Yambo Community Forum

Hi all:
I have some question about ypp results.
(1) After obtaining results of BSE from yambo I ploted the figure of absorption spectra. Then I try to use ypp to analyze it. I did ypp -e s and ypp -e a. I have file o.exc_I.sorted, o.exc_E.sorted, o.exc_weighs_at_1, and o.exc_amplitude_at-1. I found the location of maximum peak from yambo BSE results are different from the file o.exc_I.sorted. For example BSE results give maximum peak at 10 eV, however the first line in the o.exc_I.sorted is at 5 eV. Should I use o.exc_E.sorted to replot the spectra? I think two should have same maximum peak.
(2) About o.exc_weights_at_1 I do not clearly understand the parameters such as K ibz (equals 1), Symm (=1) Energy(0.33285). I think energy is in unit Ha. it is the energy difference between Band_V (valence band) and Band_C (conduct band). But from where we start to account the Band_V, from Femi level or from bottom of valence band?
(3) In the o.exc_amplitude_at_1 file what is the meaning of amplitude?
(4) In this forum I read the message that in order to plot the DOS for QP we should use GfnQPdb="E<./SAVE/db.QP". But this is only correct if yambo is compiled with netcdf. When we run yambo for GW+BSE we also need to use KfnQPdb="E<./SAVE/db.QP" . Does it work if compiled yambo without including netcdf?


Thanks

Zhifan Chen
Dept. of Physics
Clark Atlanta University
USA

Dear Zhifan Chen,

Something strange is happening to yout post processing, be sure that the absorption output you are looking
comes from the same BS matrix you are doing the post processing:

(1) After obtaining results of BSE from yambo I ploted the figure of absorption spectra. Then I try to use ypp to analyze it. I did ypp -e s and ypp -e a. I have file o.exc_I.sorted, o.exc_E.sorted, o.exc_weighs_at_1, and o.exc_amplitude_at-1. I found the location of maximum peak from yambo BSE results are different from the file o.exc_I.sorted. For example BSE results give maximum peak at 10 eV, however the first line in the o.exc_I.sorted is at 5 eV. Should I use o.exc_E.sorted to replot the spectra? I think two should have same maximum peak.

The two o.exc_E files do contains the same information, they are just differently sorted, one by increasing energy and the other by increasing intensity.
o.exc_E_sorted is in general useful to look if there are low energy excitations that you do not see in the absorption spectrum because they have zero or very small oscillator strengths. If you find a peak at 10eV that is stronger than one at 5 eV something strange is happening.

(2) About o.exc_weights_at_1 I do not clearly understand the parameters such as K ibz (equals 1), Symm (=1) Energy(0.33285). I think energy is in unit Ha. it is the energy difference between Band_V (valence band) and Band_C (conduct band). But from where we start to account the Band_V, from Femi level or from bottom of valence band?

Here you have the electron-hole pairs that contribute to your excitation: the excitation you have chosen from the input ypp.in: for example. This number are the exciton indexes that you find in the o.exc_E_sorted file. K,Symm, Energy are not parameter but for that excitation (index 1 in your case) you have the weights for each contributions (bigger than 5%), so you have the label of the k-point, the symm (as you sample in the Ibz and then the k points are expanded in the whole Bz by symmetries) the conduction and valence bands. Of course, if you have only the gamma point, the Kibz will be always one. Energy is the energy difference of that KS states in eV. I think you have a system with a small KS gap, and most probably you are not looking at the excitations at 5eV, you have to check the index of your excitations!! The zero is usually taken at the top of the valence bands, have a look at E0 in the report, anyway, as it is a difference this is not important.

(4) In this forum I read the message that in order to plot the DOS for QP we should use GfnQPdb="E<./SAVE/db.QP". But this is only correct if yambo is compiled with netcdf. When we run yambo for GW+BSE we also need to use KfnQP_E="E<./SAVE/db.QP" . Does it work if compiled yambo without including netcdf?

You can include the energy correction either by using a scissor (KfnQP_E) either by the QP database (KfnQPdb and not KfnQP_E) of a previous GW calculation. I think that in the svn version it should work also without netcdf (can someone confirm it?) anyway I strongly suggest you to install netcdf.
Anyway if the db has been read or not it is written in the report file of the BS calculation.

Bests,
Daniele

Dr. Daniele Varsano:
Thank you for your quick responce. I found different peaks between files o.eps_q1_haydock_bse, which from yambo BSE results and the file o.exc_E_sorted. Files o.exc_E_sorted and o.exc_I_sorted have the same maximum peak.
I still have question about the meaning of amplitude in the file o.exc_amplitude_at_1.

Thanks

Zhifan Chen
Dept of Physics
Clark Atlanta University
USA

Dear Zhifan,

the file file o.exc_amplitude_at_1 contains the amplitude of the contribution of the KS electron-hole pairs
referred to the index exciton 1. If you plot it and compare with the o.exc_weights_at_1 you will recognize
that you have poles in correspondence of the KS energy differences of the states that do contribute to that
excitation with their respective weights.

amplitue = \sum weight_i /(w-deltaE_i)**2+damping**2

About your discrepancies, I cannot say anything at this stage, please post
all yours o.exc* files together with the absorption output and the report of the bse calculations, and we will have a look at it.

Bests,

Daniele

Dr. Daniele Varsano :
Thank you very much for your time. I will check other systems to find any hint.

Zhifan Chen
Dept. of Physics
Clark Atlanta University
USA

Dear Yamboers,

A user has mentioned in this thread that apart from optical absorption spectra, JDOS (joint density of states) was also calculated. Therefore, can someone please paste the command for the run-level or the input parameter which I need to get JDOS data?

And can I also get PDOS plot from yambo ypp? I mean, how can I get the electronic states responsible for the transitions?


Thanks,

Dear Haseeb,
I suggest you to go through the tutorial step by step and play a bit by yourself with the code. Here you can find the tutorials of the last school:
http://www.yambo-code.org/wiki/index.php?title=ICTP2020
and in particular this for what concern exciton analysis:
http://www.yambo-code.org/wiki/index.ph ... e_excitons


1) There is no command needed for the JDOS as it is calculated and reported in the o.jdos* file together with absorption and eels (o.eps*, o.eels*).

2)

And can I also get PDOS plot from yambo ypp? I mean, how can I get the electronic states responsible for the transitions?

Electronic states responsible for the transitions is not related to the PDOS of the system.
In the same tutorial above it is explained how to look at the transition forming the excitations.

Best,
Daniele

Thank you dear Daniele , I am follwoing the Yambo tutorials and they are very helpful, my question is:

There is no command needed for the JDOS as it is calculated and reported in the o.jdos* file together with absorption and eels (o.eps*, o.eels*).

1: Shouldn't I get o.jdos in in the RPA and TDDFT absorption spectra? I am getting o.eps and o.eel files but not o.jdos!

Thank you dear Daniele , I am follwoing the Yambo tutorials and they are very helpful, my question is:

There is no command needed for the JDOS as it is calculated and reported in the o.jdos* file together with absorption and eels (o.eps*, o.eels*).

1: Shouldn't I get o.jdos in in the RPA and TDDFT absorption spectra also? I am getting o.eps and o.eel files but not o.jdos!

Thanks,

1: Shouldn't I get o.jdos in in the RPA and TDDFT absorption spectra also? I am getting o.eps and o.eel files but not o.jdos!

No, you have the o.jdos when performing calculations in transition space. You can also do RPA and TDDFT in transition space.
Best,
Daniele