Re: [SIESTA-L] << two different values for charge same output >>

Dear Camps, did you read this article? https://www.cup.uni-muenchen.de/oc/zipse/site/assets/files/1130/zipse_2005_97.pdf Sincerely. I. Camps , 5 Eyl 2019 Per, 23:00 tarihinde şunu yazdı: > Thank you Nick for your help. > > []'s > > Camps > > Em qua, 4 de set de 2019 17:00, Nick Papior > escrev

Re: [SIESTA-L] << two different values for charge same output >>

Thank you Nick for your help. []'s Camps Em qua, 4 de set de 2019 17:00, Nick Papior escreveu: > Ok, I see the mistake now. > > It is because you calculate the LDOS. The first value is the correct > value, the second value corresponds to the V/H charges for the LDOS charge, > so not really use

Re: [SIESTA-L] << two different values for charge same output >>

Ok, I see the mistake now. It is because you calculate the LDOS. The first value is the correct value, the second value corresponds to the V/H charges for the LDOS charge, so not really useful here. :) I have submitted a patch for this! Thanks! Den tir. 3. sep. 2019 kl. 22.01 skrev I. Camps :

Re: [SIESTA-L] << two different values for charge same output >>

Could you share your input fdf? And also which version of siesta you are using? Den søn. 1. sep. 2019 kl. 22.01 skrev I. Camps : > Hello SIESTers, > > I am trying to analyze the charge transfer when a metal is absorbed on a > surface. In order to do that, I calculated the charges using different

Re: [SIESTA-L] << two different values for charge same output >>

Dear Camps, The issue is not one of software related problems.Each methods have different poulation schemes. https://www.ncbi.nlm.nih.gov/pubmed/14648618 http://www.demon-software.com/public_html/support/htmlug/ug-node105.html Sincerely, Berna Uyanık I. Camps , 1 Eyl 2019 Paz, 23:00 tarihinde şu

Re: [SIESTA-L] Relaxation of borophene nanoribbon

I had a similar problem with convergence for other system using boron. The solution I found was to disable the Pulay mixing, maybe this work for you too. []'s, Camps On Wed, Aug 14, 2019 at 5:01 PM Najmeh Honari wrote: > > > Dear Siesta Users > I am trying to relax 8-pmmn borophene nanoribb

Re: [SIESTA-L] << Spin polarization output >>

I will recalculate everything again :) The polarization of my system is not total as shown. []'s, Camps On Sat, Aug 10, 2019 at 5:01 PM Nick Papior wrote: > Well, you could read in the DM and overlap matrix in sisl and manually > calculate the spin-polarization. > > Otherwise you have to rec

Re: [SIESTA-L] << Spin polarization output >>

Well, you could read in the DM and overlap matrix in sisl and manually calculate the spin-polarization. Otherwise you have to recalculate with this option XML.Write. But why don't just use: *spin moment: S , {S} =2.0 0.0 0.0 2.0* ? Den fre. 9. aug. 2019 kl. 22.01 skrev I. Cam

Re: [SIESTA-L] << Spin polarization output >>

Thanks Nick. Unfortunately, the only xml output that I have is related to the ion files :(. Should I have to re-calculate? []'s, Camps On Thu, Aug 8, 2019 at 5:00 PM Nick Papior wrote: > If you also store the xml output you can get the spin polarization > information there, key=siesta:stot

Re: [SIESTA-L] << Spin polarization output >>

If you also store the xml output you can get the spin polarization information there, key=siesta:stot and key=siesta:svec (only for non-colinear). Den tir. 6. aug. 2019 kl. 22.00 skrev I. Camps : > Dear SIESTers, > > In previous versions of SIESTA (aka 3.1), when running a spin polarized > calcul

Re: [SIESTA-L] With or without gold in the scattering region

No, you probably cannot do this since you need a "screening" layer which ensures the electrode has the electronic structure of a bulk part. Den man. 8. jul. 2019 kl. 22.04 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Good afternoon all. > I was wondering if I calculate a system made of

Re: [SIESTA-L] pseudopotential

Hello, Did you compile the ATOM program? (https://departments.icmab.es/leem/siesta/Pseudopotentials/index.html) []'s, Camps On Wed, Jul 10, 2019 at 5:05 PM batoul wrote: > Dear all > > I'm trying to generate the pseudopotential but i have this problem .how > can i fix it > > > > ../../Utils

Re: [SIESTA-L] Non-orthogonal Electrodes

Hello There Seyed, Based on the fdf files you have sent the error is expected because the electrodes you have defined are also repeated into the scattering region. In my opinion i would have made sure first that the system is in z increasing order and then create 2 electrode folders in which you

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

: Wednesday, 3 July 2019 6:05 AM To: siesta-l Subject: Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans Den tir. 2. jul. 2019 kl. 22.01 skrev El-abed Haidar mailto:ehai2...@uni.sydney.edu.au>>: THank you again for the reply Nick I wanted to ask you then if PDOS siesta vs PDOS Tbtra

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

> > -- > *From:* siesta-l-requ...@uam.es on behalf of > Nick Papior > *Sent:* Monday, 24 June 2019 8:23 PM > *To:* siesta-l > *Subject:* Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans > > In general, > > A 0 bias calculation

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

| 2006 From: siesta-l-requ...@uam.es on behalf of Nick Papior Sent: Monday, 24 June 2019 8:23 PM To: siesta-l Subject: Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans In general, A 0 bias calculation should yield a somewhat equivalent PDOS in siesta vs

Re: [SIESTA-L] Difference of K point for ribbons and layer in .TBtrans

Hi, Den ons. 26. jun. 2019 kl. 22.02 skrev Fazle Subhan : > Dear Dr. Nick > > Previously I work on some nanoribbons for calculating the I-V curve where > I simply use k-points along the z-direction. Therefore in the P.TRANS file > I get only one k point (means is it due to the one dimension case?

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

; -- > *From:* siesta-l-requ...@uam.es on behalf of > Nick Papior > *Sent:* Monday, 24 June 2019 8:23 PM > *To:* siesta-l > *Subject:* Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans > > In general, > > A 0 bias calculation should yi

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: siesta-l-requ...@uam.es on behalf of Nick Papior Sent: Monday, 24 June 2019 8:23 PM To: siesta-l Subject: Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans In

Re: [SIESTA-L] pDOS spin up vs spin down in tbrans

Den fre. 21. jun. 2019 kl. 22.02 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Good evening, > I was wondering for the spin PDOS extracted from Tbtrans, should I > multiply the values obtained by -1 > No! > because I have noticed PDOS spin down calculated via TBTRANs for many > different

Re: [SIESTA-L] Thoughts on PDOS siesta vs PDOS tbtrans

In general, A 0 bias calculation should yield a somewhat equivalent PDOS in siesta vs. tbtrans. If this is the case it means that you have set up your system in a sufficient manner. This is to say that the electrodes already screen off the junction sufficiently (please spend some time on why this

Re: [SIESTA-L] segmentation fault

thank you for your suggestion ,it was due to limited stack size and I have added this line to the sbatch file and the error solved ulimit -s unlimited ‫في الاثنين، 17 يونيو 2019 في 10:00 م تمت كتابة ما يلي بواسطة ‪El-abed Haidar‬‏ <‪ehai2...@uni.sydney.edu.au‬‏>:‬ > Hey doaa > Can you send

Re: [SIESTA-L] segmentation fault

Hey doaa Can you send us the bash file in which you sent this siesta job? It could be that you have to Just increase the amount of memory given But I could be wrong. Looking forward to your reply El abed Sent from my iPhone > On 17 Jun 2019, at 6:00 am, doaa haleem wrote: > > Dears > > how co

Re: [SIESTA-L] Ionization potential and electron affinities

Dear Peter, thank you for your reply! Best regards, Koussai LAZAAR ᐧ

Re:[SIESTA-L]

Thank you for your reply! Best regards, Koussai LAZAAR ᐧ

Re: [SIESTA-L] compiling the PSML-compatible version

Thanks Alberto, that was it. I had a typo in my arch.make and wasn't passing the flags correctly, thanks for pointing me in the right direction! Pablo On Sat, Jun 8, 2019 at 9:01 PM Alberto Garcia wrote: > Hi, > > The code in siesta_init is: > > #ifdef MPI > call gridxc_init(comm=MPI_Comm

Re: [SIESTA-L] compiling the PSML-compatible version

Hi, The code in siesta_init is: #ifdef MPI call gridxc_init(comm=MPI_Comm_World, $ time_mpi_calls=fdf_get('gridxc-time-mpi-calls',.false.)) #else call gridxc_init() #endif Thus, you seem not to have used the -DMPI compilation flag, while you are using an MPI-enabled version

Re: [SIESTA-L] Siesta error, regarding

On Fri, Jun 7, 2019 at 1:32 AM sullah wrote: > Dear Rahul, > > Why did you send .out of another system? Please check once again your .fdf > and .out files are for different systems. How can someone suggest anything > without looking at the error (problem)? > I am really sorry, I didn't notice th

Re: [SIESTA-L] Siesta error, regarding

Thank you Mr Camps. I will work on it. Thank you On Fri, Jun 7, 2019 at 1:30 AM I. Camps wrote: > Hello Rahul, > > The error you are having is because SIESTA is not finding the > corresponding pseudopotentials files. > > This consist in two steps: > - You need to insert in your input the info

Re: [SIESTA-L] Siesta error, regarding

Dear Rahul, Why did you send .out of another system? Please check once again your .fdf and .out files are for different systems. How can someone suggest anything without looking at the error (problem)? I believe (which I'm not sure, just a shot in the dark) you are getting ghost states? If yes,

Re: [SIESTA-L] Siesta error, regarding

Hello Rahul, The error you are having is because SIESTA is not finding the corresponding pseudopotentials files. This consist in two steps: - You need to insert in your input the information about the pseudopotentials you want to use. - You need to put the corresponding files (psf extension) toge

Re: [SIESTA-L] Siesta error, regarding

Hi I got your second comment. Is there any visualizer which could generate the coordiantes in the format for siesta code? About your first comment, I havent mentioned C.hsc anywhere in my fdf file. I have one more querry, I want ot run this simulation with GGA-PBE functional and PAW method for

Re: [SIESTA-L] Ionization potential and electron affinities

Dear Koussai, You could you Delta SCF approach. SIESTA accepts NetCharge parameter. Best regards, Peter On Wed, May 29, 2019 at 10:02 PM Koussai LAZAAR wrote: > Dear Siesta users, > > How can I calculate ionization potential (vertical and adiabatic) and > electron > affinities (vertical an

Re:[SIESTA-L]

hello Koussai Lazaar To do calculation ionization potential ( vertical) and electron affinities (vertical ) using siesta (GGA) of a molecule, you can use the comment NetCharge. NetCharge (real): Specify the net charge of the system (in units of |e|). For charged systems, the energy converges ver

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > -- > *From:* siesta-l-requ...@uam.es on behalf of > Ali Roohforouz > *Sent:* Saturday, 4 May 2019 10:02 AM > *To:* siesta-l@uam.es > *Subject:* Re: [SIESTA-L] How to rotate translate or move molecule from > one

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

atter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: siesta-l-requ...@uam.es on behalf of Ali Roohforouz Sent: Saturday, 4 May 2019 10:02 AM To: siesta-l@uam.es Subject: Re: [SIESTA-L] How to rotate translate or move molecule

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

This is a typical problem when one tries to relax a molecular transistor. I suggest that you do the following steps: 1- relax electrodes and molecule separately 2- Build the sandwich device 3- relax the device with geometry constraints( rigid the electrodes and molecule but no constraints on the el

Re: [SIESTA-L] Installation Problem

Hello Vipin, Just type "f77" at the command prompt to find out if it is there or not. Anyway, f77 is not what you want, but something like mpif90 or mpifort or ..., to be assigned to variable FC in arch.make. Suggestion: grab one of those arch.make in Src/Sys that best suits your system (you'd b

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

: siesta-l@uam.es Subject: Re: [SIESTA-L] How to rotate translate or move molecule from one position to another? Dear El-Habed, I am not quite sure what you mean with "sandwiched" and what plane you want the molecule to lie in, but one tool you might want to look at is gdis. It's a

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

Dear El-Habed, I am not quite sure what you mean with "sandwiched" and what plane you want the molecule to lie in, but one tool you might want to look at is gdis. It's a viewer that can read and write fdf files. You can select your molecule in the gap and rotate (ctrl-right-mousebutton) or tr

Re: [SIESTA-L] How to rotate translate or move molecule from one position to another?

Dear El-Abed, you can use Avogadro software (it is free) to rotate your molecule. The easiest way would be to select molecule, then use option add center of atoms, a usually copy coordinates to Origin, move center of atoms to 0,0,0 then return it to Avogadro, this step is because Avogardo rota

Re: [SIESTA-L] << error compiling TBtrans-4.1-b4 >>

Try a make clean, otherwise you may have some problematic flags in your arch.make. One should not need to edit the arch.make to compile tbtrans. Den ons. 24. apr. 2019 kl. 22.07 skrev I. Camps : > Hello, > > After successfully compiled siesta-4.1-b4, I moved to > *siesta-4.1-b4/Util/TS/TBtrans* i

Re: [SIESTA-L] << Debian 9.8+Intel+NetCDF >>

Great, yes, MUMPS can be quite tricky. It isn't necessary anyways. :) Den ons. 24. apr. 2019 kl. 22.00 skrev I. Camps : > Dear Nick, > > After cleaned up the arch.make, I successfully (semi)compiled > siesta-4.1-b4. I wrote (semi) because I got several errors with MUMPS that > I "solved" removing

Re: [SIESTA-L] << Debian 9.8+Intel+NetCDF >>

Dear Nick, After cleaned up the arch.make, I successfully (semi)compiled siesta-4.1-b4. I wrote (semi) because I got several errors with MUMPS that I "solved" removing from arch.make. Thank you very much. Camps On Mon, Apr 22, 2019 at 5:01 PM Nick Papior wrote: > You have a mixed usage of FPP

Re: [SIESTA-L] Atom binary

Hi, I think you have to got to: https://departments.icmab.es/leem/siesta/Pseudopotentials/atom_licence.html In order to get atom. []'s, Camps On Tue, Apr 23, 2019 at 5:03 PM Максим Арсентьев wrote: > Dear siesta users and developers, > > > Does anybody have binary file for the latest versio

Re: [SIESTA-L] << Debian 9.8+Intel+NetCDF >>

Dear siesta users and developers, Does anybody have binary file for the latest version of atom program. Bests, Maxim Arsentev, ISC RAS пн, 22 апр 2019 г., 23:03 Nick Papior : > You have a mixed usage of FPPFLAGS_* and LDFLAGS. So in the end you don't > have the include directories for NetCDF (

Re: [SIESTA-L] << Debian 9.8+Intel+NetCDF >>

You have a mixed usage of FPPFLAGS_* and LDFLAGS. So in the end you don't have the include directories for NetCDF (or any of your other libraries) in your FPPFLAGS variable (since you do FPPFLAGS = ... which overwrites what you did). Simply carefully go through your variables/flags and either appe

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Dear SIESTA experts, Here provided some part of my calculations for the band structure, following your explanation for kpoints I don't know why my data don't have a similar trend to the above sample kpoints for the hexagonal lattice, I mean from Gamma to M ky values are not zero as you said above..

Re: [SIESTA-L] << Reduce number of nodes? >>

Dear Nick, I compiled siesta-4.1-b4 with -O1 and used unbuffer as recommended. It is running with 7 processor since yesterday (almost 24h now) but I can not see any information in the output file (I imaging that the file will be updated at the end). Hopping everything goes well. []'s, Camps

Re: [SIESTA-L] << Reduce number of nodes? >>

Could you: 0) Send the FORCE_STRESS file? 1) Use siesta-4.1 b4 (you are using b3) 2) Add MinSCFIterations 3 to the options 3) I would probably try and relax the system a bit first in a non-polarized calculation (but this is unrelated to the failure) Also, you are compiling with Intel -O3 which I

Re: [SIESTA-L] << Reduce number of nodes? >>

Could you please do a tar.gz or zip file? rar is horrible ;) Den lør. 13. apr. 2019 kl. 22.01 skrev I. Camps : > Hello Nick, > > Here are the files. > > []'s, > > Camps > > > On Fri, Apr 12, 2019 at 5:02 PM Nick Papior wrote: > >> Could you attach the output, fdf and psf files? >> >> Den tor. 11

Re: [SIESTA-L] << Reduce number of nodes? >>

Could you attach the output, fdf and psf files? Den tor. 11. apr. 2019 kl. 22.01 skrev I. Camps : > Hello, > > My system is a nanotube with 123 atoms (B, N, Ni). I am running a geometry > optimization and the calculations are stopped (after 10 CG steps) with the > following message: > > "*Sparse

Re: [SIESTA-L] Peroveskites using siesta

I am really grateful for your notes, I will try it. thank you Doaa ‫في الجمعة، 5 أبريل 2019 في 10:08 م تمت كتابة ما يلي بواسطة ‪Leonardo Fonseca‬‏ <‪fonsecal...@gmail.com‬‏>:‬ > Looks pretty bad to me. I am not used to GGA+U since in many cases the > adjusted U parameter is unphysical. You can c

Re: [SIESTA-L] Peroveskites using siesta

Looks pretty bad to me. I am not used to GGA+U since in many cases the adjusted U parameter is unphysical. You can check in the literature for other GGA+U attempts in peroveskites. Another possibility is to do GGA-1/2 correcting only the oxygen self-interaction energy. It gives quite accurate resul

Re: [SIESTA-L] Converting HSX file into a readable file

Probably the easiest way is to use sisl (www.github.com/zerothi/sisl) which is a Python module. Something like this: import sisl H = sisl.get_sile('RUN.fdf').read_hamiltonian() print(H[0, 1]) # the Hamiltonian element between orbital 1 and 2 Since H is a sparse matrix you can also loop the matri

Re: [SIESTA-L] Peroveskites using siesta

thank you for your patience I have another question How could I decrease the 2 eV difference between theoretical and experimental value ? ‫في الأربعاء، 3 أبريل 2019 في 10:02 م تمت كتابة ما يلي بواسطة ‪Leonardo Fonseca‬‏ <‪fonsecal...@gmail.com‬‏>:‬ > There is no such a thing as the exact band g

Re: [SIESTA-L] Peroveskites using siesta

Hey Doaa, 2 eV is still a large gap difference which is why as Leonardo said there is no such exact gap calculation. A great agreement would be having be experimental and computational results differ by around 0.2 not 2 eV. Hope that makes sense. El abed Sent from my iPhone On 5 Apr 2019, at 7:

Re: [SIESTA-L] Peroveskites using siesta

Thank you for your reply I understand your point, but The experimental band gap for my structure is 4.8 eV , after using GGA+U it becomes 2.8 eV...so is the 2 eV difference acceptable ? On Wed, 3 Apr 2019, 10:02 p.m. Leonardo Fonseca, wrote: > There is no such a thing as the exact band ga

Re: [SIESTA-L] Peroveskites using siesta

There is no such a thing as the exact band gap if you employ DFT within the various approximations for the exchange-correlation. For most cases DFT underestimates it. GGA+U is an approximation which in many cases improves the band gap considerably over plain GGA, but it is not exact. In fact not ev

Re: [SIESTA-L] Defining block for band structure

Dear researchers, I have defined blockbandline for my system as follow: BandLinesScale ReciprocalLatticeVectors %block BandLines 1 0.5 0.0 0.0 X 20 0.0 0.0 0.0 \Gamma 20 0.0 0.5 0.0 Y 1 0.5 0.5 0.0 L 25 0.0 0.0 0.0 \Gamma 20 0.0 0.0 0.5 Z 1 0.5 0.0 0.5 N 25 0.0 0.0 0.0 \Gamma 25 0.0 0.5 0.5

Re: [SIESTA-L] Strange force/stress behavior in transiesta 4.1-b4

Dear Nick, Thanks for your answers. We see then that some of the workarounds we had been considering with little justification (ie constraining atoms in the device close to the electrodes) may not be as unjustified, after all! Thanks again, Xavier On 03/29/2019 07:38 AM, Nick Papior wr

Re: [SIESTA-L] PHtrans

Hi, Den søn. 31. mar. 2019 kl. 22.02 skrev Rodrigo Garcia Amorim < rgamo...@id.uff.br>: > Dear developers, > > I saw in the manual that is possible calculate the phonon > transmission. Regarding this topic, my questions are: > > 1) Could I use similar setup of transport calculation? > Yes and

Re: [SIESTA-L] Defining block for band structure

Dear all, Could you please guide me how I can define "%block BandPoints" for a crystalline system with the following parameters: a=17.70 b=26.5 c=44 alpha=78.72 beta=101.79 gamma=122.33 Thank you for any help in advance. Best regards, Mina From: sies

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Thank you so much. [image: Mailtrack] Sender notified by Mailtrack 03/31/19, 12:48:02 AM On Sat, Mar 30, 2

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

The data looks like representing the path K -> Gamma -> M -> K: (b1/3 b2/3 0) -> (0 0 0 ) -> (b1/2 0 0) -> (b1/3 b2/3 0 []'s, Camps On Thu, Mar 28, 2019 at 6:03 PM ziba torkashvand wrote: > Thank you very much. your explanation is exactly what I mean. Now my > question: from M to K is the val

Re: [SIESTA-L] Strange force/stress behavior in transiesta 4.1-b4

There are many issues in relaxing a geometry with TranSiesta, besides the system you have chosen which has a band-gap. 1) For gapped electrodes one cannot be sure the electrostatics in your electrode calculation and in the device calculation coincide *perfectly* and hence you will have a mismatch

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Thank you very much. your explanation is exactly what I mean. Now my question: from M to K is the value of kx must be constant and again for ky repeat the above procedure or something else. If yes, I can not see this trend in the attached data after G to M path because the value of kx is increasing

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Dear Ziba, I think I get what are you asking for. Following the reference (10.1016/j.commatsci.2010.05.010 ) we have for the hexagonal lattice (table 13): Gamma point: 0 0 0 M point: b1/2 0 0 (b1, b2, b3 are the lattice parameters). In order to

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

are of a general nature, and do not relate to the code specifically. Best regards, -Salvador From: siesta-l-requ...@uam.es on behalf of saul...@iitk.ac.in Sent: Monday, March 25, 2019 11:56:33 PM To: siesta-l@uam.es Subject: Re: [SIESTA-L] kpoints i

Re: [SIESTA-L] Qtot is not zero

basis and non-spin polarized state. Thank you so much in advance. Regards, Mina From: siesta-l-requ...@uam.es on behalf of sullah Sent: March 25, 2019 6:45:16 PM To: siesta-l@uam.es Subject: Re: [SIESTA-L] Qtot is not zero Dear Mine, Could you please sen

Re: [SIESTA-L] TBTrans segfaults

Hi, No, said line shouldn't be the cause of anything... :( And fdf inputs shouldn't generate a seg-fault. Another try for debugging would be to add full traceback calls: Intel: FFLAGS = -O0 -g -check bounds -traceback Which should be more informative. Also, Intel is notorious for using the

Re: [SIESTA-L] Qtot is not zero

Dear Mine, Could you please send the first and last geometry of your structure? The output file might also be helpful. Regards, Saif Ullah Departamento de Física Instituto de Ciências Exatas - ICE Universidade Federal de Juiz de Fora - UFJF Juiz de Fora - MG - Brazil - CEP 36036-330 Cell# +

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Sym points are governed by the lattice vectors. Please read kittel' book on solid state physics chapters 1 and 2 > Thank you for your response. I see but in this references, the high > symmetry points are provided just in term of lattice vectors now, my > question is how kx, ky, and kz are vary

Re: [SIESTA-L] TBTrans segfaults

Deleting the TBTGF files did not solve the problem. So, my two guesses now are that there is an issue with the compilation of TBTrans (but it's compiled with stock Intel compiler, so I imagine someone else would have run into this) or there is an error in the input code. Would an error in the input

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Thank you for your response. I see but in this references, the high symmetry points are provided just in term of lattice vectors now, my question is how kx, ky, and kz are vary along this pathes? I have found a file with some data (below) but I can't find my understood relation (mensioned in my pre

Re: [SIESTA-L] Qtot is not zero

Hi, Den lør. 23. mar. 2019 kl. 22.01 skrev Mina Sedighi : > Dear Nick, > > Thank you for your reply. It is good news. But what is the reason of > destroying MnO2 structure (Oxygen atoms are opened from the structure). > I don't know, I am no expert in your system. > And how can I calculate Mull

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

in 2019-03-23 23:48:01,"ziba torkashvand" Compose: >Dear all SIESTA users, >I'm trying to find kpoint coordinates (kx,ky,kz) inside the Gamma-M-K-Gamma >path for my structure. I have found kpoints coordinates in siesta output file. >I think the kpoints coordinates in a hexagonal structure m

Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

Please, take look in the main reference paper at the link below, it has all the high symmetry points to build your path. Link: https://en.m.wikipedia.org/wiki/Brillouin_zone []'s Camps Em sáb, 23 de mar de 2019 18:03, ziba torkashvand escreveu: > Dear all SIESTA users, > I'm trying to find kp

Re: [SIESTA-L] Qtot is not zero

Dear Nick, Thank you for your reply. It is good news. But what is the reason of destroying MnO2 structure (Oxygen atoms are opened from the structure). And how can I calculate Mulliken charge distribution on the system? Best regards Mina Get Outlook for Android On Fr

Re: [SIESTA-L] Qtot is not zero

Qtot is the valence charge for your system. So everything seems fine! NetCharge is an additional charge added to your system and thus would change Qtot correspondingly. Den tor. 21. mar. 2019 kl. 22.11 skrev Mina Sedighi : > Dear all, > > > I solved SCF convergence problem by playing with SCF.Mix

Re: [SIESTA-L] Hamiltonian&hopping parameter

http://zerothi.github.io/sisl/docs/latest/index.html or https://github.com/cfm-mpc/pyscf On Wed, Mar 20, 2019 at 10:01 PM zhy wrote: > Dear All， >Can anyone know how to extract hamiltonian and matrices data from > HSX file and how to express the wave functions of atomic- orbital > ba

Re: [SIESTA-L] GGA+U

Dear Mina, Yes, for sure, assuming that you already know LDA+U. Best, Em 15.03.2019 17:13, Mina Sedighi escreveu: > Dear Siesta users and developers, > > Is there any possibility of performing GGA+U simulations by Siesta? > > Regards, > > Mina

Re: [SIESTA-L] pseudo-potential for K atom

LDA+U simulation. Can I use this GGA > pseudo-potential for that? > > Thank you so much. > > Best regards, > > Mina > - > > FROM: siesta-l-requ...@uam.es on behalf of sullah > > SENT: March 12, 2019 6:42:17 PM > TO: sie

RE: [SIESTA-L] GGA+U

Sure Mohan Sent from Mail for Windows 10 From: Mina Sedighi Sent: 16 March 2019 02:33 To: siesta-l Subject: [SIESTA-L] GGA+U Dear Siesta users and developers, Is there any possibility of performing GGA+U simulations by Siesta? Regards, Mina

RE: [SIESTA-L] Procedure to calculate electron localization functionand charge density plot

Go through my website www.drmlv.in It may help you. Sent from Mail for Windows 10 From: Ananya Rajpoot Sent: 14 March 2019 02:39 To: siesta-l@uam.es Subject: [SIESTA-L] Procedure to calculate electron localization functionand charge density plot Dear users, Can anyone suggest tutorials explai

Re: [SIESTA-L] pseudo-potential for K atom

-l-requ...@uam.es on behalf of > sullah > *Sent:* March 12, 2019 6:42:17 PM > *To:* siesta-l@uam.es > *Subject:* Re: [SIESTA-L] pseudo-potential for K atom > > > Dear Mina, > > As mentioned earlier, this is a PBE flavor of GGA. This PP is checked > during the mak

Re: [SIESTA-L] Test shows "DIFFERENCE FOUND"

Hi again, checking the results from the test I found some of them to be big. Once again I ask the same as above. Is this caused by something in the way I compile the program. Any clue will be appreciated. The compilation flags can be found at the top. Thank you very much. El mar., 26 feb. 2019 a

Re: [SIESTA-L] Difference between PDOS in SIESTA vs TbTrans??

Yes, there is a difference between the siesta and tbtrans. Siesta is a fully periodic calculation. TBtrans is a semi-infinite calculation where one or more directions are replaced by bulk electrodes. Additionally, TBtrans allows non-equilibrium calculations. These two systems are not equivalent a

Re: [SIESTA-L] Error when running fmpdos.x - Fail to read integer number from positions

Hello there the mistake is here: Extract data for atom index (enter atom NUMBER, or 0 to select all), or for all atoms of given species (enter its chemical LABEL): 492 504 you have to choose only one number. EL-Abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT)

Re: [SIESTA-L] pseudo-potential for K atom

Dear Mina, As mentioned earlier, this is a PBE flavor of GGA. This PP is checked during the making of (10.1016/j.cplett.2018.06.028 [3]) and (10.1016/j.apsusc.2018.12.020 [4]). I think we did not add SIESTA-PBE results there but we check all our PPs and compare with the available data and other A

Re: [SIESTA-L] pseudo-potential for K atom

Dear Sir/Madam, Thank you so much for your help. Have this potential tested before? And which exchange correlation is supported by this? LDA or GGA?Thank you so much. Regards, Mina Get Outlook for Android On Sat, Mar 9, 2019 at 4:02 PM -0500, "sullah" mailto:sul...@f

Re: [SIESTA-L] problem

Dear doaa haleem : in your “111” case, your unit cell is twice longer in the X direction than in other two(did you have a look at the structure figure??) In other two cases, the lattice vectors are more cubic, yet you have Hf in the “A” positionand Ba in the “B” position (in the oxygen octahedron

Re: [SIESTA-L] Question about extracting energy transferred to electrons

Dear Tan Shi Yes, the kind of things you mention have been obtained from SIESTA. Check Pruneda et al, PRL 2007, Zeb et al, PRL 2012 etc. But in your email it seems you are looking at energy terms for a time-independent equilibrium calculation. You will have to read quite a bit from the backgroun

Re: [SIESTA-L] TBTrans segfaults

Could you please delete all TBTGF* files, and rerun the calculation? Alternatively, see if increasing the eta value helps. Den fre. 8. mar. 2019 kl. 22.02 skrev Day, Zacharie : > Hello, > > A user on my cluster is trying to process something with Siesta 4.0.2 > TBTrans_rep. The process works up

Re: [SIESTA-L] ERROR in extraction of BANDS

Did exactly that. It worked. Thank you. On Thu, Mar 7, 2019, 22:03 Junquera Quintana, Francisco Javier < javier.junqu...@unican.es> wrote: > Go to > Util/Bands > > Edit gnubands.F > > Increase the parameter pointing to the maximum number of bands > > Recompile > > Javier > > Javier Junquera > C

Re: [SIESTA-L] ERROR in extraction of BANDS

it helps much. thank you. On Thu, Mar 7, 2019, 22:01 sullah wrote: > Hi, > > You need to increase some parameters, such as maxk and maxb in gnubands.f > and please don't forget to recompile it again. > > I hope it helps. > > Best, > > Saif > Departamento de Física > Instituto de Ciências Exatas

Re: [SIESTA-L] ERROR in extraction of BANDS

Go to Util/Bands Edit gnubands.F Increase the parameter pointing to the maximum number of bands Recompile Javier Javier Junquera CITIMAC Universidad de Cantabria El 06/03/2019, a las 16:02, "SIFUNA JAMES" mailto:sifunaja...@gmail.com>> escribió: Greetings, I am trying to extract the bands u

Re: [SIESTA-L] ERROR in extraction of BANDS

Hi, You need to increase some parameters, such as maxk and maxb in gnubands.f and please don't forget to recompile it again. I hope it helps. Best, Saif Departamento de Física Instituto de Ciências Exatas - ICE Universidade Federal de Juiz de Fora - UFJF Juiz de Fora - MG - Brazil - CEP 36

Re: [SIESTA-L] ERROR in extraction of BANDS

I found away out. Thank you all. had to increase maxb Best wishes, J. On Tue, Mar 5, 2019 at 11:38 PM SIFUNA JAMES wrote: > Greetings, > I am trying to extract the bands using gnubands.x gnuplot.dat. > > > I get > > STOP Dimensions in gnubands too small > > > how do I go a bout it? > Best wis

Re: [SIESTA-L] Folding of H and S is implicitly performed

Hi, It is not an error, nor a bug in the code. It is just an informational message that is printed whenever you are running a calculation without k-point sampling for a system whose unit cell is not large enough to allow the representation of all orbital interactions (matrix elements of H and S

<    1   2   3   4   5   6   7   8   9   10   >