NAME¶
g_tcaf - calculates viscosities of liquids
VERSION 4.5.4-dev-20110404-bc5695c
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 -[no]version -nice int
-b time -e time -dt time
-[no]w -xvg enum -[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, 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 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 values of tau and
eta. The fit weights decay with time as exp(-t/wt), and the TCAF and fit are
calculated up to time 5*wt. The eta values 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
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting:
xmgrace,
xmgr or
none
-[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,
exp9 or
erffit
-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 until
the end
SEE ALSO¶
gromacs(7)
More information about
GROMACS is available at
<
http://www.gromacs.org/>.