Removed include of types/ifunc.h from typedefs.h
[gromacs.git] / src / gromacs / mdlib / mdebin.cpp
blob4a11853d47bc40e756fdfeeb51ac6b27726763e7
1 /*
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37 #include "gmxpre.h"
39 #include "gromacs/legacyheaders/mdebin.h"
41 #include <float.h>
42 #include <stdlib.h>
43 #include <string.h>
45 #include "gromacs/fileio/enxio.h"
46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/xvgr.h"
48 #include "gromacs/legacyheaders/disre.h"
49 #include "gromacs/legacyheaders/mdrun.h"
50 #include "gromacs/legacyheaders/names.h"
51 #include "gromacs/legacyheaders/network.h"
52 #include "gromacs/legacyheaders/orires.h"
53 #include "gromacs/legacyheaders/typedefs.h"
54 #include "gromacs/legacyheaders/types/fcdata.h"
55 #include "gromacs/legacyheaders/types/group.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/constr.h"
59 #include "gromacs/mdlib/mdebin_bar.h"
60 #include "gromacs/pbcutil/pbc.h"
61 #include "gromacs/pulling/pull.h"
62 #include "gromacs/topology/mtop_util.h"
63 #include "gromacs/utility/arraysize.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/smalloc.h"
67 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
69 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
71 static const char *tricl_boxs_nm[] = {
72 "Box-XX", "Box-YY", "Box-ZZ",
73 "Box-YX", "Box-ZX", "Box-ZY"
76 static const char *vol_nm[] = { "Volume" };
78 static const char *dens_nm[] = {"Density" };
80 static const char *pv_nm[] = {"pV" };
82 static const char *enthalpy_nm[] = {"Enthalpy" };
84 static const char *boxvel_nm[] = {
85 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
86 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
89 #define NBOXS asize(boxs_nm)
90 #define NTRICLBOXS asize(tricl_boxs_nm)
92 t_mdebin *init_mdebin(ener_file_t fp_ene,
93 const gmx_mtop_t *mtop,
94 const t_inputrec *ir,
95 FILE *fp_dhdl)
97 const char *ener_nm[F_NRE];
98 static const char *vir_nm[] = {
99 "Vir-XX", "Vir-XY", "Vir-XZ",
100 "Vir-YX", "Vir-YY", "Vir-YZ",
101 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
103 static const char *sv_nm[] = {
104 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
105 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
106 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
108 static const char *fv_nm[] = {
109 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
110 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
111 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
113 static const char *pres_nm[] = {
114 "Pres-XX", "Pres-XY", "Pres-XZ",
115 "Pres-YX", "Pres-YY", "Pres-YZ",
116 "Pres-ZX", "Pres-ZY", "Pres-ZZ"
118 static const char *surft_nm[] = {
119 "#Surf*SurfTen"
121 static const char *mu_nm[] = {
122 "Mu-X", "Mu-Y", "Mu-Z"
124 static const char *vcos_nm[] = {
125 "2CosZ*Vel-X"
127 static const char *visc_nm[] = {
128 "1/Viscosity"
130 static const char *baro_nm[] = {
131 "Barostat"
134 char **grpnms;
135 const gmx_groups_t *groups;
136 char **gnm;
137 char buf[256];
138 const char *bufi;
139 t_mdebin *md;
140 int i, j, ni, nj, n, k, kk, ncon, nset;
141 gmx_bool bBHAM, b14;
143 snew(md, 1);
145 md->bVir = TRUE;
146 md->bPress = TRUE;
147 md->bSurft = TRUE;
148 md->bMu = TRUE;
150 if (EI_DYNAMICS(ir->eI))
152 md->delta_t = ir->delta_t;
154 else
156 md->delta_t = 0;
159 groups = &mtop->groups;
161 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
162 b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
163 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
165 ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
166 nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
167 md->bConstr = (ncon > 0 || nset > 0);
168 md->bConstrVir = FALSE;
169 if (md->bConstr)
171 if (ncon > 0 && ir->eConstrAlg == econtLINCS)
173 if (ir->eI == eiSD2)
175 md->nCrmsd = 2;
177 else
179 md->nCrmsd = 1;
182 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
184 else
186 md->nCrmsd = 0;
189 /* Energy monitoring */
190 for (i = 0; i < egNR; i++)
192 md->bEInd[i] = FALSE;
195 for (i = 0; i < F_NRE; i++)
197 md->bEner[i] = FALSE;
198 if (i == F_LJ)
200 md->bEner[i] = !bBHAM;
202 else if (i == F_BHAM)
204 md->bEner[i] = bBHAM;
206 else if (i == F_EQM)
208 md->bEner[i] = ir->bQMMM;
210 else if (i == F_COUL_LR)
212 md->bEner[i] = (ir->rcoulomb > ir->rlist);
214 else if (i == F_LJ_LR)
216 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
218 else if (i == F_BHAM_LR)
220 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
222 else if (i == F_RF_EXCL)
224 md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC && ir->cutoff_scheme == ecutsGROUP);
226 else if (i == F_COUL_RECIP)
228 md->bEner[i] = EEL_FULL(ir->coulombtype);
230 else if (i == F_LJ_RECIP)
232 md->bEner[i] = EVDW_PME(ir->vdwtype);
234 else if (i == F_LJ14)
236 md->bEner[i] = b14;
238 else if (i == F_COUL14)
240 md->bEner[i] = b14;
242 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
244 md->bEner[i] = FALSE;
246 else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
247 (i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
248 (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
249 (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
250 (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
251 (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
253 md->bEner[i] = (ir->efep != efepNO);
255 else if ((interaction_function[i].flags & IF_VSITE) ||
256 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
258 md->bEner[i] = FALSE;
260 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i == F_EQM))
262 md->bEner[i] = TRUE;
264 else if ((i == F_GBPOL) && ir->implicit_solvent == eisGBSA)
266 md->bEner[i] = TRUE;
268 else if ((i == F_NPSOLVATION) && ir->implicit_solvent == eisGBSA && (ir->sa_algorithm != esaNO))
270 md->bEner[i] = TRUE;
272 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
274 md->bEner[i] = FALSE;
276 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
278 md->bEner[i] = EI_DYNAMICS(ir->eI);
280 else if (i == F_DISPCORR || i == F_PDISPCORR)
282 md->bEner[i] = (ir->eDispCorr != edispcNO);
284 else if (i == F_DISRESVIOL)
286 md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
288 else if (i == F_ORIRESDEV)
290 md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
292 else if (i == F_CONNBONDS)
294 md->bEner[i] = FALSE;
296 else if (i == F_COM_PULL)
298 md->bEner[i] = (ir->bPull && pull_have_potential(ir->pull_work));
300 else if (i == F_ECONSERVED)
302 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
303 (ir->epc == epcNO || ir->epc == epcMTTK));
305 else
307 md->bEner[i] = (gmx_mtop_ftype_count(mtop, i) > 0);
311 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
312 if (ir->bAdress && !debug)
314 for (i = 0; i < F_NRE; i++)
316 md->bEner[i] = FALSE;
317 if (i == F_EKIN)
319 md->bEner[i] = TRUE;
321 if (i == F_TEMP)
323 md->bEner[i] = TRUE;
326 md->bVir = FALSE;
327 md->bPress = FALSE;
328 md->bSurft = FALSE;
329 md->bMu = FALSE;
332 md->f_nre = 0;
333 for (i = 0; i < F_NRE; i++)
335 if (md->bEner[i])
337 ener_nm[md->f_nre] = interaction_function[i].longname;
338 md->f_nre++;
342 md->epc = ir->epc;
343 md->bDiagPres = !TRICLINIC(ir->ref_p);
344 md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
345 md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
346 md->bDynBox = DYNAMIC_BOX(*ir);
347 md->etc = ir->etc;
348 md->bNHC_trotter = IR_NVT_TROTTER(ir);
349 md->bPrintNHChains = ir->bPrintNHChains;
350 md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
351 md->bMu = NEED_MUTOT(*ir);
353 md->ebin = mk_ebin();
354 /* Pass NULL for unit to let get_ebin_space determine the units
355 * for interaction_function[i].longname
357 md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, NULL);
358 if (md->nCrmsd)
360 /* This should be called directly after the call for md->ie,
361 * such that md->iconrmsd follows directly in the list.
363 md->iconrmsd = get_ebin_space(md->ebin, md->nCrmsd, conrmsd_nm, "");
365 if (md->bDynBox)
367 md->ib = get_ebin_space(md->ebin,
368 md->bTricl ? NTRICLBOXS : NBOXS,
369 md->bTricl ? tricl_boxs_nm : boxs_nm,
370 unit_length);
371 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
372 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
373 if (md->bDiagPres)
375 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
376 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
379 if (md->bConstrVir)
381 md->isvir = get_ebin_space(md->ebin, asize(sv_nm), sv_nm, unit_energy);
382 md->ifvir = get_ebin_space(md->ebin, asize(fv_nm), fv_nm, unit_energy);
384 if (md->bVir)
386 md->ivir = get_ebin_space(md->ebin, asize(vir_nm), vir_nm, unit_energy);
388 if (md->bPress)
390 md->ipres = get_ebin_space(md->ebin, asize(pres_nm), pres_nm, unit_pres_bar);
392 if (md->bSurft)
394 md->isurft = get_ebin_space(md->ebin, asize(surft_nm), surft_nm,
395 unit_surft_bar);
397 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
399 md->ipc = get_ebin_space(md->ebin, md->bTricl ? 6 : 3,
400 boxvel_nm, unit_vel);
402 if (md->bMu)
404 md->imu = get_ebin_space(md->ebin, asize(mu_nm), mu_nm, unit_dipole_D);
406 if (ir->cos_accel != 0)
408 md->ivcos = get_ebin_space(md->ebin, asize(vcos_nm), vcos_nm, unit_vel);
409 md->ivisc = get_ebin_space(md->ebin, asize(visc_nm), visc_nm,
410 unit_invvisc_SI);
413 /* Energy monitoring */
414 for (i = 0; i < egNR; i++)
416 md->bEInd[i] = FALSE;
418 md->bEInd[egCOULSR] = TRUE;
419 md->bEInd[egLJSR ] = TRUE;
421 if (ir->rcoulomb > ir->rlist)
423 md->bEInd[egCOULLR] = TRUE;
425 if (!bBHAM)
427 if (ir->rvdw > ir->rlist)
429 md->bEInd[egLJLR] = TRUE;
432 else
434 md->bEInd[egLJSR] = FALSE;
435 md->bEInd[egBHAMSR] = TRUE;
436 if (ir->rvdw > ir->rlist)
438 md->bEInd[egBHAMLR] = TRUE;
441 if (b14)
443 md->bEInd[egLJ14] = TRUE;
444 md->bEInd[egCOUL14] = TRUE;
446 md->nEc = 0;
447 for (i = 0; (i < egNR); i++)
449 if (md->bEInd[i])
451 md->nEc++;
455 n = groups->grps[egcENER].nr;
456 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
457 if (!ir->bAdress)
459 /*standard simulation*/
460 md->nEg = n;
461 md->nE = (n*(n+1))/2;
463 else if (!debug)
465 /*AdResS simulation*/
466 md->nU = 0;
467 md->nEg = 0;
468 md->nE = 0;
469 md->nEc = 0;
470 md->isvir = FALSE;
472 snew(md->igrp, md->nE);
473 if (md->nE > 1)
475 n = 0;
476 snew(gnm, md->nEc);
477 for (k = 0; (k < md->nEc); k++)
479 snew(gnm[k], STRLEN);
481 for (i = 0; (i < groups->grps[egcENER].nr); i++)
483 ni = groups->grps[egcENER].nm_ind[i];
484 for (j = i; (j < groups->grps[egcENER].nr); j++)
486 nj = groups->grps[egcENER].nm_ind[j];
487 for (k = kk = 0; (k < egNR); k++)
489 if (md->bEInd[k])
491 sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
492 *(groups->grpname[ni]), *(groups->grpname[nj]));
493 kk++;
496 md->igrp[n] = get_ebin_space(md->ebin, md->nEc,
497 (const char **)gnm, unit_energy);
498 n++;
501 for (k = 0; (k < md->nEc); k++)
503 sfree(gnm[k]);
505 sfree(gnm);
507 if (n != md->nE)
509 gmx_incons("Number of energy terms wrong");
513 md->nTC = groups->grps[egcTC].nr;
514 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
515 if (md->bMTTK)
517 md->nTCP = 1; /* assume only one possible coupling system for barostat
518 for now */
520 else
522 md->nTCP = 0;
524 if (md->etc == etcNOSEHOOVER)
526 if (md->bNHC_trotter)
528 md->mde_n = 2*md->nNHC*md->nTC;
530 else
532 md->mde_n = 2*md->nTC;
534 if (md->epc == epcMTTK)
536 md->mdeb_n = 2*md->nNHC*md->nTCP;
539 else
541 md->mde_n = md->nTC;
542 md->mdeb_n = 0;
545 snew(md->tmp_r, md->mde_n);
546 snew(md->tmp_v, md->mde_n);
547 snew(md->grpnms, md->mde_n);
548 grpnms = md->grpnms;
550 for (i = 0; (i < md->nTC); i++)
552 ni = groups->grps[egcTC].nm_ind[i];
553 sprintf(buf, "T-%s", *(groups->grpname[ni]));
554 grpnms[i] = gmx_strdup(buf);
556 md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
557 unit_temp_K);
559 if (md->etc == etcNOSEHOOVER)
561 if (md->bPrintNHChains)
563 if (md->bNHC_trotter)
565 for (i = 0; (i < md->nTC); i++)
567 ni = groups->grps[egcTC].nm_ind[i];
568 bufi = *(groups->grpname[ni]);
569 for (j = 0; (j < md->nNHC); j++)
571 sprintf(buf, "Xi-%d-%s", j, bufi);
572 grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
573 sprintf(buf, "vXi-%d-%s", j, bufi);
574 grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
577 md->itc = get_ebin_space(md->ebin, md->mde_n,
578 (const char **)grpnms, unit_invtime);
579 if (md->bMTTK)
581 for (i = 0; (i < md->nTCP); i++)
583 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
584 for (j = 0; (j < md->nNHC); j++)
586 sprintf(buf, "Xi-%d-%s", j, bufi);
587 grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
588 sprintf(buf, "vXi-%d-%s", j, bufi);
589 grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
592 md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
593 (const char **)grpnms, unit_invtime);
596 else
598 for (i = 0; (i < md->nTC); i++)
600 ni = groups->grps[egcTC].nm_ind[i];
601 bufi = *(groups->grpname[ni]);
602 sprintf(buf, "Xi-%s", bufi);
603 grpnms[2*i] = gmx_strdup(buf);
604 sprintf(buf, "vXi-%s", bufi);
605 grpnms[2*i+1] = gmx_strdup(buf);
607 md->itc = get_ebin_space(md->ebin, md->mde_n,
608 (const char **)grpnms, unit_invtime);
612 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
613 md->etc == etcVRESCALE)
615 for (i = 0; (i < md->nTC); i++)
617 ni = groups->grps[egcTC].nm_ind[i];
618 sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
619 grpnms[i] = gmx_strdup(buf);
621 md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
624 sfree(grpnms);
627 md->nU = groups->grps[egcACC].nr;
628 if (md->nU > 1)
630 snew(grpnms, 3*md->nU);
631 for (i = 0; (i < md->nU); i++)
633 ni = groups->grps[egcACC].nm_ind[i];
634 sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
635 grpnms[3*i+XX] = gmx_strdup(buf);
636 sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
637 grpnms[3*i+YY] = gmx_strdup(buf);
638 sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
639 grpnms[3*i+ZZ] = gmx_strdup(buf);
641 md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel);
642 sfree(grpnms);
645 if (fp_ene)
647 do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
650 md->print_grpnms = NULL;
652 /* check whether we're going to write dh histograms */
653 md->dhc = NULL;
654 if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
656 /* Currently dh histograms are only written with dynamics */
657 if (EI_DYNAMICS(ir->eI))
659 snew(md->dhc, 1);
661 mde_delta_h_coll_init(md->dhc, ir);
663 md->fp_dhdl = NULL;
664 snew(md->dE, ir->fepvals->n_lambda);
666 else
668 md->fp_dhdl = fp_dhdl;
669 snew(md->dE, ir->fepvals->n_lambda);
671 if (ir->bSimTemp)
673 int i;
674 snew(md->temperatures, ir->fepvals->n_lambda);
675 for (i = 0; i < ir->fepvals->n_lambda; i++)
677 md->temperatures[i] = ir->simtempvals->temperatures[i];
680 return md;
683 /* print a lambda vector to a string
684 fep = the inputrec's FEP input data
685 i = the index of the lambda vector
686 get_native_lambda = whether to print the native lambda
687 get_names = whether to print the names rather than the values
688 str = the pre-allocated string buffer to print to. */
689 static void print_lambda_vector(t_lambda *fep, int i,
690 gmx_bool get_native_lambda, gmx_bool get_names,
691 char *str)
693 int j, k = 0;
694 int Nsep = 0;
696 for (j = 0; j < efptNR; j++)
698 if (fep->separate_dvdl[j])
700 Nsep++;
703 str[0] = 0; /* reset the string */
704 if (Nsep > 1)
706 str += sprintf(str, "("); /* set the opening parenthesis*/
708 for (j = 0; j < efptNR; j++)
710 if (fep->separate_dvdl[j])
712 if (!get_names)
714 if (get_native_lambda && fep->init_lambda >= 0)
716 str += sprintf(str, "%.4f", fep->init_lambda);
718 else
720 str += sprintf(str, "%.4f", fep->all_lambda[j][i]);
723 else
725 str += sprintf(str, "%s", efpt_singular_names[j]);
727 /* print comma for the next item */
728 if (k < Nsep-1)
730 str += sprintf(str, ", ");
732 k++;
735 if (Nsep > 1)
737 /* and add the closing parenthesis */
738 sprintf(str, ")");
743 extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
744 const gmx_output_env_t *oenv)
746 FILE *fp;
747 const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
748 *lambdastate = "\\lambda state";
749 char title[STRLEN], label_x[STRLEN], label_y[STRLEN];
750 int i, nps, nsets, nsets_de, nsetsbegin;
751 int n_lambda_terms = 0;
752 t_lambda *fep = ir->fepvals; /* for simplicity */
753 t_expanded *expand = ir->expandedvals;
754 char **setname;
755 char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
756 int bufplace = 0;
758 int nsets_dhdl = 0;
759 int s = 0;
760 int nsetsextend;
761 gmx_bool write_pV = FALSE;
763 /* count the number of different lambda terms */
764 for (i = 0; i < efptNR; i++)
766 if (fep->separate_dvdl[i])
768 n_lambda_terms++;
772 if (fep->n_lambda == 0)
774 sprintf(title, "%s", dhdl);
775 sprintf(label_x, "Time (ps)");
776 sprintf(label_y, "%s (%s %s)",
777 dhdl, unit_energy, "[\\lambda]\\S-1\\N");
779 else
781 sprintf(title, "%s and %s", dhdl, deltag);
782 sprintf(label_x, "Time (ps)");
783 sprintf(label_y, "%s and %s (%s %s)",
784 dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
786 fp = gmx_fio_fopen(filename, "w+");
787 xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
789 if (!(ir->bSimTemp))
791 bufplace = sprintf(buf, "T = %g (K) ",
792 ir->opts.ref_t[0]);
794 if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
796 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
798 /* compatibility output */
799 sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
801 else
803 print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
804 lambda_vec_str);
805 print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
806 lambda_name_str);
807 sprintf(&(buf[bufplace]), "%s %d: %s = %s",
808 lambdastate, fep->init_fep_state,
809 lambda_name_str, lambda_vec_str);
812 xvgr_subtitle(fp, buf, oenv);
815 nsets_dhdl = 0;
816 if (fep->dhdl_derivatives == edhdlderivativesYES)
818 nsets_dhdl = n_lambda_terms;
820 /* count the number of delta_g states */
821 nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
823 nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
825 if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
827 nsets += 1; /*add fep state for expanded ensemble */
830 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
832 nsets += 1; /* add energy to the dhdl as well */
835 nsetsextend = nsets;
836 if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
838 nsetsextend += 1; /* for PV term, other terms possible if required for
839 the reduced potential (only needed with foreign
840 lambda, and only output when init_lambda is not
841 set in order to maintain compatibility of the
842 dhdl.xvg file) */
843 write_pV = TRUE;
845 snew(setname, nsetsextend);
847 if (expand->elmcmove > elmcmoveNO)
849 /* state for the fep_vals, if we have alchemical sampling */
850 sprintf(buf, "%s", "Thermodynamic state");
851 setname[s] = gmx_strdup(buf);
852 s += 1;
855 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
857 switch (fep->edHdLPrintEnergy)
859 case edHdLPrintEnergyPOTENTIAL:
860 sprintf(buf, "%s (%s)", "Potential Energy", unit_energy);
861 break;
862 case edHdLPrintEnergyTOTAL:
863 case edHdLPrintEnergyYES:
864 default:
865 sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
867 setname[s] = gmx_strdup(buf);
868 s += 1;
871 if (fep->dhdl_derivatives == edhdlderivativesYES)
873 for (i = 0; i < efptNR; i++)
875 if (fep->separate_dvdl[i])
878 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
880 /* compatibility output */
881 sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
883 else
885 double lam = fep->init_lambda;
886 if (fep->init_lambda < 0)
888 lam = fep->all_lambda[i][fep->init_fep_state];
890 sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
891 lam);
893 setname[s] = gmx_strdup(buf);
894 s += 1;
899 if (fep->n_lambda > 0)
901 /* g_bar has to determine the lambda values used in this simulation
902 * from this xvg legend.
905 if (expand->elmcmove > elmcmoveNO)
907 nsetsbegin = 1; /* for including the expanded ensemble */
909 else
911 nsetsbegin = 0;
914 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
916 nsetsbegin += 1;
918 nsetsbegin += nsets_dhdl;
920 for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
922 print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
923 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
925 /* for compatible dhdl.xvg files */
926 nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
928 else
930 nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
933 if (ir->bSimTemp)
935 /* print the temperature for this state if doing simulated annealing */
936 sprintf(&buf[nps], "T = %g (%s)",
937 ir->simtempvals->temperatures[s-(nsetsbegin)],
938 unit_temp_K);
940 setname[s] = gmx_strdup(buf);
941 s++;
943 if (write_pV)
945 sprintf(buf, "pV (%s)", unit_energy);
946 setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
947 nsets */
950 xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
952 for (s = 0; s < nsetsextend; s++)
954 sfree(setname[s]);
956 sfree(setname);
959 return fp;
962 static void copy_energy(t_mdebin *md, real e[], real ecpy[])
964 int i, j;
966 for (i = j = 0; (i < F_NRE); i++)
968 if (md->bEner[i])
970 ecpy[j++] = e[i];
973 if (j != md->f_nre)
975 gmx_incons("Number of energy terms wrong");
979 void upd_mdebin(t_mdebin *md,
980 gmx_bool bDoDHDL,
981 gmx_bool bSum,
982 double time,
983 real tmass,
984 gmx_enerdata_t *enerd,
985 t_state *state,
986 t_lambda *fep,
987 t_expanded *expand,
988 matrix box,
989 tensor svir,
990 tensor fvir,
991 tensor vir,
992 tensor pres,
993 gmx_ekindata_t *ekind,
994 rvec mu_tot,
995 gmx_constr_t constr)
997 int i, j, k, kk, n, gid;
998 real crmsd[2], tmp6[6];
999 real bs[NTRICLBOXS], vol, dens, pv, enthalpy;
1000 real eee[egNR];
1001 real ecopy[F_NRE];
1002 double store_dhdl[efptNR];
1003 real store_energy = 0;
1004 real tmp;
1006 /* Do NOT use the box in the state variable, but the separate box provided
1007 * as an argument. This is because we sometimes need to write the box from
1008 * the last timestep to match the trajectory frames.
1010 copy_energy(md, enerd->term, ecopy);
1011 add_ebin(md->ebin, md->ie, md->f_nre, ecopy, bSum);
1012 if (md->nCrmsd)
1014 crmsd[0] = constr_rmsd(constr, FALSE);
1015 if (md->nCrmsd > 1)
1017 crmsd[1] = constr_rmsd(constr, TRUE);
1019 add_ebin(md->ebin, md->iconrmsd, md->nCrmsd, crmsd, FALSE);
1021 if (md->bDynBox)
1023 int nboxs;
1024 if (md->bTricl)
1026 bs[0] = box[XX][XX];
1027 bs[1] = box[YY][YY];
1028 bs[2] = box[ZZ][ZZ];
1029 bs[3] = box[YY][XX];
1030 bs[4] = box[ZZ][XX];
1031 bs[5] = box[ZZ][YY];
1032 nboxs = NTRICLBOXS;
1034 else
1036 bs[0] = box[XX][XX];
1037 bs[1] = box[YY][YY];
1038 bs[2] = box[ZZ][ZZ];
1039 nboxs = NBOXS;
1041 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
1042 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
1043 add_ebin(md->ebin, md->ib, nboxs, bs, bSum);
1044 add_ebin(md->ebin, md->ivol, 1, &vol, bSum);
1045 add_ebin(md->ebin, md->idens, 1, &dens, bSum);
1047 if (md->bDiagPres)
1049 /* This is pV (in kJ/mol). The pressure is the reference pressure,
1050 not the instantaneous pressure */
1051 pv = vol*md->ref_p/PRESFAC;
1053 add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
1054 enthalpy = pv + enerd->term[F_ETOT];
1055 add_ebin(md->ebin, md->ienthalpy, 1, &enthalpy, bSum);
1058 if (md->bConstrVir)
1060 add_ebin(md->ebin, md->isvir, 9, svir[0], bSum);
1061 add_ebin(md->ebin, md->ifvir, 9, fvir[0], bSum);
1063 if (md->bVir)
1065 add_ebin(md->ebin, md->ivir, 9, vir[0], bSum);
1067 if (md->bPress)
1069 add_ebin(md->ebin, md->ipres, 9, pres[0], bSum);
1071 if (md->bSurft)
1073 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
1074 add_ebin(md->ebin, md->isurft, 1, &tmp, bSum);
1076 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
1078 tmp6[0] = state->boxv[XX][XX];
1079 tmp6[1] = state->boxv[YY][YY];
1080 tmp6[2] = state->boxv[ZZ][ZZ];
1081 tmp6[3] = state->boxv[YY][XX];
1082 tmp6[4] = state->boxv[ZZ][XX];
1083 tmp6[5] = state->boxv[ZZ][YY];
1084 add_ebin(md->ebin, md->ipc, md->bTricl ? 6 : 3, tmp6, bSum);
1086 if (md->bMu)
1088 add_ebin(md->ebin, md->imu, 3, mu_tot, bSum);
1090 if (ekind && ekind->cosacc.cos_accel != 0)
1092 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
1093 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
1094 add_ebin(md->ebin, md->ivcos, 1, &(ekind->cosacc.vcos), bSum);
1095 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
1096 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
1097 *dens*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
1098 add_ebin(md->ebin, md->ivisc, 1, &tmp, bSum);
1100 if (md->nE > 1)
1102 n = 0;
1103 for (i = 0; (i < md->nEg); i++)
1105 for (j = i; (j < md->nEg); j++)
1107 gid = GID(i, j, md->nEg);
1108 for (k = kk = 0; (k < egNR); k++)
1110 if (md->bEInd[k])
1112 eee[kk++] = enerd->grpp.ener[k][gid];
1115 add_ebin(md->ebin, md->igrp[n], md->nEc, eee, bSum);
1116 n++;
1121 if (ekind)
1123 for (i = 0; (i < md->nTC); i++)
1125 md->tmp_r[i] = ekind->tcstat[i].T;
1127 add_ebin(md->ebin, md->itemp, md->nTC, md->tmp_r, bSum);
1129 if (md->etc == etcNOSEHOOVER)
1131 /* whether to print Nose-Hoover chains: */
1132 if (md->bPrintNHChains)
1134 if (md->bNHC_trotter)
1136 for (i = 0; (i < md->nTC); i++)
1138 for (j = 0; j < md->nNHC; j++)
1140 k = i*md->nNHC+j;
1141 md->tmp_r[2*k] = state->nosehoover_xi[k];
1142 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
1145 add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
1147 if (md->bMTTK)
1149 for (i = 0; (i < md->nTCP); i++)
1151 for (j = 0; j < md->nNHC; j++)
1153 k = i*md->nNHC+j;
1154 md->tmp_r[2*k] = state->nhpres_xi[k];
1155 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
1158 add_ebin(md->ebin, md->itcb, md->mdeb_n, md->tmp_r, bSum);
1161 else
1163 for (i = 0; (i < md->nTC); i++)
1165 md->tmp_r[2*i] = state->nosehoover_xi[i];
1166 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
1168 add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
1172 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
1173 md->etc == etcVRESCALE)
1175 for (i = 0; (i < md->nTC); i++)
1177 md->tmp_r[i] = ekind->tcstat[i].lambda;
1179 add_ebin(md->ebin, md->itc, md->nTC, md->tmp_r, bSum);
1183 if (ekind && md->nU > 1)
1185 for (i = 0; (i < md->nU); i++)
1187 copy_rvec(ekind->grpstat[i].u, md->tmp_v[i]);
1189 add_ebin(md->ebin, md->iu, 3*md->nU, md->tmp_v[0], bSum);
1192 ebin_increase_count(md->ebin, bSum);
1194 /* BAR + thermodynamic integration values */
1195 if ((md->fp_dhdl || md->dhc) && bDoDHDL)
1197 for (i = 0; i < enerd->n_lambda-1; i++)
1199 /* zero for simulated tempering */
1200 md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
1201 if (md->temperatures != NULL)
1203 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1204 /* is this even useful to have at all? */
1205 md->dE[i] += (md->temperatures[i]/
1206 md->temperatures[state->fep_state]-1.0)*
1207 enerd->term[F_EKIN];
1211 if (md->fp_dhdl)
1213 fprintf(md->fp_dhdl, "%.4f", time);
1214 /* the current free energy state */
1216 /* print the current state if we are doing expanded ensemble */
1217 if (expand->elmcmove > elmcmoveNO)
1219 fprintf(md->fp_dhdl, " %4d", state->fep_state);
1221 /* total energy (for if the temperature changes */
1223 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
1225 switch (fep->edHdLPrintEnergy)
1227 case edHdLPrintEnergyPOTENTIAL:
1228 store_energy = enerd->term[F_EPOT];
1229 break;
1230 case edHdLPrintEnergyTOTAL:
1231 case edHdLPrintEnergyYES:
1232 default:
1233 store_energy = enerd->term[F_ETOT];
1235 fprintf(md->fp_dhdl, " %#.8g", store_energy);
1238 if (fep->dhdl_derivatives == edhdlderivativesYES)
1240 for (i = 0; i < efptNR; i++)
1242 if (fep->separate_dvdl[i])
1244 /* assumes F_DVDL is first */
1245 fprintf(md->fp_dhdl, " %#.8g", enerd->term[F_DVDL+i]);
1249 for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
1251 fprintf(md->fp_dhdl, " %#.8g", md->dE[i]);
1253 if (md->bDynBox &&
1254 md->bDiagPres &&
1255 (md->epc != epcNO) &&
1256 (enerd->n_lambda > 0) &&
1257 (fep->init_lambda < 0))
1259 fprintf(md->fp_dhdl, " %#.8g", pv); /* PV term only needed when
1260 there are alternate state
1261 lambda and we're not in
1262 compatibility mode */
1264 fprintf(md->fp_dhdl, "\n");
1265 /* and the binary free energy output */
1267 if (md->dhc && bDoDHDL)
1269 int idhdl = 0;
1270 for (i = 0; i < efptNR; i++)
1272 if (fep->separate_dvdl[i])
1274 /* assumes F_DVDL is first */
1275 store_dhdl[idhdl] = enerd->term[F_DVDL+i];
1276 idhdl += 1;
1279 store_energy = enerd->term[F_ETOT];
1280 /* store_dh is dE */
1281 mde_delta_h_coll_add_dh(md->dhc,
1282 (double)state->fep_state,
1283 store_energy,
1285 store_dhdl,
1286 md->dE + fep->lambda_start_n,
1287 time);
1293 void upd_mdebin_step(t_mdebin *md)
1295 ebin_increase_count(md->ebin, FALSE);
1298 static void npr(FILE *log, int n, char c)
1300 for (; (n > 0); n--)
1302 fprintf(log, "%c", c);
1306 static void pprint(FILE *log, const char *s, t_mdebin *md)
1308 char CHAR = '#';
1309 int slen;
1310 char buf1[22], buf2[22];
1312 slen = strlen(s);
1313 fprintf(log, "\t<====== ");
1314 npr(log, slen, CHAR);
1315 fprintf(log, " ==>\n");
1316 fprintf(log, "\t<==== %s ====>\n", s);
1317 fprintf(log, "\t<== ");
1318 npr(log, slen, CHAR);
1319 fprintf(log, " ======>\n\n");
1321 fprintf(log, "\tStatistics over %s steps using %s frames\n",
1322 gmx_step_str(md->ebin->nsteps_sim, buf1),
1323 gmx_step_str(md->ebin->nsum_sim, buf2));
1324 fprintf(log, "\n");
1327 void print_ebin_header(FILE *log, gmx_int64_t steps, double time, real lambda)
1329 char buf[22];
1331 fprintf(log, " %12s %12s %12s\n"
1332 " %12s %12.5f %12.5f\n\n",
1333 "Step", "Time", "Lambda", gmx_step_str(steps, buf), time, lambda);
1336 void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
1337 FILE *log,
1338 gmx_int64_t step, double time,
1339 int mode, gmx_bool bCompact,
1340 t_mdebin *md, t_fcdata *fcd,
1341 gmx_groups_t *groups, t_grpopts *opts)
1343 /*static char **grpnms=NULL;*/
1344 char buf[246];
1345 int i, j, n, ni, nj, b;
1346 int ndisre = 0;
1347 real *disre_rm3tav, *disre_rt;
1349 /* these are for the old-style blocks (1 subblock, only reals), because
1350 there can be only one per ID for these */
1351 int nr[enxNR];
1352 int id[enxNR];
1353 real *block[enxNR];
1355 t_enxframe fr;
1357 switch (mode)
1359 case eprNORMAL:
1360 init_enxframe(&fr);
1361 fr.t = time;
1362 fr.step = step;
1363 fr.nsteps = md->ebin->nsteps;
1364 fr.dt = md->delta_t;
1365 fr.nsum = md->ebin->nsum;
1366 fr.nre = (bEne) ? md->ebin->nener : 0;
1367 fr.ener = md->ebin->e;
1368 ndisre = bDR ? fcd->disres.npair : 0;
1369 disre_rm3tav = fcd->disres.rm3tav;
1370 disre_rt = fcd->disres.rt;
1371 /* Optional additional old-style (real-only) blocks. */
1372 for (i = 0; i < enxNR; i++)
1374 nr[i] = 0;
1376 if (fcd->orires.nr > 0 && bOR)
1378 diagonalize_orires_tensors(&(fcd->orires));
1379 nr[enxOR] = fcd->orires.nr;
1380 block[enxOR] = fcd->orires.otav;
1381 id[enxOR] = enxOR;
1382 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
1383 fcd->orires.nr : 0;
1384 block[enxORI] = fcd->orires.oinsl;
1385 id[enxORI] = enxORI;
1386 nr[enxORT] = fcd->orires.nex*12;
1387 block[enxORT] = fcd->orires.eig;
1388 id[enxORT] = enxORT;
1391 /* whether we are going to wrte anything out: */
1392 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1395 /* the old-style blocks go first */
1396 fr.nblock = 0;
1397 for (i = 0; i < enxNR; i++)
1399 if (nr[i] > 0)
1401 fr.nblock = i + 1;
1404 add_blocks_enxframe(&fr, fr.nblock);
1405 for (b = 0; b < fr.nblock; b++)
1407 add_subblocks_enxblock(&(fr.block[b]), 1);
1408 fr.block[b].id = id[b];
1409 fr.block[b].sub[0].nr = nr[b];
1410 #ifndef GMX_DOUBLE
1411 fr.block[b].sub[0].type = xdr_datatype_float;
1412 fr.block[b].sub[0].fval = block[b];
1413 #else
1414 fr.block[b].sub[0].type = xdr_datatype_double;
1415 fr.block[b].sub[0].dval = block[b];
1416 #endif
1419 /* check for disre block & fill it. */
1420 if (ndisre > 0)
1422 int db = fr.nblock;
1423 fr.nblock += 1;
1424 add_blocks_enxframe(&fr, fr.nblock);
1426 add_subblocks_enxblock(&(fr.block[db]), 2);
1427 fr.block[db].id = enxDISRE;
1428 fr.block[db].sub[0].nr = ndisre;
1429 fr.block[db].sub[1].nr = ndisre;
1430 #ifndef GMX_DOUBLE
1431 fr.block[db].sub[0].type = xdr_datatype_float;
1432 fr.block[db].sub[1].type = xdr_datatype_float;
1433 fr.block[db].sub[0].fval = disre_rt;
1434 fr.block[db].sub[1].fval = disre_rm3tav;
1435 #else
1436 fr.block[db].sub[0].type = xdr_datatype_double;
1437 fr.block[db].sub[1].type = xdr_datatype_double;
1438 fr.block[db].sub[0].dval = disre_rt;
1439 fr.block[db].sub[1].dval = disre_rm3tav;
1440 #endif
1442 /* here we can put new-style blocks */
1444 /* Free energy perturbation blocks */
1445 if (md->dhc)
1447 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1450 /* we can now free & reset the data in the blocks */
1451 if (md->dhc)
1453 mde_delta_h_coll_reset(md->dhc);
1456 /* do the actual I/O */
1457 do_enx(fp_ene, &fr);
1458 if (fr.nre)
1460 /* We have stored the sums, so reset the sum history */
1461 reset_ebin_sums(md->ebin);
1464 free_enxframe(&fr);
1465 break;
1466 case eprAVER:
1467 if (log)
1469 pprint(log, "A V E R A G E S", md);
1471 break;
1472 case eprRMS:
1473 if (log)
1475 pprint(log, "R M S - F L U C T U A T I O N S", md);
1477 break;
1478 default:
1479 gmx_fatal(FARGS, "Invalid print mode (%d)", mode);
1482 if (log)
1484 for (i = 0; i < opts->ngtc; i++)
1486 if (opts->annealing[i] != eannNO)
1488 fprintf(log, "Current ref_t for group %s: %8.1f\n",
1489 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1490 opts->ref_t[i]);
1493 if (mode == eprNORMAL && fcd->orires.nr > 0)
1495 print_orires_log(log, &(fcd->orires));
1497 fprintf(log, " Energies (%s)\n", unit_energy);
1498 pr_ebin(log, md->ebin, md->ie, md->f_nre+md->nCrmsd, 5, mode, TRUE);
1499 fprintf(log, "\n");
1501 if (!bCompact)
1503 if (md->bDynBox)
1505 pr_ebin(log, md->ebin, md->ib, md->bTricl ? NTRICLBOXS : NBOXS, 5,
1506 mode, TRUE);
1507 fprintf(log, "\n");
1509 if (md->bConstrVir)
1511 fprintf(log, " Constraint Virial (%s)\n", unit_energy);
1512 pr_ebin(log, md->ebin, md->isvir, 9, 3, mode, FALSE);
1513 fprintf(log, "\n");
1514 fprintf(log, " Force Virial (%s)\n", unit_energy);
1515 pr_ebin(log, md->ebin, md->ifvir, 9, 3, mode, FALSE);
1516 fprintf(log, "\n");
1518 if (md->bVir)
1520 fprintf(log, " Total Virial (%s)\n", unit_energy);
1521 pr_ebin(log, md->ebin, md->ivir, 9, 3, mode, FALSE);
1522 fprintf(log, "\n");
1524 if (md->bPress)
1526 fprintf(log, " Pressure (%s)\n", unit_pres_bar);
1527 pr_ebin(log, md->ebin, md->ipres, 9, 3, mode, FALSE);
1528 fprintf(log, "\n");
1530 if (md->bMu)
1532 fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
1533 pr_ebin(log, md->ebin, md->imu, 3, 3, mode, FALSE);
1534 fprintf(log, "\n");
1537 if (md->nE > 1)
1539 if (md->print_grpnms == NULL)
1541 snew(md->print_grpnms, md->nE);
1542 n = 0;
1543 for (i = 0; (i < md->nEg); i++)
1545 ni = groups->grps[egcENER].nm_ind[i];
1546 for (j = i; (j < md->nEg); j++)
1548 nj = groups->grps[egcENER].nm_ind[j];
1549 sprintf(buf, "%s-%s", *(groups->grpname[ni]),
1550 *(groups->grpname[nj]));
1551 md->print_grpnms[n++] = gmx_strdup(buf);
1555 sprintf(buf, "Epot (%s)", unit_energy);
1556 fprintf(log, "%15s ", buf);
1557 for (i = 0; (i < egNR); i++)
1559 if (md->bEInd[i])
1561 fprintf(log, "%12s ", egrp_nm[i]);
1564 fprintf(log, "\n");
1565 for (i = 0; (i < md->nE); i++)
1567 fprintf(log, "%15s", md->print_grpnms[i]);
1568 pr_ebin(log, md->ebin, md->igrp[i], md->nEc, md->nEc, mode,
1569 FALSE);
1571 fprintf(log, "\n");
1573 if (md->nTC > 1)
1575 pr_ebin(log, md->ebin, md->itemp, md->nTC, 4, mode, TRUE);
1576 fprintf(log, "\n");
1578 if (md->nU > 1)
1580 fprintf(log, "%15s %12s %12s %12s\n",
1581 "Group", "Ux", "Uy", "Uz");
1582 for (i = 0; (i < md->nU); i++)
1584 ni = groups->grps[egcACC].nm_ind[i];
1585 fprintf(log, "%15s", *groups->grpname[ni]);
1586 pr_ebin(log, md->ebin, md->iu+3*i, 3, 3, mode, FALSE);
1588 fprintf(log, "\n");
1595 void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin)
1597 int i;
1599 enerhist->nsteps = mdebin->ebin->nsteps;
1600 enerhist->nsum = mdebin->ebin->nsum;
1601 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1602 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1603 enerhist->nener = mdebin->ebin->nener;
1605 if (mdebin->ebin->nsum > 0)
1607 /* Check if we need to allocate first */
1608 if (enerhist->ener_ave == NULL)
1610 snew(enerhist->ener_ave, enerhist->nener);
1611 snew(enerhist->ener_sum, enerhist->nener);
1614 for (i = 0; i < enerhist->nener; i++)
1616 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1617 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1621 if (mdebin->ebin->nsum_sim > 0)
1623 /* Check if we need to allocate first */
1624 if (enerhist->ener_sum_sim == NULL)
1626 snew(enerhist->ener_sum_sim, enerhist->nener);
1629 for (i = 0; i < enerhist->nener; i++)
1631 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1634 if (mdebin->dhc)
1636 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1640 void restore_energyhistory_from_state(t_mdebin * mdebin,
1641 energyhistory_t * enerhist)
1643 int i;
1645 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1646 mdebin->ebin->nener != enerhist->nener)
1648 gmx_fatal(FARGS, "Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1649 mdebin->ebin->nener, enerhist->nener);
1652 mdebin->ebin->nsteps = enerhist->nsteps;
1653 mdebin->ebin->nsum = enerhist->nsum;
1654 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1655 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1657 for (i = 0; i < mdebin->ebin->nener; i++)
1659 mdebin->ebin->e[i].eav =
1660 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1661 mdebin->ebin->e[i].esum =
1662 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1663 mdebin->ebin->e_sim[i].esum =
1664 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1666 if (mdebin->dhc)
1668 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);