Re: [SIESTA-L] PDOS

1. The system cannot have less atoms. 2. It definetely is converged, the CG number is 0. Thanks, Cherry --- Oleksandr Voznyy <[EMAIL PROTECTED]> wrote: > > I tried to calculate the PDOS of a Si nanowire (~1400 atoms, SZP). > Hmmm... I wouldn't even continue to waste my time with SZ - it is f

[SIESTA-L] PDOS

Dear SIESTA guys, I tried to calculate the PDOS of a Si nanowire (~1400 atoms, SZP). The self-consistent calculation only takes a few hours to finish, however it is run for a few WEEKs and still running to obtain the PDOS. Is it right? Somwthing is wrong? Any way to boost? Thanks a lot! Cherry

Re: [SIESTA-L] vmem issue?

red during rdiag As you see, the maximum dynamic memory allocated jumps from 188 MB to 2146 MB. Is it all right? Thanks, Cherry --- "Cherry Y. Yates" <[EMAIL PROTECTED]> wrote: > Dear SIESTA developers > > Actually I tested the memory usage wi

Re: [SIESTA-L] vmem issue?

? Please give me some hints! Thanks, Cherry --- "Cherry Y. Yates" <[EMAIL PROTECTED]> wrote: > Dear SIESTA developers, > > I am running SIESTA for some silicon nanowires, the > memory of each node in my cluster is 4GB. when the > atom is less than 1000, the vmem and

[SIESTA-L] vmem issue?

Dear SIESTA developers, I am running SIESTA for some silicon nanowires, the memory of each node in my cluster is 4GB. when the atom is less than 1000, the vmem and mem is roughly the same, for example: resources_used.mem = 2213804kb resources_used.vmem = 2258976kb Then after that, the vm

[SIESTA-L] electron N+1 and N-1

Dear develpoers, I wonder if SIESTA can do electron N+1 and N-1 calculation, i.e., add an electron and remove an electron. Thanks, Cherry __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

[SIESTA-L] denchar: only generate specified orbital

Dear developer, I wonder if you know a simple way to use denchar to generate only the wavefunctions for specified states. Now It calculates all these states one by one, and my system is huge, taking very long time to reach the atates I need. Thanks, Zhigang

[SIESTA-L] denchar HELP!

Dear developer, I was trying to use denchar utility to plot Wavefunctions. I copied the .DM, .DIM, .ion, .PLD, .WFS files to a directory, and the input.fdf is attached. It showed the following error message: $ ./denchar < input.fdf Species number: 1 Label: H Atomic number:

[SIESTA-L] WrieWaveFunctions

Dear Siesta developers, I was using siesta to get wavefunctions. From the manu, if WriteWaveFunctions is .false., it will generate a .WFS file, which can be read by the utility READWFS, but I can not find this file. If WriteWaveFunctions is .true., it will write eigenvectors in the main output fil

Re: [SIESTA-L] RE : [SIESTA-L] calclations stopped /slabs

Please write in English so that we can understand. Thanks, Cherry --- mahtout sofiane <[EMAIL PROTECTED]> wrote: > il faut s'assurer de la défintion des coordonées > atomique de votre système. ce problème s'afiche > généralement lorsqu'il ya deux ou plusieurs atomes > qui ont les même coordonnés

Re: [SIESTA-L] Nanotube-Relaxation

This is not a reply. --- Michael Shin <[EMAIL PROTECTED]> wrote: > Hello Users > I want to find the relax atomic coordinates of > (5,5) Nanotubes and I did some calculations on > Carbon nanotubes (5,5) using CG for atomic > relaxation. After calculations I got relaxed atomic > cordinates. I use

Re: [SIESTA-L] Siesta-2.0 parallel version

It is not worth compiling it parallelly if you donot use a large number of k points (thousands). Its parallelism on gamma-point only is pretty poor. I found the best it can do is deceasing 30% time if running on a single node with two CPUs. If more nodes or more CPUs are used, essentially parallel

[SIESTA-L] electron DOS from the tetrahedron method

Dear All, I wonder if SIESTA implements the tetrahedron method to compute the electron DOS? I prefer this method to the smearing. Thanks, Cherry __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.co

[SIESTA-L] how to calculate DOS of individual atom?

Dear all, I wonder if anyone know how to calculate electron DOS of individual atom? I know there is a projected DOS block, but that one only records total DOS. For example, I have a system with 1000 atoms, I can calculate its total DOS, so that I can get band structure; but if I would like to

[SIESTA-L] system type

I found that SIESTA can identify if the system is a 1-D chain, 2-D slab, 0-D molecule, or 3-D solid. I wonder if siesta restrains the periodic boundary conditions (PBC) along the non-periodic direction. If so, when a partially PBC system, such as a chain is charged, how does SIESTA apply a neutr

[SIESTA-L] ZnO

I want to calculate a ZnO nanowire, does anyone have an optimized basis for Zn? Many thanks!!!

[SIESTA-L] Lithium basis

Hi SIESTA guys, Does anyone has good TZP basis for lithium? Many thanks, Cherry

[SIESTA-L] optimized babsis for Au?

Does anyone have optimized basis for Au? Thanks! Cherry Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shoppin

[SIESTA-L] pseudopotential for Ga and As

Please send them to me if you happen to have these pseudopotentials. Thanks!!! Cherry Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_y

Re: [SIESTA-L] pseudopotential for gold (Au)

st regards, > Vardha Srinivasan. > Computational Nanoscience Group > Univ. of California, Berkeley. > > > On Nov 15, 2007, at 1:52 PM, Cherry Y. Yates wrote: > > > Does any

[SIESTA-L] pseudopotential for gold (Au)

Does any one have a good pseudopotential for gold (Au)? Thanks. Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

[SIESTA-L] optical matrix

Dear SIESTA, I found SIESTA can calculate the imaginary part of the dielectric function. I wonder how I can output the calculated matrix element M_ij = . Please let me know where to heck the code... Thanks, Cherry _

[SIESTA-L] parallel writewave for big systems

Hi Alberto, Do you still try to figure out the issue with parallel writewave for big systems? I am waiting for your new version of writewave.F so that it is possible to write wavefunctions for big systems I calculated. Many thanks and have a nice weekend, Cherry >Cherry: > >Let's see if this ve

[SIESTA-L] external electric field

Dear SIESTA, I put an external electric field to a Si NW system (actually it is molecular like with both ends passivated by H atoms): %block ExternalElectricField 0.000 0.000 -0.050 V/Ang %endblock ExternalElectricField However, I found the energy can never get converged, even I set very smal

[SIESTA-L] parallel writewave for big systems

Dear SIESTA, I don't remember who I contacted, but I think someone promised to take a further look at the parallel issues of the writewave routine a month ago or so. I wonder if you get any progress. I really need it to generate the WFS files for a big system, which is so big that the sequential c

[SIESTA-L] fermi energy

Dear Siesta, I wonder how SIESTA determines the Fermi Energy for insulator. Is E_f defined as the highest occupied energy level? I found actually it is not. Thanks, Cherry Looking for a deal? Find gr

[SIESTA-L] band structures: anything wrong?

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 BandLines LatticeConstant 188.650178 Bohr %block LatticeVectors 0.375 0.000 0. 0.000 0.375

[SIESTA-L] band structure

I calculated a band structure along gamma to Z (0 0 0.5). I have a lattice: LatticeConstant 7.255775 Bohr %block LatticeVectors 4.1346376 0.000 0. 0.000 4.1346376 0. 0.000 0.000 1.0 %endblock LatticeVectors and %block BandLines 1 0.000 0.000 0.0

[SIESTA-L] potential unit

What is the potential unit in the .VT file? Thanks, Cherry Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&c

Re: [SIESTA-L] potential

`pgqcir_' /tmp/ifortRI8dCZ.o(.text+0x22a7): In function `grays_': : undefined reference to `pgscr_' /tmp/ifortRI8dCZ.o(.text+0x3f2f): In function `pltr3d_': : undefined reference to `pgqwin_' /tmp/ifortRI8dCZ.o(.text+0x3f4e): In function `pltr3d_': : undefined refe

Re: [SIESTA-L] potential

I actually found plrho can do the job. But I cannot compile it, and it complains "could not find -lpgplot library". Anyone knows what is that pgplot library??? Cherry --- "Cherry Y. Yates" <[EMAIL PROTECTED]> wrote: > Dear SIESTA, > > I have made a .VT file

[SIESTA-L] potential

Dear SIESTA, I have made a .VT file. Do you know how to plot them? How to make a .cube file from it? Thanks, Cherry Food fight? Enjoy some healthy debate in the Yahoo! Answers Food & Drink Q&A. http://answer

[SIESTA-L] SCF convergence issue

Dear SIESTA guys, I am trying to relax a big structure using CG and diag. At first few steps, it looks pretty good, something like this: siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) siesta:1 -258035.2072 -258036.9370 -258036.9370 0.0275 -4.3651 siesta:2 -258

Re: [SIESTA-L] Error in Cholesky factorisation in cdiag

First I compiled it with mkl and I got a lot of NAN in the output files. Then I changed to acml, and everything is fine. Cherry --- Sergey Lisenkov <[EMAIL PROTECTED]> wrote: > >Use acml library (you can download it from AMD website) instead of mkl. I > found > >mkl library doesn't work at all f

Re: [SIESTA-L] Error in Cholesky factorisation in cdiag

Use acml library (you can download it from AMD website) instead of mkl. I found mkl library doesn't work at all for SIESTA 2.00. GOOD LUCK, Cherry --- bipul rakshit <[EMAIL PROTECTED]> wrote: > hello siesta, > I am doing calculation on beta Sn... > but i get the > Error in Cholesky factorisati

[SIESTA-L] mixing

Dear All, I wonder if anyone know how to do a linear mixing for the first a few steps then do the Pulay or Broyden mixing for the rest? I know you can write two .fdf files, the first one does linear, then the second one does Pulay using the .DM file. But in a relaxation process, you cannot do that

[SIESTA-L] specify k-point?

Dear siesta helpers, Could you please tell me how to specify a given k-pont then do the SCF computation at this point only? I found the only way siesta taking k-pt is through some k-mesh, but I need to calculate some k-points around the GAMMA point to determint the effective mass... Thanks! Cher

[SIESTA-L] electron and hole effective mass?

Does anyone know how to calculate electron and hole effective mass using SIESTA? THANKS, Cherry TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/

Re: [SIESTA-L] writewave

Dear Alberto, I tried the new version, it still doesn't work. Actually I found the writewave.F is the same as that I downloaded before from that website. Thanks, Cherry --- Alberto Garcia <[EMAIL PROTECTED]> wrote: > Cherry: > > Could you please try to run the beta version of siesta-2.0.2 (l

Re: [SIESTA-L] writing the wavefunction

n the parallel operation of writewave.F. Please go to > > http://fisica.ehu.es/ag/siesta-extra/issues.html > > to download an interim fix. > > Regards, > > Alberto > > On 6/6/07, Cherry Y. Yates <[EMAIL PROTECTED]> wrote: > > Sergey, &

Re: [SIESTA-L] Fwd: [SIESTA-L] writing the wavefunction

e... > > sergey > > -- Forwarded message -- > From: Cherry Y. Yates <[EMAIL PROTECTED]> > Date: Thu, 07 Jun 2007 21:27:16 GMT > Subject: Re: [SIESTA-L] writing the wavefunction > To: SIESTA-L@listserv.uam.es > > > > > > 07.06.07, 21

Re: [SIESTA-L] writing the wavefunction

t; > Alberto > > On 6/6/07, Cherry Y. Yates <[EMAIL PROTECTED]> wrote: > > Sergey, > > > > Let's get the bottom of this. My machine is Intel(R) Xeon(TM) CPU 3.60GHz. > I > > found the initial setting of the stack size is 10240 kb. When I se

[SIESTA-L] mpi denchar won't work

Dear SIESTA developers, Because denchar is rather slow to generate the .cube files for large systems, I would like to use the MPI version, and I think it should be very efficient. But I got the following error: forrtl: Illegal seek forrtl: severe (20): REWIND error, unit 5, file stdin Image

Re: [SIESTA-L] writing the wavefunction

Sergey, Let's get the bottom of this. My machine is Intel(R) Xeon(TM) CPU 3.60GHz. I found the initial setting of the stack size is 10240 kb. When I set the stack size to unlimited, it did make the sequential ifort code as fast as the pgi one, and it can generate the wavefunction. The previous err

Re: [SIESTA-L] writing the wavefunction

Dear Sergey, This is the output of the ulimit: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited pending signals (-i) 1024 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m)

Re: [SIESTA-L] writing the wavefunction

Dear Sergey, I ckecked the command ulimit, and it outputs "unlimited". It looks like not the stack issue. Any further suggestions? Thanks, Cherry --- Sergey Lisenkov <[EMAIL PROTECTED]> wrote: > Cherry, > > It is well known now that intel compiler uses a very small stack space. So, > probably

Re: [SIESTA-L] writing the wavefunction

Cherry --- Sergey Lisenkov <[EMAIL PROTECTED]> wrote: > Cherry, > > What kind of fortran compiler doesn't work for you? What is an output from > 'ulimit' ? > > sergey > > 06.06.07, 03:41, Cherry Y. Yates <[EMAIL PROTECTED]>: > > >

Re: [SIESTA-L] writing the wavefunction

--- "Cherry Y. Yates" <[EMAIL PROTECTED]> wrote: > Dear SIESTA developers, > > I found a very wired issue of SIESTA. I compiled BLAS and LAPACK (or use > linalg.a) for the lapack and blas. It can write .WFS functions for small > systems(< ~ 1000 orbitals), but for larg

[SIESTA-L] writing the wavefunction

Dear SIESTA developers, I found a very wired issue of SIESTA. I compiled BLAS and LAPACK (or use linalg.a) for the lapack and blas. It can write .WFS functions for small systems(< ~ 1000 orbitals), but for large systems (such as ~ 3000 orbitals), it cannot wite the wavefunctions anymore! I have th

Re: [SIESTA-L] LAM SCALAPACK

parallel should be very much linear, what else I need to set up? It looks like single k-point scaling (Gamma only) ... Thanks, Cherry --- Sebastien LeRoux <[EMAIL PROTECTED]> wrote: > Cherry Y. Yates a écrit : > > DEAR Developer, > > > > Do you have any suggestions for comp

Re: [SIESTA-L] LAM SCALAPACK

rtyukhov : >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, Cher

Re: [SIESTA-L] LAM SCALAPACK

It doesn't help. I compiled everything with mpif77 -O3 (SIESTA, BLACS, and SCALAPACK), but I still got the same errors. Thanks, Cherry --- Yurko Natanzon <[EMAIL PROTECTED]> wrote: > Try removing -Bstatic flag, it causes such errors on many compilers > > On 02/06/07, Che

[SIESTA-L] LAM SCALAPACK

DEAR Developer, Do you have any suggestions for compiling a parallel version of SIESTA using LAM-MPI? I always got the following error messages: rdiag.o(.text+0x2a77): In function `rdiag_': : undefined reference to `blacs_gridinit__' libscalapack.a(descinit.o)(.text+0x54): In function `descinit_':