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| import pandas as pd | |
| import os | |
| import periodictable | |
| from .vasp_utils import get_band_structure | |
| from .structure_propriety import DBPropriety, Source | |
| def get_atomic_number(element_name): | |
| # Find the element | |
| element = getattr(periodictable, element_name, None) | |
| # Check if the element exists | |
| if element is not None and hasattr(element, 'number'): | |
| return element.number | |
| else: | |
| return "Element not found" | |
| def read_jarvis(file_path): | |
| db = pd.read_json(file_path) | |
| return db | |
| def get_jarvis_instance(jr_data, jr_id): | |
| jarvis_el = jr_data[jr_data['jid'] == jr_id] | |
| return jarvis_el | |
| def from_jarvis_formula(jarvis_el): | |
| return jarvis_el["formula"].values[0] | |
| def from_jarvis_structure(jarvis_el): | |
| structure = { | |
| 'cell': jarvis_el["atoms"].values[0]['lattice_mat'], | |
| 'atoms': [get_atomic_number(e) for e in jarvis_el["atoms"].values[0]['elements']], | |
| 'positions': jarvis_el["atoms"].values[0]['coords'], | |
| 'pbc': [True, True, False] | |
| } | |
| return structure | |
| def from_jarvis_energy(jarvis_el): | |
| return None | |
| def from_jarvis_band_gap(jarvis_el): | |
| return None | |
| def from_jarvis_band_structure(jarvis_el): | |
| jid=jarvis_el["jid"].values[0] | |
| vasp_xml_path="DB/Databases/JARVIS/JARVIS2D/OPT-Bandst/{}/vasprun.xml".format(jid) | |
| if os.path.isfile(vasp_xml_path): | |
| try: | |
| band_structure, numerics=get_band_structure(vasp_xml_path) | |
| source = Source(tipe="computation", | |
| author_id="JARVIS", | |
| description={"calculator": "VASP", | |
| "calculator_files": vasp_xml_path, }, | |
| cite="https://jarvis.nist.gov") | |
| band_structure = DBPropriety(name="band_structure", | |
| value=numerics, | |
| source=source) | |
| return band_structure | |
| except: | |
| return None | |
| return None | |
| def from_jarvis_density_of_states(jarvis_el): | |
| return None | |
| # | |
| # file_path = "/Users/voicutomut/Documents/GitLab/bespoke-interface/DB_experiments/JARVIS2D/d2-12-12-2022.json" | |
| # jar = read_jarvis(file_path) | |
| # print(jar.head()) | |
| # jr = get_jarvis_instance(jar, "JVASP-76515") | |
| # | |
| # print(jr) | |
| # print(jr.head()) | |
| # print(from_jarvis_formula(jr)) | |
| # print(jr["atoms"].values[0]['cartesian']) | |
| # print(jr["atoms"].values[0].keys()) | |