Refactor System class #4816
Refactor System class #4816
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Remove the non-bonded IA parameters global variable. Replace upper triangular matrix with lower triangular matrix indexing, which is more efficient and doesn't require re-ordering stored objects when resizing the container. Store the actual particle type in global variable max_seen_particle_type.
Remove partCfg singleton. Rewrite the remaining analysis methods that ran only on MPI rank 0 to run in parallel, or to stream only the relevant data structures to MPI rank 0 (instead of the entire particle data).
Give each member of ScriptInterface::System a handle to the core System class. Refactor AutoParameters serialization. The System class can now handle checkpointing of its ObjectHandle members.
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CellStructure::set_verlet_skina call of may lead to a situaoitn, where the ParticleDecompositoin needs to be rebuild, or at least the Verlet list becomes invalid. Can we safeguard, that this is not called without hte necessary steps being taken? |
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As I understand it, there is code in src/core/energy.cpp that implements member functions of the System class. Should we move all files that direclty contribute to the system class into a common directory src/core/system or the like? |
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void integrator_sanity_checks() should probably check for time_step <= 0 |
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Could you please add some notes as to the purpose of code in leaf.hpp |
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Aside form previous commens, LGTM. This PR is a big step towards getting rid of globals and allowing more than one system in a script. Thanks alot. |
Dependency inversion: let CellStructure manage the Verlet skin and the on_verlet_skin_change() event. Encapsulation: the core System class now has access to its own shared_ptr and can bind Leaf objects during construction. Remove the EspressoSystemStandAlone class, which is now redundant.
Done.
Done. I also took this opportunity to move the Verlet skin management and ghost update logic to
Done. Can be found in a self-contained .dox file that generates
I thought about it, in fact pressure, forces and tuning also implement |
Description of changes:
SystemclassSystemclassSystemclassSystemclassEspressoSystemStandAloneclassespressomd.galilei.GalileiTransformis now a member of theSystemclass, accessible viasystem.galilei