GA-project

Simple genetic algorithm used to study thermodynamic properties of evolutionary processes. See GA-entropy.tex for a write-up of the science and the conclusions.

Running an evolution

Pick parameters and start the run

You can run an evolution by adjusting the values of mate_func, initial_func, and fit_func in the main() function of GA-func-max.py

Then you can run it with:

./GA-func-max.py

The output will tell you what your output file name will be, for example: GA-gen-info_pid3554872.out

Plotting the evolution

You can (at any time during the run) get a view of what's happening with a command like:

./plot_ga_output.py GA-gen-info_pid3554872.out &

You could also view all the output files in the current directory with

./plot_ga_output.py &

or you can give a few GA-gen-info_pid????.out file names on the command line and it will make plots for those files. The plots are shown interactively, and they are also saved as .pdf files.

Building the paper

Right now we are using this figure as an example:

GA-gen-info_pid3095791.out.pdf

with that pdf file present you can run:

latexmk -pdf GA-entropy.tex

to generate GA-entropy.pdf

Building the slides

latexmk -pdf GA-entropy-slides.tex

will generate GA-entropy-slides.pdf

Prerequisites

The python packages we used for the code are:

• matplotlib for the graphs,
• pandas for the data frame,
• shortuuid for unique identifiying strings,
• numpy for population creation and advanced math,
• struct for binary editing,
• os and sys for nan removal as well as file creation,
• and math for regular arithmetic