Dear all:

I used a timestep=0.01 fs and set units real at the beginning of the input file, then used following commands to output velocity and pressure:

fix 3 all ave/spatial 100 10 1000 y 0.0 0.05 vx vz norm sample file vel.profile units reduced

thermo_style custom step temp pe etotal press v_pxy v_pxz v_pyz vol

I got the vel.profile like following:

# Bin Coord Ncount vx vz

1686000 20
1 0.025 155.4 -0.00298486 0.00103305
2 0.075 138.3 -0.00243176 0.000875931
3 0.125 167 -0.00283857 -0.000606894
4 0.175 134.5 -0.00202667 -0.000261809
5 0.225 153.5 -0.000897068 -0.000449544
6 0.275 144.9 -0.000929967 0.000227871
7 0.325 135.4 -0.000960776 8.03187e-06
8 0.375 158.2 -0.000113666 -0.000210768
9 0.425 155.6 0.000451149 6.38153e-05
10 0.475 147.9 0.000825888 0.000468251
11 0.525 140.2 0.000603921 0.000214347
12 0.575 168.2 -0.000223195 -0.000249969
13 0.625 140.7 0.000387531 0.000434509
14 0.675 135.4 0.000850526 -0.000758939
15 0.725 181.7 0.00130753 0.000166064
16 0.775 130 0.00226866 0.000342283
17 0.825 176.1 0.00281829 -0.000476322
18 0.875 136.9 0.00256782 -0.000735984
19 0.925 138.5 0.00350704 0.000524304
20 0.975 161.6 0.00370607 0.00144112

Here, the vx units should be A/fs, which already takes into consideration of the timestep=0.01 fs, although the z distance (second column) used reduced units in the output(0-1), right? The pressure unit should be 1 atm (=1.01E05 Pa.s). right? I just need to confirm. Using above units information, I always found the shear viscosity I calculated was smaller than the reference in an order to 10 to 100. I need to find out where was wrong. Thanks a lot.

You are correct about the units. The timestep is unrelated
to the velocity output. It is Ang/fs, regardless of the timestep.
And reduced units for the bin means a fraction of the box length.

Steve