GMSO 0.3.0

Breaking Change

• Integrate Pydantic for gmso.abc abstract classes (#431)

Features

• Improve GROMACS top writer (#306, #330, #423)
• Add method to get Site’s index (#343, #365)
• Add Improper Connection and ImproperType Potential (#338)
• Improve LAMMPS writer (#339, #331)
• Add LAMMPS data file reader (#351)
• Add method to convert to and from ParmEd Structure (#334)
• Add a class method in potential.py to create Potential object (#362)
• Add MCF writer (#340)
• Refactor PotentialTemplates (#359)
• Simplify Potential object such that the potential Expression is handled by a separate class (#419)
• Add __hash__ method for Element class (#428)
• Validate site positions and change default to np.nan (#405)
• Extend XML schema to create ConnectionType based on AtomClass (#442)
• Use networkx to enumerate connectivity in Topology (#356)
• Provide ImproperType and group names in Forcefield XML/XSD (#444)
• Ensure duplicate connections are pruned (#460)

Bug Fixes

• Fix element parsing to work with lark parser >0.8.5 (#420)
• Fix bug found in LAMMPS writer (#453)
• Prevent a nondeterministic AssertionError in unit tests (#471)

Maintenance

• Set up CI pipeline (#316, #326, #398, #409, #421)
• Build and update documentation (#322, #328, #353, #391, #429, #457, #468)
• Clean up import statements (#327, #412)
• Update setup.py (#329)
• Include package data in MANIFEST.in (#376)
• Update pytest fixtures in base_test.py (#383, #368)
• Replace allclose with unyt.array.allclose_unit in unit tests (#413)
• Update README (#422)
• Provide Dockerfile for automated image uploads (#401)
• Use bump2version for version management (#434)
• Support docker and pypi publishing from AZP (#437)
• Remove logging functions and configurations (#449)
• Update requirements files (#454, #467)
• Remove Pypi publish script (#476)

GMSO 0.2.0

This is the first public release of GMSO (previously named Topology)

Changes include

• Add a force field class with a defined XML schema (#186)
• Add sample XML files (#241, #259, #245, #263)
• Improve element class (#159, #180)
• Add moe potential templates (#233)
  • Mie non-bonded potential
  • Harmonic torsion
  • OPLS-style torsion
  • Harmonic improper torsion
• Improve support for writing to LAMMPS and GROMACS files (#244, #121, #252)
• Add examples preparing simulations of liquid argon for LAMMPS (#274) and GROMACS (#266)
• Run CI on Azure Pipelines (#251)

Documentation is available at https://gmso.mosdef.org

topology 0.1.0

Improved handling of discrete CoreTypes and clarified hashing on an id or property basis (#183)

Added dihedral class (#146)

Hollow mixing rule support (#132)

Initial definition of typed vs. un-typed Topology (#128)

Added potential templates (#134)

Several improvements to element module (#159, #166, #180)

Set default values of some mutable arguments to None (#176)

Fix a minor bug introduced by unyt 2.4 (#178)

Improved validation of some Connection types (#188)

topology 0.0.0

Features

Current status of supported file formats

Extension	Status	Support
.xyz	Fully supported	✅ 8bc9360
.gro	Mostly supported	✅#26
.data	Partially supported	✅ #28
.gsd	Mostly supported	✅ #47

Partial conversion between Topology objects and objects in OpenMM (#99) mBuild (#9) and ParmEd (#29 #12) is supported

An abstract class Potential stores the potential associated with an interaction, which can be used to describe bonded, non-bonded, etc. interactions (#96)

Bonds, Angles, and their corresponding potentials are stored (#97)

A box class, including triclinic support (#20 )

Physical values are stored with units using the unyt package (#4)

Major missing features

No dihedrals are supported

No concept of partial topologies (i.e. residues, molecules) are considered