parser.add_option("--pmdexec",
dest="pmdexec",
type="string",
default='../pmd/pmd',
help="path to the pmd executable.")
(options, args) = parser.parse_args()
displace = options.displace
print ' displacement = ', displace, ' Ang.'
rcut = options.rcut
print ' rcut = ', rcut, ' Ang.'
pmdexec = options.pmdexec
infname = args[0]
sys0 = NAPSystem()
sys0.read_pmd(infname)
sys0.write_POSCAR()
print ' POSCAR was written.'
natm0 = sys0.num_atoms()
h0 = np.zeros((3, 3))
h0[0] = sys0.a1 * sys0.alc
h0[1] = sys0.a2 * sys0.alc
h0[2] = sys0.a3 * sys0.alc
n1, n2, n3 = calc_extention_ratio(h0, rcut)
r1 = 2 * n1 + 1
r2 = 2 * n2 + 1
r3 = 2 * n3 + 1
print ' num of cells in each axis=', r1, r2, r3
return n1,n2,n3
################################################ Main routine ##########
if __name__ == "__main__":
args= docopt(__doc__)
rcut= float(args['--cutoff'])
pmddir= args['--pmddir']
execname= args['--exec']
infname= args['PMDFILE']
plot= args['--plot']
#print(args)
sys0= NAPSystem()
sys0.read_pmd(infname)
sys0.write_POSCAR()
print(' POSCAR was written.')
natm0= sys0.num_atoms()
h0=np.zeros((3,3))
h0[0]= sys0.a1 *sys0.alc
h0[1]= sys0.a2 *sys0.alc
h0[2]= sys0.a3 *sys0.alc
n1,n2,n3= calc_extention_ratio(h0,rcut)
print("n1,n2,n3 = {0:d} {1:d} {2:d}".format(n1,n2,n3))
# Make displaced POSCARS via phonopy
os.system("phonopy -d --dim=\"{0:d} {1:d} {2:d}\"".format(n1,n2,n3))
with open('disp.yaml','r') as f:
