How to use the qcelemental.testing.compare_values function in qcelemental
To help you get started, we’ve selected a few qcelemental examples, based on popular ways it is used in public projects.
Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
psi4 / psi4 / tests / pytests / test_qcng_dftd3.py View on Github 
'molecule': mol,
'driver': 'gradient',
'model': {
'method': inp['name']
},
'keywords': {},
}
jrec = qcng.compute(resinp, 'dftd3', raise_error=True)
jrec = jrec.dict()
assert len(jrec['extras']['qcvars']) == 8
assert compare_values(expected, jrec['extras']['qcvars']['CURRENT ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars']['DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars']['2-BODY DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars'][inp['lbl'] + ' DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['CURRENT GRADIENT'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['DISPERSION CORRECTION GRADIENT'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['2-BODY DISPERSION CORRECTION GRADIENT'], atol=1.e-7)
assert compare_values(
gexpected, jrec['extras']['qcvars'][inp['lbl'] + ' DISPERSION CORRECTION GRADIENT'], atol=1.e-7)'driver': 'gradient',
'model': {
'method': inp['name']
},
'keywords': {},
}
jrec = qcng.compute(resinp, 'mp2d', raise_error=True)
jrec = jrec.dict()
#assert len(jrec['extras']['qcvars']) == 8
assert compare_values(expected, jrec['extras']['qcvars']['CURRENT ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars']['DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars'][inp['lbl'] + ' DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['CURRENT GRADIENT'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['DISPERSION CORRECTION GRADIENT'], atol=1.e-7)
assert compare_values(
gexpected, jrec['extras']['qcvars'][inp['lbl'] + ' DISPERSION CORRECTION GRADIENT'], atol=1.e-7)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())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())p4mol = qcel.models.Molecule.from_data(p4_hooh_xyz)
c4mol = qcel.models.Molecule.from_data(c4_hooh_xyz)
aqmol, data = p4mol.align(c4mol, atoms_map=False, mols_align=True, verbose=4)
mill = data["mill"]
assert compare([0, 3, 1, 2], mill.atommap)
p2cgeom = mill.align_coordinates(p4mol.geometry)
assert compare_values(c4mol.geometry, p2cgeom, atol=1.0e-6)
p2c_dipder_x, p2c_dipder_y, p2c_dipder_z = mill.align_vector_gradient(p4_hooh_dipder)
assert compare_values(c4_hooh_dipder_x, p2c_dipder_x, atol=1.0e-5)
assert compare_values(c4_hooh_dipder_y, p2c_dipder_y, atol=1.0e-5)
assert compare_values(c4_hooh_dipder_z, p2c_dipder_z, atol=1.0e-5)resinp = {
'schema_name': 'qcschema_input',
'schema_version': 1,
'molecule': mol,
'driver': 'gradient',
'model': {
'method': inp['name']
},
'keywords': {},
}
jrec = qcng.compute(resinp, 'dftd3', raise_error=True)
jrec = jrec.dict()
assert len(jrec['extras']['qcvars']) == 8
assert compare_values(expected, jrec['extras']['qcvars']['CURRENT ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars']['DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(expected, jrec['extras']['qcvars']['3-BODY DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(
expected, jrec['extras']['qcvars']['AXILROD-TELLER-MUTO 3-BODY DISPERSION CORRECTION ENERGY'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['CURRENT GRADIENT'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['DISPERSION CORRECTION GRADIENT'], atol=1.e-7)
assert compare_values(gexpected, jrec['extras']['qcvars']['3-BODY DISPERSION CORRECTION GRADIENT'], atol=1.e-7)
assert compare_values(
gexpected, jrec['extras']['qcvars']['AXILROD-TELLER-MUTO 3-BODY DISPERSION CORRECTION GRADIENT'], atol=1.e-7)def test_kabsch_identity():
oco10 = qcel.molparse.from_string(soco10)
oco12 = qcel.molparse.from_string(soco10)
oco10_geom_au = oco10["qm"]["geom"].reshape((-1, 3)) / qcel.constants.bohr2angstroms
oco12_geom_au = oco12["qm"]["geom"].reshape((-1, 3)) / qcel.constants.bohr2angstroms
rmsd, rot, shift = qcel.molutil.kabsch_align(oco10_geom_au, oco12_geom_au)
assert compare_values(0.0, rmsd, "identical")
assert compare_values(np.identity(3), rot, "identity rotation matrix")
assert compare_values(np.zeros(3), shift, "identical COM")fix_orientation=True,
)
amol = Molecule(validate=False, **to_schema(adict, dtype=2))
# TODO -- can probably do more with fragments in amol now that
# Mol is something with non-contig frags. frags now discarded.
assert compare_values(
concern_mol.nuclear_repulsion_energy(),
amol.nuclear_repulsion_energy(),
"Q: concern_mol-->returned_mol NRE uncorrupted",
atol=1.0e-4,
quiet=(verbose > 1),
)
if mols_align:
assert compare_values(
ref_mol.nuclear_repulsion_energy(),
amol.nuclear_repulsion_energy(),
"Q: concern_mol-->returned_mol NRE matches ref_mol",
atol=1.0e-4,
quiet=(verbose > 1),
)
assert compare(
True,
np.allclose(ref_mol.geometry, amol.geometry, atol=4),
"Q: concern_mol-->returned_mol geometry matches ref_mol",
quiet=(verbose > 1),
)
return amol, {"rmsd": rmsd, "mill": solution}if do_plot:
# TODO Missing import
plot_coord(ref=rgeom, cand=ageom, orig=cgeom, comment="Final RMSD = {:8.4f}".format(final_rmsd))
# sanity checks
assert compare_values(
_pseudo_nre(cuniq, cgeom),
_pseudo_nre(auniq, ageom),
"D: concern_mol-->returned_mol pNRE uncorrupted",
atol=1.0e-4,
quiet=(verbose < 2),
)
if mols_align is True:
assert compare_values(
_pseudo_nre(runiq, rgeom),
_pseudo_nre(auniq, ageom),
"D: concern_mol-->returned_mol pNRE matches ref_mol",
atol=1.0e-4,
quiet=(verbose < 2),
)
assert compare_values(
rgeom, ageom, "D: concern_mol-->returned_mol geometry matches ref_mol", atol=1.0e-4, quiet=(verbose < 2)
)
assert compare_values(0.0, final_rmsd, "D: null RMSD", atol=1.0e-4, quiet=(verbose < 2))
return final_rmsd, hold_solution# final presentation & plotting
if verbose >= 2:
print("<<< Aligned:")
for at, hsh in enumerate(auniq):
print(atomfmt2.format(auniq[at][:6], *ageom[at]))
print("<<< Aligned Diff:")
for at, hsh in enumerate(auniq):
print(atomfmt2.format(auniq[at][:6], *[ageom[at][i] - rgeom[at][i] for i in range(3)]))
if do_plot:
# TODO Missing import
plot_coord(ref=rgeom, cand=ageom, orig=cgeom, comment="Final RMSD = {:8.4f}".format(final_rmsd))
# sanity checks
assert compare_values(
_pseudo_nre(cuniq, cgeom),
_pseudo_nre(auniq, ageom),
"D: concern_mol-->returned_mol pNRE uncorrupted",
atol=1.0e-4,
quiet=(verbose < 2),
)
if mols_align is True:
assert compare_values(
_pseudo_nre(runiq, rgeom),
_pseudo_nre(auniq, ageom),
"D: concern_mol-->returned_mol pNRE matches ref_mol",
atol=1.0e-4,
quiet=(verbose < 2),
)
assert compare_values(qcelemental
Core data structures for Quantum Chemistry.
Package Health Score
72 / 100Popular qcelemental functions
- qcelemental.constants
- qcelemental.constants.conversion_factor
- qcelemental.Datum
- qcelemental.exceptions.ValidationError
- qcelemental.models
- qcelemental.models.AtomicResult
- qcelemental.models.basemodels.ProtoModel
- qcelemental.models.Molecule
- qcelemental.models.ResultInput
- qcelemental.molparse
- qcelemental.molparse.from_string
- qcelemental.molparse.to_schema
- qcelemental.periodictable
- qcelemental.periodictable.to_E
- qcelemental.testing.compare_values
- qcelemental.util.safe_version
- qcelemental.util.serialization.deserialize
- qcelemental.util.unnp
- qcelemental.util.which
- qcelemental.util.which_import