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43 #include "types/commrec.h"
53 #include "gromacs/math/units.h"
55 #include "gromacs/topology/mtop_util.h"
56 #include "chargegroup.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/pbcutil/mshift.h"
61 #include "gromacs/pbcutil/pbc.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/smalloc.h"
67 atom_id shell; /* The shell id */
68 atom_id nucl1, nucl2, nucl3; /* The nuclei connected to the shell */
69 /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
70 real k; /* force constant */
71 real k_1; /* 1 over force constant */
77 typedef struct gmx_shellfc {
78 int nshell_gl; /* The number of shells in the system */
79 t_shell *shell_gl; /* All the shells (for DD only) */
80 int *shell_index_gl; /* Global shell index (for DD only) */
81 gmx_bool bInterCG; /* Are there inter charge-group shells? */
82 int nshell; /* The number of local shells */
83 t_shell *shell; /* The local shells */
84 int shell_nalloc; /* The allocation size of shell */
85 gmx_bool bPredict; /* Predict shell positions */
86 gmx_bool bRequireInit; /* Require initialization of shell positions */
87 int nflexcon; /* The number of flexible constraints */
88 rvec *x[2]; /* Array for iterative minimization */
89 rvec *f[2]; /* Array for iterative minimization */
90 int x_nalloc; /* The allocation size of x and f */
91 rvec *acc_dir; /* Acceleration direction for flexcon */
92 rvec *x_old; /* Old coordinates for flexcon */
93 int flex_nalloc; /* The allocation size of acc_dir and x_old */
94 rvec *adir_xnold; /* Work space for init_adir */
95 rvec *adir_xnew; /* Work space for init_adir */
96 int adir_nalloc; /* Work space for init_adir */
100 static void pr_shell(FILE *fplog, int ns, t_shell s[])
104 fprintf(fplog, "SHELL DATA\n");
105 fprintf(fplog, "%5s %8s %5s %5s %5s\n",
106 "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
107 for (i = 0; (i < ns); i++)
109 fprintf(fplog, "%5d %8.3f %5d", s[i].shell, 1.0/s[i].k_1, s[i].nucl1);
112 fprintf(fplog, " %5d\n", s[i].nucl2);
114 else if (s[i].nnucl == 3)
116 fprintf(fplog, " %5d %5d\n", s[i].nucl2, s[i].nucl3);
120 fprintf(fplog, "\n");
125 static void predict_shells(FILE *fplog, rvec x[], rvec v[], real dt,
127 real mass[], gmx_mtop_t *mtop, gmx_bool bInit)
129 int i, m, s1, n1, n2, n3;
130 real dt_1, dt_2, dt_3, fudge, tm, m1, m2, m3;
132 gmx_mtop_atomlookup_t alook = NULL;
137 alook = gmx_mtop_atomlookup_init(mtop);
140 /* We introduce a fudge factor for performance reasons: with this choice
141 * the initial force on the shells is about a factor of two lower than
150 fprintf(fplog, "RELAX: Using prediction for initial shell placement\n");
161 for (i = 0; (i < ns); i++)
172 for (m = 0; (m < DIM); m++)
174 x[s1][m] += ptr[n1][m]*dt_1;
187 /* Not the correct masses with FE, but it is just a prediction... */
192 for (m = 0; (m < DIM); m++)
194 x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
209 /* Not the correct masses with FE, but it is just a prediction... */
210 gmx_mtop_atomnr_to_atom(alook, n1, &atom);
212 gmx_mtop_atomnr_to_atom(alook, n2, &atom);
214 gmx_mtop_atomnr_to_atom(alook, n3, &atom);
217 tm = dt_1/(m1+m2+m3);
218 for (m = 0; (m < DIM); m++)
220 x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
224 gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
230 gmx_mtop_atomlookup_destroy(alook);
234 gmx_shellfc_t init_shell_flexcon(FILE *fplog,
235 gmx_mtop_t *mtop, int nflexcon,
238 struct gmx_shellfc *shfc;
240 int *shell_index = NULL, *at2cg;
242 int n[eptNR], ns, nshell, nsi;
243 int i, j, nmol, type, mb, mt, a_offset, cg, mol, ftype, nra;
245 int aS, aN = 0; /* Shell and nucleus */
246 int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
247 #define NBT asize(bondtypes)
249 gmx_mtop_atomloop_block_t aloopb;
250 gmx_mtop_atomloop_all_t aloop;
251 gmx_ffparams_t *ffparams;
252 gmx_molblock_t *molb;
256 /* Count number of shells, and find their indices */
257 for (i = 0; (i < eptNR); i++)
262 aloopb = gmx_mtop_atomloop_block_init(mtop);
263 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
265 n[atom->ptype] += nmol;
270 /* Print the number of each particle type */
271 for (i = 0; (i < eptNR); i++)
275 fprintf(fplog, "There are: %d %ss\n", n[i], ptype_str[i]);
280 nshell = n[eptShell];
282 if (nshell == 0 && nflexcon == 0)
284 /* We're not doing shells or flexible constraints */
289 shfc->nflexcon = nflexcon;
296 /* We have shells: fill the shell data structure */
298 /* Global system sized array, this should be avoided */
299 snew(shell_index, mtop->natoms);
301 aloop = gmx_mtop_atomloop_all_init(mtop);
303 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
305 if (atom->ptype == eptShell)
307 shell_index[i] = nshell++;
313 /* Initiate the shell structures */
314 for (i = 0; (i < nshell); i++)
316 shell[i].shell = NO_ATID;
318 shell[i].nucl1 = NO_ATID;
319 shell[i].nucl2 = NO_ATID;
320 shell[i].nucl3 = NO_ATID;
321 /* shell[i].bInterCG=FALSE; */
326 ffparams = &mtop->ffparams;
328 /* Now fill the structures */
329 shfc->bInterCG = FALSE;
332 for (mb = 0; mb < mtop->nmolblock; mb++)
334 molb = &mtop->molblock[mb];
335 molt = &mtop->moltype[molb->type];
338 snew(at2cg, molt->atoms.nr);
339 for (cg = 0; cg < cgs->nr; cg++)
341 for (i = cgs->index[cg]; i < cgs->index[cg+1]; i++)
347 atom = molt->atoms.atom;
348 for (mol = 0; mol < molb->nmol; mol++)
350 for (j = 0; (j < NBT); j++)
352 ia = molt->ilist[bondtypes[j]].iatoms;
353 for (i = 0; (i < molt->ilist[bondtypes[j]].nr); )
356 ftype = ffparams->functype[type];
357 nra = interaction_function[ftype].nratoms;
359 /* Check whether we have a bond with a shell */
362 switch (bondtypes[j])
369 if (atom[ia[1]].ptype == eptShell)
374 else if (atom[ia[2]].ptype == eptShell)
381 aN = ia[4]; /* Dummy */
382 aS = ia[5]; /* Shell */
385 gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
392 /* Check whether one of the particles is a shell... */
393 nsi = shell_index[a_offset+aS];
394 if ((nsi < 0) || (nsi >= nshell))
396 gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d",
399 if (shell[nsi].shell == NO_ATID)
401 shell[nsi].shell = a_offset + aS;
404 else if (shell[nsi].shell != a_offset+aS)
406 gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
409 if (shell[nsi].nucl1 == NO_ATID)
411 shell[nsi].nucl1 = a_offset + aN;
413 else if (shell[nsi].nucl2 == NO_ATID)
415 shell[nsi].nucl2 = a_offset + aN;
417 else if (shell[nsi].nucl3 == NO_ATID)
419 shell[nsi].nucl3 = a_offset + aN;
425 pr_shell(fplog, ns, shell);
427 gmx_fatal(FARGS, "Can not handle more than three bonds per shell\n");
429 if (at2cg[aS] != at2cg[aN])
431 /* shell[nsi].bInterCG = TRUE; */
432 shfc->bInterCG = TRUE;
435 switch (bondtypes[j])
439 shell[nsi].k += ffparams->iparams[type].harmonic.krA;
442 shell[nsi].k += ffparams->iparams[type].cubic.kb;
446 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
448 gmx_fatal(FARGS, "polarize can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
450 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
451 ffparams->iparams[type].polarize.alpha;
454 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
456 gmx_fatal(FARGS, "water_pol can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
458 alpha = (ffparams->iparams[type].wpol.al_x+
459 ffparams->iparams[type].wpol.al_y+
460 ffparams->iparams[type].wpol.al_z)/3.0;
461 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
464 gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
472 a_offset += molt->atoms.nr;
474 /* Done with this molecule type */
478 /* Verify whether it's all correct */
481 gmx_fatal(FARGS, "Something weird with shells. They may not be bonded to something");
484 for (i = 0; (i < ns); i++)
486 shell[i].k_1 = 1.0/shell[i].k;
491 pr_shell(debug, ns, shell);
495 shfc->nshell_gl = ns;
496 shfc->shell_gl = shell;
497 shfc->shell_index_gl = shell_index;
499 shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
500 shfc->bRequireInit = FALSE;
505 fprintf(fplog, "\nWill never predict shell positions\n");
510 shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
511 if (shfc->bRequireInit && fplog)
513 fprintf(fplog, "\nWill always initiate shell positions\n");
521 predict_shells(fplog, x, NULL, 0, shfc->nshell_gl, shfc->shell_gl,
529 fprintf(fplog, "\nNOTE: there all shells that are connected to particles outside thier own charge group, will not predict shells positions during the run\n\n");
531 /* Prediction improves performance, so we should implement either:
532 * 1. communication for the atoms needed for prediction
533 * 2. prediction using the velocities of shells; currently the
534 * shell velocities are zeroed, it's a bit tricky to keep
535 * track of the shell displacements and thus the velocity.
537 shfc->bPredict = FALSE;
544 void make_local_shells(t_commrec *cr, t_mdatoms *md,
545 struct gmx_shellfc *shfc)
548 int a0, a1, *ind, nshell, i;
549 gmx_domdec_t *dd = NULL;
551 if (DOMAINDECOMP(cr))
559 /* Single node: we need all shells, just copy the pointer */
560 shfc->nshell = shfc->nshell_gl;
561 shfc->shell = shfc->shell_gl;
566 ind = shfc->shell_index_gl;
570 for (i = a0; i < a1; i++)
572 if (md->ptype[i] == eptShell)
574 if (nshell+1 > shfc->shell_nalloc)
576 shfc->shell_nalloc = over_alloc_dd(nshell+1);
577 srenew(shell, shfc->shell_nalloc);
581 shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
585 shell[nshell] = shfc->shell_gl[ind[i]];
588 /* With inter-cg shells we can no do shell prediction,
589 * so we do not need the nuclei numbers.
593 shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
594 if (shell[nshell].nnucl > 1)
596 shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
598 if (shell[nshell].nnucl > 2)
600 shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
603 shell[nshell].shell = i;
608 shfc->nshell = nshell;
612 static void do_1pos(rvec xnew, rvec xold, rvec f, real step)
630 static void do_1pos3(rvec xnew, rvec xold, rvec f, rvec step)
648 static void directional_sd(rvec xold[], rvec xnew[], rvec acc_dir[],
649 int start, int homenr, real step)
653 for (i = start; i < homenr; i++)
655 do_1pos(xnew[i], xold[i], acc_dir[i], step);
659 static void shell_pos_sd(rvec xcur[], rvec xnew[], rvec f[],
660 int ns, t_shell s[], int count)
662 const real step_scale_min = 0.8,
663 step_scale_increment = 0.2,
664 step_scale_max = 1.2,
665 step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
669 real step_min, step_max;
674 for (i = 0; (i < ns); i++)
679 for (d = 0; d < DIM; d++)
681 s[i].step[d] = s[i].k_1;
683 step_min = min(step_min, s[i].step[d]);
684 step_max = max(step_max, s[i].step[d]);
690 for (d = 0; d < DIM; d++)
692 dx = xcur[shell][d] - s[i].xold[d];
693 df = f[shell][d] - s[i].fold[d];
694 /* -dx/df gets used to generate an interpolated value, but would
695 * cause a NaN if df were binary-equal to zero. Values close to
696 * zero won't cause problems (because of the min() and max()), so
697 * just testing for binary inequality is OK. */
701 /* Scale the step size by a factor interpolated from
702 * step_scale_min to step_scale_max, as k_est goes from 0 to
703 * step_scale_multiple * s[i].step[d] */
705 step_scale_min * s[i].step[d] +
706 step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
711 if (gmx_numzero(dx)) /* 0 == dx */
713 /* Likely this will never happen, but if it does just
714 * don't scale the step. */
718 s[i].step[d] *= step_scale_max;
722 step_min = min(step_min, s[i].step[d]);
723 step_max = max(step_max, s[i].step[d]);
727 copy_rvec(xcur[shell], s[i].xold);
728 copy_rvec(f[shell], s[i].fold);
730 do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
734 fprintf(debug, "shell[%d] = %d\n", i, shell);
735 pr_rvec(debug, 0, "fshell", f[shell], DIM, TRUE);
736 pr_rvec(debug, 0, "xold", xcur[shell], DIM, TRUE);
737 pr_rvec(debug, 0, "step", s[i].step, DIM, TRUE);
738 pr_rvec(debug, 0, "xnew", xnew[shell], DIM, TRUE);
742 printf("step %.3e %.3e\n", step_min, step_max);
746 static void decrease_step_size(int nshell, t_shell s[])
750 for (i = 0; i < nshell; i++)
752 svmul(0.8, s[i].step, s[i].step);
756 static void print_epot(FILE *fp, gmx_int64_t mdstep, int count, real epot, real df,
757 int ndir, real sf_dir)
761 fprintf(fp, "MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
762 gmx_step_str(mdstep, buf), count, epot, df);
765 fprintf(fp, ", dir. rmsF: %6.2e\n", sqrt(sf_dir/ndir));
774 static real rms_force(t_commrec *cr, rvec f[], int ns, t_shell s[],
775 int ndir, real *sf_dir, real *Epot)
781 for (i = 0; i < ns; i++)
784 buf[0] += norm2(f[shell]);
793 gmx_sumd(4, buf, cr);
794 ntot = (int)(buf[1] + 0.5);
800 return (ntot ? sqrt(buf[0]/ntot) : 0);
803 static void check_pbc(FILE *fp, rvec x[], int shell)
808 for (m = 0; (m < DIM); m++)
810 if (fabs(x[shell][m]-x[now][m]) > 0.3)
812 pr_rvecs(fp, 0, "SHELL-X", x+now, 5);
818 static void dump_shells(FILE *fp, rvec x[], rvec f[], real ftol, int ns, t_shell s[])
825 for (i = 0; (i < ns); i++)
828 ff2 = iprod(f[shell], f[shell]);
831 fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
832 shell, f[shell][XX], f[shell][YY], f[shell][ZZ], sqrt(ff2));
834 check_pbc(fp, x, shell);
838 static void init_adir(FILE *log, gmx_shellfc_t shfc,
839 gmx_constr_t constr, t_idef *idef, t_inputrec *ir,
840 t_commrec *cr, int dd_ac1,
841 gmx_int64_t step, t_mdatoms *md, int start, int end,
842 rvec *x_old, rvec *x_init, rvec *x,
843 rvec *f, rvec *acc_dir,
844 gmx_bool bMolPBC, matrix box,
845 real *lambda, real *dvdlambda, t_nrnb *nrnb)
852 unsigned short *ptype;
855 if (DOMAINDECOMP(cr))
863 if (n > shfc->adir_nalloc)
865 shfc->adir_nalloc = over_alloc_dd(n);
866 srenew(shfc->adir_xnold, shfc->adir_nalloc);
867 srenew(shfc->adir_xnew, shfc->adir_nalloc);
869 xnold = shfc->adir_xnold;
870 xnew = shfc->adir_xnew;
876 /* Does NOT work with freeze or acceleration groups (yet) */
877 for (n = start; n < end; n++)
879 w_dt = md->invmass[n]*dt;
881 for (d = 0; d < DIM; d++)
883 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
885 xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
886 xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
890 xnold[n-start][d] = x[n][d];
891 xnew[n-start][d] = x[n][d];
895 constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
896 x, xnold-start, NULL, bMolPBC, box,
897 lambda[efptBONDED], &(dvdlambda[efptBONDED]),
898 NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
899 constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
900 x, xnew-start, NULL, bMolPBC, box,
901 lambda[efptBONDED], &(dvdlambda[efptBONDED]),
902 NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
904 for (n = start; n < end; n++)
906 for (d = 0; d < DIM; d++)
909 -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/sqr(dt)
910 - f[n][d]*md->invmass[n];
912 clear_rvec(acc_dir[n]);
915 /* Project the acceleration on the old bond directions */
916 constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
917 x_old, xnew-start, acc_dir, bMolPBC, box,
918 lambda[efptBONDED], &(dvdlambda[efptBONDED]),
919 NULL, NULL, nrnb, econqDeriv_FlexCon, FALSE, 0, 0);
922 int relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose,
923 gmx_int64_t mdstep, t_inputrec *inputrec,
924 gmx_bool bDoNS, int force_flags,
927 gmx_enerdata_t *enerd, t_fcdata *fcd,
928 t_state *state, rvec f[],
931 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
933 gmx_groups_t *groups,
934 struct gmx_shellfc *shfc,
937 double t, rvec mu_tot,
938 gmx_bool *bConverged,
945 rvec *pos[2], *force[2], *acc_dir = NULL, *x_old = NULL;
949 real ftol, xiH, xiS, dum = 0;
951 gmx_bool bCont, bInit;
952 int nat, dd_ac0, dd_ac1 = 0, i;
953 int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1;
954 int nflexcon, g, number_steps, d, Min = 0, count = 0;
955 #define Try (1-Min) /* At start Try = 1 */
957 bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
958 bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
959 ftol = inputrec->em_tol;
960 number_steps = inputrec->niter;
961 nshell = shfc->nshell;
963 nflexcon = shfc->nflexcon;
967 if (DOMAINDECOMP(cr))
969 nat = dd_natoms_vsite(cr->dd);
972 dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
973 nat = max(nat, dd_ac1);
981 if (nat > shfc->x_nalloc)
983 /* Allocate local arrays */
984 shfc->x_nalloc = over_alloc_dd(nat);
985 for (i = 0; (i < 2); i++)
987 srenew(shfc->x[i], shfc->x_nalloc);
988 srenew(shfc->f[i], shfc->x_nalloc);
991 for (i = 0; (i < 2); i++)
994 force[i] = shfc->f[i];
997 if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
999 /* This is the only time where the coordinates are used
1000 * before do_force is called, which normally puts all
1001 * charge groups in the box.
1003 if (inputrec->cutoff_scheme == ecutsVERLET)
1005 put_atoms_in_box_omp(fr->ePBC, state->box, md->homenr, state->x);
1011 put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
1012 &(top->cgs), state->x, fr->cg_cm);
1017 mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
1021 /* After this all coordinate arrays will contain whole charge groups */
1024 shift_self(graph, state->box, state->x);
1029 if (nat > shfc->flex_nalloc)
1031 shfc->flex_nalloc = over_alloc_dd(nat);
1032 srenew(shfc->acc_dir, shfc->flex_nalloc);
1033 srenew(shfc->x_old, shfc->flex_nalloc);
1035 acc_dir = shfc->acc_dir;
1036 x_old = shfc->x_old;
1037 for (i = 0; i < homenr; i++)
1039 for (d = 0; d < DIM; d++)
1042 state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
1047 /* Do a prediction of the shell positions */
1048 if (shfc->bPredict && !bCont)
1050 predict_shells(fplog, state->x, state->v, inputrec->delta_t, nshell, shell,
1051 md->massT, NULL, bInit);
1054 /* do_force expected the charge groups to be in the box */
1057 unshift_self(graph, state->box, state->x);
1060 /* Calculate the forces first time around */
1063 pr_rvecs(debug, 0, "x b4 do_force", state->x + start, homenr);
1065 do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, groups,
1066 state->box, state->x, &state->hist,
1067 force[Min], force_vir, md, enerd, fcd,
1068 state->lambda, graph,
1069 fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
1070 (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
1075 init_adir(fplog, shfc,
1076 constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
1077 shfc->x_old-start, state->x, state->x, force[Min],
1078 shfc->acc_dir-start,
1079 fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
1081 for (i = start; i < end; i++)
1083 sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
1087 Epot[Min] = enerd->term[F_EPOT];
1089 df[Min] = rms_force(cr, shfc->f[Min], nshell, shell, nflexcon, &sf_dir, &Epot[Min]);
1093 fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
1098 pr_rvecs(debug, 0, "force0", force[Min], md->nr);
1101 if (nshell+nflexcon > 0)
1103 /* Copy x to pos[Min] & pos[Try]: during minimization only the
1104 * shell positions are updated, therefore the other particles must
1107 memcpy(pos[Min], state->x, nat*sizeof(state->x[0]));
1108 memcpy(pos[Try], state->x, nat*sizeof(state->x[0]));
1111 if (bVerbose && MASTER(cr))
1113 print_epot(stdout, mdstep, 0, Epot[Min], df[Min], nflexcon, sf_dir);
1118 fprintf(debug, "%17s: %14.10e\n",
1119 interaction_function[F_EKIN].longname, enerd->term[F_EKIN]);
1120 fprintf(debug, "%17s: %14.10e\n",
1121 interaction_function[F_EPOT].longname, enerd->term[F_EPOT]);
1122 fprintf(debug, "%17s: %14.10e\n",
1123 interaction_function[F_ETOT].longname, enerd->term[F_ETOT]);
1124 fprintf(debug, "SHELLSTEP %s\n", gmx_step_str(mdstep, sbuf));
1127 /* First check whether we should do shells, or whether the force is
1128 * low enough even without minimization.
1130 *bConverged = (df[Min] < ftol);
1132 for (count = 1; (!(*bConverged) && (count < number_steps)); count++)
1136 construct_vsites(vsite, pos[Min], inputrec->delta_t, state->v,
1137 idef->iparams, idef->il,
1138 fr->ePBC, fr->bMolPBC, cr, state->box);
1143 init_adir(fplog, shfc,
1144 constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
1145 x_old-start, state->x, pos[Min], force[Min], acc_dir-start,
1146 fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
1148 directional_sd(pos[Min], pos[Try], acc_dir-start, start, end,
1152 /* New positions, Steepest descent */
1153 shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
1155 /* do_force expected the charge groups to be in the box */
1158 unshift_self(graph, state->box, pos[Try]);
1163 pr_rvecs(debug, 0, "RELAX: pos[Min] ", pos[Min] + start, homenr);
1164 pr_rvecs(debug, 0, "RELAX: pos[Try] ", pos[Try] + start, homenr);
1166 /* Try the new positions */
1167 do_force(fplog, cr, inputrec, 1, nrnb, wcycle,
1168 top, groups, state->box, pos[Try], &state->hist,
1169 force[Try], force_vir,
1170 md, enerd, fcd, state->lambda, graph,
1171 fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
1176 pr_rvecs(debug, 0, "RELAX: force[Min]", force[Min] + start, homenr);
1177 pr_rvecs(debug, 0, "RELAX: force[Try]", force[Try] + start, homenr);
1182 init_adir(fplog, shfc,
1183 constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
1184 x_old-start, state->x, pos[Try], force[Try], acc_dir-start,
1185 fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
1187 for (i = start; i < end; i++)
1189 sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
1193 Epot[Try] = enerd->term[F_EPOT];
1195 df[Try] = rms_force(cr, force[Try], nshell, shell, nflexcon, &sf_dir, &Epot[Try]);
1199 fprintf(debug, "df = %g %g\n", df[Min], df[Try]);
1206 pr_rvecs(debug, 0, "F na do_force", force[Try] + start, homenr);
1210 fprintf(debug, "SHELL ITER %d\n", count);
1211 dump_shells(debug, pos[Try], force[Try], ftol, nshell, shell);
1215 if (bVerbose && MASTER(cr))
1217 print_epot(stdout, mdstep, count, Epot[Try], df[Try], nflexcon, sf_dir);
1220 *bConverged = (df[Try] < ftol);
1222 if ((df[Try] < df[Min]))
1226 fprintf(debug, "Swapping Min and Try\n");
1230 /* Correct the velocities for the flexible constraints */
1231 invdt = 1/inputrec->delta_t;
1232 for (i = start; i < end; i++)
1234 for (d = 0; d < DIM; d++)
1236 state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
1244 decrease_step_size(nshell, shell);
1247 if (MASTER(cr) && !(*bConverged))
1249 /* Note that the energies and virial are incorrect when not converged */
1253 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1254 gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
1257 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1258 gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
1261 /* Copy back the coordinates and the forces */
1262 memcpy(state->x, pos[Min], nat*sizeof(state->x[0]));
1263 memcpy(f, force[Min], nat*sizeof(f[0]));