hoomd4.2.1-mod
HOOMD-blue version 4.2.1 modified for Rheoinformatic colloid simulations
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary
Keywords
Repository
HOOMD-blue version 4.2.1 modified for Rheoinformatic colloid simulations
Statistics
- Stars: 1
- Watchers: 0
- Forks: 3
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
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 * Admin tasks including pull requests, upgrading, adding changes, and compiling for Google Colab
Additional branches are available, tho they may be incomplete: - branch "hoomd4.2wwall": modifications for flat and sinusoidal walls - branch "noshear": clean version of original DPDMorse and virialind 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: - [ ] update Lifetime.h @Rob - [ ] add wall mods @Josh @Rob
- [ ] add bond rigidity @Paniz
Installation
To install hoomd4.2.1-mod on Explorer:
Login and move to the location you want to put hoomd4.2-mod
bash
ssh your-username@login.explorer.northeastern.edu
bash
cd /projects/props/your-name/software/
Make a new directory for hoomd4.2.1-mod
bash
mkdir hoomd4.2.1-mod
Clone the repository
bash
git clone git@github.com:procf/hoomd4.2.1-mod.git
Run the install-hoomd-mod-4.2.1 script with sbatch
bash
cd /scripts/install-update/ && sbatch install-hoomd-mod-4.2.1
Owner
- Name: PRO-CF
- Login: procf
- Kind: organization
- Email: PROCF.NU@gmail.com
- Location: United States of America
- Website: https://web.northeastern.edu/complexfluids/
- Twitter: PROCF_NU
- Repositories: 2
- Profile: https://github.com/procf
Physics and Rheology of Complex Fluids Research Group
GitHub Events
Total
- Watch event: 1
- Delete event: 1
- Push event: 8
- Pull request event: 4
- Fork event: 2
- Create event: 3
Last Year
- Watch event: 1
- Delete event: 1
- Push event: 8
- Pull request event: 4
- Fork event: 2
- Create event: 3
Dependencies
- furo *
- ipython *
- ipython_genutils *
- nbconvert *
- nbsphinx *
- numpy *
- pandoc *
- sphinx *
- tornado *