def test_curvature2(testdir):
'''This test has two atoms spinning counter-clockwise around eachother. the
The radius (1/curvature) is less obviously pair_distance*sqrt(2)/2.
This is the simplest multi-body analytic curvature test.'''
name = 'test_curvature2'
radius = pair_distance * np.sqrt(2) / 2
atoms = Al_atom_pair(pair_distance)
atoms.set_velocities([[0, -1, 0], [0, 1, 0]])
dyn = ContourExploration(
atoms,
maxstep=1.0,
parallel_drift=0.0,
angle_limit=30,
trajectory=name + '.traj',
logfile=name + '.log',
)
print("Target Radius (1/curvature) {: .6f} Ang".format(radius))
for i in range(5):
dyn.run(30)
print('Radius (1/curvature) {: .6f} Ang'.format(1 / dyn.curvature))
assert radius == pytest.approx(1.0 / dyn.curvature, abs=2e-3)
def test_curvature1(testdir):
'''This basic test has an atom spinning counter-clockwise around a fixed
atom. The radius (1/curvature) must therefore be very
close the pair_distance.'''
name = 'test_curvature1'
radius = pair_distance
atoms = Al_atom_pair(pair_distance)
atoms.set_constraint(FixAtoms(indices=[0]))
atoms.set_velocities([[0, 0, 0], [0, 1, 0]])
dyn = ContourExploration(
atoms,
maxstep=1.5,
parallel_drift=0.0,
angle_limit=30,
trajectory=name + '.traj',
logfile=name + '.log',
)
print("Target Radius (1/curvature) {: .6f} Ang".format(radius))
for i in range(5):
dyn.run(30)
print('Radius (1/curvature) {: .6f} Ang'.format(1 / dyn.curvature))
assert radius == pytest.approx(1.0 / dyn.curvature, abs=2e-3)
def test_potentiostat(testdir):
'''This is very realistic and stringent test of the potentiostatic accuracy
with 32 atoms at ~235 meV/atom above the ground state.'''
name = 'test_potentiostat'
seed = 19460926
atoms = Al_block()
E0 = atoms.get_potential_energy()
atoms.rattle(stdev=0.18, seed=seed)
initial_energy = atoms.get_potential_energy()
rng = np.random.RandomState(seed)
MaxwellBoltzmannDistribution(atoms, temperature_K=300, rng=rng)
dyn = ContourExploration(
atoms,
**bulk_Al_settings,
energy_target=initial_energy,
rng=rng,
trajectory=name + '.traj',
logfile=name + '.log',
)
print("Energy Above Ground State: {: .4f} eV/atom".format(
(initial_energy - E0) / len(atoms)))
for i in range(5):
dyn.run(5)
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_potentiostat_no_fs(testdir):
'''This test ensures that the potentiostat is working even when curvature
extrapolation (use_fs) is turned off.'''
name = 'test_potentiostat_no_fs'
atoms = Al_atom_pair()
atoms.set_momenta([[0, -1, 0], [0, 1, 0]])
initial_energy = atoms.get_potential_energy()
dyn = ContourExploration(
atoms,
maxstep=0.2,
parallel_drift=0.0,
remove_translation=False,
energy_target=initial_energy,
potentiostat_step_scale=None,
use_frenet_serret=False,
trajectory=name + '.traj',
logfile=name + '.log',
)
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_logging(testdir):
seed = 19460926
atoms = Al_block()
atoms.rattle(stdev=0.18, seed=seed)
rng = np.random.RandomState(seed)
initial_energy = atoms.get_potential_energy()
name = 'test_logging'
traj_name = name + '.traj'
log_name = name + '.log'
dyn = ContourExploration(atoms,
**bulk_Al_settings,
rng=rng,
trajectory=traj_name,
logfile=log_name,
)
energy_target = initial_energy
dev = (atoms.get_potential_energy() - energy_target) / len(atoms)
energy_targets = [energy_target]
curvatures = [dyn.curvature]
stepsizes = [dyn.step_size]
deviation_per_atom = [dev]
# we shift the target_energy to ensure it's actaully being logged when it
# changes.
de = 0.001 * len(atoms)
# these print statements, mirror the log file.
# print(energy_target, dyn.curvature, dyn.step_size, dev)
for i in range(0, 5):
energy_target = initial_energy + de * i
dyn.energy_target = energy_target
dyn.run(1)
dev = (atoms.get_potential_energy() - energy_target) / len(atoms)
# print(energy_target, dyn.curvature, dyn.step_size, dev)
energy_targets.append(energy_target)
curvatures.append(dyn.curvature)
stepsizes.append(dyn.step_size)
deviation_per_atom.append(dev)
# Now we check the contents of the log file
# assert log file has correct length
with open(log_name) as fd:
length = len(fd.readlines())
assert length == 7, length
with io.Trajectory(traj_name, 'r') as traj, open(log_name, 'r') as fd:
# skip the first line because it's a small initialization step
lines = fd.readlines()[1:]
for i, (im, line) in enumerate(zip(traj, lines)):
lineparts = [float(part) for part in line.split()]
log_energy_target = lineparts[1]
assert 0 == pytest.approx(
log_energy_target - energy_targets[i], abs=1e-5)
log_energy = lineparts[2]
assert 0 == pytest.approx(
log_energy - im.get_potential_energy(), abs=1e-5)
log_curvature = lineparts[3]
assert 0 == pytest.approx(log_curvature - curvatures[i], abs=1e-5)
log_step_size = lineparts[4]
assert 0 == pytest.approx(log_step_size - stepsizes[i], abs=1e-5)
log_dev = lineparts[5]
assert 0 == pytest.approx(log_dev - deviation_per_atom[i], abs=1e-5)