[Pw_forum] Charge analysis in QE

Yang, Chi-Ta chita-yang at uiowa.edu
Thu Feb 11 17:16:29 CET 2016


Dear Matic,

Thanks for your help and suggestion. I'll look into what you suggested, and check if I am wrong with the parameters I am using.

Best,
Chi-Ta
UI  

________________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Matic Poberznik <matic.poberznik at gmail.com>
Sent: Thursday, February 11, 2016 9:48 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Charge analysis in QE

Dear Chi-Ta,

The cartesian coordinates in the Bader output file in Bohr and not
Angstrom, and they do match the coordinates in your pp.in file,
The first three:

alat=10.76944268

0.252079033*alat = 2.714751 (x)
0.141015163*alat = 1.518655 (y)
0.817121712*alat = 8.799945 (z)

However these coordinates do not match those in your input file (i.e.
the first coordinate would be 0.247414 in alat units) why that is I
don't know, perhaps check how the scf.out read the coordinates (or if it
is a relax run check the final set of coordinates).

Hope this helps,

Best regards,
Matic


Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia

On 02/10/2016 06:35 PM, Yang, Chi-Ta wrote:
> 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
>>
>> ********************************************************
>> - Article premier - Les hommes naissent et demeurent
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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
>>    E-mail: <giuseppe.mattioli at ism.cnr.it>
>>    http://www.ism.cnr.it/english/staff/mattiolig
>>    ResearcherID: F-6308-2012
>>
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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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