Adjust input and include PBC

Signed-off-by: Rafael Ravedutti Lucio Machado <rafael.r.ravedutti@fau.de>

data/minimd_setup_4x4x4.input

--2.8,9.5184,-2.8,9.5184,-2.8,9.5184
+0,6.7184,0,6.7184,0,6.7184
 1,0,0,0,-1.13216,0.0489689,-2.03943
 1,1.6796,0,0,0.689294,0.210488,-1.97539
 1,3.3592,0,0,-1.6486,0.372007,-1.91135

sim/particle_simulation.py

@@ -175,8 +175,8 @@ class ParticleSimulation:
     def generate(self):
         timestep = Timestep(self, self.ntimesteps, [
             (EnforcePBC(self.pbc).lower(), 20),
-            #(SetupPBC(self.pbc).lower(), 20),
-            #UpdatePBC(self.pbc).lower(),
+            (SetupPBC(self.pbc).lower(), 20),
+            UpdatePBC(self.pbc).lower(),
             (CellListsBuild(self.cell_lists).lower(), 20),
             PropertiesResetVolatile(self).lower(),
             self.kernels.lower()
@@ -188,8 +188,8 @@ class ParticleSimulation:
             CellListsStencilBuild(self.cell_lists).lower(),
             self.setups.lower(),
             EnforcePBC(self.pbc).lower(),
-            #SetupPBC(self.pbc).lower(),
-            #UpdatePBC(self.pbc).lower(),
+            SetupPBC(self.pbc).lower(),
+            UpdatePBC(self.pbc).lower(),
             CellListsBuild(self.cell_lists).lower(),
             Block(self, VTKWrite(self, self.vtk_file, 0)),
             timestep.as_block()