def test_c2pk_cell_opt() -> None:
"""Test CP2K cell optimization calculations with the :class:`CP2K_MM` class."""
mol = Molecule(PATH / 'cspbbr3_3d.xyz')
s = Settings()
s.specific.cp2k += cell_opt.specific.cp2k_mm.copy()
s.specific.cp2k.motion.cell_opt.max_iter = 10
s.specific.cp2k.motion.print['forces low'].filename = ''
s.gmax = [22, 22, 22]
s.cell_parameters = [25.452, 35.995, 24.452]
s.charge = {
'param': 'charge',
'Cs': 0.2,
'Pb': 0.4,
'Br': -0.2,
}
s.lennard_jones = {
'param': ('sigma', 'epsilon'),
'unit': ('nm', 'kjmol'),
'Cs Cs': (0.585, 1),
'Cs Pb': (0.510, 1),
'Br Se': (0.385, 1),
'Pb Pb': (0.598, 1),
'Br Pb': (0.290, 1),
'Br Br': (0.426, 1),
}
job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_cell_opt')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
def test_prm_to_df() -> None:
"""Tests for :func:`prm_to_df`."""
s = Settings()
s.lennard_jones = {
'param': ('epsilon', 'sigma'),
'unit': ('kcalmol', 'angstrom'),
'Cs': (1, 1),
'Cd': (2, 2),
'O': (3, 3),
'H': (4, 4)
}
ref = {
'param': {
'epsilon': 'epsilon',
'sigma': 'sigma'
},
'unit': {
'epsilon': 'kcalmol',
'sigma': 'angstrom'
},
'Cs': {
'epsilon': 1.0,
'sigma': 1.0
},
'Cd': {
'epsilon': 2.0,
'sigma': 2.0
},
'O': {
'epsilon': 3.0,
'sigma': 3.0
},
'H': {
'epsilon': 4.0,
'sigma': 4.0
}
}
prm_to_df(s)
assertion.eq(s['lennard_jones'].to_dict(), ref)
# The 'param' key is missing
s2 = {'lennard-jones': {'Cs': (1, 2)}}
assertion.assert_(prm_to_df, s2, exception=KeyError)
def test_c2pk_cell_opt_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
mol = Molecule(PATH / 'cspbbr3_3d.xyz')
s = Settings()
s.specific.cp2k += cell_opt.specific.cp2k_mm.copy()
s.specific.cp2k.motion.cell_opt.max_iter = 10
s.specific.cp2k.motion.print['forces low'].filename = ''
s.gmax = [22, 22, 22]
s.cell_parameters = [25.452, 35.995, 24.452]
s.charge = {
'param': 'charge',
'Cs': 0.2,
'Pb': 0.4,
'Br': -0.2,
}
s.lennard_jones = {
'param': ('sigma', 'epsilon'),
'unit': ('nm', 'kjmol'),
'Cs Cs': (0.585, 1),
'Cs Pb': (0.510, 1),
'Br Se': (0.385, 1),
'Pb Pb': (0.598, 1),
'Br Pb': (0.290, 1),
'Br Br': (0.426, 1),
}
job = cp2k_mm(s, mol)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_cell_opt")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
ref_volume = np.load(PATH / 'volume.npy')
ref_coordinates = np.load(PATH / 'coordinates.npy')
ref_forces = np.load(PATH / 'forces.npy')
ref_lattice = np.load(PATH / 'lattice.npy')
np.testing.assert_allclose(result.volume, ref_volume)
np.testing.assert_allclose(result.coordinates, ref_coordinates)
np.testing.assert_allclose(result.forces, ref_forces)
np.testing.assert_allclose(result.lattice, ref_lattice)