atomate2 / OpenMM OPLS-AA Enhancements

[shehan807]

Summary

This PR resolves the first two enhancements proposed in Issue #1102:

• Feature 1: Implements the correct geometric combination rules for OPLS MD simulations via opls_lj()

I've changed create_system_from_xml to create_ff_from_xml in src/atomate2/openmm/jobs/generate.py. Why? The OPLS geometric combination rules have two requirements, (1) a CustomNonbondedForce in OpenMM that combines the sigma and eps parameters geometrically, and (2) the coulomb14scale and lj14scale attributes of the ForceField are both 0.5. The latter was enough justification for raising an error if not the case--to do so, the ForceField object would need to be accessible in generate_openmm_interchange (instead of adding unsuitable arguments to create_system_from_xml). Originally, create_system_from_xml created both the ForceField and System within the same function; now, system and ff are separate variables in generate_openmm_interchange.

• Feature 2: Allows users to create OPLS forcefield files via generate_opls_xml() via LigParGen and BOSS source code directly. To do so, users would need to follow the steps in the docs from this fork.

Currently, generate_opls_xml is only functional so long as the user has a local installation of Docker and created a private (for now, pending approval for pushing to public registries) image of LigParGen. The documentation is provided to completion in docs/user/codes/openmm.md.

• Feature 3: All changes from Generalize download_opls_xml Function #1054 have been merged into this fork (i.e., extending the download_opls_xml to handle charges, number of optimization iterations, and charge method).

Additional dependencies introduced

• defusedxml, resolves ruff failures for safely loading XML files, e.g.,

self.tree = DiffET.parse(xml_string)

• textwrap, enables easier text wrapping of long warnings/errors printed for the user, e.g.,

        if (c14 != 0.5) or (lj14 != 0.5):
            raise ValueError(
                textwrap.dedent(f"""\
                    NonbondedForce class in XML,
                    <NonbondedForce coulomb14scale="0.5" lj14scale="0.5">,
                    does not match OPLS convention,
                    <NonbondedForce coulomb14scale="{c14}" lj14scale="{lj14}">.""")
            )

CC'ing @utf, @orionarcher