def test_adf_parser():
"""Test the adf output readers."""
energy = kfreader(path_t21, section="Energy", prop="Bond Energy")
charge = kfreader(path_t21,
section="Properties",
prop="AtomCharge Mulliken")
assertion.isclose(np.sum(charge), 0.0, abs_tol=1e-8)
assertion.isfinite(energy)
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_orca_mock(mocker: MockFixture):
"""Mock a call to orca."""
methanol = Molecule(PATH_MOLECULES / "methanol.xyz")
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt NumFreq TightSCF SmallPrint"
# print the orbitals
s.specific.orca.scf = " print[p_mos] 1"
job = orca(s, methanol)
run_mocked = mocker.patch("qmflows.run")
jobname = "ORCAjob"
dill_path = WORKDIR / jobname / "ORCAjob.dill"
plams_dir = WORKDIR / jobname
run_mocked.return_value = ORCA_Result(s,
methanol,
jobname,
dill_path=dill_path,
plams_dir=plams_dir)
rs = run_mocked(job)
assertion.isfinite(rs.energy)
assertion.isfinite(rs.runtime)
assertion.isfinite(np.sum(rs.dipole))
# steps until convergence
assertion.eq(rs.optcycles, 8)
# Check that hessian is symmetric
hess = rs.hessian
assertion.isclose(np.sum(hess - hess.T), 0.0)
# frequencies
frequencies = rs.frequencies
assertion.len_eq(frequencies, 18)
# Normal modes
normal_modes = rs.normal_modes
assertion.shape_eq(normal_modes, (18, 18))
# Orbitals
orbs = rs.orbitals
assert np.isfinite(np.sum(orbs.eigenvalues)) # eigenvalues
# Molecule
mol = rs.molecule
assertion.isinstance(mol, Molecule)
assertion.len_eq(mol, 6) # there are 6 atoms
def test_dftb_freq_mock(mocker: MockFixture):
"""Mock a geometry optimization using DFTB."""
jobname = "dftb_freq"
job = dftb(templates.geometry, WATER, job_name=jobname)
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# Check that hessian is symmetric
hess_list = rs.hessian
dim = int(np.sqrt(len(hess_list)))
hess = np.array(hess_list).reshape(dim, dim)
assertion.isclose(np.sum(hess - hess.T), 0.0)
# enthalpy and Gibbs free energy
assertion.isfinite(rs.enthalpy)
assertion.isfinite(rs.free_energy)
# frequencies
assertion.isfinite(np.sum(rs.frequencies))
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 _validate(atom: str, value: float, param: pd.Series) -> None:
"""Validate the moves of :func:`test_constraint_blocks`."""
ident = f"{atom}={value}"
assertion.isclose(param[atom],
value,
abs_tol=0.001,
message=f'{atom} ({ident})')
for min_, max_, (key, v) in zip(PRM_MIN, PRM_MAX, param.items()):
assertion.le(min_, v, message=f'{key} ({ident})')
assertion.ge(max_, v, message=f'{key} ({ident})')
assertion.isclose((param * COUNT).sum(),
0,
abs_tol=0.001,
message=f"net charge ({ident})")
for key in EXCLUDE:
assertion.eq(param[key], PARAM[key], message=f'{key} ({ident})')
idx1 = ATOM_COEFS[0].index
idx2 = ATOM_COEFS[1].index
v1 = (param[idx1] * ATOM_COEFS[0]).sum()
v2 = (param[idx2] * ATOM_COEFS[1]).sum()
assertion.isclose(v1,
v2,
abs_tol=0.001,
message=f"{idx1} and {idx2} ({ident})")
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)