Addign editor to fix atomic positions in x,y,z #1397
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1397 +/- ##
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- Coverage 72.40% 71.29% -1.12%
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Files 109 109
Lines 7317 7468 +151
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+ Hits 5298 5324 +26
- Misses 2019 2144 +125
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| # Try to get fixed_atoms from AiiDA StructureData attributes | ||
| fixed_atoms = None | ||
| try: | ||
| fixed_atoms = self.structure.base.attributes.all['fixed_atoms'] |
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Could you do something like fixed_atoms = self.structure.base.attributes.all.get('fixed_atoms', None) ?
| chemical_symbols = ase_atoms.get_chemical_symbols() | ||
| tags = ase_atoms.get_tags() | ||
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| def fmt_free(mask): |
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I think here, you can put a condition if mask is not an instance , mask = (0,0,0) and then you do return f"({' '.join('✓' if val else 'x' for val in mask)})"
src/aiidalab_qe/common/widgets.py
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| self.input_selection = deepcopy(self.selection) | ||
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| class AddingFixedAtomsEditor(ipw.VBox): |
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I think you could name this editor, as ConstraintEditor , so in the future new constraints as implemented
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Done @AndresOrtegaGuerrero, thanks for the comments.
I have in mind how to modify the Editor to allow for other constraints, such as "distance", "torsion",..., but before we can do so, we would need such features implemented in the aiida plugin. Anyone willing to take the challenge @mbercx @superstar54 @edan-bainglass @AndresOrtegaGuerrero ?
We will also have to think about some warnings, since in QE, with symmetries, constraints can break the optimization.
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Tables in the editor and in the result page now look like this: |
connected to aiidalab/aiidalab-widgets-base#706
Constraints on x,y,z for each atom are stored in the ASE array 'fixed_atoms' .
The additional column is not present in case no constraints were specified
I need help (I would prefer in a separate PR), e.g. @edan-bainglass @superstar54, to add some warning logics:
If I load a structure that has constraints and I try to do phonons-related properties, I should get a warning. The warning can disappear only if 1)I remove the constraints, and 2) I do an additional geo-opt.
We should think about how to make this editor more general, including other types of constraints