"""
IO support for the qb@ll sys format.
The positions and cell dimensions are in Bohrs.
Contributed by Rafi Ullah <rraffiu@gmail.com>
"""
from re import compile
from ase.atoms import Atoms
from ase.units import Bohr
__all__ = ['read_sys', 'write_sys']
[docs]
def read_sys(fileobj):
"""
Function to read a qb@ll sys file.
fileobj: file (object) to read from.
"""
a1, a2, a3, b1, b2, b3, c1, c2, c3 = fileobj.readline().split()[2:11]
cell = []
cell.append([float(a1) * Bohr, float(a2) * Bohr, float(a3) * Bohr])
cell.append([float(b1) * Bohr, float(b2) * Bohr, float(b3) * Bohr])
cell.append([float(c1) * Bohr, float(c2) * Bohr, float(c3) * Bohr])
positions = []
symbols = []
reg = compile(r'(\d+|\s+)')
line = fileobj.readline()
while 'species' in line:
line = fileobj.readline()
while line:
# The units column is ignored.
_a, symlabel, _spec, x, y, z = line.split()[0:6]
positions.append([float(x) * Bohr, float(y) * Bohr,
float(z) * Bohr])
sym = reg.split(str(symlabel))
symbols.append(sym[0])
line = fileobj.readline()
atoms = Atoms(symbols=symbols, cell=cell, positions=positions)
return atoms
[docs]
def write_sys(fileobj, atoms):
"""
Function to write a sys file.
fileobj: file object
File to which output is written.
atoms: Atoms object
Atoms object specifying the atomic configuration.
"""
fileobj.write('set cell')
for i in range(3):
d = atoms.cell[i] / Bohr
fileobj.write((' {:6f} {:6f} {:6f}').format(*d))
fileobj.write(' bohr\n')
ch_sym = atoms.get_chemical_symbols()
atm_nm = atoms.numbers
a_pos = atoms.positions
an = list(set(atm_nm))
for i, s in enumerate(set(ch_sym)):
fileobj.write(('species {}{} {}.xml \n').format(s, an[i], s))
for i, (S, Z, (x, y, z)) in enumerate(zip(ch_sym, atm_nm, a_pos)):
fileobj.write(('atom {:5} {:5} {:12.6f} {:12.6f} {:12.6f}\
bohr\n').format(S + str(i + 1), S + str(Z), x / Bohr, y / Bohr,
z / Bohr))