Isosurface Levels

[thom...@vt.edu]

Hello, I am wondering if anyone can explain the meaning of isosurface level.  I am uploading a CHGCAR file from VASP and the default value for isosurface level is on the order of .1.  The isosurface for visualizing charge densities does not look correct in that case.  When I decrease the isosurface level to .008 the image looks much better, but I have no justification for doing so.  Can anyone explain?  I have attached images of both cases .1 first and .008 second.

Thanks,

Tom 

[Eric Isaacs]

Dear Tom,

An isosurface is a surface of constant value (of charge density in this case since you are visualizing the CHGCAR file). The "isosurface level" is that constant value of your choosing. For example, for larger isosurface level you are plotting the region in space in which the density of electrons is larger. The units of this quantity should be those used in the CHGCAR file, which you can find in the VASP manual or by searching their forum (http://cms.mpi.univie.ac.at/vasp-forum/forum.php).

In terms of different isosurfaces looking incorrect, I do not understand why in particular you think there is a problem. That said, there definitely will be values of isosurface level that are more useful to analyze the charge density.

Hope this helps,

Eric

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[Nitta]

Dear Eric:
    I have a beginner's question. I opened up the 2D electron density plo utilityt, and clicked on slice button. I get two dimensional plots. I want to know what is the meaning of saturation levels ( maximum and minimum and the percentage associated with it; the percentage goes up and down when I tinker with different values for maximum and minimum). When I click on the absolute value, the value of the minimum changes. And what is plotting colors recursively mean? When I scroll my macintosh pointer up and down the color palette, I get values at the bottom of the graphical areas - very tiny, on the order of 10e-08 to 10e-09. What are these values? I am plotting data from CHGCAR of VASP. I hope I did not ask too much.
Nitta

[Eric Isaacs]

Hi Nitta,

I have not used the 2D data display in VESTA, so I will let others
reply to your query. I would say that it appears there is some
description of these quantities in the VESTA manual, so you may want
to examine the documentation at
http://jp-minerals.org/vesta/en/doc.html

Best,
Eric

[Philip Howie]

Hi Nitta,

When you make a 2D plot, you choose a colour scheme - the default is B-G-R for blue-green-red.  The saturation values can be set either as absolute values or as percentiles of the values in your data, with 0% being the lowest value in your data and 100% the highest.  VESTA assigns one end of the colour scale (blue) to the minimum saturation value and the other (red) to the maximum saturation value.  Values in between appear somewhere on the scale.  Values less than the minimum will also appear a uniform blue; values more than the maximum will appear a uniform red.

Adjusting these saturation values therefore allows you to magnify certain data ranges.  For example, if you have extremely high electron density at the atom positions but very low in between, you might set the maximum saturation value to 50% of the largest value in your data - this will hide the data in the atom cores but allow more subtle variations between them to be seen.  I suggest playing around with the display to see how it changes as you alter the parameters.

If, on the other hand, you tick the 'assign colours recursively' box, the colour scale is repeated to include values outside the minimum and maximum saturation values.  If, say, you set the minimum and maximum saturation values to 0% and 50%, then the scale will look like this:

1% blue
25% green
50% red
51% blue
75% green
100% red

One last point: moving the pointer over the 2D display shows the value of that point at the bottom of the screen.  If you move the pointer outside the display area, VESTA assumes your crystal is periodic and simply searches in the next unit cell.  When you move the pointer over the colour palette, you are NOT seeing the value of the different colours, you are seeing the values in the next unit cell.

I hope that helps!  As for what the actual numbers represent, I'm sorry I don't know CHGCAR and can't comment on that.

Best,

Philip

[Thomas Danielson]

Hi, I have a question regarding the coloring of the isosurfaces.  The image shown is a differential charge density.  Notice that there are portions of the isosurface plot that are yellow and some that are blue.  Is there any significance to this difference in color, or is it simply for contrast?  i.e. can we attribute different colors to different orbital contributions?

Thank you for any suggestions,

Thomas Danielson

[Micah Prange]

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 (or through the properties item in the Objects menu).

HTH,

Micah

[Muhammad Ali]

I have seen very nice & useful discussion and one question to elaborate the meaning of positive and negative thresholds in detail, please?

[Sarita Ahlawat]

Dear Philip


I am using Vesta to plot differential charge density of Fe-C system as shown below. I want to use 2D data display on this final CHGCAR along some plane. When I am using 2D data display , it is not showing anything except the color bar as you can see in attached file. The steps I followed are:

1. Obtain Differential charge density (CHGCAR) using volumetric data then subtract the subsystem CHGCAR
2. goto Utilities then 2D data display then click on slice then giving input for desired plane and distance form origin
3. It is not showing anything

But if I am able to use 2D data display in CHGCAR like pure-Fe etc,. Please help me how I can use this in differential CHGCAR also. Hope to hear from you soon.

Thanks & Regards 

[Eloge MADILA]

Good evening and best wishes my friends. 

I have  synthesized a compound ans I want to calculate the distances M-O. 

 I would like to know if VESTA can do it, if so, how? 

If you know of any other software that does it, please answer me.

Thanks a lot

On Sat, 29 Dec 2018, 00:55 Yang Sun <yangs...@gmail.com wrote:

I come across this discussion when I try to understand how VESTA converts the CHGCAR value to its own isosurface value. After a few try-and-errors, I believe VESTA divides the CHGCAR value by the cell volume and transforms the angstrom unit to Bohr radius. Below is the formula.

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[Andre Childs]

Yes, Vesta can do it. You need to click on the Atoms you wish to see difference of. You have to use the 5th button down after the magnifying glass. 

[Andre Childs]

I also have a question, but it seems that many of you are using VASP, I am not using VASP I am using Quantum Expresso, and the file that I am looking at the Iso Surface level with is a .CUBE file. 

How Can I control Vesta to enhance this file?

Thank you

[Eloge MADILA]

Hi to all

I am also using Quantum-espresso. But my issue is that I don't know how can I describe K-POINTS path for a monoclinic system with P2_1/n as the space group.

It is a bit of a hassle for because I am a beginner on it.

[Andre Childs]

Let me add you to my quantum expresso group. I just made it

What is your email?

[Eloge MADILA]

elogem...@gmail.com

[Nadire Nayir]

Hi Andre,
Could you please add me to your Quantum Espresso group? I also use it in my studies - maybe we can be of help with each other at some some points.

Nadire

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Nadire Nayir
Post Doctoral Scholar
Department of Mechanical and Nuclear Engineering
135 Research East Building
Pennsylvania State University
University Park, PA 16802
Phone: (814) 863-6278
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[Eloge MADILA]

As for Quantum espresso, can we create a whatsapp group?

 Because I  notice that we give our responses lately.

Best regards

[Nychtophilian Selcouth]

Hi Sarita, 

were you able to solve this problem ? i also need assistance.

[Sarita Ahlawat]

Dear Nychtophilian

Yes I am able to plot differential charge density using Vesta now. You can ask your query on this.

Regards

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Sarita.