# Single Si layer:

Si1 = Atom('Si')
Si2 = Atom('Si')
Si3 = Atom('Si')
Si4 = Atom('Si')
Si5 = Atom('Si')
Si6 = Atom('Si')

H1 = Atom('H')
H2 = Atom('H')
H3 = Atom('H')
H4 = Atom('H')
H5 = Atom('H')
H6 = Atom('H')

b12 = Bond(Si1, Si2)
b23 = Bond(Si2, Si3)
b34 = Bond(Si3, Si4)
b45 = Bond(Si4, Si5)
b56 = Bond(Si5, Si6)
b61 = Bond(Si6, Si1)

hb1 = Bond(Si1, H1)
hb2 = Bond(Si2, H2)
hb3 = Bond(Si3, H3)
hb4 = Bond(Si4, H4)
hb5 = Bond(Si5, H5)
hb6 = Bond(Si6, H6)

da1 = Dihedral(Si1,Si2,Si3,Si4,60*deg)
da2 = Dihedral(Si2,Si3,Si4,Si5,-60*deg)
dh1 = Dihedral(Si3,Si2,Si1,H1,180*deg)
dh2 = Dihedral(Si6,Si1,Si2,H2,180*deg)
dh3 = Dihedral(Si1,Si2,Si3,H3,180*deg)
dh4 = Dihedral(Si6,Si5,Si4,H4,180*deg)
dh5 = Dihedral(Si3,Si4,Si5,H5,180*deg)
dh6 = Dihedral(Si4,Si5,Si6,H6,180*deg)

amber_atom_type = {Si1: 'SI', Si2: 'SI', Si3: 'SI', Si4: 'SI', Si5: 'SI', Si6: 'SI',
		   H1: 'HC', H2: 'HC', H3: 'HC', H4: 'HC', H5: 'HC', H6: 'HC'}

# somewhat arbitrary charges
amber_charge = {Si1: 0.,Si2: 0.,Si3: 0.,Si4: 0.,Si5: 0.,Si6: 0.,\
		H1: 0.1, H2: 0.1, H3: 0.1, H4: 0.1, H5: 0.1, H6: 0.1}

dC1a = DanglingBond(Si1, Dihedral(None,Si1,Si6,Si5,-60*deg))
dC2a = DanglingBond(Si2, Dihedral(Si6,Si1,Si2,None, 60*deg))
dC3a = DanglingBond(Si3, Dihedral(Si1,Si2,Si3,None,-60*deg))
dC4a = DanglingBond(Si4, Dihedral(Si2,Si3,Si4,None, 60*deg))
dC5a = DanglingBond(Si5, Dihedral(Si3,Si4,Si5,None,-60*deg))
dC6a = DanglingBond(Si6, Dihedral(None,Si6,Si1,Si2, 60*deg))

hookup   = Hook(None, [dC1a,dC3a,dC5a])
hookdown = Hook(None, [dC2a,dC4a,dC6a])