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 <[email protected]> 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 <[email protected]>: >> >> Dear Gabriele, >> >> Thank you in advance for your reply. >> >> Best, >> Raha >> >> >> On Wed, Dec 24, 2014 at 2:36 PM, Gabriele Sclauzero < >> [email protected]> 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 >>> >>> %%%%%%%%%%%%%%%% >>> >>> >>> -- >>> Khadije Khalili >>> Ph.D Student of Solid-State Physics >>> Department of Physics >>> University of Mazandaran >>> Babolsar, Iran >>> [email protected] >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> [email protected] >>> 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 >>> [email protected] >>> www.theory.mat.ethz.ch/people/postdocs/gsclauze >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> [email protected] >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> Khadije Khalili >> Ph.D Student of Solid-State Physics >> Department of Physics >> University of Mazandaran >> Babolsar, Iran >> [email protected] >> >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum >> > -- Khadije Khalili Ph.D Student of Solid-State Physics Department of Physics University of Mazandaran Babolsar, Iran [email protected] _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
