step
,
523 &state
->s
, state_global
, state
->f
, f_global
);
525 if (confout
!= NULL
&& MASTER(cr
))
527 if (ir
->ePBC
!= epbcNONE
&& !ir
->bPeriodicMols
&& DOMAINDECOMP(cr
))
529 /* Make molecules whole only for confout writing */
530 do_pbc_mtop(fplog
, ir
->ePBC
, state_global
->box
, top_global
,
534 write_sto_conf_mtop(confout
,
535 *top_global
->name
, top_global
,
536 state_global
->x
, NULL
, ir
->ePBC
, state_global
->box
);
540 static void do_em_step(t_commrec
*cr
, t_inputrec
*ir
, t_mdatoms
*md
,
542 em_state_t
*ems1
, real a
, rvec
*f
, em_state_t
*ems2
,
543 gmx_constr_t constr
, gmx_localtop_t
*top
,
544 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
557 if (DOMAINDECOMP(cr
) && s1
->ddp_count
!= cr
->dd
->ddp_count
)
559 gmx_incons("state mismatch in do_em_step");
562 s2
->flags
= s1
->flags
;
564 if (s2
->nalloc
!= s1
->nalloc
)
566 s2
->nalloc
= s1
->nalloc
;
567 srenew(s2
->x
, s1
->nalloc
);
568 srenew(ems2
->f
, s1
->nalloc
);
569 if (s2
->flags
& (1<<estCGP
))
571 srenew(s2
->cg_p
, s1
->nalloc
);
575 s2
->natoms
= s1
->natoms
;
576 copy_mat(s1
->box
, s2
->box
);
577 /* Copy free energy state */
578 for (i
= 0; i
< efptNR
; i
++)
580 s2
->lambda
[i
] = s1
->lambda
[i
];
582 copy_mat(s1
->box
, s2
->box
);
590 #pragma omp parallel num_threads(gmx_omp_nthreads_get(emntUpdate))
595 #pragma omp for schedule(static) nowait
596 for (i
= start
; i
< end
; i
++)
602 for (m
= 0; m
< DIM
; m
++)
604 if (ir
->opts
.nFreeze
[gf
][m
])
610 x2
[i
][m
] = x1
[i
][m
] + a
*f
[i
][m
];
615 if (s2
->flags
& (1<<estCGP
))
617 /* Copy the CG p vector */
620 #pragma omp for schedule(static) nowait
621 for (i
= start
; i
< end
; i
++)
623 copy_rvec(x1
[i
], x2
[i
]);
627 if (DOMAINDECOMP(cr
))
629 s2
->ddp_count
= s1
->ddp_count
;
630 if (s2
->cg_gl_nalloc
< s1
->cg_gl_nalloc
)
633 s2
->cg_gl_nalloc
= s1
->cg_gl_nalloc
;
634 srenew(s2
->cg_gl
, s2
->cg_gl_nalloc
);
637 s2
->ncg_gl
= s1
->ncg_gl
;
638 #pragma omp for schedule(static) nowait
639 for (i
= 0; i
< s2
->ncg_gl
; i
++)
641 s2
->cg_gl
[i
] = s1
->cg_gl
[i
];
643 s2
->ddp_count_cg_gl
= s1
->ddp_count_cg_gl
;
649 wallcycle_start(wcycle
, ewcCONSTR
);
651 constrain(NULL
, TRUE
, TRUE
, constr
, &top
->idef
,
652 ir
, NULL
, cr
, count
, 0, 1.0, md
,
653 s1
->x
, s2
->x
, NULL
, bMolPBC
, s2
->box
,
654 s2
->lambda
[efptBONDED
], &dvdl_constr
,
655 NULL
, NULL
, nrnb
, econqCoord
, FALSE
, 0, 0);
656 wallcycle_stop(wcycle
, ewcCONSTR
);
660 static void em_dd_partition_system(FILE *fplog
, int step
, t_commrec
*cr
,
661 gmx_mtop_t
*top_global
, t_inputrec
*ir
,
662 em_state_t
*ems
, gmx_localtop_t
*top
,
663 t_mdatoms
*mdatoms
, t_forcerec
*fr
,
664 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
665 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
)
667 /* Repartition the domain decomposition */
668 wallcycle_start(wcycle
, ewcDOMDEC
);
669 dd_partition_system(fplog
, step
, cr
, FALSE
, 1,
670 NULL
, top_global
, ir
,
672 mdatoms
, top
, fr
, vsite
, NULL
, constr
,
673 nrnb
, wcycle
, FALSE
);
674 dd_store_state(cr
->dd
, &ems
->s
);
675 wallcycle_stop(wcycle
, ewcDOMDEC
);
678 static void evaluate_energy(FILE *fplog
, t_commrec
*cr
,
679 gmx_mtop_t
*top_global
,
680 em_state_t
*ems
, gmx_localtop_t
*top
,
681 t_inputrec
*inputrec
,
682 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
683 gmx_global_stat_t gstat
,
684 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
686 t_graph
*graph
, t_mdatoms
*mdatoms
,
687 t_forcerec
*fr
, rvec mu_tot
,
688 gmx_enerdata_t
*enerd
, tensor vir
, tensor pres
,
689 gmx_int64_t count
, gmx_bool bFirst
)
694 tensor force_vir
, shake_vir
, ekin
;
695 real dvdl_constr
, prescorr
, enercorr
, dvdlcorr
;
698 /* Set the time to the initial time, the time does not change during EM */
699 t
= inputrec
->init_t
;
702 (DOMAINDECOMP(cr
) && ems
->s
.ddp_count
< cr
->dd
->ddp_count
))
704 /* This is the first state or an old state used before the last ns */
710 if (inputrec
->nstlist
> 0)
714 else if (inputrec
->nstlist
== -1)
716 nabnsb
= natoms_beyond_ns_buffer(inputrec
, fr
, &top
->cgs
, NULL
, ems
->s
.x
);
719 gmx_sumi(1, &nabnsb
, cr
);
727 construct_vsites(vsite
, ems
->s
.x
, 1, NULL
,
728 top
->idef
.iparams
, top
->idef
.il
,
729 fr
->ePBC
, fr
->bMolPBC
, cr
, ems
->s
.box
);
732 if (DOMAINDECOMP(cr
) && bNS
)
734 /* Repartition the domain decomposition */
735 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
736 ems
, top
, mdatoms
, fr
, vsite
, constr
,
740 /* Calc force & energy on new trial position */
741 /* do_force always puts the charge groups in the box and shifts again
742 * We do not unshift, so molecules are always whole in congrad.c
744 do_force(fplog
, cr
, inputrec
,
745 count
, nrnb
, wcycle
, top
, &top_global
->groups
,
746 ems
->s
.box
, ems
->s
.x
, &ems
->s
.hist
,
747 ems
->f
, force_vir
, mdatoms
, enerd
, fcd
,
748 ems
->s
.lambda
, graph
, fr
, vsite
, mu_tot
, t
, NULL
, NULL
, TRUE
,
749 GMX_FORCE_STATECHANGED
| GMX_FORCE_ALLFORCES
|
750 GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
|
751 (bNS
? GMX_FORCE_NS
| GMX_FORCE_DO_LR
: 0));
753 /* Clear the unused shake virial and pressure */
754 clear_mat(shake_vir
);
757 /* Communicate stuff when parallel */
758 if (PAR(cr
) && inputrec
->eI
!= eiNM
)
760 wallcycle_start(wcycle
, ewcMoveE
);
762 global_stat(fplog
, gstat
, cr
, enerd
, force_vir
, shake_vir
, mu_tot
,
763 inputrec
, NULL
, NULL
, NULL
, 1, &terminate
,
764 top_global
, &ems
->s
, FALSE
,
770 wallcycle_stop(wcycle
, ewcMoveE
);
773 /* Calculate long range corrections to pressure and energy */
774 calc_dispcorr(fplog
, inputrec
, fr
, count
, top_global
->natoms
, ems
->s
.box
, ems
->s
.lambda
[efptVDW
],
775 pres
, force_vir
, &prescorr
, &enercorr
, &dvdlcorr
);
776 enerd
->term
[F_DISPCORR
] = enercorr
;
777 enerd
->term
[F_EPOT
] += enercorr
;
778 enerd
->term
[F_PRES
] += prescorr
;
779 enerd
->term
[F_DVDL
] += dvdlcorr
;
781 ems
->epot
= enerd
->term
[F_EPOT
];
785 /* Project out the constraint components of the force */
786 wallcycle_start(wcycle
, ewcCONSTR
);
788 constrain(NULL
, FALSE
, FALSE
, constr
, &top
->idef
,
789 inputrec
, NULL
, cr
, count
, 0, 1.0, mdatoms
,
790 ems
->s
.x
, ems
->f
, ems
->f
, fr
->bMolPBC
, ems
->s
.box
,
791 ems
->s
.lambda
[efptBONDED
], &dvdl_constr
,
792 NULL
, &shake_vir
, nrnb
, econqForceDispl
, FALSE
, 0, 0);
793 if (fr
->bSepDVDL
&& fplog
)
795 gmx_print_sepdvdl(fplog
, "Constraints", t
, dvdl_constr
);
797 enerd
->term
[F_DVDL_CONSTR
] += dvdl_constr
;
798 m_add(force_vir
, shake_vir
, vir
);
799 wallcycle_stop(wcycle
, ewcCONSTR
);
803 copy_mat(force_vir
, vir
);
807 enerd
->term
[F_PRES
] =
808 calc_pres(fr
->ePBC
, inputrec
->nwall
, ems
->s
.box
, ekin
, vir
, pres
);
810 sum_dhdl(enerd
, ems
->s
.lambda
, inputrec
->fepvals
);
812 if (EI_ENERGY_MINIMIZATION(inputrec
->eI
))
814 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, ems
);
818 static double reorder_partsum(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
820 em_state_t
*s_min
, em_state_t
*s_b
)
824 int ncg
, *cg_gl
, *index
, c
, cg
, i
, a0
, a1
, a
, gf
, m
;
826 unsigned char *grpnrFREEZE
;
830 fprintf(debug
, "Doing reorder_partsum\n");
836 cgs_gl
= dd_charge_groups_global(cr
->dd
);
837 index
= cgs_gl
->index
;
839 /* Collect fm in a global vector fmg.
840 * This conflicts with the spirit of domain decomposition,
841 * but to fully optimize this a much more complicated algorithm is required.
843 snew(fmg
, mtop
->natoms
);
845 ncg
= s_min
->s
.ncg_gl
;
846 cg_gl
= s_min
->s
.cg_gl
;
848 for (c
= 0; c
< ncg
; c
++)
853 for (a
= a0
; a
< a1
; a
++)
855 copy_rvec(fm
[i
], fmg
[a
]);
859 gmx_sum(mtop
->natoms
*3, fmg
[0], cr
);
861 /* Now we will determine the part of the sum for the cgs in state s_b */
863 cg_gl
= s_b
->s
.cg_gl
;
867 grpnrFREEZE
= mtop
->groups
.grpnr
[egcFREEZE
];
868 for (c
= 0; c
< ncg
; c
++)
873 for (a
= a0
; a
< a1
; a
++)
875 if (mdatoms
->cFREEZE
&& grpnrFREEZE
)
879 for (m
= 0; m
< DIM
; m
++)
881 if (!opts
->nFreeze
[gf
][m
])
883 partsum
+= (fb
[i
][m
] - fmg
[a
][m
])*fb
[i
][m
];
895 static real
pr_beta(t_commrec
*cr
, t_grpopts
*opts
, t_mdatoms
*mdatoms
,
897 em_state_t
*s_min
, em_state_t
*s_b
)
903 /* This is just the classical Polak-Ribiere calculation of beta;
904 * it looks a bit complicated since we take freeze groups into account,
905 * and might have to sum it in parallel runs.
908 if (!DOMAINDECOMP(cr
) ||
909 (s_min
->s
.ddp_count
== cr
->dd
->ddp_count
&&
910 s_b
->s
.ddp_count
== cr
->dd
->ddp_count
))
916 /* This part of code can be incorrect with DD,
917 * since the atom ordering in s_b and s_min might differ.
919 for (i
= 0; i
< mdatoms
->homenr
; i
++)
921 if (mdatoms
->cFREEZE
)
923 gf
= mdatoms
->cFREEZE
[i
];
925 for (m
= 0; m
< DIM
; m
++)
927 if (!opts
->nFreeze
[gf
][m
])
929 sum
+= (fb
[i
][m
] - fm
[i
][m
])*fb
[i
][m
];
936 /* We need to reorder cgs while summing */
937 sum
= reorder_partsum(cr
, opts
, mdatoms
, mtop
, s_min
, s_b
);
941 gmx_sumd(1, &sum
, cr
);
944 return sum
/sqr(s_min
->fnorm
);
947 double do_cg(FILE *fplog
, t_commrec
*cr
,
948 int nfile
, const t_filenm fnm
[],
949 const output_env_t gmx_unused oenv
, gmx_bool bVerbose
, gmx_bool gmx_unused bCompact
,
950 int gmx_unused nstglobalcomm
,
951 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
952 int gmx_unused stepout
,
953 t_inputrec
*inputrec
,
954 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
955 t_state
*state_global
,
957 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
958 gmx_edsam_t gmx_unused ed
,
960 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
961 gmx_membed_t gmx_unused membed
,
962 real gmx_unused cpt_period
, real gmx_unused max_hours
,
963 const char gmx_unused
*deviceOptions
,
965 unsigned long gmx_unused Flags
,
966 gmx_walltime_accounting_t walltime_accounting
)
968 const char *CG
= "Polak-Ribiere Conjugate Gradients";
970 em_state_t
*s_min
, *s_a
, *s_b
, *s_c
;
972 gmx_enerdata_t
*enerd
;
974 gmx_global_stat_t gstat
;
976 rvec
*f_global
, *p
, *sf
, *sfm
;
977 double gpa
, gpb
, gpc
, tmp
, sum
[2], minstep
;
980 real a
, b
, c
, beta
= 0.0;
984 gmx_bool converged
, foundlower
;
986 gmx_bool do_log
= FALSE
, do_ene
= FALSE
, do_x
, do_f
;
988 int number_steps
, neval
= 0, nstcg
= inputrec
->nstcgsteep
;
990 int i
, m
, gf
, step
, nminstep
;
995 s_min
= init_em_state();
996 s_a
= init_em_state();
997 s_b
= init_em_state();
998 s_c
= init_em_state();
1000 /* Init em and store the local state in s_min */
1001 init_em(fplog
, CG
, cr
, inputrec
,
1002 state_global
, top_global
, s_min
, &top
, &f
, &f_global
,
1003 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
, vsite
, constr
,
1004 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
1006 /* Print to log file */
1007 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, CG
);
1009 /* Max number of steps */
1010 number_steps
= inputrec
->nsteps
;
1014 sp_header(stderr
, CG
, inputrec
->em_tol
, number_steps
);
1018 sp_header(fplog
, CG
, inputrec
->em_tol
, number_steps
);
1021 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1022 /* do_force always puts the charge groups in the box and shifts again
1023 * We do not unshift, so molecules are always whole in congrad.c
1025 evaluate_energy(fplog
, cr
,
1026 top_global
, s_min
, top
,
1027 inputrec
, nrnb
, wcycle
, gstat
,
1028 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1029 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1034 /* Copy stuff to the energy bin for easy printing etc. */
1035 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1036 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1037 NULL
, NULL
, vir
, pres
, NULL
, mu_tot
, constr
);
1039 print_ebin_header(fplog
, step
, step
, s_min
->s
.lambda
[efptFEP
]);
1040 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1041 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1045 /* Estimate/guess the initial stepsize */
1046 stepsize
= inputrec
->em_stepsize
/s_min
->fnorm
;
1050 fprintf(stderr
, " F-max = %12.5e on atom %d\n",
1051 s_min
->fmax
, s_min
->a_fmax
+1);
1052 fprintf(stderr
, " F-Norm = %12.5e\n",
1053 s_min
->fnorm
/sqrt(state_global
->natoms
));
1054 fprintf(stderr
, "\n");
1055 /* and copy to the log file too... */
1056 fprintf(fplog
, " F-max = %12.5e on atom %d\n",
1057 s_min
->fmax
, s_min
->a_fmax
+1);
1058 fprintf(fplog
, " F-Norm = %12.5e\n",
1059 s_min
->fnorm
/sqrt(state_global
->natoms
));
1060 fprintf(fplog
, "\n");
1062 /* Start the loop over CG steps.
1063 * Each successful step is counted, and we continue until
1064 * we either converge or reach the max number of steps.
1067 for (step
= 0; (number_steps
< 0 || (number_steps
>= 0 && step
<= number_steps
)) && !converged
; step
++)
1070 /* start taking steps in a new direction
1071 * First time we enter the routine, beta=0, and the direction is
1072 * simply the negative gradient.
1075 /* Calculate the new direction in p, and the gradient in this direction, gpa */
1080 for (i
= 0; i
< mdatoms
->homenr
; i
++)
1082 if (mdatoms
->cFREEZE
)
1084 gf
= mdatoms
->cFREEZE
[i
];
1086 for (m
= 0; m
< DIM
; m
++)
1088 if (!inputrec
->opts
.nFreeze
[gf
][m
])
1090 p
[i
][m
] = sf
[i
][m
] + beta
*p
[i
][m
];
1091 gpa
-= p
[i
][m
]*sf
[i
][m
];
1092 /* f is negative gradient, thus the sign */
1101 /* Sum the gradient along the line across CPUs */
1104 gmx_sumd(1, &gpa
, cr
);
1107 /* Calculate the norm of the search vector */
1108 get_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, p
, &pnorm
, NULL
, NULL
);
1110 /* Just in case stepsize reaches zero due to numerical precision... */
1113 stepsize
= inputrec
->em_stepsize
/pnorm
;
1117 * Double check the value of the derivative in the search direction.
1118 * If it is positive it must be due to the old information in the
1119 * CG formula, so just remove that and start over with beta=0.
1120 * This corresponds to a steepest descent step.
1125 step
--; /* Don't count this step since we are restarting */
1126 continue; /* Go back to the beginning of the big for-loop */
1129 /* Calculate minimum allowed stepsize, before the average (norm)
1130 * relative change in coordinate is smaller than precision
1133 for (i
= 0; i
< mdatoms
->homenr
; i
++)
1135 for (m
= 0; m
< DIM
; m
++)
1137 tmp
= fabs(s_min
->s
.x
[i
][m
]);
1146 /* Add up from all CPUs */
1149 gmx_sumd(1, &minstep
, cr
);
1152 minstep
= GMX_REAL_EPS
/sqrt(minstep
/(3*state_global
->natoms
));
1154 if (stepsize
< minstep
)
1160 /* Write coordinates if necessary */
1161 do_x
= do_per_step(step
, inputrec
->nstxout
);
1162 do_f
= do_per_step(step
, inputrec
->nstfout
);
1164 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, NULL
,
1165 top_global
, inputrec
, step
,
1166 s_min
, state_global
, f_global
);
1168 /* Take a step downhill.
1169 * In theory, we should minimize the function along this direction.
1170 * That is quite possible, but it turns out to take 5-10 function evaluations
1171 * for each line. However, we dont really need to find the exact minimum -
1172 * it is much better to start a new CG step in a modified direction as soon
1173 * as we are close to it. This will save a lot of energy evaluations.
1175 * In practice, we just try to take a single step.
1176 * If it worked (i.e. lowered the energy), we increase the stepsize but
1177 * the continue straight to the next CG step without trying to find any minimum.
1178 * If it didn't work (higher energy), there must be a minimum somewhere between
1179 * the old position and the new one.
1181 * Due to the finite numerical accuracy, it turns out that it is a good idea
1182 * to even accept a SMALL increase in energy, if the derivative is still downhill.
1183 * This leads to lower final energies in the tests I've done. / Erik
1185 s_a
->epot
= s_min
->epot
;
1187 c
= a
+ stepsize
; /* reference position along line is zero */
1189 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
< cr
->dd
->ddp_count
)
1191 em_dd_partition_system(fplog
, step
, cr
, top_global
, inputrec
,
1192 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
1196 /* Take a trial step (new coords in s_c) */
1197 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, c
, s_min
->s
.cg_p
, s_c
,
1198 constr
, top
, nrnb
, wcycle
, -1);
1201 /* Calculate energy for the trial step */
1202 evaluate_energy(fplog
, cr
,
1203 top_global
, s_c
, top
,
1204 inputrec
, nrnb
, wcycle
, gstat
,
1205 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1206 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1208 /* Calc derivative along line */
1212 for (i
= 0; i
< mdatoms
->homenr
; i
++)
1214 for (m
= 0; m
< DIM
; m
++)
1216 gpc
-= p
[i
][m
]*sf
[i
][m
]; /* f is negative gradient, thus the sign */
1219 /* Sum the gradient along the line across CPUs */
1222 gmx_sumd(1, &gpc
, cr
);
1225 /* This is the max amount of increase in energy we tolerate */
1226 tmp
= sqrt(GMX_REAL_EPS
)*fabs(s_a
->epot
);
1228 /* Accept the step if the energy is lower, or if it is not significantly higher
1229 * and the line derivative is still negative.
1231 if (s_c
->epot
< s_a
->epot
|| (gpc
< 0 && s_c
->epot
< (s_a
->epot
+ tmp
)))
1234 /* Great, we found a better energy. Increase step for next iteration
1235 * if we are still going down, decrease it otherwise
1239 stepsize
*= 1.618034; /* The golden section */
1243 stepsize
*= 0.618034; /* 1/golden section */
1248 /* New energy is the same or higher. We will have to do some work
1249 * to find a smaller value in the interval. Take smaller step next time!
1252 stepsize
*= 0.618034;
1258 /* OK, if we didn't find a lower value we will have to locate one now - there must
1259 * be one in the interval [a=0,c].
1260 * The same thing is valid here, though: Don't spend dozens of iterations to find
1261 * the line minimum. We try to interpolate based on the derivative at the endpoints,
1262 * and only continue until we find a lower value. In most cases this means 1-2 iterations.
1264 * I also have a safeguard for potentially really patological functions so we never
1265 * take more than 20 steps before we give up ...
1267 * If we already found a lower value we just skip this step and continue to the update.
1275 /* Select a new trial point.
1276 * If the derivatives at points a & c have different sign we interpolate to zero,
1277 * otherwise just do a bisection.
1279 if (gpa
< 0 && gpc
> 0)
1281 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
1288 /* safeguard if interpolation close to machine accuracy causes errors:
1289 * never go outside the interval
1291 if (b
<= a
|| b
>= c
)
1296 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
1298 /* Reload the old state */
1299 em_dd_partition_system(fplog
, -1, cr
, top_global
, inputrec
,
1300 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
1304 /* Take a trial step to this new point - new coords in s_b */
1305 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
, s_min
, b
, s_min
->s
.cg_p
, s_b
,
1306 constr
, top
, nrnb
, wcycle
, -1);
1309 /* Calculate energy for the trial step */
1310 evaluate_energy(fplog
, cr
,
1311 top_global
, s_b
, top
,
1312 inputrec
, nrnb
, wcycle
, gstat
,
1313 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1314 mu_tot
, enerd
, vir
, pres
, -1, FALSE
);
1316 /* p does not change within a step, but since the domain decomposition
1317 * might change, we have to use cg_p of s_b here.
1322 for (i
= 0; i
< mdatoms
->homenr
; i
++)
1324 for (m
= 0; m
< DIM
; m
++)
1326 gpb
-= p
[i
][m
]*sf
[i
][m
]; /* f is negative gradient, thus the sign */
1329 /* Sum the gradient along the line across CPUs */
1332 gmx_sumd(1, &gpb
, cr
);
1337 fprintf(debug
, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
1338 s_a
->epot
, s_b
->epot
, s_c
->epot
, gpb
);
1341 epot_repl
= s_b
->epot
;
1343 /* Keep one of the intervals based on the value of the derivative at the new point */
1346 /* Replace c endpoint with b */
1347 swap_em_state(s_b
, s_c
);
1353 /* Replace a endpoint with b */
1354 swap_em_state(s_b
, s_a
);
1360 * Stop search as soon as we find a value smaller than the endpoints.
1361 * Never run more than 20 steps, no matter what.
1365 while ((epot_repl
> s_a
->epot
|| epot_repl
> s_c
->epot
) &&
1368 if (fabs(epot_repl
- s_min
->epot
) < fabs(s_min
->epot
)*GMX_REAL_EPS
||
1371 /* OK. We couldn't find a significantly lower energy.
1372 * If beta==0 this was steepest descent, and then we give up.
1373 * If not, set beta=0 and restart with steepest descent before quitting.
1383 /* Reset memory before giving up */
1389 /* Select min energy state of A & C, put the best in B.
1391 if (s_c
->epot
< s_a
->epot
)
1395 fprintf(debug
, "CGE: C (%f) is lower than A (%f), moving C to B\n",
1396 s_c
->epot
, s_a
->epot
);
1398 swap_em_state(s_b
, s_c
);
1406 fprintf(debug
, "CGE: A (%f) is lower than C (%f), moving A to B\n",
1407 s_a
->epot
, s_c
->epot
);
1409 swap_em_state(s_b
, s_a
);
1419 fprintf(debug
, "CGE: Found a lower energy %f, moving C to B\n",
1422 swap_em_state(s_b
, s_c
);
1427 /* new search direction */
1428 /* beta = 0 means forget all memory and restart with steepest descents. */
1429 if (nstcg
&& ((step
% nstcg
) == 0))
1435 /* s_min->fnorm cannot be zero, because then we would have converged
1439 /* Polak-Ribiere update.
1440 * Change to fnorm2/fnorm2_old for Fletcher-Reeves
1442 beta
= pr_beta(cr
, &inputrec
->opts
, mdatoms
, top_global
, s_min
, s_b
);
1444 /* Limit beta to prevent oscillations */
1445 if (fabs(beta
) > 5.0)
1451 /* update positions */
1452 swap_em_state(s_min
, s_b
);
1455 /* Print it if necessary */
1460 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
1461 step
, s_min
->epot
, s_min
->fnorm
/sqrt(state_global
->natoms
),
1462 s_min
->fmax
, s_min
->a_fmax
+1);
1464 /* Store the new (lower) energies */
1465 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1466 mdatoms
->tmass
, enerd
, &s_min
->s
, inputrec
->fepvals
, inputrec
->expandedvals
, s_min
->s
.box
,
1467 NULL
, NULL
, vir
, pres
, NULL
, mu_tot
, constr
);
1469 do_log
= do_per_step(step
, inputrec
->nstlog
);
1470 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
1472 /* Prepare IMD energy record, if bIMD is TRUE. */
1473 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, step
, TRUE
);
1477 print_ebin_header(fplog
, step
, step
, s_min
->s
.lambda
[efptFEP
]);
1479 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
1480 do_log
? fplog
: NULL
, step
, step
, eprNORMAL
,
1481 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1484 /* Send energies and positions to the IMD client if bIMD is TRUE. */
1485 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state_global
->box
, state_global
->x
, inputrec
, 0, wcycle
) && MASTER(cr
))
1487 IMD_send_positions(inputrec
->imd
);
1490 /* Stop when the maximum force lies below tolerance.
1491 * If we have reached machine precision, converged is already set to true.
1493 converged
= converged
|| (s_min
->fmax
< inputrec
->em_tol
);
1495 } /* End of the loop */
1497 /* IMD cleanup, if bIMD is TRUE. */
1498 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
1502 step
--; /* we never took that last step in this case */
1505 if (s_min
->fmax
> inputrec
->em_tol
)
1509 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1510 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
1517 /* If we printed energy and/or logfile last step (which was the last step)
1518 * we don't have to do it again, but otherwise print the final values.
1522 /* Write final value to log since we didn't do anything the last step */
1523 print_ebin_header(fplog
, step
, step
, s_min
->s
.lambda
[efptFEP
]);
1525 if (!do_ene
|| !do_log
)
1527 /* Write final energy file entries */
1528 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
1529 !do_log
? fplog
: NULL
, step
, step
, eprNORMAL
,
1530 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1534 /* Print some stuff... */
1537 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
1541 * For accurate normal mode calculation it is imperative that we
1542 * store the last conformation into the full precision binary trajectory.
1544 * However, we should only do it if we did NOT already write this step
1545 * above (which we did if do_x or do_f was true).
1547 do_x
= !do_per_step(step
, inputrec
->nstxout
);
1548 do_f
= (inputrec
->nstfout
> 0 && !do_per_step(step
, inputrec
->nstfout
));
1550 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
1551 top_global
, inputrec
, step
,
1552 s_min
, state_global
, f_global
);
1554 fnormn
= s_min
->fnorm
/sqrt(state_global
->natoms
);
1558 print_converged(stderr
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1559 s_min
->epot
, s_min
->fmax
, s_min
->a_fmax
, fnormn
);
1560 print_converged(fplog
, CG
, inputrec
->em_tol
, step
, converged
, number_steps
,
1561 s_min
->epot
, s_min
->fmax
, s_min
->a_fmax
, fnormn
);
1563 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
1566 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
1568 /* To print the actual number of steps we needed somewhere */
1569 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
1572 } /* That's all folks */
1575 double do_lbfgs(FILE *fplog
, t_commrec
*cr
,
1576 int nfile
, const t_filenm fnm
[],
1577 const output_env_t gmx_unused oenv
, gmx_bool bVerbose
, gmx_bool gmx_unused bCompact
,
1578 int gmx_unused nstglobalcomm
,
1579 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
1580 int gmx_unused stepout
,
1581 t_inputrec
*inputrec
,
1582 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
1585 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1586 gmx_edsam_t gmx_unused ed
,
1588 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
1589 gmx_membed_t gmx_unused membed
,
1590 real gmx_unused cpt_period
, real gmx_unused max_hours
,
1591 const char gmx_unused
*deviceOptions
,
1593 unsigned long gmx_unused Flags
,
1594 gmx_walltime_accounting_t walltime_accounting
)
1596 static const char *LBFGS
= "Low-Memory BFGS Minimizer";
1598 gmx_localtop_t
*top
;
1599 gmx_enerdata_t
*enerd
;
1601 gmx_global_stat_t gstat
;
1604 int ncorr
, nmaxcorr
, point
, cp
, neval
, nminstep
;
1605 double stepsize
, gpa
, gpb
, gpc
, tmp
, minstep
;
1606 real
*rho
, *alpha
, *ff
, *xx
, *p
, *s
, *lastx
, *lastf
, **dx
, **dg
;
1607 real
*xa
, *xb
, *xc
, *fa
, *fb
, *fc
, *xtmp
, *ftmp
;
1608 real a
, b
, c
, maxdelta
, delta
;
1609 real diag
, Epot0
, Epot
, EpotA
, EpotB
, EpotC
;
1610 real dgdx
, dgdg
, sq
, yr
, beta
;
1612 gmx_bool converged
, first
;
1615 gmx_bool do_log
, do_ene
, do_x
, do_f
, foundlower
, *frozen
;
1617 int start
, end
, number_steps
;
1619 int i
, k
, m
, n
, nfmax
, gf
, step
;
1626 gmx_fatal(FARGS
, "Cannot do parallel L-BFGS Minimization - yet.\n");
1631 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).");
1634 n
= 3*state
->natoms
;
1635 nmaxcorr
= inputrec
->nbfgscorr
;
1637 /* Allocate memory */
1638 /* Use pointers to real so we dont have to loop over both atoms and
1639 * dimensions all the time...
1640 * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
1641 * that point to the same memory.
1654 snew(rho
, nmaxcorr
);
1655 snew(alpha
, nmaxcorr
);
1658 for (i
= 0; i
< nmaxcorr
; i
++)
1664 for (i
= 0; i
< nmaxcorr
; i
++)
1673 init_em(fplog
, LBFGS
, cr
, inputrec
,
1674 state
, top_global
, &ems
, &top
, &f
, &f_global
,
1675 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
, vsite
, constr
,
1676 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
1677 /* Do_lbfgs is not completely updated like do_steep and do_cg,
1678 * so we free some memory again.
1683 xx
= (real
*)state
->x
;
1687 end
= mdatoms
->homenr
;
1689 /* Print to log file */
1690 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, LBFGS
);
1692 do_log
= do_ene
= do_x
= do_f
= TRUE
;
1694 /* Max number of steps */
1695 number_steps
= inputrec
->nsteps
;
1697 /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
1699 for (i
= start
; i
< end
; i
++)
1701 if (mdatoms
->cFREEZE
)
1703 gf
= mdatoms
->cFREEZE
[i
];
1705 for (m
= 0; m
< DIM
; m
++)
1707 frozen
[3*i
+m
] = inputrec
->opts
.nFreeze
[gf
][m
];
1712 sp_header(stderr
, LBFGS
, inputrec
->em_tol
, number_steps
);
1716 sp_header(fplog
, LBFGS
, inputrec
->em_tol
, number_steps
);
1721 construct_vsites(vsite
, state
->x
, 1, NULL
,
1722 top
->idef
.iparams
, top
->idef
.il
,
1723 fr
->ePBC
, fr
->bMolPBC
, cr
, state
->box
);
1726 /* Call the force routine and some auxiliary (neighboursearching etc.) */
1727 /* do_force always puts the charge groups in the box and shifts again
1728 * We do not unshift, so molecules are always whole
1733 evaluate_energy(fplog
, cr
,
1734 top_global
, &ems
, top
,
1735 inputrec
, nrnb
, wcycle
, gstat
,
1736 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1737 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
1742 /* Copy stuff to the energy bin for easy printing etc. */
1743 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
1744 mdatoms
->tmass
, enerd
, state
, inputrec
->fepvals
, inputrec
->expandedvals
, state
->box
,
1745 NULL
, NULL
, vir
, pres
, NULL
, mu_tot
, constr
);
1747 print_ebin_header(fplog
, step
, step
, state
->lambda
[efptFEP
]);
1748 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
, FALSE
, FALSE
, fplog
, step
, step
, eprNORMAL
,
1749 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
1753 /* This is the starting energy */
1754 Epot
= enerd
->term
[F_EPOT
];
1760 /* Set the initial step.
1761 * since it will be multiplied by the non-normalized search direction
1762 * vector (force vector the first time), we scale it by the
1763 * norm of the force.
1768 fprintf(stderr
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1769 fprintf(stderr
, " F-max = %12.5e on atom %d\n", fmax
, nfmax
+1);
1770 fprintf(stderr
, " F-Norm = %12.5e\n", fnorm
/sqrt(state
->natoms
));
1771 fprintf(stderr
, "\n");
1772 /* and copy to the log file too... */
1773 fprintf(fplog
, "Using %d BFGS correction steps.\n\n", nmaxcorr
);
1774 fprintf(fplog
, " F-max = %12.5e on atom %d\n", fmax
, nfmax
+1);
1775 fprintf(fplog
, " F-Norm = %12.5e\n", fnorm
/sqrt(state
->natoms
));
1776 fprintf(fplog
, "\n");
1780 for (i
= 0; i
< n
; i
++)
1784 dx
[point
][i
] = ff
[i
]; /* Initial search direction */
1792 stepsize
= 1.0/fnorm
;
1795 /* Start the loop over BFGS steps.
1796 * Each successful step is counted, and we continue until
1797 * we either converge or reach the max number of steps.
1802 /* Set the gradient from the force */
1804 for (step
= 0; (number_steps
< 0 || (number_steps
>= 0 && step
<= number_steps
)) && !converged
; step
++)
1807 /* Write coordinates if necessary */
1808 do_x
= do_per_step(step
, inputrec
->nstxout
);
1809 do_f
= do_per_step(step
, inputrec
->nstfout
);
1814 mdof_flags
|= MDOF_X
;
1819 mdof_flags
|= MDOF_F
;
1824 mdof_flags
|= MDOF_IMD
;
1827 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
,
1828 top_global
, step
, (real
)step
, state
, state
, f
, f
);
1830 /* Do the linesearching in the direction dx[point][0..(n-1)] */
1832 /* pointer to current direction - point=0 first time here */
1835 /* calculate line gradient */
1836 for (gpa
= 0, i
= 0; i
< n
; i
++)
1841 /* Calculate minimum allowed stepsize, before the average (norm)
1842 * relative change in coordinate is smaller than precision
1844 for (minstep
= 0, i
= 0; i
< n
; i
++)
1854 minstep
= GMX_REAL_EPS
/sqrt(minstep
/n
);
1856 if (stepsize
< minstep
)
1862 /* Store old forces and coordinates */
1863 for (i
= 0; i
< n
; i
++)
1872 for (i
= 0; i
< n
; i
++)
1877 /* Take a step downhill.
1878 * In theory, we should minimize the function along this direction.
1879 * That is quite possible, but it turns out to take 5-10 function evaluations
1880 * for each line. However, we dont really need to find the exact minimum -
1881 * it is much better to start a new BFGS step in a modified direction as soon
1882 * as we are close to it. This will save a lot of energy evaluations.
1884 * In practice, we just try to take a single step.
1885 * If it worked (i.e. lowered the energy), we increase the stepsize but
1886 * the continue straight to the next BFGS step without trying to find any minimum.
1887 * If it didn't work (higher energy), there must be a minimum somewhere between
1888 * the old position and the new one.
1890 * Due to the finite numerical accuracy, it turns out that it is a good idea
1891 * to even accept a SMALL increase in energy, if the derivative is still downhill.
1892 * This leads to lower final energies in the tests I've done. / Erik
1897 c
= a
+ stepsize
; /* reference position along line is zero */
1899 /* Check stepsize first. We do not allow displacements
1900 * larger than emstep.
1906 for (i
= 0; i
< n
; i
++)
1909 if (delta
> maxdelta
)
1914 if (maxdelta
> inputrec
->em_stepsize
)
1919 while (maxdelta
> inputrec
->em_stepsize
);
1921 /* Take a trial step */
1922 for (i
= 0; i
< n
; i
++)
1924 xc
[i
] = lastx
[i
] + c
*s
[i
];
1928 /* Calculate energy for the trial step */
1929 ems
.s
.x
= (rvec
*)xc
;
1931 evaluate_energy(fplog
, cr
,
1932 top_global
, &ems
, top
,
1933 inputrec
, nrnb
, wcycle
, gstat
,
1934 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
1935 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
1938 /* Calc derivative along line */
1939 for (gpc
= 0, i
= 0; i
< n
; i
++)
1941 gpc
-= s
[i
]*fc
[i
]; /* f is negative gradient, thus the sign */
1943 /* Sum the gradient along the line across CPUs */
1946 gmx_sumd(1, &gpc
, cr
);
1949 /* This is the max amount of increase in energy we tolerate */
1950 tmp
= sqrt(GMX_REAL_EPS
)*fabs(EpotA
);
1952 /* Accept the step if the energy is lower, or if it is not significantly higher
1953 * and the line derivative is still negative.
1955 if (EpotC
< EpotA
|| (gpc
< 0 && EpotC
< (EpotA
+tmp
)))
1958 /* Great, we found a better energy. Increase step for next iteration
1959 * if we are still going down, decrease it otherwise
1963 stepsize
*= 1.618034; /* The golden section */
1967 stepsize
*= 0.618034; /* 1/golden section */
1972 /* New energy is the same or higher. We will have to do some work
1973 * to find a smaller value in the interval. Take smaller step next time!
1976 stepsize
*= 0.618034;
1979 /* OK, if we didn't find a lower value we will have to locate one now - there must
1980 * be one in the interval [a=0,c].
1981 * The same thing is valid here, though: Don't spend dozens of iterations to find
1982 * the line minimum. We try to interpolate based on the derivative at the endpoints,
1983 * and only continue until we find a lower value. In most cases this means 1-2 iterations.
1985 * I also have a safeguard for potentially really patological functions so we never
1986 * take more than 20 steps before we give up ...
1988 * If we already found a lower value we just skip this step and continue to the update.
1997 /* Select a new trial point.
1998 * If the derivatives at points a & c have different sign we interpolate to zero,
1999 * otherwise just do a bisection.
2002 if (gpa
< 0 && gpc
> 0)
2004 b
= a
+ gpa
*(a
-c
)/(gpc
-gpa
);
2011 /* safeguard if interpolation close to machine accuracy causes errors:
2012 * never go outside the interval
2014 if (b
<= a
|| b
>= c
)
2019 /* Take a trial step */
2020 for (i
= 0; i
< n
; i
++)
2022 xb
[i
] = lastx
[i
] + b
*s
[i
];
2026 /* Calculate energy for the trial step */
2027 ems
.s
.x
= (rvec
*)xb
;
2029 evaluate_energy(fplog
, cr
,
2030 top_global
, &ems
, top
,
2031 inputrec
, nrnb
, wcycle
, gstat
,
2032 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2033 mu_tot
, enerd
, vir
, pres
, step
, FALSE
);
2038 for (gpb
= 0, i
= 0; i
< n
; i
++)
2040 gpb
-= s
[i
]*fb
[i
]; /* f is negative gradient, thus the sign */
2043 /* Sum the gradient along the line across CPUs */
2046 gmx_sumd(1, &gpb
, cr
);
2049 /* Keep one of the intervals based on the value of the derivative at the new point */
2052 /* Replace c endpoint with b */
2056 /* swap coord pointers b/c */
2066 /* Replace a endpoint with b */
2070 /* swap coord pointers a/b */
2080 * Stop search as soon as we find a value smaller than the endpoints,
2081 * or if the tolerance is below machine precision.
2082 * Never run more than 20 steps, no matter what.
2086 while ((EpotB
> EpotA
|| EpotB
> EpotC
) && (nminstep
< 20));
2088 if (fabs(EpotB
-Epot0
) < GMX_REAL_EPS
|| nminstep
>= 20)
2090 /* OK. We couldn't find a significantly lower energy.
2091 * If ncorr==0 this was steepest descent, and then we give up.
2092 * If not, reset memory to restart as steepest descent before quitting.
2104 /* Search in gradient direction */
2105 for (i
= 0; i
< n
; i
++)
2107 dx
[point
][i
] = ff
[i
];
2109 /* Reset stepsize */
2110 stepsize
= 1.0/fnorm
;
2115 /* Select min energy state of A & C, put the best in xx/ff/Epot
2121 for (i
= 0; i
< n
; i
++)
2132 for (i
= 0; i
< n
; i
++)
2146 for (i
= 0; i
< n
; i
++)
2154 /* Update the memory information, and calculate a new
2155 * approximation of the inverse hessian
2158 /* Have new data in Epot, xx, ff */
2159 if (ncorr
< nmaxcorr
)
2164 for (i
= 0; i
< n
; i
++)
2166 dg
[point
][i
] = lastf
[i
]-ff
[i
];
2167 dx
[point
][i
] *= stepsize
;
2172 for (i
= 0; i
< n
; i
++)
2174 dgdg
+= dg
[point
][i
]*dg
[point
][i
];
2175 dgdx
+= dg
[point
][i
]*dx
[point
][i
];
2180 rho
[point
] = 1.0/dgdx
;
2183 if (point
>= nmaxcorr
)
2189 for (i
= 0; i
< n
; i
++)
2196 /* Recursive update. First go back over the memory points */
2197 for (k
= 0; k
< ncorr
; k
++)
2206 for (i
= 0; i
< n
; i
++)
2208 sq
+= dx
[cp
][i
]*p
[i
];
2211 alpha
[cp
] = rho
[cp
]*sq
;
2213 for (i
= 0; i
< n
; i
++)
2215 p
[i
] -= alpha
[cp
]*dg
[cp
][i
];
2219 for (i
= 0; i
< n
; i
++)
2224 /* And then go forward again */
2225 for (k
= 0; k
< ncorr
; k
++)
2228 for (i
= 0; i
< n
; i
++)
2230 yr
+= p
[i
]*dg
[cp
][i
];
2234 beta
= alpha
[cp
]-beta
;
2236 for (i
= 0; i
< n
; i
++)
2238 p
[i
] += beta
*dx
[cp
][i
];
2248 for (i
= 0; i
< n
; i
++)
2252 dx
[point
][i
] = p
[i
];
2262 /* Test whether the convergence criterion is met */
2263 get_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, f
, &fnorm
, &fmax
, &nfmax
);
2265 /* Print it if necessary */
2270 fprintf(stderr
, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
2271 step
, Epot
, fnorm
/sqrt(state
->natoms
), fmax
, nfmax
+1);
2273 /* Store the new (lower) energies */
2274 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)step
,
2275 mdatoms
->tmass
, enerd
, state
, inputrec
->fepvals
, inputrec
->expandedvals
, state
->box
,
2276 NULL
, NULL
, vir
, pres
, NULL
, mu_tot
, constr
);
2277 do_log
= do_per_step(step
, inputrec
->nstlog
);
2278 do_ene
= do_per_step(step
, inputrec
->nstenergy
);
2281 print_ebin_header(fplog
, step
, step
, state
->lambda
[efptFEP
]);
2283 print_ebin(mdoutf_get_fp_ene(outf
), do_ene
, FALSE
, FALSE
,
2284 do_log
? fplog
: NULL
, step
, step
, eprNORMAL
,
2285 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2288 /* Send x and E to IMD client, if bIMD is TRUE. */
2289 if (do_IMD(inputrec
->bIMD
, step
, cr
, TRUE
, state
->box
, state
->x
, inputrec
, 0, wcycle
) && MASTER(cr
))
2291 IMD_send_positions(inputrec
->imd
);
2294 /* Stop when the maximum force lies below tolerance.
2295 * If we have reached machine precision, converged is already set to true.
2298 converged
= converged
|| (fmax
< inputrec
->em_tol
);
2300 } /* End of the loop */
2302 /* IMD cleanup, if bIMD is TRUE. */
2303 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2307 step
--; /* we never took that last step in this case */
2310 if (fmax
> inputrec
->em_tol
)
2314 warn_step(stderr
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2315 warn_step(fplog
, inputrec
->em_tol
, step
-1 == number_steps
, FALSE
);
2320 /* If we printed energy and/or logfile last step (which was the last step)
2321 * we don't have to do it again, but otherwise print the final values.
2323 if (!do_log
) /* Write final value to log since we didn't do anythin last step */
2325 print_ebin_header(fplog
, step
, step
, state
->lambda
[efptFEP
]);
2327 if (!do_ene
|| !do_log
) /* Write final energy file entries */
2329 print_ebin(mdoutf_get_fp_ene(outf
), !do_ene
, FALSE
, FALSE
,
2330 !do_log
? fplog
: NULL
, step
, step
, eprNORMAL
,
2331 TRUE
, mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2334 /* Print some stuff... */
2337 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2341 * For accurate normal mode calculation it is imperative that we
2342 * store the last conformation into the full precision binary trajectory.
2344 * However, we should only do it if we did NOT already write this step
2345 * above (which we did if do_x or do_f was true).
2347 do_x
= !do_per_step(step
, inputrec
->nstxout
);
2348 do_f
= !do_per_step(step
, inputrec
->nstfout
);
2349 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, ftp2fn(efSTO
, nfile
, fnm
),
2350 top_global
, inputrec
, step
,
2355 print_converged(stderr
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2356 number_steps
, Epot
, fmax
, nfmax
, fnorm
/sqrt(state
->natoms
));
2357 print_converged(fplog
, LBFGS
, inputrec
->em_tol
, step
, converged
,
2358 number_steps
, Epot
, fmax
, nfmax
, fnorm
/sqrt(state
->natoms
));
2360 fprintf(fplog
, "\nPerformed %d energy evaluations in total.\n", neval
);
2363 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2365 /* To print the actual number of steps we needed somewhere */
2366 walltime_accounting_set_nsteps_done(walltime_accounting
, step
);
2369 } /* That's all folks */
2372 double do_steep(FILE *fplog
, t_commrec
*cr
,
2373 int nfile
, const t_filenm fnm
[],
2374 const output_env_t gmx_unused oenv
, gmx_bool bVerbose
, gmx_bool gmx_unused bCompact
,
2375 int gmx_unused nstglobalcomm
,
2376 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2377 int gmx_unused stepout
,
2378 t_inputrec
*inputrec
,
2379 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2380 t_state
*state_global
,
2382 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2383 gmx_edsam_t gmx_unused ed
,
2385 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
2386 gmx_membed_t gmx_unused membed
,
2387 real gmx_unused cpt_period
, real gmx_unused max_hours
,
2388 const char gmx_unused
*deviceOptions
,
2390 unsigned long gmx_unused Flags
,
2391 gmx_walltime_accounting_t walltime_accounting
)
2393 const char *SD
= "Steepest Descents";
2394 em_state_t
*s_min
, *s_try
;
2396 gmx_localtop_t
*top
;
2397 gmx_enerdata_t
*enerd
;
2399 gmx_global_stat_t gstat
;
2401 real stepsize
, constepsize
;
2405 gmx_bool bDone
, bAbort
, do_x
, do_f
;
2410 int steps_accepted
= 0;
2414 s_min
= init_em_state();
2415 s_try
= init_em_state();
2417 /* Init em and store the local state in s_try */
2418 init_em(fplog
, SD
, cr
, inputrec
,
2419 state_global
, top_global
, s_try
, &top
, &f
, &f_global
,
2420 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
, vsite
, constr
,
2421 nfile
, fnm
, &outf
, &mdebin
, imdport
, Flags
, wcycle
);
2423 /* Print to log file */
2424 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, SD
);
2426 /* Set variables for stepsize (in nm). This is the largest
2427 * step that we are going to make in any direction.
2429 ustep
= inputrec
->em_stepsize
;
2432 /* Max number of steps */
2433 nsteps
= inputrec
->nsteps
;
2437 /* Print to the screen */
2438 sp_header(stderr
, SD
, inputrec
->em_tol
, nsteps
);
2442 sp_header(fplog
, SD
, inputrec
->em_tol
, nsteps
);
2445 /**** HERE STARTS THE LOOP ****
2446 * count is the counter for the number of steps
2447 * bDone will be TRUE when the minimization has converged
2448 * bAbort will be TRUE when nsteps steps have been performed or when
2449 * the stepsize becomes smaller than is reasonable for machine precision
2454 while (!bDone
&& !bAbort
)
2456 bAbort
= (nsteps
>= 0) && (count
== nsteps
);
2458 /* set new coordinates, except for first step */
2461 do_em_step(cr
, inputrec
, mdatoms
, fr
->bMolPBC
,
2462 s_min
, stepsize
, s_min
->f
, s_try
,
2463 constr
, top
, nrnb
, wcycle
, count
);
2466 evaluate_energy(fplog
, cr
,
2467 top_global
, s_try
, top
,
2468 inputrec
, nrnb
, wcycle
, gstat
,
2469 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2470 mu_tot
, enerd
, vir
, pres
, count
, count
== 0);
2474 print_ebin_header(fplog
, count
, count
, s_try
->s
.lambda
[efptFEP
]);
2479 s_min
->epot
= s_try
->epot
+ 1;
2482 /* Print it if necessary */
2487 fprintf(stderr
, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
2488 count
, ustep
, s_try
->epot
, s_try
->fmax
, s_try
->a_fmax
+1,
2489 (s_try
->epot
< s_min
->epot
) ? '\n' : '\r');
2492 if (s_try
->epot
< s_min
->epot
)
2494 /* Store the new (lower) energies */
2495 upd_mdebin(mdebin
, FALSE
, FALSE
, (double)count
,
2496 mdatoms
->tmass
, enerd
, &s_try
->s
, inputrec
->fepvals
, inputrec
->expandedvals
,
2497 s_try
->s
.box
, NULL
, NULL
, vir
, pres
, NULL
, mu_tot
, constr
);
2499 /* Prepare IMD energy record, if bIMD is TRUE. */
2500 IMD_fill_energy_record(inputrec
->bIMD
, inputrec
->imd
, enerd
, count
, TRUE
);
2502 print_ebin(mdoutf_get_fp_ene(outf
), TRUE
,
2503 do_per_step(steps_accepted
, inputrec
->nstdisreout
),
2504 do_per_step(steps_accepted
, inputrec
->nstorireout
),
2505 fplog
, count
, count
, eprNORMAL
, TRUE
,
2506 mdebin
, fcd
, &(top_global
->groups
), &(inputrec
->opts
));
2511 /* Now if the new energy is smaller than the previous...
2512 * or if this is the first step!
2513 * or if we did random steps!
2516 if ( (count
== 0) || (s_try
->epot
< s_min
->epot
) )
2520 /* Test whether the convergence criterion is met... */
2521 bDone
= (s_try
->fmax
< inputrec
->em_tol
);
2523 /* Copy the arrays for force, positions and energy */
2524 /* The 'Min' array always holds the coords and forces of the minimal
2526 swap_em_state(s_min
, s_try
);
2532 /* Write to trn, if necessary */
2533 do_x
= do_per_step(steps_accepted
, inputrec
->nstxout
);
2534 do_f
= do_per_step(steps_accepted
, inputrec
->nstfout
);
2535 write_em_traj(fplog
, cr
, outf
, do_x
, do_f
, NULL
,
2536 top_global
, inputrec
, count
,
2537 s_min
, state_global
, f_global
);
2541 /* If energy is not smaller make the step smaller... */
2544 if (DOMAINDECOMP(cr
) && s_min
->s
.ddp_count
!= cr
->dd
->ddp_count
)
2546 /* Reload the old state */
2547 em_dd_partition_system(fplog
, count
, cr
, top_global
, inputrec
,
2548 s_min
, top
, mdatoms
, fr
, vsite
, constr
,
2553 /* Determine new step */
2554 stepsize
= ustep
/s_min
->fmax
;
2556 /* Check if stepsize is too small, with 1 nm as a characteristic length */
2558 if (count
== nsteps
|| ustep
< 1e-12)
2560 if (count
== nsteps
|| ustep
< 1e-6)
2565 warn_step(stderr
, inputrec
->em_tol
, count
== nsteps
, constr
!= NULL
);
2566 warn_step(fplog
, inputrec
->em_tol
, count
== nsteps
, constr
!= NULL
);
2571 /* Send IMD energies and positions, if bIMD is TRUE. */
2572 if (do_IMD(inputrec
->bIMD
, count
, cr
, TRUE
, state_global
->box
, state_global
->x
, inputrec
, 0, wcycle
) && MASTER(cr
))
2574 IMD_send_positions(inputrec
->imd
);
2578 } /* End of the loop */
2580 /* IMD cleanup, if bIMD is TRUE. */
2581 IMD_finalize(inputrec
->bIMD
, inputrec
->imd
);
2583 /* Print some data... */
2586 fprintf(stderr
, "\nwriting lowest energy coordinates.\n");
2588 write_em_traj(fplog
, cr
, outf
, TRUE
, inputrec
->nstfout
, ftp2fn(efSTO
, nfile
, fnm
),
2589 top_global
, inputrec
, count
,
2590 s_min
, state_global
, f_global
);
2592 fnormn
= s_min
->fnorm
/sqrt(state_global
->natoms
);
2596 print_converged(stderr
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2597 s_min
->epot
, s_min
->fmax
, s_min
->a_fmax
, fnormn
);
2598 print_converged(fplog
, SD
, inputrec
->em_tol
, count
, bDone
, nsteps
,
2599 s_min
->epot
, s_min
->fmax
, s_min
->a_fmax
, fnormn
);
2602 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2604 /* To print the actual number of steps we needed somewhere */
2605 inputrec
->nsteps
= count
;
2607 walltime_accounting_set_nsteps_done(walltime_accounting
, count
);
2610 } /* That's all folks */
2613 double do_nm(FILE *fplog
, t_commrec
*cr
,
2614 int nfile
, const t_filenm fnm
[],
2615 const output_env_t gmx_unused oenv
, gmx_bool bVerbose
, gmx_bool gmx_unused bCompact
,
2616 int gmx_unused nstglobalcomm
,
2617 gmx_vsite_t
*vsite
, gmx_constr_t constr
,
2618 int gmx_unused stepout
,
2619 t_inputrec
*inputrec
,
2620 gmx_mtop_t
*top_global
, t_fcdata
*fcd
,
2621 t_state
*state_global
,
2623 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2624 gmx_edsam_t gmx_unused ed
,
2626 int gmx_unused repl_ex_nst
, int gmx_unused repl_ex_nex
, int gmx_unused repl_ex_seed
,
2627 gmx_membed_t gmx_unused membed
,
2628 real gmx_unused cpt_period
, real gmx_unused max_hours
,
2629 const char gmx_unused
*deviceOptions
,
2631 unsigned long gmx_unused Flags
,
2632 gmx_walltime_accounting_t walltime_accounting
)
2634 const char *NM
= "Normal Mode Analysis";
2636 int natoms
, atom
, d
;
2639 gmx_localtop_t
*top
;
2640 gmx_enerdata_t
*enerd
;
2642 gmx_global_stat_t gstat
;
2644 real t
, t0
, lambda
, lam0
;
2649 gmx_bool bSparse
; /* use sparse matrix storage format */
2651 gmx_sparsematrix_t
* sparse_matrix
= NULL
;
2652 real
* full_matrix
= NULL
;
2653 em_state_t
* state_work
;
2655 /* added with respect to mdrun */
2656 int i
, j
, k
, row
, col
;
2657 real der_range
= 10.0*sqrt(GMX_REAL_EPS
);
2663 gmx_fatal(FARGS
, "Constraints present with Normal Mode Analysis, this combination is not supported");
2666 state_work
= init_em_state();
2668 /* Init em and store the local state in state_minimum */
2669 init_em(fplog
, NM
, cr
, inputrec
,
2670 state_global
, top_global
, state_work
, &top
,
2672 nrnb
, mu_tot
, fr
, &enerd
, &graph
, mdatoms
, &gstat
, vsite
, constr
,
2673 nfile
, fnm
, &outf
, NULL
, imdport
, Flags
, wcycle
);
2675 natoms
= top_global
->natoms
;
2683 "NOTE: This version of Gromacs has been compiled in single precision,\n"
2684 " which MIGHT not be accurate enough for normal mode analysis.\n"
2685 " Gromacs now uses sparse matrix storage, so the memory requirements\n"
2686 " are fairly modest even if you recompile in double precision.\n\n");
2690 /* Check if we can/should use sparse storage format.
2692 * Sparse format is only useful when the Hessian itself is sparse, which it
2693 * will be when we use a cutoff.
2694 * For small systems (n<1000) it is easier to always use full matrix format, though.
2696 if (EEL_FULL(fr
->eeltype
) || fr
->rlist
== 0.0)
2698 md_print_info(cr
, fplog
, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
2701 else if (top_global
->natoms
< 1000)
2703 md_print_info(cr
, fplog
, "Small system size (N=%d), using full Hessian format.\n", top_global
->natoms
);
2708 md_print_info(cr
, fplog
, "Using compressed symmetric sparse Hessian format.\n");
2714 sz
= DIM
*top_global
->natoms
;
2716 fprintf(stderr
, "Allocating Hessian memory...\n\n");
2720 sparse_matrix
= gmx_sparsematrix_init(sz
);
2721 sparse_matrix
->compressed_symmetric
= TRUE
;
2725 snew(full_matrix
, sz
*sz
);
2729 /* Initial values */
2730 t0
= inputrec
->init_t
;
2731 lam0
= inputrec
->fepvals
->init_lambda
;
2739 /* Write start time and temperature */
2740 print_em_start(fplog
, cr
, walltime_accounting
, wcycle
, NM
);
2742 /* fudge nr of steps to nr of atoms */
2743 inputrec
->nsteps
= natoms
*2;
2747 fprintf(stderr
, "starting normal mode calculation '%s'\n%d steps.\n\n",
2748 *(top_global
->name
), (int)inputrec
->nsteps
);
2751 nnodes
= cr
->nnodes
;
2753 /* Make evaluate_energy do a single node force calculation */
2755 evaluate_energy(fplog
, cr
,
2756 top_global
, state_work
, top
,
2757 inputrec
, nrnb
, wcycle
, gstat
,
2758 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2759 mu_tot
, enerd
, vir
, pres
, -1, TRUE
);
2760 cr
->nnodes
= nnodes
;
2762 /* if forces are not small, warn user */
2763 get_state_f_norm_max(cr
, &(inputrec
->opts
), mdatoms
, state_work
);
2765 md_print_info(cr
, fplog
, "Maximum force:%12.5e\n", state_work
->fmax
);
2766 if (state_work
->fmax
> 1.0e-3)
2768 md_print_info(cr
, fplog
,
2769 "The force is probably not small enough to "
2770 "ensure that you are at a minimum.\n"
2771 "Be aware that negative eigenvalues may occur\n"
2772 "when the resulting matrix is diagonalized.\n\n");
2775 /***********************************************************
2777 * Loop over all pairs in matrix
2779 * do_force called twice. Once with positive and
2780 * once with negative displacement
2782 ************************************************************/
2784 /* Steps are divided one by one over the nodes */
2785 for (atom
= cr
->nodeid
; atom
< natoms
; atom
+= nnodes
)
2788 for (d
= 0; d
< DIM
; d
++)
2790 x_min
= state_work
->s
.x
[atom
][d
];
2792 state_work
->s
.x
[atom
][d
] = x_min
- der_range
;
2794 /* Make evaluate_energy do a single node force calculation */
2796 evaluate_energy(fplog
, cr
,
2797 top_global
, state_work
, top
,
2798 inputrec
, nrnb
, wcycle
, gstat
,
2799 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2800 mu_tot
, enerd
, vir
, pres
, atom
*2, FALSE
);
2802 for (i
= 0; i
< natoms
; i
++)
2804 copy_rvec(state_work
->f
[i
], fneg
[i
]);
2807 state_work
->s
.x
[atom
][d
] = x_min
+ der_range
;
2809 evaluate_energy(fplog
, cr
,
2810 top_global
, state_work
, top
,
2811 inputrec
, nrnb
, wcycle
, gstat
,
2812 vsite
, constr
, fcd
, graph
, mdatoms
, fr
,
2813 mu_tot
, enerd
, vir
, pres
, atom
*2+1, FALSE
);
2814 cr
->nnodes
= nnodes
;
2816 /* x is restored to original */
2817 state_work
->s
.x
[atom
][d
] = x_min
;
2819 for (j
= 0; j
< natoms
; j
++)
2821 for (k
= 0; (k
< DIM
); k
++)
2824 -(state_work
->f
[j
][k
] - fneg
[j
][k
])/(2*der_range
);
2832 #define mpi_type MPI_DOUBLE
2834 #define mpi_type MPI_FLOAT
2836 MPI_Send(dfdx
[0], natoms
*DIM
, mpi_type
, MASTERNODE(cr
), cr
->nodeid
,
2837 cr
->mpi_comm_mygroup
);
2842 for (node
= 0; (node
< nnodes
&& atom
+node
< natoms
); node
++)
2848 MPI_Recv(dfdx
[0], natoms
*DIM
, mpi_type
, node
, node
,
2849 cr
->mpi_comm_mygroup
, &stat
);
2854 row
= (atom
+ node
)*DIM
+ d
;
2856 for (j
= 0; j
< natoms
; j
++)
2858 for (k
= 0; k
< DIM
; k
++)
2864 if (col
>= row
&& dfdx
[j
][k
] != 0.0)
2866 gmx_sparsematrix_increment_value(sparse_matrix
,
2867 row
, col
, dfdx
[j
][k
]);
2872 full_matrix
[row
*sz
+col
] = dfdx
[j
][k
];
2879 if (bVerbose
&& fplog
)
2884 /* write progress */
2885 if (MASTER(cr
) && bVerbose
)
2887 fprintf(stderr
, "\rFinished step %d out of %d",
2888 min(atom
+nnodes
, natoms
), natoms
);
2895 fprintf(stderr
, "\n\nWriting Hessian...\n");
2896 gmx_mtxio_write(ftp2fn(efMTX
, nfile
, fnm
), sz
, sz
, full_matrix
, sparse_matrix
);
2899 finish_em(cr
, outf
, walltime_accounting
, wcycle
);
2901 walltime_accounting_set_nsteps_done(walltime_accounting
, natoms
*2);