.. _gmx tcaf:

gmx tcaf
========

Synopsis
--------

.. parsed-literal::

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

Description
-----------

``gmx tcaf`` 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.

Options
-------

Options to specify input files:

``-f`` [<.trr/.cpt/...>] (traj.trr)
    Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` 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)
    First frame (ps) to read from trajectory
``-e`` <time> (0)
    Last frame (ps) to read from trajectory
``-dt`` <time> (0)
    Only use frame when t MOD dt = first time (ps)
``-[no]w``  (no)
    View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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