Re: [SIESTA-L] URGENT (supercell for bulk)

Dear Catrina, Mind that you have periodical boundary conditions so your unit cell is repeated infinite number of times in all directions. So, you only need to construct a supercell if you want to break the symmetry (i.e. introduce defects). Or if you want to imitate zero boundary conditions (i.e.

Re: [SIESTA-L] Converting .vps to .psf

Dear Carsten, I guess the only way to convert is to generate the pseudopotential from scratch using atom program. The cutoff radii as well as other parameters you will find in the beginning of the .vps file. regards, Yurko 2008/10/31 Carsten Rostgaard [EMAIL PROTECTED]: Hi I have some old

Re: [SIESTA-L] Comparing energy outputs between siesta and gaussian

Dear John, One would not expect that total energy obtained by different calculation methods (and different exchange-correlation functional!) will be the same, thus such comparison has no physical sense. I'd rather recommend to compare the measurable physical quantities, i.e. lattice constants or

Re: [SIESTA-L] rgarding Bulkmodulus

I'd recommend rather +/- 3% of the equilibrium volume. I've used this tool: http://www.fhi-berlin.mpg.de/th/fhi98md/toolkit/murn.tar It works well for noncubic lattices also. 2008/6/21 Sushil Auluck [EMAIL PROTECTED]: hi, bulk modulus is defined near the equilibrium volume. so calculate total

Re: [SIESTA-L] bulk modulus

There is a link to the SIESTA Tutorials which may be helpful: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/tutorials.html Tutorials contain both lecture notes and exercises (bulkmodulus calculation was done at the Tutorial in Lyon, at least). Bulk modulus calculation: You may

Re: [SIESTA-L] Rejected postings

For sure this happens. But I've the notification turned on and see that my message was succesfully distributed despite the rejection. This is a kind of bug but you just ignore the rejection message because it's not rejected in fact. On 11/03/2008, R.C.Pasianot [EMAIL PROTECTED] wrote: Hello

Re: [SIESTA-L] Parellelization overview

See, a colleague of mine says she's not seeing a (significant) performance gain while running in parallel (10 or so nodes) with respect to the serial case. The performance is noticable when using larger supercells. The larger cell is the bigger is the performance with respect to serial

Re: [SIESTA-L] Problem with optical properties

: 0.00172457 0.00169353 Ry/Bohr**3 siesta: 0.15834379 0.15549400 eV/Ang**3 siesta: 253.69747052249.13154735 kBar Does any bady know what did I wrong?! Thanks in advance NH -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute

Re: [SIESTA-L] UseStructFile

.. I think UseStructFile .true. is in coorect way. Am i right Unlimited freedom, unlimited storage. Get it now -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31

Re: [SIESTA-L] pseudopotential basis for Sulfur.

in directory S.tm2 == Pseudopotential in S.tm2.vps and S.tm2.psf and I could not find the S.tm2.vps and S.tm2.psf files. How could I fix this ? Thanks Best, Jingbin -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul

Re: [SIESTA-L] A naive question

atoms, but its not working. I am quite novice in using SIESTA. I would appreciate if anyone could help me. I am sorry if I am asking stupid question. Thanks, Zubaer -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul

[SIESTA-L] failed to get XV file

mailing list archives, I found I'm not the one who has faced this problem: there were reports, that SIESTA 2.0 doesn't produce XV for large systems. Can this issue somehow be solved? -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul

Re: [SIESTA-L] LAM SCALAPACK

! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

Re: [SIESTA-L] Not enough memory in isolated molecule calcs

mail2web.com – Enhanced email for the mobile individual based on Microsoft(r) Exchange - http://link.mail2web.com/Personal/EnhancedEmail -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish

Re: [SIESTA-L] LDA pseudopotential for GGA calculations?

? Or, could anybody kindly tell me how can I get a good GGA/PBE pps? Any suggestions or solutions would be greatly appreciated. Thanks in advance. C. Zhou -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342

Re: [SIESTA-L] parallel run

! Messenger -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

Re: [SIESTA-L] Performing relaxation correctly

users briefly how do you perform relaxation and whether you relax atomic coordinates and unit cell volume at the same time. -- Yurko Natanzon PhD Student Henryk Niewodnicza?ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email

[SIESTA-L] Performing relaxation correctly

briefly how do you perform relaxation and whether you relax atomic coordinates and unit cell volume at the same time. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED

Re: [SIESTA-L] SCF convergence problem on large system

with Adam, that if you have some partially filled states in the gap you would have problems with SCF convergence, so that more k-points would be needed, or try to increase ElectronicTemperature (by the way MP mixing has never worked for me, neither for GaAs nor for gold). -- Yurko Natanzon PhD

Re: [SIESTA-L] net charge calculation

/07, Yurko Natanzon [EMAIL PROTECTED] wrote: Dear Adam Gali, Andrei Postnikov, thank you for explanation. Actually, I'm not interested in particular numbers, but want to observe changes in ionic charges of atoms, neighboring to dopant and the dependence of such changes on a dopant concentration

[SIESTA-L] Fwd: [SIESTA-L] net charge calculation

their influence on net charges of nieghboring atoms? On 19/04/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Yurko Natanzon, take care! Mulliken-charges could be meaningless by using diffusing orbitals. Draw the net charge density around the atoms (you can do it by SIESTA and utility programs

Re: [SIESTA-L] net charge calculation

. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set

[SIESTA-L] net charge calculation

in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

Re: [SIESTA-L] How to fix some of the atoms while doing relaxation

only relax in z direction but are fixed in x and y direction. Can SIESTA do this? Thanks in advance. Yours Clutch 远离垃圾邮件？免费帮你过滤98％的垃圾邮件！www.126.com -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy

Re: [SIESTA-L] xmgrace

and select the correct range of energy. Now the problem is what is xmgrace.I did not find it in my out files and not anywhere in siesta software.Please help me a send some material about solution of these problems in future. best regards -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute

Re: [SIESTA-L] Restrict geometry optimization

don't change. Regards Pablo -- --- Pablo Aguado Puente [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy

Re: [SIESTA-L] how to calculate the values of strain tensor from forces or stress tensor?

tolerance. Note that since you are using a finite integration grid, no one can guarantee that you will ever get zero stresses. So, check for the integration grid cutoff as well, you might have to increase it at some point. 2007/3/27, Yurko Natanzon [EMAIL PROTECTED]: Dear siesters, I'm thinking

Re: [SIESTA-L] gnubands

? please help.i am waiting for your reply... with regards, Saswata Here's a new way to find what you're looking for - Yahoo! Answers -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152

Re: [SIESTA-L] SPAM : Re: [SIESTA-L] Diag.ParallelOverK

label). Emilio Yurko Natanzon wrote: dear bipul, it seems you have a mistake in your input file: Diag.PatallelOverK.true. you should correct into Diag.ParallelOverK .true. On 22/03/07, bipul rakshit [EMAIL PROTECTED] wrote: hello siesta user, i am running siesta in parallel AIX machine

Re: [SIESTA-L] Diag.ParallelOverK

dear bipul, it seems you have a mistake in your input file: Diag.PatallelOverK.true. you should correct into Diag.ParallelOverK .true. On 22/03/07, bipul rakshit [EMAIL PROTECTED] wrote: hello siesta user, i am running siesta in parallel AIX machine. I use the Diag.ParallelOverK .true.

Re: [SIESTA-L] Cu slab

-potential T save-hs T -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

Re: [SIESTA-L] how to increase accuracy of bulk modulus calculations?

the total energies. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

[SIESTA-L] how to increase accuracy of bulk modulus calculations?

, with best regards, -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

[SIESTA-L] Convergence vs MeshCutoff problem

-8637.1387 140 -8637.1375 150 -8637.1375 200 -8637.1380 250 -8637.1369 I'd be grateful if anyone can give me any advice on this. A sample of input file is attached -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul

[SIESTA-L] Fwd: [SIESTA-L] In running parallel siesta the energy is too large...

Dear bipul rakshit, I see you are using Portland compiler with -fast flag. It is known for causing problems like crashes and bad results for siesta 2.0 at least. I suggest to play with optimization flags, for example, change to -O2, -O1 or so. On 21/02/07, bipul rakshit [EMAIL PROTECTED] wrote:

Re: [SIESTA-L] input file for parallel siesta

in the input of the *.fdf file for parallel seista. if yes then can any body send a copy of fdf file. plz Here's a new way to find what you're looking for - Yahoo! Answers -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish

Re: [SIESTA-L] MPI compilation problem

it. It is better to use '-i-static' option instead. On 2/8/07, Yurko Natanzon [EMAIL PROTECTED] wrote: Dear Sebastien, Acttually the same problem I have as a result: mpif90 -o kind_explorer -Vaxlib -static kind_explorer.o /opt/intel/fc/lib/libifcore.a(for_open_proc.o): In function `for__compute_filename

Re: [SIESTA-L] MPI compilation problem

/lib/libc.a(iofwrite.o):(.eh_frame+0xde): undefined reference to `__gcc_personality_v0' On 08/02/07, Sebastien LeRoux [EMAIL PROTECTED] wrote: Yurko Natanzon a écrit : Dear Sebastien, thank you for your help. I was confused with mpif90 output and thought that it didn't work. Now I've recompiled

Re: [SIESTA-L] MPI compilation problem

`backtrace': ... I attach arch.make once again. My yesterdays arch.make was the same, but I used ifort instead of mpif90. However, with ifort I get the same errors. On 08/02/07, Sebastien LeRoux [EMAIL PROTECTED] wrote: Yurko Natanzon a écrit : So I compiled everything with ifort and icc

Re: [SIESTA-L] MPI compilation problem

. And by the way, compile mpich 2.0 by yourself could help too. On Wed, 7 Feb 2007, Yurko Natanzon wrote: LAPACK=-lmkl_lapack BLAS=-lmkl_ia32 These are the intel mkls, aren't they? Better try your own compiled. Regards Marcel -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute

Re: [SIESTA-L] MPI compilation problem

Dear colleagues, Actually I have the same problem with parallel compilation of SIESTA on Intel Core Duo machine. I've downloaded and installed Intel Fortran Compiler (ifort), Intel MKL Libraries Cluster Edition, Intel MPI. I've also compiled scalapack and blas from scratch, but still have lots of

Re: [SIESTA-L] A Question About Pseu

0.00 43 0.00 0.00 1.15 1.15 1.15 1.15 # Where does the number 2.0 come from ? Is there any differences between different jobcodes (pg and pe )? Thanks in advance! -- Yurko Natanzon PhD Student Henryk Niewodnicza��ski Institute of Nuclear Physics Polish Academy

Re: [SIESTA-L] Construction of GGA pseudopotential from LDA inputdata

, they are then varied during the calculations. On 16/12/06, Yurko Natanzon [EMAIL PROTECTED] wrote: Dear Vasilii, thank you for the information. Yes, there are some input file templates available together with ADPACK sources, so I can take cutoff radii. Unfortunately, not all the elements I need

Re: [SIESTA-L] Construction of GGA pseudopotential from LDA inputdata

in some pseudos in the database are just non-sensical. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

[SIESTA-L] Construction of GGA pseudopotential from LDA input data

to construct GGA pseudo? I'm interested, if I should change core radii and in what way. Thanks in advance -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]

Re: [SIESTA-L] Pseudos from ABINIT

Trieste, Italy I have become so addicted to vi that I try to exit OpenOffice by typing :wq! -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL

Re: [SIESTA-L] Zr and Y pseudopotentials needed

with ATOM. Marcos -- Yurko Natanzon PhD Student Henryk Niewodnicza?ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter

[SIESTA-L] Zr and Y pseudopotentials needed

Hello, SIESTA users! I'd be grateful if any of you can provide me a good GGA pseudopotential for Yttrium (Y), and also for Zirconium (Zr). There are some at ABINIT web page, but I don't know how to convert those pseudos to SIESTA psf/vps format. Is there any software for doing it? -- Yurko