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Table 2 A description of each command line argument and their default values

From: Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Command line parameter Description Which methods use it Default value
Filename NetCDF file name All None
Random Seed The random number generator's seed value. All Randomized (system dependent)
Epsilon (ε) Minimum number of molecules of both reactant & product species for approximation to a continuous Markov process All HyJCMSS simulation methods 100 molecules
Lambda (λ) Minimum rate of reaction for approximation to a continuous Markov process All HyJCMSS simulation methods 10 molecules/sec
MSR Tolerance Maximum relative effect of slow reactions per numerical integration of SDEs All HyJCMSS simulation methods 1/ε
SDE Tolerance Maximum values of drift& diffusion error criteria Adaptive Methods 1e-4
SDE time step Maximum time step of numerical integrator Fixed Methods 0.10 seconds or Save Time