Remove ase/pymatgen/... inputs from constructor in favor of from_ classmethods
#10
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Hi @mbercx , I will work on this 🚀 today |
mikibonacci
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This is implemented following the pydantic PR for aiida-core: aiidateam/aiida-core#6255
agoscinski
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This is implemented following the pydantic PR for aiida-core: aiidateam/aiida-core#6255
mikibonacci
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* Introducing the kind checks. In principle, we can also not define the kinds, in that case it is up to the plugin to use the get_kinds() method of the StructureData to define kinds. * Starting to migrate to mkdocs * StructureData developer guide, missing: PropertyCollector and properties. * First profiling for the atomistic vs orm StructureData generation. Need more profiling for low-atoms systems, where it seems orm is better * Comment on profiling * Additional notes on profilings * Adding a last scaling test, to be commented and inserted in the github issue * Adding the automatic kind generation. Missing: deactivate this automatism. * Adding the `allow_kinds` input in the StructureData init. used to deactivate the automatic kind generation. * Adding the `to_legacy_structuredata` method in atomistc.StructureData This is provided in temporary way in order to make easier to migrate the plugin gradually to this new Data. In a first step, we should use this method anytime the plugin uses the StructureData. Then add the properties setting. * - Adding the developer docs - Adding some bugfixing for the empty StructureData init. * Added user guide with examples * Fixing #16 * This solves issue #10 This is implemented following the pydantic PR for aiida-core: aiidateam/aiida-core#6255 * New implementation, following the pydantic PR. adding the `charges` properties, in the same way as we have the cell and pbc: hard-coding the getter and setter methods. For now, no data validation is there. * Added the support to read charges also from ASE Atoms object. Added the map_kinds method, which return the mapping for the kinds as contained in the sites attribute. * Reverting back to non-pydantic implementation (Just removing the Model attribute from the StructureData class, nothing else changed) Added also the charges in the get_ase method. * Attaching the properties to the Sites. - code refactored: now `StructureData` and `Site` classes are in separated files, as well as the utils; `Kind` class is removed - `Site` class now contains the properties: `symbol`, `position`, `mass`, `charge`, `magnetization`, `kind_name`; `kind_name` should be removed. The properties are defined via the `property` decorator - `from_ase`, `to_ase` methods are added - `from_pymatgen`, `to_pymatgen` methods are added (**TOBE fixed to add also the magnetization**) - `from_file`, `to_file` methods are added. They rely on ASE `io.read` and `io.write` functions. - the `orm.StructureData` (the old one) now has a method `to_atomistic` - the `utils.py` file contains also the `to_kinds` and `get_kinds` functions, to automatically generate kinds. The user should only use the `get_kinds` function. **TOBE refined: kind names, and remove the other kinds methods from the StructureData class.** - the `StructureData` constructor now works in this way: we provide the pbc, cell. Then we should use the `append_atom` method afterwards. **TOBE discussed, I guess we cann add lists contaning site-wise value for properties** - slicing of structure data: defined the __getitem__ method, to obtain a sliced structuredata instance from the initial one. - TOBE added: `to_supercell` method. * adding the possiblity to provide lists in the constructor BUT we are gonna change this by providing the possibility to provide list of sites (each of them is a dictionary), in the same format as they are represented in the database * Moving the get_kinds and _to_kinds (now a private method) into the StructureData class. * Removed kind related methods which now are no more needed in the StructureData * Utilities for cell and sites update * New StructureData and StructureDataMutable both inheriting from StructureDataCore. Added properties: - charge - magmom Relevant added methods: - from/to ASE/Pymatgen - to_legacy - to_structuredata - to_mutable_structuredata Added single page for API tutorial. Added tests for basic functionalities of both Structure Classes. * Allowing also magmom to be provided as floats: they are then stored as [magmom,0,0] * Improving mutability and minor changes. Mutability is improved by removing all the setter methods, both in StructureDataCore and Site classes. Moreover, lists and tuples are returned as np.array with flags.writeable=False, meaning that we cannot even modify the internal arrays/lists. Other minor changes: - Now in StructureDataCore we have to define the pbc, cell and sites keywords to initialise it (and so the other subclasses), this is helpful to then document the inputs. - `get_kinds` routine fixed to work also with magmoms (arrays) - docu and tests updated with respect to these changes. * Adding type hinting and minor fixes removing mutable attribute in Site class adding a get_global_properties method in StructureDataCore, not used now but in the future to have a list of the properties in the database (not only attached to the single sites), to make easy to query wrt a property. * Improving flexibility, automatic get_kinds and pymatgen fixings. Providing full flexibility in the StructureDataMutable while preserving same data structure of StructureData. - adding the parent and index when we initialise the Site class (i.e. when we access structure.sites). This is helpful to be able to change directly properties in the StructureDataMutable class. - in the same direction, we implemented the ObservedArray class which basically allows to trigger the setter methods of arrays/lists even if we modify only one element (for example: structure.sites[0].position[0] = 5). In this way, changes are written into the structure._data, which represents the real data stored in the instance. `get_kinds` method now is stable. Fixing pymatgen problems with oxi_state and magmom. * Adding in the tutorial markdown also the get_kinds method, and minimal update of the pytests.
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Currently the constructor of the
StructureDatastill has e.g. theaseinput to initialize an instance from an ASEAtomsobject:aiida-atomistic/src/aiida_atomistic/data/structure/__init__.py
Lines 717 to 727 in 1af101e
I would instead want to see a
from_ase()class method, e.g.:The text was updated successfully, but these errors were encountered: