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#1 2018-11-30 02:19:05

Stom
Member
Registered: 2018-11-30
Posts: 4

Electron density redistribution

I study the adsorption of organic acids on FeOOH mineral surfaces. Using Gaussian16, I run where the molecule is adsorbed on the FeOOH, the molecule alone, and the FeOOH alone. Using cubegen and GaussView6, I can can get the the *.cub file that represents the electron density redistribution when the molecule is adsorbed to the mineral by adsorbed - molecule alone - FeOOH alone.

Can multiwfn read the *.cub file for electron redistribution and produce a contour plot showing where the regions of of density gain and loss?  Thank you.

Last edited by Stom (2018-11-30 02:23:09)

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#2 2018-11-30 03:12:52

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 138
Website

Re: Electron density redistribution

In fact you do not need to use cubegen at all. The main function 5 of Multiwfn, which is used to calculate grid data, is by far more powerful, flexible and easy-to-use than cubegen.

If you want to plot isosurface map or contour line map of density difference corresponding to ρ(complex) - ρ(FeOOH) - ρ(acid), please simply follow the example in Section 4.5.5 of Multiwfn manual, you will find the procedure is quite easy. The .fch files that you already have, could be directly used as input file.

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#3 2018-11-30 15:19:20

Stom
Member
Registered: 2018-11-30
Posts: 4

Re: Electron density redistribution

Thank you very much, Tian!  I was focused on section 4.4, not 4.5.  I was able to follow the example provided in the manual very easily with my files which shows how well the manual is written.  I used Option -6 to export the calculated plane to a text file which is also a very nice feature to have:

15.42593   8.11226  -0.17794   0.00000   0.00000  2.4373344965E-03
15.38293   8.10101  -0.17471   0.00000   0.04456  2.6856696917E-03
15.33993   8.08977  -0.17148   0.00000   0.08912  2.9467572067E-03
.
.
.

I have a 200 X 200 grid so the rows cycles in 200 units.  I think the 1st column is the x-axis value, 2nd column is the y-axis value, 3rd column is the z-axis value for the electron density redistribution.  I can't quite figure out what the 4th, 5th, and 6th columns are.  Can you help me out here.

Again, thanks for making this electronic structure analyzer available to the public.  It is most appreciated.

Stom

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#4 2018-12-01 05:59:05

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 138
Website

Re: Electron density redistribution

Please carefully check the outputted information on screen, Multiwfn always explicitly inform users the meaning of each column in the outputted file when exporting the file.

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#5 2018-12-03 18:18:06

Stom
Member
Registered: 2018-11-30
Posts: 4

Re: Electron density redistribution

Thanks, Tian.  The column labels scroll on so fast I missed them above the new set of options.  The graph that I get plotted goes 0 to 14.81 Bohr on the x-axis, and 16.76 on the y-axis.  In the text file, the 4th column (x) goes from 0 to 7.83896 and the 5th column goes from 0 to 8.86786 in the sets of 200 for the grid points. 

I don't understand why the graph axis values and text file axis values are so different.  Can you clarify why the difference between the plot and the saved file?  Thank you.

Stom

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#6 2018-12-03 19:17:12

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 138
Website

Re: Electron density redistribution

The units are different. 1 Bohr = 0.5292 Angstrom, therefore 14.81*0.5292=7.83.

By default, the length unit in the plotted map is Bohr, while the unit in the exported file is Angstrom.

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#7 2018-12-03 21:50:20

Stom
Member
Registered: 2018-11-30
Posts: 4

Re: Electron density redistribution

Thank you.

Stom

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