Re: [SIESTA-L] ANNOUNCE: LDA & GGA pseudo databases
To Eduardo: I have tried to get the Si ' s pseudo but it's said " *ATENCIÓN*: *La página solicitada no se ha encontrado o el vínculo seguido es erróneo. Por favor, disculpe la molestia.* *WARNING*: *The requested object does not exist on this server. The link you followed is either outdated, inaccurate. Please, excuse the inconvenience.* " I can only see your update of this kind: ' Pseudopotentials with and without core electrons promoted to the valence (semicore) available. SIESTA can use these pseudos.' what's the matter, can you tell me ? Thank you very much :) shanghui
Re: [SIESTA-L] Fw: [SIESTA-L] help in band structure
Dear Sonia, You have 5 atomic orbital in your Basis therefore you will get 5 bands. You should change the basis to get more bands. Regards, Reza - Original Message From: Sonia Mehra <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Thursday, April 3, 2008 3:37:25 AM Subject: [SIESTA-L] Fw: [SIESTA-L] help in band structure - Forwarded Message From: Sonia Mehra <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Wednesday, 2 April, 2008 5:40:15 PM Subject: [SIESTA-L] help in band structure Dear Users, Please help me out in band structure .I m working on MgS I got stuck up,at bandlines of MgS I am getting only 5 bandlines of MgS but according to the experimental values it should be around 8.Can anyone tell where is my mistake in input file which I have attached so that I could sort out the problem.I am also attachinf file of bands and my output file waiting for your reply soon Why delete messages? Unlimited storage is just a click away. Get the freedom to save as many mails as you wish. Click here to know how. You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. http://tc.deals.yahoo.com/tc/blockbuster/text5.com
Re: [SIESTA-L] Spin polarization
Dear Eduardo Anglada, Last month I have posted asimilar question about Qtot in some spin polarized GGA calculations. in my case Qup = 126.5 and Qdown = 126.5. The correct values shold be 127 and 126. I did not have incomplete scf convergence or an excesive electronic temperature. Do you think that my problem was because of incomplete DM normalization? How serious is that issue? Many Thanks! I have been trying to figure out this for several months... With my best regards, Pablo - Original Message - From: Eduardo Anglada To: SIESTA-L@listserv.uam.es Sent: Thursday, April 03, 2008 4:52 PM Subject: Re: [SIESTA-L] Spin polarization Hi! This is José Soler answer: "Without discarding the effect of imperfect density matrix normalization, it seems to me that the most likely cause of that small deviation from 1 is an incomplete scf convergence, or an excessive electronic temperature." Regards, Eduardo On 02/04/2008, at 11:59, Vasilii Artyukhov wrote: That's how many spin-up electrons than spin-down there are in your system. It seems to me that these figures long after comma should probably be discarded, they must be due to slightly incomplete normalization of the density. Hence, a question to the developers: Is the above correct & how many significant figures should we keep in this number & how small is the effect of such normalization on the accuracy? 2008/4/2, Jiaye, Li <[EMAIL PROTECTED]>: Dear Users This is the copied line from the output file of siesta: siesta: Total spin polarization (Qup-Qdown) =1.35 What does "Qup-Qdown' mean? 1.35 is the value of unpaired electrons? Thanks in advance! ps. I performed calculations with Pt metal, SpinPolarized flag was set .true. -- Sincerely James Li __ NOD32 2998 (20080403) Information __ This message was checked by NOD32 antivirus system. http://www.eset.com
Re: [SIESTA-L] Fw: [SIESTA-L] help in band structure
Hi Sonia, First, I don't know the exact meaning of your 'bandline'. I guess, you are talking about energy band. If yes, then your results are OK. The total number of energy bands is equal to the total number of basis orbitals. In your case you have 5 orbitals ( 1 for Mg 3s, 1 for S 3s, 3 for S 3p (px,py,pz)). If you want to get more energy bands you should use a larger basis, like DZP. regards, Xiaobing Quoting Sonia Mehra <[EMAIL PROTECTED]>: > > > - Forwarded Message > From: Sonia Mehra <[EMAIL PROTECTED]> > To: SIESTA-L@listserv.uam.es > Sent: Wednesday, 2 April, 2008 5:40:15 PM > Subject: [SIESTA-L] help in band structure > > Dear Users, > Please help me out in band structure .I m working on MgS > I got stuck up,at bandlines of MgS > I am getting only 5 bandlines of MgS but according to the experimental values > it should be around 8.Can anyone tell where is my mistake in input file which > I have attached so that I could sort out the problem.I am also attachinf file > of bands and my output file > > waiting for your reply soon > > > > > >Why delete messages? Unlimited storage is just a click away. > > > > > > Bollywood, fun, friendship, sports and more. You name it, we have it on > http://in.promos.yahoo.com/groups This message was sent using IMP, the Internet Messaging Program.
Re: [SIESTA-L] Spin polarization
Dear Eduardo (and José), I don't think I can imagine some way in which incomplete scf convergence could cause the deviation, since the DM is supposed to be normalized at each step, correct me if I'm wrong... The electronic temperature might be able to cause such thing, but I'm definitely getting these small deviations even with it set to zero. I converge SCF to 1.d-5 by density. So, should I still blame the normalization? 2008/4/3, Eduardo Anglada <[EMAIL PROTECTED]>: > > > Hi! > > This is José Soler answer: > > "Without discarding the effect of imperfect density matrix > normalization, it seems to me that the most likely cause > of that small deviation from 1 is an incomplete scf > convergence, or an excessive electronic temperature." > > Regards, > Eduardo > > > On 02/04/2008, at 11:59, Vasilii Artyukhov wrote: > > That's how many spin-up electrons than spin-down there are in your system. > > It seems to me that these figures long after comma should probably be > discarded, they must be due to slightly incomplete normalization of the > density. Hence, a question to the developers: > > Is the above correct & how many significant figures should we keep in this > number & how small is the effect of such normalization on the accuracy? > > 2008/4/2, Jiaye, Li <[EMAIL PROTECTED]>: > > > > Dear Users > > > > This is the copied line from the output file of siesta: > > > > *siesta: Total spin polarization (Qup-Qdown) =1.35* > > > > What does "Qup-Qdown' mean? 1.35 is the value of unpaired electrons? > > Thanks in advance! > > > > ps. I performed calculations with Pt metal, SpinPolarized flag was set > > .true. > > > > -- > > Sincerely > > > > James Li > > > > > > > > > > >
Re: [SIESTA-L] ANNOUNCE: LDA & GGA pseudo databases
Dear users, I've uploaded the new version of the database. Now each pseudo has it's own web page with info about the matching radii, occupations, plots of the pseudos, and, if present the core charge density with its corresponding radius. As always any comments/suggestions are really welcome. Best, Eduardo On 12/03/2008, at 18:22, Eduardo Anglada wrote: Dear Users of Siesta, There is a new collection of pseudopotentials available for SIESTA! I have translated the LDA/GGA pseudos in the Fritz-Haber-Instute (FHI) format of ABINIT's database found in http://www.abinit.org/Psps/?text=psps so now they can be used with SIESTA. The database can be found In the siesta web page: http://www.uam.es/siesta Follow the link "Pseudos & Basis" in the left menu. I would like to thank the ABINIT team for sharing their pseudos with the community. If you encounter any problems feel free to post them in the list. Best regards, Eduardo
Re: [SIESTA-L] Spin polarization
Hi! This is José Soler answer: "Without discarding the effect of imperfect density matrix normalization, it seems to me that the most likely cause of that small deviation from 1 is an incomplete scf convergence, or an excessive electronic temperature." Regards, Eduardo On 02/04/2008, at 11:59, Vasilii Artyukhov wrote: That's how many spin-up electrons than spin-down there are in your system. It seems to me that these figures long after comma should probably be discarded, they must be due to slightly incomplete normalization of the density. Hence, a question to the developers: Is the above correct & how many significant figures should we keep in this number & how small is the effect of such normalization on the accuracy? 2008/4/2, Jiaye, Li <[EMAIL PROTECTED]>: Dear Users This is the copied line from the output file of siesta: siesta: Total spin polarization (Qup-Qdown) =1.35 What does "Qup-Qdown' mean? 1.35 is the value of unpaired electrons? Thanks in advance! ps. I performed calculations with Pt metal, SpinPolarized flag was set .true. -- Sincerely James Li
[SIESTA-L] Problems with grid2cube
I am trying to do visualizations of the charge density for non-spin-polarized silicon nanowire. After relaxation, I try to run grid2cube with the following syntax (my input file for g2c is SiNW.g2c and for simplicity's sake, my system label will be referred to as S_L): ./grid2cube.out < SiNW.g2c S_L.XV S_L.RHO > g2c.out but when I do this, it returns that my nspin=0 and thus does not make a .cube file at all. My input file for g2c is: - S_L rho 0.0 0.0 0.0 1 unformatted -- This is the standard output of the command that I issued above: -- Cell vectors 46.1754762584164 0.000E+000 0.000E+000 0.000E+000 46.1754762584164 0.000E+000 0.000E+000 0.000E+000 17.7734538727118 Grid mesh: 216 x 0 x 216 nspin =0 --- Something seems strange to me about that '0' in the grid mesh, too. I tried editing the fortran code for grid2cube.f, setting nspin=1 manually inside the code, recompiling and running again, but this is what I get: - 680.000.000.00 2160.2137750.000.00 0 NaN InfinityNaN 2160.000.000.082285 140.009.433099 NaN0.903102 140.009.432789 NaN5.318021 140.00 13.033586 NaN6.808950 140.00 13.015757 NaN 11.235454 140.00 13.015924 NaN 12.758808 140.00 13.034385 NaN 17.185759 140.00 16.618908 NaN0.904276 140.00 16.618154 NaN5.315916 140.00 13.005918 NaN0.916227 140.00 13.038506 NaN5.327205 140.00 16.613020 NaN6.851160 140.00 16.601408 NaN 11.252581 140.005.860178 NaN0.916193 140.005.827284 NaN5.327166 140.009.433099 NaN6.820480 140.009.432860 NaN 11.246750 140.009.432089 NaN 12.764217 140.009.432765 NaN 17.163633 140.002.246604 NaN0.904218 140.002.245486 NaN5.316090 140.005.830740 NaN6.808691 140.005.849300 NaN 11.235654 140.005.848824 NaN 12.758320 140.005.831752 NaN 17.185301 140.005.828020 NaN0.893063 140.005.859017 NaN5.304081 140.009.431658 NaN6.829797 140.009.431909 NaN 11.229134 -- And this is obviously a non-result. Additionally, I read on the boards something about using a program called WSxM for visualization of SIESTA output. I downloaded the program, but could not get it to load any of my output files for plotting. Anybody use this regularly for plotting SIESTA output? I also could not find the keywords to save RHO, DRHO, etc. in formatted output. I think that may have something to do with this, at least maybe for the WSxM part. My fdf file is attached for any who wish to help me tackle my problem. Any suggestions would be appreciated, and I understand that in the past few days there has been a lot of activity in the email list. Thank you in advance for your kind help, Abraham Hmiel Research Assistant in Theoretical and Computational Nanoscience Center for Nanoscale Science and Engineering at the State University of New York at Albany SiNW.fdf Description: application/vnd.fdf
Re: [SIESTA-L] problem in band structure of SmTe
I don't know anything about SmTe, but I would suggest that the band structure does not depend on pseudos, but rather on the symmetry of the crystal. If you expect to see 8 bands then check the lowest 8 bands and compare them to previously published ones - if the symmetry of the crystal is correct then the shapes of the bands should be correct too. I believe that due to some other parameters you have a 0 band gap (which is quite possible in DFT, if expt value is 0.67) instead of 10eV which is likely to be the second (higher) bandgap - in the band model, bands become narrower when you go higher in energy, while bandgaps become bigger.
