fail to diagonalize matrix

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renren123123:
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!!!

Nordland:
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:
Alternative you can try inspecting the system in VNL Nanoscope to see if there is anything wrong with the geometry.

renren123123:
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:
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.

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