def test_global_quadratic_from_file_fmo_h2o_anion_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -1.93118022E-01, -2.69116912E-01, -7.635212549312298E+01
with path("chemtools.data", "h2o_q-1_ub3lyp_ccpvtz.fchk") as fname:
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
model2 = GlobalConceptualDFT.from_file([fname], "quadratic")
# check quadratic global conceptual DFT model from a fname given as string
check_global_reactivity_quadratic(model1, ip, ea, energy, 11)
# check quadratic global conceptual DFT model from a fname given as a list of string
check_global_reactivity_quadratic(model2, ip, ea, energy, 11)
def test_global_linear_from_file_fmo_h2o_anion_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -1.93118022E-01, -2.69116912E-01, -7.635212549312298E+01
with path('chemtools.data', 'h2o_q-1_ub3lyp_ccpvtz.fchk') as fname:
model1 = GlobalConceptualDFT.from_file(fname, "linear")
model2 = GlobalConceptualDFT.from_file([fname], "linear")
# check from_file
check_global_reactivity_linear(model1, ip, ea, energy, 11)
# check from_file given as a list
check_global_reactivity_linear(model2, ip, ea, energy, 11)
def test_global_quadratic_from_file_fmo_h2o_cation_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(-8.47044131E-01), -(
-6.19391831E-01), -7.599493522312368E+01
with path("chemtools.data", "h2o_q+1_ub3lyp_ccpvtz.fchk") as fname:
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
model2 = GlobalConceptualDFT.from_file([fname], "quadratic")
# check quadratic global conceptual DFT model from a fname given as string
check_global_reactivity_quadratic(model1, ip, ea, energy, 9)
# check quadratic global conceptual DFT model from a fname given as a list of string
check_global_reactivity_quadratic(model2, ip, ea, energy, 9)
def test_global_quadratic_from_file_fmo_h2o_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(
-3.09871604E-01), -2.48704636E-02, -7.645980351270224E+01
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as fname:
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
model2 = GlobalConceptualDFT.from_file([fname], "quadratic")
# check from_file
check_global_reactivity_quadratic(model1, ip, ea, energy, 10)
# check from_file given as a list
check_global_reactivity_quadratic(model2, ip, ea, energy, 10)
def test_global_quadratic_from_file_fmo_ch4_wfn():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(
-5.43101269E-01), -1.93295185E-01, -4.019868797400735E+01
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
model2 = GlobalConceptualDFT.from_file([fname], "quadratic")
# check from_file
check_global_reactivity_quadratic(model1, ip, ea, energy, 10)
# check from_file given as a list
check_global_reactivity_quadratic(model2, ip, ea, energy, 10)
def test_global_linear_from_file_fmo_h2o_cation_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(-8.47044131E-01), -(
-6.19391831E-01), -7.599493522312368E+01
with path('chemtools.data', 'h2o_q+1_ub3lyp_ccpvtz.fchk') as fname:
model1 = GlobalConceptualDFT.from_file(fname, "linear")
model2 = GlobalConceptualDFT.from_file([fname], "linear")
# check from_file
check_global_reactivity_linear(model1, ip, ea, energy, 9)
# check from_file given as a list
check_global_reactivity_linear(model2, ip, ea, energy, 9)
def test_global_quadratic_from_molecule_fmo_ch4_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(
-5.43101269E-01), -1.93295185E-01, -4.019868797400735E+01
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
molecule = Molecule.from_file(fname)
# check from_molecule
model = GlobalConceptualDFT.from_molecule(molecule, "quadratic")
check_global_reactivity_quadratic(model, ip, ea, energy, 10)
# check from_molecule given as a list
model = GlobalConceptualDFT.from_molecule([molecule], "quadratic")
check_global_reactivity_quadratic(model, ip, ea, energy, 10)
def test_global_linear_from_molecule_fmo_h2o_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(
-3.09871604E-01), -2.48704636E-02, -7.645980351270224E+01
with path('chemtools.data', 'h2o_q+0_ub3lyp_ccpvtz.fchk') as fname:
molecule = Molecule.from_file(fname)
# check from_molecule
model = GlobalConceptualDFT.from_molecule(molecule, "linear")
check_global_reactivity_linear(model, ip, ea, energy, 10)
# check from_molecule given as a list
model = GlobalConceptualDFT.from_molecule([molecule], "linear")
check_global_reactivity_linear(model, ip, ea, energy, 10)
def test_global_linear_from_file_fmo_ch4_fchk():
# FMO: ip = -E(H**O) & ea = -E(LUMO)
ip, ea, energy = -(
-5.43101269E-01), -1.93295185E-01, -4.019868797400735E+01
# check from_file
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
model = GlobalConceptualDFT.from_file(fname, "linear")
check_global_reactivity_linear(model, ip, ea, energy, 10)
# check from_file given as a list
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
model = GlobalConceptualDFT.from_file([fname], "linear")
check_global_reactivity_linear(model, ip, ea, energy, 10)
def test_global_conceptual_raises():
# dictionary of energy values
values = {0.0: 0.0, 1.0: -0.5, 2.0: -0.45}
# check invalid model
assert_raises(ValueError, GlobalConceptualDFT, values, "quad")
assert_raises(ValueError, GlobalConceptualDFT, values, "Gibberish")
assert_raises(NotImplementedError, GlobalConceptualDFT, values, "general")
# check invalid coordinates
assert_raises(ValueError, GlobalConceptualDFT, values, "linear",
np.array([0., 0., 0.]))
assert_raises(ValueError, GlobalConceptualDFT, values, "linear",
np.array([[0., 0.]]))
# check invalid atomic numbers
coord = np.array([[0., 0., 0.]])
assert_raises(ValueError, GlobalConceptualDFT, values, "linear", coord, [])
assert_raises(ValueError, GlobalConceptualDFT, values, "linear", coord,
[1, 1])
# check invalid number of electrons
values = {"0": 0.0, 1: -0.5, 2: -0.45}
assert_raises(ValueError, GlobalConceptualDFT, values, "linear", coord)
assert_raises(ValueError, GlobalConceptualDFT, values, "quadratic", coord)
values = {0.5: 0.0, 1.3: -0.5, 2: -0.45}
assert_raises(ValueError, GlobalConceptualDFT, values, "linear", coord)
assert_raises(ValueError, GlobalConceptualDFT, values, "quadratic", coord)
values = {0: 0.0, 1: -0.5, 3: -0.45}
assert_raises(ValueError, GlobalConceptualDFT, values, "linear")
assert_raises(ValueError, GlobalConceptualDFT, values, "quadratic")
values = {0: 0.0, 1: -0.5, 2: -0.45, 3: -0.4}
assert_raises(ValueError, GlobalConceptualDFT, values, "linear", coord)
assert_raises(ValueError, GlobalConceptualDFT, values, "quadratic", coord)
# check non-existing attribute
model = GlobalConceptualDFT({0.0: 0.0, 1.0: -0.5, 2.0: -0.45}, "quadratic")
assert_raises(AttributeError, getattr, model, "mu_plus")
assert_raises(AttributeError, getattr, model, "gibberish")
# check molecule file inconsistency
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as file1:
with path('chemtools.data', 'o2_uhf.fchk') as file2:
fnames = [file1, file2]
assert_raises(ValueError, GlobalConceptualDFT.from_file, fnames,
"linear")
assert_raises(ValueError, GlobalConceptualDFT.from_file, fnames,
"quadratic")
with path('chemtools.data', 'ch4_uhf_ccpvdz.fchk') as fname:
assert_raises(ValueError, GlobalConceptualDFT.from_file,
[fname, fname], "linear")
assert_raises(ValueError, GlobalConceptualDFT.from_file,
[fname, fname], "quadratic")
assert_raises(ValueError, GlobalConceptualDFT.from_file,
[fname, fname, fname], "linear")
assert_raises(ValueError, GlobalConceptualDFT.from_file,
[fname, fname, fname], "quadratic")
def test_global_quadratic_fd_h2o_fchk():
ep, e0, en = -7.599493522312368E+01, -7.645980351270224E+01, -7.635212549312298E+01
ip, ea, energy = ep - e0, e0 - en, e0
# check quadratic global conceptual DFT model
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 = GlobalConceptualDFT.from_file(fname, "quadratic")
molecule = [Molecule.from_file(item) for item in fname]
model2 = GlobalConceptualDFT.from_molecule(
molecule, "quadratic")
# cehck from_file
check_global_reactivity_quadratic(model1, ip, ea, energy, 10)
# check from_molecule
check_global_reactivity_quadratic(model2, ip, ea, energy, 10)
# rearrange input files
with path("chemtools.data", "h2o_q+1_ub3lyp_ccpvtz.fchk") as file1:
with path("chemtools.data", "h2o_q+0_ub3lyp_ccpvtz.fchk") as file2:
with path("chemtools.data", "h2o_q-1_ub3lyp_ccpvtz.fchk") as file3:
fname = [file1, file2, file3]
# check from_file
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
molecule = [Molecule.from_file(item) for item in fname]
model2 = GlobalConceptualDFT.from_molecule(
molecule, "quadratic")
check_global_reactivity_quadratic(model1, ip, ea, energy, 10)
# check from_molecule
check_global_reactivity_quadratic(model2, ip, ea, energy, 10)
# rearrange input files
with path("chemtools.data", "h2o_q-1_ub3lyp_ccpvtz.fchk") as file1:
with path("chemtools.data", "h2o_q+1_ub3lyp_ccpvtz.fchk") as file2:
with path("chemtools.data", "h2o_q+0_ub3lyp_ccpvtz.fchk") as file3:
fname = [file1, file2, file3]
model1 = GlobalConceptualDFT.from_file(fname, "quadratic")
molecule = [Molecule.from_file(item) for item in fname]
model2 = GlobalConceptualDFT.from_molecule(
molecule, "quadratic")
# check from_file
check_global_reactivity_quadratic(model1, ip, ea, energy, 10)
# check from_molecule
check_global_reactivity_quadratic(model2, ip, ea, energy, 10)