[Pw_forum] Too big atomic spheres error

[raha khalili]

Dear Dr. Sclauzero

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?





On Mon, Apr 14, 2014 at 5:04 PM, Gabriele Sclauzero <
gabriele.sclauzero at mat.ethz.ch> wrote:

>  Dear Khadije,
>
>     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).
>
> Are you sure you have understood the setup for a transmission calculation?
> I would strongly suggest you to go through examples 1 and 2 in
> PWCOND/examples and make sure you understand them.
> 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.
>
> HTH
>
> GS
>
>
> On 04/14/2014 10:08 AM, raha khalili wrote:
>
> Dear PW users
>
>  I am trying to calculate transmission coefficient of a molecular wire using espresso-5.0.2. The output returns with the error
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       Error in routine init_orbitals (1):
>      Too big atomic spheres
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Below is the input for scf calculation and pwcond.x:
>
> &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
>
> &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
>
> I appreciate any help.
>
> Regards
>
> Khadije Khalili
>
>  Ph.D Student of Solid-State Physics
> Department of Physics
> University of Mazandaran
> Babolsar, Iran
> kh.khalili at stu.umz.ac.ir
>
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> 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 59gabriele.sclauzero at mat.ethz.chhttp://www.theory.mat.ethz.ch/people/postdocs/gsclauze
>
>
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>



-- 
Khadije Khalili
Ph.D Student of Solid-State Physics
Department of Physics
University of Mazandaran
Babolsar, Iran
kh.khalili at stu.umz.ac.ir
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