gmx-tcaf - Calculate viscosities of liquids

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                       GMX-TCAF(1)

gmxtcaf  computes  tranverse current autocorrelations.  These are used to estimate the shear viscosity,
       eta.  For details see: Palmer, Phys. Rev. E 49 (1994) pp 359-366.

       Transverse currents are calculated using the k-vectors (1,0,0) and  (2,0,0)  each  also  in  the  y-  and
       z-direction, (1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors are not independent) and
       (1,1,1)  and  the 3 other box diagonals (also not independent). For each k-vector the sine and cosine are
       used, in combination with the velocity in 2 perpendicular directions. This gives  a  total  of  16*2*2=64
       transverse  currents.  One  autocorrelation is calculated fitted for each k-vector, which gives 16 TCAFs.
       Each of these TCAFs is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 -  4
       tau  eta/rho  k^2),  which  gives 16 values of tau and eta. The fit weights decay exponentially with time
       constant w (given with -wt) as exp(-t/w), and the TCAF and fit are calculated up to time  5*w.   The  eta
       values should be fitted to 1 - a eta(k) k^2, from which one can estimate the shear viscosity at k=0.

       When  the  box is cubic, one can use the option -oc, which averages the TCAFs over all k-vectors with the
       same length.  This results in more accurate TCAFs.  Both the cubic TCAFs and fits are written to -oc  The
       cubic eta estimates are also written to -ov.

       With  option  -mol, the transverse current is determined of molecules instead of atoms. In this case, the
       index group should consist of molecule numbers instead of atom numbers.

       The k-dependent viscosities in the -ov file should be fitted to eta(k) = eta_0 (1 - a k^2) to obtain  the
       viscosity at infinite wavelength.

       Note: make sure you write coordinates and velocities often enough.  The initial, non-exponential, part of
       the autocorrelation function is very important for obtaining a good fit.

       gmx-tcaf - Calculate viscosities of liquids

       Options to specify input files:

       -f[<.trr/.cpt/...>](traj.trr)
              Full precision trajectory: trrcpttng-s[<.tpr/.gro/...>](topol.tpr)(Optional)
              Structure+mass(db): tprgrog96pdb brk ent

       -n[<.ndx>](index.ndx)(Optional)
              Index file

       Options to specify output files:

       -ot[<.xvg>](transcur.xvg)(Optional)
              xvgr/xmgr file

       -oa[<.xvg>](tcaf_all.xvg)
              xvgr/xmgr file

       -o[<.xvg>](tcaf.xvg)
              xvgr/xmgr file

       -of[<.xvg>](tcaf_fit.xvg)
              xvgr/xmgr file

       -oc[<.xvg>](tcaf_cub.xvg)(Optional)
              xvgr/xmgr file

       -ov[<.xvg>](visc_k.xvg)
              xvgr/xmgr file

       Other options:

       -b<time>(0)
              Time of first frame to read from trajectory (default unit ps)

       -e<time>(0)
              Time of last frame to read from trajectory (default unit ps)

       -dt<time>(0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w(no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg<enum>(xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -[no]mol(no)
              Calculate TCAF of molecules

       -[no]k34(no)
              Also use k=(3,0,0) and k=(4,0,0)

       -wt<real>(5)
              Exponential decay time for the TCAF fit weights

       -acflen<int>(-1)
              Length of the ACF, default is half the number of frames

       -[no]normalize(yes)
              Normalize ACF

       -P<enum>(0)
              Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

       -fitfn<enum>(none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -beginfit<real>(0)
              Time where to begin the exponential fit of the correlation function

       -endfit<real>(-1)
              Time where to end the exponential fit of the correlation function, -1 is until the end

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          gmx tcaf [-f[<.trr/.cpt/...>]] [-s[<.tpr/.gro/...>]] [-n[<.ndx>]]
                   [-ot[<.xvg>]] [-oa[<.xvg>]] [-o[<.xvg>]] [-of[<.xvg>]]
                   [-oc[<.xvg>]] [-ov[<.xvg>]] [-b<time>] [-e<time>]
                   [-dt<time>] [-[no]w] [-xvg<enum>] [-[no]mol] [-[no]k34]
                   [-wt<real>] [-acflen<int>] [-[no]normalize] [-P<enum>]
                   [-fitfn<enum>] [-beginfit<real>] [-endfit<real>]