add missing data in format atoms

[lory-w]

Related to #275
Part of the problem is ase atoms is missing ptr and batch when converting to dictionary.

[laserkelvin]

LGTM

[melo-gonzo]

A note for the future if any other errors pop up around this : we can also use concatenate_keys from matsciml.datasets.utils to add these attributes in a more robust way.

[laserkelvin]

@melo-gonzo can you elaborate?

Just checking to make sure I understand what you mean

[melo-gonzo]

I patched this in my mp-tests branch by just using that function as a final step before passing into .predict in the calculate function. Just wanted to note it in case we see any issues again

    def calculate(
        self,
        atoms=None,
        properties: list[Literal["energy", "forces"]] = ["energy", "forces"],
        system_changes=...,
    ) -> None:
        # retrieve atoms even if not passed
        Calculator.calculate(self, atoms)
        # get into format ready for matsciml model
        data_dict = self._format_pipeline(atoms)
        # run the data structure through the model
        data_dict = concatenate_keys([data_dict])
        output = self.task_module.predict(data_dict)
        ...