def expand(self,n1,n2,n3):
#...expand unit vectors
self.a1= self.a1*n1
self.a2= self.a2*n2
self.a3= self.a3*n3
n123= n1*n2*n3
nsid= 0
for ai in self.atoms:
nsid= max(nsid,ai.sid)
natm_per_spcs= np.zeros((nsid,),dtype=int)
for ai in self.atoms:
sid= ai.sid -1
natm_per_spcs[sid] += 1
natm0= self.num_atoms()
atoms0= copy.copy(self.atoms)
self.atoms= []
aid= 0
for ai0 in atoms0:
ai0.pos[0] /= n1
ai0.pos[1] /= n2
ai0.pos[2] /= n3
for i1 in range(n1):
for i2 in range(n2):
for i3 in range(n3):
aid += 1
ai= Atom()
ai.sid= ai0.sid
x= ai0.pos[0]+1.0/n1*i1
y= ai0.pos[1]+1.0/n2*i2
z= ai0.pos[2]+1.0/n3*i3
ai.set_pos(x,y,z)
ai.set_auxd(ai0.auxd)
ai.set_id(aid)
self.atoms.append(ai)
amax = options.amax print ' amax = ', amax distance = options.distance print ' distance = ', distance, ' Ang.' pmdexec = options.pmdexec asys = AtomSystem() a1 = np.array([2.0, 0.0, 0.0]) a2 = np.array([0.0, 2.0, 0.0]) a3 = np.array([0.0, 0.0, 1.0]) alc = rcut asys.set_lattice(alc, a1, a2, a3) atom1 = Atom() atom1.set_pos(0.0, 0.0, 0.0) atom1.set_id(1) asys.add_atom(atom1) hd = distance / (alc * 2) atom2 = Atom() atom2.set_pos(hd, 0.0, 0.0) atom2.set_id(2) asys.add_atom(atom2) atom3 = Atom() atom3.set_pos(0.0, 0.0, 0.0) atom3.set_id(3) asys.add_atom(atom3) da = (amax - amin) / nsmpl
print ' rcut = ', rcut, ' Ang.'
rmin = options.rmin
print ' rmin = ', rmin, ' Ang.'
pmdexec = options.pmdexec
asys = AtomSystem()
a1 = np.array([2.0, 0.0, 0.0])
a2 = np.array([0.0, 1.0, 0.0])
a3 = np.array([0.0, 0.0, 1.0])
alc = rcut
asys.set_lattice(alc, a1, a2, a3)
atom1 = Atom()
atom2 = Atom()
atom1.set_pos(0.0, 0.0, 0.0)
atom1.set_id(1)
asys.add_atom(atom1)
atom2.set_pos(0.5, 0.0, 0.0)
atom2.set_id(2)
asys.add_atom(atom2)
hmin = rmin / (2 * rcut)
hd = (0.5 - hmin) / nsmpl
fout = open('out.2body', 'w')
for ip in range(nsmpl + 1):
print '.',
d = hmin + hd * ip
asys.atoms[1].pos[0] = d
asys.write_pmd('0000/pmd00000')
os.system(pmdexec + ' > out.pmd')
