[DFTB-Plus-User] R: Spin polarized NEGF calculation on iron nanocontact

Wynand Dednam wdednam at gmail.com
Thu May 24 19:40:34 CEST 2018


Hi Alex,

Thanks for your reply. If you don't mind, could you please give me some
tips on how to fix the bug when you have found it?

Thank you very much in advance :)

Kind regards
Wynand

On Thu, May 24, 2018 at 7:30 PM, alessandro.pecchia <
alessandro.pecchia at ismn.cnr.it> wrote:

> Hello,
>
> Right in these days I am debugging the spin-polarized transport. The
> density matrix and scc charges converge and seem to work. Transmission
> instead does not make sense. I am searching the problem.
>
>  In principles it is like a spin polarized dftb calculation but using negf
> as solver.
>
> Alex
>
>
>
> Inviato dal mio dispositivo Samsung
>
>
> -------- Messaggio originale --------
> Da: Wynand Dednam <wdednam at gmail.com>
> Data: 24/05/18 7:01 PM (GMT+01:00)
> A: User list for DFTB+ related questions <dftb-plus-user at mailman.zfn.
> uni-bremen.de>
> Oggetto: [DFTB-Plus-User] Spin polarized NEGF calculation on iron
> nanocontact
>
> Dear DFTB+ users,
>
> I want to calculate the spin-polarized transport through an iron
> nanocontact in a  NEGF calculation.
>
> I used the SiNW cluster example as inspiration, read all the relevant
> parts of the manual, including the 2D Carbon tutorial. But I could not find
> an example with spin polarization.
>
> The lead calculations run correctly, but the GreensFunction calculation
> crashes just when the SCC cycles are about to begin, with the following
> error:
>
> forrtl: severe (24): end-of-file during read, unit 29, file
> /home/dednamw/DFTB+/Fe/Fe1004Ktiptip308/Fe1004Ktiptip308frame5524000_
> spinpol/shiftcont_source.dat
> Image              PC                Routine            Line
> Source
> dftb+              00000000009243C3  Unknown               Unknown  Unknown
> dftb+              000000000095D9ED  Unknown               Unknown  Unknown
> dftb+              000000000095BA4E  Unknown               Unknown  Unknown
> dftb+              0000000000447FB4  dftbplus_mp_uploa        3083
> dftb+.F90
> dftb+              0000000000430DEA  dftbplus_mp_dftbp         413
> dftb+.F90
> dftb+              000000000040803C  MAIN__                      8
> main.F90
> dftb+              0000000000407FDE  Unknown               Unknown  Unknown
> libc.so.6          0000003F69C1ED1D  Unknown               Unknown  Unknown
> dftb+              0000000000407EE9  Unknown               Unknown  Unknown
>
> It seems like the shiftcont_drain.dat and shiftcont_source.dat, which I
> generated in two separate calculations, cannot be read during the
> GreensFunction calculation, or that some information is missing from these
> files? Below I paste the input device file:
>
> Geometry = GenFormat {
> <<< 'iron_contact.gen'
> }
>
> Transport {
>     Device {
>       AtomRange = 1 208
>       FirstLayerAtoms = 1 208
>     }
>     Contact {
>       Id = "source"
>       AtomRange = 209 308
>       FermiLevel [eV] = -0.4658
>       Potential = 0.0
>     }
>     Contact {
>       Id = "drain"
>       AtomRange = 309 408
>       FermiLevel [eV] = -0.4658
>       Potential = 0.0
>     }
>   Task = UploadContacts{}
>
> }
>
> Hamiltonian = DFTB {
>   SCC = Yes
>   MaxSCCIterations = 1000
>   SCCTolerance = 1.0E-8
>   MaxAngularMomentum = {
>     Fe = "d"
>   }
>
>   #ReadInitialCharges = Yes
>
>   SpinPolarisation = Colinear {
>     UnpairedElectrons = 300.0
>    }
>
>
>   SpinConstants = {
>     Fe = {
>        -0.016 -0.012 -0.003
>          -0.012 -0.029 -0.001
>          -0.003 -0.001 -0.015
>     }
>   }
>   Filling = Fermi {
>     Temperature [Kelvin] = 20
>   }
>   SlaterKosterFiles = {
>     Fe-Fe = "./Fe-Fe.skf"
>   }
>
>   Electrostatics = Poisson {
>     Poissonbox [Angstrom] = 30.0 30.0 30.0
>     MinimalGrid [Angstrom] = 0.4 0.4 0.4
>     AtomDensityTolerance = 1e-5
>     BuildBulkPotential = Yes
>     SavePotential = Yes
>     PoissonAccuracy = 1e-5
>     BoundaryRegion = Circle{}
>   }
>
>   Eigensolver = GreensFunction {
>   #  FirstLayerAtoms =  1 25
>     Delta [eV] = 1e-4
>     ContourPoints = 20 20
>     LowestEnergy [eV] = -60.0
>     EnclosedPoles = 3
>     }
> }
>
> And the input geometry:
>
> 408  C
>  Fe
> 1   1    3.5274      9.5586     -1.2772
> 2   1    6.3974      6.6886     -1.2772
> 3   1    3.5274      6.6886     -1.2772
> 4   1    9.2674      6.6886     -1.2772
> 5   1   12.1374      6.6886     -1.2772
> 6   1    0.6574      9.5586     -1.2772
> 7   1    6.3974      9.5586     -1.2772
> 8   1    9.2674     12.4286     -1.2772
> 9   1   12.1374      9.5586     -1.2772
> 10   1    0.6574     12.4286     -1.2772
> 11   1    3.5274     12.4286     -1.2772
> 12   1    6.3974     12.4286     -1.2772
> 13   1   12.1374     12.4286     -1.2772
> 14   1    0.6574      6.6886     -1.2772
> 15   1    9.2674      9.5586     -1.2772
> 16   1    9.2674      3.8186     -1.2772
> 17   1   12.1374      3.8186     -1.2772
> 18   1    0.6574      3.8186     -1.2772
> 19   1    3.5274      0.9486     -1.2772
> 20   1    6.3974      3.8186     -1.2772
> 21   1    9.2674      0.9486     -1.2772
> 22   1   12.1374      0.9486     -1.2772
> 23   1    0.6574      0.9486     -1.2772
> 24   1    3.5274      3.8186     -1.2772
> 25   1    6.3974      0.9486     -1.2772
> 26   1   13.3313     13.9132     -0.0856
> 27   1   13.6576      8.1170      0.0144
> 28   1   13.6123     11.0149      0.0283
> 29   1   13.4880      2.6040      0.0508
> 30   1   13.6096      5.2677      0.0544
> 31   1    7.8596      8.1207      0.1267
> 32   1   10.7121      8.1244      0.1287
> 33   1    2.1232      2.4115      0.1297
> 34   1    4.9650     10.9550      0.1301
> 35   1    7.8314     10.9404      0.1448
> 36   1    4.9719      5.2630      0.1469
> 37   1    4.9401      8.1127      0.1502
> 38   1    2.1169      5.2735      0.1510
> 39   1    2.0914      8.1220      0.1536
> 40   1    4.9798      2.4070      0.1593
> 41   1    2.1270     11.0120      0.1641
> 42   1    2.3170     13.6701      0.1652
> 43   1   10.7050     11.0462      0.1666
> 44   1   10.7092      2.4345      0.1720
> 45   1    7.8441      2.4063      0.1755
> 46   1    7.8378      5.2486      0.1766
> 47   1   10.6785     13.7532      0.1949
> 48   1   10.7366      5.2188      0.2239
> 49   1    4.9921     13.3451      0.6106
> 50   1    7.8303     13.2916      0.6559
> 51   1   12.1970      9.5346      1.4788
> 52   1    6.4051      9.5027      1.5209
> 53   1   12.1966      6.7397      1.5362
> 54   1    6.4141      6.7712      1.5438
> 55   1    9.3028      6.7022      1.5694
> 56   1    9.3324      9.5534      1.5814
> 57   1    3.5373      9.5449      1.5908
> 58   1    3.5706      3.8543      1.6055
> 59   1    6.4291      3.8283      1.6646
> 60   1    3.5222      6.7346      1.6661
> 61   1    9.2429      3.8724      1.6985
> 62   1    5.1365     11.2521      2.6034
> 63   1    7.8527     11.1759      2.6821
> 64   1    5.0428      5.4414      2.7521
> 65   1    7.8510      8.2371      2.9252
> 66   1   10.7486      8.1196      2.9508
> 67   1    7.8165      5.4068      3.0154
> 68   1    4.9677      8.2681      3.0633
> 69   1   10.7100      5.4604      3.2306
> 70   1    3.7215      3.8028      4.1450
> 71   1    6.4619      9.8522      4.2125
> 72   1    6.3235      6.9087      4.2651
> 73   1    9.1779      6.8809      4.4239
> 74   1    9.2936      9.4338      4.5065
> 75   1    3.9574      6.2888      4.5526
> 76   1    9.0681      3.9991      4.5677
> 77   1    6.1425      4.3513      4.5937
> 78   1   11.3972      7.5382      5.2472
> 79   1    7.4772      8.2405      5.6720
> 80   1    7.8461      5.6938      5.8040
> 81   1    5.0512      8.4709      5.8890
> 82   1   10.4043      5.4598      6.1757
> 83   1    5.5846      6.1998      6.5872
> 84   1    4.1252      4.4751      6.6028
> 85   1    3.1358      7.0834      6.7280
> 86   1    9.4372      7.6011      6.8433
> 87   1    6.5156      3.8517      7.0421
> 88   1    9.0790      3.6259      7.2587
> 89   1   11.6391      7.5687      7.8479
> 90   1    7.0840      7.5463      7.9155
> 91   1    8.1443      5.5375      8.0203
> 92   1    4.7337      7.8711      8.5128
> 93   1    3.5187      5.6907      8.6827
> 94   1   10.4069      5.7175      8.7706
> 95   1    5.7735      5.5403      8.9145
> 96   1    4.6928      3.3915      8.9369
> 97   1    9.1599      7.7430      9.3233
> 98   1    7.2091      3.4623      9.3814
> 99   1    9.5330      3.7622      9.8316
> 100   1    7.8018      5.8347     10.2198
> 101   1    6.7562      8.0486     10.2641
> 102   1   11.2901      7.6028     10.5030
> 103   1    5.0346      6.7084     10.8694
> 104   1    3.6286      4.6542     10.8938
> 105   1    5.9695      4.3517     11.3191
> 106   1    9.9014      5.7743     11.3606
> 107   1    8.7703      7.9158     11.8002
> 108   1    8.2849      3.9671     12.0059
> 109   1    7.1432      6.2560     12.4541
> 110   1    6.0711      8.2332     12.7103
> 111   1   10.7753      7.4165     13.0771
> 112   1    4.7415      5.6582     13.0777
> 113   1    9.1248      5.6603     13.7561
> 114   1    6.8440      4.5126     14.0949
> 115   1    8.2233      7.8680     14.2319
> 116   1    6.0302      6.8405     14.7953
> 117   1    7.9560      5.9963     16.0204
> 118   1    7.1901      6.6256     18.9572
> 119   1    7.0961      4.5246     20.3433
> 120   1    5.5866      6.4009     20.9586
> 121   1    6.8550      8.5428     21.0032
> 122   1    8.2451      6.5574     21.2521
> 123   1    4.6764      8.4171     22.1945
> 124   1    8.3235      4.4603     22.5309
> 125   1    5.8627      4.5407     22.6270
> 126   1    8.7747      8.6675     22.7040
> 127   1    6.6598      6.8159     23.1983
> 128   1    4.0266      6.2843     23.2138
> 129   1    6.5316      9.5390     23.3977
> 130   1    9.4038      6.4417     23.6110
> 131   1    5.0598      8.0120     24.7227
> 132   1    8.3974     10.4929     24.7308
> 133   1   10.4300      8.4090     24.7800
> 134   1    7.6291      5.1753     24.8077
> 135   1    7.8738      8.0215     24.8910
> 136   1    5.0587      5.1761     24.9120
> 137   1   11.9190      6.8309     26.1314
> 138   1    3.5240      6.7291     26.1318
> 139   1    6.4197      9.5207     26.1652
> 140   1    3.5861      9.4583     26.2100
> 141   1    9.2798      6.5684     26.2150
> 142   1    6.4094      6.6564     26.2490
> 143   1    9.1857      3.8239     26.2563
> 144   1   12.1286      9.4010     26.3628
> 145   1    6.4191      3.7043     26.3900
> 146   1    9.2551      9.3568     26.4766
> 147   1    7.8283     10.9867     27.5817
> 148   1    5.0156     10.9523     27.6320
> 149   1   10.6487     10.9660     27.6377
> 150   1    4.9666      8.1028     27.6400
> 151   1    4.9136      5.2714     27.6406
> 152   1    7.8126      8.0799     27.6697
> 153   1   10.6813      5.2493     27.6808
> 154   1    2.0725      8.0470     27.6928
> 155   1    7.8092      5.2165     27.6961
> 156   1    2.0872      5.3114     27.6973
> 157   1   10.6223      8.0662     27.7221
> 158   1    7.8671      2.2724     27.7454
> 159   1    3.5028      9.5747     29.0404
> 160   1   12.1271      9.5455     29.0421
> 161   1   12.1546      6.6878     29.0461
> 162   1    6.3778      3.7686     29.0574
> 163   1    3.5223     12.3841     29.0624
> 164   1    6.3993      9.5520     29.0649
> 165   1    3.5111      3.7748     29.0700
> 166   1    9.2804      3.7677     29.0722
> 167   1    9.2528     12.4134     29.0768
> 168   1   12.1153      3.7901     29.0859
> 169   1    6.3975     12.4180     29.0878
> 170   1   12.1143     12.4034     29.0889
> 171   1    3.5232      6.6895     29.0933
> 172   1    6.3750      6.6753     29.0946
> 173   1    9.2428      9.5691     29.1048
> 174   1    9.2462      6.6635     29.1091
> 175   1    0.6655      3.7927     29.1447
> 176   1    0.6355      9.5396     29.1732
> 177   1    0.7399     12.2183     29.1857
> 178   1    0.5997      6.6804     29.2038
> 179   1    6.3931      0.8955     29.2120
> 180   1    3.5255      0.8699     29.2494
> 181   1    9.2613      0.8501     29.2596
> 182   1   11.9236      0.9292     29.2934
> 183   1    0.8558      0.8977     29.3657
> 184   1    7.8324     10.9936     30.5103
> 185   1    4.9624     13.8636     30.5103
> 186   1   10.7024     13.8636     30.5103
> 187   1    2.0924     13.8636     30.5103
> 188   1   13.5724     13.8636     30.5103
> 189   1    7.8324     13.8636     30.5103
> 190   1   10.7024     10.9936     30.5103
> 191   1   13.5724     10.9936     30.5103
> 192   1    7.8324      5.2536     30.5103
> 193   1    2.0924     10.9936     30.5103
> 194   1    2.0924      2.3836     30.5103
> 195   1    4.9624      2.3836     30.5103
> 196   1    7.8324      2.3836     30.5103
> 197   1   10.7024      2.3836     30.5103
> 198   1   13.5724      2.3836     30.5103
> 199   1    2.0924      5.2536     30.5103
> 200   1    4.9624      5.2536     30.5103
> 201   1    4.9624     10.9936     30.5103
> 202   1   13.5724      5.2536     30.5103
> 203   1    2.0924      8.1236     30.5103
> 204   1    4.9624      8.1236     30.5103
> 205   1    7.8324      8.1236     30.5103
> 206   1   10.7024      8.1236     30.5103
> 207   1   13.5724      8.1236     30.5103
> 208   1   10.7024      5.2536     30.5103
> 1   1    0.6574      6.6886     31.9453
> 2   1    3.5274      6.6886     31.9453
> 3   1    6.3974      6.6886     31.9453
> 4   1    9.2674      6.6886     31.9453
> 5   1   12.1374      6.6886     31.9453
> 6   1    0.6574      9.5586     31.9453
> 7   1   12.1374      9.5586     31.9453
> 8   1    6.3974      9.5586     31.9453
> 9   1    9.2674      9.5586     31.9453
> 10  1    0.6574     12.4286     31.9453
> 11  1    3.5274     12.4286     31.9453
> 12  1    6.3974     12.4286     31.9453
> 13  1   12.1374      3.8186     31.9453
> 14  1    3.5274      9.5586     31.9453
> 15  1    9.2674     12.4286     31.9453
> 16  1    9.2674      3.8186     31.9453
> 17  1    6.3974      3.8186     31.9453
> 18  1   12.1374     12.4286     31.9453
> 19  1    0.6574      0.9486     31.9453
> 20  1    3.5274      0.9486     31.9453
> 21  1    6.3974      0.9486     31.9453
> 22  1   12.1374      0.9486     31.9453
> 23  1    0.6574      3.8186     31.9453
> 24  1    9.2674      0.9486     31.9453
> 25  1    3.5274      3.8186     31.9453
> 26  1   10.7024     13.8636     33.3803
> 27  1   10.7024      5.2536     33.3803
> 28  1    7.8324     13.8636     33.3803
> 29  1    4.9624      5.2536     33.3803
> 30  1    4.9624     13.8636     33.3803
> 31  1    2.0924      2.3836     33.3803
> 32  1    2.0924     13.8636     33.3803
> 33  1   13.5724      5.2536     33.3803
> 34  1   13.5724     10.9936     33.3803
> 35  1    4.9624      2.3836     33.3803
> 36
>
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