Coverage for /builds/ase/ase/ase/io/sys.py: 100.00%

1# fmt: off 

2 

3""" 

4IO support for the qb@ll sys format. 

5 

6The positions and cell dimensions are in Bohrs. 

7 

8Contributed by Rafi Ullah <rraffiu@gmail.com> 

9""" 

10 

11from re import compile 

12 

13from ase.atoms import Atoms 

14from ase.units import Bohr 

15 

16__all__ = ['read_sys', 'write_sys'] 

17 

18 

19def read_sys(fileobj): 

20 """ 

21 Function to read a qb@ll sys file. 

22 

23 fileobj: file (object) to read from. 

24 """ 

25 a1, a2, a3, b1, b2, b3, c1, c2, c3 = fileobj.readline().split()[2:11] 

26 cell = [] 

27 cell.append([float(a1) * Bohr, float(a2) * Bohr, float(a3) * Bohr]) 

28 cell.append([float(b1) * Bohr, float(b2) * Bohr, float(b3) * Bohr]) 

29 cell.append([float(c1) * Bohr, float(c2) * Bohr, float(c3) * Bohr]) 

30 positions = [] 

31 symbols = [] 

32 reg = compile(r'(\d+|\s+)') 

33 line = fileobj.readline() 

34 while 'species' in line: 

35 line = fileobj.readline() 

36 while line: 

37 # The units column is ignored. 

38 _a, symlabel, _spec, x, y, z = line.split()[0:6] 

39 positions.append([float(x) * Bohr, float(y) * Bohr, 

40 float(z) * Bohr]) 

41 sym = reg.split(str(symlabel)) 

42 symbols.append(sym[0]) 

43 line = fileobj.readline() 

44 atoms = Atoms(symbols=symbols, cell=cell, positions=positions) 

45 return atoms 

46 

47 

48def write_sys(fileobj, atoms): 

49 """ 

50 Function to write a sys file. 

51 

52 fileobj: file object 

53 File to which output is written. 

54 atoms: Atoms object 

55 Atoms object specifying the atomic configuration. 

56 """ 

57 fileobj.write('set cell') 

58 for i in range(3): 

59 d = atoms.cell[i] / Bohr 

60 fileobj.write((' {:6f} {:6f} {:6f}').format(*d)) 

61 fileobj.write(' bohr\n') 

62 

63 ch_sym = atoms.get_chemical_symbols() 

64 atm_nm = atoms.numbers 

65 a_pos = atoms.positions 

66 an = list(set(atm_nm)) 

67 

68 for i, s in enumerate(set(ch_sym)): 

69 fileobj.write(('species {}{} {}.xml \n').format(s, an[i], s)) 

70 for i, (S, Z, (x, y, z)) in enumerate(zip(ch_sym, atm_nm, a_pos)): 

71 fileobj.write(('atom {:5} {:5} {:12.6f} {:12.6f} {:12.6f}\ 

72 bohr\n').format(S + str(i + 1), S + str(Z), x / Bohr, y / Bohr, 

73 z / Bohr))