How to plot electron density and color by electrostatic potential on VESTA

[Kristen Wang]

I currently use VASP for my calculations and I have written out the CHGCAR file for the perovskite system I am studying. I was wondering:

1) how do I plot the electron density and color it by electrostatic potential on VESTA? 

ie. I want a plot for my perovskite system to be similar to the attached Gaussian output file that shows the electron density for imidazole where the red region indicates a greater electron density and the blue region indicates less electron density

2) Is the CHGCAR file enough to produce the electron density plot or are there other additional files that are required?

Thank you!

[abed haidar]

Hi Kristen,

If I understand correctly you need to use the property isosurface as shown below: The screen shot is for one my studies. Once you open you CHGCAR you should be able to access the files properties. From Properties head over to Isosurfaces where you can identify the positive density from the negative ones and choose your favourable colours from simply pressing the new button. 

Hope that helps!

EL-abed

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[Kristen Wang]

Hi Abed,

Thank you for your response!

I actually had a few question about the blue and yellow colors as I am still confused with its meaning. In another post I read: "The yellow surfaces bound regions in which the plotted quantity is greater than a (positive) threshold, and the blue surfaces bound regions where the plotted quantity is less than a different (negative) threshold. The threshold values, colors, etc. can be set from the isosurfaces tab of the dialog box that is called up by the properties button near the bottom left of the Vesta window." 

My questions are:

1) What do these threshold values physically mean?

2) When you say that the colors represent positive/ negative densities, does the blue represent the negative density? 

3) Does negative density refer to charge accumulation or does it just indicate the phases of the orbital involved (ie. like how p-orbitals are made of two lobes with each lobe usually differentiated by a + or -)

Thank you for your help!

Best,

Kristen

On Friday, June 21, 2019 at 4:04:29 PM UTC-7, abed haidar wrote:

Hi Kristen,

If I understand correctly you need to use the property isosurface as shown below: The screen shot is for one my studies. Once you open you CHGCAR you should be able to access the files properties. From Properties head over to Isosurfaces where you can identify the positive density from the negative ones and choose your favourable colours from simply pressing the new button. 

Hope that helps!

EL-abed

On Sat, Jun 22, 2019 at 2:43 AM Kristen Wang <kriste...@gmail.com> wrote:

I currently use VASP for my calculations and I have written out the CHGCAR file for the perovskite system I am studying. I was wondering:

1) how do I plot the electron density and color it by electrostatic potential on VESTA? 

ie. I want a plot for my perovskite system to be similar to the attached Gaussian output file that shows the electron density for imidazole where the red region indicates a greater electron density and the blue region indicates less electron density

2) Is the CHGCAR file enough to produce the electron density plot or are there other additional files that are required?

Thank you!

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[abed haidar]

Hello again Kristen,

As for the colors you can choose them to be either positive or negative. 

Now as the science behind those figures, well in my field I am projecting the Hamiltonian onto the molecule. THose isosurfaces are called in our field molecular projected self-consistent Hamiltonian (MPSH) states. Those states enable us to analyze transmission properties by studying two features: the degree of localization or delocalization of the orbital. I can go more into it but not sure which field are you in.

Hope that helps. Be free to email me for more information or questions.

EL-abed

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[K K Sram]

hi all

i too have the exact doubt raised by Kristen.  in simple terms... What exactly the "POSITIVE" and "NEGATIVE" means represented by colors (whatever might be color).

does "Positive ' = 'More charge in those regions? i.e. more electrons remained there so it is finally (-ve charge accumulation? i.e. synomymous to electron transfer?

similarly 'Negative' = has opposite to above? i.e. synoonymous to hole transfer?

can some one explain?

also 

the density unit as per the VASP calculation its unit is e/Bohr^3. 

if we change the unit does the visualisation in VESTA changes?

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