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Maybe it is not part of computational chemistry, but how do you do explorative analysis? More than half my time working with data is spend grouping and summaris
by wodenokoto 4y ago
Maybe it is not part of computational chemistry, but how do you do explorative analysis? More than half my time working with data is spend grouping and summarising data, typically in Pandas and drawing interactive graphs in plotly.
- the__alchemist 4y agoPlots and visualizations in 3D. (Vulkan / WGPU) For example, to compare wave function solutions, I use surface plots of a 2D slice. I have a UI that can change the slice of the non-mapped axis. Plots of psi'', the potential etc too. Or for simulating molecular motion, draw it out in 3D, with 6DOF FPS-style camera controls etc. I imagine Pandas would be OOM too slow for this. Compared to Numpy, Pandas is, in my experience far too slow. Another speed limitation is Matplotlib's 3D plots make my computer crawl when rotating them etc; and they're not very interactive, at least on their own. When dealing with these systems, a particular computational challenge is that they're 3D, so computation scales with precision^3. (This also adds complications to visualization, as I alluded to above)
- legerdemain 4y agoDid you write your own visualizations using wgpu? I don't think its goals include providing visualization out of the box.
- the__alchemist 4y agoYep! So, took some work upfront. Basic rendering/navigation engine. `egui` for the GUI.