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import numpy as np
import pytest
from ase import Atoms
@pytest.mark.calculator_lite()
def test_cutoff_skin(KIM, testdir):
"""
To test that the calculator handles skin and cutoffs correctly.
Specifically, note that the neighbor skin distance must be added onto
both the model influence distance *and* each of the model cutoffs. If
the skin is not added onto the cutoffs, then an atom lying in between
the largest cutoff and the skinned influence distance will not register
as a neighbor if it hasn't already.
The cutoff (and influence distance) for the model
ex_model_Ar_P_Morse_07C is 8.15 Angstroms and the default skin distance
when using the kimpy neighbor list library (which is the default when
using a KIM portable model with this calculator) is 0.2 times the cutoff
distance (1.63 Angstroms for this model). Here, we construct a dimer
with a separation falling just beyond the model cutoff but inside of the
skinned influence distance. We then compute the energy, which we expect
to be zero in any case. Next, we reduce the dimer separation by less
than the skin distance so that the atoms fall within the cutoff of one
another but without triggering a neighbor list rebuild. If the atom had
properly registered as a neighbor when it was outside of the cutoff but
still inside of the skinned influence distance, then the energy in this
case should be significantly far off from zero. However, if the atom
had failed to ever register as a neighbor, then we'll get zero once
again.
"""
calc = KIM("ex_model_Ar_P_Morse_07C")
# Create dimer with separation just beyond cutoff distance. We *want*
# these atoms to register as neighbors of one another since they fall
# within the skinned influence distance of 9.78 Angstroms.
model_cutoff = 8.15
skin_distance = 0.2 * model_cutoff
distance_orig = model_cutoff + 0.1 * skin_distance
atoms = Atoms("Ar2", positions=[[0, 0, 0], [distance_orig, 0, 0]])
atoms.calc = calc
# Get energy -- should be zero
e_outside_cutoff = atoms.get_potential_energy()
# Now reduce the separation distance to something well within the model
# cutoff -- should get something significantly non-zero
atoms.positions[1, 0] -= 0.5 * skin_distance
# Get new energy
e_inside_cutoff = atoms.get_potential_energy()
assert not np.isclose(e_outside_cutoff, e_inside_cutoff)
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