HOOMD-Blue handling Virtual sites for TIP4P water xml#956
HOOMD-Blue handling Virtual sites for TIP4P water xml#956CalCraven wants to merge 9 commits intomosdef-hub:mainfrom
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…r some of the inputs in test files, fix bug in xyz reader
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## main #956 +/- ##
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- Coverage 93.96% 93.54% -0.43%
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Files 67 67
Lines 7693 7883 +190
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+ Hits 7229 7374 +145
- Misses 464 509 +45 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| yield site | ||
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| def iter_sites(self, key, value): | ||
| """Iterate through this topology's sites and virtual_sites based on certain attribute and their values. |
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Is this doc string mixed up with the one in iter_sites_and_virtual_sites?
| ) | ||
| # attach potential to VirtualSitType | ||
| virtualsite_group.append(virtual_type.etree(params_units_def)) | ||
| # potential_group.append(virtual_type.virtual_potential.etree(potential_params_units_def)) |
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Can these commented lines be removed?
| xyz = u.unyt_array( | ||
| [site.position.to_value(base_units["length"]) for site in top.sites] | ||
| ) | ||
| if shift_coords: |
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Why are we removing the coordiante shift? Is this being handled somewhere else? shift_coords is still a parameter in to_gsd_snapshot and to_hoomd_snapshot
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Thanks or re-working this to support virtual sites. I'll test it out some this week, but it looks pretty close to complete from what I can tell. |
| return potential | ||
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| def _organize_generate_topology_molecule_info(top): |
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I was just thinking thismight be better suited as a method in Topology as there might be use cases other than writing rigid bodies in HOOMD.
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Or, if we don't want to add it as a class method for Topology (to reduce clutter) maybe this should live in a utils module instead.
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PR Summary: This PR should enable passing of various TIP-4P, and other forcefield models, enabling efficient handling of both virtual sites and rigid bodies.
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