¶ Xponge.helper.math
This module is used to provide basic common math functions
¶ subpackages
¶ submodules
¶ functions
¶ get_rotate_matrix
This function is used to get the rotation matrix by the axis and the angle
| parameters |
explanation |
| r0 |
the axis to rotate around |
| angle |
the angle to rotate |
| return |
the rotation matrix |
¶ kabsch
This function uses Kabsch algorithm to align two sets of positions
| parameters |
explanation |
| positions1 |
the first set of positions, a numpy array with shape (N,3) |
| positions2 |
the second set of positions, a numpy array with shape (N,3) |
| return |
a tuple of 3 numpy arrays |
¶ get_fibonacci_grid
This function is used to get the sphere grid by fibonacci algorithm
| parameters |
explanation |
| n |
the number of grids |
| origin |
the origin of the sphere |
| radius |
the radius of the sphere |
| return |
a numpy array of grid coordinates |
¶ guess_element_from_mass
This function is used to guess element from its mass
| parameters |
explanation |
| mass |
an int or a float, the mass |
¶ get_basis_vectors_from_length_and_angle
This function is used to get the basis vectors from the cell lengths and cell angles.
| parameters |
explanation |
| a |
the length of the first basis vector |
| b |
the length of the second basis vector |
| c |
the length of the third basis vector |
| alpha |
the angle between the second and the third basis vectors |
| beta |
the angle between the first and the third basis vectors |
| gamma |
the angle between the first and the second basis vectors |
| angle_in_degree |
whether the unit of the angles is degree, True for default. |
| return |
a 3x3 numpy array, and every row is one basis vector |
