Re: [SIESTA-L] About SIESTA and wannier90 interface.

Dear Javier, Thank you. I hope it will be implemented soon. Regards, Jigneshkumar On Tue, 18 Jun, 2024, 1:30 am Junquera Quintana, Francisco Javier, < javier.junqu...@unican.es> wrote: > > Dear Jigneshkumar: > > The interface between SIESTA and WANNIER90 for spinors has not been >

Re: [SIESTA-L] About SIESTA and wannier90 interface.

Dear Jigneshkumar: The interface between SIESTA and WANNIER90 for spinors has not been implemented yet. Best regards, Javier [logoweb] [logocitimac] Javier Junquera Catedrático de Universidad Departamento de

Re: [SIESTA-L] << Siesta 5.0 + LibXC >>

Hi, Could you share more information, like the full output of the cmake invocation, it is hard (if not impossible) to work out what went wrong in this case. Den ons. 29. maj 2024 kl. 22.00 skrev I. Camps : > Hello, > > I downloaded SIESTA version 5.0 from Gitlab ( >

Re: [SIESTA-L] Issues with building and compiling new siesta

Thanks Alberto; the "Deferred-length character" error vanishes with a modern gcc. On Fri, 7 Jun 2024 at 22:00, Alberto Garcia wrote: > You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version. > > Best regards, > > Alberto > > > - El 6 de Junio de 2024, a las

Re: [SIESTA-L] Issues with building and compiling new siesta

You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version. Best regards, Alberto - El 6 de Junio de 2024, a las 19:09, Boubacar Traore escribió: | I finally sorted out the issue of scalapack linking by adding its path to | LIBRARY_PATH instead of LD_LIBRARY_PATH

Re: [SIESTA-L] Issues with building and compiling new siesta

Hi Camps, Thanks for the reply. I have already gone through that link but those known issues do not seem to be related to the compilation errors that I encounter. In particular, there is "Error: Deferred-length character component 'message' at (1) is not yet supported " error message. I am not

Re: [SIESTA-L] Issues with building and compiling new siesta

Hi Boubacar, Take a look at this link, it may help: https://urldefense.com/v3/__https://docs.siesta-project.org/projects/siesta/en/stable/installation/build-issues.html__;!!D9dNQwwGXtA!W7_FwTUE6tqp6WrQ8D3wsJLjE9muIaDjVOCP95FNi--GCwPavq6Ac4fosYmMJSd8pCIVgsxT9gQk$ . []'s, Camps On Wed, Jun 5,

Re: [SIESTA-L] Issues with building and compiling new siesta

More specifically it stops at scalapack stage when : "-- Performing Test scalapack_has_blacs_gridinit - Failed" The config routine finds scalapack but it fails in "SiestaCheckLinalg.cmake" routine. All the dependencies were installed according to the doc. So, I am not sure if I still missed

Re: [SIESTA-L] Issues with building and compiling new siesta

I finally sorted out the issue of scalapack linking by adding its path to LIBRARY_PATH instead of LD_LIBRARY_PATH (more info here:

Re: [SIESTA-L] Tbtrans not printing Volatge and current output

Hi There Did you have to use 4.1.5 ? The reason i am saying this is because 4.1.3 had its own bugs El abed Sent from my iPhone On 25 May 2024, at 6:01 AM, RUPESH TIWARI wrote:  Dear users and developers, I am performing a transport calculation using the transiesta 4.1-b3 version. The

Re: [SIESTA-L] siesta with miniconda3

Hi, Which version of siesta did you install with conda? Could you try and upgrade the siesta installation. The latest version should have this enabled. Den tors. 16. maj 2024 kl. 22.00 skrev Aleksandra Oranskaia < aleksandra.oransk...@kaust.edu.sa>: > Dear users and developers, > > I am a

Re: [SIESTA-L] Hole pockets in Bi

Hi Roland, I would highly recommend using psml pseudos: https://urldefense.com/v3/__http://www.pseudo-dojo.org/__;!!D9dNQwwGXtA!RrBjENfaENy8ZMudSEjcZAXbM2fn5MOyEJ82THnRwER5QrSWiV4QR4EMegYaKl394GIDwNSAlunD3CJh$ . I have used the Bi pseudos from here (different system) and got good agreement

Re: [SIESTA-L] Regarding SCF convergence issue during optimization

rds, Daniel Bennett From: siesta-l-requ...@uam.es on behalf of Andrei Postnikov Sent: 23 April 2024 07:09 To: Siesta-l Cc: deb.jyotirmo...@gmail.com Subject: Re: [SIESTA-L] Regarding SCF convergence issue during optimization Hi, you provide too few information. Of course just i

Re: [SIESTA-L] Regarding SCF convergence issue during optimization

Hi, you provide too few information. Of course just increasing the number of iterations won't bring you further if there is no convergence. General advises might be as follows: - Check that you are using diagonalisation and NOT order-N scheme before you fix the things and "know what you are

Re: [SIESTA-L] << SIESTA workflows systems >>

Hi Camps, I answered this here: https://urldefense.com/v3/__https://mattermodeling.stackexchange.com/questions/12525/better-siesta-workflows-system__;!!D9dNQwwGXtA!RWrxZFGKJWOZ8ctQOqm5xNu4uLBq4jJbEsHb4oO6F3frBvWox134brbqZH3Oztkn93T9SXQa-Ke3uiBrgw$ Thanks! Den ons. 6. mar. 2024 kl. 22.00 skrev

Re: [SIESTA-L] learning

STOP On Tue, 26 Dec, 2023, 2:30 am M Mohammadi, wrote: > how can i learn siesta from the biggening? > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence >

Re: [SIESTA-L] Grimm parameters

Hi, I don't see a problem, I think you misinterpret what the numbers should be? The values are the sum of atomic vdW radii. Please see discussion in Grimme paper ~ Eq. 12. So it looks correct, no? Thanks. / Nick Den fre. 15. dec. 2023 kl. 22.00 skrev Reza Behjatmanesh-Ardakani <

Re: [SIESTA-L] converge problem in long voltage range

Hello Yelda, I hope you are doing well! Try to decrease the bias step. For instance, if you are trying to get convergence in -1.6 V using the "*.TSDE" and "*.TSHS" files of -1.5 V, do the calculation for -1.55 V using the -1.50 V files, and then use the -1.55 V files to get the -1.60 V

Re: [SIESTA-L] converge problem in long voltage range

Good evening Yelda I have been facing similar issues and at this stage Nick would tell you its a trial and error situation since at lower voltages your calculations worked. So you might want to try instead of 2.1 V try 2.13V Or changing mixing weight again could work Hope that helps El abed Sent

Re: [SIESTA-L] Passing constraint harmonic energy through constr.f

Hi Francisco, You could define new "species" for the atoms you are interested in, and then put in the MM.Potentials block the right information for those species. A simple example. Say that you want to constrain harmonically one of the H atoms and the O atom in a water molecule. Then:

Re: [SIESTA-L] Passing constraint harmonic energy through constr.f

Dear Prof. Garcia Many thanks for your response. I looked up the MM.Potentials block but I couldn't figure out how to apply the harmonic potential to selected atoms. Any assistance would be appreciated. Thanks! Francisco On Mon, Nov 13, 2023 at 1:51 AM Alberto Garcia wrote: > Hi Francisco,

Re: [SIESTA-L] Passing constraint harmonic energy through constr.f

Hi Francisco, You could indeed modify the constr.f file to include what you need, but first check the section of the manual entitled "Auxiliary Force Field". In there you can find a discussion of the MM.Potentials block, in which you can define the parameters of, among others, a harmonic

Re: [SIESTA-L] Siesta fatbands / building utilities in 5.0

Write true and Save-HS true in > separate calculations and got the same error. Is there another way to get > the *.HSX file? > > > -- > *From:* siesta-l-requ...@uam.es on behalf of > Alberto Garcia > *Sent:* 24 October 2023 03:20 > *To:* siesta-l@uam.es

Re: [SIESTA-L] Siesta fatbands / building utilities in 5.0

2023 03:20 To: siesta-l@uam.es Subject: Re: [SIESTA-L] Siesta fatbands / building utilities in 5.0 Hi Daniel, In Siesta 5.0 the CMake system builds all the utilities by default. If you install the package after building they will all be in the /path/to/installation/bin directory, together

Re: [SIESTA-L] Siesta fatbands / building utilities in 5.0

Hi Daniel, In Siesta 5.0 the CMake system builds all the utilities by default. If you install the package after building they will all be in the /path/to/installation/bin directory, together with the siesta executable itself. If you do not install, they will be in _build/Util/, where

Re: [SIESTA-L] [EXTERNAL] Re: 3 Terminal STM device.

Hello Prof. Nick, Found my mistake. The calculations are running now. Regards, Ghadiyali Mohammed Kader Post Doctoral Fellow King Abdullah University of Science and Technology On 29 Sep 2023 at 11:00 PM +0300, Nick Papior , wrote: > No transfer matrix generally happens when you do electrode runs

Re: [SIESTA-L] Error in compiling siesta-master (28 Sep. 2023)

Hi, Please note that the master branch has received a lot of new commits in the past week. You might have downloaded a version with a temporary glitch. I suggest you now re-run the build step in the same directory with the option '-j 1' instead of '-j 44', so that the compilation's last

Re: [SIESTA-L] 3 Terminal STM device.

No transfer matrix generally happens when you do electrode runs without k-points, or if you are using a vacuum region along the semi-infinite direction (which is clearly wrong). Try and figure out these two conditions for your input files. Den tors. 28. sep. 2023 kl. 22.00 skrev Mohammed

Re: [SIESTA-L] Error in tselecs.sh

Thanks for reporting. You should be able to download a working script from here:

RE: [SIESTA-L] Problem using Vibra utility

al-computational-infrastructure/__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VW6jSi4R$ > [NCI Australia logo black PNG transparent] [MHFAider Accredited Digital Badge] From: Sunetra Das<mailto:sunetra.das...@gmail.com> Sent: Friday, 15 September 2023 6:00 AM To: sie

Re: [SIESTA-L] Problem using Vibra utility

Hello, I want to unsubscribe from Siesta emails. Kindly cancel my email address from subscription. Thank you. Regards, Sunetra Das. On Thu, 14 Sep, 2023, 1:30 am Andrei Postnikov, < andrei.postni...@univ-lorraine.fr> wrote: > Dear Diego, > > as your case is q=0 only, you can try your luck >

Re: [SIESTA-L] Problem using Vibra utility

Dear Diego, as your case is q=0 only, you can try your luck with my shortcut version of vibra, to be compiled from the attached zip. It does not need an .fdf file, just .XV and .FC (.XV serves just to identify the atoms; exact coordinates are not important). Tell me if you'd encounter any

Re: [SIESTA-L] GPU install siesta

Hello, Any update on my query? Regards, Ghadiyali Mohammed Kader Post Doctoral Fellow King Abdullah University of Science and Technology On 20 Aug 2023 at 4:54 PM +0300, Mohammed Ghadiyali , wrote: > Hello, > > I’m trying to install siesta on GPU and using the attached make file. I’ve > used

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

I've learned that, and it helps me a lot. Thank you Nick Papior and Yuefei Huang for your reply. | | 肖威 | | xiaowei951...@163.com | Replied Message | From | Nick Papior | | Date | 9/3/2023 04:00 | | To | | | Subject | Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

Fmail-online.nosdn.127.net*2Fqiyelogo*2FdefaultAvatar.png=*5B*22xiaowei951020*40163.com*22*5D__;6IKW5aiBJSUlJSUlJSUlJSU!!D9dNQwwGXtA!QJE7m5jLqhlIUxQ3cUJUVfPUq4gmfp-PANjZdaBrw6Regb7NzfLExWoIZBrwGXI0WQy0XJO4_X-iqiCdQRjP7Q$> > Replied Message > From yh46 > Date 8/29/2023 04:00

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

| 8/29/2023 04:00 | | To | | | Subject | Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA | Wei, The normal vector in this case is just (1.0, 0.5, 0.2). There is nothing to do with the line "1.0 1.0 1.0 Ang". If you still don't

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

5B*22xiaowei951020*40163.com*22*5D__;6IKW5aiBJSUlJSUlJSUlJSU!!D9dNQwwGXtA!URpSF7zEPUo2pgnDAu-R8G2ylzEB4WJvVMj6ieteqAMMZPkxWDoJvxO4K0mmRZZT9CKicYpb-gKpQV9QpZ8gtg$> > Replied Message > From Nick Papior > Date 8/27/2023 04:00 > To siesta-l > Subject Re: [SIESTA-L] ***SPAM*** Re: ***SPAM**

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

bject | Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA | Your understanding is wrong, it is not inserted into the box before determining the direction. It is a direction first. On Fri, 25 Aug 2023, 22:00 肖威, wrote: Dear Nick Papior, Here is

Re: [SIESTA-L] ***SPAM*** Re: ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

Dear Nick Papior, Please give me some more guidance on the direction of the plane's normal vector. (Gate, Infinite plane) Many thanks. Wei | | 肖威 | | xiaowei951...@163.com | Replied Message | From | Nick Papior | | Date | 8/27/2023 04:00 | | To | siesta-l | | Subject | Re: [SIESTA

Re: [SIESTA-L] Compiling siesta 4.1.5b, problem with libfdf

Subject: Re: [SIESTA-L] Compiling siesta 4.1.5b, problem with libfdf Hi, 4.1.5b does not contain the psml stuff.. So I am not fully sure what you mean? Secondly, - if you want a stable release, use 4.1.5, this does NOT contain PSML. - if you want psml support, download the latest 'master' commit

Re: [SIESTA-L] Compiling siesta 4.1.5b, problem with libfdf

Hi, 4.1.5b does not contain the psml stuff.. So I am not fully sure what you mean? Secondly, - if you want a stable release, use 4.1.5, this does NOT contain PSML. - if you want psml support, download the latest 'master' commit at gitlab.com/siesta-project/siesta Den tors. 24. aug. 2023 kl.

Re: [SIESTA-L] ***SPAM*** Re: Question about Gate (Infinite plane) in SIESTA

Dear Nick Papior, Take the blue font below for example: The normal vector consists of two points, pointing from (1.0 1.0 1.0) to (1.0 0.5 0.2). What I want to ask is whether the unit of (1.0 0.5 0.2) is Ang. Here is an example of the use of (Infinite plane) in the SIESTA 4.1.5

Re: [SIESTA-L] Transmission Spectrum

It is hard to know what went wrong. But! You seem to be mixing old flags (pre 4.1) and new flags (4.1 and newer). As far as I remember LDA+U was first introduced in 4.1. And your TS options are for 4.0 or older. Please double check your output whether all your options are correct, this is vital.

Re: [SIESTA-L] Question about (TS.Voltage, %block TS.Elecs) in TRANSIESTA

dashi.163.com/projects/signature-manager/detail/index.html?ftlId=1=**E=xiaowei951020*40163.com=https*3A*2F*2Fmail-online.nosdn.127.net*2Fqiyelogo*2FdefaultAvatar.png=*5B*22xiaowei951020*40163.com*22*5D__;6IKW5aiBJSUlJSUlJSUlJSU!!D9dNQwwGXtA!SxLyWC01B6AeL3kmEC1A3xVpoGpwQIBsrLylYVlBspzJ2WlwjZ

Re: [SIESTA-L] Question about (TS.Voltage, %block TS.Elecs) in TRANSIESTA

--- | From | Nick Papior | | Date | 8/16/2023 04:00 | | To | | | Subject | Re: [SIESTA-L] Question about (TS.Voltage, %block TS.Elecs) in TRANSIESTA | Hi Wei, Have you read the manual? If not, I would highly recommend you to read that, and if there are still some clarifications needed, then

Re: [SIESTA-L] Question about (TS.Voltage, %block TS.Elecs) in TRANSIESTA

Hi Wei, Have you read the manual? If not, I would highly recommend you to read that, and if there are still some clarifications needed, then please let us know: 1. What was not clear enough in the manual 2. A possible suggestion to improve it Thanks! Den lør. 12. aug. 2023 kl. 22.00 skrev 肖威 :

Re: [SIESTA-L] Error in specifying the type of an atom!. Atoms specified is above the total number of atoms!

I did that and now it says Erroneous electrode setup, check out-put On Sat, Aug 5, 2023 at 3:00 PM Nick Papior wrote: > You are requesting the last electrode to start at the last atom, thus > resulting in requesting non-existing atoms. It should be "elec-pos end -1". > > Den fre. 4. aug. 2023

Re: [SIESTA-L] Error in specifying the type of an atom!. Atoms specified is above the total number of atoms!

You are requesting the last electrode to start at the last atom, thus resulting in requesting non-existing atoms. It should be "elec-pos end -1". Den fre. 4. aug. 2023 kl. 22.00 skrev El-Abed Haidar < ehai2...@uni.sydney.edu.au>: > Good evening all, > > I am studying a graphene system and would

Re: [SIESTA-L] Dipole correction for slab calculation

Dear Emilio, Thanks for your suggestions. Finally I could converge the symmetric slab after many SCF iterations, but I noticed that the Slab.DipoleCorrection keyword is not helping my calculations. I noticed that at each SCF iteration the applied E field is different, so the calculation

Re: [SIESTA-L] Dipole correction for slab calculation

Dear Diego 1. Depending how you make the surface you may be breaking bonds, which can give SCF trouble. (not sure about garnet, and depending on particular surface). You may need to saturate bonds, depending on what makes sense chemically, and/or you would expect of that garnet surface in

RE: [SIESTA-L] Error in specifying the type of an atom

dited Digital Badge] From: I. Camps<mailto:ica...@gmail.com> Sent: Wednesday, 26 July 2023 6:00 AM To: siesta-l@uam.es<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] Error in specifying the type of an atom Hi, In the AtomicCoordinatesAndAtomicSpecies block, you only have 32 atoms, but you

Re: [SIESTA-L] Error in specifying the type of an atom

Hi, In the AtomicCoordinatesAndAtomicSpecies block, you only have 32 atoms, but you declared that there are 94. []'s Camps Em sex., 21 de jul. de 2023 17:00, El-Abed Haidar < ehai2...@uni.sydney.edu.au> escreveu: > Good day all, > > I was wondering if anyone could help me understand why I

Re: [SIESTA-L] Lattice parameters shorter than crystal after optimization

It is not an issue that you find lattice parameters smaller than the experimental ones. This may depend on several factors, including the selection of the functional you use. The k-points should be inverse proportional to the lattice parameters. They don't have to be equal. The energy for

Re: [SIESTA-L] Lattice parameters shorter than crystal after optimization

Dear, Making some tests, I observed 2 things:  1- The system takes ~1800 steps to converge the optimization. During ~700 steps the lattice parameters (a, b, c) increase (beta almost isn't changing). It takes some more steps to the beta angle starts to change, while a, b, c decrease. It

Re: [SIESTA-L] Lattice parameters shorter than crystal after optimization

Maybe the selection of an improper pseudopotential can cause problems. You may have a look here https://departments.icmab.es/leem/siesta/Pseudopotentials/index.html for pseudopotentials for SIESTA. An option is to use the "atoms" code to produce your own pseudopotential, but this is something that

Re: [SIESTA-L] Lattice parameters shorter than crystal after optimization

Dear Dr. Fthenakis, Thank you again for answering my questions.  My main doubt isn't only the beta angle, but the whole changes in the lattice parameters. There are several crystal structures obtained for this neurotransmitter, and all of them have closer lattice parameters. Besides, it's

Re: [SIESTA-L] Lattice parameters shorter than crystal after optimization

I can not find any mistake in your calculations. Maybe you can use a different base. But, how do you know that the correct angle is 96^o and not 99^o ? Is this difference very important for you? I mean several theoretical approaches may have some differences with respect to the experiment, but

Re: [SIESTA-L] How to increase the number of significant figures of energy values in .out file

In addition, is it possible to increase significant digits of energy in .band file? Currently, it is limited to 4 decimal places only. Regards, Anshu On 27-04-2023 14:37, Fanmiao Kong wrote: Dear Siesta users, Does anyone know how to increase the number of significant figures of the

Re: [SIESTA-L] Constraints in positive or negative z-direction

Dear Daniel, I aim to try to induce some sp3 bonds between the layers, forcing them by hydrogenating (or by other chemical groups) a couple of carbon atoms (the non-constrained atoms) and strain. In fact, I'm trying to obtain the 2D diamond structure and then trying to use the same methodology in

Re: [SIESTA-L] Constraints in positive or negative z-direction

Hi Ramon, I'm not sure if this is such a good idea, at least in your example. If I understand correctly, you freeze the first graphene layer (in the z=0 plane say), then the second graphene layer is at some z which is larger than the optimal one which minimizes the van der Waals energy. Then

Re: [SIESTA-L] What is ADOS?

Hello Srest, I think ADOS measures how much the DOS of a certain electrode is spilled onto a certain set of orbitals. So it is related to the DOS of the electrode, and how strong the orbitals are coupleed to the electrode. If the scattering region is not connected in the same way to the

Re: [SIESTA-L] about the 'Electrode connectivity is not perfect'

Please see this question on matter modelling: https://urldefense.com/v3/__https://mattermodeling.stackexchange.com/questions/9424/tbt-transiesta-calculation-error__;!!D9dNQwwGXtA!Q0B4ku0Ggr5WGLRlqQanAhMDQgCsmcwv4nk4V4yVTmXyu0RdrGo-Nwh_WVdR97nasmLA7ityvqMRA22Sjg$ Den tirs. 21. mar. 2023 kl.

Re: [SIESTA-L] About Work Function Calculation on Au

Hello SIESTA users, I found that this is due to choice of PAO.EnergyShift, the work function value is very sensitive to the selection of this parameter. With PAO.EnergyShift = 0.02 Ry I get 3.5 eV. With PAO.EnergyShift = 0.001 Ry, I get 5.1eV. I know that the role of this parameter is

Re: [SIESTA-L] About Work Function Calculation on Au

Hi, Your 'slab' is just three layers thick... that is not nearly enough to have a good representation of a "bulk" region in the center and a "surface" region. After you fix that, you probably need to process the .VH file and obtain a potential profile along z to check that you reach a flat

Re: [SIESTA-L] Memory problems with SOC

on behalf of Nick Papior Sent: 27 February 2023 03:07 To: siesta-l@uam.es Subject: Re: [SIESTA-L] Memory problems with SOC I think that this is a memory leak in MKL, could you try a later revision? Please see details here: https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta

Re: [SIESTA-L] Memory problems with SOC

I think that this is a memory leak in MKL, could you try a later revision? Please see details here: https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/issues/29__;!!D9dNQwwGXtA!VJ6dNL-0-ztPLYjo9nyf0U6oWg9E4yUL2dpwIavhqG8_fCPtLxlZBt0ZW4ZCD8oJSNuN_S5CVgp2mkfOgg$ So I think it

Re: [SIESTA-L] Does siesta consider periodicity in scattering region?

Hi, Yes, transiesta considers periodicity in the transverse directions to the transport direction (if it is unidirectional). If you want to remove periodic images (which inherently contains your scattering region) and retain a pristine electrode surrounding your device, then you could use the

Re: [SIESTA-L] Radial part of basis orbital

Isn't this information explicitly included in .ion files - after a general header, one basis function after the other? You just need to cut whichever you want and feed it to a plotting program... Best regards, A.P. ... # PAOs:__ 0 2 1 0 2.00 #orbital l, n, z,

Re: [SIESTA-L] Radial part of basis orbital

Check the WriteIonPlotFiles option E On 14 Feb 2023, at 06:17, Francisco Garcia mailto:garcia.ff@gmail.com>> wrote: Dear Users, I would like to know how to obtain the data for the radial part of a given basis orbital for plotting. E.g. the radial part of Al 3s and Al 3p for SZ basis.

Re: [SIESTA-L] Radial part of basis orbital

Hi Probably the easiest is to use sisl to read in the geometry + orbital information. Then something like this: R = np.linspace(0, 10, 100) geometry.atoms[0].orbitals[0].radial(R) this should give you the radial component for the first orbital on the first atom. The indexing should be

Re: [SIESTA-L] Specify file path for pseudos?

Currently this is not implemented. But, we have an issue for this and it will most likely be in the next major release of Siesta! :) Thanks for bringing this up! Den fre. 3. feb. 2023 kl. 22.04 skrev Daniel Bennett : > Hi all, > > I was wondering if anybody knows if there is a way to specify a

Re: [SIESTA-L] Specify file path for pseudos?

Hi, This is something that we are planning to implement. For now, if file space is a problem, you could use symbolic links from a central location to each execution directory. Best regards, Alberto - El 3 de Feb de 2023, a las 19:33, Daniel Bennett escribió: | Hi all, | I was

Re: [SIESTA-L] Restarting calculations with different spin orientations

Thank you, Nick. I had used sisl previously and didn't know it could do that. I was able to converge the other spin configurations without issues. Best, Andres. On Wed, Feb 1, 2023 at 4:11 PM Nick Papior wrote: > Hi, > > You should be able to use sisl to rotate the spin-box matrices. > sisl

Re: [SIESTA-L] Restarting calculations with different spin orientations

Hi, You should be able to use sisl to rotate the spin-box matrices. sisl is a python tool aiding dft calculations and has a root in the siesta environment.

Re: [SIESTA-L] Restarting calculations with different spin orientations

Dear Andres Tellez, my DMtune tool was written having similar tasks in mind; please feel free to download it from [

Re: [SIESTA-L] DFT-D3 in Siesta package

Yes! The latest development included this: https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/merge_requests/70__;!!D9dNQwwGXtA!Q99mAou4w_f6DS5APAYiRuFOwHe_dR4vyLSsRG6A9YjMGfDR6qQ-in8aTdRcju9oCo2JHrn_QylshcJ7Qw$ The next major release will have this enabled! Den ons. 25.

Re: [SIESTA-L] DFT-D3 in Siesta package

You can check the list of vdW functionals in the siesta manual: https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/siesta-4.1-b4.pdf pages 48-49 Daniel Bennett From: siesta-l-requ...@uam.es on behalf of Mahbubeh Amiri Sent: 25 January 2023 05:43

Re: [SIESTA-L] should I choose the conda-version of siesta?

There should be a performance difference between manually compiled siesta. But the conda version is most useful for testing and getting to play with siesta. :) Den tir. 7. jun. 2022 kl. 22.02 skrev LQChen : > Dear Community; > > Is the conda-version of siesta for learning? Or it is suit for real

Re: [SIESTA-L] Plotting Spin Density in Supercell

Hi, It depends on what you want to do. For instance if you have already stored the RHO file (or Rho.grid.nc) file you could do the following to get the spin density along z for a polarized calculation. sgrid Rho.grid.nc{0} --diff Rho.grid.nc{1} --geometry RUN.fdf --tile 10 a test.cube or,

Re: [SIESTA-L] Need help with Phonon Dispersion Band Lines in Vibra

Dear Francisco, so your AFM structure is of CuAu type. This is fine but of course this is not the only AFM structure possible (and I don't know whether it is realistic at all, but this of course depends on your objectives). Now, if you want the q-path to be the same in your two settings, you

Re: [SIESTA-L] Need help with Phonon Dispersion Band Lines in Vibra

Dear Prof. Postnikov, Many thanks and appreciation for your response. I believe I found a solution to my problem but I want to run it by you. First, an FCC cell with 2 unique atoms is equivalent to a tetragonal cell (this is the smallest unit cell to model antiferromagnetism). Using the website

Re: [SIESTA-L] Need help with Phonon Dispersion Band Lines in Vibra

Dear Prof. Postnikov, Special thanks again for your kind and prompt response. (i) The q-paths in input 2 must be rotated by 45 degrees to maintain consistency with the paths in input 1. I would like to kindly know the axis about which the rotation should be performed. (ii) Regarding your

Re: [SIESTA-L] Need help with Phonon Dispersion Band Lines in Vibra

Dear Francisco, it is difficult to give a useful advice on the basis of very limited information you provide, but my impression is that your problems are not obviously related with Vibra. Some questions: 1. What (magnetic) structure are you modelling? How comes you have four atoms per AFM

Re: [SIESTA-L] Current or transmission direction

This is defined via the semi-inf-direction option provided for each of the electrodes. The output of siesta (transiesta) clearly denotes which semi-infinite directions each electrode has. Please note, that there is *per see* not a transport direction. There is only semi-infinite directions, and

Re:[SIESTA-L]

I think the problem is that you are using a semicolon instead of a point for decimal separation. []'s, Camps On Mon, Nov 7, 2022 at 6:05 PM Amal Yassin wrote: > Dear siesta users > can you help me? i did the run for fdf file, and i found this error.. > > > coor: Atomic-coordinates input

Re:[SIESTA-L]

Hi, For some reason, you are using commas (",") instead of dots (".") as decimal separators. In fortran, a comma in an input line separates items. This confuses the program. You should check your 'locale' settings. Alberto - El 7 de Noviembre de 2022, a las 17:18, Amal Yassin

Re: [SIESTA-L] (Wrong block specification)

Hi, You should remove the comment character from: #%endblock LatticeVectors Alberto - El 21 de Septiembre de 2022, a las 12:23, Amal Yassin escribió: | Dear Siesta Users | I make run to carbone nanotube armchair, but i find an error, can anyone helle | me to solve this error? ( I

Re: [SIESTA-L] (problems with polarization orbital when using Mg.psml)

Dear Alberto, Many thanks for the guidance. I was looking for that section (%block PAO.PolarizationScheme) in the manual v. 4.1-b4 but couldn't find any. However, I entered as you wrote and it worked, but it goes only for one CG steps and ends. Then I tried with "PAO.oldstylepolorbs to be false

Re: [SIESTA-L] (problems with polarization orbital when using Mg.psml)

Dear Rajesh, I quote from (the source of) the Siesta manual: \item The default perturbative scheme for polarization orbitals can fail in very specific cases. When the polarization orbital has to have a node due to the presence of a lower-lying orbital with the same $l$, the program can (if

RE: [SIESTA-L] [***Posible SPAM***] RE: number of k-points in denchar

-Original Message- From: Rajesh_Dutta Sent: 2022年9月7日 14:50 To: Fanmiao Kong ; siesta-l@uam.es Subject: Re: [SIESTA-L] [***Posible SPAM***] RE: number of k-points in denchar Dear Fanmiao, Many thanks for the information, I exactly needed thatinfo. BTW, I was playing with different PP format (.psf

Re: [SIESTA-L] [***Posible SPAM***] RE: number of k-points in denchar

Dear Fanmiao, Many thanks for the information, I exactly needed thatinfo. BTW, I was playing with different PP format (.psf and .psml) to have a test on result. Mg.psml downloaded from pseudo dojo through some following error:

Re:[SIESTA-L]

Dear Amal Yassin: Your unit cell vectors are all zeros; your atom belongs to specie Nr zero (must be 1), and there seems to be a problem with its coordinate. All this is evident from your output file if you read it beyond the first line. The absence of XV file is just a warning; it's no

Re: [SIESTA-L] Installing Siesta GPU acclerated version

Dear All, Thank you very much for introducing me to a wonderful forum. I am new in Siesta. Please let me know how I calculate free energy change of a reaction, I am interested in calculating free energy profile for CO2 reduction steps. Thanks in advance. Regards, Dr. N N Ghsoh University of Gour

Re: [SIESTA-L] Question about Gate in SIESTA

Dear Nick Papior, Thank you very much for your reply. Please take a moment to see if I misunderstood your response. As shown in the comments section below (red font) : 1. Please confirm whether the comments in red font below are correct. This will help me a lot. %block Geometry.Hartree plane 1.

Re: [SIESTA-L] Question about Gate in SIESTA

Hi, On Fri, 1 Jul 2022, 22:00 肖威, wrote: > Dear SIESTA developers and users, > > I recently read Papior et al. 's article on Phys. Chem. Chem. Phys. > entitled "Manipulating the voltage drop in graphene nanojunctions using a > gate potential (DOI: 10.1039/C5CP04613K)". I am very interested in

Re: [SIESTA-L] TBtrans and broadening matrix

Hi, thank you very much for provided material! Kind regards, Aleksandar Tomovic -- 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] TBtrans and broadening matrix

Hi, As for details regarding the projected transmissions and other scalar quantities, you may find this useful: https://www.youtube.com/watch?v=ERGksOfikb8=PLwM2jMcWDGDAMkCAmGOi19Pe8rL0-CJtU=15 Also, the discussion related to the tutorial on projected transmissions is still present on the

Re: [SIESTA-L] Installing Siesta GPU acclerated version

Hello, Thanks for the information, I’ll try to install it as per the instructions provided. Regards, Ghadiyali Mohammed Kader Post Doctoral Fellow King Abdullah University of Science and Technology On 29 Jun 2022, 11:06 PM +0300, Alberto Garcia , wrote: > Hello, > > We are writing a section on

Re: [SIESTA-L] Question on VCA approach

Hi Roberto, The first reference is the closest in spirit, except that we incorporate the mix as the pseudopotential of a new "alchemical" species instead of keeping separate "pure" ghost atoms and using a weight factor for each. The second reference imposes extra conditions on the

Re: [SIESTA-L] Installing Siesta GPU acclerated version

Hello, We are writing a section on GPUs in the documentation, but until it is ready you can use the ideas below: There are two ways to take advantage of GPUs (enabled only for the solver stage, which typically takes up the most time): -- Using the ELPA library and its native interface in

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