Re: [SIESTA-L] pseudo plot

2009-01-16 Thread Julie Smart
Hi, do you mean pseudo.gplot , but how can we plot a pseudo.psf with it? regards From: Marcos Verissimo Alves marcos.veriss...@uclouvain.be To: SIESTA-L@listserv.uam.es Sent: Thursday, January 15, 2009 11:41:58 PM Subject: Re: [SIESTA-L] pseudo plot Julie,

Re: [SIESTA-L] pseudo plot

2009-01-16 Thread Marcos Verissimo Alves
One does not plot the psf file. When you generate the pseudo, separate files for the different channels are generated, and this is what the scripts plot. Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Julie Smart Hi, do you mean pseudo.gplot , but how can we plot a

[SIESTA-L] Dissociation energy calculation

2009-01-16 Thread Roberto Veiga
Hello all, I want to calculate the adsorption energy of two oxygen atoms which originally formed an O2 molecule onto a surface. I think I have to take into account the energy required to break the O2 bond before forming the surface-O bonds. Could anyone give me an idea about how to do that?

Re: [SIESTA-L] Dissociation energy calculation

2009-01-16 Thread Danil Bukhvalov
Dear Roberto, I did it as described in this paper: http://arxiv.org/abs/0809.5257 There you can also find refs. to similar calculations for oxidation. Danil. Hello all, I want to calculate the adsorption energy of two oxygen atoms which originally formed an O2 molecule onto a surface. I

Re: [SIESTA-L] BornCharge, PolarizationGrid, Parallel

2009-01-16 Thread Miguel
Why don't you calculate the Born-charges in the unit cell?? The only reason to do supercell calculations for the phonons is to get the phonon-dispersion, right?. For the Born-charges you can use the same values than for the unit cell for each equivalent atom in the supercell. Cheers, On Thu, Jan

[SIESTA-L] Hess's law

2009-01-16 Thread Roberto Veiga
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

Re: [SIESTA-L] Hess's law

2009-01-16 Thread N H
If you have correwctly calculated all intial and finals states the answer is yes! On Fri, Jan 16, 2009 at 10:02 PM, Roberto Veiga roberto.ve...@ymail.comwrote: Hello, if I have a substitution reaction as follows: AB+CD--AC+BD and I calculate the four systems isolated with Siesta, can I

Re: [SIESTA-L] Hess's law

2009-01-16 Thread Roberto Veiga
Ok, so I have how to know if the reaction is endothermic or not just by calculating the four isolated systems (the two reactants and the two products). But in order to know if the reaction is spontaneous for T0, I have to compute also the change in the entropy. It is not that easy, I guess...

Re: [SIESTA-L] Hess's law

2009-01-16 Thread N H
If the reaction is in gas phase u can use [A] = [A0] + RTln(p/p0) and this should give u the chemical potential ... if u have solid reagents the chemical potentials are not sensitive to the temperature, and I guess u dont have anything in solution. Best Regards NH On Fri, Jan 16, 2009 at 10:27

Re: [SIESTA-L] Hess's law

2009-01-16 Thread Roberto Veiga
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 neyh...@gmail.com To: SIESTA-L@listserv.uam.es Sent: Friday, January 16, 2009 10:51:27 PM Subject:

Re: [SIESTA-L] BornCharge, PolarizationGrid, Parallel

2009-01-16 Thread Lydia Nemec
Hello! Thanks for your help! Maybe it is just Friday night and I am to tired or it isn't obvious. Could you please give me a more detailed advice? Thanks again. How do I include the Born charges in my Calculation? I couldn't find something like UseSave... As far as I understand the output, it