copy_rvec(xcm[grp1][j], xk);
rvec_add(xj, mu[gi], xi);
rvec_add(xk, mu[gj], xl);
- phi = dih_angle(xi, xj, xk, xl, &pbc, r_ij, r_kj, r_kl, mm, nn, /* out */
- &t1, &t2, &t3);
+ phi = dih_angle(xi,
+ xj,
+ xk,
+ xl,
+ &pbc,
+ r_ij,
+ r_kj,
+ r_kl,
+ mm,
+ nn, /* out */
+ &t1,
+ &t2,
+ &t3);
cosa = std::cos(phi);
}
else
fprintf(debug ? debug : stderr,
"mu[%d] = %5.2f %5.2f %5.2f |mi| = %5.2f, mu[%d] = %5.2f %5.2f %5.2f "
"|mj| = %5.2f rr = %5.2f cosa = %5.2f\n",
- gi, mu[gi][XX], mu[gi][YY], mu[gi][ZZ], norm(mu[gi]), gj, mu[gj][XX],
- mu[gj][YY], mu[gj][ZZ], norm(mu[gj]), rr, cosa);
+ gi,
+ mu[gi][XX],
+ mu[gi][YY],
+ mu[gi][ZZ],
+ norm(mu[gi]),
+ gj,
+ mu[gj][XX],
+ mu[gj][YY],
+ mu[gj][ZZ],
+ norm(mu[gj]),
+ rr,
+ cosa);
}
add2gkr(gb, rr, cosa, phi);
/*2.0*j/(gb->ny-1.0)-1.0;*/
}
out = gmx_ffopen(cmap, "w");
- write_xpm(out, 0, "Dipole Orientation Distribution", "Fraction", "r (nm)", gb->bPhi ? "Phi" : "Alpha",
- gb->nx, gb->ny, xaxis, yaxis, gb->cmap, 0, hi, rlo, rhi, nlevels);
+ write_xpm(out,
+ 0,
+ "Dipole Orientation Distribution",
+ "Fraction",
+ "r (nm)",
+ gb->bPhi ? "Phi" : "Alpha",
+ gb->nx,
+ gb->ny,
+ xaxis,
+ yaxis,
+ gb->cmap,
+ 0,
+ hi,
+ rlo,
+ rhi,
+ nlevels);
gmx_ffclose(out);
sfree(xaxis);
sfree(yaxis);
fprintf(stderr,
"Something strange: expected %d entries in energy file at step %s\n(time %g) but "
"found %d entries\n",
- nre, gmx_step_str(fr->step, buf), fr->t, fr->nre);
+ nre,
+ gmx_step_str(fr->step, buf),
+ fr->t,
+ fr->nre);
}
if (bCont)
char buf[STRLEN];
int i;
real mutot;
- const char* leg_dim[4] = { "\\f{12}m\\f{4}\\sX\\N", "\\f{12}m\\f{4}\\sY\\N",
- "\\f{12}m\\f{4}\\sZ\\N", "\\f{12}m\\f{4}\\stot\\N" };
+ const char* leg_dim[4] = { "\\f{12}m\\f{4}\\sX\\N",
+ "\\f{12}m\\f{4}\\sY\\N",
+ "\\f{12}m\\f{4}\\sZ\\N",
+ "\\f{12}m\\f{4}\\stot\\N" };
sprintf(buf, "Box-%c (nm)", 'X' + idim);
fp = xvgropen(fn, "Average dipole moment per slab", buf, "\\f{12}m\\f{4} (D)", oenv);
for (i = 0; (i < nslice); i++)
{
mutot = norm(slab_dipole[i]) / nframes;
- fprintf(fp, "%10.3f %10.3f %10.3f %10.3f %10.3f\n",
- ((i + 0.5) * box[idim][idim]) / nslice, slab_dipole[i][XX] / nframes,
- slab_dipole[i][YY] / nframes, slab_dipole[i][ZZ] / nframes, mutot);
+ fprintf(fp,
+ "%10.3f %10.3f %10.3f %10.3f %10.3f\n",
+ ((i + 0.5) * box[idim][idim]) / nslice,
+ slab_dipole[i][XX] / nframes,
+ slab_dipole[i][YY] / nframes,
+ slab_dipole[i][ZZ] / nframes,
+ mutot);
}
xvgrclose(fp);
do_view(oenv, fn, "-autoscale xy -nxy");
#define NLEGMTOT asize(leg_mtot)
const char* leg_eps[] = { "epsilon", "G\\sk", "g\\sk" };
#define NLEGEPS asize(leg_eps)
- const char* leg_aver[] = { "< |M|\\S2\\N >", "< |M| >\\S2\\N", "< |M|\\S2\\N > - < |M| >\\S2\\N",
+ const char* leg_aver[] = { "< |M|\\S2\\N >",
+ "< |M| >\\S2\\N",
+ "< |M|\\S2\\N > - < |M| >\\S2\\N",
"< |M| >\\S2\\N / < |M|\\S2\\N >" };
#define NLEGAVER asize(leg_aver)
- const char* leg_cosaver[] = { "\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>", "RMSD cos",
+ const char* leg_cosaver[] = { "\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>",
+ "RMSD cos",
"\\f{4}<|cos\\f{12}q\\f{4}\\siX\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siY\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siZ\\N|>" };
mulsq = gmx_stats_init();
/* Open all the files */
- outmtot = xvgropen(out_mtot, "Total dipole moment of the simulation box vs. time", "Time (ps)",
- "Total Dipole Moment (Debye)", oenv);
+ outmtot = xvgropen(out_mtot,
+ "Total dipole moment of the simulation box vs. time",
+ "Time (ps)",
+ "Total Dipole Moment (Debye)",
+ oenv);
outeps = xvgropen(out_eps, "Epsilon and Kirkwood factors", "Time (ps)", "", oenv);
outaver = xvgropen(out_aver, "Total dipole moment", "Time (ps)", "D", oenv);
if (bSlab)
}
if (cosaver)
{
- caver = xvgropen(cosaver, bPairs ? "Average pair orientation" : "Average absolute dipole orientation",
- "Time (ps)", "", oenv);
+ caver = xvgropen(cosaver,
+ bPairs ? "Average pair orientation" : "Average absolute dipole orientation",
+ "Time (ps)",
+ "",
+ oenv);
xvgr_legend(caver, NLEGCOSAVER, bPairs ? leg_cosaver : &(leg_cosaver[1]), oenv);
}
{
fprintf(dip3d,
"set arrow %d from %f, %f, %f to %f, %f, %f lt %d # %d %d\n",
- i + 1, x[ind0][XX], x[ind0][YY], x[ind0][ZZ],
- x[ind0][XX] + dipole[i][XX] / 25, x[ind0][YY] + dipole[i][YY] / 25,
- x[ind0][ZZ] + dipole[i][ZZ] / 25, ncolour, ind0, i);
+ i + 1,
+ x[ind0][XX],
+ x[ind0][YY],
+ x[ind0][ZZ],
+ x[ind0][XX] + dipole[i][XX] / 25,
+ x[ind0][YY] + dipole[i][YY] / 25,
+ x[ind0][ZZ] + dipole[i][ZZ] / 25,
+ ncolour,
+ ind0,
+ i);
}
}
} /* End loop of all molecules in frame */
+ gmx::square(dipaxis[ZZ] - 0.5));
if (bPairs)
{
- fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n", t, dd, rms_cos,
- dipaxis[XX], dipaxis[YY], dipaxis[ZZ]);
+ fprintf(caver,
+ "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
+ t,
+ dd,
+ rms_cos,
+ dipaxis[XX],
+ dipaxis[YY],
+ dipaxis[ZZ]);
}
else
{
- fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e\n", t, rms_cos, dipaxis[XX],
- dipaxis[YY], dipaxis[ZZ]);
+ fprintf(caver,
+ "%10.3e %10.3e %10.3e %10.3e %10.3e\n",
+ t,
+ rms_cos,
+ dipaxis[XX],
+ dipaxis[YY],
+ dipaxis[ZZ]);
}
}
*/
if ((skip == 0) || ((teller % skip) == 0))
{
- fprintf(outmtot, "%10g %12.8e %12.8e %12.8e %12.8e\n", t, M_av[XX], M_av[YY], M_av[ZZ],
+ fprintf(outmtot,
+ "%10g %12.8e %12.8e %12.8e %12.8e\n",
+ t,
+ M_av[XX],
+ M_av[YY],
+ M_av[ZZ],
std::sqrt(M_av2[XX] + M_av2[YY] + M_av2[ZZ]));
}
* the two. Here M is sum mu_i. Further write the finite system
* Kirkwood G factor and epsilon.
*/
- fprintf(outaver, "%10g %10.3e %10.3e %10.3e %10.3e\n", t, M2_ave, M_ave2, M_diff,
- M_ave2 / M2_ave);
+ fprintf(outaver, "%10g %10.3e %10.3e %10.3e %10.3e\n", t, M2_ave, M_ave2, M_diff, M_ave2 / M2_ave);
if (fnadip)
{
if (bTotal)
{
- do_autocorr(corf, oenv, "Autocorrelation Function of Total Dipole", teller, 1,
- muall, dt, mode, TRUE);
+ do_autocorr(
+ corf, oenv, "Autocorrelation Function of Total Dipole", teller, 1, muall, dt, mode, TRUE);
}
else
{
- do_autocorr(corf, oenv, "Dipole Autocorrelation Function", teller, gnx_tot, muall,
- dt, mode, std::strcmp(corrtype, "molsep") != 0);
+ do_autocorr(corf,
+ oenv,
+ "Dipole Autocorrelation Function",
+ teller,
+ gnx_tot,
+ muall,
+ dt,
+ mode,
+ std::strcmp(corrtype, "molsep") != 0);
}
}
}
}
if (m == mols->nr)
{
- gmx_fatal(FARGS, "index[%d]=%d does not correspond to the first atom of a molecule",
- i + 1, index[i] + 1);
+ gmx_fatal(FARGS,
+ "index[%d]=%d does not correspond to the first atom of a molecule",
+ i + 1,
+ index[i] + 1);
}
for (j = mols->index[m]; j < mols->index[m + 1]; j++)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
sfree(ppa);
return 0;
}
nFF[0] = nFA;
nFF[1] = nFB;
- do_dip(top, pbcType, det(box), ftp2fn(efTRX, NFILE, fnm), opt2fn("-o", NFILE, fnm),
- opt2fn("-eps", NFILE, fnm), opt2fn("-a", NFILE, fnm), opt2fn("-d", NFILE, fnm),
- opt2fn_null("-cos", NFILE, fnm), opt2fn_null("-dip3d", NFILE, fnm),
- opt2fn_null("-adip", NFILE, fnm), bPairs, corrtype[0], opt2fn("-c", NFILE, fnm), bGkr,
- opt2fn("-g", NFILE, fnm), bPhi, &nlevels, ndegrees, ncos, opt2fn("-cmap", NFILE, fnm),
- rcmax, bQuad, bMU, opt2fn("-en", NFILE, fnm), gnx, grpindex, mu_max, mu_aver, epsilonRF,
- temp, nFF, skip, bSlab, nslices, axtitle, opt2fn("-slab", NFILE, fnm), oenv);
+ do_dip(top,
+ pbcType,
+ det(box),
+ ftp2fn(efTRX, NFILE, fnm),
+ opt2fn("-o", NFILE, fnm),
+ opt2fn("-eps", NFILE, fnm),
+ opt2fn("-a", NFILE, fnm),
+ opt2fn("-d", NFILE, fnm),
+ opt2fn_null("-cos", NFILE, fnm),
+ opt2fn_null("-dip3d", NFILE, fnm),
+ opt2fn_null("-adip", NFILE, fnm),
+ bPairs,
+ corrtype[0],
+ opt2fn("-c", NFILE, fnm),
+ bGkr,
+ opt2fn("-g", NFILE, fnm),
+ bPhi,
+ &nlevels,
+ ndegrees,
+ ncos,
+ opt2fn("-cmap", NFILE, fnm),
+ rcmax,
+ bQuad,
+ bMU,
+ opt2fn("-en", NFILE, fnm),
+ gnx,
+ grpindex,
+ mu_max,
+ mu_aver,
+ epsilonRF,
+ temp,
+ nFF,
+ skip,
+ bSlab,
+ nslices,
+ axtitle,
+ opt2fn("-slab", NFILE, fnm),
+ oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-autoscale xy -nxy");
do_view(oenv, opt2fn("-eps", NFILE, fnm), "-autoscale xy -nxy");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff