Closed KitchenSong closed 6 years ago
It can be done by following the example in the documentation (just added).
So for instance if you already have a device.TBT.nc
one may do the following which adds $1 \mathrm{eV}$ on the diagonal terms for all orbitals on atoms 10, 11, 12 and 13:
import numpy as np
import sisl
# The important thing is that we should know the number of orbitals per atom
geom = sisl.get_sile('device.TBT.nc').read_geometry()
dH = sisl.Hamiltonian(geom, dtype=np.complex128)
orb_diag = geom.a2o(range(10, 14), all=True)
for o in orb_diag:
dH[o, o] = 1.j
sisl.get_sile('delta.dH.nc', 'w').write_delta(dH)
Let me know if you have other inquiries.
I test it and think it is working. This code explains a lot. Thank you.
Great, will mark as resolved.
Sorry for not doing the test carefully. I do get the delta.dH.nc fil. However, when redoing the tbtrans calculation, I get
tbtrans: Using buffer atoms with dH method. tbtrans: Ensure no buffer orbitals used in dH!
and
Error occured in NCDF: NetCDF: Invalid argument Status number: -36 ncdf: Stopped due to error in NetCDF file ncdf-Node 0
I checked the atom index and I thought it should not be in the buffer atom list. Just wondering what leads to this problem.
It most definitely is in the buffer list.
Remember, when you do programming in Python it is 0-based indexing, while in the input it is 1-based.
However, note that in future versions of tbtrans, this check has been removed because it is not important. However, it should still run.
Hmm, I do check the atom and orbital index carefully... Even I only assign delta to only an atom and looped the index of this atom, the same error exists. I notice the file delta.dH.nc is not large, can I print all the file contents to see if anything is going wrong?
The error message posted:
`Error occured in NCDF: Retrieving information about: RedH in file: delta.dH.nc
Error occured in NCDF: Retrieving information about: RedH in file: delta.dH.nc
Error occured in NCDF: NetCDF: Variable not found Status number: -49 NetCDF: Variable not found Status number: -49 NetCDF: Variable not found Status number: -49 ncdf: Stopped due to error in NetCDF file ncdf-Node 8 ncdf: Stopped due to error in NetCDF file ncdf-Node 2`
Ah, yes.
This is my mistake.
I would suggest you to download the latest commit for siesta-4.1 and use the TBtrans in that version.
https://bazaar.launchpad.net/~siesta-maint/siesta/rel-4.1/tarball/846
The reason is that I found out that the $\delta H$ term should have been expressed in two separate terms: $\delta H$ and $\delta \Sigma$. The first contributes to bond-currents, while the last term does not. This is a necessity and is enabled in the coming 4.1-b4 release. As for sisl, I quickly adopted this convention, hence the variable name change.
So, please download the latest 4.1 commit and use that.
I used 4.1-b3. Will have a try on the new version.
Exactly. ;)
That version you mentioned works properly.
In this paper (Computer Physics Communications, 212, pp.8-24), there is a section regarding adding a correction term $\delta H$ in the Hamiltonian. In practice, I guess that you can generate a 'delta.nc' file and add tag 'TBT.dH delta.nc' in the input file for tbtrans.
Meanwhile, I realize this python code is capable of adding $delta H$ or $delta \Sigma$ term as well, which is nice. I assume this can be realized by defining class
sisl.io.tbtrans.deltancSileTBtransare
.My question is given that I have a 'device.TBT.nc' file from a standard tbtrans calculation, how to properly generate this delta H/Sigma class, say e.g. a k-dependent E-dependent delta Sigma, such that I can further calculate the transmission based on the modified Hamiltonian. Or do I have to re-run the tbtrans code to get the transport properties of interest based on the modified Hamiltonian?