[Bug]: Lattice objects created are inconsistent with existing ones

[laserkelvin]

Expected behavior

The periodic properties calculation workflow currently creates a new pymatgen.core.Structure object, regardless of whether it exists or not, and based either on an existing lattice matrix or from parameters.

When using MaterialsProjectDataset and children, @melo-gonzo pointed out that the serialized structures are not identical to the ones produced by the matsciml workflow, which is not what we would expect as it then leads to a mismatch in input structures and labels.

Actual behavior

In a set of notebook tests, the image below shows the creation of a Lattice object from parameters, versus passing an existing Structure's lattice matrix directly: note the differences in the resulting matrix.

If you inspect the resulting structure's coordinates, nothing immediately stands out but if you visualize the structure, they are very different. This is a huge issue for force prediction, as the atoms are switched: the top panel below shows the matsciml emitted structure, and the lower panel is from the serialized structure.

As it turns out, at some point, pymatgen introduced a vesta argument to Lattice.from_parameters. The default value is False, but if set to True, the generated and serialized structures are then consistent.

Steps to reproduce the problem

Code snippets shown above; compare serialized structure with that produced by the PeriodicPropertiesTransform workflow.

Specifications

Mainly relevant here is pymatgen==2023.9.25