Addign editor to fix atomic positions in x,y,z and to add constraints - #1397
Addign editor to fix atomic positions in x,y,z and to add constraints#1397cpignedoli wants to merge 6 commits into
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## 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)})"
| 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: |
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Should we finish reviewing this PR to merge it ? I think it could be of great help for heterojunctions |
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we do it at the conding week for sure |
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Hi @cpignedoli , sorry for the late response. Is this PR ready for review? |
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hi @superstar54 it was working but my plan was to revise it during the coding days |
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Thanks for adding this feature!
I have a quick run on the app.
- Change the tab name "Edit Constrains" to "Constrains" directly, and same for the other tabs, because they already in the "Edit structure" section.
- If we also support other type of contrains, better to move current code in a subsection (or tab), e.g., "Fix positions"
- Would be nice to have a table, with atom index, and contraints (x, y, z), which the user can edit/save/reset directly.
- If the
angle, anddistancecontrains are not supported byaiida-quantumespresso, we remove them in the text. - in my tests, the contrains are not shown in the table of the results panel.
- add tests
Lets do that in another PR , and we keep this one only about the constraints.
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3 participants
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