How to use the mendeleev.get_all_elements function in mendeleev

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github SUNCAT-Center / CatalysisHubBackend / apps / prototypeSearch / ingest.py View on Github external
import pprint
import sys
import time
import statistics

from sqlalchemy.sql.expression import Tuple

import models
import mendeleev

# create table if it hasn't already happened
models.metadata.create_all(models.engine)
models.session.commit()

scarcity_data = {}
for element in mendeleev.get_all_elements():
    scarcity_data[element.symbol] = 1./(element.abundance_crust or 1e-9)


#@profile
def bulk_upsert(db, geometries):
    geometries_dict = {
            (geometry.repository, geometry.handle): geometry
                 for geometry in geometries
            }
    existing = db.Geometry.query.filter(
            Tuple(db.Geometry.repository, db.Geometry.handle).in_(
                (geometry.repository, geometry.handle)
                for geometry in geometries
                )
            )
    for each in existing.all():
github SUNCAT-Center / CatalysisHubBackend / apps / catKitDemo / __init__.py View on Github external
"turbomole",
    "v-sim",
    "vasp",
    "xsf",
    "xyz"]


# safe settings for non-cubic large gas phase cell
GAS_PHASE_CELL = [15, 16, 17]

atomic_radii = {
    element.symbol:
    (element.atomic_radius
     or element.covalent_radius_cordero
     or element.covalent_radius_pyykko)
    for element in mendeleev.get_all_elements()}


class MockRequest(object):

    def __init__(self, args):
        self.args = json.dumps(args)

    def __repr__(self):
        return '[MockRequest] ' + pprint.pformat(self.args)


@catKitDemo.route('/generate_bulk_cif/', methods=['GET', 'POST'])
def generate_bulk_cif(request=None, return_atoms=False):
    request = flask.request if request is None else request
    if isinstance(request.args, str):
        request.args = json.loads(request.args)

mendeleev

Pythonic periodic table of elements

MIT
Latest version published 1 month ago

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