def test_potentiostat():
size = 2
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Al',
size=(size, size, size),
pbc=True)
atoms.set_calculator(EMT())
E0 = atoms.get_potential_energy()
atoms.rattle(stdev=0.18, seed=312)
md_temp = 300
rng = np.random.RandomState(60622)
MaxwellBoltzmannDistribution(atoms, temperature_K=md_temp, rng=rng)
initial_energy = atoms.get_potential_energy()
print("Energy Above Ground State: {: .4f} eV/atom".format(
(initial_energy - E0) / len(atoms)))
name = 'test_potentiostat'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = contour_exploration(
atoms,
maxstep=1.0,
parallel_drift=0.05,
remove_translation=True,
force_parallel_step_scale=None,
energy_target=initial_energy,
angle_limit=20,
use_tangent_curvature=False,
#trajectory = traj_name,
#logfile = log_name,
)
for i in range(5):
dyn.run(10)
energy_error = (atoms.get_potential_energy() -
initial_energy) / len(atoms)
print('Potentiostat Error {: .4f} eV/atom'.format(energy_error))
assert 0 == pytest.approx(energy_error, abs=0.01)
def test_momentum_conservation2():
d = 1.9
atoms = Atoms('Al4',
positions=[[d, 0, 0], [0, d, 0], [-d, 0, 0], [0, -d, 0]])
atoms.center(vacuum=10)
atoms.calc = EMT()
#atoms.set_momenta([[1,0,0],[0,0,0],[0,0,0],[0,0,0]])
atoms.set_momenta([[0, 1, 0], [-1, 0, 0], [0, -1, 0], [1, 0, 0]])
atoms.set_momenta(atoms.get_momenta() * 1 + np.array([0, 0, 4]))
momentum_target = atoms.get_momenta().sum(axis=0)
atoms.set_calculator(EMT())
initial_energy = atoms.get_potential_energy()
#io.write('debug.traj', atoms)
print("Target Momentum: [{: .6f} {: .6f} {: .6f}]".format(
*tuple(momentum_target)))
name = 'test_momentum_conservation2'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = contour_exploration(
atoms,
maxstep=1.0,
parallel_drift=0.0,
remove_translation=False,
force_parallel_step_scale=None,
energy_target=initial_energy,
angle_limit=15,
use_tangent_curvature=False,
trajectory=traj_name,
#logfile = log_name,
)
for i in range(10):
dyn.run(30)
momentum = atoms.get_momenta().sum(axis=0)
print("Momentum: [{: .6f} {: .6f} {: .6f}]".format(*tuple(momentum)))
assert 0 == pytest.approx(np.linalg.norm(momentum_target - momentum),
abs=1e2)
def test_momentum_conservation1():
pair_distance = 2.6
atoms = Atoms('AlAl',
positions=[[0, -pair_distance / 2, 0],
[0, pair_distance / 2, 0]])
atoms.center(vacuum=10)
atoms.calc = EMT()
atoms.set_momenta([[1, 0, 0], [0, 0, 0]])
momentum_target = atoms.get_momenta().sum(axis=0)
atoms.set_calculator(EMT())
initial_energy = atoms.get_potential_energy()
print("Target Momentum: [{: .6f} {: .6f} {: .6f}]".format(
*tuple(momentum_target)))
name = 'test_momentum_conservation1'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = contour_exploration(
atoms,
maxstep=1.0,
parallel_drift=0.0,
remove_translation=False,
force_parallel_step_scale=None,
energy_target=initial_energy,
angle_limit=15,
use_tangent_curvature=False,
trajectory=traj_name,
#logfile = log_name,
)
for i in range(5):
dyn.run(30)
momentum = atoms.get_momenta().sum(axis=0)
print("Momentum: [{: .6f} {: .6f} {: .6f}]".format(*tuple(momentum)))
assert 0 == pytest.approx(np.linalg.norm(momentum_target - momentum),
abs=1e-0)
def test_kappa2():
pair_distance = 2.6
radius = pair_distance * np.sqrt(2) / 2
atoms = Atoms('AlAl',
positions=[[-pair_distance / 2, 0, 0],
[pair_distance / 2, 0, 0]])
atoms.center(vacuum=10)
atoms.calc = EMT()
atoms.set_momenta([[0, -10, 0], [0, 10, 0]])
atoms.set_calculator(EMT())
initial_energy = atoms.get_potential_energy()
print("Target Radius (1/kappa) {: .6f} Ang".format(radius))
name = 'test_kappa2'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = contour_exploration(
atoms,
maxstep=1.0,
parallel_drift=0.0,
remove_translation=False,
force_parallel_step_scale=None,
energy_target=initial_energy,
angle_limit=15,
use_tangent_curvature=False,
#trajectory = traj_name,
#logfile = log_name,
)
for i in range(5):
dyn.run(30)
print('Radius (1/kappa) {: .6f} Ang'.format(1 / dyn.kappa))
assert 0 == pytest.approx(radius - 1 / dyn.kappa, abs=1e-3)
def test_potentiostat_no_FS():
radius = 2.6
atoms = Atoms('AlAl', positions=[[-radius / 2, 0, 0], [radius / 2, 0, 0]])
atoms.center(vacuum=10)
atoms.calc = EMT()
atoms.set_momenta([[0, -10, 0], [0, 10, 0]])
atoms.set_calculator(EMT())
initial_energy = atoms.get_potential_energy()
print("Pair distance {: .6f} Ang".format(radius))
name = 'test_potentiostat_no_FS'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = contour_exploration(
atoms,
maxstep=0.2,
parallel_drift=0.0,
remove_translation=False,
force_parallel_step_scale=None,
energy_target=initial_energy,
use_FS=False,
#trajectory = traj_name,
#logfile = log_name,
)
for i in range(5):
dyn.run(10)
energy_error = (atoms.get_potential_energy() -
initial_energy) / len(atoms)
print('Potentiostat Error {: .4f} eV/atom'.format(energy_error))
assert 0 == pytest.approx(energy_error, abs=0.01)