I’m trying to use the fix ave/spatial command to get the average (x,y) coordinates in separate cylindrical cut-out sections of a CNT in order to define the geometrical parameters of my simulation. For the origin in the ave/spatial fix I’m using the com of each disk, and outputting the average x and y coordinates, in order to get an average radius of each of the disks, “sqrt(x^2 + y^2)” to monitor and use later on.

My confusion is with the documentation for the fix ave/spatial section, specifically in sections that give geometrical descriptions of the bins for 1,2, or 3-dimensions. Since I’m using the origin, and delta settings twice for the x and y coordinates, I have two-dimensional bins, but I’m having difficulty picturing what a 2-D “pencil” is.

The doc states for 1,2, and 3-D the bins are surfaces/slabs, pencils, and boxes, respectively.

Should it be 1-D pencils, and 2-D slabs?

I’ve been repeatedly reading the doc, and searching elsewhere.

respectfully,

dc

10-2-cnt.lmp (5.34 KB)

I don't think so.

Say you've got an orthorhombic simulation box extending from (0, 0, 0) to (X, Y, Z).

If you do a 1D ave/spatial, with something like "x lower delta_x", you'll get a series of subvolumes of dimensions (delta_x, Y, Z). Their extent in y and z is much larger than their extent in x, so we call them surfaces/slabs.

When the second dimension is introduced, with "x lower delta_x y lower delta_y", you get subvolumes of dimensions (delta_x, delta_y, Z). Now you have one "large" dimension (z), and two small ones (x and y), so we call it a pencil (long in one direction, thin in the other two).

Finally, when you make the third set of cuts (x lower delta_x y lower delta_y z lower delta_z) you get subvolumes of size (delta_x, delta_y, delta_z). These are of comparable size in all three dimensions, so we call them boxes.

Thanks, Niall,

For your time, and the explanation. To show that I’ve “got it”, the cylindrical cross-section in my simulation is filled with thin rectangular boxes extending along the axial z-direction of the simulation domain, with the majority of them empty, and only the few boxes on the edges containing particles in the histogram count.

Apologies, if the question is naive.

Thanks, again,

respectfully,