Python tnm Examples

Example #1

File: test_qcng_dftd3_mp2d.py Project: ymshi449/psi4

def test_qcdb__energy_d3():
    eneyne = qcdb.set_molecule(seneyne)
    eneyne.update_geometry()

    E, jrec = qcdb.energy('d3-b3lyp-d2', return_wfn=True)
    assert compare_values(ref['eneyne']['B3LYP-D2']['dimer'], E, 7,
                          'P: Ethene-Ethyne -D2')
    assert compare_values(ref['eneyne']['B3LYP-D2']['dimer'],
                          jrec['qcvars']['DISPERSION CORRECTION ENERGY'].data,
                          7, tnm())
    assert compare_values(
        ref['eneyne']['B3LYP-D2']['dimer'],
        jrec['qcvars']['B3LYP-D2 DISPERSION CORRECTION ENERGY'].data, 7, tnm())

    mA = eneyne.extract_subsets(1)

    E, jrec = qcdb.energy('d3-b3lyp-d3bj', return_wfn=True, molecule=mA)
    assert compare_values(ref['eneyne']['B3LYP-D3(BJ)']['mA'], E, 7, tnm())
    assert compare_values(ref['eneyne']['B3LYP-D3(BJ)']['mA'],
                          jrec['qcvars']['DISPERSION CORRECTION ENERGY'].data,
                          7, tnm())
    assert compare_values(
        ref['eneyne']['B3LYP-D3(BJ)']['mA'],
        jrec['qcvars']['B3LYP-D3(BJ) DISPERSION CORRECTION ENERGY'].data, 7,
        tnm())

Example #2

File: test_molparse_pubchem.py Project: sjrl/QCElemental

def test_pubchem_4a():
    subject = subject4
    fullans = copy.deepcopy(fullans4)
    fullans["provenance"] = _string_prov_stamp

    final, intermed = qcelemental.molparse.from_string(subject, return_processed=True)
    assert compare_molrecs(ans4, intermed, tnm() + ": intermediate")
    assert compare_molrecs(fullans, final["qm"], tnm() + ": full")

Example #3

File: test_molparse_pubchem.py Project: nuwandesilva/QCElemental

def test_pubchem_13i():
    subject = "PubChem:223"
    fullans = copy.deepcopy(fullans13)
    fullans['provenance'] = _string_prov_stamp

    final, intermed = qcelemental.molparse.from_string(subject,
                                                       return_processed=True)
    assert compare_molrecs(ans13, intermed, tnm() + ': intermediate')
    assert compare_molrecs(fullans, final['qm'], tnm() + ': full')

Example #4

File: test_molparse_pubchem.py Project: pk-organics/QCElemental

def test_pubchem_13i():
    subject = "PubChem:223"
    fullans = copy.deepcopy(fullans13)
    fullans["provenance"] = _string_prov_stamp

    with xfail_on_pubchem_busy():
        final, intermed = qcelemental.molparse.from_string(subject, return_processed=True)
    assert compare_molrecs(ans13, intermed, tnm() + ": intermediate")
    assert compare_molrecs(fullans, final["qm"], tnm() + ": full")

Example #5

File: test_molparse_pubchem.py Project: sjrl/QCElemental

def test_pubchem_4c():
    subject = """
pubchem  : 241
"""
    ans = copy.deepcopy(ans4)
    ans["name"] = "benzene"
    fullans = copy.deepcopy(fullans4)
    fullans["name"] = "benzene"
    fullans["provenance"] = _string_prov_stamp

    final, intermed = qcelemental.molparse.from_string(subject, return_processed=True, name="benzene", verbose=2)
    assert compare_molrecs(ans, intermed, tnm() + ": intermediate")
    assert compare_molrecs(fullans, final["qm"], tnm() + ": full")

Example #6

File: test_molparse_pubchem.py Project: nuwandesilva/QCElemental

def test_pubchem_4c():
    subject = """
pubchem  : 241
"""
    ans = copy.deepcopy(ans4)
    ans['name'] = 'benzene'
    fullans = copy.deepcopy(fullans4)
    fullans['name'] = 'benzene'
    fullans['provenance'] = _string_prov_stamp

    final, intermed = qcelemental.molparse.from_string(subject,
                                                       return_processed=True,
                                                       name='benzene',
                                                       verbose=2)
    assert compare_molrecs(ans, intermed, tnm() + ': intermediate')
    assert compare_molrecs(fullans, final['qm'], tnm() + ': full')

Example #7

File: test_dftd3_mp2d.py Project: ChemRacer/QCEngine

def test_dftd3__from_arrays(inp, expected):
    res = empirical_dispersion_resources.from_arrays(**inp[0])
    assert compare_recursive(expected, res, atol=1.e-4)
    assert compare(inp[1], _compute_key(res), 'key')
    res = empirical_dispersion_resources.from_arrays(name_hint=res['fctldash'],
                                                     level_hint=res['dashlevel'],
                                                     param_tweaks=res['dashparams'])
    assert compare_recursive(expected, res, tnm() + ' idempotent', atol=1.e-4)

Example #8

File: test_qcng_dftd3.py Project: fevangelista/psi4

def test_qcdb__energy_d3():
    eneyne = qcdb.set_molecule(seneyne)
    eneyne.update_geometry()

    E, jrec = qcdb.energy('d3-b3lyp-d2', return_wfn=True)
    assert compare_values(ref['eneyne']['B3LYP-D2']['dimer'], E, 7, 'P: Ethene-Ethyne -D2')
    assert compare_values(ref['eneyne']['B3LYP-D2']['dimer'], jrec['qcvars']['DISPERSION CORRECTION ENERGY'].data, 7,
                          tnm())
    assert compare_values(ref['eneyne']['B3LYP-D2']['dimer'],
                          jrec['qcvars']['B3LYP-D2 DISPERSION CORRECTION ENERGY'].data, 7, tnm())

    mA = eneyne.extract_subsets(1)

    E, jrec = qcdb.energy('d3-b3lyp-d3bj', return_wfn=True, molecule=mA)
    assert compare_values(ref['eneyne']['B3LYP-D3(BJ)']['mA'], E, 7, tnm())
    assert compare_values(ref['eneyne']['B3LYP-D3(BJ)']['mA'], jrec['qcvars']['DISPERSION CORRECTION ENERGY'].data, 7,
                          tnm())
    assert compare_values(ref['eneyne']['B3LYP-D3(BJ)']['mA'],
                          jrec['qcvars']['B3LYP-D3(BJ) DISPERSION CORRECTION ENERGY'].data, 7, tnm())

Example #9

def test_dftd3__from_arrays__supplement():
    ans = {
        'dashlevel': 'chg',
        'dashparams': {
            's6': 4.05
        },
        'fctldash': 'asdf-d4',
        'dashparams_citation': '    mypaper\n'
    }
    supp = {'chg': {'definitions': {'asdf-d4': {'params': {'s6': 4.05}, 'citation': '    mypaper\n'}}}}

    res = dftd3.from_arrays(name_hint='asdf-d4', level_hint='chg', dashcoeff_supplement=supp)
    assert compare_recursive(ans, res, atol=1.e-4)
    with pytest.raises(ValueError) as e:
        dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
    assert "Can't guess -D correction level" in str(e)
    res = dftd3.from_arrays(
        name_hint=res['fctldash'],
        level_hint=res['dashlevel'],
        param_tweaks=res['dashparams'],
        dashcoeff_supplement=supp)
    assert compare_recursive(ans, res, tnm() + ' idempotent', atol=1.e-4)

Example #10

File: test_qcng_dftd3.py Project: fevangelista/psi4

def test_dftd3__from_arrays__supplement():
    ans = {
        'dashlevel': 'chg',
        'dashparams': {
            's6': 4.05
        },
        'fctldash': 'asdf-d4',
        'dashparams_citation': '    mypaper\n'
    }
    supp = {'chg': {'definitions': {'asdf-d4': {'params': {'s6': 4.05}, 'citation': '    mypaper\n'}}}}

    res = dftd3.from_arrays(name_hint='asdf-d4', level_hint='chg', dashcoeff_supplement=supp)
    assert compare_recursive(ans, res, atol=1.e-4)
    with pytest.raises(ValueError) as e:
        dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
    assert "Can't guess -D correction level" in str(e)
    res = dftd3.from_arrays(
        name_hint=res['fctldash'],
        level_hint=res['dashlevel'],
        param_tweaks=res['dashparams'],
        dashcoeff_supplement=supp)
    assert compare_recursive(ans, res, tnm() + ' idempotent', atol=1.e-4)

Example #11

File: test_qcng_dftd3.py Project: fevangelista/psi4

def test_dftd3__from_arrays(inp, expected):
    res = dftd3.from_arrays(**inp[0])
    assert compare_recursive(expected, res, atol=1.e-4)
    assert compare(inp[1], _compute_key(res), 'key')
    res = dftd3.from_arrays(name_hint=res['fctldash'], level_hint=res['dashlevel'], param_tweaks=res['dashparams'])
    assert compare_recursive(expected, res, tnm() + ' idempotent', atol=1.e-4)