mamico-cfg: Fix support for different boundary conditions

[rubenhorn]

TODO:

• Add new option for boundary condition XY-periodic [1]
• Rename current checkpoint to CheckpointSimpleMD_10000_XY-periodic_0.checkpoint
• Create new checkpoint CheckpointSimpleMD_10000_fully_periodic_0.checkpoint
• Select checkpoint based on the boundary condition during couette.xml.template substitution
• Apply boudary condition settings appropriately (Usher, massflux, Zhou force)
  For XY-periodic: Usher disabled, massflux only XY, Zhou only Z ie
  <boundary-force type="zhou-boundary-force" west="no" east="no" north="no" south="no" bottom="yes" top="yes" density="0.81" temperature="1.1" />
• Better checkpoint formats #85

[1]: XY-periodic boundary condition:

bottom-south-west="reflecting"
bottom-south="reflecting"
bottom-south-east="reflecting"
bottom-west="reflecting"
bottom="reflecting"
bottom-east="reflecting"
bottom-north-west="reflecting"
bottom-north="reflecting"
bottom-north-east="reflecting"

south-west="periodic"
south="periodic"
south-east="periodic"
west="periodic"
east="periodic"
north-west="periodic"
north="periodic"
north-east="periodic"

top-south-west="reflecting"
top-south="reflecting"
top-south-east="reflecting"
top-west="reflecting"
top="reflecting" 
top-east="reflecting"
top-north-west="reflecting"
top-north="reflecting"
top-north-east="reflecting"