Fixes to mamico plugin after mamico refactor

[amartyads]

Description

After the mamico coding week, some files and functions were renamed. The plugin is now fixed to use these new names.

Fixes Issue #290

[amartyads]

Since this fixes issue #290, which can only be done after the PR MaMiCo 45 is merged, I've turned this into draft.

[rubenhorn]

Seems not compatible with current MaMiCo master:

MaMiCo/ls1/src/Simulation.cpp: In member function ‘void Simulation::readXML(XMLfileUnits&)’:
MaMiCo/ls1/src/Simulation.cpp:321:87: error: ‘class coupling::interface::LS1StaticCommData’ has no member named ‘getSubdomainWeights’
  321 |                                 coupling::interface::LS1StaticCommData::getInstance().getSubdomainWeights()
      |                                                                                       ^~~~~~~~~~~~~~~~~~~

And also on the MaMiCo side:

MaMiCo/coupling/interface/impl/ls1/LS1MDSolverInterface.h: In member function ‘virtual void coupling::interface::LS1MDSolverInterface::synchronizeMoleculesAfterMassModification()’:
MaMiCo/coupling/interface/impl/ls1/LS1MDSolverInterface.h:189:46: error: ‘class DomainDecompBase’ has no member named ‘removeNonPeriodicHalos’
  189 |     global_simulation->domainDecomposition().removeNonPeriodicHalos();
      |                                              ^~~~~~~~~~~~~~~~~~~~~~

[amartyads]

The problem is that a bunch of these commits now depend on each other. Mamico master only works with the reflective-boundaries branch on ls1, which I didn't want to merge until I got this current PR merged, and pulled into reflective-boundaries.

And on mamico side, the irregular domain decomp needs some bugfixing, and since the getSubdomainWeights() function is part of that, pushing that on master right now would mean there's code on master that technically doesn't work.

I guess I can finish and merge irreg-dd-fix first before merging this, then mamico master will work with reflective-boundaries atleast.

[amartyads]

@cniethammer could you please check this PR?

The base branch was changed.