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    <div class="moz-cite-prefix">Dear Khadije,<br>
      <br>
          If you withheld the atomic positions is difficult to
      understand your problem and give suggestions. I guess the one
      below is the scattering region. What about the leads? If you
      specify prefixt, then you need to use bdl to compute transmission
      (assuming that your cell also contains the leads). <br>
      <br>
      Are you sure you have understood the setup for a transmission
      calculation?<br>
      I would strongly suggest you to go through examples 1 and 2 in
      PWCOND/examples and make sure you understand them.<br>
      Then you can go back to your system. Also, I would suggest to
      start with the collinear calculation, because calculations
      including spin-orbit are much more costly and you might just waste
      a lot of computer time if you are not sure of what you are doing.<br>
      <br>
      HTH<br>
      <br>
      GS<br>
      <br>
      On 04/14/2014 10:08 AM, raha khalili wrote:<br>
    </div>
    <blockquote
cite="mid:CAC-SUbsQ9WzdQXkU-Mq8Ps2y2tKdgkmKEKdFSR__bQ=KCHRVRg@mail.gmail.com"
      type="cite">
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      <div dir="ltr"><font face="arial, helvetica, sans-serif">Dear PW
          users</font>
        <div><font face="arial, helvetica, sans-serif"><br>
          </font></div>
        <div>
          <pre style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif">I am trying to calculate transmission coefficient of a molecular wire using espresso-5.0.2. The output returns with the error</font></pre>
          <div>
            <div><font face="arial, helvetica, sans-serif">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
              </font></div>
            <div><font face="arial, helvetica, sans-serif">     Error in
                routine init_orbitals (1):</font></div>
            <div><font face="arial, helvetica, sans-serif">     Too big
                atomic spheres</font></div>
            <div><font face="arial, helvetica, sans-serif"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div>
          </div>
          <div>
            <pre style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif">Below is the input for scf calculation and pwcond.x:</font></pre>
            <pre><font color="#000000" face="arial, helvetica, sans-serif">&control
    calculation = 'scf'
    restart_mode='from_scratch',
    prefix='adn',
    tprnfor = .true.
    pseudo_dir = '/home/khalili/espresso-5.0.2/pseudo',
    outdir='./'
 /
 &system
    ibrav= 0, celldm(1)=5.613142761,
    nat= 21, ntyp= 5,
    ecutwfc = 27,
    ecutrho = 391,
    occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
    lspinorb=.true.
    noncolin = .true.
 /
 &electrons
    diagonalization='david'
    electron_maxstep = 500,
    mixing_mode = 'plain'
    mixing_beta = 0.3
    conv_thr =  1.0d-7
/
ATOMIC_SPECIES
 C   12.0107   C.pz-rrkjus.UPF
 H   1.0       H.pz-rrkjus.UPF
 N   14.0067   N.pz-rrkjus.UPF
 S   32.065    S.pz-n-rrkjus_psl.0.1.UPF
 Au  196.966   Au.rel-pz-dn-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS
...
CELL_PARAMETERS cubic 
 5.613142761   0.0   0.0
 0.0   5.613142761   0.0
 0.0   0.0   5.613142761
K_POINTS {Automatic}
 1 1 4 1 1 1
</font></pre>
            <pre><font color="#000000" face="arial, helvetica, sans-serif">&INPUTCOND
    outdir = './',
    prefixt = 'adn',
    tran_file = 'trans.AdnAu',
    ikind = 1,
    energy0 = 1.d0,
    denergy=-0.4d0,
    ewind=1.d0,
    epsproj=1.d-3,
    nz1 = 1,
 /
    1
    0.0  0.0  1.0
    100
</font></pre>
            <pre style="color:rgb(0,0,0)">I appreciate any help.</pre>
            <pre style="color:rgb(0,0,0)">Regards</pre>
            <pre style="color:rgb(0,0,0)">Khadije Khalili</pre>
          </div>
          <div dir="ltr">
            <div>Ph.D Student of Solid-State Physics</div>
            <div>Department of Physics</div>
            <div>University of Mazandaran</div>
            <div>Babolsar, Iran</div>
            <div><a moz-do-not-send="true"
                href="mailto:kh.khalili@stu.umz.ac.ir" target="_blank">kh.khalili@stu.umz.ac.ir</a></div>
            <div> </div>
          </div>
        </div>
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      <br>
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      <br>
      <pre wrap="">_______________________________________________
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    </blockquote>
    <br>
    <br>
    <pre class="moz-signature" cols="72">-- 
Dr. Gabriele Sclauzero
ETH Zurich
Materials Theory
HIT G 43.2
Wolfgang-Pauli-Str. 27
8093 Zürich, Switzerland

Phone +41 44 633 94 10
Fax +41 44 633 14 59
<a class="moz-txt-link-abbreviated" href="mailto:gabriele.sclauzero@mat.ethz.ch">gabriele.sclauzero@mat.ethz.ch</a>
<a class="moz-txt-link-freetext" href="http://www.theory.mat.ethz.ch/people/postdocs/gsclauze">http://www.theory.mat.ethz.ch/people/postdocs/gsclauze</a></pre>
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