[SIESTA-L] Koh-Sham eigenvalues

Dear all, I would like to kindly ask if it is possible to calculate the orbital resolved Koh-Sham eigenvalues and corresponding occupation number using siesta code? If so, how to do it? I want to calculate the spin constant coupling for Ti atom (Wss, Wsp, Wsd, Wps, Wpp, Wpd, Wds, Wdp, Wdd), u

[SIESTA-L] range of the basis function

Dear all, please how to "extract" the range of the basis function in Angstroms from *.psf file? best regards

[SIESTA-L] bug siesta 4.1

Dear, there is a bug in m_matio.F90 while compiling siesta 4.1 error #6285: There is no matching specific subroutine for this generic subroutine call. [MPI_REDUCE] call MPI_Reduce(no_l,no_u,1,MPI_integer,MPI_sum,0,SIESTA_Comm,MPIerror) in m_matio.F90 : integer, intent(in) :: no_l call

[SIESTA-L] Left electrode file does not exist. Please create electrode 'NOT REQUESTED' first.

Dear transiesta users, i am using SIESTA 4.1-b1 to do transport calculations. for scattering calculations, i define the electrodes like this : = #define electrodes %block TS.Elecs Left Right %endblock TS.Elecs = #define

[SIESTA-L] manual of new version transiesta

Dear all, Please can anyone give more clarification of this section : 9.8 Matching TranSIESTA coordinates: basic rules of the user guide SIESTA 4.1-b1. best regards

RE: [SIESTA-L] *.TBTGFL and *.TBTGFR files

f you do many transport calculations with the same electrodes, same energy grid and same k-point sampling, then the TBTGF files may be reused which will drastically reduce computation time. In this case it is highly recommended to do so. -- Kind regards Nick Papior On 27 Sep 2016 09:50, &q

[SIESTA-L] *.TBTGFL and *.TBTGFR files

Dear all, what is the role of *.TBTGFL and *.TBTGFR files from tbtrans?? they are very large files. kind regards

[SIESTA-L] non symmetric values of current for symmetric junction

Dear all, is it "normal" to get non symmetric valus of current for symmetric junction? symmetric here means left electrode is the same as right electrode. i am getting different absolute values; i.e == Results: Voltage, Current(A)

[SIESTA-L] error while changing bias

Dear all, i want to present the I-V characteristics, it works fine for biases between -1.5 to -8 (step : 0.1) and also without bias. But for the bias -0.7 it gives the following error : Valence Band Bottom: -10.1950 eV Atoms available/ used atoms : 6 / 6 Orbitals available /

RE: [SIESTA-L] z coordinates from output differnt from input

same folder, please check. On 10-Sep-2016 7:58 pm, "toufik esssakhri" mailto:tou...@hotmail.fr>> wrote: Dear TRansiesta users, i am getting z coordinates in output file different to those in input file in the scatternig calculations and the code prints the following error

[SIESTA-L] z coordinates from output differnt from input

Dear TRansiesta users, i am getting z coordinates in output file different to those in input file in the scatternig calculations and the code prints the following error Structure of the Left electrode | System electrode: X (Ang) Y (Ang) Z (Ang) | X (Ang) Y (Ang) Z (Ang) 0.0 0.0 0.00

[SIESTA-L] "The electrodes are not situated in the same coordinates. Please correct." error

Dear all, i am using siesta-4.0 to do transport calculations,it prints thsi error and stops "The electrodes are not situated in the same coordinates. Please correct." wha siesta is saying means that the the coordinates of electrodes from elect.TSHS are "different" from those in the system. w

[SIESTA-L] Dear all,

i am using tbtrans to calculate transmission function the job is fine with 0 bias voltage but when applaying a non-zero bias the job ends with this error: Starting K-Point loop for spin: 1 Transport for spin -> 1 , kxy-point -> 1, of Node 1 kxy=(-.372 0.000 0.000 ),w= 0

[SIESTA-L] electrode and scattering setup

Dear all, please can anyone verify my electrode and scattering of Fe/MgO junction i am using siesta-3.2-pl-5 # electrode == # UNIT CELL AND ATOMIC POSITIONS LatticeConstant 1 Ang %block LatticeVectors 2.98000.00 0.00 00.002.980

[SIESTA-L] restart tbtrans

Dear all, i am using tbtrans from siesta-3.2-pl-5 to do transport calculation my question is how to restart calculation when using tbtrans? for transiesta we should set : MD.UseSaveXV .true. DM.UseSaveDM.true. is it the case for tbtrans? bests taoufik

RE: [SIESTA-L] TRANS to XSF

excuse me i forget to attach the file From: nickpap...@gmail.com Date: Thu, 12 Nov 2015 10:56:57 +0100 To: siesta-l@uam.es Subject: Re: [SIESTA-L] TRANS to XSF those are the kpoints, so kxy =-.239 0. meanskx =-0.239 andky=0. 2015-11-12 10:40 GMT+01:00 toufik esssakhri : yes this what i want

RE: [SIESTA-L] TRANS to XSF

: siesta-l@uam.es Subject: Re: [SIESTA-L] TRANS to XSF those are the kpoints, so kxy =-.239 0. meanskx =-0.239 andky=0. 2015-11-12 10:40 GMT+01:00 toufik esssakhri : yes this what i want to do, but the file is organized asfollws: # kxy=-.318 0.000 , w= 0.0100 -1.0 0.10869385E-04

RE: [SIESTA-L] TRANS to XSF

TRANS == T(E,k)so extract all T(0,k) and plot that in a contour plot. 2015-11-12 10:29 GMT+01:00 toufik esssakhri : thank you, i want to present the transmission at Fermi level as function as Kx and Ky, there is any idea how to proceed i really appreciate your help From: nickpap...@gmail.com Date

RE: [SIESTA-L] TRANS to XSF

) data file, XSF is a coordinate data file describing a molecule or periodic system. 2015-11-12 9:59 GMT+01:00 toufik esssakhri : Dear all, i am wondring if there is a program to convert .TRANS generated by TRANSIESTA en XSF format i want to plot the kresolved transmission. cheers taoufik

[SIESTA-L] TRANS to XSF

Dear all, i am wondring if there is a program to convert .TRANS generated by TRANSIESTA en XSF format i want to plot the kresolved transmission. cheers taoufik

RE: [SIESTA-L] k resolved transmission

15-10-29 16:22 GMT+01:00 toufik esssakhri : The .TRANS ile is organized like this: # Kxy-point:1 # kxy=-.318 0.000 , w= 0.0100 # Kxy-point:2 # kxy=-.239 0.000 , w= 0.0100 # Kxy-point:3 # kxy=-.159 0.000 , w= 0.0100 # Kxy-point:4 # kxy=

RE: [SIESTA-L] k resolved transmission

transmission The TRANS file contains the k-resolved transmissionAVTRANS contains the k-averaged transmission. 2015-10-29 16:04 GMT+01:00 toufik esssakhri : Dear all, please, can you give me some guide to plot the k resolved transmission cheers taoufik

[SIESTA-L] k resolved transmission

Dear all, please, can you give me some guide to plot the k resolved transmission cheers taoufik

RE: [SIESTA-L] dI/dV

-0500 To: siesta-l@uam.es Subject: Re: [SIESTA-L] dI/dV You can use the tbtrans post processing code (http://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node103.html) Alex On Tue, Jun 9, 2015 at 3:29 AM, toufik esssakhri wrote: Dear all, in many paper, we can

[SIESTA-L] dI/dV

Dear all, in many paper, we can see that we can present the conductance G=dI/dV my question is how to get G from Transiesta calculation at 0 bias and under finite bias voltage? best

RE: [SIESTA-L] how to fix spin TS calculations

up. 2015-05-22 14:43 GMT+02:00 toufik esssakhri : What kind of constraints?? because you can see with this %block DM.InitSpin 1 + %endblock DM.InitSpin all Fe atoms are imposed to be up and vice-versa From: nickpap...@gmail.com Date: Fri, 22 May 2015 14:24:25 +0200 To: siesta-l@uam.es

RE: [SIESTA-L] how to fix spin TS calculations

calculations Have you checked that the spin configurations _are_ different? If not, then try and impose more constraints on the initspin block. 2015-05-22 14:08 GMT+02:00 toufik esssakhri : I try by using block DM.InitSpin right electrode: %block ChemicalSpeciesLabel 1 26 Fe %endblock

RE: [SIESTA-L] how to fix spin TS calculations

individually in transiesta. You have to go by using other methods.I.e. try and converge towards the spin-configuration you want, then proceed. 2015-05-22 13:51 GMT+02:00 toufik esssakhri : Dear all, I am using transiesta to do transport calculation, i want to fix all spin in right electrode to be

[SIESTA-L] how to fix spin TS calculations

Dear all, I am using transiesta to do transport calculation, i want to fix all spin in right electrode to be up and all spin in left one to be down i set the flag FixSpin to be .true. but i faced that error Begin: TS CHECKS AND WARNINGS Fixe

[SIESTA-L] paralel antiparalel with DM.InitSpin

Dear all, i am trying to calculate the TMR for a ferromagnetic/oxide/ferromagnetic junction. i should do calculation for parallel and antiparallel configurations, so i initialize the spin by using the block DM.InitSpin %block Chemical_Species_Label 1 26 Fe_up 2 26 Fe_down %endblock

RE: [SIESTA-L] compiling plrho utility

Dear, i am also trying to compile plrho, i use this command : gfortran -o plrho plrho.f -L/usr/local/pgplot -L/usr/X11/lib -lpgplot -lX11 i faced this error icolor.f:179.72: Included a

RE: [SIESTA-L] TMR and TMR

2015 21:04:59 +0200 To: siesta-l@uam.es Subject: Re: [SIESTA-L] TMR and TMR I haven't tried myself, but you should be able to do this with DM.InitSpin (if the configurations converge to their respective anti-parallel and parallel magnetizations). 2015-04-08 20:04 GMT+02:00 toufik esss

[SIESTA-L] TMR and TMR

Dear all, The tunneling magnetoresistance is defined as TMR=(Iparallel-Iantiparallel)/(Iparallel+Iantiparallel), it's known that intensensity versus bias can be done with tbtrans my question is how to set the structure to the parallel and antiparallel configuration with transiesta. cheers

[SIESTA-L] k-point resolved transmission

Dear all, in this paper http://dx.doi.org/10.1088/0957-4484/25/34/345703, the authors presented in figure4 the k-point resolved transmission function at Fermi level. my question is : which file have been used to do such figure? is there a special software to present it?

RE: [SIESTA-L] Re : Re: wrong solution method

2015 at 00:57, toufik esssakhri wrote: Ok i will talk to our system administrator to install it thanks a lot From: nickpap...@gmail.com Date: Thu, 12 Feb 2015 19:07:41 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] wrong solution method Sorry, that is probably wrong, I do not kn

[SIESTA-L] Re : Re: wrong solution method

s.html > > 2015-02-12 19:04 GMT+00:00 Nick Papior Andersen : > > I think your system administrator needs to do the previous steps I said, > it seems like you have a corrupt executable. (it reads it in correctly > first, then dies later...) :( > > 2015-02-12 19:00 GMT+00

RE: [SIESTA-L] wrong solution method

, it seems like you have a corrupt executable. (it reads it in correctly first, then dies later...) :( 2015-02-12 19:00 GMT+00:00 toufik esssakhri : it gives the same error siesta: ERROR: wrong solution method From: nickpap...@gmail.com Date: Thu, 12 Feb 2015 18:54:02 + To: siesta-l@uam.es

RE: [SIESTA-L] wrong solution method

it gives the same error siesta: ERROR: wrong solution method From: nickpap...@gmail.com Date: Thu, 12 Feb 2015 18:54:02 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] wrong solution method try and change solutionmethod to:transi 2015-02-12 18:44 GMT+00:00 toufik esssakhri : all done by our

RE: [SIESTA-L] wrong solution method

ke cleanmake transiesta Else try and compile transiesta again by doing the above. 2015-02-12 18:28 GMT+00:00 toufik esssakhri : Dear all, i want to redo examples from http://departments.icmab.es/leem/siesta/tlv14/ using siesta-3.2-pl-5, i begun with the first example (00-chain), i do not make a

[SIESTA-L] wrong solution method

Dear all, i want to redo examples from http://departments.icmab.es/leem/siesta/tlv14/ using siesta-3.2-pl-5, i begun with the first example (00-chain), i do not make any change to the *fdf files the first step (electrode) is done correctally and i have the elect.TSHS, now to do calculation fo

RE: [SIESTA-L] Transmission doesn't change

guess what happens from graphs... 2015-02-10 9:26 GMT+01:00 toufik esssakhri : what do you mean by "saturation"? for 7, 9 and 11 layers i have exactally the same results > Date: Tue, 10 Feb 2015 13:51:21 +0530 > From: saul...@iitk.ac.in > To: siesta-l@uam.es > Subject: Re:

RE: [SIESTA-L] Transmission doesn't change

what do you mean by "saturation"? for 7, 9 and 11 layers i have exactally the same results > Date: Tue, 10 Feb 2015 13:51:21 +0530 > From: saul...@iitk.ac.in > To: siesta-l@uam.es > Subject: Re: [SIESTA-L] Transmission doesn't change > > hi, > the 5 layer looks very different. > could you have re

[SIESTA-L] Transmission doesn't change

Dear all transiesta/tbtrans users, i am doing transport properties of Fe/MgO junctions, at 0 bias you can see that the transmission coeffiecient doesn't change when increasing the thickness of the substrate (MgO) from 5 to 11 monolayers, the same for 7, 9 and 11. i can not undersatand what

[SIESTA-L] same input but different results

Dear all, I am performing some transiesta (tbtrans) calculations Why when i do calcutions using same input with different cluster i do not have the same results??

[SIESTA-L] restart TRANSIESTA

Dear all, i do some transiesta calculations, i want to restart calculation so i use these flags: UseSaveData .true. DM.UseSaveDM .true. MD.UseSaveCG .true. but the job restarts from the begening kindly help me to restart the job from where it was terminated? Bests taouf

[SIESTA-L] tbtrans suddenly STOPS

Dear all, i am using tbtrans to calculate the transmission, the calculation stops suddenly --- --- > tail -5 scat-tbt.out Start

[SIESTA-L] How to define atomic positions for TRANSIESTA?

Dear all, I want to use transiesta do transport properties of some metal/oxide junctions. i have done siesta calculations to obtain electronic properties, please, how can i define atomic positions for electrode and the scattering. here the atomic positions for the hole junction used in siesta cal

RE: [SIESTA-L] Unexpected no. orbs. in L elec.

many atoms as an electrode.If this doesn't help, please compare how an electrode is defined for the examples in the Tests directory. Reading the manual while comparing to an existing working setup should clarify any issues you might have. 2014-11-10 8:45 GMT+00:00 toufik esssakhri : I

[SIESTA-L] Unexpected no. orbs. in L elec.

I'm trying to run transport calculations for metal/oxide junction. Calculation for electrode is done corrctally and it gave *.TSHS without any problem, but when i go to do calculations for the scattering region i got an error like this: === ERROR:

RE: [SIESTA-L] electrode model calculation

​Dear: so if I build by electrode like the pic. attached, is that OK?the z direction is in (111) direction​ -- Best Regards 邱芳瑜 Chiu Fang Yu 國立成功大學 材料科學與工程學系碩一 MOBILE：0930287221(中華) GMAIL：joyce79...@gmail.com 2014-08-26 21:26 GMT+08:00 toufik esssakhri : dear, PBC = Periodic Bondairy

RE: [SIESTA-L] electrode model calculation

dear, PBC = Periodic Bondairy Condition in my knowledge, the electrode should be periodic only in the z-direction (z here is the direction of transport) Date: Tue, 26 Aug 2014 21:18:58 +0800 From: dxshao...@gmail.com To: siesta-l@uam.es Subject: Re: [SIESTA-L] electrode model calculation What

RE: [SIESTA-L] version 3.2 : siesta = transiesta??

well explained.(you are using siesta, not transiesta in your calculation) 2014-08-08 8:54 GMT+00:00 toufik esssakhri : what's exactally gone wrong?? this is the first lines of the output Siesta Version:siesta-3.2-pl-5 Architecture : x86_64-c

RE: [SIESTA-L] version 3.2 : siesta = transiesta??

u have done something wrong. The output will tell you whether it has transiesta supported or not (check the first 5 lines of the output) 2014-08-07 20:34 GMT+00:00 toufik esssakhri : Thanks, one other question : To do transiesta calculation should i do export executable= transiesta

[SIESTA-L] Re : Re: version 3.2 : siesta = transiesta??

n" Envoyé : 7 août 2014 23:30 A : siesta-l@uam.es Objet : Re: [SIESTA-L] version 3.2 : siesta = transiesta?? 2014-08-07 13:23 GMT+00:00 toufik esssakhri : > dear all, > > i have one question please > > In version 3.2, is *transiesta = siesta* (which is included)?? > transi

[SIESTA-L] version 3.2 : siesta = transiesta??

dear all, i have one question please In version 3.2, is transiesta = siesta (which is included)?? cheers, Taoufik

[SIESTA-L] non zero exit code

dear all, i want to do transiesta calculation for graphen with 4 nodes in parallel, the process craches and i have this error in the last of graphen.out * Maximum dynamic memory allocated = 126 MB *** Note: ParallelOverK option

RE: [SIESTA-L] error tbtrans

trans. You could try the TBtrans_rep in the trunk-versions. 2014-07-18 1:32 GMT+02:00 toufik esssakhri : i attached the ouput file From: nickpap...@gmail.com Date: Thu, 17 Jul 2014 19:41:19 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] error tbtrans Do the output of tbtrans show anyt

RE: [SIESTA-L] error tbtrans

i attached the ouput file From: nickpap...@gmail.com Date: Thu, 17 Jul 2014 19:41:19 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] error tbtrans Do the output of tbtrans show anything? Else it seems like you call tbtrans erroneously. 2014-07-17 12:55 GMT+00:00 toufik esssakhri

[SIESTA-L] error tbtrans

Dear all, i want to to transport properties using transiesta and tbtrans, so i start with rerun example of H in the siesta package electrode and scattering are done with transiesat, fine when i want to do tbtras calculations, i have this error in the out file : --

RE: [SIESTA-L] can not have band structure with gnubands??

not have band structure with gnubands?? Hello Firstly run .bands files with gnubands I.e executable file then plot by using gnuplot. On 17 Jul 2014 12:52, "toufik esssakhri" wrote: Hi, this is my file *.fdf, you can check it i do not understand why i don't have band struc

RE: [SIESTA-L] structual optimization

check atomic positions with xcrysden for example taoufik Date: Thu, 17 Jul 2014 17:01:03 +0800 From: dxshao...@gmail.com To: siesta-l@uam.es Subject: [SIESTA-L] structual optimization Dear everyone:I‘m now considering make a defect in the original structure.However,when I come to the structual o

RE: [SIESTA-L] can not have band structure with gnubands??

> line in your input file. > > Regards, > > Alberto > > > On 16 Jul 2014, at 15:42, toufik esssakhri wrote: > > > yes, that's exactally what i do, > > also i try : gnubands < prefix.BONDS > output > > and no result > > i use a s

RE: [SIESTA-L] can not have band structure with gnubands??

th gnubands?? Dear taoufik, Please use like this: gnubands < prefix.BONDS | tee output then you can see output using gnuplot. all the best Hui 2014-07-16 14:06 GMT+02:00 toufik esssakhri : Dear alla, i want to present th e band structure of my system, in my prefix.fdf file i put

[SIESTA-L] can not have band structure with gnubands??

Dear alla, i want to present th e band structure of my system, in my prefix.fdf file i put : WriteKbands .true. WriteBands.true. BandLinesScale pi/a = %block BandLines 1 0.0 0.00 0.00 \Gamma 40

[SIESTA-L] transport calculation

Dear all, i want to do transport properties in the metal/oxyde junction using TRANSIESTA, i don't find documentation. Please, there is anyone help me how to proceed?? cheers

RE: [SIESTA-L] 4zGNR

coherent with the block DM.InitSpin?? what i see that Fe1 and Fe2 not reconized! thaks taoufik Date: Tue, 24 Jun 2014 15:24:39 +0800 From: xhzh...@theory.issp.ac.cn To: siesta-l@uam.es Subject: Re: [SIESTA-L] 4zGNR Do it in the "DM.InitSpin" block. From: toufik esssakhri

RE: [SIESTA-L] 4zGNR

Dear, i am intrested on this subject >InitSpinAf only sets every second atom spin up, and every other second spin >down. this is true to configurate the hole system as antiferromagnetic. now for exemple i have one system with two atom, one antiferromagnetic and one nonmagnetic (for example FeR

RE: [SIESTA-L] FeRh antiferromagnetic system

Dear all, i want to study a binary alloy FeRh, this system have two magnetic configuration one ferromagnetic and one antiferromagnetic. The structure is the same (CsCl) i begin with the ferromagnetic so i set SpinPolarized to true, all it's fine. now to do calculations for the antiferromagnetic co

RE: [SIESTA-L] how to compile the TBTrans in the version siesta-trunk-458

Dear all, I am a beginner user of Siesta and I am trying to do calculations for the very known hybrid system metal/oxyde junction. i need to use a tetragonal supercell, so how can i build it or define the atomic positions with siesta. i can extract the positions using XCrySDen for example but h