Re: [SIESTA-L] How to calculate charge density difference using siesta?

The macroave utility can be used to plot the charge density and electrostatic potential in real space. So for a bilayer system you can get the density in the out-of-plane direction, averaged in the in-plane directions. In your input.fdf file you need flags like SaveElectrostaticPotential true, etc.

Re: [SIESTA-L] Inconsistency in polarization orbital error for Fe

Of course, here's the file attached. Thanks!! El sáb, 12 dic 2020 a las 16:33, Alejandra Chavarría () escribió: > Of course, here's attached. > > Thanks!! > > Alejandra > > El sáb, 12 dic 2020 a las 7:13, Emilio Artacho () > escribió: > >> Hi Alejandra >> >> if you could post the fdf input we m

Re: [SIESTA-L] SIESTA (GitLab version) installation failure

Dear Prof. Papior, Thank you for your quick response. Please find arch.make attached. For your information: this file was auto-generated by my home-made pkg. manager which added all flags for all the dependencies. The code is based on my understanding of Obj/DOCUMENTED-TEMPLATE.make. I appreciat

Re: [SIESTA-L] Inconsistency in polarization orbital error for Fe

Hi Alejandra if you could post the fdf input we may get a better chance to see the problem thanks Emilio > On 11 Dec 2020, at 19:51, Alejandra Chavarría > wrote: > > Hi, > I am using siesta v4.1-b4-148 and I'm having problems with the polarization > orbital for an iron perovskite. First, I

Re: [SIESTA-L] SIESTA (GitLab version) installation failure

Please attach your arch.make file On Fri, 11 Dec 2020, 22:03 Tamas Karpati, wrote: > Dear fellow developers, > > > Please help my first attempt to build SIESTA as I'm stuck after > several attempts. No similar symptoms I could find in the archives. > > Shortly: make stops without both executable

Re: [SIESTA-L] spin polarized bands

Hello sir I am using siesta -3.2 I will try with latest version. Thank you sir On Wed, 9 Dec 2020, 8:21 am veerpal kaur dhiman, wrote: > Hello sir , > I will try with latest version > Thank you sir > > > > > On Wed, 9 Dec 2020, 2:32 am Sankushkrishna Maheshuni, < > sankushnov2...@gmail.com> wr

Re: [SIESTA-L] spin polarized bands

Hello sir Thank you so much both of you. It worked with latest version siesta -4.1 . I got separate up and down bands successfully. Thank you On Wed, Dec 9, 2020 at 8:23 AM veerpal kaur dhiman wrote: > Hello sir > > I am using siesta -3.2 > I will try with latest version. > > Thank you sir > > O

Re: [SIESTA-L] spin polarized bands

Hello sir , I will try with latest version Thank you sir On Wed, 9 Dec 2020, 2:32 am Sankushkrishna Maheshuni, < sankushnov2...@gmail.com> wrote: > Hello Veerpal kaur dhiman. I've gone through your .bands file. I had no > trouble generating the spin bandstructure. The problem might be with you

Re: [SIESTA-L] spin polarized bands

Which version of siesta are you using. When I do gnubands -s 1 ... gnubands -s 2 ... it works as expected! And the bands are different in up and down channel. Den man. 7. dec. 2020 kl. 22.03 skrev veerpal kaur dhiman < v.veerpa...@gmail.com>: > Please find attached the .bands file > > Thank you

Re: [SIESTA-L] Denchar software inquiry

No, denchar is sadly not MPI parallelised. Den man. 7. dec. 2020 kl. 22.01 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Good afternoon, > > I was wondering when utilizing the Denchar software, if the system is very > large can we use mpirun? > > I tried but it does not seem to be going f

Re: [SIESTA-L] spin polarized bands

Hello Veerpal Kaur Dhiman. Could you please send your ". bands" file so that I can have a clear idea of the bandstructure you are getting. On Fri, Dec 4, 2020, 2:31 AM veerpal kaur dhiman wrote: > Dear Siesa users , > I have been trying to calculate the spin polarized band structure for > my sy

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

hello sir, I got only two columns in band.dat file one for k and another for E. There is no column for spin. I also tried this gnubands -s 1 < .bands > band_up.dat gnubands -s 2 < .bands > band_dn.dat But i got the exactly same bands for up and down. Where may be the problem ? Please help. Than

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Thank u sir But i got only two columns in bands file On Tue, 1 Dec 2020, 2:34 am Nick Papior, wrote: > The spin index is the last value in each row. > > So everything is compressed as a flat file format. > > Alternatively you can do: > > gnubands -s 1 < .bands > band_up.dat > gnubands -s 2 < .

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

The spin index is the last value in each row. So everything is compressed as a flat file format. Alternatively you can do: gnubands -s 1 < .bands > band_up.dat gnubands -s 2 < .bands > band_dn.dat to split them in two files. Den fre. 27. nov. 2020 kl. 22.00 skrev veerpal kaur dhiman < v.veerpa

Re: [SIESTA-L] Parallel siesta crashing during SCF

Hi, Without more information we can't help, 1) compiler and library versions 2) your arch.make 3) your input files Den tir. 17. nov. 2020 kl. 22.01 skrev D. Bennett : > Dear siesta users, > > I'm running some calculations using a parallel version of siesta-psml, > and I'm finding that some of

Re: [SIESTA-L] Performance issue in Pd slab calculation

Hi, This is not totally unsurprising. When you hit 128 cores you are effectively only having 30 orbitals per core. This means when the diagonalization takes place it's blocks will be ~30x30 matrices. You are reaching the bottleneck of the diagonalization routines which takes up a considerable amo

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

I don't know if you did it correctly. A plot does not show this! But from what you describe it sounds correct to me. However, it seems that you have a dipole in the system, i.e. you should add the dipole correction for this calculation. Den lør. 3. okt. 2020 kl. 11.19 skrev Harkishan Dua : > Dea

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Dear sir, I have generated the data set (VH_z.dat file) for my structure using SISL and generated its plot using gnuplot. And from that plot, I have taken points 1 and 2 (given in the 1.5.png file) for calculating the potential difference for my structure. But the potential difference that i am ge

Re: [SIESTA-L] VDW+U in siesta and TRANSIESTA calculation

Dear Iran, your question is not clear. I have not understood if you read the manual or not. Do you want to add U correction to vdW functional or to use the two corrections on the same fdf file? The second one easy. For the second solution you need only vdW pseudos and values for LDAU blocks. You ca

Re: [SIESTA-L] Question about the number of electrons considered in the pseudopotential

Hello How will decide PAO.EnergyShift On Mon, 28 Sep 2020, 08:08 Premlata Narwaria, wrote: > How we create SiC nanoribbon structure > > On Mon, 28 Sep 2020, 01:38 berna uyanık, wrote: > >> Dear Shi, There is also all electron approach. How do you prepare the >> pseudopotential files. If

Re: [SIESTA-L] Question about the number of electrons considered in the pseudopotential

How we create SiC nanoribbon structure On Mon, 28 Sep 2020, 01:38 berna uyanık, wrote: > Dear Shi, There is also all electron approach. How do you prepare the > pseudopotential files. If you use "Atom", you should look at the manual. > > 26 Eyl 2020 Cts 23:00 tarihinde shi tan şunu > yazdı: > >

Re: [SIESTA-L] Question about the number of electrons considered in the pseudopotential

Dear Shi, There is also all electron approach. How do you prepare the pseudopotential files. If you use "Atom", you should look at the manual. 26 Eyl 2020 Cts 23:00 tarihinde shi tan şunu yazdı: > Dear SIESTA experts, > > For Fe, I noticed that the available pseudopotential from the siesta

Re: [SIESTA-L] Question about the number of electrons considered in the pseudopotential

Dear Tan Shi, the issue of importance of 3p for Fe has been discussed in Eur. Phys. J. D 25, 261–270 (2003) -DOI: 10.1140/epjd/e2003-00209-3 The pseudopotentials I used there were straightforward – generated with r = 2.00, 2.00, 2.00, 1.50, 0.0, 0.7for both cases, 4 1 0.00and 4 1 6.00 Best regard

Re: [SIESTA-L] Question about the number of electrons considered in the pseudopotential

On Sun, 27 Sep 2020, 20:21 Premlata Narwaria, wrote: > How to create SiC nanoribbon structure??? Help me sir > > On Sun, 27 Sep 2020, 01:30 shi tan, wrote: > >> Dear SIESTA experts, >> >> For Fe, I noticed that the available pseudopotential from the >> siesta website only includes 4s2

Re: [SIESTA-L] antiparallel calculation of the leads

Please have a look at DM.InitSpin to initialize a spin configuration. However, converging this in transiesta is probably difficult due to the abrupt spin-boundary. But you could try this. Den tor. 24. sep. 2020 kl. 22.02 skrev rayan moukhadder < rayanroro321...@gmail.com>: > I mean that I want to

Re: [SIESTA-L] antiparallel calculation of the leads

I mean that I want to make a calculation for the leads two times..one time with spin up and the other time with all spins down how can I make such thing ? In other words what are the options that I should add to the input file of the leads ? On Wed, Sep 23, 2020 at 11:01 PM Nick Papior wrote: >

Re: [SIESTA-L] antiparallel calculation of the leads

Please be more specific in your question, it isn't clear to us what anti-parallel means? Den tir. 22. sep. 2020 kl. 22.05 skrev rayan moukhadder < rayanroro321...@gmail.com>: > Dear siesta users, > I want to perform a calculation in transiesta code with two graphene > sheets sandwiching a cobalt

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

How did you do it? How were your unit conversions etc.? Remember that sisl automatically converts to eV and Ang when reading siesta files. Den man. 21. sep. 2020 kl. 15.22 skrev Harkishan Dua : > We are working on a system similar to the paper attached. In the paper it > can be seen in Figure 1.

Re: [SIESTA-L] some questions about NEGF

Den fre. 4. sep. 2020 kl. 22.00 skrev zhyphy : > Dear All， > I have some questions in the process of learning Green's function.I hope > someone can help me. > (1) The surface Green function contains all the informations about > interaction between electrodes and scatter region, but for Transiest

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Hi, Den søn. 6. sep. 2020 kl. 16.36 skrev Harkishan Dua : > Dear sir, > I am trying to generate the potential plot for monolayer CdS and Bilayer > CdS systems using sisl. and with that I am getting the plots of the ones I > have attached with this mail.There are some queries that I wished to > cl

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Dear sir, I am trying to generate the potential plot for monolayer CdS and Bilayer CdS systems using sisl. and with that I am getting the plots of the ones I have attached with this mail.There are some queries that I wished to clarify: 1. As both structures are planar Z coordinates are fixed for al

Re: [SIESTA-L] Question about continuing TranSIESTA job

The same flag applies to transiesta. :) On Tue, 1 Sep 2020, 22:01 El-abed Haidar, wrote: > Good afternoon, > > In siesta you can use UseData to continue a siesta job, what command > should I use to make sure that TranSIESTA continues from where it stops > especially if the job was not completed?

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Thanks Nick for this update on sisl :-) On Tue, 1 Sep 2020 at 22:00, Nick Papior wrote: > Hi, > > In this it seems you don't need the filtering that macroave is capable of. > In that case you can use sisl to create the data for you. > > The command would be something like this: > > sgrid siesta.

Re: [SIESTA-L] Command for scattering region calculation

You simply do "siesta xxx.fdf" TranSiesta is enabled through the fdf-option "SolutionMethod". As for the I-V curve, yes, I would recommend you to compile siesta with NetCDF4 support. Den fre. 28. aug. 2020 kl. 22.00 skrev MANISH KR MOHANTA < manish.ph16...@inst.ac.in>: > Dear Experts, > > I am

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Hi, In this it seems you don't need the filtering that macroave is capable of. In that case you can use sisl to create the data for you. The command would be something like this: sgrid siesta.VH --average 0 --average 1 --out VH_z.dat which will write a 2 column data file with z coordinates (in

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Hi, > I am trying to generate the potential plot using macroave and for that I > have taken the .XV file and made it to run it with the macroave.in file. > But there are some queries that I have not understood regarding the > macroave.in file. And I would be very glad if any one could help me in >

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Dear sir/ma'am I am trying to generate the potential plot using macroave and for that I have taken the .XV file and made it to run it with the macroave.in file. But there are some queries that I have not understood regarding the macroave.in file. And I would be very glad if any one could help me in

Re: [SIESTA-L] How to find find variation of potential with distance in siesta

Hi, For this, you need to activate this tag "SaveElectrostaticPotential" to true for siesta to generate the total electrostatic potential file named SystemLabel.VH. Then you use siesta utility "macroave" from Util/macroave directory to plot the variation of the potential along the layers. Best, B

Re: [SIESTA-L] Pseudos for vdW functional?

Hi. Is there a source for pseudos for dft+1/2? 26 Ağu 2020 Çar 23:00 tarihinde şunu yazdı: > Hi Danny, > > Have a look at this, > https://forum.simuneatomistics.com/t/van-der-waals-functional-and-pseudo/276 > > Regards, > > Federico. > > -Original Message- > From: siesta-l-requ...@uam.es

Re: [SIESTA-L] Pseudos for vdW functional?

Hi. Is there a source for pseudos for dft+1/2? berna uyanık , 27 Ağu 2020 Per, 06:34 tarihinde şunu yazdı: > Hi. Is there a source for pseudos for dft+1/2? > > 26 Ağu 2020 Çar 23:00 tarihinde şunu yazdı: > >> Hi Danny, >> >> Have a look at this, >> https://forum.simuneatomistics.com/t/van-der-wa

RE: [SIESTA-L] Pseudos for vdW functional?

Hi Danny, Have a look at this, https://forum.simuneatomistics.com/t/van-der-waals-functional-and-pseudo/276 Regards, Federico. -Original Message- From: siesta-l-requ...@uam.es On Behalf Of D. Bennett Sent: 05 August 2020 11:32 To: siesta-l@uam.es Subject: [SIESTA-L] Pseudos for vdW fu

Re: [SIESTA-L] Pseudos for vdW functional?

Please, use PBE pseudos with vdW functionals. It is difficult to generate a vdW pseudo. Good luck, Peter El mié., 5 ago. 2020 22:00, D. Bennett escribió: > Hi all, > > I wanted to try out the van der Waals in siesta (DRSLL/DF1 by > Román-Pérez and Soler), but wasn't sure about what to use for

Re: [SIESTA-L] tbtrans errors

Could you try with a nonzero eta for the electrodes? Same goes for transiesta calculations with bias. Say a value of 1e-4 eV. One cannot use eta==0 since the dos explodes if you hit an eigenstate. On Sat, 25 Jul 2020, 07:12 赵鸿远, wrote: > Dear all, > I am using siesta4.1-b4 version. I want t

Re: [SIESTA-L] PDOS Up and Down

Dear Rayan,in a spin-polarized case, the script writes several columns of PDOS (2, or 4 for non-collinear case)into the output file:C --- write down accumulated DOS values: - if (isferm) write (io1,310) efermi write (io1,304) do it=1,nt write (io1,305) ene(it),(dos(it,ispin),ispin

RE: [SIESTA-L] PDOS Up and Down

Hello Rayan You do not need to worry about that because once you choose n,l, and m, you will have 3 columns: energy, spin up, and spin down. If you plot using gnuplot you can use the following command: plot 'Up.dat' using ($1):($2) title "pdosUP" since the 1st 2 columns are energy and spin up an

RE: [SIESTA-L] E(Fermi)

No shift is needed TbTrans does that. In other words when you plot T(E) you are plotting T(E-EF) Good luck! El-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: rayan moukhadder

RE: [SIESTA-L] Fw: How to read WFSX file

?Thank you Nick Best Regards, Linda From: siesta-l-requ...@uam.es on behalf of Nick Papior Sent: 06 July 2020 14:36 To: siesta-l Subject: Re: [SIESTA-L] Fw: How to read WFSX file How do you want to read it? In sisl there is a recent addition which allows you

Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question

tness you are aiming for?* > Yeah, sounds correct. > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > *From: *Nick Papior > *Sent: *Friday, 10 July

RE: [SIESTA-L] K points in TranSIESTA vs TbTrans question

abed Haidar<mailto:ehai2...@uni.sydney.edu.au> Cc: siesta-l@uam.es<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question Hi, Den fre. 10. jul. 2020 kl. 05.00 skrev El-abed Haidar mailto:ehai2...@uni.sydney.edu.au>>: Thank you a lot for the outline

Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question

hank you all ! > > EL-abed > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > *From: *Nick Papior > *Sent: *Friday, 10 July 2020 6:04 AM > *To:

RE: [SIESTA-L] K points in TranSIESTA vs TbTrans question

s THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Nick Papior<mailto:nickpap...@gmail.com> Sent: Friday, 10 July 2020 6:04 AM To: siesta-l<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question The basic principle of transiesta is as with siesta. A roug

Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question

The basic principle of transiesta is as with siesta. A rough outline would be this: 0) Create your system, decide upon the electrodes. Ensure your device screens off the defect towards the electrodes (meaning you'll need some additional electrode layers) 1) You converge your density in your elect

Re: [SIESTA-L] K points in TranSIESTA vs TbTrans question

Dear Eı-abed, How many k-points you should use depends on number of k-points through transport directions. If less number of k-points covers all k-points along transport direction than you do not need bigger number of k-points. El-abed Haidar , 8 Tem 2020 Çar, 23:00 tarihinde şunu yazdı: > Good

Re: [SIESTA-L] Fw: How to read WFSX file

How do you want to read it? In sisl there is a recent addition which allows you to iterate the values in the file python import sisl as si wfsx = si.get_sile("file.WFSX") for es in wfsx.yield_eigenstate(): print(es, es.shape) ### This lets you use the values in the file, if needed :) Th

RE: [SIESTA-L] Conductance plot

Hi Rayan That is correct it is from a TbTrans run where you will have a AVTRANS file to plot T(E) vs V Hope that helps. Good luck! EL-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: rayan

Re: [SIESTA-L] Conductance plot

You can use Bolztrap. 4 Tem 2020 Cmt 23:02 tarihinde rayan moukhadder şunu yazdı: > Dear siesta users, > > I want to use transiesta in order to plot Energy-conductance plot but from the > > mail archive I knew that transiesta did not calculate the conductance, > > So how can i do that? > > Best

RE: [SIESTA-L] [***RedIris: Posible SPAM***] .AVTRANS

AVTRANS gives you only the average transmission only. To get PDOS you can use sisl which can extract PDOS of any region of your desire from the nc file. Good luck! EL-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF S

Re: [SIESTA-L] SCF not converging for Cr2O3

Dear Yuvam:It might be a good idea to fix first the small periodic Cr2O3 with less than 720 atoms... then if it works and your cluster don't,I'd say, you have problem with your structure (positions of atoms);try to look at them.By the way, how about the magnetic moments?An idea to try all differ

Re: [SIESTA-L] how to define the value of rc to generate pseudo potential

Hi, Have a look at ./Contrib/atom_table.txt within the Atom tree, that file provides sensible values to start. bye, Roberto On 27/06/20 06:11, niuniubiubiu chen wrote: Hi, As I am trying to generate pseudopotential from Atom. Will any body please spare your valuable time to guide me that how

Re: [SIESTA-L] PDOS and EIG files in transiesta

Thanks for your reply, I really found that useful. ‫في الخميس، 25 يونيو 2020 في 11:08 م تمت كتابة ما يلي بواسطة ‪Nick Papior‬‏ <‪nickpap...@gmail.com‬‏>:‬ > TranSiesta does not use the same file formats. > > 1) Eigenvalues cannot be calculated using the NEGF formalism, so you won't > get the eig

Re: [SIESTA-L] PDOS and EIG files in transiesta

TranSiesta does not use the same file formats. 1) Eigenvalues cannot be calculated using the NEGF formalism, so you won't get the eig file, ever. 2) If you use siesta-4.1 or later you will only get a projected DOS output from TBtrans in the *.TBT.nc files. Subsequently you should use sisl, https:/

RE: [SIESTA-L] PDOS and EIG files in transiesta

Hello Rayan, 1. For Eigen files you may have forgot WriteEigenvalues true. 2. In order to extract PDOS, I am using sisl. Have a look at siesta mail or nick Papior GitHub page for more details about that. You just have to install sisl onto your terminal and then use the command sdata. Hope

Re: [SIESTA-L] [SIESTA-user] Problem while installing psml compatible SIESTA

Thank you Dr. Papior, I was successful in installing psml enable siesta in parallel execution using your bash files. But there is a problem arising that system is still searching for psf pseudopotetials instead of psml. I installed it multiple times hoping it would fix it but it doesn't. Is there a

Re: [SIESTA-L] [SIESTA-user] Problem while installing psml compatible SIESTA

Could you attach the full output? Also, never run siesta as root. It makes no sense, and HPC centers will not allow it (at least they shouldn't). If the executable is installed in another location, just make sure it is executable by "others". Den tor. 25. jun. 2020 kl. 20.16 skrev Yuvam Bhateja

Re: [SIESTA-L] [SIESTA-user] Problem while installing psml compatible SIESTA

In conjunction with making Siesta easier to install (and the future PSML incorporation) I have made some scripts which should ease this. I here attach the scripts which I have tested (only a few times), any feedback is very welcome. They should more or less be self-contained. :) @Nicolas please

RE: [SIESTA-L] Pseudo potentials for Mg and O

-- De : siesta-l-requ...@uam.es De la part de aguado Envoyé : jeudi 18 juin 2020 22:46 À : siesta-l@uam.es Objet : Re: [SIESTA-L] Pseudo potentials for Mg and O Hi, in my experience it is essentially unbelievable that such a huge error comes from the pseudopotential. I suggest to analyze carefull

RE: [SIESTA-L] [SIESTA-user] Problem while installing psml compatible SIESTA

Hello, Has anyone have a users’ guide for the installation of siesta latest version for full parallel computing ? Where can I find this info ? Regards Nicolas Fourches From: siesta-l-requ...@uam.es On Behalf Of Yuvam Bhateja Sent: vendredi 19 juin 2020 10:49 To: siesta-l@uam.es Subject: [S

Re: [SIESTA-L] [SIESTA-USER] Error in setting up psml supported SIESTA

I would reccommend following Javier Junquera's tutorial on compiling siesta/abinit for use with PSML pseudos: https://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Pseudos/Siesta-abinit/Siesta-Abinit-PSML.pdf You'll have to compile 4 programs (libxc, libgridxc, libpsml, xmlf90) t

Re: [SIESTA-L] Pseudo potentials for Mg and O

Hi, in my experience it is essentially unbelievable that such a huge error comes from the pseudopotential. I suggest to analyze carefully the convergence of the calculation with respect to other parameters such as k-point sampling, basis set size, mesh cutoff, etc. Improving any of these sho

Re: [SIESTA-L] << Materials Modeling Stack Exchange >>

Thanks for bringing this to the attention of the community! Den ons. 17. jun. 2020 kl. 22.06 skrev I. Camps : > Dear SIESTers, > > I would like to invite you to visit the Materials Modeling Stack Exchange > forum (in public beta). > > The site is dedicated for those interested in building a commu

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: rayan moukhadder<mailto:rayanroro321...@gmail.com> Sent: Wednesday, 17 June 2020 6:15 AM To: siesta-l@uam.es<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Re: [SIESTA-L] Transiesta DM does not converge

Hi, Den tir. 16. jun. 2020 kl. 22.00 skrev Seyed Mohammad Tabatabaei < smt...@gmail.com>: > Thank you so much for your answer. > > Do I need to use more buffer layers? > Maybe, first change to metallic MoS2, then see. > > I am currently using semiconducting MoS2 nanoribbons (1D system) with a >

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Transport is along the z-direction, thanks for your help I will try to make use of those options. ‫في الاثنين، 15 يونيو 2020 في 11:02 م تمت كتابة ما يلي بواسطة ‪El-abed Haidar‬‏ <‪ehai2...@uni.sydney.edu.au‬‏>:‬ > Hi Rayan > > Quick question what is the transport direction? > > I feel there are s

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

uesday, 16 June 2020 4:41 PM To: siesta-l<mailto:siesta-l@uam.es>; El-abed Haidar<mailto:ehai2...@uni.sydney.edu.au> Subject: Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank Hi, 1. Original poster. Could you please try read the manual. Your problem are multiple, the el

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

T) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > *From: *Nick Papior > *Sent: *Tuesday, 16 June 2020 11:35 PM > *To: *El-abed Haidar > *Cc: *siesta-l > *Subject: *Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi, 1. Original poster. Could you please try read the manual. Your problem are multiple, the electronic structure parameters are insufficient and you are not using the electrodes as they should. I.e. they are not bulk like. Your simulation requires the use of real-space self-energies, see https:/

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

bed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > *From: *Nick Papior > *Sent: *Tuesday, 16 June 2020 4:41 PM > *To: *siesta-l ; El-abed Haidar > > *Subject:

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

o:nickpap...@gmail.com>; siesta-l<mailto:siesta-l@uam.es> Subject: RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank Thank you very much Nick! No wonder my calculations were taking that much long! El-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT

Re: [SIESTA-L] Transiesta DM does not converge

Thank you so much for your answer. Do I need to use more buffer layers? I am currently using semiconducting MoS2 nanoribbons (1D system) with a bandgap of about 0.5 eV. Would changing to metallic MoS2 nanoribbons improve convergence? Do you mean I should increase the cutt-off energy? On Tue

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

; Sent: Tuesday, 16 June 2020 10:43 PM To: Nick Papior<mailto:nickpap...@gmail.com>; siesta-l<mailto:siesta-l@uam.es> Subject: RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank Thank you very much Nick! No wonder my calculations were taking that much long! El-abed

Re: [SIESTA-L] Transiesta DM does not converge

Hi, 1. Great that you are using buffer atoms to get the *correct* behaviour of your electrodes 2. However, you are using MoS2 as electrodes, which is semiconducting. This is not a good idea since the NEGF formalism requires the electrodes are *bulk-like* and this cannot be enforced if the screenin

RE: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi Rayan Quick question what is the transport direction? I feel there are some essential blocks missing. Those are generally required for a TranSIESTA and TbTrans calculation. Good luck! %block TS.ChemPots Left Right %endblock TS.ChemPots %block TS.ChemPot.Left mu V/2 contour.eq begin

Re: [SIESTA-L] Transiesta DM does not converge

Thank you for your answer. 1-The electrodes are connected to the scattering region. However, the scattering region has a vertical gap in which you can see a molecule. I want to simulate the cross-plane electrical current across the gap both in the absence and presence of the molecule. 2-Thank you

RE: [SIESTA-L] Transiesta DM does not converge

Hello Seyed, 1. Is there a reason the electrodes and scattering regions are not connected? Is it relaxed in SIESTA? 2. Is there a reason you chose DM.OccupancyTolerance 0.10E-11 that is very small to be honest. Also DM.Tolerance 1.d-5 also seems very small I would cut

RE: [SIESTA-L] PDOS at a vacuum on top of a slab

Good evening Dr. Haldar, Mainly it is a siesta run where you need to be using the following block in the fdf file: %block ProjectedDensityOfStates -20.00 10.00 0.200 500 eV %endblock ProjectedDensityOfStates -[20, 10] is the energy interval in eV, 0.2 as the peak width and 500 is the number of

Re: [SIESTA-L] PDOS at a vacuum on top of a slab

Dear Soumyajyoti,the easiest approximation to what you probably want (especially as you mentionempty spheres) might be to use ghost atoms, see the end of the description ofPAO.Basis block in the manual. Notably the atom number -100 is supposed to add the basis of spherical Bessel functionsto wh

Re: [SIESTA-L] [SIESTA] Performing geometrical optimization

Good Evening Everyone, Thank you for all your great advice. Dr. Roberto Dr. Camps Dr. Haider Dr. Postikov I will consider every piece of advice while doing my calculations. Glad to be finally a part of the SIESTA family. Regards Yuvam Bhateja On Mon, Jun 8, 2020 at 1:38 AM Andrei Postnikov < and

Re: [SIESTA-L] [SIESTA] Performing geometrical optimization

Dear Yuvam, if you are new to the code it might be more "robust" to test parts of your system (just a single-cell graphene; separately a single-cell oxide; ... ) before making and relaxing a supercell out of them. The point is, the choice of basis functions might be critical in Siesta because i

Re: [SIESTA-L] [SIESTA] Performing geometrical optimization

Hi, In your main fdf data file set keywords MD.TypeOfRun CG (conjugate gradients) MD.VariableCell .true. (fully flexible box) This will do using default values for other parameters. Have a look at the user's guide for other choices and fine tuning. Goo

RE: [SIESTA-L] [SIESTA] Performing geometrical optimization

Hello Yuvam, Since you have some experience in quantum espresso, then all you need to do is just go through the optimization section in the latest siesta manual and choose the appropriate parameters. Bare in mind that QE, like VASP, is a plane wave DFT software unlike SIESTA which is LCAO based

Re: [SIESTA-L] [SIESTA] Performing geometrical optimization

Hello Yuvam, Normally, there is no need to use scripts for geometry optimization. There are keywords in order to set up the type of optimization you want. For example, the keyword *MD.VariableCell* if set to *.true.* (together with the keyword *MD.NumCGsteps* with a value different than cero), ind

Re: [SIESTA-L] Transietsa/sisl problem

Hi, Den ons. 20. maj 2020 kl. 22.04 skrev shirin zandi < shirinzandi1...@gmail.com>: > Dear Nick, > The sgeom works and it produces: > info:0: SislInfo: Scaling vector by: 2.7056029424251387 > > What was wrong with the sdata command? and also how I can scaling all the > bond current vectors by s

Re: [SIESTA-L] << Error compiling Util/COOP >>

I can't recall if we *may* have fixed some things since then. Could you try and download the latest commit on the 4.1 branch? Here: https://gitlab.com/siesta-project/siesta/-/archive/rel-4.1/siesta-rel-4.1.tar.bz2 Den ons. 20. maj 2020 kl. 22.08 skrev I. Camps : > The output of "make dep" at t

Re: [SIESTA-L] << Error compiling Util/COOP >>

The output of "make dep" at the util folder was: *make: *** No rule to make target 'dep'. Stop.* Inside the COOP folder was: *sfmakedepend --depend=obj --modext=o \ /home/icamps/temp/SIESTA/siesta-4.1-b4/Util/COOP/../../Src/*.f /home/icamps/temp/SIESTA/siesta-4.1-b4/Util/COOP/../../Src/*.f9

Re: [SIESTA-L] Transietsa/sisl problem

Dear Nick, The sgeom works and it produces: info:0: SislInfo: Scaling vector by: 2.7056029424251387 What was wrong with the sdata command? and also how I can scaling all the bond current vectors by specific values (multiple by 3, 4, and ..) And one more question! is there any graphical package

RE: [SIESTA-L] Transietsa/sisl problem

(CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Nick Papior<mailto:nickpap...@gmail.com> Sent: Wednesday, 20 May 2020 6:00 AM To: siesta-l<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] Transietsa/sisl problem Den man. 18. maj 2020 kl. 22.00 skrev El

Re: [SIESTA-L] Transietsa/sisl problem

(Science) > Condensed Matter Theory (CMT) Group > > | School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > *From: *Nick Papior > *Sent: *Monday, 18 May 2020 6:01 AM > *To: *siesta-l > *Subject: *Re: [SIESTA-L] Transietsa/sisl problem > > > >

Re: [SIESTA-L] Transietsa/sisl problem

Could you try with: sgeom instead of sdata? That forces the interpreter to recognize geometry output settings. Den man. 18. maj 2020 kl. 22.02 skrev shirin zandi < shirinzandi1...@gmail.com>: > Dear Nick, > > Many thanks. > > I did the data por.TBT.nc --info command and thi

Re: [SIESTA-L] Transietsa/sisl problem

Dear Nick, Many thanks. I did the data por.TBT.nc --info command and this is what code produces: Device information: - number of kpoints: 1 <- [ A = 1 , B = 1 , C = 1 ] (time-reversal unknown) - energy range: -4.99950 -- 4.99950 eV [1.000 meV] - imaginary part

RE: [SIESTA-L] Transietsa/sisl problem

El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Nick Papior<mailto:nickpap...@gmail.com> Sent: Monday, 18 May 2020 6:01 AM To: siesta-l<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L

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