def equilibrated(asap3, berendsenparams):
"""Make an atomic system with equilibrated temperature and pressure."""
rng = np.random.RandomState(42)
with seterr(all='raise'):
print()
# Must be big enough to avoid ridiculous fluctuations
atoms = bulk('Au', cubic=True).repeat((3, 3, 3))
#a[5].symbol = 'Ag'
print(atoms)
atoms.calc = asap3.EMT()
MaxwellBoltzmannDistribution(atoms,
temperature_K=100,
force_temp=True,
rng=rng)
Stationary(atoms)
assert abs(atoms.get_temperature() - 100) < 0.0001
md = NPTBerendsen(atoms,
timestep=20 * fs,
logfile='-',
loginterval=200,
**berendsenparams['npt'])
# Equilibrate for 20 ps
md.run(steps=1000)
T = atoms.get_temperature()
pres = -atoms.get_stress(
include_ideal_gas=True)[:3].sum() / 3 / GPa * 10000
print("Temperature: {:.2f} K Pressure: {:.2f} bar".format(T, pres))
return atoms
def __init__(self, atoms, timestep, temperature, taut=0.5e3,
pressure=1.01325, taup=1e3,
compressibility=4.57e-5, fixcm=True, trajectory=None,
**kwargs):
NPTBerendsen.__init__(self, atoms, timestep, temperature, taut,
pressure, taup,
compressibility, fixcm, trajectory)
OTF.__init__(self, **kwargs)
self.md_engine = 'NPTBerendsen'
def testWithNumericalStressWithPBCEnabled(self):
# Run NPT dynamics for some steps and periodically check that the
# numerical and analytical stresses agree up to a given
# absolute difference
filename = os.path.join(
path, '../tools/generate-unit-test-expect/others/Benzene.json')
benzene = read(filename)
# set velocities to a very small value to avoid division by zero
# warning due to initial zero temperature.
#
# Note that there are 4 benzene molecules, thus, 48 atoms in
# Benzene.json
benzene.set_velocities(np.full((48, 3), 1e-15))
calculator = self.model.ase()
benzene.set_calculator(calculator)
dyn = NPTBerendsen(benzene,
timestep=0.1 * units.fs,
temperature=300 * units.kB,
taut=0.1 * 1000 * units.fs,
pressure=1.01325,
taup=1.0 * 1000 * units.fs,
compressibility=4.57e-5)
def test_stress():
stress = benzene.get_stress()
numerical_stress = calculator.calculate_numerical_stress(benzene)
self.assertEqual(stress, numerical_stress)
dyn.attach(test_stress, interval=30)
dyn.run(120)
def testWithNumericalStressWithPBCEnabled(self):
filename = os.path.join(path, '../tools/generate-unit-test-expect/others/Benzene.cif')
benzene = read(filename)
calculator = self.model.ase()
benzene.set_calculator(calculator)
dyn = NPTBerendsen(benzene, timestep=0.1 * units.fs,
temperature=300 * units.kB,
taut=0.1 * 1000 * units.fs, pressure=1.01325,
taup=1.0 * 1000 * units.fs, compressibility=4.57e-5)
def test_stress():
stress = benzene.get_stress()
numerical_stress = calculator.calculate_numerical_stress(benzene)
diff = torch.from_numpy(stress - numerical_stress).abs().max().item()
self.assertLess(diff, tol)
dyn.attach(test_stress, interval=30)
dyn.run(120)