Molecules connectivity + compatibility with manybody interactions #91
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Added LAMMPSData class that handles the input/output to LAMMPS data text files to/from numpy arrays, and a Molecules class that (so far) provides access to the connectivity and types for bonds/angles/dihedrals.
Currently only computes potential energies for bonds, angles and dihedrals.
The classes CutoffNeighbourhood wraps around the neighbour_list and triplet_list functions. MolecularNeighbourhood mimics CutoffNeighbourhood in the quantities it returns, but takes pair information from the connectivity defined by the Molecules class.
The C extension functions only accept int32 types.
Out of plane components of the Hessian should be 0, but for short bond lengths the analytical expression of the Hessian accumulates floating point errors. There may be an optimal implementation of the analytical expression to minimze floating point error.
When calling neighbour_list with an integer cutoff, the previous behavior was to raise a ValueError exception with an obscure error message.
pastewka
requested changes
Mar 5, 2022
pastewka
approved these changes
Mar 7, 2022
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Thanks for the contribution @prs513rosewood |
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Hi all,
Here's the start of my work on bonded interactions (pair bonds, angles, dihedrals). It is currently composed of two parts:
LAMMPSDataclass in theio.lammps_datasubmodule.Moleculesclass in themoleculessubmodule, which also provides convenience functions for geometry calculations.I also added a few simple calculators (mainly for testing), but I'll end up removing them once I get the manybody calculator to play nice with molecule connectivity. For that, I think I'll create a class with an interface that abstracts away whether pairs and triplets come from neighbor lists or a prescribed connectivity. Any feedback welcome.