len_bond,
'efjc',
ibp,
sep=sep)
iatm += 1
config.add_bond(bnd_t_bs, ibp, iatm - 1)
ibnd += 1
ia_br_beg = iatm - 1
else:
config.append_atom_bonded(atm_t_sc,
0.0,
len_bond,
'efjc',
iatm - 1,
sep=sep)
iatm += 1
config.add_bond(bnd_t_ss, iatm - 2, iatm - 1)
ibnd += 1
#Set branch
config.set_branch(ibp, ia_br_beg, na_sc)
#Add molecule
config.add_molecule(1, iatm - 1, iatm_beg, ibnd - 1, ibnd_beg, 0, 0, 0, 0)
config.update_simbox()
config.to_center(1)
config.add_flow_field(0, np.array([]))
write_ldf(config, 'tfr.txt', title='test_brush')
write_cfg(config, 'bb-sus-%d-%d.cfg' % (na_bbone, na_sc), title='brush')
sep = 1.95 # Must be <= len_bond
#Loop over all molecules
imol = 1
iatm = 1
ibnd = 1
iang = 1 #Index of one past the last atom, bond, etc. added
for imol in range(1, num_mols_A + 1):
iatm_beg = iatm
ibnd_beg = ibnd
iang_beg = iang
config.append_atom_unbonded(atm_t_a, 1.0, sep=sep)
iatm += 1
config.add_molecule(mol_t_A, natm, iatm_beg, 0, ibnd_beg, 0, iang_beg, 0,
0)
for imol in range(1, num_mols_B + 1):
iatm_beg = iatm
ibnd_beg = ibnd
iang_beg = iang
config.append_atom_unbonded(atm_t_b, -1.0, sep=sep)
iatm += 1
config.add_molecule(mol_t_B, natm, iatm_beg, 0, ibnd_beg, 0, iang_beg, 0,
0)
config.apply_pbc()
write_ldf(config, 'tfr.txt', title='test_frame')
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]) )
write_ldf(config, 'tfr.txt', title='test_frame')
write_cfg(config, 'lin-%d.cfg'%natm, title='test_cfg')
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)
#No bonds & angles. Let's keep sep same as before. Put these counterions
#randomly within the box.
for imol in range(1, num_mols + 1):
iatm_beg = iatm + 1
iatm = config.append_atom_unbonded(atm_t_c, 0.0, sep=sep)
#Add the whole molecule
config.add_molecule(mol_t_ci, 1, iatm_beg, 0, 0, 0, 0, 0, 0)
#Randomly assign charge, while keeping the whole system neutral.
