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"""Tests for ``Tersoff``."""
import numpy as np
import pytest
from ase import Atoms
from ase.build import bulk
from ase.calculators.calculator import PropertyNotImplementedError
from ase.calculators.fd import (
calculate_numerical_forces,
calculate_numerical_stress,
)
from ase.calculators.tersoff import Tersoff, TersoffParameters
@pytest.fixture
def si_parameters():
"""Fixture providing the Silicon parameters.
Parameters taken from: Tersoff, Phys Rev B, 37, 6991 (1988)
"""
return {
('Si', 'Si', 'Si'): TersoffParameters(
A=3264.7,
B=95.373,
lambda1=3.2394,
lambda2=1.3258,
lambda3=1.3258,
beta=0.33675,
gamma=1.00,
m=3.00,
n=22.956,
c=4.8381,
d=2.0417,
h=0.0000,
R=3.00,
D=0.20,
)
}
@pytest.fixture(name='atoms_si')
def fixture_atoms_si(
si_parameters: dict[tuple[str, str, str], TersoffParameters],
) -> Atoms:
"""Make Atoms for Si with a small displacement on the first atom."""
atoms = bulk('Si', a=5.43, cubic=True)
# pertubate first atom to get substantial forces
atoms.positions[0] += [0.03, 0.02, 0.01]
atoms.calc = Tersoff(si_parameters)
return atoms
def test_initialize_from_params_from_dict(si_parameters):
"""Test initializing Tersoff calculator from dictionary of parameters."""
calc = Tersoff(si_parameters)
assert calc.parameters == si_parameters
diamond = bulk('Si', 'diamond', a=5.43)
diamond.calc = calc
potential_energy = diamond.get_potential_energy()
np.testing.assert_allclose(potential_energy, -9.260818674314585, atol=1e-8)
def test_set_parameters(
si_parameters: dict[tuple[str, str, str], TersoffParameters],
) -> None:
"""Test updating parameters of the Tersoff calculator."""
calc = Tersoff(si_parameters)
key = ('Si', 'Si', 'Si')
calc.set_parameters(key, m=2.0)
assert calc.parameters[key].m == 2.0
calc.set_parameters(key, R=2.90, D=0.25)
assert calc.parameters[key].R == 2.90
assert calc.parameters[key].D == 0.25
new_params = TersoffParameters(
m=si_parameters[key].m,
gamma=si_parameters[key].gamma,
lambda3=si_parameters[key].lambda3,
c=si_parameters[key].c,
d=si_parameters[key].d,
h=si_parameters[key].h,
n=si_parameters[key].n,
beta=si_parameters[key].beta,
lambda2=si_parameters[key].lambda2,
B=si_parameters[key].B,
R=3.00, # Reset cutoff radius
D=si_parameters[key].D,
lambda1=si_parameters[key].lambda1,
A=si_parameters[key].A,
)
calc.set_parameters(key, params=new_params)
assert calc.parameters[key] == new_params
def test_isolated_atom(si_parameters: dict) -> None:
"""Test if an isolated atom can be computed correctly."""
atoms = Atoms('Si')
atoms.calc = Tersoff(si_parameters)
energy = atoms.get_potential_energy()
energies = atoms.get_potential_energies()
forces = atoms.get_forces()
np.testing.assert_almost_equal(energy, 0.0)
np.testing.assert_allclose(energies, [0.0], rtol=1e-5)
np.testing.assert_allclose(forces, [[0.0] * 3], rtol=1e-5)
with pytest.raises(PropertyNotImplementedError):
atoms.get_stress()
def test_unary(atoms_si: Atoms) -> None:
"""Test if energy, forces, and stress of a unary system agree with LAMMPS.
The reference values are obtained in the following way.
>>> from ase.calculators.lammpslib import LAMMPSlib
>>>
>>> atoms = bulk('Si', a=5.43, cubic=True)
>>> atoms.positions[0] += [0.03, 0.02, 0.01]
>>> lmpcmds = ['pair_style tersoff', 'pair_coeff * * Si.tersoff Si']
>>> atoms.calc = LAMMPSlib(lmpcmds=lmpcmds)
>>> energy = atoms.get_potential_energy()
>>> energies = atoms.get_potential_energies()
>>> forces = atoms.get_forces()
>>> stress = atoms.get_stress()
"""
energy_ref = -37.03237572778589
energies_ref = [
-4.62508202,
-4.62242901,
-4.63032346,
-4.63028909,
-4.63037555,
-4.63147495,
-4.63040683,
-4.63199482,
]
forces_ref = [
[-4.63805736e-01, -3.17112011e-01, -1.79345801e-01],
[+2.34142607e-01, +2.29060580e-01, +2.24142706e-01],
[-2.79544489e-02, +1.31289732e-03, +3.99485914e-04],
[+1.85144670e-02, +1.48017753e-02, +8.47421196e-03],
[+2.06558877e-03, -1.86613107e-02, +3.98039278e-04],
[+8.68756690e-02, -5.15405628e-02, +7.32472691e-02],
[+2.06388309e-03, +1.30960793e-03, -9.30764103e-03],
[+1.48097970e-01, +1.40829025e-01, -1.18008270e-01],
]
stress_ref = [
-0.00048610,
-0.00056779,
-0.00061684,
-0.00342602,
-0.00231541,
-0.00124569,
]
energy = atoms_si.get_potential_energy()
energies = atoms_si.get_potential_energies()
forces = atoms_si.get_forces()
stress = atoms_si.get_stress()
np.testing.assert_almost_equal(energy, energy_ref)
np.testing.assert_allclose(energies, energies_ref, rtol=1e-5)
np.testing.assert_allclose(forces, forces_ref, rtol=1e-5)
np.testing.assert_allclose(stress, stress_ref, rtol=1e-5)
def test_binary(datadir) -> None:
"""Test if energy, forces, and stress of a binary system agree with LAMMPS.
The reference values are obtained in the following way.
>>> from ase.calculators.lammpslib import LAMMPSlib
>>>
>>> atoms = bulk('Si', a=5.43, cubic=True)
>>> atoms.symbols[1] = 'C'
>>> atoms.symbols[2] = 'C'
>>> atoms.positions[0] += [0.03, 0.02, 0.01]
>>> lmpcmds = ['pair_style tersoff', 'pair_coeff * * SiC.tersoff Si C']
>>> atoms.calc = LAMMPSlib(lmpcmds=lmpcmds)
>>> energy = atoms.get_potential_energy()
>>> energies = atoms.get_potential_energies()
>>> forces = atoms.get_forces()
>>> stress = atoms.get_stress()
"""
atoms = bulk('Si', a=5.43, cubic=True)
atoms.symbols[1] = 'C'
atoms.symbols[2] = 'C'
# pertubate first atom to get substantial forces
atoms.positions[0] += [0.03, 0.02, 0.01]
potential_file = datadir / 'tersoff' / 'SiC.tersoff'
atoms.calc = Tersoff.from_lammps(potential_file)
energy_ref = -28.780184609451915
energies_ref = [
-4.33637575,
-2.02218449,
-1.80044260,
-4.12192108,
-4.12650203,
-4.12473794,
-4.12677193,
-4.12124880,
]
forces_ref = [
[+6.40479511, +6.64830387, +6.83733140],
[+6.93259841, -7.29932178, -7.32986722],
[-7.09646214, +7.17384006, +7.15478087],
[-6.63906798, -6.62943844, -6.64034900],
[-6.48323569, +6.55237593, -6.52463929],
[+6.64668748, +6.56474714, -6.55390547],
[-6.47026652, -6.50615747, +6.53977908],
[+6.70495132, -6.50434930, +6.51686963],
]
stress_ref = [
+0.35188635,
+0.35366730,
+0.35444532,
-0.11629806,
+0.11665436,
+0.11668285,
]
energy = atoms.get_potential_energy()
energies = atoms.get_potential_energies()
forces = atoms.get_forces()
stress = atoms.get_stress()
np.testing.assert_almost_equal(energy, energy_ref)
np.testing.assert_allclose(energies, energies_ref, rtol=1e-5)
np.testing.assert_allclose(forces, forces_ref, rtol=1e-5)
np.testing.assert_allclose(stress, stress_ref, rtol=1e-5)
def test_forces_and_stress(atoms_si: Atoms) -> None:
"""Test if analytical forces and stress agree with numerical ones."""
forces = atoms_si.get_forces()
numerical_forces = calculate_numerical_forces(atoms_si, eps=1e-5)
np.testing.assert_allclose(forces, numerical_forces, atol=1e-5)
stress = atoms_si.get_stress()
numerical_stress = calculate_numerical_stress(atoms_si, eps=1e-5)
np.testing.assert_allclose(stress, numerical_stress, atol=1e-5)
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