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 can use them at the same time. 30 Eyl 2020 Çar 23:00 tarihinde Mehr Iran şunu yazdı: > Dear SIESTA and TranSIESTA users, > > > Can I use VDW+U in my calculation? I noticed there is possibility to use > U correction for LDA, is there the same correction for VDW functional? > > > All the best, > M. > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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 > website only includes 4s2 and 3d6 electrons. But in some published works > with other codes, 3p6 electrons are also included. I suppose that it is > more accurate with more electrons taken into account. Where can I find > those pseudopotentials with more electrons or should I construct one by > myself? This happens to a lot of metals, is it accurate to just use > those pseudopotentials from the SIESTA website to describe metal behavior? > I would really appreciate your help! Thank you! > > Sincerely, > -- > Tan SHI > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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 On Behalf Of D. > Bennett > Sent: 05 August 2020 11:32 > To: siesta-l@uam.es > Subject: [SIESTA-L] Pseudos for vdW functional? > > 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 the pseudopotentials. > I've been using the PSML pseudos from pseudo-dojo for LDA, PBE, etc. Would > it be ok to use those (PBE say) for the vdW functional, or should I > generate my own? I checked the PRL by Román-Pérez and Soler but couldn't > find any info about the pseudos. Any advice would be much appreciated > > Thanks, > > Danny Bennett > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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-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 functional? >> >> 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 the pseudopotentials. >> I've been using the PSML pseudos from pseudo-dojo for LDA, PBE, etc. Would >> it be ok to use those (PBE say) for the vdW functional, or should I >> generate my own? I checked the PRL by Román-Pérez and Soler but couldn't >> find any info about the pseudos. Any advice would be much appreciated >> >> Thanks, >> >> Danny Bennett >> >> >> -- >> SIESTA is supported by the Spanish Research Agency (AEI) and by the >> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >> > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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 afternoon, > > I was wondering about the following: > >1. I have done a TranSIESTA + TbTrans calculation using 1 1 100 and >had a look at transmission curves and PDOS. I got certain results but I >then increased k points to 5 1 100. And only ran a TbTrans. The NEW >results saw some changes. >2. I decided then to restart from scratch the same Transiesta + >Tbtrans calculation with 5 1 100 instead of 1 1 100. I got almost the same >results as the NEW in step 1. Is that expected? If so why ? >3. If so also does that mean I could start with less k points and just >increase them in the TbTrans run by using TBT.k [a b c]? > > > > I just want to make sure that my results are feasible and acceptable. > > Thank you and looking forward to your reply. > > EL-abed > > 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/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] DFT-half method and pseudopotential files
In this mail group,Mr. Fonseca said that all I need is to generate self-energy potential and add it to Zn elements pseudofile. There are calculations in Ferreira's articles but I do not know how I represent dft-1/2 parameters such as power index and strip. Could you give me a sample inp file for dft-1/2 or at least an explanation? Thank you. -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] DFT-1/2
Hello. I am trying to create a Zn ion (for DFT-1/2) file via http://www.eedevice.com/siesta-sh-inner.aspx. I chose the element as Zn and uploaded the necessary ion file. But there was only this message: "The corresponding self-energy potential is not found." Is there any way to create ion files for dft-1/2? Regards. -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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 regards > > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] To compile siesta in Windows
Hi dear siesta users, Is there a way to compile siesta source code in windows via Visual Studio? -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] If you need help for running your job
Hi, if anybody needs help, I may help them (for unknown time). I assume, I can use 16-32 cores. Good luck humanity. -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] scf not converged
Hi. You can use molecular dynamics. Could you post your fdf and pseudopotantial files? RAHUL SURESH , 8 Oca 2020 Çar, 00:00 tarihinde şunu yazdı: > Hi > On optimizing a geometry, after 50 steps, i get the notification that scf > is not converged. What can be done now to get the relaxed structure? > > Another clarification, Is there any tool to final structure from Siesta? > > Thank you > -- > *Regards,* > *Rahul * > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
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 > 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 useful here. :) >> >> I have submitted a patch for this! >> >> Thanks! >> >> Den tir. 3. sep. 2019 kl. 22.01 skrev I. Camps : >> >>> Thank you for your reply. >>> >>> @Nick: I attached both files: input and output. >>> @Berna: They are different schemes but the output is shown twice with >>> different values. >>> >>> >>> []'s, >>> >>> Camps >>> >>> >>> On Mon, Sep 2, 2019 at 5:09 PM Nick Papior wrote: >>> 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 > schemes implemented in SIESTA (Mulliken, Hirshfeld, Voronoi and Bader). > > At the end of the output (bellow), I got two values for the Hirshfeld > and Voronoi. > > My question is: why did I got two values instead of one? > > # Output for Pb > > > > > > > > > > > > > > > > > > *Hirshfeld Net Atomic Populations:Atom #Qatom Species 1 > -0.000 PbVoronoi Net Atomic Populations:Atom #Qatom Species 1 > -0.000 PbBader Analysis core-charge setup. Radii (standard, H): 1.000 > 0.600dhscf: Vacuum level (max, mean) =0.0033770.003376 eVHirshfeld > Net Atomic Populations:Atom #Qatom Species 16.000 PbVoronoi > Net Atomic Populations:Atom #Qatom Species 16.000 Pb* > # Output for Pb > > []'s, > > Camps > -- Kind regards Nick >>> >> >> -- >> Kind regards Nick >> >
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 şunu yazdı: > 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 > schemes implemented in SIESTA (Mulliken, Hirshfeld, Voronoi and Bader). > > At the end of the output (bellow), I got two values for the Hirshfeld and > Voronoi. > > My question is: why did I got two values instead of one? > > # Output for Pb > > > > > > > > > > > > > > > > > > *Hirshfeld Net Atomic Populations:Atom #Qatom Species 1 -0.000 > PbVoronoi Net Atomic Populations:Atom #Qatom Species 1 -0.000 > PbBader Analysis core-charge setup. Radii (standard, H): 1.000 > 0.600dhscf: Vacuum level (max, mean) =0.0033770.003376 eVHirshfeld > Net Atomic Populations:Atom #Qatom Species 16.000 PbVoronoi > Net Atomic Populations:Atom #Qatom Species 16.000 Pb* > # Output for Pb > > []'s, > > Camps >
[SIESTA-L] AWS cloud
Hello, dear siesta users. Did anyone try to set up siesta with mpi library in Amazon cloud (AWS) and/or google cloud? I could try in two months because of my exam. But I wonder whether there is somebody set up siesta in AWS/google clouds or not. Sincerely.
[SIESTA-L] Siesta as a package of Anaconda
Hi, siesta users. I have installed siesta using Anaconda. My system is ubuntu 18.04. You should install Anaconda without sudo command otherwise installing siesta breaks with permission denied error. After installation, siesta, transiesta, denchar, Eig2DOS, eigfat2plot executable files can be seen in the anaconda3(or anaconda2)\bin folder. But I couldn't find examples, tutorials, manuals for siesta. Sincerely, Berna Uyanık
Re: [SIESTA-L] Release of siesta-4.0.2
I think, my question is somehow stupid. https://anaconda.org/anaconda/netcdf4 I am trying anaconda siesta version. Thank you. berna uyanık , 20 Tem 2018 Cum, 23:12 tarihinde şunu yazdı: > Thank you. Could we use netcdf files with anaconda version of siesta? >
Re: [SIESTA-L] Release of siesta-4.0.2
Thank you. Could we use netcdf files with anaconda version of siesta?
Re: [SIESTA-L] running steps
Dear Fatemeh, Please follow steps in the manual which they are in docs folder. But, I think you may have a problem with arch.make file because the new version has few differences. Make sure you have installed fortran (for linux systems) ant change the name of gfortran.make file in obj folder to arch.make. The other steps are same with older versions. Sincerely, Berna Uyanık fatemeh , 24 Haz 2018 Paz, 23:01 tarihinde şunu yazdı: > any advice? >
Re: [SIESTA-L] new version
Dear Fatemah, If you want to use gollum, you should use old versions. But using new versions have always more advances like less bugs and new properties like transport properties with netcdf files.Which property do you want calculate? fatemeh ghorbani , 24 Haz 2018 Paz, 23:00 tarihinde şunu yazdı: > Hi everyone, > I worked with siesta-2.0.2 six years ago and now I want to start working > again. I have some questions about it, please help me. > first, should I work with new version i.e. ? or I can use siesta-4.0 ? > secondly, how can I install it? I've tried a lot but I can't. > Thanks for helping, > Best regards, > Fatemeh > >
Re: [SIESTA-L] file running for long time without error
Dear Harsh, Optimization of the structure can spend long time. You may try molecular dynamics methods for quick optimization. Sincerely, Berna Uyanık 6 Haz 2018 Çar 23:04 tarihinde Harsh Shah şunu yazdı: > Dear Siesta user, > > I am running a file in parallel with around 110 atoms in stampede2 > supercomputer and it has been running for quite a some time. > > It has been running without giving any error and I think it should not > take that much time. > > Is this a problem with MPI or there might be a bug in siesta4? > This is just the possibility which I m stating,it might be due to other > issues also. > > > I would really appreciate if you could help me out. > > With Best Wishes, > Harsh >
Re: [SIESTA-L] file running for long time without error
Dear Harsh, I am sorry, your later posts came late. I saw your first post too early. I understood you do not have optimization or convergence problem. Then what type of method do you use? Spin polarize methods take a long time. Do you use different pseudo potential files? Sincerely, Berna Uyanık 10 Haz 2018 09:07 tarihinde "berna uyanık" yazdı: Dear Harsh, Optimization of the structure can spend long time. You may try molecular dynamics methods for quick optimization. Sincerely, Berna Uyanık 6 Haz 2018 Çar 23:04 tarihinde Harsh Shah şunu yazdı: > Dear Siesta user, > > I am running a file in parallel with around 110 atoms in stampede2 > supercomputer and it has been running for quite a some time. > > It has been running without giving any error and I think it should not > take that much time. > > Is this a problem with MPI or there might be a bug in siesta4? > This is just the possibility which I m stating,it might be due to other > issues also. > > > I would really appreciate if you could help me out. > > With Best Wishes, > Harsh >
Re: [SIESTA-L] transport for 2D materials
Dear Zara, Transiesta using NEGF method which could not successful in high temperature. What is the degree of temperature you used? Sincerely, Berna Uyanık 2018-05-23 10:07 GMT+03:00 Zara Nosh : > Dear Nick, > > But in reality, it is possible to have an applied bias between two ends of > a pristine material without any defects, isn't it? > > What is wrong with this system? Is the problem non-metallic electrodes? > can we study pristine metal materials under an applied bias? In these > cases, the length dependent behavior does not occur? > > The last question, the device transmission at equilibrium (zero bias) is > similar for any length of the scattering region. Can I just consider this > transmission spectrum and conclude about the I-V curve of the system at > higher biases? > > I really appreciate your help in advance. > > Regards, > Zara > > On Tue, May 22, 2018 at 11:20 AM, Nick Papior > wrote: > >> >> >> 2018-05-21 2:25 GMT+02:00 Zara Nosh : >> >>> Dear Nick, >>> >>> Thank you very much for your response. >>> >>> So how should we study the transport properties of the pristine system >>> under bias? >>> >> It is an unphysical system if you are studying a pristine system with >> applied bias. For exactly the reason you see in your initial question. The >> junction only has the potential drop across the full system length, in >> which case the system is length dependent (which it shouldn't). >> >>> Maybe just by considering the zero-bias transmission; but in this >>> regards, we cannot find for example NDR characteristic of a system. >>> >>> Regards, >>> Zara >>> >>> On Sun, May 20, 2018 at 12:18 PM, Nick Papior >>> wrote: >>> >>>> Dear Zara, >>>> >>>> On Sat, 19 May 2018, 22:03 Zara Nosh, wrote: >>>> >>>>> Dear expert, >>>>> >>>>> My results show that calculating the current under bias voltage in a >>>>> pure 2D system depends on the length of scattering region. Also, this >>>>> dependent is not linear, for example, under bias voltage 2V the calculated >>>>> current in the larger system is 1/3 of the current of the smaller system >>>>> but under bias voltage 3 this ratio could be different. >>>>> >>>>> As the system is pure and there is no scatterer in the system, what is >>>>> the reason of this behavior? >>>>> >>>> Because simulating a pristine system with bias is physically wrong. >>>> >>>>> >>>>> Second question: is transiesta method valid for such a study >>>>> (calculating current under bias-voltage in a 2D system)? >>>>> >>>> Transiesta is valid for 2D systems. One cannot apply bias to pristine >>>> systems, but otherwise you can. >>>> >>>>> >>>>> I really appreciate your help in advance. >>>>> >>>>> Best regards, >>>>> Zara >>>>> >>>> >>> >> >> >> -- >> Kind regards Nick >> > >
Re: [SIESTA-L] Vdw pseudopotential
Siesta no longer include the atom. 2018-05-21 17:56 GMT+03:00 Azadeh Ayatollahie : > Dear all > I am going to make vdw pseudo with siesta4-0, but when I installed > siesta4-0, the pseudo directory was empty and there was not atom directory > in it. How can I get the atom4-0 directory? > > Best, > Azadeh > >
Re: [SIESTA-L] DFT+1/2
Dear Nick, Thank you for the answer. Some siesta users said that they used dft+1/2 method. I hope they can add their contribute to launch pad. For now, I found these codes: http://exciting-code.org/boron10-dft05 http://www.gmsn.ita.br/?q=en/node/16 If I handle using siesta with dft+1/2, I will add my contributionts on hosting site. Sincerely, Berna 2018-04-19 9:20 GMT+03:00 Nick Papior : > Dear Berna, > > The siesta code is officially hosted on this Launchpad site: > https://launchpad.net/siesta > > We highly encourage developers to contribute their work on this site. > Currently a DFT+1/2 implementation is not hosted on Launchpad, nor is it > actively developed by any known contributors. > > 2018-04-18 19:05 GMT+02:00 berna uyanık : > >> Dear Siesta users? >> Could you please add DFT+1/2 package or code to mail group. Or, I think, >> adfingvthese packages at github service is better. >> Best >> > > > > -- > Kind regards Nick >
[SIESTA-L] DFT+1/2
Dear Siesta users? Could you please add DFT+1/2 package or code to mail group. Or, I think, adfingvthese packages at github service is better. Best
Re: [SIESTA-L] DFT-1/2 vs DFT-U
I calculated band gap of the wurtzit ZnO crystal as 1.74 eV via GGA+U (for Zn 3d = 9 eV) and 2.87 eV via SGGA+1/2. Maybe, some parameters for Hubbard U term in literature give more accurate results, but I think, in case of defects like vacancies, parameter independent band correction method will be more safe because of missing bonds. 27 Oca 2018 00:01 tarihinde "Julian Niño" yazdı: > why? > > 2018-01-25 3:40 GMT-03:00 berna uyanık : > >> Hi, again. I used both DFT-1/2 and DFT-U methods to calculate ZnO band >> gap. I think the first method is more succesful. Then, siesta should >> include DFT-1/2 method. Best. >> > > > > -- > > - > > - > > - > > - > > - > > - >
[SIESTA-L] DFT-1/2 Method
Hi. I wonder is there an unpublished siesta version which is contains DFT-1/2 method implemented by Kohn and Sham? Sincerely, BernaUyanık
[SIESTA-L] SUBSCRIBE SIESTA-L Berna Uyanık
[SIESTA-L] DFT-1/2 vs DFT-U
Hi, again. I used both DFT-1/2 and DFT-U methods to calculate ZnO band gap. I think the first method is more succesful. Then, siesta should include DFT-1/2 method. Best.
[SIESTA-L] DFT-1/2
Hi. How can DFT-1/2 method be adapted to siesta?
Re: [SIESTA-L] structure optimization
May be, decreasing value of MaxForceTol helps. 2017-04-14 23:17 GMT+03:00 : > Is there any physical reason why you think that the hexagonal symmetry > must preserve? > > Ruslan Zhachuk > > Sent from my iPhone > > On 14 апр. 2017 г., at 17:09, Sunetra Das > wrote: > > Hello SIESTA users, > > I am facing a difficulty during while trying to fully relax a 32 atom > graphene like 2D system with and without a single vacancy, in the middle of > the srtucture. > A part of my input .fdf file is given below: > > > > > > > > > > > > > > > > > > > > > *DM.Tolerance 1.d-3DM.Require.Energy.Convergence > TDM.Energy.Tolerance 1.d-5 eVPAO.BasisSize DZPPAO.EnergyShift 0.3 > eVMD.TypeOfRun CGMaxSCFIterations 3000MD.NumCGsteps > 3000MD.VariableCell TMD.MaxForceTol0.02 eV/AngMeshCutoff300 > RyDM.MixingWeight 0.02DM.NumberPulay 3WriteCoorXmol > TWriteMullikenPop0XC.functional GGAXC.authors > PBESolutionMethod diagonElectronicTemperature 300 K* > The lattice constant of the system, the bond length and bond angle used by > me has already been reported in a reputed journal, as a stable one. I have > not used any constraints in my structure. I have created a 4x4x1 supercell > using the reported dimensions and trying to optimize the structure with the > siesta code version 3.2-pl-5. The problem I am facing is that the optimized > structure is no longer of the symmetry I started with. The structure is no > longer a hexagonal honeycomb one anymore. > Also while using a vacancy defect in the structure the atoms are getting > asymmetrically arranged breaking any symmetry that was present there. > Now my question is, are there any more parameters that I should have > specified in the input .fdf file? > Or, will a change in the .psf file can bring about any improvement in the > optimization? > Also, if I apply some constraints like fixing the bond angles or that my > structure should relax only in a single plane, then how can I say that all > the atoms in my structure are FULLY relaxed? > > Please kindly help me in this regard. I feel like I am missing some > important parameter in my .fdf file. > Thank you. > > Regards, > Sunetra Das. > >
Re: [SIESTA-L] structure optimization
Dear Sunetra, did you have log or output file? In these files, there should be a clue for what wrong is. Best. 2017-04-14 19:09 GMT+03:00 Sunetra Das : > Hello SIESTA users, > > I am facing a difficulty during while trying to fully relax a 32 atom > graphene like 2D system with and without a single vacancy, in the middle of > the srtucture. > A part of my input .fdf file is given below: > > > > > > > > > > > > > > > > > > > > > *DM.Tolerance 1.d-3DM.Require.Energy.Convergence > TDM.Energy.Tolerance 1.d-5 eVPAO.BasisSize DZPPAO.EnergyShift 0.3 > eVMD.TypeOfRun CGMaxSCFIterations 3000MD.NumCGsteps > 3000MD.VariableCell TMD.MaxForceTol0.02 eV/AngMeshCutoff300 > RyDM.MixingWeight 0.02DM.NumberPulay 3WriteCoorXmol > TWriteMullikenPop0XC.functional GGAXC.authors > PBESolutionMethod diagonElectronicTemperature 300 K* > The lattice constant of the system, the bond length and bond angle used by > me has already been reported in a reputed journal, as a stable one. I have > not used any constraints in my structure. I have created a 4x4x1 supercell > using the reported dimensions and trying to optimize the structure with the > siesta code version 3.2-pl-5. The problem I am facing is that the optimized > structure is no longer of the symmetry I started with. The structure is no > longer a hexagonal honeycomb one anymore. > Also while using a vacancy defect in the structure the atoms are getting > asymmetrically arranged breaking any symmetry that was present there. > Now my question is, are there any more parameters that I should have > specified in the input .fdf file? > Or, will a change in the .psf file can bring about any improvement in the > optimization? > Also, if I apply some constraints like fixing the bond angles or that my > structure should relax only in a single plane, then how can I say that all > the atoms in my structure are FULLY relaxed? > > Please kindly help me in this regard. I feel like I am missing some > important parameter in my .fdf file. > Thank you. > > Regards, > Sunetra Das. >
Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2
I do not know how did you understand I do not know how to install siesta. Because I can write all steps of installing siesta without looking into manual. But I know siesta includes lapack and scalapack. Then why does siesta not include another essential package? Some years ago siesta included also atom. Now we should download separately these programs. Maybe you think less you consider more to your students. 2017-03-25 10:45 GMT+03:00 : > hi, > i think what you want to know is..how to install siesta WITHOUT netcdf. > > s.auluck > > > Hi. I am sorry my grammar mistakes. Actually I want to try asking why > > have > > *not *siesta been coming with netcdf? Or why doesn't siesta include > netcdf > > package? > > > > 2017-03-23 7:26 GMT+03:00 berna uyanık : > > > >> Hi. I wonder why have siesta been coming with netcdf? > >> > >> 23 Mar 2017 00:00 tarihinde "Nick Papior" yazdı: > >> > >>> Please see this post which contains a script to install netcdf4. > >>> > >>> http://www.mail-archive.com/siesta-l@uam.es/msg09275.html > >>> > >>> If you have problems with it consult your local administrator or ask on > >>> the NetCDF mailing lists. > >>> > >>> 2017-03-21 10:00 GMT+01:00 Ankita Joshi : > >>> > >>>> Dear SIESTA users, > >>>> > >>>> I want to compile tbtrans using netcdf4 in siesta 4.1b2. Can someone > >>>> send me a link to install netcdf4 ? > >>>> > >>>> Thanks in advance, > >>>> > >>>> Ankita Joshi > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> -- > >>> Kind regards Nick > >>> > >> > > > > > -- > Prof. Sushil Auluck Phone:+91-512-6797092/6148 > Department of Physics +91-512-6798177(Home) > Indian Institute of Technology Cell :+91-9305548667 > Kanpur 208016 (UP) Fax :+91-512-6790914 > IndiaE-mail:saul...@iitk.ac.in > ...:saul...@gmail.com > http://www.nplindia.org/prof-sushil-auluck > http://www.iitk.ac.in/phy/index.php/component/content/ > article/2-uncategorised/124-sushil-auluck > http://www.iitk.ac.in/phy/People/phy_facvis.html > http://www.iitk.ac.in/phy/New01/profile_SA.html > http://www.iitk.ac.in/phy/index.php/people/faculty > http://www.iitk.ac.in/phy/index.php/people/faculty/12- > people/faculty/profile/88-sushil-auluck > ... > ~ >
Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2
Hi. I am sorry my grammar mistakes. Actually I want to try asking why have *not *siesta been coming with netcdf? Or why doesn't siesta include netcdf package? 2017-03-23 7:26 GMT+03:00 berna uyanık : > Hi. I wonder why have siesta been coming with netcdf? > > 23 Mar 2017 00:00 tarihinde "Nick Papior" yazdı: > >> Please see this post which contains a script to install netcdf4. >> >> http://www.mail-archive.com/siesta-l@uam.es/msg09275.html >> >> If you have problems with it consult your local administrator or ask on >> the NetCDF mailing lists. >> >> 2017-03-21 10:00 GMT+01:00 Ankita Joshi : >> >>> Dear SIESTA users, >>> >>> I want to compile tbtrans using netcdf4 in siesta 4.1b2. Can someone >>> send me a link to install netcdf4 ? >>> >>> Thanks in advance, >>> >>> Ankita Joshi >>> >>> >>> >>> >> >> >> -- >> Kind regards Nick >> >
Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2
Hi. I wonder why have siesta been coming with netcdf? 23 Mar 2017 00:00 tarihinde "Nick Papior" yazdı: > Please see this post which contains a script to install netcdf4. > > http://www.mail-archive.com/siesta-l@uam.es/msg09275.html > > If you have problems with it consult your local administrator or ask on > the NetCDF mailing lists. > > 2017-03-21 10:00 GMT+01:00 Ankita Joshi : > >> Dear SIESTA users, >> >> I want to compile tbtrans using netcdf4 in siesta 4.1b2. Can someone send >> me a link to install netcdf4 ? >> >> Thanks in advance, >> >> Ankita Joshi >> >> >> >> > > > -- > Kind regards Nick >
Re: [SIESTA-L] Fwd: transport in ballistic regime for nano structures
Dear Zara, e-e interaction is a Coulomb interaction. There is slave boson method to ignore this term. But so far, I do not know why, any software did not use this method. For theory, you can look Nordlander's and Langreth's articles.Also, you can find experimental results of this group if you search old presentations. Best wishes. 8 Mar 2017 12:12 AM tarihinde "Zara Nosh" yazdı: > Dear all, > I have a question about the studying the transport in nanostructures in > the ballistic regimes. > > As screening reduces in nano structures and e-e interaction is more > important than balk materials, how much ignoring the e-e interactions is > acceptable or reasonable? > Would please any one introduce some comparisons between experimental > results and theory results (in ballistic regimes)? > > I really appreciate your help in advance. > -Zara > >
[SIESTA-L] Supercell
Hi. Should I add supercell definition for geometry optimization of one or two atom doped structure? Thanks for any helps.
Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf
I think tbtrans need netcdf. I used 4.1b1 with transiesta. All functions worked without netcdf. Tbtrans also seemed worked but trans files were empty. 17 Şub 2017 23:00 tarihinde "Riya Rogers" yazdı: > Dear Dr Nick > > Also as I wont be able to manipulate the server packages hence I am > running without netcdf support I think without netcdf it works fine. > > I am also interested in b2 version but in my proj i used B1 version hence > fr now i m using B1 version > > Thanks > > Regards > Riya > > On 17-Feb-2017 2:36 AM, "Riya Rogers" wrote: > >> Dear Dr Nick >> >> Actually I tested few sample prog without netcdf its Working fine thats >> why I asked. >> >> Thanks >> >> Regards >> Riya >> >> On 17-Feb-2017 2:34 AM, "Nick Papior" wrote: >> >>> It is not a must, but it is highly recommendable. >>> >>> Also, the second beta release of siesta 4.1 has been released. >>> When testing with a beta release you are encouraged to follow the new >>> releases, closely. >>> >>> 2017-02-15 15:25 GMT+01:00 Riya Rogers : >>> Dear All Is it must to compile Siesta 4.1b1 with netcdf? Regards Riya >>> >>> >>> >>> -- >>> Kind regards Nick >>> >>
Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf
Has netcdf to be installed for tbtrans? 2017-02-16 0:06 GMT+03:00 Nick Papior : > It is not a must, but it is highly recommendable. > > Also, the second beta release of siesta 4.1 has been released. > When testing with a beta release you are encouraged to follow the new > releases, closely. > > 2017-02-15 15:25 GMT+01:00 Riya Rogers : > >> Dear All >> >> Is it must to compile Siesta 4.1b1 with netcdf? >> >> Regards >> Riya >> > > > > -- > Kind regards Nick >
[SIESTA-L] Semicore pseudopotential files
Hi, I need a semicore pseudopotential file for Zn. But the occupation is 3d10 4s1 4p0.1. I try without 4f. I used atom to make the psp file. But siesta does not accept it. Then, how can I find radii of 4f based on this occupation state? Thanks.
[SIESTA-L] Bash Script
Hi. I prepared a script for k grid optimization. One can improve to other cases. Because of differences between sh and bash commands, the command below should be used: bash template.sh After the task finished And this could be useful: cp *.out ../file_dir Best regards. B. Uyanık template.sh Description: Bourne shell script
Re: [SIESTA-L] Band line with ase-siesta calculator
Dear Boubacar,
The code below worked fine:
calc = Siesta(label='Si',
xc='PBE',
mesh_cutoff=200 * Ry,
energy_shift=0.01 * Ry,
basis_set='DZ',
kpts=[10, 10, 10],
fdf_arguments={'DM.MixingWeight': 0.10,
'MaxSCFIterations': 100,
'BandLines': [ ' 10.0 0.0 -0.5 ',
# gamma point
'200.0 0.0 0.5 ' ]},
)
Thanks for the answer. It inspired me alot.
Regards,
Berna Uyanık
2016-12-28 18:18 GMT+03:00 Boubacar Traore :
> Hi,
>
> To add bandlines block or any other similar block in ASE-siesta (by adding
> the right block name with the proper entries), you may use this example:
>
> I assume that you have attached siesta calculator to calc and we would
> like the band structure at [0 0 0], [0.5 0.5 0.5] and [0.5 0 0] k points:
>
> calc.set_fdf('BandLines', [ ' 10.0 0.0 0.0 ',# gamma
> point
> ' 20 0.5 0.5 0.5 ',#
> another k point with 20 points from gamma, etc
> ' 20 0.5 0.0 0.0 ' ])
>
> ASE siesta interprets this as a block with the entries of the block
> defined in the content of the list (the comma separated strings correspond
> to entries in different lines).
> One remark : This way of block definition worked for ase3.9.0 and
> hopefully did not change with the new versions of ASE (to be checked) ...
>
> Best regards,
> Boubacar
>
> On Sun, Dec 25, 2016 at 1:17 PM, berna uyanık
> wrote:
>
>> Hi. I want to get band lines with ase-siesta calculator. But there is no
>> notation or parameter for siesta block BandLines on web page of ase-siesta
>> calculator. Then I tried
>>
>> "% block BandLines
>> ...
>> % endblock BandLines"
>>
>>
>> "% block BandLines
>> " ..."
>> % endblock BandLines"
>>
>> BandLines("..
>> ..")
>>
>> But neither of them worked.
>> What should I do to plot band lines with ase-siesta calculator?
>> Thanks.
>>
>
>
[SIESTA-L] Band line with ase-siesta calculator
Hi. I want to get band lines with ase-siesta calculator. But there is no
notation or parameter for siesta block BandLines on web page of ase-siesta
calculator. Then I tried
"% block BandLines
...
% endblock BandLines"
"% block BandLines
" ..."
% endblock BandLines"
BandLines("..
..")
But neither of them worked.
What should I do to plot band lines with ase-siesta calculator?
Thanks.
Re: [SIESTA-L] Not convergence in transiesta
Hi. First, you should optimize geometry of structure. http://departments.icmab.es/dmmis/leem/siesta/tlv14/slides15.pdf 2016-12-11 1:48 GMT+03:00 Максим Арсентьев : > play with those two > > 2016-12-11 1:48 GMT+03:00 Максим Арсентьев : > >> hi, >> play with DM.MixingWeight and DM.NumberPulay. >> I recently had the same problem - when I set DM.MixingWeight 0.05 and >> DM.NumberPulay to 2 all come better. >> >> 2016-12-10 23:38 GMT+03:00 Leila Mikaeilzadeh : >> >>> >>> I'm using siesta 4.0b-485 version of siesta/transiesta with the >>> following scf parameters: >>> # SCF variables >>> >>> #DM.MixSCF1 F >>> MixHamiltonian T #changed newly >>> MaxSCFIterations 1 # Maximum number of SCF iter >>> DM.MixingWeight 0.005 # New DM amount for next SCF cycle >>> DM.Tolerance 0.02 # Tolerance in maximum difference >>> DM.Require.Energy.Convergence .true. >>> DM.Energy.Tolerance 0.01 eV >>> DM.UseSaveDM true # to use continuation files >>> DM.NumberPulay 10 #changed >>> Diag.DivideAndConquer no >>> Diag.ParallelOverKyes >>> #Diag.NoExpert T >>> Although with these parameters, electrod calculation is converged >>> rarely fast, but for scattering calculation run up to 3000 scf cycles >>> without convergence the energy. How can I solve this problem? >>> Thank you in advance. >>> >> >> >> >> -- >> Best wishes, >> Maxim Arsent'ev, Ph.D. (Chemistry) >> Laboratory of research of nanostructures >> Institute of Silicate Chemistry of RAS >> > > > > -- > Best wishes, > Maxim Arsent'ev, Ph.D. (Chemistry) > Laboratory of research of nanostructures > Institute of Silicate Chemistry of RAS >
Re: [SIESTA-L] Fwd: Transiesta error in electrode size
Dear Anita, Is your question about "transiesta error in electrode size" or about zGNR zGNR is suitable for device electronics because of its semiconductor properties. There are articles in scholar.google.com for zGNR devices. Regards. 2016-12-05 1:34 GMT+02:00 berna uyanık : > http://docs.quantumwise.com/tutorials/intro_vnl_atk3/intro_vnl_atk3.html > There is a little information in quantumwise.com. But I think, you should > write maunally lengths of electrodes for zGNR. In my opinion, you can > create zGNR nanodevices. > > 2016-12-05 1:12 GMT+02:00 berna uyanık : > >> Tbtrans has been using netcdf4 since siesta4.1. There are changes in fdf >> files. >> But, I had same error which was fixed by "TS.NumUsedAtomsRight/Left " in >> siesta4.0. >> For transport calculations you can also try abinit and wanT together. >> And compere results. >> Bests. >> >> 2016-12-04 0:54 GMT+02:00 berna uyanık : >> >>> Could you try with siesta 4.0? >>> >>> 2016-12-03 12:01 GMT+02:00 anita dameh : >>> >>>> >>>> -- Forwarded message -- >>>> From: anita dameh >>>> Date: 3 December 2016 at 10:52 >>>> Subject: Transiesta error in electrode size >>>> To: siesta-l@uam.es >>>> >>>> >>>> Dear Transiesta users, >>>> >>>> In the new version of Transiesta when I use the zigzag graphene >>>> nannoribbon (zGNR) as electrodes with the length 4.992 Å it represented >>>> errors that imply the electrode length is small. While I noticed there is >>>> no such error in siesta 3.2 and also this size of electrodes can describe >>>> electronic properties of zigzag nanoriboons such as DOS pick in Fermi >>>> energy levels. >>>> >>>> In your opinion this size of zGNR can be suitable for device set up >>>> application or NOT? >>>> >>>> >>>> >>>> >>>> Regards, >>>> >>>> Anita >>>> >>>> >>> >> >
Re: [SIESTA-L] Fwd: Transiesta error in electrode size
Tbtrans has been using netcdf4 since siesta4.1. There are changes in fdf files. But, I had same error which was fixed by "TS.NumUsedAtomsRight/Left " in siesta4.0. For transport calculations you can also try abinit and wanT together. And compere results. Bests. 2016-12-04 0:54 GMT+02:00 berna uyanık : > Could you try with siesta 4.0? > > 2016-12-03 12:01 GMT+02:00 anita dameh : > >> >> -- Forwarded message -- >> From: anita dameh >> Date: 3 December 2016 at 10:52 >> Subject: Transiesta error in electrode size >> To: siesta-l@uam.es >> >> >> Dear Transiesta users, >> >> In the new version of Transiesta when I use the zigzag graphene >> nannoribbon (zGNR) as electrodes with the length 4.992 Å it represented >> errors that imply the electrode length is small. While I noticed there is >> no such error in siesta 3.2 and also this size of electrodes can describe >> electronic properties of zigzag nanoriboons such as DOS pick in Fermi >> energy levels. >> >> In your opinion this size of zGNR can be suitable for device set up >> application or NOT? >> >> >> >> >> Regards, >> >> Anita >> >> >
Re: [SIESTA-L] Fwd: Transiesta error in electrode size
http://docs.quantumwise.com/tutorials/intro_vnl_atk3/intro_vnl_atk3.html There is a little information in quantumwise.com. But I think, you should write maunally lengths of electrodes for zGNR. In my opinion, you can create zGNR nanodevices. 2016-12-05 1:12 GMT+02:00 berna uyanık : > Tbtrans has been using netcdf4 since siesta4.1. There are changes in fdf > files. > But, I had same error which was fixed by "TS.NumUsedAtomsRight/Left " in > siesta4.0. > For transport calculations you can also try abinit and wanT together. > And compere results. > Bests. > > 2016-12-04 0:54 GMT+02:00 berna uyanık : > >> Could you try with siesta 4.0? >> >> 2016-12-03 12:01 GMT+02:00 anita dameh : >> >>> >>> -- Forwarded message -- >>> From: anita dameh >>> Date: 3 December 2016 at 10:52 >>> Subject: Transiesta error in electrode size >>> To: siesta-l@uam.es >>> >>> >>> Dear Transiesta users, >>> >>> In the new version of Transiesta when I use the zigzag graphene >>> nannoribbon (zGNR) as electrodes with the length 4.992 Å it represented >>> errors that imply the electrode length is small. While I noticed there is >>> no such error in siesta 3.2 and also this size of electrodes can describe >>> electronic properties of zigzag nanoriboons such as DOS pick in Fermi >>> energy levels. >>> >>> In your opinion this size of zGNR can be suitable for device set up >>> application or NOT? >>> >>> >>> >>> >>> Regards, >>> >>> Anita >>> >>> >> >
Re: [SIESTA-L] Fwd: Transiesta error in electrode size
Could you try with siesta 4.0? 2016-12-03 12:01 GMT+02:00 anita dameh : > > -- Forwarded message -- > From: anita dameh > Date: 3 December 2016 at 10:52 > Subject: Transiesta error in electrode size > To: siesta-l@uam.es > > > Dear Transiesta users, > > In the new version of Transiesta when I use the zigzag graphene > nannoribbon (zGNR) as electrodes with the length 4.992 Å it represented > errors that imply the electrode length is small. While I noticed there is > no such error in siesta 3.2 and also this size of electrodes can describe > electronic properties of zigzag nanoriboons such as DOS pick in Fermi > energy levels. > > In your opinion this size of zGNR can be suitable for device set up > application or NOT? > > > > > Regards, > > Anita > >
[SIESTA-L] Stars in the output file
Hi. There are stars in ny out file along dDmax and Ef columns. Is that mean these quantities weren't calculated or digits in a number too much? scat.out Description: Binary data
[SIESTA-L] Siesta In Windows
I am using siesta in windows (with cygwin). Is there any different result in linux? Thanks for answers?
[SIESTA-L] Primitive Cell
There are two atoms in graphen's primitive cell. Can I use "NumberOfAtoms 2" for graphene? Thanks for answers.
Re: [SIESTA-L] Difficulty in plotting Band structure in SIESTA using gnubands.f
Hi, http://departments.icmab.es/leem/siesta/Documentation/Tutorials/Barcelona-2007/intro.html Find zip files of exercises open Ex2 folder and use this gnubands.f file. Good lock! 2014-08-27 22:36 GMT+03:00 Saheli Sarkar : > Hello Everyone! > I am a new user of SIESTA . I ran some transiesta jobs and I want to plot > band structure with "8AGNRwire.bands" file.So, I complied the 'gnubands.f' > file with gfortran , but while running the executable, it is showing this > error: > At line 34 of file gnubands.f (unit = 5, file = 'stdin') > Fortran runtime error: Bad real number in item 1 of list input > > Some part of my band structure file '8AGNRwire.bands' is as follow: > > -5.08822475973784 > 0.000E+000 0.780496983871844 > -24.5573270944525112.132171155951 > 160 1 161 > 0.00-23.2828-22.9441-22.5321-22.1938-21.4026 > -21.0609-20.0505-19.6809-17.8503-17.5864 > -15.9972-15.7075-14.1372-13.8170-13.1548 > -12.7664-12.3499-12.2073-12.0498-11.8797 > -11.8784-11.6604-11.2786-11.0484-10.9777 > -10.8026-10.7708-10.5190 -9.9897 -9.7329 >-8.8533 -8.5881 -7.7067 -7.4291 -3.2399 > -2.9647 -1.5979 -1.2958 0.2702 0.6062 > 1.5518 1.9144 1.9424 2.2611 > 2.5260 2. 3.0681 3.3366 3.8311 3.9462 > 4.3610 4.5450 6.0775 6.4844 > 7.0922 7.4849 8.2826 8.6825 9.8889 10.1862 >10.3856 10.3912 11.4923 11.6654 11.9481 > 12.1080 12.2123 12.3194 12.9147 13.0235 >13.1439 13.3469 13.5638 13.6230 13.9119 > 14.4664 15.1507 15.2875 15.4478 15.5400 >15.6579 15.8633 16.7591 17.2966 18.2066 > 18.2901 18.3519 18.7067 19.2839 19.3566 >21.2272 21.4511 21.5498 21.6936 23.0794 > 23.2304 25.0598 25.3692 25.3706 25.4635 >27.4843 27.9680 28.9448 29.3525 29.3742 > 29.6231 31.1160 31.6707 33.4992 34.3139 >34.8484 35.7136 36.0541 36.8756 37.3555 > 37.9084 38.5999 39.3164 40.4543 40.8405 >40.8721 41.4302 42.6732 43.1500 44.4510 > 44.6546 44.7629 44.9399 46.2572 46.5622 >46.6414 47.0428 49.2733 50.1010 53.5866 > 54.4021 55.4737 56.2953 59.8435 60.8530 >64.9607 66.1577 67.0146 67.8963 68.9845 > 70.3779 70.4591 71.3078 72.6434 73.9072 >75.0948 75.8140 81.7366 82.1139 87.5197 > 87.7895 93.9892 94.6691 98.9801 99.8796 > > > I am not being able to understand the error.Could anyone help me with > this?That will be very helpful for me.Can the band structure be plotted in > some other way? > Thanks! > Saheli >
[SIESTA-L] Crystalmaker Files
Hi all. I would like to know whether siesta is able to read / load cmdf file (crystalmaker file). I shall be thankful for replies. Sincerely
Re: [SIESTA-L] charge density
Hi. VMD's supporting files is here: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ You should convert your files to supporting files. On Wed, Jun 4, 2014 at 9:38 AM, Suman Chowdhury wrote: > Dear user, > Can anyone know how to plot charge density through siesta by using vmd > visualization tool. > > -- > > > > *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- > 79, West Bengal, India.* > * Ph no-+91-9830512232 <%2B91-9830512232>* > >
