Re: [Pw_forum] Ion

[Mostafa Youssef]

Hi Ashkan,

Click on the title your thread or alternatively search the forum with the 
keyword ion and you will find detailed answers to your question.

See for example:

http://www.mail-archive.com/pw_forum%40pwscf.org/msg09585.html


and also the manual entry:

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idp110032


Mostafa Youssef
MIT
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[Pw_forum] Ion

[ashkan shekaari]

Dear all
Does any one know is it possible to define ions in QE?

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
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[Pw_forum] ion problem

[Cyrille Barreteau]

Dear Nicola

Thank you for this interesting reference which is exactly the
subject of my "worries"..

cyrille

-- 
==
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay | fax   : +33 (0)1 69 08 84 46
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== 



Nicola Marzari wrote:

>Dear Cyrille,
>
>if you are interested in this problem, you might want to
>have a look at http://arxiv.org/abs/0709.4647 , and in
>particular at Fig 5.
>
>The published Makov-Payne correction is actually incorrect
>in the charge*quadrupole term.
>
>   nicola
>
>
>Cyrille Barreteau wrote:
>  
>
>>Dear all
>>
>>I have a question related to this problem.
>>I am interested in the study of charged clusters.
>>If I understand well, due to to the periodicity of the plane wave codes
>>one has to substract the correct "background" in order to keep the
>>energy from going to infinity..
>>
>>I would like to compare the energy of clusters with different
>>charges -e -2e etc... Do you have some advices to do such calculation?
>>Is it necessary to take even larger supercells than for neutral clusters?
>>
>>thanks in advance
>>
>>  cyrille
>>
>>
>>
>
>
>  
>

[Pw_forum] ion problem

[Nicola Marzari]

> Rudra Banerjee wrote:
>> dear PWSCF users,
>> I am new to pwscf and stuck in a question...is there any way to 
>> put anion   or cationas a unit?the total cluster is charge less 
>> but have two different types of ion...can anyone tell me what to 
>> do in this situation?
>> Regards


  Dear Rudra,

  several have answered this question. Let me add, though, that
  standard approximation to the exact exchange-correlation functional
  will often fail in "depositing" the right amount of charge on
  an ion. This becomes a very relevant failure if you have in the
  same unit cell ions of the same type, but of different valence,
  e.g. Fe 2+ and Fe 3+ in an oxide, or as ferrous/ferric ions in
  solution.

  GGA+U formulations help to correct this failure in the solid state
  (see e.g. Cococcioni / de Gironcoli, PRB 2005);  charge constraints
  can also be implemented successfully (see Sit, Cococcioni, Marzari,
  PRL 2006, and Van Voorhis PRA 72 024502 (2005)). Other references
  are given below.

  Best,

  nicola


  Van Voorhis J. Chem. Theo. Comp. 2 765 (2006); JPCA
  110 9212 (2006).

  Akai, Blugel, Zeller and Dederichs PRL 1986

  Hybertsen, Schluter and Christensen, PRB 1989

  Zhang and Satpathy PRB 1991

  Ujfalussy, Wang, Nicholson, Shelton, Stocks, Wang and Gyory J. App.
  Phys. 1999

  Prezhdo, Kindt and Tully JCP 1999

  Behler, Delley, Lorenz, Reuter and Scheffler PRL 2005, and
  Behler et al PRB 2007

-- 
-
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

[Pw_forum] ion problem

[Nicola Marzari]

Rudra Banerjee wrote:
> dear PWSCF users,
> I am new to pwscf and stuck in a question...is there any way to put 
> anion   or cationas a unit?the total cluster is charge less but have 
> two different types of ion...can anyone tell me what to do in this 
> situation?
> Regards


Dear Rudra,

several have answered this question. Let me add, though, that
standard approximation to the exact exchange-correlation functional
will often fail in "depositing" the right amount of charge on
an ion. This becomes a very relevant failure if you have in the
same unit cell ions of the same type, but of different valence,
e.g. Fe 2+ and Fe 3+ in an oxide, or as ferrous/ferric ions in
solution.

GGA+U formulations help to correct this failure in the solid state
(see e.g. Cococcioni / de Gironcoli, PRB 2005);  charge constraints
can also be implemented successfully (see Sit, Cococcioni, Marzari,
PRL 2006, and Van Voorhis PRA 72 024502 (2005)). Other references
are given below.

Best,

nicola


Van Voorhis J. Chem. Theo. Comp. 2 765 (2006); JPCA
110 9212 (2006).

Akai, Blugel, Zeller and Dederichs PRL 1986

Hybertsen, Schluter and Christensen, PRB 1989

Zhang and Satpathy PRB 1991

Ujfalussy, Wang, Nicholson, Shelton, Stocks, Wang and Gyory J. App. 
Phys. 1999

Prezhdo, Kindt and Tully JCP 1999

Behler, Delley, Lorenz, Reuter and Scheffler PRL 2005, and
Behler et al PRB 2007


-
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

[Pw_forum] ion problem

[Nicola Marzari]

Dear Cyrille,

if you are interested in this problem, you might want to
have a look at http://arxiv.org/abs/0709.4647 , and in
particular at Fig 5.

The published Makov-Payne correction is actually incorrect
in the charge*quadrupole term.

nicola


Cyrille Barreteau wrote:
> Dear all
> 
> I have a question related to this problem.
> I am interested in the study of charged clusters.
> If I understand well, due to to the periodicity of the plane wave codes
> one has to substract the correct "background" in order to keep the
> energy from going to infinity..
> 
> I would like to compare the energy of clusters with different
> charges -e -2e etc... Do you have some advices to do such calculation?
> Is it necessary to take even larger supercells than for neutral clusters?
> 
> thanks in advance
> 
>   cyrille
> 


-- 
-
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

[Pw_forum] ion problem

[Axel Kohlmeyer]

On Wed, 14 Nov 2007, Rudra Banerjee wrote:

RB> dear PWSCF users,

dear rudra,

RB> I am new to pwscf and stuck in a question..is there any way 
RB> toput anion or cation as a unit?the total cluster is charge less but 
RB> have two different types of ion...can anyone tell me what to do 

let me guess: you did classical MD before?
in a first principles calculation, there is usually no
need to distinguish between atoms and ions. you put in
the core charges (as point charges or pseudopotentials)
and then add the proper number of electrons, and the
QM calculation (in DFT approximation when using PWSCF)
will take care of how the electrons are distributed.

so you only have to take care of the total charge,
because it determines in combination with the sum
of the core charges how many electrons need to be added.

HTH,
  axel. 

RB> in this situation?

Regards
 
-- 
Rudra
Have a Nice Time
http://www.bose.res.in/~rudra
Please, if possible, don't  send me MS Word or PowerPoint attachments
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-- 
===
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
===
If you make something idiot-proof, the universe creates a better idiot.

[Pw_forum] ion problem

[Cyrille Barreteau]

Thanks a lot for this detailed explanation...
Hopefully I will succeed to follow this tortuous way,
else I will wait for the next release :-)

   cyrille

Giovanni Cantele wrote:

>Cyrille Barreteau wrote:
>  
>
>>Dear all
>>
>>I have a question related to this problem.
>>I am interested in the study of charged clusters.
>>If I understand well, due to to the periodicity of the plane wave codes
>>one has to substract the correct "background" in order to keep the
>>energy from going to infinity..
>>  
>>
>>
>This is automatically done by the code, as you may read in the INPUT_PW
>documentation file:
>nelec  REAL
>   number of electron in the unit cell
>   (may be noninteger if you wish)
>   Default: the same as ionic charge (neutral cell)
>   A compensating jellium background is inserted
>   to remove divergences if the cell is not neutral
>
>So, you set nelec in the input file, and that should be enough.
>
>  
>
>>I would like to compare the energy of clusters with different
>>charges -e -2e etc... Do you have some advices to do such calculation?
>>Is it necessary to take even larger supercells than for neutral clusters?
>>  
>>
>>
>The problem with charged clusters is that spurious interactions are 
>introduced by the
>periodic boundary conditions, so as convergence would be achieved at 
>very large supercells.
>Neverthelessm the total energy can be corrected, to get rid of such 
>interactions, as
>described by Makov-Payne, PRB (1995). Such corrections are currently 
>implemented
>in Quantum-ESPRESSO, with the only warning that, as far as I know, 
>corrections are
>applied to the total energy but are not to the forces.
>
>If you are using espresso-3.2, you should
>- run a self-consistent calculation for you charged cluster
>- run post-processing code pp.x, for obtaining the total charge density 
>(plot_num=0) in
>a suitable format
>- run dipole.x, you may read the header of PP/dipole.f90 for very short 
>explanation
>
>You finally end up with a Makov-Payne correction that must be added to 
>the total energy
>WITH its sign.
>You may try the same charged cluster with two different supercells, and 
>compare the
>two uncorrected energies, as well as the corrected ones, finding the 
>latter much more
>converged.
>
>Next releases will probably have an easier procedure. In the CVS version 
>I understand that a new variable
>(assume_isolated) has been added to the pw.x input, that, if set to 
>.TRUE., should allow to get
>the MP correction directly within the scf loop (so post-processing is 
>not mandatory).
>
>Giovanni
>
>
>  
>


-- 
==
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462   |
91191 Gif sur Yvette Cedex  FRANCE
  
http://www-drecam.cea.fr/spcsi/index.php
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php
== 

[Pw_forum] ion problem

[Giovanni Cantele]

Cyrille Barreteau wrote:
> Dear all
>
> I have a question related to this problem.
> I am interested in the study of charged clusters.
> If I understand well, due to to the periodicity of the plane wave codes
> one has to substract the correct "background" in order to keep the
> energy from going to infinity..
>   
This is automatically done by the code, as you may read in the INPUT_PW
documentation file:
nelec  REAL
   number of electron in the unit cell
   (may be noninteger if you wish)
   Default: the same as ionic charge (neutral cell)
   A compensating jellium background is inserted
   to remove divergences if the cell is not neutral

So, you set nelec in the input file, and that should be enough.

> I would like to compare the energy of clusters with different
> charges -e -2e etc... Do you have some advices to do such calculation?
> Is it necessary to take even larger supercells than for neutral clusters?
>   
The problem with charged clusters is that spurious interactions are 
introduced by the
periodic boundary conditions, so as convergence would be achieved at 
very large supercells.
Neverthelessm the total energy can be corrected, to get rid of such 
interactions, as
described by Makov-Payne, PRB (1995). Such corrections are currently 
implemented
in Quantum-ESPRESSO, with the only warning that, as far as I know, 
corrections are
applied to the total energy but are not to the forces.

If you are using espresso-3.2, you should
- run a self-consistent calculation for you charged cluster
- run post-processing code pp.x, for obtaining the total charge density 
(plot_num=0) in
a suitable format
- run dipole.x, you may read the header of PP/dipole.f90 for very short 
explanation

You finally end up with a Makov-Payne correction that must be added to 
the total energy
WITH its sign.
You may try the same charged cluster with two different supercells, and 
compare the
two uncorrected energies, as well as the corrected ones, finding the 
latter much more
converged.

Next releases will probably have an easier procedure. In the CVS version 
I understand that a new variable
(assume_isolated) has been added to the pw.x input, that, if set to 
.TRUE., should allow to get
the MP correction directly within the scf loop (so post-processing is 
not mandatory).

Giovanni


-- 



Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: Giovanni.Cantele at na.infn.it
Web: http://people.na.infn.it/~cantele

[Pw_forum] ion problem

[Stefano de Gironcoli]

The Makov-Payne correction (assume_isolated flag in &electrons) corrects 
for the leading term in the  cluster-backgound interaction .
This should reduce the size of the supercell needed, which should 
however be large and cheched for conergence.
stefano

Cyrille Barreteau wrote:
> Dear all
>
> I have a question related to this problem.
> I am interested in the study of charged clusters.
> If I understand well, due to to the periodicity of the plane wave codes
> one has to substract the correct "background" in order to keep the
> energy from going to infinity..
>
> I would like to compare the energy of clusters with different
> charges -e -2e etc... Do you have some advices to do such calculation?
> Is it necessary to take even larger supercells than for neutral clusters?
>
> thanks in advance
>
>   cyrille
>
>   

[Pw_forum] ion problem

[Cyrille Barreteau]

Dear all

I have a question related to this problem.
I am interested in the study of charged clusters.
If I understand well, due to to the periodicity of the plane wave codes
one has to substract the correct "background" in order to keep the
energy from going to infinity..

I would like to compare the energy of clusters with different
charges -e -2e etc... Do you have some advices to do such calculation?
Is it necessary to take even larger supercells than for neutral clusters?

thanks in advance

  cyrille

-- 
==
Cyrille Barreteau  | phone : +33 (0)1 69 08 29 51
CEA Saclay | fax   : +33 (0)1 69 08 84 46
DSM/DRECAM/SPCSI   | email cyrille.barreteau at cea.fr
Batiment 462   |
91191 Gif sur Yvette Cedex  FRANCE
  
http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html
== 



Stefano de Gironcoli wrote:

>Unless you put some constraint the code will distribute the charge 
>density so as to minimize the total energy. If the atoms behaves as ions 
>in your cluster this will be automatically found by the code.
>A way (one of the many arbitrary ways) to measure this atomic charge is 
>to project the wfc on atomic orbitals and counts how many electrons are 
>projected on each atom... this is done by projwfc.x in the PP directory.
>If you want to force the system to do something else w.r.t. what it 
>would do automatically you need to add some constraint. For instance in 
>a non collinear magnetic calculation one can constraint the size of the 
>atomic magnetization, its direction or one of its commponents. In the 
>cvs version magnetization size can be constrained also in the collinear 
>case.
>Currently there is no constraint on the atomic charge but using the 
>constrained_magnetization part as template should not be too difficult 
>implement such a feature.
>
>Hope this helps,
>
>Don't forget to sign your posts including your affilation.
>
>Stefano de Gironcoli, SISSA and DEMOCRITOS
>
>Rudra Banerjee wrote:
>  
>
>>dear PWSCF users,
>>I am new to pwscf and stuck in a question...is there any way to 
>>put anion   or cationas a unit?the total cluster is charge less 
>>but have two different types of ion...can anyone tell me what to 
>>do in this situation?
>>Regards
>> 
>>-- 
>>Rudra
>>Have a Nice Time
>>http://www.bose.res.in/~rudra 
>>Please, if possible, don't send me MS Word or PowerPoint attachments
>>Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>>
>>
>>Forgot the famous last words? Access your message archive online. 
>>Click here. 
>>
>> 
>>
>>
>>
>>___
>>Pw_forum mailing list
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>>  
>>
>>
>
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>http://www.democritos.it/mailman/listinfo/pw_forum
>  
>

[Pw_forum] ion problem

[Rudra Banerjee]

dear PWSCF users,
I am new to pwscf and stuck in a question..is there any way to put anion   
or cationas a unit?the total cluster is charge less but have two different 
types of ion...can anyone tell me what to do in this situation? 
Regards
 
-- 
Rudra
Have a Nice Time
http://www.bose.res.in/~rudra
Please, if possible, don't  send me MS Word or PowerPoint attachments
Why?See:  http://www.gnu.org/philosophy/no-word-attachments.html






  Forgot the famous last words? Access your message archive online at 
http://in.messenger.yahoo.com/webmessengerpromo.php
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[Pw_forum] ion problem

[Stefano de Gironcoli]

Unless you put some constraint the code will distribute the charge 
density so as to minimize the total energy. If the atoms behaves as ions 
in your cluster this will be automatically found by the code.
A way (one of the many arbitrary ways) to measure this atomic charge is 
to project the wfc on atomic orbitals and counts how many electrons are 
projected on each atom... this is done by projwfc.x in the PP directory.
If you want to force the system to do something else w.r.t. what it 
would do automatically you need to add some constraint. For instance in 
a non collinear magnetic calculation one can constraint the size of the 
atomic magnetization, its direction or one of its commponents. In the 
cvs version magnetization size can be constrained also in the collinear 
case.
Currently there is no constraint on the atomic charge but using the 
constrained_magnetization part as template should not be too difficult 
implement such a feature.

Hope this helps,

Don't forget to sign your posts including your affilation.

Stefano de Gironcoli, SISSA and DEMOCRITOS

Rudra Banerjee wrote:
> dear PWSCF users,
> I am new to pwscf and stuck in a question...is there any way to 
> put anion   or cationas a unit?the total cluster is charge less 
> but have two different types of ion...can anyone tell me what to 
> do in this situation?
> Regards
>  
> -- 
> Rudra
> Have a Nice Time
> http://www.bose.res.in/~rudra 
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>
> 
> Forgot the famous last words? Access your message archive online. 
> Click here. 
> 
>  
>
> 
>
> ___
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>