[SIESTA-L] STM Utility Inquiry

Hi, I want to plot the LDOS of my system including a 2D material by using stm utility within the siesta-3.2 package. So I tried some of the examples included in the corresponding doc in the Util/stm/ol-stm/Examples. According to the user's guide of STM.1.0.1, at first WFSX was converted to WFS usin

Re: [SIESTA-L] Optical properties

e utility in the Optical directory > and in the coming 4.0.2 release this update will make it easier to build > the utilities there. > > However, you shouldn't use the yagiuda utility. It has nothing to do with > Siesta. > > Den lør. 16. jun. 2018 kl. 22.01 skrev Nadia Salami &

Re: [SIESTA-L] Optical properties

سلام خوشبختانه مشکل حل شد. با احترام سلامی On Sat, Jun 16, 2018 at 9:36 PM, Nadia Salami wrote: > Dear Siesta users > > I want to calculate the optical properties of some molecules. > > > > In order to compile input.f code at Optical folder, the following command > is

[SIESTA-L] Optical properties

t I don't find an answer. Your help is highly appreciated to get rid of the problem. Thanks in advance, Kind regards Nadia Salami

[SIESTA-L] Optical properties

Dear Siesta users I want to calculate the optical properties of some molecules. In order to compile input.f code at Optical folder, the following command is written in the terminal: "gfortran input.f -o input" But it sounds that installing yagiuda requires using the following command: "sudo

[SIESTA-L] Should spin-polarized calculations be done for DFT investigations of a slab?

Dear Siesta users, I am trying to model a slab using Siesta code. I think that spin-polarized calculations should be done due to dangling bonds on the slab surface. Is it correct? Your comments will be highly appreciated. Best regards, Nadia

[SIESTA-L] How to model two electrons induced due to the chemical interaction

simulated before and after the chemical interaction using DFT calculation. But, Who can be considered the two electrons induced due to the chemical interaction. Your guidance will be highly appreciated. Best regards, Nadia Salami

[SIESTA-L] Fortran runtime error: I/O past end of record on unformatted file

(unit=2, file='A.RHO') Fortran runtime error: I/O past end of record on unformatted file Also, I have attached the executable file of code. I don't know how to get rid of the problem. Could you help me, please? Thanks in advance, Kind regards. Nadia Salami charge-transfer Desc

Re: [SIESTA-L] Incorrect Fermi energy for the electrode

Dear Mads, Thanks for your comment and guidance. I will try to explore its reason. Kind regards, Nadia Salami On Tue, Sep 15, 2015 at 8:38 PM, Mads Engelund wrote: > Dear Nadia, > I encountered something similar. Be aware that it might not be an error > but could actually reflect th

[SIESTA-L] Incorrect Fermi energy for the electrode

I must to add that when I do electrode calculation for same system by setting the following values, %block kgrid_Monkhorst_Pack 1 0 0 0.0 0 3 0 0.0 0 0 50 0.0 %endblock kgrid_Monkhorst_Pack SpinPolarized false I have obtained the correct Fermi energy. Thanks in advance.

[SIESTA-L] incorrect Fermi energy for the electrode

sampling to obtain elec.TSHS file, 1 0 0 0 3 0 0 0 50 I have obtained incorrect value for the Fermi energy. I don't know how to solve this problem. Your guidance and suggestion will be highly appreciated. Thanks in advance, Best regards. Nadia Salami

[SIESTA-L] incorrect Fermi energy for the electrode

sampling to obtain elec.TSHS file, 1 0 0 0 3 0 0 0 50 I have obtained incorrect value for the Fermi energy. I don't know to solve this problem. Your guidance and suggestion will be highly appreciated. Thanks in advance, Best regards. Nadia Salami

[SIESTA-L] Marcoave or plrho utility

Dear siesta users, I want to explore the electrostatic potential at edge of a small supercell at various conditions. The supercell contains of 12 atoms. Is it convenirnt to utilize plrho utillity or marcoave utility? Your guidance is highly appreciated. Thanks in advance, Best regards. Nadia

Re: [SIESTA-L] correct k point sampling for the electrode, scattering and Tbtrans calculations

e used to calculate the transmission. Am I right? > > > > Thanks in advance, > > > > Best regards, > > Nadia Salami > > > > On Sun, Jul 26, 2015 at 11:53 AM, Nadia Salami > > wrote: > > > >> Dear Dr. Papior, > >> > >> S

Re: [SIESTA-L] correct k point sampling for the electrode, scattering and Tbtrans calculations

? Thanks in advance, Best regards, Nadia Salami On Sun, Jul 26, 2015 at 11:53 AM, Nadia Salami wrote: > Dear Dr. Papior, > > Since my system is a slab, so the scattering occurs in two dimensions (the > transport direction and also the transverse direction), According to two > direction

Re: [SIESTA-L] correct k point sampling for the electrode, scattering and Tbtrans calculations

, Nadia Salami On Sat, Jul 25, 2015 at 11:46 AM, Nick Papior wrote: > > > 2015-07-25 6:55 GMT+00:00 Nadia Salami : > >> Dear Transiesta users, >> >> I don’t know how to determine correct k point sampling for the Transiesta >> as well as Tbtrans calculatio

Re: [SIESTA-L] correct k point sampling for the electrode, scattering and Tbtrans calculations

Dear Dr. Papior, Thank you very for your helpful guidance. Best regards, Nadia Salami On Sat, Jul 25, 2015 at 11:46 AM, Nick Papior wrote: > > > 2015-07-25 6:55 GMT+00:00 Nadia Salami : > >> Dear Transiesta users, >> >> I don’t know how to determine correct k poi

[SIESTA-L] correct k point sampling for the electrode, scattering and Tbtrans calculations

transmission calculation? It will be highly appreciated your comments and guidances. Thanks in advance, Best regards, Nadia Salami

Re: [SIESTA-L] Qsol and Qtot are different

Dear Dr. Papior, Thank you very much for your useful guidance. I will check them and try to solve. Best regards. On Fri, Jul 10, 2015 at 12:03 AM, Nick Papior wrote: > > > 2015-07-09 17:06 GMT+00:00 Nadia Salami : > >> Dear Transiesta users, >> >> I want

[SIESTA-L] Qsol and Qtot are different

tions. Thanks in advance. Best regards. Nadia Salami

Re: [SIESTA-L] convergence test in the level broadening and number of grid points to obtain the non-equilibrium part of density matrix

Dear Dr. Papior, Thanks so much for your reply. Must I do the energy convergence test? Thanks in advance, Best regards. Nadia Salami On Fri, Jul 3, 2015 at 11:58 AM, Nick Papior wrote: > As you said, convergence tests is the way to go. > > 2015-07-03 9:06 GMT+02:00 Nadia Salami : >

Re: [SIESTA-L] convergence test in the level broadening and number of grid points to obtain the non-equilibrium part of density matrix

Dear Dr. Papior, Thank you very much for your reply. I have applied these options, TS.BiasContour.Eta 0.0001 Ry TS.BiasContour.NumPoints 10 But I don't know how to obtain the optimized value. Your Guidance will be highly appreciated. Thanks a lot. Best, Nadia Salami On Fri,

[SIESTA-L] convergence test in the level broadening and number of grid points to obtain the non-equilibrium part of density matrix

ow to do the convergence test? Any comments and guidance will be appreciated. Best, Nadia Salami

Re: [SIESTA-L] plotting the 3D charge density difference

in charge densities. It reads label. cube file. You can subtract the two > *.cube files. > > nd > On Jun 21, 2015 1:32 AM, "Nadia Salami" wrote: > >> Dear siesta users, >> >> I want to plot the difference between self-consistent charge density of >

[SIESTA-L] plotting the 3D charge density difference

lp is most welcome. Thanks in advance, Best regards. Nadia Salami

Re: [SIESTA-L] How to correct the Berry phase to calculate piezoelectric coefficient for 2D structure

Namely, I don't know how to estimate the polarization using the berry-phase method. Could you guide me, please? Thanks in advance. Best regards. On Thu, Jun 11, 2015 at 9:02 PM, Nadia Salami wrote: > Dear users, > Let me know how to apply the results of Electric dipole in cas

[SIESTA-L] How to correct the Berry phase to calculate piezoelectric coefficient for 2D structure

dance will be highly appreciated. Thanks in advance, Best. Nadia salami

Re: [SIESTA-L] TranSiesta: Qsol,Qtot: NaN 1260.000 1.000

015-06-05 10:45 GMT+02:00 Nadia Salami : > >> Dear Nick, >> .fdf file is attached. >> Thanks in advance, >> >> On Fri, Jun 5, 2015 at 1:05 PM, Nick Papior Andersen < >> nickpap...@gmail.com> wrote: >> >>> Provide your fdf... >>

Re: [SIESTA-L] TranSiesta: Qsol,Qtot: NaN 1260.000 1.000

Dear Nick, .fdf file is attached. Thanks in advance, On Fri, Jun 5, 2015 at 1:05 PM, Nick Papior Andersen wrote: > Provide your fdf... > > 2015-06-05 10:28 GMT+02:00 Nadia Salami : > >> Dear transiesta users, >> >> Following output appears in the transiesta ca

[SIESTA-L] TranSiesta: Qsol,Qtot: NaN 1260.000 1.000

.759s sys 0m27.482s I don' know what's the matter, and any comments and advice will be appreciated. Best, Nadia Salami

[SIESTA-L] How to compile constr.f for my system

have deleted constr.f in the directory. I have faced to the following error: Error: constr.o: No such file or directory Could you help me to get rid of the problem, please? Thanks in advance, Beat regards. Nadia Salami

[SIESTA-L] compiling plrho utility

(1) (scalar and rank-1) plrho.f:206.24: . nt, colmin, colavg, colmax ) 1 Warning: Rank mismatch in argument 'colmin' at (1) (rank-1 and scalar) /usr/bin/ld: cannot find -lpgplot collect2: error: ld returned 1 exit status How can I solve the pr

Re: [SIESTA-L] how to compile constr.f file for my system

formatted) > 2) Change the fortran format to fortran 90, this is easier as there are > less restrictions on the formatting, if you do this, change the file ending > to .f90 instead of .f, and be sure to only have Src/constr.f90 and not > Src/constr.f in the directory. > > 2015-04-28

[SIESTA-L] how to compile constr.f file for my system

= fz * amass(14)/tmass 1 Error: 'fa' at (1) is not a variable ~/siesta-3.2/Src/constr.f:59. fa(3,15) = fz * amass(15)/tmass 1 Error: 'fa' at (1) is not a variable Fatal Error: Error count reached limit of 25. make: *** [constr.o] Error 1 Also, I h

[SIESTA-L] how to compile constr.f file for my system

Dear users I want to relax part of my system using constr.f file. At first step, I don’t know how to compile constr.f file for my system. At next step, is the compiled constr.f file included in my work directory? Could you help me please? Thanks in advance, Regards. Nadia Salami

[SIESTA-L] question about k-point sampling and displacements

Dear Siesta users Good time, I would be really grateful if you help me about this problem, There is a question about k-point sampling and displacements for calculating the correct transmission of graphene in the siesta mailing list. http://www.mail-archive.com/siesta-l@uam.es/msg07134.

Re: [SIESTA-L] Fwd: Hirshfeld Charges

Hi, In my Knowledge, the partial charge can be obtained from difference between the atomic total charge before and after bonding using Mulliken population analysis. Best regards, Nadia On Wed, Mar 11, 2015 at 7:37 AM, BingHuang wrote: > Hi, Mohammad, > > i have to say that doing this is comple

[SIESTA-L] Electric Dipole

I want to add that the following link can be useful. http://www.mail-archive.com/siesta-l%40uam.es/msg00498.html Thanks

[SIESTA-L] Electric Dipole

st regards, Nadia Salami PhD student

Re: [SIESTA-L] the association of each level (orbital) in a specific band

band-orbital. > > ••• > > On 17:40, Fri, Dec 12, 2014 Nadia Salami wrote: > >> Dear siesta users, >> >> How to determine the association of each level (orbital) in a specific >> band in the bandstructure curve? >> It will be highly appreciated any help and comment. >> Thanks in advance, >> Best. >> Nadia Salami >> >

Re: [SIESTA-L] interaction between two electrodes

If the bond length of atoms in two electrodes don't change due to the scattering region, So can be say that there aren't any interaction between them? Is it correct? It will be highly appreciated any guidance. Thanks in advance. Nadia Salami On Sat, Dec 13, 2014 at 7:40 AM, Nadia Sal

Re: [SIESTA-L] interaction between two electrodes

Thanks a lot for your guidance. There are bond lengths between each two atoms in the .BONDS file. Is it correct? Thanks a lot. Nadia Salami On Sat, Dec 13, 2014 at 12:38 AM, Nick Papior Andersen wrote: > > Just to mention two, you can either calculate it from the orbital range or >

[SIESTA-L] the association of each level (orbital) in a specific band

Dear siesta users, How to determine the association of each level (orbital) in a specific band in the bandstructure curve? It will be highly appreciated any help and comment. Thanks in advance, Best. Nadia Salami

[SIESTA-L] interaction between two electrodes

Dear siesta users, How to test exactly that the left and right electrodes don't interact to each other from the output files of transiesta calculations? Thanks in advance. Best regards. Nadia salami

Re: [SIESTA-L] electronic and magnetic properties

umns. The first one will be the energy in eV. The next one > will be dos for spin up, then dos for spin down and the last one will be > the dos for spin up + spin down. > > On Tue, Dec 2, 2014 at 1:03 PM, Nadia Salami > wrote: > >> I think that the density of states of spin u

Re: [SIESTA-L] electronic and magnetic properties

I think that the density of states of spin up and down are same. On Tue, Dec 2, 2014 at 9:05 AM, Nadia Salami wrote: > Dear Siesta users, > > I want to obtain the electronic and magnetic properties of my system. So I > have used "SpinPolarized true " option. But

[SIESTA-L] electronic and magnetic properties

mic and Orbital Populations for all species with up and down spins in the output file. It will be highly appreciated any help and comment. Thanks in advance, Best regards. Nadia Salami PhD student

[SIESTA-L] one question

lease? It will be highly appreciated any comment and help. Thanks in advance. Kind regards. Nadia Salami PHD student

[SIESTA-L] one question

ighly appreciated any comment and help. Thanks in advance. Kind regards. Nadia Salami PHD student

[SIESTA-L] some questions

Dear siesta users, In order to calculate the transport properties of a monolayer composed 2D hexagonal lattice such as TMDs, I want to do the geometry relaxation for a super-cell 5*7*1. I have two different questions: First question that, I have used the following options for the structural relax

[SIESTA-L] the geometry relaxation for the transiesta calculation & k-pint sampling

Dear siesta users, In order to calculate the transport properties of a monolayer such as TMDs, I want to do the geometry relaxation for a super-cell 5*7*1. I have two different questions: First question that, I have used the following options for the structural relaxations of monolayer: # MD va

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

Dear huazhong, Thank you very much, Best regards. Nadia On Sat, Oct 25, 2014 at 5:51 AM, huazhong guo wrote: > The atomic positions in the electrode file are not consistent with the SR > file. > > 2014-10-25 2:00 GMT+08:00, Nadia Salami : > > Dear Alex > > > > Tha

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

gt; same in the scat and elec files. Please look at atom 15. > > Alex > > On Fri, Oct 24, 2014 at 11:47 AM, Nadia Salami > wrote: > >> Dear transiesta users, >> >> I have set up the scattering region as bellow: >> >> Left electrode/contact/right electro

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

Dear transiesta users, I have set up the scattering region as bellow: Left electrode/contact/right electrode The number of atoms in the electrodes are 30 atoms. I have set the following theoptions as bellow: TS.NumUsedAtomsLeft30 TS.NumUsedAtomsRight30 The same k point sampling

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

ation. > > 2014-10-24 19:36 GMT+08:00, Nadia Salami : > > Dear transiesta users, > > > > > > I'm trying to do the transport calculations for MoS2-ML ( node=1, ppn=8) > . > > The > > number of atoms in the electrodes are 30 and I got same k-points i

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

Dear transiesta users, I'm trying to do the transport calculations for MoS2-ML ( node=1, ppn=8) . The number of atoms in the electrodes are 30 and I got same k-points in the x and y directions in the electrodes and the scattering regions. I have done DFT calculations for electrodes and TSHS file

[SIESTA-L] parallel spin calculation

nPolarized .true." in the fdf file. when is it used "NonCollinearSpin"? It will be greatly appreciated your help and comments. Best Regards. Nadia Salami