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| """ | |
| Structure of our main database: | |
| DB | |
| ├── unique_id.json :(dictionary) | |
| │ ├── unique_id [str] | |
| │ ├── formula [str] | |
| │ ├── key_words [list(str)] | |
| │ ├── source: (dictionary) | |
| │ │ ├── name: [str](ex: JARVIS /C2DB /None etc) | |
| │ │ └── source_id:[str] | |
| │ ├── structure:(dictionary) | |
| │ │ ├── atoms [list(int)] | |
| │ │ ├── lattice_vectors [3x3[array]] | |
| │ │ ├── pbc [bool, bool ,bool] | |
| │ │ └── position [nx3[array]] n-nr of atoms | |
| │ ├── sub_components: [list(str)] (list of parents ids ) | |
| │ ├── propriety: (dictionary) | |
| │ │ ├── energy: (list[prop_dictionary]) | |
| │ │ ├── band gap: (list[prop_dictionary]) | |
| │ │ ├── band structure:(list[prop_dictionary]) | |
| │ │ ├── .... | |
| │ │ └── density of states:(list[prop_dictionary]) | |
| │ │ | |
| │ ├── citation:"str" | |
| │ └── author: (dictionary) | |
| │ ├── name | |
| │ └── id | |
| ├──────────────────────────────────────────────────────────────────────────────── | |
| │ | |
| ├── prop_dictionary | |
| │ ├── name :(str) energy | |
| │ ├── value: (int float list ) | |
| │ └── source: (dictionary) | |
| │ ├── tipe: (DB/computation/author_enforce) | |
| │ ├── citation:"str" | |
| │ └── description: (dictionary) | |
| │ ├── author_id : (str) | |
| │ └── method_name : (str) | |
| │ ├── hyperparameters :(dictionary) | |
| │ └── inputs :(dictionary) | |
| │ | |
| └───────────────────────────────────────────────────────────────────────────────── | |
| """ | |
| from .utils import read_json , process_chemical_formula | |
| from .parse_c2db import * | |
| from .parse_jarvis import * | |
| # Constants: | |
| JARVIS_DB_path = "/Users/voicutomut/Documents/GitLab/bespoke-interface/DB_experiments/JARVIS2D/d2-12-12-2022.json" | |
| class DBInstance: | |
| def __init__(self): | |
| self.unique_id = None | |
| self.formula = None | |
| self.key_words = [] | |
| self.source = None | |
| self.structure = {} | |
| self.sub_components = [] | |
| self.propriety = {} | |
| self.author = {} | |
| def from_json_file(self, file_name): | |
| data = read_json(file_name) | |
| self.unique_id = data["unique_id"] | |
| self.formula = data["formula"] | |
| self.key_words = data["key_words"] | |
| self.structure = data["structure"] | |
| self.sub_components = data["sub_components"] | |
| self.source = data["source"] | |
| prop = {} | |
| for key in data["propriety"].keys(): | |
| prop[key] = [] | |
| read_prop = data["propriety"][key] | |
| for pro in read_prop: | |
| source = Source(pro["source"]["tipe"], | |
| pro["source"]["author_id"], | |
| pro["source"]["description"], | |
| pro["source"]["cite"]) | |
| r_pro = DBPropriety(pro["name"], pro["value"], source) | |
| prop[key].append(r_pro) | |
| self.propriety = prop | |
| self.author = data["author"] | |
| return self | |
| def from_c2db_jason(self, file_path): | |
| c2 = read_c2db_json(file_path) | |
| self.unique_id = from_c2db_unique_id(c2['structure.json']) | |
| self.formula = from_c2db_formula(c2['structure.json']) | |
| self.structure = from_c2db_structure(c2['structure.json']) | |
| self.source = { | |
| "name": "C2DB", | |
| "id": from_c2db_unique_id(c2['structure.json']), | |
| "file": file_path.split("/")[-1], | |
| "cite": "DOI 10.1088/2053-1583/aacfc1" | |
| } | |
| self.propriety = { | |
| "energy": [from_c2db_energy(c2['structure.json'])], | |
| "band_gap": [from_c2db_band_gap(c2)], | |
| "band_structure": [from_c2db_band_structure(c2)], | |
| "density_of_states": [from_c2db_density_of_states(c2)], | |
| } | |
| # Todo: | |
| self.key_words = process_chemical_formula(self.formula) | |
| self.sub_components = {} | |
| self.author = {"name": "c2db", | |
| "id": "c2db"} | |
| return self | |
| def from_jarvis_json(self, jarvis_id, jarvis_data=JARVIS_DB_path): | |
| self.unique_id = jarvis_id | |
| jr_data = read_jarvis(jarvis_data) | |
| jr = get_jarvis_instance(jr_data, jarvis_id) | |
| self.formula = from_jarvis_formula(jr) | |
| self.structure = from_jarvis_structure(jr) | |
| self.source = { | |
| "name": "Jarvis", | |
| "id": jarvis_id, | |
| "file": jarvis_data.split("/")[-1], | |
| "cite": "https://jarvis.nist.gov" | |
| } | |
| self.propriety = { | |
| "energy": [from_jarvis_energy(jr)], | |
| "band_gap": [from_jarvis_band_gap(jr)], | |
| "band_structure": [from_jarvis_band_structure(jr)], | |
| "density_of_states": [from_jarvis_density_of_states(jr)], | |
| } | |
| print("band_structure:", self.propriety) | |
| self.key_words = process_chemical_formula(self.formula) | |
| self.sub_components = {} | |
| self.author = {"name": "jarvis", | |
| "id": "jarvis"} | |
| return self | |
| def json_descript(self): | |
| propriety = {} | |
| for key in self.propriety.keys(): | |
| propriety[key] = [prop.json_descript() for prop in self.propriety[key] if prop is not None] | |
| data_instance = {"unique_id": self.unique_id, | |
| "formula": self.formula, | |
| "key_words": self.key_words, | |
| "source": self.source, | |
| "structure": self.structure, | |
| "sub_components": self.sub_components, | |
| "propriety": propriety, | |
| "author": self.author} | |
| return data_instance | |
| # inst = DBInstance().from_c2db_jason("/Users/voicutomut/Desktop/WS2-64090c9845f8_data.json") | |
| # print(inst.propriety["energy"][0].value) | |