densities / blob Goto Github PK

It seems that centers stay behind.

To reset isovalue and camera position. Thanks to Gosia for the idea.

To make it easier to select an isovalue. Also document how the default isovalue is computed.

• https://3dmol.csb.pitt.edu
• https://github.com/arose/nglview

(good question/feedback received via Twitter)

It would be great if this could be embedded in a Jupyter notebook.

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 may not be obvious.

• x toggles fullscreen
• arrows move the origin

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.

To show time evolution or iterative changes

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
...

All stays in the browser.

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.

Until then only screenshots but I believe there must be libraries and solutions for exporting three.js stuff.

It would be great to be able to point to an URL and plot directly from there.

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)

• I think the data is not aligned with the meshing triple loops
• The meshing algorithm loops over all voxels but for typical molecular densities we could screen away many voxels or entire planes

It would be great to have a cube file tracing an orbital to test/debug this.

The mesh color can be changed directly without recomputing.

Where the visualization could be exported as JS or JSON and embed in interactive papers or presentations (like Authorea papers). Related to #20.

And perhaps give them different colors.

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.