Add table potential class to forcefields library #65
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Additional details and impacted files@@ Coverage Diff @@
## main #65 +/- ##
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- Coverage 93.75% 93.54% -0.22%
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Files 20 20
Lines 1410 1533 +123
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+ Hits 1322 1434 +112
- Misses 88 99 +11
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chrisjonesBSU
commented
Sep 27, 2023
| pair_dict[pair_type] = dict() | ||
| pair_dict[pair_type]["U"] = table[:, 1] | ||
| pair_dict[pair_type]["F"] = table[:, 2] | ||
| if len(r_min) != len(r_max) != 1: |
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Technically, we can handle pair tables with different r_mins and r_maxs if we set the rmax on a per-pair basis in _create_forcefield
chrisjonesBSU
commented
Sep 28, 2023
marjanalbooyeh
approved these changes
Oct 2, 2023
| bonds: dict, optional, default None | ||
| angles: dict, optional, default None | ||
| dihedrals: dict, optional, default None | ||
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probably it's worth mentioning r_min in the docstrings. I think it's the first time we have it in hoomd-organics
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Yeah, I forgot that I need to finish this part of the doc strings still.
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This PR adds a class that creates hoomd table potentials. In hoomd, the table potentials are just created from arrays (i.e. you don't give hoomd the txt or npy file). So, this class is designed to accept dictionaries of
{type: {}}where the inside dictionary has keys and values of{parameter: parameter_value}for all of the hoomd parameters (force, energy, etc...). However, since the use case is most commonly going to be loading table potential files, I added afrom_filesclass method that handles building up of the these dictionaries.To Do: