Showing posts with label isosurfaces. Show all posts
Showing posts with label isosurfaces. Show all posts
Tuesday, March 24, 2015
Rendering Voids in a Molecular Dynamics Simulation
It's been a while since I've posted. I still need to make that post about X-ray scattering but in the mean time, I'd like to share a picture that I helped make. Katherine Sebeck wanted to render the voids in her epoxy simulation in smooth organic way. I generalized the way Kirke handles grids and my metaball code to handle density grids. The density grid for her epoxy simulation was generated from my smoothed meshing code in Kirke. I talk a bit more about it here. I'll show a movie if Katie says it's okay, but for now here is a large picture (~41 MiB):
Sunday, September 21, 2014
My Problem with Isosurfaces of Molecular Orbitals
When people plot their MO's, they show us an isosurface in electron density. It is common procedure to use a density (or wavefunction) value for this surface and report that (Hopefully). I take issue with this.
By not having a standard, we may or may not be missing features of our MO's. Or worse, undesirable features could be hidden. I propose that the fraction of the MO contained by the isosurface be listed. Because we can create a cumulative distribution function for the MO density, specifying the fraction contained by the surface is a sufficient condition for specifying an isosurface density reproducibly.
To demonstrate this loss of detail, I have two isosurfaces from the same series of calculations. These isosurfaces are of the highest occupied MO (HOMO) for a pair of molecules SubPc and C60. The first animation shows an isosurface containing 80 % of the HOMO as the molecules are separated. This is the percentage that I have used to present at conferences.
80 % of the HOMO looks great! You can clearly see the lobes associated the pi orbitals. Next, I'll render the 99 % isosurface of the HOMO.
You can clearly see that some of the HOMO has tunneled to the C60 and that the amount that has tunneled decreases with separation distance. This has an actual affect on some of my calculations. Since we as field have MO's of varying size, the total fraction contained seems to be a more general metric to allow us to more quickly evaluate the works of others.
Or maybe I am just being pedantic?
If you are wondering, I detailed how I render MO's in another post. The series of images was animates with ImageMagick. In any case, I am feeling very under the weather so do pardon any grammatical errors in this post.
By not having a standard, we may or may not be missing features of our MO's. Or worse, undesirable features could be hidden. I propose that the fraction of the MO contained by the isosurface be listed. Because we can create a cumulative distribution function for the MO density, specifying the fraction contained by the surface is a sufficient condition for specifying an isosurface density reproducibly.
To demonstrate this loss of detail, I have two isosurfaces from the same series of calculations. These isosurfaces are of the highest occupied MO (HOMO) for a pair of molecules SubPc and C60. The first animation shows an isosurface containing 80 % of the HOMO as the molecules are separated. This is the percentage that I have used to present at conferences.
Or maybe I am just being pedantic?
If you are wondering, I detailed how I render MO's in another post. The series of images was animates with ImageMagick. In any case, I am feeling very under the weather so do pardon any grammatical errors in this post.
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