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Workflow ideas for 2018 Avogadro UGM
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workflow-ideas.md

Avogadro

  • get / modify selection (e.g., enlarge by x Å)
  • create enantiomer
  • “Random alloy” - Replace x% atom X -> atom Y

Scikit-nano https://docs.scikit-nano.org

  • MWNT
  • Graphene or TMDC multilayers?

Pymatgen https://github.com/materialsproject/pymatgen

  • create a slab
  • nanoparticle with Wulff

STK https://lukasturcani.github.io/stk/docs/build/html/

  • polymers
  • cages
  • COF
    • hexagonal, honeycomb, kagome, square

RDKit http://www.rdkit.org/docs/GettingStartedInPython.html

  • get ETKDG conformer

ASE

GenIce - https://github.com/vitroid/GenIce/

  • Generate ice unit cell

PackMol https://github.com/choderalab/openmoltools/blob/master/openmoltools/packmol.py

Glycam(?)

  • Sugar / oligosaccaride builder?
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