from atom import Atom from napsys import NAPSystem __author__ = 'Ryo KOBAYASHI' __version__ = '160510' if __name__ == '__main__': args = docopt(__doc__,version=__version__) infile = args['INFILE'] specorder = args['--specorder'].split(',') psys = NAPSystem(fname=infile,specorder=specorder) psys.assign_pbc() psys.a1 = psys.a1 *psys.alc psys.a2 = psys.a2 *psys.alc psys.a3 = psys.a3 *psys.alc psys.alc = 1.0 print('a1 = ',psys.a1) print('a2 = ',psys.a2) print('a3 = ',psys.a3) pos = psys.get_real_positions() spos = psys.get_scaled_positions() for i in range(min(len(psys.atoms),100)): a = psys.atoms[i] print('{0:5d} {1:s}'.format(a.id,a.symbol) +' {0:12.5f} {1:12.5f} {2:12.5f}'.format(spos[i,0], spos[i,1], spos[i,2]) +' {0:12.5f} {1:12.5f} {2:12.5f}'.format(pos[i,0],