Re: [SIESTA-L] electrostatic potential
A Zahra sugeriu mais ou menos a mesma coisa. Porém, se tu puder somar manualmente o potencial de Hartree mais os três pseudopotenciais locais o problema estaria resolvido. Mas não sei se isso é válido. Como te falei, que eu saiba quem calcula o potencial eletrostático é o Transiesta, mas de repente a soma pode ser feita manualmente também e o Transiesta entraria na jogada somente para facilitar. Eu lembro que na época do Mestrado fiz várias somas manualmente para não ter que instalar bibliotecas e programas adicionais. Julio. De: siesta-l-requ...@uam.es em nome de Laura O. Enviado: sexta-feira, 13 de abril de 2018 22:34 Para: siesta-l@uam.es Assunto: Re: [SIESTA-L] electrostatic potential Obrigada Julio! Estou indo por essas dicas também.. - Dear Zahra, The value of the total electrostatic potential of a molecule is defined as the sum of the hartree potential plus the local pseudopotential. So.. could I use the Hartree and the local pseudopotential of each atom that is in the .out file? Final energy Hartree (eV):+ VLOCAL (Ry) I'm not sure about the Vlocal. .out : Final energy Hartree =9401.996956 VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry (atom: C) VLOCAL1: 99.9% of the norm of Vloc inside 46.372 Ry (atom: N) VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry (atom: C) Best, Laura 2018-04-10 17:38 GMT-03:00 Zara Nosh mailto:z.nr...@gmail.com>>: Dear Laura, If you have installed siesta with netcdf support, my suggestion is using sisl utility. In this regard, you need to work with ElectrostaticPotential.grid.nc<http://ElectrostaticPotential.grid.nc> file (created by transiesta), and sgrid command in sisl. for more information see https://doi.org/10.5281/zenodo.597181; https://github.com/zerothi/sisl. Good luck, Zahra On Wed, Apr 11, 2018 at 12:31 AM, mailto:laura.o.vendr...@gmail.com>> wrote: Dear users, I need to know the value of the total electrostatic potential of a molecule, defined as the sum of the hartree potential plus the local pseudopotential. I produced SystemLabel.VH. How can I do it? Best, Laura
Re: [SIESTA-L] electrostatic potential
Obrigada Julio! Estou indo por essas dicas também.. - Dear Zahra, The value of the total electrostatic potential of a molecule is defined as the sum of the hartree potential plus the local pseudopotential. So.. could I use the Hartree and the local pseudopotential of each atom that is in the .out file? Final energy Hartree (eV):+ VLOCAL (Ry) I'm not sure about the Vlocal. .out : Final energy Hartree =9401.996956 VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry (atom: C) VLOCAL1: 99.9% of the norm of Vloc inside 46.372 Ry (atom: N) VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry (atom: C) Best, Laura 2018-04-10 17:38 GMT-03:00 Zara Nosh : > Dear Laura, > If you have installed siesta with netcdf support, my suggestion is using > sisl utility. > In this regard, you need to work with ElectrostaticPotential.grid.nc file > (created by transiesta), and sgrid command in sisl. > > for more information see > https://doi.org/10.5281/zenodo.597181; > https://github.com/zerothi/sisl. > > Good luck, > Zahra > > On Wed, Apr 11, 2018 at 12:31 AM, wrote: > >> Dear users, >> >> I need to know the value of the total electrostatic potential of a >> molecule, >> defined as the sum of the hartree potential plus the local >> pseudopotential. >> I produced SystemLabel.VH. >> How can I do it? >> >> Best, >> Laura >> >> >
Re: [SIESTA-L] electrostatic potential
Dear Laura, If you have installed siesta with netcdf support, my suggestion is using sisl utility. In this regard, you need to work with ElectrostaticPotential.grid.nc file (created by transiesta), and sgrid command in sisl. for more information see https://doi.org/10.5281/zenodo.597181; https://github.com/zerothi/sisl. Good luck, Zahra On Wed, Apr 11, 2018 at 12:31 AM, wrote: > Dear users, > > I need to know the value of the total electrostatic potential of a > molecule, > defined as the sum of the hartree potential plus the local pseudopotential. > I produced SystemLabel.VH. > How can I do it? > > Best, > Laura > >
Re: [SIESTA-L] electrostatic potential
Dear Nick, Thank you for your clarification. Best, Zara On Fri, Oct 6, 2017 at 12:39 PM, Nick Papior wrote: > The difference between the Hartree electrostatic potential VH(v) - VH(0) > is the potential induced by the applied bias. You may refer to this as the > potential profile or potential drop in the device region. > > For instance the potential profile shown in this article > www.doi.org/10.1039/c5cp04613k is calculated as you write it (disclaimer > I am author on the paper). > > Note that the default output of the potential is in Ry and thus needs > conversion to eV. If you do this you will find that the difference between > the left and right lead regions should amount to the applied bias. > > Whether it drops linearly or not, depends on the system. > > 2017-10-05 21:08 GMT+02:00 Zara Nosh : > >> Dear all, >> >> If we consider for example pure GNR device, we expect that the Hartee >> electrostatic potential drops linearly through the device length. In the >> situation that we have some p-dope or n-dope impurity atoms the >> electrostatic potential evolution is not linearly anymore , however if we >> consider "the difference of electrostatic potential of finite bias with >> zero-bias", it will change linearly. >> >> it seems that charge transport behavior comes from the "VH(v)-VH(0)", so >> what is the physical >> meaning and importance of VH(v)? >> >> Best regards, >> Zara >> > > > > -- > Kind regards Nick >
Re: [SIESTA-L] electrostatic potential
The difference between the Hartree electrostatic potential VH(v) - VH(0) is the potential induced by the applied bias. You may refer to this as the potential profile or potential drop in the device region. For instance the potential profile shown in this article www.doi.org/10.1039/c5cp04613k is calculated as you write it (disclaimer I am author on the paper). Note that the default output of the potential is in Ry and thus needs conversion to eV. If you do this you will find that the difference between the left and right lead regions should amount to the applied bias. Whether it drops linearly or not, depends on the system. 2017-10-05 21:08 GMT+02:00 Zara Nosh : > Dear all, > > If we consider for example pure GNR device, we expect that the Hartee > electrostatic potential drops linearly through the device length. In the > situation that we have some p-dope or n-dope impurity atoms the > electrostatic potential evolution is not linearly anymore , however if we > consider "the difference of electrostatic potential of finite bias with > zero-bias", it will change linearly. > > it seems that charge transport behavior comes from the "VH(v)-VH(0)", so > what is the physical > meaning and importance of VH(v)? > > Best regards, > Zara > -- Kind regards Nick
Re: [SIESTA-L] electrostatic potential
Dear Nick Thanks for you answer. Best regards, Zara On Sun, Aug 13, 2017 at 11:41 PM, Nick Papior wrote: > If your system is a semi-conductor (gapped nano-ribbon) then the fermi > level of the electrodes and the device need not coincide. > In such cases there is an intrinsic offset in the potential between the > two calculations and the band-bending you see is introduced. This is what I > *presume* is the cause of your calculation, but I could be wrong. > > I.e. if your system is a gapped nano-ribbon, then it is not easy to > perform such calculations in the current transiesta implementation. > > 2017-08-09 15:58 GMT+02:00 Zara Nosh : > >> Dear transiesta users, >> I am studying the transport properties of phosphorene nanoribbons, and I >> have calculated the electrostatic potential vs the transport direction. >> As my electrodes are same as scattering region, it is expected that the >> electrostatic potential of the scattering region, at the zero bias, were >> equal to the electrodes potential. >> But in my calculation the electrostatic potential of the electrodes are >> same but they are about 0.1eV higher that the scattering region ( something >> like this: \___/ ). >> Please look at the attached picture. >> Would anyone please explain the reason >> of this behavior >> ? >> >> >> Bests, >> Zara >> >> >> > > > -- > Kind regards Nick >
Re: [SIESTA-L] electrostatic potential
Maybe it is the influence of the semi-infinite leads but I am not sure. Have you done your calculation of electrostatic potential with SIESTA? Also, perhaps, you can subtract this potential from the potential you get at higher voltages. On Sun, Aug 13, 2017 at 11:41 PM, Nick Papior wrote: > If your system is a semi-conductor (gapped nano-ribbon) then the fermi > level of the electrodes and the device need not coincide. > In such cases there is an intrinsic offset in the potential between the > two calculations and the band-bending you see is introduced. This is what I > *presume* is the cause of your calculation, but I could be wrong. > > I.e. if your system is a gapped nano-ribbon, then it is not easy to > perform such calculations in the current transiesta implementation. > > 2017-08-09 15:58 GMT+02:00 Zara Nosh : > >> Dear transiesta users, >> I am studying the transport properties of phosphorene nanoribbons, and I >> have calculated the electrostatic potential vs the transport direction. >> As my electrodes are same as scattering region, it is expected that the >> electrostatic potential of the scattering region, at the zero bias, were >> equal to the electrodes potential. >> But in my calculation the electrostatic potential of the electrodes are >> same but they are about 0.1eV higher that the scattering region ( something >> like this: \___/ ). >> Please look at the attached picture. >> Would anyone please explain the reason >> of this behavior >> ? >> >> >> Bests, >> Zara >> >> >> > > > -- > Kind regards Nick >
Re: [SIESTA-L] electrostatic potential
If your system is a semi-conductor (gapped nano-ribbon) then the fermi level of the electrodes and the device need not coincide. In such cases there is an intrinsic offset in the potential between the two calculations and the band-bending you see is introduced. This is what I *presume* is the cause of your calculation, but I could be wrong. I.e. if your system is a gapped nano-ribbon, then it is not easy to perform such calculations in the current transiesta implementation. 2017-08-09 15:58 GMT+02:00 Zara Nosh : > Dear transiesta users, > I am studying the transport properties of phosphorene nanoribbons, and I > have calculated the electrostatic potential vs the transport direction. > As my electrodes are same as scattering region, it is expected that the > electrostatic potential of the scattering region, at the zero bias, were > equal to the electrodes potential. > But in my calculation the electrostatic potential of the electrodes are > same but they are about 0.1eV higher that the scattering region ( something > like this: \___/ ). > Please look at the attached picture. > Would anyone please explain the reason > of this behavior > ? > > > Bests, > Zara > > > -- Kind regards Nick
