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"""This test ensures that logging to a text file and to the trajectory file are
reporting the same values as in the ContourExploration object."""
import pytest
from ase.md.contour_exploration import ContourExploration
import numpy as np
from ase import io
from .test_ce_potentiostat import Al_block, bulk_Al_settings
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'
with ContourExploration(
atoms,
**bulk_Al_settings,
rng=rng,
trajectory=traj_name,
logfile=log_name,
) as dyn:
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)
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