Bader Analysis 1

Steps and considerations to be completed before Bader Analysis:

The first step, the static calculation parameters before Bader analysis: LAECHG;

In a statically computed Incar, set laechg=. TRUE. (Note also: icharg=2). After the calculation is completed, a aeccar0,aeccar1 is generated, AECCAR2 these 3 files for subsequent analysis to use.

The second step, Bader analysis required two post-processing tools: chgsum.pl and Bader;

(1) Go to "VASP TST Tools" page download chgsum.pl file, Link: http://theory.cm.utexas.edu/vasp/scripts.html

(2) Go to "Bader Charge analysis" page download Bader program, Link: http://theory.cm.utexas.edu/henkelman/code/bader/recommended the use of Linux version, After downloading with the following command decompression: TAR-ZXVF bader_lnx_64.tar.gz Download details system: Using 360 browser download is bader_lnx_64.gz, using the Firefox browser download is bader_lnx_64. Tar.gz, both of these formats are available with the unzip command above.    The third step, the use of post-processing tools. (1) The following methods of chgsum.pl are used:

run: chgsum.pl AECCAR0 AECCAR2, get chgcar_sum file(2) The following methods of Bader are used:

Bader [-C Bader | Voronoi]          [-N Bader | Voronoi]          [-B neargrid | ongrid]          [-R Refine_edge_method]          [- Ref Reference_charge]          [-vac off | auto | vacuum_density]          [-P all_atom | all_bader]          [-P sel_atom | sel_ba Der] [Volume list or range]          [-P sum_atom | sum_bader] [Volume list or range]          [-P atom_index | bader_index]          [-I cube | chgcar]          [-h] [-V]          Chargefile

run: Bader-ref chgcar_sum chgcar, get ACF.dat (including the price of electronic charge information), BCF.dat, AVF.dat these 3 files.

Some of the posts used: Bader Chgcar-ref Chgcar_sum, this is also possible.

Precautions:

(1) Bader only support paw method, need vasp4.6.31 and above version.

(2) When calculating the charge layout analysis, a relatively dense FFT mesh is required, which can be adjusted by ng (x, y, z) f to increase the amount until the total number of charges is correct. In general, there is no problem with using the default FFT grid settings.

(3) The Bader charge density is based on the distribution of charges. and Mulliken, Hirhfeld analysis and comparison, atomic charge: Hirshfeld <mulliken<bader. (This comparison is qualitative).

(4) It is not possible to analyze the charge settlement of a certain track, but it will be available soon, and the new version would have this feature (temporarily not verifying that the new version has this feature and is being updated later).

You probably already knew this, but a quick comment about the example in Bader analysis here:

Https://github.com/jkitchin/dft-book/blob/master/dft.org#bader-analysis

If you reference the charge-to-core charge it seems to give a reasonable answer. You have the to run vasp with Laechg=true. Then chgsum the AECCAR0 and AECCAR2 files and use it as reference to Bader. Then it seems-give values comparable to https://wiki.fysik.dtu.dk/gpaw/tutorials/bader/bader.html

Also, the Attach_charges function from Ase.io.bader references the charge to the atomic number, which might leads to Mislea Ding results for VASP due to only using the valence charge density.

See below. http://theory.cm.utexas.edu/henkelman/code/bader/

Note for VASP users
One major issue with the charge density (chgcar) files from the VASP code are that they only contain the valance charge den Sity. The Bader analysis assumes that charge density Maxima is located at atomic centers (or at pseudoatoms). Aggressive pseudopotentials remove charge from atomic centers where it's both expensive to calculate and irrelevant for t He important bonding properties of atoms.

Recently, the VASP developers has added a module (aedens) which allows for the core charge to being written out from PAW Cal Culations. This module was included in vasp version 4.6.31 08feb07 and later. By adding the laechg=. TRUE. To the Incar file, the core charge are written to AECCAR0 and the valance charge to AECCAR2. These charge density files can be summed using the chgsum.pl script:

chgsum.pl AECCAR0 AECCAR2
The total charge is written to Chgcar_sum.
The Bader analysis can-then is-do-on-this-total charge density file:

Bader Chgcar-ref Chgcar_sum
One finally note is this need a fine FFT grid to accurately reproduce the correct total core charge. It is essential to do a few calculations, increasing NG (x, Y, z) F until the total charge is correct.

Reference Links:

[1] VASP TST tools:http://ma.cms-initiative.jp/en/application-list/vasp-tst-tools/vasp-tst-tools

[2] vasp under Bader Charge calculation: http://wangzongguo122.blog.163.com/blog/static/2914191220143191224847/

[3] vasp_bader_charge:http://blog.163.com/[email protected]/blog/static/ 186172302011874443402

[4] Bader Analysis: http://blog.chinaunix.net/uid-7726704-id-2045378.html

[5] Science Bader Some details of the charge analysis: http://simulation.haotui.com/viewthread.php?tid=25750

[6] Bader analysis #2: HTTPS://GITHUB.COM/JKITCHIN/DFT-BOOK/ISSUES/2

Bader Analysis 1