[Pw_forum] zns/zno surface

Mon Aug 13 20:24:07 CEST 2012

Dear Amin,
Sure it is better to saturate both surfaces - that is why i suggested to put the hydrogens on the dangling bond on each surface. In my understanding it is not realistic to have some unsaturated (dangling) bonds, especially on the surface (which is exposed lets say to the air). The bulk surface (in your case bottom) is not exposed to reactive components, so it maybe ok from the chemical point of view not to saturate them. However, from the computational point of view, that may(and will) lead to different charge density. To cure this you can put hydrogens on all unsaturated surface atoms.  

Best regards,
Alexey  

----- Original Message -----
From: "Amin Torabi" <mtorabi at uwo.ca>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Monday, August 13, 2012 7:27:35 AM
Subject: Re: [Pw_forum] zns/zno surface

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 
**************************************** 

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-- 
Dr. Alexey V. Akimov 

Postdoctoral Research Associate 
Department of Chemistry 
University of Rochester 

aakimov at z.rochester.edu 
_______________________________________________ 
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-- 

*************************************** 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 