Use the examples of AuH2

[QinglangL]

In the examples of AuH2/L9.68/TSrun, I run the command $EigenChannels ECrun, and I get a error:

SiestaIO.ReadTSHS: Reading TSHS header from ./Chain.TSHS STOP Unsupported TSHS version file

So, what should I do to to solve this?

[tfrederiksen]

Which versions of Inelastica and TranSIESTA are you using?

[QinglangL]

Inelastica is 1.3.3, and transiesta is 4.1

[tfrederiksen]

This combination should work. But are you sure you are using Inelastica-1.3.3? I doubt it because the line with SiestaIO.ReadTSHS was modified to print io.siesta.ReadTSHS in v1.3.3. Please also check that the file Chain.TSHS exists and is not corrupt. In any case it could be helpful to see the full log files.

[QinglangL]

I am sure that. /Downloads/inelastica-1.3.3/Examples/AuH2/L9.68/TSrun and this is my address of inelastica. I try to open the Chain.TSHS, but it is empty. So I copy the Electrode.TSHS from the ELEC folder and rename it with Chain.TSHS. Then I try again the command $EigenChannels ECrun , it gives me an error:

SiestaIO.ReadXVFile: Reading ./Chain.XV SiestaIO.HS.init: Reading ././ELEC/Electrode.TSHS Found 4 atoms, (1620, 60) orbitals in super-, unit-cell SiestaIO.HS.init: Reading ././ELEC/Electrode.TSHS Found 4 atoms, (1620, 60) orbitals in super-, unit-cell SiestaIO.HS.init: Reading ./Chain.TSHS Found 4 atoms, (1620, 60) orbitals in super-, unit-cell GF: UseBulk= True Traceback (most recent call last): File "/home/qing/anaconda3/envs/inelastica/bin/EigenChannels", line 11, in Module.main(options) File "/home/qing/anaconda3/envs/inelastica/lib/python2.7/site-packages/Inelastica/EigenChannels.py", line 127, in main BufferAtoms=options.buffer) File "/home/qing/anaconda3/envs/inelastica/lib/python2.7/site-packages/Inelastica/NEGF.py", line 516, in init self.DeviceOrbs = [self.HS.lasto[DeviceAtoms[0]-1]+1, self.HS.lasto[DeviceAtoms[1]]] IndexError: index 8 is out of bounds for axis 0 with size 5

And I check the file, not find the index of 8. Now , what should I do ?

[tfrederiksen]

You can't replace Chain.TSHS by Electrode.TSHS - these are two different systems, which explains why you get the index error above. Did you try to rerun TranSIESTA? Make sure this calculation finishes correctly.

[QinglangL]

That' right, I know I should make transiesta, but when I try this in /TSrun,mpirun -np 1 transiesta < RUN.fdf > output.dat, it will point thatCould not find electrode: Left. In the same time, I have successfully compiled siesta in the /TSrun/ElEC with mpirun -np 1 siesta < RUN.fdf >output.dat and get Job completed.

[tfrederiksen]

OK, the issue is then your TranSIESTA calculation, not EigenChannels.

[bookkiy]

Hi,my name is Bookkiy .In the examples of CO/Cu(111), after running the command “STM -F 64 -L 87 -n 1 -x 5 -y 5 STM5x5”,I get the STMimage.nc file .But I have no idea how to draw the the STM image.The version of Inelastica is 3.0, and transiesta is siesta-MAX-1.2.1 So, how can I draw the STM image using the STMIimage.nc file? Thank you very much and looking forward to your replay.

[tfrederiksen]

Hi,my name is Bookkiy .In the examples of CO/Cu(111), after running the command “STM -F 64 -L 87 -n 1 -x 5 -y 5 STM5x5”,I get the STMimage.nc file .But I have no idea how to draw the the STM image.The version of Inelastica is 3.0, and transiesta is siesta-MAX-1.2.1 So, how can I draw the STM image using the STMIimage.nc file? Thank you very much and looking forward to your replay.

You can use Mathematica to draw the images, please have a look here: https://github.com/tfrederiksen/inelastica/tree/master/Examples/STMimage