def plot_full_rad(self, step, rotation=0):
x, y, z = self._ranges
Z, Y = np.meshgrid(z, y)
density_slide = self.fn_electronic_density(np.array([[rotations.rotate_align_z([0, j, k],
rotation,
center=self._center,
align=self._align,
radial=self._radial
) for k in z] for j in y]))
for val in np.arange(self._ranges[0][0]+step, self._ranges[0][-1], step):
density_slide += self.fn_electronic_density(np.array([[rotations.rotate_align_z([i, j, val],
rotation,
center=self._center,
align=self._align,
radial=self._radial
) for j in y] for i in x]))
density_slide *=step
plt.contourf(Y, Z, density_slide)
if self._radial:
plt.xlabel("Angle (Radian)")
plt.ylabel("Radius (Bohr)")
else:
plt.xlabel("Bohr")
plt.ylabel("Bohr")
plt.colorbar().set_label("Electronic density (e-/Bohr^3)")
plt.show()
def get_density(self):
if self._density is None:
x, y, z = self._ranges
self._density = self.fn_electronic_density(np.array([[[rotations.rotate_align_z([i, j, k],
0,
center=self._center,
align=self._align,
radial=self._radial,
) for k in z] for j in y] for i in x]))
return self._density
def plot_full(self, step, rotation=0):
x, y, z = self._ranges_cart
Y, X = np.meshgrid(y, x)
density_slide = self.fn_electronic_density(np.array([[rotations.rotate_align_z([i, j, 0],
rotation,
center=self._center,
align=self._align
) for j in y] for i in x]))
for val in np.arange(self._ranges[0][0]+step, self._ranges[0][-1], step):
density_slide += self.fn_electronic_density(np.array([[rotations.rotate_align_z([i, j, val],
rotation,
center=self._center,
align=self._align
) for j in y] for i in x]))
density_slide *=step
# levels = np.linspace(0, 0.5, 40)
plt.xlabel("Bohr")
plt.ylabel("Bohr")
plt.contourf(X, Y, density_slide)
plt.colorbar().set_label("Electronic density (e-/Bohr^2)")
plt.show()
def get_total_overlap(self):
if self._total_overlap is None:
# print('getting_overlap')
x, y, z = self._ranges
overlappings = []
for i in range(self._order):
# print('overlap: {0}'.format(i))
angle = 2*np.pi/self._order * i
dens_rot = self.fn_electronic_density(np.array([[[rotations.rotate_align_z([i, j, k],
angle, center=self._center,
align=self._align,
radial=self._radial
) for k in z] for j in y] for i in x]))
overlappings.append(np.multiply(self.get_density(), dens_rot))
self._total_overlap = sum(overlappings)/self._order
return self._total_overlap
def plot_slide_rad(self, val, rotation=0):
x, y, z = self._ranges
Z, Y = np.meshgrid(z, y)
density_slide = self.fn_electronic_density(np.array([[rotations.rotate_align_z([val, j, k],
rotation,
center=self._center,
align=self._align,
radial=self._radial
) for k in z] for j in y]))
plt.contourf(Y, Z, density_slide)
if self._radial:
plt.xlabel("Angle (Radian)")
plt.ylabel("Radius (Bohr)")
else:
plt.xlabel("Bohr")
plt.ylabel("Bohr")
plt.colorbar().set_label("Electronic density (e-/Bohr^3)")
plt.show()