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)
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
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