search

shankar1729 / jdftx

JDFTx: software for joint density functional theory
http://jdftx.org
84 stars 54 forks source link

In-situ or "streaming" visualization? #358

Open mmarchywka opened 1 month ago

mmarchywka commented 1 month ago

( the old forum said to bring "general discussion" topics here so I'm posting this here ).

I was re-installing jdftx after not using it for many years. IIRC, in the past, I could monitor the output such as ion positions as it was generated rather than accumulating output until the end of a run. However, it does not appear this capability exists in the tools supported here. I probably converted the output to a pdb or other file as each iteration was output but I'm still digging through my old code. This "real time" or streaming support does not seem to be normal but apparently it is called in-situ visualization. FreeFEM has a simple form of this and some viewer, see paraview thread below, have means to accommodate it. The package described below also allows "streering" or user input back to the code, jdftx , to modifcy simulation parameters on the fly.

https://discourse.paraview.org/t/does-or-can-paraview-support-streaming-input/13637/7

This generally is a lot more informative than viewing once everything is done curious what people do or would use in this regard. Thanks.

shankar1729 commented 1 month ago

Hi Mike,

The createXSF script with the animated option should output all ionic coordinates up to the current point. You'd just need to run it on the in-process log. Is there something beyond that which is needed to visualize on the fly?

Best, Shankar

mmarchywka commented 3 weeks ago

Sorry I was hoping my memory would improve before getting back to this. JDFTx normally does not do a lot of stuff that may benefit from on-the-fly or as they say in-situ imaging. However, I seem to recall I was playing with some code I made up to follow ions as they relaxed. Velocity was based on jdftx calculated forces positions updated to next time step and forces calculated again. This leads to a movie you'd like to watch during execution. Thanks.

shankar1729 commented 3 weeks ago

You can also do ab initio molecular dynamics calculations using ionic-dynamics, which could be useful to visualize on a stream as you mention. This should be possible using createXSF and some piping, hopefully.