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_c2pk_npt_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = Settings()
job = cp2k_mm(s, None)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_npt")
result = run_mocked(job)
ref_pressure = np.load(PATH / 'pressure.npy')
np.testing.assert_allclose(result.pressure, ref_pressure)
def test_c2pk_md_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = SETTINGS.copy()
s.specific.cp2k += md.specific.cp2k_mm
job = cp2k_mm(s, MOL)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_md")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
assertion.isfile(result.results['cp2k-1_1000.restart'])
def test_singlepoint() -> None:
"""Test CP2K singlepoint calculations with the :class:`CP2K_MM` class."""
s = SETTINGS.copy()
s.specific.cp2k += singlepoint.specific.cp2k_mm
job = cp2k_mm(settings=s, mol=MOL, job_name='cp2k_mm_sp')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
# Compare energies
ref = -15.4431781758
assertion.isclose(result.energy, ref, rel_tol=10**-4)
def test_cp2k_singlepoint_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = SETTINGS.copy()
s.specific.cp2k += geometry.specific.cp2k_mm
job = cp2k_mm(s, MOL)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_sp")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
# Compare energies
ref = -15.4431781758
assertion.isclose(result.energy, ref, rel_tol=10**-4)
def test_md() -> None:
"""Test CP2K molecular dynamics calculations with the :class:`CP2K_MM` class."""
mol = Molecule(
PATH_MOLECULES /
'Cd68Cl26Se55__26_acetate.freq.xyz') # Optimized coordinates
s = SETTINGS.copy()
s.specific.cp2k += md.specific.cp2k_mm
s.specific.cp2k.motion.md.steps = 1000
job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_md')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
plams_results = result.results
assertion.isfile(plams_results['cp2k-1_1000.restart'])
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)
def _multi_ligand_job(mol: Molecule, psf: PSFContainer, settings: QmSettings,
workdir: str, db_file: str,
**kwargs: Any) -> CP2KMM_Result:
"""Helper function for :func:`multi_ligand_job`."""
# Run MATCH on all unique ligands
lig_dict = _lig_from_psf(mol, psf)
ff: str = kwargs.pop('forcefield', 'top_all36_cgenff_new')
rtf_list, prm = _run_match(lig_dict.values(), forcefield=ff)
# Update the .psf file with all MATCH results
initial_charge = psf.charge.sum()
for id_range, rtf_file in zip(lig_dict.keys(), rtf_list):
overlay_rtf_file(psf, rtf_file, id_range)
# Update the charge
_constrain_charge(psf, settings, initial_charge)
# Fill in all missing core/ligand lennard-jones parameters with those from UFF
# TODO: Connect this with the newly improved Auto-FOX 0.8 parameter guessing schemes
prm_to_df(settings)
if settings.get('lennard_jones') is not None:
_fill_uff(psf, settings['lennard_jones'])
elif settings.get('lennard-jones') is not None:
_fill_uff(psf, settings['lennard-jones'])
# Write the new .prm and .psf files and update the CP2K settings
prm_name = join(workdir, 'mol.prm')
psf_name = join(workdir, 'mol.psf')
prm.write(prm_name)
psf.write(psf_name)
settings.prm = prm_name
settings.psf = psf_name
# Run the actual CP2K job
with SET_CONFIG_STDOUT:
job = cp2k_mm(mol=mol, settings=settings, **kwargs)
return run_parallel(job,
db_file=db_file,
n_threads=1,
always_cache=True,
registry=registry,
echo_log=False)
def test_c2pk_freq_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = SETTINGS.copy()
s.specific.cp2k += freq.specific.cp2k_mm
job = cp2k_mm(s, MOL)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_freq")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
freqs = result.frequencies
freqs_ref = np.load(PATH / 'Cd68Cl26Se55__26_acetate.freq.npy')
np.testing.assert_allclose(freqs, freqs_ref, rtol=0, atol=5.0)
G = result.free_energy
H = result.enthalpy
H_ref = -8642.371633064053
assertion.isnan(G)
assertion.isclose(H, H_ref, rel_tol=0.1)
def test_freq() -> None:
"""Test CP2K frequency calculations with the :class:`CP2K_MM` class."""
mol = Molecule(
PATH_MOLECULES /
'Cd68Cl26Se55__26_acetate.freq.xyz') # Optimized coordinates
s = SETTINGS.copy()
s.specific.cp2k += freq.specific.cp2k_mm
job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_freq')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
freqs = result.frequencies
freqs_ref = np.load(PATH / 'Cd68Cl26Se55__26_acetate.freq.npy')
np.testing.assert_allclose(freqs, freqs_ref, rtol=0, atol=5.0)
G = result.free_energy
H = result.enthalpy
H_ref = -8642.371633064053
assertion.isnan(G)
assertion.isclose(H, H_ref, rel_tol=0.1)
def test_geometry() -> None:
"""Test CP2K geometry optimization calculations with the :class:`CP2K_MM` class."""
s = SETTINGS.copy()
s.specific.cp2k += geometry.specific.cp2k_mm
job = cp2k_mm(settings=s, mol=MOL, job_name='cp2k_mm_opt')
result = run(job, path=PATH)
assertion.eq(result.status, 'successful')
# Compare energies
ref = -16.865587192150834
assertion.isclose(result.energy, ref, rel_tol=10**-4)
# Compare geometries
xyz_ref = np.load(PATH_MOLECULES / 'Cd68Cl26Se55__26_acetate.npy')
_xyz = np.array(result.geometry)
_xyz -= _xyz.mean(axis=0)[None, ...]
xyz = overlap_coords(_xyz, xyz_ref)
r_mean = np.linalg.norm(xyz - xyz_ref, axis=1).mean()
assertion.le(r_mean, 0.1)
def test_c2pk_opt_mock(mocker: MockFixture) -> None:
"""Mock a call to CP2K."""
s = SETTINGS.copy()
s.specific.cp2k += singlepoint.specific.cp2k_mm
job = cp2k_mm(s, MOL)
run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_opt")
result = run_mocked(job)
assertion.eq(result.status, 'successful')
# Compare energies
ref = -16.865587192150834
energy = result.energy
assertion.isclose(energy, ref, rel_tol=10**-4)
# Compare geometries
xyz_ref = np.load(PATH_MOLECULES / 'Cd68Cl26Se55__26_acetate.npy')
_xyz = np.array(result.geometry)
_xyz -= _xyz.mean(axis=0)[None, ...]
xyz = overlap_coords(_xyz, xyz_ref)
r_mean = np.linalg.norm(xyz - xyz_ref, axis=1).mean()
assertion.le(r_mean, 0.1)