February 05
Doing some physical simulations I could abstract the Gillespie algorithm, see


which may be useful.

The number of algorithms able to model physical (continuous) time during an ongoing (reaction) process is rather limited. The announced algorithm is known to provide this feature. There are very much manifestations and improvements of the original Gillespie. In general, the improvements try to improve the speed of the algorithm either via
- faster timing generation
- faster next reaction look up
- approximating the output by assumptions

Compared to the standard Gillespie algorithm two enhancements were implemented:
- for the case, reaction propensities are known, interarrival timings do not necessarily depend on a random number and its logarithm. This makes each time query faster.
- If the governing simulation can handle non-nogc algorithm instantiation, a dedicated working array can be handled inside the algorithm. This provides faster next reaction search for all operations.

All issues are of course welcome and will be tackled in my spare time. I hope, for this library, many further improvements, and applications could be found in future.