def test_MMM2D(self):
self.S.box_l = (10, 10, 10)
self.S.cell_system.set_layered(n_layers=10,use_verlet_lists=False)
self.S.periodicity=1,1,0
mmm2d=(el.MMM2D(prefactor=1,maxPWerror=1E-7))
self.S.actors.add(mmm2d)
self.S.integrator.run(0)
if self.generate_data:
n=len(self.S.part)
data=np.hstack((self.S.part[:].id.reshape((n,1)),self.S.part[:].pos_folded,self.S.part[:].q.reshape((n,1)),self.S.part[:].f))
np.savetxt(tests_common.abspath(
"data/coulomb_mixed_periodicity_system.data"),data)
self.compare("mmm2d (compared to stored data)", energy=True)
self.S.actors.remove(mmm2d)
WCA_cut = 2.**(1. / 6.)
system.non_bonded_inter[0, 1].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=WCA_cut,
shift="auto")
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1.0,
sigma=1.0,
cutoff=WCA_cut,
shift="auto")
energy = system.analysis.energy()
print("Before Minimization: E_total=", energy['total'])
system.minimize_energy.init(f_max=10,
gamma=50.0,
max_steps=1000,
max_displacement=0.2)
system.minimize_energy.minimize()
energy = system.analysis.energy()
print("After Minimization: E_total=", energy['total'])
system.thermostat.set_langevin(kT=0.1, gamma=1.0)
mmm2d = electrostatics.MMM2D(prefactor=10.0,
maxPWerror=1e-3,
const_pot=1,
pot_diff=50.0)
system.actors.add(mmm2d)
visualizer.run(1)