Hi, Den søn. 3. maj 2020 kl. 22.03 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>:
> Thank you for the compliment Nick, > I was seeking an answer from yourself on why does the k points change from > 100 to 1 in tbtrans. > The answer seems to be in the physics where the system is not being > periodic (semi periodic to be precise) therefore the kpoints from tbtrans > changes automatically to 1. But we use the 100 in the electrode calculation > and transiesta to find the Hamiltonian of both electrodes and scattering > region. Is that correct? > In the electrode calculation you do use a high number of k-points along the semiinfinite direction. Not in the scattering region. Please try and understand my question in 2. > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group > | School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > ------------------------------ > *From:* siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of > Nick Papior <nickpap...@gmail.com> > *Sent:* Saturday, 2 May 2020 7:07 PM > *To:* siesta-l <siesta-l@uam.es> > *Subject:* Re: [SIESTA-L] Still confused about K points in siesta, > transiesta and tbtrans in siesta 4.1b4 > > Hi, > > Great you have tried to fully understand this issue. > > Den man. 20. apr. 2020 kl. 22.01 skrev El-abed Haidar < > ehai2...@uni.sydney.edu.au>: > > Following up on that: In the manual it says that if we use* TBT kgrid > Monkhorst Pack (block):* > This means it would act as the same as * kgrid Monkhorst Pack*, however, > this is used to have a separate k-sampling in the tbtrans utility. If it > does not exist it will use kgrid Monkhorst Pack > But as i look into the output it seems to make it back to the default of 1 > 1 1. > Not sure why? > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group > | School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > ------------------------------ > *From:* El-abed Haidar > *Sent:* Friday, 17 April 2020 2:44 AM > *To:* siesta-l@uam.es <siesta-l@uam.es> > *Subject:* Still confused about K points in siesta, transiesta and > tbtrans in siesta 4.1b4 > > Good afternoon to whom it may concern, > i really want to understand the in depth behind the kpoints in electron > transport. I still feel after going through the siesta mail where I have > asked about it before in > https://www.mail-archive.com/siesta-l@uam.es/msg10916.html > <https://protect-au.mimecast.com/s/j_mvCP7LAXf9oqZ6UzLfZ4?domain=mail-archive.com> > leading > to https://www.mail-archive.com/siesta-l@uam.es/msg09386.html > <https://protect-au.mimecast.com/s/IzB8CQnMBZfg3m9RCPzoD8?domain=mail-archive.com> > . > However, the answers were not clear to be honest as i did not get the > complete understanding out of this. I went back and read more about > periodicity as suggested back here in > https://www.mail-archive.com/siesta-l@uam.es/msg08489.html > <https://protect-au.mimecast.com/s/VqxvCROND2uoR8QOSPmrq4?domain=mail-archive.com> > and as Cubot mentioned its not about periodicity that is usually defined in > solid states.* Any resources on k points for transport we can rely on or > tutorials? Because* > I am more confused on the k points when defined for electron transport > study. So im trying really and really would appreciate if there is a > tutorial in the future for the latest siesta version to how we use k points > BECAUSE > > So far i understand that we will go through 3 steps > 1-transiesta <electrod.fdf >electrode.out to calculate Hamiltonian and > overlap matrix of electrodes > 2-transiesta <scat.fdf >scattering.out to calculate density matrix of > scattering region ] > 3-tbtran <scat.fdf >.tbtrans.out to calculate current and transmission > When papers define the k points to be 1 1 100 along electron transport i > would assume we use in all siesta versions %block Monkhorst Pack and > through out the 3 steps i assume i am using 1 1 100 in my entire > calculation. *I found out recently that once siesta run is done in step > 2 and starts a transiesta run the k points change suddenly to 1 1 1. > WHY???? It was > mentioned https://answers.launchpad.net/siesta/+question/686603 > <https://protect-au.mimecast.com/s/-9yOCVARKgCm51XZiJdbmo?domain=answers.launchpad.net> > but > not enough explanation on the reason why. * > > I am not sure why especially that i want my study to be infinite along x > and y ( or lattice vector a and b) and finite in z ( or c vector). > *Now if I am suppose to add a block in each step above mentioned, what > should I do to make sure all 3 steps have 1 1 100? IF NOT AGAIN WHY?* > *I fully understand that i should do convergence tests for k points but i > need to know also if that is always the case. Because i read that 1 1 100 > is more than enough (based on literature and reading around the siesta > mail)* > > *Would anyone be able to give their in sight thoughts as detailed as > possible. Thank you* > > > I would suggest you to first conceptually figure out what the NEGF code > does. As per your 3 steps above > 1. transiesta elec.fdf > This calculates a _truly_ bulk electrode. Ask your selve this: > a) how do you approach the truly bulk charge density in a regular > calculation? Which parameter should be *tuned* to find the truly bulk > electrode? > b) You want the electrode to be added to a device region. In the device > calculation you have a particular direction of the electrodes that are > "semi-infinite". You want the two systems to be commensurate in terms of > calculation parameters. How does this relate to a)? What does this imply > for the semi-infinite direction, and for the transverse directions? > 2. transiesta scat.fdf > Here you calculate the device region where you place your _truly_ bulk > electrodes. What does the NEGF implementation state about electrodes? What > does an electrode mean in a device region system? And more importantly, if > you have 2 electrodes both with the same semi-infinite direction. What does > this mean for the k-point sampling along that direction? Why shouldn't it > matter whether you use any number of k-points? (once you figure > out/understand this it means you understand the NEGF concept ;) ) > 3. tbtrans scat.fdf > This calculates the spectroscopic quantities, such as DOS. > There is no conceptual difference from TBtrans and from a regular PDOS > calculation using Siesta. > E.g. if you use a k-point sampling [nx=3 ny=3 nz=3] in siesta, would that > be enough to get a good PDOS estimate? > If not, why? And how do you resolve this? > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group > | School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/ > <https://protect-au.mimecast.com/s/vnC5CWLVXkUZPvx4SmRk7M?domain=max-centre.eu/> > ) > > > > -- > Kind regards Nick > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
