Clone the repository using the following command:
git clone https://github.com/DaVinkie/ComplexSystems.git
After having cloned the repository, you need to collect the submodule cromosim. This is done by running the following command:
git submodule update --init --recursive
The repository assumes you're using SSH to identify yourself and will throw a key-error when you are not. If you use the standard password for Git, go to the file .git/config and change the URL underneath submodules (line 20) to:
https://github.com/DaVinkie/cromosim.git
Afterwards run the previous command again.
In cromosim/requirements.txt you will find the required packages to run cromosim. These are relatively standard packages, but it is important to have update to the latest version of numpy.
To run a model simulation there are two options:
- Run a single simulation:
The simulation_demo.json contains the parameters of the model. Adjust these to your liking. Of note are the background under domain and velocity distribution underneath groups and new_groups. Full documentation on the parameters can be found in the simulation_demo.py
To run a simulation, run the following command from the terminal:
python model_simulation.py --json model_simulation.json
- Run our experiments:
To replicate our experiments, run the following commands - without the json flag:
python run_simulation_a.py
python run_simulation_b.py
(Results from the experiment are already stored within the results folder. The complete runtime is about 380 CPU hours. The simulation_a_loop.txt / simulation_b_loop.txt files allow for running parallel simulation on one machine by keeping track of simulations that's currently being executed.)
Data handling is done in R (due to it's superior features for analyzing and working with data :): The analysis folder contains the folowing scripts:
analyze_a.R analyze_b.R
each of which is designated for collecting, cleaning, visializing, and analyzing results from the respective simulations. The analysis scripts can be run interactively to produce all required figures.
The generate_sims.R creates settings file for running the simulations and the results_animation.R file joins output from the cromosim with a calculated thoughput for creating a joint animation of the simulation and the increasing throughput.
