def test_load():
xyz_path = os.path.join(here, 'data', 'configs.xyz')
configs = ConfigurationSet()
configs.load(xyz_path)
assert len(configs) == 2
# Should default to uncharged singlet
for config in configs:
assert config.box is not None
assert config.charge == 0
assert config.mult == 1
zn_aq = System(gt.Ion('Zn', charge=2), box_size=[12, 12, 12])
zn_aq.add_solvent('h2o', n=52)
configs = ConfigurationSet()
configs.load(xyz_path, system=zn_aq)
for config in configs:
assert config.box is not None
assert config.charge == 2
assert config.mult == 1
configs = ConfigurationSet()
configs.load(xyz_path, charge=2)
for config in configs:
assert config.box is not None
assert config.charge == 2
assert config.mult == 1
with open('tmp.xyz', 'w') as test_xyz:
print('1\n', file=test_xyz)
# Should fail to load with no atoms in the xyz file
configs = ConfigurationSet()
with pytest.raises(LoadingFailed):
configs.load(filename='tmp.xyz')
os.remove('tmp.xyz')
from gaptrain.loss import RMSE
from gaptrain.configurations import ConfigurationSet
from gaptrain.systems import System
import numpy as np
system = System(box_size=[10, 10, 10])
system.add_solvent('h2o', n=3)
def test_rmse():
configs = ConfigurationSet()
for _ in range(2):
configs += system.random()
configs[0].energy = 1
configs[1].energy = 2
true_configs = configs.copy()
true_configs[0].energy = 1.1
true_configs[1].energy = 1.8
rmse = RMSE(configs, true_configs)
expected = np.sqrt(((1 - 1.1)**2 + (2 - 1.8)**2) / 2.0)
assert np.abs(rmse.energy - expected) < 1E-6