minimal-diamond.py

#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
"""
Set up a diamond-structured polymer network.
"""
import espressomd
espressomd.assert_features(["WCA"])
from espressomd import interactions, polymer
from espressomd.io.writer import vtf  # pylint: disable=import-error

import numpy as np

# System parameters
#############################################################

system = espressomd.System(box_l=[1.0, 1.0, 1.0])
system.set_random_state_PRNG()
system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
np.seed = system.seed
system.time_step = 0.01
system.cell_system.skin = 0.4
system.cell_system.set_n_square(use_verlet_lists=False)

system.non_bonded_inter[0, 0].wca.set_params(epsilon=1, sigma=1)
system.non_bonded_inter[0, 1].wca.set_params(epsilon=1, sigma=1)
system.non_bonded_inter[1, 1].wca.set_params(epsilon=1, sigma=1)

# create stiff FENE bonds
fene = interactions.FeneBond(k=30, d_r_max=1.5)
system.bonded_inter.add(fene)

# The call to diamond.Diamond() creates 16 connected polymers.
# These polymers are initialized in a straight line connected to crosslink nodes
# Furthermore they are connected to one another across simulation boxes in a periodic fashion.
# It is crucial that the simulation box, chain length and a-parameters be
# chosen such that the arrangement will not break bonds.

# monomers per chain
MPC = 15

# length for Kremer-Grest chain
bond_length = 0.966

# The physical distance between 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 = 3 * [a]
print("box now at ", system.box_l)

# We can now call diamond to place the monomers, crosslinks and bonds.
polymer.setup_diamond_polymer(system=system, bond=fene, MPC=MPC)

#############################################################
#      Warmup                                               #
#############################################################

# minimize energy using min_dist as the convergence criterion
system.integrator.set_steepest_descent(f_max=0, gamma=1e-3,
                                       max_displacement=0.01)
while system.analysis.min_dist() < 0.9:
    print("minimization: {:+.2e}".format(system.analysis.energy()["total"]))
    system.integrator.run(20)

print("minimization: {:+.2e}".format(system.analysis.energy()["total"]))
print()
system.integrator.set_vv()

# activate thermostat
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)


#############################################################
#      Integration                                          #
#############################################################

sim_steps = 100
print("simulating...")
system.integrator.run(sim_steps)

# because stretched polymers are not too impressive...
print("simulating a slow compression...")
for d in np.arange(1, 15):
    system.change_volume_and_rescale_particles(
        d_new=system.box_l[0] - 1, dir='xyz')
    print("box now at ", system.box_l)
    system.integrator.run(sim_steps)

# visualize at a smaller box size
outfile = open('diamond.vtf', 'w')
vtf.writevsf(system, outfile)
vtf.writevcf(system, outfile)
t_steps = 100
for t in range(t_steps):
    print("step {} of {}".format(t + 1, t_steps), end='\r', flush=True)
    system.integrator.run(sim_steps)
    vtf.writevcf(system, outfile)
outfile.close()
print()