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Welcome to Active Matter DEM Simulator

This is a versatile classical particle dynamics simulation code that focuses on numerically modelling particulate systems/ granular matter. The system can be anything ranging from materials like colloids, grains to active and living systems like cellular assemblies. This code incorporates Discrete-Element-Method (DEM) simulation techniques 2 for application to both passive and active granular matter.

Key features

  • Simulates a diverse range of physical systems including colloids, cellular assemblies, spinners etc.
  • Availability of various integration schemes (Velocity-Verlet, Leimkuhler-Matthews etc.) and force calculation algorithms.
  • Realistic Contact force models predefined.
  • Customizable and extendable codebase for specific research needs.
  • Easy to use

Organization of this documentaion

This documentation is organized into the following parts:

  1. The Physics Guide with information about general physics that goes behind this simulation code.
  2. The Programmer Guide with information about code structure: header files and methods.
  3. The Hands-on examples with some working examples to illustrate the use of this code.

Organization of this material is simple and as readable as it can be.

The following examples depict the cases where this simulation code was used to reproduce results from the literature of Active matter and Granular matter physics.

MIPS
Motility Induced Phase Separation (Cates, M. E., & Tailleur, J. (2015). "Motility-induced phase separation.")
My caption
Directed percolation [1, see footnote] (Grober et al. "Unconventional colloidal aggregation in chiral bacterial baths." Nature Physics).
CG
Phase-separation in Chiral Lennard-Jones Fluid (Claudio B. Caporusso, et al. "Phase Coexistence and Edge Currents in the Chiral Lennard-Jones Fluid").
CG
Confined gas of active spinners (Tsai, J-C., et al. "A chiral granular gas").

  1. Pabitra Masanta worked on this for his master's thesis work at IIT Bombay ↩

  2. H Pꎬ Zhu, Zongyan Y Zhou, RY Yang, and AB Yu. Discrete particle simulation of particulate systems: theoretical developments. Chemical engineering science, 62(13):3378–3396, 2007. ↩