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],
pos[i,1],
pos[i,2]))
# print(psys.get_scaled_positions())
# print(psys.get_real_positions())
sa1new = np.zeros(3,dtype=float)
sa2new = np.zeros(3,dtype=float)
