chunk/atom

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1

I want to calculate potential energy /atom of the surface atoms of spherical particle of radius 20 nm. So I create chunks by using following command:

compute 3 all chunk/atom bin/sphere 0 0 0 0.0 20.0 5 discard yes units box

So 5 chunks are created. Then I use following command to calculate pe/atom

compute PE all pe/atom
fix 1 all ave/chunk 1 50000 60000 3 c_PE file chunk.profile

The output of chunk file is

Chunk-averaged data for fix 1 and group all

Timestep Number-of-chunks Total-count

Chunk Coord1 Ncount c_myPE

60000 5 3821.84
1 2 32 -6.51265
2 6 219.785 -6.27414
3 10 594.058 -6.33778
4 14 1120.24 -6.34645
5 18 1855.76 -6.16513

I find Total Count=3821.84 as less than the total no of atoms(3973) in the particle. Is it that the particles at the surface not included. Should I extend the rmax of chunk. Also there is vacuum above the particle

What is meant my Coord1 in the output?

Thanks

2

Apparently some of the particles some of the time lie outside the (20 A? 20 nm?) sphere, in which cases, they are “discarded,” as you explicitly requested:

compute 3 all chunk/atom bin/sphere 0 0 0 0.0 20.0 5 discard yes units box

“For the bin/sphere style the details are as follows. If discard is set to yes, an out-of-domain atom will have its chunk ID set to 0. If discard is set to no or mixed, the atom will have its chunk ID set to the first or last bin, i.e. the innermost or outermost spherical shell. If the distance of the atom from the origin is less than rmin, it will be assigned to the first bin. If the distance of the atom from the origin is greater than rmax, it will be assigned to the last bin.”

Yes, you should probably increase rmax somewhat, or use discard no

Aidan