Multithreaded Gephi Force Atlas2 Layout in 2D or 3D

Features

• Parallel Barnes-Hut tree building
• Computes total distance that all points move at each iteration in order to determine when the algorithm has converged
• Parallel force, attraction, and speed computations
• Option to rebuild Barnes-Hut tree every n iterations
• Option to update Barnes-Hut tree centers every n iterations
• Command line interface

Building

mvn package

Command Line Usage

There are two options:

1. from within the source code project:

   mvn exec:java -Djava.awt.headless=true -Xmx8g -Dexec.args="[FLAG]..."

2. using the JAR built with mvn package:

   java -Djava.awt.headless=true -Xmx8g -jar target/forceatlas2-*-jar-with-dependencies.jar [FLAG]...

where possible values for [FLAG]... are:

Flag	Description	Default Value
--input	Input graph in one of Gephi input file formats
--output	Output file; see also --format
--nsteps	Number of iterations. Mutually exclusive with --targetChangePerNode
--targetChangePerNode	Target distance change per node before stop the algorithm. Mutually exclusive with --nsteps
--targetSteps	Maximum number of iterations before stopping the algoritm. This option is together with --targetChangePerNode	10000
--2d	Whether to produce a 2d layout	false
--directed	Whether input graph is directed	false
--nthreads	Number of threads to use.	All cores
--format	Output file format. One of csv, gdf, gexf, gml, graphml, pajek, txt	txt
--coords	Tab separated file, containing initial coordinates with headers id, x, y, z
--seed	Seed for random number generation for initial node position	timestamp
--barnesHutSplits	Rounds of splits to use for Barnes-Hut tree building. Number of regions after splitting is (2^2)^barnesHutSplits for 2D, and (2^3)^barnesHutSplits for 3D
--barnesHutTheta	Theta of the Barnes Hut optimization	1.2
--barnesHutUpdateIter	Update Barnes-Hut tree every barnesHutUpdateIter iterations	1
--updateCenter	Update Barnes-Hut region centers when not rebuilding Barnes-Hut tree	false
--jitterTolerance	How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.	1.0
--linLogMode	Switch ForceAtlas' model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.	false
--scalingRatio	How much repulsion you want. More makes a more sparse graph	2.0 if # nodes >= 100, otherwise 10.0
--gravity	Attracts nodes to the center	1.0
--strongGravityMode	A stronger gravity law	false
--outboundAttractionDistribution	Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.	false

Example Datasets

Gephi example datasets