<div dir="ltr">Dear Alexey,<div>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.</div>
<div><br><div><br><br><div class="gmail_quote">On Sat, Aug 11, 2012 at 1:12 PM, Alexey Akimov <span dir="ltr"><<a href="mailto:aakimov@z.rochester.edu" target="_blank">aakimov@z.rochester.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Amin,<br>
<br>
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).<br>
<div><div class="h5"><br>
<br>
<br>
----- Original Message -----<br>
From: "Amin Torabi" <<a href="mailto:mtorabi@uwo.ca">mtorabi@uwo.ca</a>><br>
To: "PWSCF Forum" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Sent: Friday, August 10, 2012 9:22:55 AM<br>
Subject: [Pw_forum] zns/zno surface<br>
<br>
<br>
<br>
<br>
Dear PWSCF experts,<br>
<br>
<br>
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.<br>
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?<br>
<br>
<br>
Can you please take a look on my input file and let me know if you have any suggestion? Thanks<br>
<br>
<br>
<br>
&CONTROL<br>
calculation = 'relax'<br>
prefix = 'orig'<br>
pseudo_dir = '/home/p/'<br>
outdir = './tmp'<br>
tstress = .true<br>
tprnfor = .true<br>
/<br>
&SYSTEM<br>
ibrav = 12<br>
A = 11.3772<br>
B = 11.3772<br>
C = 40.0<br>
cosAB = -0.5<br>
nat = 153<br>
ntyp = 3<br>
ecutwfc = 30<br>
ecutrho = 300<br>
occupations = 'smearing'<br>
degauss = 0.01<br>
smearing = 'gauss'<br>
/<br>
&ELECTRONS<br>
mixing_mode = 'local-TF'<br>
mixing_beta = 0.3<br>
/<br>
&IONS<br>
/<br>
ATOMIC_SPECIES<br>
Zn 65.409 Zn.pbe-van.UPF<br>
S 32.066 S.pbe-van_bm.UPF<br>
O 15.9994 O.pbe-van_ak.UPF<br>
ATOMIC_POSITIONS angstrom<br>
Zn 1.896209796 1.094779514 3.1132225450 0 0 0<br>
S 0.000002678 2.189555203 2.3306235650 0 0 0<br>
S 1.896209090 1.094779922 5.4413927710 0 0 0<br>
Zn 0.000001973 2.189555611 6.2239919760 0 0 0<br>
Zn 1.896209796 1.094779514 9.3347611820 0 0 0<br>
S 0.000002678 2.189555203 8.5521622020 0 0 0<br>
S 1.896209090 1.094779922 11.662931408 0 0 0<br>
Zn 0.000001973 2.189555611 12.445530613 0 0 0<br>
Zn 1.896209796 1.094779514 15.556299819 0 0 0<br>
S 0.000002678 2.189555203 14.773700839 0 0 0<br>
S 1.896209090 1.094779922 17.884470045 0 0 0<br>
Zn 0.000001973 2.189555611 18.667069250 0 0 0<br>
Zn 1.896209796 1.094779514 21.777838456<br>
S 0.000002678 2.189555203 20.995239476<br>
S 1.896209090 1.094779922 24.106008682<br>
Zn 0.000001973 2.189555611 24.888607887<br>
S 0.000002678 2.189555203 27.216778113<br>
Zn 0.000005649 4.379109319 3.1132225450 0 0 0<br>
S -1.896201469 5.473885008 2.3306235650 0 0 0<br>
S 0.000004943 4.379109727 5.4413927710 0 0 0<br>
Zn -1.896202174 5.473885416 6.2239919760 0 0 0<br>
Zn 0.000005649 4.379109319 9.3347611820 0 0 0<br>
S -1.896201469 5.473885008 8.5521622020 0 0 0<br>
S 0.000004943 4.379109727 11.662931408 0 0 0<br>
Zn -1.896202174 5.473885416 12.445530613 0 0 0<br>
Zn 0.000005649 4.379109319 15.556299819 0 0 0<br>
S -1.896201469 5.473885008 14.773700839 0 0 0<br>
S 0.000004943 4.379109727 17.884470045 0 0 0<br>
Zn -1.896202174 5.473885416 18.667069250 0 0 0<br>
Zn 0.000005649 4.379109319 21.777838456<br>
S -1.896201469 5.473885008 20.995239476<br>
S 0.000004943 4.379109727 24.106008682<br>
Zn -1.896202174 5.473885416 24.888607887<br>
S -1.896201469 5.473885008 27.216778113<br>
Zn -1.896198498 7.663439124 3.1132225450 0 0 0<br>
S -3.792405616 8.758214813 2.3306235650 0 0 0<br>
S -1.896199204 7.663439532 5.4413927710 0 0 0<br>
Zn -3.792406321 8.758215221 6.2239919760 0 0 0<br>
Zn -1.896198498 7.663439124 9.3347611820 0 0 0<br>
S -3.792405616 8.758214813 8.5521622020 0 0 0<br>
S -1.896199204 7.663439532 11.662931408 0 0 0<br>
Zn -3.792406321 8.758215221 12.445530613 0 0 0<br>
Zn -1.896198498 7.663439124 15.556299819 0 0 0<br>
S -3.792405616 8.758214813 14.773700839 0 0 0<br>
S -1.896199204 7.663439532 17.884470045 0 0 0<br>
Zn -3.792406321 8.758215221 18.667069250 0 0 0<br>
Zn -1.896198498 7.663439124 21.777838456<br>
S -3.792405616 8.758214813 20.995239476<br>
S -1.896199204 7.663439532 24.106008682<br>
Zn -3.792406321 8.758215221 24.888607887<br>
S -3.792405616 8.758214813 27.216778113<br>
Zn 5.688625711 1.094783325 3.1132225450 0 0 0<br>
S 3.792418593 2.189559014 2.3306235650 0 0 0<br>
S 5.688625005 1.094783733 5.4413927710 0 0 0<br>
Zn 3.792417888 2.189559422 6.2239919760 0 0 0<br>
Zn 5.688625711 1.094783325 9.3347611820 0 0 0<br>
S 3.792418593 2.189559014 8.5521622020 0 0 0<br>
S 5.688625005 1.094783733 11.662931408 0 0 0<br>
Zn 3.792417888 2.189559422 12.445530613 0 0 0<br>
Zn 5.688625711 1.094783325 15.556299819 0 0 0<br>
S 3.792418593 2.189559014 14.773700839 0 0 0<br>
S 5.688625005 1.094783733 17.884470045 0 0 0<br>
Zn 3.792417888 2.189559422 18.667069250 0 0 0<br>
Zn 5.688625711 1.094783325 21.777838456<br>
S 3.792418593 2.189559014 20.995239476<br>
S 5.688625005 1.094783733 24.106008682<br>
Zn 3.792417888 2.189559422 24.888607887<br>
S 3.792418593 2.189559014 27.216778113<br>
Zn 3.792421564 4.379113130 3.1132225450 0 0 0<br>
S 1.896214446 5.473888819 2.3306235650 0 0 0<br>
S 3.792420858 4.379113538 5.4413927710 0 0 0<br>
Zn 1.896213741 5.473889227 6.2239919760 0 0 0<br>
Zn 3.792421564 4.379113130 9.3347611820 0 0 0<br>
S 1.896214446 5.473888819 8.5521622020 0 0 0<br>
S 3.792420858 4.379113538 11.662931408 0 0 0<br>
Zn 1.896213741 5.473889227 12.445530613 0 0 0<br>
Zn 3.792421564 4.379113130 15.556299819 0 0 0<br>
S 1.896214446 5.473888819 14.773700839 0 0 0<br>
S 3.792420858 4.379113538 17.884470045 0 0 0<br>
Zn 1.896213741 5.473889227 18.667069250 0 0 0<br>
Zn 3.792421564 4.379113130 21.777838456<br>
S 1.896214446 5.473888819 20.995239476<br>
O 3.792420858 4.379113538 23.706008682<br>
Zn 1.896213741 5.473889227 24.888607887<br>
O 1.896214446 5.473888819 26.816778113<br>
Zn 1.896217417 7.663442935 3.1132225450 0 0 0<br>
S 0.000010299 8.758218624 2.3306235650 0 0 0<br>
S 1.896216711 7.663443343 5.4413927710 0 0 0<br>
Zn 0.000009594 8.758219032 6.2239919760 0 0 0<br>
Zn 1.896217417 7.663442935 9.3347611820 0 0 0<br>
S 0.000010299 8.758218624 8.5521622020 0 0 0<br>
S 1.896216711 7.663443343 11.662931408 0 0 0<br>
Zn 0.000009594 8.758219032 12.445530613 0 0 0<br>
Zn 1.896217417 7.663442935 15.556299819 0 0 0<br>
S 0.000010299 8.758218624 14.773700839 0 0 0<br>
S 1.896216711 7.663443343 17.884470045 0 0 0<br>
Zn 0.000009594 8.758219032 18.667069250 0 0 0<br>
Zn 1.896217417 7.663442935 21.777838456<br>
S 0.000010299 8.758218624 20.995239476<br>
S 1.896216711 7.663443343 24.106008682<br>
Zn 0.000009594 8.758219032 24.888607887<br>
S 0.000010299 8.758218624 27.216778113<br>
Zn 9.481041626 1.094787136 3.1132225450 0 0 0<br>
S 7.584834508 2.189562825 2.3306235650 0 0 0<br>
S 9.481040920 1.094787544 5.4413927710 0 0 0<br>
Zn 7.584833803 2.189563233 6.2239919760 0 0 0<br>
Zn 9.481041626 1.094787136 9.3347611820 0 0 0<br>
S 7.584834508 2.189562825 8.5521622020 0 0 0<br>
S 9.481040920 1.094787544 11.662931408 0 0 0<br>
Zn 7.584833803 2.189563233 12.445530613 0 0 0<br>
Zn 9.481041626 1.094787136 15.556299819 0 0 0<br>
S 7.584834508 2.189562825 14.773700839 0 0 0<br>
S 9.481040920 1.094787544 17.884470045 0 0 0<br>
Zn 7.584833803 2.189563233 18.667069250 0 0 0<br>
Zn 9.481041626 1.094787136 21.777838456<br>
S 7.584834508 2.189562825 20.995239476<br>
S 9.481040920 1.094787544 24.106008682<br>
Zn 7.584833803 2.189563233 24.888607887<br>
S 7.584834508 2.189562825 27.216778113<br>
Zn 7.584837479 4.379116941 3.1132225450 0 0 0<br>
S 5.688630361 5.473892630 2.3306235650 0 0 0<br>
S 7.584836773 4.379117349 5.4413927710 0 0 0<br>
Zn 5.688629656 5.473893038 6.2239919760 0 0 0<br>
Zn 7.584837479 4.379116941 9.3347611820 0 0 0<br>
S 5.688630361 5.473892630 8.5521622020 0 0 0<br>
S 7.584836773 4.379117349 11.662931408 0 0 0<br>
Zn 5.688629656 5.473893038 12.445530613 0 0 0<br>
Zn 7.584837479 4.379116941 15.556299819 0 0 0<br>
S 5.688630361 5.473892630 14.773700839 0 0 0<br>
S 7.584836773 4.379117349 17.884470045 0 0 0<br>
Zn 5.688629656 5.473893038 18.667069250 0 0 0<br>
Zn 7.584837479 4.379116941 21.777838456<br>
S 5.688630361 5.473892630 20.995239476<br>
S 7.584836773 4.379117349 24.106008682<br>
Zn 5.688629656 5.473893038 24.888607887<br>
S 5.688630361 5.473892630 27.216778113<br>
Zn 5.688633332 7.663446746 3.1132225450 0 0 0<br>
S 3.792426214 8.758222435 2.3306235650 0 0 0<br>
S 5.688632626 7.663447154 5.4413927710 0 0 0<br>
Zn 3.792425509 8.758222843 6.2239919760 0 0 0<br>
Zn 5.688633332 7.663446746 9.3347611820 0 0 0<br>
S 3.792426214 8.758222435 8.5521622020 0 0 0<br>
S 5.688632626 7.663447154 11.662931408 0 0 0<br>
Zn 3.792425509 8.758222843 12.445530613 0 0 0<br>
Zn 5.688633332 7.663446746 15.556299819 0 0 0<br>
S 3.792426214 8.758222435 14.773700839 0 0 0<br>
S 5.688632626 7.663447154 17.884470045 0 0 0<br>
Zn 3.792425509 8.758222843 18.667069250 0 0 0<br>
Zn 5.688633332 7.663446746 21.777838456<br>
S 3.792426214 8.758222435 20.995239476<br>
S 5.688632626 7.663447154 24.106008682<br>
Zn 3.792425509 8.758222843 24.888607887<br>
S 3.792426214 8.758222435 27.216778113<br>
K_POINTS automatic<br>
3 3 1 0 0 0<br>
<br>
<br>
--<br>
<br>
<br>
*************************************** Amin Torabi<br>
Ph.D. Student<br>
Chemistry Dept.<br>
Western University<br>
London, On Canada, N6A 5B7<br>
Phone: 519-661-2111 Ext: 87871<br>
****************************************<br>
<br>
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--<br>
Dr. Alexey V. Akimov<br>
<br>
Postdoctoral Research Associate<br>
Department of Chemistry<br>
University of Rochester<br>
<br>
<a href="mailto:aakimov@z.rochester.edu">aakimov@z.rochester.edu</a><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div><span style="color:rgb(32,32,32);font-family:'Droid Sans',arial,sans-serif;font-size:13px">***************************************</span></div>
Amin Torabi<br>Ph.D. Student<br>Chemistry Dept.<br>Western University<br>London, On Canada, N6A 5B7<br><span style="font-family:'Droid Sans',arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(32,32,32)">Phone: <a value="+15196612111" style="color:rgb(103,117,58)">519-661-2111</a> Ext: 87871</span><div>
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