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materialsvirtuallab
Question about radius in BOWSR readme example
This might be a dumb question. In the BOWSR readme example, why the rounding? And is the 0.6 factor an approximation for getting the larger element's radius?
expected_radius() might be better named expected_diameter() since it gives the sum of 2 radii.
https://github.com/materialsvirtuallab/maml/blob/a37f78a090c338a79f4c0644e5e267c60c50a8d1/maml/apps/bowsr/README.md?plain=1#L75-L81
@JiQi535 In case you rename the function, I think it can also be simplified from this:
def expected_radius(struct):
element_list = struct.composition.chemical_system.split("-")
element_list = [get_el_sp(e) for e in element_list]
ele1, ele2 = sorted(element_list, key=lambda x: x.atomic_radius)[:2]
return ele1.atomic_radius + ele2.atomic_radius
to this:
def expected_diameter(structure: Structure) -> float:
elem_1, elem_2, *_ = sorted(structure.composition.elements, key=lambda x: x.atomic_radius)
return elem_1.atomic_radius + elem_2.atomic_radius
Btw, this function fails for unary structures.
ValueError: not enough values to unpack (expected at least 2, got 1)
@JiQi535 I suggest you fix these problems and submit a PR. We shouldn't let this issue fester for so long. This is not a difficult fix.
why the rounding? And is the 0.6 factor an approximation for getting the larger element's radius?
After checking through the codes, I believe this 0.6 factor is just a customizable factor to define the minimum allowed atomic distance in an optimized structure. It provides a reasonable guess of the shortest bond length in a structure that is not unphysical. As in the example of README, we provide a cutoff value for the minimum allowed atomic distance as argument to the method compressed_optimizer.get_optimized_structure_and_energy(radius=radius) . The returned optimized structure will have shortest bond length larger than this cutoff "radius".
To make it more clear, I can change the name of the "radius" variable to "cutoff_distance".
@YunxingZuo @shyuep Please kindly correct me if my understanding is not correct. Thanks!
@JiQi535 The bigger issue is the unary structure failure. That can be easily fixed?
@shyuep The BOWSER optimizer doesn't have this kind of limitation. The previous example function expected_radius to get an estimated shortest allowed atomic distance in the README does have this limitation, and it has already been modified in the PR to work with unary structures.