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-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of > Giuseppe Mattioli <giuseppe.matti...@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-y...@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-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on >> behalf of Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> >> Sent: Monday, February 8, 2016 9:50 AM >> To: pw_forum@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.matti...@ism.cnr.it> >> http://www.ism.cnr.it/english/staff/mattiolig >> ResearcherID: F-6308-2012 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > -- > ******************************************************** > - 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.matti...@ism.cnr.it> > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > ResearcherID: F-6308-2012 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum