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
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
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
? 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
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
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
__
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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
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:
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
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
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
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
Dear All,
I wonder if SIESTA implements the tetrahedron method
to compute the electron DOS? I prefer this method to
the smearing. Thanks,
Cherry
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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
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
I want to calculate a ZnO nanowire, does anyone have an optimized basis for Zn?
Many thanks!!!
Hi SIESTA guys,
Does anyone has good TZP basis for lithium? Many thanks,
Cherry
Does anyone have optimized basis for Au? Thanks!
Cherry
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Please send them to me if you happen to have these pseudopotentials.
Thanks!!!
Cherry
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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
Does any one have a good pseudopotential for gold (Au)?
Thanks.
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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
_
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
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
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
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
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
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
What is the potential unit in the .VT file? Thanks,
Cherry
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`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
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
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
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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
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
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
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
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
Does anyone know how to calculate electron and hole effective mass using
SIESTA?
THANKS,
Cherry
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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
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,
&
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
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
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
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
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)
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
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]>:
>
> >
--- "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
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
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
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
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
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_':
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