NAME
g_tcaf - calculates viscosities of liquids
VERSION 4.0.1
SYNOPSIS
g_tcaf -f traj.trr -s topol.tpr -n index.ndx -ot transcur.xvg -oa
tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg -oc tcaf_cub.xvg -ov
visc_k.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr
-[no]mol -[no]k34 -wt real -acflen int -[no]normalize -P enum -fitfn
enum -ncskip int -beginfit real -endfit real
DESCRIPTION
g_tcaf computes tranverse current autocorrelations. These are used to
estimate the shear viscosity eta. For details see: Palmer, JCP 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 plains (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 tcaf’s. Each of these tcaf’s is fitted to f(t)
= exp(-v)(cosh(Wv) + 1/W sinh(Wv)), v = -t/(2 tau), W = sqrt(1 - 4 tau
eta/rho k2), which gives 16 tau’s and eta’s. The fit weights decay with
time as exp(-t/wt), the tcaf and fit are calculated up to time 5*wt.
The eta’s should be fitted to 1 - a eta(k) k2, 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
tcaf’s over all k-vectors with the same length. This results in more
accurate tcaf’s. Both the cubic tcaf’s 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)
= eta0 (1 - a k2) 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.
FILES
-f traj.trr Input
Full precision trajectory: trr trj cpt
-s topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-ot transcur.xvg Output, Opt.
xvgr/xmgr file
-oa tcaf_all.xvg Output
xvgr/xmgr file
-o tcaf.xvg Output
xvgr/xmgr file
-of tcaf_fit.xvg Output
xvgr/xmgr file
-oc tcaf_cub.xvg Output, Opt.
xvgr/xmgr file
-ov visc_k.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 19
Set the nicelevel
-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]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[no]molno
Calculate tcaf of molecules
-[no]k34no
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]normalizeyes
Normalize ACF
-P enum 0
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or
3
-fitfn enum none
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7 or
exp9
-ncskip int 0
Skip N points in the output file of correlation functions
-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 till the end
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_tcaf(1)