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Pruning in RMG- Py

Pruning in RMG- Py. Kehang Han 7 /10/2014. Why to Do Pruning. For complex systems, memory limitation Most memory occupied by edge species Most edge species won’t be included in final model Pruning is trying to get rid of edge species which have least possibility of entering core.

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Pruning in RMG- Py

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  1. Pruning in RMG-Py Kehang Han 7/10/2014

  2. Why to Do Pruning • For complex systems, memory limitation • Most memory occupied by edge species • Most edge species won’t be included in final model • Pruning is trying to get rid of edge species which have least possibility of entering core

  3. Key Params in Pruning • toleranceInterruptSimulation • toleranceMoveToCore • toleranceKeepInEdge • maximumEdgeSpecies

  4. How Pruning Works

  5. Which Species to Prune

  6. Which Species to Prune toleranceKeepInEdge

  7. Simulation Runs to Termination terminationConversion

  8. ToleranceInterruptSimulation InterruptSimulation terminationConversion

  9. ToleranceMoveToCore InterruptSimulation MoveToCore terminationConversion

  10. ToleranceInterruptSimulation InterruptSimulation terminationConversion

  11. Normal Rules for Params • toleranceInterruptSimulationtoleranceMoveToCore • Otherwise, always interruption without enlarging core • Special cases: equal to each other; Interruption tolinfinity • toleranceKeepInEdge has the unit for flux • Not convenient, maybe can do pruning just based on rank • maximumEdgeSpecies • Start deleting species with lowest fluxes if total edge species number exceeds maximumEdgeSpecies

  12. Further Questions to Ask • How effective it can save memory when dealing with complex kinetics system? • How it affects model generation/model content? • By compare models with and without pruning • ….

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