def get_soap_fingerprint(self):
qp = self.ctx.quippy_atoms
soapargs = self.inputs.soapargs.get_dict()
spkit = get_spkit(qp)
soap = get_soap(qp, spkit=spkit,
spkitMax=self.inputs.spkit_max.get_dict(), **kwargs)
self.out('soap', Dict(soap))
def get_raw_soap_wrapper(kwargs):
fpointer = kwargs.pop('fpointer')
# need to copy the frame to avoid seg fault in quip if rerun the procedure on the same name space
frame = qp.Atoms(fpointer=fpointer).copy()
kwargs.update({'atoms': frame, 'spkit': get_spkit(frame)})
idx = kwargs.pop('idx')
return (idx, get_soap(**kwargs))
def get_soap_fingerprint(self):
qp = self.ctx.quippy_atoms
soapargs = self.inputs.soapargs.get_dict()
spkit = get_spkit(qp)
soap = get_soap(qp, spkit=spkit,
spkitMax=self.inputs.spkit_max.get_dict(), **soapargs)
soap_array = np.array(soap.values())
self.out('soap', ArraData(soap_array))
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_raw_soap_dim(frame, soap_params):
raw_soap = get_soap(frame, spkit=get_spkit(frame), **soap_params)
Ncenter, Ncoef = raw_soap.shape
return Ncoef