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PySAGES (Python Suite for Advanced General Ensemble Simulations) is a Pythonimplementation ofSSAGES with support for GPUs.

PySAGES currently supportsHOOMD-blue,LAMMPS,ASE, andOpenMM. We plan to add support for other engines that have a pythonAPI, including those supported by the original SSAGES.

Before installing PySAGES, you need to install one of the following plugins, depending onyour molecular dynamics engine of choice:

• DLPack Plugin for HOOMD-blue
• DLPack Plugin for OpenMM
• DLPack Plugin for LAMMPS
• No plugin needed for ASE

You also need to installJAX, a library forhigh-performance numerical computing. Follow their installation guide and make sure youhave it installed before using PySAGES. Depending on your local setup, you may needto install the CPU version or the CUDA compatible version.

For GPU support, JAX and any backend (HOOMD-blue, LAMMPS, or OpenMM) need to be built orinstalled with CUDA support.

You can follow our installation tutorial on Google Colab to see how PySAGES, HOOMD-blue,and OpenMM can be built and installed in such an environment.

PySAGES provides a straightforward interface to set up collective variables and enhancedsampling methods in your MD simulations. See thedocumentation to learn more.

We provide ready-to-go examples for common methods. Check out theexamplessubfolder to look at different script and notebook examples. These include pre-setsimulations and a tutorial on how to install PySAGES along with the supported MD engines.

We believe in good software engineering and collaboration. We welcome all contributions.To ease collaboration, we usetrunk as a development tool free foropen-source software. This includes version-checked linters that can be run automatically.We ship a launcher for trunk with this repo:./trunk, no installation required. Fordetails about how to use./trunk fmt to format existing code into this style and./trunk check to verify a consistent code style, check out thetrunk documentationpage.