# do the warmup until the particles have at least the distance min_dist
min_dist = 0.9
# integration
int_steps = 1000
int_n_times = 20
#############################################################
# Setup System #
#############################################################
# structure factor file
structurefactor_type_list = [0, 1]
structurefactor_order = 20
structurefactor_file = open("pylj_liquid_structurefactor.dat", "w")
structurefactor_file.write("# k\tS(k)\n")
structurefactor_bins = len(
system.analysis.structure_factor([0], structurefactor_order)[0])
structurefactor_k = np.zeros(structurefactor_bins)
structurefactor_Sk = np.zeros(structurefactor_bins)
# Interaction setup
#############################################################
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=lj_eps,
sigma=lj_sig,
cutoff=lj_cut,
shift="auto")
system.force_cap = lj_cap
print("LJ-parameters:")
print("\nSCRIPT--->P3M parameter:\n")
p3m_params = p3m.get_params()
for key in list(p3m_params.keys()):
print("{} = {}".format(key, p3m_params[key]))
# elc=electrostatic_extensions.ELC(maxPWerror=1.0,gap_size=1.0)
# system.actors.add(elc)
print(system.actors)
#############################################################
# 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))
# set LJ cap
lj_cap = 20
system.force_cap = lj_cap
print(system.non_bonded_inter[0, 0].lennard_jones)
# Warmup Integration Loop
i = 0
int_n_times = 5
#############################################################
# Setup System #
#############################################################
# distribution file
distr_type_list_a = [0]
distr_type_list_b = [1]
distr_r_min = 0.1
distr_r_max = box_l / 2.0
distr_r_bins = 200
distr_log_flag = 0
distr_int_flag = 1
distr_file = open("pylj_liquid_distribution.dat", "w")
distr_file.write("# r\tdistribution\n")
distr_r = np.zeros(distr_r_bins)
distr_values = np.zeros(distr_r_bins)
# Interaction setup
#############################################################
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=lj_eps,
sigma=lj_sig,
cutoff=lj_cut,
shift="auto")
system.force_cap = lj_cap
print("LJ-parameters:")
print(system.non_bonded_inter[0, 0].lennard_jones.get_params())
system.analysis.dist_to(0)
print("Simulate {} monovalent salt in a cubic simulation box {} at molar concentration {}."
.format(n_part, box_l, mol_dens).strip())
print("Interactions:\n")
act_min_dist = system.analysis.min_dist()
print("Start with minimal distance {}".format(act_min_dist))
system.cell_system.max_num_cells = 2744
#############################################################
# Warmup Integration #
#############################################################
# open Observable file
obs_file = open("pydebye_hueckel.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))
# set LJ cap
lj_cap = 20
system.force_cap = lj_cap
print(system.non_bonded_inter[0, 0].lennard_jones)
# Warmup Integration Loop
i = 0