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Open Source Science

https://github.com/cmelab/p3ht_validation

https://github.com/cmelab/p3ht_validation

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
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    .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: cmelab
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 29.7 MB
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  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed about 4 years ago
Metadata Files
Readme License

README.md

P3HT validation

P3HT dataset: DOI

P3HT dataset was generated using PlanckTon container v0.6.1 and PlanckTon-flow

Each simulation run took about 9 hours on NVIDIA P100 GPUs. The analysis (including figure generation and coarse-grain trajectory creation) takes around 1-2 hours.

The steps to reproduce this study are as follows. If you want to re-run the MD simulations, follow the steps in this first block--otherwise the complete simulation data can be downloaded from United-atom P3HT workspace on Zenodo and you can skip to the analysis block: 1. Pull our docker container (docker pull cmelab/planckton_gpu:v0.6.1). 1. Clone planckton-flow (git clone https://github.com/cmelab/planckton-flow) 1. Set the init file parameters (the exact init file is included in the zenodo dataset) 1. Initialize and submit the workspace

The analysis can be run as follows: 1. Clone the analysis notebook (git clone https://github.com/cmelab/p3ht_validation) 1. Create and activate the conda environment using the environment file provided (conda create -f environment.yml) 1. Move the planckton-flow directory into the analysis directory 1. Run the notebook

Owner

  • Name: Computational Materials Engineering Laboratory
  • Login: cmelab
  • Kind: organization
  • Location: Boise, ID

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Dependencies

environment.yml conda
  • ele
  • fresnel >=0.13
  • freud
  • gsd
  • jupyterlab
  • matplotlib
  • mbuild
  • numpy
  • openbabel
  • pillow
  • pip
  • py3dmol
  • pyside2 >=5.13
  • python 3.8.*
  • rdkit
  • rowan
  • signac
  • signac-flow