gen.parRep (v1.2)
The first available C++ implementation of the Generalized Parallel Replica algorithm.
Main repository :
Link to the project gitlab page (includes more resources):
You will find on this wiki main page links to other wiki pages containing (hopefully useful) test cases / tutorials, documentation, etc.
Quick start (basic tutorial)
TODO
How to write a simple Lua input file
TODO
Lua/C++ binding reference
See Lua Cpp binding reference where you will find a listing of all the implicit variables and implicit functions the C++ code exposes to the Lua scripting interface : you can use them for writing the mandatory functions (see How to write a simple Lua input file) called for detecting state exits and observables collecting, and also functions for saving data.
Publications
See the following articles:
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A generalized parallel replica dynamics: Binder, Lelièvre & Simpson, 2015: https://doi.org/10.1016/j.jcp.2015.01.002
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gen.parRep: a first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems: Hédin & Lelièvre, 2018: https://arxiv.org/abs/1807.02431 and https://doi.org/10.1016/j.cpc.2019.01.005
Reporting Bugs and Issues :
If you find any error, bug, or limitation, please open an issue on https://gitlab.inria.fr/parallel-replica/gen.parRep/issues so that the community can benefit from its correction ; also feel free to clone/fork the repo and perform the modifications yourself if you have the programming abilities to do so !
Continous Integration :
Continuous Integration is performed on a test case system (see ./ci), ensuring that no release breaks the ability to compile the software; furthermore reference results from a previous run are available in ./ci/ref.sim in an attempt to achieve reproducibility whenever possible.
