Asynchronous τ-leaping, Zbigniew Jędrzejewski-Szmek, Kim T. Blackwell, Journal of Chemical Physics, 144, 125104 (2016)

To run the examples:

1. clone this repository:

   git clone https://github.com/neurord/jcp2016-examples

2. download NeuroRD v. 3.0:

   wget https://github.com/neurord/stochdiff/releases/download/v3.0/stochdiff-3.0.0-all-deps.jar

3. pick one of the examples, e.g.:

   cd jcp2016-examples/a_b_2d_c_annihilation/

4. run the simulation:

   java -Dstochdiff.writers=h5,text -jar ../../stochdiff-3.0.0-all-deps.jar model-async-0.01.xml

This produces output of

• *.h5 — the HDF5 file with simulation results (numbers of particles as specified times)
• *.out — the same but in tabular text format
• *.log — a copy of the screen output

See https://github.com/neurord/stochdiff/blob/v3.0/README.rst for documentation about the model file format and runtime options.