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55 #include "mtop_util.h"
59 #include "mdebin_bar.h"
62 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
64 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
66 static const char *tricl_boxs_nm[] = {
67 "Box-XX", "Box-YY", "Box-ZZ",
68 "Box-YX", "Box-ZX", "Box-ZY"
71 static const char *vol_nm[] = { "Volume" };
73 static const char *dens_nm[] = {"Density" };
75 static const char *pv_nm[] = {"pV" };
77 static const char *enthalpy_nm[] = {"Enthalpy" };
79 static const char *boxvel_nm[] = {
80 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
81 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
84 #define NBOXS asize(boxs_nm)
85 #define NTRICLBOXS asize(tricl_boxs_nm)
87 static gmx_bool bTricl,bDynBox;
88 static int f_nre=0,epc,etc,nCrmsd;
94 t_mdebin *init_mdebin(ener_file_t fp_ene,
95 const gmx_mtop_t *mtop,
99 const char *ener_nm[F_NRE];
100 static const char *vir_nm[] = {
101 "Vir-XX", "Vir-XY", "Vir-XZ",
102 "Vir-YX", "Vir-YY", "Vir-YZ",
103 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
105 static const char *sv_nm[] = {
106 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
107 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
108 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
110 static const char *fv_nm[] = {
111 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
112 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
113 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
115 static const char *pres_nm[] = {
116 "Pres-XX","Pres-XY","Pres-XZ",
117 "Pres-YX","Pres-YY","Pres-YZ",
118 "Pres-ZX","Pres-ZY","Pres-ZZ"
120 static const char *surft_nm[] = {
123 static const char *mu_nm[] = {
124 "Mu-X", "Mu-Y", "Mu-Z"
126 static const char *vcos_nm[] = {
129 static const char *visc_nm[] = {
132 static const char *baro_nm[] = {
137 const gmx_groups_t *groups;
142 int i,j,ni,nj,n,nh,k,kk,ncon,nset;
143 gmx_bool bBHAM,bNoseHoover,b14;
147 if (EI_DYNAMICS(ir->eI))
149 md->delta_t = ir->delta_t;
156 groups = &mtop->groups;
158 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
159 b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
160 gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
162 ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
163 nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
164 md->bConstr = (ncon > 0 || nset > 0);
165 md->bConstrVir = FALSE;
167 if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
173 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
178 /* Energy monitoring */
185 for(i=0; i<F_NRE; i++)
187 md->bEner[i] = FALSE;
189 md->bEner[i] = !bBHAM;
190 else if (i == F_BHAM)
191 md->bEner[i] = bBHAM;
193 md->bEner[i] = ir->bQMMM;
194 else if (i == F_COUL_LR)
195 md->bEner[i] = (ir->rcoulomb > ir->rlist);
196 else if (i == F_LJ_LR)
197 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
198 else if (i == F_BHAM_LR)
199 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
200 else if (i == F_RF_EXCL)
201 md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
202 else if (i == F_COUL_RECIP)
203 md->bEner[i] = EEL_FULL(ir->coulombtype);
204 else if (i == F_LJ14)
206 else if (i == F_COUL14)
208 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
209 md->bEner[i] = FALSE;
210 else if ((i == F_DVDL) || (i == F_DKDL))
211 md->bEner[i] = (ir->efep != efepNO);
212 else if (i == F_DHDL_CON)
213 md->bEner[i] = (ir->efep != efepNO && md->bConstr);
214 else if ((interaction_function[i].flags & IF_VSITE) ||
215 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
216 md->bEner[i] = FALSE;
217 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
219 else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
221 else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
223 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
224 md->bEner[i] = FALSE;
225 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
226 md->bEner[i] = EI_DYNAMICS(ir->eI);
228 md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
229 else if (i == F_DISPCORR || i == F_PDISPCORR)
230 md->bEner[i] = (ir->eDispCorr != edispcNO);
231 else if (i == F_DISRESVIOL)
232 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
233 else if (i == F_ORIRESDEV)
234 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
235 else if (i == F_CONNBONDS)
236 md->bEner[i] = FALSE;
237 else if (i == F_COM_PULL)
238 md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
239 else if (i == F_ECONSERVED)
240 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
241 (ir->epc == epcNO || ir->epc==epcMTTK));
243 md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
246 /* OpenMM always produces only the following 4 energy terms */
247 md->bEner[F_EPOT] = TRUE;
248 md->bEner[F_EKIN] = TRUE;
249 md->bEner[F_ETOT] = TRUE;
250 md->bEner[F_TEMP] = TRUE;
254 for(i=0; i<F_NRE; i++)
258 /* FIXME: The constness should not be cast away */
259 /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
260 ener_nm[md->f_nre]=interaction_function[i].longname;
270 md->ref_p[i][j] = ir->ref_p[i][j];
273 md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
274 md->bDynBox = DYNAMIC_BOX(*ir);
276 md->bNHC_trotter = IR_NVT_TROTTER(ir);
277 md->bMTTK = IR_NPT_TROTTER(ir);
279 md->ebin = mk_ebin();
280 /* Pass NULL for unit to let get_ebin_space determine the units
281 * for interaction_function[i].longname
283 md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
286 /* This should be called directly after the call for md->ie,
287 * such that md->iconrmsd follows directly in the list.
289 md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
293 md->ib = get_ebin_space(md->ebin,
294 md->bTricl ? NTRICLBOXS : NBOXS,
295 md->bTricl ? tricl_boxs_nm : boxs_nm,
297 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
298 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
299 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
300 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
304 md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
305 md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
307 md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
308 md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
309 md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
311 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
313 md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
316 md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
317 if (ir->cos_accel != 0)
319 md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
320 md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
324 /* Energy monitoring */
327 md->bEInd[i] = FALSE;
329 md->bEInd[egCOULSR] = TRUE;
330 md->bEInd[egLJSR ] = TRUE;
332 if (ir->rcoulomb > ir->rlist)
334 md->bEInd[egCOULLR] = TRUE;
338 if (ir->rvdw > ir->rlist)
340 md->bEInd[egLJLR] = TRUE;
345 md->bEInd[egLJSR] = FALSE;
346 md->bEInd[egBHAMSR] = TRUE;
347 if (ir->rvdw > ir->rlist)
349 md->bEInd[egBHAMLR] = TRUE;
354 md->bEInd[egLJ14] = TRUE;
355 md->bEInd[egCOUL14] = TRUE;
358 for(i=0; (i<egNR); i++)
366 n=groups->grps[egcENER].nr;
369 snew(md->igrp,md->nE);
374 for(k=0; (k<md->nEc); k++)
378 for(i=0; (i<groups->grps[egcENER].nr); i++)
380 ni=groups->grps[egcENER].nm_ind[i];
381 for(j=i; (j<groups->grps[egcENER].nr); j++)
383 nj=groups->grps[egcENER].nm_ind[j];
384 for(k=kk=0; (k<egNR); k++)
388 sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
389 *(groups->grpname[ni]),*(groups->grpname[nj]));
393 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
394 (const char **)gnm,unit_energy);
398 for(k=0; (k<md->nEc); k++)
406 gmx_incons("Number of energy terms wrong");
410 md->nTC=groups->grps[egcTC].nr;
411 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
414 md->nTCP = 1; /* assume only one possible coupling system for barostat
422 if (md->etc == etcNOSEHOOVER) {
423 if (md->bNHC_trotter) {
424 md->mde_n = 2*md->nNHC*md->nTC;
428 md->mde_n = 2*md->nTC;
430 if (md->epc == epcMTTK)
432 md->mdeb_n = 2*md->nNHC*md->nTCP;
439 snew(md->tmp_r,md->mde_n);
440 snew(md->tmp_v,md->mde_n);
441 snew(md->grpnms,md->mde_n);
444 for(i=0; (i<md->nTC); i++)
446 ni=groups->grps[egcTC].nm_ind[i];
447 sprintf(buf,"T-%s",*(groups->grpname[ni]));
448 grpnms[i]=strdup(buf);
450 md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
453 bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to print Nose-Hoover chains */
455 if (md->etc == etcNOSEHOOVER)
459 if (md->bNHC_trotter)
461 for(i=0; (i<md->nTC); i++)
463 ni=groups->grps[egcTC].nm_ind[i];
464 bufi = *(groups->grpname[ni]);
465 for(j=0; (j<md->nNHC); j++)
467 sprintf(buf,"Xi-%d-%s",j,bufi);
468 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
469 sprintf(buf,"vXi-%d-%s",j,bufi);
470 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
473 md->itc=get_ebin_space(md->ebin,md->mde_n,
474 (const char **)grpnms,unit_invtime);
477 for(i=0; (i<md->nTCP); i++)
479 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
480 for(j=0; (j<md->nNHC); j++)
482 sprintf(buf,"Xi-%d-%s",j,bufi);
483 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
484 sprintf(buf,"vXi-%d-%s",j,bufi);
485 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
488 md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
489 (const char **)grpnms,unit_invtime);
494 for(i=0; (i<md->nTC); i++)
496 ni=groups->grps[egcTC].nm_ind[i];
497 bufi = *(groups->grpname[ni]);
498 sprintf(buf,"Xi-%s",bufi);
499 grpnms[2*i]=strdup(buf);
500 sprintf(buf,"vXi-%s",bufi);
501 grpnms[2*i+1]=strdup(buf);
503 md->itc=get_ebin_space(md->ebin,md->mde_n,
504 (const char **)grpnms,unit_invtime);
508 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
509 md->etc == etcVRESCALE)
511 for(i=0; (i<md->nTC); i++)
513 ni=groups->grps[egcTC].nm_ind[i];
514 sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
515 grpnms[i]=strdup(buf);
517 md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
523 md->nU=groups->grps[egcACC].nr;
526 snew(grpnms,3*md->nU);
527 for(i=0; (i<md->nU); i++)
529 ni=groups->grps[egcACC].nm_ind[i];
530 sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
531 grpnms[3*i+XX]=strdup(buf);
532 sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
533 grpnms[3*i+YY]=strdup(buf);
534 sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
535 grpnms[3*i+ZZ]=strdup(buf);
537 md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
543 do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
546 md->print_grpnms=NULL;
548 /* check whether we're going to write dh histograms */
550 if (ir->separate_dhdl_file == sepdhdlfileNO )
555 mde_delta_h_coll_init(md->dhc, ir);
560 md->fp_dhdl = fp_dhdl;
562 md->dhdl_derivatives = (ir->dhdl_derivatives==dhdlderivativesYES);
566 FILE *open_dhdl(const char *filename,const t_inputrec *ir,
567 const output_env_t oenv)
570 const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda";
571 char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
575 sprintf(label_x,"%s (%s)","Time",unit_time);
576 if (ir->n_flambda == 0)
578 sprintf(title,"%s",dhdl);
579 sprintf(label_y,"%s (%s %s)",
580 dhdl,unit_energy,"[\\lambda]\\S-1\\N");
584 sprintf(title,"%s, %s",dhdl,deltag);
585 sprintf(label_y,"(%s)",unit_energy);
587 fp = gmx_fio_fopen(filename,"w+");
588 xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
590 if (ir->delta_lambda == 0)
592 sprintf(buf,"T = %g (K), %s = %g",
593 ir->opts.ref_t[0],lambda,ir->init_lambda);
597 sprintf(buf,"T = %g (K)",
600 xvgr_subtitle(fp,buf,oenv);
602 if (ir->n_flambda > 0)
605 /* g_bar has to determine the lambda values used in this simulation
606 * from this xvg legend. */
607 nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) +
610 if (ir->dhdl_derivatives == dhdlderivativesYES)
612 sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
613 setname[nsi++] = gmx_strdup(buf);
615 for(s=0; s<ir->n_flambda; s++)
617 sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]);
618 setname[nsi++] = gmx_strdup(buf);
620 xvgr_legend(fp,nsets,(const char**)setname,oenv);
622 for(s=0; s<nsets; s++)
632 static void copy_energy(t_mdebin *md, real e[],real ecpy[])
636 for(i=j=0; (i<F_NRE); i++)
640 gmx_incons("Number of energy terms wrong");
643 void upd_mdebin(t_mdebin *md, gmx_bool write_dhdl,
647 gmx_enerdata_t *enerd,
654 gmx_ekindata_t *ekind,
658 int i,j,k,kk,m,n,gid;
659 real crmsd[2],tmp6[6];
660 real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
664 gmx_bool bNoseHoover;
666 /* Do NOT use the box in the state variable, but the separate box provided
667 * as an argument. This is because we sometimes need to write the box from
668 * the last timestep to match the trajectory frames.
670 copy_energy(md, enerd->term,ecopy);
671 add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
674 crmsd[0] = constr_rmsd(constr,FALSE);
677 crmsd[1] = constr_rmsd(constr,TRUE);
679 add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
701 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
702 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
704 /* This is pV (in kJ/mol). The pressure is the reference pressure,
705 not the instantaneous pressure */
713 pv += box[i][j]*md->ref_p[i][j]/PRESFAC;
717 pv += box[j][i]*md->ref_p[j][i]/PRESFAC;
722 add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
723 add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
724 add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
725 add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
726 enthalpy = pv + enerd->term[F_ETOT];
727 add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
731 add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
732 add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
734 add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
735 add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
736 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
737 add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
738 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
740 tmp6[0] = state->boxv[XX][XX];
741 tmp6[1] = state->boxv[YY][YY];
742 tmp6[2] = state->boxv[ZZ][ZZ];
743 tmp6[3] = state->boxv[YY][XX];
744 tmp6[4] = state->boxv[ZZ][XX];
745 tmp6[5] = state->boxv[ZZ][YY];
746 add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
748 add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
749 if (ekind && ekind->cosacc.cos_accel != 0)
751 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
752 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
753 add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
754 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
755 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
756 *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
757 add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
762 for(i=0; (i<md->nEg); i++)
764 for(j=i; (j<md->nEg); j++)
766 gid=GID(i,j,md->nEg);
767 for(k=kk=0; (k<egNR); k++)
771 eee[kk++] = enerd->grpp.ener[k][gid];
774 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
782 for(i=0; (i<md->nTC); i++)
784 md->tmp_r[i] = ekind->tcstat[i].T;
786 add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
788 /* whether to print Nose-Hoover chains: */
789 bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL);
791 if (md->etc == etcNOSEHOOVER)
795 if (md->bNHC_trotter)
797 for(i=0; (i<md->nTC); i++)
799 for (j=0;j<md->nNHC;j++)
802 md->tmp_r[2*k] = state->nosehoover_xi[k];
803 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
806 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
809 for(i=0; (i<md->nTCP); i++)
811 for (j=0;j<md->nNHC;j++)
814 md->tmp_r[2*k] = state->nhpres_xi[k];
815 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
818 add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
824 for(i=0; (i<md->nTC); i++)
826 md->tmp_r[2*i] = state->nosehoover_xi[i];
827 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
829 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
833 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
834 md->etc == etcVRESCALE)
836 for(i=0; (i<md->nTC); i++)
838 md->tmp_r[i] = ekind->tcstat[i].lambda;
840 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
844 if (ekind && md->nU > 1)
846 for(i=0; (i<md->nU); i++)
848 copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
850 add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
853 ebin_increase_count(md->ebin,bSum);
855 /* BAR + thermodynamic integration values */
860 fprintf(md->fp_dhdl,"%.4f", time);
862 if (md->dhdl_derivatives)
864 fprintf(md->fp_dhdl," %g", enerd->term[F_DVDL]+
866 enerd->term[F_DHDL_CON]);
868 for(i=1; i<enerd->n_lambda; i++)
870 fprintf(md->fp_dhdl," %g",
871 enerd->enerpart_lambda[i]-enerd->enerpart_lambda[0]);
873 fprintf(md->fp_dhdl,"\n");
875 /* and the binary BAR output */
878 mde_delta_h_coll_add_dh(md->dhc,
879 enerd->term[F_DVDL]+ enerd->term[F_DKDL]+
880 enerd->term[F_DHDL_CON],
881 enerd->enerpart_lambda, time,
887 void upd_mdebin_step(t_mdebin *md)
889 ebin_increase_count(md->ebin,FALSE);
892 static void npr(FILE *log,int n,char c)
894 for(; (n>0); n--) fprintf(log,"%c",c);
897 static void pprint(FILE *log,const char *s,t_mdebin *md)
901 char buf1[22],buf2[22];
904 fprintf(log,"\t<====== ");
906 fprintf(log," ==>\n");
907 fprintf(log,"\t<==== %s ====>\n",s);
908 fprintf(log,"\t<== ");
910 fprintf(log," ======>\n\n");
912 fprintf(log,"\tStatistics over %s steps using %s frames\n",
913 gmx_step_str(md->ebin->nsteps_sim,buf1),
914 gmx_step_str(md->ebin->nsum_sim,buf2));
918 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb)
922 fprintf(log," %12s %12s %12s\n"
923 " %12s %12.5f %12.5f\n\n",
924 "Step","Time","Lambda",gmx_step_str(steps,buf),time,lamb);
927 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
929 gmx_large_int_t step,double time,
930 int mode,gmx_bool bCompact,
931 t_mdebin *md,t_fcdata *fcd,
932 gmx_groups_t *groups,t_grpopts *opts)
934 /*static char **grpnms=NULL;*/
936 int i,j,n,ni,nj,ndr,nor,b;
938 real *disre_rm3tav, *disre_rt;
940 /* these are for the old-style blocks (1 subblock, only reals), because
941 there can be only one per ID for these */
946 /* temporary arrays for the lambda values to write out */
947 double enxlambda_data[2];
957 fr.nsteps = md->ebin->nsteps;
959 fr.nsum = md->ebin->nsum;
960 fr.nre = (bEne) ? md->ebin->nener : 0;
961 fr.ener = md->ebin->e;
962 ndisre = bDR ? fcd->disres.npair : 0;
963 disre_rm3tav = fcd->disres.rm3tav;
964 disre_rt = fcd->disres.rt;
965 /* Optional additional old-style (real-only) blocks. */
966 for(i=0; i<enxNR; i++)
970 if (fcd->orires.nr > 0 && bOR)
972 diagonalize_orires_tensors(&(fcd->orires));
973 nr[enxOR] = fcd->orires.nr;
974 block[enxOR] = fcd->orires.otav;
976 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
978 block[enxORI] = fcd->orires.oinsl;
980 nr[enxORT] = fcd->orires.nex*12;
981 block[enxORT] = fcd->orires.eig;
985 /* whether we are going to wrte anything out: */
986 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
989 /* the old-style blocks go first */
991 for(i=0; i<enxNR; i++)
998 add_blocks_enxframe(&fr, fr.nblock);
999 for(b=0;b<fr.nblock;b++)
1001 add_subblocks_enxblock(&(fr.block[b]), 1);
1002 fr.block[b].id=id[b];
1003 fr.block[b].sub[0].nr = nr[b];
1005 fr.block[b].sub[0].type = xdr_datatype_float;
1006 fr.block[b].sub[0].fval = block[b];
1008 fr.block[b].sub[0].type = xdr_datatype_double;
1009 fr.block[b].sub[0].dval = block[b];
1013 /* check for disre block & fill it. */
1018 add_blocks_enxframe(&fr, fr.nblock);
1020 add_subblocks_enxblock(&(fr.block[db]), 2);
1021 fr.block[db].id=enxDISRE;
1022 fr.block[db].sub[0].nr=ndisre;
1023 fr.block[db].sub[1].nr=ndisre;
1025 fr.block[db].sub[0].type=xdr_datatype_float;
1026 fr.block[db].sub[1].type=xdr_datatype_float;
1027 fr.block[db].sub[0].fval=disre_rt;
1028 fr.block[db].sub[1].fval=disre_rm3tav;
1030 fr.block[db].sub[0].type=xdr_datatype_double;
1031 fr.block[db].sub[1].type=xdr_datatype_double;
1032 fr.block[db].sub[0].dval=disre_rt;
1033 fr.block[db].sub[1].dval=disre_rm3tav;
1036 /* here we can put new-style blocks */
1038 /* Free energy perturbation blocks */
1041 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1044 /* do the actual I/O */
1046 gmx_fio_check_file_position(enx_file_pointer(fp_ene));
1049 /* We have stored the sums, so reset the sum history */
1050 reset_ebin_sums(md->ebin);
1053 /* we can now free & reset the data in the blocks */
1055 mde_delta_h_coll_reset(md->dhc);
1062 pprint(log,"A V E R A G E S",md);
1068 pprint(log,"R M S - F L U C T U A T I O N S",md);
1072 gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
1077 for(i=0;i<opts->ngtc;i++)
1079 if(opts->annealing[i]!=eannNO)
1081 fprintf(log,"Current ref_t for group %s: %8.1f\n",
1082 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1086 if (mode==eprNORMAL && fcd->orires.nr>0)
1088 print_orires_log(log,&(fcd->orires));
1090 fprintf(log," Energies (%s)\n",unit_energy);
1091 pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
1098 pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
1104 fprintf(log," Constraint Virial (%s)\n",unit_energy);
1105 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
1107 fprintf(log," Force Virial (%s)\n",unit_energy);
1108 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
1111 fprintf(log," Total Virial (%s)\n",unit_energy);
1112 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
1114 fprintf(log," Pressure (%s)\n",unit_pres_bar);
1115 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
1117 fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
1118 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
1123 if (md->print_grpnms==NULL)
1125 snew(md->print_grpnms,md->nE);
1127 for(i=0; (i<md->nEg); i++)
1129 ni=groups->grps[egcENER].nm_ind[i];
1130 for(j=i; (j<md->nEg); j++)
1132 nj=groups->grps[egcENER].nm_ind[j];
1133 sprintf(buf,"%s-%s",*(groups->grpname[ni]),
1134 *(groups->grpname[nj]));
1135 md->print_grpnms[n++]=strdup(buf);
1139 sprintf(buf,"Epot (%s)",unit_energy);
1140 fprintf(log,"%15s ",buf);
1141 for(i=0; (i<egNR); i++)
1145 fprintf(log,"%12s ",egrp_nm[i]);
1149 for(i=0; (i<md->nE); i++)
1151 fprintf(log,"%15s",md->print_grpnms[i]);
1152 pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
1159 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
1164 fprintf(log,"%15s %12s %12s %12s\n",
1165 "Group","Ux","Uy","Uz");
1166 for(i=0; (i<md->nU); i++)
1168 ni=groups->grps[egcACC].nm_ind[i];
1169 fprintf(log,"%15s",*groups->grpname[ni]);
1170 pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
1179 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
1183 enerhist->nsteps = mdebin->ebin->nsteps;
1184 enerhist->nsum = mdebin->ebin->nsum;
1185 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1186 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1187 enerhist->nener = mdebin->ebin->nener;
1189 if (mdebin->ebin->nsum > 0)
1191 /* Check if we need to allocate first */
1192 if(enerhist->ener_ave == NULL)
1194 snew(enerhist->ener_ave,enerhist->nener);
1195 snew(enerhist->ener_sum,enerhist->nener);
1198 for(i=0;i<enerhist->nener;i++)
1200 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1201 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1205 if (mdebin->ebin->nsum_sim > 0)
1207 /* Check if we need to allocate first */
1208 if(enerhist->ener_sum_sim == NULL)
1210 snew(enerhist->ener_sum_sim,enerhist->nener);
1213 for(i=0;i<enerhist->nener;i++)
1215 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1220 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1224 void restore_energyhistory_from_state(t_mdebin * mdebin,
1225 energyhistory_t * enerhist)
1229 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1230 mdebin->ebin->nener != enerhist->nener)
1232 gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1233 mdebin->ebin->nener,enerhist->nener);
1236 mdebin->ebin->nsteps = enerhist->nsteps;
1237 mdebin->ebin->nsum = enerhist->nsum;
1238 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1239 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1241 for(i=0; i<mdebin->ebin->nener; i++)
1243 mdebin->ebin->e[i].eav =
1244 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1245 mdebin->ebin->e[i].esum =
1246 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1247 mdebin->ebin->e_sim[i].esum =
1248 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1252 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);