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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,95 +1,65 @@ | ||
| import os.path | ||
| from monty.serialization import loadfn | ||
|
|
||
| from pymatgen.core.structure import Structure | ||
| from pymatgen.analysis.bond_valence import BVAnalyzer | ||
| from pymatgen.core.periodic_table import Specie | ||
| from pymatgen import __version__ as pymatgen_version | ||
|
|
||
| from maggma.builder import Builder | ||
| from maggma.examples.builders import MapBuilder | ||
| from maggma.validator import JSONSchemaValidator | ||
|
|
||
|
|
||
| BOND_VALENCE_SCHEMA = { | ||
| "title": "bond_valence", | ||
| "type": "object", | ||
| "properties": | ||
| { | ||
| "task_id": {"type": "string"}, | ||
| "method": {"type": "string"}, | ||
| "possible_species": {"type": "array", "items": {"type": "strinig"}}, | ||
| "possible_valences": {"type": "array", "items": {"type": "number"}}, | ||
| "successful": {"type": "boolean"}, | ||
| "pymatgen_version": {"type": "string"}, | ||
| }, | ||
| "required": ["task_id", "successful", "pymatgen_version"] | ||
| } | ||
| MODULE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__))) | ||
| BOND_VALENCE_SCHEMA = os.path.join(MODULE_DIR, "schema", "bond_valence.json") | ||
|
|
||
|
|
||
| class BondValenceBuilder(Builder): | ||
| class BondValenceBuilder(MapBuilder): | ||
| """ | ||
| Calculate plausible oxidation states from structures. | ||
| """ | ||
|
|
||
| def __init__(self, materials, bond_valence, | ||
| query=None, **kwargs): | ||
| def __init__(self, materials, bond_valence, **kwargs): | ||
|
|
||
| self.materials = materials | ||
| self.bond_valence = bond_valence | ||
| self.query = query or {} | ||
|
|
||
| super().__init__(sources=[materials], | ||
| targets=[bond_valence], | ||
| **kwargs) | ||
|
|
||
| def get_items(self): | ||
| self.bond_valence.validator = JSONSchemaValidator(loadfn(BOND_VALENCE_SCHEMA)) | ||
| super().__init__(source=materials, target=bond_valence, ufn=self.calc, projection=["structure"], **kwargs) | ||
|
|
||
| materials = self.materials.query(criteria=self.query, | ||
| properties=["task_id", "structure"]) | ||
| # All relevant materials that have been updated since bond valences | ||
| # were last calculated | ||
| q = dict(self.query) | ||
| q.update(self.materials.lu_filter(self.bond_valence)) | ||
| new_keys = list(self.materials.distinct(self.materials.key, q)) | ||
|
|
||
| materials = self.materials.query(criteria={self.materials.key: {'$in': new_keys}}, | ||
| properties=["task_id", "structure"]) | ||
|
|
||
| self.total = materials.count() | ||
| self.logger.info("Found {} new materials for bond valence analysis".format(self.total)) | ||
| def calc(self, item): | ||
| s = Structure.from_dict(item['structure']) | ||
|
|
||
| for material in materials: | ||
| yield material | ||
| d = {"pymatgen_version": pymatgen_version, "successful": False} | ||
|
|
||
| def process_item(self, item): | ||
| s = Structure.from_dict(item['structure']) | ||
| try: | ||
| bva = BVAnalyzer() | ||
| valences = bva.get_valences(s) | ||
| possible_species = {str(Specie(s[idx].specie, oxidation_state=valence)) | ||
| for idx, valence in enumerate(valences)} | ||
| possible_species = { | ||
| str(Specie(s[idx].specie, oxidation_state=valence)) for idx, valence in enumerate(valences) | ||
| } | ||
|
|
||
| method = "BVAnalyzer" | ||
|
|
||
| d["successful"] = True | ||
| d["bond_valence"] = { | ||
| "possible_species": list(possible_species), | ||
| "possible_valences": valences, | ||
| "method": "oxi_state_guesses" | ||
| } | ||
|
|
||
| except ValueError: | ||
| try: | ||
| first_oxi_state_guess = s.composition.oxi_state_guesses()[0] | ||
| valences = [first_oxi_state_guess[site.species_string] for site in s] | ||
| possible_species = {str(Specie(el, oxidation_state=valence)) | ||
| for el, valence in first_oxi_state_guess.items()} | ||
| method = "oxi_state_guesses" | ||
| except: | ||
| return { | ||
| "task_id": item['task_id'], | ||
| "pymatgen_version": pymatgen_version, | ||
| "successful": False | ||
| possible_species = { | ||
| str(Specie(el, oxidation_state=valence)) for el, valence in first_oxi_state_guess.items() | ||
| } | ||
| d["successful"] = True | ||
| d["bond_valence"] = { | ||
| "possible_species": list(possible_species), | ||
| "possible_valences": valences, | ||
| "method": "oxi_state_guesses" | ||
| } | ||
| except: | ||
| pass | ||
|
|
||
| return { | ||
| "task_id": item['task_id'], | ||
| "possible_species": list(possible_species), | ||
| "possible_valences": valences, | ||
| "method": method, | ||
| "pymatgen_version": pymatgen_version, | ||
| "successful": True | ||
| } | ||
|
|
||
| def update_targets(self, items): | ||
| self.logger.debug("Updating {} bond valence documents".format(len(items))) | ||
| self.bond_valence.update(docs=items, key=['task_id']) | ||
| return d |
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