A Python wrapper around PLUMED.
This package uses numpy style docstrings and type hinting.
Use t.Literal[] instead of plain strings for fixed options.
To run tests, use uv run pytest tests/.
There must be unit tests added for all new functionality!
The test should expect the full output like
expected = [
"d12_g1_0_com: COM ATOMS=1,2,3,4,5,6,7,8,9",
"d12_g2_0_com: COM ATOMS=19,20,21",
"d12: DISTANCE ATOMS=d12_g1_0_com,d12_g2_0_com",
]
assert plumed_str == expected
and not just parts of it, e.g.
assert any("COM ATOMS=1,2,3,4,5,6,7,8,9" in cmd for cmd in plumed_str)
The goal of the package is to provide abstractions for collective variables and biases and to interface with ASE and ZnTrack.
The package uses ASE units, e.g. distances are in Angstrom, energies in eV and time in fs.
If available, reference the https://www.plumed.org/doc-master/user-doc/html/ inside the docstrings to get more information about the underlying PLUMED functionality!
This is a new package, backwards compatibility is not required! Make design decisions for good code structure and usability, not for backwards compatibility! Use KISS, DRY, SOLID and YAGNI principles.
Ask before you create or plan summary documents!