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Pad Representation with zeros for non-present species #350

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rosecers opened this issue May 6, 2021 · 5 comments · May be fixed by #353
Open

Pad Representation with zeros for non-present species #350

rosecers opened this issue May 6, 2021 · 5 comments · May be fixed by #353
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@max-veit
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documentation Needs addtional documentation enhancement New feature or request

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@rosecers
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rosecers commented May 6, 2021

I have this problem quite often, where I'm computing a subset of SOAP vectors for who species ABCD are present, then another subset where only ABD are present. I know that I can use the species pair dictionary to collect SOAPs per species pair, but it would be far, far more convenient to do something like this:

hyperparameters = {
    "soap_type": "PowerSpectrum",
    ...

    # I know this keyword exists, but seems to only affect `expansion_by_species_method`
    "global_species": [A, B, C, D, ...] 
}
soap = SOAP(**hyperparameters)

featuresABCD = soap.transform(framesABCD).get_features(soap)
featuresABD = soap.transform(framesABD).get_features(soap)

where featuresABCD and featuresABD have the same indexing and shape.
@rosecers rosecers added the enhancement New feature or request label May 6, 2021
@max-veit
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max-veit commented May 6, 2021

For global_species to work, I think you also have to set expansion_by_species_method="user defined" in the hypers. Is that what you meant by the comment in your example?

@max-veit max-veit added the documentation Needs addtional documentation label May 6, 2021
@ceriottm
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ceriottm commented May 6, 2021 via email

@rosecers
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rosecers commented May 7, 2021 via email

@max-veit max-veit self-assigned this May 7, 2021
max-veit added a commit that referenced this issue May 7, 2021
@max-veit
Make 'global_species' work as expected and improve documentation
eac950c 
(it was ignored before if 'expansion_by_species_method' was not set
appropriately; this is now done automatically)

Fix #350
@max-veit
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max-veit commented May 7, 2021

Ok, this is now implemented in bugfix/soap_global_species. Let me know if you want to add tests as well; I think that could be a good idea.

@rosecers
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Looking at the code, I have a few thoughts (first of which is turning the branch into a draft PR).

  • Is there a need to have the two separate input parameters (global_species and expansion_by_species_method) if inputting one overrides the other? Why not have an option to expansion_by_species_method that anticipates a list of global species?
  • If kept two parameters, I would suggest a warning in lines 219-220

@max-veit max-veit linked a pull request May 10, 2021 that will close this issue
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Make SOAP initialization more intuitive w.r.t. species lists lab-cosmo/librascal
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@max-veit @ceriottm @rosecers