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zerothi / sisl

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations
https://zerothi.github.io/sisl
Mozilla Public License 2.0
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How to output Green function of expanded molecule by transiesta+TBtrans+sisl? #344

Closed tomato151 closed 3 years ago

tomato151 commented 3 years ago

Siesta-Max-1.2.0 & sisl v0.10.0 We try to use the following codes to output the spectral function of the expanded molecule, but we are not sure whether this matrix is the spectral function (i.e. the image part of the Green function) or not? import sisl nc = sisl.get_sile('Cwire.TBT.nc') d = nc.Adensity_matrix(0,0) If not, how can we get it? Thanks!

zerothi commented 3 years ago

This is the spectral density matrix, please note the difference between the spectral matrix (G Gamma G^\dagger) and the density matrix Re[G Gamma G^\dagger * e^(i k r)].

the *density_matrix is the latter, hence it is only a real matrix. Since it is expanded in the full supercell the returned matrix has a [no, no * n_s] shape such that one can find the overlap density matrix elements coupling between supercells.

If you want the Green's function density matrix, use nc.density_matrix.

Please see the manual for the differences: https://zerothi.github.io/sisl/api/io/generated/sisl.io.tbtrans.tbtncSileTBtrans.html?highlight=adensity_matrix#sisl.io.tbtrans.tbtncSileTBtrans.Adensity_matrix

tomato151 commented 3 years ago

I've got it now! Thank you!