def mol_tester(lbl, molstr, pg, sigma, refgeomang, isbohr=False, iso=False):
symmol = qcdb.Molecule(molstr)
if iso is not False:
if isinstance(iso, int):
iso = [iso]
for at in iso:
# mass needn't make sense for element, just breaking the symmetry
symmol.set_mass(at, 2.014)
symmol.update_geometry()
symmol.axis_representation()
assert compare_strings(pg, symmol.get_full_point_group(), pg + " point group: " + lbl)
assert compare_integers(sigma, symmol.rotational_symmetry_number(), pg + " sigma")
if isbohr:
geom_now = symmol.full_geometry()
else:
geom_now = qcdb.mscale(symmol.full_geometry(), qcel.constants.bohr2angstroms)
if refgeomang:
assert compare_matrices(refgeomang, geom_now, 6, pg + " orientation")
[ -0.707106781187, -0.000000000000, -0.627971015380]]
geom_h2of = \
[[ 0.000000000000, 0.000000000000, -0.079135765807],
[ -0.000000000000, 0.707106781187, 0.627971015380],
[ 0.000000000000, -0.707106781187, 0.627971015380]]
h2oA = qcdb.Molecule("""
O
H 1 1.0
H 1 1.0 2 90.0
""")
h2oA.update_geometry()
#h2oA.print_out()
geom_now = qcdb.mscale(h2oA.geometry(), qcdb.psi_bohr2angstroms)
qcdb.compare_matrices(geom_h2oa, geom_now, 6,
"H2O A geometry and orientation") #TEST
h2oB = qcdb.Molecule("""
O 0.000000000000 0.000000000000 -0.079135765807
H 0.000000000000 -0.707106781187 0.627971015380
H 0.000000000000 0.707106781187 0.627971015380
""")
h2oB.update_geometry()
#h2oB.print_out()
geom_now = qcdb.mscale(h2oB.geometry(), qcdb.psi_bohr2angstroms)
qcdb.compare_matrices(geom_h2ob, geom_now, 6,
"H2O B geometry and orientation") #TEST
h2oC = qcdb.Molecule("""
def test_mints4():
#! A demonstration of mixed Cartesian/ZMatrix geometry specification, using variables, for
#! the benzene-hydronium complex. Atoms can be placed using ZMatrix coordinates, whether they belong
#! to the same fragment or not. Note that the Cartesian specification must come before the ZMatrix entries
#! because the former define absolute positions, while the latter are relative.
refENuc = 268.617178206572646
refGEOM = \
[[ 0.710500000000, -0.794637665924, -1.230622098778],
[ 1.421000000000, -0.794637665924, 0.000000000000],
[ 0.710500000000, -0.794637665924, 1.230622098778],
[ -0.710500000000, -0.794637665924, 1.230622098778],
[ 1.254500000000, -0.794637665924, -2.172857738095],
[ -1.254500000000, -0.794637665924, 2.172857738095],
[ -0.710500000000, -0.794637665924, -1.230622098778],
[ -1.421000000000, -0.794637665924, 0.000000000000],
[ 2.509000000000, -0.794637665924, 0.000000000000],
[ 1.254500000000, -0.794637665924, 2.172857738095],
[ -1.254500000000, -0.794637665924, -2.172857738095],
[ -2.509000000000, -0.794637665924, 0.000000000000],
[ 0.000000000000, 3.205362334076, 0.000000000000],
[ 0.494974746831, 3.555362334076, -0.857321409974],
[ 0.494974746831, 3.555362334076, 0.857321409974],
[ -0.989949493661, 3.555362334076, 0.000000000000]]
dimer = qcdb.Molecule("""
1 1
# This part is just a normal Cartesian geometry specification for benzene
C 0.710500000000 -0.794637665924 -1.230622098778
C 1.421000000000 -0.794637665924 0.000000000000
C 0.710500000000 -0.794637665924 1.230622098778
C -0.710500000000 -0.794637665924 1.230622098778
H 1.254500000000 -0.794637665924 -2.172857738095
H -1.254500000000 -0.794637665924 2.172857738095
C -0.710500000000 -0.794637665924 -1.230622098778
C -1.421000000000 -0.794637665924 0.000000000000
H 2.509000000000 -0.794637665924 0.000000000000
H 1.254500000000 -0.794637665924 2.172857738095
H -1.254500000000 -0.794637665924 -2.172857738095
H -2.509000000000 -0.794637665924 0.000000000000
# And the hydronium part is specified using a zmatrix, referencing the benzene coordinates
X 1 CC 3 30 2 A2
O 13 R 1 90 2 90
H 14 OH 13 TDA 1 0
H 14 OH 15 TDA 13 A1
H 14 OH 15 TDA 13 -A1
CC = 1.421
CH = 1.088
A1 = 120.0
A2 = 180.0
OH = 1.05
R = 4.0
units angstrom
""")
dimer.update_geometry()
assert compare_values(refENuc, dimer.nuclear_repulsion_energy(), 9, "Bz-H3O+: nuclear repulsion energy")
geom_now = qcdb.mscale(dimer.geometry(), qcdb.psi_bohr2angstroms)
assert compare_matrices(refGEOM, geom_now, 6, "Bz-H3O+: geometry and orientation")
def test_mints4():
#! A demonstration of mixed Cartesian/ZMatrix geometry specification, using variables, for
#! the benzene-hydronium complex. Atoms can be placed using ZMatrix coordinates, whether they belong
#! to the same fragment or not. Note that the Cartesian specification must come before the ZMatrix entries
#! because the former define absolute positions, while the latter are relative.
refENuc = 268.6171792624
refGEOM = \
[[ 0.710500000000, -0.794637665924, -1.230622098778],
[ 1.421000000000, -0.794637665924, 0.000000000000],
[ 0.710500000000, -0.794637665924, 1.230622098778],
[ -0.710500000000, -0.794637665924, 1.230622098778],
[ 1.254500000000, -0.794637665924, -2.172857738095],
[ -1.254500000000, -0.794637665924, 2.172857738095],
[ -0.710500000000, -0.794637665924, -1.230622098778],
[ -1.421000000000, -0.794637665924, 0.000000000000],
[ 2.509000000000, -0.794637665924, 0.000000000000],
[ 1.254500000000, -0.794637665924, 2.172857738095],
[ -1.254500000000, -0.794637665924, -2.172857738095],
[ -2.509000000000, -0.794637665924, 0.000000000000],
[ 0.000000000000, 3.205362334076, 0.000000000000],
[ 0.494974746831, 3.555362334076, -0.857321409974],
[ 0.494974746831, 3.555362334076, 0.857321409974],
[ -0.989949493661, 3.555362334076, 0.000000000000]]
dimer = qcdb.Molecule("""
1 1
# This part is just a normal Cartesian geometry specification for benzene
C 0.710500000000 -0.794637665924 -1.230622098778
C 1.421000000000 -0.794637665924 0.000000000000
C 0.710500000000 -0.794637665924 1.230622098778
C -0.710500000000 -0.794637665924 1.230622098778
H 1.254500000000 -0.794637665924 -2.172857738095
H -1.254500000000 -0.794637665924 2.172857738095
C -0.710500000000 -0.794637665924 -1.230622098778
C -1.421000000000 -0.794637665924 0.000000000000
H 2.509000000000 -0.794637665924 0.000000000000
H 1.254500000000 -0.794637665924 2.172857738095
H -1.254500000000 -0.794637665924 -2.172857738095
H -2.509000000000 -0.794637665924 0.000000000000
# And the hydronium part is specified using a zmatrix, referencing the benzene coordinates
X 1 CC 3 30 2 A2
O 13 R 1 90 2 90
H 14 OH 13 TDA 1 0
H 14 OH 15 TDA 13 A1
H 14 OH 15 TDA 13 -A1
CC = 1.421
CH = 1.088
A1 = 120.0
A2 = 180.0
OH = 1.05
R = 4.0
units angstrom
""")
dimer.update_geometry()
assert compare_values(refENuc, dimer.nuclear_repulsion_energy(), 9,
"Bz-H3O+: nuclear repulsion energy")
geom_now = qcdb.mscale(dimer.geometry(), qcdb.psi_bohr2angstroms)
assert compare_matrices(refGEOM, geom_now, 6,
"Bz-H3O+: geometry and orientation")