def makestruct(dims, angles):
result = []
zdir = np.array([0,0,1.0])
xdir = np.array([1.0,0,0])
for ix in range(dims[0]):
for iy in range(dims[1]):
for iz in range(dims[2]):
#first rotate H
ch31 = ss.rot(zdir,angles[ix,iy,iz,0,2],ch3)
ch32 = ss.rot(zdir,angles[ix,iy,iz,1,2],ch3)
ch33 = ss.rot(zdir,angles[ix,iy,iz,2,2],ch3)
ch34 = ss.rot(zdir,angles[ix,iy,iz,3,2],ch3)
nh31 = ss.rot(zdir,angles[ix,iy,iz,0,3],nh3)
nh32 = ss.rot(zdir,angles[ix,iy,iz,1,3],nh3)
nh33 = ss.rot(zdir,angles[ix,iy,iz,2,3],nh3)
nh34 = ss.rot(zdir,angles[ix,iy,iz,3,3],nh3)
mol1 = ch31+nh31+cn
mol2 = ch32+nh32+cn
mol3 = ch33+nh33+cn
mol4 = ch34+nh34+cn
#next, rotate CN axis
mol1r = ss.rot(xdir,angles[ix,iy,iz,0,0],mol1)
mol2r = ss.rot(xdir,angles[ix,iy,iz,1,0],mol2)
mol3r = ss.rot(xdir,angles[ix,iy,iz,2,0],mol3)
mol4r = ss.rot(xdir,angles[ix,iy,iz,3,0],mol4)
mol1r = ss.rot(zdir,angles[ix,iy,iz,0,1],mol1r)
mol2r = ss.rot(zdir,angles[ix,iy,iz,1,1],mol2r)
mol3r = ss.rot(zdir,angles[ix,iy,iz,2,1],mol3r)
mol4r = ss.rot(zdir,angles[ix,iy,iz,3,1],mol4r)
# finally, translate CN to new position
t1 = 0.5*lattdim[0,:]+0.0*lattdim[1,:]+0.25*lattdim[2,:]
t2 = 0.0*lattdim[0,:]+0.5*lattdim[1,:]+0.25*lattdim[2,:]
t3 = 0.5*lattdim[0,:]+0.0*lattdim[1,:]+0.75*lattdim[2,:]
t4 = 0.0*lattdim[0,:]+0.5*lattdim[1,:]+0.75*lattdim[2,:]
d = ix*lattdim[0,:] + iy*lattdim[1,:] + iz*lattdim[2,:]
t1 = t1 + d
t2 = t2 + d
t3 = t3 + d
t4 = t4 + d
mol1t = ss.trans(t1,mol1r)
mol2t = ss.trans(t2,mol2r)
mol3t = ss.trans(t3,mol3r)
mol4t = ss.trans(t4,mol4r)
#make PbI3 lattice
pbi3t = ss.trans(d,pbi3)
result = result + mol1t
result = result + mol2t
result = result + mol3t
result = result + mol4t
result = result + pbi3t
return result
dims = [2,1,1]
mol = []
mol.append(ss.Atom("C",np.array([4.424499989,0.000000000,4.449984046])))
mol.append(ss.Atom("N",np.array([4.424499989,0.000000000,3.059364031])))
mol.append(ss.Atom("H",np.array([4.424499989,7.7889999771-8.8489999771,4.683952399])))
mol.append(ss.Atom("H",np.array([3.524499989,0.470000000,4.822151273])))
mol.append(ss.Atom("H",np.array([5.324499989,0.470000000,4.822151273])))
mol.append(ss.Atom("H",np.array([4.424499989,7.7889999771-8.8489999771,2.825395693])))
mol.append(ss.Atom("H",np.array([3.524499989,0.470000000,2.687196819])))
mol.append(ss.Atom("H",np.array([5.324499989,0.470000000,2.687196819])))
zpos = 0.5*(4.449984046+3.059364031)
#translate the molecule to the origin
mol0 = ss.trans(np.array([-4.424499989,0.0,-zpos]),mol)
cn = mol0[0:2]
ch3 = mol0[2:5]
nh3 = mol0[5:8]
#PbI3 lattice
pbi3 = []
pbi3.append(ss.Atom("Pb",np.array([0,0,0])))
pbi3.append(ss.Atom("Pb",np.array([0.000000000,0.000000000,6.321000099])))
pbi3.append(ss.Atom("Pb",np.array([4.424499989,4.424499989,6.321000099])))
pbi3.append(ss.Atom("Pb",np.array([4.424499989,4.424499989,0.000000000])))
pbi3.append(ss.Atom("I",np.array([0.000000000,0.000000000,3.125102415])))
pbi3.append(ss.Atom("I",np.array([0.000000000,0.000000000,9.446102703])))
pbi3.append(ss.Atom("I",np.array([4.424499989,4.424499989,9.446102703])))
pbi3.append(ss.Atom("I",np.array([4.424499989,4.424499989,3.125102415])))
