Hack in bonded interactions #236
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Ensure bond exclusions are only enforced if bonds are not None.
mphoward
requested changes
Feb 16, 2024
src/relentless/simulate/hoomd.py
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| self._assert_dimension_safe(sim, snap) | ||
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| # create the potentials, defer attaching until later | ||
| neighbor_list = hoomd.md.nlist.Tree(buffer=sim.potentials.pair.neighbor_buffer) |
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One thing we do still want to do is make sure we can specify the neighbor list exclusions, and then only do the exclusions in the thermo if they are active. I think we talked about adding that as an argument / property of the PairPotentialTabulator, like the neighbor_buffer, and then we would set it here by setting the exclusions option.
src/relentless/simulate/hoomd.py
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| ) | ||
| .toNeighborList() | ||
| ) | ||
| if snap.bonds is not None: |
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Here you would add a check if bonds are in the exclusion list as well. Probably you need to have that forwarded to this action though, since we would normally grab it from the sim.
clpetix
commented
Apr 19, 2024
… feature/bonds
clpetix
commented
Oct 9, 2024
src/relentless/simulate/hoomd.py
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| @@ -64,6 +64,8 @@ def _call_v3(self, sim): | |||
| # parse masses by type | |||
| snap = sim["engine"]["_hoomd"].state.get_snapshot() | |||
| sim.masses = self._get_masses_from_snapshot(sim, snap) | |||
| sim[self]["_bonds"] = self._get_bonds_from_snapshot(sim, snap) | |||
| sim[self]["_angles"] = self._get_angles_from_snapshot(sim, snap) | |||
| self._assert_dimension_safe(sim, snap) | |||
| # create the potentials, defer attaching until later | |||
| neighbor_list = hoomd.md.nlist.Tree(buffer=sim.potentials.pair.neighbor_buffer) | |||
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add in exclusions=('bond', 'angle')
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