# [Pw_forum] Pwcond error

raha khalili khadije.khalili at gmail.com
Thu Dec 25 20:29:46 CET 2014

```Dear Alex,

Thank you so much for your kind helping.
My structure is consist of an adenine molecule connected to Au
electrodes via sulphur atoms. I used one scf calculation for my
structure and based on your examples I am not sure I am in right way.

Could you help me please?
Thank you in advance.

Best,
Raha

On 12/24/14, Alex Smogunov <asmogunov at gmail.com> wrote:
> Dear Raha.
> What is your system? It does not seem to be correct to me ...
> Look at examples at my home page, for examples, how to run pwcond.
> regards,
> Alexander
>
>
>
> 2014-12-24 11:52 GMT+01:00 raha khalili <khadije.khalili at gmail.com>:
>>
>> Dear Gabriele,
>>
>>
>> Best,
>> Raha
>>
>>
>> On Wed, Dec 24, 2014 at 2:36 PM, Gabriele Sclauzero <
>> gabriele.sclauzero at gmail.com> wrote:
>>
>>>
>>> Please try to increase slightly ewind (set it to 3-4 eV), and surely you
>>> need to decrease epsproj to something between 10^-5 and 10^-6. You
>>> should
>>> in principle check how the solution converges with those parameters.
>>> They
>>> influence the choice of the 2d basis set (i.e., confront n2d with
>>> ngper*npol as you change those parameters).
>>>
>>> HTH
>>>
>>> GS
>>>
>>> Hi,
>>>
>>> I am doing a transmission calculation for a molecular wire, but I get an
>>> error when I doing it.
>>>
>>> Could anyone kindly help me?
>>>
>>> error:
>>>
>>>  ngper, shell number =         1473         168
>>>  ngper, ngper*npol, n2d =         1473        2946         328
>>> ---  E-Ef =    3.0000000  k =    0.0000000   0.0000000
>>> ---  ie =          1  ik =          1
>>>  Nchannels of the left tip =            2
>>>  Right moving states:
>>>    k1(2pi/a)   k2(2pi/a)   E-Ef (eV)
>>>    0.1633443  -0.0000000   3.0000000
>>>    0.2266696  -0.0000000   3.0000000
>>>  Left moving states:
>>>    k1(2pi/a)   k2(2pi/a)   E-Ef (eV)
>>>   -0.1632933  -0.0000000   3.0000000
>>>   -0.2267428  -0.0000000   3.0000000
>>>
>>>  to transmit
>>>
>>>
>>>
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>      Error in routine transmit (34):
>>>      problems with the linear system
>>>
>>> mu input:
>>>
>>> &control
>>>     calculation = 'scf'
>>>     restart_mode='from_scratch',
>>>     prefix='mw',
>>>     tprnfor = .true.
>>>     pseudo_dir = '/home/khalili/espresso-5.1/pseudo',
>>>     outdir='./'
>>>  /
>>>  &system
>>>     ibrav= 0, celldm(1)=4.5,
>>>     nat= 24, ntyp= 5,
>>>     ecutwfc = 45,
>>>     ecutrho = 500,
>>>     occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
>>>     lspinorb=.true.
>>>     noncolin = .true.
>>> /
>>>  &electrons
>>>     diagonalization='david'
>>>     electron_maxstep = 500,
>>>     mixing_mode = 'plain'
>>>     mixing_beta = 0.6
>>>     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 {angstrom}
>>> N       -0.353885581  -0.284530022  9.162225589
>>> C       -0.281708039   1.038485778  9.315183662
>>> N       -0.022776117   1.703055915  10.458923909
>>> C        0.075422399   0.923947533  11.506837715
>>> C       -0.001416426  -0.482408098  11.482010936
>>> C       -0.204711524  -1.072155864  10.210377760
>>> N       -0.258687676  -2.391631349  10.077810212
>>> H       -0.161415486  -2.984008141  10.898364819
>>> H       -0.428159859  -2.790814768  9.158725471
>>> N        0.175939828  -1.012146204  12.687653784
>>> C        0.409994429   0.022569581  13.509380042
>>> N        0.322592635   1.213066330  12.817588267
>>> H        0.495699180   2.134366675  13.215223866
>>> S        1.014669480  -0.259337326  15.065655567
>>> S       -0.649524699   2.087736257  7.994874608
>>> Au       0.432081833   0.894194978  16.910713462
>>> Au      -0.571024380   1.058278724   6.000617954
>>> Au      -0.000000000  -0.441406607  19.131983492
>>> Au       0.000000000   2.229796563  19.131983492
>>> Au      -0.000000000  -0.441406607   3.779347924
>>> Au       0.000000000   2.229796563   3.779347924
>>> Au       0.000000000  -1.661486286   1.513165648
>>> Au       0.000000000   3.449876242   1.513165648
>>> Au       0.000000000   0.894194978   1.513165648
>>> CELL_PARAMETERS
>>>  4.5   0.0   0.0
>>>  0.0   4.5   0.0
>>>  0.0   0.0   9.333103959
>>> K_POINTS {Automatic}
>>>  1 1 4 1 1 1
>>>
>>> %%%%%%%%%%%%
>>>  &INPUTCOND
>>>     outdir = './',
>>>     prefixt = 'mw',
>>>     tran_file = 'trans.mw',
>>>     ikind = 1,
>>>     energy0 = 3.d0,
>>>     denergy=-0.01d0,
>>>     ewind=1.d0,
>>>     epsproj=1.d-3,
>>>     nz1 = 1,
>>>  /
>>>     1
>>>     0.0  0.0  1.0
>>>     500
>>>
>>> %%%%%%%%%%%%%%%%
>>>
>>>
>>> --
>>> 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 list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>> Dr. Gabriele Sclauzero
>>> Materials Theory (D_MATL)
>>> ETH Zurich, HIT G 43.2
>>> Wolfgang-Pauli-Str. 27
>>> 8093 Zürich, Switzerland
>>>
>>> Phone +41 44 633 94 10
>>> Fax +41 44 633 14 59
>>> gabriele.sclauzero at mat.ethz.ch
>>> www.theory.mat.ethz.ch/people/postdocs/gsclauze
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> 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 list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>

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