[Pw_forum] zns/zno surface

Mon Aug 13 16:27:35 CEST 2012

Dear Alexey,
How could a calculation without saturation be fine? My understanding is
that an unsaturated bottom layer will produce a spurious dipole moment
which can be large, and can interact with the corresponding dipole moment
in other unit cells.

On Sat, Aug 11, 2012 at 1:12 PM, Alexey Akimov <aakimov at z.rochester.edu>wrote:

> Dear Amin,
>
> If you want to saturate bottom (and maybe even top) sulfur/oxygen atoms I
> would try to put hydrogens on them. This way you can localize electron
> density on the sulfur/oxigen atoms and avoid dangling bonds. In reality you
> of course will not see unsaturated O/S atoms on the surface - they will be
> protonated anyway or carry some other groups on them. However it may be
> fine to do calculations even without such saturation (especially for the
> bottom layer).
>
>
>
> ----- Original Message -----
> From: "Amin Torabi" <mtorabi at uwo.ca>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Friday, August 10, 2012 9:22:55 AM
> Subject: [Pw_forum] zns/zno surface
>
>
>
>
> Dear PWSCF experts,
>
>
> I am willing to find out how doping of oxygen in a surface of ZnS
> (wurtzite) changes its band structure. I have a slab model composed of 8
> layers of ZnS, in which 2 sulfur atoms are replace with oxygen, and a 15
> Angstrom vacuum on top of the surface. I am relaxing only the first two
> layers.
> Now, my question is the sulfur or oxygen atoms on the top level resembles
> the surface that I am interested in; however, the sulfur (or zinc) atoms at
> the bottom are artifact of the model. How should I saturate them?
>
>
> Can you please take a look on my input file and let me know if you have
> any suggestion? Thanks
>
>
>
> &CONTROL
> calculation = 'relax'
> prefix = 'orig'
> pseudo_dir = '/home/p/'
> outdir = './tmp'
> tstress = .true
> tprnfor = .true
> /
> &SYSTEM
> ibrav = 12
> A = 11.3772
> B = 11.3772
> C = 40.0
> cosAB = -0.5
> nat = 153
> ntyp = 3
> ecutwfc = 30
> ecutrho = 300
> occupations = 'smearing'
> degauss = 0.01
> smearing = 'gauss'
> /
> &ELECTRONS
> mixing_mode = 'local-TF'
> mixing_beta = 0.3
> /
> &IONS
> /
> ATOMIC_SPECIES
> Zn 65.409 Zn.pbe-van.UPF
> S 32.066 S.pbe-van_bm.UPF
> O 15.9994 O.pbe-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> Zn 1.896209796 1.094779514 3.1132225450 0 0 0
> S 0.000002678 2.189555203 2.3306235650 0 0 0
> S 1.896209090 1.094779922 5.4413927710 0 0 0
> Zn 0.000001973 2.189555611 6.2239919760 0 0 0
> Zn 1.896209796 1.094779514 9.3347611820 0 0 0
> S 0.000002678 2.189555203 8.5521622020 0 0 0
> S 1.896209090 1.094779922 11.662931408 0 0 0
> Zn 0.000001973 2.189555611 12.445530613 0 0 0
> Zn 1.896209796 1.094779514 15.556299819 0 0 0
> S 0.000002678 2.189555203 14.773700839 0 0 0
> S 1.896209090 1.094779922 17.884470045 0 0 0
> Zn 0.000001973 2.189555611 18.667069250 0 0 0
> Zn 1.896209796 1.094779514 21.777838456
> S 0.000002678 2.189555203 20.995239476
> S 1.896209090 1.094779922 24.106008682
> Zn 0.000001973 2.189555611 24.888607887
> S 0.000002678 2.189555203 27.216778113
> Zn 0.000005649 4.379109319 3.1132225450 0 0 0
> S -1.896201469 5.473885008 2.3306235650 0 0 0
> S 0.000004943 4.379109727 5.4413927710 0 0 0
> Zn -1.896202174 5.473885416 6.2239919760 0 0 0
> Zn 0.000005649 4.379109319 9.3347611820 0 0 0
> S -1.896201469 5.473885008 8.5521622020 0 0 0
> S 0.000004943 4.379109727 11.662931408 0 0 0
> Zn -1.896202174 5.473885416 12.445530613 0 0 0
> Zn 0.000005649 4.379109319 15.556299819 0 0 0
> S -1.896201469 5.473885008 14.773700839 0 0 0
> S 0.000004943 4.379109727 17.884470045 0 0 0
> Zn -1.896202174 5.473885416 18.667069250 0 0 0
> Zn 0.000005649 4.379109319 21.777838456
> S -1.896201469 5.473885008 20.995239476
> S 0.000004943 4.379109727 24.106008682
> Zn -1.896202174 5.473885416 24.888607887
> S -1.896201469 5.473885008 27.216778113
> Zn -1.896198498 7.663439124 3.1132225450 0 0 0
> S -3.792405616 8.758214813 2.3306235650 0 0 0
> S -1.896199204 7.663439532 5.4413927710 0 0 0
> Zn -3.792406321 8.758215221 6.2239919760 0 0 0
> Zn -1.896198498 7.663439124 9.3347611820 0 0 0
> S -3.792405616 8.758214813 8.5521622020 0 0 0
> S -1.896199204 7.663439532 11.662931408 0 0 0
> Zn -3.792406321 8.758215221 12.445530613 0 0 0
> Zn -1.896198498 7.663439124 15.556299819 0 0 0
> S -3.792405616 8.758214813 14.773700839 0 0 0
> S -1.896199204 7.663439532 17.884470045 0 0 0
> Zn -3.792406321 8.758215221 18.667069250 0 0 0
> Zn -1.896198498 7.663439124 21.777838456
> S -3.792405616 8.758214813 20.995239476
> S -1.896199204 7.663439532 24.106008682
> Zn -3.792406321 8.758215221 24.888607887
> S -3.792405616 8.758214813 27.216778113
> Zn 5.688625711 1.094783325 3.1132225450 0 0 0
> S 3.792418593 2.189559014 2.3306235650 0 0 0
> S 5.688625005 1.094783733 5.4413927710 0 0 0
> Zn 3.792417888 2.189559422 6.2239919760 0 0 0
> Zn 5.688625711 1.094783325 9.3347611820 0 0 0
> S 3.792418593 2.189559014 8.5521622020 0 0 0
> S 5.688625005 1.094783733 11.662931408 0 0 0
> Zn 3.792417888 2.189559422 12.445530613 0 0 0
> Zn 5.688625711 1.094783325 15.556299819 0 0 0
> S 3.792418593 2.189559014 14.773700839 0 0 0
> S 5.688625005 1.094783733 17.884470045 0 0 0
> Zn 3.792417888 2.189559422 18.667069250 0 0 0
> Zn 5.688625711 1.094783325 21.777838456
> S 3.792418593 2.189559014 20.995239476
> S 5.688625005 1.094783733 24.106008682
> Zn 3.792417888 2.189559422 24.888607887
> S 3.792418593 2.189559014 27.216778113
> Zn 3.792421564 4.379113130 3.1132225450 0 0 0
> S 1.896214446 5.473888819 2.3306235650 0 0 0
> S 3.792420858 4.379113538 5.4413927710 0 0 0
> Zn 1.896213741 5.473889227 6.2239919760 0 0 0
> Zn 3.792421564 4.379113130 9.3347611820 0 0 0
> S 1.896214446 5.473888819 8.5521622020 0 0 0
> S 3.792420858 4.379113538 11.662931408 0 0 0
> Zn 1.896213741 5.473889227 12.445530613 0 0 0
> Zn 3.792421564 4.379113130 15.556299819 0 0 0
> S 1.896214446 5.473888819 14.773700839 0 0 0
> S 3.792420858 4.379113538 17.884470045 0 0 0
> Zn 1.896213741 5.473889227 18.667069250 0 0 0
> Zn 3.792421564 4.379113130 21.777838456
> S 1.896214446 5.473888819 20.995239476
> O 3.792420858 4.379113538 23.706008682
> Zn 1.896213741 5.473889227 24.888607887
> O 1.896214446 5.473888819 26.816778113
> Zn 1.896217417 7.663442935 3.1132225450 0 0 0
> S 0.000010299 8.758218624 2.3306235650 0 0 0
> S 1.896216711 7.663443343 5.4413927710 0 0 0
> Zn 0.000009594 8.758219032 6.2239919760 0 0 0
> Zn 1.896217417 7.663442935 9.3347611820 0 0 0
> S 0.000010299 8.758218624 8.5521622020 0 0 0
> S 1.896216711 7.663443343 11.662931408 0 0 0
> Zn 0.000009594 8.758219032 12.445530613 0 0 0
> Zn 1.896217417 7.663442935 15.556299819 0 0 0
> S 0.000010299 8.758218624 14.773700839 0 0 0
> S 1.896216711 7.663443343 17.884470045 0 0 0
> Zn 0.000009594 8.758219032 18.667069250 0 0 0
> Zn 1.896217417 7.663442935 21.777838456
> S 0.000010299 8.758218624 20.995239476
> S 1.896216711 7.663443343 24.106008682
> Zn 0.000009594 8.758219032 24.888607887
> S 0.000010299 8.758218624 27.216778113
> Zn 9.481041626 1.094787136 3.1132225450 0 0 0
> S 7.584834508 2.189562825 2.3306235650 0 0 0
> S 9.481040920 1.094787544 5.4413927710 0 0 0
> Zn 7.584833803 2.189563233 6.2239919760 0 0 0
> Zn 9.481041626 1.094787136 9.3347611820 0 0 0
> S 7.584834508 2.189562825 8.5521622020 0 0 0
> S 9.481040920 1.094787544 11.662931408 0 0 0
> Zn 7.584833803 2.189563233 12.445530613 0 0 0
> Zn 9.481041626 1.094787136 15.556299819 0 0 0
> S 7.584834508 2.189562825 14.773700839 0 0 0
> S 9.481040920 1.094787544 17.884470045 0 0 0
> Zn 7.584833803 2.189563233 18.667069250 0 0 0
> Zn 9.481041626 1.094787136 21.777838456
> S 7.584834508 2.189562825 20.995239476
> S 9.481040920 1.094787544 24.106008682
> Zn 7.584833803 2.189563233 24.888607887
> S 7.584834508 2.189562825 27.216778113
> Zn 7.584837479 4.379116941 3.1132225450 0 0 0
> S 5.688630361 5.473892630 2.3306235650 0 0 0
> S 7.584836773 4.379117349 5.4413927710 0 0 0
> Zn 5.688629656 5.473893038 6.2239919760 0 0 0
> Zn 7.584837479 4.379116941 9.3347611820 0 0 0
> S 5.688630361 5.473892630 8.5521622020 0 0 0
> S 7.584836773 4.379117349 11.662931408 0 0 0
> Zn 5.688629656 5.473893038 12.445530613 0 0 0
> Zn 7.584837479 4.379116941 15.556299819 0 0 0
> S 5.688630361 5.473892630 14.773700839 0 0 0
> S 7.584836773 4.379117349 17.884470045 0 0 0
> Zn 5.688629656 5.473893038 18.667069250 0 0 0
> Zn 7.584837479 4.379116941 21.777838456
> S 5.688630361 5.473892630 20.995239476
> S 7.584836773 4.379117349 24.106008682
> Zn 5.688629656 5.473893038 24.888607887
> S 5.688630361 5.473892630 27.216778113
> Zn 5.688633332 7.663446746 3.1132225450 0 0 0
> S 3.792426214 8.758222435 2.3306235650 0 0 0
> S 5.688632626 7.663447154 5.4413927710 0 0 0
> Zn 3.792425509 8.758222843 6.2239919760 0 0 0
> Zn 5.688633332 7.663446746 9.3347611820 0 0 0
> S 3.792426214 8.758222435 8.5521622020 0 0 0
> S 5.688632626 7.663447154 11.662931408 0 0 0
> Zn 3.792425509 8.758222843 12.445530613 0 0 0
> Zn 5.688633332 7.663446746 15.556299819 0 0 0
> S 3.792426214 8.758222435 14.773700839 0 0 0
> S 5.688632626 7.663447154 17.884470045 0 0 0
> Zn 3.792425509 8.758222843 18.667069250 0 0 0
> Zn 5.688633332 7.663446746 21.777838456
> S 3.792426214 8.758222435 20.995239476
> S 5.688632626 7.663447154 24.106008682
> Zn 3.792425509 8.758222843 24.888607887
> S 3.792426214 8.758222435 27.216778113
> K_POINTS automatic
> 3 3 1 0 0 0
>
>
> --
>
>
> *************************************** Amin Torabi
> Ph.D. Student
> Chemistry Dept.
> Western University
> London, On Canada, N6A 5B7
> Phone: 519-661-2111 Ext: 87871
> ****************************************
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> Dr. Alexey V. Akimov
>
> Postdoctoral Research Associate
> Department of Chemistry
> University of Rochester
>
> aakimov at z.rochester.edu
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
***************************************
Amin Torabi
Ph.D. Student
Chemistry Dept.
Western University
London, On Canada, N6A 5B7
Phone: 519-661-2111 Ext: 87871
****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20120813/0763596a/attachment.html>