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Partially addresses #109

  • LinkedCells are stored in a Kokkos View (shared, host pinned)
  • LinkedCells are converted to POS (cell molecules are stored in the MoleculeService)

@rubenhorn rubenhorn marked this pull request as draft July 24, 2025 19:16
@rubenhorn rubenhorn changed the base branch from master to refactor2507-WIP July 24, 2025 19:16
@rubenhorn rubenhorn marked this pull request as ready for review July 24, 2025 19:16
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INFO SimpleMDBench: SUCCESS Checksum is correct :-)

🚀 👍

_moleculeIndex--;
return tmp;
}
bool operator!=(const Iterator& other) const {
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There is a if(_moleculeService != other._moleculeService) return true; missing here!


private:
std::list<Molecule*> _molecules;
unsigned int _index;
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Is there a reason why the simplemd::services::MoleculeService* _moleculeService; is stored in the Iterator but not in the LinkedCell? Having it here (passed in via constructor) would have the advantage that you could do

for(Molecule& m : cell)

instead of

    for (auto it = cell.begin(_moleculeService); it != cell.end(); it++) {
      Molecule* m = (*it);
      ....

@rubenhorn rubenhorn marked this pull request as draft July 25, 2025 10:40
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Obsolete 👉 delete this branch!

@rubenhorn rubenhorn closed this Aug 9, 2025
@rubenhorn rubenhorn deleted the kokkos/simpleMD-datastructures-WIP branch August 9, 2025 12:03
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3 participants