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PatchedPhaseDiagram mimic PhaseDiagram Serialization
Summary
This avoids the duplication of data when loading a ppd as so allows for serialization to text which is much more robust than using pickle.
Attempts to type hint phase diagrams better hence touching more files to get mypy consistency.
#3940 #4414
Checklist
- [x] Google format doc strings added. Check with
ruff. - [x] Type annotations included. Check with
mypy. - [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have
duecredit@due.dcitedecorators to reference relevant papers by DOI (example)
Tip: Install pre-commit hooks to auto-check types and linting before every commit:
pip install -U pre-commit
pre-commit install
This does make some breaking changes to #4414 as some of the objects there were left hydrated after as_dict and this also changes that behavior for the PhaseDiagram.
examples of code and new (breaking?) outputs
from pprint import pprint
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram, PhaseDiagram, PDEntry
from pymatgen.core.composition import Composition
# %%
entries = [
PDEntry(Composition("Li"), energy=-1.0),
PDEntry(Composition("O2"), energy=-6.0),
PDEntry(Composition("Li2O"), energy=-12.0),
PDEntry(Composition("LiO2"), energy=-9.0),
PDEntry("He", -1.23)
]
# %%
pd = PhaseDiagram(entries)
ppd = PatchedPhaseDiagram(entries)
# %%
pd_dict = pd.as_dict()
pprint(pd_dict)
# %%
ppd_dict = ppd.as_dict()
pprint(ppd_dict)
{'@class': 'PhaseDiagram',
'@module': 'pymatgen.analysis.phase_diagram',
'computed_data': {'all_entries': [{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'He': 1.0},
'energy': -1.23,
'name': 'He'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'O': 2.0},
'energy': -6.0,
'name': 'O2'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 1.0},
'energy': -1.0,
'name': 'Li'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 1.0, 'O': 2.0},
'energy': -9.0,
'name': 'LiO2'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 2.0, 'O': 1.0},
'energy': -12.0,
'name': 'Li2O'}],
'el_refs': [('He', 0), ('O', 1), ('Li', 2)],
'facets': [[1, 3, 2], [4, 1, 2]],
'qhull_data': [[0.6666666666666666, 0.0, -3.0],
[0.3333333333333333, 0.0, -4.0],
[0.0, 1.0, -1.23],
[1.0, 0.0, -3.0],
[0.0, 0.0, -1.0],
[0.3333333333333333,
0.3333333333333333,
2.0]],
'qhull_entries': [3, 4, 0, 1, 2]},
'elements': ['Li', 'O', 'He']}
{'@class': 'PatchedPhaseDiagram',
'@module': 'pymatgen.analysis.phase_diagram',
'computed_data': {'all_entries': [{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'He': 1.0},
'energy': -1.23,
'name': 'He'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'O': 2.0},
'energy': -6.0,
'name': 'O2'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 1.0},
'energy': -1.0,
'name': 'Li'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 1.0, 'O': 2.0},
'energy': -9.0,
'name': 'LiO2'},
{'@class': 'PDEntry',
'@module': 'pymatgen.analysis.phase_diagram',
'attribute': None,
'composition': {'Li': 2.0, 'O': 1.0},
'energy': -12.0,
'name': 'Li2O'}],
'el_refs': [('He', 0), ('O', 1), ('Li', 2)],
'pds': {'Li-O': {'all_entries': [1, 2, 3, 4],
'el_refs': [('O', 1), ('Li', 2)],
'elements': ['Li', 'O'],
'facets': [[1, 3], [1, 2]],
'qhull_data': [[0.6666666666666666, -3.0],
[0.3333333333333333, -4.0],
[1.0, -3.0],
[0.0, -1.0],
[0.5, 2.0]],
'qhull_entries': [3, 4, 1, 2]}},
'qhull_entries': [3, 4, 0, 1, 2],
'spaces': [('Li', 'O')]},
'elements': ['Li', 'O', 'He']}