g_tcaf_d (1) - Linux Manuals

g_tcaf_d: calculates viscosities of liquids


g_tcaf - calculates viscosities of liquids



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


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.


-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 


 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

 Calculate tcaf of molecules

 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

 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



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