def test_cp2k_singlepoint_mock(mocker: MockFixture):
"""Mock a call to CP2K."""
# single point calculation
s = fill_cp2k_defaults(templates.singlepoint)
# print orbitals
s.specific.cp2k.force_eval.dft.print.mo.filename = (
PATH / "orbitals.out").as_posix()
s.specific.cp2k.force_eval.dft.print.mo.mo_index_range = "7 46"
s.specific.cp2k.force_eval.dft.scf.added_mos = 20
# Construct a result objects
job = cp2k(s, ETHYLENE)
jobname = "cp2k_job"
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# electronic energy
assertion.isfinite(rs.energy)
# Molecular orbitals
orbs = rs.orbitals
assertion.assert_(np.isfinite, orbs.eigenvectors,
post_process=np.all) # eigenvalues
assertion.shape_eq(orbs.eigenvectors, (46, 40))
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_dftb_opt_mock(mocker: MockFixture):
"""Mock a geometry optimization using DFTB."""
jobname = "dftb_geometry"
job = dftb(templates.geometry, WATER, job_name=jobname)
run_mocked = mock_runner(mocker, jobname)
rs = run_mocked(job)
# check the properties
assertion.isfinite(rs.energy)
assertion.len_eq(rs.dipole, 3)
assertion.isinstance(rs.molecule, Molecule)
def test_adf_mock(mocker: MockFixture):
"""Mock the ADF output."""
mol = Molecule(PATH_MOLECULES / "acetonitrile.xyz")
job = adf(templates.geometry, mol)
run_mocked = mocker.patch("qmflows.run")
jobname = "ADFjob"
dill_path = WORKDIR / jobname / "ADFjob.dill"
plams_dir = WORKDIR / jobname
run_mocked.return_value = ADF_Result(templates.geometry,
mol,
jobname,
dill_path=dill_path,
work_dir=plams_dir,
plams_dir=plams_dir)
rs = run_mocked(job)
assertion.isfinite(rs.energy)
assertion.isfinite(rs.h**o)
assertion.isfinite(rs.lumo)
# Array of runtime for each optimization
assertion.isfinite(rs.runtime[-1])
# 3-dimensional vector
assertion.len_eq(rs.dipole, 3)
# number of steps until convergence
assertion.eq(rs.optcycles, 8)
# Test molecule
# Molecule
mol = rs.molecule
assertion.isinstance(mol, Molecule)
assertion.len_eq(mol, 6) # there are 6 atoms
def test_c2pk_freq_mock(mocker: MockFixture):
"""Mock a call to CP2K."""
# Frequency calculation
s = fill_cp2k_defaults(templates.singlepoint)
s.specific.cp2k.vibrational_analysis.thermochemistry = ".TRUE."
s.specific.cp2k["global"]["run_type"] = "VIBRATIONAL_ANALYSIS"
jobname = "cp2k_freq"
run_mocked = mock_runner(mocker, jobname)
job = cp2k(s, ETHYLENE, job_name=jobname)
rs = run_mocked(job)
# check properties
assertion.isfinite(rs.enthalpy)
assertion.isfinite(rs.free_energy)
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_isfinite() -> None:
"""Test :meth:`AssertionManager.isfinite`."""
assertion.isfinite(0)
assertion.isfinite(0.0)
assertion.isfinite(98)
assertion.isfinite(nan, invert=True)
assertion.isfinite(inf, invert=True)
assertion.isfinite(-inf, invert=True)
assertion.isfinite(1, 1, 1, exception=TypeError)
assertion.isfinite('bob', exception=TypeError)
def test_line_extraction():
"""Test the line extraction function for ADF."""
h**o = extract_line_value(path_output, pattern="H**O", pos=4)
assertion.isfinite(h**o)
def test_adf_awk():
"""Test the awk parser for ADF."""
script = r"/Total Used/ {print $9}"
filename = path_output.as_posix()
results = np.array(awk_file(filename, script=script))
assertion.isfinite(np.sum(results))
def test_orca_awk():
"""Test the Awk reader for orca."""
script = r"/Sum of individual times/ {runtime = $6} END {print runtime}"
filename = PATH_OUTPUT.as_posix()
result = awk_file(filename, script=script)
assertion.isfinite(result)