def test_condense_from_molecule_fd_rmf_mulliken_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array(
[3.49417097E-01, 3.25291762E-01, 3.25291141E-01])
expected_0 = np.array([8, 1, 1]) - np.array(
[-4.32227787E-01, 2.16114060E-01, 2.16113727E-01])
expected_p = np.array([8, 1, 1]) - np.array(
[-2.64833827E-01, -3.67583325E-01, -3.67582849E-01])
molecule = []
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
molecule.append(Molecule.from_file(file1))
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
molecule.append(Molecule.from_file(file2))
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
molecule.append(Molecule.from_file(file3))
# check from_molecule linear
model = CondensedConceptualDFT.from_molecule(molecule, "linear", "RMF",
"mulliken")
check_condensed_reactivity(model, "linear", expected_0, expected_p,
expected_m, 10, 0.572546)
# check from_molecule quadratic
model = CondensedConceptualDFT.from_molecule(molecule, "quadratic", "RMF",
"mulliken")
check_condensed_reactivity(model, "quadratic", expected_0, expected_p,
expected_m, 10, 0.572546)
def test_condense_from_molecule_fd_rmf_esp_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array(
[4.14233893E-02, 4.79288419E-01, 4.79288192E-01])
expected_0 = np.array([8, 1, 1]) - np.array(
[-7.00779373E-01, 3.50389629E-01, 3.50389744E-01])
expected_p = np.array([8, 1, 1]) - np.array(
[-5.81613550E-01, -2.09193820E-01, -2.09192630E-01])
molecule = []
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
molecule.append(Molecule.from_file(file1))
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
molecule.append(Molecule.from_file(file2))
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
molecule.append(Molecule.from_file(file3))
# check from_molecule linear
model = CondensedConceptualDFT.from_molecule(molecule, "linear", "RMF",
"esp")
check_condensed_reactivity(model, "linear", expected_0, expected_p,
expected_m, 10, 0.572546)
# check from_molecule quadratic
model = CondensedConceptualDFT.from_molecule(molecule, "quadratic", "RMF",
"esp")
check_condensed_reactivity(model, "quadratic", expected_0, expected_p,
expected_m, 10, 0.572546)
def test_condense_from_molecule_fd_rmf_npa_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array(
[-3.64452391E-02, 5.18222784E-01, 5.18222455E-01])
expected_0 = np.array([8, 1, 1]) - np.array(
[-9.00876494E-01, 4.50438267E-01, 4.50438227E-01])
expected_p = np.array([8, 1, 1]) - np.array(
[-1.11332869E+00, 5.66635486E-02, 5.66651430E-02])
molecule = []
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
molecule.append(Molecule.from_file(file1))
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
molecule.append(Molecule.from_file(file2))
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
molecule.append(Molecule.from_file(file3))
# check from_molecule linear
model = CondensedConceptualDFT.from_molecule(molecule, "linear", "RMF",
"npa")
check_condensed_reactivity(model, "linear", expected_0, expected_p,
expected_m, 10, 0.572546)
# check from_molecule quadratic
model = CondensedConceptualDFT.from_molecule(molecule, "quadratic", "RMF",
"npa")
check_condensed_reactivity(model, "quadratic", expected_0, expected_p,
expected_m, 10, 0.572546)
def test_condense_quadratic_from_molecule_fmr_mbis_ch4_fchk():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
mol = Molecule.from_file(fname)
expected = np.array(
[6.46038055, 0.88489494, 0.88492901, 0.88493897, 0.88492396])
# check from_molecule
model = CondensedConceptualDFT.from_molecule(mol, "quadratic", "FMR",
"mbis")
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
# check from_molecule given as a list
model = CondensedConceptualDFT.from_molecule([mol], "quadratic", "FMR",
"mbis")
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
# check from_molecule & passing grid
grid = MolecularGrid(mol.coordinates, mol.numbers, mol.pseudo_numbesr,
'insane', 3, False)
model = CondensedConceptualDFT.from_molecule(mol,
"quadratic",
"FMR",
"mbis",
grid=grid)
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
# check from_molecule given as a list & passing grid
model = CondensedConceptualDFT.from_molecule([mol],
"quadratic",
"FMR",
"mbis",
grid=grid)
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
def test_condense_linear_from_molecule_fmr_h_ch4_wfn():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
mol = Molecule.from_file(fname)
expected = np.array(
[6.11301651, 0.97175462, 0.97175263, 0.9717521, 0.97174353])
# check from_molecule
model = CondensedConceptualDFT.from_molecule(mol, "linear", "FMR", "h")
check_condensed_reactivity(model, "linear", expected, None, None, 10,
0.736396)
# check from_molecule given as a list
model = CondensedConceptualDFT.from_molecule([mol], "linear", "FMR", "h")
check_condensed_reactivity(model, "linear", expected, None, None, 10,
0.736396)
# check from_molecule & passing grid
grid = MolecularGrid(mol.coordinates, mol.numbers, mol.pseudo_numbesr,
'insane', 3, False)
model = CondensedConceptualDFT.from_molecule(mol,
"linear",
"FMR",
"h",
grid=grid)
check_condensed_reactivity(model, "linear", expected, None, None, 10,
0.736396)
# check from_molecule given as a list & passing grid
model = CondensedConceptualDFT.from_molecule([mol],
"linear",
"FMR",
"h",
grid=grid)
check_condensed_reactivity(model, "linear", expected, None, None, 10,
0.736396)
def test_condense_linear_from_file_fmr_mbis_ch4_fchk():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
model1 = CondensedConceptualDFT.from_file(fname, "linear", "FMR",
"mbis")
model2 = CondensedConceptualDFT.from_file([fname], "linear", "FMR",
"mbis")
mol = Molecule.from_file(fname)
grid = MolecularGrid(mol.coordinates, mol.numbers, mol.pseudo_numbesr,
'insane', 3, False)
model3 = CondensedConceptualDFT.from_file(fname,
"linear",
"FMR",
"mbis",
grid=grid)
model4 = CondensedConceptualDFT.from_file([fname],
"linear",
"FMR",
"mbis",
grid=grid)
expected = np.array(
[6.46038055, 0.88489494, 0.88492901, 0.88493897, 0.88492396])
# check using fname given as a string
check_condensed_reactivity(model1, "linear", expected, None, None, 10,
0.736396)
# check using fname given as a list
check_condensed_reactivity(model2, "linear", expected, None, None, 10,
0.736396)
# check using fname as a string & passing grid
check_condensed_reactivity(model3, "linear", expected, None, None, 10,
0.736396)
# check using fname as a list & passing grid
check_condensed_reactivity(model4, "linear", expected, None, None, 10,
0.736396)
def test_condense_linear_from_file_fmr_h_ch4_fchk():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
model1 = CondensedConceptualDFT.from_file(fname, "linear", "FMR", "h")
model2 = CondensedConceptualDFT.from_file([fname], "linear", "FMR",
"h")
mol = Molecule.from_file(fname)
grid = MolecularGrid.from_molecule(mol, specs='insane', rotate=False)
model3 = CondensedConceptualDFT.from_file(fname,
"linear",
"FMR",
"h",
grid=grid)
model4 = CondensedConceptualDFT.from_file([fname],
"linear",
"FMR",
"h",
grid=grid)
expected = np.array(
[6.11301651, 0.97175462, 0.97175263, 0.9717521, 0.97174353])
# check using fname given as a string
check_condensed_reactivity(model1, "linear", expected, None, None, 10,
0.736396)
# check using fname given as a list
check_condensed_reactivity(model2, "linear", expected, None, None, 10,
0.736396)
# check using fname as a string & passing grid
check_condensed_reactivity(model3, "linear", expected, None, None, 10,
0.736396)
# check using fname as a list & passing grid
check_condensed_reactivity(model4, "linear", expected, None, None, 10,
0.736396)
def test_condense_quadratic_from_file_fmr_mbis_ch4_wfn():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
model1 = CondensedConceptualDFT.from_file(fname, "quadratic", "FMR", "mbis")
model2 = CondensedConceptualDFT.from_file([fname], "quadratic", "FMR", "mbis")
expected = np.array([6.46038055, 0.88489494, 0.88492901, 0.88493897, 0.88492396])
# check using fname given as a string
check_condensed_reactivity(model1, "quadratic", expected, None, None, 10)
# check using fname given as a list
check_condensed_reactivity(model2, "quadratic", expected, None, None, 10)
def test_condense_from_file_fd_rmf_mulliken_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array([ 3.49417097E-01, 3.25291762E-01, 3.25291141E-01])
expected_0 = np.array([8, 1, 1]) - np.array([-4.32227787E-01, 2.16114060E-01, 2.16113727E-01])
expected_p = np.array([8, 1, 1]) - np.array([-2.64833827E-01,-3.67583325E-01,-3.67582849E-01])
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
fname = [file1, file2, file3]
model1 = CondensedConceptualDFT.from_file(fname, "linear", "RMF", "mulliken")
model2 = CondensedConceptualDFT.from_file(fname, "quadratic", "RMF", "mulliken")
# check from_file linear
check_condensed_reactivity(model1, "linear", expected_0, expected_p, expected_m, 10)
# check from_file quadratic
check_condensed_reactivity(model2, "quadratic", expected_0, expected_p, expected_m, 10)
def test_condense_from_file_fd_rmf_npa_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array([-3.64452391E-02, 5.18222784E-01, 5.18222455E-01])
expected_0 = np.array([8, 1, 1]) - np.array([-9.00876494E-01, 4.50438267E-01, 4.50438227E-01])
expected_p = np.array([8, 1, 1]) - np.array([-1.11332869E+00, 5.66635486E-02, 5.66651430E-02])
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
fname = [file1, file2, file3]
# check from_file linear
model1 = CondensedConceptualDFT.from_file(fname, "linear", "RMF", "npa")
model2 = CondensedConceptualDFT.from_file(fname, "quadratic", "RMF", "npa")
check_condensed_reactivity(model1, "linear", expected_0, expected_p, expected_m, 10)
# check from_file quadratic
check_condensed_reactivity(model2, "quadratic", expected_0, expected_p, expected_m, 10)
def test_condense_from_file_fd_rmf_esp_h2o_fchk():
# expected populations of H2O from fchk file
expected_m = np.array([8, 1, 1]) - np.array([ 4.14233893E-02, 4.79288419E-01, 4.79288192E-01])
expected_0 = np.array([8, 1, 1]) - np.array([-7.00779373E-01, 3.50389629E-01, 3.50389744E-01])
expected_p = np.array([8, 1, 1]) - np.array([-5.81613550E-01,-2.09193820E-01,-2.09192630E-01])
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as file1:
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as file2:
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as file3:
fname = [file1, file2, file3]
# check from_file linear
model1 = CondensedConceptualDFT.from_file(fname, "linear", "RMF", "esp")
model2 = CondensedConceptualDFT.from_file(fname, "quadratic", "RMF", "esp")
check_condensed_reactivity(model1, "linear", expected_0, expected_p, expected_m, 10)
# check from_file quadratic
check_condensed_reactivity(model2, "quadratic", expected_0, expected_p, expected_m, 10)
def test_condense_quadratic_from_molecule_fmr_mbis_ch4_wfn():
# expected populations of CH4 computed with HORTON
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
molecule = Molecule.from_file(fname)
expected = np.array(
[6.46038055, 0.88489494, 0.88492901, 0.88493897, 0.88492396])
# check from_molecule given as a string
model = CondensedConceptualDFT.from_molecule(molecule, "quadratic", "FMR",
"mbis")
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
# check from_molecule given as a list
model = CondensedConceptualDFT.from_molecule([molecule], "quadratic",
"FMR", "mbis")
check_condensed_reactivity(model, "quadratic", expected, None, None, 10,
0.736396)
