Dear all,
I am trying to plot 1D charge density difference using vasputil. As per as instruction it says " Use the vasputil_chgarith tool to create a suitable input charge density file (e.g. the charge density difference when some species adsorbs on a surface), and then use the lev00 utility to create the charge density data in a plane. The data is written to a file (default name out.dat_1) that can be read with the vasputil_chgplaneplot utility which can then plot this data."
Can anybody explain me the step by step procedure ? My system is already minimized and has CHGCAR files generated. I want to plot the planar charge density difference upon adsorption.
Hello Suraj,
In order to obtain the charge density difference (CDD) one CHGCAR file will not be enough.
In short, what you've got in your CHGCAR is the charge density of your optimized system as a whole ( lets say this system as AB). To get the CDD, you will also need the CHGCAR of your adsorbate (A) (without the adsorbent B) and CHGCAR of you adsorbent (B) (without the adsorbate A). Then you can calculate the CDD is as,
rho(AB)-rho(A)-rho(B), or in terms of CHGCAR
CHGCAR(AB)-CHGCAR(A)-CHGCAR(B)
The plot can easily be made in VESTA (either 2D or 3D), a detail instruction is provied very nicely here: http://vaspnotes.blogspot.com/2013/10/charge-density-difference-plots.html
Dear Turbasu,
Thank you for your reply. I have done it using VESTA. But I want to plot something like this ( Right Hand side )
Hello Suraj ,
There are many toolkit available to generate the plot (Planer average Charge Density). I think VASPKIT(http://vaspkit.sourceforge.net/) may be one of the easiest. You can generate the deformation charge density (CDD) in VASPKIT from the three CHGCAR file by option 31>314 (Vaspkit version 0.72p1). The process is straightforward otherwise you can take a look at section 3.4 in the Manual(Chinese) provided with the download. VASPKIT will save the CDD as CHGDIFF.vasp,(which can be viewed by VESTA). Copy this file in some folder and rename as CHGCAR, then rerun VASPKIT in the folder and select option 31>316, then select the desired direction (x,y or z). It will save the plotdata in CHGPAVG.dat file which you can plot in any plotting software.
Thank you so much Turbasu.
Here is what i did. I utilized chgdiff.pl code available in the vtst tools to compute charge density difference of the system ( AB-B-A). Then used vaspkit code to generate planar charge density (using option 41) which generated me CHGPAVG.dat file.
My .dat file shows only positive numbers. There are no negative numbers (neg charges).
It is difficult to say without seeing the files. However, Can you explain how you're getting your CDD through VTST tools. I'll suggest (In case you've done differently) first add A and B, then subtract from AB. e.g:
Step 1: chgsumf.pl A/CHGCAR B/CHGCAR which will generate CHGCAR_sum
then Step 2: chgdiff.pl AB/CHGCAR CHGCAR_sum to generate the CDD CHGCAR_diff
You can plot this CHGCAR_diff in VESTA to check whether the plot has two different colors (negative and positive). Then feed to VASPKIT to get CHGPAVG.dat
Let me know.
Here is what i did,
step 1: chgdiff.pl AB/CHGCAR A/CHGCAR
step 2: change the name of the result CHGCAR_diff to CHGCAR
step 3: chgdiff.pl CHGCAR(step2) B/CHGCAR
Then used VASPKIT to get CHGPAVG.dat.
I got it right for one of my system. I think i made some mistake previously while choosing CHCGAR file.
Thank you very much for help.
Actually after testing I've found that for some reason if you follow the procedure which you've mentioned, the final CDD is incorrect (It has no negative value for some system as you've already noticed). Which may be due to how the file being read by the script. I'll therefore advice first add A+B by chgsum.pl to generate a CHGCAR and then finally subtract from AB CHGCAR.
You can also check whether you have obtained right CDD or not by opening the final CHGCAR via VESTA.
Yup you are correct. I did the samething that you have mentioned previously and got my planar CCD.
Chgsum.pl CHGCAR(A) CHGCAR(B)
chgdiff.pl CHGCAR(AB) CHGCAR_sum
and utilized vaspkit.
I got the idea of plotting of CDD using VESTA and vtsttools scripts. Can anybody explain me , how to resolve the data grid error in CDD of adsorbed systems?
Thanks for your consideration in advance.
Did you encounter this problem using vesta or vtst-tools ?
if Using vesta then make sure that the size of the box for every species is same.
Yes, it's different. I have generated CHGCAR of adsorbed molecule as a cluster (gamma point) and substrate as a monolayer. How can we make same data grid?
Please try to follow the instructions mention here
http://renqinzhang.weebly.com/uploads/9/6/1/9/9619514/charge_density_difference.pdf
Make sure you pay special attention to slides 5, 6, and 7.
Thanks for your useful suggestions, now getting the proper results. Working on it.
With Regards.