[Pw_forum] Charge analysis in QE
Yang, Chi-Ta
chita-yang at uiowa.edu
Wed Feb 10 18:35:56 CET 2016
Dear Giuseppe,
I tried to check the new cartesian coordinates with xcrysden, but could not open and gave me error message - Error: wrong # args: should be"pwInputPreset file". I checked the structure with xyz file ,and found that the structure with new coordinates expands. The distances between atoms are almost twice longer than the original ones. I am not sure if bader charge is reasonable upon this.
Please see below the first 5 coordinates of my system from original QE.in to final bader ACF file.
Thanks,
Chi-Ta
UI
------------------------------------------------------------------------------------original.in
CELL_PARAMETERS {angstrom}
5.698943615 0.0000000000 0.0000000000
-4.2742077111 7.4031449178 0.0000000000
0.0000000000 0.0000000000 32.000000000
ATOMIC_POSITIONS {angstrom}
Li 1.409999974 0.814063944 4.686666946
Li -0.000000069 1.628127888 9.373333892
Li -0.000000011 3.256255557 4.686666946
Li -1.409999949 4.070319174 9.373333892
Li -1.410000059 5.698447280 4.686666946
--------------------------------------------------------------------------------------pp.in fileplot
75 120 432 75 120 432 66 5
0 10.76944268 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
1.00000000000000 0.000000000000000E+000 0.000000000000000E+000
-0.749999999973679 1.29903810564372 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 5.61507573364542
1410.1585948767 12.0000000000 40.0000000000 0
1 Li 3.00
2 Ni 10.00
3 Mn 15.00
4 Co 9.00
5 O 6.00
1 0.252079033 0.141015163 0.817121712 1
2 0.005082174 0.280355405 1.656190248 1
3 0.006369515 0.579747049 0.813824987 1
4 -0.249162597 0.719321092 1.657458257 1
5 -0.247504790 1.007537235 0.811527088 1
------------------------------------------------------------------------------------------cube
Cubfile created from PWScf calculation
Total SCF Density
66 0.000000 0.000000 0.000000
75 0.143593 0.000000 0.000000
120 -0.067309 0.116583 0.000000
432 0.000000 0.000000 0.139980
3 3.000000 2.714751 1.518655 8.799945
3 3.000000 0.054732 3.019271 17.836246
3 3.000000 0.068596 6.243553 8.764442
3 3.000000 -2.683342 7.746687 17.849902
3 3.000000 -2.665489 10.850615 8.739694
------------------------------------------------------------------------------------------------bader
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 2.7147510 1.5186550 8.7999450 2.0988754 1.2593539 20.4268562
2 0.0547320 3.0192710 17.8362460 2.1011053 1.2504756 20.1011325
3 0.0685960 6.2435530 8.7644420 2.0990261 1.2389623 20.4596629
4 -2.6833420 7.7466870 17.8499020 2.1025553 1.2311932 19.5598220
5 -2.6654890 10.8506150 8.7396940 2.0998684 1.2281964 20.4315428
________________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
Sent: Tuesday, February 9, 2016 9:01 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Charge analysis in QE
Dear Chi-Ta
> ".cube" shows a new set of cartesian coordinates based on fileout,
> which is different from my original cartesian coordinates.
Check whether the refolding of coordinates into your supercell
possibly made by pw.x or pp.x yielded a different but equivalent set
of cartesian coordinates.
> Is it normal to have a new set of cartesian coordinates? In this
> case, will it affect bader charge?
It is in cube files, and no, it does not affect the results of Bader analysis.
HTH
Giuseppe
Quoting "Yang, Chi-Ta" <chita-yang at uiowa.edu>:
> Dear Giuseppe,
>
> Thanks for your replay. I tried bader charge analysis, but have a
> concern about it.
> I used cartesian coordinates in my pw.x input file. I noticed that
> the coordinate systems in the output files of pp.x (fileout and.cube
> ) are different.
>
> "fileout" shows crystal coordinates
>
> ".cube" shows a new set of cartesian coordinates based on fileout,
> which is different from my original cartesian coordinates.
>
> Is it normal to have a new set of cartesian coordinates? In this
> case, will it affect bader charge?
>
> Thanks a lot,
> Chi-Ta Yang
> University of Iowa
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on
> behalf of Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Sent: Monday, February 8, 2016 9:50 AM
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Charge analysis in QE
>
> Dear Chi-Ta Yang
>
>> For the charge analysis in QE, is it fine to use the charge values
>> from the .out files?
>
> No, it is a fast on-the-fly calculation. You can post-process your
> results a) with projwfc.x to obtain Lowdin charges or b) with pp.x
> to export the
> total charge density as a .cube file and then with an external tool
> you find here (http://theory.cm.utexas.edu/henkelman/code/bader) to
> calculate the
> Bader charges from the cube files. Better results are obtained by
> using denser FFT grids than default ones and by using NC or PAW PPs
> in the case of
> the Bader tool.
>
> HTH
> Giuseppe
>
> On Monday, February 08, 2016 03:26:32 PM Yang, Chi-Ta wrote:
>> Dear All,
>>
>>
>> For the charge analysis in QE, is it fine to use the charge values
>> from the .out files? (below)
>>
>> If yes, do you recommend to use high K point for a better quality
>> of these values or other recommendations? What kind of charge is
>> this (ex:
>> bader...) ?
>>
>>
>>
>> Magnetic moment per site:
>> atom: 1 charge: 2.1845 magn: 0.1742 constr: 0.0000
>> atom: 2 charge: 2.1716 magn: 0.1740 constr: 0.0000
>> atom: 3 charge: 2.1820 magn: 0.1742 constr: 0.0000
>> atom: 4 charge: 2.1826 magn: 0.1743 constr: 0.0000
>> atom: 5 charge: 2.1711 magn: 0.1739 constr: 0.0000
>> atom: 6 charge: 2.1841 magn: 0.1741 constr: 0.0000
>> atom: 7 charge: 7.3535 magn: 1.9625 constr: 0.0000
>> atom: 8 charge: 7.3507 magn: 2.0039 constr: 0.0000
>>
>> Thanks a lot,
>> Chi-Ta Yang
>> University of Iowa
>
> ********************************************************
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> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> v. Salaria Km 29,300 - C.P. 10
> I 00015 - Monterotondo Stazione (RM), Italy
> Tel + 39 06 90672836 - Fax +39 06 90672316
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>
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--
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
********************************************************
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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