openchemistry / chemicaljson Goto Github PK

Development of the Chemical JSON data representation

Python 100.00%

chemistry fileformat json json-representation science

chemicaljson's Introduction

Open Chemistry

Introduction

The Open Chemistry project is a collection of open source, cross platform libraries and applications for the exploration, analysis and generation of chemical data. The project builds upon various efforts by collaborators and innovators in open chemistry such as the Blue Obelisk, Quixote and the associated projects. We aim to improve the state of the art, and facilitate the open exchange of ideas and exchange of chemical data leveraging the best technologies ranging from quantum chemistry codes, molecular dynamics, informatics and visualization.

This repository contains git submodules for the Open Chemistry projects: Avogadro, MoleQueue and MongoChem. It can be used to download all relevant source files as well as building many of the necessary dependencies. Please see the documentation in the submodules for more details about each project.

Installing

We provide nightly binaries built by our dashboards for Mac OS X and Windows. If you would like to build from source we recommend that you follow our building Open Chemistry guide that will take care of building most dependencies.

Contributing

Our project uses the standard GitHub pull request process for code review and integration. Please check our development guide for more details on developing and contributing to the project. The GitHub issue tracker can be used to report bugs, make feature requests, etc.

Our wiki is used to document features, flesh out designs and host other documentation. Our API is [documented using Doxygen][Doxygen] with updated documentation generated nightly. We have several mailing lists to coordinate development and to provide support.

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schamnad cryos mcocdawc langner certik skeptycal fieldplay nazaalopez pk-organics ghutchis berquist amandadumi caiyingchun hexcreator

chemicaljson's Issues

Connections reflexive?

Thank you for this project!
Could you please specify the reflexivity of the connections object.
So if atom 1 is bonded to atom 0, then atom 0 is bonded to atom 1.
In your minimal example it is non reflexive.

I think there are three options:

Non reflexive
Reflexive
Could be both and code may not rely on one property

Atomic gradients?

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 my own syntax (e.g., adding an attribute to atoms) or adopting existing practice.

Clarify orbital properties for open-shell systems

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 other lists ambiguous.

Consider writing a json schema file

https://github.com/tangram-js/json-schema-editor
https://json-schema.org/

Not sure if relevant, if it's not, please close this issue.

Clarify relative energies for 3dSets

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 do handle this.

Specification not in sync with avogadrolibs implementation

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 the implementation in avogadrolibs the source of truth for this format?

Support orbital sets with energies

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 could also vary during a trajectory

Do we need to have varying orbital occupations?

Example with multiple coordinate sets / animations?

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

Unit cell => Translation Axes

Currently, the unit cell is written as alpha, beta, gamma, a, b, c. But this is 6 degrees of freedom, but many solid state codes use translation vectors.

For use with solid-state codes, it would be ideal if CJSON:

Always wrote out real-space Cartesian coordinates (in addition to fractional)
Wrote out the 3x3 translation matrix either in addition to the unit cell parameters or instead of the parameters.

Otherwise, it's hard to implement CP2K or VASP or ABINIT input generators in Avo2 (among other things)