bin volume for chunk/atom with region

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1

Hi,

I am wondering what bin volume is used when density is determined with the following compute and fix,

region r_slit block 43.969997 82.279999 0.032451 35.277549 38.310001 76.320000

compute c_ow ow chunk/atom bin/1d z 38.310001 0.317 region r_slit

fix f_rho_ow ow ave/chunk 500 1 500 c_ow density/number file rho_ow.dat ave running overwrite

As per my understanding, for 1d bins in z direction for a specified region, the bin volume should be dz*(xhi-xlo)*(yhi-ylo), where lo and hi are from the region specifications.

However, after a quick peek into the source code, I guess the the bin volume, for 1-d bins in z dim, is computed based on the xy surface area of the box, and it does not consider any region condition.

So to get desired densities in the specified region, I should scale the densities as rho(z) * xy surface are of the box / xy surface area of the region. With this, the density values that I get are in the expected value range.

I would appreciate if someone could comment on this.

Thanks,

Sikandar

2

There is no logic in the code to calculate the intersection
of a region with a 1d slab, 2d pencil, 3d brick to get what
you are thinking of as the “exact” volume. That would be
very hard to do for arbitrary regions, even a sphere is not
simple. If the region is a union/intersection, then much
harder.

We should put a comment on the doc page about this …

Steve

3

There is no logic in the code to calculate the intersection
of a region with a 1d slab, 2d pencil, 3d brick to get what
you are thinking of as the “exact” volume. That would be
very hard to do for arbitrary regions, even a sphere is not
simple. If the region is a union/intersection, then much
harder.

While doing and exact determination is hard, getting a decent approximation should be straightforward via monte carlo integration. Since binned data has large statistical error bars anyway, it would not be as bad even with a small number of samples.

Axel

4

Thanks Steve and Axel for clarifications.

A note in the doc would be helpful.

I guess, since determining volume of a generic region may not be straightforward, in that case fix ave/chunk … density/* … should only write average particle number or mass in the bins and let user scale it with appropriate volume.

Thanks,

Sikandar