[SIESTA-L] Surface Energy
Dear all, I hope that there is some of you who has studied surfaces or thin layers and has an idea on how to calculate the energy of the surface, specifically the surface of the Au. I have calculated the energy surface of the Au (100), (110) and (111), with 8, 12 and 15 layers and 4 plans empty. I am expecting that surface energy would converge when increasing the number of layers but it is not the case in my calculations. The energy always increase when adding layers in the case of (100) and (110) and always decrease in the case of (111). Has anyone any idea of the problem?
[SIESTA-L] LDA overestimates lattice constant of CdSe
Hello everyone I am calculating CdSe. Also I have a reasonable agreement from bulk modulus (55.6 GPa (calc) vs. 53.8 (exp)), I find a slight overstimation of 1 % in lattice constant. I know that LDA is often known to have an overbinding, that should result in an underestimation of the lattice constant. How serious should I take this overestimated lattice constant? Kind regards Marcel Marcel Mohr Institut für Festkörperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin
Re: [SIESTA-L] Surface Energy
Hi Jafar,
I've done a convergence study for a SiC surface and Ni[100], but I guess
the general features will be the same, quite independently of the
material. The nice thing about siesta is that vacuum layers come virtually
for free, as opposed to plane-waves calculation.
So, maybe the first thing to do is to determine which is the minimum
vacuum layer thicness to have an isolated slab of gold. I guess 10 Ang
would already be a good choice, but of course this has to be checked. Once
I determined the optimum vacuum thickness, I determined the largest slab
thickness, and built the supercell for my largest slab thickness. The
lattice vectors of this supercell were the standard for all slab
thicknesses, because then I could guarantee that the effective k-point
sampling would be the same for all supercells. Since in siesta you
practically don't pay for the vacuum, it's ok to exaggerate and have the
exact same sampling for all cells
After all the slabs had been relaxed, I calculated the surface formation
energy for each of the slabs (equation in LaTeX):
$E^s_n=\frac{E_n-nE_{bulk}}{A}$
where n is the number of layers of the material in the slab, E_{bulk} is
the energy of one layer of the material for the bulk crystal and A is the
surface area of the supercell.
Hope this helps.
Marcos
Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Ali
Jaafar
> Dear all,
> I hope that there is some of you who has studied surfaces or thin
> layers and has an idea on how to calculate the energy of the surface,
> specifically the surface of the Au. I have calculated the energy surface
> of the Au (100), (110) and (111), with 8, 12 and 15 layers and 4 plans
> empty.
>
> I am expecting that surface energy would converge when increasing the
> number of layers but it is not the case in my calculations. The energy
> always increase when adding layers in the case of (100) and (110) and
> always decrease in the case of (111).
> Has anyone any idea of the problem?
>
--
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Unité de Physico-Chimie et de Physique des Matériaux (PCPM)
Université Catholique de Louvain
1 Place Croix du Sud, B-1348
Louvain-la-Neuve
Belgique
--
Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto.
[SIESTA-L] Zr GGA + basis
Hello everybody, This is a sort of newby question. I'm looking for a consistent pair of GGA Zr pseudo plus the basis for Siesta. Does anybody possess such a thing and is willing to share ?. Would it be ok to use the (LDA) basis already available for Siesta together with a GGA Zr ( such the recently available from ABINIT ) ?. Thanks a lot, Roberto
Re: [SIESTA-L] LDA overestimates lattice constant of CdSe
On the contrary, overbinding should cause an overestimation of the l.c. A simplified explanation would be that LDA doesn't care about the gradients, only the local density value is taken into account, and stretching the atoms apart lowers that. Hence the overbinding - because unlike a solid, you can't stretch a single atom much and lower its energy in the same manner :) 2008/4/10, Marcel Mohr <[EMAIL PROTECTED]>: > > Hello everyone > > I am calculating CdSe. > Also I have a reasonable agreement from bulk modulus > (55.6 GPa (calc) vs. 53.8 (exp)), I find a slight overstimation of 1 % in > lattice constant. > > I know that LDA is often known to have an overbinding, that should result > in an underestimation of the lattice constant. > How serious should I take this overestimated lattice constant? > > Kind regards > Marcel > > > Marcel Mohr Institut für Festkörperphysik, TU Berlin > marcel(at)physik.tu-berlin.de Sekr. EW 5-4 > TEL: +49-30-314 24442 Hardenbergstr. 36 > FAX: +49-30-314 27705 10623 Berlin > >
Re: [SIESTA-L] WARNING: Qtot, Tr[D*S] differ
Hi Salvador, Could you post your fdf and pseudo? (if you prefer you send them directly to me) Best, Eduardo On 09/04/2008, at 21:06, Salvador Barraza-Lopez wrote: Hello list, I am doing a calculation where a gold surface is covered with a magnetic molecule, via sulfur (thiol). I first performed a calculation with a gold pseudo and basis including the 5d electrons. My basis was built explicitly and had 2zetas for the 6s, and 1 zeta for 6p and 5s channels. The band structure I get is very similar to that from plane-wave codes. Then, I built a pseudo without the 5d channel. I built my basis explicitly once again. For reasons I do not completely understand I am getting the following warning: siesta:1 -208997.1679 -208235.0221 -208235.0221 1.2912 -5.5563 timer: Routine,Calls,Time,% = IterSCF1 107338.054 20.77 siesta: WARNING: Qtot, Tr[D*S] = 870.00 859.492781 There is something not quite right. Could you share your experience on the problem, and perhaps point out what could be wrong with my basis? Thank you, -Salvador.
Re: [SIESTA-L] compiling error
Dear Ricardo, In the ld.so.conf you set up the variables for dynamic linking, while on the compiler command line option you requested static linking (the a at the end of libmkl_intel.a corresponds to a static library). So you don't have to mix both options (static/dynamic) use only one of them. Regards, Eduardo On 09/04/2008, at 21:05, Ricardo Faccio wrote: Dear Users After setting all the enviroment variables in our dual-core machine, the compilation process stops with this error: ld: cannot find libmkl_intel.a make: *** [siesta] Error 1 the ifort and mkl enviroment variables are ok the ld.so.conf includes: /opt/intel/fc/10.1.012/lib/ /opt/intel/mkl/10.0.1.014/lib/32/ /opt/intel/mkl/10.0.1.014/lib/emt64/ Any hint? Best regards Ricardo - - Dr. Ricardo Faccio Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: [EMAIL PROTECTED] Phone: 598 2 9241860 Int. 109 598 2 9290705 Fax:598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
Re: [SIESTA-L] Is there a psf for La
Dear Siesta user, I have recently installed Ubuntu 7.1 on a core 2 duo machine. I would like to know if somebody has installed siesta on it? I have been able to install ifort and mkl but when I try to compile the atom program or siesta the congifure.log tells me that he cannot created the executable variables. I have installed all the packages recommended at the ubuntu site (g++ build essential, 32bit libs etc.). So I guess that the problem may be related with the bash.bahsrc (I have added the path of ifort and mkl to the bash.bashrc and .bashrc) Any cluet? Many thanks! Pablo
Re: [SIESTA-L] Valence configuration of samarium
> Hi, > > I have made the changes according to u and defined the pseudo of Sm as Hi - If "u" refers to me, mind that I never advised you on the pseudo radii for Sm... I only meant that inclusing 4f is technically no error - but it will probably lead to physically wrong results. Whatever... Regarding your problems with calculations which sometimes stop at an error in basis block, sometimes not: you should carefully read the SIESTA doc file about the syntaxis of the basis block. Namely: > but when I define the PAO basis like > %block PAO.Basis > Sm 2 # Label, l-shells > n=6 0 2 P 1 # n, l, Nzeta, Polarization,NzetaPol > 0.000 0.000 > 1.000 1.000 > n=6 1 2 > 0.000 0.000 > 1.000 1.000 > n=5 2 2 > 0.000 0.000 > 1.000 1.000 > n=4 3 2 > 0.000 0.000 > 1.000 1.000 - yes, it fails, because you declared 2 l-shells (1st line of the Sm block) but in the following you pass the info for 4 l-shells. I thought we were already past this problem... > Again I mabe the changes in PAO basis as > %block PAO.Basis > Sm 2 # Label, l-shells > n=6 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol >0.000 0.000 >1.000 1.000 > n=4 3 2 >0.000 0.000 >1.000 1.000 > Te 2# Species label, number of l-shells > n=5 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol >0.000 0.000 >1.000 1.000 > n=5 1 2 # n, l, Nzeta >0.000 0.000 >1.000 1.000 > %endblock PAO.Basis > > then the program run successfully but lattice parameter and band gap is > far from our expt values. Now this is formally correct (number of l-shells declared equals number of l-shells passed), but the basis (at least for Sm) is not complete enough - you'd need 5d in the basis. And after you do this, do not expect to get band structure right, because 4f states will most probably be at a wrong energy... Good luck Andrei Postnikov
Re: [SIESTA-L] Valence configuration of samarium
> Many thanks for your kind reply guiding me for corrections. I will try
> according to the suggestions given by you.
> I will like ask
Nidhi:
your question is not about "Valence configuration of samarium" anymore.
Why not mark in correspondingly, to make the mailing list better lisible?
> I wish to compute the band structure of LaS and LaAs (in first case La is
> +2 and in the later is +3)
> n=La c=car # Symbol, XC flavor,{ |r|s}
>0.0 0.0 0.0 0.0 0.0 0.0
>114 # norbs_core, norbs_valence
> 60 2.00 0.00 # 6s2
> 61 0.00 0.00 # 6p0
> 52 1.00 0.00 # 5d1
> 43 0.00 0.00 # 4f0
> 3.47 4.13 3.00 2.75 0.00 0.00
> It is for La+3. How to define it in pseudo file for La+2 ?
This looks like a definition of a pseudo (I don't know if it is good)
for a perferctly neutral La atom - and this is perfectly OK.
Why you say it is for La+3 ???
An ionicity arises in the course of chemical bonding - one atom loses
electrons, another gains; this is chemistry.
You don't need to know this in advance, when creating pseudos.
Yes you can generate a pseudo for an ionic configuration,
but it yet yon't force your atom (in a compound) into this configuration.
> And How to decide, in band structure which particular bands belong to
> which shell (s,p,d,f)
>From the analysis of eigenvectors in each k-point. Since this is not
automatized in Siesta (i.e., an option to plot "orbital-labelled bands"
or "fat bands" do not exist), a look at the partial DOS may give a clue.
Best regards
Andrei Postnikov
Re: [SIESTA-L] Is there a psf for La
Thank you for your help. 2008/4/10, Pablo Aguado <[EMAIL PROTECTED]>: > > Hi, > > You can find LDA pseudo and basis for La in the SIESTA web. Just in > case you are interested I send you also those generated by me both for > LDA and GGA calculations (the LDA pseudo I use is the one in the > website). In the tar files I attach you can find the pseudo and basis > files, pseudo tests, graphs and descriptions. > > Best regards, > > Pablo > > > > On Sun, Apr 6, 2008 at 4:29 PM, ding yi <[EMAIL PROTECTED]> wrote: > > > > > > Hi everyone. > > > > I'm trying to use SIESTA to cal LaOFeAs and I would like to know if > > there is somebody here able to give me an input file to generate La > > pseudo potentials, which can not be found in the web now. Suggestions > > concerning about works using SIESTA and testing La pseudo with it are > > welcome to. > > > > Thank you very much in advance. > > > > > > > > -- > --- > Pablo Aguado Puente > [EMAIL PROTECTED] > > >
Re: [SIESTA-L] WARNING: Qtot, Tr[D*S] differ
Dear Eduardo, I was using siesta1.3p with no patches, hence the error (I found a 2004 post by Pablo Ordejon mentioning this problem). I switched to siesta-2.0 and it is gone. Thank you for your assistance. -Salvador. On Thu, 10 Apr 2008, Eduardo Anglada wrote: Hi Salvador, Could you post your fdf and pseudo? (if you prefer you send them directly to me) Best, Eduardo On 09/04/2008, at 21:06, Salvador Barraza-Lopez wrote: Hello list, I am doing a calculation where a gold surface is covered with a magnetic molecule, via sulfur (thiol). I first performed a calculation with a gold pseudo and basis including the 5d electrons. My basis was built explicitly and had 2zetas for the 6s, and 1 zeta for 6p and 5s channels. The band structure I get is very similar to that from plane-wave codes. Then, I built a pseudo without the 5d channel. I built my basis explicitly once again. For reasons I do not completely understand I am getting the following warning: siesta:1 -208997.1679 -208235.0221 -208235.0221 1.2912 -5.5563 timer: Routine,Calls,Time,% = IterSCF1 107338.054 20.77 siesta: WARNING: Qtot, Tr[D*S] = 870.00 859.492781 There is something not quite right. Could you share your experience on the problem, and perhaps point out what could be wrong with my basis? Thank you, -Salvador.
