/NERDSS

NonEquilibrium Reaction-Diffusion Self-assembly Simulator

Primary LanguageC++GNU General Public License v3.0GPL-3.0

NERDSS

Structure-Resolved Reaction-Diffusion Simulation Software by Johnson Lab, JHU

Installation

To build NERDSS, you need:

  1. A C++ compiler:
    • For macOS, install XCode
    • For Ubuntu, install a compiler through apt
  2. GNU Scientific Library (GSL) version 1.0 or higher:
    • For macOS, install via Homebrew
    • For Ubuntu, install via apt
  3. To compile using make:
    • Navigate to the main directory
    • Run make serial
    • The executable will be placed in the ./bin directory

Running Simulations

  1. Example input files are located in the subdirectories within the sample_inputs folder. They can also be generated using the python GUI program, which is also included in the ioNERDSS tool.

  2. To start the simulation, use the command ./nerdss -f parms.inp.

Analyzing Results

  1. Use the ioNERDSS PyPi library for visualizing simulation results.
  2. Install ioNERDSS with pip install ioNERDSS.
  3. Refer to the ioNERDSS repository for more details.