opening .amp files?

[Alireza Khorshidi]

I was wondering how we can open up ".amp" files? They seem to be not readable, what is their format?

v0.5 seems to be calculating neighbors incorrectly. It seems that even if the atomic configuration is non-periodic, v0.5 behaves it as being periodic for calculating neighbors!

[andrew_peterson]

Sounds like two separate issues...

[Alireza Khorshidi]

Sorry, I did not well enough describe the issue.

I am seeing that the values of fingerprints calculated in v0.5 and v0.4 are not consistent. Thus, I decided to check first the calculated neighborlists. If I realize how to open up ".amp" files, my job will get easier.

[andrew_peterson]

I don't think fingerprints are in the .amp files. But the .amp format should be pretty clear from here. It is just a text file using ase.calculator.Parameters.write.

Did you mean to ask about the format the fingerprints are saved in? That is a shelve, as shown here.

[Alireza Khorshidi]

So, how can I read say "fingerprints.amp"?

Reading files seems to be useful for debugging.

[andrew_peterson]

Are you sure that filename ends in ".amp"? The ".amp" extension should only be for the calculator parameters, not the database.

In any case, the way to open that is described in the link I sent above. There is even an example in the docstring, which I pasted below. Just give Data the filename where the dots are.

>>> data = Data(...)
>>> data.open()
>>> keys = data.d.keys()
>>> values = data.d.values()

[Alireza Khorshidi]

Sorry, I was careless. Only parameters are saved in the ".amp" format. Anyway, I could open up neighborlists, fingerprints, and fingerprint-derivatives. Thanks for your comments.

There seems to be an inconsistency between the results of master and those of v0.4. I just checked and realized that it is not coming from these files. There must be some bug somewhere else. I will try to catch it.

Thanks again!