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# fmt: off
import numpy as np
import pytest
from scipy.optimize import check_grad
from ase import Atoms
from ase.build import bulk
from ase.calculators.fd import (
calculate_numerical_forces,
calculate_numerical_stress,
)
from ase.calculators.morse import MorsePotential, fcut, fcut_d
from ase.vibrations import Vibrations
De = 5.
Re = 3.
rho0 = 2.
def test_gs_minimum_energy():
atoms = Atoms('H2', positions=[[0, 0, 0], [0, 0, Re]])
atoms.calc = MorsePotential(epsilon=De, r0=Re)
assert atoms.get_potential_energy() == -De
def test_gs_vibrations(testdir):
# check ground state vibrations
atoms = Atoms('H2', positions=[[0, 0, 0], [0, 0, Re]])
atoms.calc = MorsePotential(epsilon=De, r0=Re, rho0=rho0)
vib = Vibrations(atoms)
vib.run()
def test_cutoff():
# check that fcut_d is the derivative of fcut
r1 = 2.0
r2 = 3.0
r = np.linspace(r1 - 0.5, r2 + 0.5, 100)
for R in r:
assert check_grad(fcut, fcut_d, np.array([R]), r1, r2) < 1e-5
def test_forces_and_stress():
atoms = bulk('Cu', cubic=True)
atoms.calc = MorsePotential(A=4.0, epsilon=1.0, r0=2.55)
atoms.rattle(0.1)
forces = atoms.get_forces()
numerical_forces = calculate_numerical_forces(atoms, eps=1e-5)
np.testing.assert_allclose(forces, numerical_forces, atol=1e-5)
stress = atoms.get_stress()
numerical_stress = calculate_numerical_stress(atoms, eps=1e-5)
np.testing.assert_allclose(stress, numerical_stress, atol=1e-5)
def fake_neighbor_list(*args, **kwargs):
raise RuntimeError('test_neighbor_list')
def test_override_neighbor_list():
with pytest.raises(RuntimeError, match='test_neighbor_list'):
atoms = bulk('Cu', cubic=True)
atoms.calc = MorsePotential(A=4.0, epsilon=1.0, r0=2.55,
neighbor_list=fake_neighbor_list)
_ = atoms.get_potential_energy()
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