Coverage for ase / optimize / test / systems.py: 16.07%

1# fmt: off 

2 

3from math import cos, pi, sin 

4 

5from ase import Atoms 

6from ase.build import add_adsorbate, fcc100, fcc111 

7from ase.cluster import wulff_construction 

8from ase.constraints import FixAtoms 

9from ase.db import connect 

10from ase.lattice.cubic import FaceCenteredCubic 

11 

12 

13def get_systems(): 

14 systems = [] 

15 

16 cell = (5, 5, 5) 

17 atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell) 

18 atoms.center() 

19 systems.append((atoms, 'Hydrogen molecule')) 

20 

21 atoms = FaceCenteredCubic( 

22 directions=[[1, -1, 0], [1, 1, 0], [0, 0, 1]], 

23 size=(2, 2, 2), 

24 symbol='Cu', 

25 pbc=(1, 1, 1)) 

26 atoms.rattle(stdev=0.1, seed=42) 

27 systems.append((atoms, 'Shaken bulk copper')) 

28 

29 a = 2.70 

30 c = 1.59 * a 

31 

32 slab = Atoms('2Cu', [(0., 0., 0.), (1 / 3., 1 / 3., -0.5 * c)], 

33 tags=(0, 1), 

34 pbc=(1, 1, 0)) 

35 slab.set_cell([(a, 0, 0), 

36 (a / 2, 3**0.5 * a / 2, 0), 

37 (0, 0, 1)]) 

38 slab.center(vacuum=3, axis=2) 

39 mask = [a.tag == 1 for a in slab] 

40 slab.set_constraint(FixAtoms(mask=mask)) 

41 systems.append((slab, 'Distorted Cu(111) surface')) 

42 

43 zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197 

44 xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19 

45 co = Atoms('CO', positions=[(-xpos + 1.2, 0, -zpos), 

46 (-xpos + 1.2, -1.1, -zpos)]) 

47 slab = fcc111('Au', size=(2, 2, 2), orthogonal=True) 

48 add_adsorbate(slab, co, 1.5, 'bridge') 

49 slab.center(vacuum=6, axis=2) 

50 slab.set_pbc((True, True, False)) 

51 constraint = FixAtoms(mask=[a.tag == 2 for a in slab]) 

52 slab.set_constraint(constraint) 

53 systems.append((slab, 'CO on Au(111) surface')) 

54 

55 atoms = Atoms(symbols='C5H12', 

56 cell=[16.83752497, 12.18645905, 11.83462179], 

57 positions=[[5.90380523, 5.65545388, 5.91569796], 

58 [7.15617518, 6.52907738, 5.91569796], 

59 [8.41815022, 5.66384716, 5.92196554], 

60 [9.68108996, 6.52891016, 5.91022362], 

61 [10.93006206, 5.65545388, 5.91569796], 

62 [5.00000011, 6.30002353, 5.9163716], 

63 [5.88571848, 5.0122839, 6.82246859], 

64 [5.88625613, 5.01308931, 5.01214155], 

65 [7.14329342, 7.18115393, 6.81640316], 

66 [7.14551332, 7.17200869, 5.00879027], 

67 [8.41609966, 5.00661165, 5.02355167], 

68 [8.41971183, 5.0251482, 6.83462168], 

69 [9.69568096, 7.18645894, 6.8078633], 

70 [9.68914668, 7.16663649, 5.00000011], 

71 [10.95518898, 5.02163182, 6.8289018], 

72 [11.83752486, 6.29836826, 5.90274952], 

73 [10.94464142, 5.00000011, 5.01802495]]) 

74 systems.append((atoms, 'Pentane molecule')) 

75 

76 slab = fcc100('Cu', size=(2, 2, 2), vacuum=3.5) 

77 add_adsorbate(slab, 'C', 1.5, 'hollow') 

78 mask = [a.tag > 1 for a in slab] 

79 constraint = FixAtoms(mask=mask) 

80 slab.set_constraint(constraint) 

81 systems.append((slab, 'C/Cu(100)')) 

82 

83 surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)] 

84 esurf = [0.9151, 0.9771, 0.7953] # Surface energies 

85 size = 10 # number of atoms 

86 atoms = wulff_construction('Al', surfaces, esurf, size, 'fcc', 

87 rounding='above') 

88 atoms.center(vacuum=6) 

89 atoms.rattle(0.2) 

90 systems.append((atoms, 'Alumninum cluster')) 

91 return systems 

92 

93 

94def create_database(): 

95 systems = get_systems() 

96 db = connect('systems.db', append=False) 

97 for atoms, description in systems: 

98 name = atoms.get_chemical_formula() 

99 db.write(atoms, description=description, name=name) 

100 

101 

102if __name__ == '__main__': 

103 create_database()