gmx_bool bPhi, int *nlevels, int ndegrees,
int ncos,
const char *cmap, real rcmax,
- gmx_bool bQuad, const char *quadfn,
+ gmx_bool bQuad,
gmx_bool bMU, const char *mufn,
int *gnx, int *molindex[],
real mu_max, real mu_aver,
};
real mu_max = 5, mu_aver = -1, rcmax = 0;
real epsilonRF = 0.0, temp = 300;
- gmx_bool bAverCorr = FALSE, bMolCorr = FALSE, bPairs = TRUE, bPhi = FALSE;
+ gmx_bool bAverCorr = FALSE, bMolCorr = FALSE, bPairs = TRUE, bPhi = FALSE, bQuad = FALSE;
const char *corrtype[] = {NULL, "none", "mol", "molsep", "total", NULL};
const char *axtitle = "Z";
int nslices = 10; /* nr of slices defined */
"Correlation function to calculate" },
{ "-pairs", FALSE, etBOOL, {&bPairs},
"Calculate [MAG][COS][GRK]theta[grk][cos][mag] between all pairs of molecules. May be slow" },
+ { "-quad", FALSE, etBOOL, {&bQuad},
+ "Take quadrupole into account"},
{ "-ncos", FALSE, etINT, {&ncos},
"Must be 1 or 2. Determines whether the [CHEVRON][COS][GRK]theta[grk][cos][chevron] is computed between all molecules in one group, or between molecules in two different groups. This turns on the [TT]-g[tt] flag." },
{ "-axis", FALSE, etSTR, {&axtitle},
int nFF[2];
atom_id **grpindex;
char **grpname = NULL;
- gmx_bool bCorr, bQuad, bGkr, bMU, bSlab;
+ gmx_bool bCorr, bGkr, bMU, bSlab;
t_filenm fnm[] = {
{ efEDR, "-en", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-dip3d", "dip3d", ffOPTWR },
{ efXVG, "-cos", "cosaver", ffOPTWR },
{ efXPM, "-cmap", "cmap", ffOPTWR },
- { efXVG, "-q", "quadrupole", ffOPTWR },
{ efXVG, "-slab", "slab", ffOPTWR }
};
#define NFILE asize(fnm)
{
gmx_fatal(FARGS, "Due to new ways of treating molecules in GROMACS the total dipole in the energy file may be incorrect, because molecules can be split over periodic boundary conditions before computing the dipole. Please use your trajectory file.");
}
- bQuad = opt2bSet("-q", NFILE, fnm);
bGkr = opt2bSet("-g", NFILE, fnm);
if (opt2parg_bSet("-ncos", asize(pa), pa))
{
bPhi, &nlevels, ndegrees,
ncos,
opt2fn("-cmap", NFILE, fnm), rcmax,
- bQuad, opt2fn("-q", NFILE, fnm),
- bMU, opt2fn("-en", NFILE, fnm),
+ bQuad, bMU, opt2fn("-en", NFILE, fnm),
gnx, grpindex, mu_max, mu_aver, epsilonRF, temp, nFF, skip,
bSlab, nslices, axtitle, opt2fn("-slab", NFILE, fnm), oenv);