Author Topic: fail to diagonalize matrix  (Read 6763 times)

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renren123123

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fail to diagonalize matrix
« on: December 23, 2008, 13:11 »
I faced  a problem such as the following :

I want to calculation MPSH of my model using ATK 2008.02 trail
, but it displays after running few minitues:

ATKError: solveSymmetricGeneralizedEigenProblem: Failed to

diagonalize matrix!

In the model , I used (8,8) as left electrode, and Au111(4*4)

as right electrode!  Can it calculate model of different twoprobe

system? I can use it calcute current and transmission coefficient.

Thank you very much!!!
« Last Edit: December 23, 2008, 13:13 by renren123123 »

Nordland

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Re: fail to diagonalize matrix
« Reply #1 on: December 24, 2008, 11:17 »
Usally this problem happens when two atoms are placed on top of one another. Perhaps if you post the script, I can try to see if I can see the error.

Nordland

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Re: fail to diagonalize matrix
« Reply #2 on: December 24, 2008, 12:39 »
Alternative you can try inspecting the system in VNL Nanoscope to see if there is anything wrong with the geometry.

renren123123

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Re: fail to diagonalize matrix
« Reply #3 on: December 25, 2008, 02:55 »
Thank you for your help! however, it remain. so I recently have another problem:

how to deal with the different electrodes?  as we known, we define electrode unit cell

from origin for example :

left_electrode_elements =[Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon]

right_electrode_elements =[Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold]

left_electrode_coordinates = [[ 20.59671,  15.00612,   1.93976],
[ 18.95344,  18.96174,   1.93976],
[ 14.99389,  20.59671,   1.93976],
[ 11.03827,  18.95344,   1.93976],
[  9.40328,  14.99389,   1.93976],
[ 11.04655,  11.03827,   1.93976],
[ 15.00612,   9.40328,   1.93976],
[ 18.96174,  11.04655,   1.93976],
[ 20.40761,  16.44389,   1.93976],
[ 17.80258,  19.84399,   1.93976],
[ 13.55612,  20.40761,   1.93976],
[ 10.15602,  17.80258,   1.93976],
[  9.59238,  13.55612,   1.93976],
[ 12.19743,  10.15602,   1.93976],
[ 16.44389,   9.59238,   1.93976],
[ 19.84399,  12.19743,   1.93976],
[ 20.16871,  17.14749,   3.17   ],
[ 17.13606,  20.1724 ,   3.17   ],
[ 12.85252,  20.16871,   3.17   ],
[  9.82761,  17.13606,   3.17   ],
[  9.8313 ,  12.85252,   3.17   ],
[ 12.86393,   9.82761,   3.17   ],
[ 17.14749,   9.8313 ,   3.17   ],
[ 20.1724 ,  12.86393,   3.17   ],
[ 19.44356,  18.40328,   3.17   ],
[ 15.73536,  20.54793,   3.17   ],
[ 11.59673,  19.44356,   3.17   ],
[  9.45206,  15.73536,   3.17   ],
[ 10.55644,  11.59673,   3.17   ],
[ 14.26464,   9.45206,   3.17   ],
[ 18.40328,  10.55644,   3.17   ],
[ 20.54793,  14.26464,   3.17   ]]*Angstrom

left_electrode_cell = [[ 30.0000000,  0.        ,  0.        ],
[ 0.        ,  30.0000000,  0.        ],
[ 0.        ,  0.        ,  2.46000000]]*Angstrom

right_electrode_cell = [[ 30.0000000,  0.        ,  0.        ],
[ 0.        ,  30.0000000,  0.         ],
[ 0.        ,  0.        ,  7.06373621 ]]*Angstrom

right_electrode_coordinates =  [ [ 10.66613,  15.66886,  41.29911],
[ 12.10911,  13.16954,  41.29911],
[ 13.5521 ,  10.67021,  41.29911],
[ 14.99509,   8.17089,  41.29911],
[ 12.10911,  18.16819,  41.29911],
[ 13.5521 ,  15.66886,  41.29911],
[ 14.99509,  13.16954,  41.29911],
[ 16.43807,  10.67021,  41.29911],
[ 13.5521 ,  20.66751,  41.29911],
[ 14.99509,  18.16819,  41.29911],
[ 16.43807,  15.66886,  41.29911],
[ 17.88106,  13.16954,  41.29911],
[ 14.99509,  23.16684,  41.29911],
[ 16.43807,  20.66751,  41.29911],
[ 17.88106,  18.16819,  41.29911],
[ 19.32404,  15.66886,  41.29911],
[ 10.66613,  17.33508,  43.6555 ],
[ 12.10911,  14.83575,  43.6555 ],
[ 13.5521 ,  12.33643,  43.6555 ],
[ 14.99509,   9.8371 ,  43.6555 ],
[ 12.10911,  19.8344 ,  43.6555 ],
[ 13.5521 ,  17.33508,  43.6555 ],
[ 14.99509,  14.83575,  43.6555 ],
[ 16.43807,  12.33643,  43.6555 ],
[ 13.5521 ,  22.33373,  43.6555 ],
[ 14.99509,  19.8344 ,  43.6555 ],
[ 16.43807,  17.33508,  43.6555 ],
[ 17.88106,  14.83575,  43.6555 ],
[ 14.99509,  24.83305,  43.6555 ],
[ 16.43807,  22.33373,  43.6555 ],
[ 17.88106,  19.8344 ,  43.6555 ],
[ 19.32404,  17.33508,  43.6555 ],
[  9.22314,  16.50197,  46.01188],
[ 10.66613,  14.00265,  46.01188],
[ 12.10911,  11.50332,  46.01188],
[ 13.5521 ,   9.004  ,  46.01188],
[ 10.66613,  19.00129,  46.01188],
[ 12.10911,  16.50197,  46.01188],
[ 13.5521 ,  14.00265,  46.01188],
[ 14.99509,  11.50332,  46.01188],
[ 12.10911,  21.50062,  46.01188],
[ 13.5521 ,  19.00129,  46.01188],
[ 14.99509,  16.50197,  46.01188],
[ 16.43807,  14.00265,  46.01188],
[ 13.5521 ,  23.99994,  46.01188],
[ 14.99509,  21.50062,  46.01188],
[ 16.43807,  19.00129,  46.01188],
[ 17.88106,  16.50197,  46.01188]]*Angstrom

# Set up electrodes
left_electrode_configuration = PeriodicAtomConfiguration(
left_electrode_cell,
left_electrode_elements,
left_electrode_coordinates
)

# Set up electrodes
right_electrode_configuration = PeriodicAtomConfiguration(
right_electrode_cell,
right_electrode_elements,
right_electrode_coordinates
)

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(left_electrode_configuration,right_electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[1,1],[1,1]],
equivalent_atoms=([-1,31],[-1,-1])
)

so a problem occurs i.e. left electrode unitcell and right one will superpose

Nordland

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Re: fail to diagonalize matrix
« Reply #4 on: December 25, 2008, 12:19 »
Looking at the electrode by themself, they look correct.

1) When does the error happen exactly ? In the electrode calculation, in the equvialent bulk calculation or twoprobe calculation?
Or is it first when you are trying to do the MPSH calculation the error happens?

2) If there is anything that could be wrong judging from the file, since I don't have the scattering region, it could be the equvialent atoms that are incorrect.
However if the systems looks correct in VNL, it is properly not the case, and must be something different.

renren123123

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Re: fail to diagonalize matrix
« Reply #5 on: December 26, 2008, 14:26 »
The error occurs in the MPSH calculation! Before this , I have calculated its current and transmission and DOS, it is not problem, however, for MPSH  I can not calculate which displays fail to diagonalize matrix!

renren123123

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Re: fail to diagonalize matrix
« Reply #6 on: December 26, 2008, 14:32 »
my scattering region sets such as:
# Scattering elements and coordinates
scattering_elements = [Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Hydrogen, Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Hydrogen, Hydrogen,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Hydrogen, Hydrogen, Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon,   Carbon,
Carbon,   Carbon,   Carbon, ......
Carbon,   Sulfur,   Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold,     Gold,     Gold,
Gold,     Gold]
scattering_coordinates = [[ 10.1542 ,  17.79887,   4.3963 ],
[  9.40356,  14.99802,   4.39632],
[ 14.99799,  20.59658,   4.39635],
[ 11.04127,  18.95645,   4.39636],
[  9.59362,  13.55203,   4.39637],
[ 17.79879,  19.84584,   4.39638],
[ 11.04375,  11.04132,   4.39639],
[ 13.55195,  20.40656,   4.3964 ],
[ 18.95638,  18.9587 ,   4.39641],
[ 15.00208,   9.40356,   4.39646],
[ 12.20131,  10.1542 ,   4.39647],
[ 20.59647,  15.00199,   4.39652],
[ 18.9587 ,  11.04374,   4.39653],
[ 20.40644,  16.44807,   4.39654],
[ 19.84583,  12.20137,   4.39659],
[ 16.44814,   9.59365,   4.3966 ],
[  9.46795,  15.73236,   5.62482],
[  9.84276,  17.13084,   5.62484],
[  9.84529,  12.85918,   5.62486],
[ 11.6053 ,  19.43097,   5.62488],
[ 12.85902,  20.15504,   5.6249 ],
[ 17.13071,  20.15741,   5.62492],
[ 10.56937,  11.60544,   5.62492],
[ 15.73221,  20.53224,   5.62494],
[ 19.43072,  18.39465,   5.62499],
[ 12.86939,   9.84269,   5.62509],
[ 20.15489,  17.14095,   5.62514],
[ 14.26797,   9.46789,   5.62521],
[ 17.14106,   9.84531,   5.62523],
[ 20.15735,  12.86945,   5.62529],
[ 18.3948 ,  10.56953,   5.6253 ],
[ 20.53209,  14.26799,   5.62533],
[  9.40915,  14.99163,   6.86067],
[  9.59719,  13.55967,   6.86068],
[ 11.04045,  18.94825,   6.86075],
[ 10.16229,  17.80168,   6.86075],
[ 14.99133,  20.59109,   6.86085],
[ 11.05213,  11.04068,   6.86085],
[ 17.8014 ,  19.83787,   6.86087],
[ 13.55931,  20.40312,   6.8609 ],
[ 18.94782,  18.95947,   6.86091],
[ 12.19861,  10.16228,   6.86105],
[ 15.00883,   9.40919,   6.86125],
[ 20.40293,  16.44084,   6.86127],
[ 18.95972,  11.05248,   6.86131],
[ 16.44093,   9.59733,   6.86138],
[ 20.59091,  15.00885,   6.86142],
[ 19.83805,  12.199  ,   6.86153],
[  9.44415,  15.73562,   8.09055],
[  9.82297,  12.85002,   8.09058],
[  9.8206 ,  17.13986,   8.09059],
[ 10.55004,  11.5911 ,   8.09059],
[ 17.13951,  20.17951,   8.09077],
[ 11.59054,  19.45001,   8.09078],
[ 12.8495 ,  20.17719,   8.09079],
[ 15.73513,  20.55607,   8.09089],
[ 19.44962,  18.40941,   8.09091],
[ 12.86047,   9.82088,   8.09112],
[ 20.17692,  17.15055,   8.09126],
[ 17.1509 ,   9.82364,   8.09133],
[ 14.26493,   9.44441,   8.09133],
[ 20.17991,  12.86103,   8.09153],
[ 18.40987,  10.55094,   8.09157],
[ 20.55623,  14.26541,   8.09177],
[  9.5806 ,  13.55325,   9.31832],
[  9.39175,  14.99388,   9.31837],
[ 11.02953,  18.96159,   9.31852],
[ 10.14594,  17.80824,   9.31856],
[ 17.80792,  19.85386,   9.31857],
[ 11.038  ,  11.03045,   9.31862],
[ 18.96138,  18.97041,   9.31865],
[ 14.99313,  20.60796,   9.31871],
[ 12.19168,  10.14702,   9.31878],
[ 13.55245,  20.41888,   9.31885],
[ 15.00707,   9.39315,   9.31927],
[ 18.97134,  11.03966,   9.31934],
[ 20.41896,  16.44803,   9.31948],
[ 16.448  ,   9.58234,   9.31953],
[ 20.60863,  15.00748,   9.31978],
[ 19.85486,  12.19323,   9.31989],
[ 10.54584,  11.59281,  10.5495 ],
[  9.82143,  12.84706,  10.54967],
[  9.8174 ,  17.13776,  10.54973],
[  9.44249,  15.73866,  10.54973],
[ 17.13719,  20.18168,  10.5499 ],
[ 12.846  ,  20.17644,  10.54999],
[ 15.73794,  20.55607,  10.55   ],
[ 19.45282,  18.4089 ,  10.55004],
[ 11.59156,  19.4523 ,  10.55009],
[ 12.86256,   9.82064,  10.55037],
[ 14.26213,   9.44648,  10.55044],
[ 17.15499,   9.82535,  10.55046],
[ 20.1773 ,  17.15477,  10.55081],
[ 18.40976,  10.54924,  10.5511 ],
[ 20.18344,  12.86445,  10.55131],
[ 20.55812,  14.26376,  10.55187],
[  9.57939,  13.55349,  11.78089],
[ 12.1916 ,  10.15055,  11.78093],
[ 17.808  ,  19.85401,  11.78101],
[ 11.0367 ,  11.03157,  11.78104],
[  9.3909 ,  14.99401,  11.78105],
[ 18.96238,  18.97185,  11.78115],
[ 11.02907,  18.9609 ,  11.78118],
[ 10.14515,  17.80798,  11.78123],
[ 14.99309,  20.60481,  11.78131],
[ 13.5526 ,  20.41597,  11.7815 ],
[ 15.00748,   9.40029,  11.78154],
[ 16.44812,   9.58745,  11.78196],
[ 18.97235,  11.04167,  11.78211],
[ 20.41927,  16.44991,  11.78293],
[ 19.85552,  12.19522,  11.78313],
[ 20.60875,  15.00928,  11.78335],
[ 14.84204,  14.79224,  12.33445],
[ 10.54797,  11.59227,  13.00886],
[ 17.13917,  20.17754,  13.00894],
[  9.82062,  12.85087,  13.00905],
[ 14.26605,   9.45897,  13.00906],
[ 15.73463,  20.55051,  13.00918],
[  9.81962,  17.13957,  13.00919],
[  9.44294,  15.73542,  13.00922],
[ 12.86145,   9.83091,  13.00924],
[ 19.45187,  18.41337,  13.00925],
[ 12.85002,  20.17231,  13.0093 ],
[ 11.59009,  19.44772,  13.00945],
[ 17.15103,   9.83171,  13.00953],
[ 20.17853,  17.15436,  13.01054],
[ 18.41132,  10.55596,  13.01054],
[ 20.17859,  12.8657 ,  13.01131],
[ 20.55454,  14.26986,  13.0125 ],
[ 14.84255,  14.8158 ,  13.52167],
[ 14.84264,  17.10607,  13.59541],
[ 14.83714,  12.5247 ,  13.70109],
[ 14.84385,  16.08874,  14.20981],
[ 15.00897,   9.4274 ,  14.23899],
[ 11.05001,  11.04391,  14.23914],
[ 18.95111,  18.9649 ,  14.23921],
[ 16.44042,   9.61055,  14.23921],
[ 17.80174,  19.83863,  14.23923],
[ 12.1996 ,  10.1708 ,  14.23925],
[ 14.99125,  20.58357,  14.23938],
[  9.40756,  14.99199,  14.23942],
[  9.59512,  13.56   ,  14.23945],
[ 13.55984,  20.39591,  14.23951],
[ 11.03965,  18.9468 ,  14.23953],
[ 10.16078,  17.80104,  14.23956],
[ 18.96011,  11.05883,  14.24096],
[ 20.40429,  16.44749,  14.24221],
[ 19.83622,  12.2072 ,  14.24239],
[ 20.58773,  15.01527,  14.24291],
[ 14.84089,  13.57302,  14.26428],
[ 14.26887,   9.48407,  15.47451],
[ 12.87064,   9.85339,  15.47472],
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[ 17.13606,  20.1724 ,  17.93   ],
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[  9.82761,  17.13606,  17.93   ],
[  9.8313 ,  12.85252,  17.93   ],
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...................
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[ 16.43808,  19.00129,  38.94272],
[ 16.43808,  14.00264,  38.94272],
[ 17.88106,  16.50197,  38.94272]]*Angstrom

Nordland

• QuantumATK Staff
• Supreme ATK Wizard
• Posts: 812
• Reputation: 18
Re: fail to diagonalize matrix
« Reply #7 on: December 26, 2008, 16:27 »
Hey!

I have looked a little into your system, but I haven't figured out the troubles yet. However I spotted a fatal error in your script.
The electrode cell of the nanotube must be repeated at least 3-4 times more or else you will get incorret transport results!
I have written in another post the reason and the way it is seen (Incorrect transport for short electrodes)