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

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1

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,

Hamed.

2

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.

Steve

3

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?

Regards,

Hamed.

4

Answers below.

Steve