def testCuFcc(self):
cu_fcc = bulk('Cu', 'fcc', a=3.6, cubic=True)
config = TurboSOAPSpecie(rcut=2.5)
turbosoap = TurboSOAP(species = {'Cu': config}, lmax=8)
turbosoap_fcc = turbosoap.create(cu_fcc, periodic=True)
self.assertEqual(turbosoap_fcc.shape[0], len(cu_fcc))
self.assertEqual(turbosoap_fcc.shape[1], 324)
self.assertAlmostEqual(np.dot(turbosoap_fcc[0], turbosoap_fcc[1]), 1.0, delta=1e-7)
def testWaterMolecule(self):
H_config = TurboSOAPSpecie(rcut=5.0, nmax=8, buffer=0.5, atom_sigma_r = 0.3, atom_sigma_t = 0.5,
atom_sigma_r_scaling = 0.05, atom_sigma_t_scaling = 0.025)
O_config = TurboSOAPSpecie(rcut=5.0, nmax=8, buffer=0.5, atom_sigma_r = 0.2, atom_sigma_t = 0.3,
atom_sigma_r_scaling = 0.03, atom_sigma_t_scaling = 0.020)
turbosoap = TurboSOAP(species = {'H': H_config, 'O': O_config}, lmax=10)
water = molecule("H2O")
turbosoap_water = turbosoap.create(water)
self.assertAlmostEqual(np.dot(turbosoap_water[1], turbosoap_water[2]), 1.0, delta=1e-7)
self.assertAlmostEqual(np.dot(turbosoap_water[0], turbosoap_water[1]), 0.0, delta=1e-3)
def testWaterMoleculeSymbols(self):
turbosoap = TurboSOAP(species = {'H': None, 'O': None}, lmax=8)
water = molecule("H2O")
turbosoap_water = turbosoap.create(water)
self.assertEqual(turbosoap_water.shape[0], 3)
self.assertEqual(turbosoap_water.shape[1], 1224)
def testRcut(self):
config = TurboSOAPSpecie(rcut=0.9)
with self.assertRaises(ValueError):
turbosoap = TurboSOAP(species = {'H': config, 'O': None}, lmax=8)
def testMultipleSpeciesDefs(self):
with self.assertRaises(ValueError):
turbosoap = TurboSOAP(species = {'G': None, 'O': None}, lmax=8)
with self.assertRaises(ValueError):
turbosoap = TurboSOAP(species = {'G': None, 'O': None}, lmax=8)
def testSpeciesMissing(self):
turbosoap = TurboSOAP(species = {'H': None}, lmax=8)
water = molecule("H2O")
with self.assertRaises(ValueError):
turbosoap_water = turbosoap.create(water)
def testInvalidSymbols(self):
with self.assertRaises(ValueError):
turbosoap = TurboSOAP(species = {'G': None, 'O': None}, lmax=8)
def testWaterMoleculeAtomicNumbers(self):
turbosoap = TurboSOAP(species = {1: None, 8: None}, lmax=8)
water = molecule("H2O")
turbosoap_water = turbosoap.create(water)
self.assertEqual(turbosoap_water.shape[0], 3)
self.assertEqual(turbosoap_water.shape[1], 1224)
from dscribe.descriptors import TurboSOAP
turbosoap = TurboSOAP(species={'H': None, 'O': None}, lmax=8)
from ase.build import molecule
#Water molecule
water = molecule("H2O")
#Create TurboSOAP output for water
turbosoap_water = turbosoap.create(water)
print(turbosoap_water.shape)
print(turbosoap_water)
from dscribe.descriptors.turbosoap import TurboSOAPSpecie
# More control on each species
H_config = TurboSOAPSpecie(rcut=5.0,
nmax=8,
buffer=0.5,
atom_sigma_r=0.3,
atom_sigma_t=0.5,
atom_sigma_r_scaling=0.05,
atom_sigma_t_scaling=0.025)
O_config = TurboSOAPSpecie(rcut=5.0,
nmax=8,
buffer=0.5,
atom_sigma_r=0.2,
atom_sigma_t=0.3,
atom_sigma_r_scaling=0.03,