为什么更改变量中的参数对转换后的坐标没有影响？

Question

我编写了这段代码，将六边形连接晶格的一组 2d 坐标包装到 3d 圆柱体中：

import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d.axes3d as axes3d
import matplotlib.colors 

with open("test_A_aux.dat", "r") as aux:
    dim = np.genfromtxt(aux, skip_header =3, max_rows = 1)

n = int(input("Enter the value for n: ")) 
m = int(input("Enter the value for m: "))

# Open coordinate file and import data to array
with open("test_A_crds.dat", "r") as crds:
    array = np.genfromtxt(crds)

# Defines the chiral angle based on a1 and a2 vectors 
# This is then used to manipulate x,y coords onto the vector  
def chiral_angle(n, m):
    # a1 vector is set along x axis 
    a1 = np.array([np.sqrt(3),0])
    a2 = np.array([np.sqrt(3)/2, 3/2])
    # chiral vector is the dot product of n * a1 and m * a2
    chiral_vector = np.add(np.multiply(a1, n), np.multiply(a2, m))
    # magnitude of chiral vector
    mag = np.linalg.norm(chiral_vector)
    # dot product formula to find cos theta
    cos_theta = np.dot(chiral_vector, np.array([1,0])) / mag
    theta = np.arccos(cos_theta)
    return theta

# This function wraps the 2d coordinates into a cylinder by maniuplating
# the y cooridnates and generating z coordinates 
# x coordinates unchaged
def wrap(n, m):
    # normalises to max length of the dimensions of the input cell
    normalise = matplotlib.colors.Normalize(0, dim[1])
    X = array[:,0]
    THETA = np.array([2*np.pi * normalise(i) for i in array[:,1]])
    r = dim[1] / (2 * np.pi)
    Y = np.array([r * np.sin(angle) for angle in THETA])
    Z = np.array([r * np.cos(angle) for angle in THETA])
    # stacks X and Y into n*2 array
    tube = np.vstack((X, Y))
    # stacks above n*2 array with Z to make n*3 array
    tube = np.vstack((tube, Z))
    # transposes array to make 3*n array of 3D coordinates
    tube = np.transpose(tube)
    return tube

# Plotting function
def plot_tube():
    fig = plt.figure()
    ax = fig.add_subplot(1,1,1, projection='3d')
    plot = ax.scatter(tube[:,0], tube[:,1], tube[:,2])
    plt.show()
    return



# creates file and writes it to vmd for visualisation
# with open("nanotube.xyz", "w") as vmd:
#    vmd.write("{:}\n\n " .format(array.shape[0]))
#    for i in range(array.shape[0]):
#       vmd.write("{:} {:<10} {:<10} {:<10}\n" .format(i, tube[i,0], tube[i,1], tube[i,2]))

tube = wrap(n, m)        
print(tube)
plot_tube()

但是更改 n 和 m 变量对输出的 3d 坐标没有影响。作为参考，手性向量如下所示：

a1 沿 x 轴设置。

如何使 n 和 m 影响手性矢量，从而影响角度 theta 和管子的最终形状？

数据：https://www.dropbox.com/scl/fi/m16rn9uxgsahsysj8y50l/test_A_crds.dat?rlkey=44dtrzxbcwapalntyqv24ox56&dl=0

Answer 1

您没有在wrap 函数中使用chiral_angle 计算。我无法测试，没有数据，但在我看来，你需要在 THETA 计算行中使用 chiral_angle(n, m) 而不是 2*np.pi 。