How to use chunk/atom bin/cylinder to calculate velocity, density, etc

Dear all,

I need to calculate the mass density of water in CNT. The radius of CNT is 5.45 Angs and the height of tube changes between 32-58.26 Angs. Based on these dimensions, I set the coordinates of the computational domain with real units in the input file as:

-6.5 6.5 xlo xhi
-6.5 6.5 ylo yhi
31.0 58.8 zlo zhi

To calculate the density of water, I used the following command:

compute cc1 mobile chunk/atom bin/cylinder z lower 26.26 0 0 0.0 5.4 30 units box
fix 1 mobile ave/chunk 1 20000 20000 cc1 vx vy vz density/number density/mass file vel1.profile

In the output file, I get the following numbers:

Chunk Coord1 Coord2 Ncount vx vy vz density/number density/mass

40000 60 231
1 0.09 44.13 9.34205 -4.33601e-05 -5.36655e-05 6.57059e-06 3.49504 71.2459
2 0.09 70.39 0.10235 -0.000372728 -0.000419092 -0.000203393 0.0382911 1.01591
3 0.27 44.13 5.735 3.71229e-05 -3.98979e-05 2.37601e-05 0.715192 8.56079
4 0.27 70.39 0.15325 -0.000426444 -1.19502e-05 2.08448e-05 0.0191113 0.471264
5 0.45 44.13 2.1103 3.9363e-05 0.00031698 -0.000120481 0.157901 0.672219

My question is that what are those two numbers as Corrd2 (44.13 and 70.39)? Do they represent two sections at the entrance and exit of tube? If so, I didn’t apply this in the command of chunk/atom. I just divided the tube in radial direction and why these two numbers are not same as what I applied as the height of tube (32 to 58.26)?

To get the right density at each radial section, do I need to get average between densities at two heights?

E.g. at radius=0.09: Mass Density=0.5 *(71.2459+1.01591)=36.13.

Thanks and regards,


The 1st 3 args of bin/cylinder are dim origin delta = z lower 26.26 in your

case. The doc page explains that 26.26 is the bin distance along

the axis of the cylinder. So you have 2 bins in that dir, along with

the radial binning. The 44/70 are the center points of those

z-axis bins.


Dear Dr. Plimpton,

Thanks for clarifying the args.

I just wanted to make sure: The density of water over the whole of z-axis, is the value only at center point of 44=((32+58.26)/2). Therefore, I don’t need to get the average of densities between two center points of 44 and 70 at each radial binning. Am I right?

My second question is that I specified the coordinates of the box (-6.5 6.5 xlo xhi, -6.5 6.5 ylo yhi, 31.0 58.8 zlo zhi) a little big larger than the dimensions of CNT. How can I make sure that these numbers are right values and don’t change the simulation results significantly?



Answers below.