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45 #ifdef HAVE_SYS_TIME_H
50 #include "gromacs/utility/cstringutil.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "chargegroup.h"
55 #include "gromacs/math/vec.h"
60 #include "gromacs/math/units.h"
73 #include "nbnxn_atomdata.h"
74 #include "nbnxn_search.h"
75 #include "nbnxn_kernels/nbnxn_kernel_ref.h"
76 #include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
77 #include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
78 #include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
79 #include "nonbonded.h"
80 #include "../gmxlib/nonbonded/nb_kernel.h"
81 #include "../gmxlib/nonbonded/nb_free_energy.h"
83 #include "gromacs/legacyheaders/types/commrec.h"
84 #include "gromacs/pbcutil/ishift.h"
85 #include "gromacs/pbcutil/mshift.h"
86 #include "gromacs/timing/wallcycle.h"
87 #include "gromacs/timing/walltime_accounting.h"
88 #include "gromacs/utility/gmxmpi.h"
89 #include "gromacs/utility/smalloc.h"
90 #include "gromacs/essentialdynamics/edsam.h"
91 #include "gromacs/pulling/pull.h"
92 #include "gromacs/pulling/pull_rotation.h"
93 #include "gromacs/imd/imd.h"
97 #include "gmx_omp_nthreads.h"
99 #include "nbnxn_cuda_data_mgmt.h"
100 #include "nbnxn_cuda/nbnxn_cuda.h"
102 void print_time(FILE *out
,
103 gmx_walltime_accounting_t walltime_accounting
,
106 t_commrec gmx_unused
*cr
)
109 char timebuf
[STRLEN
];
110 double dt
, elapsed_seconds
, time_per_step
;
113 #ifndef GMX_THREAD_MPI
119 fprintf(out
, "step %s", gmx_step_str(step
, buf
));
120 if ((step
>= ir
->nstlist
))
122 double seconds_since_epoch
= gmx_gettime();
123 elapsed_seconds
= seconds_since_epoch
- walltime_accounting_get_start_time_stamp(walltime_accounting
);
124 time_per_step
= elapsed_seconds
/(step
- ir
->init_step
+ 1);
125 dt
= (ir
->nsteps
+ ir
->init_step
- step
) * time_per_step
;
131 finish
= (time_t) (seconds_since_epoch
+ dt
);
132 gmx_ctime_r(&finish
, timebuf
, STRLEN
);
133 sprintf(buf
, "%s", timebuf
);
134 buf
[strlen(buf
)-1] = '\0';
135 fprintf(out
, ", will finish %s", buf
);
139 fprintf(out
, ", remaining wall clock time: %5d s ", (int)dt
);
144 fprintf(out
, " performance: %.1f ns/day ",
145 ir
->delta_t
/1000*24*60*60/time_per_step
);
148 #ifndef GMX_THREAD_MPI
158 void print_date_and_time(FILE *fplog
, int nodeid
, const char *title
,
161 char time_string
[STRLEN
];
170 char timebuf
[STRLEN
];
171 time_t temp_time
= (time_t) the_time
;
173 gmx_ctime_r(&temp_time
, timebuf
, STRLEN
);
174 for (i
= 0; timebuf
[i
] >= ' '; i
++)
176 time_string
[i
] = timebuf
[i
];
178 time_string
[i
] = '\0';
181 fprintf(fplog
, "%s on node %d %s\n", title
, nodeid
, time_string
);
184 void print_start(FILE *fplog
, t_commrec
*cr
,
185 gmx_walltime_accounting_t walltime_accounting
,
190 sprintf(buf
, "Started %s", name
);
191 print_date_and_time(fplog
, cr
->nodeid
, buf
,
192 walltime_accounting_get_start_time_stamp(walltime_accounting
));
195 static void sum_forces(int start
, int end
, rvec f
[], rvec flr
[])
201 pr_rvecs(debug
, 0, "fsr", f
+start
, end
-start
);
202 pr_rvecs(debug
, 0, "flr", flr
+start
, end
-start
);
204 for (i
= start
; (i
< end
); i
++)
206 rvec_inc(f
[i
], flr
[i
]);
211 * calc_f_el calculates forces due to an electric field.
213 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
215 * Et[] contains the parameters for the time dependent
216 * part of the field (not yet used).
217 * Ex[] contains the parameters for
218 * the spatial dependent part of the field. You can have cool periodic
219 * fields in principle, but only a constant field is supported
221 * The function should return the energy due to the electric field
222 * (if any) but for now returns 0.
225 * There can be problems with the virial.
226 * Since the field is not self-consistent this is unavoidable.
227 * For neutral molecules the virial is correct within this approximation.
228 * For neutral systems with many charged molecules the error is small.
229 * But for systems with a net charge or a few charged molecules
230 * the error can be significant when the field is high.
231 * Solution: implement a self-consitent electric field into PME.
233 static void calc_f_el(FILE *fp
, int start
, int homenr
,
234 real charge
[], rvec f
[],
235 t_cosines Ex
[], t_cosines Et
[], double t
)
241 for (m
= 0; (m
< DIM
); m
++)
248 Ext
[m
] = cos(Et
[m
].a
[0]*(t
-t0
))*exp(-sqr(t
-t0
)/(2.0*sqr(Et
[m
].a
[2])));
252 Ext
[m
] = cos(Et
[m
].a
[0]*t
);
261 /* Convert the field strength from V/nm to MD-units */
262 Ext
[m
] *= Ex
[m
].a
[0]*FIELDFAC
;
263 for (i
= start
; (i
< start
+homenr
); i
++)
265 f
[i
][m
] += charge
[i
]*Ext
[m
];
275 fprintf(fp
, "%10g %10g %10g %10g #FIELD\n", t
,
276 Ext
[XX
]/FIELDFAC
, Ext
[YY
]/FIELDFAC
, Ext
[ZZ
]/FIELDFAC
);
280 static void calc_virial(int start
, int homenr
, rvec x
[], rvec f
[],
281 tensor vir_part
, t_graph
*graph
, matrix box
,
282 t_nrnb
*nrnb
, const t_forcerec
*fr
, int ePBC
)
287 /* The short-range virial from surrounding boxes */
289 calc_vir(SHIFTS
, fr
->shift_vec
, fr
->fshift
, vir_part
, ePBC
== epbcSCREW
, box
);
290 inc_nrnb(nrnb
, eNR_VIRIAL
, SHIFTS
);
292 /* Calculate partial virial, for local atoms only, based on short range.
293 * Total virial is computed in global_stat, called from do_md
295 f_calc_vir(start
, start
+homenr
, x
, f
, vir_part
, graph
, box
);
296 inc_nrnb(nrnb
, eNR_VIRIAL
, homenr
);
298 /* Add position restraint contribution */
299 for (i
= 0; i
< DIM
; i
++)
301 vir_part
[i
][i
] += fr
->vir_diag_posres
[i
];
304 /* Add wall contribution */
305 for (i
= 0; i
< DIM
; i
++)
307 vir_part
[i
][ZZ
] += fr
->vir_wall_z
[i
];
312 pr_rvecs(debug
, 0, "vir_part", vir_part
, DIM
);
316 static void posres_wrapper(FILE *fplog
,
322 matrix box
, rvec x
[],
323 gmx_enerdata_t
*enerd
,
331 /* Position restraints always require full pbc */
332 set_pbc(&pbc
, ir
->ePBC
, box
);
334 v
= posres(top
->idef
.il
[F_POSRES
].nr
, top
->idef
.il
[F_POSRES
].iatoms
,
335 top
->idef
.iparams_posres
,
336 (const rvec
*)x
, fr
->f_novirsum
, fr
->vir_diag_posres
,
337 ir
->ePBC
== epbcNONE
? NULL
: &pbc
,
338 lambda
[efptRESTRAINT
], &dvdl
,
339 fr
->rc_scaling
, fr
->ePBC
, fr
->posres_com
, fr
->posres_comB
);
342 gmx_print_sepdvdl(fplog
, interaction_function
[F_POSRES
].longname
, v
, dvdl
);
344 enerd
->term
[F_POSRES
] += v
;
345 /* If just the force constant changes, the FEP term is linear,
346 * but if k changes, it is not.
348 enerd
->dvdl_nonlin
[efptRESTRAINT
] += dvdl
;
349 inc_nrnb(nrnb
, eNR_POSRES
, top
->idef
.il
[F_POSRES
].nr
/2);
351 if ((ir
->fepvals
->n_lambda
> 0) && (flags
& GMX_FORCE_DHDL
))
353 for (i
= 0; i
< enerd
->n_lambda
; i
++)
355 real dvdl_dum
, lambda_dum
;
357 lambda_dum
= (i
== 0 ? lambda
[efptRESTRAINT
] : ir
->fepvals
->all_lambda
[efptRESTRAINT
][i
-1]);
358 v
= posres(top
->idef
.il
[F_POSRES
].nr
, top
->idef
.il
[F_POSRES
].iatoms
,
359 top
->idef
.iparams_posres
,
360 (const rvec
*)x
, NULL
, NULL
,
361 ir
->ePBC
== epbcNONE
? NULL
: &pbc
, lambda_dum
, &dvdl
,
362 fr
->rc_scaling
, fr
->ePBC
, fr
->posres_com
, fr
->posres_comB
);
363 enerd
->enerpart_lambda
[i
] += v
;
368 static void fbposres_wrapper(t_inputrec
*ir
,
371 matrix box
, rvec x
[],
372 gmx_enerdata_t
*enerd
,
378 /* Flat-bottomed position restraints always require full pbc */
379 set_pbc(&pbc
, ir
->ePBC
, box
);
380 v
= fbposres(top
->idef
.il
[F_FBPOSRES
].nr
, top
->idef
.il
[F_FBPOSRES
].iatoms
,
381 top
->idef
.iparams_fbposres
,
382 (const rvec
*)x
, fr
->f_novirsum
, fr
->vir_diag_posres
,
383 ir
->ePBC
== epbcNONE
? NULL
: &pbc
,
384 fr
->rc_scaling
, fr
->ePBC
, fr
->posres_com
);
385 enerd
->term
[F_FBPOSRES
] += v
;
386 inc_nrnb(nrnb
, eNR_FBPOSRES
, top
->idef
.il
[F_FBPOSRES
].nr
/2);
389 static void pull_potential_wrapper(FILE *fplog
,
393 matrix box
, rvec x
[],
397 gmx_enerdata_t
*enerd
,
404 /* Calculate the center of mass forces, this requires communication,
405 * which is why pull_potential is called close to other communication.
406 * The virial contribution is calculated directly,
407 * which is why we call pull_potential after calc_virial.
409 set_pbc(&pbc
, ir
->ePBC
, box
);
411 enerd
->term
[F_COM_PULL
] +=
412 pull_potential(ir
->ePull
, ir
->pull
, mdatoms
, &pbc
,
413 cr
, t
, lambda
[efptRESTRAINT
], x
, f
, vir_force
, &dvdl
);
416 gmx_print_sepdvdl(fplog
, "Com pull", enerd
->term
[F_COM_PULL
], dvdl
);
418 enerd
->dvdl_lin
[efptRESTRAINT
] += dvdl
;
421 static void pme_receive_force_ener(FILE *fplog
,
424 gmx_wallcycle_t wcycle
,
425 gmx_enerdata_t
*enerd
,
428 real e_q
, e_lj
, v
, dvdl_q
, dvdl_lj
;
429 float cycles_ppdpme
, cycles_seppme
;
431 cycles_ppdpme
= wallcycle_stop(wcycle
, ewcPPDURINGPME
);
432 dd_cycles_add(cr
->dd
, cycles_ppdpme
, ddCyclPPduringPME
);
434 /* In case of node-splitting, the PP nodes receive the long-range
435 * forces, virial and energy from the PME nodes here.
437 wallcycle_start(wcycle
, ewcPP_PMEWAITRECVF
);
440 gmx_pme_receive_f(cr
, fr
->f_novirsum
, fr
->vir_el_recip
, &e_q
,
441 fr
->vir_lj_recip
, &e_lj
, &dvdl_q
, &dvdl_lj
,
445 gmx_print_sepdvdl(fplog
, "Electrostatic PME mesh", e_q
, dvdl_q
);
446 gmx_print_sepdvdl(fplog
, "Lennard-Jones PME mesh", e_lj
, dvdl_lj
);
448 enerd
->term
[F_COUL_RECIP
] += e_q
;
449 enerd
->term
[F_LJ_RECIP
] += e_lj
;
450 enerd
->dvdl_lin
[efptCOUL
] += dvdl_q
;
451 enerd
->dvdl_lin
[efptVDW
] += dvdl_lj
;
455 dd_cycles_add(cr
->dd
, cycles_seppme
, ddCyclPME
);
457 wallcycle_stop(wcycle
, ewcPP_PMEWAITRECVF
);
460 static void print_large_forces(FILE *fp
, t_mdatoms
*md
, t_commrec
*cr
,
461 gmx_int64_t step
, real pforce
, rvec
*x
, rvec
*f
)
465 char buf
[STEPSTRSIZE
];
468 for (i
= 0; i
< md
->homenr
; i
++)
471 /* We also catch NAN, if the compiler does not optimize this away. */
472 if (fn2
>= pf2
|| fn2
!= fn2
)
474 fprintf(fp
, "step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
475 gmx_step_str(step
, buf
),
476 ddglatnr(cr
->dd
, i
), x
[i
][XX
], x
[i
][YY
], x
[i
][ZZ
], sqrt(fn2
));
481 static void post_process_forces(t_commrec
*cr
,
483 t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
485 matrix box
, rvec x
[],
490 t_forcerec
*fr
, gmx_vsite_t
*vsite
,
497 /* Spread the mesh force on virtual sites to the other particles...
498 * This is parallellized. MPI communication is performed
499 * if the constructing atoms aren't local.
501 wallcycle_start(wcycle
, ewcVSITESPREAD
);
502 spread_vsite_f(vsite
, x
, fr
->f_novirsum
, NULL
,
503 (flags
& GMX_FORCE_VIRIAL
), fr
->vir_el_recip
,
505 &top
->idef
, fr
->ePBC
, fr
->bMolPBC
, graph
, box
, cr
);
506 wallcycle_stop(wcycle
, ewcVSITESPREAD
);
508 if (flags
& GMX_FORCE_VIRIAL
)
510 /* Now add the forces, this is local */
513 sum_forces(0, fr
->f_novirsum_n
, f
, fr
->f_novirsum
);
517 sum_forces(0, mdatoms
->homenr
,
520 if (EEL_FULL(fr
->eeltype
))
522 /* Add the mesh contribution to the virial */
523 m_add(vir_force
, fr
->vir_el_recip
, vir_force
);
525 if (EVDW_PME(fr
->vdwtype
))
527 /* Add the mesh contribution to the virial */
528 m_add(vir_force
, fr
->vir_lj_recip
, vir_force
);
532 pr_rvecs(debug
, 0, "vir_force", vir_force
, DIM
);
537 if (fr
->print_force
>= 0)
539 print_large_forces(stderr
, mdatoms
, cr
, step
, fr
->print_force
, x
, f
);
543 static void do_nb_verlet(t_forcerec
*fr
,
544 interaction_const_t
*ic
,
545 gmx_enerdata_t
*enerd
,
546 int flags
, int ilocality
,
549 gmx_wallcycle_t wcycle
)
551 int nnbl
, kernel_type
, enr_nbnxn_kernel_ljc
, enr_nbnxn_kernel_lj
;
553 nonbonded_verlet_group_t
*nbvg
;
556 if (!(flags
& GMX_FORCE_NONBONDED
))
558 /* skip non-bonded calculation */
562 nbvg
= &fr
->nbv
->grp
[ilocality
];
564 /* CUDA kernel launch overhead is already timed separately */
565 if (fr
->cutoff_scheme
!= ecutsVERLET
)
567 gmx_incons("Invalid cut-off scheme passed!");
570 bCUDA
= (nbvg
->kernel_type
== nbnxnk8x8x8_CUDA
);
574 wallcycle_sub_start(wcycle
, ewcsNONBONDED
);
576 switch (nbvg
->kernel_type
)
578 case nbnxnk4x4_PlainC
:
579 nbnxn_kernel_ref(&nbvg
->nbl_lists
,
585 enerd
->grpp
.ener
[egCOULSR
],
587 enerd
->grpp
.ener
[egBHAMSR
] :
588 enerd
->grpp
.ener
[egLJSR
]);
591 case nbnxnk4xN_SIMD_4xN
:
592 nbnxn_kernel_simd_4xn(&nbvg
->nbl_lists
,
599 enerd
->grpp
.ener
[egCOULSR
],
601 enerd
->grpp
.ener
[egBHAMSR
] :
602 enerd
->grpp
.ener
[egLJSR
]);
604 case nbnxnk4xN_SIMD_2xNN
:
605 nbnxn_kernel_simd_2xnn(&nbvg
->nbl_lists
,
612 enerd
->grpp
.ener
[egCOULSR
],
614 enerd
->grpp
.ener
[egBHAMSR
] :
615 enerd
->grpp
.ener
[egLJSR
]);
618 case nbnxnk8x8x8_CUDA
:
619 nbnxn_cuda_launch_kernel(fr
->nbv
->cu_nbv
, nbvg
->nbat
, flags
, ilocality
);
622 case nbnxnk8x8x8_PlainC
:
623 nbnxn_kernel_gpu_ref(nbvg
->nbl_lists
.nbl
[0],
628 nbvg
->nbat
->out
[0].f
,
630 enerd
->grpp
.ener
[egCOULSR
],
632 enerd
->grpp
.ener
[egBHAMSR
] :
633 enerd
->grpp
.ener
[egLJSR
]);
637 gmx_incons("Invalid nonbonded kernel type passed!");
642 wallcycle_sub_stop(wcycle
, ewcsNONBONDED
);
645 if (EEL_RF(ic
->eeltype
) || ic
->eeltype
== eelCUT
)
647 enr_nbnxn_kernel_ljc
= eNR_NBNXN_LJ_RF
;
649 else if ((!bCUDA
&& nbvg
->ewald_excl
== ewaldexclAnalytical
) ||
650 (bCUDA
&& nbnxn_cuda_is_kernel_ewald_analytical(fr
->nbv
->cu_nbv
)))
652 enr_nbnxn_kernel_ljc
= eNR_NBNXN_LJ_EWALD
;
656 enr_nbnxn_kernel_ljc
= eNR_NBNXN_LJ_TAB
;
658 enr_nbnxn_kernel_lj
= eNR_NBNXN_LJ
;
659 if (flags
& GMX_FORCE_ENERGY
)
661 /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
662 enr_nbnxn_kernel_ljc
+= 1;
663 enr_nbnxn_kernel_lj
+= 1;
666 inc_nrnb(nrnb
, enr_nbnxn_kernel_ljc
,
667 nbvg
->nbl_lists
.natpair_ljq
);
668 inc_nrnb(nrnb
, enr_nbnxn_kernel_lj
,
669 nbvg
->nbl_lists
.natpair_lj
);
670 /* The Coulomb-only kernels are offset -eNR_NBNXN_LJ_RF+eNR_NBNXN_RF */
671 inc_nrnb(nrnb
, enr_nbnxn_kernel_ljc
-eNR_NBNXN_LJ_RF
+eNR_NBNXN_RF
,
672 nbvg
->nbl_lists
.natpair_q
);
674 if (ic
->vdw_modifier
== eintmodFORCESWITCH
)
676 /* We add up the switch cost separately */
677 inc_nrnb(nrnb
, eNR_NBNXN_ADD_LJ_FSW
+((flags
& GMX_FORCE_ENERGY
) ? 1 : 0),
678 nbvg
->nbl_lists
.natpair_ljq
+ nbvg
->nbl_lists
.natpair_lj
);
680 if (ic
->vdw_modifier
== eintmodPOTSWITCH
)
682 /* We add up the switch cost separately */
683 inc_nrnb(nrnb
, eNR_NBNXN_ADD_LJ_PSW
+((flags
& GMX_FORCE_ENERGY
) ? 1 : 0),
684 nbvg
->nbl_lists
.natpair_ljq
+ nbvg
->nbl_lists
.natpair_lj
);
686 if (ic
->vdwtype
== evdwPME
)
688 /* We add up the LJ Ewald cost separately */
689 inc_nrnb(nrnb
, eNR_NBNXN_ADD_LJ_EWALD
+((flags
& GMX_FORCE_ENERGY
) ? 1 : 0),
690 nbvg
->nbl_lists
.natpair_ljq
+ nbvg
->nbl_lists
.natpair_lj
);
694 static void do_nb_verlet_fep(nbnxn_pairlist_set_t
*nbl_lists
,
701 gmx_enerdata_t
*enerd
,
704 gmx_wallcycle_t wcycle
)
707 nb_kernel_data_t kernel_data
;
709 real dvdl_nb
[efptNR
];
714 /* Add short-range interactions */
715 donb_flags
|= GMX_NONBONDED_DO_SR
;
717 /* Currently all group scheme kernels always calculate (shift-)forces */
718 if (flags
& GMX_FORCE_FORCES
)
720 donb_flags
|= GMX_NONBONDED_DO_FORCE
;
722 if (flags
& GMX_FORCE_VIRIAL
)
724 donb_flags
|= GMX_NONBONDED_DO_SHIFTFORCE
;
726 if (flags
& GMX_FORCE_ENERGY
)
728 donb_flags
|= GMX_NONBONDED_DO_POTENTIAL
;
730 if (flags
& GMX_FORCE_DO_LR
)
732 donb_flags
|= GMX_NONBONDED_DO_LR
;
735 kernel_data
.flags
= donb_flags
;
736 kernel_data
.lambda
= lambda
;
737 kernel_data
.dvdl
= dvdl_nb
;
739 kernel_data
.energygrp_elec
= enerd
->grpp
.ener
[egCOULSR
];
740 kernel_data
.energygrp_vdw
= enerd
->grpp
.ener
[egLJSR
];
742 /* reset free energy components */
743 for (i
= 0; i
< efptNR
; i
++)
748 assert(gmx_omp_nthreads_get(emntNonbonded
) == nbl_lists
->nnbl
);
750 wallcycle_sub_start(wcycle
, ewcsNONBONDED
);
751 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
752 for (th
= 0; th
< nbl_lists
->nnbl
; th
++)
754 gmx_nb_free_energy_kernel(nbl_lists
->nbl_fep
[th
],
755 x
, f
, fr
, mdatoms
, &kernel_data
, nrnb
);
758 if (fepvals
->sc_alpha
!= 0)
760 enerd
->dvdl_nonlin
[efptVDW
] += dvdl_nb
[efptVDW
];
761 enerd
->dvdl_nonlin
[efptCOUL
] += dvdl_nb
[efptCOUL
];
765 enerd
->dvdl_lin
[efptVDW
] += dvdl_nb
[efptVDW
];
766 enerd
->dvdl_lin
[efptCOUL
] += dvdl_nb
[efptCOUL
];
769 /* If we do foreign lambda and we have soft-core interactions
770 * we have to recalculate the (non-linear) energies contributions.
772 if (fepvals
->n_lambda
> 0 && (flags
& GMX_FORCE_DHDL
) && fepvals
->sc_alpha
!= 0)
774 kernel_data
.flags
= (donb_flags
& ~(GMX_NONBONDED_DO_FORCE
| GMX_NONBONDED_DO_SHIFTFORCE
)) | GMX_NONBONDED_DO_FOREIGNLAMBDA
;
775 kernel_data
.lambda
= lam_i
;
776 kernel_data
.energygrp_elec
= enerd
->foreign_grpp
.ener
[egCOULSR
];
777 kernel_data
.energygrp_vdw
= enerd
->foreign_grpp
.ener
[egLJSR
];
778 /* Note that we add to kernel_data.dvdl, but ignore the result */
780 for (i
= 0; i
< enerd
->n_lambda
; i
++)
782 for (j
= 0; j
< efptNR
; j
++)
784 lam_i
[j
] = (i
== 0 ? lambda
[j
] : fepvals
->all_lambda
[j
][i
-1]);
786 reset_foreign_enerdata(enerd
);
787 #pragma omp parallel for schedule(static) num_threads(nbl_lists->nnbl)
788 for (th
= 0; th
< nbl_lists
->nnbl
; th
++)
790 gmx_nb_free_energy_kernel(nbl_lists
->nbl_fep
[th
],
791 x
, f
, fr
, mdatoms
, &kernel_data
, nrnb
);
794 sum_epot(&(enerd
->foreign_grpp
), enerd
->foreign_term
);
795 enerd
->enerpart_lambda
[i
] += enerd
->foreign_term
[F_EPOT
];
799 wallcycle_sub_stop(wcycle
, ewcsNONBONDED
);
802 void do_force_cutsVERLET(FILE *fplog
, t_commrec
*cr
,
803 t_inputrec
*inputrec
,
804 gmx_int64_t step
, t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
806 gmx_groups_t gmx_unused
*groups
,
807 matrix box
, rvec x
[], history_t
*hist
,
811 gmx_enerdata_t
*enerd
, t_fcdata
*fcd
,
812 real
*lambda
, t_graph
*graph
,
813 t_forcerec
*fr
, interaction_const_t
*ic
,
814 gmx_vsite_t
*vsite
, rvec mu_tot
,
815 double t
, FILE *field
, gmx_edsam_t ed
,
823 gmx_bool bSepDVDL
, bStateChanged
, bNS
, bFillGrid
, bCalcCGCM
, bBS
;
824 gmx_bool bDoLongRange
, bDoForces
, bSepLRF
, bUseGPU
, bUseOrEmulGPU
;
825 gmx_bool bDiffKernels
= FALSE
;
827 rvec vzero
, box_diag
;
829 float cycles_pme
, cycles_force
, cycles_wait_gpu
;
830 nonbonded_verlet_t
*nbv
;
835 nb_kernel_type
= fr
->nbv
->grp
[0].kernel_type
;
838 homenr
= mdatoms
->homenr
;
840 bSepDVDL
= (fr
->bSepDVDL
&& do_per_step(step
, inputrec
->nstlog
));
842 clear_mat(vir_force
);
845 if (DOMAINDECOMP(cr
))
847 cg1
= cr
->dd
->ncg_tot
;
858 bStateChanged
= (flags
& GMX_FORCE_STATECHANGED
);
859 bNS
= (flags
& GMX_FORCE_NS
) && (fr
->bAllvsAll
== FALSE
);
860 bFillGrid
= (bNS
&& bStateChanged
);
861 bCalcCGCM
= (bFillGrid
&& !DOMAINDECOMP(cr
));
862 bDoLongRange
= (fr
->bTwinRange
&& bNS
&& (flags
& GMX_FORCE_DO_LR
));
863 bDoForces
= (flags
& GMX_FORCE_FORCES
);
864 bSepLRF
= (bDoLongRange
&& bDoForces
&& (flags
& GMX_FORCE_SEPLRF
));
865 bUseGPU
= fr
->nbv
->bUseGPU
;
866 bUseOrEmulGPU
= bUseGPU
|| (nbv
->grp
[0].kernel_type
== nbnxnk8x8x8_PlainC
);
870 update_forcerec(fr
, box
);
872 if (NEED_MUTOT(*inputrec
))
874 /* Calculate total (local) dipole moment in a temporary common array.
875 * This makes it possible to sum them over nodes faster.
877 calc_mu(start
, homenr
,
878 x
, mdatoms
->chargeA
, mdatoms
->chargeB
, mdatoms
->nChargePerturbed
,
883 if (fr
->ePBC
!= epbcNONE
)
885 /* Compute shift vectors every step,
886 * because of pressure coupling or box deformation!
888 if ((flags
& GMX_FORCE_DYNAMICBOX
) && bStateChanged
)
890 calc_shifts(box
, fr
->shift_vec
);
895 put_atoms_in_box_omp(fr
->ePBC
, box
, homenr
, x
);
896 inc_nrnb(nrnb
, eNR_SHIFTX
, homenr
);
898 else if (EI_ENERGY_MINIMIZATION(inputrec
->eI
) && graph
)
900 unshift_self(graph
, box
, x
);
904 nbnxn_atomdata_copy_shiftvec(flags
& GMX_FORCE_DYNAMICBOX
,
905 fr
->shift_vec
, nbv
->grp
[0].nbat
);
908 if (!(cr
->duty
& DUTY_PME
))
910 /* Send particle coordinates to the pme nodes.
911 * Since this is only implemented for domain decomposition
912 * and domain decomposition does not use the graph,
913 * we do not need to worry about shifting.
918 wallcycle_start(wcycle
, ewcPP_PMESENDX
);
920 bBS
= (inputrec
->nwall
== 2);
924 svmul(inputrec
->wall_ewald_zfac
, boxs
[ZZ
], boxs
[ZZ
]);
927 if (EEL_PME(fr
->eeltype
))
929 pme_flags
|= GMX_PME_DO_COULOMB
;
932 if (EVDW_PME(fr
->vdwtype
))
934 pme_flags
|= GMX_PME_DO_LJ
;
937 gmx_pme_send_coordinates(cr
, bBS
? boxs
: box
, x
,
938 mdatoms
->nChargePerturbed
, mdatoms
->nTypePerturbed
, lambda
[efptCOUL
], lambda
[efptVDW
],
939 (flags
& (GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
)),
942 wallcycle_stop(wcycle
, ewcPP_PMESENDX
);
946 /* do gridding for pair search */
949 if (graph
&& bStateChanged
)
951 /* Calculate intramolecular shift vectors to make molecules whole */
952 mk_mshift(fplog
, graph
, fr
->ePBC
, box
, x
);
956 box_diag
[XX
] = box
[XX
][XX
];
957 box_diag
[YY
] = box
[YY
][YY
];
958 box_diag
[ZZ
] = box
[ZZ
][ZZ
];
960 wallcycle_start(wcycle
, ewcNS
);
963 wallcycle_sub_start(wcycle
, ewcsNBS_GRID_LOCAL
);
964 nbnxn_put_on_grid(nbv
->nbs
, fr
->ePBC
, box
,
966 0, mdatoms
->homenr
, -1, fr
->cginfo
, x
,
968 nbv
->grp
[eintLocal
].kernel_type
,
969 nbv
->grp
[eintLocal
].nbat
);
970 wallcycle_sub_stop(wcycle
, ewcsNBS_GRID_LOCAL
);
974 wallcycle_sub_start(wcycle
, ewcsNBS_GRID_NONLOCAL
);
975 nbnxn_put_on_grid_nonlocal(nbv
->nbs
, domdec_zones(cr
->dd
),
977 nbv
->grp
[eintNonlocal
].kernel_type
,
978 nbv
->grp
[eintNonlocal
].nbat
);
979 wallcycle_sub_stop(wcycle
, ewcsNBS_GRID_NONLOCAL
);
982 if (nbv
->ngrp
== 1 ||
983 nbv
->grp
[eintNonlocal
].nbat
== nbv
->grp
[eintLocal
].nbat
)
985 nbnxn_atomdata_set(nbv
->grp
[eintLocal
].nbat
, eatAll
,
986 nbv
->nbs
, mdatoms
, fr
->cginfo
);
990 nbnxn_atomdata_set(nbv
->grp
[eintLocal
].nbat
, eatLocal
,
991 nbv
->nbs
, mdatoms
, fr
->cginfo
);
992 nbnxn_atomdata_set(nbv
->grp
[eintNonlocal
].nbat
, eatAll
,
993 nbv
->nbs
, mdatoms
, fr
->cginfo
);
995 wallcycle_stop(wcycle
, ewcNS
);
998 /* initialize the GPU atom data and copy shift vector */
1003 wallcycle_start_nocount(wcycle
, ewcLAUNCH_GPU_NB
);
1004 nbnxn_cuda_init_atomdata(nbv
->cu_nbv
, nbv
->grp
[eintLocal
].nbat
);
1005 wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1008 wallcycle_start_nocount(wcycle
, ewcLAUNCH_GPU_NB
);
1009 nbnxn_cuda_upload_shiftvec(nbv
->cu_nbv
, nbv
->grp
[eintLocal
].nbat
);
1010 wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1013 /* do local pair search */
1016 wallcycle_start_nocount(wcycle
, ewcNS
);
1017 wallcycle_sub_start(wcycle
, ewcsNBS_SEARCH_LOCAL
);
1018 nbnxn_make_pairlist(nbv
->nbs
, nbv
->grp
[eintLocal
].nbat
,
1021 nbv
->min_ci_balanced
,
1022 &nbv
->grp
[eintLocal
].nbl_lists
,
1024 nbv
->grp
[eintLocal
].kernel_type
,
1026 wallcycle_sub_stop(wcycle
, ewcsNBS_SEARCH_LOCAL
);
1030 /* initialize local pair-list on the GPU */
1031 nbnxn_cuda_init_pairlist(nbv
->cu_nbv
,
1032 nbv
->grp
[eintLocal
].nbl_lists
.nbl
[0],
1035 wallcycle_stop(wcycle
, ewcNS
);
1039 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1040 wallcycle_sub_start(wcycle
, ewcsNB_X_BUF_OPS
);
1041 nbnxn_atomdata_copy_x_to_nbat_x(nbv
->nbs
, eatLocal
, FALSE
, x
,
1042 nbv
->grp
[eintLocal
].nbat
);
1043 wallcycle_sub_stop(wcycle
, ewcsNB_X_BUF_OPS
);
1044 wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1049 wallcycle_start(wcycle
, ewcLAUNCH_GPU_NB
);
1050 /* launch local nonbonded F on GPU */
1051 do_nb_verlet(fr
, ic
, enerd
, flags
, eintLocal
, enbvClearFNo
,
1053 wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1056 /* Communicate coordinates and sum dipole if necessary +
1057 do non-local pair search */
1058 if (DOMAINDECOMP(cr
))
1060 bDiffKernels
= (nbv
->grp
[eintNonlocal
].kernel_type
!=
1061 nbv
->grp
[eintLocal
].kernel_type
);
1065 /* With GPU+CPU non-bonded calculations we need to copy
1066 * the local coordinates to the non-local nbat struct
1067 * (in CPU format) as the non-local kernel call also
1068 * calculates the local - non-local interactions.
1070 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1071 wallcycle_sub_start(wcycle
, ewcsNB_X_BUF_OPS
);
1072 nbnxn_atomdata_copy_x_to_nbat_x(nbv
->nbs
, eatLocal
, TRUE
, x
,
1073 nbv
->grp
[eintNonlocal
].nbat
);
1074 wallcycle_sub_stop(wcycle
, ewcsNB_X_BUF_OPS
);
1075 wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1080 wallcycle_start_nocount(wcycle
, ewcNS
);
1081 wallcycle_sub_start(wcycle
, ewcsNBS_SEARCH_NONLOCAL
);
1085 nbnxn_grid_add_simple(nbv
->nbs
, nbv
->grp
[eintNonlocal
].nbat
);
1088 nbnxn_make_pairlist(nbv
->nbs
, nbv
->grp
[eintNonlocal
].nbat
,
1091 nbv
->min_ci_balanced
,
1092 &nbv
->grp
[eintNonlocal
].nbl_lists
,
1094 nbv
->grp
[eintNonlocal
].kernel_type
,
1097 wallcycle_sub_stop(wcycle
, ewcsNBS_SEARCH_NONLOCAL
);
1099 if (nbv
->grp
[eintNonlocal
].kernel_type
== nbnxnk8x8x8_CUDA
)
1101 /* initialize non-local pair-list on the GPU */
1102 nbnxn_cuda_init_pairlist(nbv
->cu_nbv
,
1103 nbv
->grp
[eintNonlocal
].nbl_lists
.nbl
[0],
1106 wallcycle_stop(wcycle
, ewcNS
);
1110 wallcycle_start(wcycle
, ewcMOVEX
);
1111 dd_move_x(cr
->dd
, box
, x
);
1113 /* When we don't need the total dipole we sum it in global_stat */
1114 if (bStateChanged
&& NEED_MUTOT(*inputrec
))
1116 gmx_sumd(2*DIM
, mu
, cr
);
1118 wallcycle_stop(wcycle
, ewcMOVEX
);
1120 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1121 wallcycle_sub_start(wcycle
, ewcsNB_X_BUF_OPS
);
1122 nbnxn_atomdata_copy_x_to_nbat_x(nbv
->nbs
, eatNonlocal
, FALSE
, x
,
1123 nbv
->grp
[eintNonlocal
].nbat
);
1124 wallcycle_sub_stop(wcycle
, ewcsNB_X_BUF_OPS
);
1125 cycles_force
+= wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1128 if (bUseGPU
&& !bDiffKernels
)
1130 wallcycle_start(wcycle
, ewcLAUNCH_GPU_NB
);
1131 /* launch non-local nonbonded F on GPU */
1132 do_nb_verlet(fr
, ic
, enerd
, flags
, eintNonlocal
, enbvClearFNo
,
1134 cycles_force
+= wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1140 /* launch D2H copy-back F */
1141 wallcycle_start_nocount(wcycle
, ewcLAUNCH_GPU_NB
);
1142 if (DOMAINDECOMP(cr
) && !bDiffKernels
)
1144 nbnxn_cuda_launch_cpyback(nbv
->cu_nbv
, nbv
->grp
[eintNonlocal
].nbat
,
1145 flags
, eatNonlocal
);
1147 nbnxn_cuda_launch_cpyback(nbv
->cu_nbv
, nbv
->grp
[eintLocal
].nbat
,
1149 cycles_force
+= wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1152 if (bStateChanged
&& NEED_MUTOT(*inputrec
))
1156 gmx_sumd(2*DIM
, mu
, cr
);
1159 for (i
= 0; i
< 2; i
++)
1161 for (j
= 0; j
< DIM
; j
++)
1163 fr
->mu_tot
[i
][j
] = mu
[i
*DIM
+ j
];
1167 if (fr
->efep
== efepNO
)
1169 copy_rvec(fr
->mu_tot
[0], mu_tot
);
1173 for (j
= 0; j
< DIM
; j
++)
1176 (1.0 - lambda
[efptCOUL
])*fr
->mu_tot
[0][j
] +
1177 lambda
[efptCOUL
]*fr
->mu_tot
[1][j
];
1181 /* Reset energies */
1182 reset_enerdata(fr
, bNS
, enerd
, MASTER(cr
));
1183 clear_rvecs(SHIFTS
, fr
->fshift
);
1185 if (DOMAINDECOMP(cr
) && !(cr
->duty
& DUTY_PME
))
1187 wallcycle_start(wcycle
, ewcPPDURINGPME
);
1188 dd_force_flop_start(cr
->dd
, nrnb
);
1193 /* Enforced rotation has its own cycle counter that starts after the collective
1194 * coordinates have been communicated. It is added to ddCyclF to allow
1195 * for proper load-balancing */
1196 wallcycle_start(wcycle
, ewcROT
);
1197 do_rotation(cr
, inputrec
, box
, x
, t
, step
, wcycle
, bNS
);
1198 wallcycle_stop(wcycle
, ewcROT
);
1201 /* Start the force cycle counter.
1202 * This counter is stopped in do_forcelow_level.
1203 * No parallel communication should occur while this counter is running,
1204 * since that will interfere with the dynamic load balancing.
1206 wallcycle_start(wcycle
, ewcFORCE
);
1209 /* Reset forces for which the virial is calculated separately:
1210 * PME/Ewald forces if necessary */
1211 if (fr
->bF_NoVirSum
)
1213 if (flags
& GMX_FORCE_VIRIAL
)
1215 fr
->f_novirsum
= fr
->f_novirsum_alloc
;
1218 clear_rvecs(fr
->f_novirsum_n
, fr
->f_novirsum
);
1222 clear_rvecs(homenr
, fr
->f_novirsum
+start
);
1227 /* We are not calculating the pressure so we do not need
1228 * a separate array for forces that do not contribute
1235 /* Clear the short- and long-range forces */
1236 clear_rvecs(fr
->natoms_force_constr
, f
);
1237 if (bSepLRF
&& do_per_step(step
, inputrec
->nstcalclr
))
1239 clear_rvecs(fr
->natoms_force_constr
, fr
->f_twin
);
1242 clear_rvec(fr
->vir_diag_posres
);
1245 if (inputrec
->ePull
== epullCONSTRAINT
)
1247 clear_pull_forces(inputrec
->pull
);
1250 /* We calculate the non-bonded forces, when done on the CPU, here.
1251 * We do this before calling do_force_lowlevel, as in there bondeds
1252 * forces are calculated before PME, which does communication.
1253 * With this order, non-bonded and bonded force calculation imbalance
1254 * can be balanced out by the domain decomposition load balancing.
1259 /* Maybe we should move this into do_force_lowlevel */
1260 do_nb_verlet(fr
, ic
, enerd
, flags
, eintLocal
, enbvClearFYes
,
1264 if (fr
->efep
!= efepNO
)
1266 /* Calculate the local and non-local free energy interactions here.
1267 * Happens here on the CPU both with and without GPU.
1269 if (fr
->nbv
->grp
[eintLocal
].nbl_lists
.nbl_fep
[0]->nrj
> 0)
1271 do_nb_verlet_fep(&fr
->nbv
->grp
[eintLocal
].nbl_lists
,
1273 inputrec
->fepvals
, lambda
,
1274 enerd
, flags
, nrnb
, wcycle
);
1277 if (DOMAINDECOMP(cr
) &&
1278 fr
->nbv
->grp
[eintNonlocal
].nbl_lists
.nbl_fep
[0]->nrj
> 0)
1280 do_nb_verlet_fep(&fr
->nbv
->grp
[eintNonlocal
].nbl_lists
,
1282 inputrec
->fepvals
, lambda
,
1283 enerd
, flags
, nrnb
, wcycle
);
1287 if (!bUseOrEmulGPU
|| bDiffKernels
)
1291 if (DOMAINDECOMP(cr
))
1293 do_nb_verlet(fr
, ic
, enerd
, flags
, eintNonlocal
,
1294 bDiffKernels
? enbvClearFYes
: enbvClearFNo
,
1304 aloc
= eintNonlocal
;
1307 /* Add all the non-bonded force to the normal force array.
1308 * This can be split into a local a non-local part when overlapping
1309 * communication with calculation with domain decomposition.
1311 cycles_force
+= wallcycle_stop(wcycle
, ewcFORCE
);
1312 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1313 wallcycle_sub_start(wcycle
, ewcsNB_F_BUF_OPS
);
1314 nbnxn_atomdata_add_nbat_f_to_f(nbv
->nbs
, eatAll
, nbv
->grp
[aloc
].nbat
, f
);
1315 wallcycle_sub_stop(wcycle
, ewcsNB_F_BUF_OPS
);
1316 cycles_force
+= wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1317 wallcycle_start_nocount(wcycle
, ewcFORCE
);
1319 /* if there are multiple fshift output buffers reduce them */
1320 if ((flags
& GMX_FORCE_VIRIAL
) &&
1321 nbv
->grp
[aloc
].nbl_lists
.nnbl
> 1)
1323 nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv
->grp
[aloc
].nbat
,
1328 /* update QMMMrec, if necessary */
1331 update_QMMMrec(cr
, fr
, x
, mdatoms
, box
, top
);
1334 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_POSRES
].nr
> 0)
1336 posres_wrapper(fplog
, flags
, bSepDVDL
, inputrec
, nrnb
, top
, box
, x
,
1340 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_FBPOSRES
].nr
> 0)
1342 fbposres_wrapper(inputrec
, nrnb
, top
, box
, x
, enerd
, fr
);
1345 /* Compute the bonded and non-bonded energies and optionally forces */
1346 do_force_lowlevel(fplog
, step
, fr
, inputrec
, &(top
->idef
),
1347 cr
, nrnb
, wcycle
, mdatoms
,
1348 x
, hist
, f
, bSepLRF
? fr
->f_twin
: f
, enerd
, fcd
, top
, fr
->born
,
1349 &(top
->atomtypes
), bBornRadii
, box
,
1350 inputrec
->fepvals
, lambda
, graph
, &(top
->excls
), fr
->mu_tot
,
1351 flags
, &cycles_pme
);
1355 if (do_per_step(step
, inputrec
->nstcalclr
))
1357 /* Add the long range forces to the short range forces */
1358 for (i
= 0; i
< fr
->natoms_force_constr
; i
++)
1360 rvec_add(fr
->f_twin
[i
], f
[i
], f
[i
]);
1365 cycles_force
+= wallcycle_stop(wcycle
, ewcFORCE
);
1369 do_flood(cr
, inputrec
, x
, f
, ed
, box
, step
, bNS
);
1372 if (bUseOrEmulGPU
&& !bDiffKernels
)
1374 /* wait for non-local forces (or calculate in emulation mode) */
1375 if (DOMAINDECOMP(cr
))
1381 wallcycle_start(wcycle
, ewcWAIT_GPU_NB_NL
);
1382 nbnxn_cuda_wait_gpu(nbv
->cu_nbv
,
1383 nbv
->grp
[eintNonlocal
].nbat
,
1385 enerd
->grpp
.ener
[egLJSR
], enerd
->grpp
.ener
[egCOULSR
],
1387 cycles_tmp
= wallcycle_stop(wcycle
, ewcWAIT_GPU_NB_NL
);
1388 cycles_wait_gpu
+= cycles_tmp
;
1389 cycles_force
+= cycles_tmp
;
1393 wallcycle_start_nocount(wcycle
, ewcFORCE
);
1394 do_nb_verlet(fr
, ic
, enerd
, flags
, eintNonlocal
, enbvClearFYes
,
1396 cycles_force
+= wallcycle_stop(wcycle
, ewcFORCE
);
1398 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1399 wallcycle_sub_start(wcycle
, ewcsNB_F_BUF_OPS
);
1400 /* skip the reduction if there was no non-local work to do */
1401 if (nbv
->grp
[eintLocal
].nbl_lists
.nbl
[0]->nsci
> 0)
1403 nbnxn_atomdata_add_nbat_f_to_f(nbv
->nbs
, eatNonlocal
,
1404 nbv
->grp
[eintNonlocal
].nbat
, f
);
1406 wallcycle_sub_stop(wcycle
, ewcsNB_F_BUF_OPS
);
1407 cycles_force
+= wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1411 if (bDoForces
&& DOMAINDECOMP(cr
))
1413 /* Communicate the forces */
1414 wallcycle_start(wcycle
, ewcMOVEF
);
1415 dd_move_f(cr
->dd
, f
, fr
->fshift
);
1416 /* Do we need to communicate the separate force array
1417 * for terms that do not contribute to the single sum virial?
1418 * Position restraints and electric fields do not introduce
1419 * inter-cg forces, only full electrostatics methods do.
1420 * When we do not calculate the virial, fr->f_novirsum = f,
1421 * so we have already communicated these forces.
1423 if (EEL_FULL(fr
->eeltype
) && cr
->dd
->n_intercg_excl
&&
1424 (flags
& GMX_FORCE_VIRIAL
))
1426 dd_move_f(cr
->dd
, fr
->f_novirsum
, NULL
);
1430 /* We should not update the shift forces here,
1431 * since f_twin is already included in f.
1433 dd_move_f(cr
->dd
, fr
->f_twin
, NULL
);
1435 wallcycle_stop(wcycle
, ewcMOVEF
);
1440 /* wait for local forces (or calculate in emulation mode) */
1443 wallcycle_start(wcycle
, ewcWAIT_GPU_NB_L
);
1444 nbnxn_cuda_wait_gpu(nbv
->cu_nbv
,
1445 nbv
->grp
[eintLocal
].nbat
,
1447 enerd
->grpp
.ener
[egLJSR
], enerd
->grpp
.ener
[egCOULSR
],
1449 cycles_wait_gpu
+= wallcycle_stop(wcycle
, ewcWAIT_GPU_NB_L
);
1451 /* now clear the GPU outputs while we finish the step on the CPU */
1453 wallcycle_start_nocount(wcycle
, ewcLAUNCH_GPU_NB
);
1454 nbnxn_cuda_clear_outputs(nbv
->cu_nbv
, flags
);
1455 wallcycle_stop(wcycle
, ewcLAUNCH_GPU_NB
);
1459 wallcycle_start_nocount(wcycle
, ewcFORCE
);
1460 do_nb_verlet(fr
, ic
, enerd
, flags
, eintLocal
,
1461 DOMAINDECOMP(cr
) ? enbvClearFNo
: enbvClearFYes
,
1463 wallcycle_stop(wcycle
, ewcFORCE
);
1465 wallcycle_start(wcycle
, ewcNB_XF_BUF_OPS
);
1466 wallcycle_sub_start(wcycle
, ewcsNB_F_BUF_OPS
);
1467 if (nbv
->grp
[eintLocal
].nbl_lists
.nbl
[0]->nsci
> 0)
1469 /* skip the reduction if there was no non-local work to do */
1470 nbnxn_atomdata_add_nbat_f_to_f(nbv
->nbs
, eatLocal
,
1471 nbv
->grp
[eintLocal
].nbat
, f
);
1473 wallcycle_sub_stop(wcycle
, ewcsNB_F_BUF_OPS
);
1474 wallcycle_stop(wcycle
, ewcNB_XF_BUF_OPS
);
1477 if (DOMAINDECOMP(cr
))
1479 dd_force_flop_stop(cr
->dd
, nrnb
);
1482 dd_cycles_add(cr
->dd
, cycles_force
-cycles_pme
, ddCyclF
);
1485 dd_cycles_add(cr
->dd
, cycles_wait_gpu
, ddCyclWaitGPU
);
1492 if (IR_ELEC_FIELD(*inputrec
))
1494 /* Compute forces due to electric field */
1495 calc_f_el(MASTER(cr
) ? field
: NULL
,
1496 start
, homenr
, mdatoms
->chargeA
, fr
->f_novirsum
,
1497 inputrec
->ex
, inputrec
->et
, t
);
1500 /* If we have NoVirSum forces, but we do not calculate the virial,
1501 * we sum fr->f_novirum=f later.
1503 if (vsite
&& !(fr
->bF_NoVirSum
&& !(flags
& GMX_FORCE_VIRIAL
)))
1505 wallcycle_start(wcycle
, ewcVSITESPREAD
);
1506 spread_vsite_f(vsite
, x
, f
, fr
->fshift
, FALSE
, NULL
, nrnb
,
1507 &top
->idef
, fr
->ePBC
, fr
->bMolPBC
, graph
, box
, cr
);
1508 wallcycle_stop(wcycle
, ewcVSITESPREAD
);
1512 wallcycle_start(wcycle
, ewcVSITESPREAD
);
1513 spread_vsite_f(vsite
, x
, fr
->f_twin
, NULL
, FALSE
, NULL
,
1515 &top
->idef
, fr
->ePBC
, fr
->bMolPBC
, graph
, box
, cr
);
1516 wallcycle_stop(wcycle
, ewcVSITESPREAD
);
1520 if (flags
& GMX_FORCE_VIRIAL
)
1522 /* Calculation of the virial must be done after vsites! */
1523 calc_virial(0, mdatoms
->homenr
, x
, f
,
1524 vir_force
, graph
, box
, nrnb
, fr
, inputrec
->ePBC
);
1528 if (inputrec
->ePull
== epullUMBRELLA
|| inputrec
->ePull
== epullCONST_F
)
1530 pull_potential_wrapper(fplog
, bSepDVDL
, cr
, inputrec
, box
, x
,
1531 f
, vir_force
, mdatoms
, enerd
, lambda
, t
);
1534 /* Add the forces from enforced rotation potentials (if any) */
1537 wallcycle_start(wcycle
, ewcROTadd
);
1538 enerd
->term
[F_COM_PULL
] += add_rot_forces(inputrec
->rot
, f
, cr
, step
, t
);
1539 wallcycle_stop(wcycle
, ewcROTadd
);
1542 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
1543 IMD_apply_forces(inputrec
->bIMD
, inputrec
->imd
, cr
, f
, wcycle
);
1545 if (PAR(cr
) && !(cr
->duty
& DUTY_PME
))
1547 /* In case of node-splitting, the PP nodes receive the long-range
1548 * forces, virial and energy from the PME nodes here.
1550 pme_receive_force_ener(fplog
, bSepDVDL
, cr
, wcycle
, enerd
, fr
);
1555 post_process_forces(cr
, step
, nrnb
, wcycle
,
1556 top
, box
, x
, f
, vir_force
, mdatoms
, graph
, fr
, vsite
,
1560 /* Sum the potential energy terms from group contributions */
1561 sum_epot(&(enerd
->grpp
), enerd
->term
);
1564 void do_force_cutsGROUP(FILE *fplog
, t_commrec
*cr
,
1565 t_inputrec
*inputrec
,
1566 gmx_int64_t step
, t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
1567 gmx_localtop_t
*top
,
1568 gmx_groups_t
*groups
,
1569 matrix box
, rvec x
[], history_t
*hist
,
1573 gmx_enerdata_t
*enerd
, t_fcdata
*fcd
,
1574 real
*lambda
, t_graph
*graph
,
1575 t_forcerec
*fr
, gmx_vsite_t
*vsite
, rvec mu_tot
,
1576 double t
, FILE *field
, gmx_edsam_t ed
,
1577 gmx_bool bBornRadii
,
1583 gmx_bool bSepDVDL
, bStateChanged
, bNS
, bFillGrid
, bCalcCGCM
, bBS
;
1584 gmx_bool bDoLongRangeNS
, bDoForces
, bDoPotential
, bSepLRF
;
1585 gmx_bool bDoAdressWF
;
1587 rvec vzero
, box_diag
;
1588 real e
, v
, dvdlambda
[efptNR
];
1590 float cycles_pme
, cycles_force
;
1593 homenr
= mdatoms
->homenr
;
1595 bSepDVDL
= (fr
->bSepDVDL
&& do_per_step(step
, inputrec
->nstlog
));
1597 clear_mat(vir_force
);
1600 if (DOMAINDECOMP(cr
))
1602 cg1
= cr
->dd
->ncg_tot
;
1613 bStateChanged
= (flags
& GMX_FORCE_STATECHANGED
);
1614 bNS
= (flags
& GMX_FORCE_NS
) && (fr
->bAllvsAll
== FALSE
);
1615 /* Should we update the long-range neighborlists at this step? */
1616 bDoLongRangeNS
= fr
->bTwinRange
&& bNS
;
1617 /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
1618 bFillGrid
= (bNS
&& bStateChanged
);
1619 bCalcCGCM
= (bFillGrid
&& !DOMAINDECOMP(cr
));
1620 bDoForces
= (flags
& GMX_FORCE_FORCES
);
1621 bDoPotential
= (flags
& GMX_FORCE_ENERGY
);
1622 bSepLRF
= ((inputrec
->nstcalclr
> 1) && bDoForces
&&
1623 (flags
& GMX_FORCE_SEPLRF
) && (flags
& GMX_FORCE_DO_LR
));
1625 /* should probably move this to the forcerec since it doesn't change */
1626 bDoAdressWF
= ((fr
->adress_type
!= eAdressOff
));
1630 update_forcerec(fr
, box
);
1632 if (NEED_MUTOT(*inputrec
))
1634 /* Calculate total (local) dipole moment in a temporary common array.
1635 * This makes it possible to sum them over nodes faster.
1637 calc_mu(start
, homenr
,
1638 x
, mdatoms
->chargeA
, mdatoms
->chargeB
, mdatoms
->nChargePerturbed
,
1643 if (fr
->ePBC
!= epbcNONE
)
1645 /* Compute shift vectors every step,
1646 * because of pressure coupling or box deformation!
1648 if ((flags
& GMX_FORCE_DYNAMICBOX
) && bStateChanged
)
1650 calc_shifts(box
, fr
->shift_vec
);
1655 put_charge_groups_in_box(fplog
, cg0
, cg1
, fr
->ePBC
, box
,
1656 &(top
->cgs
), x
, fr
->cg_cm
);
1657 inc_nrnb(nrnb
, eNR_CGCM
, homenr
);
1658 inc_nrnb(nrnb
, eNR_RESETX
, cg1
-cg0
);
1660 else if (EI_ENERGY_MINIMIZATION(inputrec
->eI
) && graph
)
1662 unshift_self(graph
, box
, x
);
1667 calc_cgcm(fplog
, cg0
, cg1
, &(top
->cgs
), x
, fr
->cg_cm
);
1668 inc_nrnb(nrnb
, eNR_CGCM
, homenr
);
1671 if (bCalcCGCM
&& gmx_debug_at
)
1673 pr_rvecs(debug
, 0, "cgcm", fr
->cg_cm
, top
->cgs
.nr
);
1677 if (!(cr
->duty
& DUTY_PME
))
1679 /* Send particle coordinates to the pme nodes.
1680 * Since this is only implemented for domain decomposition
1681 * and domain decomposition does not use the graph,
1682 * we do not need to worry about shifting.
1687 wallcycle_start(wcycle
, ewcPP_PMESENDX
);
1689 bBS
= (inputrec
->nwall
== 2);
1692 copy_mat(box
, boxs
);
1693 svmul(inputrec
->wall_ewald_zfac
, boxs
[ZZ
], boxs
[ZZ
]);
1696 if (EEL_PME(fr
->eeltype
))
1698 pme_flags
|= GMX_PME_DO_COULOMB
;
1701 if (EVDW_PME(fr
->vdwtype
))
1703 pme_flags
|= GMX_PME_DO_LJ
;
1706 gmx_pme_send_coordinates(cr
, bBS
? boxs
: box
, x
,
1707 mdatoms
->nChargePerturbed
, mdatoms
->nTypePerturbed
, lambda
[efptCOUL
], lambda
[efptVDW
],
1708 (flags
& (GMX_FORCE_VIRIAL
| GMX_FORCE_ENERGY
)),
1711 wallcycle_stop(wcycle
, ewcPP_PMESENDX
);
1713 #endif /* GMX_MPI */
1715 /* Communicate coordinates and sum dipole if necessary */
1716 if (DOMAINDECOMP(cr
))
1718 wallcycle_start(wcycle
, ewcMOVEX
);
1719 dd_move_x(cr
->dd
, box
, x
);
1720 wallcycle_stop(wcycle
, ewcMOVEX
);
1723 /* update adress weight beforehand */
1724 if (bStateChanged
&& bDoAdressWF
)
1726 /* need pbc for adress weight calculation with pbc_dx */
1727 set_pbc(&pbc
, inputrec
->ePBC
, box
);
1728 if (fr
->adress_site
== eAdressSITEcog
)
1730 update_adress_weights_cog(top
->idef
.iparams
, top
->idef
.il
, x
, fr
, mdatoms
,
1731 inputrec
->ePBC
== epbcNONE
? NULL
: &pbc
);
1733 else if (fr
->adress_site
== eAdressSITEcom
)
1735 update_adress_weights_com(fplog
, cg0
, cg1
, &(top
->cgs
), x
, fr
, mdatoms
,
1736 inputrec
->ePBC
== epbcNONE
? NULL
: &pbc
);
1738 else if (fr
->adress_site
== eAdressSITEatomatom
)
1740 update_adress_weights_atom_per_atom(cg0
, cg1
, &(top
->cgs
), x
, fr
, mdatoms
,
1741 inputrec
->ePBC
== epbcNONE
? NULL
: &pbc
);
1745 update_adress_weights_atom(cg0
, cg1
, &(top
->cgs
), x
, fr
, mdatoms
,
1746 inputrec
->ePBC
== epbcNONE
? NULL
: &pbc
);
1750 if (NEED_MUTOT(*inputrec
))
1757 gmx_sumd(2*DIM
, mu
, cr
);
1759 for (i
= 0; i
< 2; i
++)
1761 for (j
= 0; j
< DIM
; j
++)
1763 fr
->mu_tot
[i
][j
] = mu
[i
*DIM
+ j
];
1767 if (fr
->efep
== efepNO
)
1769 copy_rvec(fr
->mu_tot
[0], mu_tot
);
1773 for (j
= 0; j
< DIM
; j
++)
1776 (1.0 - lambda
[efptCOUL
])*fr
->mu_tot
[0][j
] + lambda
[efptCOUL
]*fr
->mu_tot
[1][j
];
1781 /* Reset energies */
1782 reset_enerdata(fr
, bNS
, enerd
, MASTER(cr
));
1783 clear_rvecs(SHIFTS
, fr
->fshift
);
1787 wallcycle_start(wcycle
, ewcNS
);
1789 if (graph
&& bStateChanged
)
1791 /* Calculate intramolecular shift vectors to make molecules whole */
1792 mk_mshift(fplog
, graph
, fr
->ePBC
, box
, x
);
1795 /* Do the actual neighbour searching */
1797 groups
, top
, mdatoms
,
1798 cr
, nrnb
, bFillGrid
,
1801 wallcycle_stop(wcycle
, ewcNS
);
1804 if (inputrec
->implicit_solvent
&& bNS
)
1806 make_gb_nblist(cr
, inputrec
->gb_algorithm
,
1807 x
, box
, fr
, &top
->idef
, graph
, fr
->born
);
1810 if (DOMAINDECOMP(cr
) && !(cr
->duty
& DUTY_PME
))
1812 wallcycle_start(wcycle
, ewcPPDURINGPME
);
1813 dd_force_flop_start(cr
->dd
, nrnb
);
1818 /* Enforced rotation has its own cycle counter that starts after the collective
1819 * coordinates have been communicated. It is added to ddCyclF to allow
1820 * for proper load-balancing */
1821 wallcycle_start(wcycle
, ewcROT
);
1822 do_rotation(cr
, inputrec
, box
, x
, t
, step
, wcycle
, bNS
);
1823 wallcycle_stop(wcycle
, ewcROT
);
1826 /* Start the force cycle counter.
1827 * This counter is stopped in do_forcelow_level.
1828 * No parallel communication should occur while this counter is running,
1829 * since that will interfere with the dynamic load balancing.
1831 wallcycle_start(wcycle
, ewcFORCE
);
1835 /* Reset forces for which the virial is calculated separately:
1836 * PME/Ewald forces if necessary */
1837 if (fr
->bF_NoVirSum
)
1839 if (flags
& GMX_FORCE_VIRIAL
)
1841 fr
->f_novirsum
= fr
->f_novirsum_alloc
;
1844 clear_rvecs(fr
->f_novirsum_n
, fr
->f_novirsum
);
1848 clear_rvecs(homenr
, fr
->f_novirsum
+start
);
1853 /* We are not calculating the pressure so we do not need
1854 * a separate array for forces that do not contribute
1861 /* Clear the short- and long-range forces */
1862 clear_rvecs(fr
->natoms_force_constr
, f
);
1863 if (bSepLRF
&& do_per_step(step
, inputrec
->nstcalclr
))
1865 clear_rvecs(fr
->natoms_force_constr
, fr
->f_twin
);
1868 clear_rvec(fr
->vir_diag_posres
);
1870 if (inputrec
->ePull
== epullCONSTRAINT
)
1872 clear_pull_forces(inputrec
->pull
);
1875 /* update QMMMrec, if necessary */
1878 update_QMMMrec(cr
, fr
, x
, mdatoms
, box
, top
);
1881 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_POSRES
].nr
> 0)
1883 posres_wrapper(fplog
, flags
, bSepDVDL
, inputrec
, nrnb
, top
, box
, x
,
1887 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_FBPOSRES
].nr
> 0)
1889 fbposres_wrapper(inputrec
, nrnb
, top
, box
, x
, enerd
, fr
);
1892 /* Compute the bonded and non-bonded energies and optionally forces */
1893 do_force_lowlevel(fplog
, step
, fr
, inputrec
, &(top
->idef
),
1894 cr
, nrnb
, wcycle
, mdatoms
,
1895 x
, hist
, f
, bSepLRF
? fr
->f_twin
: f
, enerd
, fcd
, top
, fr
->born
,
1896 &(top
->atomtypes
), bBornRadii
, box
,
1897 inputrec
->fepvals
, lambda
,
1898 graph
, &(top
->excls
), fr
->mu_tot
,
1904 if (do_per_step(step
, inputrec
->nstcalclr
))
1906 /* Add the long range forces to the short range forces */
1907 for (i
= 0; i
< fr
->natoms_force_constr
; i
++)
1909 rvec_add(fr
->f_twin
[i
], f
[i
], f
[i
]);
1914 cycles_force
= wallcycle_stop(wcycle
, ewcFORCE
);
1918 do_flood(cr
, inputrec
, x
, f
, ed
, box
, step
, bNS
);
1921 if (DOMAINDECOMP(cr
))
1923 dd_force_flop_stop(cr
->dd
, nrnb
);
1926 dd_cycles_add(cr
->dd
, cycles_force
-cycles_pme
, ddCyclF
);
1932 if (IR_ELEC_FIELD(*inputrec
))
1934 /* Compute forces due to electric field */
1935 calc_f_el(MASTER(cr
) ? field
: NULL
,
1936 start
, homenr
, mdatoms
->chargeA
, fr
->f_novirsum
,
1937 inputrec
->ex
, inputrec
->et
, t
);
1940 if (bDoAdressWF
&& fr
->adress_icor
== eAdressICThermoForce
)
1942 /* Compute thermodynamic force in hybrid AdResS region */
1943 adress_thermo_force(start
, homenr
, &(top
->cgs
), x
, fr
->f_novirsum
, fr
, mdatoms
,
1944 inputrec
->ePBC
== epbcNONE
? NULL
: &pbc
);
1947 /* Communicate the forces */
1948 if (DOMAINDECOMP(cr
))
1950 wallcycle_start(wcycle
, ewcMOVEF
);
1951 dd_move_f(cr
->dd
, f
, fr
->fshift
);
1952 /* Do we need to communicate the separate force array
1953 * for terms that do not contribute to the single sum virial?
1954 * Position restraints and electric fields do not introduce
1955 * inter-cg forces, only full electrostatics methods do.
1956 * When we do not calculate the virial, fr->f_novirsum = f,
1957 * so we have already communicated these forces.
1959 if (EEL_FULL(fr
->eeltype
) && cr
->dd
->n_intercg_excl
&&
1960 (flags
& GMX_FORCE_VIRIAL
))
1962 dd_move_f(cr
->dd
, fr
->f_novirsum
, NULL
);
1966 /* We should not update the shift forces here,
1967 * since f_twin is already included in f.
1969 dd_move_f(cr
->dd
, fr
->f_twin
, NULL
);
1971 wallcycle_stop(wcycle
, ewcMOVEF
);
1974 /* If we have NoVirSum forces, but we do not calculate the virial,
1975 * we sum fr->f_novirum=f later.
1977 if (vsite
&& !(fr
->bF_NoVirSum
&& !(flags
& GMX_FORCE_VIRIAL
)))
1979 wallcycle_start(wcycle
, ewcVSITESPREAD
);
1980 spread_vsite_f(vsite
, x
, f
, fr
->fshift
, FALSE
, NULL
, nrnb
,
1981 &top
->idef
, fr
->ePBC
, fr
->bMolPBC
, graph
, box
, cr
);
1982 wallcycle_stop(wcycle
, ewcVSITESPREAD
);
1986 wallcycle_start(wcycle
, ewcVSITESPREAD
);
1987 spread_vsite_f(vsite
, x
, fr
->f_twin
, NULL
, FALSE
, NULL
,
1989 &top
->idef
, fr
->ePBC
, fr
->bMolPBC
, graph
, box
, cr
);
1990 wallcycle_stop(wcycle
, ewcVSITESPREAD
);
1994 if (flags
& GMX_FORCE_VIRIAL
)
1996 /* Calculation of the virial must be done after vsites! */
1997 calc_virial(0, mdatoms
->homenr
, x
, f
,
1998 vir_force
, graph
, box
, nrnb
, fr
, inputrec
->ePBC
);
2002 if (inputrec
->ePull
== epullUMBRELLA
|| inputrec
->ePull
== epullCONST_F
)
2004 pull_potential_wrapper(fplog
, bSepDVDL
, cr
, inputrec
, box
, x
,
2005 f
, vir_force
, mdatoms
, enerd
, lambda
, t
);
2008 /* Add the forces from enforced rotation potentials (if any) */
2011 wallcycle_start(wcycle
, ewcROTadd
);
2012 enerd
->term
[F_COM_PULL
] += add_rot_forces(inputrec
->rot
, f
, cr
, step
, t
);
2013 wallcycle_stop(wcycle
, ewcROTadd
);
2016 /* Add forces from interactive molecular dynamics (IMD), if bIMD == TRUE. */
2017 IMD_apply_forces(inputrec
->bIMD
, inputrec
->imd
, cr
, f
, wcycle
);
2019 if (PAR(cr
) && !(cr
->duty
& DUTY_PME
))
2021 /* In case of node-splitting, the PP nodes receive the long-range
2022 * forces, virial and energy from the PME nodes here.
2024 pme_receive_force_ener(fplog
, bSepDVDL
, cr
, wcycle
, enerd
, fr
);
2029 post_process_forces(cr
, step
, nrnb
, wcycle
,
2030 top
, box
, x
, f
, vir_force
, mdatoms
, graph
, fr
, vsite
,
2034 /* Sum the potential energy terms from group contributions */
2035 sum_epot(&(enerd
->grpp
), enerd
->term
);
2038 void do_force(FILE *fplog
, t_commrec
*cr
,
2039 t_inputrec
*inputrec
,
2040 gmx_int64_t step
, t_nrnb
*nrnb
, gmx_wallcycle_t wcycle
,
2041 gmx_localtop_t
*top
,
2042 gmx_groups_t
*groups
,
2043 matrix box
, rvec x
[], history_t
*hist
,
2047 gmx_enerdata_t
*enerd
, t_fcdata
*fcd
,
2048 real
*lambda
, t_graph
*graph
,
2050 gmx_vsite_t
*vsite
, rvec mu_tot
,
2051 double t
, FILE *field
, gmx_edsam_t ed
,
2052 gmx_bool bBornRadii
,
2055 /* modify force flag if not doing nonbonded */
2056 if (!fr
->bNonbonded
)
2058 flags
&= ~GMX_FORCE_NONBONDED
;
2061 switch (inputrec
->cutoff_scheme
)
2064 do_force_cutsVERLET(fplog
, cr
, inputrec
,
2080 do_force_cutsGROUP(fplog
, cr
, inputrec
,
2095 gmx_incons("Invalid cut-off scheme passed!");
2100 void do_constrain_first(FILE *fplog
, gmx_constr_t constr
,
2101 t_inputrec
*ir
, t_mdatoms
*md
,
2102 t_state
*state
, t_commrec
*cr
, t_nrnb
*nrnb
,
2103 t_forcerec
*fr
, gmx_localtop_t
*top
)
2105 int i
, m
, start
, end
;
2107 real dt
= ir
->delta_t
;
2111 snew(savex
, state
->natoms
);
2118 fprintf(debug
, "vcm: start=%d, homenr=%d, end=%d\n",
2119 start
, md
->homenr
, end
);
2121 /* Do a first constrain to reset particles... */
2122 step
= ir
->init_step
;
2125 char buf
[STEPSTRSIZE
];
2126 fprintf(fplog
, "\nConstraining the starting coordinates (step %s)\n",
2127 gmx_step_str(step
, buf
));
2131 /* constrain the current position */
2132 constrain(NULL
, TRUE
, FALSE
, constr
, &(top
->idef
),
2133 ir
, NULL
, cr
, step
, 0, md
,
2134 state
->x
, state
->x
, NULL
,
2135 fr
->bMolPBC
, state
->box
,
2136 state
->lambda
[efptBONDED
], &dvdl_dum
,
2137 NULL
, NULL
, nrnb
, econqCoord
,
2138 ir
->epc
== epcMTTK
, state
->veta
, state
->veta
);
2141 /* constrain the inital velocity, and save it */
2142 /* also may be useful if we need the ekin from the halfstep for velocity verlet */
2143 /* might not yet treat veta correctly */
2144 constrain(NULL
, TRUE
, FALSE
, constr
, &(top
->idef
),
2145 ir
, NULL
, cr
, step
, 0, md
,
2146 state
->x
, state
->v
, state
->v
,
2147 fr
->bMolPBC
, state
->box
,
2148 state
->lambda
[efptBONDED
], &dvdl_dum
,
2149 NULL
, NULL
, nrnb
, econqVeloc
,
2150 ir
->epc
== epcMTTK
, state
->veta
, state
->veta
);
2152 /* constrain the inital velocities at t-dt/2 */
2153 if (EI_STATE_VELOCITY(ir
->eI
) && ir
->eI
!= eiVV
)
2155 for (i
= start
; (i
< end
); i
++)
2157 for (m
= 0; (m
< DIM
); m
++)
2159 /* Reverse the velocity */
2160 state
->v
[i
][m
] = -state
->v
[i
][m
];
2161 /* Store the position at t-dt in buf */
2162 savex
[i
][m
] = state
->x
[i
][m
] + dt
*state
->v
[i
][m
];
2165 /* Shake the positions at t=-dt with the positions at t=0
2166 * as reference coordinates.
2170 char buf
[STEPSTRSIZE
];
2171 fprintf(fplog
, "\nConstraining the coordinates at t0-dt (step %s)\n",
2172 gmx_step_str(step
, buf
));
2175 constrain(NULL
, TRUE
, FALSE
, constr
, &(top
->idef
),
2176 ir
, NULL
, cr
, step
, -1, md
,
2177 state
->x
, savex
, NULL
,
2178 fr
->bMolPBC
, state
->box
,
2179 state
->lambda
[efptBONDED
], &dvdl_dum
,
2180 state
->v
, NULL
, nrnb
, econqCoord
,
2181 ir
->epc
== epcMTTK
, state
->veta
, state
->veta
);
2183 for (i
= start
; i
< end
; i
++)
2185 for (m
= 0; m
< DIM
; m
++)
2187 /* Re-reverse the velocities */
2188 state
->v
[i
][m
] = -state
->v
[i
][m
];
2197 integrate_table(real vdwtab
[], real scale
, int offstart
, int rstart
, int rend
,
2198 double *enerout
, double *virout
)
2200 double enersum
, virsum
;
2201 double invscale
, invscale2
, invscale3
;
2202 double r
, ea
, eb
, ec
, pa
, pb
, pc
, pd
;
2204 int ri
, offset
, tabfactor
;
2206 invscale
= 1.0/scale
;
2207 invscale2
= invscale
*invscale
;
2208 invscale3
= invscale
*invscale2
;
2210 /* Following summation derived from cubic spline definition,
2211 * Numerical Recipies in C, second edition, p. 113-116. Exact for
2212 * the cubic spline. We first calculate the negative of the
2213 * energy from rvdw to rvdw_switch, assuming that g(r)=1, and then
2214 * add the more standard, abrupt cutoff correction to that result,
2215 * yielding the long-range correction for a switched function. We
2216 * perform both the pressure and energy loops at the same time for
2217 * simplicity, as the computational cost is low. */
2221 /* Since the dispersion table has been scaled down a factor
2222 * 6.0 and the repulsion a factor 12.0 to compensate for the
2223 * c6/c12 parameters inside nbfp[] being scaled up (to save
2224 * flops in kernels), we need to correct for this.
2235 for (ri
= rstart
; ri
< rend
; ++ri
)
2239 eb
= 2.0*invscale2
*r
;
2243 pb
= 3.0*invscale2
*r
;
2244 pc
= 3.0*invscale
*r
*r
;
2247 /* this "8" is from the packing in the vdwtab array - perhaps
2248 should be defined? */
2250 offset
= 8*ri
+ offstart
;
2251 y0
= vdwtab
[offset
];
2252 f
= vdwtab
[offset
+1];
2253 g
= vdwtab
[offset
+2];
2254 h
= vdwtab
[offset
+3];
2256 enersum
+= y0
*(ea
/3 + eb
/2 + ec
) + f
*(ea
/4 + eb
/3 + ec
/2) + g
*(ea
/5 + eb
/4 + ec
/3) + h
*(ea
/6 + eb
/5 + ec
/4);
2257 virsum
+= f
*(pa
/4 + pb
/3 + pc
/2 + pd
) + 2*g
*(pa
/5 + pb
/4 + pc
/3 + pd
/2) + 3*h
*(pa
/6 + pb
/5 + pc
/4 + pd
/3);
2259 *enerout
= 4.0*M_PI
*enersum
*tabfactor
;
2260 *virout
= 4.0*M_PI
*virsum
*tabfactor
;
2263 void calc_enervirdiff(FILE *fplog
, int eDispCorr
, t_forcerec
*fr
)
2265 double eners
[2], virs
[2], enersum
, virsum
, y0
, f
, g
, h
;
2266 double r0
, r1
, r
, rc3
, rc9
, ea
, eb
, ec
, pa
, pb
, pc
, pd
;
2267 double invscale
, invscale2
, invscale3
;
2268 int ri0
, ri1
, ri
, i
, offstart
, offset
;
2269 real scale
, *vdwtab
, tabfactor
, tmp
;
2271 fr
->enershiftsix
= 0;
2272 fr
->enershifttwelve
= 0;
2273 fr
->enerdiffsix
= 0;
2274 fr
->enerdifftwelve
= 0;
2276 fr
->virdifftwelve
= 0;
2278 if (eDispCorr
!= edispcNO
)
2280 for (i
= 0; i
< 2; i
++)
2285 if (fr
->vdwtype
== evdwSWITCH
|| fr
->vdwtype
== evdwSHIFT
||
2286 fr
->vdw_modifier
== eintmodPOTSWITCH
||
2287 fr
->vdw_modifier
== eintmodFORCESWITCH
)
2289 if (fr
->rvdw_switch
== 0)
2292 "With dispersion correction rvdw-switch can not be zero "
2293 "for vdw-type = %s", evdw_names
[fr
->vdwtype
]);
2296 scale
= fr
->nblists
[0].table_elec_vdw
.scale
;
2297 vdwtab
= fr
->nblists
[0].table_vdw
.data
;
2299 /* Round the cut-offs to exact table values for precision */
2300 ri0
= floor(fr
->rvdw_switch
*scale
);
2301 ri1
= ceil(fr
->rvdw
*scale
);
2307 if (fr
->vdwtype
== evdwSHIFT
||
2308 fr
->vdw_modifier
== eintmodFORCESWITCH
)
2310 /* Determine the constant energy shift below rvdw_switch.
2311 * Table has a scale factor since we have scaled it down to compensate
2312 * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
2314 fr
->enershiftsix
= (real
)(-1.0/(rc3
*rc3
)) - 6.0*vdwtab
[8*ri0
];
2315 fr
->enershifttwelve
= (real
)( 1.0/(rc9
*rc3
)) - 12.0*vdwtab
[8*ri0
+ 4];
2317 /* Add the constant part from 0 to rvdw_switch.
2318 * This integration from 0 to rvdw_switch overcounts the number
2319 * of interactions by 1, as it also counts the self interaction.
2320 * We will correct for this later.
2322 eners
[0] += 4.0*M_PI
*fr
->enershiftsix
*rc3
/3.0;
2323 eners
[1] += 4.0*M_PI
*fr
->enershifttwelve
*rc3
/3.0;
2324 for (i
= 0; i
< 2; i
++)
2328 integrate_table(vdwtab
, scale
, (i
== 0 ? 0 : 4), ri0
, ri1
, &enersum
, &virsum
);
2329 eners
[i
] -= enersum
;
2333 /* now add the correction for rvdw_switch to infinity */
2334 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
2335 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
2336 virs
[0] += 8.0*M_PI
/rc3
;
2337 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
2339 else if (fr
->vdwtype
== evdwCUT
||
2340 EVDW_PME(fr
->vdwtype
) ||
2341 fr
->vdwtype
== evdwUSER
)
2343 if (fr
->vdwtype
== evdwUSER
&& fplog
)
2346 "WARNING: using dispersion correction with user tables\n");
2349 /* Note that with LJ-PME, the dispersion correction is multiplied
2350 * by the difference between the actual C6 and the value of C6
2351 * that would produce the combination rule.
2352 * This means the normal energy and virial difference formulas
2356 rc3
= fr
->rvdw
*fr
->rvdw
*fr
->rvdw
;
2358 /* Contribution beyond the cut-off */
2359 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
2360 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
2361 if (fr
->vdw_modifier
== eintmodPOTSHIFT
)
2363 /* Contribution within the cut-off */
2364 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
2365 eners
[1] += 4.0*M_PI
/(3.0*rc9
);
2367 /* Contribution beyond the cut-off */
2368 virs
[0] += 8.0*M_PI
/rc3
;
2369 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
2374 "Dispersion correction is not implemented for vdw-type = %s",
2375 evdw_names
[fr
->vdwtype
]);
2378 /* TODO: remove this code once we have group LJ-PME kernels
2379 * that calculate the exact, full LJ param C6/r^6 within the cut-off,
2380 * as the current nbnxn kernels do.
2382 if (fr
->vdwtype
== evdwPME
&& fr
->cutoff_scheme
== ecutsGROUP
)
2384 /* Calculate self-interaction coefficient (assuming that
2385 * the reciprocal-space contribution is constant in the
2386 * region that contributes to the self-interaction).
2388 fr
->enershiftsix
= pow(fr
->ewaldcoeff_lj
, 6) / 6.0;
2390 eners
[0] += -pow(sqrt(M_PI
)*fr
->ewaldcoeff_lj
, 3)/3.0;
2391 virs
[0] += pow(sqrt(M_PI
)*fr
->ewaldcoeff_lj
, 3);
2394 fr
->enerdiffsix
= eners
[0];
2395 fr
->enerdifftwelve
= eners
[1];
2396 /* The 0.5 is due to the Gromacs definition of the virial */
2397 fr
->virdiffsix
= 0.5*virs
[0];
2398 fr
->virdifftwelve
= 0.5*virs
[1];
2402 void calc_dispcorr(FILE *fplog
, t_inputrec
*ir
, t_forcerec
*fr
,
2403 gmx_int64_t step
, int natoms
,
2404 matrix box
, real lambda
, tensor pres
, tensor virial
,
2405 real
*prescorr
, real
*enercorr
, real
*dvdlcorr
)
2407 gmx_bool bCorrAll
, bCorrPres
;
2408 real dvdlambda
, invvol
, dens
, ninter
, avcsix
, avctwelve
, enerdiff
, svir
= 0, spres
= 0;
2418 if (ir
->eDispCorr
!= edispcNO
)
2420 bCorrAll
= (ir
->eDispCorr
== edispcAllEner
||
2421 ir
->eDispCorr
== edispcAllEnerPres
);
2422 bCorrPres
= (ir
->eDispCorr
== edispcEnerPres
||
2423 ir
->eDispCorr
== edispcAllEnerPres
);
2425 invvol
= 1/det(box
);
2428 /* Only correct for the interactions with the inserted molecule */
2429 dens
= (natoms
- fr
->n_tpi
)*invvol
;
2434 dens
= natoms
*invvol
;
2435 ninter
= 0.5*natoms
;
2438 if (ir
->efep
== efepNO
)
2440 avcsix
= fr
->avcsix
[0];
2441 avctwelve
= fr
->avctwelve
[0];
2445 avcsix
= (1 - lambda
)*fr
->avcsix
[0] + lambda
*fr
->avcsix
[1];
2446 avctwelve
= (1 - lambda
)*fr
->avctwelve
[0] + lambda
*fr
->avctwelve
[1];
2449 enerdiff
= ninter
*(dens
*fr
->enerdiffsix
- fr
->enershiftsix
);
2450 *enercorr
+= avcsix
*enerdiff
;
2452 if (ir
->efep
!= efepNO
)
2454 dvdlambda
+= (fr
->avcsix
[1] - fr
->avcsix
[0])*enerdiff
;
2458 enerdiff
= ninter
*(dens
*fr
->enerdifftwelve
- fr
->enershifttwelve
);
2459 *enercorr
+= avctwelve
*enerdiff
;
2460 if (fr
->efep
!= efepNO
)
2462 dvdlambda
+= (fr
->avctwelve
[1] - fr
->avctwelve
[0])*enerdiff
;
2468 svir
= ninter
*dens
*avcsix
*fr
->virdiffsix
/3.0;
2469 if (ir
->eDispCorr
== edispcAllEnerPres
)
2471 svir
+= ninter
*dens
*avctwelve
*fr
->virdifftwelve
/3.0;
2473 /* The factor 2 is because of the Gromacs virial definition */
2474 spres
= -2.0*invvol
*svir
*PRESFAC
;
2476 for (m
= 0; m
< DIM
; m
++)
2478 virial
[m
][m
] += svir
;
2479 pres
[m
][m
] += spres
;
2484 /* Can't currently control when it prints, for now, just print when degugging */
2489 fprintf(debug
, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
2495 "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
2496 *enercorr
, spres
, svir
);
2500 fprintf(debug
, "Long Range LJ corr.: Epot %10g\n", *enercorr
);
2504 if (fr
->bSepDVDL
&& do_per_step(step
, ir
->nstlog
))
2506 gmx_print_sepdvdl(fplog
, "Dispersion correction", *enercorr
, dvdlambda
);
2508 if (fr
->efep
!= efepNO
)
2510 *dvdlcorr
+= dvdlambda
;
2515 void do_pbc_first(FILE *fplog
, matrix box
, t_forcerec
*fr
,
2516 t_graph
*graph
, rvec x
[])
2520 fprintf(fplog
, "Removing pbc first time\n");
2522 calc_shifts(box
, fr
->shift_vec
);
2525 mk_mshift(fplog
, graph
, fr
->ePBC
, box
, x
);
2528 p_graph(debug
, "do_pbc_first 1", graph
);
2530 shift_self(graph
, box
, x
);
2531 /* By doing an extra mk_mshift the molecules that are broken
2532 * because they were e.g. imported from another software
2533 * will be made whole again. Such are the healing powers
2536 mk_mshift(fplog
, graph
, fr
->ePBC
, box
, x
);
2539 p_graph(debug
, "do_pbc_first 2", graph
);
2544 fprintf(fplog
, "Done rmpbc\n");
2548 static void low_do_pbc_mtop(FILE *fplog
, int ePBC
, matrix box
,
2549 gmx_mtop_t
*mtop
, rvec x
[],
2554 gmx_molblock_t
*molb
;
2556 if (bFirst
&& fplog
)
2558 fprintf(fplog
, "Removing pbc first time\n");
2563 for (mb
= 0; mb
< mtop
->nmolblock
; mb
++)
2565 molb
= &mtop
->molblock
[mb
];
2566 if (molb
->natoms_mol
== 1 ||
2567 (!bFirst
&& mtop
->moltype
[molb
->type
].cgs
.nr
== 1))
2569 /* Just one atom or charge group in the molecule, no PBC required */
2570 as
+= molb
->nmol
*molb
->natoms_mol
;
2574 /* Pass NULL iso fplog to avoid graph prints for each molecule type */
2575 mk_graph_ilist(NULL
, mtop
->moltype
[molb
->type
].ilist
,
2576 0, molb
->natoms_mol
, FALSE
, FALSE
, graph
);
2578 for (mol
= 0; mol
< molb
->nmol
; mol
++)
2580 mk_mshift(fplog
, graph
, ePBC
, box
, x
+as
);
2582 shift_self(graph
, box
, x
+as
);
2583 /* The molecule is whole now.
2584 * We don't need the second mk_mshift call as in do_pbc_first,
2585 * since we no longer need this graph.
2588 as
+= molb
->natoms_mol
;
2596 void do_pbc_first_mtop(FILE *fplog
, int ePBC
, matrix box
,
2597 gmx_mtop_t
*mtop
, rvec x
[])
2599 low_do_pbc_mtop(fplog
, ePBC
, box
, mtop
, x
, TRUE
);
2602 void do_pbc_mtop(FILE *fplog
, int ePBC
, matrix box
,
2603 gmx_mtop_t
*mtop
, rvec x
[])
2605 low_do_pbc_mtop(fplog
, ePBC
, box
, mtop
, x
, FALSE
);
2608 void finish_run(FILE *fplog
, t_commrec
*cr
,
2609 t_inputrec
*inputrec
,
2610 t_nrnb nrnb
[], gmx_wallcycle_t wcycle
,
2611 gmx_walltime_accounting_t walltime_accounting
,
2612 wallclock_gpu_t
*gputimes
,
2613 gmx_bool bWriteStat
)
2616 t_nrnb
*nrnb_tot
= NULL
;
2619 double elapsed_time
,
2620 elapsed_time_over_all_ranks
,
2621 elapsed_time_over_all_threads
,
2622 elapsed_time_over_all_threads_over_all_ranks
;
2623 wallcycle_sum(cr
, wcycle
);
2629 MPI_Allreduce(nrnb
->n
, nrnb_tot
->n
, eNRNB
, MPI_DOUBLE
, MPI_SUM
,
2630 cr
->mpi_comm_mysim
);
2638 elapsed_time
= walltime_accounting_get_elapsed_time(walltime_accounting
);
2639 elapsed_time_over_all_ranks
= elapsed_time
;
2640 elapsed_time_over_all_threads
= walltime_accounting_get_elapsed_time_over_all_threads(walltime_accounting
);
2641 elapsed_time_over_all_threads_over_all_ranks
= elapsed_time_over_all_threads
;
2645 /* reduce elapsed_time over all MPI ranks in the current simulation */
2646 MPI_Allreduce(&elapsed_time
,
2647 &elapsed_time_over_all_ranks
,
2648 1, MPI_DOUBLE
, MPI_SUM
,
2649 cr
->mpi_comm_mysim
);
2650 elapsed_time_over_all_ranks
/= cr
->nnodes
;
2651 /* Reduce elapsed_time_over_all_threads over all MPI ranks in the
2652 * current simulation. */
2653 MPI_Allreduce(&elapsed_time_over_all_threads
,
2654 &elapsed_time_over_all_threads_over_all_ranks
,
2655 1, MPI_DOUBLE
, MPI_SUM
,
2656 cr
->mpi_comm_mysim
);
2662 print_flop(fplog
, nrnb_tot
, &nbfs
, &mflop
);
2669 if ((cr
->duty
& DUTY_PP
) && DOMAINDECOMP(cr
))
2671 print_dd_statistics(cr
, inputrec
, fplog
);
2676 wallcycle_print(fplog
, cr
->nnodes
, cr
->npmenodes
,
2677 elapsed_time_over_all_ranks
,
2680 if (EI_DYNAMICS(inputrec
->eI
))
2682 delta_t
= inputrec
->delta_t
;
2691 print_perf(fplog
, elapsed_time_over_all_threads_over_all_ranks
,
2692 elapsed_time_over_all_ranks
,
2693 walltime_accounting_get_nsteps_done(walltime_accounting
),
2694 delta_t
, nbfs
, mflop
);
2698 print_perf(stderr
, elapsed_time_over_all_threads_over_all_ranks
,
2699 elapsed_time_over_all_ranks
,
2700 walltime_accounting_get_nsteps_done(walltime_accounting
),
2701 delta_t
, nbfs
, mflop
);
2706 extern void initialize_lambdas(FILE *fplog
, t_inputrec
*ir
, int *fep_state
, real
*lambda
, double *lam0
)
2708 /* this function works, but could probably use a logic rewrite to keep all the different
2709 types of efep straight. */
2712 t_lambda
*fep
= ir
->fepvals
;
2714 if ((ir
->efep
== efepNO
) && (ir
->bSimTemp
== FALSE
))
2716 for (i
= 0; i
< efptNR
; i
++)
2728 *fep_state
= fep
->init_fep_state
; /* this might overwrite the checkpoint
2729 if checkpoint is set -- a kludge is in for now
2731 for (i
= 0; i
< efptNR
; i
++)
2733 /* overwrite lambda state with init_lambda for now for backwards compatibility */
2734 if (fep
->init_lambda
>= 0) /* if it's -1, it was never initializd */
2736 lambda
[i
] = fep
->init_lambda
;
2739 lam0
[i
] = lambda
[i
];
2744 lambda
[i
] = fep
->all_lambda
[i
][*fep_state
];
2747 lam0
[i
] = lambda
[i
];
2753 /* need to rescale control temperatures to match current state */
2754 for (i
= 0; i
< ir
->opts
.ngtc
; i
++)
2756 if (ir
->opts
.ref_t
[i
] > 0)
2758 ir
->opts
.ref_t
[i
] = ir
->simtempvals
->temperatures
[*fep_state
];
2764 /* Send to the log the information on the current lambdas */
2767 fprintf(fplog
, "Initial vector of lambda components:[ ");
2768 for (i
= 0; i
< efptNR
; i
++)
2770 fprintf(fplog
, "%10.4f ", lambda
[i
]);
2772 fprintf(fplog
, "]\n");
2778 void init_md(FILE *fplog
,
2779 t_commrec
*cr
, t_inputrec
*ir
, const output_env_t oenv
,
2780 double *t
, double *t0
,
2781 real
*lambda
, int *fep_state
, double *lam0
,
2782 t_nrnb
*nrnb
, gmx_mtop_t
*mtop
,
2784 int nfile
, const t_filenm fnm
[],
2785 gmx_mdoutf_t
*outf
, t_mdebin
**mdebin
,
2786 tensor force_vir
, tensor shake_vir
, rvec mu_tot
,
2787 gmx_bool
*bSimAnn
, t_vcm
**vcm
, unsigned long Flags
)
2792 /* Initial values */
2793 *t
= *t0
= ir
->init_t
;
2796 for (i
= 0; i
< ir
->opts
.ngtc
; i
++)
2798 /* set bSimAnn if any group is being annealed */
2799 if (ir
->opts
.annealing
[i
] != eannNO
)
2806 update_annealing_target_temp(&(ir
->opts
), ir
->init_t
);
2809 /* Initialize lambda variables */
2810 initialize_lambdas(fplog
, ir
, fep_state
, lambda
, lam0
);
2814 *upd
= init_update(ir
);
2820 *vcm
= init_vcm(fplog
, &mtop
->groups
, ir
);
2823 if (EI_DYNAMICS(ir
->eI
) && !(Flags
& MD_APPENDFILES
))
2825 if (ir
->etc
== etcBERENDSEN
)
2827 please_cite(fplog
, "Berendsen84a");
2829 if (ir
->etc
== etcVRESCALE
)
2831 please_cite(fplog
, "Bussi2007a");
2839 *outf
= init_mdoutf(fplog
, nfile
, fnm
, Flags
, cr
, ir
, mtop
, oenv
);
2841 *mdebin
= init_mdebin((Flags
& MD_APPENDFILES
) ? NULL
: mdoutf_get_fp_ene(*outf
),
2842 mtop
, ir
, mdoutf_get_fp_dhdl(*outf
));
2847 please_cite(fplog
, "Fritsch12");
2848 please_cite(fplog
, "Junghans10");
2850 /* Initiate variables */
2851 clear_mat(force_vir
);
2852 clear_mat(shake_vir
);