Krdytkyu

How can I visualize the normal mode vibrations of a molecule in Mathematica?
Something like the gif shown in the following link.benzene b_2u vibrational mode.
I have the XYZ fileben-xyz-file of the benzene molecule and the normal mode coordinates normal-mode.

Using a few undocumented functions that have been discussed here on the stack exchange before,

{atoms, coords} = Import[

    "https://www.dropbox.com/s/q3rwpedngv5wbqi/ben.xyz?dl=1",

    {"XYZ", {"VertexTypes", "VertexCoordinates"}}

];

mode = Most @ Import[

    "https://www.dropbox.com/s/3pjxams7ndr0l7h/19.mode?dl=1", "Table"

];

mode = 100 * mode;

bonds = Graphics`MoleculePlotDump`InferBonds[atoms, coords, 40, 25];

range = Range[-0.5, 0.5, 0.025];

range = Join[range, Reverse @ range];

plot[v_] := ImportExport`MoleculePlot3D[

    {

        "VertexCoordinates" -> (coords + v * mode),

        "VertexTypes" -> atoms, "EdgeRules" -> bonds

    }

];

ListAnimate @ Map[plot, range] 

When importing the mode file, it returns an empty list as the last element so I need to use Most to make it a matrix. Then I multiplied it by 100 to convert to picometers. Finally I had to precompute the bonds, because as the molecule moves along the normal coordinate, the atoms could get far enough apart that the bonds wouldn't be detected by MoleculePlot3D.

Sources:

1. Connectivity in a molecule and permutations


2. How can I access the internal function that plots a molecule from a formatted XYZ file?


3. Visualizing .xyz file in Mathematica