[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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