14 votes
Accepted

Extract coordination sphere from crystal structure

Yes, there is! Pymatgen is ideally suited for this task. Specifically, I highly recommend the local environment module. Given a CIF, you can calculate the coordination environment around a given atom ...
Andrew Rosen's user avatar
  • 7,361
4 votes

Extract coordination sphere from crystal structure

I don't think there is a predefined tool right away or at least I'm not aware of that, but this problem seems a pretty easy task to do with TCL in VMD (Visual Molecular Dynamics) software. Basically ...
Mithridates the Great's user avatar
4 votes

Continuous Coordination Number Definition

Continuous coordination numbers are very commonly used in the enhanced sampling/free energy world, where they form the basis of different types of collective variables (e.g., coarse-grained reaction ...
Kristof Bal's user avatar
  • 1,331
4 votes

Continuous Coordination Number Definition

One can start with the definition of the usual, integer coordination number (which as the OP said is not a continuous function of the geometry), and smoothen its discontinuities. The (integer) ...
wzkchem5's user avatar
  • 9,621
4 votes
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How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter?

Sticking with ase you can use the built-in get_distance function. It supports non-orthogonal unit cells. An example to get the distance between atom number ...
Hebo's user avatar
  • 1,675
3 votes
Accepted

Model coordination complex using GROMACS or CP2K

Here is how you can get the structure from PubChem, read the SMILES into Avogadro2, do a MMFF94 (classical) optimization, and then a single-point energy calculation using NWChem (RHF, 6-31G*). The ...
Todd Minehardt's user avatar
3 votes
Accepted

Is hexaamminecobalt(III) chloride thermodynamically stable in pure water?

I think it is tricky to do the analysis in "pure water", since you cannot have a charged solution. Maybe what you mean is an aqueous solution at neutral pH? Based on what I saw in the ...
Stephen's user avatar
  • 721
3 votes

How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter?

Have you tried using the Ovito where there are built in functions to evaluate both RDF and CN of a system? Additionally, it might be possible to use Vesta to convert the unit cell to a rectangular one ...
PBH's user avatar
  • 2,653

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