iatm_beg = iatm
ibnd_beg = ibnd
iang_beg = iang
config.append_atom_unbonded( atm_t_bb, 0.0 )
iatm += 1
config.append_atom_bonded(1, 0.0, len_bond, 'efjc', iatm-1, sep=sep)
iatm += 1
for i in range(3,natm+1):
config.append_atom_bonded(atm_t_bb, 0.0, len_bond, 'efjc',
iatm-1, im2=iatm-2, theta=theta, sep=sep)
iatm += 1
for i in range(1, nbnd+1):
j = iatm_beg + i - 1
config.add_bond(bnd_t_bb, j, j+1)
ibnd += 1
for i in range(1, nang+1):
j = iatm_beg + i - 1
config.add_angle(ang_t_bb, j, j+1, j+2)
iang += 1
config.add_molecule(1, natm, iatm_beg, nbnd, ibnd_beg, nang, iang_beg, 0, 0)
#config.add_tether(teth_t, 1, np.zeros((3,)) )
config.update_simbox()
config.to_center(1)
config.add_flow_field( 1, np.array([0.1]) )
iatm += 1
#Put the rest of the backbone atoms
for i in range(3, na_bbone + 1):
config.append_atom_bonded(atm_t_bb,
0.0,
len_bond,
'alignx',
iatm - 1,
im2=iatm - 2,
theta=theta_bb,
sep=sep)
iatm += 1
#Backbone bonds
nbnd = na_bbone - 1
for i in range(1, nbnd + 1):
config.add_bond(bnd_t_bb, i, i + 1)
ibnd += 1
#Set backbone branch
config.set_branch(-1, 1, na_bbone)
#Side chains (arranged as efjc)
for i in range(1, na_bbone + 1, na_sp + 1):
ibp = i #Branch point
for i_sc in range(1, f + 1):
for ia_sc in range(1, na_sc + 1):
if ia_sc == 1:
config.append_atom_bonded(atm_t_sc,
0.0,
len_bond,
'efjc',
iatm,
sep=sep)
#Add rest of the atoms as freely rotating links
for i in range(3, natm + 1):
iatm = config.append_atom_bonded(atm_t_m,
0.0,
len_bond,
'efrc',
iatm,
im2=iatm - 1,
theta=theta,
sep=sep)
#Add bonds
for i in range(1, nbnd + 1):
j = iatm_beg + i - 1
ibnd = config.add_bond(bnd_t_chn, j, j + 1)
#Add angles
for i in range(1, nang + 1):
j = iatm_beg + i - 1
iang = config.add_angle(ang_t_chn, j, j + 1, j + 2)
#Add the whole molecule
config.add_molecule(mol_t_chn, natm, iatm_beg, nbnd, ibnd_beg, nang,
iang_beg, 0, 0)
#Now add counterions. These are monoatomic molecules. Let's keep their name same
#as the atomic species.
#Let there be 50 counterions.
num_mols = 50
mol_t_ci = config.add_molecule_type('C', num_mols)
