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optimization_type
property for structures #455base: develop
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optimization_type
property for structures #455Changes from 9 commits
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I find the current classification scheme to be too vague and too poorly undefined to be satisfactory as a standard for a database implementation, especially for the automated application. In particular, what is "observed experimentally" is very much dependent on the field of research (e.g., in what sense was the Ds element, with the half life below a millisecond and abundances of several atoms actually observed?), and "consensus" and "structure exists" are in the eye of the beholder.
An alternative suggestion comes from our discussion with Rickard (@rartino) during the lunch-time discussion of the 2023 CECAM workshop. We notice that most of the structures we are interested in comes from some sort of a minimization procedure, when the atomic coordinates are refined against a chosen target function. This target function essentially defined the physical meaning of the refined structure (and thus the conclusions we an draw from it); closeness to the optimum can be evaluated and serves as a quality criterion. The target function can be specified regardless to the minimization procedures (algorithms, programs) that were employed. The target function is unique for a given structure and specific to a given methods, thus it can be used for broad classification of the structures.
The current examples of the classes could be:
min sum_h,k,l ||F_obs| - |F_calc||
; see https://dictionary.iucr.org/R_factor. Subclasses can be introduced depending on the radiation type (X-rays, neutrons, electrons);min E(rho(x,y,z))
; subclasses can be introduced depending on the exact form of the hamiltonian, and on the aproximations that were in place;min E(bonds, angles, dihedrals)
;Finally, there might be structures that were not optimised in any way, and these can be designated as "fantsy structures"
Note that the classes introduced in this way will be unambiguous, non-overlapping, and structures withing a single class will be easier comparable between themselves as the structures from different classes.
Should we go this direction as a more tractable one?
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I must say that I'm not sure this differs much from our current proposal, though we could certainly adopt some of your wording. Is it the PR you disagree with in its current state or just the suggestion in the comment you are replying to?
The important distinction missing from you suggestion is the mechanism for a database to indicate that they believe a structure to be globally stable when compared to other structures in the same database; whilst we can handle this with the eventual "stability" namespace, I think it would be a shame to exclude e.g., generative structures with high predicted stability probability, or phases that cannot easily be exhaustively screened for stability from our definition (the "stability" namespace would strictly boil this down to a distance from a well-defined locally completed convex hull).
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To me the difference is fundamental.
The suggested definitions, unlike the current PR wording, are unambiguous (IMHO) and mathematically well defined. We just need to double check what exactly minima are meant by different methods. I am pretty sure for experimental crystallography, not so sure about other methods.
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I wold strongly suggest that
stability
is conveyed by another, numeric property. As you suggest, it should give energy above the convex hull, and would give a possibility to search for quantitative results.