Re: [SIESTA-L] Spin-polarized band structure

Hi, Juliana, you can find attached a slightly modified version of the program gnubands. It generates two files, bands-up.dat and bands-down.dat. Best regards, Roberto From: Juliana Morbec To: siest...@listserv.uam..es Sent: Sunday, January 25, 2009 2:13:09

Re: [SIESTA-L] Hess's law

I am interested on oxidation of a solid surface (SiC), where an O replaces a C atom, forming a Si-O-Si onto the surface, with CO desorption. Roberto From: N H To: SIESTA-L@listserv.uam.es Sent: Friday, January 16, 2009 10:51:27 PM Subject: Re: [SIESTA-L

Re: [SIESTA-L] Hess's law

ess... Roberto From: N H To: SIESTA-L@listserv.uam.es Sent: Friday, January 16, 2009 10:11:41 PM Subject: Re: [SIESTA-L] Hess's law If you have correwctly calculated all intial and finals states the answer is yes! On Fri, Jan 16, 2009 at 10:02 PM, Rober

[SIESTA-L] Hess's law

Hello, if I have a substitution reaction as follows: AB+CD-->AC+BD and I calculate the four systems isolated with Siesta, can I calculate the enthalpy of such a reaction as stated by the Hess's law? Or there is any subtlety? Thanks in advance, Roberto

[SIESTA-L] Dissociation energy calculation

? Thanks in advance, Roberto Veiga

Re: [SIESTA-L] Still energy differences and BSSE corrections

discrepancy in the energy differences is due to BSSE. What I do not know is where to put the ghost atoms and if I have to add other terms in the equation (and, if so, which ones). Roberto From: Oleksandr Voznyy To: SIESTA-L@listserv.uam.es Sent: Thursday, January

Re: [SIESTA-L] Still energy differences and BSSE corrections

Thanks, Victor. In the PAO.Basis bellow, is it 4p instead of 3p? 4p is empty in the iron ground state, no? Roberto From: "Garcia-Suarez, Victor" To: SIESTA-L@listserv.uam.es Sent: Thursday, January 8, 2009 12:51:44 PM Subject: Re: [SIESTA-L] St

Re: [SIESTA-L] Still energy differences and BSSE corrections

btained for C interstitial in iron was without any BSSE correction. C'est ça. Roberto From: Oleksandr Voznyy To: SIESTA-L@listserv.uam.es Sent: Wednesday, January 7, 2009 6:10:47 PM Subject: Re: [SIESTA-L] Still energy differences and BSSE corrections H_

Re: [SIESTA-L] Still energy differences and BSSE corrections

-DZP basis set nor if this is the best protocol to minimize basis sets. Roberto From: Oleksandr Voznyy To: SIESTA-L@listserv.uam.es Sent: Wednesday, January 7, 2009 7:38:02 PM Subject: Re: [SIESTA-L] Still energy differences and BSSE corrections Dear Victor, I

Re: [SIESTA-L] Still energy differences and BSSE corrections

l or physically speaking, in doing so? Anyway, once again, bad results, compared to those given by VASP. Thanks and sorry if I am bothering everyone with this subject. Roberto From: Oleksandr Voznyy To: SIESTA-L@listserv.uam.es Sent: Saturday, December 6, 2008 7:01:

Re: [SIESTA-L] Still energy differences and BSSE corrections

you cannot reach a quantitative agreement at all, neither with experiments nor PW. Of course, I know you cannot apply the correction only when it interests you... Thanks, Roberto Veiga From: Oleksandr Voznyy <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es

[SIESTA-L] Still energy differences and BSSE corrections

out how to apply the correction. If I replace E(Fe16) by E(Fe16+C_ghost) and E(C) by E(C+Fe16_ghost), things become worst. Does anyone have any idea on how apply a BSSE correction in this case? Thanks in advance, Roberto Veiga

Re: [SIESTA-L] Bulk cohesion energy

Ok, but how to know that, a priori, before starting a simulation? I mean, how many atoms besides the ones explicitly defined in my input should I take into account? Roberto From: Eduardo Anglada <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: T

Re: [SIESTA-L] Bulk cohesion energy

Thank you, Eduardo. How do I obtain the total number of basis functions for a condensed system? Should I take into account more than the atoms explicitly defined in my input? Roberto From: Eduardo Anglada <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.e

Re: [SIESTA-L] Bulk cohesion energy

Where in the output can I find the number of basis functions? Roberto From: Oleksandr Voznyy <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Monday, November 3, 2008 3:41:53 PM Subject: Re: [SIESTA-L] Bulk cohesion energy > I did like that:

Re: [SIESTA-L] Bulk cohesion energy

4.78 eV, and the experimental value is 4.28 eV. So I think that in this case the BSSE correction is negligible. Thanks, Roberto Veiga PhD student INSA-Lyon PS.: As a suggestion: it would be nice if some Siesta advanced users provide us with some useful examples on how to calculate things like bi

Re: [SIESTA-L] Bulk cohesion energy

, the bcc Fe unit (primitive) cell has only one atom. If I include ghost atoms in the calculation of the isolated atom, I will have a basis set in this case larger than that used for the bulk calculation. Roberto

[SIESTA-L] Bulk cohesion energy

Hi: I would like to know how to calculate the bulk cohesion energy of a crystalline solid (in my case, Fe) with Siesta. I guess it is the difference between the total energies of the atom in the bulk and the isolated atom. Thanks, Roberto

[SIESTA-L] How to generate a pseudo with core electrons?

Hello: I would like to know how to generate a pseudopotential including some of the core electrons in it, besides the usual valence ones. A simple sample input would be nice. Thanks in advance, Roberto

Re: [SIESTA-L] Vacancy formation energy

I got a problem doing that... the formation of a vacancy is exothermic! If I do the calculation in this way: Ef=Et(64)-Et(63)-Et(64)/64 C'est bizarre! Roberto Veiga PhD student INSA-Lyon - Original Message From: Pablo A. Denis <[EMAIL PROTECTED]> To: SIESTA-L@listserv.

Re: [SIESTA-L] Vacancy formation energy

Ok, but allowing the system to relax with the ghost? I mean, would not the ghost atom have any (artificial) affect to the final optimized geometry? []s, Roberto Veiga - Original Message From: Oleksandr Voznyy <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Wednesday, Au

Re: [SIESTA-L] Vacancy formation energy

Dear Pablo: thank you. However, in this case, I think we will have some undesirable contribution to the formation energy thanks to the basis set superposition error, don't you think so? Regards, Roberto - Original Message From: Pablo A. Denis <[EMAIL PROTECTED]> T

Re: [SIESTA-L] Vacancy formation energy

Well... so... coming back to my initial question, what should I do to calculate the formation energy of a single vacancy in a 64-atoms bcc lattice? []s, Roberto - Original Message From: Pablo A. Denis <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Monday, September 1

[SIESTA-L] Vacancy formation energy

? Is it completely wrong? Roberto Veiga PhD student INSA-Lyon

Re: [SIESTA-L] Failure to converge standard eigenproblem

Dear Eduardo: it works! Thank you very much. Roberto - Original Message From: Eduardo Anglada <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Friday, July 11, 2008 6:35:06 AM Subject: Re: [SIESTA-L] Failure to converge standard eigenproblem Hi Roberto, Tr

Re: [SIESTA-L] Ag pseudopotential

Dear Eduardo: are those pseudopotentials for metals, without partial core correction, suitable for, ahn, "useful" calculations? []s, Roberto Veiga PhD student INSA-Lyon - Original Message From: Eduardo Anglada <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent:

[SIESTA-L] Failure to converge standard eigenproblem

anymore. Besides, if you remove the SuperCell block, it works like a charm. A+, Roberto - Original Message From: Alexandre Lebon <[EMAIL PROTECTED]> To: "Siesta, Self-Consistent DFT LCAO program, [EMAIL PROTECTED] http://www.uam.es/siesta"; <[EMAIL PROTECTED]>;

[SIESTA-L] Failure to converge standard eigenproblem

Sorry. I forgot to give a title to the message. Roberto - Forwarded Message From: Roberto Veiga <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Thursday, July 10, 2008 1:17:31 PM Subject: [SIESTA-L] Hello everybody: I had the following problem when trying to perfor, a

[SIESTA-L]

works if the SuperCell block is not available. As one can see, it is based on the input for Fe in Siesta examples directory. Any idea? []s, Roberto Veiga PhD student INSA-Lyon

[SIESTA-L] Basis for Fe

Hello everyone: does any of you have (and would like to share) optimized basis for bcc-Fe? Regards, Roberto PhD student INSA-Lyon

[SIESTA-L] Total energy vs. Energy Shift convergence

s and isolated atoms. On the other hand, I found, for the ribbon (a 1D periodic system), that the minimum for the total energy occurs for an energy shift around 0.05 eV. Why such a difference? With my best regards, Roberto

Re: [SIESTA-L] List-directed I/O syntax error

Dear all: sorry, it was an error in the input file, as Marcel said. []s, Roberto

[SIESTA-L] List-directed I/O syntax error

known Unknown Unknown Unknown002A959EDA9D Unknown Unknown Unknown siesta 004033EA Unknown Unknown Unknown Any idea? Siesta was compiled with Intel Fortran and has been running since then with no problem but the one above. []s, Roberto

Re: [SIESTA-L] Charged molecule adsorbed onto a surface

Ok. So, if I simply replace the periodic surface by a a large non-periodic cluster is not an option, is not it? The problem is we do not have how to specify the charged part of the system. []s, Roberto 2008/4/24 lan haiping <[EMAIL PROTECTED]>: > I donot think we can deal such situa

[SIESTA-L] Charged molecule adsorbed onto a surface

Hi, everybody: I'd like to know if there is a way to define in Siesta a charged molecule that would be adsorbed onto a neutral surface (slab or chain). Best regards, Roberto

Re: [SIESTA-L] Bromine pseudo

Eduardo: thank you or, as you say in Spain, muchas gracias. []s, Roberto 2008/4/15, Eduardo Anglada <[EMAIL PROTECTED]>: > > > Hi Roberto, > I attach the output of Bromine pseudo generation using the Fritz Habber > Institute (fhi) code. > The input was taken from Ab

[SIESTA-L] Bromine pseudo

Has anyone generated a pseudo for bromine? Regards, Roberto

Re: [SIESTA-L] MD.VariableCell with slabs and chains

Just a computational challenge or also it leads to incorrect results? That is what I'm worried about... []s, Roberto 2008/3/19, lan haiping <[EMAIL PROTECTED]>: > > I think variable cell calculation even is a challenge for bulk system > calculations. > > On Wed, Mar 19

[SIESTA-L] MD.VariableCell with slabs and chains

Hi everybody: is MD.VariableCell also suitble for chains and slabs, or just for bulk systems? []s, Roberto

Re: [SIESTA-L] problem about the polarized system!

Dear Jianbao: it follows, attached to this mail. Regards, Roberto 2008/3/9, Jianbao Wu <[EMAIL PROTECTED]>: > > Dear Roberto: > > Thanks for your answering, up to now I have not find any way to solve this > porblem which bother me for a long time. Could you send me the m

Re: [SIESTA-L] problem about the polarized system!

Dear Jianbao: in order to plot the bands "up" and "down" separately, I changed the gnubands utility that comes with Siesta. I don't know if there is another way to do that easier. If not and you want, I can send you the modified gnubands. With the best regards, Robe

[SIESTA-L] GGA calculations and BSSE corrections

binding energies (equilibrium distances) calculated within GGA are strongly under(over)estimated with respect to the same results obtained by using LDA. Does anyone have an experience with that? []s, Roberto -- "If I have seen farther than others it is because of a myopia surgery."

[SIESTA-L] BSSE-corrected calculation of binding energy for chemisorption

perfect surface? Regards, Roberto

Re: [SIESTA-L] LDA and GGA pseudo

Anyway, it is at least a good starting point, I guess. []s, Roberto 2008/2/14, Marcos Verissimo Alves <[EMAIL PROTECTED]>: > David, > > It is not simply a matter of changing the xc label, otherwise there would > be no reason for generating new functional forms and parametriz

Re: [SIESTA-L] Binding energy O2 with GGA

possible with a bad pseudo? []s, Roberto 2008/2/13, Oleksandr Voznyy <[EMAIL PROTECTED]>: > > I had similar experience with ammonia borane molecular crystal. Cohesive > > energy was about 2 eV with GGA functionals and about 3 eV with LDA > > functionals in SIESTA. >

Re: [SIESTA-L] Binding energy O2 with GGA

Dear Riccardo: I'll try to do that. But I think I have to use the same EnergyShift for both the molecule and the isolated atom, sure? []s, Roberto 2008/2/13, Riccardo Rurali <[EMAIL PROTECTED]>: > Dear Roberto, > > the localized basis used in Siesta were thought for solid

Re: [SIESTA-L] Binding energy O2 with GGA

14.40 The experimental value is 5.1 eV, information I also obtained in Gianozzi's paper. []s, Roberto 2008/2/13, N H <[EMAIL PROTECTED]>: > I suppose u are using spin polarized calculations ... well, what about > your energy shift for the isolated atoms?! ... Are

[SIESTA-L] Binding energy O2 with GGA

s two oxygen atoms separated by a very large distance and kept frozen. Could anyone with a previous experience with O2 tell me how he/she calculated the binding energy of the molecule? Thanks in advance, Roberto

Re: [SIESTA-L] Titanium dioxide nanotubes

Dear Kugan: it looks quite different, indeed. If you don't know any algorithm (like the White et al. for carbon nanotubes) to help you to write a program to build the structure, you will have to do some hard ball and stick modelling... []s, Roberto 2008/1/25, navaratnarajah kuganathan &l

Re: [SIESTA-L] Titanium dioxide nanotubes

Are they similar in structure with carbon or boron nitride nanotubes (honeycomb cylinders)? If so, you can just generate a cabon nanotube and manually replace the carbon atoms by the appropriate ones. []s, Roberto 2008/1/25, navaratnarajah kuganathan <[EMAIL PROTECTED]>: > Hi, >

Re: [SIESTA-L] pseudopotential for Pt

There is a web application that generates pseudopotentials for Siesta: http://www.tddft.org/programs/octopus/wiki/index.php/Pseudopotentials. It seems to be much easier than atom to carry out this task. Regards, Roberto 2008/1/24, Bozidar <[EMAIL PROTECTED]>: > Dear Mohammad, > &

Re: [SIESTA-L] Differences in the spin polarization

Dear Vasilii: thank you. Do you have any reference on this subject? Thanks again, in advance, Roberto 2007/12/22, Vasilii Artyukhov <[EMAIL PROTECTED]>: > There sure is. LDA is known to predict qualitatively incorrect magnetic > properties for a number of systems, perhaps the most

[SIESTA-L] Differences in the spin polarization

ation of a single atom by integrating PDOS_up-PDOS_down up to Fermi energy. Is there any good reason for that difference? []s, Roberto -- "If I have seen farther than others it is because of a myopia surgery."

Re: [SIESTA-L] Band structure

Yes, there is a post-processing tool for PDOS in the Util directory (pdosxml, somehting like that). The only problem with it is... you have to change the code and make it every time you want to plot another orbital. That is boring, hehehe! Regards, Roberto 2007/10/16, Lindsay Shuller <[EM

[SIESTA-L] Oxygen (triplet)

Hi: I'm gonna do some spin polarized calculations in which molecular oxygen is adsorbed onto a surface. I'd like to know how to represent triplet oxygen (as initial state) in the Siesta's input. Regards, Roberto -- "If I have seen farther than others it is because of a myopia surgery."

[SIESTA-L] pdosxml for SpinPolarized systems

Dear users, I am trying to use the "pdos.f90" code, within "Util/pdosxml". But noticed that it is not working for spinpolarized "PDOS" files. I don't know if there is any line I have to change in "m_orbital_chooser.f90". Thanks for your attention. Roberto Hiroki Miwa Brazil.

[SIESTA-L] A simple input file for a graphene sheet

Dear all: can anyone suggest to me a simples input file for a graphene sheet? Regards, Roberto Veiga

Re: [SIESTA-L] Nanotube coordinates

Dear Navaratnarajah: here you have capped (5,5) and (10,0) nanotubes. I hope it be useful for you. Regards, Roberto 2006/7/13, navaratnarajah kuganathan <[EMAIL PROTECTED]>: Dear Siesta users, I am performing calcualtions on carbon nanotubes.Could you please suggest any meth

Re: [SIESTA-L] [SIESTA-] Nanotubes cordinates-broadening

radially deformed. Regards, Roberto Veiga 2006/6/26, Michael Shin <[EMAIL PROTECTED]>: Thank you much *navaratnarajah kuganathan * I solved that problem now, but I observed one thing that how can we find the width of the Gaussian broadening for Nanotubes bcos wen I chnage Gaussian broadening

[SIESTA-L] Pseudo for Fe

Hi, does anyone have a LDA pseudo for Fe? []s, Roberto

Re: [SIESTA-L] Mulliken population

Thank you very much, Wolfgang. You surely noticed that, despite the inversion of charge transfer, the absolute values you have obtained are in the same order... []s, Roberto 2005/7/20, Wolfgang Voegeli <[EMAIL PROTECTED]>: > Dear Roberto, > > It seems to depend very much on th

[SIESTA-L] Mulliken population

0.561 0.450 0.582 0.139 0.386 0.269 0.116 0.144 0.206 0.261 0.125 But, of course, I was expecting a charge transfer from Si to C. What may be wrong? []s, Roberto

[SIESTA-L] F pseudopotential

Hi does anybody have a LDA (CA) pseudopotential for F? []s, Roberto

[SIESTA-L] BandLines for carbon nanotubes

Does anyone have an example of block BandLines for carbon nanotubes? Best regards, Roberto

[SIESTA-L] Parallel Siesta problems

it? Thanks in advance, Roberto Veiga