man g_tcaf (Commandes) - g_tcaf VERSION 3.3_beta_20050823
NAME
g_tcaf VERSION 3.3_beta_20050823
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
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-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]h no 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]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-[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 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