f"compute cna all cna/atom {1.207*self.a0}",
"variable disordered atom 'c_cna != 3'",
"group cascade dynamic all var disordered every 50",
f"dump all_dump all custom 50 {self.dir_out}/full.xyz id type x y z c_cna",
"compute myRDF cascade rdf 50",
So the radial distribution function (RDF) is calculated in cascade group. However, my question is that if in the calculation of the RDF only atoms in cascade are considered or also the atoms around cascade that are inside the cutoff distance of RDF calculation.
I have already read that, but it is not clear to me if the RDF includes or not the surrounding atoms:
Define a computation that calculates […] for a group of particles.
My logic would say that you need to include them because of the cutoff distance of the interatomic potential, but other software (OVITO) ignore surroundings (they clearly stablish “unselected particles will be treated as if they did not exist during the calculation”, I miss such a sentence in LAMMPS documentation, which I guess does the same).
Please consider that the condition of inclusion of atom pairs are listed as a bullet list in the doc page:
Pairwise distances are generated by looping over a pairwise neighbor list, just as they would be in a pair_style computation. The distance between two atoms I and J is included in a specific histogram if the following criteria are met:
* atoms i and j are both in the specified compute group
* the distance between atoms i and j is less than the maximum force cutoff
* the type of the I atom matches itypeN (one or a range of types)
* the type of the j atom matches jtypeN (one or a range of types)
It is OK if a particular pairwise distance is included in more than one individual histogram, due to the way the itypeN and jtypeN arguments are specified.
Also note that Ovito’s RDF uses different normalisation than LAMMPS to allow for partial RDF computation. This is also documented.