0.12.0 Release

What's Changed

Improvements

• Convert all amber ions (see openmm/openmm#3663 for more detail) one-to-one using Amber ion frcmod files (from AmberTools 22) into OpenMM xml files with the same names and the same contents. by @mattwthompson & @aizvorski in #242 & #239
• SystemGenerator should only add barostat if system is periodic. Solves #252 by @jchodera in #253
• Fix OPC3 bond length. In the Amber implementation of the OPC3 water model at ffxml/amber/opc3.xml, the H-O bond length was too large by a factor of 10. by @mattwthompson in #273
• raise ForceException if a custom force is found. by @mattwthompson in #292
• Allow an offxml string to be used as a small molecule force field for the SystemGenerator and SMIRNOFFTemplateGenerator for example:

"Try and load a OFFXML string into a system generator object"
from openmmforcefields.generators import SystemGenerator
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.topology import Molecule
import openmm

# load the ff
ff = ForceField("openff-2.0.0.offxml")
# create a system generator
system_gen = SystemGenerator(
    forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml'],
    small_molecule_forcefield=ff.to_string()
)
mol = Molecule.from_smiles("CC")
system = system_gen.create_system(topology=mol.to_topology().to_openmm(), molecules=mol)
with open("system.xml", "w") as output:
    output.write(openmm.XmlSerializer.serialize(system))

by @jthorton in #288

• Support system and template generator for Espaloma 0.3.* (espaloma 0.2.* is no longer supported) by @ijpulidos in #293

CI

• Bump codecov/codecov-action from 3.1.0 to 3.1.1 by @dependabot in #238
• Switch to setup-micromamba by @mattwthompson in #274
• Scattered fixes to get CI running by @mattwthompson in #290

Docs

• Update docstrings, run in CI by @mattwthompson in #240

New Contributors

• @jthorton made their first contribution in #288

Full Changelog: 0.11.2...0.12.0