[Smeagol-discuss] Strange transmission
XIAOHONG ZHENG
exhzheng at gmail.com
Mon Apr 7 21:06:14 IST 2008
Dear Ivan,
Thank you for your suggestion. I insert 8 more atoms into the scattering
region on the two sides. The transmission is better now. But still there
are some problems. Especially, the density matrix does not converge. I
repeated the calculations with different DM.MixingWeight. Every time, it
did not converge and the transmission is different. The input file and
the converging information is pasted here while the transmission is sent
by an attachment. Could you have a look into it, please?
input file:
=================================================================
SystemName benzene
SystemLabel benzene
NumberOfAtoms 30
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 6 C
2 1 H
%endblock ChemicalSpeciesLabel
PAO.BasisSize SZP
PAO.EnergyShift 300 meV
LatticeConstant 1.0 Bohr
%block LatticeVectors
27.00 0.000 0.000
0.000 18.00 0.000
0.000 0.000 56.2535
%endblock LatticeVectors
MeshCutoff 40.0 Ry
MaxSCFIterations 80
DM.MixingWeight 0.1
DM.NumberPulay 1
DM.Tolerance 1.d-6
DM.UseSaveDM F
SolutionMethod diagon
ElectronicTemperature 25 meV
MD.TypeOfRun cg
MD.NumCGsteps 0
MD.MaxCGDispl 0.1 Ang
MD.MaxForceTol 0.04 eV/Ang
AtomicCoordinatesFormat Bohr
%block AtomicCoordinatesAndAtomicSpecies
13.5000000 9.00000 0.00000000 1
13.5000000 9.00000 2.28590470 1
13.5000000 9.00000 4.86715480 1
13.5000000 9.00000 7.15333470 1
13.5000000 9.00000 9.73604030 1
13.5000000 9.00000 12.02204100 1
13.5000000 9.00000 14.60290250 1
13.5000000 9.00000 16.88907190 1
13.5000000 9.00000 19.47000000 1
13.5000000 9.00000 21.75318770 1
13.5000000 9.00000 24.41991040 1
15.8180875 9.00000 26.18780090 1
17.5680899 9.00000 24.61085210 2
11.1817067 9.00000 25.68727470 1
9.4320393 9.00000 24.60998160 2
15.8183374 9.00000 28.31488420 1
17.5682682 9.00000 29.39133060 2
11.1829912 9.00000 28.31473760 1
9.4318671 9.00000 29.39117500 2
13.5000000 9.00000 29.58468970 1
13.5000000 9.00000 32.25399430 1
13.5000000 9.00000 34.53707160 1
13.5000000 9.00000 37.07856538 1
13.5000000 9.00000 39.36447008 1
13.5000000 9.00000 41.94572018 1
13.5000000 9.00000 44.23190008 1
13.5000000 9.00000 46.81460568 1
13.5000000 9.00000 49.10060638 1
13.5000000 9.00000 51.68146788 1
13.5000000 9.00000 53.96763728 1
%endblock AtomicCoordinatesAndAtomicSpecies
SaveElectrostaticPotential T
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 2 0.0
%endblock kgrid_Monkhorst_Pack
EMTransport T
InitTransport T
NEnergReal 1000
NEnergImCircle 400
NEnergImLine 100
NPoles 20
TrCoefficients T
UseLeadsGF F
HartreeLeadsLeft 0.000000000 Bohr
HartreeLeadsRight 17.60856538 Bohr
HartreeLeadsBottom -0.700000000000 Ry
VInitial 0.00 eV
VFinal 0.10 eV
NIVPoints 1
InitTransmRange -8.436770000 eV
FinalTransmRange -4.43677000 eV
NTransmPoints 400
The converging information:
DM.MixingWeight = 0.2
=================================================================
siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
siesta: 1 -4227.3725 -4005.3329 -4005.3329
1.5146 0.0000
timer: Routine,Calls,Time,% = IterSCF 1 308.300 99.56
siesta: 2 -7543.2057 -3514.6466 -3514.6466
6.4490 0.0000
siesta: 3 3198.2436 4465.6178 4465.6178
28.0857 0.0000
siesta: 4 -3983.1694 -3844.9989 -3844.9989
4.6522 0.0000
siesta: 5 -3825.0191 -3873.8132 -3873.8132
3.6673 0.0000
siesta: 6 -4064.7821 -3908.9941 -3908.9941
3.6093 0.0000
siesta: 7 -3886.5341 -3931.9508 -3931.9508
3.2275 0.0000
siesta: 8 -4062.9256 -3996.7554 -3996.7554
2.2184 0.0000
siesta: 9 -4012.2556 -4034.4161 -4034.4161
0.9899 0.0000
siesta: 10 -4059.0849 -4042.5946 -4042.5946
0.5201 0.0000
siesta: 11 -4026.0745 -4040.8760 -4040.8760
0.4970 0.0000
siesta: 12 -4059.4396 -4042.2673 -4042.2673
0.5150 0.0000
siesta: 13 -4025.4239 -4040.5512 -4040.5512
0.5106 0.0000
siesta: 14 -4059.5614 -4042.0593 -4042.0593
0.5198 0.0000
siesta: 15 -4025.1937 -4040.4159 -4040.4159
0.5165 0.0000
siesta: 16 -4059.6145 -4041.9762 -4041.9762
0.5213 0.0000
siesta: 17 -4025.0902 -4040.3560 -4040.3560
0.5196 0.0000
siesta: 18 -4059.6450 -4041.9412 -4041.9412
0.5220 0.0000
siesta: 19 -4025.0423 -4040.3308 -4040.3308
0.5211 0.0000
siesta: 20 -4059.6634 -4041.9272 -4041.9272
0.5223 0.0000
siesta: 21 -4025.0199 -4040.3207 -4040.3207
0.5220 0.0000
siesta: 22 -4059.6746 -4041.9221 -4041.9221
0.5225 0.0000
siesta: 23 -4025.0096 -4040.3172 -4040.3172
0.5224 0.0000
siesta: 24 -4059.6816 -4041.9207 -4041.9207
0.5226 0.0000
siesta: 25 -4025.0047 -4040.3163 -4040.3163
0.5226 0.0000
siesta: 26 -4059.6860 -4041.9206 -4041.9206
0.5227 0.0000
siesta: 27 -4025.0025 -4040.3164 -4040.3164
0.5227 0.0000
siesta: 28 -4059.6887 -4041.9210 -4041.9210
0.5228 0.0000
siesta: 29 -4025.0015 -4040.3168 -4040.3168
0.5228 0.0000
siesta: 30 -4059.6904 -4041.9213 -4041.9213
0.5228 0.0000
siesta: 31 -4025.0010 -4040.3171 -4040.3171
0.5228 0.0000
siesta: 32 -4059.6915 -4041.9217 -4041.9217
0.5228 0.0000
siesta: 33 -4025.0008 -4040.3174 -4040.3174
0.5229 0.0000
siesta: 34 -4059.6922 -4041.9220 -4041.9220
0.5228 0.0000
siesta: 35 -4025.0007 -4040.3176 -4040.3176
0.5229 0.0000
siesta: 36 -4059.6927 -4041.9222 -4041.9222
0.5229 0.0000
siesta: 37 -4025.0006 -4040.3178 -4040.3178
0.5229 0.0000
siesta: 38 -4059.6929 -4041.9223 -4041.9223
0.5229 0.0000
siesta: 39 -4025.0006 -4040.3179 -4040.3179
0.5229 0.0000
siesta: 40 -4059.6931 -4041.9224 -4041.9224
0.5229 0.0000
siesta: 41 -4025.0006 -4040.3180 -4040.3180
0.5229 0.0000
siesta: 42 -4059.6932 -4041.9224 -4041.9224
0.5229 0.0000
siesta: 43 -4025.0006 -4040.3180 -4040.3180
0.5229 0.0000
siesta: 44 -4059.6933 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 45 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 46 -4059.6933 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 47 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 48 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 49 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 50 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 51 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 52 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 53 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 54 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 55 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 56 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 57 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 58 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 59 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 60 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 61 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 62 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 63 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 64 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 65 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 66 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 67 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 68 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 69 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 70 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 71 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 72 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 73 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 74 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 75 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 76 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 77 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
siesta: 78 -4059.6934 -4041.9225 -4041.9225
0.5229 0.0000
siesta: 79 -4025.0006 -4040.3181 -4040.3181
0.5229 0.0000
DM.MixingWeight = 0.1
=================================================================
siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
siesta: 1 -4227.3725 -4005.3329 -4005.3329
1.5146 0.0000
timer: Routine,Calls,Time,% = IterSCF 1 280.810 99.65
siesta: 2 -7543.2057 -3514.6466 -3514.6466
6.4490 0.0000
siesta: 3 4477.0713 4465.6178 4465.6178
28.0857 0.0000
siesta: 4 1275.1669 1588.6792 1588.6792
23.1953 0.0000
siesta: 5 -2822.0117 -2284.4926 -2284.4926
13.0474 0.0000
siesta: 6 -3798.4137 -3837.4175 -3837.4175
4.2451 0.0000
siesta: 7 -4030.8252 -4040.7285 -4040.7285
0.6530 0.0000
siesta: 8 -4049.6215 -4045.2726 -4045.2726
0.4870 0.0000
siesta: 9 -4040.0791 -4045.0711 -4045.0711
0.3367 0.0000
siesta: 10 -4052.4265 -4046.0065 -4046.0065
0.3171 0.0000
siesta: 11 -4034.1083 -4043.1146 -4043.1146
0.3649 0.0000
siesta: 12 -4053.2498 -4045.2646 -4045.2646
0.3059 0.0000
siesta: 13 -4035.0265 -4043.2948 -4043.2948
0.3019 0.0000
siesta: 14 -4053.9650 -4044.9502 -4044.9502
0.2845 0.0000
siesta: 15 -4033.0496 -4042.4277 -4042.4277
0.3518 0.0000
siesta: 16 -4054.0878 -4044.5327 -4044.5327
0.3172 0.0000
siesta: 17 -4032.7967 -4042.2354 -4042.2354
0.3429 0.0000
siesta: 18 -4054.1963 -4044.3069 -4044.3069
0.3308 0.0000
siesta: 19 -4032.3546 -4041.9909 -4041.9909
0.3479 0.0000
siesta: 20 -4054.2428 -4044.1407 -4044.1407
0.3405 0.0000
siesta: 21 -4032.1060 -4041.8394 -4041.8394
0.3498 0.0000
siesta: 22 -4054.2643 -4044.0305 -4044.0305
0.3461 0.0000
siesta: 23 -4031.9408 -4041.7347 -4041.7347
0.3514 0.0000
siesta: 24 -4054.2734 -4043.9569 -4043.9569
0.3494 0.0000
siesta: 25 -4031.8317 -4041.6629 -4041.6629
0.3526 0.0000
siesta: 26 -4054.2771 -4043.9077 -4043.9077
0.3513 0.0000
siesta: 27 -4031.7590 -4041.6139 -4041.6139
0.3534 0.0000
......
siesta: 54 -4054.2912 -4043.8096 -4043.8096
0.3552 0.0000
siesta: 55 -4031.6024 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 56 -4054.2917 -4043.8096 -4043.8096
0.3552 0.0000
siesta: 57 -4031.6021 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 58 -4054.2921 -4043.8097 -4043.8097
0.3552 0.0000
siesta: 59 -4031.6019 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 60 -4054.2924 -4043.8098 -4043.8098
0.3553 0.0000
siesta: 61 -4031.6017 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 62 -4054.2927 -4043.8098 -4043.8098
0.3553 0.0000
siesta: 63 -4031.6015 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 64 -4054.2929 -4043.8099 -4043.8099
0.3553 0.0000
siesta: 65 -4031.6014 -4041.5101 -4041.5101
0.3553 0.0000
siesta: 66 -4054.2931 -4043.8099 -4043.8099
0.3553 0.0000
siesta: 67 -4031.6013 -4041.5102 -4041.5102
0.3553 0.0000
siesta: 68 -4054.2932 -4043.8100 -4043.8100
0.3553 0.0000
siesta: 69 -4031.6013 -4041.5102 -4041.5102
0.3553 0.0000
siesta: 70 -4054.2933 -4043.8100 -4043.8100
0.3553 0.0000
siesta: 71 -4031.6013 -4041.5102 -4041.5102
0.3553 0.0000
siesta: 72 -4054.2935 -4043.8101 -4043.8101
0.3553 0.0000
siesta: 73 -4031.6013 -4041.5103 -4041.5103
0.3553 0.0000
siesta: 74 -4054.2935 -4043.8101 -4043.8101
0.3553 0.0000
siesta: 75 -4031.6012 -4041.5103 -4041.5103
0.3553 0.0000
siesta: 76 -4054.2936 -4043.8102 -4043.8102
0.3553 0.0000
siesta: 77 -4031.6012 -4041.5103 -4041.5103
0.3553 0.0000
siesta: 78 -4054.2937 -4043.8102 -4043.8102
0.3553 0.0000
siesta: 79 -4031.6012 -4041.5103 -4041.5103
0.3553 0.0000
DM.MixingWeight = 0.01
=================================================================
siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
siesta: 1 -4227.3725 -4005.3329 -4005.3329
1.5146 0.0000
timer: Routine,Calls,Time,% = IterSCF 1 309.150 99.56
siesta: 2 -7543.2057 -3514.6466 -3514.6466
6.4490 0.0000
siesta: 3 4477.0060 4465.6178 4465.6178
28.0857 0.0000
siesta: 4 4373.2234 4360.1435 4360.1435
27.7535 0.0000
siesta: 5 4245.4590 4230.5163 4230.5163
27.4107 0.0000
siesta: 6 4087.7708 4070.9341 4070.9341
27.0528 0.0000
siesta: 7 3893.9234 3875.4444 3875.4444
26.6747 0.0000
siesta: 8 3659.0988 3639.6043 3639.6043
26.2707 0.0000
siesta: 9 3385.2005 3362.7484 3362.7484
25.8360 0.0000
siesta: 10 3047.8454 3025.5322 3025.5322
25.3582 0.0000
siesta: 11 2658.7850 2644.9828 2644.9828
24.8195 0.0000
siesta: 12 2325.7499 2317.3861 2317.3861
24.3060 0.0000
siesta: 13 2034.9402 2031.7042 2031.7042
23.8099 0.0000
siesta: 14 1804.8305 1805.3256 1805.3256
23.3543 0.0000
siesta: 15 1775.6551 1639.1566 1639.1566
22.9507 0.0000
siesta: 16 5814.0229 5690.6438 5690.6438
28.9349 0.0000
siesta: 17 8619.8755 8832.8441 8832.8441
30.6452 0.0000
siesta: 18 4591.3050 4835.5268 4835.5268
25.7401 0.0000
siesta: 19 1682.5619 1749.5589 1749.5589
22.2170 0.0000
siesta: 20 1135.6760 1191.9123 1191.9123
21.3383 0.0000
siesta: 21 188.2386 235.4582 235.4582
19.9248 0.0000
siesta: 22 -762.1576 -734.4629 -734.4629
17.5510 0.0000
siesta: 23 -1250.9626 -1211.6215 -1211.6215
16.2802 0.0000
siesta: 24 -1979.4178 -1955.8973 -1955.8973
14.1220 0.0000
siesta: 25 -2362.1518 -2311.4056 -2311.4056
12.8877 0.0000
siesta: 26 -3134.0363 -3098.0941 -3098.0941
9.6859 0.0000
siesta: 27 -3521.5369 -3489.0820 -3489.0820
7.8640 0.0000
siesta: 28 -3776.3337 -3773.0503 -3773.0503
5.7232 0.0000
siesta: 29 -3801.3239 -3798.2185 -3798.2185
5.4582 0.0000
siesta: 30 -3832.8755 -3822.4495 -3822.4495
5.1865 0.0000
siesta: 31 -3911.1420 -3892.5369 -3892.5369
4.3499 0.0000
siesta: 32 -3994.7434 -3990.1925 -3990.1925
2.4226 0.0000
siesta: 33 -4012.8782 -4006.4445 -4006.4445
2.0267 0.0000
siesta: 34 -4023.4144 -4022.6821 -4022.6821
1.5621 0.0000
siesta: 35 -4025.7546 -4025.1959 -4025.1959
1.4763 0.0000
siesta: 36 -4027.7782 -4027.2589 -4027.2589
1.4167 0.0000
......
siesta: 132 -4044.9191 -4044.9423 -4044.9423
0.0990 0.0000
siesta: 133 -4044.9040 -4044.9267 -4044.9267
0.0972 0.0000
siesta: 134 -4044.8892 -4044.9113 -4044.9113
0.0955 0.0000
siesta: 135 -4044.8744 -4044.8961 -4044.8961
0.0938 0.0000
siesta: 136 -4044.8600 -4044.8812 -4044.8812
0.0921 0.0000
siesta: 137 -4044.8457 -4044.8665 -4044.8665
0.0905 0.0000
siesta: 138 -4044.8316 -4044.8519 -4044.8519
0.0889 0.0000
siesta: 139 -4044.8178 -4044.8376 -4044.8376
0.0873 0.0000
siesta: 140 -4044.8042 -4044.8236 -4044.8236
0.0858 0.0000
siesta: 141 -4044.7907 -4044.8097 -4044.8097
0.0843 0.0000
siesta: 142 -4044.7775 -4044.7961 -4044.7961
0.0828 0.0000
siesta: 143 -4044.7643 -4044.7825 -4044.7825
0.0813 0.0000
siesta: 144 -4044.7515 -4044.7692 -4044.7692
0.0799 0.0000
siesta: 145 -4044.7388 -4044.7562 -4044.7562
0.0785 0.0000
siesta: 146 -4044.7263 -4044.7433 -4044.7433
0.0771 0.0000
siesta: 147 -4044.7140 -4044.7306 -4044.7306
0.0758 0.0000
siesta: 148 -4044.7019 -4044.7182 -4044.7182
0.0745 0.0000
siesta: 149 -4044.6899 -4044.7059 -4044.7059
0.0732 0.0000
siesta: 150 -4044.6782 -4044.6938 -4044.6938
0.0719 0.0000
siesta: 151 -4044.6666 -4044.6819 -4044.6819
0.0706 0.0000
siesta: 152 -4044.6552 -4044.6701 -4044.6701
0.0694 0.0000
siesta: 153 -4044.6439 -4044.6586 -4044.6586
0.0682 0.0000
siesta: 154 -4044.6328 -4044.6472 -4044.6472
0.0670 0.0000
siesta: 155 -4044.6219 -4044.6360 -4044.6360
0.0659 0.0000
siesta: 156 -4044.6112 -4044.6250 -4044.6250
0.0647 0.0000
siesta: 157 -4044.6006 -4044.6141 -4044.6141
0.0636 0.0000
siesta: 158 -4044.5902 -4044.6035 -4044.6035
0.0625 0.0000
siesta: 159 -4044.5801 -4044.5930 -4044.5930
0.0614 0.0000
We can see that for DM.MixingWeight = 0.2 or 0.1, dDmax does not go to
the DM.Tolerance, but stays at a fixed value, not decreasing, not
increasing. If I use 0.01, then it decrease very slowly. However, if we
set "EMTransport F" and do a general siesta calculation, it converges
very well and very fast. Do you know why, please?
Sincerely,
Xiaohong
Ivan Rungger wrote:
> Dear Xiaonhong,
>
> I went through your input file, there is a problem in the atomic
> coordinates. In smeagol you need one slice of leads on each side of the
> scattering region, you only add 4 c atoms on each end, but you have to
> add at least 8.
>
> Cheers,
>
> Ivan
>
>
> XIAOHONG ZHENG wrote:
>
>> Hello, Dear All,
>>
>> I am trying a simple system to get familiar with Smeagol. This system is
>> a benzene molecule connected to a carbon atomic chain. I compared the
>> result of smeagol with that of TranSIESTAC.
>>
>> The transmission for the lead ( an infinite lead) is perfect except for
>> a small shift of the Fermi energy. Both of these two methods give the
>> same results. However, the transmission for the chain/benzene/chain
>> system is totally different. I know the result of the TranSIESTAC is
>> right since I use another method and also I get this figure. I think
>> there must be some mistakes in my input file for the scattering region.
>> I checked for several times but I cannot find where is the mistake. I
>> have attached the input files and the figures to this email. Could you
>> help me to have a look into it and show me what's wrong in it, please?
>>
>> Thank you very much!
>>
>> Sincerely,
>> Xiaohong
>>
>>
>
>
>
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