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Move disre.* and orires.* to listed-forces/
[gromacs.git] / src / gromacs / mdlib / update.cpp
blob5b57a4d49d3f3db4f524e8878e1ec591134e6aef
1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
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36 */
37 #include "gmxpre.h"
38
39 #include "update.h"
40
41 #include <math.h>
42 #include <stdio.h>
43
44 #include <algorithm>
45
46 #include "gromacs/domdec/domdec_struct.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
49 #include "gromacs/gmxlib/network.h"
50 #include "gromacs/gmxlib/nrnb.h"
51 #include "gromacs/listed-forces/disre.h"
52 #include "gromacs/listed-forces/orires.h"
53 #include "gromacs/math/units.h"
54 #include "gromacs/math/vec.h"
55 #include "gromacs/math/vecdump.h"
56 #include "gromacs/mdlib/constr.h"
57 #include "gromacs/mdlib/force.h"
58 #include "gromacs/mdlib/mdrun.h"
59 #include "gromacs/mdlib/sim_util.h"
60 #include "gromacs/mdlib/tgroup.h"
61 #include "gromacs/mdtypes/commrec.h"
62 #include "gromacs/mdtypes/group.h"
63 #include "gromacs/mdtypes/inputrec.h"
64 #include "gromacs/mdtypes/md_enums.h"
65 #include "gromacs/pbcutil/boxutilities.h"
66 #include "gromacs/pbcutil/mshift.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/pulling/pull.h"
69 #include "gromacs/random/random.h"
70 #include "gromacs/timing/wallcycle.h"
71 #include "gromacs/utility/exceptions.h"
72 #include "gromacs/utility/fatalerror.h"
73 #include "gromacs/utility/futil.h"
74 #include "gromacs/utility/gmxassert.h"
75 #include "gromacs/utility/gmxomp.h"
76 #include "gromacs/utility/smalloc.h"
77
78 /*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
79 /*#define STARTFROMDT2*/
80
81 typedef struct {
82 double gdt;
83 double eph;
84 double emh;
85 double em;
86 double b;
87 double c;
88 double d;
89 } gmx_sd_const_t;
90
91 typedef struct {
92 real V;
93 real X;
94 real Yv;
95 real Yx;
96 } gmx_sd_sigma_t;
97
98 typedef struct {
99 /* BD stuff */
100 real *bd_rf;
101 /* SD stuff */
102 gmx_sd_const_t *sdc;
103 gmx_sd_sigma_t *sdsig;
104 rvec *sd_V;
105 int sd_V_nalloc;
106 /* andersen temperature control stuff */
107 gmx_bool *randomize_group;
108 real *boltzfac;
109 } gmx_stochd_t;
110
111 typedef struct gmx_update
112 {
113 gmx_stochd_t *sd;
114 /* xprime for constraint algorithms */
115 rvec *xp;
116 int xp_nalloc;
117
118 /* Variables for the deform algorithm */
119 gmx_int64_t deformref_step;
120 matrix deformref_box;
121 } t_gmx_update;
122
123
124 static void do_update_md(int start, int nrend, double dt,
125 t_grp_tcstat *tcstat,
126 double nh_vxi[],
127 gmx_bool bNEMD, t_grp_acc *gstat, rvec accel[],
128 ivec nFreeze[],
129 real invmass[],
130 unsigned short ptype[], unsigned short cFREEZE[],
131 unsigned short cACC[], unsigned short cTC[],
132 rvec x[], rvec xprime[], rvec v[],
133 rvec f[], matrix M,
134 gmx_bool bNH, gmx_bool bPR)
135 {
136 double imass, w_dt;
137 int gf = 0, ga = 0, gt = 0;
138 rvec vrel;
139 real vn, vv, va, vb, vnrel;
140 real lg, vxi = 0, u;
141 int n, d;
142
143 if (bNH || bPR)
144 {
145 /* Update with coupling to extended ensembles, used for
146 * Nose-Hoover and Parrinello-Rahman coupling
147 * Nose-Hoover uses the reversible leap-frog integrator from
148 * Holian et al. Phys Rev E 52(3) : 2338, 1995
149 */
150 for (n = start; n < nrend; n++)
151 {
152 imass = invmass[n];
153 if (cFREEZE)
154 {
155 gf = cFREEZE[n];
156 }
157 if (cACC)
158 {
159 ga = cACC[n];
160 }
161 if (cTC)
162 {
163 gt = cTC[n];
164 }
165 lg = tcstat[gt].lambda;
166 if (bNH)
167 {
168 vxi = nh_vxi[gt];
169 }
170 rvec_sub(v[n], gstat[ga].u, vrel);
171
172 for (d = 0; d < DIM; d++)
173 {
174 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
175 {
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;
180 v[n][d] = vn;
181 xprime[n][d] = x[n][d]+vn*dt;
182 }
183 else
184 {
185 v[n][d] = 0.0;
186 xprime[n][d] = x[n][d];
187 }
188 }
189 }
190 }
191 else if (cFREEZE != NULL ||
192 nFreeze[0][XX] || nFreeze[0][YY] || nFreeze[0][ZZ] ||
193 bNEMD)
194 {
195 /* Update with Berendsen/v-rescale coupling and freeze or NEMD */
196 for (n = start; n < nrend; n++)
197 {
198 w_dt = invmass[n]*dt;
199 if (cFREEZE)
200 {
201 gf = cFREEZE[n];
202 }
203 if (cACC)
204 {
205 ga = cACC[n];
206 }
207 if (cTC)
208 {
209 gt = cTC[n];
210 }
211 lg = tcstat[gt].lambda;
212
213 for (d = 0; d < DIM; d++)
214 {
215 vn = v[n][d];
216 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
217 {
218 vv = lg*vn + f[n][d]*w_dt;
219
220 /* do not scale the mean velocities u */
221 u = gstat[ga].u[d];
222 va = vv + accel[ga][d]*dt;
223 vb = va + (1.0-lg)*u;
224 v[n][d] = vb;
225 xprime[n][d] = x[n][d]+vb*dt;
226 }
227 else
228 {
229 v[n][d] = 0.0;
230 xprime[n][d] = x[n][d];
231 }
232 }
233 }
234 }
235 else
236 {
237 /* Plain update with Berendsen/v-rescale coupling */
238 for (n = start; n < nrend; n++)
239 {
240 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
241 {
242 w_dt = invmass[n]*dt;
243 if (cTC)
244 {
245 gt = cTC[n];
246 }
247 lg = tcstat[gt].lambda;
248
249 for (d = 0; d < DIM; d++)
250 {
251 vn = lg*v[n][d] + f[n][d]*w_dt;
252 v[n][d] = vn;
253 xprime[n][d] = x[n][d] + vn*dt;
254 }
255 }
256 else
257 {
258 for (d = 0; d < DIM; d++)
259 {
260 v[n][d] = 0.0;
261 xprime[n][d] = x[n][d];
262 }
263 }
264 }
265 }
266 }
267
268 static void do_update_vv_vel(int start, int nrend, double dt,
269 rvec accel[], ivec nFreeze[], real invmass[],
270 unsigned short ptype[], unsigned short cFREEZE[],
271 unsigned short cACC[], rvec v[], rvec f[],
272 gmx_bool bExtended, real veta, real alpha)
273 {
274 double w_dt;
275 int gf = 0, ga = 0;
276 int n, d;
277 double g, mv1, mv2;
278
279 if (bExtended)
280 {
281 g = 0.25*dt*veta*alpha;
282 mv1 = exp(-g);
283 mv2 = series_sinhx(g);
284 }
285 else
286 {
287 mv1 = 1.0;
288 mv2 = 1.0;
289 }
290 for (n = start; n < nrend; n++)
291 {
292 w_dt = invmass[n]*dt;
293 if (cFREEZE)
294 {
295 gf = cFREEZE[n];
296 }
297 if (cACC)
298 {
299 ga = cACC[n];
300 }
301
302 for (d = 0; d < DIM; d++)
303 {
304 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
305 {
306 v[n][d] = mv1*(mv1*v[n][d] + 0.5*(w_dt*mv2*f[n][d]))+0.5*accel[ga][d]*dt;
307 }
308 else
309 {
310 v[n][d] = 0.0;
311 }
312 }
313 }
314 } /* do_update_vv_vel */
315
316 static void do_update_vv_pos(int start, int nrend, double dt,
317 ivec nFreeze[],
318 unsigned short ptype[], unsigned short cFREEZE[],
319 rvec x[], rvec xprime[], rvec v[],
320 gmx_bool bExtended, real veta)
321 {
322 int gf = 0;
323 int n, d;
324 double g, mr1, mr2;
325
326 /* Would it make more sense if Parrinello-Rahman was put here? */
327 if (bExtended)
328 {
329 g = 0.5*dt*veta;
330 mr1 = exp(g);
331 mr2 = series_sinhx(g);
332 }
333 else
334 {
335 mr1 = 1.0;
336 mr2 = 1.0;
337 }
338
339 for (n = start; n < nrend; n++)
340 {
341
342 if (cFREEZE)
343 {
344 gf = cFREEZE[n];
345 }
346
347 for (d = 0; d < DIM; d++)
348 {
349 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
350 {
351 xprime[n][d] = mr1*(mr1*x[n][d]+mr2*dt*v[n][d]);
352 }
353 else
354 {
355 xprime[n][d] = x[n][d];
356 }
357 }
358 }
359 } /* do_update_vv_pos */
360
361 static void do_update_visc(int start, int nrend, double dt,
362 t_grp_tcstat *tcstat,
363 double nh_vxi[],
364 real invmass[],
365 unsigned short ptype[], unsigned short cTC[],
366 rvec x[], rvec xprime[], rvec v[],
367 rvec f[], matrix M, matrix box, real
368 cos_accel, real vcos,
369 gmx_bool bNH, gmx_bool bPR)
370 {
371 double imass, w_dt;
372 int gt = 0;
373 real vn, vc;
374 real lg, vxi = 0, vv;
375 real fac, cosz;
376 rvec vrel;
377 int n, d;
378
379 fac = 2*M_PI/(box[ZZ][ZZ]);
380
381 if (bNH || bPR)
382 {
383 /* Update with coupling to extended ensembles, used for
384 * Nose-Hoover and Parrinello-Rahman coupling
385 */
386 for (n = start; n < nrend; n++)
387 {
388 imass = invmass[n];
389 if (cTC)
390 {
391 gt = cTC[n];
392 }
393 lg = tcstat[gt].lambda;
394 cosz = cos(fac*x[n][ZZ]);
395
396 copy_rvec(v[n], vrel);
397
398 vc = cosz*vcos;
399 vrel[XX] -= vc;
400 if (bNH)
401 {
402 vxi = nh_vxi[gt];
403 }
404 for (d = 0; d < DIM; d++)
405 {
406 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
407 {
408 vn = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
409 - iprod(M[d], vrel)))/(1 + 0.5*vxi*dt);
410 if (d == XX)
411 {
412 vn += vc + dt*cosz*cos_accel;
413 }
414 v[n][d] = vn;
415 xprime[n][d] = x[n][d]+vn*dt;
416 }
417 else
418 {
419 xprime[n][d] = x[n][d];
420 }
421 }
422 }
423 }
424 else
425 {
426 /* Classic version of update, used with berendsen coupling */
427 for (n = start; n < nrend; n++)
428 {
429 w_dt = invmass[n]*dt;
430 if (cTC)
431 {
432 gt = cTC[n];
433 }
434 lg = tcstat[gt].lambda;
435 cosz = cos(fac*x[n][ZZ]);
436
437 for (d = 0; d < DIM; d++)
438 {
439 vn = v[n][d];
440
441 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
442 {
443 if (d == XX)
444 {
445 vc = cosz*vcos;
446 /* Do not scale the cosine velocity profile */
447 vv = vc + lg*(vn - vc + f[n][d]*w_dt);
448 /* Add the cosine accelaration profile */
449 vv += dt*cosz*cos_accel;
450 }
451 else
452 {
453 vv = lg*(vn + f[n][d]*w_dt);
454 }
455 v[n][d] = vv;
456 xprime[n][d] = x[n][d]+vv*dt;
457 }
458 else
459 {
460 v[n][d] = 0.0;
461 xprime[n][d] = x[n][d];
462 }
463 }
464 }
465 }
466 }
467
468 static gmx_stochd_t *init_stochd(t_inputrec *ir)
469 {
470 gmx_stochd_t *sd;
471 gmx_sd_const_t *sdc;
472 int ngtc, n;
473 real y;
474
475 snew(sd, 1);
476
477 ngtc = ir->opts.ngtc;
478
479 if (ir->eI == eiBD)
480 {
481 snew(sd->bd_rf, ngtc);
482 }
483 else if (EI_SD(ir->eI))
484 {
485 snew(sd->sdc, ngtc);
486 snew(sd->sdsig, ngtc);
487
488 sdc = sd->sdc;
489 for (n = 0; n < ngtc; n++)
490 {
491 if (ir->opts.tau_t[n] > 0)
492 {
493 sdc[n].gdt = ir->delta_t/ir->opts.tau_t[n];
494 sdc[n].eph = exp(sdc[n].gdt/2);
495 sdc[n].emh = exp(-sdc[n].gdt/2);
496 sdc[n].em = exp(-sdc[n].gdt);
497 }
498 else
499 {
500 /* No friction and noise on this group */
501 sdc[n].gdt = 0;
502 sdc[n].eph = 1;
503 sdc[n].emh = 1;
504 sdc[n].em = 1;
505 }
506 if (sdc[n].gdt >= 0.05)
507 {
508 sdc[n].b = sdc[n].gdt*(sdc[n].eph*sdc[n].eph - 1)
509 - 4*(sdc[n].eph - 1)*(sdc[n].eph - 1);
510 sdc[n].c = sdc[n].gdt - 3 + 4*sdc[n].emh - sdc[n].em;
511 sdc[n].d = 2 - sdc[n].eph - sdc[n].emh;
512 }
513 else
514 {
515 y = sdc[n].gdt/2;
516 /* Seventh order expansions for small y */
517 sdc[n].b = y*y*y*y*(1/3.0+y*(1/3.0+y*(17/90.0+y*7/9.0)));
518 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))));
519 sdc[n].d = y*y*(-1+y*y*(-1/12.0-y*y/360.0));
520 }
521 if (debug)
522 {
523 fprintf(debug, "SD const tc-grp %d: b %g c %g d %g\n",
524 n, sdc[n].b, sdc[n].c, sdc[n].d);
525 }
526 }
527 }
528 else if (ETC_ANDERSEN(ir->etc))
529 {
530 int ngtc;
531 t_grpopts *opts;
532 real reft;
533
534 opts = &ir->opts;
535 ngtc = opts->ngtc;
536
537 snew(sd->randomize_group, ngtc);
538 snew(sd->boltzfac, ngtc);
539
540 /* for now, assume that all groups, if randomized, are randomized at the same rate, i.e. tau_t is the same. */
541 /* since constraint groups don't necessarily match up with temperature groups! This is checked in readir.c */
542
543 for (n = 0; n < ngtc; n++)
544 {
545 reft = std::max<real>(0, opts->ref_t[n]);
546 if ((opts->tau_t[n] > 0) && (reft > 0)) /* tau_t or ref_t = 0 means that no randomization is done */
547 {
548 sd->randomize_group[n] = TRUE;
549 sd->boltzfac[n] = BOLTZ*opts->ref_t[n];
550 }
551 else
552 {
553 sd->randomize_group[n] = FALSE;
554 }
555 }
556 }
557 return sd;
558 }
559
560 gmx_update_t init_update(t_inputrec *ir)
561 {
562 t_gmx_update *upd;
563
564 snew(upd, 1);
565
566 if (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE || ETC_ANDERSEN(ir->etc))
567 {
568 upd->sd = init_stochd(ir);
569 }
570
571 upd->xp = NULL;
572 upd->xp_nalloc = 0;
573
574 return upd;
575 }
576
577 static void do_update_sd1(gmx_stochd_t *sd,
578 int start, int nrend, double dt,
579 rvec accel[], ivec nFreeze[],
580 real invmass[], unsigned short ptype[],
581 unsigned short cFREEZE[], unsigned short cACC[],
582 unsigned short cTC[],
583 rvec x[], rvec xprime[], rvec v[], rvec f[],
584 int ngtc, real ref_t[],
585 gmx_bool bDoConstr,
586 gmx_bool bFirstHalfConstr,
587 gmx_int64_t step, int seed, int* gatindex)
588 {
589 gmx_sd_const_t *sdc;
590 gmx_sd_sigma_t *sig;
591 real kT;
592 int gf = 0, ga = 0, gt = 0;
593 real ism;
594 int n, d;
595
596 sdc = sd->sdc;
597 sig = sd->sdsig;
598
599 for (n = 0; n < ngtc; n++)
600 {
601 kT = BOLTZ*ref_t[n];
602 /* The mass is encounted for later, since this differs per atom */
603 sig[n].V = sqrt(kT*(1 - sdc[n].em*sdc[n].em));
604 }
605
606 if (!bDoConstr)
607 {
608 for (n = start; n < nrend; n++)
609 {
610 real rnd[3];
611 int ng = gatindex ? gatindex[n] : n;
612
613 ism = sqrt(invmass[n]);
614 if (cFREEZE)
615 {
616 gf = cFREEZE[n];
617 }
618 if (cACC)
619 {
620 ga = cACC[n];
621 }
622 if (cTC)
623 {
624 gt = cTC[n];
625 }
626
627 gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
628
629 for (d = 0; d < DIM; d++)
630 {
631 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
632 {
633 real sd_V, vn;
634
635 sd_V = ism*sig[gt].V*rnd[d];
636 vn = v[n][d] + (invmass[n]*f[n][d] + accel[ga][d])*dt;
637 v[n][d] = vn*sdc[gt].em + sd_V;
638 /* Here we include half of the friction+noise
639 * update of v into the integration of x.
640 */
641 xprime[n][d] = x[n][d] + 0.5*(vn + v[n][d])*dt;
642 }
643 else
644 {
645 v[n][d] = 0.0;
646 xprime[n][d] = x[n][d];
647 }
648 }
649 }
650 }
651 else
652 {
653 /* We do have constraints */
654 if (bFirstHalfConstr)
655 {
656 /* First update without friction and noise */
657 real im;
658
659 for (n = start; n < nrend; n++)
660 {
661 im = invmass[n];
662
663 if (cFREEZE)
664 {
665 gf = cFREEZE[n];
666 }
667 if (cACC)
668 {
669 ga = cACC[n];
670 }
671
672 for (d = 0; d < DIM; d++)
673 {
674 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
675 {
676 v[n][d] = v[n][d] + (im*f[n][d] + accel[ga][d])*dt;
677 xprime[n][d] = x[n][d] + v[n][d]*dt;
678 }
679 else
680 {
681 v[n][d] = 0.0;
682 xprime[n][d] = x[n][d];
683 }
684 }
685 }
686 }
687 else
688 {
689 /* Update friction and noise only */
690 for (n = start; n < nrend; n++)
691 {
692 real rnd[3];
693 int ng = gatindex ? gatindex[n] : n;
694
695 ism = sqrt(invmass[n]);
696 if (cFREEZE)
697 {
698 gf = cFREEZE[n];
699 }
700 if (cTC)
701 {
702 gt = cTC[n];
703 }
704
705 gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
706
707 for (d = 0; d < DIM; d++)
708 {
709 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
710 {
711 real sd_V, vn;
712
713 sd_V = ism*sig[gt].V*rnd[d];
714 vn = v[n][d];
715 v[n][d] = vn*sdc[gt].em + sd_V;
716 /* Add the friction and noise contribution only */
717 xprime[n][d] = xprime[n][d] + 0.5*(v[n][d] - vn)*dt;
718 }
719 }
720 }
721 }
722 }
723 }
724
725 static void check_sd2_work_data_allocation(gmx_stochd_t *sd, int nrend)
726 {
727 if (nrend > sd->sd_V_nalloc)
728 {
729 sd->sd_V_nalloc = over_alloc_dd(nrend);
730 srenew(sd->sd_V, sd->sd_V_nalloc);
731 }
732 }
733
734 static void do_update_sd2_Tconsts(gmx_stochd_t *sd,
735 int ngtc,
736 const real tau_t[],
737 const real ref_t[])
738 {
739 /* This is separated from the update below, because it is single threaded */
740 gmx_sd_const_t *sdc;
741 gmx_sd_sigma_t *sig;
742 int gt;
743 real kT;
744
745 sdc = sd->sdc;
746 sig = sd->sdsig;
747
748 for (gt = 0; gt < ngtc; gt++)
749 {
750 kT = BOLTZ*ref_t[gt];
751 /* The mass is encounted for later, since this differs per atom */
752 sig[gt].V = sqrt(kT*(1-sdc[gt].em));
753 sig[gt].X = sqrt(kT*sqr(tau_t[gt])*sdc[gt].c);
754 sig[gt].Yv = sqrt(kT*sdc[gt].b/sdc[gt].c);
755 sig[gt].Yx = sqrt(kT*sqr(tau_t[gt])*sdc[gt].b/(1-sdc[gt].em));
756 }
757 }
758
759 static void do_update_sd2(gmx_stochd_t *sd,
760 gmx_bool bInitStep,
761 int start, int nrend,
762 rvec accel[], ivec nFreeze[],
763 real invmass[], unsigned short ptype[],
764 unsigned short cFREEZE[], unsigned short cACC[],
765 unsigned short cTC[],
766 rvec x[], rvec xprime[], rvec v[], rvec f[],
767 rvec sd_X[],
768 const real tau_t[],
769 gmx_bool bFirstHalf, gmx_int64_t step, int seed,
770 int* gatindex)
771 {
772 gmx_sd_const_t *sdc;
773 gmx_sd_sigma_t *sig;
774 /* The random part of the velocity update, generated in the first
775 * half of the update, needs to be remembered for the second half.
776 */
777 rvec *sd_V;
778 int gf = 0, ga = 0, gt = 0;
779 real vn = 0, Vmh, Xmh;
780 real ism;
781 int n, d, ng;
782
783 sdc = sd->sdc;
784 sig = sd->sdsig;
785 sd_V = sd->sd_V;
786
787 for (n = start; n < nrend; n++)
788 {
789 real rnd[6], rndi[3];
790 ng = gatindex ? gatindex[n] : n;
791 ism = sqrt(invmass[n]);
792 if (cFREEZE)
793 {
794 gf = cFREEZE[n];
795 }
796 if (cACC)
797 {
798 ga = cACC[n];
799 }
800 if (cTC)
801 {
802 gt = cTC[n];
803 }
804
805 gmx_rng_cycle_6gaussian_table(step*2+(bFirstHalf ? 1 : 2), ng, seed, RND_SEED_UPDATE, rnd);
806 if (bInitStep)
807 {
808 gmx_rng_cycle_3gaussian_table(step*2, ng, seed, RND_SEED_UPDATE, rndi);
809 }
810 for (d = 0; d < DIM; d++)
811 {
812 if (bFirstHalf)
813 {
814 vn = v[n][d];
815 }
816 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
817 {
818 if (bFirstHalf)
819 {
820 if (bInitStep)
821 {
822 sd_X[n][d] = ism*sig[gt].X*rndi[d];
823 }
824 Vmh = sd_X[n][d]*sdc[gt].d/(tau_t[gt]*sdc[gt].c)
825 + ism*sig[gt].Yv*rnd[d*2];
826 sd_V[n][d] = ism*sig[gt].V*rnd[d*2+1];
827
828 v[n][d] = vn*sdc[gt].em
829 + (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 - sdc[gt].em)
830 + sd_V[n][d] - sdc[gt].em*Vmh;
831
832 xprime[n][d] = x[n][d] + v[n][d]*tau_t[gt]*(sdc[gt].eph - sdc[gt].emh);
833 }
834 else
835 {
836 /* Correct the velocities for the constraints.
837 * This operation introduces some inaccuracy,
838 * since the velocity is determined from differences in coordinates.
839 */
840 v[n][d] =
841 (xprime[n][d] - x[n][d])/(tau_t[gt]*(sdc[gt].eph - sdc[gt].emh));
842
843 Xmh = sd_V[n][d]*tau_t[gt]*sdc[gt].d/(sdc[gt].em-1)
844 + ism*sig[gt].Yx*rnd[d*2];
845 sd_X[n][d] = ism*sig[gt].X*rnd[d*2+1];
846
847 xprime[n][d] += sd_X[n][d] - Xmh;
848
849 }
850 }
851 else
852 {
853 if (bFirstHalf)
854 {
855 v[n][d] = 0.0;
856 xprime[n][d] = x[n][d];
857 }
858 }
859 }
860 }
861 }
862
863 static void do_update_bd_Tconsts(double dt, real friction_coefficient,
864 int ngtc, const real ref_t[],
865 real *rf)
866 {
867 /* This is separated from the update below, because it is single threaded */
868 int gt;
869
870 if (friction_coefficient != 0)
871 {
872 for (gt = 0; gt < ngtc; gt++)
873 {
874 rf[gt] = sqrt(2.0*BOLTZ*ref_t[gt]/(friction_coefficient*dt));
875 }
876 }
877 else
878 {
879 for (gt = 0; gt < ngtc; gt++)
880 {
881 rf[gt] = sqrt(2.0*BOLTZ*ref_t[gt]);
882 }
883 }
884 }
885
886 static void do_update_bd(int start, int nrend, double dt,
887 ivec nFreeze[],
888 real invmass[], unsigned short ptype[],
889 unsigned short cFREEZE[], unsigned short cTC[],
890 rvec x[], rvec xprime[], rvec v[],
891 rvec f[], real friction_coefficient,
892 real *rf, gmx_int64_t step, int seed,
893 int* gatindex)
894 {
895 /* note -- these appear to be full step velocities . . . */
896 int gf = 0, gt = 0;
897 real vn;
898 real invfr = 0;
899 int n, d;
900
901 if (friction_coefficient != 0)
902 {
903 invfr = 1.0/friction_coefficient;
904 }
905
906 for (n = start; (n < nrend); n++)
907 {
908 real rnd[3];
909 int ng = gatindex ? gatindex[n] : n;
910
911 if (cFREEZE)
912 {
913 gf = cFREEZE[n];
914 }
915 if (cTC)
916 {
917 gt = cTC[n];
918 }
919 gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
920 for (d = 0; (d < DIM); d++)
921 {
922 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
923 {
924 if (friction_coefficient != 0)
925 {
926 vn = invfr*f[n][d] + rf[gt]*rnd[d];
927 }
928 else
929 {
930 /* NOTE: invmass = 2/(mass*friction_constant*dt) */
931 vn = 0.5*invmass[n]*f[n][d]*dt
932 + sqrt(0.5*invmass[n])*rf[gt]*rnd[d];
933 }
934
935 v[n][d] = vn;
936 xprime[n][d] = x[n][d]+vn*dt;
937 }
938 else
939 {
940 v[n][d] = 0.0;
941 xprime[n][d] = x[n][d];
942 }
943 }
944 }
945 }
946
947 static void dump_it_all(FILE gmx_unused *fp, const char gmx_unused *title,
948 int gmx_unused natoms, rvec gmx_unused x[], rvec gmx_unused xp[],
949 rvec gmx_unused v[], rvec gmx_unused f[])
950 {
951 #ifdef DEBUG
952 if (fp)
953 {
954 fprintf(fp, "%s\n", title);
955 pr_rvecs(fp, 0, "x", x, natoms);
956 pr_rvecs(fp, 0, "xp", xp, natoms);
957 pr_rvecs(fp, 0, "v", v, natoms);
958 pr_rvecs(fp, 0, "f", f, natoms);
959 }
960 #endif
961 }
962
963 static void calc_ke_part_normal(rvec v[], t_grpopts *opts, t_mdatoms *md,
964 gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
965 {
966 int g;
967 t_grp_tcstat *tcstat = ekind->tcstat;
968 t_grp_acc *grpstat = ekind->grpstat;
969 int nthread, thread;
970
971 /* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also
972 an option, but not supported now.
973 bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
974 */
975
976 /* group velocities are calculated in update_ekindata and
977 * accumulated in acumulate_groups.
978 * Now the partial global and groups ekin.
979 */
980 for (g = 0; (g < opts->ngtc); g++)
981 {
982 copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
983 if (bEkinAveVel)
984 {
985 clear_mat(tcstat[g].ekinf);
986 tcstat[g].ekinscalef_nhc = 1.0; /* need to clear this -- logic is complicated! */
987 }
988 else
989 {
990 clear_mat(tcstat[g].ekinh);
991 }
992 }
993 ekind->dekindl_old = ekind->dekindl;
994 nthread = gmx_omp_nthreads_get(emntUpdate);
995
996 #pragma omp parallel for num_threads(nthread) schedule(static)
997 for (thread = 0; thread < nthread; thread++)
998 {
999 // This OpenMP only loops over arrays and does not call any functions
1000 // or memory allocation. It should not be able to throw, so for now
1001 // we do not need a try/catch wrapper.
1002 int start_t, end_t, n;
1003 int ga, gt;
1004 rvec v_corrt;
1005 real hm;
1006 int d, m;
1007 matrix *ekin_sum;
1008 real *dekindl_sum;
1009
1010 start_t = ((thread+0)*md->homenr)/nthread;
1011 end_t = ((thread+1)*md->homenr)/nthread;
1012
1013 ekin_sum = ekind->ekin_work[thread];
1014 dekindl_sum = ekind->dekindl_work[thread];
1015
1016 for (gt = 0; gt < opts->ngtc; gt++)
1017 {
1018 clear_mat(ekin_sum[gt]);
1019 }
1020 *dekindl_sum = 0.0;
1021
1022 ga = 0;
1023 gt = 0;
1024 for (n = start_t; n < end_t; n++)
1025 {
1026 if (md->cACC)
1027 {
1028 ga = md->cACC[n];
1029 }
1030 if (md->cTC)
1031 {
1032 gt = md->cTC[n];
1033 }
1034 hm = 0.5*md->massT[n];
1035
1036 for (d = 0; (d < DIM); d++)
1037 {
1038 v_corrt[d] = v[n][d] - grpstat[ga].u[d];
1039 }
1040 for (d = 0; (d < DIM); d++)
1041 {
1042 for (m = 0; (m < DIM); m++)
1043 {
1044 /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
1045 ekin_sum[gt][m][d] += hm*v_corrt[m]*v_corrt[d];
1046 }
1047 }
1048 if (md->nMassPerturbed && md->bPerturbed[n])
1049 {
1050 *dekindl_sum +=
1051 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
1052 }
1053 }
1054 }
1055
1056 ekind->dekindl = 0;
1057 for (thread = 0; thread < nthread; thread++)
1058 {
1059 for (g = 0; g < opts->ngtc; g++)
1060 {
1061 if (bEkinAveVel)
1062 {
1063 m_add(tcstat[g].ekinf, ekind->ekin_work[thread][g],
1064 tcstat[g].ekinf);
1065 }
1066 else
1067 {
1068 m_add(tcstat[g].ekinh, ekind->ekin_work[thread][g],
1069 tcstat[g].ekinh);
1070 }
1071 }
1072
1073 ekind->dekindl += *ekind->dekindl_work[thread];
1074 }
1075
1076 inc_nrnb(nrnb, eNR_EKIN, md->homenr);
1077 }
1078
1079 static void calc_ke_part_visc(matrix box, rvec x[], rvec v[],
1080 t_grpopts *opts, t_mdatoms *md,
1081 gmx_ekindata_t *ekind,
1082 t_nrnb *nrnb, gmx_bool bEkinAveVel)
1083 {
1084 int start = 0, homenr = md->homenr;
1085 int g, d, n, m, gt = 0;
1086 rvec v_corrt;
1087 real hm;
1088 t_grp_tcstat *tcstat = ekind->tcstat;
1089 t_cos_acc *cosacc = &(ekind->cosacc);
1090 real dekindl;
1091 real fac, cosz;
1092 double mvcos;
1093
1094 for (g = 0; g < opts->ngtc; g++)
1095 {
1096 copy_mat(ekind->tcstat[g].ekinh, ekind->tcstat[g].ekinh_old);
1097 clear_mat(ekind->tcstat[g].ekinh);
1098 }
1099 ekind->dekindl_old = ekind->dekindl;
1100
1101 fac = 2*M_PI/box[ZZ][ZZ];
1102 mvcos = 0;
1103 dekindl = 0;
1104 for (n = start; n < start+homenr; n++)
1105 {
1106 if (md->cTC)
1107 {
1108 gt = md->cTC[n];
1109 }
1110 hm = 0.5*md->massT[n];
1111
1112 /* Note that the times of x and v differ by half a step */
1113 /* MRS -- would have to be changed for VV */
1114 cosz = cos(fac*x[n][ZZ]);
1115 /* Calculate the amplitude of the new velocity profile */
1116 mvcos += 2*cosz*md->massT[n]*v[n][XX];
1117
1118 copy_rvec(v[n], v_corrt);
1119 /* Subtract the profile for the kinetic energy */
1120 v_corrt[XX] -= cosz*cosacc->vcos;
1121 for (d = 0; (d < DIM); d++)
1122 {
1123 for (m = 0; (m < DIM); m++)
1124 {
1125 /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
1126 if (bEkinAveVel)
1127 {
1128 tcstat[gt].ekinf[m][d] += hm*v_corrt[m]*v_corrt[d];
1129 }
1130 else
1131 {
1132 tcstat[gt].ekinh[m][d] += hm*v_corrt[m]*v_corrt[d];
1133 }
1134 }
1135 }
1136 if (md->nPerturbed && md->bPerturbed[n])
1137 {
1138 /* The minus sign here might be confusing.
1139 * The kinetic contribution from dH/dl doesn't come from
1140 * d m(l)/2 v^2 / dl, but rather from d p^2/2m(l) / dl,
1141 * where p are the momenta. The difference is only a minus sign.
1142 */
1143 dekindl -= 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
1144 }
1145 }
1146 ekind->dekindl = dekindl;
1147 cosacc->mvcos = mvcos;
1148
1149 inc_nrnb(nrnb, eNR_EKIN, homenr);
1150 }
1151
1152 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
1153 gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
1154 {
1155 if (ekind->cosacc.cos_accel == 0)
1156 {
1157 calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel);
1158 }
1159 else
1160 {
1161 calc_ke_part_visc(state->box, state->x, state->v, opts, md, ekind, nrnb, bEkinAveVel);
1162 }
1163 }
1164
1165 extern void init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir)
1166 {
1167 ekinstate->ekin_n = ir->opts.ngtc;
1168 snew(ekinstate->ekinh, ekinstate->ekin_n);
1169 snew(ekinstate->ekinf, ekinstate->ekin_n);
1170 snew(ekinstate->ekinh_old, ekinstate->ekin_n);
1171 snew(ekinstate->ekinscalef_nhc, ekinstate->ekin_n);
1172 snew(ekinstate->ekinscaleh_nhc, ekinstate->ekin_n);
1173 snew(ekinstate->vscale_nhc, ekinstate->ekin_n);
1174 ekinstate->dekindl = 0;
1175 ekinstate->mvcos = 0;
1176 }
1177
1178 void update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind)
1179 {
1180 int i;
1181
1182 for (i = 0; i < ekinstate->ekin_n; i++)
1183 {
1184 copy_mat(ekind->tcstat[i].ekinh, ekinstate->ekinh[i]);
1185 copy_mat(ekind->tcstat[i].ekinf, ekinstate->ekinf[i]);
1186 copy_mat(ekind->tcstat[i].ekinh_old, ekinstate->ekinh_old[i]);
1187 ekinstate->ekinscalef_nhc[i] = ekind->tcstat[i].ekinscalef_nhc;
1188 ekinstate->ekinscaleh_nhc[i] = ekind->tcstat[i].ekinscaleh_nhc;
1189 ekinstate->vscale_nhc[i] = ekind->tcstat[i].vscale_nhc;
1190 }
1191
1192 copy_mat(ekind->ekin, ekinstate->ekin_total);
1193 ekinstate->dekindl = ekind->dekindl;
1194 ekinstate->mvcos = ekind->cosacc.mvcos;
1195
1196 }
1197
1198 void restore_ekinstate_from_state(t_commrec *cr,
1199 gmx_ekindata_t *ekind, const ekinstate_t *ekinstate)
1200 {
1201 int i, n;
1202
1203 if (MASTER(cr))
1204 {
1205 for (i = 0; i < ekinstate->ekin_n; i++)
1206 {
1207 copy_mat(ekinstate->ekinh[i], ekind->tcstat[i].ekinh);
1208 copy_mat(ekinstate->ekinf[i], ekind->tcstat[i].ekinf);
1209 copy_mat(ekinstate->ekinh_old[i], ekind->tcstat[i].ekinh_old);
1210 ekind->tcstat[i].ekinscalef_nhc = ekinstate->ekinscalef_nhc[i];
1211 ekind->tcstat[i].ekinscaleh_nhc = ekinstate->ekinscaleh_nhc[i];
1212 ekind->tcstat[i].vscale_nhc = ekinstate->vscale_nhc[i];
1213 }
1214
1215 copy_mat(ekinstate->ekin_total, ekind->ekin);
1216
1217 ekind->dekindl = ekinstate->dekindl;
1218 ekind->cosacc.mvcos = ekinstate->mvcos;
1219 n = ekinstate->ekin_n;
1220 }
1221
1222 if (PAR(cr))
1223 {
1224 gmx_bcast(sizeof(n), &n, cr);
1225 for (i = 0; i < n; i++)
1226 {
1227 gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinh[0][0]),
1228 ekind->tcstat[i].ekinh[0], cr);
1229 gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinf[0][0]),
1230 ekind->tcstat[i].ekinf[0], cr);
1231 gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinh_old[0][0]),
1232 ekind->tcstat[i].ekinh_old[0], cr);
1233
1234 gmx_bcast(sizeof(ekind->tcstat[i].ekinscalef_nhc),
1235 &(ekind->tcstat[i].ekinscalef_nhc), cr);
1236 gmx_bcast(sizeof(ekind->tcstat[i].ekinscaleh_nhc),
1237 &(ekind->tcstat[i].ekinscaleh_nhc), cr);
1238 gmx_bcast(sizeof(ekind->tcstat[i].vscale_nhc),
1239 &(ekind->tcstat[i].vscale_nhc), cr);
1240 }
1241 gmx_bcast(DIM*DIM*sizeof(ekind->ekin[0][0]),
1242 ekind->ekin[0], cr);
1243
1244 gmx_bcast(sizeof(ekind->dekindl), &ekind->dekindl, cr);
1245 gmx_bcast(sizeof(ekind->cosacc.mvcos), &ekind->cosacc.mvcos, cr);
1246 }
1247 }
1248
1249 void set_deform_reference_box(gmx_update_t upd, gmx_int64_t step, matrix box)
1250 {
1251 upd->deformref_step = step;
1252 copy_mat(box, upd->deformref_box);
1253 }
1254
1255 static void deform(gmx_update_t upd,
1256 int start, int homenr, rvec x[], matrix box,
1257 const t_inputrec *ir, gmx_int64_t step)
1258 {
1259 matrix bnew, invbox, mu;
1260 real elapsed_time;
1261 int i, j;
1262
1263 elapsed_time = (step + 1 - upd->deformref_step)*ir->delta_t;
1264 copy_mat(box, bnew);
1265 for (i = 0; i < DIM; i++)
1266 {
1267 for (j = 0; j < DIM; j++)
1268 {
1269 if (ir->deform[i][j] != 0)
1270 {
1271 bnew[i][j] =
1272 upd->deformref_box[i][j] + elapsed_time*ir->deform[i][j];
1273 }
1274 }
1275 }
1276 /* We correct the off-diagonal elements,
1277 * which can grow indefinitely during shearing,
1278 * so the shifts do not get messed up.
1279 */
1280 for (i = 1; i < DIM; i++)
1281 {
1282 for (j = i-1; j >= 0; j--)
1283 {
1284 while (bnew[i][j] - box[i][j] > 0.5*bnew[j][j])
1285 {
1286 rvec_dec(bnew[i], bnew[j]);
1287 }
1288 while (bnew[i][j] - box[i][j] < -0.5*bnew[j][j])
1289 {
1290 rvec_inc(bnew[i], bnew[j]);
1291 }
1292 }
1293 }
1294 m_inv_ur0(box, invbox);
1295 copy_mat(bnew, box);
1296 mmul_ur0(box, invbox, mu);
1297
1298 for (i = start; i < start+homenr; i++)
1299 {
1300 x[i][XX] = mu[XX][XX]*x[i][XX]+mu[YY][XX]*x[i][YY]+mu[ZZ][XX]*x[i][ZZ];
1301 x[i][YY] = mu[YY][YY]*x[i][YY]+mu[ZZ][YY]*x[i][ZZ];
1302 x[i][ZZ] = mu[ZZ][ZZ]*x[i][ZZ];
1303 }
1304 }
1305
1306 void update_tcouple(gmx_int64_t step,
1307 t_inputrec *inputrec,
1308 t_state *state,
1309 gmx_ekindata_t *ekind,
1310 t_extmass *MassQ,
1311 t_mdatoms *md)
1312
1313 {
1314 gmx_bool bTCouple = FALSE;
1315 real dttc;
1316 int i, offset;
1317
1318 /* if using vv with trotter decomposition methods, we do this elsewhere in the code */
1319 if (inputrec->etc != etcNO &&
1320 !(inputrecNvtTrotter(inputrec) || inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)))
1321 {
1322 /* We should only couple after a step where energies were determined (for leapfrog versions)
1323 or the step energies are determined, for velocity verlet versions */
1324
1325 if (EI_VV(inputrec->eI))
1326 {
1327 offset = 0;
1328 }
1329 else
1330 {
1331 offset = 1;
1332 }
1333 bTCouple = (inputrec->nsttcouple == 1 ||
1334 do_per_step(step+inputrec->nsttcouple-offset,
1335 inputrec->nsttcouple));
1336 }
1337
1338 if (bTCouple)
1339 {
1340 dttc = inputrec->nsttcouple*inputrec->delta_t;
1341
1342 switch (inputrec->etc)
1343 {
1344 case etcNO:
1345 break;
1346 case etcBERENDSEN:
1347 berendsen_tcoupl(inputrec, ekind, dttc);
1348 break;
1349 case etcNOSEHOOVER:
1350 nosehoover_tcoupl(&(inputrec->opts), ekind, dttc,
1351 state->nosehoover_xi, state->nosehoover_vxi, MassQ);
1352 break;
1353 case etcVRESCALE:
1354 vrescale_tcoupl(inputrec, step, ekind, dttc,
1355 state->therm_integral);
1356 break;
1357 }
1358 /* rescale in place here */
1359 if (EI_VV(inputrec->eI))
1360 {
1361 rescale_velocities(ekind, md, 0, md->homenr, state->v);
1362 }
1363 }
1364 else
1365 {
1366 /* Set the T scaling lambda to 1 to have no scaling */
1367 for (i = 0; (i < inputrec->opts.ngtc); i++)
1368 {
1369 ekind->tcstat[i].lambda = 1.0;
1370 }
1371 }
1372 }
1373
1374 void update_pcouple(FILE *fplog,
1375 gmx_int64_t step,
1376 t_inputrec *inputrec,
1377 t_state *state,
1378 matrix pcoupl_mu,
1379 matrix M,
1380 gmx_bool bInitStep)
1381 {
1382 gmx_bool bPCouple = FALSE;
1383 real dtpc = 0;
1384 int i;
1385
1386 /* if using Trotter pressure, we do this in coupling.c, so we leave it false. */
1387 if (inputrec->epc != epcNO && (!(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec))))
1388 {
1389 /* We should only couple after a step where energies were determined */
1390 bPCouple = (inputrec->nstpcouple == 1 ||
1391 do_per_step(step+inputrec->nstpcouple-1,
1392 inputrec->nstpcouple));
1393 }
1394
1395 clear_mat(pcoupl_mu);
1396 for (i = 0; i < DIM; i++)
1397 {
1398 pcoupl_mu[i][i] = 1.0;
1399 }
1400
1401 clear_mat(M);
1402
1403 if (bPCouple)
1404 {
1405 dtpc = inputrec->nstpcouple*inputrec->delta_t;
1406
1407 switch (inputrec->epc)
1408 {
1409 /* We can always pcoupl, even if we did not sum the energies
1410 * the previous step, since state->pres_prev is only updated
1411 * when the energies have been summed.
1412 */
1413 case (epcNO):
1414 break;
1415 case (epcBERENDSEN):
1416 if (!bInitStep)
1417 {
1418 berendsen_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, state->box,
1419 pcoupl_mu);
1420 }
1421 break;
1422 case (epcPARRINELLORAHMAN):
1423 parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev,
1424 state->box, state->box_rel, state->boxv,
1425 M, pcoupl_mu, bInitStep);
1426 break;
1427 default:
1428 break;
1429 }
1430 }
1431 }
1432
1433 static rvec *get_xprime(const t_state *state, gmx_update_t upd)
1434 {
1435 if (state->nalloc > upd->xp_nalloc)
1436 {
1437 upd->xp_nalloc = state->nalloc;
1438 srenew(upd->xp, upd->xp_nalloc);
1439 }
1440
1441 return upd->xp;
1442 }
1443
1444 void update_constraints(FILE *fplog,
1445 gmx_int64_t step,
1446 real *dvdlambda, /* the contribution to be added to the bonded interactions */
1447 t_inputrec *inputrec, /* input record and box stuff */
1448 t_mdatoms *md,
1449 t_state *state,
1450 gmx_bool bMolPBC,
1451 t_graph *graph,
1452 rvec force[], /* forces on home particles */
1453 t_idef *idef,
1454 tensor vir_part,
1455 t_commrec *cr,
1456 t_nrnb *nrnb,
1457 gmx_wallcycle_t wcycle,
1458 gmx_update_t upd,
1459 gmx_constr_t constr,
1460 gmx_bool bFirstHalf,
1461 gmx_bool bCalcVir)
1462 {
1463 gmx_bool bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
1464 double dt;
1465 int start, homenr, nrend, i, m;
1466 tensor vir_con;
1467 rvec *xprime = NULL;
1468 int nth, th;
1469
1470 if (constr)
1471 {
1472 bDoConstr = TRUE;
1473 }
1474 if (bFirstHalf && !EI_VV(inputrec->eI))
1475 {
1476 bDoConstr = FALSE;
1477 }
1478
1479 /* for now, SD update is here -- though it really seems like it
1480 should be reformulated as a velocity verlet method, since it has two parts */
1481
1482 start = 0;
1483 homenr = md->homenr;
1484 nrend = start+homenr;
1485
1486 dt = inputrec->delta_t;
1487
1488 /*
1489 * Steps (7C, 8C)
1490 * APPLY CONSTRAINTS:
1491 * BLOCK SHAKE
1492
1493 * When doing PR pressure coupling we have to constrain the
1494 * bonds in each iteration. If we are only using Nose-Hoover tcoupling
1495 * it is enough to do this once though, since the relative velocities
1496 * after this will be normal to the bond vector
1497 */
1498
1499 if (bDoConstr)
1500 {
1501 /* clear out constraints before applying */
1502 clear_mat(vir_part);
1503
1504 xprime = get_xprime(state, upd);
1505
1506 bLastStep = (step == inputrec->init_step+inputrec->nsteps);
1507 bLog = (do_per_step(step, inputrec->nstlog) || bLastStep || (step < 0));
1508 bEner = (do_per_step(step, inputrec->nstenergy) || bLastStep);
1509 /* Constrain the coordinates xprime */
1510 wallcycle_start(wcycle, ewcCONSTR);
1511 if (EI_VV(inputrec->eI) && bFirstHalf)
1512 {
1513 constrain(NULL, bLog, bEner, constr, idef,
1514 inputrec, cr, step, 1, 1.0, md,
1515 state->x, state->v, state->v,
1516 bMolPBC, state->box,
1517 state->lambda[efptBONDED], dvdlambda,
1518 NULL, bCalcVir ? &vir_con : NULL, nrnb, econqVeloc);
1519 }
1520 else
1521 {
1522 constrain(NULL, bLog, bEner, constr, idef,
1523 inputrec, cr, step, 1, 1.0, md,
1524 state->x, xprime, NULL,
1525 bMolPBC, state->box,
1526 state->lambda[efptBONDED], dvdlambda,
1527 state->v, bCalcVir ? &vir_con : NULL, nrnb, econqCoord);
1528 }
1529 wallcycle_stop(wcycle, ewcCONSTR);
1530
1531 where();
1532
1533 dump_it_all(fplog, "After Shake",
1534 state->natoms, state->x, xprime, state->v, force);
1535
1536 if (bCalcVir)
1537 {
1538 if (inputrec->eI == eiSD2)
1539 {
1540 /* A correction factor eph is needed for the SD constraint force */
1541 /* Here we can, unfortunately, not have proper corrections
1542 * for different friction constants, so we use the first one.
1543 */
1544 for (i = 0; i < DIM; i++)
1545 {
1546 for (m = 0; m < DIM; m++)
1547 {
1548 vir_part[i][m] += upd->sd->sdc[0].eph*vir_con[i][m];
1549 }
1550 }
1551 }
1552 else
1553 {
1554 m_add(vir_part, vir_con, vir_part);
1555 }
1556 if (debug)
1557 {
1558 pr_rvecs(debug, 0, "constraint virial", vir_part, DIM);
1559 }
1560 }
1561 }
1562
1563 where();
1564
1565 if (inputrec->eI == eiSD1 && bDoConstr && !bFirstHalf)
1566 {
1567 wallcycle_start(wcycle, ewcUPDATE);
1568 xprime = get_xprime(state, upd);
1569
1570 nth = gmx_omp_nthreads_get(emntUpdate);
1571
1572 #pragma omp parallel for num_threads(nth) schedule(static)
1573 for (th = 0; th < nth; th++)
1574 {
1575 try
1576 {
1577 int start_th, end_th;
1578
1579 start_th = start + ((nrend-start)* th )/nth;
1580 end_th = start + ((nrend-start)*(th+1))/nth;
1581
1582 /* The second part of the SD integration */
1583 do_update_sd1(upd->sd,
1584 start_th, end_th, dt,
1585 inputrec->opts.acc, inputrec->opts.nFreeze,
1586 md->invmass, md->ptype,
1587 md->cFREEZE, md->cACC, md->cTC,
1588 state->x, xprime, state->v, force,
1589 inputrec->opts.ngtc, inputrec->opts.ref_t,
1590 bDoConstr, FALSE,
1591 step, inputrec->ld_seed,
1592 DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
1593 }
1594 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1595 }
1596 inc_nrnb(nrnb, eNR_UPDATE, homenr);
1597 wallcycle_stop(wcycle, ewcUPDATE);
1598
1599 if (bDoConstr)
1600 {
1601 /* Constrain the coordinates xprime for half a time step */
1602 wallcycle_start(wcycle, ewcCONSTR);
1603
1604 constrain(NULL, bLog, bEner, constr, idef,
1605 inputrec, cr, step, 1, 0.5, md,
1606 state->x, xprime, NULL,
1607 bMolPBC, state->box,
1608 state->lambda[efptBONDED], dvdlambda,
1609 state->v, NULL, nrnb, econqCoord);
1610
1611 wallcycle_stop(wcycle, ewcCONSTR);
1612 }
1613 }
1614
1615 if ((inputrec->eI == eiSD2) && !(bFirstHalf))
1616 {
1617 wallcycle_start(wcycle, ewcUPDATE);
1618 xprime = get_xprime(state, upd);
1619
1620 nth = gmx_omp_nthreads_get(emntUpdate);
1621
1622 #pragma omp parallel for num_threads(nth) schedule(static)
1623 for (th = 0; th < nth; th++)
1624 {
1625 try
1626 {
1627 int start_th, end_th;
1628
1629 start_th = start + ((nrend-start)* th )/nth;
1630 end_th = start + ((nrend-start)*(th+1))/nth;
1631
1632 /* The second part of the SD integration */
1633 do_update_sd2(upd->sd,
1634 FALSE, start_th, end_th,
1635 inputrec->opts.acc, inputrec->opts.nFreeze,
1636 md->invmass, md->ptype,
1637 md->cFREEZE, md->cACC, md->cTC,
1638 state->x, xprime, state->v, force, state->sd_X,
1639 inputrec->opts.tau_t,
1640 FALSE, step, inputrec->ld_seed,
1641 DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
1642 }
1643 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1644 }
1645 inc_nrnb(nrnb, eNR_UPDATE, homenr);
1646 wallcycle_stop(wcycle, ewcUPDATE);
1647
1648 if (bDoConstr)
1649 {
1650 /* Constrain the coordinates xprime */
1651 wallcycle_start(wcycle, ewcCONSTR);
1652 constrain(NULL, bLog, bEner, constr, idef,
1653 inputrec, cr, step, 1, 1.0, md,
1654 state->x, xprime, NULL,
1655 bMolPBC, state->box,
1656 state->lambda[efptBONDED], dvdlambda,
1657 NULL, NULL, nrnb, econqCoord);
1658 wallcycle_stop(wcycle, ewcCONSTR);
1659 }
1660 }
1661
1662
1663 /* We must always unshift after updating coordinates; if we did not shake
1664 x was shifted in do_force */
1665
1666 if (!(bFirstHalf)) /* in the first half of vv, no shift. */
1667 {
1668 /* NOTE This part of the update actually does not belong with
1669 * the constraints, since we also call it without constraints.
1670 * But currently we always integrate to a temporary buffer and
1671 * then copy the results back here.
1672 */
1673 wallcycle_start_nocount(wcycle, ewcUPDATE);
1674
1675 if (graph && (graph->nnodes > 0))
1676 {
1677 unshift_x(graph, state->box, state->x, upd->xp);
1678 if (TRICLINIC(state->box))
1679 {
1680 inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
1681 }
1682 else
1683 {
1684 inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
1685 }
1686 }
1687 else
1688 {
1689 #ifndef __clang_analyzer__
1690 // cppcheck-suppress unreadVariable
1691 nth = gmx_omp_nthreads_get(emntUpdate);
1692 #endif
1693 #pragma omp parallel for num_threads(nth) schedule(static)
1694 for (i = start; i < nrend; i++)
1695 {
1696 // Trivial statement, does not throw
1697 copy_rvec(upd->xp[i], state->x[i]);
1698 }
1699 }
1700 wallcycle_stop(wcycle, ewcUPDATE);
1701
1702 dump_it_all(fplog, "After unshift",
1703 state->natoms, state->x, upd->xp, state->v, force);
1704 }
1705 /* ############# END the update of velocities and positions ######### */
1706 }
1707
1708 void update_box(FILE *fplog,
1709 gmx_int64_t step,
1710 t_inputrec *inputrec, /* input record and box stuff */
1711 t_mdatoms *md,
1712 t_state *state,
1713 rvec force[], /* forces on home particles */
1714 matrix pcoupl_mu,
1715 t_nrnb *nrnb,
1716 gmx_update_t upd)
1717 {
1718 double dt;
1719 int start, homenr, i, n, m;
1720
1721 start = 0;
1722 homenr = md->homenr;
1723
1724 dt = inputrec->delta_t;
1725
1726 where();
1727
1728 /* now update boxes */
1729 switch (inputrec->epc)
1730 {
1731 case (epcNO):
1732 break;
1733 case (epcBERENDSEN):
1734 /* We should only scale after a step where the pressure (kinetic
1735 * energy and virial) was calculated. This happens after the
1736 * coordinate update, whereas the current routine is called before
1737 * that, so we scale when step % nstpcouple = 1 instead of 0.
1738 */
1739 if (inputrec->nstpcouple == 1 || (step % inputrec->nstpcouple == 1))
1740 {
1741 berendsen_pscale(inputrec, pcoupl_mu, state->box, state->box_rel,
1742 start, homenr, state->x, md->cFREEZE, nrnb);
1743 }
1744 break;
1745 case (epcPARRINELLORAHMAN):
1746 /* The box velocities were updated in do_pr_pcoupl in the update
1747 * iteration, but we dont change the box vectors until we get here
1748 * since we need to be able to shift/unshift above.
1749 */
1750 for (i = 0; i < DIM; i++)
1751 {
1752 for (m = 0; m <= i; m++)
1753 {
1754 state->box[i][m] += dt*state->boxv[i][m];
1755 }
1756 }
1757 preserve_box_shape(inputrec, state->box_rel, state->box);
1758
1759 /* Scale the coordinates */
1760 for (n = start; (n < start+homenr); n++)
1761 {
1762 tmvmul_ur0(pcoupl_mu, state->x[n], state->x[n]);
1763 }
1764 break;
1765 case (epcMTTK):
1766 switch (inputrec->epct)
1767 {
1768 case (epctISOTROPIC):
1769 /* DIM * eta = ln V. so DIM*eta_new = DIM*eta_old + DIM*dt*veta =>
1770 ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) =>
1771 Side length scales as exp(veta*dt) */
1772
1773 msmul(state->box, exp(state->veta*dt), state->box);
1774
1775 /* Relate veta to boxv. veta = d(eta)/dT = (1/DIM)*1/V dV/dT.
1776 o If we assume isotropic scaling, and box length scaling
1777 factor L, then V = L^DIM (det(M)). So dV/dt = DIM
1778 L^(DIM-1) dL/dt det(M), and veta = (1/L) dL/dt. The
1779 determinant of B is L^DIM det(M), and the determinant
1780 of dB/dt is (dL/dT)^DIM det (M). veta will be
1781 (det(dB/dT)/det(B))^(1/3). Then since M =
1782 B_new*(vol_new)^(1/3), dB/dT_new = (veta_new)*B(new). */
1783
1784 msmul(state->box, state->veta, state->boxv);
1785 break;
1786 default:
1787 break;
1788 }
1789 break;
1790 default:
1791 break;
1792 }
1793
1794 if (inputrecDeform(inputrec))
1795 {
1796 deform(upd, start, homenr, state->x, state->box, inputrec, step);
1797 }
1798 where();
1799 dump_it_all(fplog, "After update",
1800 state->natoms, state->x, upd->xp, state->v, force);
1801 }
1802
1803 void update_coords(FILE *fplog,
1804 gmx_int64_t step,
1805 t_inputrec *inputrec, /* input record and box stuff */
1806 t_mdatoms *md,
1807 t_state *state,
1808 rvec *f, /* forces on home particles */
1809 t_fcdata *fcd,
1810 gmx_ekindata_t *ekind,
1811 matrix M,
1812 gmx_update_t upd,
1813 gmx_bool bInitStep,
1814 int UpdatePart,
1815 t_commrec *cr, /* these shouldn't be here -- need to think about it */
1816 gmx_constr_t constr)
1817 {
1818 gmx_bool bNH, bPR, bDoConstr = FALSE;
1819 double dt, alpha;
1820 int start, homenr, nrend;
1821 rvec *xprime;
1822 int nth, th;
1823
1824 bDoConstr = (NULL != constr);
1825
1826 /* Running the velocity half does nothing except for velocity verlet */
1827 if ((UpdatePart == etrtVELOCITY1 || UpdatePart == etrtVELOCITY2) &&
1828 !EI_VV(inputrec->eI))
1829 {
1830 gmx_incons("update_coords called for velocity without VV integrator");
1831 }
1832
1833 start = 0;
1834 homenr = md->homenr;
1835 nrend = start+homenr;
1836
1837 xprime = get_xprime(state, upd);
1838
1839 dt = inputrec->delta_t;
1840
1841 /* We need to update the NMR restraint history when time averaging is used */
1842 if (state->flags & (1<<estDISRE_RM3TAV))
1843 {
1844 update_disres_history(fcd, &state->hist);
1845 }
1846 if (state->flags & (1<<estORIRE_DTAV))
1847 {
1848 update_orires_history(fcd, &state->hist);
1849 }
1850
1851
1852 bNH = inputrec->etc == etcNOSEHOOVER;
1853 bPR = ((inputrec->epc == epcPARRINELLORAHMAN) || (inputrec->epc == epcMTTK));
1854
1855 /* ############# START The update of velocities and positions ######### */
1856 where();
1857 dump_it_all(fplog, "Before update",
1858 state->natoms, state->x, xprime, state->v, f);
1859
1860 if (inputrec->eI == eiSD2)
1861 {
1862 check_sd2_work_data_allocation(upd->sd, nrend);
1863
1864 do_update_sd2_Tconsts(upd->sd,
1865 inputrec->opts.ngtc,
1866 inputrec->opts.tau_t,
1867 inputrec->opts.ref_t);
1868 }
1869 if (inputrec->eI == eiBD)
1870 {
1871 do_update_bd_Tconsts(dt, inputrec->bd_fric,
1872 inputrec->opts.ngtc, inputrec->opts.ref_t,
1873 upd->sd->bd_rf);
1874 }
1875
1876 nth = gmx_omp_nthreads_get(emntUpdate);
1877
1878 #pragma omp parallel for num_threads(nth) schedule(static) private(alpha)
1879 for (th = 0; th < nth; th++)
1880 {
1881 try
1882 {
1883 int start_th, end_th;
1884
1885 start_th = start + ((nrend-start)* th )/nth;
1886 end_th = start + ((nrend-start)*(th+1))/nth;
1887
1888 switch (inputrec->eI)
1889 {
1890 case (eiMD):
1891 if (ekind->cosacc.cos_accel == 0)
1892 {
1893 do_update_md(start_th, end_th, dt,
1894 ekind->tcstat, state->nosehoover_vxi,
1895 ekind->bNEMD, ekind->grpstat, inputrec->opts.acc,
1896 inputrec->opts.nFreeze,
1897 md->invmass, md->ptype,
1898 md->cFREEZE, md->cACC, md->cTC,
1899 state->x, xprime, state->v, f, M,
1900 bNH, bPR);
1901 }
1902 else
1903 {
1904 do_update_visc(start_th, end_th, dt,
1905 ekind->tcstat, state->nosehoover_vxi,
1906 md->invmass, md->ptype,
1907 md->cTC, state->x, xprime, state->v, f, M,
1908 state->box,
1909 ekind->cosacc.cos_accel,
1910 ekind->cosacc.vcos,
1911 bNH, bPR);
1912 }
1913 break;
1914 case (eiSD1):
1915 /* With constraints, the SD1 update is done in 2 parts */
1916 do_update_sd1(upd->sd,
1917 start_th, end_th, dt,
1918 inputrec->opts.acc, inputrec->opts.nFreeze,
1919 md->invmass, md->ptype,
1920 md->cFREEZE, md->cACC, md->cTC,
1921 state->x, xprime, state->v, f,
1922 inputrec->opts.ngtc, inputrec->opts.ref_t,
1923 bDoConstr, TRUE,
1924 step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
1925 break;
1926 case (eiSD2):
1927 /* The SD2 update is always done in 2 parts,
1928 * because an extra constraint step is needed
1929 */
1930 do_update_sd2(upd->sd,
1931 bInitStep, start_th, end_th,
1932 inputrec->opts.acc, inputrec->opts.nFreeze,
1933 md->invmass, md->ptype,
1934 md->cFREEZE, md->cACC, md->cTC,
1935 state->x, xprime, state->v, f, state->sd_X,
1936 inputrec->opts.tau_t,
1937 TRUE, step, inputrec->ld_seed,
1938 DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
1939 break;
1940 case (eiBD):
1941 do_update_bd(start_th, end_th, dt,
1942 inputrec->opts.nFreeze, md->invmass, md->ptype,
1943 md->cFREEZE, md->cTC,
1944 state->x, xprime, state->v, f,
1945 inputrec->bd_fric,
1946 upd->sd->bd_rf,
1947 step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
1948 break;
1949 case (eiVV):
1950 case (eiVVAK):
1951 alpha = 1.0 + DIM/((double)inputrec->opts.nrdf[0]); /* assuming barostat coupled to group 0. */
1952 switch (UpdatePart)
1953 {
1954 case etrtVELOCITY1:
1955 case etrtVELOCITY2:
1956 do_update_vv_vel(start_th, end_th, dt,
1957 inputrec->opts.acc, inputrec->opts.nFreeze,
1958 md->invmass, md->ptype,
1959 md->cFREEZE, md->cACC,
1960 state->v, f,
1961 (bNH || bPR), state->veta, alpha);
1962 break;
1963 case etrtPOSITION:
1964 do_update_vv_pos(start_th, end_th, dt,
1965 inputrec->opts.nFreeze,
1966 md->ptype, md->cFREEZE,
1967 state->x, xprime, state->v,
1968 (bNH || bPR), state->veta);
1969 break;
1970 }
1971 break;
1972 default:
1973 gmx_fatal(FARGS, "Don't know how to update coordinates");
1974 break;
1975 }
1976 }
1977 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1978 }
1979
1980 }
1981
1982
1983 void correct_ekin(FILE *log, int start, int end, rvec v[], rvec vcm, real mass[],
1984 real tmass, tensor ekin)
1985 {
1986 /*
1987 * This is a debugging routine. It should not be called for production code
1988 *
1989 * The kinetic energy should calculated according to:
1990 * Ekin = 1/2 m (v-vcm)^2
1991 * However the correction is not always applied, since vcm may not be
1992 * known in time and we compute
1993 * Ekin' = 1/2 m v^2 instead
1994 * This can be corrected afterwards by computing
1995 * Ekin = Ekin' + 1/2 m ( -2 v vcm + vcm^2)
1996 * or in hsorthand:
1997 * Ekin = Ekin' - m v vcm + 1/2 m vcm^2
1998 */
1999 int i, j, k;
2000 real m, tm;
2001 rvec hvcm, mv;
2002 tensor dekin;
2003
2004 /* Local particles */
2005 clear_rvec(mv);
2006
2007 /* Processor dependent part. */
2008 tm = 0;
2009 for (i = start; (i < end); i++)
2010 {
2011 m = mass[i];
2012 tm += m;
2013 for (j = 0; (j < DIM); j++)
2014 {
2015 mv[j] += m*v[i][j];
2016 }
2017 }
2018 /* Shortcut */
2019 svmul(1/tmass, vcm, vcm);
2020 svmul(0.5, vcm, hvcm);
2021 clear_mat(dekin);
2022 for (j = 0; (j < DIM); j++)
2023 {
2024 for (k = 0; (k < DIM); k++)
2025 {
2026 dekin[j][k] += vcm[k]*(tm*hvcm[j]-mv[j]);
2027 }
2028 }
2029 pr_rvecs(log, 0, "dekin", dekin, DIM);
2030 pr_rvecs(log, 0, " ekin", ekin, DIM);
2031 fprintf(log, "dekin = %g, ekin = %g vcm = (%8.4f %8.4f %8.4f)\n",
2032 trace(dekin), trace(ekin), vcm[XX], vcm[YY], vcm[ZZ]);
2033 fprintf(log, "mv = (%8.4f %8.4f %8.4f)\n",
2034 mv[XX], mv[YY], mv[ZZ]);
2035 }
2036
2037 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr,
2038 t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr_t constr)
2039 {
2040
2041 real rate = (ir->delta_t)/ir->opts.tau_t[0];
2042
2043 if (ir->etc == etcANDERSEN && constr != NULL)
2044 {
2045 /* Currently, Andersen thermostat does not support constrained
2046 systems. Functionality exists in the andersen_tcoupl
2047 function in GROMACS 4.5.7 to allow this combination. That
2048 code could be ported to the current random-number
2049 generation approach, but has not yet been done because of
2050 lack of time and resources. */
2051 gmx_fatal(FARGS, "Normal Andersen is currently not supported with constraints, use massive Andersen instead");
2052 }
2053
2054 /* proceed with andersen if 1) it's fixed probability per
2055 particle andersen or 2) it's massive andersen and it's tau_t/dt */
2056 if ((ir->etc == etcANDERSEN) || do_per_step(step, (int)(1.0/rate)))
2057 {
2058 andersen_tcoupl(ir, step, cr, md, state, rate,
2059 upd->sd->randomize_group, upd->sd->boltzfac);
2060 return TRUE;
2061 }
2062 return FALSE;
2063 }
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