hoomd4.2.1-mod

This repository contains the modified version of HOOMD-blue v4.2 used for colloid simulations in the Rheoinformatic group. It also includes:

• Installation instructions
• Background Reading about how these simulations work
• Example scripts for installing and running simulations on an HPC research cluster
• Citation information for papers published using this simulation platform
• A Changelog summarizing what was changed, and a full list of the files that were changed

Additional branches are available, tho they may be incomplete:

• branch "hoomd4.2_w_wall": modifications for flat and sinusoidal walls
• branch "no_shear": clean version of original DPDMorse and virial_ind tracking without shear, bond-tracking, or other mods.

[Last Updated: June 2024]

Contact: Rob Campbell (campbell.r@northeastern.edu)

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For any questions, or to help with modifications, contact Rob.

To-Do:

• fix bond trackign to work correctly @Rob
  • and add bond tracking to BD/Langevin sims?
• copy in wall mods @Josh @Rob
  • test compile wall mods
  • test DPD initialization, equilibrium, and gelation w/ walls
  • test BD/Langevin sims w/ walls
• add bond contraints and associated bond tracking @Paniz
• remove AO from README or add AO mods @Rob

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Installation

To install hoomd4.2.1-mod on Discovery:

Login and move to the location you want to put hoomd4.2-mod

ssh your-username@login.discovery.neu.edu

cd /work/props/your-name/software/

Make a new directory for hoomd4.2.1-mod

mkdir hoomd4.2.1-mod

Clone the repository

git clone git@github.com:procf/hoomd4.2.1-mod.git

Run the install-hoomd-mod-4.2.1 script with sbatch

cd /scripts/install-update/ && sbatch install-hoomd-mod-4.2.1