Re: [SIESTA-L] order-N method

[Vasilii Artyukhov]

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 of a system consisting of 128
atoms.But the SCF results vibrate siginificantly, then to an infinit
value  and can't converge.
In the manual of siesta, it is said that we should adjust ON.eta
parameter so that the total charge is conserved. Does anyone know how
to achieve it?Also, is there any other parameter that should be
adjusted or set up?
Thank you very much.
Mu J.Helien

Re: [SIESTA-L] order-N method

[Nichols A. Romero]

At a system size of 128 atoms, there is very little advantage in using the
orderN method.

On 4/23/07, Mu J. Helien <[EMAIL PROTECTED]> wrote:


Dear siestausers,
Is there anyone who has experience in using orderN method?
I just want to calculate the total energy of a system consisting of 128
atoms.But the SCF results vibrate siginificantly, then to an infinit
value  and can't converge.
In the manual of siesta, it is said that we should adjust ON.eta
parameter so that the total charge is conserved. Does anyone know how
to achieve it?Also, is there any other parameter that should be
adjusted or set up?
Thank you very much.
Mu J.Helien





--
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)

[SIESTA-L] order-N method

[Mu J. Helien]

Dear siestausers,
Is there anyone who has experience in using orderN method?
I just want to calculate the total energy of a system consisting of 128 
atoms.But the SCF results vibrate siginificantly, then to an infinit 
value  and can't converge.
In the manual of siesta, it is said that we should adjust ON.eta 
parameter so that the total charge is conserved. Does anyone know how 
to achieve it?Also, is there any other parameter that should be 
adjusted or set up?

Thank you very much.
Mu J.Helien

[SIESTA-L] SaveHS option

[Eduardo Cruz]

Hello Siesterers...

I have been writing a subroutine to read the HS file and reconstruct
the Hamiltonian and overlap matrices, and I noticed that in Siesta,
the iohs subroutine that writes this file is called from inside the
SCF loop.  If Siesta does not read this file, is there a reason why to
write it on each SCF cycle??? Wouldn't it be better to have it written
at the end of each MD step or just once after the MD loop?

Saludos
Eduardo Cruz

Re: [SIESTA-L] comparing total energies between programs

[Nichols A. Romero]

Marcos,

You are correct that the local potential scheme is different between SIESTA
and that typically
used in a PW implementation.

I took a look back at Figure 3 of the SIESTA method paper (on the website).
It clearly shows that as
the basis size increases from DZP, TZP, TZDP, TZTP, etc. the total energy
curves approaches the PW
result from _above_. Even at the DZP level, the example used here suggests
that there is still a difference
of ~0.1 eV/atom in the absolute total energy. So, let me be more precise in
my formulation of the question.

If the NL pseudopotential is decomposed identicaly (local and non-local
parts), can one directly compare
the total energies between SIESTA and a PW code, e.g. ABINIT? (Or is the
some reference energy
that needs to be substracte out.) Also, will the PW total energy be in
general lower the SIESTA energy
barring an overcompleteness of the local basis set.

Thanks for pointing out the work of Jean-Christophe Charlier. If there is a
specific published work or
online presentation, it would be nice if you can send us a link for more
information.

On 4/23/07, Marcos Verissimo Alves <[EMAIL PROTECTED]> wrote:


Hi Nichols,

While this would not be an authoritative answer to your question, I guess
it would be possible to compare the total energies directly, even if you
do not make the local potential exactly the same - there are articles on
the siesta methodology (I do not remember the references now) in which
total energies (as a function of the basis set size) are compared to PW
calculations. Also, the way siesta determines the local potential seems to
be a bit different from that of usual PW codes.

Regarding binding energies, I remember having seen a presentation by
Jean-Christophe Charlier in October, in which he had adsorbed atoms in the
system and used siesta. After BSSE his results agreed very well with the
ones obtained with plane waves. But, of course, this is something to be
checked.

Regarding your last question, this is something that I have always
wondered about. Hopefully someone with more expertise on the list will be
able to answer it...

Best regards,

Marcos

> Hi,
>
> Say that one was able to make everything identical (pseudpotential,
local
> potential, k-poins, T_el, SCF tol, etc.)
>
> Is it possible to directly compare the total energies between SIESTA &
PW
> code (e.g. ABINIT)? What should
> be used as a reference energy? Would binding energies between the two
codes
> agree by including the
> BSSE?
>
> --
> Nichols A. Romero, Ph.D.
> 1613 Denise Dr. Apt. D
> Forest Hill, MD 21050
> 443-567-8328 (C)
> 410-306-0709 (O)
>


--
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy



I have become so addicted to vi that I try to exit OpenOffice by typing
:wq!





--
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)

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

[Vasilii Artyukhov]

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 discussion on the list in the last few
days... Using the mulliken populations would be one way of doing it.
Another would be to use Andrei Postnikov's tools for integration of charge
density over atomic spheres. Yet another way would be to calculate the
PDOS for each atom with a small smearing, then integrate over the energies
up to the Fermi level. Seems complicated but with some shell scripting,
sed and a small fortran/c program to integrate the PDOS it can be
accomplished without too much difficulty.

Cheers,

Marcos


> Is it right if only use the value of "SPIN-UP - SPIN-DOWN" in Mulliken
> population analysis?
>
>> Dear Siesta usrers,
>>
>> How to get the local magnetic moment of each atom in the clusters,
>> molecules, or solids using siesta code?
>>
>> Best regards,
>> C. H. Hu
>>
>>
>
>


--
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy



I have become so addicted to vi that I try to exit OpenOffice by typing
:wq!

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

[Marcos Verissimo Alves]

This question has just come to discussion on the list in the last few
days... Using the mulliken populations would be one way of doing it.
Another would be to use Andrei Postnikov's tools for integration of charge
density over atomic spheres. Yet another way would be to calculate the
PDOS for each atom with a small smearing, then integrate over the energies
up to the Fermi level. Seems complicated but with some shell scripting,
sed and a small fortran/c program to integrate the PDOS it can be
accomplished without too much difficulty.

Cheers,

Marcos


> Is it right if only use the value of "SPIN-UP - SPIN-DOWN" in Mulliken
> population analysis?
>
>> Dear Siesta usrers,
>>
>> How to get the local magnetic moment of each atom in the clusters,
>> molecules, or solids using siesta code?
>>
>> Best regards,
>> C. H. Hu
>>
>>
>
>


-- 
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy



I have become so addicted to vi that I try to exit OpenOffice by typing :wq!

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

[Gul Rahman]

Hello Chahao
  Yes U can use and you can see the local magnetic momnet of each atom  and at 
the end you can also  see total magnetic momnet of your unit cell i.e 
  Total spin polarization (Qup-Qdown) =
  

Chaohao Hu <[EMAIL PROTECTED]> wrote:
Is it right if only use the value of "SPIN-UP - SPIN-DOWN" in Mulliken 
population analysis?
  
> Dear Siesta usrers, 
>   
> How to get the local magnetic moment of each atom in the clusters, molecules, 
> or solids using siesta code?  
>   
> Best regards, 
> C. H. Hu  
>  
> 







Gul Rahman   
Gul Rahman
Computational Physics Lab
Department of Physics 
University of Ulsan 
Republic of Korea
 
















   
-
Ahhh...imagining that irresistible "new car" smell?
 Check outnew cars at Yahoo! Autos.

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

[Vasilii Artyukhov]

Mulliken populations are dependent on the basis set (see another discussion
that takes place these days). Then, I guess that only the difference of
total populations can be used in a strict sense, gibing you the total
magnetization of the molecule or unit cell. For partial spin charges, this
can only be used as a 'hint'. I suggest that you use the postprocessing
utility by Dr. Postnikov (see recent mailing list archives), there the spin
density difference is integrated over a sphere around an atom; this should
be more exact. Although some tool that takes the topology of spin density
into account would clearly be desirable to establish a more or less strict
description of local moments, as spherical integration is still a somewhat
arbitrary choice of atomic 'shape'.

2007/4/23, Chaohao Hu <[EMAIL PROTECTED]>:


Is it right if only use the value of "SPIN-UP - SPIN-DOWN" in Mulliken
population analysis?


> Dear Siesta usrers,
>
> How to get the local magnetic moment of each atom in the clusters, molecules, 
or solids using siesta code?

>
> Best regards,
> C. H. Hu
>
>

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

[Chaohao Hu]

Is it right if only use the value of "SPIN-UP - SPIN-DOWN" in Mulliken 
population analysis?

> Dear Siesta usrers, 
>   
> How to get the local magnetic moment of each atom in the clusters, molecules, 
> or solids using siesta code?  
>   
> Best regards, 
> C. H. Hu  
>  
>  

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

[Oleksandr Voznyy]

I cannot agree that observing the relative change in Mulliken charges 
instead of absolute values would be correct. I had experience that DZP 
showed transfer of charge from surface to molecule, while TZP showed 
the opposite (though the charge transfer itself was very smal - about 
0.1e)


Was this an effect only in the Mulliken populations, or was it something 
from the calculation?  Did you checked was was really happening with the 
charge transfer?


I believe, yes. The binding energies (if BSSE corrections are taken) and 
the geometry were the same. I haven't checked too much, but I believe 
that if I were to draw DRHO it would be pretty the same (at least 
difference would not be noticeable by a naked eye).
While the Mulliken charges themselves were very different. And their 
difference (i.e. charge transfer) was a little bit different.

[SIESTA-L] A question about local magnetic moment

[Chaohao Hu]

Dear Siesta usrers,
 
How to get the local magnetic moment of each atom in the clusters, molecules, 
or solids using siesta code? 
 
Best regards,
C. H. Hu 

Re: [SIESTA-L] pw vs. localized basis and pseudopotentials

[Eduardo Anglada]

This is José M. Soler answer to this question:

Dear Nichols:

The basis set and the pseudopotentials are completely
independent things:
- If you have no l=d pseudo projector, but you use l=d basis
functions, they  will feel only the local part of the
pseudopotential, exactly like in a PW program (the SIESTA
local part of the pseudopotential is rather non-standard, but
this is a separate issue and not very relevant in practice).
- If you have no l=d basis, but you use a l=d pseudo projector,
it will still act on the l=s,p functions of neighbor atoms.
If these were very rich, they might 'in principle' represent
the l=d part of the wavefunction around the atom.

In summary: there is no difference on how the pseudopotentials
act in SIESTA and PW codes. If the wavefunctions are the same
(though expanded in different basis) the results are the same.

Best wishes,
Jose M. Soler



Hi,

This is a conceptual question about basis sets (pw vs. localized  
basis) and pseudopotentials as implemented in SIESTA. The best way  
to ask my question

is by a very simple example.

Consider Si where L = d states are important. In SIESTA,  
contributions from L= d states require L=d basis functions _plus_  
the d-pseudopotential. As opposed to a code like ABINIT, where the  
PW have this variational freedom builtin. One would get  
contributions from L=d states, even without the d-pseudopotential.  
(One can do a PDOS per angular momentum and see this.)


So in SIESTA, unless you actually have L=d basis functions  
including the d-pseudopotential would _not_ do anything. Or to put  
it another way, does the
d-pseudopotential act on the basis functions of different symmetry  
in the localized basis set?


Thanks,

--
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)

Re: [SIESTA-L] innovative program

[Bailey, Steven]

Dear Sirs
 
Yes I use quantum mechanical simulations throughout the year along with my PhD 
students, so please send me some info about USPEX.
Steve
 

Dr S Bailey 
L & C IoP Branch Secretary 
Physics Department 
Lancaster University 
Lancaster, UK. 
LA1 4YB 
Tel. +44(0)1524592844 

 



From: Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta 
[mailto:[EMAIL PROTECTED] On Behalf Of mphilipp
Sent: 23 April 2007 09:43
To: SIESTA-L@listserv.uam.es
Subject: [SIESTA-L] innovative program


Dear Sir or Madam, 

As far as we know, you are working with a quantum-mechanical simulation, such 
as VASP, SIESTA or GULP. Therefor you might be interested in the software 
called USPEX.

USPEX is a new program which was recently developed at the Swiss Federal 
Institute of Technology, ETH Zurich. It allows you to predict crystal 
structures at a given temperature and pressure. Through combination of 
evolutionary algorithms and quantum-mechanical simulations, it is not only 
faster but also is no initial guess needed. As a result researchers no longer 
have to predict starting structures because USPEX will do that. By selecting 
the fittest structures, optimizing them locally and then  recombining them, 
USPEX is able to generate new structures with even lower free energy. This 
evolutionary process results in crystal structure that is stable under the 
given conditions.

For detailed technical information see attachment.

Within a first market survey we would like to know

*   How often you are using quantum-mechanical simulation within a year 
*   If you are interested in USPEX 
*   If you prefer your own USPEX or a  service which is calculating data 
for you 


If you are interested in the software please contact us. 

We are looking forward to hearing from you.
 


Philipp Matzinger & Christoph Mäder



ETH Zurich
ETH transfer, HG E48.2
Raemistrasse 101
8092 Zurich, Switzerland
Phone: +41 44 632 61 65
Fax: +41 44 632 11 84
[EMAIL PROTECTED]
[EMAIL PROTECTED] 

[SIESTA-L] innovative program

[mphilipp]

Dear Sir or Madam,

As far as we know, you are working with a quantum-mechanical simulation, 
such as VASP, SIESTA or GULP. Therefor you might be interested in the 
software called USPEX.


USPEX is a new program which was recently developed at the Swiss Federal 
Institute of Technology, ETH Zurich. It allows you to predict crystal 
structures at a given temperature and pressure. Through combination of 
evolutionary algorithms and quantum-mechanical simulations, it is not 
only faster but also is no initial guess needed. As a result researchers 
no longer have to predict starting structures because USPEX will do 
that. By selecting the fittest structures, optimizing them locally and 
then  recombining them, USPEX is able to generate new structures with 
even lower free energy. This evolutionary process results in crystal 
structure that is stable under the given conditions.


For detailed technical information see attachment.

Within a first market survey we would like to know

   * How often you are using quantum-mechanical simulation within a year
   * If you are interested in USPEX
   * If you prefer your own USPEX or a  service which is calculating
 data for you


If you are interested in the software please contact us.

We are looking forward to hearing from you.


Philipp Matzinger & Christoph Mäder

ETH Zurich
ETH transfer, HG E48.2
Raemistrasse 101
8092 Zurich, Switzerland
Phone: +41 44 632 61 65
Fax: +41 44 632 11 84
[EMAIL PROTECTED] 
[EMAIL PROTECTED]


uspex.pdf
Description: Adobe PDF document

Re: [SIESTA-L] comparing total energies between programs

[Marcos Verissimo Alves]

Hi Nichols,

While this would not be an authoritative answer to your question, I guess
it would be possible to compare the total energies directly, even if you
do not make the local potential exactly the same - there are articles on
the siesta methodology (I do not remember the references now) in which
total energies (as a function of the basis set size) are compared to PW
calculations. Also, the way siesta determines the local potential seems to
be a bit different from that of usual PW codes.

Regarding binding energies, I remember having seen a presentation by
Jean-Christophe Charlier in October, in which he had adsorbed atoms in the
system and used siesta. After BSSE his results agreed very well with the
ones obtained with plane waves. But, of course, this is something to be
checked.

Regarding your last question, this is something that I have always
wondered about. Hopefully someone with more expertise on the list will be
able to answer it...

Best regards,

Marcos

> Hi,
>
> Say that one was able to make everything identical (pseudpotential, local
> potential, k-poins, T_el, SCF tol, etc.)
>
> Is it possible to directly compare the total energies between SIESTA & PW
> code (e.g. ABINIT)? What should
> be used as a reference energy? Would binding energies between the two codes
> agree by including the
> BSSE?
>
> --
> Nichols A. Romero, Ph.D.
> 1613 Denise Dr. Apt. D
> Forest Hill, MD 21050
> 443-567-8328 (C)
> 410-306-0709 (O)
>


-- 
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy



I have become so addicted to vi that I try to exit OpenOffice by typing :wq!

[SIESTA-L] comparing total energies between programs

[Nichols A. Romero]

Hi,

Say that one was able to make everything identical (pseudpotential, local
potential, k-poins, T_el, SCF tol, etc.)

Is it possible to directly compare the total energies between SIESTA & PW
code (e.g. ABINIT)? What should
be used as a reference energy? Would binding energies between the two codes
agree by including the
BSSE?

--
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)

[SIESTA-L] pw vs. localized basis and pseudopotentials

[Nichols A. Romero]

Hi,

This is a conceptual question about basis sets (pw vs. localized basis) and
pseudopotentials as implemented in SIESTA. The best way to ask my question
is by a very simple example.

Consider Si where L = d states are important. In SIESTA, contributions from
L= d states require L=d basis functions _plus_ the d-pseudopotential. As
opposed to a code like ABINIT, where the PW have this variational freedom
builtin. One would get contributions from L=d states, even without the
d-pseudopotential. (One can do a PDOS per angular momentum and see this.)

So in SIESTA, unless you actually have L=d basis functions including the
d-pseudopotential would _not_ do anything. Or to put it another way, does
the
d-pseudopotential act on the basis functions of different symmetry in the
localized basis set?

Thanks,

--
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)