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ReaDDy Welcome to the website of ReaDDy - a particle-based reaction-diffusion simulator, written in C++ with python bindings ReaDDy is an open-source project, developed and maintained by Moritz Hoffmann, Christoph Fröhner and Frank Noé of the AI4Science (former CMB) group at the Freie Universität Berlin
Simulation - GitHub Pages Reactions in ReaDDy are evaluated per time step, meaning that each particle might have multiple possible reaction partners In order to solve this, one can chose between two different reaction handlers:
Install readdy - GitHub Pages If this does not return an error, you are ready to readdy Latest build To obtain the latest but possibly unstable build you can build from source by using conda-build on the recipe
Practical sessions - GitHub Pages Task 3) ReaDDy intro II: Reactions, observables and checkpoints Follow along the readdy-observables The notebook covers the following: adding reaction to system adding observable to simulation reading back the observable from trajectory file using checkpoints to continue a simulation Task 4) Crowded mixture, MSD
System configuration - GitHub Pages Potentials in ReaDDy are divided into first-order potentials external potentials, i e , those that depend only on the position of one particle, and second-order potentials pair potentials, i e , those that depend on the relative position of two particles
Demonstration - readdy. github. io ReaDDy - A particle-based reaction-diffusion simulator HomeInstall readdy API System configurationSimulationPost-processing Examples
Development - GitHub Pages This section shall be a DevGuide, i e there will be implementation-related information which is not required for using ReaDDy, but for understanding how it works
ReaDDy documentation ReaDDy - A particle-based reaction-diffusion simulator Home Install readdy API System configuration Simulation Post-processing Examples Demonstration Validation Benchmark Advanced topics Cookbook Development Legal notices Imprint Software license ReaDDy on GitHub
Cookbook - GitHub Pages import os import numpy as np import readdy system = readdy ReactionDiffusionSystem (box_size= [10 , 10 , 10 ]) system add_species ("A", 1 0) sim = system simulation ("SingleCPU") sim output_file = "out h5" if os path exists ("checkpoints "): # load checkpoint sim load_particles_from_latest_checkpoint ("checkpoints ") else: # new positions
Simple example - readdy. github. io Simple example In [1]: import readdy print(readdy __version__) v2 0 3-27 Step 1: Set up a reaction diffusion system In [2]: system = readdy ReactionDiffusionSystem([25 ,25 ,25 ], temperature=300 *readdy units kelvin) system add_species("A", 1 0) Define reactions In [3]: system reactions add("myfusion: A +(2) A -> A", rate=10 ) system reactions