Molecular Dynamics

Please go to https://github.com/deepmodeling/deepmd-kit/discussions to ask questions. Before asking questions, you can

• search the previous discussions
• check the document, especially training parameters

Please provide necessary information including the version of software and installation way,

Is your feature request related to a problem? Please describe.
Some, likely many, I/O operations work on path strings but not pathlib.Path objects.

>>> from openforcefield.topology import Molecule
>>> from pathlib import Path
>>> Molecule.from_file('mol.sdf', file_format='sdf')
Molecule with name '' and SMILES '[H]C([H])([H])C([H])([H])O[H]'
>>> Molecule.from_file(Path('

Currently the C++ code in freud does not ensure that r_min is non-negative (>= 0) in several classes. Values of r_min < 0 should raise an error in the constructor like this:

https://github.com/glotzerlab/freud/blob/eb2a97bac302ed45236f26e0a7e6a0346071c579/cpp/density/RDF.cc#L17-L28

This applies to classes like RDF and CorrelationFunction and other classes that deal with radial dist

This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.

Low hanging fruit

Want to get involved? These issues might be the place to start:

• Speedups to the code. Both on the level of individual functions and the overall algorithm. [Getting there]
• Look over