# Interaction parameters (repulsive Lennard Jones)
#############################################################
lj_eps = 1.0
lj_sig = 1.0
lj_cut = 1.12246
lj_cap = 20
# Integration parameters
#############################################################
system = espressomd.System()
system.time_step = 0.01
system.skin = 0.4
#es._espressoHandle.Tcl_Eval('thermostat langevin 1.0 1.0')
thermostat.Thermostat().setLangevin(1.0, 1.0)
# warmup integration (with capped LJ potential)
warm_steps = 100
warm_n_times = 30
# do the warmup until the particles have at least the distance min__dist
min_dist = 0.9
# integration
int_steps = 1000
int_n_times = 10
#############################################################
# Setup System #
#############################################################
############################################################# wca_eps = 10.0 wca_sig = 1.0 wca_cap = 20 # Integration parameters ############################################################# system = espressomd.System(box_l=[box_l] * 3) system.set_random_state_PRNG() #system.seed = system.cell_system.get_state()['n_nodes'] * [1234] np.random.seed(seed=system.seed) system.time_step = 0.01 system.cell_system.skin = 0.4 thermostat.Thermostat().set_langevin(1.0, 1.0, seed=42) # warmup integration (with capped LJ potential) warm_steps = 100 warm_n_times = 30 # do the warmup until the particles have at least the distance min_dist min_dist = 0.7 # integration int_steps = 1000 int_n_times = 10 ############################################################# # Setup System # #############################################################
for i in xrange(n_part):
#posx, posy, posz = box_l*numpy.random.random(3)
q *= -1
ptype = 1 - ptype
system.part.add(id=i, type=ptype, pos=numpy.random.random(3)
* system.box_l, q=q)
# Simulation parameters
system.time_step = 0.01
system.skin = 0.3
# Thermostat
temp = 1.
gamma = 1.
thermostat.Thermostat().set_langevin(kT=temp, gamma=gamma)
# Lennard-Jones interactions
lj_sig = 1.
lj_eps = 1.
lj_cut = 2.**(1. / 6.)
system.non_bonded_inter[0, 0].lennard_jones.set_params(
epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
system.non_bonded_inter[1, 0].lennard_jones.set_params(
epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
system.non_bonded_inter[1, 1].lennard_jones.set_params(
epsilon=lj_eps, sigma=lj_sig, cutoff=lj_cut, shift="auto")
# Check if electrostatics method is clear...
if method not in implemented_methods:
print("Please select an electrostatics method in the script.")
