Example with multiple coordinate sets / animations?

OpenChemistry / chemicaljson

Development of the Chemical JSON data representation

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Example with multiple coordinate sets / animations? #5

Open ghutchis opened 7 years ago

ghutchis commented 7 years ago

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

ghutchis commented 7 years ago

Bump. There doesn't seem to be any way to support multiple coordinate sets in CJSON, which is a big problem for animations, dynamics, conformers, etc.

wadejong commented 7 years ago

One good way to introduce a series of coordinate sets would be to introduce some kind of iterator, including a keyword in the geometry identifying the type of coordinates, xyz, unit cell, and if this is a coordinate series (could be both xyz or unit cell in case of ab initio molecular dynamics). We will need to add a time stamp (from MD) or an iterator integer to ensure we can extract them in the correct time order.

Bert

On Feb 12, 2017, at 6:16 PM, Geoff Hutchison notifications@github.com wroteBump. There doesn't seem to be any way to support multiple coordinate sets in CJSON, which is a big problem for animations, dynamics, conformers, etc. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

ghutchis commented 6 years ago

Are we going to address this in CJSON or work on the new QC JSON and handle it there?

cryos commented 6 years ago

I was going to get this in here, but got distracted by switching to a more modern JSON library. I think what we do here/in QC JSON will hopefully share a lot. Thanks for the reminder, it should not have taken this long, apologies! I think this would offer a simple way of getting smaller trajectories out of other packages in that case too.

cryos commented 6 years ago

I have working code now, and will get the examples uploaded soon.

ghutchis commented 2 years ago

This seems to already be in the wild as part of 3dSets .. an array of arrays.

What's missing:

time step (from MD)
relative energies or other properties (e.g., recording forces through an optimization or MD)
a way to indicate the default set (e.g., usually with geometry optimization, the default 3d set would indicate the best, lowest-energy geometry .. but in MD, the default might duplicate the first coordinates.)
- In other words, if 3dSets is available, can something else indicate the default index?