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55 #include "mtop_util.h"
60 #include "mdebin_bar.h"
63 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
65 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
67 static const char *tricl_boxs_nm[] = {
68 "Box-XX", "Box-YY", "Box-ZZ",
69 "Box-YX", "Box-ZX", "Box-ZY"
72 static const char *vol_nm[] = { "Volume" };
74 static const char *dens_nm[] = {"Density" };
76 static const char *pv_nm[] = {"pV" };
78 static const char *enthalpy_nm[] = {"Enthalpy" };
80 static const char *boxvel_nm[] = {
81 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
82 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
85 #define NBOXS asize(boxs_nm)
86 #define NTRICLBOXS asize(tricl_boxs_nm)
88 t_mdebin *init_mdebin(ener_file_t fp_ene,
89 const gmx_mtop_t *mtop,
93 const char *ener_nm[F_NRE];
94 static const char *vir_nm[] = {
95 "Vir-XX", "Vir-XY", "Vir-XZ",
96 "Vir-YX", "Vir-YY", "Vir-YZ",
97 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
99 static const char *sv_nm[] = {
100 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
101 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
102 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
104 static const char *fv_nm[] = {
105 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
106 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
107 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
109 static const char *pres_nm[] = {
110 "Pres-XX","Pres-XY","Pres-XZ",
111 "Pres-YX","Pres-YY","Pres-YZ",
112 "Pres-ZX","Pres-ZY","Pres-ZZ"
114 static const char *surft_nm[] = {
117 static const char *mu_nm[] = {
118 "Mu-X", "Mu-Y", "Mu-Z"
120 static const char *vcos_nm[] = {
123 static const char *visc_nm[] = {
126 static const char *baro_nm[] = {
131 const gmx_groups_t *groups;
136 int i,j,ni,nj,n,nh,k,kk,ncon,nset;
137 gmx_bool bBHAM,bNoseHoover,b14;
146 if (EI_DYNAMICS(ir->eI))
148 md->delta_t = ir->delta_t;
155 groups = &mtop->groups;
157 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
158 b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
159 gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
161 ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
162 nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
163 md->bConstr = (ncon > 0 || nset > 0);
164 md->bConstrVir = FALSE;
166 if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
172 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
177 /* Energy monitoring */
184 for(i=0; i<F_NRE; i++)
186 md->bEner[i] = FALSE;
188 md->bEner[i] = !bBHAM;
189 else if (i == F_BHAM)
190 md->bEner[i] = bBHAM;
192 md->bEner[i] = ir->bQMMM;
193 else if (i == F_COUL_LR)
194 md->bEner[i] = (ir->rcoulomb > ir->rlist);
195 else if (i == F_LJ_LR)
196 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
197 else if (i == F_BHAM_LR)
198 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
199 else if (i == F_RF_EXCL)
200 md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC && ir->cutoff_scheme == ecutsGROUP);
201 else if (i == F_COUL_RECIP)
202 md->bEner[i] = EEL_FULL(ir->coulombtype);
203 else if (i == F_LJ14)
205 else if (i == F_COUL14)
207 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
208 md->bEner[i] = FALSE;
209 else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
210 (i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
211 (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
212 (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
213 (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
214 (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
215 md->bEner[i] = (ir->efep != efepNO);
216 else if ((interaction_function[i].flags & IF_VSITE) ||
217 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
218 md->bEner[i] = FALSE;
219 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
221 else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
223 else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
225 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
226 md->bEner[i] = FALSE;
227 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
228 md->bEner[i] = EI_DYNAMICS(ir->eI);
230 md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
231 else if (i == F_DISPCORR || i == F_PDISPCORR)
232 md->bEner[i] = (ir->eDispCorr != edispcNO);
233 else if (i == F_DISRESVIOL)
234 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
235 else if (i == F_ORIRESDEV)
236 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
237 else if (i == F_CONNBONDS)
238 md->bEner[i] = FALSE;
239 else if (i == F_COM_PULL)
240 md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
241 else if (i == F_ECONSERVED)
242 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
243 (ir->epc == epcNO || ir->epc==epcMTTK));
245 md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
248 /* OpenMM always produces only the following 4 energy terms */
249 md->bEner[F_EPOT] = TRUE;
250 md->bEner[F_EKIN] = TRUE;
251 md->bEner[F_ETOT] = TRUE;
252 md->bEner[F_TEMP] = TRUE;
255 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
256 if (ir->bAdress && !debug) {
257 for (i = 0; i < F_NRE; i++) {
258 md->bEner[i] = FALSE;
259 if(i == F_EKIN){ md->bEner[i] = TRUE;}
260 if(i == F_TEMP){ md->bEner[i] = TRUE;}
269 for(i=0; i<F_NRE; i++)
273 ener_nm[md->f_nre]=interaction_function[i].longname;
279 md->bDiagPres = !TRICLINIC(ir->ref_p);
280 md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
281 md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
282 md->bDynBox = DYNAMIC_BOX(*ir);
284 md->bNHC_trotter = IR_NVT_TROTTER(ir);
285 md->bPrintNHChains = ir-> bPrintNHChains;
286 md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
287 md->bMu = NEED_MUTOT(*ir);
289 md->ebin = mk_ebin();
290 /* Pass NULL for unit to let get_ebin_space determine the units
291 * for interaction_function[i].longname
293 md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
296 /* This should be called directly after the call for md->ie,
297 * such that md->iconrmsd follows directly in the list.
299 md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
303 md->ib = get_ebin_space(md->ebin,
304 md->bTricl ? NTRICLBOXS : NBOXS,
305 md->bTricl ? tricl_boxs_nm : boxs_nm,
307 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
308 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
311 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
312 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
317 md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
318 md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
321 md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
323 md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
325 md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
327 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
329 md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
334 md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
336 if (ir->cos_accel != 0)
338 md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
339 md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
343 /* Energy monitoring */
346 md->bEInd[i] = FALSE;
348 md->bEInd[egCOULSR] = TRUE;
349 md->bEInd[egLJSR ] = TRUE;
351 if (ir->rcoulomb > ir->rlist)
353 md->bEInd[egCOULLR] = TRUE;
357 if (ir->rvdw > ir->rlist)
359 md->bEInd[egLJLR] = TRUE;
364 md->bEInd[egLJSR] = FALSE;
365 md->bEInd[egBHAMSR] = TRUE;
366 if (ir->rvdw > ir->rlist)
368 md->bEInd[egBHAMLR] = TRUE;
373 md->bEInd[egLJ14] = TRUE;
374 md->bEInd[egCOUL14] = TRUE;
377 for(i=0; (i<egNR); i++)
385 n=groups->grps[egcENER].nr;
386 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
388 /*standard simulation*/
393 /*AdResS simulation*/
400 snew(md->igrp,md->nE);
405 for(k=0; (k<md->nEc); k++)
409 for(i=0; (i<groups->grps[egcENER].nr); i++)
411 ni=groups->grps[egcENER].nm_ind[i];
412 for(j=i; (j<groups->grps[egcENER].nr); j++)
414 nj=groups->grps[egcENER].nm_ind[j];
415 for(k=kk=0; (k<egNR); k++)
419 sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
420 *(groups->grpname[ni]),*(groups->grpname[nj]));
424 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
425 (const char **)gnm,unit_energy);
429 for(k=0; (k<md->nEc); k++)
437 gmx_incons("Number of energy terms wrong");
441 md->nTC=groups->grps[egcTC].nr;
442 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
445 md->nTCP = 1; /* assume only one possible coupling system for barostat
452 if (md->etc == etcNOSEHOOVER)
454 if (md->bNHC_trotter)
456 md->mde_n = 2*md->nNHC*md->nTC;
460 md->mde_n = 2*md->nTC;
462 if (md->epc == epcMTTK)
464 md->mdeb_n = 2*md->nNHC*md->nTCP;
471 snew(md->tmp_r,md->mde_n);
472 snew(md->tmp_v,md->mde_n);
473 snew(md->grpnms,md->mde_n);
476 for(i=0; (i<md->nTC); i++)
478 ni=groups->grps[egcTC].nm_ind[i];
479 sprintf(buf,"T-%s",*(groups->grpname[ni]));
480 grpnms[i]=strdup(buf);
482 md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
485 if (md->etc == etcNOSEHOOVER)
487 if (md->bPrintNHChains)
489 if (md->bNHC_trotter)
491 for(i=0; (i<md->nTC); i++)
493 ni=groups->grps[egcTC].nm_ind[i];
494 bufi = *(groups->grpname[ni]);
495 for(j=0; (j<md->nNHC); j++)
497 sprintf(buf,"Xi-%d-%s",j,bufi);
498 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
499 sprintf(buf,"vXi-%d-%s",j,bufi);
500 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
503 md->itc=get_ebin_space(md->ebin,md->mde_n,
504 (const char **)grpnms,unit_invtime);
507 for(i=0; (i<md->nTCP); i++)
509 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
510 for(j=0; (j<md->nNHC); j++)
512 sprintf(buf,"Xi-%d-%s",j,bufi);
513 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
514 sprintf(buf,"vXi-%d-%s",j,bufi);
515 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
518 md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
519 (const char **)grpnms,unit_invtime);
524 for(i=0; (i<md->nTC); i++)
526 ni=groups->grps[egcTC].nm_ind[i];
527 bufi = *(groups->grpname[ni]);
528 sprintf(buf,"Xi-%s",bufi);
529 grpnms[2*i]=strdup(buf);
530 sprintf(buf,"vXi-%s",bufi);
531 grpnms[2*i+1]=strdup(buf);
533 md->itc=get_ebin_space(md->ebin,md->mde_n,
534 (const char **)grpnms,unit_invtime);
538 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
539 md->etc == etcVRESCALE)
541 for(i=0; (i<md->nTC); i++)
543 ni=groups->grps[egcTC].nm_ind[i];
544 sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
545 grpnms[i]=strdup(buf);
547 md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
553 md->nU=groups->grps[egcACC].nr;
556 snew(grpnms,3*md->nU);
557 for(i=0; (i<md->nU); i++)
559 ni=groups->grps[egcACC].nm_ind[i];
560 sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
561 grpnms[3*i+XX]=strdup(buf);
562 sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
563 grpnms[3*i+YY]=strdup(buf);
564 sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
565 grpnms[3*i+ZZ]=strdup(buf);
567 md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
573 do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
576 md->print_grpnms=NULL;
578 /* check whether we're going to write dh histograms */
580 if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO )
582 /* Currently dh histograms are only written with dynamics */
583 if (EI_DYNAMICS(ir->eI))
587 mde_delta_h_coll_init(md->dhc, ir);
593 md->fp_dhdl = fp_dhdl;
597 snew(md->temperatures,ir->fepvals->n_lambda);
598 for (i=0;i<ir->fepvals->n_lambda;i++)
600 md->temperatures[i] = ir->simtempvals->temperatures[i];
606 extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
607 const output_env_t oenv)
610 const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
611 *lambdastate="\\lambda state",*remain="remaining";
612 char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
613 int i,np,nps,nsets,nsets_de,nsetsbegin;
626 if (fep->n_lambda == 0)
628 sprintf(title,"%s",dhdl);
629 sprintf(label_x,"Time (ps)");
630 sprintf(label_y,"%s (%s %s)",
631 dhdl,unit_energy,"[\\lambda]\\S-1\\N");
635 sprintf(title,"%s and %s",dhdl,deltag);
636 sprintf(label_x,"Time (ps)");
637 sprintf(label_y,"%s and %s (%s %s)",
638 dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
640 fp = gmx_fio_fopen(filename,"w+");
641 xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
645 bufplace = sprintf(buf,"T = %g (K) ",
648 if (ir->efep != efepSLOWGROWTH)
650 if (fep->n_lambda == 0)
652 sprintf(&(buf[bufplace]),"%s = %g",
653 lambda,fep->init_lambda);
657 sprintf(&(buf[bufplace]),"%s = %d",
658 lambdastate,fep->init_fep_state);
661 xvgr_subtitle(fp,buf,oenv);
663 for (i=0;i<efptNR;i++)
665 if (fep->separate_dvdl[i]) {nsets_dhdl++;}
668 /* count the number of delta_g states */
669 nsets_de = fep->n_lambda;
671 nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
673 if (fep->n_lambda>0 && ir->bExpanded)
675 nsets += 1; /*add fep state for expanded ensemble */
678 if (fep->bPrintEnergy)
680 nsets += 1; /* add energy to the dhdl as well */
684 if ((ir->epc!=epcNO) && (fep->n_lambda>0))
686 nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
688 snew(setname,nsetsextend);
692 /* state for the fep_vals, if we have alchemical sampling */
693 sprintf(buf,"%s","Thermodynamic state");
694 setname[s] = strdup(buf);
698 if (fep->bPrintEnergy)
700 sprintf(buf,"%s (%s)","Energy",unit_energy);
701 setname[s] = strdup(buf);
705 for (i=0;i<efptNR;i++)
707 if (fep->separate_dvdl[i]) {
708 sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
709 setname[s] = strdup(buf);
714 if (fep->n_lambda > 0)
716 /* g_bar has to determine the lambda values used in this simulation
717 * from this xvg legend.
721 nsetsbegin = 1; /* for including the expanded ensemble */
726 if (fep->bPrintEnergy)
730 nsetsbegin += nsets_dhdl;
732 for(s=nsetsbegin; s<nsets; s++)
734 nps = sprintf(buf,"%s %s (",deltag,lambda);
735 for (i=0;i<efptNR;i++)
737 if (fep->separate_dvdl[i])
739 np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
745 /* print the temperature for this state if doing simulated annealing */
746 sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
750 sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */
752 setname[s] = strdup(buf);
754 if (ir->epc!=epcNO) {
755 np = sprintf(buf,"pV (%s)",unit_energy);
756 setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */
759 xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
761 for(s=0; s<nsetsextend; s++)
771 static void copy_energy(t_mdebin *md, real e[],real ecpy[])
775 for(i=j=0; (i<F_NRE); i++)
779 gmx_incons("Number of energy terms wrong");
782 void upd_mdebin(t_mdebin *md,
787 gmx_enerdata_t *enerd,
796 gmx_ekindata_t *ekind,
800 int i,j,k,kk,m,n,gid;
801 real crmsd[2],tmp6[6];
802 real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
805 double store_dhdl[efptNR];
810 /* Do NOT use the box in the state variable, but the separate box provided
811 * as an argument. This is because we sometimes need to write the box from
812 * the last timestep to match the trajectory frames.
814 copy_energy(md, enerd->term,ecopy);
815 add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
818 crmsd[0] = constr_rmsd(constr,FALSE);
821 crmsd[1] = constr_rmsd(constr,TRUE);
823 add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
845 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
846 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
847 add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
848 add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
849 add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
853 /* This is pV (in kJ/mol). The pressure is the reference pressure,
854 not the instantaneous pressure */
855 pv = vol*md->ref_p/PRESFAC;
857 add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
858 enthalpy = pv + enerd->term[F_ETOT];
859 add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
864 add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
865 add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
868 add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
870 add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
872 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
873 add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
875 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
877 tmp6[0] = state->boxv[XX][XX];
878 tmp6[1] = state->boxv[YY][YY];
879 tmp6[2] = state->boxv[ZZ][ZZ];
880 tmp6[3] = state->boxv[YY][XX];
881 tmp6[4] = state->boxv[ZZ][XX];
882 tmp6[5] = state->boxv[ZZ][YY];
883 add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
887 add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
889 if (ekind && ekind->cosacc.cos_accel != 0)
891 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
892 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
893 add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
894 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
895 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
896 *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
897 add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
902 for(i=0; (i<md->nEg); i++)
904 for(j=i; (j<md->nEg); j++)
906 gid=GID(i,j,md->nEg);
907 for(k=kk=0; (k<egNR); k++)
911 eee[kk++] = enerd->grpp.ener[k][gid];
914 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
922 for(i=0; (i<md->nTC); i++)
924 md->tmp_r[i] = ekind->tcstat[i].T;
926 add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
928 if (md->etc == etcNOSEHOOVER)
930 /* whether to print Nose-Hoover chains: */
931 if (md->bPrintNHChains)
933 if (md->bNHC_trotter)
935 for(i=0; (i<md->nTC); i++)
937 for (j=0;j<md->nNHC;j++)
940 md->tmp_r[2*k] = state->nosehoover_xi[k];
941 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
944 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
947 for(i=0; (i<md->nTCP); i++)
949 for (j=0;j<md->nNHC;j++)
952 md->tmp_r[2*k] = state->nhpres_xi[k];
953 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
956 add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
961 for(i=0; (i<md->nTC); i++)
963 md->tmp_r[2*i] = state->nosehoover_xi[i];
964 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
966 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
970 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
971 md->etc == etcVRESCALE)
973 for(i=0; (i<md->nTC); i++)
975 md->tmp_r[i] = ekind->tcstat[i].lambda;
977 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
981 if (ekind && md->nU > 1)
983 for(i=0; (i<md->nU); i++)
985 copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
987 add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
990 ebin_increase_count(md->ebin,bSum);
992 /* BAR + thermodynamic integration values */
993 if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda > 0))
995 snew(dE,enerd->n_lambda-1);
996 for(i=0; i<enerd->n_lambda-1; i++) {
997 dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0]; /* zero for simulated tempering */
998 if (md->temperatures!=NULL)
1000 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1001 /* is this even useful to have at all? */
1002 dE[i] += (md->temperatures[i]/md->temperatures[state->fep_state]-1.0)*enerd->term[F_EKIN];
1007 if (md->fp_dhdl && bDoDHDL)
1009 fprintf(md->fp_dhdl,"%.4f",time);
1010 /* the current free energy state */
1012 /* print the current state if we are doing expanded ensemble */
1013 if (expand->elmcmove > elmcmoveNO) {
1014 fprintf(md->fp_dhdl," %4d",state->fep_state);
1016 /* total energy (for if the temperature changes */
1017 if (fep->bPrintEnergy)
1019 store_energy = enerd->term[F_ETOT];
1020 fprintf(md->fp_dhdl," %#.8g",store_energy);
1023 for (i=0;i<efptNR;i++)
1025 if (fep->separate_dvdl[i])
1027 fprintf(md->fp_dhdl," %#.8g",enerd->term[F_DVDL+i]); /* assumes F_DVDL is first */
1030 for(i=1; i<enerd->n_lambda; i++)
1032 fprintf(md->fp_dhdl," %#.8g",dE[i-1]);
1035 if ((md->epc!=epcNO) && (enerd->n_lambda > 0))
1037 fprintf(md->fp_dhdl," %#.8g",pv); /* PV term only needed when there are alternate state lambda */
1039 fprintf(md->fp_dhdl,"\n");
1040 /* and the binary free energy output */
1042 if (md->dhc && bDoDHDL)
1045 for (i=0;i<efptNR;i++)
1047 if (fep->separate_dvdl[i])
1049 store_dhdl[idhdl] = enerd->term[F_DVDL+i]; /* assumes F_DVDL is first */
1053 /* store_dh is dE */
1054 mde_delta_h_coll_add_dh(md->dhc,
1055 (double)state->fep_state,
1058 (expand->elamstats>elamstatsNO),
1059 (fep->bPrintEnergy),
1067 if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda >0))
1074 void upd_mdebin_step(t_mdebin *md)
1076 ebin_increase_count(md->ebin,FALSE);
1079 static void npr(FILE *log,int n,char c)
1081 for(; (n>0); n--) fprintf(log,"%c",c);
1084 static void pprint(FILE *log,const char *s,t_mdebin *md)
1088 char buf1[22],buf2[22];
1091 fprintf(log,"\t<====== ");
1093 fprintf(log," ==>\n");
1094 fprintf(log,"\t<==== %s ====>\n",s);
1095 fprintf(log,"\t<== ");
1097 fprintf(log," ======>\n\n");
1099 fprintf(log,"\tStatistics over %s steps using %s frames\n",
1100 gmx_step_str(md->ebin->nsteps_sim,buf1),
1101 gmx_step_str(md->ebin->nsum_sim,buf2));
1105 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lambda)
1109 fprintf(log," %12s %12s %12s\n"
1110 " %12s %12.5f %12.5f\n\n",
1111 "Step","Time","Lambda",gmx_step_str(steps,buf),time,lambda);
1114 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
1116 gmx_large_int_t step,double time,
1117 int mode,gmx_bool bCompact,
1118 t_mdebin *md,t_fcdata *fcd,
1119 gmx_groups_t *groups,t_grpopts *opts)
1121 /*static char **grpnms=NULL;*/
1123 int i,j,n,ni,nj,ndr,nor,b;
1125 real *disre_rm3tav, *disre_rt;
1127 /* these are for the old-style blocks (1 subblock, only reals), because
1128 there can be only one per ID for these */
1133 /* temporary arrays for the lambda values to write out */
1134 double enxlambda_data[2];
1144 fr.nsteps = md->ebin->nsteps;
1145 fr.dt = md->delta_t;
1146 fr.nsum = md->ebin->nsum;
1147 fr.nre = (bEne) ? md->ebin->nener : 0;
1148 fr.ener = md->ebin->e;
1149 ndisre = bDR ? fcd->disres.npair : 0;
1150 disre_rm3tav = fcd->disres.rm3tav;
1151 disre_rt = fcd->disres.rt;
1152 /* Optional additional old-style (real-only) blocks. */
1153 for(i=0; i<enxNR; i++)
1157 if (fcd->orires.nr > 0 && bOR)
1159 diagonalize_orires_tensors(&(fcd->orires));
1160 nr[enxOR] = fcd->orires.nr;
1161 block[enxOR] = fcd->orires.otav;
1163 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
1165 block[enxORI] = fcd->orires.oinsl;
1166 id[enxORI] = enxORI;
1167 nr[enxORT] = fcd->orires.nex*12;
1168 block[enxORT] = fcd->orires.eig;
1169 id[enxORT] = enxORT;
1172 /* whether we are going to wrte anything out: */
1173 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1176 /* the old-style blocks go first */
1178 for(i=0; i<enxNR; i++)
1185 add_blocks_enxframe(&fr, fr.nblock);
1186 for(b=0;b<fr.nblock;b++)
1188 add_subblocks_enxblock(&(fr.block[b]), 1);
1189 fr.block[b].id=id[b];
1190 fr.block[b].sub[0].nr = nr[b];
1192 fr.block[b].sub[0].type = xdr_datatype_float;
1193 fr.block[b].sub[0].fval = block[b];
1195 fr.block[b].sub[0].type = xdr_datatype_double;
1196 fr.block[b].sub[0].dval = block[b];
1200 /* check for disre block & fill it. */
1205 add_blocks_enxframe(&fr, fr.nblock);
1207 add_subblocks_enxblock(&(fr.block[db]), 2);
1208 fr.block[db].id=enxDISRE;
1209 fr.block[db].sub[0].nr=ndisre;
1210 fr.block[db].sub[1].nr=ndisre;
1212 fr.block[db].sub[0].type=xdr_datatype_float;
1213 fr.block[db].sub[1].type=xdr_datatype_float;
1214 fr.block[db].sub[0].fval=disre_rt;
1215 fr.block[db].sub[1].fval=disre_rm3tav;
1217 fr.block[db].sub[0].type=xdr_datatype_double;
1218 fr.block[db].sub[1].type=xdr_datatype_double;
1219 fr.block[db].sub[0].dval=disre_rt;
1220 fr.block[db].sub[1].dval=disre_rm3tav;
1223 /* here we can put new-style blocks */
1225 /* Free energy perturbation blocks */
1228 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1231 /* we can now free & reset the data in the blocks */
1234 mde_delta_h_coll_reset(md->dhc);
1237 /* do the actual I/O */
1239 gmx_fio_check_file_position(enx_file_pointer(fp_ene));
1242 /* We have stored the sums, so reset the sum history */
1243 reset_ebin_sums(md->ebin);
1251 pprint(log,"A V E R A G E S",md);
1257 pprint(log,"R M S - F L U C T U A T I O N S",md);
1261 gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
1266 for(i=0;i<opts->ngtc;i++)
1268 if(opts->annealing[i]!=eannNO)
1270 fprintf(log,"Current ref_t for group %s: %8.1f\n",
1271 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1275 if (mode==eprNORMAL && fcd->orires.nr>0)
1277 print_orires_log(log,&(fcd->orires));
1279 fprintf(log," Energies (%s)\n",unit_energy);
1280 pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
1287 pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
1293 fprintf(log," Constraint Virial (%s)\n",unit_energy);
1294 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
1296 fprintf(log," Force Virial (%s)\n",unit_energy);
1297 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
1302 fprintf(log," Total Virial (%s)\n",unit_energy);
1303 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
1308 fprintf(log," Pressure (%s)\n",unit_pres_bar);
1309 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
1314 fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
1315 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
1321 if (md->print_grpnms==NULL)
1323 snew(md->print_grpnms,md->nE);
1325 for(i=0; (i<md->nEg); i++)
1327 ni=groups->grps[egcENER].nm_ind[i];
1328 for(j=i; (j<md->nEg); j++)
1330 nj=groups->grps[egcENER].nm_ind[j];
1331 sprintf(buf,"%s-%s",*(groups->grpname[ni]),
1332 *(groups->grpname[nj]));
1333 md->print_grpnms[n++]=strdup(buf);
1337 sprintf(buf,"Epot (%s)",unit_energy);
1338 fprintf(log,"%15s ",buf);
1339 for(i=0; (i<egNR); i++)
1343 fprintf(log,"%12s ",egrp_nm[i]);
1347 for(i=0; (i<md->nE); i++)
1349 fprintf(log,"%15s",md->print_grpnms[i]);
1350 pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
1357 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
1362 fprintf(log,"%15s %12s %12s %12s\n",
1363 "Group","Ux","Uy","Uz");
1364 for(i=0; (i<md->nU); i++)
1366 ni=groups->grps[egcACC].nm_ind[i];
1367 fprintf(log,"%15s",*groups->grpname[ni]);
1368 pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
1377 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
1381 enerhist->nsteps = mdebin->ebin->nsteps;
1382 enerhist->nsum = mdebin->ebin->nsum;
1383 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1384 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1385 enerhist->nener = mdebin->ebin->nener;
1387 if (mdebin->ebin->nsum > 0)
1389 /* Check if we need to allocate first */
1390 if(enerhist->ener_ave == NULL)
1392 snew(enerhist->ener_ave,enerhist->nener);
1393 snew(enerhist->ener_sum,enerhist->nener);
1396 for(i=0;i<enerhist->nener;i++)
1398 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1399 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1403 if (mdebin->ebin->nsum_sim > 0)
1405 /* Check if we need to allocate first */
1406 if(enerhist->ener_sum_sim == NULL)
1408 snew(enerhist->ener_sum_sim,enerhist->nener);
1411 for(i=0;i<enerhist->nener;i++)
1413 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1418 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1422 void restore_energyhistory_from_state(t_mdebin * mdebin,
1423 energyhistory_t * enerhist)
1427 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1428 mdebin->ebin->nener != enerhist->nener)
1430 gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1431 mdebin->ebin->nener,enerhist->nener);
1434 mdebin->ebin->nsteps = enerhist->nsteps;
1435 mdebin->ebin->nsum = enerhist->nsum;
1436 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1437 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1439 for(i=0; i<mdebin->ebin->nener; i++)
1441 mdebin->ebin->e[i].eav =
1442 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1443 mdebin->ebin->e[i].esum =
1444 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1445 mdebin->ebin->e_sim[i].esum =
1446 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1450 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);