<div dir="ltr"><font color="#000000">Dear Dr. <span style="white-space:pre-wrap">Sclauzero</span></font><div><font color="#000000"><br></font></div><div style><font color="#000000">Thanks a lot for your help and suggestion. I studied mentioned examples and changed my input files. I separated electrodes in another file with prefix='au', molecule with prefix='adn' and pwcond.x with prefixl='au', prefixs='adn' and prefixs='au'. Could you tell if I am in right way, please?</font></div>
<div style><font color="#000000"><br></font></div><div style><br></div><div style><font color="#000000"><div style><br></div></font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 14, 2014 at 5:04 PM, Gabriele Sclauzero <span dir="ltr"><<a href="mailto:gabriele.sclauzero@mat.ethz.ch" target="_blank">gabriele.sclauzero@mat.ethz.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>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<div><div class="h5"><br>
<br>
On 04/14/2014 10:08 AM, raha khalili wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<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><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><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>I appreciate any help.</pre>
<pre style>Regards</pre>
<pre style>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 href="mailto:kh.khalili@stu.umz.ac.ir" target="_blank">kh.khalili@stu.umz.ac.ir</a></div>
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<br>
<br>
<pre 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 href="mailto:gabriele.sclauzero@mat.ethz.ch" target="_blank">gabriele.sclauzero@mat.ethz.ch</a>
<a href="http://www.theory.mat.ethz.ch/people/postdocs/gsclauze" target="_blank">http://www.theory.mat.ethz.ch/people/postdocs/gsclauze</a></pre>
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<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 href="mailto:kh.khalili@stu.umz.ac.ir" target="_blank">kh.khalili@stu.umz.ac.ir</a></div>
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