绕转矩阵和坐标变换矩阵

最近在研究原子坐标变换的时候用到了两个矩阵，就记录一下。

1. 绕转

齐次坐标系

import numpy as np

# 需要使用4 x 1的齐次坐标系，所以要把三维列补上一行（见第二句）
# theta: 绕转角；u,v,w: 归一化的绕转向量（旋转平面法向量，通过np.cross()获得）


rotationMatrix = np.array([[np.square(u)+(1-np.square(u))*np.cos(theta),u*v*(1-np.cos(theta))-w*np.sin(theta),u*w*(1-np.cos(theta))+v*np.sin(theta),0],
                           [u*v*(1-np.cos(theta))+w*np.sin(theta),np.square(v)+(1-np.square(v))*np.cos(theta),v*w*(1-np.cos(theta))-u*np.sin(theta),0],
                           [u*w*(1-np.cos(theta))-v*np.sin(theta),v*w*(1-np.cos(theta))+u*np.sin(theta),np.square(w)+(1-np.square(w))*np.cos(theta),0],
                           [0,0,0,1]])
coordinationMatrix_added = np.r_[coordinationMatrix,np.array([[1]])]

newCoordMatrix = np.dot(rotationMartix, coordinationMatrix_added)

1. 相对坐标与绝对坐标变换

import numpy as np

# oldCoordinate: oldX, oldY, oldZ
# newCoordinate: newX, newY, newZ
# a, b, c
# alpha, beta, gamma
conversionMatrix = np.array([[a, b * np.cos(gamma), c * np.cos(beta)],
                             [0, b * np.sin(gamma), c * (np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / np.sin(gamma)],
                             [0, 0, c * np.sqrt(np.sin(beta) * np.sin(beta) - np.power(
                               (np.cos(alpha) - np.cos(beta) * np.cos(gamma)) / np.sin(gamma), 2))]])