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.
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44 #include "types/commrec.h"
55 #include "gmx_random.h"
69 #include "gmx_wallcycle.h"
70 #include "gmx_omp_nthreads.h"
72 /*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
73 /*#define STARTFROMDT2*/
93 /* The random state */
99 gmx_sd_sigma_t
*sdsig
;
102 /* andersen temperature control stuff */
103 gmx_bool
*randomize_group
;
107 typedef struct gmx_update
110 /* xprime for constraint algorithms */
114 /* variable size arrays for andersen */
117 gmx_bool randatom_list_init
;
119 /* Variables for the deform algorithm */
120 gmx_large_int_t deformref_step
;
121 matrix deformref_box
;
125 static void do_update_md(int start
,int nrend
,double dt
,
126 t_grp_tcstat
*tcstat
,
128 gmx_bool bNEMD
,t_grp_acc
*gstat
,rvec accel
[],
131 unsigned short ptype
[],unsigned short cFREEZE
[],
132 unsigned short cACC
[],unsigned short cTC
[],
133 rvec x
[],rvec xprime
[],rvec v
[],
135 gmx_bool bNH
,gmx_bool bPR
)
140 real vn
,vv
,va
,vb
,vnrel
;
146 /* Update with coupling to extended ensembles, used for
147 * Nose-Hoover and Parrinello-Rahman coupling
148 * Nose-Hoover uses the reversible leap-frog integrator from
149 * Holian et al. Phys Rev E 52(3) : 2338, 1995
151 for(n
=start
; n
<nrend
; n
++)
166 lg
= tcstat
[gt
].lambda
;
170 rvec_sub(v
[n
],gstat
[ga
].u
,vrel
);
174 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
176 vnrel
= (lg
*vrel
[d
] + dt
*(imass
*f
[n
][d
] - 0.5*vxi
*vrel
[d
]
177 - iprod(M
[d
],vrel
)))/(1 + 0.5*vxi
*dt
);
178 /* do not scale the mean velocities u */
179 vn
= gstat
[ga
].u
[d
] + accel
[ga
][d
]*dt
+ vnrel
;
181 xprime
[n
][d
] = x
[n
][d
]+vn
*dt
;
186 xprime
[n
][d
] = x
[n
][d
];
191 else if (cFREEZE
!= NULL
||
192 nFreeze
[0][XX
] || nFreeze
[0][YY
] || nFreeze
[0][ZZ
] ||
195 /* Update with Berendsen/v-rescale coupling and freeze or NEMD */
196 for(n
=start
; n
<nrend
; n
++)
198 w_dt
= invmass
[n
]*dt
;
211 lg
= tcstat
[gt
].lambda
;
216 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
218 vv
= lg
*vn
+ f
[n
][d
]*w_dt
;
220 /* do not scale the mean velocities u */
222 va
= vv
+ accel
[ga
][d
]*dt
;
223 vb
= va
+ (1.0-lg
)*u
;
225 xprime
[n
][d
] = x
[n
][d
]+vb
*dt
;
230 xprime
[n
][d
] = x
[n
][d
];
237 /* Plain update with Berendsen/v-rescale coupling */
238 for(n
=start
; n
<nrend
; n
++)
240 if ((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
))
242 w_dt
= invmass
[n
]*dt
;
247 lg
= tcstat
[gt
].lambda
;
251 vn
= lg
*v
[n
][d
] + f
[n
][d
]*w_dt
;
253 xprime
[n
][d
] = x
[n
][d
] + vn
*dt
;
261 xprime
[n
][d
] = x
[n
][d
];
268 static void do_update_vv_vel(int start
,int nrend
,double dt
,
269 t_grp_tcstat
*tcstat
,t_grp_acc
*gstat
,
270 rvec accel
[],ivec nFreeze
[],real invmass
[],
271 unsigned short ptype
[],unsigned short cFREEZE
[],
272 unsigned short cACC
[],rvec v
[],rvec f
[],
273 gmx_bool bExtended
, real veta
, real alpha
)
278 real u
,vn
,vv
,va
,vb
,vnrel
;
284 g
= 0.25*dt
*veta
*alpha
;
286 mv2
= series_sinhx(g
);
293 for(n
=start
; n
<nrend
; n
++)
295 w_dt
= invmass
[n
]*dt
;
307 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
309 v
[n
][d
] = mv1
*(mv1
*v
[n
][d
] + 0.5*(w_dt
*mv2
*f
[n
][d
]))+0.5*accel
[ga
][d
]*dt
;
317 } /* do_update_vv_vel */
319 static void do_update_vv_pos(int start
,int nrend
,double dt
,
320 t_grp_tcstat
*tcstat
,t_grp_acc
*gstat
,
321 rvec accel
[],ivec nFreeze
[],real invmass
[],
322 unsigned short ptype
[],unsigned short cFREEZE
[],
323 rvec x
[],rvec xprime
[],rvec v
[],
324 rvec f
[],gmx_bool bExtended
, real veta
, real alpha
)
331 /* Would it make more sense if Parrinello-Rahman was put here? */
336 mr2
= series_sinhx(g
);
342 for(n
=start
; n
<nrend
; n
++) {
351 if ((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
353 xprime
[n
][d
] = mr1
*(mr1
*x
[n
][d
]+mr2
*dt
*v
[n
][d
]);
357 xprime
[n
][d
] = x
[n
][d
];
361 }/* do_update_vv_pos */
363 static void do_update_visc(int start
,int nrend
,double dt
,
364 t_grp_tcstat
*tcstat
,
367 unsigned short ptype
[],unsigned short cTC
[],
368 rvec x
[],rvec xprime
[],rvec v
[],
369 rvec f
[],matrix M
,matrix box
,real
371 gmx_bool bNH
,gmx_bool bPR
)
381 fac
= 2*M_PI
/(box
[ZZ
][ZZ
]);
384 /* Update with coupling to extended ensembles, used for
385 * Nose-Hoover and Parrinello-Rahman coupling
387 for(n
=start
; n
<nrend
; n
++) {
393 lg
= tcstat
[gt
].lambda
;
394 cosz
= cos(fac
*x
[n
][ZZ
]);
396 copy_rvec(v
[n
],vrel
);
408 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
))
410 vn
= (lg
*vrel
[d
] + dt
*(imass
*f
[n
][d
] - 0.5*vxi
*vrel
[d
]
411 - iprod(M
[d
],vrel
)))/(1 + 0.5*vxi
*dt
);
414 vn
+= vc
+ dt
*cosz
*cos_accel
;
417 xprime
[n
][d
] = x
[n
][d
]+vn
*dt
;
421 xprime
[n
][d
] = x
[n
][d
];
428 /* Classic version of update, used with berendsen coupling */
429 for(n
=start
; n
<nrend
; n
++)
431 w_dt
= invmass
[n
]*dt
;
436 lg
= tcstat
[gt
].lambda
;
437 cosz
= cos(fac
*x
[n
][ZZ
]);
443 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
))
448 /* Do not scale the cosine velocity profile */
449 vv
= vc
+ lg
*(vn
- vc
+ f
[n
][d
]*w_dt
);
450 /* Add the cosine accelaration profile */
451 vv
+= dt
*cosz
*cos_accel
;
455 vv
= lg
*(vn
+ f
[n
][d
]*w_dt
);
458 xprime
[n
][d
] = x
[n
][d
]+vv
*dt
;
463 xprime
[n
][d
] = x
[n
][d
];
470 static gmx_stochd_t
*init_stochd(FILE *fplog
,t_inputrec
*ir
)
479 /* Initiate random number generator for langevin type dynamics,
480 * for BD, SD or velocity rescaling temperature coupling.
482 sd
->gaussrand
= gmx_rng_init(ir
->ld_seed
);
484 ngtc
= ir
->opts
.ngtc
;
488 snew(sd
->bd_rf
,ngtc
);
490 else if (EI_SD(ir
->eI
))
493 snew(sd
->sdsig
,ngtc
);
496 for(n
=0; n
<ngtc
; n
++)
498 if (ir
->opts
.tau_t
[n
] > 0)
500 sdc
[n
].gdt
= ir
->delta_t
/ir
->opts
.tau_t
[n
];
501 sdc
[n
].eph
= exp(sdc
[n
].gdt
/2);
502 sdc
[n
].emh
= exp(-sdc
[n
].gdt
/2);
503 sdc
[n
].em
= exp(-sdc
[n
].gdt
);
507 /* No friction and noise on this group */
513 if (sdc
[n
].gdt
>= 0.05)
515 sdc
[n
].b
= sdc
[n
].gdt
*(sdc
[n
].eph
*sdc
[n
].eph
- 1)
516 - 4*(sdc
[n
].eph
- 1)*(sdc
[n
].eph
- 1);
517 sdc
[n
].c
= sdc
[n
].gdt
- 3 + 4*sdc
[n
].emh
- sdc
[n
].em
;
518 sdc
[n
].d
= 2 - sdc
[n
].eph
- sdc
[n
].emh
;
523 /* Seventh order expansions for small y */
524 sdc
[n
].b
= y
*y
*y
*y
*(1/3.0+y
*(1/3.0+y
*(17/90.0+y
*7/9.0)));
525 sdc
[n
].c
= y
*y
*y
*(2/3.0+y
*(-1/2.0+y
*(7/30.0+y
*(-1/12.0+y
*31/1260.0))));
526 sdc
[n
].d
= y
*y
*(-1+y
*y
*(-1/12.0-y
*y
/360.0));
529 fprintf(debug
,"SD const tc-grp %d: b %g c %g d %g\n",
530 n
,sdc
[n
].b
,sdc
[n
].c
,sdc
[n
].d
);
533 else if (ETC_ANDERSEN(ir
->etc
))
542 snew(sd
->randomize_group
,ngtc
);
543 snew(sd
->boltzfac
,ngtc
);
545 /* for now, assume that all groups, if randomized, are randomized at the same rate, i.e. tau_t is the same. */
546 /* since constraint groups don't necessarily match up with temperature groups! This is checked in readir.c */
548 for (n
=0;n
<ngtc
;n
++) {
549 reft
= max(0.0,opts
->ref_t
[n
]);
550 if ((opts
->tau_t
[n
] > 0) && (reft
> 0)) /* tau_t or ref_t = 0 means that no randomization is done */
552 sd
->randomize_group
[n
] = TRUE
;
553 sd
->boltzfac
[n
] = BOLTZ
*opts
->ref_t
[n
];
555 sd
->randomize_group
[n
] = FALSE
;
562 void get_stochd_state(gmx_update_t upd
,t_state
*state
)
564 gmx_rng_get_state(upd
->sd
->gaussrand
,state
->ld_rng
,state
->ld_rngi
);
567 void set_stochd_state(gmx_update_t upd
,t_state
*state
)
569 gmx_rng_set_state(upd
->sd
->gaussrand
,state
->ld_rng
,state
->ld_rngi
[0]);
572 gmx_update_t
init_update(FILE *fplog
,t_inputrec
*ir
)
578 if (ir
->eI
== eiBD
|| EI_SD(ir
->eI
) || ir
->etc
== etcVRESCALE
|| ETC_ANDERSEN(ir
->etc
))
580 upd
->sd
= init_stochd(fplog
,ir
);
585 upd
->randatom
= NULL
;
586 upd
->randatom_list
= NULL
;
587 upd
->randatom_list_init
= FALSE
; /* we have not yet cleared the data structure at this point */
592 static void do_update_sd1(gmx_stochd_t
*sd
,
593 int start
,int homenr
,double dt
,
594 rvec accel
[],ivec nFreeze
[],
595 real invmass
[],unsigned short ptype
[],
596 unsigned short cFREEZE
[],unsigned short cACC
[],
597 unsigned short cTC
[],
598 rvec x
[],rvec xprime
[],rvec v
[],rvec f
[],
600 int ngtc
,real tau_t
[],real ref_t
[])
612 if (homenr
> sd
->sd_V_nalloc
)
614 sd
->sd_V_nalloc
= over_alloc_dd(homenr
);
615 srenew(sd
->sd_V
,sd
->sd_V_nalloc
);
617 gaussrand
= sd
->gaussrand
;
619 for(n
=0; n
<ngtc
; n
++)
622 /* The mass is encounted for later, since this differs per atom */
623 sig
[n
].V
= sqrt(kT
*(1 - sdc
[n
].em
*sdc
[n
].em
));
626 for(n
=start
; n
<start
+homenr
; n
++)
628 ism
= sqrt(invmass
[n
]);
644 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
646 sd_V
= ism
*sig
[gt
].V
*gmx_rng_gaussian_table(gaussrand
);
648 v
[n
][d
] = v
[n
][d
]*sdc
[gt
].em
649 + (invmass
[n
]*f
[n
][d
] + accel
[ga
][d
])*tau_t
[gt
]*(1 - sdc
[gt
].em
)
652 xprime
[n
][d
] = x
[n
][d
] + v
[n
][d
]*dt
;
657 xprime
[n
][d
] = x
[n
][d
];
663 static void do_update_sd2(gmx_stochd_t
*sd
,gmx_bool bInitStep
,
664 int start
,int homenr
,
665 rvec accel
[],ivec nFreeze
[],
666 real invmass
[],unsigned short ptype
[],
667 unsigned short cFREEZE
[],unsigned short cACC
[],
668 unsigned short cTC
[],
669 rvec x
[],rvec xprime
[],rvec v
[],rvec f
[],
671 int ngtc
,real tau_t
[],real ref_t
[],
676 /* The random part of the velocity update, generated in the first
677 * half of the update, needs to be remembered for the second half.
689 if (homenr
> sd
->sd_V_nalloc
)
691 sd
->sd_V_nalloc
= over_alloc_dd(homenr
);
692 srenew(sd
->sd_V
,sd
->sd_V_nalloc
);
695 gaussrand
= sd
->gaussrand
;
699 for (n
=0; n
<ngtc
; n
++)
702 /* The mass is encounted for later, since this differs per atom */
703 sig
[n
].V
= sqrt(kT
*(1-sdc
[n
].em
));
704 sig
[n
].X
= sqrt(kT
*sqr(tau_t
[n
])*sdc
[n
].c
);
705 sig
[n
].Yv
= sqrt(kT
*sdc
[n
].b
/sdc
[n
].c
);
706 sig
[n
].Yx
= sqrt(kT
*sqr(tau_t
[n
])*sdc
[n
].b
/(1-sdc
[n
].em
));
710 for (n
=start
; n
<start
+homenr
; n
++)
712 ism
= sqrt(invmass
[n
]);
732 if((ptype
[n
] != eptVSite
) && (ptype
[n
] != eptShell
) && !nFreeze
[gf
][d
])
738 sd_X
[n
][d
] = ism
*sig
[gt
].X
*gmx_rng_gaussian_table(gaussrand
);
740 Vmh
= sd_X
[n
][d
]*sdc
[gt
].d
/(tau_t
[gt
]*sdc
[gt
].c
)
741 + ism
*sig
[gt
].Yv
*gmx_rng_gaussian_table(gaussrand
);
742 sd_V
[n
-start
][d
] = ism
*sig
[gt
].V
*gmx_rng_gaussian_table(gaussrand
);
744 v
[n
][d
] = vn
*sdc
[gt
].em
745 + (invmass
[n
]*f
[n
][d
] + accel
[ga
][d
])*tau_t
[gt
]*(1 - sdc
[gt
].em
)
746 + sd_V
[n
-start
][d
] - sdc
[gt
].em
*Vmh
;
748 xprime
[n
][d
] = x
[n
][d
] + v
[n
][d
]*tau_t
[gt
]*(sdc
[gt
].eph
- sdc
[gt
].emh
);
753 /* Correct the velocities for the constraints.
754 * This operation introduces some inaccuracy,
755 * since the velocity is determined from differences in coordinates.
758 (xprime
[n
][d
] - x
[n
][d
])/(tau_t
[gt
]*(sdc
[gt
].eph
- sdc
[gt
].emh
));
760 Xmh
= sd_V
[n
-start
][d
]*tau_t
[gt
]*sdc
[gt
].d
/(sdc
[gt
].em
-1)
761 + ism
*sig
[gt
].Yx
*gmx_rng_gaussian_table(gaussrand
);
762 sd_X
[n
][d
] = ism
*sig
[gt
].X
*gmx_rng_gaussian_table(gaussrand
);
764 xprime
[n
][d
] += sd_X
[n
][d
] - Xmh
;
773 xprime
[n
][d
] = x
[n
][d
];
780 static void do_update_bd(int start
,int nrend
,double dt
,
782 real invmass
[],unsigned short ptype
[],
783 unsigned short cFREEZE
[],unsigned short cTC
[],
784 rvec x
[],rvec xprime
[],rvec v
[],
785 rvec f
[],real friction_coefficient
,
786 int ngtc
,real tau_t
[],real ref_t
[],
787 real
*rf
,gmx_rng_t gaussrand
)
789 /* note -- these appear to be full step velocities . . . */
795 if (friction_coefficient
!= 0)
797 invfr
= 1.0/friction_coefficient
;
798 for(n
=0; n
<ngtc
; n
++)
800 rf
[n
] = sqrt(2.0*BOLTZ
*ref_t
[n
]/(friction_coefficient
*dt
));
805 for(n
=0; n
<ngtc
; n
++)
807 rf
[n
] = sqrt(2.0*BOLTZ
*ref_t
[n
]);
810 for(n
=start
; (n
<nrend
); n
++)
820 for(d
=0; (d
<DIM
); d
++)
822 if((ptype
[n
]!=eptVSite
) && (ptype
[n
]!=eptShell
) && !nFreeze
[gf
][d
])
824 if (friction_coefficient
!= 0) {
825 vn
= invfr
*f
[n
][d
] + rf
[gt
]*gmx_rng_gaussian_table(gaussrand
);
829 /* NOTE: invmass = 2/(mass*friction_constant*dt) */
830 vn
= 0.5*invmass
[n
]*f
[n
][d
]*dt
831 + sqrt(0.5*invmass
[n
])*rf
[gt
]*gmx_rng_gaussian_table(gaussrand
);
835 xprime
[n
][d
] = x
[n
][d
]+vn
*dt
;
840 xprime
[n
][d
] = x
[n
][d
];
846 static void dump_it_all(FILE *fp
,const char *title
,
847 int natoms
,rvec x
[],rvec xp
[],rvec v
[],rvec f
[])
852 fprintf(fp
,"%s\n",title
);
853 pr_rvecs(fp
,0,"x",x
,natoms
);
854 pr_rvecs(fp
,0,"xp",xp
,natoms
);
855 pr_rvecs(fp
,0,"v",v
,natoms
);
856 pr_rvecs(fp
,0,"f",f
,natoms
);
861 static void calc_ke_part_normal(rvec v
[], t_grpopts
*opts
,t_mdatoms
*md
,
862 gmx_ekindata_t
*ekind
,t_nrnb
*nrnb
,gmx_bool bEkinAveVel
,
863 gmx_bool bSaveEkinOld
)
866 t_grp_tcstat
*tcstat
=ekind
->tcstat
;
867 t_grp_acc
*grpstat
=ekind
->grpstat
;
870 /* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also
871 an option, but not supported now. Additionally, if we are doing iterations.
872 bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
873 bSavEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't copy over the ekinh_old.
874 If FALSE, we overrwrite it.
877 /* group velocities are calculated in update_ekindata and
878 * accumulated in acumulate_groups.
879 * Now the partial global and groups ekin.
881 for(g
=0; (g
<opts
->ngtc
); g
++)
885 copy_mat(tcstat
[g
].ekinh
,tcstat
[g
].ekinh_old
);
888 clear_mat(tcstat
[g
].ekinf
);
890 clear_mat(tcstat
[g
].ekinh
);
893 tcstat
[g
].ekinscalef_nhc
= 1.0; /* need to clear this -- logic is complicated! */
896 ekind
->dekindl_old
= ekind
->dekindl
;
898 nthread
= gmx_omp_nthreads_get(emntUpdate
);
900 #pragma omp parallel for num_threads(nthread) schedule(static)
901 for(thread
=0; thread
<nthread
; thread
++)
911 start_t
= md
->start
+ ((thread
+0)*md
->homenr
)/nthread
;
912 end_t
= md
->start
+ ((thread
+1)*md
->homenr
)/nthread
;
914 ekin_sum
= ekind
->ekin_work
[thread
];
915 dekindl_sum
= &ekind
->ekin_work
[thread
][opts
->ngtc
][0][0];
917 for(gt
=0; gt
<opts
->ngtc
; gt
++)
919 clear_mat(ekin_sum
[gt
]);
924 for(n
=start_t
; n
<end_t
; n
++)
934 hm
= 0.5*md
->massT
[n
];
936 for(d
=0; (d
<DIM
); d
++)
938 v_corrt
[d
] = v
[n
][d
] - grpstat
[ga
].u
[d
];
940 for(d
=0; (d
<DIM
); d
++)
942 for (m
=0;(m
<DIM
); m
++)
944 /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
945 ekin_sum
[gt
][m
][d
] += hm
*v_corrt
[m
]*v_corrt
[d
];
948 if (md
->nMassPerturbed
&& md
->bPerturbed
[n
])
951 0.5*(md
->massB
[n
] - md
->massA
[n
])*iprod(v_corrt
,v_corrt
);
957 for(thread
=0; thread
<nthread
; thread
++)
959 for(g
=0; g
<opts
->ngtc
; g
++)
963 m_add(tcstat
[g
].ekinf
,ekind
->ekin_work
[thread
][g
],
968 m_add(tcstat
[g
].ekinh
,ekind
->ekin_work
[thread
][g
],
973 ekind
->dekindl
+= ekind
->ekin_work
[thread
][opts
->ngtc
][0][0];
976 inc_nrnb(nrnb
,eNR_EKIN
,md
->homenr
);
979 static void calc_ke_part_visc(matrix box
,rvec x
[],rvec v
[],
980 t_grpopts
*opts
,t_mdatoms
*md
,
981 gmx_ekindata_t
*ekind
,
982 t_nrnb
*nrnb
, gmx_bool bEkinAveVel
, gmx_bool bSaveEkinOld
)
984 int start
=md
->start
,homenr
=md
->homenr
;
988 t_grp_tcstat
*tcstat
=ekind
->tcstat
;
989 t_cos_acc
*cosacc
=&(ekind
->cosacc
);
994 for(g
=0; g
<opts
->ngtc
; g
++)
996 copy_mat(ekind
->tcstat
[g
].ekinh
,ekind
->tcstat
[g
].ekinh_old
);
997 clear_mat(ekind
->tcstat
[g
].ekinh
);
999 ekind
->dekindl_old
= ekind
->dekindl
;
1001 fac
= 2*M_PI
/box
[ZZ
][ZZ
];
1004 for(n
=start
; n
<start
+homenr
; n
++)
1010 hm
= 0.5*md
->massT
[n
];
1012 /* Note that the times of x and v differ by half a step */
1013 /* MRS -- would have to be changed for VV */
1014 cosz
= cos(fac
*x
[n
][ZZ
]);
1015 /* Calculate the amplitude of the new velocity profile */
1016 mvcos
+= 2*cosz
*md
->massT
[n
]*v
[n
][XX
];
1018 copy_rvec(v
[n
],v_corrt
);
1019 /* Subtract the profile for the kinetic energy */
1020 v_corrt
[XX
] -= cosz
*cosacc
->vcos
;
1021 for (d
=0; (d
<DIM
); d
++)
1023 for (m
=0; (m
<DIM
); m
++)
1025 /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
1028 tcstat
[gt
].ekinf
[m
][d
]+=hm
*v_corrt
[m
]*v_corrt
[d
];
1032 tcstat
[gt
].ekinh
[m
][d
]+=hm
*v_corrt
[m
]*v_corrt
[d
];
1036 if(md
->nPerturbed
&& md
->bPerturbed
[n
])
1038 dekindl
-= 0.5*(md
->massB
[n
] - md
->massA
[n
])*iprod(v_corrt
,v_corrt
);
1041 ekind
->dekindl
= dekindl
;
1042 cosacc
->mvcos
= mvcos
;
1044 inc_nrnb(nrnb
,eNR_EKIN
,homenr
);
1047 void calc_ke_part(t_state
*state
,t_grpopts
*opts
,t_mdatoms
*md
,
1048 gmx_ekindata_t
*ekind
,t_nrnb
*nrnb
, gmx_bool bEkinAveVel
, gmx_bool bSaveEkinOld
)
1050 if (ekind
->cosacc
.cos_accel
== 0)
1052 calc_ke_part_normal(state
->v
,opts
,md
,ekind
,nrnb
,bEkinAveVel
,bSaveEkinOld
);
1056 calc_ke_part_visc(state
->box
,state
->x
,state
->v
,opts
,md
,ekind
,nrnb
,bEkinAveVel
,bSaveEkinOld
);
1060 extern void init_ekinstate(ekinstate_t
*ekinstate
,const t_inputrec
*ir
)
1062 ekinstate
->ekin_n
= ir
->opts
.ngtc
;
1063 snew(ekinstate
->ekinh
,ekinstate
->ekin_n
);
1064 snew(ekinstate
->ekinf
,ekinstate
->ekin_n
);
1065 snew(ekinstate
->ekinh_old
,ekinstate
->ekin_n
);
1066 snew(ekinstate
->ekinscalef_nhc
,ekinstate
->ekin_n
);
1067 snew(ekinstate
->ekinscaleh_nhc
,ekinstate
->ekin_n
);
1068 snew(ekinstate
->vscale_nhc
,ekinstate
->ekin_n
);
1069 ekinstate
->dekindl
= 0;
1070 ekinstate
->mvcos
= 0;
1073 void update_ekinstate(ekinstate_t
*ekinstate
,gmx_ekindata_t
*ekind
)
1077 for(i
=0;i
<ekinstate
->ekin_n
;i
++)
1079 copy_mat(ekind
->tcstat
[i
].ekinh
,ekinstate
->ekinh
[i
]);
1080 copy_mat(ekind
->tcstat
[i
].ekinf
,ekinstate
->ekinf
[i
]);
1081 copy_mat(ekind
->tcstat
[i
].ekinh_old
,ekinstate
->ekinh_old
[i
]);
1082 ekinstate
->ekinscalef_nhc
[i
] = ekind
->tcstat
[i
].ekinscalef_nhc
;
1083 ekinstate
->ekinscaleh_nhc
[i
] = ekind
->tcstat
[i
].ekinscaleh_nhc
;
1084 ekinstate
->vscale_nhc
[i
] = ekind
->tcstat
[i
].vscale_nhc
;
1087 copy_mat(ekind
->ekin
,ekinstate
->ekin_total
);
1088 ekinstate
->dekindl
= ekind
->dekindl
;
1089 ekinstate
->mvcos
= ekind
->cosacc
.mvcos
;
1093 void restore_ekinstate_from_state(t_commrec
*cr
,
1094 gmx_ekindata_t
*ekind
,ekinstate_t
*ekinstate
)
1100 for(i
=0;i
<ekinstate
->ekin_n
;i
++)
1102 copy_mat(ekinstate
->ekinh
[i
],ekind
->tcstat
[i
].ekinh
);
1103 copy_mat(ekinstate
->ekinf
[i
],ekind
->tcstat
[i
].ekinf
);
1104 copy_mat(ekinstate
->ekinh_old
[i
],ekind
->tcstat
[i
].ekinh_old
);
1105 ekind
->tcstat
[i
].ekinscalef_nhc
= ekinstate
->ekinscalef_nhc
[i
];
1106 ekind
->tcstat
[i
].ekinscaleh_nhc
= ekinstate
->ekinscaleh_nhc
[i
];
1107 ekind
->tcstat
[i
].vscale_nhc
= ekinstate
->vscale_nhc
[i
];
1110 copy_mat(ekinstate
->ekin_total
,ekind
->ekin
);
1112 ekind
->dekindl
= ekinstate
->dekindl
;
1113 ekind
->cosacc
.mvcos
= ekinstate
->mvcos
;
1114 n
= ekinstate
->ekin_n
;
1119 gmx_bcast(sizeof(n
),&n
,cr
);
1122 gmx_bcast(DIM
*DIM
*sizeof(ekind
->tcstat
[i
].ekinh
[0][0]),
1123 ekind
->tcstat
[i
].ekinh
[0],cr
);
1124 gmx_bcast(DIM
*DIM
*sizeof(ekind
->tcstat
[i
].ekinf
[0][0]),
1125 ekind
->tcstat
[i
].ekinf
[0],cr
);
1126 gmx_bcast(DIM
*DIM
*sizeof(ekind
->tcstat
[i
].ekinh_old
[0][0]),
1127 ekind
->tcstat
[i
].ekinh_old
[0],cr
);
1129 gmx_bcast(sizeof(ekind
->tcstat
[i
].ekinscalef_nhc
),
1130 &(ekind
->tcstat
[i
].ekinscalef_nhc
),cr
);
1131 gmx_bcast(sizeof(ekind
->tcstat
[i
].ekinscaleh_nhc
),
1132 &(ekind
->tcstat
[i
].ekinscaleh_nhc
),cr
);
1133 gmx_bcast(sizeof(ekind
->tcstat
[i
].vscale_nhc
),
1134 &(ekind
->tcstat
[i
].vscale_nhc
),cr
);
1136 gmx_bcast(DIM
*DIM
*sizeof(ekind
->ekin
[0][0]),
1139 gmx_bcast(sizeof(ekind
->dekindl
),&ekind
->dekindl
,cr
);
1140 gmx_bcast(sizeof(ekind
->cosacc
.mvcos
),&ekind
->cosacc
.mvcos
,cr
);
1144 void set_deform_reference_box(gmx_update_t upd
,gmx_large_int_t step
,matrix box
)
1146 upd
->deformref_step
= step
;
1147 copy_mat(box
,upd
->deformref_box
);
1150 static void deform(gmx_update_t upd
,
1151 int start
,int homenr
,rvec x
[],matrix box
,matrix
*scale_tot
,
1152 const t_inputrec
*ir
,gmx_large_int_t step
)
1154 matrix bnew
,invbox
,mu
;
1158 elapsed_time
= (step
+ 1 - upd
->deformref_step
)*ir
->delta_t
;
1160 for(i
=0; i
<DIM
; i
++)
1162 for(j
=0; j
<DIM
; j
++)
1164 if (ir
->deform
[i
][j
] != 0)
1167 upd
->deformref_box
[i
][j
] + elapsed_time
*ir
->deform
[i
][j
];
1171 /* We correct the off-diagonal elements,
1172 * which can grow indefinitely during shearing,
1173 * so the shifts do not get messed up.
1175 for(i
=1; i
<DIM
; i
++)
1177 for(j
=i
-1; j
>=0; j
--)
1179 while (bnew
[i
][j
] - box
[i
][j
] > 0.5*bnew
[j
][j
])
1181 rvec_dec(bnew
[i
],bnew
[j
]);
1183 while (bnew
[i
][j
] - box
[i
][j
] < -0.5*bnew
[j
][j
])
1185 rvec_inc(bnew
[i
],bnew
[j
]);
1189 m_inv_ur0(box
,invbox
);
1191 mmul_ur0(box
,invbox
,mu
);
1193 for(i
=start
; i
<start
+homenr
; i
++)
1195 x
[i
][XX
] = mu
[XX
][XX
]*x
[i
][XX
]+mu
[YY
][XX
]*x
[i
][YY
]+mu
[ZZ
][XX
]*x
[i
][ZZ
];
1196 x
[i
][YY
] = mu
[YY
][YY
]*x
[i
][YY
]+mu
[ZZ
][YY
]*x
[i
][ZZ
];
1197 x
[i
][ZZ
] = mu
[ZZ
][ZZ
]*x
[i
][ZZ
];
1201 /* The transposes of the scaling matrices are stored,
1202 * so we need to do matrix multiplication in the inverse order.
1204 mmul_ur0(*scale_tot
,mu
,*scale_tot
);
1208 static void combine_forces(int nstcalclr
,
1209 gmx_constr_t constr
,
1210 t_inputrec
*ir
,t_mdatoms
*md
,t_idef
*idef
,
1212 gmx_large_int_t step
,
1213 t_state
*state
,gmx_bool bMolPBC
,
1214 int start
,int nrend
,
1215 rvec f
[],rvec f_lr
[],
1220 /* f contains the short-range forces + the long range forces
1221 * which are stored separately in f_lr.
1224 if (constr
!= NULL
&& !(ir
->eConstrAlg
== econtSHAKE
&& ir
->epc
== epcNO
))
1226 /* We need to constrain the LR forces separately,
1227 * because due to the different pre-factor for the SR and LR
1228 * forces in the update algorithm, we can not determine
1229 * the constraint force for the coordinate constraining.
1230 * Constrain only the additional LR part of the force.
1232 /* MRS -- need to make sure this works with trotter integration -- the constraint calls may not be right.*/
1233 constrain(NULL
,FALSE
,FALSE
,constr
,idef
,ir
,NULL
,cr
,step
,0,md
,
1234 state
->x
,f_lr
,f_lr
,bMolPBC
,state
->box
,state
->lambda
[efptBONDED
],NULL
,
1235 NULL
,NULL
,nrnb
,econqForce
,ir
->epc
==epcMTTK
,state
->veta
,state
->veta
);
1238 /* Add nstcalclr-1 times the LR force to the sum of both forces
1239 * and store the result in forces_lr.
1241 nm1
= nstcalclr
- 1;
1242 for(i
=start
; i
<nrend
; i
++)
1244 for(d
=0; d
<DIM
; d
++)
1246 f_lr
[i
][d
] = f
[i
][d
] + nm1
*f_lr
[i
][d
];
1251 void update_tcouple(FILE *fplog
,
1252 gmx_large_int_t step
,
1253 t_inputrec
*inputrec
,
1255 gmx_ekindata_t
*ekind
,
1256 gmx_wallcycle_t wcycle
,
1262 gmx_bool bTCouple
=FALSE
;
1264 int i
,start
,end
,homenr
,offset
;
1266 /* if using vv with trotter decomposition methods, we do this elsewhere in the code */
1267 if (inputrec
->etc
!= etcNO
&&
1268 !(IR_NVT_TROTTER(inputrec
) || IR_NPT_TROTTER(inputrec
) || IR_NPH_TROTTER(inputrec
)))
1270 /* We should only couple after a step where energies were determined (for leapfrog versions)
1271 or the step energies are determined, for velocity verlet versions */
1273 if (EI_VV(inputrec
->eI
)) {
1278 bTCouple
= (inputrec
->nsttcouple
== 1 ||
1279 do_per_step(step
+inputrec
->nsttcouple
-offset
,
1280 inputrec
->nsttcouple
));
1285 dttc
= inputrec
->nsttcouple
*inputrec
->delta_t
;
1287 switch (inputrec
->etc
)
1292 berendsen_tcoupl(inputrec
,ekind
,dttc
);
1295 nosehoover_tcoupl(&(inputrec
->opts
),ekind
,dttc
,
1296 state
->nosehoover_xi
,state
->nosehoover_vxi
,MassQ
);
1299 vrescale_tcoupl(inputrec
,ekind
,dttc
,
1300 state
->therm_integral
,upd
->sd
->gaussrand
);
1303 /* rescale in place here */
1304 if (EI_VV(inputrec
->eI
))
1306 rescale_velocities(ekind
,md
,md
->start
,md
->start
+md
->homenr
,state
->v
);
1311 /* Set the T scaling lambda to 1 to have no scaling */
1312 for(i
=0; (i
<inputrec
->opts
.ngtc
); i
++)
1314 ekind
->tcstat
[i
].lambda
= 1.0;
1319 void update_pcouple(FILE *fplog
,
1320 gmx_large_int_t step
,
1321 t_inputrec
*inputrec
,
1325 gmx_wallcycle_t wcycle
,
1329 gmx_bool bPCouple
=FALSE
;
1333 /* if using Trotter pressure, we do this in coupling.c, so we leave it false. */
1334 if (inputrec
->epc
!= epcNO
&& (!(IR_NPT_TROTTER(inputrec
) || IR_NPH_TROTTER(inputrec
))))
1336 /* We should only couple after a step where energies were determined */
1337 bPCouple
= (inputrec
->nstpcouple
== 1 ||
1338 do_per_step(step
+inputrec
->nstpcouple
-1,
1339 inputrec
->nstpcouple
));
1342 clear_mat(pcoupl_mu
);
1343 for(i
=0; i
<DIM
; i
++)
1345 pcoupl_mu
[i
][i
] = 1.0;
1352 dtpc
= inputrec
->nstpcouple
*inputrec
->delta_t
;
1354 switch (inputrec
->epc
)
1356 /* We can always pcoupl, even if we did not sum the energies
1357 * the previous step, since state->pres_prev is only updated
1358 * when the energies have been summed.
1362 case (epcBERENDSEN
):
1365 berendsen_pcoupl(fplog
,step
,inputrec
,dtpc
,state
->pres_prev
,state
->box
,
1369 case (epcPARRINELLORAHMAN
):
1370 parrinellorahman_pcoupl(fplog
,step
,inputrec
,dtpc
,state
->pres_prev
,
1371 state
->box
,state
->box_rel
,state
->boxv
,
1372 M
,pcoupl_mu
,bInitStep
);
1380 static rvec
*get_xprime(const t_state
*state
,gmx_update_t upd
)
1382 if (state
->nalloc
> upd
->xp_nalloc
)
1384 upd
->xp_nalloc
= state
->nalloc
;
1385 srenew(upd
->xp
,upd
->xp_nalloc
);
1391 void update_constraints(FILE *fplog
,
1392 gmx_large_int_t step
,
1393 real
*dvdlambda
, /* the contribution to be added to the bonded interactions */
1394 t_inputrec
*inputrec
, /* input record and box stuff */
1395 gmx_ekindata_t
*ekind
,
1400 rvec force
[], /* forces on home particles */
1403 tensor vir
, /* tensors for virial and ekin, needed for computing */
1406 gmx_wallcycle_t wcycle
,
1408 gmx_constr_t constr
,
1410 gmx_bool bFirstHalf
,
1414 gmx_bool bExtended
,bLastStep
,bLog
=FALSE
,bEner
=FALSE
,bDoConstr
=FALSE
;
1417 int start
,homenr
,nrend
,i
,n
,m
,g
,d
;
1419 rvec
*vbuf
,*xprime
=NULL
;
1421 if (constr
) {bDoConstr
=TRUE
;}
1422 if (bFirstHalf
&& !EI_VV(inputrec
->eI
)) {bDoConstr
=FALSE
;}
1424 /* for now, SD update is here -- though it really seems like it
1425 should be reformulated as a velocity verlet method, since it has two parts */
1428 homenr
= md
->homenr
;
1429 nrend
= start
+homenr
;
1431 dt
= inputrec
->delta_t
;
1436 * APPLY CONSTRAINTS:
1439 * When doing PR pressure coupling we have to constrain the
1440 * bonds in each iteration. If we are only using Nose-Hoover tcoupling
1441 * it is enough to do this once though, since the relative velocities
1442 * after this will be normal to the bond vector
1447 /* clear out constraints before applying */
1448 clear_mat(vir_part
);
1450 xprime
= get_xprime(state
,upd
);
1452 bLastStep
= (step
== inputrec
->init_step
+inputrec
->nsteps
);
1453 bLog
= (do_per_step(step
,inputrec
->nstlog
) || bLastStep
|| (step
< 0));
1454 bEner
= (do_per_step(step
,inputrec
->nstenergy
) || bLastStep
);
1455 /* Constrain the coordinates xprime */
1456 wallcycle_start(wcycle
,ewcCONSTR
);
1457 if (EI_VV(inputrec
->eI
) && bFirstHalf
)
1459 constrain(NULL
,bLog
,bEner
,constr
,idef
,
1460 inputrec
,ekind
,cr
,step
,1,md
,
1461 state
->x
,state
->v
,state
->v
,
1463 state
->lambda
[efptBONDED
],dvdlambda
,
1464 NULL
,bCalcVir
? &vir_con
: NULL
,nrnb
,econqVeloc
,
1465 inputrec
->epc
==epcMTTK
,state
->veta
,vetanew
);
1469 constrain(NULL
,bLog
,bEner
,constr
,idef
,
1470 inputrec
,ekind
,cr
,step
,1,md
,
1471 state
->x
,xprime
,NULL
,
1473 state
->lambda
[efptBONDED
],dvdlambda
,
1474 state
->v
,bCalcVir
? &vir_con
: NULL
,nrnb
,econqCoord
,
1475 inputrec
->epc
==epcMTTK
,state
->veta
,state
->veta
);
1477 wallcycle_stop(wcycle
,ewcCONSTR
);
1481 dump_it_all(fplog
,"After Shake",
1482 state
->natoms
,state
->x
,xprime
,state
->v
,force
);
1486 if (inputrec
->eI
== eiSD2
)
1488 /* A correction factor eph is needed for the SD constraint force */
1489 /* Here we can, unfortunately, not have proper corrections
1490 * for different friction constants, so we use the first one.
1492 for(i
=0; i
<DIM
; i
++)
1494 for(m
=0; m
<DIM
; m
++)
1496 vir_part
[i
][m
] += upd
->sd
->sdc
[0].eph
*vir_con
[i
][m
];
1502 m_add(vir_part
,vir_con
,vir_part
);
1506 pr_rvecs(debug
,0,"constraint virial",vir_part
,DIM
);
1512 if ((inputrec
->eI
== eiSD2
) && !(bFirstHalf
))
1514 xprime
= get_xprime(state
,upd
);
1516 /* The second part of the SD integration */
1517 do_update_sd2(upd
->sd
,FALSE
,start
,homenr
,
1518 inputrec
->opts
.acc
,inputrec
->opts
.nFreeze
,
1519 md
->invmass
,md
->ptype
,
1520 md
->cFREEZE
,md
->cACC
,md
->cTC
,
1521 state
->x
,xprime
,state
->v
,force
,state
->sd_X
,
1522 inputrec
->opts
.ngtc
,inputrec
->opts
.tau_t
,
1523 inputrec
->opts
.ref_t
,FALSE
);
1524 inc_nrnb(nrnb
, eNR_UPDATE
, homenr
);
1528 /* Constrain the coordinates xprime */
1529 wallcycle_start(wcycle
,ewcCONSTR
);
1530 constrain(NULL
,bLog
,bEner
,constr
,idef
,
1531 inputrec
,NULL
,cr
,step
,1,md
,
1532 state
->x
,xprime
,NULL
,
1534 state
->lambda
[efptBONDED
],dvdlambda
,
1535 NULL
,NULL
,nrnb
,econqCoord
,FALSE
,0,0);
1536 wallcycle_stop(wcycle
,ewcCONSTR
);
1540 /* We must always unshift after updating coordinates; if we did not shake
1541 x was shifted in do_force */
1543 if (!(bFirstHalf
)) /* in the first half of vv, no shift. */
1545 if (graph
&& (graph
->nnodes
> 0))
1547 unshift_x(graph
,state
->box
,state
->x
,upd
->xp
);
1548 if (TRICLINIC(state
->box
))
1550 inc_nrnb(nrnb
,eNR_SHIFTX
,2*graph
->nnodes
);
1554 inc_nrnb(nrnb
,eNR_SHIFTX
,graph
->nnodes
);
1559 #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntUpdate)) schedule(static)
1560 for(i
=start
; i
<nrend
; i
++)
1562 copy_rvec(upd
->xp
[i
],state
->x
[i
]);
1566 dump_it_all(fplog
,"After unshift",
1567 state
->natoms
,state
->x
,upd
->xp
,state
->v
,force
);
1569 /* ############# END the update of velocities and positions ######### */
1572 void update_box(FILE *fplog
,
1573 gmx_large_int_t step
,
1574 t_inputrec
*inputrec
, /* input record and box stuff */
1578 rvec force
[], /* forces on home particles */
1582 gmx_wallcycle_t wcycle
,
1585 gmx_bool bFirstHalf
)
1587 gmx_bool bExtended
,bLastStep
,bLog
=FALSE
,bEner
=FALSE
;
1590 int start
,homenr
,nrend
,i
,n
,m
,g
;
1594 homenr
= md
->homenr
;
1595 nrend
= start
+homenr
;
1598 (inputrec
->etc
== etcNOSEHOOVER
) ||
1599 (inputrec
->epc
== epcPARRINELLORAHMAN
) ||
1600 (inputrec
->epc
== epcMTTK
);
1602 dt
= inputrec
->delta_t
;
1606 /* now update boxes */
1607 switch (inputrec
->epc
) {
1610 case (epcBERENDSEN
):
1611 berendsen_pscale(inputrec
,pcoupl_mu
,state
->box
,state
->box_rel
,
1612 start
,homenr
,state
->x
,md
->cFREEZE
,nrnb
);
1614 case (epcPARRINELLORAHMAN
):
1615 /* The box velocities were updated in do_pr_pcoupl in the update
1616 * iteration, but we dont change the box vectors until we get here
1617 * since we need to be able to shift/unshift above.
1623 state
->box
[i
][m
] += dt
*state
->boxv
[i
][m
];
1626 preserve_box_shape(inputrec
,state
->box_rel
,state
->box
);
1628 /* Scale the coordinates */
1629 for(n
=start
; (n
<start
+homenr
); n
++)
1631 tmvmul_ur0(pcoupl_mu
,state
->x
[n
],state
->x
[n
]);
1635 switch (inputrec
->epct
)
1637 case (epctISOTROPIC
):
1638 /* DIM * eta = ln V. so DIM*eta_new = DIM*eta_old + DIM*dt*veta =>
1639 ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) =>
1640 Side length scales as exp(veta*dt) */
1642 msmul(state
->box
,exp(state
->veta
*dt
),state
->box
);
1644 /* Relate veta to boxv. veta = d(eta)/dT = (1/DIM)*1/V dV/dT.
1645 o If we assume isotropic scaling, and box length scaling
1646 factor L, then V = L^DIM (det(M)). So dV/dt = DIM
1647 L^(DIM-1) dL/dt det(M), and veta = (1/L) dL/dt. The
1648 determinant of B is L^DIM det(M), and the determinant
1649 of dB/dt is (dL/dT)^DIM det (M). veta will be
1650 (det(dB/dT)/det(B))^(1/3). Then since M =
1651 B_new*(vol_new)^(1/3), dB/dT_new = (veta_new)*B(new). */
1653 msmul(state
->box
,state
->veta
,state
->boxv
);
1663 if ((!(IR_NPT_TROTTER(inputrec
) || IR_NPH_TROTTER(inputrec
))) && scale_tot
)
1665 /* The transposes of the scaling matrices are stored,
1666 * therefore we need to reverse the order in the multiplication.
1668 mmul_ur0(*scale_tot
,pcoupl_mu
,*scale_tot
);
1671 if (DEFORM(*inputrec
))
1673 deform(upd
,start
,homenr
,state
->x
,state
->box
,scale_tot
,inputrec
,step
);
1676 dump_it_all(fplog
,"After update",
1677 state
->natoms
,state
->x
,upd
->xp
,state
->v
,force
);
1680 void update_coords(FILE *fplog
,
1681 gmx_large_int_t step
,
1682 t_inputrec
*inputrec
, /* input record and box stuff */
1686 rvec
*f
, /* forces on home particles */
1690 gmx_ekindata_t
*ekind
,
1692 gmx_wallcycle_t wcycle
,
1696 t_commrec
*cr
, /* these shouldn't be here -- need to think about it */
1698 gmx_constr_t constr
,
1701 gmx_bool bNH
,bPR
,bLastStep
,bLog
=FALSE
,bEner
=FALSE
;
1703 real
*imass
,*imassin
;
1706 int start
,homenr
,nrend
,i
,j
,d
,n
,m
,g
;
1707 int blen0
,blen1
,iatom
,jatom
,nshake
,nsettle
,nconstr
,nexpand
;
1710 rvec
*vcom
,*xcom
,*vall
,*xall
,*xin
,*vin
,*forcein
,*fall
,*xpall
,*xprimein
,*xprime
;
1713 /* Running the velocity half does nothing except for velocity verlet */
1714 if ((UpdatePart
== etrtVELOCITY1
|| UpdatePart
== etrtVELOCITY2
) &&
1715 !EI_VV(inputrec
->eI
))
1717 gmx_incons("update_coords called for velocity without VV integrator");
1721 homenr
= md
->homenr
;
1722 nrend
= start
+homenr
;
1724 xprime
= get_xprime(state
,upd
);
1726 dt
= inputrec
->delta_t
;
1729 /* We need to update the NMR restraint history when time averaging is used */
1730 if (state
->flags
& (1<<estDISRE_RM3TAV
))
1732 update_disres_history(fcd
,&state
->hist
);
1734 if (state
->flags
& (1<<estORIRE_DTAV
))
1736 update_orires_history(fcd
,&state
->hist
);
1740 bNH
= inputrec
->etc
== etcNOSEHOOVER
;
1741 bPR
= ((inputrec
->epc
== epcPARRINELLORAHMAN
) || (inputrec
->epc
== epcMTTK
));
1743 if (bDoLR
&& inputrec
->nstcalclr
> 1 && !EI_VV(inputrec
->eI
)) /* get this working with VV? */
1745 /* Store the total force + nstcalclr-1 times the LR force
1746 * in forces_lr, so it can be used in a normal update algorithm
1747 * to produce twin time stepping.
1749 /* is this correct in the new construction? MRS */
1750 combine_forces(inputrec
->nstcalclr
,constr
,inputrec
,md
,idef
,cr
,
1752 start
,nrend
,f
,f_lr
,nrnb
);
1760 /* ############# START The update of velocities and positions ######### */
1762 dump_it_all(fplog
,"Before update",
1763 state
->natoms
,state
->x
,xprime
,state
->v
,force
);
1765 if (EI_RANDOM(inputrec
->eI
))
1767 /* We still need to take care of generating random seeds properly
1768 * when multi-threading.
1774 nth
= gmx_omp_nthreads_get(emntUpdate
);
1777 # pragma omp parallel for num_threads(nth) schedule(static) private(alpha)
1778 for(th
=0; th
<nth
; th
++)
1780 int start_th
,end_th
;
1782 start_th
= start
+ ((nrend
-start
)* th
)/nth
;
1783 end_th
= start
+ ((nrend
-start
)*(th
+1))/nth
;
1785 switch (inputrec
->eI
) {
1787 if (ekind
->cosacc
.cos_accel
== 0)
1789 do_update_md(start_th
,end_th
,dt
,
1790 ekind
->tcstat
,state
->nosehoover_vxi
,
1791 ekind
->bNEMD
,ekind
->grpstat
,inputrec
->opts
.acc
,
1792 inputrec
->opts
.nFreeze
,
1793 md
->invmass
,md
->ptype
,
1794 md
->cFREEZE
,md
->cACC
,md
->cTC
,
1795 state
->x
,xprime
,state
->v
,force
,M
,
1800 do_update_visc(start_th
,end_th
,dt
,
1801 ekind
->tcstat
,state
->nosehoover_vxi
,
1802 md
->invmass
,md
->ptype
,
1803 md
->cTC
,state
->x
,xprime
,state
->v
,force
,M
,
1805 ekind
->cosacc
.cos_accel
,
1811 do_update_sd1(upd
->sd
,start
,homenr
,dt
,
1812 inputrec
->opts
.acc
,inputrec
->opts
.nFreeze
,
1813 md
->invmass
,md
->ptype
,
1814 md
->cFREEZE
,md
->cACC
,md
->cTC
,
1815 state
->x
,xprime
,state
->v
,force
,state
->sd_X
,
1816 inputrec
->opts
.ngtc
,inputrec
->opts
.tau_t
,inputrec
->opts
.ref_t
);
1819 /* The SD update is done in 2 parts, because an extra constraint step
1822 do_update_sd2(upd
->sd
,bInitStep
,start
,homenr
,
1823 inputrec
->opts
.acc
,inputrec
->opts
.nFreeze
,
1824 md
->invmass
,md
->ptype
,
1825 md
->cFREEZE
,md
->cACC
,md
->cTC
,
1826 state
->x
,xprime
,state
->v
,force
,state
->sd_X
,
1827 inputrec
->opts
.ngtc
,inputrec
->opts
.tau_t
,inputrec
->opts
.ref_t
,
1831 do_update_bd(start
,nrend
,dt
,
1832 inputrec
->opts
.nFreeze
,md
->invmass
,md
->ptype
,
1833 md
->cFREEZE
,md
->cTC
,
1834 state
->x
,xprime
,state
->v
,force
,
1836 inputrec
->opts
.ngtc
,inputrec
->opts
.tau_t
,inputrec
->opts
.ref_t
,
1837 upd
->sd
->bd_rf
,upd
->sd
->gaussrand
);
1841 alpha
= 1.0 + DIM
/((double)inputrec
->opts
.nrdf
[0]); /* assuming barostat coupled to group 0. */
1842 switch (UpdatePart
) {
1845 do_update_vv_vel(start_th
,end_th
,dt
,
1846 ekind
->tcstat
,ekind
->grpstat
,
1847 inputrec
->opts
.acc
,inputrec
->opts
.nFreeze
,
1848 md
->invmass
,md
->ptype
,
1849 md
->cFREEZE
,md
->cACC
,
1851 (bNH
|| bPR
),state
->veta
,alpha
);
1854 do_update_vv_pos(start_th
,end_th
,dt
,
1855 ekind
->tcstat
,ekind
->grpstat
,
1856 inputrec
->opts
.acc
,inputrec
->opts
.nFreeze
,
1857 md
->invmass
,md
->ptype
,md
->cFREEZE
,
1858 state
->x
,xprime
,state
->v
,force
,
1859 (bNH
|| bPR
),state
->veta
,alpha
);
1864 gmx_fatal(FARGS
,"Don't know how to update coordinates");
1872 void correct_ekin(FILE *log
,int start
,int end
,rvec v
[],rvec vcm
,real mass
[],
1873 real tmass
,tensor ekin
)
1876 * This is a debugging routine. It should not be called for production code
1878 * The kinetic energy should calculated according to:
1879 * Ekin = 1/2 m (v-vcm)^2
1880 * However the correction is not always applied, since vcm may not be
1881 * known in time and we compute
1882 * Ekin' = 1/2 m v^2 instead
1883 * This can be corrected afterwards by computing
1884 * Ekin = Ekin' + 1/2 m ( -2 v vcm + vcm^2)
1886 * Ekin = Ekin' - m v vcm + 1/2 m vcm^2
1893 /* Local particles */
1896 /* Processor dependent part. */
1898 for(i
=start
; (i
<end
); i
++)
1902 for(j
=0; (j
<DIM
); j
++)
1908 svmul(1/tmass
,vcm
,vcm
);
1909 svmul(0.5,vcm
,hvcm
);
1911 for(j
=0; (j
<DIM
); j
++)
1913 for(k
=0; (k
<DIM
); k
++)
1915 dekin
[j
][k
] += vcm
[k
]*(tm
*hvcm
[j
]-mv
[j
]);
1918 pr_rvecs(log
,0,"dekin",dekin
,DIM
);
1919 pr_rvecs(log
,0," ekin", ekin
,DIM
);
1920 fprintf(log
,"dekin = %g, ekin = %g vcm = (%8.4f %8.4f %8.4f)\n",
1921 trace(dekin
),trace(ekin
),vcm
[XX
],vcm
[YY
],vcm
[ZZ
]);
1922 fprintf(log
,"mv = (%8.4f %8.4f %8.4f)\n",
1923 mv
[XX
],mv
[YY
],mv
[ZZ
]);
1926 extern gmx_bool
update_randomize_velocities(t_inputrec
*ir
, gmx_large_int_t step
, t_mdatoms
*md
, t_state
*state
, gmx_update_t upd
, t_idef
*idef
, gmx_constr_t constr
) {
1929 real rate
= (ir
->delta_t
)/ir
->opts
.tau_t
[0];
1930 /* proceed with andersen if 1) it's fixed probability per
1931 particle andersen or 2) it's massive andersen and it's tau_t/dt */
1932 if ((ir
->etc
==etcANDERSEN
) || do_per_step(step
,(int)(1.0/rate
)))
1934 srenew(upd
->randatom
,state
->nalloc
);
1935 srenew(upd
->randatom_list
,state
->nalloc
);
1936 if (upd
->randatom_list_init
== FALSE
) {
1937 for (i
=0;i
<state
->nalloc
;i
++) {
1938 upd
->randatom
[i
] = FALSE
;
1939 upd
->randatom_list
[i
] = 0;
1941 upd
->randatom_list_init
= TRUE
;
1943 andersen_tcoupl(ir
,md
,state
,upd
->sd
->gaussrand
,rate
,
1944 (ir
->etc
==etcANDERSEN
)?idef
:NULL
,
1945 constr
?get_nblocks(constr
):0,
1946 constr
?get_sblock(constr
):NULL
,
1947 upd
->randatom
,upd
->randatom_list
,
1948 upd
->sd
->randomize_group
,upd
->sd
->boltzfac
);