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https://github.com/cmelab/pl-validation

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

https://github.com/cmelab/pl-validation

Science Score: 57.0%

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    Links to: acs.org
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    Organization cmelab has institutional domain (coen.boisestate.edu)
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Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: cmelab
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 31.9 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Created 12 months ago · Last pushed 7 months ago
Metadata Files
Readme

README.md

pl-validation

Verifying that persistence length calculations of conjugated donor acceptor polymers using flowermd are independent of each other.
This repository is based on work completed by Dr. Paul found here: https://github.com/cmelab/forcefields/tree/main
Polymers being studied (Danielsen et al.): https://pubs.acs.org/doi/10.1021/acs.macromol.1c02229#_i2

The ff_generation.ipynb generates mbuild monomers and their forcefields using ESPALOMA. A foyer forcefield is output that should work with an uncharged mol2 file.

poly_builder.ipynb uses mbuild to polymerize the monomers.

polyminworking_example.ipynb contains code to run NVT simulations.

coarse_grain.ipynb makes CG beads in preparation for persistence length calculations.

data_analysis.ipynb has the requisite functions for calculating the persistence length of mbuild polymers.

To install environment:

git clone https://github.com/cmelab/pl-validation.git conda env create -f environment.yml conda activate p_l

Owner

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

GitHub Events

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Top Authors
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  • jbieri (6)
  • erjank (5)
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Dependencies

environment.yml conda
  • espaloma 0.3.2.*
  • flowermd
  • fresnel >=0.13.5
  • freud >=3.0
  • gmso <=0.12.4
  • grits >=0.5.1
  • gsd >=3.0
  • hoomd <=4.5
  • jupyter
  • matplotlib
  • mbuild >=0.16.4
  • mdanalysis
  • numpy
  • openbabel
  • pip
  • py3dmol
  • python >=3.10,<3.12
  • rdkit
  • signac <=1.8
  • signac-flow <=0.24