Coverage for /builds/ase/ase/ase/md/fix.py: 100.00%

1# fmt: off 

2 

3import numpy as np 

4 

5 

6class FixRotation: 

7 """Remove rotation from an atoms object. 

8 

9 This class is intended as an observer on an atoms class during 

10 a molecular dynamics simulation. When it is called, it removes 

11 any rotation around the center of mass. 

12 

13 It assumes that the system is a (nano)particle with free boundary 

14 conditions. 

15 

16 Bugs: 

17 Should check that the boundary conditions make sense. 

18 """ 

19 

20 def __init__(self, atoms): 

21 self.atoms = atoms 

22 

23 def __call__(self): 

24 atoms = self.atoms 

25 

26 r = atoms.get_positions() - atoms.get_center_of_mass() 

27 v = atoms.get_velocities() 

28 p = atoms.get_momenta() 

29 m = atoms.get_masses() 

30 

31 x = r[:, 0] 

32 y = r[:, 1] 

33 z = r[:, 2] 

34 

35 I11 = np.sum(m * (y**2 + z**2)) 

36 I22 = np.sum(m * (x**2 + z**2)) 

37 I33 = np.sum(m * (x**2 + y**2)) 

38 I12 = np.sum(-m * x * y) 

39 I13 = np.sum(-m * x * z) 

40 I23 = np.sum(-m * y * z) 

41 

42 I = np.array([[I11, I12, I13], 

43 [I12, I22, I23], 

44 [I13, I23, I33]]) 

45 

46 w = np.dot(np.linalg.inv(I), np.sum(np.cross(r, p), axis=0)) 

47 

48 self.atoms.set_velocities(v - np.cross(w, r))