Simulation code of the dynamical graph model proposed in the paper Y. Murase et al., "A simple model for skewed species-lifetime distributions", New J. Phys. (2010). http://iopscience.iop.org/article/10.1088/1367-2630/12/6/063021
The main simulation program is written in standard C++.
For making plots, Python3 and numpy and matplotlib libraries are needed.
One of the simplest way to install these would be using miniconda or anaconda.
conda install numpy matplotlib
To build the simulation code, run
make
After the program was built, execute
./run.sh 0.2 1024 65536 1234
where the arguements specify "connection probability", "initial warm-up timesteps", "simulation timesteps", and the seed of random numbers, respectively.
You'll find the simulation data as well as png files of the plots.
After you build the program, run the following command to register the simulator to OACIS.
$OACIS_ROOT/bin/oacis_ruby register_oacis.rb
Here $OACIS_ROOT refers to the path of OACIS.
If you are using the docker image of OACIS, the following command registers the simulator to the OACIS running in the container. Please use oacis/oacis_jupyter since it contains Python environments.
docker exec -it -u oacis my_oacis bash -c "git clone https://github.com/yohm/dynamical_graph_model.git && dynamical_graph_model/install.sh"
The MIT License (MIT)
Copyright (c) 2016 Yohsuke Murase
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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