Improve of betacristabolite recipe #1124
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…with freud_generate_bonds)
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Bug fixed, pending test for new use case. |
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #1124 +/- ##
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+ Coverage 87.11% 87.18% +0.06%
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Files 62 62
Lines 6451 6483 +32
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+ Hits 5620 5652 +32
Misses 831 831
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| # Bogus values provided | ||
| with pytest.raises(ValueError): | ||
| surface = Betacristobalite(dimensions="bogus") |
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Code scanning / CodeQL
Unused local variable Note
| scale_Lz = math.ceil(box.Lz / ref_dims[2]) | ||
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| silica_list = list() | ||
| for particle in list(betacristabolite.particles()): |
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don't need to turn this into a list, can just use the particles iterable.
| temp.translate(shift) | ||
| silica_list.append(temp) | ||
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| self.add(silica_list) | ||
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| count = 0 | ||
| for particle in list(self.particles()): |
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should also not generate the list first.
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| count = 0 | ||
| for particle in list(self.particles()): | ||
| if particle.name.startswith("O") and particle.pos[2] > 1.0: | ||
| if particle.name.startswith("O") and particle.pos[2] >= box.Lz: |
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So this line originally was so you could determine surface oxygens. But if we make the particles position have to be larger than the z dimension of the box, won't we generate zero ports? Seems like this should maybe be some fraction of the the box.Lz.
| assert surface.n_bonds == 2400 | ||
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| # 2D dimension provided | ||
| surface = Betacristobalite(dimensions=(5.3888 * 1.2, 4.589110 * 1.25)) |
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So something seems a bit off to me here based on these inputs. I'm worried about the bondlength distributions. What if a particle gets closely placed towards an edge and near a particle already at that edge? I'm not sure fractional values for dimensions should be allowed since this behavior could result.
I would suggest either making a smaller version of the surface so it's easier to tile with integer values, writing a call that instead of loading the mol2, actually does the carving of the amorphous surface which should account for the exact box size specified and not have this issue, or have some filter that removes particles that get within a certain cutoff radius.
| # Bogus values provided | ||
| with pytest.raises(ValueError): | ||
| surface = Betacristobalite(dimensions="bogus") | ||
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Should add the test:
| assert len(surface.available_ports()) > 1 | |
| distancesList = [] | |
| for particle in surface.particles(): | |
| assert len( | |
| surface.particles_in_range(particle, dmax=0.001, max_particles=1) | |
| ) ==0 | |
| assert np.min(distancesList) > 0.001 # 1/1000 of a nm is too close |
PR Summary:
Modify the
Betacristobaliterecipe so that it can be created with a custom size (with some borrow code fromwater_boxrecipe).PR Checklist