#Atom types
#All atoms are point particles with unit mass
atm_t_bb = config.add_atom_type('BB', 1, 1.0)
atm_t_sc = config.add_atom_type('SC', 1, 1.0)
#Vdw interaction
eps = 1.0
sigma = 2.0
rcut = 2.0**(1.0 / 6) * sigma
config.add_ia_vdw('BB', 'BB', 1, np.array([eps, sigma, rcut]))
config.add_ia_vdw('BB', 'SC', 1, np.array([eps, sigma, rcut]))
config.add_ia_vdw('SC', 'SC', 1, np.array([eps, sigma, rcut]))
#Bond types
bnd_t_bb = config.add_bond_type(
3, np.array([30 * eps / sigma**2, 1.5 * sigma, eps, sigma]))
bnd_t_bs = config.add_bond_type(
3, np.array([30 * eps / sigma**2, 1.5 * sigma, eps, sigma]))
bnd_t_ss = config.add_bond_type(
3, np.array([30 * eps / sigma**2, 1.5 * sigma, eps, sigma]))
#Angle types (No angles)
#Dihedral types (No dihedrals)
#Tether types (No tethers)
#Molecule type
num_mols = 1
config.add_molecule_type('BTLBRS', num_mols)
config.add_simbox(30.0, 30.0, 30.0, 1)
#The system consists of polymer chains and couterions.
#Atom types
#Monomer atoms as point particles with mass 1.0
atm_t_m = config.add_atom_type('M', 1, 1.0)
#Counterion atoms as point particles with mass 1.0.
atm_t_c = config.add_atom_type('C', 1, 1.0)
#Bond types
#Bonds along the chain. (Kremer-Grest)
eps = 1.0
sigma = 2.0
rcut = 2.0**(1.0 / 6) * sigma
bnd_t_chn = config.add_bond_type(
3, np.array([30 * eps / sigma**2, 1.5 * sigma, eps, sigma]))
#Angle types
#Angles along the chain. (Cosine)
ang_t_chn = config.add_angle_type(1, np.array([2.0, 1.0]))
#Vdw (pairwise) interaction. 12-6 LJ+Coulomb (cut & shifted)
#Assume same for all pairs
eps = 1.0
sigma = 2.0
rcut = 2.0**(1.0 / 6) * sigma
rcut_coul = rcut + 3.0
C = 20.0
config.add_ia_vdw('M', 'M', 5, np.array([eps, sigma, rcut, rcut_coul, C]))
config.add_ia_vdw('C', 'C', 5, np.array([eps, sigma, rcut, rcut_coul, C]))
config.add_ia_vdw('M', 'C', 5, np.array([eps, sigma, rcut, rcut_coul, C]))
