'''
import sys
import math
import numpy as np
from configuration import Configuration
from config_io import *
#-------------------------------------------------------------------------------
config = Configuration()
#Add simulation box and boundary condition. The box size can be updated later if
#necessary.
config.add_simbox(40.0, 40.0, 40.0, 0)
#Number of backbone atoms
na_bbone = 30 #int(sys.argv[1])
#Number of atoms on each side chain
na_sc = 4 #int(sys.argv[2])
#Number of atoms between consecutive branch points
na_sp = 0
#Number of side chains growing from a branch point
f = 1
#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)
Creates initial configuration for a system containing unbranched linear chains.
'''
import sys
import math
import numpy as np
from configuration import Configuration
from config_io import *
#-------------------------------------------------------------------------------
config = Configuration()
#Add simulation box and boundary condition. The box size can be updated later if
#necessary.
config.add_simbox(10.0, 10.0, 10.0, 1)
#Molecule details
num_mols_A = 60
num_mols_B = 60
mol_t_A = config.add_molecule_type('A', num_mols_A)
mol_t_B = config.add_molecule_type('B', num_mols_B)
#Total number of atoms in the molecule
natm = 1
#Atom types
# natm atoms as point particles with mass 1.0
atm_t_a = config.add_atom_type('A', 1, 1.0)
atm_t_b = config.add_atom_type('B', 1, 1.0)
chain in an unbounded domain.
'''
import sys
import math
import numpy as np
from configuration import Configuration
from config_io import *
#-------------------------------------------------------------------------------
config = Configuration()
#Add simulation box and boundary condition. The box size can be updated later if
#necessary.
config.add_simbox(20.0, 20.0, 20.0, 0)
#Molecule details
num_mols = 1
config.add_molecule_type('CHN-UB', num_mols)
#Total number of atoms in the molecule
natm = 30 #int(sys.argv[1])
#Total number of bonds
nbnd = natm - 1
#Total number of angles. If no angles set num_angles to zero.
nang = natm - 2 if natm > 2 else 0
#Atom types
'''
Creates initial configuration for a system containing charged chains and counterions.
'''
import sys
import math
import numpy as np
from configuration import Configuration
from config_io import *
#-------------------------------------------------------------------------------
config = Configuration()
#Add simulation box with PBC.
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(
