Request for Detailed Documentation on Using XYZ Files to Set Up SQLite Database for Fine-Tuning orbModel

[JinZongxiao]

Hi there,

I'm currently working on fine-tuning the orbModel using ASE, but I'm encountering difficulties when trying to write an atoms object instantiated with XYZ file content to a SQLite database.

Here's the specific issue:

1.I've successfully instantiated an atoms object using the content of an XYZ file.
2.However, when I try to write this atoms object to a SQLite database using ASE's functionalities, it doesn't work as expected.

I would appreciate it if you could provide:

1.A reference dataset or an example of a correctly formatted SQLite database that includes energy and force data.
2.Instructions or a script for building a SQLite database with energy and force data that is compatible with the orbModel fine-tuning process.

Alternatively, if there are any known issues or limitations with writing atoms objects to SQLite databases in ASE, please let me know.

Thank you for your time and assistance. Looking forward to your response.

B.R.

[benrhodes26]

Something like this should work:

with connect("your/local/path/train.db") as db:
    atoms = ...  # an ase.Atoms object
    spc = SinglePointCalculator(atoms=atoms, energy=energy, forces=forces, stress=stress)
    atoms.calc = spc
    db.write(atoms)

As a friendly note: this issue is out of scope and so I will close. If you have further troubles using ase, please consult a relevant forum / make an issue for improved documentation on the ase github repo. I hope you solve your problem!