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 |