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45 #include "gmx_fatal.h"
49 #include "gromacs/fileio/enxio.h"
57 #include "gromacs/fileio/tpxio.h"
58 #include "gromacs/fileio/trxio.h"
60 #include "mtop_util.h"
64 static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
82 gmx_large_int_t nsteps;
83 gmx_large_int_t npoints;
91 static double mypow(double x, double y)
103 static int *select_it(int nre, char *nm[], int *nset)
108 gmx_bool bVerbose = TRUE;
110 if ((getenv("VERBOSE")) != NULL)
115 fprintf(stderr, "Select the terms you want from the following list\n");
116 fprintf(stderr, "End your selection with 0\n");
120 for (k = 0; (k < nre); )
122 for (j = 0; (j < 4) && (k < nre); j++, k++)
124 fprintf(stderr, " %3d=%14s", k+1, nm[k]);
126 fprintf(stderr, "\n");
133 if (1 != scanf("%d", &n))
135 gmx_fatal(FARGS, "Error reading user input");
137 if ((n > 0) && (n <= nre))
145 for (i = (*nset) = 0; (i < nre); i++)
158 static void chomp(char *buf)
160 int len = strlen(buf);
162 while ((len > 0) && (buf[len-1] == '\n'))
169 static int *select_by_name(int nre, gmx_enxnm_t *nm, int *nset)
172 int n, k, kk, j, i, nmatch, nind, nss;
174 gmx_bool bEOF, bVerbose = TRUE, bLong = FALSE;
175 char *ptr, buf[STRLEN];
176 const char *fm4 = "%3d %-14s";
177 const char *fm2 = "%3d %-34s";
180 if ((getenv("VERBOSE")) != NULL)
185 fprintf(stderr, "\n");
186 fprintf(stderr, "Select the terms you want from the following list by\n");
187 fprintf(stderr, "selecting either (part of) the name or the number or a combination.\n");
188 fprintf(stderr, "End your selection with an empty line or a zero.\n");
189 fprintf(stderr, "-------------------------------------------------------------------\n");
193 for (k = 0; k < nre; k++)
195 newnm[k] = strdup(nm[k].name);
196 /* Insert dashes in all the names */
197 while ((ptr = strchr(newnm[k], ' ')) != NULL)
207 fprintf(stderr, "\n");
210 for (kk = k; kk < k+4; kk++)
212 if (kk < nre && strlen(nm[kk].name) > 14)
220 fprintf(stderr, " ");
224 fprintf(stderr, fm4, k+1, newnm[k]);
233 fprintf(stderr, fm2, k+1, newnm[k]);
244 fprintf(stderr, "\n\n");
250 while (!bEOF && (fgets2(buf, STRLEN-1, stdin)))
252 /* Remove newlines */
258 /* Empty line means end of input */
259 bEOF = (strlen(buf) == 0);
267 /* First try to read an integer */
268 nss = sscanf(ptr, "%d", &nind);
271 /* Zero means end of input */
276 else if ((1 <= nind) && (nind <= nre))
282 fprintf(stderr, "number %d is out of range\n", nind);
287 /* Now try to read a string */
290 for (nind = 0; nind < nre; nind++)
292 if (gmx_strcasecmp(newnm[nind], ptr) == 0)
302 for (nind = 0; nind < nre; nind++)
304 if (gmx_strncasecmp(newnm[nind], ptr, i) == 0)
312 fprintf(stderr, "String '%s' does not match anything\n", ptr);
317 /* Look for the first space, and remove spaces from there */
318 if ((ptr = strchr(ptr, ' ')) != NULL)
323 while (!bEOF && (ptr && (strlen(ptr) > 0)));
328 for (i = (*nset) = 0; (i < nre); i++)
340 gmx_fatal(FARGS, "No energy terms selected");
343 for (i = 0; (i < nre); i++)
352 static void get_dhdl_parms(const char *topnm, t_inputrec *ir)
359 /* all we need is the ir to be able to write the label */
360 read_tpx(topnm, ir, box, &natoms, NULL, NULL, NULL, &mtop);
363 static void get_orires_parms(const char *topnm,
364 int *nor, int *nex, int **label, real **obs)
375 read_tpx(topnm, &ir, box, &natoms, NULL, NULL, NULL, &mtop);
376 top = gmx_mtop_generate_local_top(&mtop, &ir);
378 ip = top->idef.iparams;
379 iatom = top->idef.il[F_ORIRES].iatoms;
381 /* Count how many distance restraint there are... */
382 nb = top->idef.il[F_ORIRES].nr;
385 gmx_fatal(FARGS, "No orientation restraints in topology!\n");
392 for (i = 0; i < nb; i += 3)
394 (*label)[i/3] = ip[iatom[i]].orires.label;
395 (*obs)[i/3] = ip[iatom[i]].orires.obs;
396 if (ip[iatom[i]].orires.ex >= *nex)
398 *nex = ip[iatom[i]].orires.ex+1;
401 fprintf(stderr, "Found %d orientation restraints with %d experiments",
405 static int get_bounds(const char *topnm,
406 real **bounds, int **index, int **dr_pair, int *npairs,
407 gmx_mtop_t *mtop, gmx_localtop_t **ltop, t_inputrec *ir)
410 t_functype *functype;
412 int natoms, i, j, k, type, ftype, natom;
420 read_tpx(topnm, ir, box, &natoms, NULL, NULL, NULL, mtop);
422 top = gmx_mtop_generate_local_top(mtop, ir);
425 functype = top->idef.functype;
426 ip = top->idef.iparams;
428 /* Count how many distance restraint there are... */
429 nb = top->idef.il[F_DISRES].nr;
432 gmx_fatal(FARGS, "No distance restraints in topology!\n");
435 /* Allocate memory */
440 /* Fill the bound array */
442 for (i = 0; (i < top->idef.ntypes); i++)
445 if (ftype == F_DISRES)
448 label1 = ip[i].disres.label;
449 b[nb] = ip[i].disres.up1;
456 /* Fill the index array */
458 disres = &(top->idef.il[F_DISRES]);
459 iatom = disres->iatoms;
460 for (i = j = k = 0; (i < disres->nr); )
463 ftype = top->idef.functype[type];
464 natom = interaction_function[ftype].nratoms+1;
465 if (label1 != top->idef.iparams[type].disres.label)
468 label1 = top->idef.iparams[type].disres.label;
478 gmx_incons("get_bounds for distance restraints");
487 static void calc_violations(real rt[], real rav3[], int nb, int index[],
488 real bounds[], real *viol, double *st, double *sa)
490 const real sixth = 1.0/6.0;
492 double rsum, rav, sumaver, sumt;
496 for (i = 0; (i < nb); i++)
500 for (j = index[i]; (j < index[i+1]); j++)
504 viol[j] += mypow(rt[j], -3.0);
507 rsum += mypow(rt[j], -6);
509 rsum = max(0.0, mypow(rsum, -sixth)-bounds[i]);
510 rav = max(0.0, mypow(rav, -sixth)-bounds[i]);
519 static void analyse_disre(const char *voutfn, int nframes,
520 real violaver[], real bounds[], int index[],
521 int pair[], int nbounds,
522 const output_env_t oenv)
525 double sum, sumt, sumaver;
528 /* Subtract bounds from distances, to calculate violations */
529 calc_violations(violaver, violaver,
530 nbounds, pair, bounds, NULL, &sumt, &sumaver);
533 fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
535 fprintf(stdout, "Largest violation averaged over simulation: %g nm\n\n",
538 vout = xvgropen(voutfn, "r\\S-3\\N average violations", "DR Index", "nm",
542 for (i = 0; (i < nbounds); i++)
544 /* Do ensemble averaging */
546 for (j = pair[i]; (j < pair[i+1]); j++)
548 sumaver += sqr(violaver[j]/nframes);
550 sumaver = max(0.0, mypow(sumaver, minsixth)-bounds[i]);
553 sum = max(sum, sumaver);
554 fprintf(vout, "%10d %10.5e\n", index[i], sumaver);
557 for (j = 0; (j < dr.ndr); j++)
559 fprintf(vout, "%10d %10.5e\n", j, mypow(violaver[j]/nframes, minthird));
564 fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
566 fprintf(stdout, "Largest violation averaged over simulation: %g nm\n\n", sum);
568 do_view(oenv, voutfn, "-graphtype bar");
571 static void einstein_visco(const char *fn, const char *fni, int nsets,
572 int nframes, real **sum,
573 real V, real T, int nsteps, double time[],
574 const output_env_t oenv)
577 double av[4], avold[4];
586 dt = (time[1]-time[0]);
589 for (i = 0; i <= nsets; i++)
593 fp0 = xvgropen(fni, "Shear viscosity integral",
594 "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N ps)", oenv);
595 fp1 = xvgropen(fn, "Shear viscosity using Einstein relation",
596 "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N)", oenv);
597 for (i = 1; i < nf4; i++)
599 fac = dt*nframes/nsteps;
600 for (m = 0; m <= nsets; m++)
604 for (j = 0; j < nframes-i; j++)
606 for (m = 0; m < nsets; m++)
608 di = sqr(fac*(sum[m][j+i]-sum[m][j]));
611 av[nsets] += di/nsets;
614 /* Convert to SI for the viscosity */
615 fac = (V*NANO*NANO*NANO*PICO*1e10)/(2*BOLTZMANN*T)/(nframes-i);
616 fprintf(fp0, "%10g", time[i]-time[0]);
617 for (m = 0; (m <= nsets); m++)
620 fprintf(fp0, " %10g", av[m]);
623 fprintf(fp1, "%10g", 0.5*(time[i]+time[i-1])-time[0]);
624 for (m = 0; (m <= nsets); m++)
626 fprintf(fp1, " %10g", (av[m]-avold[m])/dt);
646 gmx_large_int_t nst_min;
649 static void clear_ee_sum(ee_sum_t *ees)
657 static void add_ee_sum(ee_sum_t *ees, double sum, int np)
663 static void add_ee_av(ee_sum_t *ees)
667 av = ees->sum/ees->np;
674 static double calc_ee2(int nb, ee_sum_t *ees)
676 return (ees->sav2/nb - dsqr(ees->sav/nb))/(nb - 1);
679 static void set_ee_av(ener_ee_t *eee)
683 char buf[STEPSTRSIZE];
684 fprintf(debug, "Storing average for err.est.: %s steps\n",
685 gmx_step_str(eee->nst, buf));
687 add_ee_av(&eee->sum);
689 if (eee->b == 1 || eee->nst < eee->nst_min)
691 eee->nst_min = eee->nst;
696 static void calc_averages(int nset, enerdata_t *edat, int nbmin, int nbmax)
699 double sum, sum2, sump, see2;
700 gmx_large_int_t steps, np, p, bound_nb;
704 double x, sx, sy, sxx, sxy;
707 /* Check if we have exact statistics over all points */
708 for (i = 0; i < nset; i++)
711 ed->bExactStat = FALSE;
712 if (edat->npoints > 0)
714 /* All energy file sum entries 0 signals no exact sums.
715 * But if all energy values are 0, we still have exact sums.
718 for (f = 0; f < edat->nframes && !ed->bExactStat; f++)
720 if (ed->ener[i] != 0)
724 ed->bExactStat = (ed->es[f].sum != 0);
728 ed->bExactStat = TRUE;
734 for (i = 0; i < nset; i++)
745 for (nb = nbmin; nb <= nbmax; nb++)
748 clear_ee_sum(&eee[nb].sum);
752 for (f = 0; f < edat->nframes; f++)
758 /* Add the sum and the sum of variances to the totals. */
764 sum2 += dsqr(sum/np - (sum + es->sum)/(np + p))
770 /* Add a single value to the sum and sum of squares. */
776 /* sum has to be increased after sum2 */
780 /* For the linear regression use variance 1/p.
781 * Note that sump is the sum, not the average, so we don't need p*.
783 x = edat->step[f] - 0.5*(edat->steps[f] - 1);
789 for (nb = nbmin; nb <= nbmax; nb++)
791 /* Check if the current end step is closer to the desired
792 * block boundary than the next end step.
794 bound_nb = (edat->step[0]-1)*nb + edat->nsteps*(eee[nb].b+1);
795 if (eee[nb].nst > 0 &&
796 bound_nb - edat->step[f-1]*nb < edat->step[f]*nb - bound_nb)
806 eee[nb].nst += edat->step[f] - edat->step[f-1];
810 add_ee_sum(&eee[nb].sum, es->sum, edat->points[f]);
814 add_ee_sum(&eee[nb].sum, edat->s[i].ener[f], 1);
816 bound_nb = (edat->step[0]-1)*nb + edat->nsteps*(eee[nb].b+1);
817 if (edat->step[f]*nb >= bound_nb)
824 edat->s[i].av = sum/np;
827 edat->s[i].rmsd = sqrt(sum2/np);
831 edat->s[i].rmsd = sqrt(sum2/np - dsqr(edat->s[i].av));
834 if (edat->nframes > 1)
836 edat->s[i].slope = (np*sxy - sx*sy)/(np*sxx - sx*sx);
840 edat->s[i].slope = 0;
845 for (nb = nbmin; nb <= nbmax; nb++)
847 /* Check if we actually got nb blocks and if the smallest
848 * block is not shorter than 80% of the average.
852 char buf1[STEPSTRSIZE], buf2[STEPSTRSIZE];
853 fprintf(debug, "Requested %d blocks, we have %d blocks, min %s nsteps %s\n",
855 gmx_step_str(eee[nb].nst_min, buf1),
856 gmx_step_str(edat->nsteps, buf2));
858 if (eee[nb].b == nb && 5*nb*eee[nb].nst_min >= 4*edat->nsteps)
860 see2 += calc_ee2(nb, &eee[nb].sum);
866 edat->s[i].ee = sqrt(see2/nee);
876 static enerdata_t *calc_sum(int nset, enerdata_t *edat, int nbmin, int nbmax)
887 snew(s->ener, esum->nframes);
888 snew(s->es, esum->nframes);
890 s->bExactStat = TRUE;
892 for (i = 0; i < nset; i++)
894 if (!edat->s[i].bExactStat)
896 s->bExactStat = FALSE;
898 s->slope += edat->s[i].slope;
901 for (f = 0; f < edat->nframes; f++)
904 for (i = 0; i < nset; i++)
906 sum += edat->s[i].ener[f];
910 for (i = 0; i < nset; i++)
912 sum += edat->s[i].es[f].sum;
918 calc_averages(1, esum, nbmin, nbmax);
923 static char *ee_pr(double ee, char *buf)
930 sprintf(buf, "%s", "--");
934 /* Round to two decimals by printing. */
935 sprintf(tmp, "%.1e", ee);
936 sscanf(tmp, "%lf", &rnd);
937 sprintf(buf, "%g", rnd);
943 static void remove_drift(int nset, int nbmin, int nbmax, real dt, enerdata_t *edat)
945 /* Remove the drift by performing a fit to y = ax+b.
946 Uses 5 iterations. */
948 double delta, d, sd, sd2;
950 edat->npoints = edat->nframes;
951 edat->nsteps = edat->nframes;
953 for (k = 0; (k < 5); k++)
955 for (i = 0; (i < nset); i++)
957 delta = edat->s[i].slope*dt;
961 fprintf(debug, "slope for set %d is %g\n", i, edat->s[i].slope);
964 for (j = 0; (j < edat->nframes); j++)
966 edat->s[i].ener[j] -= j*delta;
967 edat->s[i].es[j].sum = 0;
968 edat->s[i].es[j].sum2 = 0;
971 calc_averages(nset, edat, nbmin, nbmax);
975 static void calc_fluctuation_props(FILE *fp,
976 gmx_bool bDriftCorr, real dt,
978 char **leg, enerdata_t *edat,
979 int nbmin, int nbmax)
982 double vvhh, vv, v, h, hh2, vv2, varv, hh, varh, tt, cv, cp, alpha, kappa, dcp, et, varet;
985 eVol, eEnth, eTemp, eEtot, eNR
987 const char *my_ener[] = { "Volume", "Enthalpy", "Temperature", "Total Energy" };
990 NANO3 = NANO*NANO*NANO;
993 fprintf(fp, "\nYou may want to use the -driftcorr flag in order to correct\n"
994 "for spurious drift in the graphs. Note that this is not\n"
995 "a substitute for proper equilibration and sampling!\n");
999 remove_drift(nset, nbmin, nbmax, dt, edat);
1001 for (i = 0; (i < eNR); i++)
1003 for (ii[i] = 0; (ii[i] < nset &&
1004 (gmx_strcasecmp(leg[ii[i]], my_ener[i]) != 0)); ii[i]++)
1008 /* if (ii[i] < nset)
1009 fprintf(fp,"Found %s data.\n",my_ener[i]);
1011 /* Compute it all! */
1012 vvhh = alpha = kappa = cp = dcp = cv = NOTSET;
1016 if (ii[eTemp] < nset)
1018 tt = edat->s[ii[eTemp]].av;
1022 if ((ii[eVol] < nset) && (ii[eTemp] < nset))
1024 vv = edat->s[ii[eVol]].av*NANO3;
1025 varv = dsqr(edat->s[ii[eVol]].rmsd*NANO3);
1026 kappa = (varv/vv)/(BOLTZMANN*tt);
1030 if ((ii[eEnth] < nset) && (ii[eTemp] < nset))
1032 hh = KILO*edat->s[ii[eEnth]].av/AVOGADRO;
1033 varh = dsqr(KILO*edat->s[ii[eEnth]].rmsd/AVOGADRO);
1034 cp = AVOGADRO*((varh/nmol)/(BOLTZMANN*tt*tt));
1037 et = varet = NOTSET;
1038 if ((ii[eEtot] < nset) && (hh == NOTSET) && (tt != NOTSET))
1040 /* Only compute cv in constant volume runs, which we can test
1041 by checking whether the enthalpy was computed.
1043 et = edat->s[ii[eEtot]].av;
1044 varet = sqr(edat->s[ii[eEtot]].rmsd);
1045 cv = KILO*((varet/nmol)/(BOLTZ*tt*tt));
1048 if ((ii[eVol] < nset) && (ii[eEnth] < nset) && (ii[eTemp] < nset))
1051 for (j = 0; (j < edat->nframes); j++)
1053 v = edat->s[ii[eVol]].ener[j]*NANO3;
1054 h = KILO*edat->s[ii[eEnth]].ener[j]/AVOGADRO;
1057 vvhh /= edat->nframes;
1058 alpha = (vvhh-vv*hh)/(vv*BOLTZMANN*tt*tt);
1059 dcp = (vv*AVOGADRO/nmol)*tt*sqr(alpha)/(kappa);
1066 fprintf(fp, "\nWARNING: nmol = %d, this may not be what you want.\n",
1069 fprintf(fp, "\nTemperature dependent fluctuation properties at T = %g.\n", tt);
1070 fprintf(fp, "\nHeat capacities obtained from fluctuations do *not* include\n");
1071 fprintf(fp, "quantum corrections. If you want to get a more accurate estimate\n");
1072 fprintf(fp, "please use the g_dos program.\n\n");
1073 fprintf(fp, "WARNING: Please verify that your simulations are converged and perform\n"
1074 "a block-averaging error analysis (not implemented in g_energy yet)\n");
1080 fprintf(fp, "varv = %10g (m^6)\n", varv*AVOGADRO/nmol);
1084 fprintf(fp, "vvhh = %10g (m^3 J)\n", vvhh);
1089 fprintf(fp, "Volume = %10g m^3/mol\n",
1094 fprintf(fp, "Enthalpy = %10g kJ/mol\n",
1095 hh*AVOGADRO/(KILO*nmol));
1097 if (alpha != NOTSET)
1099 fprintf(fp, "Coefficient of Thermal Expansion Alpha_P = %10g (1/K)\n",
1102 if (kappa != NOTSET)
1104 fprintf(fp, "Isothermal Compressibility Kappa = %10g (J/m^3)\n",
1106 fprintf(fp, "Adiabatic bulk modulus = %10g (m^3/J)\n",
1111 fprintf(fp, "Heat capacity at constant pressure Cp = %10g J/mol K\n",
1116 fprintf(fp, "Heat capacity at constant volume Cv = %10g J/mol K\n",
1121 fprintf(fp, "Cp-Cv = %10g J/mol K\n",
1124 please_cite(fp, "Allen1987a");
1128 fprintf(fp, "You should select the temperature in order to obtain fluctuation properties.\n");
1132 static void analyse_ener(gmx_bool bCorr, const char *corrfn,
1133 gmx_bool bFee, gmx_bool bSum, gmx_bool bFluct,
1134 gmx_bool bVisco, const char *visfn, int nmol,
1135 gmx_large_int_t start_step, double start_t,
1136 gmx_large_int_t step, double t,
1137 double time[], real reftemp,
1139 int nset, int set[], gmx_bool *bIsEner,
1140 char **leg, gmx_enxnm_t *enm,
1141 real Vaver, real ezero,
1142 int nbmin, int nbmax,
1143 const output_env_t oenv)
1146 /* Check out the printed manual for equations! */
1147 double Dt, aver, stddev, errest, delta_t, totaldrift;
1148 enerdata_t *esum = NULL;
1149 real xxx, integral, intBulk, Temp = 0, Pres = 0;
1150 real sfrac, oldfrac, diffsum, diffav, fstep, pr_aver, pr_stddev, pr_errest;
1151 double beta = 0, expE, expEtot, *fee = NULL;
1152 gmx_large_int_t nsteps;
1153 int nexact, nnotexact;
1157 char buf[256], eebuf[100];
1159 nsteps = step - start_step + 1;
1162 fprintf(stdout, "Not enough steps (%s) for statistics\n",
1163 gmx_step_str(nsteps, buf));
1167 /* Calculate the time difference */
1168 delta_t = t - start_t;
1170 fprintf(stdout, "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
1171 gmx_step_str(nsteps, buf), start_t, t, nset);
1173 calc_averages(nset, edat, nbmin, nbmax);
1177 esum = calc_sum(nset, edat, nbmin, nbmax);
1180 if (edat->npoints == 0)
1189 for (i = 0; (i < nset); i++)
1191 if (edat->s[i].bExactStat)
1204 fprintf(stdout, "All statistics are over %s points\n",
1205 gmx_step_str(edat->npoints, buf));
1207 else if (nexact == 0 || edat->npoints == edat->nframes)
1209 fprintf(stdout, "All statistics are over %d points (frames)\n",
1214 fprintf(stdout, "The term%s", nnotexact == 1 ? "" : "s");
1215 for (i = 0; (i < nset); i++)
1217 if (!edat->s[i].bExactStat)
1219 fprintf(stdout, " '%s'", leg[i]);
1222 fprintf(stdout, " %s has statistics over %d points (frames)\n",
1223 nnotexact == 1 ? "is" : "are", edat->nframes);
1224 fprintf(stdout, "All other statistics are over %s points\n",
1225 gmx_step_str(edat->npoints, buf));
1227 fprintf(stdout, "\n");
1229 fprintf(stdout, "%-24s %10s %10s %10s %10s",
1230 "Energy", "Average", "Err.Est.", "RMSD", "Tot-Drift");
1233 fprintf(stdout, " %10s\n", "-kT ln<e^(E/kT)>");
1237 fprintf(stdout, "\n");
1239 fprintf(stdout, "-------------------------------------------------------------------------------\n");
1241 /* Initiate locals, only used with -sum */
1245 beta = 1.0/(BOLTZ*reftemp);
1248 for (i = 0; (i < nset); i++)
1250 aver = edat->s[i].av;
1251 stddev = edat->s[i].rmsd;
1252 errest = edat->s[i].ee;
1257 for (j = 0; (j < edat->nframes); j++)
1259 expE += exp(beta*(edat->s[i].ener[j] - aver)/nmol);
1263 expEtot += expE/edat->nframes;
1266 fee[i] = log(expE/edat->nframes)/beta + aver/nmol;
1268 if (strstr(leg[i], "empera") != NULL)
1272 else if (strstr(leg[i], "olum") != NULL)
1276 else if (strstr(leg[i], "essure") != NULL)
1282 pr_aver = aver/nmol-ezero;
1283 pr_stddev = stddev/nmol;
1284 pr_errest = errest/nmol;
1293 /* Multiply the slope in steps with the number of steps taken */
1294 totaldrift = (edat->nsteps - 1)*edat->s[i].slope;
1300 fprintf(stdout, "%-24s %10g %10s %10g %10g",
1301 leg[i], pr_aver, ee_pr(pr_errest, eebuf), pr_stddev, totaldrift);
1304 fprintf(stdout, " %10g", fee[i]);
1307 fprintf(stdout, " (%s)\n", enm[set[i]].unit);
1311 for (j = 0; (j < edat->nframes); j++)
1313 edat->s[i].ener[j] -= aver;
1319 totaldrift = (edat->nsteps - 1)*esum->s[0].slope;
1320 fprintf(stdout, "%-24s %10g %10s %10s %10g (%s)",
1321 "Total", esum->s[0].av/nmol, ee_pr(esum->s[0].ee/nmol, eebuf),
1322 "--", totaldrift/nmol, enm[set[0]].unit);
1323 /* pr_aver,pr_stddev,a,totaldrift */
1326 fprintf(stdout, " %10g %10g\n",
1327 log(expEtot)/beta + esum->s[0].av/nmol, log(expEtot)/beta);
1331 fprintf(stdout, "\n");
1335 /* Do correlation function */
1336 if (edat->nframes > 1)
1338 Dt = delta_t/(edat->nframes - 1);
1346 const char* leg[] = { "Shear", "Bulk" };
1351 /* Assume pressure tensor is in Pxx Pxy Pxz Pyx Pyy Pyz Pzx Pzy Pzz */
1353 /* Symmetrise tensor! (and store in first three elements)
1354 * And subtract average pressure!
1357 for (i = 0; i < 12; i++)
1359 snew(eneset[i], edat->nframes);
1362 for (i = 0; i < 3; i++)
1364 snew(enesum[i], edat->nframes);
1366 for (i = 0; (i < edat->nframes); i++)
1368 eneset[0][i] = 0.5*(edat->s[1].ener[i]+edat->s[3].ener[i]);
1369 eneset[1][i] = 0.5*(edat->s[2].ener[i]+edat->s[6].ener[i]);
1370 eneset[2][i] = 0.5*(edat->s[5].ener[i]+edat->s[7].ener[i]);
1371 for (j = 3; j <= 11; j++)
1373 eneset[j][i] = edat->s[j].ener[i];
1375 eneset[11][i] -= Pres;
1376 enesum[0][i] = 0.5*(edat->s[1].es[i].sum+edat->s[3].es[i].sum);
1377 enesum[1][i] = 0.5*(edat->s[2].es[i].sum+edat->s[6].es[i].sum);
1378 enesum[2][i] = 0.5*(edat->s[5].es[i].sum+edat->s[7].es[i].sum);
1381 einstein_visco("evisco.xvg", "eviscoi.xvg",
1382 3, edat->nframes, enesum, Vaver, Temp, nsteps, time, oenv);
1384 /*do_autocorr(corrfn,buf,nenergy,3,eneset,Dt,eacNormal,TRUE);*/
1385 /* Do it for shear viscosity */
1386 strcpy(buf, "Shear Viscosity");
1387 low_do_autocorr(corrfn, oenv, buf, edat->nframes, 3,
1388 (edat->nframes+1)/2, eneset, Dt,
1389 eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
1391 /* Now for bulk viscosity */
1392 strcpy(buf, "Bulk Viscosity");
1393 low_do_autocorr(corrfn, oenv, buf, edat->nframes, 1,
1394 (edat->nframes+1)/2, &(eneset[11]), Dt,
1395 eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
1397 factor = (Vaver*1e-26/(BOLTZMANN*Temp))*Dt;
1398 fp = xvgropen(visfn, buf, "Time (ps)", "\\8h\\4 (cp)", oenv);
1399 xvgr_legend(fp, asize(leg), leg, oenv);
1401 /* Use trapezium rule for integration */
1404 nout = get_acfnout();
1405 if ((nout < 2) || (nout >= edat->nframes/2))
1407 nout = edat->nframes/2;
1409 for (i = 1; (i < nout); i++)
1411 integral += 0.5*(eneset[0][i-1] + eneset[0][i])*factor;
1412 intBulk += 0.5*(eneset[11][i-1] + eneset[11][i])*factor;
1413 fprintf(fp, "%10g %10g %10g\n", (i*Dt), integral, intBulk);
1421 strcpy(buf, "Autocorrelation of Energy Fluctuations");
1425 strcpy(buf, "Energy Autocorrelation");
1428 do_autocorr(corrfn, oenv, buf, edat->nframes,
1430 bSum ? &edat->s[nset-1].ener : eneset,
1431 (delta_t/edat->nframes), eacNormal, FALSE);
1437 static void print_time(FILE *fp, double t)
1439 fprintf(fp, "%12.6f", t);
1442 static void print1(FILE *fp, gmx_bool bDp, real e)
1446 fprintf(fp, " %16.12f", e);
1450 fprintf(fp, " %10.6f", e);
1454 static void fec(const char *ene2fn, const char *runavgfn,
1455 real reftemp, int nset, int set[], char *leg[],
1456 enerdata_t *edat, double time[],
1457 const output_env_t oenv)
1459 const char * ravgleg[] = {
1460 "\\8D\\4E = E\\sB\\N-E\\sA\\N",
1461 "<e\\S-\\8D\\4E/kT\\N>\\s0..t\\N"
1465 int nre, timecheck, step, nenergy, nenergy2, maxenergy;
1471 gmx_enxnm_t *enm = NULL;
1475 /* read second energy file */
1478 enx = open_enx(ene2fn, "r");
1479 do_enxnms(enx, &(fr->nre), &enm);
1481 snew(eneset2, nset+1);
1487 /* This loop searches for the first frame (when -b option is given),
1488 * or when this has been found it reads just one energy frame
1492 bCont = do_enx(enx, fr);
1496 timecheck = check_times(fr->t);
1500 while (bCont && (timecheck < 0));
1502 /* Store energies for analysis afterwards... */
1503 if ((timecheck == 0) && bCont)
1507 if (nenergy2 >= maxenergy)
1510 for (i = 0; i <= nset; i++)
1512 srenew(eneset2[i], maxenergy);
1515 if (fr->t != time[nenergy2])
1517 fprintf(stderr, "\nWARNING time mismatch %g!=%g at frame %s\n",
1518 fr->t, time[nenergy2], gmx_step_str(fr->step, buf));
1520 for (i = 0; i < nset; i++)
1522 eneset2[i][nenergy2] = fr->ener[set[i]].e;
1528 while (bCont && (timecheck == 0));
1531 if (edat->nframes != nenergy2)
1533 fprintf(stderr, "\nWARNING file length mismatch %d!=%d\n",
1534 edat->nframes, nenergy2);
1536 nenergy = min(edat->nframes, nenergy2);
1538 /* calculate fe difference dF = -kT ln < exp(-(E_B-E_A)/kT) >_A */
1542 fp = xvgropen(runavgfn, "Running average free energy difference",
1543 "Time (" unit_time ")", "\\8D\\4E (" unit_energy ")", oenv);
1544 xvgr_legend(fp, asize(ravgleg), ravgleg, oenv);
1546 fprintf(stdout, "\n%-24s %10s\n",
1547 "Energy", "dF = -kT ln < exp(-(EB-EA)/kT) >A");
1549 beta = 1.0/(BOLTZ*reftemp);
1550 for (i = 0; i < nset; i++)
1552 if (gmx_strcasecmp(leg[i], enm[set[i]].name) != 0)
1554 fprintf(stderr, "\nWARNING energy set name mismatch %s!=%s\n",
1555 leg[i], enm[set[i]].name);
1557 for (j = 0; j < nenergy; j++)
1559 dE = eneset2[i][j] - edat->s[i].ener[j];
1560 sum += exp(-dE*beta);
1563 fprintf(fp, "%10g %10g %10g\n",
1564 time[j], dE, -BOLTZ*reftemp*log(sum/(j+1)) );
1567 aver = -BOLTZ*reftemp*log(sum/nenergy);
1568 fprintf(stdout, "%-24s %10g\n", leg[i], aver);
1578 static void do_dhdl(t_enxframe *fr, t_inputrec *ir, FILE **fp_dhdl,
1579 const char *filename, gmx_bool bDp,
1580 int *blocks, int *hists, int *samples, int *nlambdas,
1581 const output_env_t oenv)
1583 const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda";
1584 char title[STRLEN], label_x[STRLEN], label_y[STRLEN], legend[STRLEN];
1586 gmx_bool first = FALSE;
1587 int nblock_hist = 0, nblock_dh = 0, nblock_dhcoll = 0;
1590 double temp = 0, start_time = 0, delta_time = 0, start_lambda = 0, delta_lambda = 0;
1591 static int setnr = 0;
1592 double *native_lambda_vec = NULL;
1593 const char **lambda_components = NULL;
1594 int n_lambda_vec = 0;
1595 gmx_bool changing_lambda = FALSE;
1596 int lambda_fep_state;
1598 /* now count the blocks & handle the global dh data */
1599 for (i = 0; i < fr->nblock; i++)
1601 if (fr->block[i].id == enxDHHIST)
1605 else if (fr->block[i].id == enxDH)
1609 else if (fr->block[i].id == enxDHCOLL)
1612 if ( (fr->block[i].nsub < 1) ||
1613 (fr->block[i].sub[0].type != xdr_datatype_double) ||
1614 (fr->block[i].sub[0].nr < 5))
1616 gmx_fatal(FARGS, "Unexpected block data");
1619 /* read the data from the DHCOLL block */
1620 temp = fr->block[i].sub[0].dval[0];
1621 start_time = fr->block[i].sub[0].dval[1];
1622 delta_time = fr->block[i].sub[0].dval[2];
1623 start_lambda = fr->block[i].sub[0].dval[3];
1624 delta_lambda = fr->block[i].sub[0].dval[4];
1625 changing_lambda = (delta_lambda != 0);
1626 if (fr->block[i].nsub > 1)
1628 lambda_fep_state = fr->block[i].sub[1].ival[0];
1629 if (n_lambda_vec == 0)
1631 n_lambda_vec = fr->block[i].sub[1].ival[1];
1635 if (n_lambda_vec != fr->block[i].sub[1].ival[1])
1638 "Unexpected change of basis set in lambda");
1641 if (lambda_components == NULL)
1643 snew(lambda_components, n_lambda_vec);
1645 if (native_lambda_vec == NULL)
1647 snew(native_lambda_vec, n_lambda_vec);
1649 for (j = 0; j < n_lambda_vec; j++)
1651 native_lambda_vec[j] = fr->block[i].sub[0].dval[5+j];
1652 lambda_components[j] =
1653 efpt_singular_names[fr->block[i].sub[1].ival[2+j]];
1659 if (nblock_hist == 0 && nblock_dh == 0)
1661 /* don't do anything */
1664 if (nblock_hist > 0 && nblock_dh > 0)
1666 gmx_fatal(FARGS, "This energy file contains both histogram dhdl data and non-histogram dhdl data. Don't know what to do.");
1672 /* we have standard, non-histogram data --
1673 call open_dhdl to open the file */
1674 /* TODO this is an ugly hack that needs to be fixed: this will only
1675 work if the order of data is always the same and if we're
1676 only using the g_energy compiled with the mdrun that produced
1678 *fp_dhdl = open_dhdl(filename, ir, oenv);
1682 sprintf(title, "N(%s)", deltag);
1683 sprintf(label_x, "%s (%s)", deltag, unit_energy);
1684 sprintf(label_y, "Samples");
1685 *fp_dhdl = xvgropen_type(filename, title, label_x, label_y, exvggtXNY, oenv);
1686 sprintf(buf, "T = %g (K), %s = %g", temp, lambda, start_lambda);
1687 xvgr_subtitle(*fp_dhdl, buf, oenv);
1691 (*hists) += nblock_hist;
1692 (*blocks) += nblock_dh;
1693 (*nlambdas) = nblock_hist+nblock_dh;
1695 /* write the data */
1696 if (nblock_hist > 0)
1698 gmx_large_int_t sum = 0;
1700 for (i = 0; i < fr->nblock; i++)
1702 t_enxblock *blk = &(fr->block[i]);
1703 if (blk->id == enxDHHIST)
1705 double foreign_lambda, dx;
1707 int nhist, derivative;
1709 /* check the block types etc. */
1710 if ( (blk->nsub < 2) ||
1711 (blk->sub[0].type != xdr_datatype_double) ||
1712 (blk->sub[1].type != xdr_datatype_large_int) ||
1713 (blk->sub[0].nr < 2) ||
1714 (blk->sub[1].nr < 2) )
1716 gmx_fatal(FARGS, "Unexpected block data in file");
1718 foreign_lambda = blk->sub[0].dval[0];
1719 dx = blk->sub[0].dval[1];
1720 nhist = blk->sub[1].lval[0];
1721 derivative = blk->sub[1].lval[1];
1722 for (j = 0; j < nhist; j++)
1725 x0 = blk->sub[1].lval[2+j];
1729 sprintf(legend, "N(%s(%s=%g) | %s=%g)",
1730 deltag, lambda, foreign_lambda,
1731 lambda, start_lambda);
1735 sprintf(legend, "N(%s | %s=%g)",
1736 dhdl, lambda, start_lambda);
1740 xvgr_new_dataset(*fp_dhdl, setnr, 1, lg, oenv);
1742 for (k = 0; k < blk->sub[j+2].nr; k++)
1747 hist = blk->sub[j+2].ival[k];
1750 fprintf(*fp_dhdl, "%g %d\n%g %d\n", xmin, hist,
1754 /* multiple histogram data blocks in one histogram
1755 mean that the second one is the reverse of the first one:
1756 for dhdl derivatives, it's important to know both the
1757 maximum and minimum values */
1762 (*samples) += (int)(sum/nblock_hist);
1768 char **setnames = NULL;
1769 int nnames = nblock_dh;
1771 for (i = 0; i < fr->nblock; i++)
1773 t_enxblock *blk = &(fr->block[i]);
1774 if (blk->id == enxDH)
1778 len = blk->sub[2].nr;
1782 if (len != blk->sub[2].nr)
1784 gmx_fatal(FARGS, "Length inconsistency in dhdl data");
1791 for (i = 0; i < len; i++)
1793 double time = start_time + delta_time*i;
1795 fprintf(*fp_dhdl, "%.4f ", time);
1797 for (j = 0; j < fr->nblock; j++)
1799 t_enxblock *blk = &(fr->block[j]);
1800 if (blk->id == enxDH)
1803 if (blk->sub[2].type == xdr_datatype_float)
1805 value = blk->sub[2].fval[i];
1809 value = blk->sub[2].dval[i];
1811 /* we need to decide which data type it is based on the count*/
1813 if (j == 1 && ir->bExpanded)
1815 fprintf(*fp_dhdl, "%4d", (int)value); /* if expanded ensembles and zero, this is a state value, it's an integer. We need a cleaner conditional than if j==1! */
1821 fprintf(*fp_dhdl, " %#.12g", value); /* print normal precision */
1825 fprintf(*fp_dhdl, " %#.8g", value); /* print normal precision */
1830 fprintf(*fp_dhdl, "\n");
1836 int gmx_energy(int argc, char *argv[])
1838 const char *desc[] = {
1840 "[TT]g_energy[tt] extracts energy components or distance restraint",
1841 "data from an energy file. The user is prompted to interactively",
1842 "select the desired energy terms.[PAR]",
1844 "Average, RMSD, and drift are calculated with full precision from the",
1845 "simulation (see printed manual). Drift is calculated by performing",
1846 "a least-squares fit of the data to a straight line. The reported total drift",
1847 "is the difference of the fit at the first and last point.",
1848 "An error estimate of the average is given based on a block averages",
1849 "over 5 blocks using the full-precision averages. The error estimate",
1850 "can be performed over multiple block lengths with the options",
1851 "[TT]-nbmin[tt] and [TT]-nbmax[tt].",
1852 "[BB]Note[bb] that in most cases the energy files contains averages over all",
1853 "MD steps, or over many more points than the number of frames in",
1854 "energy file. This makes the [TT]g_energy[tt] statistics output more accurate",
1855 "than the [TT].xvg[tt] output. When exact averages are not present in the energy",
1856 "file, the statistics mentioned above are simply over the single, per-frame",
1857 "energy values.[PAR]",
1859 "The term fluctuation gives the RMSD around the least-squares fit.[PAR]",
1861 "Some fluctuation-dependent properties can be calculated provided",
1862 "the correct energy terms are selected, and that the command line option",
1863 "[TT]-fluct_props[tt] is given. The following properties",
1864 "will be computed:[BR]",
1865 "Property Energy terms needed[BR]",
1866 "---------------------------------------------------[BR]",
1867 "Heat capacity C[SUB]p[sub] (NPT sims): Enthalpy, Temp [BR]",
1868 "Heat capacity C[SUB]v[sub] (NVT sims): Etot, Temp [BR]",
1869 "Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp[BR]",
1870 "Isothermal compressibility: Vol, Temp [BR]",
1871 "Adiabatic bulk modulus: Vol, Temp [BR]",
1872 "---------------------------------------------------[BR]",
1873 "You always need to set the number of molecules [TT]-nmol[tt].",
1874 "The C[SUB]p[sub]/C[SUB]v[sub] computations do [BB]not[bb] include any corrections",
1875 "for quantum effects. Use the [TT]g_dos[tt] program if you need that (and you do).[PAR]"
1876 "When the [TT]-viol[tt] option is set, the time averaged",
1877 "violations are plotted and the running time-averaged and",
1878 "instantaneous sum of violations are recalculated. Additionally",
1879 "running time-averaged and instantaneous distances between",
1880 "selected pairs can be plotted with the [TT]-pairs[tt] option.[PAR]",
1882 "Options [TT]-ora[tt], [TT]-ort[tt], [TT]-oda[tt], [TT]-odr[tt] and",
1883 "[TT]-odt[tt] are used for analyzing orientation restraint data.",
1884 "The first two options plot the orientation, the last three the",
1885 "deviations of the orientations from the experimental values.",
1886 "The options that end on an 'a' plot the average over time",
1887 "as a function of restraint. The options that end on a 't'",
1888 "prompt the user for restraint label numbers and plot the data",
1889 "as a function of time. Option [TT]-odr[tt] plots the RMS",
1890 "deviation as a function of restraint.",
1891 "When the run used time or ensemble averaged orientation restraints,",
1892 "option [TT]-orinst[tt] can be used to analyse the instantaneous,",
1893 "not ensemble-averaged orientations and deviations instead of",
1894 "the time and ensemble averages.[PAR]",
1896 "Option [TT]-oten[tt] plots the eigenvalues of the molecular order",
1897 "tensor for each orientation restraint experiment. With option",
1898 "[TT]-ovec[tt] also the eigenvectors are plotted.[PAR]",
1900 "Option [TT]-odh[tt] extracts and plots the free energy data",
1901 "(Hamiltoian differences and/or the Hamiltonian derivative dhdl)",
1902 "from the [TT]ener.edr[tt] file.[PAR]",
1904 "With [TT]-fee[tt] an estimate is calculated for the free-energy",
1905 "difference with an ideal gas state: [BR]",
1906 " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
1907 " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
1908 "where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
1909 "the average is over the ensemble (or time in a trajectory).",
1910 "Note that this is in principle",
1911 "only correct when averaging over the whole (Boltzmann) ensemble",
1912 "and using the potential energy. This also allows for an entropy",
1913 "estimate using:[BR]",
1914 " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T[BR]",
1915 " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = ([CHEVRON]U[SUB]pot[sub][chevron] + pV - [GRK]Delta[grk] G)/T",
1918 "When a second energy file is specified ([TT]-f2[tt]), a free energy",
1919 "difference is calculated [BR] dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
1920 "where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
1921 "files, and the average is over the ensemble A. The running average",
1922 "of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
1923 "[BB]Note[bb] that the energies must both be calculated from the same trajectory."
1926 static gmx_bool bSum = FALSE, bFee = FALSE, bPrAll = FALSE, bFluct = FALSE, bDriftCorr = FALSE;
1927 static gmx_bool bDp = FALSE, bMutot = FALSE, bOrinst = FALSE, bOvec = FALSE, bFluctProps = FALSE;
1928 static int skip = 0, nmol = 1, nbmin = 5, nbmax = 5;
1929 static real reftemp = 300.0, ezero = 0;
1931 { "-fee", FALSE, etBOOL, {&bFee},
1932 "Do a free energy estimate" },
1933 { "-fetemp", FALSE, etREAL, {&reftemp},
1934 "Reference temperature for free energy calculation" },
1935 { "-zero", FALSE, etREAL, {&ezero},
1936 "Subtract a zero-point energy" },
1937 { "-sum", FALSE, etBOOL, {&bSum},
1938 "Sum the energy terms selected rather than display them all" },
1939 { "-dp", FALSE, etBOOL, {&bDp},
1940 "Print energies in high precision" },
1941 { "-nbmin", FALSE, etINT, {&nbmin},
1942 "Minimum number of blocks for error estimate" },
1943 { "-nbmax", FALSE, etINT, {&nbmax},
1944 "Maximum number of blocks for error estimate" },
1945 { "-mutot", FALSE, etBOOL, {&bMutot},
1946 "Compute the total dipole moment from the components" },
1947 { "-skip", FALSE, etINT, {&skip},
1948 "Skip number of frames between data points" },
1949 { "-aver", FALSE, etBOOL, {&bPrAll},
1950 "Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)" },
1951 { "-nmol", FALSE, etINT, {&nmol},
1952 "Number of molecules in your sample: the energies are divided by this number" },
1953 { "-fluct_props", FALSE, etBOOL, {&bFluctProps},
1954 "Compute properties based on energy fluctuations, like heat capacity" },
1955 { "-driftcorr", FALSE, etBOOL, {&bDriftCorr},
1956 "Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties."},
1957 { "-fluc", FALSE, etBOOL, {&bFluct},
1958 "Calculate autocorrelation of energy fluctuations rather than energy itself" },
1959 { "-orinst", FALSE, etBOOL, {&bOrinst},
1960 "Analyse instantaneous orientation data" },
1961 { "-ovec", FALSE, etBOOL, {&bOvec},
1962 "Also plot the eigenvectors with [TT]-oten[tt]" }
1964 const char * drleg[] = {
1968 static const char *setnm[] = {
1969 "Pres-XX", "Pres-XY", "Pres-XZ", "Pres-YX", "Pres-YY",
1970 "Pres-YZ", "Pres-ZX", "Pres-ZY", "Pres-ZZ", "Temperature",
1971 "Volume", "Pressure"
1974 FILE *out = NULL, *fp_pairs = NULL, *fort = NULL, *fodt = NULL, *foten = NULL;
1975 FILE *fp_dhdl = NULL;
1980 gmx_localtop_t *top = NULL;
1984 gmx_enxnm_t *enm = NULL;
1985 t_enxframe *frame, *fr = NULL;
1987 #define NEXT (1-cur)
1988 int nre, teller, teller_disre, nfr;
1989 gmx_large_int_t start_step;
1990 int nor = 0, nex = 0, norfr = 0, enx_i = 0;
1992 real *bounds = NULL, *violaver = NULL, *oobs = NULL, *orient = NULL, *odrms = NULL;
1993 int *index = NULL, *pair = NULL, norsel = 0, *orsel = NULL, *or_label = NULL;
1994 int nbounds = 0, npairs;
1995 gmx_bool bDisRe, bDRAll, bORA, bORT, bODA, bODR, bODT, bORIRE, bOTEN, bDHDL;
1996 gmx_bool bFoundStart, bCont, bEDR, bVisco;
1997 double sum, sumaver, sumt, ener, dbl;
1998 double *time = NULL;
2000 int *set = NULL, i, j, k, nset, sss;
2001 gmx_bool *bIsEner = NULL;
2002 char **pairleg, **odtleg, **otenleg;
2005 char *anm_j, *anm_k, *resnm_j, *resnm_k;
2006 int resnr_j, resnr_k;
2007 const char *orinst_sub = "@ subtitle \"instantaneous\"\n";
2010 t_enxblock *blk = NULL;
2011 t_enxblock *blk_disre = NULL;
2013 int dh_blocks = 0, dh_hists = 0, dh_samples = 0, dh_lambdas = 0;
2016 { efEDR, "-f", NULL, ffREAD },
2017 { efEDR, "-f2", NULL, ffOPTRD },
2018 { efTPX, "-s", NULL, ffOPTRD },
2019 { efXVG, "-o", "energy", ffWRITE },
2020 { efXVG, "-viol", "violaver", ffOPTWR },
2021 { efXVG, "-pairs", "pairs", ffOPTWR },
2022 { efXVG, "-ora", "orienta", ffOPTWR },
2023 { efXVG, "-ort", "orientt", ffOPTWR },
2024 { efXVG, "-oda", "orideva", ffOPTWR },
2025 { efXVG, "-odr", "oridevr", ffOPTWR },
2026 { efXVG, "-odt", "oridevt", ffOPTWR },
2027 { efXVG, "-oten", "oriten", ffOPTWR },
2028 { efXVG, "-corr", "enecorr", ffOPTWR },
2029 { efXVG, "-vis", "visco", ffOPTWR },
2030 { efXVG, "-ravg", "runavgdf", ffOPTWR },
2031 { efXVG, "-odh", "dhdl", ffOPTWR }
2033 #define NFILE asize(fnm)
2038 ppa = add_acf_pargs(&npargs, pa);
2039 if (!parse_common_args(&argc, argv,
2040 PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
2041 NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
2046 bDRAll = opt2bSet("-pairs", NFILE, fnm);
2047 bDisRe = opt2bSet("-viol", NFILE, fnm) || bDRAll;
2048 bORA = opt2bSet("-ora", NFILE, fnm);
2049 bORT = opt2bSet("-ort", NFILE, fnm);
2050 bODA = opt2bSet("-oda", NFILE, fnm);
2051 bODR = opt2bSet("-odr", NFILE, fnm);
2052 bODT = opt2bSet("-odt", NFILE, fnm);
2053 bORIRE = bORA || bORT || bODA || bODR || bODT;
2054 bOTEN = opt2bSet("-oten", NFILE, fnm);
2055 bDHDL = opt2bSet("-odh", NFILE, fnm);
2060 fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
2061 do_enxnms(fp, &nre, &enm);
2065 bVisco = opt2bSet("-vis", NFILE, fnm);
2067 if ((!bDisRe) && (!bDHDL))
2071 nset = asize(setnm);
2073 /* This is nasty code... To extract Pres tensor, Volume and Temperature */
2074 for (j = 0; j < nset; j++)
2076 for (i = 0; i < nre; i++)
2078 if (strstr(enm[i].name, setnm[j]))
2086 if (gmx_strcasecmp(setnm[j], "Volume") == 0)
2088 printf("Enter the box volume (" unit_volume "): ");
2089 if (1 != scanf("%lf", &dbl))
2091 gmx_fatal(FARGS, "Error reading user input");
2097 gmx_fatal(FARGS, "Could not find term %s for viscosity calculation",
2105 set = select_by_name(nre, enm, &nset);
2107 /* Print all the different units once */
2108 sprintf(buf, "(%s)", enm[set[0]].unit);
2109 for (i = 1; i < nset; i++)
2111 for (j = 0; j < i; j++)
2113 if (strcmp(enm[set[i]].unit, enm[set[j]].unit) == 0)
2121 strcat(buf, enm[set[i]].unit);
2125 out = xvgropen(opt2fn("-o", NFILE, fnm), "Gromacs Energies", "Time (ps)", buf,
2129 for (i = 0; (i < nset); i++)
2131 leg[i] = enm[set[i]].name;
2135 leg[nset] = strdup("Sum");
2136 xvgr_legend(out, nset+1, (const char**)leg, oenv);
2140 xvgr_legend(out, nset, (const char**)leg, oenv);
2143 snew(bIsEner, nset);
2144 for (i = 0; (i < nset); i++)
2147 for (j = 0; (j <= F_ETOT); j++)
2149 bIsEner[i] = bIsEner[i] ||
2150 (gmx_strcasecmp(interaction_function[j].longname, leg[i]) == 0);
2154 if (bPrAll && nset > 1)
2156 gmx_fatal(FARGS, "Printing averages can only be done when a single set is selected");
2161 if (bORIRE || bOTEN)
2163 get_orires_parms(ftp2fn(efTPX, NFILE, fnm), &nor, &nex, &or_label, &oobs);
2187 fprintf(stderr, "Select the orientation restraint labels you want (-1 is all)\n");
2188 fprintf(stderr, "End your selection with 0\n");
2195 if (1 != scanf("%d", &(orsel[j])))
2197 gmx_fatal(FARGS, "Error reading user input");
2200 while (orsel[j] > 0);
2203 fprintf(stderr, "Selecting all %d orientation restraints\n", nor);
2206 for (i = 0; i < nor; i++)
2213 /* Build the selection */
2215 for (i = 0; i < j; i++)
2217 for (k = 0; k < nor; k++)
2219 if (or_label[k] == orsel[i])
2228 fprintf(stderr, "Orientation restraint label %d not found\n",
2233 snew(odtleg, norsel);
2234 for (i = 0; i < norsel; i++)
2236 snew(odtleg[i], 256);
2237 sprintf(odtleg[i], "%d", or_label[orsel[i]]);
2241 fort = xvgropen(opt2fn("-ort", NFILE, fnm), "Calculated orientations",
2242 "Time (ps)", "", oenv);
2245 fprintf(fort, "%s", orinst_sub);
2247 xvgr_legend(fort, norsel, (const char**)odtleg, oenv);
2251 fodt = xvgropen(opt2fn("-odt", NFILE, fnm),
2252 "Orientation restraint deviation",
2253 "Time (ps)", "", oenv);
2256 fprintf(fodt, "%s", orinst_sub);
2258 xvgr_legend(fodt, norsel, (const char**)odtleg, oenv);
2264 foten = xvgropen(opt2fn("-oten", NFILE, fnm),
2265 "Order tensor", "Time (ps)", "", oenv);
2266 snew(otenleg, bOvec ? nex*12 : nex*3);
2267 for (i = 0; i < nex; i++)
2269 for (j = 0; j < 3; j++)
2271 sprintf(buf, "eig%d", j+1);
2272 otenleg[(bOvec ? 12 : 3)*i+j] = strdup(buf);
2276 for (j = 0; j < 9; j++)
2278 sprintf(buf, "vec%d%s", j/3+1, j%3 == 0 ? "x" : (j%3 == 1 ? "y" : "z"));
2279 otenleg[12*i+3+j] = strdup(buf);
2283 xvgr_legend(foten, bOvec ? nex*12 : nex*3, (const char**)otenleg, oenv);
2288 nbounds = get_bounds(ftp2fn(efTPX, NFILE, fnm), &bounds, &index, &pair, &npairs,
2290 snew(violaver, npairs);
2291 out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
2292 "Time (ps)", "nm", oenv);
2293 xvgr_legend(out, 2, drleg, oenv);
2296 fp_pairs = xvgropen(opt2fn("-pairs", NFILE, fnm), "Pair Distances",
2297 "Time (ps)", "Distance (nm)", oenv);
2298 if (output_env_get_print_xvgr_codes(oenv))
2300 fprintf(fp_pairs, "@ subtitle \"averaged (tau=%g) and instantaneous\"\n",
2307 get_dhdl_parms(ftp2fn(efTPX, NFILE, fnm), &ir);
2310 /* Initiate energies and set them to zero */
2319 /* Initiate counters */
2322 bFoundStart = FALSE;
2327 /* This loop searches for the first frame (when -b option is given),
2328 * or when this has been found it reads just one energy frame
2332 bCont = do_enx(fp, &(frame[NEXT]));
2335 timecheck = check_times(frame[NEXT].t);
2338 while (bCont && (timecheck < 0));
2340 if ((timecheck == 0) && bCont)
2342 /* We read a valid frame, so we can use it */
2343 fr = &(frame[NEXT]);
2347 /* The frame contains energies, so update cur */
2350 if (edat.nframes % 1000 == 0)
2352 srenew(edat.step, edat.nframes+1000);
2353 memset(&(edat.step[edat.nframes]), 0, 1000*sizeof(edat.step[0]));
2354 srenew(edat.steps, edat.nframes+1000);
2355 memset(&(edat.steps[edat.nframes]), 0, 1000*sizeof(edat.steps[0]));
2356 srenew(edat.points, edat.nframes+1000);
2357 memset(&(edat.points[edat.nframes]), 0, 1000*sizeof(edat.points[0]));
2359 for (i = 0; i < nset; i++)
2361 srenew(edat.s[i].ener, edat.nframes+1000);
2362 memset(&(edat.s[i].ener[edat.nframes]), 0,
2363 1000*sizeof(edat.s[i].ener[0]));
2364 srenew(edat.s[i].es, edat.nframes+1000);
2365 memset(&(edat.s[i].es[edat.nframes]), 0,
2366 1000*sizeof(edat.s[i].es[0]));
2371 edat.step[nfr] = fr->step;
2376 /* Initiate the previous step data */
2377 start_step = fr->step;
2379 /* Initiate the energy sums */
2380 edat.steps[nfr] = 1;
2381 edat.points[nfr] = 1;
2382 for (i = 0; i < nset; i++)
2385 edat.s[i].es[nfr].sum = fr->ener[sss].e;
2386 edat.s[i].es[nfr].sum2 = 0;
2393 edat.steps[nfr] = fr->nsteps;
2395 if (fr->step - start_step + 1 == edat.nsteps + fr->nsteps)
2399 edat.points[nfr] = 1;
2400 for (i = 0; i < nset; i++)
2403 edat.s[i].es[nfr].sum = fr->ener[sss].e;
2404 edat.s[i].es[nfr].sum2 = 0;
2410 edat.points[nfr] = fr->nsum;
2411 for (i = 0; i < nset; i++)
2414 edat.s[i].es[nfr].sum = fr->ener[sss].esum;
2415 edat.s[i].es[nfr].sum2 = fr->ener[sss].eav;
2417 edat.npoints += fr->nsum;
2422 /* The interval does not match fr->nsteps:
2423 * can not do exact averages.
2427 edat.nsteps = fr->step - start_step + 1;
2430 for (i = 0; i < nset; i++)
2432 edat.s[i].ener[nfr] = fr->ener[set[i]].e;
2436 * Define distance restraint legends. Can only be done after
2437 * the first frame has been read... (Then we know how many there are)
2439 blk_disre = find_block_id_enxframe(fr, enxDISRE, NULL);
2440 if (bDisRe && bDRAll && !leg && blk_disre)
2445 fa = top->idef.il[F_DISRES].iatoms;
2446 ip = top->idef.iparams;
2447 if (blk_disre->nsub != 2 ||
2448 (blk_disre->sub[0].nr != blk_disre->sub[1].nr) )
2450 gmx_incons("Number of disre sub-blocks not equal to 2");
2453 ndisre = blk_disre->sub[0].nr;
2454 if (ndisre != top->idef.il[F_DISRES].nr/3)
2456 gmx_fatal(FARGS, "Number of disre pairs in the energy file (%d) does not match the number in the run input file (%d)\n",
2457 ndisre, top->idef.il[F_DISRES].nr/3);
2459 snew(pairleg, ndisre);
2460 for (i = 0; i < ndisre; i++)
2462 snew(pairleg[i], 30);
2465 gmx_mtop_atominfo_global(&mtop, j, &anm_j, &resnr_j, &resnm_j);
2466 gmx_mtop_atominfo_global(&mtop, k, &anm_k, &resnr_k, &resnm_k);
2467 sprintf(pairleg[i], "%d %s %d %s (%d)",
2468 resnr_j, anm_j, resnr_k, anm_k,
2469 ip[fa[3*i]].disres.label);
2471 set = select_it(ndisre, pairleg, &nset);
2473 for (i = 0; (i < nset); i++)
2476 sprintf(leg[2*i], "a %s", pairleg[set[i]]);
2477 snew(leg[2*i+1], 32);
2478 sprintf(leg[2*i+1], "i %s", pairleg[set[i]]);
2480 xvgr_legend(fp_pairs, 2*nset, (const char**)leg, oenv);
2484 * Store energies for analysis afterwards...
2486 if (!bDisRe && !bDHDL && (fr->nre > 0))
2488 if (edat.nframes % 1000 == 0)
2490 srenew(time, edat.nframes+1000);
2492 time[edat.nframes] = fr->t;
2496 * Printing time, only when we do not want to skip frames
2498 if (!skip || teller % skip == 0)
2502 /*******************************************
2503 * D I S T A N C E R E S T R A I N T S
2504 *******************************************/
2508 float *disre_rt = blk_disre->sub[0].fval;
2509 float *disre_rm3tav = blk_disre->sub[1].fval;
2511 double *disre_rt = blk_disre->sub[0].dval;
2512 double *disre_rm3tav = blk_disre->sub[1].dval;
2515 print_time(out, fr->t);
2516 if (violaver == NULL)
2518 snew(violaver, ndisre);
2521 /* Subtract bounds from distances, to calculate violations */
2522 calc_violations(disre_rt, disre_rm3tav,
2523 nbounds, pair, bounds, violaver, &sumt, &sumaver);
2525 fprintf(out, " %8.4f %8.4f\n", sumaver, sumt);
2528 print_time(fp_pairs, fr->t);
2529 for (i = 0; (i < nset); i++)
2532 fprintf(fp_pairs, " %8.4f", mypow(disre_rm3tav[sss], minthird));
2533 fprintf(fp_pairs, " %8.4f", disre_rt[sss]);
2535 fprintf(fp_pairs, "\n");
2542 do_dhdl(fr, &ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
2545 /*******************************************
2547 *******************************************/
2554 /* We skip frames with single points (usually only the first frame),
2555 * since they would result in an average plot with outliers.
2559 print_time(out, fr->t);
2560 print1(out, bDp, fr->ener[set[0]].e);
2561 print1(out, bDp, fr->ener[set[0]].esum/fr->nsum);
2562 print1(out, bDp, sqrt(fr->ener[set[0]].eav/fr->nsum));
2568 print_time(out, fr->t);
2572 for (i = 0; i < nset; i++)
2574 sum += fr->ener[set[i]].e;
2576 print1(out, bDp, sum/nmol-ezero);
2580 for (i = 0; (i < nset); i++)
2584 print1(out, bDp, (fr->ener[set[i]].e)/nmol-ezero);
2588 print1(out, bDp, fr->ener[set[i]].e);
2595 blk = find_block_id_enxframe(fr, enx_i, NULL);
2599 xdr_datatype dt = xdr_datatype_float;
2601 xdr_datatype dt = xdr_datatype_double;
2605 if ( (blk->nsub != 1) || (blk->sub[0].type != dt) )
2607 gmx_fatal(FARGS, "Orientational restraints read in incorrectly");
2610 vals = blk->sub[0].fval;
2612 vals = blk->sub[0].dval;
2615 if (blk->sub[0].nr != (size_t)nor)
2617 gmx_fatal(FARGS, "Number of orientation restraints in energy file (%d) does not match with the topology (%d)", blk->sub[0].nr);
2621 for (i = 0; i < nor; i++)
2623 orient[i] += vals[i];
2628 for (i = 0; i < nor; i++)
2630 odrms[i] += sqr(vals[i]-oobs[i]);
2635 fprintf(fort, " %10f", fr->t);
2636 for (i = 0; i < norsel; i++)
2638 fprintf(fort, " %g", vals[orsel[i]]);
2640 fprintf(fort, "\n");
2644 fprintf(fodt, " %10f", fr->t);
2645 for (i = 0; i < norsel; i++)
2647 fprintf(fodt, " %g", vals[orsel[i]]-oobs[orsel[i]]);
2649 fprintf(fodt, "\n");
2653 blk = find_block_id_enxframe(fr, enxORT, NULL);
2657 xdr_datatype dt = xdr_datatype_float;
2659 xdr_datatype dt = xdr_datatype_double;
2663 if ( (blk->nsub != 1) || (blk->sub[0].type != dt) )
2665 gmx_fatal(FARGS, "Orientational restraints read in incorrectly");
2668 vals = blk->sub[0].fval;
2670 vals = blk->sub[0].dval;
2673 if (blk->sub[0].nr != (size_t)(nex*12))
2675 gmx_fatal(FARGS, "Number of orientation experiments in energy file (%g) does not match with the topology (%d)",
2676 blk->sub[0].nr/12, nex);
2678 fprintf(foten, " %10f", fr->t);
2679 for (i = 0; i < nex; i++)
2681 for (j = 0; j < (bOvec ? 12 : 3); j++)
2683 fprintf(foten, " %g", vals[i*12+j]);
2686 fprintf(foten, "\n");
2693 while (bCont && (timecheck == 0));
2695 fprintf(stderr, "\n");
2717 out = xvgropen(opt2fn("-ora", NFILE, fnm),
2718 "Average calculated orientations",
2719 "Restraint label", "", oenv);
2722 fprintf(out, "%s", orinst_sub);
2724 for (i = 0; i < nor; i++)
2726 fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr);
2732 out = xvgropen(opt2fn("-oda", NFILE, fnm),
2733 "Average restraint deviation",
2734 "Restraint label", "", oenv);
2737 fprintf(out, "%s", orinst_sub);
2739 for (i = 0; i < nor; i++)
2741 fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr-oobs[i]);
2747 out = xvgropen(opt2fn("-odr", NFILE, fnm),
2748 "RMS orientation restraint deviations",
2749 "Restraint label", "", oenv);
2752 fprintf(out, "%s", orinst_sub);
2754 for (i = 0; i < nor; i++)
2756 fprintf(out, "%5d %g\n", or_label[i], sqrt(odrms[i]/norfr));
2767 analyse_disre(opt2fn("-viol", NFILE, fnm),
2768 teller_disre, violaver, bounds, index, pair, nbounds, oenv);
2775 printf("\n\nWrote %d lambda values with %d samples as ",
2776 dh_lambdas, dh_samples);
2779 printf("%d dH histograms ", dh_hists);
2783 printf("%d dH data blocks ", dh_blocks);
2785 printf("to %s\n", opt2fn("-odh", NFILE, fnm));
2790 gmx_fatal(FARGS, "No dH data in %s\n", opt2fn("-f", NFILE, fnm));
2796 double dt = (frame[cur].t-start_t)/(edat.nframes-1);
2797 analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
2798 bFee, bSum, opt2parg_bSet("-nmol", npargs, ppa),
2799 bVisco, opt2fn("-vis", NFILE, fnm),
2801 start_step, start_t, frame[cur].step, frame[cur].t,
2802 time, reftemp, &edat,
2803 nset, set, bIsEner, leg, enm, Vaver, ezero, nbmin, nbmax,
2807 calc_fluctuation_props(stdout, bDriftCorr, dt, nset, nmol, leg, &edat,
2811 if (opt2bSet("-f2", NFILE, fnm))
2813 fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm),
2814 reftemp, nset, set, leg, &edat, time, oenv);
2818 const char *nxy = "-nxy";
2820 do_view(oenv, opt2fn("-o", NFILE, fnm), nxy);
2821 do_view(oenv, opt2fn_null("-ravg", NFILE, fnm), nxy);
2822 do_view(oenv, opt2fn_null("-ora", NFILE, fnm), nxy);
2823 do_view(oenv, opt2fn_null("-ort", NFILE, fnm), nxy);
2824 do_view(oenv, opt2fn_null("-oda", NFILE, fnm), nxy);
2825 do_view(oenv, opt2fn_null("-odr", NFILE, fnm), nxy);
2826 do_view(oenv, opt2fn_null("-odt", NFILE, fnm), nxy);
2827 do_view(oenv, opt2fn_null("-oten", NFILE, fnm), nxy);
2828 do_view(oenv, opt2fn_null("-odh", NFILE, fnm), nxy);