def make_cone_path(file1, file2, save, N=20):
save = Path(save)
container1 = magnes.io.load(str(file1))
system = container1.extract_system()
s0 = container1["PATH"][0]
size = s0.shape
path = []
path_len = N - 1
for n in range(N):
state = system.field3D()
theta = np.pi * (1 + n / path_len) * (
1 - np.linspace(0, 1, size[2])) - np.pi
phi_0 = 4 * n * (path_len - n) / (path_len * path_len
) #(0,1) 1 at n=path_len/2
phi = np.arcsin(phi_0 * (1 - np.linspace(0, 1, size[2])))
print(
f'{theta.min() = },{theta.max() = },{np.sin(phi.min()) = },{np.sin(phi.max()) = }'
)
x, y, z = cs.sp2cart(r=1, theta=phi, phi=theta)
s = np.zeros([1, 1, size[2], 1, 3])
s[0, 0, :, 0, 0] = x
s[0, 0, :, 0, 1] = y
s[0, 0, :, 0, 2] = z
state.upload(s)
path.append(state)
path = magnes.Path(path)
path = path.interpolate(relative_positions=np.linspace(0, 1, N))
container = magnes.io.container('.npz')
container.store_system(system)
container["PATH"] = path.download()
container.save(str(save))
# Radius of Hydrogen atom
r_H = 53e-12 # m
# Carbon - Hydrogen Bond Length
BL_CH = 160e-12 # m
r_min, r_max = -BL_CH * 2, BL_CH * 2
# Tetrahedral angle (109.4 deg) - 90 deg
tet_theta = -asin(1 / 3)
# Charge Districution for C atom
C_chargeArray = [4 * e] + [-e] * 4
C_chargePosArray = np.array(
sp2cart([0] + [r_C] * 4, [0, pi / 2] + [tet_theta] * 3,
[0, 0, -pi / 3, pi / 3, pi])).transpose()
C_ChargeDist = ChargeDistribution(C_chargeArray, C_chargePosArray)
# Array of positions of H atoms
H_PosArray = np.array(
sp2cart([BL_CH] * 4, [pi / 2] + [tet_theta] * 3,
[0, -pi / 3, pi / 3, pi])).transpose()
# Array of positions of electron of H atom
# assuming them to be farther away from the C atom
H_e_PosArray = np.array(
sp2cart([BL_CH + r_H] * 4, [pi / 2] + [tet_theta] * 3,
[0, -pi / 3, pi / 3, pi])).transpose()
# H atom Dipoles
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.ticker import FormatStrFormatter
import matplotlib.pyplot as plt
a = 38e-12 # m
n_frames = 50
frequency = 10 # Hz
r_min, r_max = a * 10, a * 15
chargeArray = [4 * e] + [-e] * 4
tet_theta = -asin(1 / 3)
chargePosArray = np.array(
sp2cart([0] + [a] * 4, [0, pi / 2] + [tet_theta] * 3,
[0, 0, -pi / 3, pi / 3, pi])).transpose()
myChargeDist = ChargeDistribution(chargeArray, chargePosArray)
n_points = 20
r_array = np.linspace(r_min, r_max, n_points)
theta_array = np.linspace(tet_theta, pi / 2, n_points)
phi_array = np.linspace(-pi / 3, pi / 3, n_frames)
V_Tensor = np.zeros((n_frames, n_points, n_points))
print('Started calculating V_Tensor')
for i in range(n_frames):
print('Started calculating V_Tensor')
for i in range(n_frames) :
phi = phi_array[i]
for j in range(n_points) :
r = r_array[j]
for k in range(n_points) :
theta = theta_array[k]
pos = np.array(sp2cart(r, theta, phi))
V_Tensor[i][j][k] = myChargeDist.V(pos)
print('Finished calculating V_Tensor')
X, Y = np.meshgrid(r_array, theta_array * 180 / np.pi, indexing='ij')
fig = plt.figure(figsize=(16,10))
ax = fig.gca(projection='3d')
surf = [ ax.plot_surface(X, Y, V_Tensor[0], cmap='magma', rstride=1, cstride=1) ]
def update(i) :
Axes3D.set_title(ax, label=(r'$\phi$ = ' + str(round(phi_array[i] * 180 / np.pi)) + r'$^o$'))
def set_theta_phi(self, theta, phi) :
self.p = sp2cart(np.linalg.norm(self.p), theta, phi)
pass
from electric_multipoles import ChargeDistribution, e
from mayavi.mlab import contour3d
from ai.cs import sp2cart
from math import asin, pi
import numpy as np
a = 38e-12 # m
r_min, r_max = -2*a, 2*a
chargeArray = [4*e] + [-e]*4
tet_theta = - asin(1/3)
chargePosArray = np.array( sp2cart([0] + [a]*4, [0, pi/2] + [tet_theta] * 3, [0, 0, -pi/3, pi/3, pi]) ).transpose()
myChargeDist = ChargeDistribution(chargeArray, chargePosArray)
n_points = 20
x_array = np.linspace(r_min, r_max, n_points)
y_array = np.linspace(r_min, r_max, n_points)
z_array = np.linspace(r_min, r_max, n_points)
V_Tensor = np.zeros((n_points, n_points, n_points))
print('Started calculating V_Tensor')
for i in range(n_points) :
x = x_array[i]
from electric_multipoles import ChargeDistribution, e
from ai.cs import sp2cart
from math import asin, pi
import numpy as np
a = 38e-12 # m
r_o = np.array([0, 0, 0]) * 1e-10
chargeArray = [4 * e] + [-e] * 4
tet_theta = -asin(1 / 3)
chargePosArray = np.array(
sp2cart([0] + [a] * 4, [0, pi / 2] + [tet_theta] * 3,
[0, 0, -pi / 3, pi / 3, pi])).transpose()
myChargeDist = ChargeDistribution(chargeArray, chargePosArray)
print('\nP_e : ')
print(myChargeDist.P_e(r_o))
print('\nq_e : ')
print(myChargeDist.q_e(r_o))
print('\nQ_e : ')
print(myChargeDist.Q_e(r_o))
r_H = 53e-12 # m
# Carbon - Hydrogen Bond Length
BL_CH = 160e-12 # m
n_frames = 50
r_min, r_max = BL_CH * 10, BL_CH * 15
# Tetrahedral angle (109.4 deg) - 90 deg
tet_theta = -asin(1 / 3)
# Charge Districution for C atom
C_chargeArray = [4 * e] + [-e] * 4
C_chargePosArray = np.array(
sp2cart([0] + [r_C] * 4, [0, pi / 2] + [tet_theta] * 3,
[0, 0, -pi / 3, pi / 3, pi])).transpose()
C_ChargeDist = ChargeDistribution(C_chargeArray, C_chargePosArray)
# Array of positions of H atoms
H_PosArray = np.array(
sp2cart([BL_CH] * 4, [pi / 2] + [tet_theta] * 3,
[0, -pi / 3, pi / 3, pi])).transpose()
# Array of positions of electron of H atom
# assuming them to be farther away from the C atom
H_e_PosArray = np.array(
sp2cart([BL_CH + r_H] * 4, [pi / 2] + [tet_theta] * 3,
[0, -pi / 3, pi / 3, pi])).transpose()
# H atom Dipoles
