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9 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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32 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
41 #include "gmx_fatal.h"
56 #include "mtop_util.h"
57 #include "chargegroup.h"
62 atom_id shell; /* The shell id */
63 atom_id nucl1,nucl2,nucl3; /* The nuclei connected to the shell */
64 /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
65 real k; /* force constant */
66 real k_1; /* 1 over force constant */
72 typedef struct gmx_shellfc {
73 int nshell_gl; /* The number of shells in the system */
74 t_shell *shell_gl; /* All the shells (for DD only) */
75 int *shell_index_gl; /* Global shell index (for DD only) */
76 gmx_bool bInterCG; /* Are there inter charge-group shells? */
77 int nshell; /* The number of local shells */
78 t_shell *shell; /* The local shells */
79 int shell_nalloc; /* The allocation size of shell */
80 gmx_bool bPredict; /* Predict shell positions */
81 gmx_bool bForceInit; /* Force initialization of shell positions */
82 int nflexcon; /* The number of flexible constraints */
83 rvec *x[2]; /* Array for iterative minimization */
84 rvec *f[2]; /* Array for iterative minimization */
85 int x_nalloc; /* The allocation size of x and f */
86 rvec *acc_dir; /* Acceleration direction for flexcon */
87 rvec *x_old; /* Old coordinates for flexcon */
88 int flex_nalloc; /* The allocation size of acc_dir and x_old */
89 rvec *adir_xnold; /* Work space for init_adir */
90 rvec *adir_xnew; /* Work space for init_adir */
91 int adir_nalloc; /* Work space for init_adir */
95 static void pr_shell(FILE *fplog,int ns,t_shell s[])
99 fprintf(fplog,"SHELL DATA\n");
100 fprintf(fplog,"%5s %8s %5s %5s %5s\n",
101 "Shell","Force k","Nucl1","Nucl2","Nucl3");
102 for(i=0; (i<ns); i++) {
103 fprintf(fplog,"%5d %8.3f %5d",s[i].shell,1.0/s[i].k_1,s[i].nucl1);
105 fprintf(fplog," %5d\n",s[i].nucl2);
106 else if (s[i].nnucl == 3)
107 fprintf(fplog," %5d %5d\n",s[i].nucl2,s[i].nucl3);
113 static void predict_shells(FILE *fplog,rvec x[],rvec v[],real dt,
115 real mass[],gmx_mtop_t *mtop,gmx_bool bInit)
118 real dt_1,dt_2,dt_3,fudge,tm,m1,m2,m3;
122 /* We introduce a fudge factor for performance reasons: with this choice
123 * the initial force on the shells is about a factor of two lower than
130 fprintf(fplog,"RELAX: Using prediction for initial shell placement\n");
139 for(i=0; (i<ns); i++) {
143 switch (s[i].nnucl) {
146 for(m=0; (m<DIM); m++)
147 x[s1][m]+=ptr[n1][m]*dt_1;
156 /* Not the correct masses with FE, but it is just a prediction... */
161 for(m=0; (m<DIM); m++)
162 x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
173 /* Not the correct masses with FE, but it is just a prediction... */
174 gmx_mtop_atomnr_to_atom(mtop,n1,&atom);
176 gmx_mtop_atomnr_to_atom(mtop,n2,&atom);
178 gmx_mtop_atomnr_to_atom(mtop,n3,&atom);
181 tm = dt_1/(m1+m2+m3);
182 for(m=0; (m<DIM); m++)
183 x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
186 gmx_fatal(FARGS,"Shell %d has %d nuclei!",i,s[i].nnucl);
191 gmx_shellfc_t init_shell_flexcon(FILE *fplog,
192 gmx_mtop_t *mtop,int nflexcon,
195 struct gmx_shellfc *shfc;
197 int *shell_index=NULL,*at2cg;
199 int n[eptNR],ns,nshell,nsi;
200 int i,j,nmol,type,mb,mt,a_offset,cg,mol,ftype,nra;
202 int aS,aN=0; /* Shell and nucleus */
203 int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_WATER_POL };
204 #define NBT asize(bondtypes)
206 gmx_mtop_atomloop_block_t aloopb;
207 gmx_mtop_atomloop_all_t aloop;
208 gmx_ffparams_t *ffparams;
209 gmx_molblock_t *molb;
213 /* Count number of shells, and find their indices */
214 for(i=0; (i<eptNR); i++) {
218 aloopb = gmx_mtop_atomloop_block_init(mtop);
219 while (gmx_mtop_atomloop_block_next(aloopb,&atom,&nmol)) {
220 n[atom->ptype] += nmol;
224 /* Print the number of each particle type */
225 for(i=0; (i<eptNR); i++) {
227 fprintf(fplog,"There are: %d %ss\n",n[i],ptype_str[i]);
232 nshell = n[eptShell];
234 if (nshell == 0 && nflexcon == 0) {
239 shfc->nflexcon = nflexcon;
245 /* We have shells: fill the shell data structure */
247 /* Global system sized array, this should be avoided */
248 snew(shell_index,mtop->natoms);
250 aloop = gmx_mtop_atomloop_all_init(mtop);
252 while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
253 if (atom->ptype == eptShell) {
254 shell_index[i] = nshell++;
260 /* Initiate the shell structures */
261 for(i=0; (i<nshell); i++) {
262 shell[i].shell = NO_ATID;
264 shell[i].nucl1 = NO_ATID;
265 shell[i].nucl2 = NO_ATID;
266 shell[i].nucl3 = NO_ATID;
267 /* shell[i].bInterCG=FALSE; */
272 ffparams = &mtop->ffparams;
274 /* Now fill the structures */
275 shfc->bInterCG = FALSE;
278 for(mb=0; mb<mtop->nmolblock; mb++) {
279 molb = &mtop->molblock[mb];
280 molt = &mtop->moltype[molb->type];
283 snew(at2cg,molt->atoms.nr);
284 for(cg=0; cg<cgs->nr; cg++) {
285 for(i=cgs->index[cg]; i<cgs->index[cg+1]; i++) {
290 atom = molt->atoms.atom;
291 for(mol=0; mol<molb->nmol; mol++) {
292 for(j=0; (j<NBT); j++) {
293 ia = molt->ilist[bondtypes[j]].iatoms;
294 for(i=0; (i<molt->ilist[bondtypes[j]].nr); ) {
296 ftype = ffparams->functype[type];
297 nra = interaction_function[ftype].nratoms;
299 /* Check whether we have a bond with a shell */
302 switch (bondtypes[j]) {
307 if (atom[ia[1]].ptype == eptShell) {
311 else if (atom[ia[2]].ptype == eptShell) {
317 aN = ia[4]; /* Dummy */
318 aS = ia[5]; /* Shell */
321 gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
327 /* Check whether one of the particles is a shell... */
328 nsi = shell_index[a_offset+aS];
329 if ((nsi < 0) || (nsi >= nshell))
330 gmx_fatal(FARGS,"nsi is %d should be within 0 - %d. aS = %d",
332 if (shell[nsi].shell == NO_ATID) {
333 shell[nsi].shell = a_offset + aS;
336 else if (shell[nsi].shell != a_offset+aS)
337 gmx_fatal(FARGS,"Weird stuff in %s, %d",__FILE__,__LINE__);
339 if (shell[nsi].nucl1 == NO_ATID) {
340 shell[nsi].nucl1 = a_offset + aN;
341 } else if (shell[nsi].nucl2 == NO_ATID) {
342 shell[nsi].nucl2 = a_offset + aN;
343 } else if (shell[nsi].nucl3 == NO_ATID) {
344 shell[nsi].nucl3 = a_offset + aN;
347 pr_shell(fplog,ns,shell);
348 gmx_fatal(FARGS,"Can not handle more than three bonds per shell\n");
350 if (at2cg[aS] != at2cg[aN]) {
351 /* shell[nsi].bInterCG = TRUE; */
352 shfc->bInterCG = TRUE;
355 switch (bondtypes[j]) {
358 shell[nsi].k += ffparams->iparams[type].harmonic.krA;
361 shell[nsi].k += ffparams->iparams[type].cubic.kb;
364 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
365 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);
366 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
367 ffparams->iparams[type].polarize.alpha;
370 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
371 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);
372 alpha = (ffparams->iparams[type].wpol.al_x+
373 ffparams->iparams[type].wpol.al_y+
374 ffparams->iparams[type].wpol.al_z)/3.0;
375 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
378 gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
386 a_offset += molt->atoms.nr;
388 /* Done with this molecule type */
392 /* Verify whether it's all correct */
394 gmx_fatal(FARGS,"Something weird with shells. They may not be bonded to something");
396 for(i=0; (i<ns); i++)
397 shell[i].k_1 = 1.0/shell[i].k;
400 pr_shell(debug,ns,shell);
403 shfc->nshell_gl = ns;
404 shfc->shell_gl = shell;
405 shfc->shell_index_gl = shell_index;
407 shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
408 shfc->bForceInit = FALSE;
409 if (!shfc->bPredict) {
411 fprintf(fplog,"\nWill never predict shell positions\n");
413 shfc->bForceInit = (getenv("GMX_FORCEINIT") != NULL);
414 if (shfc->bForceInit && fplog)
415 fprintf(fplog,"\nWill always initiate shell positions\n");
418 if (shfc->bPredict) {
420 predict_shells(fplog,x,NULL,0,shfc->nshell_gl,shfc->shell_gl,
424 if (shfc->bInterCG) {
426 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");
427 shfc->bPredict = FALSE;
434 void make_local_shells(t_commrec *cr,t_mdatoms *md,
435 struct gmx_shellfc *shfc)
438 int a0,a1,*ind,nshell,i;
439 gmx_domdec_t *dd=NULL;
442 if (DOMAINDECOMP(cr)) {
447 pd_at_range(cr,&a0,&a1);
450 /* Single node: we need all shells, just copy the pointer */
451 shfc->nshell = shfc->nshell_gl;
452 shfc->shell = shfc->shell_gl;
457 ind = shfc->shell_index_gl;
461 for(i=a0; i<a1; i++) {
462 if (md->ptype[i] == eptShell) {
463 if (nshell+1 > shfc->shell_nalloc) {
464 shfc->shell_nalloc = over_alloc_dd(nshell+1);
465 srenew(shell,shfc->shell_nalloc);
468 shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
470 shell[nshell] = shfc->shell_gl[ind[i]];
472 /* With inter-cg shells we can no do shell prediction,
473 * so we do not need the nuclei numbers.
475 if (!shfc->bInterCG) {
476 shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
477 if (shell[nshell].nnucl > 1)
478 shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
479 if (shell[nshell].nnucl > 2)
480 shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
482 shell[nshell].shell = i;
487 shfc->nshell = nshell;
491 static void do_1pos(rvec xnew,rvec xold,rvec f,real step)
509 static void do_1pos3(rvec xnew,rvec xold,rvec f,rvec step)
527 static void directional_sd(FILE *log,rvec xold[],rvec xnew[],rvec acc_dir[],
528 int start,int homenr,real step)
532 for(i=start; i<homenr; i++)
533 do_1pos(xnew[i],xold[i],acc_dir[i],step);
536 static void shell_pos_sd(FILE *log,rvec xcur[],rvec xnew[],rvec f[],
537 int ns,t_shell s[],int count)
539 const real step_scale_min = 0.8,
540 step_scale_increment = 0.2,
541 step_scale_max = 1.2,
542 step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
546 real step_min,step_max;
551 for(i=0; (i<ns); i++) {
554 for(d=0; d<DIM; d++) {
555 s[i].step[d] = s[i].k_1;
557 step_min = min(step_min,s[i].step[d]);
558 step_max = max(step_max,s[i].step[d]);
562 for(d=0; d<DIM; d++) {
563 dx = xcur[shell][d] - s[i].xold[d];
564 df = f[shell][d] - s[i].fold[d];
565 /* -dx/df gets used to generate an interpolated value, but would
566 * cause a NaN if df were binary-equal to zero. Values close to
567 * zero won't cause problems (because of the min() and max()), so
568 * just testing for binary inequality is OK. */
572 /* Scale the step size by a factor interpolated from
573 * step_scale_min to step_scale_max, as k_est goes from 0 to
574 * step_scale_multiple * s[i].step[d] */
576 step_scale_min * s[i].step[d] +
577 step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
582 if (gmx_numzero(dx)) /* 0 == dx */
584 /* Likely this will never happen, but if it does just
585 * don't scale the step. */
589 s[i].step[d] *= step_scale_max;
593 step_min = min(step_min,s[i].step[d]);
594 step_max = max(step_max,s[i].step[d]);
598 copy_rvec(xcur[shell],s[i].xold);
599 copy_rvec(f[shell], s[i].fold);
601 do_1pos3(xnew[shell],xcur[shell],f[shell],s[i].step);
604 fprintf(debug,"shell[%d] = %d\n",i,shell);
605 pr_rvec(debug,0,"fshell",f[shell],DIM,TRUE);
606 pr_rvec(debug,0,"xold",xcur[shell],DIM,TRUE);
607 pr_rvec(debug,0,"step",s[i].step,DIM,TRUE);
608 pr_rvec(debug,0,"xnew",xnew[shell],DIM,TRUE);
612 printf("step %.3e %.3e\n",step_min,step_max);
616 static void decrease_step_size(int nshell,t_shell s[])
620 for(i=0; i<nshell; i++)
621 svmul(0.8,s[i].step,s[i].step);
624 static void print_epot(FILE *fp,gmx_large_int_t mdstep,int count,real epot,real df,
625 int ndir,real sf_dir)
629 fprintf(fp,"MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
630 gmx_step_str(mdstep,buf),count,epot,df);
632 fprintf(fp,", dir. rmsF: %6.2e\n",sqrt(sf_dir/ndir));
638 static real rms_force(t_commrec *cr,rvec f[],int ns,t_shell s[],
639 int ndir,real *sf_dir,real *Epot)
645 for(i=0; i<ns; i++) {
647 buf[0] += norm2(f[shell]);
656 ntot = (int)(buf[1] + 0.5);
662 return (ntot ? sqrt(buf[0]/ntot) : 0);
665 static void check_pbc(FILE *fp,rvec x[],int shell)
670 for(m=0; (m<DIM); m++)
671 if (fabs(x[shell][m]-x[now][m]) > 0.3) {
672 pr_rvecs(fp,0,"SHELL-X",x+now,5);
677 static void dump_shells(FILE *fp,rvec x[],rvec f[],real ftol,int ns,t_shell s[])
684 for(i=0; (i<ns); i++) {
686 ff2 = iprod(f[shell],f[shell]);
688 fprintf(fp,"SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
689 shell,f[shell][XX],f[shell][YY],f[shell][ZZ],sqrt(ff2));
690 check_pbc(fp,x,shell);
694 static void init_adir(FILE *log,gmx_shellfc_t shfc,
695 gmx_constr_t constr,t_idef *idef,t_inputrec *ir,
696 t_commrec *cr,int dd_ac1,
697 gmx_large_int_t step,t_mdatoms *md,int start,int end,
698 rvec *x_old,rvec *x_init,rvec *x,
699 rvec *f,rvec *acc_dir,matrix box,
700 real lambda,real *dvdlambda,t_nrnb *nrnb)
707 unsigned short *ptype;
710 if (DOMAINDECOMP(cr))
714 if (n > shfc->adir_nalloc) {
715 shfc->adir_nalloc = over_alloc_dd(n);
716 srenew(shfc->adir_xnold,shfc->adir_nalloc);
717 srenew(shfc->adir_xnew ,shfc->adir_nalloc);
719 xnold = shfc->adir_xnold;
720 xnew = shfc->adir_xnew;
726 /* Does NOT work with freeze or acceleration groups (yet) */
727 for (n=start; n<end; n++) {
728 w_dt = md->invmass[n]*dt;
730 for (d=0; d<DIM; d++) {
731 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) {
732 xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
733 xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
735 xnold[n-start][d] = x[n][d];
736 xnew[n-start][d] = x[n][d];
740 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
741 x,xnold-start,NULL,box,
742 lambda,dvdlambda,NULL,NULL,nrnb,econqCoord,FALSE,0,0);
743 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
744 x,xnew-start,NULL,box,
745 lambda,dvdlambda,NULL,NULL,nrnb,econqCoord,FALSE,0,0);
747 /* Set xnew to minus the acceleration */
748 for (n=start; n<end; n++) {
751 -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/sqr(dt)
752 - f[n][d]*md->invmass[n];
753 clear_rvec(acc_dir[n]);
756 /* Project the acceleration on the old bond directions */
757 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
758 x_old,xnew-start,acc_dir,box,
759 lambda,dvdlambda,NULL,NULL,nrnb,econqDeriv_FlexCon,FALSE,0,0);
762 int relax_shell_flexcon(FILE *fplog,t_commrec *cr,gmx_bool bVerbose,
763 gmx_large_int_t mdstep,t_inputrec *inputrec,
764 gmx_bool bDoNS,int force_flags,
769 gmx_enerdata_t *enerd,t_fcdata *fcd,
770 t_state *state,rvec f[],
773 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
775 gmx_groups_t *groups,
776 struct gmx_shellfc *shfc,
779 double t,rvec mu_tot,
780 int natoms,gmx_bool *bConverged,
787 rvec *pos[2],*force[2],*acc_dir=NULL,*x_old=NULL;
791 real ftol,xiH,xiS,dum=0;
793 gmx_bool bCont,bInit;
794 int nat,dd_ac0,dd_ac1=0,i;
795 int start=md->start,homenr=md->homenr,end=start+homenr,cg0,cg1;
796 int nflexcon,g,number_steps,d,Min=0,count=0;
797 #define Try (1-Min) /* At start Try = 1 */
799 bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
800 bInit = (mdstep == inputrec->init_step) || shfc->bForceInit;
801 ftol = inputrec->em_tol;
802 number_steps = inputrec->niter;
803 nshell = shfc->nshell;
805 nflexcon = shfc->nflexcon;
809 if (DOMAINDECOMP(cr)) {
810 nat = dd_natoms_vsite(cr->dd);
812 dd_get_constraint_range(cr->dd,&dd_ac0,&dd_ac1);
813 nat = max(nat,dd_ac1);
819 if (nat > shfc->x_nalloc) {
820 /* Allocate local arrays */
821 shfc->x_nalloc = over_alloc_dd(nat);
822 for(i=0; (i<2); i++) {
823 srenew(shfc->x[i],shfc->x_nalloc);
824 srenew(shfc->f[i],shfc->x_nalloc);
827 for(i=0; (i<2); i++) {
829 force[i] = shfc->f[i];
832 /* With particle decomposition this code only works
833 * when all particles involved with each shell are in the same cg.
836 if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr)) {
837 /* This is the only time where the coordinates are used
838 * before do_force is called, which normally puts all
839 * charge groups in the box.
841 if (PARTDECOMP(cr)) {
842 pd_cg_range(cr,&cg0,&cg1);
847 put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,state->box,
848 &(top->cgs),state->x,fr->cg_cm);
850 mk_mshift(fplog,graph,fr->ePBC,state->box,state->x);
853 /* After this all coordinate arrays will contain whole molecules */
855 shift_self(graph,state->box,state->x);
858 if (nat > shfc->flex_nalloc) {
859 shfc->flex_nalloc = over_alloc_dd(nat);
860 srenew(shfc->acc_dir,shfc->flex_nalloc);
861 srenew(shfc->x_old,shfc->flex_nalloc);
863 acc_dir = shfc->acc_dir;
865 for(i=0; i<homenr; i++) {
868 state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
872 /* Do a prediction of the shell positions */
873 if (shfc->bPredict && !bCont) {
874 predict_shells(fplog,state->x,state->v,inputrec->delta_t,nshell,shell,
875 md->massT,NULL,bInit);
878 /* do_force expected the charge groups to be in the box */
880 unshift_self(graph,state->box,state->x);
882 /* Calculate the forces first time around */
884 pr_rvecs(debug,0,"x b4 do_force",state->x + start,homenr);
886 do_force(fplog,cr,inputrec,mdstep,nrnb,wcycle,top,mtop,groups,
887 state->box,state->x,&state->hist,
888 force[Min],force_vir,md,enerd,fcd,
890 fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
891 (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
895 init_adir(fplog,shfc,
896 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
897 shfc->x_old-start,state->x,state->x,force[Min],
898 shfc->acc_dir-start,state->box,state->lambda,&dum,nrnb);
900 for(i=start; i<end; i++)
901 sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
904 Epot[Min] = enerd->term[F_EPOT];
906 df[Min]=rms_force(cr,shfc->f[Min],nshell,shell,nflexcon,&sf_dir,&Epot[Min]);
909 fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
913 pr_rvecs(debug,0,"force0",force[Min],md->nr);
916 if (nshell+nflexcon > 0) {
917 /* Copy x to pos[Min] & pos[Try]: during minimization only the
918 * shell positions are updated, therefore the other particles must
921 memcpy(pos[Min],state->x,nat*sizeof(state->x[0]));
922 memcpy(pos[Try],state->x,nat*sizeof(state->x[0]));
925 if (bVerbose && MASTER(cr))
926 print_epot(stdout,mdstep,0,Epot[Min],df[Min],nflexcon,sf_dir);
929 fprintf(debug,"%17s: %14.10e\n",
930 interaction_function[F_EKIN].longname,enerd->term[F_EKIN]);
931 fprintf(debug,"%17s: %14.10e\n",
932 interaction_function[F_EPOT].longname,enerd->term[F_EPOT]);
933 fprintf(debug,"%17s: %14.10e\n",
934 interaction_function[F_ETOT].longname,enerd->term[F_ETOT]);
935 fprintf(debug,"SHELLSTEP %s\n",gmx_step_str(mdstep,sbuf));
938 /* First check whether we should do shells, or whether the force is
939 * low enough even without minimization.
941 *bConverged = (df[Min] < ftol);
943 for(count=1; (!(*bConverged) && (count < number_steps)); count++) {
945 construct_vsites(fplog,vsite,pos[Min],nrnb,inputrec->delta_t,state->v,
946 idef->iparams,idef->il,
947 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
950 init_adir(fplog,shfc,
951 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
952 x_old-start,state->x,pos[Min],force[Min],acc_dir-start,
953 state->box,state->lambda,&dum,nrnb);
955 directional_sd(fplog,pos[Min],pos[Try],acc_dir-start,start,end,
959 /* New positions, Steepest descent */
960 shell_pos_sd(fplog,pos[Min],pos[Try],force[Min],nshell,shell,count);
962 /* do_force expected the charge groups to be in the box */
964 unshift_self(graph,state->box,pos[Try]);
967 pr_rvecs(debug,0,"RELAX: pos[Min] ",pos[Min] + start,homenr);
968 pr_rvecs(debug,0,"RELAX: pos[Try] ",pos[Try] + start,homenr);
970 /* Try the new positions */
971 do_force(fplog,cr,inputrec,1,nrnb,wcycle,
972 top,mtop,groups,state->box,pos[Try],&state->hist,
973 force[Try],force_vir,
974 md,enerd,fcd,state->lambda,graph,
975 fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
979 pr_rvecs(debug,0,"RELAX: force[Min]",force[Min] + start,homenr);
980 pr_rvecs(debug,0,"RELAX: force[Try]",force[Try] + start,homenr);
984 init_adir(fplog,shfc,
985 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
986 x_old-start,state->x,pos[Try],force[Try],acc_dir-start,
987 state->box,state->lambda,&dum,nrnb);
989 for(i=start; i<end; i++)
990 sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
993 Epot[Try] = enerd->term[F_EPOT];
995 df[Try]=rms_force(cr,force[Try],nshell,shell,nflexcon,&sf_dir,&Epot[Try]);
998 fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
1002 pr_rvecs(debug,0,"F na do_force",force[Try] + start,homenr);
1004 fprintf(debug,"SHELL ITER %d\n",count);
1005 dump_shells(debug,pos[Try],force[Try],ftol,nshell,shell);
1009 if (bVerbose && MASTER(cr))
1010 print_epot(stdout,mdstep,count,Epot[Try],df[Try],nflexcon,sf_dir);
1012 *bConverged = (df[Try] < ftol);
1014 if ((df[Try] < df[Min])) {
1016 fprintf(debug,"Swapping Min and Try\n");
1018 /* Correct the velocities for the flexible constraints */
1019 invdt = 1/inputrec->delta_t;
1020 for(i=start; i<end; i++) {
1021 for(d=0; d<DIM; d++)
1022 state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
1027 decrease_step_size(nshell,shell);
1030 if (MASTER(cr) && !(*bConverged)) {
1031 /* Note that the energies and virial are incorrect when not converged */
1034 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1035 gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
1037 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1038 gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
1041 /* Copy back the coordinates and the forces */
1042 memcpy(state->x,pos[Min],nat*sizeof(state->x[0]));
1043 memcpy(f,force[Min],nat*sizeof(f[0]));