Fix scale charges, add unit tests #33
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hoomd_organics/base/system.py
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| @@ -150,6 +150,11 @@ def mass(self): | |||
| ) | |||
| return sum(mol.mass for mol in self.all_molecules) | |||
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| @property | |||
| def net_charge(self): | |||
| if self.gmso_system: | |||
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I wonder if we still need this if self.gmso_system anymore? It's used in n_particles and mass as well. I think with the recent changes, self.gmso_system will always exist.
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So, I think we need it for the mass attribute, since that is used by set_target_box before self.gmso_system is created, but we probably don't need it in the n_particles and net_charge attributes. I'll test it out and push more changes if so.
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #33 +/- ##
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+ Coverage 89.17% 92.04% +2.86%
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Files 18 18
Lines 1303 1320 +17
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+ Hits 1162 1215 +53
+ Misses 141 105 -36
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hoomd_organics/base/system.py
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| net_charge = sum(charges) | ||
| abs_charge = sum(abs(charges)) | ||
| for site in self.gmso_system.sites: | ||
| site.charge -= abs(site.charge) * (net_charge / abs_charge) |
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probably need to take care of division by zero error for cases where abs_charge=0
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And abs(site.charge) would also cause problem if site.charge=None.
I think one way to fix this would be to have a for loop in _convert_to_gmso() that checks the site.charge and if it's None sets to 0 by default.
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Good catch, I'll fix this after we merge your PR with addl. unit tests.
This PR adds the scale charges functionality to the
Systemclass that was previously in a separate utils files, and includes some unit tests.It works so that each negative charge is slightly increased and each positive charge is slightly decreased (all by the same amount) to achieve as close to a neutral charge as possible.