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

Wynand Dednam wdednam at gmail.com
Thu May 24 19:01:00 CEST 2018


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  1   10.7024     10.9936     33.3803
37  1    2.0924      5.2536     33.3803
38  1    7.8324     10.9936     33.3803
39  1    7.8324      2.3836     33.3803
40  1    4.9624     10.9936     33.3803
41  1    7.8324      5.2536     33.3803
42  1    2.0924     10.9936     33.3803
43  1   10.7024      2.3836     33.3803
44  1   13.5724      8.1236     33.3803
45  1    2.0924      8.1236     33.3803
46  1   10.7024      8.1236     33.3803
47  1   13.5724      2.3836     33.3803
48  1    7.8324      8.1236     33.3803
49  1    4.9624      8.1236     33.3803
50  1   13.5724     13.8636     33.3803
1   1    0.6574      6.6886     34.8153
2   1    3.5274      6.6886     34.8153
3   1    6.3974      6.6886     34.8153
4   1    9.2674      6.6886     34.8153
5   1   12.1374      6.6886     34.8153
6   1    0.6574      9.5586     34.8153
7   1   12.1374      9.5586     34.8153
8   1    6.3974      9.5586     34.8153
9   1    9.2674      9.5586     34.8153
10  1    0.6574     12.4286     34.8153
11  1    3.5274     12.4286     34.8153
12  1    6.3974     12.4286     34.8153
13  1   12.1374      3.8186     34.8153
14  1    3.5274      9.5586     34.8153
15  1    9.2674     12.4286     34.8153
16  1    9.2674      3.8186     34.8153
17  1    6.3974      3.8186     34.8153
18  1   12.1374     12.4286     34.8153
19  1    0.6574      0.9486     34.8153
20  1    3.5274      0.9486     34.8153
21  1    6.3974      0.9486     34.8153
22  1   12.1374      0.9486     34.8153
23  1    0.6574      3.8186     34.8153
24  1    9.2674      0.9486     34.8153
25  1    3.5274      3.8186     34.8153
26  1   10.7024     13.8636     36.2503
27  1   10.7024      5.2536     36.2503
28  1    7.8324     13.8636     36.2503
29  1    4.9624      5.2536     36.2503
30  1    4.9624     13.8636     36.2503
31  1    2.0924      2.3836     36.2503
32  1    2.0924     13.8636     36.2503
33  1   13.5724      5.2536     36.2503
34  1   13.5724     10.9936     36.2503
35  1    4.9624      2.3836     36.2503
36  1   10.7024     10.9936     36.2503
37  1    2.0924      5.2536     36.2503
38  1    7.8324     10.9936     36.2503
39  1    7.8324      2.3836     36.2503
40  1    4.9624     10.9936     36.2503
41  1    7.8324      5.2536     36.2503
42  1    2.0924     10.9936     36.2503
43  1   10.7024      2.3836     36.2503
44  1   13.5724      8.1236     36.2503
45  1    2.0924      8.1236     36.2503
46  1   10.7024      8.1236     36.2503
47  1   13.5724      2.3836     36.2503
48  1    7.8324      8.1236     36.2503
49  1    4.9624      8.1236     36.2503
50  1   13.5724     13.8636     36.2503
1   1   10.7024     13.8636     -2.7122
2   1   10.7024      5.2536     -2.7122
3   1    7.8324     13.8636     -2.7122
4   1    4.9624      5.2536     -2.7122
5   1    4.9624     13.8636     -2.7122
6   1    2.0924      2.3836     -2.7122
7   1    2.0924     13.8636     -2.7122
8   1   13.5724      5.2536     -2.7122
9   1   13.5724     10.9936     -2.7122
10  1    4.9624      2.3836     -2.7122
11  1   10.7024     10.9936     -2.7122
12  1    2.0924      5.2536     -2.7122
13  1    7.8324     10.9936     -2.7122
14  1    7.8324      2.3836     -2.7122
15  1    4.9624     10.9936     -2.7122
16  1    7.8324      5.2536     -2.7122
17  1    2.0924     10.9936     -2.7122
18  1   10.7024      2.3836     -2.7122
19  1   13.5724      8.1236     -2.7122
20  1    2.0924      8.1236     -2.7122
21  1   10.7024      8.1236     -2.7122
22  1   13.5724      2.3836     -2.7122
23  1    7.8324      8.1236     -2.7122
24  1    4.9624      8.1236     -2.7122
25  1   13.5724     13.8636     -2.7122
26  1    0.6574      6.6886     -4.1472
27  1    3.5274      6.6886     -4.1472
28  1    6.3974      6.6886     -4.1472
29  1    9.2674      6.6886     -4.1472
30  1   12.1374      6.6886     -4.1472
31  1    0.6574      9.5586     -4.1472
32  1   12.1374      9.5586     -4.1472
33  1    6.3974      9.5586     -4.1472
34  1    9.2674      9.5586     -4.1472
35  1    0.6574     12.4286     -4.1472
36  1    3.5274     12.4286     -4.1472
37  1    6.3974     12.4286     -4.1472
38  1   12.1374      3.8186     -4.1472
39  1    3.5274      9.5586     -4.1472
40  1    9.2674     12.4286     -4.1472
41  1    9.2674      3.8186     -4.1472
42  1    6.3974      3.8186     -4.1472
43  1   12.1374     12.4286     -4.1472
44  1    0.6574      0.9486     -4.1472
45  1    3.5274      0.9486     -4.1472
46  1    6.3974      0.9486     -4.1472
47  1   12.1374      0.9486     -4.1472
48  1    0.6574      3.8186     -4.1472
49  1    9.2674      0.9486     -4.1472
50  1    3.5274      3.8186     -4.1472
1   1   10.7024     13.8636     -5.5822
2   1   10.7024      5.2536     -5.5822
3   1    7.8324     13.8636     -5.5822
4   1    4.9624      5.2536     -5.5822
5   1    4.9624     13.8636     -5.5822
6   1    2.0924      2.3836     -5.5822
7   1    2.0924     13.8636     -5.5822
8   1   13.5724      5.2536     -5.5822
9   1   13.5724     10.9936     -5.5822
10  1    4.9624      2.3836     -5.5822
11  1   10.7024     10.9936     -5.5822
12  1    2.0924      5.2536     -5.5822
13  1    7.8324     10.9936     -5.5822
14  1    7.8324      2.3836     -5.5822
15  1    4.9624     10.9936     -5.5822
16  1    7.8324      5.2536     -5.5822
17  1    2.0924     10.9936     -5.5822
18  1   10.7024      2.3836     -5.5822
19  1   13.5724      8.1236     -5.5822
20  1    2.0924      8.1236     -5.5822
21  1   10.7024      8.1236     -5.5822
22  1   13.5724      2.3836     -5.5822
23  1    7.8324      8.1236     -5.5822
24  1    4.9624      8.1236     -5.5822
25  1   13.5724     13.8636     -5.5822
26  1    0.6574      6.6886     -7.0172
27  1    3.5274      6.6886     -7.0172
28  1    6.3974      6.6886     -7.0172
29  1    9.2674      6.6886     -7.0172
30  1   12.1374      6.6886     -7.0172
31  1    0.6574      9.5586     -7.0172
32  1   12.1374      9.5586     -7.0172
33  1    6.3974      9.5586     -7.0172
34  1    9.2674      9.5586     -7.0172
35  1    0.6574     12.4286     -7.0172
36  1    3.5274     12.4286     -7.0172
37  1    6.3974     12.4286     -7.0172
38  1   12.1374      3.8186     -7.0172
39  1    3.5274      9.5586     -7.0172
40  1    9.2674     12.4286     -7.0172
41  1    9.2674      3.8186     -7.0172
42  1    6.3974      3.8186     -7.0172
43  1   12.1374     12.4286     -7.0172
44  1    0.6574      0.9486     -7.0172
45  1    3.5274      0.9486     -7.0172
46  1    6.3974      0.9486     -7.0172
47  1   12.1374      0.9486     -7.0172
48  1    0.6574      3.8186     -7.0172
49  1    9.2674      0.9486     -7.0172
50  1    3.5274      3.8186     -7.0172

I would appreciate any help, thanks. The only thing I can think might be
the problem is that the spin populations are only for the leads in the
source and drain calculations, but for the whole structure (leads + device)
in the NEGF calculation. Do they need to be consistent? If I assign 300
unpaired electrons to the leads (100 atoms each), do I  specify 1224
unpaired electrons to the whole structure (408 in total)?

Best,
Wynand
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