1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
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11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * GROwing Monsters And Cloning Shrimps
41 #include<catamount/dclock.h>
47 #ifdef HAVE_SYS_TIME_H
82 #include "pull_rotation.h"
83 #include "mpelogging.h"
86 #include "gmx_wallcycle.h"
99 typedef struct gmx_timeprint
{
108 #ifdef HAVE_GETTIMEOFDAY
110 struct timezone tz
= { 0,0 };
113 gettimeofday(&t
,&tz
);
115 seconds
= (double) t
.tv_sec
+ 1e-6*(double)t
.tv_usec
;
121 seconds
= time(NULL
);
128 #define difftime(end,start) ((double)(end)-(double)(start))
130 void print_time(FILE *out
,gmx_runtime_t
*runtime
,gmx_large_int_t step
,
131 t_inputrec
*ir
, t_commrec
*cr
)
142 fprintf(out
,"step %s",gmx_step_str(step
,buf
));
143 if ((step
>= ir
->nstlist
)) {
144 if ((ir
->nstlist
== 0) || ((step
% ir
->nstlist
) == 0)) {
145 /* We have done a full cycle let's update time_per_step */
146 runtime
->last
= gmx_gettime();
147 dt
= difftime(runtime
->last
,runtime
->real
);
148 runtime
->time_per_step
= dt
/(step
- ir
->init_step
+ 1);
150 dt
= (ir
->nsteps
+ ir
->init_step
- step
)*runtime
->time_per_step
;
153 finish
= (time_t) (runtime
->last
+ dt
);
154 sprintf(buf
,"%s",ctime(&finish
));
155 buf
[strlen(buf
)-1]='\0';
156 fprintf(out
,", will finish %s",buf
);
159 fprintf(out
,", remaining runtime: %5d s ",(int)dt
);
173 static double set_proctime(gmx_runtime_t
*runtime
)
179 prev
= runtime
->proc
;
180 runtime
->proc
= dclock();
182 diff
= runtime
->proc
- prev
;
186 prev
= runtime
->proc
;
187 runtime
->proc
= clock();
189 diff
= (double)(runtime
->proc
- prev
)/(double)CLOCKS_PER_SEC
;
193 /* The counter has probably looped, ignore this data */
200 void runtime_start(gmx_runtime_t
*runtime
)
202 runtime
->real
= gmx_gettime();
204 set_proctime(runtime
);
205 runtime
->realtime
= 0;
206 runtime
->proctime
= 0;
208 runtime
->time_per_step
= 0;
211 void runtime_end(gmx_runtime_t
*runtime
)
217 runtime
->proctime
+= set_proctime(runtime
);
218 runtime
->realtime
= now
- runtime
->real
;
222 void runtime_upd_proc(gmx_runtime_t
*runtime
)
224 runtime
->proctime
+= set_proctime(runtime
);
227 void print_date_and_time(FILE *fplog
,int nodeid
,const char *title
,
228 const gmx_runtime_t
*runtime
)
231 char *ts
,time_string
[STRLEN
];
236 tmptime
= (time_t) runtime
->real
;
237 ts
= ctime(&tmptime
);
241 tmptime
= (time_t) gmx_gettime();
242 ts
= ctime(&tmptime
);
244 for(i
=0; ts
[i
]>=' '; i
++)
246 time_string
[i
]=ts
[i
];
251 fprintf(fplog
,"%s on node %d %s\n",title
,nodeid
,time_string
);
255 static void sum_forces(int start
,int end
,rvec f
[],rvec flr
[])
260 pr_rvecs(debug
,0,"fsr",f
+start
,end
-start
);
261 pr_rvecs(debug
,0,"flr",flr
+start
,end
-start
);
263 for(i
=start
; (i
<end
); i
++)
264 rvec_inc(f
[i
],flr
[i
]);
268 * calc_f_el calculates forces due to an electric field.
270 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
272 * Et[] contains the parameters for the time dependent
273 * part of the field (not yet used).
274 * Ex[] contains the parameters for
275 * the spatial dependent part of the field. You can have cool periodic
276 * fields in principle, but only a constant field is supported
278 * The function should return the energy due to the electric field
279 * (if any) but for now returns 0.
282 * There can be problems with the virial.
283 * Since the field is not self-consistent this is unavoidable.
284 * For neutral molecules the virial is correct within this approximation.
285 * For neutral systems with many charged molecules the error is small.
286 * But for systems with a net charge or a few charged molecules
287 * the error can be significant when the field is high.
288 * Solution: implement a self-consitent electric field into PME.
290 static void calc_f_el(FILE *fp
,int start
,int homenr
,
291 real charge
[],rvec x
[],rvec f
[],
292 t_cosines Ex
[],t_cosines Et
[],double t
)
298 for(m
=0; (m
<DIM
); m
++)
305 Ext
[m
] = cos(Et
[m
].a
[0]*(t
-t0
))*exp(-sqr(t
-t0
)/(2.0*sqr(Et
[m
].a
[2])));
309 Ext
[m
] = cos(Et
[m
].a
[0]*t
);
318 /* Convert the field strength from V/nm to MD-units */
319 Ext
[m
] *= Ex
[m
].a
[0]*FIELDFAC
;
320 for(i
=start
; (i
<start
+homenr
); i
++)
321 f
[i
][m
] += charge
[i
]*Ext
[m
];
330 fprintf(fp
,"%10g %10g %10g %10g #FIELD\n",t
,
331 Ext
[XX
]/FIELDFAC
,Ext
[YY
]/FIELDFAC
,Ext
[ZZ
]/FIELDFAC
);
335 static void calc_virial(FILE *fplog
,int start
,int homenr
,rvec x
[],rvec f
[],
336 tensor vir_part
,t_graph
*graph
,matrix box
,
337 t_nrnb
*nrnb
,const t_forcerec
*fr
,int ePBC
)
342 /* The short-range virial from surrounding boxes */
344 calc_vir(fplog
,SHIFTS
,fr
->shift_vec
,fr
->fshift
,vir_part
,ePBC
==epbcSCREW
,box
);
345 inc_nrnb(nrnb
,eNR_VIRIAL
,SHIFTS
);
347 /* Calculate partial virial, for local atoms only, based on short range.
348 * Total virial is computed in global_stat, called from do_md
350 f_calc_vir(fplog
,start
,start
+homenr
,x
,f
,vir_part
,graph
,box
);
351 inc_nrnb(nrnb
,eNR_VIRIAL
,homenr
);
353 /* Add position restraint contribution */
354 for(i
=0; i
<DIM
; i
++) {
355 vir_part
[i
][i
] += fr
->vir_diag_posres
[i
];
358 /* Add wall contribution */
359 for(i
=0; i
<DIM
; i
++) {
360 vir_part
[i
][ZZ
] += fr
->vir_wall_z
[i
];
364 pr_rvecs(debug
,0,"vir_part",vir_part
,DIM
);
367 static void print_large_forces(FILE *fp
,t_mdatoms
*md
,t_commrec
*cr
,
368 gmx_large_int_t step
,real pforce
,rvec
*x
,rvec
*f
)
375 for(i
=md
->start
; i
<md
->start
+md
->homenr
; i
++) {
378 fprintf(fp
,"step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
379 gmx_step_str(step
,buf
),
380 ddglatnr(cr
->dd
,i
),x
[i
][XX
],x
[i
][YY
],x
[i
][ZZ
],sqrt(fn2
));
385 void do_force(FILE *fplog
,t_commrec
*cr
,
386 t_inputrec
*inputrec
,
387 gmx_large_int_t step
,t_nrnb
*nrnb
,gmx_wallcycle_t wcycle
,
390 gmx_groups_t
*groups
,
391 matrix box
,rvec x
[],history_t
*hist
,
395 gmx_enerdata_t
*enerd
,t_fcdata
*fcd
,
396 real lambda
,t_graph
*graph
,
397 t_forcerec
*fr
,gmx_vsite_t
*vsite
,rvec mu_tot
,
398 double t
,FILE *field
,gmx_edsam_t ed
,
405 bool bSepDVDL
,bStateChanged
,bNS
,bFillGrid
,bCalcCGCM
,bBS
;
406 bool bDoLongRange
,bDoForces
,bSepLRF
;
410 float cycles_ppdpme
,cycles_pme
,cycles_seppme
,cycles_force
;
412 start
= mdatoms
->start
;
413 homenr
= mdatoms
->homenr
;
415 bSepDVDL
= (fr
->bSepDVDL
&& do_per_step(step
,inputrec
->nstlog
));
417 clear_mat(vir_force
);
421 pd_cg_range(cr
,&cg0
,&cg1
);
426 if (DOMAINDECOMP(cr
))
428 cg1
= cr
->dd
->ncg_tot
;
440 bStateChanged
= (flags
& GMX_FORCE_STATECHANGED
);
441 bNS
= (flags
& GMX_FORCE_NS
) && (fr
->bAllvsAll
==FALSE
);
442 bFillGrid
= (bNS
&& bStateChanged
);
443 bCalcCGCM
= (bFillGrid
&& !DOMAINDECOMP(cr
));
444 bDoLongRange
= (fr
->bTwinRange
&& bNS
&& (flags
& GMX_FORCE_DOLR
));
445 bDoForces
= (flags
& GMX_FORCE_FORCES
);
446 bSepLRF
= (bDoLongRange
&& bDoForces
&& (flags
& GMX_FORCE_SEPLRF
));
450 update_forcerec(fplog
,fr
,box
);
452 /* Calculate total (local) dipole moment in a temporary common array.
453 * This makes it possible to sum them over nodes faster.
455 calc_mu(start
,homenr
,
456 x
,mdatoms
->chargeA
,mdatoms
->chargeB
,mdatoms
->nChargePerturbed
,
460 if (fr
->ePBC
!= epbcNONE
) {
461 /* Compute shift vectors every step,
462 * because of pressure coupling or box deformation!
464 if ((flags
& GMX_FORCE_DYNAMICBOX
) && bStateChanged
)
465 calc_shifts(box
,fr
->shift_vec
);
468 put_charge_groups_in_box(fplog
,cg0
,cg1
,fr
->ePBC
,box
,
469 &(top
->cgs
),x
,fr
->cg_cm
);
470 inc_nrnb(nrnb
,eNR_CGCM
,homenr
);
471 inc_nrnb(nrnb
,eNR_RESETX
,cg1
-cg0
);
473 else if (EI_ENERGY_MINIMIZATION(inputrec
->eI
) && graph
) {
474 unshift_self(graph
,box
,x
);
477 else if (bCalcCGCM
) {
478 calc_cgcm(fplog
,cg0
,cg1
,&(top
->cgs
),x
,fr
->cg_cm
);
479 inc_nrnb(nrnb
,eNR_CGCM
,homenr
);
484 move_cgcm(fplog
,cr
,fr
->cg_cm
);
487 pr_rvecs(debug
,0,"cgcm",fr
->cg_cm
,top
->cgs
.nr
);
491 if (!(cr
->duty
& DUTY_PME
)) {
492 /* Send particle coordinates to the pme nodes.
493 * Since this is only implemented for domain decomposition
494 * and domain decomposition does not use the graph,
495 * we do not need to worry about shifting.
498 wallcycle_start(wcycle
,ewcPP_PMESENDX
);
499 GMX_MPE_LOG(ev_send_coordinates_start
);
501 bBS
= (inputrec
->nwall
== 2);
504 svmul(inputrec
->wall_ewald_zfac
,boxs
[ZZ
],boxs
[ZZ
]);
507 gmx_pme_send_x(cr
,bBS
? boxs
: box
,x
,mdatoms
->nChargePerturbed
,lambda
,step
);
509 GMX_MPE_LOG(ev_send_coordinates_finish
);
510 wallcycle_stop(wcycle
,ewcPP_PMESENDX
);
514 /* Communicate coordinates and sum dipole if necessary */
517 wallcycle_start(wcycle
,ewcMOVEX
);
518 if (DOMAINDECOMP(cr
))
520 dd_move_x(cr
->dd
,box
,x
);
524 move_x(fplog
,cr
,GMX_LEFT
,GMX_RIGHT
,x
,nrnb
);
526 /* When we don't need the total dipole we sum it in global_stat */
527 if (bStateChanged
&& NEED_MUTOT(*inputrec
))
529 gmx_sumd(2*DIM
,mu
,cr
);
531 wallcycle_stop(wcycle
,ewcMOVEX
);
539 fr
->mu_tot
[i
][j
] = mu
[i
*DIM
+ j
];
543 if (fr
->efep
== efepNO
)
545 copy_rvec(fr
->mu_tot
[0],mu_tot
);
552 (1.0 - lambda
)*fr
->mu_tot
[0][j
] + lambda
*fr
->mu_tot
[1][j
];
557 reset_enerdata(&(inputrec
->opts
),fr
,bNS
,enerd
,MASTER(cr
));
558 clear_rvecs(SHIFTS
,fr
->fshift
);
562 wallcycle_start(wcycle
,ewcNS
);
564 if (graph
&& bStateChanged
)
566 /* Calculate intramolecular shift vectors to make molecules whole */
567 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
570 /* Reset long range forces if necessary */
573 /* Reset the (long-range) forces if necessary */
574 clear_rvecs(fr
->natoms_force
,bSepLRF
? fr
->f_twin
: f
);
577 /* Do the actual neighbour searching and if twin range electrostatics
578 * also do the calculation of long range forces and energies.
582 groups
,&(inputrec
->opts
),top
,mdatoms
,
583 cr
,nrnb
,lambda
,&dvdl
,&enerd
->grpp
,bFillGrid
,
584 bDoLongRange
,bDoForces
,bSepLRF
? fr
->f_twin
: f
);
587 fprintf(fplog
,sepdvdlformat
,"LR non-bonded",0.0,dvdl
);
589 enerd
->dvdl_lin
+= dvdl
;
591 wallcycle_stop(wcycle
,ewcNS
);
594 if (inputrec
->implicit_solvent
&& bNS
)
596 make_gb_nblist(cr
,mtop
->natoms
,inputrec
->gb_algorithm
,inputrec
->rlist
,
597 x
,box
,fr
,&top
->idef
,graph
,fr
->born
);
600 if (DOMAINDECOMP(cr
))
602 if (!(cr
->duty
& DUTY_PME
))
604 wallcycle_start(wcycle
,ewcPPDURINGPME
);
605 dd_force_flop_start(cr
->dd
,nrnb
);
611 /* Enforced rotation has its own cycle counter that starts after the collective
612 * coordinates have been communicated. It is added to ddCyclF */
613 do_rotation(cr
,inputrec
,box
,x
,t
,step
,wcycle
,bNS
);
616 /* Start the force cycle counter.
617 * This counter is stopped in do_forcelow_level.
618 * No parallel communication should occur while this counter is running,
619 * since that will interfere with the dynamic load balancing.
621 wallcycle_start(wcycle
,ewcFORCE
);
622 GMX_MPE_LOG(ev_forcecycles_start
);
626 /* Reset forces for which the virial is calculated separately:
627 * PME/Ewald forces if necessary */
630 if (flags
& GMX_FORCE_VIRIAL
)
632 fr
->f_novirsum
= fr
->f_novirsum_alloc
;
633 GMX_BARRIER(cr
->mpi_comm_mygroup
);
636 clear_rvecs(fr
->f_novirsum_n
,fr
->f_novirsum
);
640 clear_rvecs(homenr
,fr
->f_novirsum
+start
);
642 GMX_BARRIER(cr
->mpi_comm_mygroup
);
646 /* We are not calculating the pressure so we do not need
647 * a separate array for forces that do not contribute
656 /* Add the long range forces to the short range forces */
657 for(i
=0; i
<fr
->natoms_force
; i
++)
659 copy_rvec(fr
->f_twin
[i
],f
[i
]);
662 else if (!(fr
->bTwinRange
&& bNS
))
664 /* Clear the short-range forces */
665 clear_rvecs(fr
->natoms_force
,f
);
668 clear_rvec(fr
->vir_diag_posres
);
670 GMX_BARRIER(cr
->mpi_comm_mygroup
);
672 if (inputrec
->ePull
== epullCONSTRAINT
)
674 clear_pull_forces(inputrec
->pull
);
677 /* update QMMMrec, if necessary */
680 update_QMMMrec(cr
,fr
,x
,mdatoms
,box
,top
);
683 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_POSRES
].nr
> 0)
685 /* Position restraints always require full pbc */
686 set_pbc(&pbc
,inputrec
->ePBC
,box
);
687 v
= posres(top
->idef
.il
[F_POSRES
].nr
,top
->idef
.il
[F_POSRES
].iatoms
,
688 top
->idef
.iparams_posres
,
689 (const rvec
*)x
,fr
->f_novirsum
,fr
->vir_diag_posres
,
690 inputrec
->ePBC
==epbcNONE
? NULL
: &pbc
,lambda
,&dvdl
,
691 fr
->rc_scaling
,fr
->ePBC
,fr
->posres_com
,fr
->posres_comB
);
694 fprintf(fplog
,sepdvdlformat
,
695 interaction_function
[F_POSRES
].longname
,v
,dvdl
);
697 enerd
->term
[F_POSRES
] += v
;
698 /* This linear lambda dependence assumption is only correct
699 * when only k depends on lambda,
700 * not when the reference position depends on lambda.
701 * grompp checks for this.
703 enerd
->dvdl_lin
+= dvdl
;
704 inc_nrnb(nrnb
,eNR_POSRES
,top
->idef
.il
[F_POSRES
].nr
/2);
707 /* Compute the bonded and non-bonded energies and optionally forces */
708 do_force_lowlevel(fplog
,step
,fr
,inputrec
,&(top
->idef
),
709 cr
,nrnb
,wcycle
,mdatoms
,&(inputrec
->opts
),
710 x
,hist
,f
,enerd
,fcd
,mtop
,top
,fr
->born
,
711 &(top
->atomtypes
),bBornRadii
,box
,
712 lambda
,graph
,&(top
->excls
),fr
->mu_tot
,
715 cycles_force
= wallcycle_stop(wcycle
,ewcFORCE
);
716 GMX_BARRIER(cr
->mpi_comm_mygroup
);
720 do_flood(fplog
,cr
,x
,f
,ed
,box
,step
);
723 if (DOMAINDECOMP(cr
))
725 dd_force_flop_stop(cr
->dd
,nrnb
);
728 dd_cycles_add(cr
->dd
,cycles_force
-cycles_pme
,ddCyclF
);
734 if (IR_ELEC_FIELD(*inputrec
))
736 /* Compute forces due to electric field */
737 calc_f_el(MASTER(cr
) ? field
: NULL
,
738 start
,homenr
,mdatoms
->chargeA
,x
,fr
->f_novirsum
,
739 inputrec
->ex
,inputrec
->et
,t
);
742 /* Communicate the forces */
745 wallcycle_start(wcycle
,ewcMOVEF
);
746 if (DOMAINDECOMP(cr
))
748 dd_move_f(cr
->dd
,f
,fr
->fshift
);
749 /* Do we need to communicate the separate force array
750 * for terms that do not contribute to the single sum virial?
751 * Position restraints and electric fields do not introduce
752 * inter-cg forces, only full electrostatics methods do.
753 * When we do not calculate the virial, fr->f_novirsum = f,
754 * so we have already communicated these forces.
756 if (EEL_FULL(fr
->eeltype
) && cr
->dd
->n_intercg_excl
&&
757 (flags
& GMX_FORCE_VIRIAL
))
759 dd_move_f(cr
->dd
,fr
->f_novirsum
,NULL
);
763 /* We should not update the shift forces here,
764 * since f_twin is already included in f.
766 dd_move_f(cr
->dd
,fr
->f_twin
,NULL
);
771 pd_move_f(cr
,f
,nrnb
);
774 pd_move_f(cr
,fr
->f_twin
,nrnb
);
777 wallcycle_stop(wcycle
,ewcMOVEF
);
780 /* If we have NoVirSum forces, but we do not calculate the virial,
781 * we sum fr->f_novirum=f later.
783 if (vsite
&& !(fr
->bF_NoVirSum
&& !(flags
& GMX_FORCE_VIRIAL
)))
785 wallcycle_start(wcycle
,ewcVSITESPREAD
);
786 spread_vsite_f(fplog
,vsite
,x
,f
,fr
->fshift
,nrnb
,
787 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
788 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
792 wallcycle_start(wcycle
,ewcVSITESPREAD
);
793 spread_vsite_f(fplog
,vsite
,x
,fr
->f_twin
,NULL
,
795 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
796 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
800 if (flags
& GMX_FORCE_VIRIAL
)
802 /* Calculation of the virial must be done after vsites! */
803 calc_virial(fplog
,mdatoms
->start
,mdatoms
->homenr
,x
,f
,
804 vir_force
,graph
,box
,nrnb
,fr
,inputrec
->ePBC
);
808 if (inputrec
->ePull
== epullUMBRELLA
|| inputrec
->ePull
== epullCONST_F
)
810 /* Calculate the center of mass forces, this requires communication,
811 * which is why pull_potential is called close to other communication.
812 * The virial contribution is calculated directly,
813 * which is why we call pull_potential after calc_virial.
815 set_pbc(&pbc
,inputrec
->ePBC
,box
);
817 enerd
->term
[F_COM_PULL
] =
818 pull_potential(inputrec
->ePull
,inputrec
->pull
,mdatoms
,&pbc
,
819 cr
,t
,lambda
,x
,f
,vir_force
,&dvdl
);
822 fprintf(fplog
,sepdvdlformat
,"Com pull",enerd
->term
[F_COM_PULL
],dvdl
);
824 enerd
->dvdl_lin
+= dvdl
;
827 enerd
->term
[F_COM_PULL
] = 0.0;
829 /* Add the forces from enforced rotation potentials (if any) */
831 enerd
->term
[F_COM_PULL
] += add_rot_forces(inputrec
->rot
, f
, cr
,step
,t
);
834 if (PAR(cr
) && !(cr
->duty
& DUTY_PME
))
836 cycles_ppdpme
= wallcycle_stop(wcycle
,ewcPPDURINGPME
);
837 dd_cycles_add(cr
->dd
,cycles_ppdpme
,ddCyclPPduringPME
);
839 /* In case of node-splitting, the PP nodes receive the long-range
840 * forces, virial and energy from the PME nodes here.
842 wallcycle_start(wcycle
,ewcPP_PMEWAITRECVF
);
844 gmx_pme_receive_f(cr
,fr
->f_novirsum
,fr
->vir_el_recip
,&e
,&dvdl
,
848 fprintf(fplog
,sepdvdlformat
,"PME mesh",e
,dvdl
);
850 enerd
->term
[F_COUL_RECIP
] += e
;
851 enerd
->dvdl_lin
+= dvdl
;
854 dd_cycles_add(cr
->dd
,cycles_seppme
,ddCyclPME
);
856 wallcycle_stop(wcycle
,ewcPP_PMEWAITRECVF
);
859 if (bDoForces
&& fr
->bF_NoVirSum
)
863 /* Spread the mesh force on virtual sites to the other particles...
864 * This is parallellized. MPI communication is performed
865 * if the constructing atoms aren't local.
867 wallcycle_start(wcycle
,ewcVSITESPREAD
);
868 spread_vsite_f(fplog
,vsite
,x
,fr
->f_novirsum
,NULL
,nrnb
,
869 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
870 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
872 if (flags
& GMX_FORCE_VIRIAL
)
874 /* Now add the forces, this is local */
877 sum_forces(0,fr
->f_novirsum_n
,f
,fr
->f_novirsum
);
881 sum_forces(start
,start
+homenr
,f
,fr
->f_novirsum
);
883 if (EEL_FULL(fr
->eeltype
))
885 /* Add the mesh contribution to the virial */
886 m_add(vir_force
,fr
->vir_el_recip
,vir_force
);
890 pr_rvecs(debug
,0,"vir_force",vir_force
,DIM
);
895 /* Sum the potential energy terms from group contributions */
896 sum_epot(&(inputrec
->opts
),enerd
);
898 if (fr
->print_force
>= 0 && bDoForces
)
900 print_large_forces(stderr
,mdatoms
,cr
,step
,fr
->print_force
,x
,f
);
904 void do_constrain_first(FILE *fplog
,gmx_constr_t constr
,
905 t_inputrec
*ir
,t_mdatoms
*md
,
906 t_state
*state
,rvec
*f
,
907 t_graph
*graph
,t_commrec
*cr
,t_nrnb
*nrnb
,
908 t_forcerec
*fr
, gmx_localtop_t
*top
, tensor shake_vir
)
911 gmx_large_int_t step
;
912 double mass
,tmass
,vcm
[4];
917 snew(savex
,state
->natoms
);
920 end
= md
->homenr
+ start
;
923 fprintf(debug
,"vcm: start=%d, homenr=%d, end=%d\n",
924 start
,md
->homenr
,end
);
925 /* Do a first constrain to reset particles... */
926 step
= ir
->init_step
;
928 fprintf(fplog
,"\nConstraining the starting coordinates (step %d)\n",step
);
931 /* constrain the current position */
932 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
933 ir
,NULL
,cr
,step
,0,md
,
934 state
->x
,state
->x
,NULL
,
935 state
->box
,state
->lambda
,&dvdlambda
,
936 NULL
,NULL
,nrnb
,econqCoord
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
939 /* constrain the inital velocity, and save it */
940 /* also may be useful if we need the ekin from the halfstep for velocity verlet */
941 /* might not yet treat veta correctly */
942 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
943 ir
,NULL
,cr
,step
,0,md
,
944 state
->x
,state
->v
,state
->v
,
945 state
->box
,state
->lambda
,&dvdlambda
,
946 NULL
,NULL
,nrnb
,econqVeloc
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
948 /* constrain the inital velocities at t-dt/2 */
949 if (EI_STATE_VELOCITY(ir
->eI
) && ir
->eI
!=eiVV
)
951 for(i
=start
; (i
<end
); i
++)
953 for(m
=0; (m
<DIM
); m
++)
955 /* Reverse the velocity */
956 state
->v
[i
][m
] = -state
->v
[i
][m
];
957 /* Store the position at t-dt in buf */
958 savex
[i
][m
] = state
->x
[i
][m
] + dt
*state
->v
[i
][m
];
961 /* Shake the positions at t=-dt with the positions at t=0
962 * as reference coordinates.
966 fprintf(fplog
,"\nConstraining the coordinates at t0-dt (step %d)\n",
970 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
971 ir
,NULL
,cr
,step
,-1,md
,
973 state
->box
,state
->lambda
,&dvdlambda
,
974 state
->v
,NULL
,nrnb
,econqCoord
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
976 for(i
=start
; i
<end
; i
++) {
977 for(m
=0; m
<DIM
; m
++) {
978 /* Re-reverse the velocities */
979 state
->v
[i
][m
] = -state
->v
[i
][m
];
986 for(i
=start
; i
<end
; i
++) {
988 for(m
=0; m
<DIM
; m
++) {
989 vcm
[m
] += state
->v
[i
][m
]*mass
;
994 if (ir
->nstcomm
!= 0 || debug
) {
995 /* Compute the global sum of vcm */
997 fprintf(debug
,"vcm: %8.3f %8.3f %8.3f,"
998 " total mass = %12.5e\n",vcm
[XX
],vcm
[YY
],vcm
[ZZ
],vcm
[3]);
1002 for(m
=0; (m
<DIM
); m
++)
1005 fprintf(debug
,"vcm: %8.3f %8.3f %8.3f,"
1006 " total mass = %12.5e\n",vcm
[XX
],vcm
[YY
],vcm
[ZZ
],tmass
);
1007 if (ir
->nstcomm
!= 0) {
1008 /* Now we have the velocity of center of mass, let's remove it */
1009 for(i
=start
; (i
<end
); i
++) {
1010 for(m
=0; (m
<DIM
); m
++)
1011 state
->v
[i
][m
] -= vcm
[m
];
1019 void calc_enervirdiff(FILE *fplog
,int eDispCorr
,t_forcerec
*fr
)
1021 double eners
[2],virs
[2],enersum
,virsum
,y0
,f
,g
,h
;
1022 double r0
,r1
,r
,rc3
,rc9
,ea
,eb
,ec
,pa
,pb
,pc
,pd
;
1023 double invscale
,invscale2
,invscale3
;
1024 int ri0
,ri1
,ri
,i
,offstart
,offset
;
1027 fr
->enershiftsix
= 0;
1028 fr
->enershifttwelve
= 0;
1029 fr
->enerdiffsix
= 0;
1030 fr
->enerdifftwelve
= 0;
1032 fr
->virdifftwelve
= 0;
1034 if (eDispCorr
!= edispcNO
) {
1035 for(i
=0; i
<2; i
++) {
1039 if ((fr
->vdwtype
== evdwSWITCH
) || (fr
->vdwtype
== evdwSHIFT
)) {
1040 if (fr
->rvdw_switch
== 0)
1042 "With dispersion correction rvdw-switch can not be zero "
1043 "for vdw-type = %s",evdw_names
[fr
->vdwtype
]);
1045 scale
= fr
->nblists
[0].tab
.scale
;
1046 vdwtab
= fr
->nblists
[0].vdwtab
;
1048 /* Round the cut-offs to exact table values for precision */
1049 ri0
= floor(fr
->rvdw_switch
*scale
);
1050 ri1
= ceil(fr
->rvdw
*scale
);
1056 if (fr
->vdwtype
== evdwSHIFT
) {
1057 /* Determine the constant energy shift below rvdw_switch */
1058 fr
->enershiftsix
= (real
)(-1.0/(rc3
*rc3
)) - vdwtab
[8*ri0
];
1059 fr
->enershifttwelve
= (real
)( 1.0/(rc9
*rc3
)) - vdwtab
[8*ri0
+ 4];
1061 /* Add the constant part from 0 to rvdw_switch.
1062 * This integration from 0 to rvdw_switch overcounts the number
1063 * of interactions by 1, as it also counts the self interaction.
1064 * We will correct for this later.
1066 eners
[0] += 4.0*M_PI
*fr
->enershiftsix
*rc3
/3.0;
1067 eners
[1] += 4.0*M_PI
*fr
->enershifttwelve
*rc3
/3.0;
1069 invscale
= 1.0/(scale
);
1070 invscale2
= invscale
*invscale
;
1071 invscale3
= invscale
*invscale2
;
1073 /* following summation derived from cubic spline definition,
1074 Numerical Recipies in C, second edition, p. 113-116. Exact
1075 for the cubic spline. We first calculate the negative of
1076 the energy from rvdw to rvdw_switch, assuming that g(r)=1,
1077 and then add the more standard, abrupt cutoff correction to
1078 that result, yielding the long-range correction for a
1079 switched function. We perform both the pressure and energy
1080 loops at the same time for simplicity, as the computational
1084 enersum
= 0.0; virsum
= 0.0;
1089 for (ri
=ri0
; ri
<ri1
; ri
++) {
1092 eb
= 2.0*invscale2
*r
;
1096 pb
= 3.0*invscale2
*r
;
1097 pc
= 3.0*invscale
*r
*r
;
1100 /* this "8" is from the packing in the vdwtab array - perhaps
1101 should be #define'ed? */
1102 offset
= 8*ri
+ offstart
;
1103 y0
= vdwtab
[offset
];
1104 f
= vdwtab
[offset
+1];
1105 g
= vdwtab
[offset
+2];
1106 h
= vdwtab
[offset
+3];
1108 enersum
+= y0
*(ea
/3 + eb
/2 + ec
) + f
*(ea
/4 + eb
/3 + ec
/2)+
1109 g
*(ea
/5 + eb
/4 + ec
/3) + h
*(ea
/6 + eb
/5 + ec
/4);
1110 virsum
+= f
*(pa
/4 + pb
/3 + pc
/2 + pd
) +
1111 2*g
*(pa
/5 + pb
/4 + pc
/3 + pd
/2) + 3*h
*(pa
/6 + pb
/5 + pc
/4 + pd
/3);
1114 enersum
*= 4.0*M_PI
;
1116 eners
[i
] -= enersum
;
1120 /* now add the correction for rvdw_switch to infinity */
1121 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
1122 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
1123 virs
[0] += 8.0*M_PI
/rc3
;
1124 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
1126 else if ((fr
->vdwtype
== evdwCUT
) || (fr
->vdwtype
== evdwUSER
)) {
1127 if (fr
->vdwtype
== evdwUSER
&& fplog
)
1129 "WARNING: using dispersion correction with user tables\n");
1130 rc3
= fr
->rvdw
*fr
->rvdw
*fr
->rvdw
;
1132 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
1133 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
1134 virs
[0] += 8.0*M_PI
/rc3
;
1135 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
1138 "Dispersion correction is not implemented for vdw-type = %s",
1139 evdw_names
[fr
->vdwtype
]);
1141 fr
->enerdiffsix
= eners
[0];
1142 fr
->enerdifftwelve
= eners
[1];
1143 /* The 0.5 is due to the Gromacs definition of the virial */
1144 fr
->virdiffsix
= 0.5*virs
[0];
1145 fr
->virdifftwelve
= 0.5*virs
[1];
1149 void calc_dispcorr(FILE *fplog
,t_inputrec
*ir
,t_forcerec
*fr
,
1150 gmx_large_int_t step
,int natoms
,
1151 matrix box
,real lambda
,tensor pres
,tensor virial
,
1152 real
*prescorr
, real
*enercorr
, real
*dvdlcorr
)
1154 bool bCorrAll
,bCorrPres
;
1155 real dvdlambda
,invvol
,dens
,ninter
,avcsix
,avctwelve
,enerdiff
,svir
=0,spres
=0;
1165 if (ir
->eDispCorr
!= edispcNO
) {
1166 bCorrAll
= (ir
->eDispCorr
== edispcAllEner
||
1167 ir
->eDispCorr
== edispcAllEnerPres
);
1168 bCorrPres
= (ir
->eDispCorr
== edispcEnerPres
||
1169 ir
->eDispCorr
== edispcAllEnerPres
);
1171 invvol
= 1/det(box
);
1174 /* Only correct for the interactions with the inserted molecule */
1175 dens
= (natoms
- fr
->n_tpi
)*invvol
;
1180 dens
= natoms
*invvol
;
1181 ninter
= 0.5*natoms
;
1184 if (ir
->efep
== efepNO
)
1186 avcsix
= fr
->avcsix
[0];
1187 avctwelve
= fr
->avctwelve
[0];
1191 avcsix
= (1 - lambda
)*fr
->avcsix
[0] + lambda
*fr
->avcsix
[1];
1192 avctwelve
= (1 - lambda
)*fr
->avctwelve
[0] + lambda
*fr
->avctwelve
[1];
1195 enerdiff
= ninter
*(dens
*fr
->enerdiffsix
- fr
->enershiftsix
);
1196 *enercorr
+= avcsix
*enerdiff
;
1198 if (ir
->efep
!= efepNO
)
1200 dvdlambda
+= (fr
->avcsix
[1] - fr
->avcsix
[0])*enerdiff
;
1204 enerdiff
= ninter
*(dens
*fr
->enerdifftwelve
- fr
->enershifttwelve
);
1205 *enercorr
+= avctwelve
*enerdiff
;
1206 if (fr
->efep
!= efepNO
)
1208 dvdlambda
+= (fr
->avctwelve
[1] - fr
->avctwelve
[0])*enerdiff
;
1214 svir
= ninter
*dens
*avcsix
*fr
->virdiffsix
/3.0;
1215 if (ir
->eDispCorr
== edispcAllEnerPres
)
1217 svir
+= ninter
*dens
*avctwelve
*fr
->virdifftwelve
/3.0;
1219 /* The factor 2 is because of the Gromacs virial definition */
1220 spres
= -2.0*invvol
*svir
*PRESFAC
;
1222 for(m
=0; m
<DIM
; m
++) {
1223 virial
[m
][m
] += svir
;
1224 pres
[m
][m
] += spres
;
1229 /* Can't currently control when it prints, for now, just print when degugging */
1233 fprintf(debug
,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1239 "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
1240 *enercorr
,spres
,svir
);
1244 fprintf(debug
,"Long Range LJ corr.: Epot %10g\n",*enercorr
);
1248 if (fr
->bSepDVDL
&& do_per_step(step
,ir
->nstlog
))
1249 fprintf(fplog
,sepdvdlformat
,"Dispersion correction",
1250 *enercorr
,dvdlambda
);
1252 if (fr
->efep
!= efepNO
)
1254 *dvdlcorr
+= dvdlambda
;
1259 void do_pbc_first(FILE *fplog
,matrix box
,t_forcerec
*fr
,
1260 t_graph
*graph
,rvec x
[])
1263 fprintf(fplog
,"Removing pbc first time\n");
1264 calc_shifts(box
,fr
->shift_vec
);
1266 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
1268 p_graph(debug
,"do_pbc_first 1",graph
);
1269 shift_self(graph
,box
,x
);
1270 /* By doing an extra mk_mshift the molecules that are broken
1271 * because they were e.g. imported from another software
1272 * will be made whole again. Such are the healing powers
1275 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
1277 p_graph(debug
,"do_pbc_first 2",graph
);
1280 fprintf(fplog
,"Done rmpbc\n");
1283 static void low_do_pbc_mtop(FILE *fplog
,int ePBC
,matrix box
,
1284 gmx_mtop_t
*mtop
,rvec x
[],
1289 gmx_molblock_t
*molb
;
1291 if (bFirst
&& fplog
)
1292 fprintf(fplog
,"Removing pbc first time\n");
1296 for(mb
=0; mb
<mtop
->nmolblock
; mb
++) {
1297 molb
= &mtop
->molblock
[mb
];
1298 if (molb
->natoms_mol
== 1 ||
1299 (!bFirst
&& mtop
->moltype
[molb
->type
].cgs
.nr
== 1)) {
1300 /* Just one atom or charge group in the molecule, no PBC required */
1301 as
+= molb
->nmol
*molb
->natoms_mol
;
1303 /* Pass NULL iso fplog to avoid graph prints for each molecule type */
1304 mk_graph_ilist(NULL
,mtop
->moltype
[molb
->type
].ilist
,
1305 0,molb
->natoms_mol
,FALSE
,FALSE
,graph
);
1307 for(mol
=0; mol
<molb
->nmol
; mol
++) {
1308 mk_mshift(fplog
,graph
,ePBC
,box
,x
+as
);
1310 shift_self(graph
,box
,x
+as
);
1311 /* The molecule is whole now.
1312 * We don't need the second mk_mshift call as in do_pbc_first,
1313 * since we no longer need this graph.
1316 as
+= molb
->natoms_mol
;
1324 void do_pbc_first_mtop(FILE *fplog
,int ePBC
,matrix box
,
1325 gmx_mtop_t
*mtop
,rvec x
[])
1327 low_do_pbc_mtop(fplog
,ePBC
,box
,mtop
,x
,TRUE
);
1330 void do_pbc_mtop(FILE *fplog
,int ePBC
,matrix box
,
1331 gmx_mtop_t
*mtop
,rvec x
[])
1333 low_do_pbc_mtop(fplog
,ePBC
,box
,mtop
,x
,FALSE
);
1336 void finish_run(FILE *fplog
,t_commrec
*cr
,const char *confout
,
1337 t_inputrec
*inputrec
,
1338 t_nrnb nrnb
[],gmx_wallcycle_t wcycle
,
1339 gmx_runtime_t
*runtime
,
1343 t_nrnb
*nrnb_tot
=NULL
;
1346 double cycles
[ewcNR
];
1348 wallcycle_sum(cr
,wcycle
,cycles
);
1350 if (cr
->nnodes
> 1) {
1354 MPI_Reduce(nrnb
->n
,nrnb_tot
->n
,eNRNB
,MPI_DOUBLE
,MPI_SUM
,
1355 MASTERRANK(cr
),cr
->mpi_comm_mysim
);
1361 if (SIMMASTER(cr
)) {
1362 print_flop(fplog
,nrnb_tot
,&nbfs
,&mflop
);
1363 if (cr
->nnodes
> 1) {
1368 if ((cr
->duty
& DUTY_PP
) && DOMAINDECOMP(cr
)) {
1369 print_dd_statistics(cr
,inputrec
,fplog
);
1372 if (SIMMASTER(cr
)) {
1373 if (PARTDECOMP(cr
)) {
1374 pr_load(fplog
,cr
,nrnb_tot
);
1377 wallcycle_print(fplog
,cr
->nnodes
,cr
->npmenodes
,runtime
->realtime
,
1380 if (EI_DYNAMICS(inputrec
->eI
)) {
1381 delta_t
= inputrec
->delta_t
;
1387 print_perf(fplog
,runtime
->proctime
,runtime
->realtime
,
1388 cr
->nnodes
-cr
->npmenodes
,
1389 runtime
->nsteps_done
,delta_t
,nbfs
,mflop
);
1392 print_perf(stderr
,runtime
->proctime
,runtime
->realtime
,
1393 cr
->nnodes
-cr
->npmenodes
,
1394 runtime
->nsteps_done
,delta_t
,nbfs
,mflop
);
1398 runtime=inputrec->nsteps*inputrec->delta_t;
1400 if (cr->nnodes == 1)
1401 fprintf(stderr,"\n\n");
1402 print_perf(stderr,nodetime,realtime,runtime,&ntot,
1403 cr->nnodes-cr->npmenodes,FALSE);
1405 wallcycle_print(fplog,cr->nnodes,cr->npmenodes,realtime,wcycle,cycles);
1406 print_perf(fplog,nodetime,realtime,runtime,&ntot,cr->nnodes-cr->npmenodes,
1409 pr_load(fplog,cr,nrnb_all);
1416 void init_md(FILE *fplog
,
1417 t_commrec
*cr
,t_inputrec
*ir
,const output_env_t oenv
,
1418 double *t
,double *t0
,
1419 real
*lambda
,double *lam0
,
1420 t_nrnb
*nrnb
,gmx_mtop_t
*mtop
,
1422 int nfile
,const t_filenm fnm
[],
1423 int *fp_trn
,int *fp_xtc
,ener_file_t
*fp_ene
,const char **fn_cpt
,
1424 FILE **fp_dhdl
,FILE **fp_field
,
1426 tensor force_vir
,tensor shake_vir
,rvec mu_tot
,
1427 bool *bNEMD
,bool *bSimAnn
,t_vcm
**vcm
, t_state
*state
, unsigned long Flags
)
1433 sprintf(filemode
, (Flags
& MD_APPENDFILES
) ? "a+" : "w+");
1435 /* Initial values */
1436 *t
= *t0
= ir
->init_t
;
1437 if (ir
->efep
!= efepNO
)
1439 *lam0
= ir
->init_lambda
;
1440 *lambda
= *lam0
+ ir
->init_step
*ir
->delta_lambda
;
1444 *lambda
= *lam0
= 0.0;
1448 for(i
=0;i
<ir
->opts
.ngtc
;i
++)
1450 /* set bSimAnn if any group is being annealed */
1451 if(ir
->opts
.annealing
[i
]!=eannNO
)
1458 update_annealing_target_temp(&(ir
->opts
),ir
->init_t
);
1461 *bNEMD
= (ir
->opts
.ngacc
> 1) || (norm(ir
->opts
.acc
[0]) > 0);
1465 *upd
= init_update(fplog
,ir
);
1470 *vcm
= init_vcm(fplog
,&mtop
->groups
,ir
);
1473 if (EI_DYNAMICS(ir
->eI
) && !(Flags
& MD_APPENDFILES
))
1475 if (ir
->etc
== etcBERENDSEN
)
1477 please_cite(fplog
,"Berendsen84a");
1479 if (ir
->etc
== etcVRESCALE
)
1481 please_cite(fplog
,"Bussi2007a");
1495 *fp_trn
= open_trn(ftp2fn(efTRN
,nfile
,fnm
), filemode
);
1496 if (ir
->nstxtcout
> 0)
1498 *fp_xtc
= open_xtc(ftp2fn(efXTC
,nfile
,fnm
), filemode
);
1500 *fp_ene
= open_enx(ftp2fn(efEDR
,nfile
,fnm
), filemode
);
1501 *fn_cpt
= opt2fn("-cpo",nfile
,fnm
);
1503 if ((fp_dhdl
!= NULL
) && ir
->efep
!= efepNO
&& ir
->nstdhdl
> 0)
1505 if(Flags
& MD_APPENDFILES
)
1507 *fp_dhdl
= gmx_fio_fopen(opt2fn("-dhdl",nfile
,fnm
),filemode
);
1511 *fp_dhdl
= open_dhdl(opt2fn("-dhdl",nfile
,fnm
),ir
,oenv
);
1515 if ((fp_field
!= NULL
) &&
1516 (ir
->ex
[XX
].n
|| ir
->ex
[YY
].n
||ir
->ex
[ZZ
].n
))
1518 if(Flags
& MD_APPENDFILES
)
1520 *fp_dhdl
=gmx_fio_fopen(opt2fn("-field",nfile
,fnm
),filemode
);
1524 *fp_field
= xvgropen(opt2fn("-field",nfile
,fnm
),
1525 "Applied electric field","Time (ps)",
1530 *mdebin
= init_mdebin( (Flags
& MD_APPENDFILES
) ? NULL
: *fp_ene
,
1534 /* Initiate variables */
1535 clear_mat(force_vir
);
1536 clear_mat(shake_vir
);