[Pw_forum] Charge analysis in QE
Matic Poberznik
matic.poberznik at gmail.com
Thu Feb 11 16:48:11 CET 2016
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
>> 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), 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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