def structure2quippy(structure,
anonymize=False,
scale=False,
standardize=False,
primitivize=False,
symprec=1e-3,
from_dict=False):
'''
Convert pymatgen Structure to quippy Atoms
Args:
structure (pymatgen.core.Structure): pymatgen Structure object
anonymize (bool): replace all species with hydrogen
scale (bool): scale volume to 1 Å^3 / atom
standardize (bool): use spglib to standardize the structure
primitivize (bool): use spglib to standardize and primitivize the structure
symprec (float): symmetry tolerance factor (see spglib documentation)
Returns:
quippy.atoms.Atoms: quippy Atoms object
'''
if from_dict:
structure = Structure.from_dict(structure)
cell = structure2cell(structure, anonymize) # (matrix, positions, numbers)
if standardize or primitivize:
cell = standardize_cell(cell,
to_primitive=primitivize,
symprec=symprec)
if cell:
cell = list(cell)
else:
try:
# spglib can't make a primitive
return ase2qp(AseAtomsAdaptor.get_atoms(structure))
except ValueError as ve: # TODO: warn the user here maybe
return None # Must be either really f****d up or disordered
if scale:
cell = list(cell)
# cell[0] = matrix
volume = np.dot(np.cross(cell[0][0], cell[0][1]), cell[0][2])
# len(cell[2]) = n_atoms
cell[0] = cell[0] / np.cbrt(volume / len(cell[2]))
return ase2qp(
Atoms(cell=cell[0], positions=cell[1], numbers=list(cell[2]),
pbc=True))
def get(self):
parser = flask_restful.reqparse.RequestParser()
argument_names = [
'atoms', 'spkitMax', 'nocenters', 'gaussian_width', 'spkit',
'cutoff', 'cutoff_transition_width', 'nmax', 'lmax'
]
for argument_name in argument_names:
parser.add_argument(ARGUMENTS[argument_name])
args = parser.parse_args(strict=True)
args['atoms'] = atoms_utils.loads(args['atoms'])
args['atoms'] = ase2qp(args['atoms'])
args['spkitMax'] = json.loads(args['spkitMax'])
if not args['spkit']:
args['spkit'] = get_spkit(args['atoms'])
# args['atoms'] = [args['atoms']]
soaps = get_soap(**args)
# soaps = {key: value.tolist() for key, value in soaps.iteritems()}
soaps = soaps.tolist()
return flask.jsonify(soaps)
def get(self):
parser = flask_restful.reqparse.RequestParser()
argument_names = [
'atoms', 'nocenters', 'chem_channels', 'centerweight',
'gaussian_width', 'spkitMax', 'chemicalProjection',
'is_fast_average', 'cutoff', 'cutoff_transition_width', 'nmax',
'lmax'
]
for argument_name in argument_names:
parser.add_argument(ARGUMENTS[argument_name])
args = parser.parse_args(strict=True)
if args['spkitMax']:
args['spkitMax'] = json.loads(args['spkitMax'])
args['atoms'] = json.loads(args['atoms'])
args['atoms'] = [atoms_utils.loads(atoms) for atoms in args['atoms']]
args['atoms'] = [ase2qp(atoms) for atoms in args['atoms']]
soaps = get_Soaps(**args)
soaps = [{key: value.tolist()
for key, value in soap.iteritems()} for soap in soaps]
return flask.jsonify(soaps)
def get_quippy_atoms(self):
ase_atoms = self.inputs.anonymous_aiida_structure.get_ase()
quippy_atoms = ase2qp(ase_atoms)
self.ctx.quippy_atoms = quippy_atoms
import sys
sys.path.insert(0, '/home/app/glosim2')
from ase import Atoms
import numpy as np
from libmatch.soap import get_Soaps
from libmatch.utils import ase2qp
# Read structures and convert to ase Atoms
# raw_structures =
# ase_atoms =
quippy_atoms = [ase2qp(ase_atoms_instance) for ase_atoms_instance in ase_atoms]
# atoms: [quippy.Atoms]
# nocenters: None or [Atomic numbers to ignore]
# chem_channels: bool (whether or not to include chemical combinations)
# centerweight: float (weight of gaussian on central atom)
# gaussian_width: float (sigma of gaussian)
# cutoff: float (integration cutoff distance)
# cutoff_transition_width: float (width of sigmoid used to smooth integration cutoff)
# nmax: int (number of radial basis functions)
# lmax: int (number of spherical harmonics)
# spkitMax: dict {atomic numbers: max. number of occurrences in a structure in the set atoms}
# nprocess: int (number of subprocesses spawned)
# chemicalProjection: ???
# dispbar: bool ???
# is_fast_average: None or bool (use fast averaging to calculate average soap; no average calculated if None)
soaps = get_Soaps(atoms=quippy_atoms,
nocenters=None,
chem_channels=False,
centerweight=1.0,