Coverage for /builds/kinetik161/ase/ase/cluster/decahedron.py: 93.75%

1import numpy as np 

2 

3from ase import Atoms 

4from ase.cluster.util import get_element_info 

5 

6 

7def Decahedron(symbol, p, q, r, latticeconstant=None): 

8 """ 

9 Return a decahedral cluster. 

10 

11 Parameters 

12 ---------- 

13 symbol: Chemical symbol (or atomic number) of the element. 

14 

15 p: Number of atoms on the (100) facets perpendicular to the five 

16 fold axis. 

17 

18 q: Number of atoms on the (100) facets parallel to the five fold 

19 axis. q = 1 corresponds to no visible (100) facets. 

20 

21 r: Depth of the Marks re-entrence at the pentagon corners. r = 0 

22 corresponds to no re-entrence. 

23 

24 latticeconstant (optional): The lattice constant. If not given, 

25 then it is extracted form ase.data. 

26 """ 

27 

28 symbol, atomic_number, latticeconstant = get_element_info( 

29 symbol, latticeconstant) 

30 

31 # Check values of p, q, r 

32 if p < 1 or q < 1: 

33 raise ValueError("p and q must be greater than 0.") 

34 

35 if r < 0: 

36 raise ValueError("r must be greater than or equal to 0.") 

37 

38 # Defining constants 

39 t = 2.0 * np.pi / 5.0 

40 b = latticeconstant / np.sqrt(2.0) 

41 a = b * np.sqrt(3.0) / 2.0 

42 

43 verticies = a * np.array([[np.cos(np.pi / 2.), np.sin(np.pi / 2.), 0.], 

44 [np.cos(t * 1. + np.pi / 2.), 

45 np.sin(t * 1. + np.pi / 2.), 0.], 

46 [np.cos(t * 2. + np.pi / 2.), 

47 np.sin(t * 2. + np.pi / 2.), 0.], 

48 [np.cos(t * 3. + np.pi / 2.), 

49 np.sin(t * 3. + np.pi / 2.), 0.], 

50 [np.cos(t * 4. + np.pi / 2.), np.sin( 

51 t * 4. + np.pi / 2.), 0.]]) 

52 

53 # Number of atoms on the five fold axis and a nice constant 

54 h = p + q + 2 * r - 1 

55 g = h - q + 1 # p + 2*r 

56 

57 positions = [] 

58 # Make the five fold axis 

59 for j in range(h): 

60 pos = np.array([0.0, 0.0, j * b - (h - 1) * b / 2.0]) 

61 positions.append(pos) 

62 

63 # Make pentagon rings around the five fold axis 

64 for n in range(1, h): 

65 # Condition for (100)-planes 

66 if n < g: 

67 for m in range(5): 

68 v1 = verticies[m - 1] 

69 v2 = verticies[m] 

70 for i in range(n): 

71 # Condition for marks re-entrence 

72 if n - i < g - r and i < g - r: 

73 for j in range(h - n): 

74 pos = (n - i) * v1 + i * v2 

75 pos += np.array([0.0, 0.0, j * b - 

76 (h - n - 1) * b / 2.0]) 

77 positions.append(pos) 

78 

79 symbols = [atomic_number] * len(positions) 

80 return Atoms(symbols=symbols, positions=positions)