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Refactor particle insertion code #4493

Merged
merged 8 commits into from
Apr 11, 2022
Merged

Refactor particle insertion code #4493

merged 8 commits into from
Apr 11, 2022

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jngrad
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@jngrad jngrad commented Apr 7, 2022

Fixes #4447

Description of changes:

  • cache the largest particle id to make particle insertion run in constant time
  • fix regressions in the particle insertion code that raised NameError and numpy.VisibleDeprecationWarning
  • prevent particles from excluding themselves from non-bonded interactions and allow excluding ParticleHandle objects
  • improve separation of concerns and enforce single-responsibility principle:
    • move particle insertion/deletion/caching/tracking logic from particle_data.cpp to particle_node.cpp
    • simplify particle MPI callbacks by splitting the particle insertion code from the particle moving code

jngrad added 7 commits April 6, 2022 17:45
@jngrad
core: Separate particle storage from particle data
4f4040a 
Move particle creation, deletion, storage, cache and tracking logic
to a dedicated source file particle_node.cpp and leave particle
property setters and getters in particle_data.cpp.
@jngrad
core: Narrow interface of particle management
7af7b9c 
Narrow includes of particle_data.hpp and particle_node.hpp.
Make particle creation/deletion functions return void, since
internal details of the particle storage are irrelevant. Make
utility functions private (internal linkage). Replace MPI
primitives by their equivalent boost::mpi functions.
@jngrad
core: Use consistent argument names
b388ce5
@jngrad
core: Simplify particle callbacks
5a4c1c4 
Split callbacks that mixed multiple responsibilities via a flag
into multiple callbacks that have only one responsibility each.
@jngrad
core: Rewrite particle exclusion exception mechanism
255d0c8
@jngrad
core: Make particle insertion run in constant time
cf061d7
@jngrad
python: Fix broken particle creation logic
4054714 
The np.shape() call was raising a numpy deprecation warning on the
virtual sites relative property. The dictionary type check was not
correct and would fall through for any non-dict object.
@jngrad jngrad added this to the Espresso 4.2 milestone Apr 7, 2022
@jngrad jngrad requested a review from reinaual April 7, 2022 20:59
@jngrad jngrad added the automerge Merge with kodiak label Apr 11, 2022
@kodiakhq kodiakhq bot merged commit 32a46f6 into espressomd:python Apr 11, 2022
@jngrad jngrad deleted the particle_node branch April 11, 2022 15:56
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@reinaual reinaual reinaual approved these changes

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Successfully merging this pull request may close these issues.

Particle creation too slow in large simulations
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@jngrad @reinaual