no way to access atomic descriptors

[bernstei]

There is a function that computes atomic descriptors, compute_atomic_descriptors, and these are saved in self.atomic_desc, but from what I can tell, there is no function that retrieves those (similar to fetch_computed_descriptors which appears to only get global descriptors). This means that there's no way to generate that atomic descriptor design matrix without going through a file, since get_atomic_descriptors does appear to read them.

[bernstei]

Note that from what I can tell if you call compute_atomic_descriptors but not compute_global_descriptors, you get an ASAPXYZ object that cannot be written. If you want to write it (so you can read it back in and use get_atomic_descriptors), you have to call compute_global_descriptors with keep_atomic=True. I'll put together an example of this.

[BingqingCheng]

I think you are right. I'm a bit snowed under these couple of days but will fix it before the end of the week.

[bernstei]

On Oct 13, 2020, at 8:04 AM, Bingqing Cheng <notifications@github.com<mailto:notifications@github.com>> wrote: I think you are right. I'm a bit snowed under these couple of days but will fix it before the end of the week. In general, it would be useful to extend the howto_asaplib.rst with a complete atomic descriptor example.

[BingqingCheng]

This is done now. In summary, one can just compute atomic_descriptors using, e.g.

compute atomic descriptors only

asapxyz.compute_atomic_descriptors(desc_spec_dict=soap_spec,
sbs=[],
tag='tio2-atomic',
n_process=1)

and fetch it by:
dm = asapxyz.fetch_computed_atomic_descriptors(['soap1'])

Will update the documentation shortly