Re: [SIESTA-L] ATK and Siesta/transiesta

If you would like to know how they are different, I recommend you go > through they site and using a sheet of paper, make two columns, and write > down they features. > > > []'s, > > @mps > > On Fri, Oct 2, 2015 at 12:58 PM, Riya Rogers <rogers.riy...@gmail.com> >

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Hello everyone

[SIESTA-L] ATK and Siesta/transiesta

Hello everyone I am a using siesta for my ATK toolkit for my project work but its only available inside my university campus. I get to know about siesta and transiesta from web search. Can I use siesta/transiesta for analysis of electrical behavior MoS2 and interactions with metal atoms instead

Re: [SIESTA-L] Transiesta Convergence problem in zigzag nanoribbon of Graphene

Here is my fdf file. Regards Riya On Mon, Nov 23, 2015 at 9:20 PM, Younas Khan <younaskhan.phys...@gmail.com> wrote: > Kindly share your input file so that it becomes easy to find out where you > are making a mistake. > > Thanks > > > On Mon, Nov 23, 2015 at 4:52

Re: [SIESTA-L] Sampling scheme problem

, > > Camps > > On Thu, Jan 7, 2016 at 12:38 PM, Riya Rogers <rogers.riy...@gmail.com> > wrote: > >> Thank You Dr. Camps for your suggestion. >> But what I understood is if my supercell is having periodicity in >> Z-direction, I should took 1 X 1 X

[SIESTA-L] comment on lattice constant

Hello Everyone Is it ok to take lattice constant as 1.4336 Ang in this example (Graphene zigzag nanoribbon): http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon as 1.42 Ang is standard value. comment please. Thank you Regards Riya

[SIESTA-L] Nano cluster simulation

Dear all I want to study Gold 10 atom nano clusters with siesta, is it possible with siesta to get the structure of nano cluster? If yes then how to proceed for that? or any online resource from where I get the structure? Thanking you Regards Riya

Re: [SIESTA-L] Siesta to be released with GPL license

Dear Alberto, Is there any rules which a general user like me have to take care? Do we need to pay for GPL? if not then what is the difference between acedemic and GPL? only the difference is easy re-distribution ? what is re-distribution? Please cearify Regards Riya On Mon, May 23, 2016

[SIESTA-L] Query on relaxation using geometry constraint (electrode fixed) then transiesta run

Hello Everyone I am trying to get transmission spectrum of graphene nanoribbon with Scattering region relaxed. Can any one confirm that the following procedure which i am using is correct? 1. First I took my coordinates (electrode+scattering+electrode) and relax the structure using CG run while

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

Thanks a lot for your valuable comments Dr Nick But as Rajan pointed out, I am facing the same problem of transiesta convergence. Should I use : TS.ReplicateA2Left/Right to increase my electrode size and may cause in convergence? Please comment. With Regards Riya On Wed, Jan 20, 2016 at

Re: [SIESTA-L] 4-ZGNR transmission spectrum

operties of 8AGNR and 4ZGNR" published by > Quantum Matter > <http://www.ingentaconnect.com/content/asp/qm;jsessionid=1v6cf13vs5clq.alexandra>, > Volume 2, Number 3, June 2013, pp. 225-228(4) > > On Sat, Mar 26, 2016 at 1:17 PM, Riya Rogers <rogers.riy...@gmail.com> &

[SIESTA-L] 4-ZGNR transmission spectrum

Dear All I was simulating 4-ZGNR transmission spectrum using transisesta. Can anyone suggest some good reference paper from which I can validate my results. I was trying to find out but I wont be able to find any suitable as many write 4-zgnr but their structure is something different as shown

[SIESTA-L] compat-pre-v4-dynamics in Siesta for siesta-trunk-462 like results

Hello everyone I am using siesta-4.0 version for my calculations and I am putting : compat-pre-v4-dm-h true compat-pre-v4-dynamics true I read the documentation where it is written that for pre-4.0 version results these two should be true so I put them as true. As I was using trunk-462 version

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

[SIESTA-L] Convergence criteria of mesh cut off 0.01 eV

Dear all During mesh cutoff convergence study for graphene I am using 0.01 eV as a convergence criteria. Is that ok? please guide me. Thank u Regards Riya

[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

Re: [SIESTA-L] Band structure for doped ZGNR

Doped means is it replacement of carbon or other molecule in vicinity? On 30-Jul-2016 10:38 pm, "maryam jamaati" wrote: > Dear siesta users, > > According to helpful advices of some friends (Nick, Kamaraj,..), I reduced > geometry to unit cell for calculation of ZGNR band

Re: [SIESTA-L] Band structure for doped ZGNR

neral manner. I did not dealt with supercells but do not think your >> problem is critical. >> >> 2016-07-30 23:00 GMT+04:00 Riya Rogers <rogers.riy...@gmail.com>: >> >>> Doped means is it replacement of carbon or other molecule in vicinity? >>> >&

Re: [SIESTA-L] Band structure for doped ZGNR

should to try all >> possible combinations and the combination with the lowes energy is correct. >> This i know other researchers do, but your route is unknown for me, explain. >> >> 2016-07-31 13:30 GMT+04:00 Riya Rogers <rogers.riy...@gmail.com>: >> >>> Primi

[SIESTA-L] Restricted and unrestricted dft calculations using siesta

Dear all Can anyone tell me how to perform restricted and unrestricted dft calculation using siesta. Thank u Regards Riya

Re: [SIESTA-L] VDW Calculations

Ok tht means by using the same if i get same bond lengths etc thn? On 08-Aug-2016 9:40 pm, "gagandeep Kaur" <gaganj1...@gmail.com> wrote: > Yes u can after testing it for your system.. > > > Sent from Samsung Mobile > > > ---- Original message &g

Re: [SIESTA-L] VDW Calculations

I think for gga n lda its ok bt i m nt sure. But fr vdw etc it should change. On 08-Aug-2016 1:29 pm, "Seyed Mohammad Tabatabaei" <smt...@gmail.com> wrote: > That is also my question. It seems that no one is going to help. > > On Mon, Aug 8, 2016 at 11:49 AM, Riya Rogers

[SIESTA-L] Regarding download psedopotentials

Dear all Can we just download psedopotentials and use it? Or we need to modify it? I download from siesta site. Clarify pls. Thanks Regards Riya

Re: [SIESTA-L] VDW Calculations

Dear all If I am using GGA PBE and I used psedopotentials from siesta site. Should I generate or is it ok to proceed with it? Please clarify... Thanks On 04-Aug-2016 9:56 pm, "gagandeep Kaur" wrote: > Thanks sir..bt wat abt .psf files?? > > > Sent from Samsung Mobile >

[SIESTA-L] GGA-PBE compatible norm conserving Troullier-Martins pseudopotentials is it ok to use siesta database?

Dear All I need GGA-PBE compatible norm conserving Troullier-Martins pseudopotentials, is it ok to download them from the siesta database: https://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-gga-abinit.html actually the input file is having keyword as pe: which is

Re: [SIESTA-L] Error in the end of simulation Siesta 4.1 b1

ard it completely. > I will fix this in the 4.1-b3 release so that it simply creates a file. > > May I suggest you to try 4.1-b2 instead of b1? Numerous bug-fixes has > already been added to the 4.1 release series. And with 4.1 still being in > beta it is imperative to stay updated. >

[SIESTA-L] Error in the end of simulation Siesta 4.1 b1

Dear All I am using siesta 4.1 b1 in parallel mode, everything is fine but I am getting following errors in the end: sh: /usr/bin/touch: No such file or directory what should i do for such error? Thanks Regards Riya

Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf

AM, "Riya Rogers" <rogers.riy...@gmail.com> wrote: > Dear Dr Nick > > Actually I tested few sample prog without netcdf its Working fine thats > why I asked. > > Thanks > > Regards > Riya > > On 17-Feb-2017 2:34 AM, "Nick Papior" <nickpa

Re: [SIESTA-L] Is it must to install siesta 4.1b1 with netcdf

release of siesta 4.1 has been released. > When testing with a beta release you are encouraged to follow the new > releases, closely. > > 2017-02-15 15:25 GMT+01:00 Riya Rogers <rogers.riy...@gmail.com>: > >> Dear All >> >> Is it must to compile Siesta 4.1b1 with netcdf? >> >> Regards >> Riya >> > > > > -- > Kind regards Nick >

Re: [SIESTA-L] k-point sampling in transiesta

Usually electrode k points should be 3 times of device k points. On 06-Nov-2016 11:16 pm, "Mahmoud Hammouri" wrote: > In the electrode run you need large number of k points. In the tbtrans run > you need very large k points even if your system was converged with less k > points.

[SIESTA-L] Intel mkl libraries for siesta

Dear all I am using intel mkl library but not able to modify LIBS variable properly hence at the end of installation, i am getting error saying: No such file or directory How to modify LIBS variable? Kindly help me out... Regards Riya

Re: [SIESTA-L] Intel mkl libraries for siesta

lers (that include the > path to the MKL files): > > source /opt/intel/parallel_studio_xe_2015/psxevars.sh > > > []'s, > > Camps > > On Wed, Nov 9, 2016 at 5:52 PM, Riya Rogers <rogers.riy...@gmail.com> > wrote: > >> Dear all >> >> I am us

Re: [SIESTA-L] siesta-4.1-b1: /bin/sh: FoX/FoX-config: No such file or directory

I didnt have ifort can i put if90? On 10-Nov-2016 6:47 pm, "Ricardo Faccio" wrote: > Try including this line in your arch.make. > FC_SERIAL = Ifort > Best regards > Ricardo > > -- > Dr. Ricardo Faccio > Prof. Agregado de Física > > Av. Gral. Flores 2124.

[SIESTA-L] Peptide simulations using Siesta

Dear all Can anyone tell me about peptide simulations using siesta? Kindly suggest some papers who used siesta for peptide interactions with surfaces. Thanks Regards Riya

[SIESTA-L] How to calculate single molecule energies

Dear all Can anyone tell me how to calculate energy of one molecule of gas. Should I take molecule inside lattice? Or Should I follow the following example1: http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Basic/Basic-exercises.html Does k points n meshcutoff and basis set

[SIESTA-L] How to calculate single molecule energies

Dear all Can anyone tell me how to calculate energy of one molecule of gas. Should I take molecule inside lattice? Or Should I follow the following example1: http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Basic/Basic-exercises.html Does k points n meshcutoff and basis set

[SIESTA-L] How to calculate single molecule energies

Dear all Can anyone tell me how to calculate energy of one molecule of gas. Should I take molecule inside lattice? Or Should I follow the following example1: http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Basic/Basic-exercises.html Does k points n meshcutoff and basis set

[SIESTA-L] Cutoff radii for psedopotentials generation

Dear All In oder to generate psedopotentials for different exchange n correlation functionals, I am using ATOM program but kindly tell me how to put cutoff radii for different shells? Is there any standard values for atomic radii for each atom? Kindly suggest something. Thanks Regards Riya

[SIESTA-L] Cutoff radii for psedopotentials generation

Dear All In oder to generate psedopotentials for different exchange n correlation functionals, I am using ATOM program but kindly tell me how to put cutoff radii for different shells? Is there any standard values for atomic radii for each atom? Kindly suggest something. Thanks Regards Riya

Re: [SIESTA-L] How to calculate single molecule energies

Dear Dr Camps Thank u so much. I m taking very high cutoff greater than 340Ry. N put the Molecule in middle of big lattice. My bond lengths are lil away frm exam abt 1.2 to 1.4%. Thanking you Regards Riya On 18-Dec-2016 2:40 am, "I. Camps" wrote: > > Can anyone tell me how

[SIESTA-L] Basis set superimposition error

Dear All I have a general query for those who are involved in calculation of adsorption energies. I have gone through many recent publications in very famous journals in which adsorption energies are calculated without considering Basis set superimposition error. Also, in most of the cases the

[SIESTA-L] Interpretation of PDOS plot for adsorption

Dear All I have plotted the PDOS orbitals for atoms of a molecule which is adsorbed over a surface. Also I have plotted the orbitals of atoms of surface too. I observed little overlapping of orbitals. Can I say that due to this overlapping tht particular orbitals are interacting and hence I am

Re: [SIESTA-L] Basis set superimposition error

Thanks... Regards Riya On 17-Apr-2017 1:34 AM, "I. Camps" <ica...@gmail.com> wrote: > I think that the answer to your question can be found in the original BSSE > paper. > > On Sat, Apr 15, 2017, 17:02 Riya Rogers <rogers.riy...@gmail.com> wrote: > >

[SIESTA-L] Eig2DOS parameters

Dear All What is the default values for the following parameters in Eig2DOS: - peak width (in eV) for broadening (gaussian or lorentzian). - number of points in the energy window - energy window: Emin and Emax (wrt E_F shifted to zero) And what if I dont supply these values in .EIG file? Is

[SIESTA-L] Parameters for zeta

Dear All How to set energy shift n split norm? Also when to change this is default values are ok? Thanking you Regards Riya

[SIESTA-L] Mixing parameters for spin polarized calculation

Dear All, I am trying to perform a spin polarized calculation on doped graphene structure, my scf itearations taking toom much time. Kindly give me suggestions for following: 1. which method should I choose for mixing : SCF.Mixer.MethodPulay|Broyden|Linear if pulay then

[SIESTA-L] DOS calculation with fermi shifted to zero

Dear All, I am calculating DOS of my system using the Andrei Postnikov method (given in tutorial below) : http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Structuralproperties/PDOS-SrTiO3/Exercise-PDOS-SrTiO3.pdf I have a doubt that whether this method gives the DOS with fermi