# 2. Prune Edge Species¶

When dealing with complicated reaction systems, RMG calculation would easily hit the computer memory limitation. Memory profiling shows most memory especially during memory limitation stage is occupied by edge species. However, most edge species in fact wouldn’t be included in the core (or final model). Thus, it’s natural to get rid of some not “so useful” edge species during calculation in order to achieve both low memory consumption and mechanism accuracy. Pruning is such a way.

## 2.1. Key Parameters in Pruning¶

• toleranceKeepInEdge

Any edge species to prune should have peak flux along the whole conversion course lower than toleranceKeepInEdge $$*$$ characteristic flux. Thus, larger values will lead to smaller edge mechanisms.

• toleranceMoveToCore

Any edge species to enter core model should have flux at some point larger than toleranceMoveToCore $$*$$ characteristic flux Thus, in general, smaller values will lead to larger core mechanisms.

• toleranceInterrupSimulation

Once flux of any edge species exceeds toleranceInterruptSimulation $$*$$ characteristic flux, dynamic simulation will be stopped. Usually this tolerance will be set a very high value so that any flux’s exceeding that means mechanism is too incomplete to continue dynamic simulation.

• maximumEdgeSpecies

If dynamic simulation isn’t interrupted in half way and total number of the edge species whose peak fluxes are higher than toleranceKeepInEdge $$*$$ characteristic flux exceeds maximumEdgeSpecies, such excessive amount of edge species with lowest peak fluxes will be pruned.

• minCoreSizeForPrune

Ensures that a minimum number of species are in the core before pruning occurs, in order to avoid pruning the model when it is far away from completeness. The default value is set to 50 species.

• minSpeciesExistIterationsForPrune

Set the number of iterations an edge species must stay in the job before it can be pruned. The default value is 2 iterations.