Re: [SIESTA-L] Tips for symmetry?

There's also the GridCellSampling block that is intented for this, too. 2009/6/25 David Strubbe dstru...@berkeley.edu Ben, Your symmetry is probably not being broken by numerical noise, which is all that those tolerances will affect, but rather by the real-space mesh, i.e. the eggbox

Re: [SIESTA-L] Compilation on WIndows

Hi, You can do it in absolutely the same way as under Linux using the Cygwin environment. Unfortunately, though, you won't be able to use the nice compiler and math libs from Intel, so you'll have to use gfortran and ATLAS (link with -mno-cygwin and -static so you don't have to worry about

Re: [SIESTA-L] Band plotting in supercells

Dear Marcos, Consider a 1D system. Imagine that we have the dispersion plot for a primitive cell for k from 0 to kmax. For a 2x supercell, we have all the same bands, but now we need to squeeze them into a reciprocal cell (not the IBZ, but simply the complete 1st Brillouin zone) half the original

Re: [SIESTA-L] basis problem

You have to define two different atomic species with atomic number = 8 and different labels, and put the .psf files for both labels into your dir. It's all described in the manual. Also, I think that there was this Hfloat input example that has two different H species (if I'm not mistaken).

Re: [SIESTA-L] Basis for CdSe

2008/4/15, Marcel Mohr [EMAIL PROTECTED]: Then I get nearly linear behaviour PAOshift vs. Total energy, with 5 meV PAO shift gives lowest energy (for my range 5 tp 100 meV). Actually, as Dr. Postnikov correctly pointed out, I made a mistake here. The problem indeed is variational, but the

Re: [SIESTA-L] ANNOUNCE: LDA GGA pseudo databases

Dear Eduardo, There seems to be something wrong with the database. I'm unable to access the pseudos, the links take me to an object doesn't exist page. 2008/3/12, Eduardo Anglada [EMAIL PROTECTED]: Dear Users of Siesta, There is a new collection of pseudopotentials available for SIESTA! I

Re: [SIESTA-L] Spin polarization

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

Re: [SIESTA-L] Spin polarization

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

Re: [SIESTA-L] Segmentation fault in Broyden mixing

Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Vasilii Artyukhov Strange, I'm using Broyden all the time and never had any segmentation faults there... 2008/3/27, Marcos Verissimo Alves [EMAIL PROTECTED]: Hi all, I was trying to use the Broyden mixing scheme

Re: [SIESTA-L] Segmentation fault in Broyden mixing

Strange, I'm using Broyden all the time and never had any segmentation faults there... 2008/3/27, Marcos Verissimo Alves [EMAIL PROTECTED]: Hi all, I was trying to use the Broyden mixing scheme in siesta, in both versions 2.0 and 2.0.2-rc9, and I was getting a segmentation fault when it came

Re: [SIESTA-L] Problem FixSpin

FixSpin only fixes the total magnetization, making SIESTA very the Fermi levels for up and down spins so that the net spin population will be what you've specified in the parameter. This has nothing to do with the populations on individual atoms. Clearly, trying to impose a fixed spin on each atom

Re: [SIESTA-L] A magnetic structure going nonmagnetic

2007/11/9, Marcos Verissimo Alves [EMAIL PROTECTED]: Hi Vasilii, Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Vasilii Artyukhov Hi everybody, I have a somewhat awkward question. I'm relaxing a structure that is supposed to be magnetic. This means, a SCF run

[SIESTA-L] A magnetic structure going nonmagnetic

Hi everybody, I have a somewhat awkward question. I'm relaxing a structure that is supposed to be magnetic. This means, a SCF run with a broken initial spin symmetry gives a nonzero magnetic moment. But then, after some relaxation steps (unfortunately, SIESTA only outputs the magnetic moment at

Re: [SIESTA-L] Number of valence bands

Andrey, I'm afraid that the number of valence electrons for oxygen is really 6. 2s^2 2p^4. 2007/10/17, Semichaevsky, Andrey [EMAIL PROTECTED]: Konstantin, Oxygen valence is 2, not 6. So the number of electrons per molecule is 3*2 (In) + 2*3 (O) =12. The total number of bands for 16

Re: [SIESTA-L] Lattice relaxation and band structure calculations for In2O3

1) Did you turn the MD.UseSaveCG flag on? Also, you might want to try MD.TypeOfRun Broyden, in my experience this is really superior to CG. 1) Екн 2007/10/16, Semichaevsky, Andrey [EMAIL PROTECTED]: Dear Siesta users, I have two questions related to the calculation of the electronic

Re: [SIESTA-L] Parallel SIESTA on SMP Machine

As far as my experience goes, I've been running SIESTA on a 64-processor SMP by Hewlett-Packard. Everything was okay, although using MPI on an SMP is certainly a waste of memory. There's indeed no difference for SIESTA between an SMP and a cluster. 2007/7/19, Marcos Verissimo Alves [EMAIL

Re: [SIESTA-L] POSS nanoparticles

Could you please send a copy of your input, I'll try to have a look... 2007/7/16, Zoya Shah [EMAIL PROTECTED]: Dear all I am at the moment trying to model some Silicon-Oxygen-nanoparticles (POSS). When relaxing them I find a big variance in the Si-O-Si, bond angles, but I can not really see a

Re: [SIESTA-L] Wavefunction plot at k-point other than Gamma

There was a message from Andrei Postnikov on Jan 27: the wavefunctions in other k_points than Gamma are complex, and since they are moreover defined up to a complex exponent (as any eigenvector), a problem arises already how you'll plot them in an unambiguous way... I can think of a possible

Re: [SIESTA-L] band structures: anything wrong?

It's okay, the units of k-points in the file are 1/Bohr. 2007/7/9, Cherry Y. Yates [EMAIL PROTECTED]: Dear Siesta, I tried to calculate the bands along gamma to Z (0 0 1/2). This is my setings: %block BandLines 1 0.000 0.000 0.000 \Gamma 5 0.000 0.000 1.000 Z %endblock

Re: [SIESTA-L] Do not getting output

You're using a pseudopotential that only has angular projectors included for s and p symmetry, while your basis set is set to contain polarization functions, which means d functions as well. To overcome this, you should set nonzero populations in the pseudo generation input file for the

Re: [SIESTA-L] error when trying to compile gen-basis.F

Hmm... So far 'make gen-basis' has worked just fine for me on every machines... 2007/6/15, berkaine nabil [EMAIL PROTECTED]: Hello everyone, Can anybody tell me how to compile correctly the gen-basis.F program. In the manual it is says that it's compiled at the same time than SIESTA (like the

Re: [SIESTA-L] siesta compilation at bluegene

If you could tell us more about what exactly error messages you get, more people could help you. 2007/6/8, Haiying He [EMAIL PROTECTED]: Hi, Joachim Thank you very much for your comments. We tried with Siesta2.0.1 and so far no success. Could you please send us the arch.make file? Sincerely

Re: [SIESTA-L] LAM SCALAPACK

It seems to me that whichever MPI you're using is not to blame. Are you sure that you use the correct Fortran/C name conventions? The BLACS distribution, for instance, contains utilities to check the correct settings (in the INSTALL directory). 2007/6/3, Cherry Y. Yates [EMAIL PROTECTED]: It

Re: [SIESTA-L] More on Cholesky in parallel siesta

That's strange, since as far as I could figure out, Cholesky factorization in cdiag.o seems to be called only in parallel diagonalizations - it's related to the decomposition of matrices over processors. You can trace the error from cdiag to a ScaLAPACK routine, can't recall its name, and take a

[SIESTA-L] Problems with band structure output

Hi, I've encountered a problem when calculating the band structure with SIESTA. When I try to calculate it in parallel, the program solves the SCF equations and then just does nothing - the processes are still there but they are idle. I'm doing all this on an 64-CPU HP SuperDome under HP-UX11i

Re: [SIESTA-L] k-mesh: unexpected shift

Hi, It is not a feature, this issue has already been discussed, see the archives (12.01.2007, by Marcos Verissimo Alves): I have just received a reply from Alberto Garcia on the subject. It is indeed a bug, and I will be testing the fix. As soon as I have it tested (by the end of the day I

[SIESTA-L] SCF convergence

Dear everybody, I'm trying to converge the SCF equations, and sometimes the output can look like this: siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) siesta:1-9151.6992-9154.1412-9154.1412 0.2829 -6.6663 timer: Routine,Calls,Time,% = IterSCF1

Re: [SIESTA-L] k-point shifts

2007/5/5, Andrei Postnikov [EMAIL PROTECTED]: Well, that's how the inversion works. The BZ is cut in two by c=0 plane, and points with c0 are removed. For c0, obviously all a and b are included. Your 48 points are 4x4 planes, taken three times (for c=0, 0.5, 1). In case of shifted mesh, you's

Re: [SIESTA-L] k-point shifts

2007/5/4, Andrei Postnikov [EMAIL PROTECTED]: On Fri, 4 May 2007, Vasilii Artyukhov wrote: | I was wondering how to make k-space sampling in SIESTA efficient. Dear Vasilii: it is efficient enough... Well I'd say it's efficient in, for example, ABINIT, while SIESTA doesn't seem to use

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

Yes, it seems like a nice idea to increase the electronic temperature. After the convergence you can restart the calculation using this density matrix with a lower electronic temperature to get the most of your accuracy. And the MP smearing for some reason doesn't work for me, either. And there

Re: [SIESTA-L] A question about local magnetic moment

Hi Marcos, Yes, the arbitrariness of radius choice is exactly what I'm talking about. There's a strict way to choose the integration region using the geometrical properties of the density. I'm not very aware about the details or what codes can do it. If someone's interested in having a

Re: [SIESTA-L] order-N method

I'm not sure that your system is actually big enough do that you can gain anything from linear scaling. Do you actually need O(N)? 2007/4/23, Mu J. Helien [EMAIL PROTECTED]: Dear siestausers, Is there anyone who has experience in using orderN method? I just want to calculate the total energy

Re: [SIESTA-L] A question about local magnetic moment

Dear Marcos, It seems like a very nice idea, but doesn't PDOS depend strongly on the basis set, as well? I still think that the most reliable choice would be to work directly with the total spin density. 2007/4/23, Marcos Verissimo Alves [EMAIL PROTECTED]: This question has just come to

Re: [SIESTA-L] MPI interface

rakshit [EMAIL PROTECTED]: hello vasilii, i think you are installing it in serial mode... here is an arch.make file i send you as an attachment i use it in mu AIX IBM machine and work well but with xlf95 *Vasilii Artyukhov [EMAIL PROTECTED]* wrote: Dear everyone, I'm trying to compile SIESTA

[SIESTA-L] FDF howto's

Dear all, especially, the developers, Could someone briefly explain to me how to work with the FDF format? I'd like to use SIESTA as an external subroutine (I want to implement some simple form of metadynamics), and it seems a nice idea to make the driver program compatible with FDF. Best

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

If your system is not too large, I'd advise that you determine the relaxed lattice constants from a series of fixed-cell calculations, especially if the system is more or less symmetrical. Although your stresses seem quite low to me, I think that the only way to improve them might be, indeed, to

Re: [SIESTA-L] Posible SPAM: elastic constant calculations

I believe that if you're willing to apply strain in the c direction only, you might also want to relax the other two lattice parameters. Obviously this will decrease your values, maybe to something reasonable. 2007/3/19, Chun Li [EMAIL PROTECTED]: Dear SIESTA users, I used SIESTA to calculate

[SIESTA-L] Partial core correction; also Simplex

Dear everyone, My first question is: where can I get the celebrated Simplex script for basis set optimization? And the second is about the partial core correction in the pseodupotentials. The other day I used the web interface to Atom by the Octopus team. They offer two options for the pcc,

Re: [SIESTA-L] Bug in bands.F ?

Sorry, could you please explain this part in some more detail? 2007/2/2, Fabio Bernardini [EMAIL PROTECTED]: Hello In version 2.0 it seems there is a bug in Bands.F file. When you run a spin polarized bandstructure the values for the fermi energy in the first line of .bands are wrong. I think

Re: [SIESTA-L] User.Basis

Perhaps you should consider consulting the literature about various basis set kinds and their peculiarities: Gaussian functions, all sorts of plane waves and wavelets, localized muffin-tin orbitals, numerical atomic orbitals, finite grids and splines... -- just to understand why you don't want

Re: [SIESTA-L] User.Basis

Since SIESTA doesn't work with Gaussian bases, you can't do that. The basis orbitals automatically generated by SIESTA are atomic, Slater-like, but with a finite support. In principle, you can input any desired Gaussian function (on a finite support) as a radial table using block PAO.UserBasis,

Re: [SIESTA-L] space group implementation

Hi, I don't think that the knowledge of your system's space group will be of any use to SIESTA, since it performs grid integration, and the grid has (by default) only the symmetry of the Bravais lattice. You can use the Kgrid.Sampling block to partially correct for that, but even this is not

Re: [SIESTA-L] vmem issue?

Hi, There are some keywords that reduce the memory usage in parallel calculations, like ON.LowerMemory and a couple of others, check with the manual. Besides these, what you can do is increase the number of nodes (pretty obvious), shrink the basis set (obvious, too), use basis orbitals with a

Re: [SIESTA-L] Questions about MD.Anneal

Hi all, 2007/1/4, Andrei Postnikov [EMAIL PROTECTED]: On Thu, 4 Jan 2007, Oleksandr Voznyy wrote: | Andrei, | the temperature will start from initial temperature and will gradually change | to target T during MD.TauRelax time with a given time step (as for usual MD). Alexander, thank you

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

I think that you could use the radii from Dr. Ozaki's database of pseudopotentials for OpenMX. Since the method is essentially the same, and the database is said to be more or less tested, everything should be OK, although I didn't have the time to try this myself yet. You can find the parameters

Re: [SIESTA-L] Another compilation trouble - or is it?

Let's say that this corrects the problem *partially*. The graphite calculation is ok, but in some other cases, this doesn't help, and that still includes the BaTiO3 test. So it appears that I have to recompile the program from scratch. But it would still be interesting to know the possible

Re: [SIESTA-L] Another compilation trouble - or is it?

Well, I'm quite sure that the OS on that computer has been reinstalled this spring, so it's unlikely that something is outdated. I'm not sure if the compilation options were exactly the same, I'll have to check it. What I'm sure about is that it's not a problem of the OS or MPICH or something

Re: [SIESTA-L] About PDOS for 2p orbitals

2006/12/4, Oleksandr Voznyy [EMAIL PROTECTED]: I still haven't got any reasonable explanation from other people. The only suggestion I hear many times that hybridization concept is oversimplified and you need to think of molecular orbitals rather than simple hybridization of atomic orbitals.

Re: [SIESTA-L] Problems finding pseudopotentials in siesta2.0 -para

The first (quite stupid) idea that comes to mind is to check which atom specie names you are using. If your system has atom species named something like Z_whatever, then the program will not be satisfied by a pseudo file named Z.psf, you must also have a file named Z_whatever.psf. At any rate,

Re: [SIESTA-L] Pseudos from ABINIT

Well, I've browsed back through the list archives, I think, up to June or something, but perhaps the discussion you refer to has escaped from my attention. Of course, you can always take the pseudopotenital generation parameters from some other source and generate them - but then, why did they

[SIESTA-L] Pseudos from ABINIT

Hello everyone, I recall reading something about the fact that the pseudos from the ABINIT database could somehow be used with SIESTA, but I can't find that bit now. Is it just false memory, or is it really possible to do that? I also found out that both codes can read pseudos in XML format, but

Re: [SIESTA-L] Problem on using OrderN SolutionMethod for MD relaxation

Right now I'm trying to deal with the same problem using another order-N code, OpenMX. It does not have many advantages over SIESTA (and in fact, has certain strong disadvantages), but it has that Kerker density mixing scheme in the SCF which allows (in theory) to deal with zero-gap systems. The

[SIESTA-L] Yet another compilation trouble

Hi everyone, I seem to have a very strange problem with parallel SIESTA. The make goes okay, but the program does not read the input .fdf file. In fact, all it does is output the out.fdf file that says: fdf-debug 0 # Default value SystemName #

Re: [SIESTA-L]

, you should use the available optimized libraries. 2006/11/15, Jess Kondor [EMAIL PROTECTED]: On 11/15/06, Vasilii Artyukhov [EMAIL PROTECTED] wrote: RTFM! Everything is said in the corresponding readme's of the libraries. First, you should install MPI, then ATLAS (it is required

Re: [SIESTA-L]

RTFM! Everything is said in the corresponding readme's of the libraries. First, you should install MPI, then ATLAS (it is required for the following), then MPIBLACS and SCALAPACK. Then, in theory, you can go for SIESTA. Don't forget to specify the Add_ option when compiling the libraries and to

Re: [SIESTA-L] Au 6s pseudopotential

You have to include the Au semicore states into your calculation if you want to get some meaningful results. It is useless to do calculations for the 6s only, as 5d electrons also participate in the bonding and cannot be treated as core (which is what you're trying to do). 2006/11/15, Haiying He

[SIESTA-L] Parallel compilation

Hi everyone, I'm new to the world of Linux, therefore I'm going to be asking a couple of stupid questions. I'm trying to compile SIESTA on a 256-CPU Itanium2 LINUX machine. I've run ./configure --enable-mpi, then edited the arch.make to indicate the path to BLACS and CLAPACK. The file is below.

[SIESTA-L] Compiling ATOM under cygwin

Hello everyone, I'm trying to compile the ATOM program under cygwin and it seems that I need a fortran-90 compiler, which I don't have. The makefile has a line saying AUX_OBJS= auxf95.o # Change if you don't have a fortran-90 compiler but I'm unable to figure out what to write there. Can