Separation of concerns in Reaction Ensemble

[jngrad]

The RE needs to be moved to a submodule of the core and split in several files, one per RE class (along with their dependencies). Right now all classes are mixed together, which makes maintenance more difficult. For example:

• It is not immediately clear which utility classes are needed by each RE class. It's also unclear if RE classes depend on each other, or if they only depend on the parent class ReactionAlgorithm. Having separate files would help figure that information out by simply reading the #include statements.
• The public API of RE includes particle_data.hpp and energy.hpp, both of which shouldn't be exposed. They are actually only needed in the implementation of private methods of the CollectiveVariable classes and could easily be moved to the .cpp file (the overhead of not having them inline shouldn't matter much). particle_data.hpp in particular contains prototypes for particle communication and should only be included in .cpp files; in fact, the Particle structs were extracted from particle_data.hpp and stored in Particle.hpp in ESPResSo 4.2 to help us hide the communication logic and remove as many #include <particle_data.hpp> as possible (75ef537, 78bf03d).

The new layout could look like this:

src/core/reaction_ensemble/
                          |- CMakeLists.txt
                          |- utils.hpp
                          |- utils.cpp
                          |- ReactionAlgorithm.hpp
                          |- ReactionAlgorithm.cpp
                          |- ConstantpHEnsemble.hpp
                          |- ConstantpHEnsemble.cpp
                          |- WidomInsertion.hpp
                          |- WidomInsertion.cpp
                          |- ReactionEnsemble.hpp
                          |- ReactionEnsemble.cpp
                          |- WangLandauReactionEnsemble.hpp
                          |- WangLandauReactionEnsemble.cpp

Special files:

• utils.hpp
  • for all functions currently defined at the bottom of src/core/reaction_ensemble.hpp
• ReactionAlgorithm.hpp
  • class ReactionAlgorithm
  • class SingleReaction
  • class StoredParticleProperty
• WangLandauReactionEnsemble.hpp
  • class WangLandauReactionEnsemble
  • class CollectiveVariable
  • class EnergyCollectiveVariable
  • class DegreeOfAssociationCollectiveVariable