avold[i] = 0;
}
fp0 = xvgropen(fni, "Shear viscosity integral", "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N ps)", oenv);
- fp1 = xvgropen(fn, "Shear viscosity using Einstein relation", "Time (ps)",
- "(kg m\\S-1\\N s\\S-1\\N)", oenv);
+ fp1 = xvgropen(
+ fn, "Shear viscosity using Einstein relation", "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N)", oenv);
for (i = 0; i < nf4; i++)
{
for (m = 0; m <= nsets; m++)
if (debug)
{
char buf1[STEPSTRSIZE], buf2[STEPSTRSIZE];
- fprintf(debug, "Requested %d blocks, we have %d blocks, min %s nsteps %s\n", nb,
- eee[nb].b, gmx_step_str(eee[nb].nst_min, buf1), gmx_step_str(edat->nsteps, buf2));
+ fprintf(debug,
+ "Requested %d blocks, we have %d blocks, min %s nsteps %s\n",
+ nb,
+ eee[nb].b,
+ gmx_step_str(eee[nb].nst_min, buf1),
+ gmx_step_str(edat->nsteps, buf2));
}
if (eee[nb].b == nb && 5 * nb * eee[nb].nst_min >= 4 * edat->nsteps)
{
}
if (varh != NOTSET)
{
- fprintf(fp, "Enthalpy = %10g kJ/mol\n",
- hh * AVOGADRO / (KILO * nmol));
+ fprintf(fp, "Enthalpy = %10g kJ/mol\n", hh * AVOGADRO / (KILO * nmol));
}
if (alpha != NOTSET)
{
/* Calculate the time difference */
delta_t = t - start_t;
- fprintf(stdout, "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
- gmx_step_str(nsteps, buf), start_t, t, nset);
+ fprintf(stdout,
+ "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
+ gmx_step_str(nsteps, buf),
+ start_t,
+ t,
+ nset);
calc_averages(nset, edat, nbmin, nbmax);
fprintf(stdout, " '%s'", leg[i]);
}
}
- fprintf(stdout, " %s has statistics over %d points (frames)\n",
- nnotexact == 1 ? "is" : "are", edat->nframes);
+ fprintf(stdout,
+ " %s has statistics over %d points (frames)\n",
+ nnotexact == 1 ? "is" : "are",
+ edat->nframes);
fprintf(stdout, "All other statistics are over %s points\n", gmx_step_str(edat->npoints, buf));
}
fprintf(stdout, "\n");
- fprintf(stdout, "%-24s %10s %10s %10s %10s", "Energy", "Average", "Err.Est.", "RMSD",
+ fprintf(stdout,
+ "%-24s %10s %10s %10s %10s",
+ "Energy",
+ "Average",
+ "Err.Est.",
+ "RMSD",
"Tot-Drift");
if (bFee)
{
{
totaldrift = (edat->nsteps - 1) * esum->s[0].slope;
ee_pr(esum->s[0].ee / nmol, sizeof(eebuf), eebuf);
- fprintf(stdout, "%-24s %10g %10s %10s %10g (%s)", "Total", esum->s[0].av / nmol, eebuf,
- "--", totaldrift / nmol, enm[set[0]].unit);
+ fprintf(stdout,
+ "%-24s %10g %10s %10s %10g (%s)",
+ "Total",
+ esum->s[0].av / nmol,
+ eebuf,
+ "--",
+ totaldrift / nmol,
+ enm[set[0]].unit);
/* pr_aver,pr_stddev,a,totaldrift */
if (bFee)
{
- fprintf(stdout, " %10g %10g\n", std::log(expEtot) / beta + esum->s[0].av / nmol,
+ fprintf(stdout,
+ " %10g %10g\n",
+ std::log(expEtot) / beta + esum->s[0].av / nmol,
std::log(expEtot) / beta);
}
else
/*do_autocorr(corrfn,buf,nenergy,3,eneset,Dt,eacNormal,TRUE);*/
/* Do it for shear viscosity */
std::strcpy(buf, "Shear Viscosity");
- low_do_autocorr(corrfn, oenv, buf, edat->nframes, 3, (edat->nframes + 1) / 2, eneset,
- Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
+ low_do_autocorr(corrfn,
+ oenv,
+ buf,
+ edat->nframes,
+ 3,
+ (edat->nframes + 1) / 2,
+ eneset,
+ Dt,
+ eacNormal,
+ 1,
+ TRUE,
+ FALSE,
+ FALSE,
+ 0.0,
+ 0.0,
+ 0);
/* Now for bulk viscosity */
std::strcpy(buf, "Bulk Viscosity");
- low_do_autocorr(corrfn, oenv, buf, edat->nframes, 1, (edat->nframes + 1) / 2,
- &(eneset[11]), Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);
+ low_do_autocorr(corrfn,
+ oenv,
+ buf,
+ edat->nframes,
+ 1,
+ (edat->nframes + 1) / 2,
+ &(eneset[11]),
+ Dt,
+ eacNormal,
+ 1,
+ TRUE,
+ FALSE,
+ FALSE,
+ 0.0,
+ 0.0,
+ 0);
factor = (Vaver * 1e-26 / (BOLTZMANN * Temp)) * Dt;
fp = xvgropen(visfn, buf, "Time (ps)", "\\8h\\4 (cp)", oenv);
if (fr->t != time[nenergy2])
{
- fprintf(stderr, "\nWARNING time mismatch %g!=%g at frame %s\n", fr->t,
- time[nenergy2], gmx_step_str(fr->step, buf));
+ fprintf(stderr,
+ "\nWARNING time mismatch %g!=%g at frame %s\n",
+ fr->t,
+ time[nenergy2],
+ gmx_step_str(fr->step, buf));
}
for (i = 0; i < nset; i++)
{
fp = nullptr;
if (runavgfn)
{
- fp = xvgropen(runavgfn, "Running average free energy difference", "Time (" unit_time ")",
- "\\8D\\4E (" unit_energy ")", oenv);
+ fp = xvgropen(runavgfn,
+ "Running average free energy difference",
+ "Time (" unit_time ")",
+ "\\8D\\4E (" unit_energy ")",
+ oenv);
xvgr_legend(fp, asize(ravgleg), ravgleg, oenv);
}
fprintf(stdout, "\n%-24s %10s\n", "Energy", "dF = -kT ln < exp(-(EB-EA)/kT) >A");
if (!derivative)
{
- sprintf(legend, "N(%s(%s=%g) | %s=%g)", deltag, lambda, foreign_lambda,
- lambda, start_lambda);
+ sprintf(legend, "N(%s(%s=%g) | %s=%g)", deltag, lambda, foreign_lambda, lambda, start_lambda);
}
else
{
if (j == 1 && ir->bExpanded)
{
- fprintf(*fp_dhdl, "%4d",
- static_cast<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! */
+ fprintf(*fp_dhdl, "%4d", static_cast<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! */
}
else
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm,
- npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
}
if (bDHDL)
{
- do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists,
- &dh_samples, &dh_lambdas, oenv);
+ do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
}
/*******************************************
else
{
double dt = (frame[cur].t - start_t) / (edat.nframes - 1);
- analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
- opt2fn("-evisco", NFILE, fnm), opt2fn("-eviscoi", NFILE, fnm), bFee, bSum,
- bFluct, bVisco, opt2fn("-vis", NFILE, fnm), nmol, start_step, start_t,
- frame[cur].step, frame[cur].t, reftemp, &edat, nset, set, bIsEner, leg, enm,
- Vaver, ezero, nbmin, nbmax, oenv);
+ analyse_ener(opt2bSet("-corr", NFILE, fnm),
+ opt2fn("-corr", NFILE, fnm),
+ opt2fn("-evisco", NFILE, fnm),
+ opt2fn("-eviscoi", NFILE, fnm),
+ bFee,
+ bSum,
+ bFluct,
+ bVisco,
+ opt2fn("-vis", NFILE, fnm),
+ nmol,
+ start_step,
+ start_t,
+ frame[cur].step,
+ frame[cur].t,
+ reftemp,
+ &edat,
+ nset,
+ set,
+ bIsEner,
+ leg,
+ enm,
+ Vaver,
+ ezero,
+ nbmin,
+ nbmax,
+ oenv);
if (bFluctProps)
{
calc_fluctuation_props(stdout, bDriftCorr, dt, nset, nmol, leg, &edat, nbmin, nbmax);
}
if (opt2bSet("-f2", NFILE, fnm))
{
- fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm), reftemp, nset, set, leg, &edat,
- time, oenv);
+ fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm), reftemp, nset, set, leg, &edat, time, oenv);
}
// Clean up!
done_enerdata_t(nset, &edat);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff