andeplane / atomify Goto Github PK

If you start a simulation, pause it, then click on "New simulation" and write any number in the "Name" field, a popup will appear saying "Setting simulation speed to X.

We can leverage LAMMPS's readers and basically create a small script to read and present any LAMMPS data file.

For example, a slider which would change the target temperature of a thermostat, so one can for example see metal melting/solidifying.

Seems like visualization issues when we have a changing number of atoms. I need to have better testing for this.

This could be pretty cool. A simulation can then be embedded in an iframe or similar. Camera animation could be a part of the simulation, and keyboard/mouse can be enabled/disabled. This is step 1 to write a nice, interactive book.

Hi,
Sorry for a late response, but recently I have quite a lot of things going on. My ideas are below. I don't know if all of them can be implemented, so I didn't create separate threads. Let me know, if you want me to elaborate on the ideas or bug reports.

Ideas:

• manual describing Atomify commands (#/camera, #/atom, etc.)

• orthographic visualization mode

• add scale bar (or grid) to the visualization window

• add units to axis titles in plots

• use a shortcut to change mouse mode, e.g. after clicking "T", mouse pans the view instead of rotating it (similar as in VMD)

• plots for variables

• a way of changing simulation parameters from the visualization window, e.g. a slider which would change the target temperature of a thermostat

• parallel simulations

Bug reports:

• If you start a simulation, pause it, then click on "New simulation" and write any number in the "Name" field, a popup will appear saying "Setting simulation speed to X."
• The y-axes of plots have wrong titles, for example a plot for "thermo_temp" is titled "Potential energy"

Right now, this triggers a sync of files which for some reason breaks the state while c++ is active.

The workflow deploy.yaml is referencing action actions/checkout using references v1. However this reference is missing the commit a6747255bd19d7a757dbdda8c654a9f84db19839 which may contain fix to the some vulnerability.
The vulnerability fix that is missing by actions version could be related to:
(1) CVE fix
(2) upgrade of vulnerable dependency
(3) fix to secret leak and others.
Please consider to update the reference to the action.

There is a significant performance hit when coloring atoms by property, and the reason for this is that colors currently are being set using textures which is slower than an attribute based coloring method. A caveat here is that since LAMMPS is reordering particle indices, we would have to either detect this, or set all colors every frame, both of which is expensive. Not sure what the best solution is.

In order to support #50, I want each Simulation to consist of a JSON file with all data. The structure should be the contents of each example in the examples.json file, including inputScript and previewImage.

Then we can better setup for your simulations, where we reuse the file system of JupyterLite so we have one file system in sync.

The y-axes of plots have wrong titles, for example a plot for "thermo_temp" is titled "Potential energy".

It stops rendering when SSAO is disabled

There is clearly some pattern in the noise from SSAO

For instance, if we open the Notebook during a simulation, Atomify will sync files from wasm. For some reason I don't understand, this leads Atomify into a bad state so multiple things stops working.

Proposed fix: fix state so everything that communicates with webassembly happens during sync, or when no simulation is running.

i.e. simulations using more than one thread.

Some browsers have mouse gestures which use right mouse button, so a key to change mouse mode from rotating to panning the view would be helpful.

If a user clicks an atom, we can show all per atom quantities, show neighbors, highlight it and other niceness.

This is really to avoid updated files from LAMMPS simulation and editor disagreeing on what is latest content