system = espressomd.System(box_l=[box_l] * 3)
system.set_random_state_PRNG()
np.random.seed(seed=system.seed)
system.time_step = 0.01
system.cell_system.skin = 0.4
system.thermostat.set_langevin(kT=0.1, gamma=20.0, seed=42)
system.non_bonded_inter[0, 0].lennard_jones.set_params(
epsilon=0, sigma=1, cutoff=2, shift="auto")
system.bonded_inter[0] = HarmonicBond(k=0.5, r_0=1.0)
for i in range(n_part):
system.part.add(id=i, pos=np.random.random(3) * system.box_l)
for i in range(n_part - 1):
system.part[i].add_bond((system.bonded_inter[0], system.part[i + 1].id))
# Select visualizer
if args.visualizer == "mayavi":
visualizer = visualization.mayaviLive(system)
else:
visualizer = visualization.openGLLive(system, bond_type_radius=[0.3])
system.minimize_energy.init(
f_max=10, gamma=50.0, max_steps=1000, max_displacement=0.2)
system.minimize_energy.minimize()
visualizer.run(1)
for i in range(n_part):
system.part.add(id=i, pos=numpy.random.random(3) * system.box_l)
system.analysis.distto(0)
print("Simulate {} particles in a cubic simulation box {} at density {}."
.format(n_part, box_l, density).strip())
print("Interactions:\n")
act_min_dist = system.analysis.mindist()
print("Start with minimal distance {}".format(act_min_dist))
system.max_num_cells = 2744
#Switch between openGl/Mayavi
visualizer = visualization.mayaviLive(system)
#visualizer = visualization.openGLLive(system)
#############################################################
# Warmup Integration #
#############################################################
# open Observable file
obs_file = open("pylj_liquid.obs", "w")
obs_file.write("# Time\tE_tot\tE_kin\tE_pot\n")
print("""
Start warmup integration:
At maximum {} times {} steps
Stop if minimal distance is larger than {}
""".strip().format(warm_n_times, warm_steps, min_dist))
