Construction of the system for the NEGF transport calculation |
- Date: 2024/05/02 10:38
- Name: Kieran
<skn_neu@hotmail.co.uk>
- Dear All,
I followed the manual (https://www.openmx-square.org/openmx_man3.9/node127.html) to construct the system coordinate for the NEGF transport calculation. Since the manual says the transport direction is assumed to be a axis, I moved the z-axis coordinate for central scattering region, left and right leads to the x-axis (a-axis) position. I also shifted left and right leads by the length of the unit cell along the x axis (a-axis) so that OpenMX could connect all these three parts (central scattering region, left and right leads) together.
This is the coordinate setting for the left lead
LeftLeadAtoms.Number 30
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 O -10.228074251500001 1.4562538860000001 0.0000000000000000 2.0 4.0
2 O -3.7325744025000001 3.3027458190000001 0.0000000000000000 2.0 4.0
3 O -10.228074251500001 -0.72812694600000005 1.2611528640000000 2.0 4.0
4 O -3.7325744025000001 -1.6513729880000001 2.8602619169999999 2.0 4.0
5 O -10.228074251500001 1.6513729100000001 2.8602619169999999 2.0 4.0
6 O -3.7325744025000001 0.72812694300000003 1.2611528640000000 2.0 4.0
7 O -5.8977403035000000 3.8357539180000000 1.3738049269999999 2.0 4.0
8 O -12.393240868500001 0.92324614500000002 1.3738049269999999 2.0 4.0
9 O -5.8977403035000000 1.6513729100000001 2.6349580289999999 2.0 4.0
10 O -12.393240868500001 3.1076269150000000 0.11265206300000000 2.0 4.0
11 O -5.8977403035000000 1.6513730289999999 0.11265206300000000 2.0 4.0
12 O -12.393240868500001 3.1076269150000000 2.6349580289999999 2.0 4.0
13 O -1.5674075474999996 1.4562540049999999 2.7476098539999998 2.0 4.0
14 O -8.0629071584999998 -1.4562538860000001 2.7476098539999998 2.0 4.0
15 O -1.5674075474999996 -0.72812700299999999 4.0087628359999998 2.0 4.0
16 O -8.0629071584999998 0.72812688400000003 1.4864569900000000 2.0 4.0
17 O -1.5674075474999996 -0.72812700299999999 1.4864569900000000 2.0 4.0
18 O -8.0629071584999998 0.72812700299999999 4.0087628359999998 2.0 4.0
19 Al -8.9029921875000007 0.0000000000000000 0.0000000000000000 2.0 1.0
20 Al -5.0576562274999999 0.0000000000000000 0.0000000000000000 2.0 1.0
21 Al -11.553156196500000 0.0000000000000000 0.0000000000000000 2.0 1.0
22 Al -2.4074925775000002 0.0000000000000000 0.0000000000000000 2.0 1.0
23 Al -4.5726584785000002 2.3794999120000000 1.3738049269999999 2.0 1.0
24 Al 0.72732251750000043 2.3794999120000000 1.3738049269999999 - 2.0 1.0
25 Al -7.2228230824999997 2.3794999120000000 1.3738049269999999 2.0 1.0
26 Al -11.068159996500000 2.3794999120000000 1.3738049269999999 2.0 1.0
27 Al -13.233324616500001 0.0000000000000000 2.7476098539999998 2.0 1.0
28 Al -9.3879894605000000 0.0000000000000000 2.7476098539999998 2.0 1.0
29 Al -2.8924893724999992 0.0000000000000000 2.7476098539999998 2.0 1.0
30 Al -6.7378253335000000 0.0000000000000000 2.7476098539999998 2.0 1.0
LeftLeadAtoms.SpeciesAndCoordinates>
This is the coordinate setting for the central scattering region
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 76
<Atoms.SpeciesAndCoordinates
1 O 9.500650406 -0.728126943 1.261152864 2.0 4.0
2 O 5.170282841 -0.728150725 4.008776665 2.0 4.0
3 O 0.840215921 1.651396751 2.634944201 2.0 4.0
4 O 9.500650406 1.456253886 0.000000000 2.0 4.0
5 O 5.170282841 1.456230283 2.747623682 2.0 4.0
6 O 0.840215921 3.835777521 1.373791218 2.0 4.0
7 O 9.500650406 1.651372910 2.860261917 2.0 4.0
8 O 5.170282841 -0.728150785 1.486470580 2.0 4.0
9 O 0.840215921 1.651396751 0.112638265 2.0 4.0
10 O 3.005399466 -1.651372910 2.860261917 2.0 4.0
11 O 11.665833473 0.728103161 1.486470580 2.0 4.0
12 O 7.335466385 3.107650757 0.112638265 2.0 4.0
13 O 3.005399466 3.302745819 0.000000000 2.0 4.0
14 O 11.665833473 -1.456277847 2.747623682 2.0 4.0
15 O 7.335466385 0.923269808 1.373791218 2.0 4.0
16 O 3.005399466 0.728126943 1.261152864 2.0 4.0
17 O 11.665833473 0.728103399 4.008776665 2.0 4.0
18 O 7.335466385 3.107650518 2.634944201 2.0 4.0
19 O 20.011299133 1.456253886 0.000000000 2.0 4.0
20 O 24.341665268 3.835777521 1.373791218 2.0 4.0
21 O 28.672031403 1.456230283 2.747623682 2.0 4.0
22 O 20.011299133 -0.728126943 1.261152864 2.0 4.0
23 O 24.341665268 1.651396751 2.634944201 2.0 4.0
24 O 28.672031403 -0.728150725 4.008776665 2.0 4.0
25 O 20.011299133 1.651372910 2.860261917 2.0 4.0
26 O 24.341665268 1.651396751 0.112638265 2.0 4.0
27 O 28.672031403 -0.728150785 1.486470580 2.0 4.0
28 O 26.506849289 3.302745819 0.000000000 2.0 4.0
29 O 17.846115112 0.923269808 1.373791218 2.0 4.0
30 O 22.176481247 -1.456277847 2.747623682 2.0 4.0
31 O 26.506849289 -1.651372910 2.860261917 2.0 4.0
32 O 17.846115112 3.107650757 0.112638265 2.0 4.0
33 O 22.176481247 0.728103161 1.486470580 2.0 4.0
34 O 26.506849289 0.728126943 1.261152864 2.0 4.0
35 O 17.846115112 3.107650518 2.634944201 2.0 4.0
36 O 22.176481247 0.728103399 4.008776665 2.0 4.0
37 Al 8.175682068 0.000000000 0.000000000 2.0 1.0
38 Al 3.845315218 -0.000023842 2.747623682 2.0 1.0
39 Al 12.506049156 2.379523754 1.373791218 2.0 1.0
40 Al 10.825917244 0.000000000 0.000000000 2.0 1.0
41 Al 6.495550156 -0.000023842 2.747623682 2.0 1.0
42 Al 2.165183544 2.379523754 1.373791218 2.0 1.0
43 Al 4.330367088 0.000000000 0.000000000 2.0 1.0
44 Al 0.000000000 -0.000023842 2.747623682 2.0 1.0
45 Al 8.660734177 2.379523754 1.373791218 2.0 1.0
46 Al 1.680131912 0.000000000 0.000000000 2.0 1.0
47 Al 10.340865135 -0.000023842 2.747623682 2.0 1.0
48 Al 6.010499001 2.379523754 1.373791218 2.0 1.0
49 Al 21.336265564 0.000000000 0.000000000 2.0 1.0
50 Al 25.666633606 2.379523754 1.373791218 2.0 1.0
51 Al 17.005899429 -0.000023842 2.747623682 2.0 1.0
52 Al 18.686031342 0.000000000 0.000000000 2.0 1.0
53 Al 23.016397476 2.379523754 1.373791218 2.0 1.0
54 Al 27.346765518 -0.000023842 2.747623682 2.0 1.0
55 Al 25.181581497 0.000000000 0.000000000 2.0 1.0
56 Al 29.511947632 2.379523754 1.373791218 2.0 1.0
57 Al 20.851215363 -0.000023842 2.747623682 2.0 1.0
58 Al 27.831817627 0.000000000 0.000000000 2.0 1.0
59 Al 19.171083450 2.379523754 1.373791218 2.0 1.0
60 Al 23.501449585 -0.000023842 2.747623682 2.0 1.0
61 C 14.005899429 0.000000000 0.000000000 2.0 2.0
62 C 14.005899429 1.189726114 0.686916173 2.0 2.0
63 C 14.005899429 2.379499912 0.000000000 2.0 2.0
64 C 14.005899429 3.569226027 0.686916173 2.0 2.0
65 C 14.005899429 -1.189749956 2.060707331 2.0 2.0
66 C 14.005899429 -0.000023842 2.747623682 2.0 2.0
67 C 14.005899429 1.189749956 2.060707331 2.0 2.0
68 C 14.005899429 2.379476070 2.747623682 2.0 2.0
69 C 15.506048203 0.000000000 0.000000000 2.0 2.0
70 C 15.506048203 0.000023782 1.373791218 2.0 2.0
71 C 15.506048203 -1.189749956 2.060707331 2.0 2.0
72 C 15.506048203 -1.189726114 3.434498310 2.0 2.0
73 C 15.506048203 2.379499912 0.000000000 2.0 2.0
74 C 15.506048203 2.379523754 1.373791218 2.0 2.0
75 C 15.506048203 1.189749956 2.060707331 2.0 2.0
76 C 15.506048203 1.189773917 3.434498310 2.0 2.0
Atoms.SpeciesAndCoordinates>
This is the coordinates for the right lead.
# Lead-Right
RightLeadAtoms.Number 30
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 O 16.723574339499997 1.4562538860000001 0.0000000000000000 2.0 4.0
2 O 23.219074188499999 3.3027458190000001 0.0000000000000000 2.0 4.0
3 O 16.723574339499997 -0.72812694600000005 1.2611528640000000 2.0 4.0
4 O 23.219074188499999 -1.6513729880000001 2.8602619169999999 2.0 4.0
5 O 16.723574339499997 1.6513729100000001 2.8602619169999999 2.0 4.0
6 O 23.219074188499999 0.72812694300000003 1.2611528640000000 2.0 4.0
7 O 21.053908287500001 3.8357539180000000 1.3738049269999999 2.0 4.0
8 O 14.558407722500000 0.92324614500000002 1.3738049269999999 2.0 4.0
9 O 21.053908287500001 1.6513729100000001 2.6349580289999999 2.0 4.0
10 O 14.558407722500000 3.1076269150000000 0.11265206300000000 2.0 4.0
11 O 21.053908287500001 1.6513730289999999 0.11265206300000000 2.0 4.0
12 O 14.558407722500000 3.1076269150000000 2.6349580289999999 2.0 4.0
13 O 25.384241043499998 1.4562540049999999 2.7476098539999998 2.0 4.0
14 O 18.888741432499998 -1.4562538860000001 2.7476098539999998 2.0 4.0
15 O 25.384241043499998 -0.72812700299999999 4.0087628359999998 2.0 4.0
16 O 18.888741432499998 0.72812688400000003 1.4864569900000000 2.0 4.0
17 O 25.384241043499998 -0.72812700299999999 1.4864569900000000 2.0 4.0
18 O 18.888741432499998 0.72812700299999999 4.0087628359999998 2.0 4.0
19 Al 18.048656403499997 0.0000000000000000 0.0000000000000000 2.0 1.0
20 Al 21.893992363499997 0.0000000000000000 0.0000000000000000 2.0 1.0
21 Al 15.398492394500002 0.0000000000000000 0.0000000000000000 2.0 1.0
22 Al 24.544156013500000 0.0000000000000000 0.0000000000000000 2.0 1.0
23 Al 22.378990112499999 2.3794999120000000 1.3738049269999999 2.0 1.0
24 Al 26.224326073499999 2.3794999120000000 1.3738049269999999 2.0 1.0
25 Al 19.728825508499998 2.3794999120000000 1.3738049269999999 2.0 1.0
26 Al 15.883488594500001 2.3794999120000000 1.3738049269999999 2.0 1.0
27 Al 13.718323974500001 0.0000000000000000 2.7476098539999998 2.0 1.0
28 Al 17.563659130500000 0.0000000000000000 2.7476098539999998 2.0 1.0
29 Al 24.059159218500000 0.0000000000000000 2.7476098539999998 2.0 1.0
30 Al 20.213823257500000 0.0000000000000000 2.7476098539999998 2.0 1.0
RightLeadAtoms.SpeciesAndCoordinates>
After I launched the calculation, <seedname>.std file responded to me with the following error message.
The LEFT lead cannot be superposed on the original cell even after the translation.
Check your atomic coordinates of the LEFT lead.
Would anyone please tell what is wrong with my coordinate setting?
Thank you very much in advance.
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