def test_box_expansion():
h2o = gt.System(box_size=[7, 7, 7])
h2o.add_solvent('h2o', n=5)
ase_atoms = h2o.random().ase_atoms()
intra = gt.GAP('intra')
intra.mol_idxs = [[3*j + i for i in range(3)] for j in range(5)]
calc = IICalculator(intra=intra,
inter=gt.GAP('iter'))
new_atoms = calc.expanded_atoms(atoms=ase_atoms)
from timeit import repeat
print('Expansion runs in ',
min(repeat(lambda: calc.expanded_atoms(atoms=ase_atoms),
number=100))/100,
's')
write('tmp.xyz', new_atoms)
ade_mol = ade.Molecule('tmp.xyz')
assert ade_mol.distance(0, 1) < 2 # Å
assert ade_mol.distance(0, 3) > 5 # Å
os.remove('tmp.xyz')
def test_gap_train():
system = gt.System(box_size=[10, 10, 10])
training_data = gt.Data(name='test')
training_data.load(system=system,
filename=os.path.join(here, 'data', 'rnd_training.xyz'))
assert len(training_data) == 10
assert len(training_data[0].atoms) == 31
if 'GT_GAP' not in os.environ or not os.environ['GT_GAP'] == 'True':
return
# Run GAP train with the training data
gap = gt.GAP(name='test', system=system)
gap.train(training_data)
