<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.yiv1670408046tab
{mso-style-name:yiv1670408046tab;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Shamsu<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Your input file and parameters are fine. When you plot the DOS you need to shift your Fermi level to zero if you want the gap to show up at zero. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Add the line<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>verbosity = ‘high’ <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>to the control part of your input file and run pw.x again. Then you can grep your output file<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>less scf.out | grep ‘Fermi energy’<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>You should get a line that looks like this:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>the Fermi energy is -1.6709 ev<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>When you plot your DOS, for instance in gnuplot you would now plot<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>plot ‘Graph01.dos’ ($1-(-1.6709)):2 w l<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>and you should see your plot with the bandgap and dispersion at zero. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>When you do these calculations the Fermi level will rarely show up at exactly zero.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Robert<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> pw_forum-bounces@pwscf.org [mailto:pw_forum-bounces@pwscf.org] <b>On Behalf Of </b>Shamsu Abubakar<br><b>Sent:</b> Wednesday, April 03, 2013 8:23 PM<br><b>To:</b> pw_forum@pwscf.org<br><b>Subject:</b> [Pw_forum] Fermi energy reference point shift from 0 to -2<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div id=yiv1670408046><div><div><div><p class=MsoNormal style='background:white'><span style='font-size:14.0pt;color:black'>Dear <span class=yiv1670408046tab>Q.E Users.</span><o:p></o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>I have a system of 4x4 graphene supercell, comprising 32 carbon atoms. I sucessfully run all the calculations i.e scf,nscf and other postprocessing such as DOS and PDOS. But the main problem i'm facing currently is on the density of state. Usually, i consider zero to be my fermi reference energy point in my ./dos.x input file, forexample,from -10 and 10 as my Emin and Emax respectivily. For pristine graphene,i expect to always see the dispersion at the zero vicinity, showing a semi metallic behavior, but surprisingly, its always moving away from zero to around -2, in the valence band side which i knew is unsual for pristine graphene. However, when i combine graphene with GaAs nanostructure, most of the interesting properties interms of orbitals contributions (PDOS), also resides on similar point -2. That is some of the contributions that are supposed to be seen at the vicinity of the fermi level, now moved to another point -2. Also, i consider changing the smearing from marzari-vanderbilt to Fermi- Dirac, but similar properties were observed. I decided to consider only 1x1, and 2x2 graphene supercell alone, still similar properties i observed also. In fact, i even consider changing my pseudopotential from pw91 to pbe.rrkjus still no progress. My problem now, i don't know what really causes these shift from 0 to -2. </span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>I attached one of my graphene scf input file for your verification and advice.</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:14.0pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'> &CONTROL</span></span><span style='font-size:14.0pt;color:black'><br><span class=yiv1670408046tab> title = 'Graphene monolayer01',</span><br><span class=yiv1670408046tab> prefix = 'Graph01',</span><br><span class=yiv1670408046tab> calculation = 'scf' ,</span><br><span class=yiv1670408046tab> restart_mode = 'from_scratch' ,</span><br><span class=yiv1670408046tab> outdir = '/home//???/espresso-4.1.2/bin/' ,</span><br><span class=yiv1670408046tab> pseudo_dir = '/home//???/???/espresso-4.1.2/upf_files/' ,</span><br><span class=yiv1670408046tab> </span><br><span class=yiv1670408046tab> tstress = .true. ,</span><br><span class=yiv1670408046tab> tprnfor = .true. ,</span><br><span class=yiv1670408046tab> /</span><br><span class=yiv1670408046tab> &SYSTEM</span><br><span class=yiv1670408046tab> ibrav = 4,</span><br><span class=yiv1670408046tab> celldm(1) = 18.59490373,</span><br><span class=yiv1670408046tab> celldm(3) = 1.80,</span><br><span class=yiv1670408046tab> nat = 32,</span><br><span class=yiv1670408046tab> ntyp = 1,</span><br><span class=yiv1670408046tab> ecutwfc = 34.D0 ,</span><br><span class=yiv1670408046tab> tot_charge = 0.000000,</span><br><span class=yiv1670408046tab> occupations = 'smearing' ,</span><br><span class=yiv1670408046tab> degauss = 0.02 ,</span><br><span class=yiv1670408046tab> smearing = 'fermi-dirac' ,</span><br><span class=yiv1670408046tab> </span><br><span class=yiv1670408046tab> /</span><br><span class=yiv1670408046tab> &ELECTRONS</span><br><span class=yiv1670408046tab> conv_thr = 1.D-8 ,</span><br><span class=yiv1670408046tab> mixing_beta = 0.7D0 ,</span><br><span class=yiv1670408046tab> /</span><br><span class=yiv1670408046tab>ATOMIC_SPECIES</span><br><span class=yiv1670408046tab> C 12.00000 C.pw91-van_ak.UPF </span><br><span class=yiv1670408046tab> </span><br><span class=yiv1670408046tab>ATOMIC_POSITIONS (angstrom)</span><br><span class=yiv1670408046tab>C 1.229999657 0.709326753 1.999999753</span><br><span class=yiv1670408046tab>C 2.459999165 1.419486000 1.999999874</span><br><span class=yiv1670408046tab>C 3.689999208 0.709327391 1.999999822</span><br><span class=yiv1670408046tab>C 4.920000000 1.419486496 1.999999944</span><br><span class=yiv1670408046tab>C 4.920000000 2.839880146 2.000000125</span><br><span class=yiv1670408046tab>C 6.149999990 3.549976521 1.999999907</span><br><span class=yiv1670408046tab>C 3.690000010 3.549976521 1.999999907</span><br><span class=yiv1670408046tab>C 2.459999764 2.839879152 2.000000067</span><br><span class=yiv1670408046tab>C 6.150000792 0.709327391 1.999999822</span><br><span class=yiv1670408046tab>C 7.380000835 1.419486000 1.999999874</span><br><span class=yiv1670408046tab>C 7.380000236 2.839879152 2.000000067</span><br><span class=yiv1670408046tab>C 8.610000005 3.549975943 1.999999891</span><br><span class=yiv1670408046tab>C 8.609999654 4.970023341 2.000000208</span><br><span class=yiv1670408046tab>C 9.840000000 5.680120078 2.000000200</span><br><span class=yiv1670408046tab>C 7.379999382 5.680120770 2.000000152</span><br><span class=yiv1670408046tab>C 6.149999800 4.970024086 2.000000150</span><br><span class=yiv1670408046tab>C 4.920000000 5.680121474 2.000000132</span><br><span class=yiv1670408046tab>C 3.690000200 4.970024086 2.000000150</span><br><span class=yiv1670408046tab>C 8.610000343 0.709326753 1.999999753</span><br><span class=yiv1670408046tab>C 9.840000000 1.419485253 1.999999874</span><br><span class=yiv1670408046tab>C 9.840000000 2.839878353 2.000000070</span><br><span class=yiv1670408046tab>C 11.069999995 3.549975943 1.999999891</span><br><span class=yiv1670408046tab>C 11.070000346 4.970023341 2.000000208</span><br><span class=yiv1670408046tab>C 12.300000618 5.680120770 2.000000152</span><br><span class=yiv1670408046tab>C 12.300001137 7.100514050 2.000000166</span><br><span class=yiv1670408046tab>C 13.530000464 7.810673002 1.999999744</span><br><span class=yiv1670408046tab>C 11.070000830 7.810672948 1.999999928</span><br><span class=yiv1670408046tab>C 9.840000000 7.100514025 2.000000287</span><br><span class=yiv1670408046tab>C 8.609999170 7.810672948 1.999999928</span><br><span class=yiv1670408046tab>C 7.379998863 7.100514050 2.000000166</span><br><span class=yiv1670408046tab>C 6.149999536 7.810673002 1.999999744</span><br><span class=yiv1670408046tab>C 4.920000000 7.100514261 2.000000041</span><br><span class=yiv1670408046tab> </span><br><span class=yiv1670408046tab>K_POINTS automatic </span><br><span class=yiv1670408046tab> 6 6 1 0 0 0 </span><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:14.0pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>Thank you for your kind response.</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:14.0pt;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>Shamsu Abubakar</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>Postgraduate student</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>Department of Physics</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div><p class=MsoNormal style='background:white'><span class=yiv1670408046tab><span style='font-size:14.0pt;color:black'>University Putra Malaysia</span></span><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p></div></div></div></div></div></body></html>