I tried the following way to calculate (& visualize) the bonding charge density difference in my system.
I did the DFT calculations using LAECHG = T tag which produces AECCAR files. I then calculated the difference by subtracting AECCAR1 and AECCAR2 files (using Henkelman's 'chgdiff.pl' script) and then use VESTA programme to visualize it.
I am wondering if this this the correct way to do it? Could anyone please give some light on this topic (any general idea would also be appreciated)?
From my experience, there are two ways of doing it.
1) Through VESTA itself. First, you need to obtain charge densities* for the full system, and sub systems separately. Then load the full system's CHGCAR in VESTA. Next, go to Edit->Edit Data -> Volumetric Data, click import. At the open file menu, select and open the CHGCAR file for one of your sub system. Select subtract from current data, you can choose to convert units. Repeat for the next sub system in the system.
Density difference = Density_fullsystem - Density_subsys1 - Density_subsys2
*Perform only single point calculation to obtain the charge densities.
2) If you are using the chgdiff.pl, Subtract using CHGCARs not AECCARs. The LAECHG tag is not needed, unless you want to calculate Bader charges.
I have attached a link that I have used before. The slides provide step by step explanation utilising VESTA for charge density difference plot. Hopefully it helps.
Best wishes.
http://renqinzhang.weebly.com/uploads/9/6/1/9/9619514/charge_density_difference.pdf
Thanks for your reply. I am interested in AECCARs files which I think VESTA can't handle.
I had looked into before this slides but probably this is not the one which I want. I am more interested rather your second way/step where you do one single calculation.
So what should I do for subtracting AECCARs files and then how to visualize it in VESTA or any other visualization programme?
Have you tried to visualize the corresponding CHGCAR file with VMD?
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Upload the file with VMD and then:
Graphics-> Representations -> Drawing Method -> Isosurface
Hope it helps!
I understand your question was about how to plot a bonding charge density difference. However, there may be a better and easier approach to understanding what is going on in your system. If you are interested in understanding charge transfer between atoms, that can be more readily quantified using net atomic charges. If you are trying to understand the formation of chemical bonds (or the electron sharing between atoms), that can be more readily quantified by computing the bond orders.
You could perform DDEC6 analysis to compute the net atomic charges and bond orders. This method has a lot of useful properties. See the following papers for details:
(1) T. A. Manz and N. Gabaldon Limas, “Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology,” RSC Advances, 6 (2016) 47771-47801 (http://dx.doi.org/10.1039/C6RA04656H).
(2) N. Gabaldon Limas and T. A. Manz, “Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials,” RSC Advances, 6 (2016) 45727-45747 (http://dx.doi.org/10.1039/C6RA05507A).
(3) T. A. Manz, "Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders," RSC Advances, 7 (2017) 45552-45581 (http://dx.doi.org/10.1039/C7RA07400J ). (open access)
The DDEC6 method is available in the free Chargemol program (http://ddec.sourceforge.net) which can analyze the outputs of VASP, Gaussian, and other quantum chemistry programs.
For VASP, follow these steps:
(1) Get your desired geometry from either experiments or geometry optimization or any other method of your choice.
(2) Prepare an INCAR file with the following keywords: NSW = 0 (don't change geometry), Prec = Accurate (use an accurate integration grid), ENCUT = value greater than or equal to 400 eV, LAECHG = .TRUE. (generate the AECCAR0 and AECCAR2 files), and LCHARG = .TRUE. (generate the CHGCAR file), and any other keywords appropriate to your particular material calculation.
(3) In the KPOINTS file, set up your k-point grid so that the product of number of k-points along each lattice direction times the length of that lattice vector is at least 16 angstroms. For example, if your lattice vector lengths are 2.54 angstroms, 5.8 angstroms, and 17.2 angstroms, you could use a 7 (or 8) x 3 x 1 kpoint mesh. Usually the auto Monkhorst-Pack scheme works well; however, use Gamma point if k-point mesh is 1 x 1 x 1.
(4) Place the AECCAR0, AECCAR2, CHGCAR, and POTCAR file into a directory and add the job_control.txt file. (See above program manual for how to set up and use the job_control.txt file.)
(5) Run the Chargemol program to produce the output files containing the net atomic charges, atomic spin moments (for magnetic materials), atomic dipoles and quadrupoles, bond orders, overlap populations, etc.
Dear Prof. Manz,
I want to use above mentioned software for net atomic charge calculation. Here my query is that how much time it takes on calculating all mentioned properties. As in bader charge calculation, software takes less than a minute. How much time does chargemol software take ?
Thank You
Shilendra
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