gillespied 0.3.1

Physical time reaction propagation library in D. Based on the Gillespie algorithm of 1977 it contains various implementations and enhancements for fast reaction index and timing sampling.


To use this package, run the following command in your project's root directory:

Manual usage
Put the following dependency into your project's dependences section:

README

This repository contains a physical time reaction propagation library in D. Based on the Gillespie algorithm of 1977 it contains various implementations and enhancements for fast reaction index and timing sampling.

The algorithm models the time and reaction evolution as stated by Gillespie, see [1] and [2]. After [3], all properly or rather "related to the intended master equation" formulated algorithms, modelling physical time propagation algorithms are equivalent. This concerns algorithms with rejection as well as the ones which are rejection-free, as the current algorithm. The rejection-free algorithms form a subset of the algorithms with rejection.

The default Gillespie algorithm was enhanced by two features.

  • If the reaction propensities are known, i. e. they do not have to be estimated, one of the random numbers needed by the original algorithm can be saved. As consequence the longer logarithmic operation is cancelled. See [4].

  • The search of next reaction is done over the cumulative sum of provided propensities. This search can be enhanced by using memory space. In this case, any of available search algorithms can be applied to the cumulative sum range, which is naturally ordered. In [5] the binary search algorithm was applied, whereas in the present case, the search policy is managed by the standard library.

[1] D. T. Gillespie, J. Comput. Phys. 434, 403 (1976).

[2] D. T. Gillespie, 93555, 2340 (1977).

[3] S. A. Serebrinsky, Phys. Rev. E - Stat. Nonlinear, Soft Matter Phys. 83, 2010 (2011).

[4] W. Sandmann, Comput. Biol. Chem. J. 32, 292 (2008).

[5] H. Li and L. R. Petzold, Tech. Rep. 1 (2006). (logarithmic direct method)

Example usage:

import gillespied;
import std.random : uniform, uniform01, rndGen; 
import std.math : log, isNaN; 
import std.range; 

void main()
{
    import std.stdio; 
	real[] inputPropensities = new real[uniform(1, ubyte.max)];
    foreach(ref el; inputPropensities) 
        el = - uniform01!real.log; 
    auto algorithm = gillespieAlgorithm;
    put(algorithm, inputPropensities); 
    assert(!algorithm.tau.isNaN); 
    assert(algorithm.tau != real.infinity); 
    assert(algorithm.index != inputPropensities.length); 
}

The package provides optional dependency on the random generator of mir.random. This is done by the optional feature of dub, so that this random generator take over, if already present in the project.

Copyright: Copyright (c) 2019- Alexander Orlov. All rights reserved.

License: https://opensource.org/licenses/BSL-1.0, BSL License

Author: Alexander Orlov, sascha.orlov@gmail.com

Authors:
  • Alexander Orlov
Dependencies:
mir-random
Versions:
0.3.3 2019-Feb-08
0.3.2 2019-Feb-08
0.3.1 2019-Feb-05
0.3.0 2019-Feb-05
0.2.0 2019-Jan-27
Show all 9 versions
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