Skip to content

Repo for issue tracking, documents and release. Learn more about MEDYAN at medyan.org.

License

Notifications You must be signed in to change notification settings

medyan-dev/medyan-public

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

26 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

MEDYAN

Build Status docs website

Welcome to Papoian Lab’s Mechanochemical Dynamics of Active Networks software package.

Copyright 2015-2022, Papoian lab at the University of Maryland.

For more general information about the code, visit medyan.org or the Papoian lab page. If you have questions, you can open an issue at https://github.com/medyan-dev/medyan-public.

This code is distributed under the license found in this directory, license.txt.

Usage

The MEDYAN executable can to be built from source. Check the installation guide for more information.

After compilation, MEDYAN can be invoked with additional command line arguments. Use ./medyan -h to see the help message, which includes all the available commands and options.

To run a simulation with a given system input file, run

./medyan -s <system-input-file> [-i <input-directory>] [-o <output-directory>]

The input files are described in detail here. Example input files for various systems are provided in the examples directory. The additional referenced input files are looked up in the same directory as the system input file, unless the -i option is used to specify a different directory.

The simulation output is written to the current working directory unless the -o option is used to specify a different directory. The output files are described in detail here.

MEDYAN also comes with a native interactive visualization tool to display simulation trajectories. Run ./medyan gui to launch MEDYAN in visualization-only mode. In this mode, one can press g to toggle the GUI overlay.

Authors

Active developers:

Name Email
Haoran Ni [email protected]
Nathan Zimmerberg [email protected]

All developers:

Garegin Papoian ([email protected]), Konstantin Popov, James Komianos, Aravind Chandrasekaran, Qin Ni, Carlos Floyd, Haoran Ni, Nathan Zimmerberg, Joshua Lucker.

All general correspondence about the code and its applications should be directed to Garegin Papoian. All developer and more specific code, installation, and usage correspondence should be directed to Active developers via email or the issue tracker.

Files

This MEDYAN distribution has the following files and directories:

File/Dir Description
docs Documentation files
examples A packaged example
external External libraries used by MEDYAN
license.txt Code licensing information
papers Relevant papers
README.md Current file
restart Restart scripts
src All source files
visual Visualization scripts

See the following documentation for details:

Documentation file Description
docs/manual/installation.md Tips on compilation, etc
docs/manual/input-files.md Tips on input files
docs/manual/output-files.md Tips on output files
docs/ExampleGuide.pdf Packaged example description

About

Repo for issue tracking, documents and release. Learn more about MEDYAN at medyan.org.

Topics

Resources

License

Stars

Watchers

Forks

Packages

No packages published