[SIESTA-L] PDOS calculation

Hi I have installed a new version of siesta(siesta-4.1-b3). In my new work I need the SpinPolarized calculation. I want to plot the PDOS of different elements so I make the executable pdos with change the siesta/util/pdosxml/m_orbital_chooser file. when I run this executable file on my old project

Re: [SIESTA-L] PDOS Up and Down

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

RE: [SIESTA-L] PDOS Up and Down

f Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: rayan moukhadder<mailto:rayanroro321...@gmail.com> Sent: Wednesday, 22 July 2020 6:02 AM To: siesta-l@uam.es<mailto:siesta-l@uam.es> Subject: [SIESTA-L] PDOS Up and

[SIESTA-L] PDOS Up and Down

Dear siesta users, A successful spin polarized siesta run was done and a .PDOS file has been created. Now I would like to plot PDOS up and down for specific atoms using one of Andrei Postnikov tools which is fmpdos script. Using this script I can easily identify n,l,m quantum numbers of the atom bu

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

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

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

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

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

:siesta-l@uam.es> Subject: [SIESTA-L] PDOS and EIG files in transiesta Hello everybody, I would like to ask why .PDOS and .EIG files are not obtained by me after a successful transiesta and tbtrans run knowing that i added the options TS.TBT.AtomPDOS true TBT.DOS.A.All true Thanks in advance.

[SIESTA-L] PDOS and EIG files in transiesta

Hello everybody, I would like to ask why .PDOS and .EIG files are not obtained by me after a successful transiesta and tbtrans run knowing that i added the options TS.TBT.AtomPDOS true TBT.DOS.A.All true Thanks in advance. -- SIESTA is supported by the Spanish Research Agency (AEI) and by the Eur

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

) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Soumyajyoti Haldar<mailto:sjh...@outlook.com> Sent: Tuesday, 9 June 2020 6:03 AM To: siesta-l<mailto:siesta-l@uam.es> Subject: [SIESTA-L] PDOS at a vacuum on top of a slab Dear Sies

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

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

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

Dear Siesta Users, I am trying to calculate PDOS in the vacuum at a Z Å height above a surface. Can you suggest how to proceed with Siesta? In some other codes, I know one can use empty sphere to project DOS. Is there something similar in Siesta one can set up? If yes can you let me know how t

Re: [SIESTA-L] pDOS spin up vs spin down in tbrans

Den fre. 21. jun. 2019 kl. 22.02 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Good evening, > I was wondering for the spin PDOS extracted from Tbtrans, should I > multiply the values obtained by -1 > No! > because I have noticed PDOS spin down calculated via TBTRANs for many > different

[SIESTA-L] pDOS spin up vs spin down in tbrans

Good evening, I was wondering for the spin PDOS extracted from Tbtrans, should I multiply the values obtained by -1 because I have noticed PDOS spin down calculated via TBTRANs for many different elements tend to have a similar trend to PDOS spin up. If i should not multiply by -1 what does spin

Re: [SIESTA-L] PDOS or LDOS in Transiesta

Dear Nick Papior, Thank you for your kind answer. Best regards, Lee 2017-02-02 7:13 GMT+00:00 Nick Papior : > Dear Lee, > > In transiesta 4.0 it is not possible to further analyse the DOS > distribution among orbitals. If you want to do PDOS you need to recalculate > for each PDOS region you a

Re: [SIESTA-L] PDOS or LDOS in Transiesta

Dear Lee, In transiesta 4.0 it is not possible to further analyse the DOS distribution among orbitals. If you want to do PDOS you need to recalculate for each PDOS region you are interested in. See the TS.TBT.PDOSFrom and TS.TBT.PDOSTo flags. Let me note that since 4.1 this is now possible in a s

[SIESTA-L] PDOS or LDOS in Transiesta

Dear all, I am calculating the 2-terminal device using transiesta 4.0. For the deep analysis, I want to see the PDOS or LDOS in this device (scattering region). Is there any option or post processing binary that allows me to calculate PDOS or LDOS? Thank you for your kind help. Best regards,

Re: [SIESTA-L] pdos in siesta

Dear Amrish: Please, take a look at: http://personales.unican.es/junqueraj and follow the links: Set of self-explained Siesta exercises Computing structural and electronic properties of materials Density of states and projected density of states.

[SIESTA-L] pdos in siesta

dear user i want to plot pdos file. using partial dos block in my fdf i get .pdos file but i don't know how to proceed further kindly help. -- warm regards amrish sharma

Re: [SIESTA-L] PDOS

Thanks a lot Javier. On Sat, Jul 16, 2016 at 10:47 PM, Javier Junquera wrote: > > Dear Anju: > > Besides mprop, you can also have a look to the corresponding tutorial > exercise: > > Follow the links: > > http://personales.unican.es/junqueraj/ > Set of self-explained Siesta exercises > Com

Re: [SIESTA-L] PDOS

Dear Anju: Besides mprop, you can also have a look to the corresponding tutorial exercise: Follow the links: http://personales.unican.es/junqueraj/ Set of self-explained Siesta exercises Computing structural and electronic properties of materials Density of states and projected density

Re: [SIESTA-L] PDOS

Thanks Leone Carmo Garcia. On Sat, Jul 16, 2016 at 9:45 PM, leoqmc . wrote: > Dear Anju Saroha, > > I think MPROP program can solve the problem. > > Regards, > > Leone Carmo Garcia > > 2016-07-16 12:54 GMT-03:00 Anju Saroha : > >> Dear siesta users, >> >> I have run a calculation for NiO, and I

Re: [SIESTA-L] PDOS

Dear Anju Saroha, I think MPROP program can solve the problem. Regards, Leone Carmo Garcia 2016-07-16 12:54 GMT-03:00 Anju Saroha : > Dear siesta users, > > I have run a calculation for NiO, and I need to plot the PDOS for t2g and > eg of Ni- 3d orbital. As far as I know we can either plot for

[SIESTA-L] PDOS

Dear siesta users, I have run a calculation for NiO, and I need to plot the PDOS for t2g and eg of Ni- 3d orbital. As far as I know we can either plot for complete 3d i.e all m values or each individual m values. I need to know how we can plot it for eg and t2g separately. Looking forward for som

[SIESTA-L] PDOS

Hi, I have faced a problem in generating PDOS for NiO. In the NiO.PDOS output file the values for oxygen atom is not zero. While converting from .PDOS, using fmpdos utility program, the file for O- 2s and O-2p orbitals contains all zero. Can somebody please help me to overcome the issue. Has any

Re: [SIESTA-L] PDOS at a point in siesta

Dear Dr Javier Thank you so much for your help. Regards Riya On Tue, May 10, 2016 at 12:55 AM, Javier Junquera wrote: > > Dear Riya: > > Go to: > > http://personales.unican.es/junqueraj/siesta-tutorial.html > > There you can fin many fully self-explained exercises on the > practicalities an

Re: [SIESTA-L] PDOS at a point in siesta

Dear Riya: Go to: http://personales.unican.es/junqueraj/siesta-tutorial.html There you can fin many fully self-explained exercises on the practicalities and how-to in SIESTA. In your particular case, follow the links: Set of self-explained SIESTA exercises Computing structural and elec

[SIESTA-L] PDOS at a point in siesta

Dear all How to calculate PDOS at the edge carbon atom of graphene nanoribbon ? kindly guide me through. Thanking you Regard Riya

[SIESTA-L] PDOS

Hi I am finding PDOS for HgTe, after running the fdf file i got HgTe.PDOS file but how to get plot of pdos that i don't know please help me. On 22 Feb 2016 15:24, "Mayuri Vaghela" wrote: > thank you guys, > just now i got real ZnS structure by defining 8 atoms in unitcell. > thank you once again.

[SIESTA-L] PDOS

Dear SIESTA users, I perform a spin polarized calculation for a triplet arrangement, every seems ok when I look over the EIG file, however the PDOS plot shows the minority component closer to the Fermi energy than the majority component, please could somebody give me a clue about why this is happe

Re: [SIESTA-L] PDOS from Inelastica

pyTBT can only be runned in threaded parallelism if you have a threaded numpy/blas installation you can run it using several cores. It does not support MPI parallelism. For the eigenchannel calculation you need to figure out what you want to plot. The eigenchannel can reveal symmetries in the junc

Re: [SIESTA-L] PDOS from Inelastica

Hi Nick , I have managed to start up the new version of Inelastica. Can PyTBT be run in parallel ? also for eigenchannel is calculation do i have to match the a1, a2 k-points that i had used for transmission convergence ? On Thu, Apr 23, 2015 at 11:15 PM, Nick Papior Andersen wrote: > I guess

Re: [SIESTA-L] PDOS from Inelastica

Oh yeah, probably --compiler only works for "build", I can never remember. Try python setup.py build --help and all its variants. To check whether you are forcing links against intel, locate your numpy installation (import numpy and find its installation directory), and check if the libraries als

Re: [SIESTA-L] PDOS from Inelastica

now it says error: option --compiler not recognized On Thu, Apr 23, 2015 at 11:57 PM, ganesh sivaraman wrote: > Hi Nick, > > Its just my desktop. But we have this HTC condor installed in our > institute which makes it common libraries for all. A kind of weirdo system > . > > So what i usually d

Re: [SIESTA-L] PDOS from Inelastica

Hi Nick, Its just my desktop. But we have this HTC condor installed in our institute which makes it common libraries for all. A kind of weirdo system . So what i usually do is to like manually with the FC , CXX ...LD_LIBRARTH_PATH...etc .manually we do have an intel compiler installation. But

Re: [SIESTA-L] PDOS from Inelastica

I guess you are mixing intel compiled stuff with gnu compiled stuff. Do you have intel compiled numpy/python? It sure seems like it as libimf.so is a library from the intel compiler suite. Do you have a module to load intel, or do you manually source the intel file when needing the intel compiler?

Re: [SIESTA-L] PDOS from Inelastica

I see...there are some contradictions . gcc version 4.8.1 20130909 [ ldd /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/F90helpers.so linux-vdso.so.1 (0x7ffe4939e000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x2b36f3ff6000) libifport.so.5 => not found libi

Re: [SIESTA-L] PDOS from Inelastica

Please supply this: gcc --version gfortran --version And ldd /home/ganesh/.local/lib/python2.7/site-packages/Inelastica/F90helpers.so 2015-04-23 22:43 GMT+02:00 ganesh sivaraman : > Hi Nick, > > Please find the attachment for the same . I have included both building > and install . > > On Thu,

Re: [SIESTA-L] PDOS from Inelastica

Hi Nick, Please find the attachment for the same . I have included both building and install . On Thu, Apr 23, 2015 at 10:25 PM, Nick Papior Andersen wrote: > There should be another error message associated with the python > installation. > Please provide that. > > I.e. try and reinstall inela

Re: [SIESTA-L] PDOS from Inelastica

There should be another error message associated with the python installation. Please provide that. I.e. try and reinstall inelastica, but pipe the output (plus stderr) to a file and send that file. To pipe stderr to stdout do: python setup.py install 2>&1 > debug.out 2015-04-23 22:18 GMT+02:0

Re: [SIESTA-L] PDOS from Inelastica

Hi, I have this strange error . I don't quiet understand it . Isee that new pyTBT has pdos capability. But when i changed to the latest snapshot of inelastic i have started to get the following error. Problems encountered with F90helpers.so Falling back on a pure python (slower) implementation

Re: [SIESTA-L] PDOS from Inelastica

Thanks all. I will try On Tue, Apr 21, 2015 at 8:54 PM, Magnus Paulsson wrote: > Try: > pyTBT —help > > (SVN-version of Inelastica) > > This is the python version of tbtrans. Thomas has added a lot of PDOS > calculations and the output files should > be directly readable by xmgrace. I haven

Re: [SIESTA-L] PDOS from Inelastica

Try: pyTBT —help (SVN-version of Inelastica) This is the python version of tbtrans. Thomas has added a lot of PDOS calculations and the output files should be directly readable by xmgrace. I haven’t looked at PDOS myself so I don’t remember the details. -Magnus -

Re: [SIESTA-L] PDOS from Inelastica

Hi Nick , I am quiet familiar with EIgenchannels tools and --help for that was always helpful . Inelastica does say its for IETS. There are some flags similar to eingenchannels , when i tried the --help for inelastic . But i was not quiet sure about outputs. Its rather confusing unlike eigenchan

Re: [SIESTA-L] PDOS from Inelastica

Have you tried using the --help flag on the commands in Inelastica? They are actually pretty helpful. 2015-04-21 9:40 GMT+02:00 ganesh sivaraman : > Hi, > > I saw that Inelastica has the capability of give PDOS . Does any one have > experience how to do this ? > > T&R, > > Ganesh Sivaraman > -

[SIESTA-L] PDOS from Inelastica

Hi, I saw that Inelastica has the capability of give PDOS . Does any one have experience how to do this ? T&R, Ganesh Sivaraman

[SIESTA-L] pdos

hi dear users siesta, Hi im trying to compile Pdosxml in Util folder with make and f95 pdos.F90 -o pdos  commands but i got the following error: command make : f95  -o pdos m_orbital_chooser.o m_pdos.o f2kcli.o pdos.o  ../../Src/libxmlparser.a f2kcli.o: In function `__f2kcli_MOD_get_command_ar

[SIESTA-L] pdos

hi dear users siesta, Hi im trying to compile Pdosxml in Util folder with make and f95 pdos.F90 -o pdos  commands but i got the following error: command make : f95  -o pdos m_orbital_chooser.o m_pdos.o f2kcli.o pdos.o  ../../Src/libxmlparser.a f2kcli.o: In function `__f2kcli_MOD_get_command_argu

[SIESTA-L] PDOS calculation with tbtrans

Dear siesta users, I have performed transport calculations on GNR with some defects by siesta-3.1 package. I try to see PDOS for some specific atoms in the device region with  specifying following command:   TS.TBT.PDOSFrom   xx TS.TBT.PDOSTo    yy but after simulation :  I se

Re: [SIESTA-L] PDOS: Is there a way to specify radius of projection?

And just to complete the story, some plane-wave codes do not do the muffin-tin analysis, but do a full projection onto atomic orbitals of the PW eigenstates, based on Sanchez-Portal et al; Solid St. Commun. 95, 685 (1995), and J. Phys. Condensed Matter 8, 3859 (1996). I think CASTEP and CPMD do thi

Re: [SIESTA-L] PDOS: Is there a way to specify radius of projection?

Hi Benedikt, Alberto is right, SIESTA does not need projections, but YOU might need them; exactly for the sake of comparing the charges with those from "muffin-tin"-type codes I wrote some time ago a primitive tool http://www.home.uni-osnabrueck.de/apostnik/Software/grdint.f which "integrates" grid

Re: [SIESTA-L] PDOS: Is there a way to specify radius of projection?

Hi Benedikt, SIESTA does not need projections, as the basis orbitals are localized on the atoms. You get naturally the "chemical" information one is used to. Plane-wave codes such as vasp do need projections to get some kind of "local" information from the delocalized basis. Alberto On Mon, J

[SIESTA-L] PDOS: Is there a way to specify radius of projection?

Hello, I have a question about PDOS calculations with siesta. Is there a way to specify the radius around the atoms in which the projection is carried out? This option exists in different other dft codes like vasp (http://cms.mpi.univie.ac.at/vasp/vasp/RWIGS.html). Any help would be very welc

[SIESTA-L] PDOS and DOS

dear Bedamani thank you so much for your reply, by shifting the DOS curve, two curves were matched thanks a lot From: bedamani singh To: Mehrzad Sasanpoor Sent: Monday, October 15, 2012 8:31 AM Subject: Re: [SIESTA-L] PDOS and DOS Dear Mehrzad, I

[SIESTA-L] PDOS and DOS

dear siesta users I translated EIG file of my output to data and plotted DOS of my typical system (benzene molecule) versus of energy, then I plot PDOS of C2pz orbital of my system. I expected that the peaks of PDOS is matched with some of the DOS peaks . but I didn't have DOS peak in some PDOS

Re: [SIESTA-L] pdos of pz orbital

dear sir Riccardo thanks a lot for your reply, I can get the appropriate pdos for pz obital of methyl From: Riccardo Rurali To: siesta-l@uam.es Sent: Monday, October 8, 2012 11:41 AM Subject: Re: [SIESTA-L] pdos of pz orbital Sorry, but I don't

Re: [SIESTA-L] pdos of pz orbital

*To:* siesta-l *Sent:* Monday, October 8, 2012 12:39 AM *Subject:* Re: [SIESTA-L] pdos of pz orbital >>>in this curve I knew which energies is dominated by pz orbitals, but I want to know which energy is approximately related to pz orbital of methyle group. Does pdos help me? Of course PDO

Re: [SIESTA-L] pdos of pz orbital

attention From: Riccardo Rurali To: siesta-l Sent: Monday, October 8, 2012 12:39 AM Subject: Re: [SIESTA-L] pdos of pz orbital >>>in this curve I knew which energies is dominated by pz orbitals, but I want >>>to know which energy is approxima

Re: [SIESTA-L] pdos of pz orbital

> > Hi dear siesta users, > > I plot pdos of pz orbital of carbon for benzene molecule which is > functionalized with methyl group, > > in this curve I knew which energies is dominated by pz orbitals, but I > want to know which energy is approximately related to pz orbital of > methyle group. Does

Re: [SIESTA-L] pdos of pz orbital

>>>in this curve I knew which energies is dominated by pz orbitals, but I want >>>to know which energy is approximately related to pz orbital of methyle >>>group. Does pdos help me? Of course PDOS can help you! In the PDOS file you have the total density of states decomposed into ('projected'

[SIESTA-L] pdos of pz orbital

Hi dear siesta users, I plot pdos of pz orbital of carbon for benzene molecule which is functionalized with methyl group, in this curve I knew which energies is dominated by pz orbitals, but I want to know which energy is approximately related to pz orbital of methyle group. Does pdos

[SIESTA-L] pdos of pz orbital

Hi dear siesta users, I plot pdos of pz orbital of carbon for benzene molecule which is functionalized with methyl group, in this curve I knew which energies is dominated by pz orbitals, but I want to know which energy is approximately related to pz orbital of methyle group. Does pdos help me

Re: [SIESTA-L] pdos

by your complet explenation I am sure I can do that. > Thanks for your wonderfull guids again, > Good luck > > > > > > From: "apost...@uni-osnabrueck.de" > To: siesta-l@uam.es > Sent: Sat, July 2, 2011 1:59:58 PM > Subj

Re: [SIESTA-L] pdos

am.es Sent: Sat, July 2, 2011 1:59:58 PM Subject: Re: [SIESTA-L] pdos > hi dear root > I got fmpdos.f from internet. Dear Zahra - sorry for intervening even as I am not "dear root". The internet is big. I am glad that you find my small script worth using. It was intended to be simp

Re: [SIESTA-L] pdos+XML

g Alborto suggestion, but I am not using intel V11.Your help will solve my problem.Mic --- On Sat, 7/2/11, apost...@uni-osnabrueck.de wrote: From: apost...@uni-osnabrueck.de Subject: Re: [SIESTA-L] pdos To: siesta-l@uam.es Date: Saturday, July 2, 2011, 5:29 AM > hi dear root > I go

Re: [SIESTA-L] pdos

is self-evident. Good luck Andrei Postnikov > > > From: root > To: siesta-l@uam.es > Sent: Wed, June 29, 2011 11:58:11 PM > Subject: Re: [SIESTA-L] pdos > > Hi Zahra, > > There is a very handy script fmpdos.f. > > Follow the ins

Re: [SIESTA-L] pdos

are always 0. in the way that I know the l for orbital p is equal to 1. thank you From: root To: siesta-l@uam.es Sent: Wed, June 29, 2011 11:58:11 PM Subject: Re: [SIESTA-L] pdos Hi Zahra, There is a very handy script fmpdos.f. Follow the instruction, enter

Re: [SIESTA-L] pdos

Hi Zahra, There is a very handy script fmpdos.f. Follow the instruction, enter value of n, l, m, (n define certain atom number, l,m enter 0 for all case) define the name of output file, eg. atom 4 I define it as 4.out And you can get the DOS for any atoms you want. On Tue, Jun 28, 2011 at 1:40

Re: [SIESTA-L] pdos

-L] pdos To: "siesta-l@uam.es" Date: Tuesday, June 28, 2011, 1:53 AM hi you can go to Util folder  then pdosxml folder and study README file,into this file describe about plot PDOS From: Zahra Talebi To: siesta home Sent: Tuesday, June 28, 2011 10:10 AM Subject: [SIESTA-L] pdo

Re: [SIESTA-L] pdos

hi you can go to Util folder  then pdosxml folder and study README file,into this file describe about plot PDOS From: Zahra Talebi To: siesta home Sent: Tuesday, June 28, 2011 10:10 AM Subject: [SIESTA-L] pdos Hi every body I want to draw a diagram of my

[SIESTA-L] pdos

Hi every body I want to draw a diagram of my case.PDOS out put after running siesta and I don`t know how to do that. If any body knows let me know step by step

Re : [SIESTA-L] PDOS problem

hi yashumimi;   try to specify two decimal places. eg :   %block ProjectedDensityOfStates -10.00   5.00    0.05 200  eV %endblock ProjectedDensityOfStates   hope this can help,   Slimane De : Michael Shin À : siesta-l@uam.es Envoyé le : Samedi 25 Juin 2011 9h13 Objet : Re: [SIESTA-L] PDOS

Re: [SIESTA-L] PDOS problem

WriteXML    F if I use WriteXML    T, then I get the error message and calculations stop. Does it has any relation with PDOS. or is it a bug in siesta-3.0-rc2. I wish you will help me. --- On Fri, 6/24/11, yashumimi wrote: From: yashumimi Subject: [SIESTA-L] PDOS

[SIESTA-L] PDOS problem

what i set as follow: %block ProjectedDensityOfStates -10.0 0.0 0.05 200 eV %endblock ProjectedDensityOfStates and I get: in *.PDOS : n="2" l="2" m=" -2" z="1" 2d orbit? could u give some advice to exp

[SIESTA-L] PDOS problem

Hi,everyone, When I calculated the PDOS of siesta, it showed as follows: siesta: PDOS info: siesta: e1, e2, sigma, nhist: -20.00 eV 10.00 eV0.20 eV 1500 p0_23870: p4_error: interrupt SIGSEGV: 11 rm_l_2_23911: (8963.945312) net_send: could not write to fd=5, errno = 32 rm_l_3_23931: (8963

Re: [SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

Hi, NH and Marcos. I went back to the references of the basis construction and I understood the point that you stressed. Actually, I knew this points when I asked my questions and I was looking for an relation between the PDOS of the last occupied orbital (p) and the perturbing orbital (d), then I

Re: [SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

The orbitals is just a basis function!!! And a s, p or d orbitals are solutions just for the Hydrogen atom. Which means that basing our solutions on it is an approximation anyway! Besides ... although important to ann accurate description of the total energy, the polarization is a seccondary effe

Re: [SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

Okay. Siesta takes into account the l+1 orbital to consider the deformations induced by bonding. In my case, the last occupied orbital in Si has l=1, so the polarization orbital has l=2 (d orbital). However, if the d "perturbing" state are perturbing the 3p one, when I choose n=3 and l=1 to view th

Re: [SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

This has to do with how polarization orbitals are determined in Siesta. The subject has been discussed in the list before, I think, but in brief: in the manual, you can see that they are the solutions to the perturbation problem of an atom in a weak electric field. Now, if you look at this problem,

[SIESTA-L] PDOS showing occupation in the "d" orbital in SiN

Hello people, I'm learning how to use the pdosxml and I found one issue with the results of PDOS: I'm extracting the projected DOS from a silicon nitride calculation, and when I get the PDOS per atom species (N or Si) I have contribution of the "*d*" orbital (l = 2). However, Si and N atoms does n

Re: [SIESTA-L] PDOS for PI orbitals in graphene with different zeta-number

Neither: the sum of both orbitals, instead. Look for the orbitals with l=2 as well, to include in the sum: they will be the polarization orbitals of your system. Marcos On Sat, Jul 24, 2010 at 8:31 PM, Pouya Partovi-Azar < p.part...@nano.ipm.ac.ir> wrote: > Dear SIESTA users, > > I want to calcu

[SIESTA-L] PDOS for PI orbitals in graphene with different zeta-number

Dear SIESTA users, I want to calculate the PDOS of PI orbitals (n,l,m=2,1,0) for a specific carbon atom in graphene structure. I use DZP basis, so there are two such orbitals: (n,l,m,z=2,1,0,1) and (n,l,m,z=2,1,0,2). My question, considering the scheme used in SIESTA for building DZ basis from