chemicaljson

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I created a Python script to visualize ethane in 3D with rotation and zoom capabilities at https://colab.research.google.com/drive/1kHp3BUC7aPX-ELTDtQx2PPqBljUv3Opg. It showcases the power of this data structure and the simplicity of Python....

hexcreator

Clarify relative energies for 3dSets

3

When creating 3dSets (e.g., conformers, molecular dynamics, following an optimization or IRC) it is useful to retain multiple properties - particularly relative energies. It's not clear the best way to...

ghutchis

Support orbital sets with energies

2

The Avogadro implementation has "sets" as a nested object for orbital coefficients at each coordinate set (e.g., for following a reaction). Right now, that does not include orbital energies which...

ghutchis

Clarify orbital properties for open-shell systems

1

Currently, the specification does not clarify how to handle orbital energies, occupations or symmetries for open shell systems. For coefficients, `moCoefficients` splits into `alphaCoefficients` and `betaCoefficients` but this makes the...

ghutchis

Example with multiple coordinate sets / animations?

6

Are there examples of CJSON with multiple conformers / coordinate sets?

ghutchis

Specification not in sync with avogadrolibs implementation

16

The specification provided for chemical JSON in this repository seems to behind the actually supported implementation in https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp. Where can implementors of chemical JSON find an up-to-date specification or is...

awvwgk

Atomic gradients?

2

Is there already a specification for forces/gradients on atoms? I ask, because this would be really useful for the forcefield interface and I wanted to know if I should write...

ghutchis