def test_Plotting(self):
g = Graphics3D(image_size=[1500, 1500],
plot_range=[[-10, 10]] * 3,
backend="VTK")
h5 = Molecule.from_file(
self.test_log_h2,
# self.test_fchk,
# bonds = [
# [0, 1, 1],
# [0, 2, 1]
# ]
)
h5.plot(
figure=g
# mode='3D',
# bond_style= { "circle_points": 24 },
# atom_style= { "sphere_points": 24 }
)
m = Molecule.from_file(self.test_fchk, bonds=[[0, 1, 1], [0, 2, 1]])
m.plot(
figure=g
# mode='3D',
# bond_style= { "circle_points": 24 },
# atom_style= { "sphere_points": 24 }
)
def test_RenormalizeGaussianModes(self):
with GaussianFChkReader(self.test_HOD) as gr:
parse = gr.parse([
"Coordinates", "Gradient", "AtomicMasses", "ForceConstants",
"ForceDerivatives", "VibrationalModes", "VibrationalData"
])
coords = UnitsData.convert("Angstroms",
"AtomicUnitOfLength") * parse["Coordinates"]
masses = UnitsData.convert("AtomicMassUnits",
"AtomicUnitOfMass") * parse["AtomicMasses"]
modes = parse["VibrationalModes"].T
freqs = parse["VibrationalData"]["Frequencies"]
fcs = parse["ForceConstants"].array
sad = UnitsData.convert("Hartrees", "Wavenumbers") * np.sqrt(
np.diag(np.dot(np.dot(modes.T, fcs), modes)))
modes = modes * freqs / sad
print(
UnitsData.convert("Hartrees", "Wavenumbers") *
np.sqrt(np.diag(np.dot(np.dot(modes.T, fcs), modes))))
masses = np.broadcast_to(masses, (len(masses), 3)).T.flatten()
# print(modes-np.linalg.pinv(modes).T)
print(np.dot(np.dot(modes.T, np.diag(masses)), modes))
modes_2 = Molecule.from_file(
self.test_HOD).get_normal_modes(normalize=False)
mm = modes_2._basis.matrix
print(np.dot(np.dot(mm.T, np.diag(masses)), mm))
print(
UnitsData.convert("Hartrees", "Wavenumbers") *
np.sqrt(np.diag(np.dot(np.dot(mm.T, fcs), mm))))
def test_HODModes(self):
# oops f****d up getting D out
m = Molecule.from_file(self.test_HOD, bonds=[[0, 1, 1], [0, 2, 1]])
modes = m.normal_modes
self.assertEquals(m.atoms, ("O", "H", "D"))
self.assertEquals(tuple(np.round(modes.freqs)),
(1422.0, 2810.0, 3874.0))
def test_VisualizeNormalModes(self):
from Psience.Molecools.Vibrations import VibrationalModes, NormalModeCoordinates
from McUtils.Plots import GraphicsGrid, Graphics3D
m = Molecule.from_file(self.test_fchk, bonds=[[0, 1, 1], [0, 2, 1]])
with GaussianFChkReader(self.test_fchk) as reader:
parse = reader.parse(("VibrationalModes", "VibrationalData"))
modes = parse["VibrationalModes"].T
test_freqs = parse["VibrationalData"]["Frequencies"]
nms = m.normal_modes
realvibs = VibrationalModes(m,
basis=NormalModeCoordinates(
modes, freqs=test_freqs))
plot_vibrations = False
if plot_vibrations:
nmodes = 1
mode_start = 0
g = GraphicsGrid(nrows=2,
ncols=nmodes,
graphics_class=Graphics3D,
plot_range=[[-2, 2], [-2, 2], [-2, 2]],
fig_kw=dict(figsize=(17, 5)),
tighten=True)
for i in range(nmodes):
nms.visualize(step_size=.1,
figure=g[0, i],
which=mode_start + i,
anim_opts=dict(interval=10))
for i in range(nmodes):
realvibs.visualize(step_size=.1,
figure=g[1, i],
which=mode_start + i,
anim_opts=dict(interval=10))
g.show()
self.assertEquals(tuple(round(a, 4) for a in nms.freqs),
tuple(round(a, 4) for a in test_freqs))
def test_H2OModes(self):
m = Molecule.from_file(self.test_fchk, bonds=[[0, 1, 1], [0, 2, 1]])
modes = m.normal_modes
self.assertEquals(m.atoms, ("O", "H", "H"))
self.assertEquals(tuple(np.round(modes.freqs)),
(1622.0, 3803.0, 3938.0))
def test_AutoZMat(self):
m = Molecule.from_file(self.test_fchk)
def test_Frags(self):
m = Molecule.from_file(self.test_fchk)
self.assertEquals(len(m.prop("fragments")), 1)
def test_BondGuessing(self):
m = Molecule.from_file(self.test_fchk)
self.assertEquals(m.bonds, [[0, 1, 1], [0, 2, 1]])
def test_ImportMolecule(self):
n = 3 # water
m = Molecule.from_file(self.test_fchk)
self.assertEquals(m.atoms, ("O", "H", "H"))