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@cmelab Computational Materials Engineering Laboratory

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    49 repositories

    • cmeutils

      Public
      Useful functions by and for the CME lab
      Python
      •
      GNU General Public License v3.0
      •13•3•7•3•Updated Aug 19, 2025Aug 19, 2025

    • flowerMD

      Public
      Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics.
      polymersimulationmolecular-dynamicsmolecular-dynamics-simulationmosdef-hubhoomd-blue
      Python
      •
      GNU General Public License v3.0
      •11•21•11•3•Updated Aug 19, 2025Aug 19, 2025

    • grits

      Public
      A toolkit for working with coarse-grain systems
      smilescoarse-grainedsmartscoarse-grainingbackmappingcoarse-to-finecoarse-grain-mappings
      Python
      •
      GNU General Public License v3.0
      •10•7•7•3•Updated Aug 19, 2025Aug 19, 2025

    • pl-validation

      Public
      Verifying that the persistence length calculations are independent of each other.
      Jupyter Notebook
      •0•0•3•0•Updated Aug 18, 2025Aug 18, 2025

    • cy5-dna-md

      Public
      Home base for molecular modeling of cy5 dye and DNA using united-atom and coarse-grained molecular dynamics.
      1•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • GIXStapose

      Public
      An interactive structure viewer alongside its simulated diffraction pattern
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•18•2•2•Updated Aug 11, 2025Aug 11, 2025

    • msibi

      Public
      A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)
      Python
      •
      MIT License
      •13•7•1•0•Updated Jul 15, 2025Jul 15, 2025

    • kg-paper-validation

      Public
      Tests to validate the Kremer, Grest, Carmesin paper
      Jupyter Notebook
      •0•0•0•0•Updated May 20, 2025May 20, 2025

    • forcefields

      Public
      Jupyter Notebook
      •2•1•5•0•Updated Apr 24, 2025Apr 24, 2025

    • Molecule_random_walk

      Public
      A random walk of molecules to circumvent shrinkage step.
      Jupyter Notebook
      •0•0•1•0•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
      •1•0•1•0•Updated Oct 23, 2024Oct 23, 2024

    • quantumDNA

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • containers

      Public
      Containerized software stacks for the Computational Materials Science Lab
      dockersingularity
      GNU General Public License v3.0
      •4•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • ellipsoid_orientations

      Public
      Jupyter Notebook
      •1•1•0•0•Updated May 30, 2024May 30, 2024

    • morphct

      Public
      Python
      •
      GNU General Public License v3.0
      •6•0•12•4•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
      •7•1•9•1•Updated May 21, 2024May 21, 2024

    • flow-templates

      Public
      A place to keep some minimal signac-flow templates on hand.
      Python
      •2•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • getting-started

      Public
      Vim Script
      •11•0•10•3•Updated Feb 6, 2024Feb 6, 2024

    • pps_project

      Public
      Projects describing PPS using computational methods
      Jupyter Notebook
      •0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

    • planckton

      Public archive
      Reproducible exploration of organic photovoltaic morphology self-assembly using molecular dynamics.
      morphologycompoundssimulationssignac
      Python
      •
      GNU General Public License v3.0
      •6•5•10•0•Updated Jan 29, 2024Jan 29, 2024

    • polybinder

      Public
      Initialization of thermoplastic polymer systems to simulate thermal welding
      Python
      •
      GNU General Public License v3.0
      •5•2•9•1•Updated Aug 24, 2023Aug 24, 2023

    • Anisotropic-Particle-Simulation

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

    • parallel-tempering

      Public
      Perform parallel temping simulations using signac to manage simulations and swaps.
      Python
      •0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • pythonClasses

      Public
      A place to practice with classes in Python
      Jupyter Notebook
      •0•0•0•0•Updated Jun 14, 2023Jun 14, 2023

    • euler_practice

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 31, 2023May 31, 2023

    • CG_ML_workflow

      Public
      Machine learning models for coarse grained simulations
      Jupyter Notebook
      •0•1•0•0•Updated May 16, 2023May 16, 2023

    • Advanced-Sampling

      Public
      Python
      •2•1•5•3•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
      •1•0•2•2•Updated Feb 16, 2023Feb 16, 2023

    • polybinder-flow

      Public
      Python
      •2•0•0•0•Updated Dec 22, 2022Dec 22, 2022

    • polyellipsoid

      Public
      Python
      •
      GNU General Public License v3.0
      •3•3•2•0•Updated Dec 16, 2022Dec 16, 2022