This directory contains all of the metadata from the paper "A direct link between active matter and sheared granular systems" by P.K. Morse, S. Roy, E. Agoritsas, E. Stanifer, E.I. Corwin, and M.L. Manning. If there are any questions about the data, the corresponding author can be reached at peter.k.morse@gmail.com

Versions of programs used for Data Generation:
Python 3.6.4
GCC 7.4.0
pybind11
c++17

The data generation has been optimized and tested on UNIX systems. While it has been tested on Windows operating systems, modifications to the make file may be necessary, in particular to the linking of pybind11. See documentation of pybind11 for support.

The directory is organized as follows:
1) Data
3) Sample Script
4) monteCarloPCP

1) Data
The data here is all of the metadata from the paper, which can then be used to generate the plots. It is organized in folders labelled by the figure number and further subdivided into folders corresponding to the figure parts (a, b, c, etc.). Each figure folder has its own readme file stating the structure of the data. Due to the difficulty reading latex fonts in plaintext, references are frequently made to the x and y values of the plot. It is thus necessary to reference the paper for each (and for definitions of variable names).


2) Sample Scripts
Five sample scripts are included. Note that xi has units of the smaller particle diameter, which is 1 in the paper, but is not set to 1 in the simulations. Instead, the simulations run assuming a simulation box volume of 1 to create numerical speedups via the periodic boundary conditions. Smallest particle radius can be found by calling p.getRadii()[0] after the bidisperse radius distribution has been set.

a) To run AQRD in a system of N particles with contact power alpha and gcf correlation length xi

python3 AQRDRunGCF dim N alpha xi save_directory

b) To run AQRD in a system of N particles with contact power alpha and wcf correlation length xi 

python3 AQRDRunWCF dim N alpha xi save_directory

c) To run AQRF in a system of N particles with contact power alpha and gcf correlation length xi

python3 AQRFRunGCF dim N alpha xi save_directory

d) To run AQS in a system of N particles in dimension dim with contact power alpha

python3 AQSRun dim N alpha save_directory

3) We are not at liberty to share the initial configurations from Fig. 6, as it is borrowed from the authors of the original study cited. These authors can be contacted for configurations. However, because the force law is complex, we include a script which can run AQRD on those configurations provided they live in a location given at a location data_directory. To run AQRD with gcf correlation length xi, run the following:

python3 ninarelloRFReader xi data_directory save_directory


3) monteCarloPCP
monteCarloPCP is the code which generates the packings. It must be made by typing "make clean; make" in the folder
monteCarloPCP/Release

monteCarloPCP requires pybind11 (https://github.com/pybind/pybind11) to be included in this base folder, or else the make file must be altered to link directly to the pybind folder. It may also be necessary to locate the python folder and alter the address of it accordingly.

As this code is continually developed, an updated version of monteCarloPCP can be obtained from P.K. Morse at peter.k.morse@gmail.com. Public distribution will be provided via github at a later date.