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 ...
- 7,401
5
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 ...
- 1,401
5
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) ...
- 9,981
4
votes
Accepted
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 ...
- 1,675
4
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 ...
- 156
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 ...
- 2,934
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 ...
- 2,653
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 ...
- 721
2
votes
Accepted
How to draw the double perovskite Sr2FeMoO6 by software/hand?
Converting comments into an answer here.
Just use the structure from mp-19127 as it seems to be the one you are looking for.
Drawing structures by hand generally is best done by finding a template CIF ...
Only top scored, non community-wiki answers of a minimum length are eligible