densities / blob Goto Github PK
View Code? Open in Web Editor NEWblob: plot densities directly in your browser.
Home Page: https://densities.github.io/blob/
License: GNU Affero General Public License v3.0
blob: plot densities directly in your browser.
Home Page: https://densities.github.io/blob/
License: GNU Affero General Public License v3.0
Currently it's possible to turn axes on and off and that is nice but we should indicate more clearly which axis is which.
It would be great to be able to point to an URL and plot directly from there.
The reason why I did not do this yet is that the cube file does not "know" the structure. It only knows the positions. So we need some scheme to deduce bonds and/or additional formats.
Until then only screenshots but I believe there must be libraries and solutions for exporting three.js stuff.
Instead of storing all x, y, and z coordinates we could store the origin and number of steps in each direction together with step vectors.
It may not be obvious.
To reset isovalue and camera position. Thanks to Gosia for the idea.
And perhaps give them different colors.
All stays in the browser.
It seems that centers stay behind.
Where the visualization could be exported as JS or JSON and embed in interactive papers or presentations (like Authorea papers). Related to #20.
(good question/feedback received via Twitter)
It would be great if this could be embedded in a Jupyter notebook.
This means that some portions of the isosurface can be "in the shadow". Perhaps the light should be fixed w.r.t. the camera? (thanks Gosia for pointing it out)
It would be great to have a cube file tracing an orbital to test/debug this.
It should still be possible to add a hex code but it should not be necessary and a color picker would be convenient for users.
It seems Blob plots the function skewed compared to paraview.
I was able to get a symmetric plot of a He density with Blob using this cube header, step length computed as h = L/(n + 1) = 8.0/26 = 3.076923e-01
Cube file format
Generated by MRChem
1 -4.000000e+00 -4.000000e+00 -4.000000e+00
25 3.076923e-01 0.000000e+00 0.000000e+00
25 0.000000e+00 3.076923e-01 0.000000e+00
25 0.000000e+00 0.000000e+00 3.076923e-01
2 2.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
3.9415e-11 7.8768e-11 1.5008e-10 2.7374e-10 4.7477e-10 7.7984e-10
1.2114e-09 1.7688e-09 2.4268e-09 3.1159e-09 3.7333e-09 4.1676e-09
4.3225e-09 4.1676e-09 3.7333e-09 3.1159e-09 2.4268e-09 1.7688e-09
...
but this gives a non-symmetric plot in paraview (atomic coordinate is not at the center of the density). With paraview, on the other hand, the following cube plot becomes symmetric, step length computed as h = L/(n - 1) = 8.0/24 = 3.333333e-01
Cube file format
Generated by MRChem
1 -4.000000e+00 -4.000000e+00 -4.000000e+00
25 3.333333e-01 0.000000e+00 0.000000e+00
25 0.000000e+00 3.333333e-01 0.000000e+00
25 0.000000e+00 0.000000e+00 3.333333e-01
2 2.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
3.9415e-11 7.8768e-11 1.5008e-10 2.7374e-10 4.7477e-10 7.7984e-10
1.2114e-09 1.7688e-09 2.4268e-09 3.1159e-09 3.7333e-09 4.1676e-09
4.3225e-09 4.1676e-09 3.7333e-09 3.1159e-09 2.4268e-09 1.7688e-09
...
The mesh color can be changed directly without recomputing.
To show time evolution or iterative changes
To make it easier to select an isovalue. Also document how the default isovalue is computed.
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