Re: [SIESTA-L] Segmentation fault problem

by fixing the > libraries, i'm not familiar with this one. Thank you very much in advance > > 2016-02-23 0:27 GMT+01:00 Nick Papior <nickpap...@gmail.com>: >> >> have you fixed your libraries so not to perform threading in any places? >> >> Also which version of

Re: [SIESTA-L] Segmentation fault problem

> siesta_forces.F > siesta 012A2786 MAIN__ 23 siesta.F > siesta 0042F51E Unknown Unknown Unknown > libc.so.6 7FE713577D1D Unknown Unknown Unknown > siesta 00

Re: [SIESTA-L] Segmentation fault problem

You shouldn't compile with openmp, if the segmentation fault still occurs, compile again with debug flags (read the intel documentation for the flags or search this list for previous answers). 2016-02-22 22:34 GMT+01:00 Szendrő Márton : > Dear Siesta Users, > > I compiled

Re: [SIESTA-L] Error in Cholesky factorisation in rdiag

should i to increase cell dimension? > > On Mon, Feb 22, 2016 at 2:10 PM, Mayuri Vaghela <mayurivaghel...@gmail.com> > wrote: >> >> ok so i have to change atomic coordinate, but according to ZnS structure >> my input is correct so how should i change? >> >>

Re: [SIESTA-L] Error in Cholesky factorisation in rdiag

This is a sign of erroneous setup of coordinates: siesta: WARNING: Atoms 1 7 too close: rij =0.59 Ang Basically you have two atoms lying ontop of each other. This may cause your error. Please correct your input. 2016-02-22 9:06 GMT+01:00 Mayuri Vaghela

Re: [SIESTA-L] k-sampling in transiesta/tbtrans calculations

gt; is an overall use of kz=1. This kz-value is highly puzzling for me. > I would highly recommend you to reread the transiesta paper. Hint: The answer lies in the self-energies. > > > On Tue, Jan 19, 2016 at 10:01 PM, Nick Papior <nickpap...@gmail.com> > wrote: > >> You seem

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

ile' >> >> Reading GF file, with title: >>nanoribbon.TSGFR >> Title: 'Generated GF file' >> >> ts-charge: OL L-CC C-RR Qt >> ts-charge:4.654 133.7293.918 329.5484.652 133.346 609.847 >

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

at is > wrong. > > I am attaching my electrode and scattering .fdf files. > > Please help me with this I am doing this for several hours. > > Thank You > > Regards > Rajan Singh > > On Wed, Jan 20, 2016 at 1:47 PM, Nick Papior <nickpap...@gmail.com> wrote:

Re: [SIESTA-L] k-sampling in transiesta/tbtrans calculations

You seem to think that k-points are a generic chosen value. It is not. You should think of k-points in _exactly_ the same way as in regular siesta calculations. And what does one do with k-points in siesta? Basically, you converge them... I would highly advice you to read Kittel, Martin, or any

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

Check these slides, and see if they will help you (they are a guiding example!): http://departments.icmab.es/leem/siesta/tlv14/slides12.pdf 2016-01-19 19:04 GMT+01:00 RAJAN SINGH : > Dear Siesta Users > > Kindly give me advice on the following: > > In order to

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

> Is that right? > > Please help me. > > With Regards > Rajan > > On Tue, Jan 19, 2016 at 11:49 PM, Nick Papior <nickpap...@gmail.com> > wrote: > >> Check these slides, and see if they will help you (they are a guiding >> example!): >> >>

Re: [SIESTA-L] Problem to install siesta-trunk-462

Try a different compiler. Which version of your compiler are you using? 2016-01-15 15:42 GMT+01:00 ticu Cubot : > Dear Siesta users, > > I had the following problem by installation in the standard manner > indicated in the manual: > > pwd > > /home/ticu/siesta-trunk-462/Obj

Re: [SIESTA-L] transiesta+TSHS file contains a wrong nspin

ions. > > I couldn’t understand what other items may be effective in such > calculations? > > Warm regards > > azar > > On Fri, Jan 15, 2016 at 2:46 AM, Nick Papior <nickpap...@gmail.com> wrote: > >> As it says, it thinks the device calculation has a differe

Re: [SIESTA-L] Problem to install siesta-trunk-462

tware Foundation, Inc. >> >> make >> ... >> /usr/bin/ld: warning: libgfortran.so.1, needed by >> /usr/lib/../lib64/liblapack.so, may conflict with libgfortran.so.3 >> >> The warning is not harmless... >> >> On Fri, Jan 15, 2016 at 8:50 PM, N

Re: [SIESTA-L] Problem to install siesta-trunk-462

ortran (GCC) 4.6.3 > Copyright (C) 2011 Free Software Foundation, Inc. > > make > ... > /usr/bin/ld: warning: libgfortran.so.1, needed by > /usr/lib/../lib64/liblapack.so, may conflict with libgfortran.so.3 > > The warning is not harmless... > > On Fri, Jan 15, 2016 at 8

Re: [SIESTA-L] Problem to install siesta-trunk-462

I mean "gfortran" command... If that was confusing. 2016-01-15 21:48 GMT+01:00 Nick Papior <nickpap...@gmail.com>: > I guess this is due to the f95 standard, see e.g. > https://gcc.gnu.org/bugzilla/show_bug.cgi?id=33106 > > I do not know if your f95 forces the

Re: [SIESTA-L] transiesta+TSHS file contains a wrong nspin

As it says, it thinks the device calculation has a different number of spin components than your electrode, check your input, for both the electrode and the device. -- Kind regards Nick Papior On 14 Jan 2016 21:38, "azar ostovan" <azarosto...@gmail.com> wrote: > when

Re: [SIESTA-L] cannot reproduce results from Transiesta's original paper PRB 65, 165401 (2002)

writing this message, I went (as carefully as I could) through the > mailing list, PRB paper, the siesta manual, etc. I would greatly appreciate > a specific response and concrete details, and apologize for what I could > have overlooked by reading the aforementioned materials. > >

Re: [SIESTA-L] "allocate error" when using mpiifort

I would highly advice you not to use -i8. I have never tried it, but I doubt siesta is capable of dealing with it. At least then your mpi libraries should have been compiled as well with that, but I do not think that applies. Please remove that line, then I think you should be fine. And yes,

Re: [SIESTA-L] TRANSIESTA stuck on convergence

; there is some kind of proportion that I'm unaware of? > > Anyway, thanks for the help, I hope I can finally figure this out so that > it doesn't happen again. > > Ernesto > > El 2016-01-06 08:21, Nick Papior escribió: > >> Most likely is your device too small (you need ad

Re: [SIESTA-L] TRANSIESTA stuck on convergence

nd the > device to "hide" its effects from them, right? > It sounds correct. :) > > In any case, I'm going to test this and see what happens. > > Ernesto > > El 2016-01-06 09:33, Nick Papior escribió: > >> Sorry, I can see the confusing of "electrod

Re: [SIESTA-L] << Beta version of Siesta-4.0 vs Trunk >>

Basically siesta-4.0 is a beta release of the trunk version. Hence they are the "same" branch. I would suggest you use the siesta-4.0 version as that has some recent bug-fixes. For details of the differences between the latest trunk (462) and siesta-4.0, please see:

Re: [SIESTA-L] TRANSIESTA stuck on convergence

8 -4.5916 > > After reading all the tutorials/manuals/mailing list mails I could find > and triple checking everything, I just don't know what I may be missing > when, as I said, similar systems have converged using these parameters. I > hope you can help me. > > Best regard

Re: [SIESTA-L] external electricfield

The three quantities are along the corresponding unit-cell vectors: First quantity for the first lattice vector. Second quantity for the second lattice vector. Third quantity for the third lattice vector. 2016-01-04 15:54 GMT+01:00 Eliya Asmani : > Dear all > > I have a

Re: [SIESTA-L] cannot reproduce results from Transiesta's original paper PRB 65, 165401 (2002)

You have created the electrodes erroneously. Please carefully reread the article and manual for constructing a proper electrode. There are many questions on the list about correct electrode setups. Also try and search the mailing list. Further, the Al example can be tricky as you need to utilize

Re: [SIESTA-L] grid2cube

/zerothi/sids After installation the utility sgrid performs your required operations, difference in grids, etc. If you have any questions about the program feel free to open an issue on the github page. -- Kind regards Nick Papior On 31 Dec 2015 02:30, "Jingxian Yu" <jingxian...@ad

Re: [SIESTA-L] Untrusted transmission function

occurring there? -- Kind regards Nick Papior Dear TranSIESTA users, Now I investigated on the electron transport properties of a two-probe system with a zigzag graphene nanoribbon and an armchair graphene nanoribbion as the left and right electrodes respectively. As we know, the zigzag graphene

Re: [SIESTA-L] siesta-trunk-462

I guess you are linking against the internal lapack libraries, please do try and link against MKL, ACML, OpenBLAS+LAPACK or other linear algebra packages. Please search the mailing list for linking against BLAS/LAPACK/ScaLAPACK. 2015-12-26 19:01 GMT+01:00 Soumaia Djaadi :

Re: [SIESTA-L] Technical problem with SIESTA

Your error lies in the python script, nothing wrong with siesta here... You have to debug your python script. :) 2015-12-16 10:59 GMT+01:00 : > Dear SIESTA Users, > > While using the flags of > PAO.Filter T > VNA.Filter T > FilterCutoff 100 Ry > This error has appeared.

Re: [SIESTA-L] How to apply a gate bias perpendicular to the Z-direction in Transiesta?

e way gate-bias is considered in the next release of > TranSIESTA so that TranSIESTA users can have an overview of this > functional in advance. > > Thanks so much. > > Guangping Zhang > > > On 2015/7/26 21:13, Nick Papior wrote: > > I cannot say for sure, I hope before the

Re: [SIESTA-L] Failure compiling trunk-464--pexsi-v0.8-2

Can you compile regular siesta? I.e. the trunk version? It seems like FoX isn't build and hence siesta_cml does not compile. Please check the FoX directory and ensure that you can compile the fox library. 2015-12-08 3:12 GMT+01:00 Wei Hu : > Dear siesta users, > > I

Re: [SIESTA-L] Flag associated with proper electrode length

There is no flag to ensure this. This question has been posted several times on the mailing list, please search the mailing list. It is also addressed in the manual. Please re-read the manual as well. 2015-12-02 13:05 GMT+01:00 RAJAN SINGH : > > Dear Siesta Users > >

Re: [SIESTA-L] Flag associated with proper electrode length

and how they select the electrode > length. > > Please help me with this. > > Thank You > > Regards > Rajan Singh > > On Wed, Dec 2, 2015 at 5:41 PM, Nick Papior <nickpap...@gmail.com> wrote: > >> There is no flag to ensure this. >> This

Re: [SIESTA-L] Question about fatbands

What have you done? I have no problem aligning them? new.gnubands only prints out the k-values that you have requested, hence if you only request a subset of bands and/or energies you may or may not get the full k-space. However, this only means that there are no bands at other k for the

Re: [SIESTA-L] Max job run time

no, there isn't, siesta has implicit restart files XV and DM files. Read the manual about these two files. 2015-11-24 13:59 GMT+01:00 Thong, Aaron : > Hi all, > > I couldn't find an option to set the max runtime for jobs in the input > file. Is there such an option

Re: [SIESTA-L] TRANSIESTA stuck on convergence

@Ernesto and @Riya this should apply to you both 1. Your system should start in 0,0,0, please move your atomic coordinates to assert this. 2. Your right electrode is far too short. Please look into how to setup a good calculation. 3. Your mixing weight may be too high for this system, but please

Re: [SIESTA-L] Puzzled about ParallelOverK feature

2 0.512 1.025 0.14 > elaps: DHSCF41 71.874 71.87410.08 > elaps: dfscf 1 70.398 70.398 9.88 > elaps: overfsm 1 0.269 0.269 0.04 > elaps: optical 1 0.000 0.000 0.00

Re: [SIESTA-L] Puzzled about ParallelOverK feature

end; thus >> degrading performance. >> >> >> -Salvador >> >> >> >> >> *From:* siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of >> Nick Papior <

Re: [SIESTA-L] Puzzled about ParallelOverK feature

Oh, a last thing, timing can be dubious as that is typically inferred from clock-cycles in the cpu, hence I would advice you to time it your self. For instance by doing: date ... date It depends on the underlying timing function used. 2015-11-03 14:03 GMT+01:00 Nick Papior <nick

Re: [SIESTA-L] Puzzled about ParallelOverK feature

> code, wall-clock time derives from f95 SYSTEM_CLOCK intrinsic, > which is being handled by the master node. Rulling out programing > mistakes, would that still be dubious ?. > Well, at least I could time siesta from the shell, so that no > tinkering with the sources. > > O

Re: [SIESTA-L] Puzzled about ParallelOverK feature

> > Those elapsed times are so close ... there must be an easy explanation. > Yes, if you are using mpirun -np 5 on a quad core machine, then the explanation is easy and your numbers are irrelevant. > > Best, > > Roberto >

Re: [SIESTA-L] Puzzled about ParallelOverK feature

ine, never use more MPI processors than you have physical processors. If you still want more explanations, turn to MPI developers for more technical details, all I can say, never use more MPI processors than you have physical cores. > Best regards, > > Roberto > > > On 11/02/201

Re: [SIESTA-L] Transmission spectrum of carbon nanotube (8,8)

at the Fermi > level, instead of 2. I think that I have to play with parameters, the > electronic temperature and Kpoints. > Best regards. > > Damien > > > On 30/10/2015 12:42, Nick Papior wrote: > > Great. Note, it will not print whether your device region is too sm

Re: [SIESTA-L] scf loop break

There seems not to be any problem in your arch make if openmpi is used and compiled with the intel compiler. Else, you need to do debugging on the specific machine you have problems with, consult with your cluster-administrator to best debug this. But it could be related to some kind of memory

Re: [SIESTA-L] Transmission spectrum of carbon nanotube (8,8)

Your electrode length is almost certainly too small, you must ensure principal cell connections, only. Try and double your electrode. -- Kind regards Nick Papior On 30 Oct 2015 00:54, "Damien Tristant" <trist...@insa-toulouse.fr> wrote: > Dear Everybody > &

Re: [SIESTA-L] Transmission spectrum of carbon nanotube (8,8)

.fr>: > Thank Nick Papior for your help, but unfortunately I got the same problem. > Enclosed, I put the Transmission spectra and a picture of 3 different > systems : > - 96 atoms (1 unit cell for left electrode ; 1 unit cell for the sample ; > 1 unit cell for the right electrode)

Re: [SIESTA-L] k resolved transmission

The TRANS file contains the k-resolved transmission AVTRANS 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 > -- Kind regards

Re: [SIESTA-L] k resolved transmission

Use the TBtrans_rep from the trunk versions, the files are more understandable in that version. 2015-10-29 16:37 GMT+01:00 toufik esssakhri : > Thank you for responding, i am using siesta-3.2-pl-5 > another question: how to read thess lines : > # Kxy-point:1 > #

Re: [SIESTA-L] k resolved transmission

Energy | transmission | DOS | PDOS I can't recall that exact file format, I think it is the _old_ tbtrans format, I would suggest you use the latest version of tbtrans (TBtrans_rep from the trunk versions). 2015-10-29 16:22 GMT+01:00 toufik esssakhri : > The .TRANS ile is

Re: [SIESTA-L] SIESTA on Intel Xeon Phi

I have never heard of anybody doing this, so if you succeed please share your results. Let me note that SIESTA is currently built for MPI parallel execution with large memory blocks, hence I would not suspect any real benefit with the XeonPhi coprocessing as memory could(?) be the bottleneck for

Re: [SIESTA-L] Parallel SIESTA

We need much more information. For all we know, you could be using the serial version. Please elaborate on all you have done. -- Kind regards Nick Papior On 20 Oct 2015 23:48, "Anup Pandey" <anup.pandey...@gmail.com> wrote: > Hello everyone, > > I have a simple a

Re: [SIESTA-L] siesta crashes when running on multiple nodes

This may or may not be due to your local computer killing your application for various reasons. We simply do not know. As this hasn't been reported by any-one else I suspect you are: 1) Going beyond your time-limit (is it a cluster with an admin? Have you asked him/her first?) 2) Perhaps you are

Re: [SIESTA-L] Restart a Force constant calculation

I don't know if vibra can handle restarts, but you simply change the FCfirst flag. You possibly have to rename the new files. -- Kind regards Nick Papior On 9 Oct 2015 05:52, "Radhika Narayanan" <radhika.narayana...@gmail.com> wrote: > Dear all, > > Could anyone sugge

Re: [SIESTA-L] error running siesta parallel

< > .f90.o: > $(FC) -c $(INCFLAGS) $(FFLAGS) $< > # > > > Regards > > Aniruddha > > On Mon, Oct 5, 2015 at 4:56 PM, Nick Papior <nickpap...@gmail.com> wrote: > >> Post your arch.make file, and which version of siesta you are using. >>

Re: [SIESTA-L] Transiesta compilation error

You are missing the zgesv routine (defined in liblapack.a). Please search the mailing list, it has been asked before. 2015-10-01 18:27 GMT+00:00 RAJAN SINGH : > > Dear Siesta Users > > While doing the installation of siesta-3.2 (path level 5) version after >

Re: [SIESTA-L] TS.ComplexContour.Emin

There is now correct answer, it just have to be "well below". Test it to get a feel for it. 2015-10-03 16:27 GMT+00:00 Seyed Mohammad Tabatabaei : > Dear all, > > How many electron volts should the TS.ComplexContour.Emin be lower > than the minimum eigenvalue? > > Bests, >

Re: [SIESTA-L] How much difference between Qsol and Qtot does not ruin the calculated currents?

width of my electrodes further? > > On 10/1/15, Nick Papior <nickpap...@gmail.com> wrote: > > You may have a longer ranging screening length of your electrode. > > > > Try and add more electrode layers. Generally you just want dQ to be as > low > > as possible, but

Re: [SIESTA-L] ISSUE IN INSTALLATION SIESTA-3.2

Please reread the manual, it seems like you are missing obj_setup.sh step. 2015-09-27 10:30 GMT+00:00 RAJAN SINGH : > Dear Siesta Users > > While doing the installation of siesta-3.2 (path level 5) version after > generation of "arch.make" file using command

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

Ok, so there is a bug in diagk and pdos file when not passing a full weight of the k array. This patch fixes it (note the patch also fixes a bug in pdoskp which is related to Diag.ParallelK. Apply by: $> cd $> patch -p0 < patch_writewave_pdos 2015-09-25 7:25 GMT+02:00 Nick Papior

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

s it also > valid for Siesta 3.2-pl 5? > > Cheers, > > Marcos > > On Fri, Sep 25, 2015 at 4:40 AM, Nick Papior <nickpap...@gmail.com> wrote: > >> Ok, so there is a bug in diagk and pdos file when not passing a full >> weight of the k array. >> >>

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

You are not stating how many basis orbitals you have in your setup, so it is hard to tell whether it is a memory problem. Note that it may as well be limited disk space which _can_ trigger a SIGSEGV. Writing wave-functions is highly expensive on disk space and the fact that it runs smoothly till

Re: [SIESTA-L] SIGSEGV fault while writing COOP data

Could you try and add -fbacktrace to the flags. Any way it seems weird that it "suddenly" triggers as all memory have been allocated. Could you also attach the fdf files? -- Kind regards Nick Papior On 25 Sep 2015 02:34, "Marcos Veríssimo Alves" < marcos.verissimo.al...@

Re: [SIESTA-L] How to extract the Hamiltonian and Overlap matrix from HSX file?

h problem? > Thank You > > Regards > Rajan > > On Sun, Sep 20, 2015 at 12:32 PM, Nick Papior <nickpap...@gmail.com> > wrote: > >> In the trunk version you can check the file Src/m_hs_matrix.F90, while >> you can check the io routines that reads the HSX f

Re: [SIESTA-L] How to extract the Hamiltonian and Overlap matrix from HSX file?

In the trunk version you can check the file Src/m_hs_matrix.F90, while you can check the io routines that reads the HSX file on how to retrieve the sparse matrix in the HSX files. 2015-09-20 2:10 GMT+00:00 peter : > Hi, > I need to get the Hamiltonian and Overlap matrix

Re: [SIESTA-L] Error (parse.f?) on siesta-trunk-462

parse.F90 is a routine used to "parse" fdf input, hence you have an error in your fdf input file. I would suspect your kgrid_monkhorst_pack grid to be ill-defined. I guess you have %block kgrid_monkhorst_pack 0 0 0 %endblock which in reality should be %block kgrid_monkhorst_pack

Re: [SIESTA-L] suitable distance between two electrodes in transiesta calculations?

Short answer, at least that distance, not "exact" , but please understand the importance of electrode principal layers, then it should become obvious why the answer is yes. -- Kind regards Nick Papior On 16 Sep 2015 17:54, "azar ostovan" <azarosto...@gmail.com> wrote:

Re: [SIESTA-L] Charge Density Screening Region

Denchar also reads TSDE files, the density matrix is positioned in the same way as the DM file. PS. It is a mailing list. Please address the mailing list accordingly. :) 2015-09-16 17:29 GMT+00:00 leoqmc . : > Dear Nick, > > I am interested in obtain the charge density for the

Re: [SIESTA-L] suitable distance between two electrodes in transiesta calculations?

Once you know the length of each electrodes principal layers, so will you know the minimum distance required between the two electrodes. -- Kind regards Nick Papior On 15 Sep 2015 14:30, "azar ostovan" <azarosto...@gmail.com> wrote: > Dear transiesta users > > How

Re: [SIESTA-L] changes in the charge density inside leads under bias

Transiesta does not per default update the density in the electrode regions. So unless you have a really long extended electrode region "on-top" of your bulk electrodes, you should not see any difference. "Bias" can be anything... "TS.BiasContour.NumPoints>30" is really an arbitrary number unless

Re: [SIESTA-L] using buffer atoms

you mean usage of them is important for unsimilar > electrods? > > > kind regards > azar > > On Wed, Sep 2, 2015 at 11:31 PM, Nick Papior <nickpap...@gmail.com> wrote: > >> If, for instance, you have a left electrode of gold, and a right >> electrode of copper

Re: [SIESTA-L] using buffer atoms

If, for instance, you have a left electrode of gold, and a right electrode of copper. Then you need buffer atoms to correctly screen the electrode regions from surfaces to vacuum. 2015-09-02 18:54 GMT+00:00 azar ostovan : > Dear tranSiesta users > > > What is the purpose

Re: [SIESTA-L] [***Posible SPAM***]Fortran runtime error

Please try the latest trunk version available and see if it helps. If not report the error message that it returned. 2015-09-01 7:26 GMT+02:00 Saeed Nasiri : > Dear users > > I have a problem when I run the vibrator and the familiar "Fortran runtime > error" caused the code

Re: [SIESTA-L] select best part of lead include in scattering region

Yes, that could be one. 2015-08-27 17:15 GMT+02:00 leoqmc . leo...@gmail.com: Dear Nick, you said output. Such output would be the average transmission function (*. AVTRANS) ?. Thank you so much. Leone 2015-08-25 17:44 GMT-03:00 Nick Papior nickpap...@gmail.com: Please see this slide

Re: [SIESTA-L] k-sampling for transport calculations

This you should be able to answer yourself, 1) What does k-points implicitly mean in calculations? 2) Is that meaning compatible with your simulation? 3) In your simulation, what would be the difference between a k-point simulation and a non k-point simulation? 2015-08-28 14:14 GMT+02:00 leoqmc

Re: [SIESTA-L] Divide a large force constants (FC) calculation into small pieces

/2015 6:11 PM, Nick Papior wrote: You shouldn't need to rename the files, nor delete files, try first and do the straightforward thing. Do them separately in their own directories: FCrun_11-11 FCrun_12-12 Then do Phonons --FCwildcard=./FCrun_* ... This should work fine. 2015-08-14 8:26

Re: [SIESTA-L] [***Posible SPAM***]

Do not use that many processors for so few atoms. This may be the reason. A good advice is to use no more than the number of atoms in your system. However, in your case you use a lot of k-points. Then look up the fdf flag Diag.ParallelOverK. 2015-08-26 15:13 GMT+02:00 Barnali Bhattacharya

Re: [SIESTA-L] error:Electrodes extend into the transport direction

siesta complaining that the electrode are situated in a different coords. On Thursday, August 20, 2015 12:08 AM, Nick Papior nickpap...@gmail.com wrote: What are you asking? It says: The electrodes are not situated in the same coordinates. Please correct. Do that. Please read the output

Re: [SIESTA-L] error:Electrodes extend into the transport direction

from where these coordinates came from? so siesta complaining that the electrode are situated in a different coords. On Thursday, August 20, 2015 12:08 AM, Nick Papior nickpap...@gmail.com wrote: What are you asking? It says: The electrodes are not situated in the same coordinates. Please

Re: [SIESTA-L] error:Electrodes extend into the transport direction

-0.521458607003 5.528017823710 10.357615863662 -0.610752357764 4.991778712696 8.140904379317 -0.448790345987 4.790777885721 The electrodes are not situated in the same coordinates. Please correct. On Wednesday, August 19, 2015 5:03 AM, Nick Papior nickpap

Re: [SIESTA-L] Questions about setup for transport calculations.

Garcia 2015-08-19 14:51 GMT-03:00 leoqmc . leo...@gmail.com: Dear Nick, Thank you. I'll read the paper. Leone Carmo Garcia 2015-08-19 14:36 GMT-03:00 Nick Papior nickpap...@gmail.com: 2015-08-19 17:14 GMT+00:00 leoqmc . leo...@gmail.com: Dear Nick, I prepared my inputs following your

Re: [SIESTA-L] error:Electrodes extend into the transport direction

? On Thursday, August 20, 2015 12:32 AM, Nick Papior nickpap...@gmail.com wrote: 2015-08-20 8:27 GMT+02:00 Jaret Qi jare...@yahoo.com: and even though, this system worked well with 3.2 version and now trunk is complaining about the electrodes! this is completely weird, wrong is wrong

Re: [SIESTA-L] error:Electrodes extend into the transport direction

0.000 0.000 corrds? No, only the relative position. Their origin can be wherever you decide. On Thursday, August 20, 2015 11:06 AM, Nick Papior nickpap...@gmail.com wrote: *Structure of the Left electrode* Is, as it says, the structure read in the Left electrode *.TSHS file. *System

Re: [SIESTA-L] Questions about setup for transport calculations.

Angstroms) LatticeConstant 1.0 Ang % block LatticeVectors 31.540 0.000 0.000 25.770 29.994 0.000 0.00.0 7.06705 % endblock LatticeVectors Is this right? Nick once again thank you. 2015-08-20 9:20 GMT-03:00 Nick Papior nickpap...@gmail.com: 2015-08-20 14:14 GMT

Re: [SIESTA-L] relaxing structure with different software

Yes. -- Kind regards Nick Papior On 19 Aug 2015 12:33, azar ostovan azarosto...@gmail.com wrote: Dear tranSIESTA users Is it possible to perform electronic transport properties by tranSIESTA for structures have relaxed with different software (NO SIESTA)? Kind regards Azar Ostovan

Re: [SIESTA-L] Questions about setup for transport calculations.

will follow the tips. Leone Carmo Garcia 2015-08-18 16:42 GMT-03:00 Nick Papior nickpap...@gmail.com: 2015-08-18 19:27 GMT+00:00 leoqmc . leo...@gmail.com: Dear Nick and transiesta users, I am interested in transport calculations in single-molecule two-probe systems[Au(111)-Molecule-Au(111)]. I

Re: [SIESTA-L] error:Electrodes extend into the transport direction

to the plane containing x y. And is the skewed a matter for the trunk version, I still not sure why this issue just appear in the case of trunk version!! On Wednesday, August 19, 2015 12:52 AM, Nick Papior nickpap...@gmail.com wrote: there are x and/or y components in your third cell vector

Re: [SIESTA-L] about SOC(spin orbital coupling in Band Stucture)

Here http://www.mail-archive.com/siesta-l@uam.es/ 2015-08-20 5:12 GMT+00:00 Altaf Ur Rahman altafq...@gmail.com: How to search it , Thanks in advance On Wed, Aug 19, 2015 at 3:51 PM, I. Camps ica...@gmail.com wrote: Hello, Please, search in the list for a discussion with the subject: Spin

Re: [SIESTA-L] Qtot and Qsol

They are spin-up/down. 2015-08-16 17:40 GMT+00:00 Jaret Qi jare...@yahoo.com: Can you please clarify how collinear spin relates to transiesta. On Sunday, August 16, 2015 10:33 AM, Nick Papior nickpap...@gmail.com wrote: Same as siesta. Co-linear spin. 2015-08-16 16:32 GMT+00:00 Jaret

Re: [SIESTA-L] Qtot and Qsol

in siesta means FM calculation which in turn means spins are parallel or antiparallel, but not mixed. Thank you Jaret On Wednesday, August 5, 2015 4:20 AM, leoqmc . leo...@gmail.com wrote: Dear Nick, Thank you for your reply. Leone 2015-08-05 4:50 GMT-03:00 Nick Papior nickpap

Re: [SIESTA-L] Divide a large force constants (FC) calculation into small pieces

You shouldn't need to rename the files, nor delete files, try first and do the straightforward thing. Do them separately in their own directories: FCrun_11-11 FCrun_12-12 Then do Phonons --FCwildcard=./FCrun_* ... This should work fine. 2015-08-14 8:26 GMT+00:00 Jingxian Yu

Re: [SIESTA-L] HOW TO ADD VACUUM?

Vacuum is where no atoms exist in the unit-cell, hence creating a larger unit-cell is equivalent to vacuum. -- Kind regards Nick Papior On 13 Aug 2015 12:29, ANANT VIJAY anantvijay...@gmail.com wrote: Dear siesta users I am New in SIESTA .Please anyone can guide me how to add vacuum in siesta

Re: [SIESTA-L] Qtot and Qsol

. Please provide me some guide. Thank You Very Much. Leone 2015-08-04 17:50 GMT-03:00 Nick Papior nickpap...@gmail.com: Please read the many questions already posed about exactly this. -- Kind regards Nick Papior On 4 Aug 2015 21:13, leoqmc . leo...@gmail.com wrote: Dear siesta

Re: [SIESTA-L] spin polarized current in tbtrans

-13 22:30 GMT+08:00 Nick Papior Andersen nickpap...@gmail.com: Dear all I will here give information about the tbtrans versions. First of all there exists 2 different versions of tbtrans from trunk-424 and onwards. 1. tbtrans version from siesta-3.1 and trunk-424 (in Util/TBTrans) I have

Re: [SIESTA-L] Qtot and Qsol

Please read the many questions already posed about exactly this. -- Kind regards Nick Papior On 4 Aug 2015 21:13, leoqmc . leo...@gmail.com wrote: Dear siesta/Transiesta users, I am interested in transport calculations. My system consists of a molecule between two gold surfaces

Re: [SIESTA-L] Transiesta stops without any error message

. How can i be sure whether the program stops due to the lack of memory or not. Moreover, why i get completely different unitcell before the program stop. Thanks and regards On Tue, Jul 28, 2015 at 1:14 AM, Nick Papior nickpap...@gmail.com wrote: I would assume your electrode is too big to do

Re: [SIESTA-L] Transiesta stops without any error message

That seems like an extremely large electrode, I would guess you setup the calculation incorrectly. 2015-07-27 20:11 GMT+00:00 Fadil Iyikanat fadiliyika...@gmail.com: Hi all. I am doing transiesta calculation. My sistem is a little big. My eletrode and scattering regions consist of 114 and 342

Re: [SIESTA-L] Transiesta stops without any error message

regards Nick Papior On 27 Jul 2015 23:00, Fadil Iyikanat fadiliyika...@gmail.com wrote: Im sure from my electrodes. They are just big electrodes. But I dont know where the unitcell comes from which appeared before the last line of output. Because my unitcell of electrode is %block LatticeVectors

Re: [SIESTA-L] Electric Field

You should know which direction is the bulk one, if it becomes zero you have a fully bulk calculation. So my guess is that you have setup the fdf file incorrectly. -- Kind regards Nick Papior On 27 Jul 2015 07:21, Younas Khan younaskhan.phys...@gmail.com wrote: Thank You Nick, but I am still

Re: [SIESTA-L] generate executable file

. Auluck Respected Sir Nick Papior When I run gfortran -o eig2dos.f eig2dos from Util directory to create eig2dos executable file but command gives unexpected error gfortran: error: eig2dos: no such file or directory I can see this file by using ls -x command .I don't know how can

Re: [SIESTA-L] How to apply a gate bias perpendicular to the Z-direction in Transiesta?

I cannot say for sure, I hope before the end of the year... -- Kind regards Nick Papior On 26 Jul 2015 18:01, Nayereh Ghobadi n.ghob...@gmail.com wrote: Thank you very much for your reply. It will be very kind of you if let me know when the next release of transiesta will be available

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