Repositories list

• cmeutils

  Public
  Useful functions by and for the CME lab

  Python

  •

  GNU General Public License v3.0

  •1313 forks in cmelab/cmeutils•33 stars in cmelab/cmeutils•66 issues in cmelab/cmeutils•44 pull requests in cmelab/cmeutils•Updated Nov 9, 2026Nov 9, 2026

• grits

  Public
  A toolkit for working with coarse-grain systems

  smilescoarse-grainedsmarts+ 4

  smilescoarse-grainedsmartscoarse-grainingbackmappingcoarse-to-finecoarse-grain-mappings

  Python

  •

  GNU General Public License v3.0

  •1010 forks in cmelab/grits•77 stars in cmelab/grits•66 issues in cmelab/grits•55 pull requests in cmelab/grits•Updated Nov 9, 2026Nov 9, 2026

• flowerMD

  Public
  Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics.

  polymersimulationmolecular-dynamics+ 3

  polymersimulationmolecular-dynamicsmolecular-dynamics-simulationmosdef-hubhoomd-blue

  Python

  •

  GNU General Public License v3.0

  •1616 forks in cmelab/flowerMD•2626 stars in cmelab/flowerMD•1414 issues in cmelab/flowerMD•55 pull requests in cmelab/flowerMD•Updated Nov 9, 2026Nov 9, 2026

• PhantomWalk

  Public
  Polymer system initialization workflow that utilizes a random walk and dissipative particle dynamics as a soft push potential.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1111 forks in cmelab/PhantomWalk•00 stars in cmelab/PhantomWalk•33 issues in cmelab/PhantomWalk•11 pull request in cmelab/PhantomWalk•Updated Nov 9, 2026Nov 9, 2026

• GIXStapose

  Public
  An interactive structure viewer alongside its simulated diffraction pattern

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1111 forks in cmelab/GIXStapose•1919 stars in cmelab/GIXStapose•22 issues in cmelab/GIXStapose•22 pull requests in cmelab/GIXStapose•Updated Nov 2, 2026Nov 2, 2026

• morphct

  Public
  Python

  •

  GNU General Public License v3.0

  •99 forks in cmelab/morphct•22 stars in cmelab/morphct•1313 issues in cmelab/morphct•44 pull requests in cmelab/morphct•Updated Nov 22, 2025Nov 22, 2025

• flake-sim

  Public
  The new name of ye olde mxene project.

  Jupyter Notebook

  •88 forks in cmelab/flake-sim•00 stars in cmelab/flake-sim•22 issues in cmelab/flake-sim•11 pull request in cmelab/flake-sim•Updated Nov 20, 2025Nov 20, 2025

• cy5-dna-md

  Public
  Home base for molecular modeling of cy5 dye and DNA using united-atom and coarse-grained molecular dynamics.

  Jupyter Notebook

  •22 forks in cmelab/cy5-dna-md•00 stars in cmelab/cy5-dna-md•22 issues in cmelab/cy5-dna-md•11 pull request in cmelab/cy5-dna-md•Updated Nov 6, 2025Nov 6, 2025

• pl-validation

  Public
  Verifying that the persistence length calculations are independent of each other.

  Jupyter Notebook

  •00 forks in cmelab/pl-validation•00 stars in cmelab/pl-validation•33 issues in cmelab/pl-validation•00 pull requests in cmelab/pl-validation•Updated Aug 18, 2025Aug 18, 2025

• msibi

  Public
  A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)

  Python

  •

  MIT License

  •1616 forks in cmelab/msibi•66 stars in cmelab/msibi•11 issue in cmelab/msibi•00 pull requests in cmelab/msibi•Updated Jul 15, 2025Jul 15, 2025

• kg-paper-validation

  Public
  Tests to validate the Kremer, Grest, Carmesin paper

  Jupyter Notebook

  •00 forks in cmelab/kg-paper-validation•00 stars in cmelab/kg-paper-validation•00 issues in cmelab/kg-paper-validation•00 pull requests in cmelab/kg-paper-validation•Updated May 20, 2025May 20, 2025

• forcefields

  Public
  Jupyter Notebook

  •22 forks in cmelab/forcefields•11 star in cmelab/forcefields•55 issues in cmelab/forcefields•00 pull requests in cmelab/forcefields•Updated Apr 24, 2025Apr 24, 2025

• Molecule_random_walk

  Public
  A random walk of molecules to circumvent shrinkage step.

  Jupyter Notebook

  •00 forks in cmelab/Molecule_random_walk•00 stars in cmelab/Molecule_random_walk•11 issue in cmelab/Molecule_random_walk•00 pull requests in cmelab/Molecule_random_walk•Updated Jan 3, 2025Jan 3, 2025

• SIC

  Public
  Determining why during ultrasonic welding where there is higher crystallinity at the weld interface with higher amplitudes of vibration.

  Jupyter Notebook

  •11 fork in cmelab/SIC•00 stars in cmelab/SIC•11 issue in cmelab/SIC•00 pull requests in cmelab/SIC•Updated Oct 23, 2024Oct 23, 2024

• quantumDNA

  Public
  Jupyter Notebook

  •11 fork in cmelab/quantumDNA•00 stars in cmelab/quantumDNA•00 issues in cmelab/quantumDNA•00 pull requests in cmelab/quantumDNA•Updated Oct 18, 2024Oct 18, 2024

• containers

  Public
  Containerized software stacks for the Computational Materials Science Lab

  dockersingularity

  dockersingularity

  GNU General Public License v3.0

  •44 forks in cmelab/containers•00 stars in cmelab/containers•00 issues in cmelab/containers•00 pull requests in cmelab/containers•Updated Jul 18, 2024Jul 18, 2024

• ellipsoid_orientations

  Public
  Jupyter Notebook

  •11 fork in cmelab/ellipsoid_orientations•11 star in cmelab/ellipsoid_orientations•00 issues in cmelab/ellipsoid_orientations•00 pull requests in cmelab/ellipsoid_orientations•Updated May 30, 2024May 30, 2024

• notebook_tutorials

  Public
  A home for the Jupyter notebook tutorials created by and for our lab

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •77 forks in cmelab/notebook_tutorials•11 star in cmelab/notebook_tutorials•99 issues in cmelab/notebook_tutorials•11 pull request in cmelab/notebook_tutorials•Updated May 21, 2024May 21, 2024

• flow-templates

  Public
  A place to keep some minimal signac-flow templates on hand.

  Python

  •22 forks in cmelab/flow-templates•00 stars in cmelab/flow-templates•00 issues in cmelab/flow-templates•00 pull requests in cmelab/flow-templates•Updated Apr 12, 2024Apr 12, 2024

• getting-started

  Public
  Vim Script

  •1111 forks in cmelab/getting-started•00 stars in cmelab/getting-started•1010 issues in cmelab/getting-started•33 pull requests in cmelab/getting-started•Updated Feb 6, 2024Feb 6, 2024

• pps_project

  Public
  Projects describing PPS using computational methods

  Jupyter Notebook

  •00 forks in cmelab/pps_project•00 stars in cmelab/pps_project•00 issues in cmelab/pps_project•00 pull requests in cmelab/pps_project•Updated Feb 2, 2024Feb 2, 2024

• planckton

  Public archive
  Reproducible exploration of organic photovoltaic morphology self-assembly using molecular dynamics.

  morphologycompoundssimulations+ 1

  morphologycompoundssimulationssignac

  Python

  •

  GNU General Public License v3.0

  •66 forks in cmelab/planckton•55 stars in cmelab/planckton•1010 issues in cmelab/planckton•00 pull requests in cmelab/planckton•Updated Jan 29, 2024Jan 29, 2024

• polybinder

  Public
  Initialization of thermoplastic polymer systems to simulate thermal welding

  Python

  •

  GNU General Public License v3.0

  •55 forks in cmelab/polybinder•22 stars in cmelab/polybinder•99 issues in cmelab/polybinder•11 pull request in cmelab/polybinder•Updated Aug 24, 2023Aug 24, 2023

• Anisotropic-Particle-Simulation

  Public
  Jupyter Notebook

  •00 forks in cmelab/Anisotropic-Particle-Simulation•00 stars in cmelab/Anisotropic-Particle-Simulation•00 issues in cmelab/Anisotropic-Particle-Simulation•00 pull requests in cmelab/Anisotropic-Particle-Simulation•Updated Jul 7, 2023Jul 7, 2023

• parallel-tempering

  Public
  Perform parallel temping simulations using signac to manage simulations and swaps.

  Python

  •00 forks in cmelab/parallel-tempering•00 stars in cmelab/parallel-tempering•00 issues in cmelab/parallel-tempering•00 pull requests in cmelab/parallel-tempering•Updated Jun 20, 2023Jun 20, 2023

• pythonClasses

  Public
  A place to practice with classes in Python

  Jupyter Notebook

  •00 forks in cmelab/pythonClasses•00 stars in cmelab/pythonClasses•00 issues in cmelab/pythonClasses•00 pull requests in cmelab/pythonClasses•Updated Jun 14, 2023Jun 14, 2023

• euler_practice

  Public
  Jupyter Notebook

  •00 forks in cmelab/euler_practice•00 stars in cmelab/euler_practice•00 issues in cmelab/euler_practice•00 pull requests in cmelab/euler_practice•Updated May 31, 2023May 31, 2023

• CG_ML_workflow

  Public
  Machine learning models for coarse grained simulations

  Jupyter Notebook

  •00 forks in cmelab/CG_ML_workflow•11 star in cmelab/CG_ML_workflow•00 issues in cmelab/CG_ML_workflow•00 pull requests in cmelab/CG_ML_workflow•Updated May 16, 2023May 16, 2023

• Advanced-Sampling

  Public
  Python

  •22 forks in cmelab/Advanced-Sampling•11 star in cmelab/Advanced-Sampling•55 issues in cmelab/Advanced-Sampling•33 pull requests in cmelab/Advanced-Sampling•Updated Apr 20, 2023Apr 20, 2023

• advanced-sampling-polymers

  Public
  Repo we can use to try out advanced sampling techniques on some simple polymer systems

  Jupyter Notebook

  •11 fork in cmelab/advanced-sampling-polymers•00 stars in cmelab/advanced-sampling-polymers•22 issues in cmelab/advanced-sampling-polymers•22 pull requests in cmelab/advanced-sampling-polymers•Updated Feb 16, 2023Feb 16, 2023