hext[2] = sysext.a3 * sysext.alc
#...make extended system corresponding to the phonopy definition
for ia in range(natm0):
ai0 = sys0.atoms[ia]
for i3 in range(r3):
for i2 in range(r2):
for i1 in range(r1):
ai = Atom()
ai.set_sid(ai0.sid)
p1 = (ai0.pos[0] + i1) / r1
p2 = (ai0.pos[1] + i2) / r2
p3 = (ai0.pos[2] + i3) / r3
ai.set_pos(p1, p2, p3)
sysext.add_atom(ai)
sysext.reset_ids()
natme = sysext.num_atoms()
print ' sysext.num_atoms()=', natme
# for ai in sysext.atoms:
# print ai.pos
os.system('cp pmdini pmdorig')
#...loop for all atoms in the extended system
fcmat = np.zeros((natme, natme, 3, 3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos = np.array(sysext.atoms[ia].pos)
for ixyz in range(3):
hext[2]= sysext.a3 *sysext.alc
#...make extended system corresponding to the phonopy definition
for ia in range(natm0):
ai0= sys0.atoms[ia]
for i3 in range(r3):
for i2 in range(r2):
for i1 in range(r1):
ai= Atom()
ai.set_sid(ai0.sid)
p1= (ai0.pos[0]+i1)/r1
p2= (ai0.pos[1]+i2)/r2
p3= (ai0.pos[2]+i3)/r3
ai.set_pos(p1,p2,p3)
sysext.add_atom(ai)
sysext.reset_ids()
natme= sysext.num_atoms()
print ' sysext.num_atoms()=',natme
# for ai in sysext.atoms:
# print ai.pos
os.system('cp pmd0000 pmd0000.orig')
#...loop for all atoms in the extended system
fcmat= np.zeros((natme,natme,3,3))
for ia in range(natme):
print '.',
sys.stdout.flush()
ppos= np.array(sysext.atoms[ia].pos)
for ixyz in range(3):
