# monomers per chain MPC = 15 # length for Kremer-Grest chain bond_length = 0.966 # The physical distance beween nodes such that a line of monomers "fit" needs to be worked out. # This is done via the unit diamond lattice size parameter "a". a = (MPC + 1) * bond_length / (0.25 * np.sqrt(3)) # Lastly, the created periodic connections requires a specific simulation box. system.box_l = [a, a, a] print("box now at ", system.box_l) # We can now call diamond to place the monomers, crosslinks and bonds. diamond.Diamond(a=a, bond_length=bond_length, MPC=MPC) ############################################################# # Warmup # ############################################################# print("Warming up...") warm_steps = 10 lj_cap = 1 system.force_cap = lj_cap act_min_dist = system.analysis.min_dist() # warmp with zero temperature to remove overlaps system.thermostat.set_langevin(kT=0.0, gamma=1.0) # slowly ramp up the cap
from espressomd import integrate from espressomd import interactions from espressomd import diamond import numpy # System parameters ############################################################# system = espressomd.System() # system.seed=numpy.random.randint(low=1,high=2**31-1,size=system.n_nodes) # if no seed is provided espresso generates a seed # print system.seed system.time_step = 0.01 system.skin = 0.4 system.box_l = [100, 100, 100] system.thermostat.set_langevin(1.0, 1.0) system.cell_system.set_n_square(use_verlet_lists=False) system.non_bonded_inter[0, 0].lennard_jones.set_params( epsilon=1, sigma=1, cutoff=2**(1. / 6), shift="auto") fene = interactions.FeneBond(k=10, d_r_max=2) system.bonded_inter.add(fene) diamond.Diamond(a=20, bond_length=2, MPC=20)