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
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
31 * For more info, check our website at http://www.gromacs.org
34 * GROwing Monsters And Cloning Shrimps
41 #include<catamount/dclock.h>
47 #ifdef HAVE_SYS_TIME_H
60 #include "chargegroup.h"
83 #include "pull_rotation.h"
84 #include "mpelogging.h"
87 #include "gmx_wallcycle.h"
100 typedef struct gmx_timeprint
{
105 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
107 gmx_ctime_r(const time_t *clock
,char *buf
, int n
);
113 #ifdef HAVE_GETTIMEOFDAY
115 struct timezone tz
= { 0,0 };
118 gettimeofday(&t
,&tz
);
120 seconds
= (double) t
.tv_sec
+ 1e-6*(double)t
.tv_usec
;
126 seconds
= time(NULL
);
133 #define difftime(end,start) ((double)(end)-(double)(start))
135 void print_time(FILE *out
,gmx_runtime_t
*runtime
,gmx_large_int_t step
,
136 t_inputrec
*ir
, t_commrec
*cr
)
139 char timebuf
[STRLEN
];
149 fprintf(out
,"step %s",gmx_step_str(step
,buf
));
150 if ((step
>= ir
->nstlist
))
152 if ((ir
->nstlist
== 0) || ((step
% ir
->nstlist
) == 0))
154 /* We have done a full cycle let's update time_per_step */
155 runtime
->last
= gmx_gettime();
156 dt
= difftime(runtime
->last
,runtime
->real
);
157 runtime
->time_per_step
= dt
/(step
- ir
->init_step
+ 1);
159 dt
= (ir
->nsteps
+ ir
->init_step
- step
)*runtime
->time_per_step
;
165 finish
= (time_t) (runtime
->last
+ dt
);
166 gmx_ctime_r(&finish
,timebuf
,STRLEN
);
167 sprintf(buf
,"%s",timebuf
);
168 buf
[strlen(buf
)-1]='\0';
169 fprintf(out
,", will finish %s",buf
);
172 fprintf(out
,", remaining runtime: %5d s ",(int)dt
);
176 fprintf(out
," performance: %.1f ns/day ",
177 ir
->delta_t
/1000*24*60*60/runtime
->time_per_step
);
194 static double set_proctime(gmx_runtime_t
*runtime
)
200 prev
= runtime
->proc
;
201 runtime
->proc
= dclock();
203 diff
= runtime
->proc
- prev
;
207 prev
= runtime
->proc
;
208 runtime
->proc
= clock();
210 diff
= (double)(runtime
->proc
- prev
)/(double)CLOCKS_PER_SEC
;
214 /* The counter has probably looped, ignore this data */
221 void runtime_start(gmx_runtime_t
*runtime
)
223 runtime
->real
= gmx_gettime();
225 set_proctime(runtime
);
226 runtime
->realtime
= 0;
227 runtime
->proctime
= 0;
229 runtime
->time_per_step
= 0;
232 void runtime_end(gmx_runtime_t
*runtime
)
238 runtime
->proctime
+= set_proctime(runtime
);
239 runtime
->realtime
= now
- runtime
->real
;
243 void runtime_upd_proc(gmx_runtime_t
*runtime
)
245 runtime
->proctime
+= set_proctime(runtime
);
248 void print_date_and_time(FILE *fplog
,int nodeid
,const char *title
,
249 const gmx_runtime_t
*runtime
)
252 char timebuf
[STRLEN
];
253 char time_string
[STRLEN
];
260 tmptime
= (time_t) runtime
->real
;
261 gmx_ctime_r(&tmptime
,timebuf
,STRLEN
);
265 tmptime
= (time_t) gmx_gettime();
266 gmx_ctime_r(&tmptime
,timebuf
,STRLEN
);
268 for(i
=0; timebuf
[i
]>=' '; i
++)
270 time_string
[i
]=timebuf
[i
];
274 fprintf(fplog
,"%s on node %d %s\n",title
,nodeid
,time_string
);
278 static void sum_forces(int start
,int end
,rvec f
[],rvec flr
[])
283 pr_rvecs(debug
,0,"fsr",f
+start
,end
-start
);
284 pr_rvecs(debug
,0,"flr",flr
+start
,end
-start
);
286 for(i
=start
; (i
<end
); i
++)
287 rvec_inc(f
[i
],flr
[i
]);
291 * calc_f_el calculates forces due to an electric field.
293 * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
295 * Et[] contains the parameters for the time dependent
296 * part of the field (not yet used).
297 * Ex[] contains the parameters for
298 * the spatial dependent part of the field. You can have cool periodic
299 * fields in principle, but only a constant field is supported
301 * The function should return the energy due to the electric field
302 * (if any) but for now returns 0.
305 * There can be problems with the virial.
306 * Since the field is not self-consistent this is unavoidable.
307 * For neutral molecules the virial is correct within this approximation.
308 * For neutral systems with many charged molecules the error is small.
309 * But for systems with a net charge or a few charged molecules
310 * the error can be significant when the field is high.
311 * Solution: implement a self-consitent electric field into PME.
313 static void calc_f_el(FILE *fp
,int start
,int homenr
,
314 real charge
[],rvec x
[],rvec f
[],
315 t_cosines Ex
[],t_cosines Et
[],double t
)
321 for(m
=0; (m
<DIM
); m
++)
328 Ext
[m
] = cos(Et
[m
].a
[0]*(t
-t0
))*exp(-sqr(t
-t0
)/(2.0*sqr(Et
[m
].a
[2])));
332 Ext
[m
] = cos(Et
[m
].a
[0]*t
);
341 /* Convert the field strength from V/nm to MD-units */
342 Ext
[m
] *= Ex
[m
].a
[0]*FIELDFAC
;
343 for(i
=start
; (i
<start
+homenr
); i
++)
344 f
[i
][m
] += charge
[i
]*Ext
[m
];
353 fprintf(fp
,"%10g %10g %10g %10g #FIELD\n",t
,
354 Ext
[XX
]/FIELDFAC
,Ext
[YY
]/FIELDFAC
,Ext
[ZZ
]/FIELDFAC
);
358 static void calc_virial(FILE *fplog
,int start
,int homenr
,rvec x
[],rvec f
[],
359 tensor vir_part
,t_graph
*graph
,matrix box
,
360 t_nrnb
*nrnb
,const t_forcerec
*fr
,int ePBC
)
365 /* The short-range virial from surrounding boxes */
367 calc_vir(fplog
,SHIFTS
,fr
->shift_vec
,fr
->fshift
,vir_part
,ePBC
==epbcSCREW
,box
);
368 inc_nrnb(nrnb
,eNR_VIRIAL
,SHIFTS
);
370 /* Calculate partial virial, for local atoms only, based on short range.
371 * Total virial is computed in global_stat, called from do_md
373 f_calc_vir(fplog
,start
,start
+homenr
,x
,f
,vir_part
,graph
,box
);
374 inc_nrnb(nrnb
,eNR_VIRIAL
,homenr
);
376 /* Add position restraint contribution */
377 for(i
=0; i
<DIM
; i
++) {
378 vir_part
[i
][i
] += fr
->vir_diag_posres
[i
];
381 /* Add wall contribution */
382 for(i
=0; i
<DIM
; i
++) {
383 vir_part
[i
][ZZ
] += fr
->vir_wall_z
[i
];
387 pr_rvecs(debug
,0,"vir_part",vir_part
,DIM
);
390 static void print_large_forces(FILE *fp
,t_mdatoms
*md
,t_commrec
*cr
,
391 gmx_large_int_t step
,real pforce
,rvec
*x
,rvec
*f
)
395 char buf
[STEPSTRSIZE
];
398 for(i
=md
->start
; i
<md
->start
+md
->homenr
; i
++) {
400 /* We also catch NAN, if the compiler does not optimize this away. */
401 if (fn2
>= pf2
|| fn2
!= fn2
) {
402 fprintf(fp
,"step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
403 gmx_step_str(step
,buf
),
404 ddglatnr(cr
->dd
,i
),x
[i
][XX
],x
[i
][YY
],x
[i
][ZZ
],sqrt(fn2
));
409 void do_force(FILE *fplog
,t_commrec
*cr
,
410 t_inputrec
*inputrec
,
411 gmx_large_int_t step
,t_nrnb
*nrnb
,gmx_wallcycle_t wcycle
,
414 gmx_groups_t
*groups
,
415 matrix box
,rvec x
[],history_t
*hist
,
419 gmx_enerdata_t
*enerd
,t_fcdata
*fcd
,
420 real lambda
,t_graph
*graph
,
421 t_forcerec
*fr
,gmx_vsite_t
*vsite
,rvec mu_tot
,
422 double t
,FILE *field
,gmx_edsam_t ed
,
429 gmx_bool bSepDVDL
,bStateChanged
,bNS
,bFillGrid
,bCalcCGCM
,bBS
;
430 gmx_bool bDoLongRange
,bDoForces
,bSepLRF
;
434 float cycles_ppdpme
,cycles_pme
,cycles_seppme
,cycles_force
;
436 start
= mdatoms
->start
;
437 homenr
= mdatoms
->homenr
;
439 bSepDVDL
= (fr
->bSepDVDL
&& do_per_step(step
,inputrec
->nstlog
));
441 clear_mat(vir_force
);
445 pd_cg_range(cr
,&cg0
,&cg1
);
450 if (DOMAINDECOMP(cr
))
452 cg1
= cr
->dd
->ncg_tot
;
464 bStateChanged
= (flags
& GMX_FORCE_STATECHANGED
);
465 bNS
= (flags
& GMX_FORCE_NS
) && (fr
->bAllvsAll
==FALSE
);
466 bFillGrid
= (bNS
&& bStateChanged
);
467 bCalcCGCM
= (bFillGrid
&& !DOMAINDECOMP(cr
));
468 bDoLongRange
= (fr
->bTwinRange
&& bNS
&& (flags
& GMX_FORCE_DOLR
));
469 bDoForces
= (flags
& GMX_FORCE_FORCES
);
470 bSepLRF
= (bDoLongRange
&& bDoForces
&& (flags
& GMX_FORCE_SEPLRF
));
474 update_forcerec(fplog
,fr
,box
);
476 /* Calculate total (local) dipole moment in a temporary common array.
477 * This makes it possible to sum them over nodes faster.
479 calc_mu(start
,homenr
,
480 x
,mdatoms
->chargeA
,mdatoms
->chargeB
,mdatoms
->nChargePerturbed
,
484 if (fr
->ePBC
!= epbcNONE
) {
485 /* Compute shift vectors every step,
486 * because of pressure coupling or box deformation!
488 if ((flags
& GMX_FORCE_DYNAMICBOX
) && bStateChanged
)
489 calc_shifts(box
,fr
->shift_vec
);
492 put_charge_groups_in_box(fplog
,cg0
,cg1
,fr
->ePBC
,box
,
493 &(top
->cgs
),x
,fr
->cg_cm
);
494 inc_nrnb(nrnb
,eNR_CGCM
,homenr
);
495 inc_nrnb(nrnb
,eNR_RESETX
,cg1
-cg0
);
497 else if (EI_ENERGY_MINIMIZATION(inputrec
->eI
) && graph
) {
498 unshift_self(graph
,box
,x
);
501 else if (bCalcCGCM
) {
502 calc_cgcm(fplog
,cg0
,cg1
,&(top
->cgs
),x
,fr
->cg_cm
);
503 inc_nrnb(nrnb
,eNR_CGCM
,homenr
);
508 move_cgcm(fplog
,cr
,fr
->cg_cm
);
511 pr_rvecs(debug
,0,"cgcm",fr
->cg_cm
,top
->cgs
.nr
);
515 if (!(cr
->duty
& DUTY_PME
)) {
516 /* Send particle coordinates to the pme nodes.
517 * Since this is only implemented for domain decomposition
518 * and domain decomposition does not use the graph,
519 * we do not need to worry about shifting.
522 wallcycle_start(wcycle
,ewcPP_PMESENDX
);
523 GMX_MPE_LOG(ev_send_coordinates_start
);
525 bBS
= (inputrec
->nwall
== 2);
528 svmul(inputrec
->wall_ewald_zfac
,boxs
[ZZ
],boxs
[ZZ
]);
531 gmx_pme_send_x(cr
,bBS
? boxs
: box
,x
,
532 mdatoms
->nChargePerturbed
,lambda
,
533 ( flags
& GMX_FORCE_VIRIAL
),step
);
535 GMX_MPE_LOG(ev_send_coordinates_finish
);
536 wallcycle_stop(wcycle
,ewcPP_PMESENDX
);
540 /* Communicate coordinates and sum dipole if necessary */
543 wallcycle_start(wcycle
,ewcMOVEX
);
544 if (DOMAINDECOMP(cr
))
546 dd_move_x(cr
->dd
,box
,x
);
550 move_x(fplog
,cr
,GMX_LEFT
,GMX_RIGHT
,x
,nrnb
);
552 /* When we don't need the total dipole we sum it in global_stat */
553 if (bStateChanged
&& NEED_MUTOT(*inputrec
))
555 gmx_sumd(2*DIM
,mu
,cr
);
557 wallcycle_stop(wcycle
,ewcMOVEX
);
565 fr
->mu_tot
[i
][j
] = mu
[i
*DIM
+ j
];
569 if (fr
->efep
== efepNO
)
571 copy_rvec(fr
->mu_tot
[0],mu_tot
);
578 (1.0 - lambda
)*fr
->mu_tot
[0][j
] + lambda
*fr
->mu_tot
[1][j
];
583 reset_enerdata(&(inputrec
->opts
),fr
,bNS
,enerd
,MASTER(cr
));
584 clear_rvecs(SHIFTS
,fr
->fshift
);
588 wallcycle_start(wcycle
,ewcNS
);
590 if (graph
&& bStateChanged
)
592 /* Calculate intramolecular shift vectors to make molecules whole */
593 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
596 /* Reset long range forces if necessary */
599 /* Reset the (long-range) forces if necessary */
600 clear_rvecs(fr
->natoms_force_constr
,bSepLRF
? fr
->f_twin
: f
);
603 /* Do the actual neighbour searching and if twin range electrostatics
604 * also do the calculation of long range forces and energies.
608 groups
,&(inputrec
->opts
),top
,mdatoms
,
609 cr
,nrnb
,lambda
,&dvdl
,&enerd
->grpp
,bFillGrid
,
610 bDoLongRange
,bDoForces
,bSepLRF
? fr
->f_twin
: f
);
613 fprintf(fplog
,sepdvdlformat
,"LR non-bonded",0.0,dvdl
);
615 enerd
->dvdl_lin
+= dvdl
;
617 wallcycle_stop(wcycle
,ewcNS
);
620 if (inputrec
->implicit_solvent
&& bNS
)
622 make_gb_nblist(cr
,inputrec
->gb_algorithm
,inputrec
->rlist
,
623 x
,box
,fr
,&top
->idef
,graph
,fr
->born
);
626 if (DOMAINDECOMP(cr
))
628 if (!(cr
->duty
& DUTY_PME
))
630 wallcycle_start(wcycle
,ewcPPDURINGPME
);
631 dd_force_flop_start(cr
->dd
,nrnb
);
637 /* Enforced rotation has its own cycle counter that starts after the collective
638 * coordinates have been communicated. It is added to ddCyclF */
639 do_rotation(cr
,inputrec
,box
,x
,t
,step
,wcycle
,bNS
);
642 /* Start the force cycle counter.
643 * This counter is stopped in do_forcelow_level.
644 * No parallel communication should occur while this counter is running,
645 * since that will interfere with the dynamic load balancing.
647 wallcycle_start(wcycle
,ewcFORCE
);
648 GMX_MPE_LOG(ev_forcecycles_start
);
652 /* Reset forces for which the virial is calculated separately:
653 * PME/Ewald forces if necessary */
656 if (flags
& GMX_FORCE_VIRIAL
)
658 fr
->f_novirsum
= fr
->f_novirsum_alloc
;
659 GMX_BARRIER(cr
->mpi_comm_mygroup
);
662 clear_rvecs(fr
->f_novirsum_n
,fr
->f_novirsum
);
666 clear_rvecs(homenr
,fr
->f_novirsum
+start
);
668 GMX_BARRIER(cr
->mpi_comm_mygroup
);
672 /* We are not calculating the pressure so we do not need
673 * a separate array for forces that do not contribute
682 /* Add the long range forces to the short range forces */
683 for(i
=0; i
<fr
->natoms_force_constr
; i
++)
685 copy_rvec(fr
->f_twin
[i
],f
[i
]);
688 else if (!(fr
->bTwinRange
&& bNS
))
690 /* Clear the short-range forces */
691 clear_rvecs(fr
->natoms_force_constr
,f
);
694 clear_rvec(fr
->vir_diag_posres
);
696 GMX_BARRIER(cr
->mpi_comm_mygroup
);
698 if (inputrec
->ePull
== epullCONSTRAINT
)
700 clear_pull_forces(inputrec
->pull
);
703 /* update QMMMrec, if necessary */
706 update_QMMMrec(cr
,fr
,x
,mdatoms
,box
,top
);
709 if ((flags
& GMX_FORCE_BONDED
) && top
->idef
.il
[F_POSRES
].nr
> 0)
711 /* Position restraints always require full pbc */
712 set_pbc(&pbc
,inputrec
->ePBC
,box
);
713 v
= posres(top
->idef
.il
[F_POSRES
].nr
,top
->idef
.il
[F_POSRES
].iatoms
,
714 top
->idef
.iparams_posres
,
715 (const rvec
*)x
,fr
->f_novirsum
,fr
->vir_diag_posres
,
716 inputrec
->ePBC
==epbcNONE
? NULL
: &pbc
,lambda
,&dvdl
,
717 fr
->rc_scaling
,fr
->ePBC
,fr
->posres_com
,fr
->posres_comB
);
720 fprintf(fplog
,sepdvdlformat
,
721 interaction_function
[F_POSRES
].longname
,v
,dvdl
);
723 enerd
->term
[F_POSRES
] += v
;
724 /* This linear lambda dependence assumption is only correct
725 * when only k depends on lambda,
726 * not when the reference position depends on lambda.
727 * grompp checks for this.
729 enerd
->dvdl_lin
+= dvdl
;
730 inc_nrnb(nrnb
,eNR_POSRES
,top
->idef
.il
[F_POSRES
].nr
/2);
733 /* Compute the bonded and non-bonded energies and optionally forces */
734 do_force_lowlevel(fplog
,step
,fr
,inputrec
,&(top
->idef
),
735 cr
,nrnb
,wcycle
,mdatoms
,&(inputrec
->opts
),
736 x
,hist
,f
,enerd
,fcd
,mtop
,top
,fr
->born
,
737 &(top
->atomtypes
),bBornRadii
,box
,
738 lambda
,graph
,&(top
->excls
),fr
->mu_tot
,
741 cycles_force
= wallcycle_stop(wcycle
,ewcFORCE
);
742 GMX_BARRIER(cr
->mpi_comm_mygroup
);
746 do_flood(fplog
,cr
,x
,f
,ed
,box
,step
);
749 if (DOMAINDECOMP(cr
))
751 dd_force_flop_stop(cr
->dd
,nrnb
);
754 dd_cycles_add(cr
->dd
,cycles_force
-cycles_pme
,ddCyclF
);
760 if (IR_ELEC_FIELD(*inputrec
))
762 /* Compute forces due to electric field */
763 calc_f_el(MASTER(cr
) ? field
: NULL
,
764 start
,homenr
,mdatoms
->chargeA
,x
,fr
->f_novirsum
,
765 inputrec
->ex
,inputrec
->et
,t
);
768 /* Communicate the forces */
771 wallcycle_start(wcycle
,ewcMOVEF
);
772 if (DOMAINDECOMP(cr
))
774 dd_move_f(cr
->dd
,f
,fr
->fshift
);
775 /* Do we need to communicate the separate force array
776 * for terms that do not contribute to the single sum virial?
777 * Position restraints and electric fields do not introduce
778 * inter-cg forces, only full electrostatics methods do.
779 * When we do not calculate the virial, fr->f_novirsum = f,
780 * so we have already communicated these forces.
782 if (EEL_FULL(fr
->eeltype
) && cr
->dd
->n_intercg_excl
&&
783 (flags
& GMX_FORCE_VIRIAL
))
785 dd_move_f(cr
->dd
,fr
->f_novirsum
,NULL
);
789 /* We should not update the shift forces here,
790 * since f_twin is already included in f.
792 dd_move_f(cr
->dd
,fr
->f_twin
,NULL
);
797 pd_move_f(cr
,f
,nrnb
);
800 pd_move_f(cr
,fr
->f_twin
,nrnb
);
803 wallcycle_stop(wcycle
,ewcMOVEF
);
806 /* If we have NoVirSum forces, but we do not calculate the virial,
807 * we sum fr->f_novirum=f later.
809 if (vsite
&& !(fr
->bF_NoVirSum
&& !(flags
& GMX_FORCE_VIRIAL
)))
811 wallcycle_start(wcycle
,ewcVSITESPREAD
);
812 spread_vsite_f(fplog
,vsite
,x
,f
,fr
->fshift
,nrnb
,
813 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
814 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
818 wallcycle_start(wcycle
,ewcVSITESPREAD
);
819 spread_vsite_f(fplog
,vsite
,x
,fr
->f_twin
,NULL
,
821 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
822 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
826 if (flags
& GMX_FORCE_VIRIAL
)
828 /* Calculation of the virial must be done after vsites! */
829 calc_virial(fplog
,mdatoms
->start
,mdatoms
->homenr
,x
,f
,
830 vir_force
,graph
,box
,nrnb
,fr
,inputrec
->ePBC
);
834 if (inputrec
->ePull
== epullUMBRELLA
|| inputrec
->ePull
== epullCONST_F
)
836 /* Calculate the center of mass forces, this requires communication,
837 * which is why pull_potential is called close to other communication.
838 * The virial contribution is calculated directly,
839 * which is why we call pull_potential after calc_virial.
841 set_pbc(&pbc
,inputrec
->ePBC
,box
);
843 enerd
->term
[F_COM_PULL
] =
844 pull_potential(inputrec
->ePull
,inputrec
->pull
,mdatoms
,&pbc
,
845 cr
,t
,lambda
,x
,f
,vir_force
,&dvdl
);
848 fprintf(fplog
,sepdvdlformat
,"Com pull",enerd
->term
[F_COM_PULL
],dvdl
);
850 enerd
->dvdl_lin
+= dvdl
;
853 enerd
->term
[F_COM_PULL
] = 0.0;
855 /* Add the forces from enforced rotation potentials (if any) */
857 enerd
->term
[F_COM_PULL
] += add_rot_forces(inputrec
->rot
, f
, cr
,step
,t
);
860 if (PAR(cr
) && !(cr
->duty
& DUTY_PME
))
862 cycles_ppdpme
= wallcycle_stop(wcycle
,ewcPPDURINGPME
);
863 dd_cycles_add(cr
->dd
,cycles_ppdpme
,ddCyclPPduringPME
);
865 /* In case of node-splitting, the PP nodes receive the long-range
866 * forces, virial and energy from the PME nodes here.
868 wallcycle_start(wcycle
,ewcPP_PMEWAITRECVF
);
870 gmx_pme_receive_f(cr
,fr
->f_novirsum
,fr
->vir_el_recip
,&e
,&dvdl
,
874 fprintf(fplog
,sepdvdlformat
,"PME mesh",e
,dvdl
);
876 enerd
->term
[F_COUL_RECIP
] += e
;
877 enerd
->dvdl_lin
+= dvdl
;
880 dd_cycles_add(cr
->dd
,cycles_seppme
,ddCyclPME
);
882 wallcycle_stop(wcycle
,ewcPP_PMEWAITRECVF
);
885 if (bDoForces
&& fr
->bF_NoVirSum
)
889 /* Spread the mesh force on virtual sites to the other particles...
890 * This is parallellized. MPI communication is performed
891 * if the constructing atoms aren't local.
893 wallcycle_start(wcycle
,ewcVSITESPREAD
);
894 spread_vsite_f(fplog
,vsite
,x
,fr
->f_novirsum
,NULL
,nrnb
,
895 &top
->idef
,fr
->ePBC
,fr
->bMolPBC
,graph
,box
,cr
);
896 wallcycle_stop(wcycle
,ewcVSITESPREAD
);
898 if (flags
& GMX_FORCE_VIRIAL
)
900 /* Now add the forces, this is local */
903 sum_forces(0,fr
->f_novirsum_n
,f
,fr
->f_novirsum
);
907 sum_forces(start
,start
+homenr
,f
,fr
->f_novirsum
);
909 if (EEL_FULL(fr
->eeltype
))
911 /* Add the mesh contribution to the virial */
912 m_add(vir_force
,fr
->vir_el_recip
,vir_force
);
916 pr_rvecs(debug
,0,"vir_force",vir_force
,DIM
);
921 /* Sum the potential energy terms from group contributions */
922 sum_epot(&(inputrec
->opts
),enerd
);
924 if (fr
->print_force
>= 0 && bDoForces
)
926 print_large_forces(stderr
,mdatoms
,cr
,step
,fr
->print_force
,x
,f
);
930 void do_constrain_first(FILE *fplog
,gmx_constr_t constr
,
931 t_inputrec
*ir
,t_mdatoms
*md
,
932 t_state
*state
,rvec
*f
,
933 t_graph
*graph
,t_commrec
*cr
,t_nrnb
*nrnb
,
934 t_forcerec
*fr
, gmx_localtop_t
*top
, tensor shake_vir
)
937 gmx_large_int_t step
;
938 double mass
,tmass
,vcm
[4];
943 snew(savex
,state
->natoms
);
946 end
= md
->homenr
+ start
;
949 fprintf(debug
,"vcm: start=%d, homenr=%d, end=%d\n",
950 start
,md
->homenr
,end
);
951 /* Do a first constrain to reset particles... */
952 step
= ir
->init_step
;
955 char buf
[STEPSTRSIZE
];
956 fprintf(fplog
,"\nConstraining the starting coordinates (step %s)\n",
957 gmx_step_str(step
,buf
));
961 /* constrain the current position */
962 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
963 ir
,NULL
,cr
,step
,0,md
,
964 state
->x
,state
->x
,NULL
,
965 state
->box
,state
->lambda
,&dvdlambda
,
966 NULL
,NULL
,nrnb
,econqCoord
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
969 /* constrain the inital velocity, and save it */
970 /* also may be useful if we need the ekin from the halfstep for velocity verlet */
971 /* might not yet treat veta correctly */
972 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
973 ir
,NULL
,cr
,step
,0,md
,
974 state
->x
,state
->v
,state
->v
,
975 state
->box
,state
->lambda
,&dvdlambda
,
976 NULL
,NULL
,nrnb
,econqVeloc
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
978 /* constrain the inital velocities at t-dt/2 */
979 if (EI_STATE_VELOCITY(ir
->eI
) && ir
->eI
!=eiVV
)
981 for(i
=start
; (i
<end
); i
++)
983 for(m
=0; (m
<DIM
); m
++)
985 /* Reverse the velocity */
986 state
->v
[i
][m
] = -state
->v
[i
][m
];
987 /* Store the position at t-dt in buf */
988 savex
[i
][m
] = state
->x
[i
][m
] + dt
*state
->v
[i
][m
];
991 /* Shake the positions at t=-dt with the positions at t=0
992 * as reference coordinates.
996 char buf
[STEPSTRSIZE
];
997 fprintf(fplog
,"\nConstraining the coordinates at t0-dt (step %s)\n",
998 gmx_step_str(step
,buf
));
1001 constrain(NULL
,TRUE
,FALSE
,constr
,&(top
->idef
),
1002 ir
,NULL
,cr
,step
,-1,md
,
1003 state
->x
,savex
,NULL
,
1004 state
->box
,state
->lambda
,&dvdlambda
,
1005 state
->v
,NULL
,nrnb
,econqCoord
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
1007 for(i
=start
; i
<end
; i
++) {
1008 for(m
=0; m
<DIM
; m
++) {
1009 /* Re-reverse the velocities */
1010 state
->v
[i
][m
] = -state
->v
[i
][m
];
1015 for(m
=0; (m
<4); m
++)
1017 for(i
=start
; i
<end
; i
++) {
1018 mass
= md
->massT
[i
];
1019 for(m
=0; m
<DIM
; m
++) {
1020 vcm
[m
] += state
->v
[i
][m
]*mass
;
1025 if (ir
->nstcomm
!= 0 || debug
) {
1026 /* Compute the global sum of vcm */
1028 fprintf(debug
,"vcm: %8.3f %8.3f %8.3f,"
1029 " total mass = %12.5e\n",vcm
[XX
],vcm
[YY
],vcm
[ZZ
],vcm
[3]);
1033 for(m
=0; (m
<DIM
); m
++)
1036 fprintf(debug
,"vcm: %8.3f %8.3f %8.3f,"
1037 " total mass = %12.5e\n",vcm
[XX
],vcm
[YY
],vcm
[ZZ
],tmass
);
1038 if (ir
->nstcomm
!= 0) {
1039 /* Now we have the velocity of center of mass, let's remove it */
1040 for(i
=start
; (i
<end
); i
++) {
1041 for(m
=0; (m
<DIM
); m
++)
1042 state
->v
[i
][m
] -= vcm
[m
];
1050 void calc_enervirdiff(FILE *fplog
,int eDispCorr
,t_forcerec
*fr
)
1052 double eners
[2],virs
[2],enersum
,virsum
,y0
,f
,g
,h
;
1053 double r0
,r1
,r
,rc3
,rc9
,ea
,eb
,ec
,pa
,pb
,pc
,pd
;
1054 double invscale
,invscale2
,invscale3
;
1055 int ri0
,ri1
,ri
,i
,offstart
,offset
;
1058 fr
->enershiftsix
= 0;
1059 fr
->enershifttwelve
= 0;
1060 fr
->enerdiffsix
= 0;
1061 fr
->enerdifftwelve
= 0;
1063 fr
->virdifftwelve
= 0;
1065 if (eDispCorr
!= edispcNO
) {
1066 for(i
=0; i
<2; i
++) {
1070 if ((fr
->vdwtype
== evdwSWITCH
) || (fr
->vdwtype
== evdwSHIFT
)) {
1071 if (fr
->rvdw_switch
== 0)
1073 "With dispersion correction rvdw-switch can not be zero "
1074 "for vdw-type = %s",evdw_names
[fr
->vdwtype
]);
1076 scale
= fr
->nblists
[0].tab
.scale
;
1077 vdwtab
= fr
->nblists
[0].vdwtab
;
1079 /* Round the cut-offs to exact table values for precision */
1080 ri0
= floor(fr
->rvdw_switch
*scale
);
1081 ri1
= ceil(fr
->rvdw
*scale
);
1087 if (fr
->vdwtype
== evdwSHIFT
) {
1088 /* Determine the constant energy shift below rvdw_switch */
1089 fr
->enershiftsix
= (real
)(-1.0/(rc3
*rc3
)) - vdwtab
[8*ri0
];
1090 fr
->enershifttwelve
= (real
)( 1.0/(rc9
*rc3
)) - vdwtab
[8*ri0
+ 4];
1092 /* Add the constant part from 0 to rvdw_switch.
1093 * This integration from 0 to rvdw_switch overcounts the number
1094 * of interactions by 1, as it also counts the self interaction.
1095 * We will correct for this later.
1097 eners
[0] += 4.0*M_PI
*fr
->enershiftsix
*rc3
/3.0;
1098 eners
[1] += 4.0*M_PI
*fr
->enershifttwelve
*rc3
/3.0;
1100 invscale
= 1.0/(scale
);
1101 invscale2
= invscale
*invscale
;
1102 invscale3
= invscale
*invscale2
;
1104 /* following summation derived from cubic spline definition,
1105 Numerical Recipies in C, second edition, p. 113-116. Exact
1106 for the cubic spline. We first calculate the negative of
1107 the energy from rvdw to rvdw_switch, assuming that g(r)=1,
1108 and then add the more standard, abrupt cutoff correction to
1109 that result, yielding the long-range correction for a
1110 switched function. We perform both the pressure and energy
1111 loops at the same time for simplicity, as the computational
1115 enersum
= 0.0; virsum
= 0.0;
1120 for (ri
=ri0
; ri
<ri1
; ri
++) {
1123 eb
= 2.0*invscale2
*r
;
1127 pb
= 3.0*invscale2
*r
;
1128 pc
= 3.0*invscale
*r
*r
;
1131 /* this "8" is from the packing in the vdwtab array - perhaps
1132 should be #define'ed? */
1133 offset
= 8*ri
+ offstart
;
1134 y0
= vdwtab
[offset
];
1135 f
= vdwtab
[offset
+1];
1136 g
= vdwtab
[offset
+2];
1137 h
= vdwtab
[offset
+3];
1139 enersum
+= y0
*(ea
/3 + eb
/2 + ec
) + f
*(ea
/4 + eb
/3 + ec
/2)+
1140 g
*(ea
/5 + eb
/4 + ec
/3) + h
*(ea
/6 + eb
/5 + ec
/4);
1141 virsum
+= f
*(pa
/4 + pb
/3 + pc
/2 + pd
) +
1142 2*g
*(pa
/5 + pb
/4 + pc
/3 + pd
/2) + 3*h
*(pa
/6 + pb
/5 + pc
/4 + pd
/3);
1145 enersum
*= 4.0*M_PI
;
1147 eners
[i
] -= enersum
;
1151 /* now add the correction for rvdw_switch to infinity */
1152 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
1153 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
1154 virs
[0] += 8.0*M_PI
/rc3
;
1155 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
1157 else if ((fr
->vdwtype
== evdwCUT
) || (fr
->vdwtype
== evdwUSER
)) {
1158 if (fr
->vdwtype
== evdwUSER
&& fplog
)
1160 "WARNING: using dispersion correction with user tables\n");
1161 rc3
= fr
->rvdw
*fr
->rvdw
*fr
->rvdw
;
1163 eners
[0] += -4.0*M_PI
/(3.0*rc3
);
1164 eners
[1] += 4.0*M_PI
/(9.0*rc9
);
1165 virs
[0] += 8.0*M_PI
/rc3
;
1166 virs
[1] += -16.0*M_PI
/(3.0*rc9
);
1169 "Dispersion correction is not implemented for vdw-type = %s",
1170 evdw_names
[fr
->vdwtype
]);
1172 fr
->enerdiffsix
= eners
[0];
1173 fr
->enerdifftwelve
= eners
[1];
1174 /* The 0.5 is due to the Gromacs definition of the virial */
1175 fr
->virdiffsix
= 0.5*virs
[0];
1176 fr
->virdifftwelve
= 0.5*virs
[1];
1180 void calc_dispcorr(FILE *fplog
,t_inputrec
*ir
,t_forcerec
*fr
,
1181 gmx_large_int_t step
,int natoms
,
1182 matrix box
,real lambda
,tensor pres
,tensor virial
,
1183 real
*prescorr
, real
*enercorr
, real
*dvdlcorr
)
1185 gmx_bool bCorrAll
,bCorrPres
;
1186 real dvdlambda
,invvol
,dens
,ninter
,avcsix
,avctwelve
,enerdiff
,svir
=0,spres
=0;
1196 if (ir
->eDispCorr
!= edispcNO
) {
1197 bCorrAll
= (ir
->eDispCorr
== edispcAllEner
||
1198 ir
->eDispCorr
== edispcAllEnerPres
);
1199 bCorrPres
= (ir
->eDispCorr
== edispcEnerPres
||
1200 ir
->eDispCorr
== edispcAllEnerPres
);
1202 invvol
= 1/det(box
);
1205 /* Only correct for the interactions with the inserted molecule */
1206 dens
= (natoms
- fr
->n_tpi
)*invvol
;
1211 dens
= natoms
*invvol
;
1212 ninter
= 0.5*natoms
;
1215 if (ir
->efep
== efepNO
)
1217 avcsix
= fr
->avcsix
[0];
1218 avctwelve
= fr
->avctwelve
[0];
1222 avcsix
= (1 - lambda
)*fr
->avcsix
[0] + lambda
*fr
->avcsix
[1];
1223 avctwelve
= (1 - lambda
)*fr
->avctwelve
[0] + lambda
*fr
->avctwelve
[1];
1226 enerdiff
= ninter
*(dens
*fr
->enerdiffsix
- fr
->enershiftsix
);
1227 *enercorr
+= avcsix
*enerdiff
;
1229 if (ir
->efep
!= efepNO
)
1231 dvdlambda
+= (fr
->avcsix
[1] - fr
->avcsix
[0])*enerdiff
;
1235 enerdiff
= ninter
*(dens
*fr
->enerdifftwelve
- fr
->enershifttwelve
);
1236 *enercorr
+= avctwelve
*enerdiff
;
1237 if (fr
->efep
!= efepNO
)
1239 dvdlambda
+= (fr
->avctwelve
[1] - fr
->avctwelve
[0])*enerdiff
;
1245 svir
= ninter
*dens
*avcsix
*fr
->virdiffsix
/3.0;
1246 if (ir
->eDispCorr
== edispcAllEnerPres
)
1248 svir
+= ninter
*dens
*avctwelve
*fr
->virdifftwelve
/3.0;
1250 /* The factor 2 is because of the Gromacs virial definition */
1251 spres
= -2.0*invvol
*svir
*PRESFAC
;
1253 for(m
=0; m
<DIM
; m
++) {
1254 virial
[m
][m
] += svir
;
1255 pres
[m
][m
] += spres
;
1260 /* Can't currently control when it prints, for now, just print when degugging */
1264 fprintf(debug
,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1270 "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
1271 *enercorr
,spres
,svir
);
1275 fprintf(debug
,"Long Range LJ corr.: Epot %10g\n",*enercorr
);
1279 if (fr
->bSepDVDL
&& do_per_step(step
,ir
->nstlog
))
1281 fprintf(fplog
,sepdvdlformat
,"Dispersion correction",
1282 *enercorr
,dvdlambda
);
1284 if (fr
->efep
!= efepNO
)
1286 *dvdlcorr
+= dvdlambda
;
1291 void do_pbc_first(FILE *fplog
,matrix box
,t_forcerec
*fr
,
1292 t_graph
*graph
,rvec x
[])
1295 fprintf(fplog
,"Removing pbc first time\n");
1296 calc_shifts(box
,fr
->shift_vec
);
1298 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
1300 p_graph(debug
,"do_pbc_first 1",graph
);
1301 shift_self(graph
,box
,x
);
1302 /* By doing an extra mk_mshift the molecules that are broken
1303 * because they were e.g. imported from another software
1304 * will be made whole again. Such are the healing powers
1307 mk_mshift(fplog
,graph
,fr
->ePBC
,box
,x
);
1309 p_graph(debug
,"do_pbc_first 2",graph
);
1312 fprintf(fplog
,"Done rmpbc\n");
1315 static void low_do_pbc_mtop(FILE *fplog
,int ePBC
,matrix box
,
1316 gmx_mtop_t
*mtop
,rvec x
[],
1321 gmx_molblock_t
*molb
;
1323 if (bFirst
&& fplog
)
1324 fprintf(fplog
,"Removing pbc first time\n");
1328 for(mb
=0; mb
<mtop
->nmolblock
; mb
++) {
1329 molb
= &mtop
->molblock
[mb
];
1330 if (molb
->natoms_mol
== 1 ||
1331 (!bFirst
&& mtop
->moltype
[molb
->type
].cgs
.nr
== 1)) {
1332 /* Just one atom or charge group in the molecule, no PBC required */
1333 as
+= molb
->nmol
*molb
->natoms_mol
;
1335 /* Pass NULL iso fplog to avoid graph prints for each molecule type */
1336 mk_graph_ilist(NULL
,mtop
->moltype
[molb
->type
].ilist
,
1337 0,molb
->natoms_mol
,FALSE
,FALSE
,graph
);
1339 for(mol
=0; mol
<molb
->nmol
; mol
++) {
1340 mk_mshift(fplog
,graph
,ePBC
,box
,x
+as
);
1342 shift_self(graph
,box
,x
+as
);
1343 /* The molecule is whole now.
1344 * We don't need the second mk_mshift call as in do_pbc_first,
1345 * since we no longer need this graph.
1348 as
+= molb
->natoms_mol
;
1356 void do_pbc_first_mtop(FILE *fplog
,int ePBC
,matrix box
,
1357 gmx_mtop_t
*mtop
,rvec x
[])
1359 low_do_pbc_mtop(fplog
,ePBC
,box
,mtop
,x
,TRUE
);
1362 void do_pbc_mtop(FILE *fplog
,int ePBC
,matrix box
,
1363 gmx_mtop_t
*mtop
,rvec x
[])
1365 low_do_pbc_mtop(fplog
,ePBC
,box
,mtop
,x
,FALSE
);
1368 void finish_run(FILE *fplog
,t_commrec
*cr
,const char *confout
,
1369 t_inputrec
*inputrec
,
1370 t_nrnb nrnb
[],gmx_wallcycle_t wcycle
,
1371 gmx_runtime_t
*runtime
,
1372 gmx_bool bWriteStat
)
1375 t_nrnb
*nrnb_tot
=NULL
;
1378 double cycles
[ewcNR
];
1380 wallcycle_sum(cr
,wcycle
,cycles
);
1382 if (cr
->nnodes
> 1) {
1386 MPI_Reduce(nrnb
->n
,nrnb_tot
->n
,eNRNB
,MPI_DOUBLE
,MPI_SUM
,
1387 MASTERRANK(cr
),cr
->mpi_comm_mysim
);
1393 if (SIMMASTER(cr
)) {
1394 print_flop(fplog
,nrnb_tot
,&nbfs
,&mflop
);
1395 if (cr
->nnodes
> 1) {
1400 if ((cr
->duty
& DUTY_PP
) && DOMAINDECOMP(cr
)) {
1401 print_dd_statistics(cr
,inputrec
,fplog
);
1413 snew(nrnb_all
,cr
->nnodes
);
1414 nrnb_all
[0] = *nrnb
;
1415 for(s
=1; s
<cr
->nnodes
; s
++)
1417 MPI_Recv(nrnb_all
[s
].n
,eNRNB
,MPI_DOUBLE
,s
,0,
1418 cr
->mpi_comm_mysim
,&stat
);
1420 pr_load(fplog
,cr
,nrnb_all
);
1425 MPI_Send(nrnb
->n
,eNRNB
,MPI_DOUBLE
,MASTERRANK(cr
),0,
1426 cr
->mpi_comm_mysim
);
1431 if (SIMMASTER(cr
)) {
1432 wallcycle_print(fplog
,cr
->nnodes
,cr
->npmenodes
,runtime
->realtime
,
1435 if (EI_DYNAMICS(inputrec
->eI
)) {
1436 delta_t
= inputrec
->delta_t
;
1442 print_perf(fplog
,runtime
->proctime
,runtime
->realtime
,
1443 cr
->nnodes
-cr
->npmenodes
,
1444 runtime
->nsteps_done
,delta_t
,nbfs
,mflop
);
1447 print_perf(stderr
,runtime
->proctime
,runtime
->realtime
,
1448 cr
->nnodes
-cr
->npmenodes
,
1449 runtime
->nsteps_done
,delta_t
,nbfs
,mflop
);
1453 runtime=inputrec->nsteps*inputrec->delta_t;
1455 if (cr->nnodes == 1)
1456 fprintf(stderr,"\n\n");
1457 print_perf(stderr,nodetime,realtime,runtime,&ntot,
1458 cr->nnodes-cr->npmenodes,FALSE);
1460 wallcycle_print(fplog,cr->nnodes,cr->npmenodes,realtime,wcycle,cycles);
1461 print_perf(fplog,nodetime,realtime,runtime,&ntot,cr->nnodes-cr->npmenodes,
1464 pr_load(fplog,cr,nrnb_all);
1471 void init_md(FILE *fplog
,
1472 t_commrec
*cr
,t_inputrec
*ir
,const output_env_t oenv
,
1473 double *t
,double *t0
,
1474 real
*lambda
,double *lam0
,
1475 t_nrnb
*nrnb
,gmx_mtop_t
*mtop
,
1477 int nfile
,const t_filenm fnm
[],
1478 gmx_mdoutf_t
**outf
,t_mdebin
**mdebin
,
1479 tensor force_vir
,tensor shake_vir
,rvec mu_tot
,
1480 gmx_bool
*bSimAnn
,t_vcm
**vcm
, t_state
*state
, unsigned long Flags
)
1485 /* Initial values */
1486 *t
= *t0
= ir
->init_t
;
1487 if (ir
->efep
!= efepNO
)
1489 *lam0
= ir
->init_lambda
;
1490 *lambda
= *lam0
+ ir
->init_step
*ir
->delta_lambda
;
1494 *lambda
= *lam0
= 0.0;
1498 for(i
=0;i
<ir
->opts
.ngtc
;i
++)
1500 /* set bSimAnn if any group is being annealed */
1501 if(ir
->opts
.annealing
[i
]!=eannNO
)
1508 update_annealing_target_temp(&(ir
->opts
),ir
->init_t
);
1513 *upd
= init_update(fplog
,ir
);
1518 *vcm
= init_vcm(fplog
,&mtop
->groups
,ir
);
1521 if (EI_DYNAMICS(ir
->eI
) && !(Flags
& MD_APPENDFILES
))
1523 if (ir
->etc
== etcBERENDSEN
)
1525 please_cite(fplog
,"Berendsen84a");
1527 if (ir
->etc
== etcVRESCALE
)
1529 please_cite(fplog
,"Bussi2007a");
1537 *outf
= init_mdoutf(nfile
,fnm
,Flags
,cr
,ir
,oenv
);
1539 *mdebin
= init_mdebin((Flags
& MD_APPENDFILES
) ? NULL
: (*outf
)->fp_ene
,
1540 mtop
,ir
, (*outf
)->fp_dhdl
);
1543 /* Initiate variables */
1544 clear_mat(force_vir
);
1545 clear_mat(shake_vir
);