digichem-core 6.0.0rc1__py3-none-any.whl

digichem/test/util.py

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+"""Common testing utilities and convenience functions."""
+
+import pytest
+from pathlib import Path
+
+import digichem.config
+from digichem.datas import get_resource
+
+
+def data_directory():
+    """
+    Get a path to the test data directory.
+    """
+    return get_resource('test/data')
+
+
+# Input files.
+benzene_cdx = Path(data_directory(), "Input", "Benzene.cdx")
+pyridine_cml = Path(data_directory(), "Input", "Pyridine.cml")
+cyclopentane_com = Path(data_directory(), "Input", "Cyclopentane.com")
+water_xyz = Path(data_directory(), "Input", "Water.xyz")
+ethane_xyz = Path(data_directory(), "Input", "Ethane.xyz")
+pyridine_si_v2 = Path(data_directory(), "Input/Pyridine.v2.si")
+pyridine_si_v1 = Path(data_directory(), "Input/Pyridine.v1.si")
+
+
+# Result files for testing parsing.
+result_files = {
+    "gaussian": [Path(data_directory(), datum) for datum in [
+        'Naphthalene/Gaussian 16 Optimisation Frequencies PBE1PBE (GD3BJ) Toluene 6-31G(d,p)',
+        'Naphthalene/Gaussian 16 Excited States TDA 10 Singlets 10 Triplets PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz',
+        'Naphthalene/Gaussian 16 Excited States TDA Optimised S(1) PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz',  
+    ]],
+    "turbomole": [Path(data_directory(), datum) for datum in [
+        'Naphthalene/Turbomole Optimisation ADC(2) cc-pVDZ.tar.gz',
+        'Naphthalene/Turbomole Excited States ADC(2) S(1) and S(2) cc-pVDZ.tar.gz',
+        'Naphthalene/Turbomole Excited States ADC(2) T(1) and T(2) cc-pVDZ.tar.gz',
+    ]],
+    "orca": [Path(data_directory(), datum) for datum in [
+        'Pyridine/Orca Single Point PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca Gradient PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca Optimisation PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca Optimisation Frequencies PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca Frequencies PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca NMR PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz',
+        'Pyridine/Orca Excited States TDA 10 Singlets 10 Triplets PBE0 (GD3BJ) Gas Phase Pople Basis Sets STO-3G.tar.gz'
+    ]]
+}
+
+@pytest.fixture(scope="package")
+def digichem_options(tmpdir_factory):
+    config = digichem.config.get_config()
+    
+    # Change the default DB locations to prevent SPAM.
+    config['databases'] = [
+        "{{name: test1, path: {}}}".format(
+            Path(tmpdir_factory.mktemp("silico_database1"), "tmp.db")
+        ),
+        "{{name: test2, path: {}}}".format(
+            Path(tmpdir_factory.mktemp("silico_database2"), "tmp.db")
+        ),
+        "{{name: test3, auto_fill: False, path: {}}}".format(
+            Path(tmpdir_factory.mktemp("silico_database3"), "tmp.db")
+        ),
+    ]
+    config.logging['render_logging'] = True
+    config.validate()
+    return config
+
+
+def check_float_list(test_list, expected_list, abs = 1e-4):
+    """
+    Helper function to compare to lists of floats.
+    """
+    # Pytest bug #9921 prevents this comparison from working for now...
+    #assert test_list == pytest.approx(expected_list, abs=abs)
+    for list_index in range(0,len(expected_list)):
+        assert test_list[list_index] == pytest.approx(expected_list[list_index], abs=abs)
+
+
+def check_dipole(dipole_moment, coords, abs = 1e-4):
+    """
+    Helper function to check a dipole moment (PDM, TEDM or TMDM) matches some expected values.
+    """
+    check_float_list(dipole_moment.vector_coords, coords, abs)
+        
+    # Check total
+    assert dipole_moment.total == pytest.approx((coords[0] **2 + coords[1] **2 + coords[2] **2) **0.5, abs = abs)
+
+
+def check_orbitals(orbitals, num_occ, num_unocc, homo, lumo):
+    """Helper function for checking orbital energies"""
+    # Check numbers.
+    assert len(orbitals) == num_occ + num_unocc
+    assert len(orbitals.occupied) == num_occ
+    assert len(orbitals.virtual) == num_unocc
+    
+    # Check energies.
+    assert orbitals.HOMO_energy == pytest.approx(homo)
+    assert orbitals.LUMO_energy == pytest.approx(lumo)
+    assert orbitals.HOMO_LUMO_energy == pytest.approx(lumo - homo)
+    
+    # Check ordering.
+    assert [orbital.level for orbital in orbitals] == list(range(1, num_occ + num_unocc +1))
+
+
+def check_rendered_image(base_name):
+    """Check whether the eight separate images of a given rendered image have been created."""
+    for extension in ["jpg", "png"]:
+        for orientation in ["x0y0z0", "x0y90z0", "x45y45z45", "x90y0z0"]:
+            assert Path(base_name.parent, f"{base_name.name}.{orientation}.{extension}").exists()
+
+
+def check_report(report_folder, base_name, *,
+    unrestricted = False,
+    optimisation = False,
+    dipole = True,
+    vibrations = False,
+    excited_states = False,
+    absorption = False,
+    nmr = False,
+    s1_tdm = False,
+    s1_diff = False,
+    t1_diff = False,
+    s1_nto = False,
+    t1_nto = False,
+    vertical_emission = False,
+    adiabatic_emission = False):
+    """
+    Check that certain report and image files have been correctly rendered.
+    """
+    # First, check the report file itself is there
+    assert (Path(report_folder, f"{base_name}.journal.pdf").exists() and Path(report_folder, f"{base_name}.traditional.pdf").exists()) or Path(report_folder, f"{base_name}.pdf").exists()
+    
+    # Now check for images.
+    image_folder = Path(report_folder, "image")
+    # HOMO and LUMO
+    for image in (["HOMO", "LUMO"] if not unrestricted else ["HOMO (alpha)", "HOMO (beta)", "LUMO (alpha)", "LUMO (beta)"]):
+        check_rendered_image(Path(image_folder, f"{image}", f"{base_name}.{image}"))
+    
+    # HOMO-LUMO overlap
+    if not unrestricted:
+        check_rendered_image(Path(image_folder, "HOMO LUMO", f"{base_name}.HOMO_LUMO"))
+    
+    else:
+        check_rendered_image(Path(image_folder, "HOMO LUMO", f"{base_name}.alpha_HOMO_LUMO"))
+        check_rendered_image(Path(image_folder, "HOMO LUMO", f"{base_name}.beta_HOMO_LUMO"))
+    
+    # Structure and density.
+    check_rendered_image(Path(image_folder, "Structure", f"{base_name}.structure"))
+    check_rendered_image(Path(image_folder, "Density", f"{base_name}.SCF"))
+    
+    # Dipole.
+    if dipole:
+        check_rendered_image(Path(image_folder, "Dipole Moment", f"{base_name}.dipole"))
+    
+    if optimisation:
+        assert Path(image_folder, f"{base_name}.SCF_graph.png").exists()
+    
+    # HOMO-LUMO diagrams.
+    if not unrestricted:
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.HOMO_LUMO.png").exists()
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.orbitals.png").exists()
+    
+    else:
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.alpha_HOMO_LUMO.png").exists()
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.beta_HOMO_LUMO.png").exists()
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.alpha_orbitals.png").exists()
+        assert Path(image_folder, "Orbital Diagram", f"{base_name}.beta_orbitals.png").exists()
+        
+    # NMR.
+    if nmr:
+        assert len(Path(image_folder, "NMR").iterdir()) != 0
+    
+    # Excited state stuff.
+    if s1_tdm:
+        check_rendered_image(Path(image_folder, "S(1) Transition Dipole Moment", f"{base_name}.S(1)_dipole"))
+    
+    if s1_diff:
+        check_rendered_image(Path(image_folder, "S(1)", f"{base_name}.S(1)_difference_density"))
+    
+    if t1_diff:
+        check_rendered_image(Path(image_folder, "T(1)", f"{base_name}.T(1)_difference_density"))
+        
+    if s1_nto:
+        check_rendered_image(Path(image_folder, "S(1)", f"{base_name}.S(1)_NTO"))
+    
+    if t1_nto:
+        check_rendered_image(Path(image_folder, "T(1)", f"{base_name}.T(1)_NTO"))
+        
+    if excited_states:
+        assert Path(image_folder, f"{base_name}.excited_states.png").exists()
+    
+    if absorption:
+        assert Path(image_folder, f"{base_name}.simulated_absorption_spectrum.png").exists()
+        
+    if vertical_emission:
+        assert Path(image_folder, f"{base_name}.vertical_S(1)_emission_states.png").exists()
+        assert Path(image_folder, f"{base_name}.simulated_vertical_S(1)_emission_spectrum.png").exists()
+    
+    if adiabatic_emission:
+        assert Path(image_folder, f"{base_name}.adiabatic_S(1)_emission_states.png").exists()
+        assert Path(image_folder, f"{base_name}.simulated_adiabatic_S(1)_emission_spectrum.png").exists()
+    
+    # Vibrations.
+    if vibrations:
+        assert Path(image_folder, f"{base_name}.simulated_frequencies.png").exists()