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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"
63 atom_id shell; /* The shell id */
64 atom_id nucl1,nucl2,nucl3; /* The nuclei connected to the shell */
65 /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
66 real k; /* force constant */
67 real k_1; /* 1 over force constant */
73 typedef struct gmx_shellfc {
74 int nshell_gl; /* The number of shells in the system */
75 t_shell *shell_gl; /* All the shells (for DD only) */
76 int *shell_index_gl; /* Global shell index (for DD only) */
77 gmx_bool bInterCG; /* Are there inter charge-group shells? */
78 int nshell; /* The number of local shells */
79 t_shell *shell; /* The local shells */
80 int shell_nalloc; /* The allocation size of shell */
81 gmx_bool bPredict; /* Predict shell positions */
82 gmx_bool bRequireInit; /* Require initialization of shell positions */
83 int nflexcon; /* The number of flexible constraints */
84 rvec *x[2]; /* Array for iterative minimization */
85 rvec *f[2]; /* Array for iterative minimization */
86 int x_nalloc; /* The allocation size of x and f */
87 rvec *acc_dir; /* Acceleration direction for flexcon */
88 rvec *x_old; /* Old coordinates for flexcon */
89 int flex_nalloc; /* The allocation size of acc_dir and x_old */
90 rvec *adir_xnold; /* Work space for init_adir */
91 rvec *adir_xnew; /* Work space for init_adir */
92 int adir_nalloc; /* Work space for init_adir */
96 static void pr_shell(FILE *fplog,int ns,t_shell s[])
100 fprintf(fplog,"SHELL DATA\n");
101 fprintf(fplog,"%5s %8s %5s %5s %5s\n",
102 "Shell","Force k","Nucl1","Nucl2","Nucl3");
103 for(i=0; (i<ns); i++) {
104 fprintf(fplog,"%5d %8.3f %5d",s[i].shell,1.0/s[i].k_1,s[i].nucl1);
106 fprintf(fplog," %5d\n",s[i].nucl2);
107 else if (s[i].nnucl == 3)
108 fprintf(fplog," %5d %5d\n",s[i].nucl2,s[i].nucl3);
114 static void predict_shells(FILE *fplog,rvec x[],rvec v[],real dt,
116 real mass[],gmx_mtop_t *mtop,gmx_bool bInit)
119 real dt_1,dt_2,dt_3,fudge,tm,m1,m2,m3;
121 gmx_mtop_atomlookup_t alook=NULL;
125 alook = gmx_mtop_atomlookup_init(mtop);
128 /* We introduce a fudge factor for performance reasons: with this choice
129 * the initial force on the shells is about a factor of two lower than
136 fprintf(fplog,"RELAX: Using prediction for initial shell placement\n");
145 for(i=0; (i<ns); i++) {
149 switch (s[i].nnucl) {
152 for(m=0; (m<DIM); m++)
153 x[s1][m]+=ptr[n1][m]*dt_1;
162 /* Not the correct masses with FE, but it is just a prediction... */
167 for(m=0; (m<DIM); m++)
168 x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
179 /* Not the correct masses with FE, but it is just a prediction... */
180 gmx_mtop_atomnr_to_atom(alook,n1,&atom);
182 gmx_mtop_atomnr_to_atom(alook,n2,&atom);
184 gmx_mtop_atomnr_to_atom(alook,n3,&atom);
187 tm = dt_1/(m1+m2+m3);
188 for(m=0; (m<DIM); m++)
189 x[s1][m]+=(m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
192 gmx_fatal(FARGS,"Shell %d has %d nuclei!",i,s[i].nnucl);
197 gmx_mtop_atomlookup_destroy(alook);
201 gmx_shellfc_t init_shell_flexcon(FILE *fplog,
202 gmx_mtop_t *mtop,int nflexcon,
205 struct gmx_shellfc *shfc;
207 int *shell_index=NULL,*at2cg;
209 int n[eptNR],ns,nshell,nsi;
210 int i,j,nmol,type,mb,mt,a_offset,cg,mol,ftype,nra;
212 int aS,aN=0; /* Shell and nucleus */
213 int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
214 #define NBT asize(bondtypes)
216 gmx_mtop_atomloop_block_t aloopb;
217 gmx_mtop_atomloop_all_t aloop;
218 gmx_ffparams_t *ffparams;
219 gmx_molblock_t *molb;
223 /* Count number of shells, and find their indices */
224 for(i=0; (i<eptNR); i++) {
228 aloopb = gmx_mtop_atomloop_block_init(mtop);
229 while (gmx_mtop_atomloop_block_next(aloopb,&atom,&nmol)) {
230 n[atom->ptype] += nmol;
234 /* Print the number of each particle type */
235 for(i=0; (i<eptNR); i++) {
237 fprintf(fplog,"There are: %d %ss\n",n[i],ptype_str[i]);
242 nshell = n[eptShell];
244 if (nshell == 0 && nflexcon == 0) {
249 shfc->nflexcon = nflexcon;
255 /* We have shells: fill the shell data structure */
257 /* Global system sized array, this should be avoided */
258 snew(shell_index,mtop->natoms);
260 aloop = gmx_mtop_atomloop_all_init(mtop);
262 while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
263 if (atom->ptype == eptShell) {
264 shell_index[i] = nshell++;
270 /* Initiate the shell structures */
271 for(i=0; (i<nshell); i++) {
272 shell[i].shell = NO_ATID;
274 shell[i].nucl1 = NO_ATID;
275 shell[i].nucl2 = NO_ATID;
276 shell[i].nucl3 = NO_ATID;
277 /* shell[i].bInterCG=FALSE; */
282 ffparams = &mtop->ffparams;
284 /* Now fill the structures */
285 shfc->bInterCG = FALSE;
288 for(mb=0; mb<mtop->nmolblock; mb++) {
289 molb = &mtop->molblock[mb];
290 molt = &mtop->moltype[molb->type];
293 snew(at2cg,molt->atoms.nr);
294 for(cg=0; cg<cgs->nr; cg++) {
295 for(i=cgs->index[cg]; i<cgs->index[cg+1]; i++) {
300 atom = molt->atoms.atom;
301 for(mol=0; mol<molb->nmol; mol++) {
302 for(j=0; (j<NBT); j++) {
303 ia = molt->ilist[bondtypes[j]].iatoms;
304 for(i=0; (i<molt->ilist[bondtypes[j]].nr); ) {
306 ftype = ffparams->functype[type];
307 nra = interaction_function[ftype].nratoms;
309 /* Check whether we have a bond with a shell */
312 switch (bondtypes[j]) {
318 if (atom[ia[1]].ptype == eptShell) {
322 else if (atom[ia[2]].ptype == eptShell) {
328 aN = ia[4]; /* Dummy */
329 aS = ia[5]; /* Shell */
332 gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
338 /* Check whether one of the particles is a shell... */
339 nsi = shell_index[a_offset+aS];
340 if ((nsi < 0) || (nsi >= nshell))
341 gmx_fatal(FARGS,"nsi is %d should be within 0 - %d. aS = %d",
343 if (shell[nsi].shell == NO_ATID) {
344 shell[nsi].shell = a_offset + aS;
347 else if (shell[nsi].shell != a_offset+aS)
348 gmx_fatal(FARGS,"Weird stuff in %s, %d",__FILE__,__LINE__);
350 if (shell[nsi].nucl1 == NO_ATID) {
351 shell[nsi].nucl1 = a_offset + aN;
352 } else if (shell[nsi].nucl2 == NO_ATID) {
353 shell[nsi].nucl2 = a_offset + aN;
354 } else if (shell[nsi].nucl3 == NO_ATID) {
355 shell[nsi].nucl3 = a_offset + aN;
358 pr_shell(fplog,ns,shell);
359 gmx_fatal(FARGS,"Can not handle more than three bonds per shell\n");
361 if (at2cg[aS] != at2cg[aN]) {
362 /* shell[nsi].bInterCG = TRUE; */
363 shfc->bInterCG = TRUE;
366 switch (bondtypes[j]) {
369 shell[nsi].k += ffparams->iparams[type].harmonic.krA;
372 shell[nsi].k += ffparams->iparams[type].cubic.kb;
376 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
377 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);
378 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
379 ffparams->iparams[type].polarize.alpha;
382 if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
383 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);
384 alpha = (ffparams->iparams[type].wpol.al_x+
385 ffparams->iparams[type].wpol.al_y+
386 ffparams->iparams[type].wpol.al_z)/3.0;
387 shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
390 gmx_fatal(FARGS,"Death Horror: %s, %d",__FILE__,__LINE__);
398 a_offset += molt->atoms.nr;
400 /* Done with this molecule type */
404 /* Verify whether it's all correct */
406 gmx_fatal(FARGS,"Something weird with shells. They may not be bonded to something");
408 for(i=0; (i<ns); i++)
409 shell[i].k_1 = 1.0/shell[i].k;
412 pr_shell(debug,ns,shell);
415 shfc->nshell_gl = ns;
416 shfc->shell_gl = shell;
417 shfc->shell_index_gl = shell_index;
419 shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
420 shfc->bRequireInit = FALSE;
421 if (!shfc->bPredict) {
423 fprintf(fplog,"\nWill never predict shell positions\n");
425 shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
426 if (shfc->bRequireInit && fplog)
427 fprintf(fplog,"\nWill always initiate shell positions\n");
430 if (shfc->bPredict) {
432 predict_shells(fplog,x,NULL,0,shfc->nshell_gl,shfc->shell_gl,
436 if (shfc->bInterCG) {
438 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");
439 shfc->bPredict = FALSE;
446 void make_local_shells(t_commrec *cr,t_mdatoms *md,
447 struct gmx_shellfc *shfc)
450 int a0,a1,*ind,nshell,i;
451 gmx_domdec_t *dd=NULL;
454 if (DOMAINDECOMP(cr)) {
459 pd_at_range(cr,&a0,&a1);
462 /* Single node: we need all shells, just copy the pointer */
463 shfc->nshell = shfc->nshell_gl;
464 shfc->shell = shfc->shell_gl;
469 ind = shfc->shell_index_gl;
473 for(i=a0; i<a1; i++) {
474 if (md->ptype[i] == eptShell) {
475 if (nshell+1 > shfc->shell_nalloc) {
476 shfc->shell_nalloc = over_alloc_dd(nshell+1);
477 srenew(shell,shfc->shell_nalloc);
480 shell[nshell] = shfc->shell_gl[ind[dd->gatindex[i]]];
482 shell[nshell] = shfc->shell_gl[ind[i]];
484 /* With inter-cg shells we can no do shell prediction,
485 * so we do not need the nuclei numbers.
487 if (!shfc->bInterCG) {
488 shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
489 if (shell[nshell].nnucl > 1)
490 shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
491 if (shell[nshell].nnucl > 2)
492 shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
494 shell[nshell].shell = i;
499 shfc->nshell = nshell;
503 static void do_1pos(rvec xnew,rvec xold,rvec f,real step)
521 static void do_1pos3(rvec xnew,rvec xold,rvec f,rvec step)
539 static void directional_sd(FILE *log,rvec xold[],rvec xnew[],rvec acc_dir[],
540 int start,int homenr,real step)
544 for(i=start; i<homenr; i++)
545 do_1pos(xnew[i],xold[i],acc_dir[i],step);
548 static void shell_pos_sd(FILE *log,rvec xcur[],rvec xnew[],rvec f[],
549 int ns,t_shell s[],int count)
551 const real step_scale_min = 0.8,
552 step_scale_increment = 0.2,
553 step_scale_max = 1.2,
554 step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
558 real step_min,step_max;
563 for(i=0; (i<ns); i++) {
566 for(d=0; d<DIM; d++) {
567 s[i].step[d] = s[i].k_1;
569 step_min = min(step_min,s[i].step[d]);
570 step_max = max(step_max,s[i].step[d]);
574 for(d=0; d<DIM; d++) {
575 dx = xcur[shell][d] - s[i].xold[d];
576 df = f[shell][d] - s[i].fold[d];
577 /* -dx/df gets used to generate an interpolated value, but would
578 * cause a NaN if df were binary-equal to zero. Values close to
579 * zero won't cause problems (because of the min() and max()), so
580 * just testing for binary inequality is OK. */
584 /* Scale the step size by a factor interpolated from
585 * step_scale_min to step_scale_max, as k_est goes from 0 to
586 * step_scale_multiple * s[i].step[d] */
588 step_scale_min * s[i].step[d] +
589 step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
594 if (gmx_numzero(dx)) /* 0 == dx */
596 /* Likely this will never happen, but if it does just
597 * don't scale the step. */
601 s[i].step[d] *= step_scale_max;
605 step_min = min(step_min,s[i].step[d]);
606 step_max = max(step_max,s[i].step[d]);
610 copy_rvec(xcur[shell],s[i].xold);
611 copy_rvec(f[shell], s[i].fold);
613 do_1pos3(xnew[shell],xcur[shell],f[shell],s[i].step);
616 fprintf(debug,"shell[%d] = %d\n",i,shell);
617 pr_rvec(debug,0,"fshell",f[shell],DIM,TRUE);
618 pr_rvec(debug,0,"xold",xcur[shell],DIM,TRUE);
619 pr_rvec(debug,0,"step",s[i].step,DIM,TRUE);
620 pr_rvec(debug,0,"xnew",xnew[shell],DIM,TRUE);
624 printf("step %.3e %.3e\n",step_min,step_max);
628 static void decrease_step_size(int nshell,t_shell s[])
632 for(i=0; i<nshell; i++)
633 svmul(0.8,s[i].step,s[i].step);
636 static void print_epot(FILE *fp,gmx_large_int_t mdstep,int count,real epot,real df,
637 int ndir,real sf_dir)
641 fprintf(fp,"MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
642 gmx_step_str(mdstep,buf),count,epot,df);
644 fprintf(fp,", dir. rmsF: %6.2e\n",sqrt(sf_dir/ndir));
650 static real rms_force(t_commrec *cr,rvec f[],int ns,t_shell s[],
651 int ndir,real *sf_dir,real *Epot)
657 for(i=0; i<ns; i++) {
659 buf[0] += norm2(f[shell]);
668 ntot = (int)(buf[1] + 0.5);
674 return (ntot ? sqrt(buf[0]/ntot) : 0);
677 static void check_pbc(FILE *fp,rvec x[],int shell)
682 for(m=0; (m<DIM); m++)
683 if (fabs(x[shell][m]-x[now][m]) > 0.3) {
684 pr_rvecs(fp,0,"SHELL-X",x+now,5);
689 static void dump_shells(FILE *fp,rvec x[],rvec f[],real ftol,int ns,t_shell s[])
696 for(i=0; (i<ns); i++) {
698 ff2 = iprod(f[shell],f[shell]);
700 fprintf(fp,"SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
701 shell,f[shell][XX],f[shell][YY],f[shell][ZZ],sqrt(ff2));
702 check_pbc(fp,x,shell);
706 static void init_adir(FILE *log,gmx_shellfc_t shfc,
707 gmx_constr_t constr,t_idef *idef,t_inputrec *ir,
708 t_commrec *cr,int dd_ac1,
709 gmx_large_int_t step,t_mdatoms *md,int start,int end,
710 rvec *x_old,rvec *x_init,rvec *x,
711 rvec *f,rvec *acc_dir,
712 gmx_bool bMolPBC,matrix box,
713 real *lambda,real *dvdlambda,t_nrnb *nrnb)
720 unsigned short *ptype;
723 if (DOMAINDECOMP(cr))
727 if (n > shfc->adir_nalloc) {
728 shfc->adir_nalloc = over_alloc_dd(n);
729 srenew(shfc->adir_xnold,shfc->adir_nalloc);
730 srenew(shfc->adir_xnew ,shfc->adir_nalloc);
732 xnold = shfc->adir_xnold;
733 xnew = shfc->adir_xnew;
739 /* Does NOT work with freeze or acceleration groups (yet) */
740 for (n=start; n<end; n++) {
741 w_dt = md->invmass[n]*dt;
743 for (d=0; d<DIM; d++) {
744 if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) {
745 xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
746 xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
748 xnold[n-start][d] = x[n][d];
749 xnew[n-start][d] = x[n][d];
753 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
754 x,xnold-start,NULL,bMolPBC,box,
755 lambda[efptBONDED],&(dvdlambda[efptBONDED]),
756 NULL,NULL,nrnb,econqCoord,FALSE,0,0);
757 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
758 x,xnew-start,NULL,bMolPBC,box,
759 lambda[efptBONDED],&(dvdlambda[efptBONDED]),
760 NULL,NULL,nrnb,econqCoord,FALSE,0,0);
762 for (n=start; n<end; n++) {
765 -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/sqr(dt)
766 - f[n][d]*md->invmass[n];
767 clear_rvec(acc_dir[n]);
770 /* Project the acceleration on the old bond directions */
771 constrain(log,FALSE,FALSE,constr,idef,ir,NULL,cr,step,0,md,
772 x_old,xnew-start,acc_dir,bMolPBC,box,
773 lambda[efptBONDED],&(dvdlambda[efptBONDED]),
774 NULL,NULL,nrnb,econqDeriv_FlexCon,FALSE,0,0);
777 int relax_shell_flexcon(FILE *fplog,t_commrec *cr,gmx_bool bVerbose,
778 gmx_large_int_t mdstep,t_inputrec *inputrec,
779 gmx_bool bDoNS,int force_flags,
784 gmx_enerdata_t *enerd,t_fcdata *fcd,
785 t_state *state,rvec f[],
788 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
790 gmx_groups_t *groups,
791 struct gmx_shellfc *shfc,
794 double t,rvec mu_tot,
795 int natoms,gmx_bool *bConverged,
802 rvec *pos[2],*force[2],*acc_dir=NULL,*x_old=NULL;
806 real ftol,xiH,xiS,dum=0;
808 gmx_bool bCont,bInit;
809 int nat,dd_ac0,dd_ac1=0,i;
810 int start=md->start,homenr=md->homenr,end=start+homenr,cg0,cg1;
811 int nflexcon,g,number_steps,d,Min=0,count=0;
812 #define Try (1-Min) /* At start Try = 1 */
814 bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
815 bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
816 ftol = inputrec->em_tol;
817 number_steps = inputrec->niter;
818 nshell = shfc->nshell;
820 nflexcon = shfc->nflexcon;
824 if (DOMAINDECOMP(cr)) {
825 nat = dd_natoms_vsite(cr->dd);
827 dd_get_constraint_range(cr->dd,&dd_ac0,&dd_ac1);
828 nat = max(nat,dd_ac1);
834 if (nat > shfc->x_nalloc) {
835 /* Allocate local arrays */
836 shfc->x_nalloc = over_alloc_dd(nat);
837 for(i=0; (i<2); i++) {
838 srenew(shfc->x[i],shfc->x_nalloc);
839 srenew(shfc->f[i],shfc->x_nalloc);
842 for(i=0; (i<2); i++) {
844 force[i] = shfc->f[i];
847 /* With particle decomposition this code only works
848 * when all particles involved with each shell are in the same cg.
851 if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr)) {
852 /* This is the only time where the coordinates are used
853 * before do_force is called, which normally puts all
854 * charge groups in the box.
856 if (PARTDECOMP(cr)) {
857 pd_cg_range(cr,&cg0,&cg1);
862 put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,state->box,
863 &(top->cgs),state->x,fr->cg_cm);
865 mk_mshift(fplog,graph,fr->ePBC,state->box,state->x);
868 /* After this all coordinate arrays will contain whole molecules */
870 shift_self(graph,state->box,state->x);
873 if (nat > shfc->flex_nalloc) {
874 shfc->flex_nalloc = over_alloc_dd(nat);
875 srenew(shfc->acc_dir,shfc->flex_nalloc);
876 srenew(shfc->x_old,shfc->flex_nalloc);
878 acc_dir = shfc->acc_dir;
880 for(i=0; i<homenr; i++) {
883 state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
887 /* Do a prediction of the shell positions */
888 if (shfc->bPredict && !bCont) {
889 predict_shells(fplog,state->x,state->v,inputrec->delta_t,nshell,shell,
890 md->massT,NULL,bInit);
893 /* do_force expected the charge groups to be in the box */
895 unshift_self(graph,state->box,state->x);
897 /* Calculate the forces first time around */
899 pr_rvecs(debug,0,"x b4 do_force",state->x + start,homenr);
901 do_force(fplog,cr,inputrec,mdstep,nrnb,wcycle,top,mtop,groups,
902 state->box,state->x,&state->hist,
903 force[Min],force_vir,md,enerd,fcd,
905 fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
906 (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
910 init_adir(fplog,shfc,
911 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
912 shfc->x_old-start,state->x,state->x,force[Min],
914 fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
916 for(i=start; i<end; i++)
917 sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
920 Epot[Min] = enerd->term[F_EPOT];
922 df[Min]=rms_force(cr,shfc->f[Min],nshell,shell,nflexcon,&sf_dir,&Epot[Min]);
925 fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
929 pr_rvecs(debug,0,"force0",force[Min],md->nr);
932 if (nshell+nflexcon > 0) {
933 /* Copy x to pos[Min] & pos[Try]: during minimization only the
934 * shell positions are updated, therefore the other particles must
937 memcpy(pos[Min],state->x,nat*sizeof(state->x[0]));
938 memcpy(pos[Try],state->x,nat*sizeof(state->x[0]));
941 if (bVerbose && MASTER(cr))
942 print_epot(stdout,mdstep,0,Epot[Min],df[Min],nflexcon,sf_dir);
945 fprintf(debug,"%17s: %14.10e\n",
946 interaction_function[F_EKIN].longname,enerd->term[F_EKIN]);
947 fprintf(debug,"%17s: %14.10e\n",
948 interaction_function[F_EPOT].longname,enerd->term[F_EPOT]);
949 fprintf(debug,"%17s: %14.10e\n",
950 interaction_function[F_ETOT].longname,enerd->term[F_ETOT]);
951 fprintf(debug,"SHELLSTEP %s\n",gmx_step_str(mdstep,sbuf));
954 /* First check whether we should do shells, or whether the force is
955 * low enough even without minimization.
957 *bConverged = (df[Min] < ftol);
959 for(count=1; (!(*bConverged) && (count < number_steps)); count++) {
961 construct_vsites(fplog,vsite,pos[Min],nrnb,inputrec->delta_t,state->v,
962 idef->iparams,idef->il,
963 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
966 init_adir(fplog,shfc,
967 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
968 x_old-start,state->x,pos[Min],force[Min],acc_dir-start,
969 fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
971 directional_sd(fplog,pos[Min],pos[Try],acc_dir-start,start,end,
975 /* New positions, Steepest descent */
976 shell_pos_sd(fplog,pos[Min],pos[Try],force[Min],nshell,shell,count);
978 /* do_force expected the charge groups to be in the box */
980 unshift_self(graph,state->box,pos[Try]);
983 pr_rvecs(debug,0,"RELAX: pos[Min] ",pos[Min] + start,homenr);
984 pr_rvecs(debug,0,"RELAX: pos[Try] ",pos[Try] + start,homenr);
986 /* Try the new positions */
987 do_force(fplog,cr,inputrec,1,nrnb,wcycle,
988 top,mtop,groups,state->box,pos[Try],&state->hist,
989 force[Try],force_vir,
990 md,enerd,fcd,state->lambda,graph,
991 fr,vsite,mu_tot,t,fp_field,NULL,bBornRadii,
995 pr_rvecs(debug,0,"RELAX: force[Min]",force[Min] + start,homenr);
996 pr_rvecs(debug,0,"RELAX: force[Try]",force[Try] + start,homenr);
1000 init_adir(fplog,shfc,
1001 constr,idef,inputrec,cr,dd_ac1,mdstep,md,start,end,
1002 x_old-start,state->x,pos[Try],force[Try],acc_dir-start,
1003 fr->bMolPBC,state->box,state->lambda,&dum,nrnb);
1005 for(i=start; i<end; i++)
1006 sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
1009 Epot[Try] = enerd->term[F_EPOT];
1011 df[Try]=rms_force(cr,force[Try],nshell,shell,nflexcon,&sf_dir,&Epot[Try]);
1014 fprintf(debug,"df = %g %g\n",df[Min],df[Try]);
1018 pr_rvecs(debug,0,"F na do_force",force[Try] + start,homenr);
1020 fprintf(debug,"SHELL ITER %d\n",count);
1021 dump_shells(debug,pos[Try],force[Try],ftol,nshell,shell);
1025 if (bVerbose && MASTER(cr))
1026 print_epot(stdout,mdstep,count,Epot[Try],df[Try],nflexcon,sf_dir);
1028 *bConverged = (df[Try] < ftol);
1030 if ((df[Try] < df[Min])) {
1032 fprintf(debug,"Swapping Min and Try\n");
1034 /* Correct the velocities for the flexible constraints */
1035 invdt = 1/inputrec->delta_t;
1036 for(i=start; i<end; i++) {
1037 for(d=0; d<DIM; d++)
1038 state->v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
1043 decrease_step_size(nshell,shell);
1046 if (MASTER(cr) && !(*bConverged)) {
1047 /* Note that the energies and virial are incorrect when not converged */
1050 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1051 gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
1053 "step %s: EM did not converge in %d iterations, RMS force %.3f\n",
1054 gmx_step_str(mdstep,sbuf),number_steps,df[Min]);
1057 /* Copy back the coordinates and the forces */
1058 memcpy(state->x,pos[Min],nat*sizeof(state->x[0]));
1059 memcpy(f,force[Min],nat*sizeof(f[0]));