Re: [Wien] Whether structure optimization can achieve global minimization?

[Víctor Luaña Cabal]

* 丁一凡  [2018-09-08 16:35:01 +0800]:
> I browsed almost all of the mailing lists, but I didn't find this topic, I 
> would like to inquire about the structure of the optimization of the global 
> minimum. 
> 
> 
> It is difficult to find the global minimum in the high dimensional potential 
> energy surface. It requires us to traverse the potential energy surface, 
> eliminate many local minimums, and finally find the global minimum. Some 
> algorithms for searching for global minimization include genetic evolution 
> algorithm, random searching, simulated annealing and so on.
> 
> 
>  My question is whether Wien2k can achieve global minimization, and if so, 
> how do I need to do that? Any comment(s) would be highly appreciated.

Few codes, either in solid state calculations or in molecular structure,
try to find the global minimum. That is a quite special task and it has
its own community. If you describe your intentions with some detail
there is easier to address you in the right direction: ¿do you want to
get a contact in the field? ¿Find a code? ¿Learn on the subject?

Remember that the optimal geometry depends heavily on the thermodynamic
conditions. Finding phase transitions is a highly relevant topic on the
wien2k community.

Cheers,
Víctor Luaña
--
.  . What you wish upon others, you should wish upon yourself  
   / `' \(Golden rule of ethics)
  /(o)(o)\   
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
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|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
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! Universidad de Oviedo, 33006-Oviedo, Spain ! "Never let your sense of morals
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Re: [Wien] Problem with XCrySDen for Electron Desity plot (Wien2k_18)

[Víctor Luaña Cabal]

* Dr. K. Balamurugan  [2018-07-18 15:27:07 +0530]:
> Dear Wien2k Developers and Users,
> 
> I could get Electron Density (ED) maps using w2web; but, while I tried to do
> the same using XCrySDen, I got the following issue allowing me not get a ED
> map.
> 

Dr, Balamurugan,

Please, check critic2 in github. The code is open source and free, and
it can perform all kind of QTAIM tasks incuding, of course, Bader
analysis of the ED, and using wien2k and *many other* ED formats,

Best regards,
 Víctor Luaña
--
.  . One should not treat others in ways that one would not like
   / `' \to be treated
  /(o)(o)\   (Golden rule of ethics)
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! "Never let your sense of morals
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! phone: +34-984080927fax: +34-985103125 ! right." 
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Re: [Wien] Reg: How to change the Oxidation state of an element in a compound

[Víctor Luaña Cabal]

* pachineela rambabu  [2018-07-17 09:35:49 +0530]:
> Dear Users,
> I am working on CaCdGe compound. I want to do the
> calculation with Ca in 2+ and 3+ oxidation states. How to get 3+ from
> Wien2k.

Rambabu,

Solid state is made of neutral molecules. In gas phase you can think of a
+3 charged molecule. In a solid that's not realistic. You must design or
determine a crystalline structure in which the oxidation state of the atom
you want to study appears. Even your language "How to get 3+ from Wien2k"
makes the spine tremble. Have you received any kind of instruction on
solid state?

May I recommend you a nice book on the subject?

Richard M. Martin, "Electronic structure", basic theory and practical
methods, (Cambridge University Press, 2004)


Good luck,
Víctor Luaña
--
.  . One should not treat others in ways that one would not like
   / `' \to be treated
  /(o)(o)\   (Golden rule of ethics)
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! "Never let your sense of morals
! e-mail:! prevent you from doing what is
! phone: +34-984080927fax: +34-985103125 ! right." 
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 GroupPage: 
 Articles:  
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Re: [Wien] scan xc functional

[Víctor Luaña Cabal]

* sandeep arora  [2018-06-29 09:29:52 +]:
> 
> Dear Prof Victor
> My problem is to calculate the band gap at optimized lattice 
> constant using SCAN functional.
>  >  May I suggest you to elaborate a 2D grid or even a multidimensional 
> grid...
> I'll try first to perform geometry optimization for different rmt's,ifft 
> factors in addition to different rkmax and k-points.(correct me if i was 
> wrong in interpreting your suggestion).

Sandeep,

Of course, you decide how to do your project. Determining which parameters
influence most your final objective is my zero-th step in a project.

Best luck,
  Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
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 Articles:  
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Re: [Wien] scan xc functional

[Víctor Luaña Cabal]

* sandeep arora  [2018-06-29 06:44:48 +]:
> Dear wien2k users
> I want to use scan exchange correlation for optimization of binary 
> semiconductors(GaP).But the lattice constant varies with Rkmax at third 
> decimal place even on increasing rkmax up to 11 and increasing ifft 
> enhancement factor up to 4 in case.in0.although the E-V graph is smooth. 
> Please suggest some solution to converge the lattice constant with rkmax.
>  the results obtained are
> RK
> 8.0   5.4663
> 8.5   5.4651
> 9.5   5.4642
> 10.0  5.4633

Sandeep,

When you have a problem in which several factors are relevant I prefer
exp0loring the several variables that are relevant, You are interested
in the band gap and your exploration so far shows that geometry is most
relevant.

May I suggest you to elaborate a 2D grid or even a multidimensional grid
if that is required and examine your main property in the nodes of the
grid? For instance the distance variable provides a relevant range from
4.5 to 6.0, the RK grid range from 7 to 10, maybe, and so on.

That would be my way of exploring your problem, if I was able to explain
my idea.

Thanks,
   Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
 GroupPage: 
 Articles:  
 git-hub:   
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Re: [Wien] Transition-State/NEB Calculations

[Víctor Luaña Cabal]

* Laurence Marks  [2018-06-15 08:19:30 -0500]:
> Dear Victor,
> 
> Thanks for the email. The very specific question I am asking is whether it
> is "well known" with Vasp, Ab-init, Gaussian etc that one needs "good"
> parameters such as k-mesh etc for the transition state. I am hoping that
> there are people who have done NEB (for instance) calculations on this
> mailing list.

Laurence,

Let me go back to the subject. The method finally working in molecular
codes is best thna NEB and it is based in the idea that coming to a TS
the surface profile of a minimum changes into a transition state ;-)
That means that, if you are looking for a first-order transition state
(the one involved in most reactions), one of the eigenvalues of the
hessian matrix changes sign.

The solution prefered in most molecular codes consist in modifying
artificially the sign of the incumbent eigenvalue and converting the
problem into a false minimum exploration.

You can find an old code implementing this idea in navigator
, an in-house
code never published. The idea of navigator, optim and derive is making
available the algorithms and being able to use data comming from every
kind of electronic code you may have at hand.

Let me invite you to examine
 in our web page
, Maybe you find it useful.

On a different subject I was thinking into organizing a CECAM
worshop/school on "computer tools for computational scientists" and my
idea was showing the students how computational science is created.
Might this issue interest you? We don't need bothering the wien2k
list and you have my email at the signature.

Cheers,
   Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
 GroupPage: 
 Articles:  
 git-hub:   
 ORCID: -0003-4585-4627; RID: H-2045-2015
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Re: [Wien] Transition-State/NEB Calculations

[Víctor Luaña Cabal]

* Laurence Marks  [2018-06-15 07:49:51 -0500]:
> Dear All,
> 
> I am part way through developing new code for transition-state (TS)
> calculations. I observed one thing which may be "well-known" with other
> codes; since currently WIen2k cannot do such calculations I have no
> experience. The observation is that at/near the TS one needs a fairly good
> k-mesh, just using gamma fails. (This may be a Wien2k phenomenon.) Has
> anyone heard of this?

Prof. Marks,

I have no experience in solid state calculations but, regarding
molecules, it is kind of normal that TS become problematic to find.
In a minimum all gradient paths arrive to the critical point you are
looking for. In a TS you have gradient paths coming to but also a
gradient line escaping from the critical point.

Under "morse theory gradient flow" you will find scores of material.

Good luck developing the TS code! It will be a much appreciated addition
to wien2k, imho.

Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
 GroupPage: 
 Articles:  
 git-hub:   
 ORCID: -0003-4585-4627; RID: H-2045-2015
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Re: [Wien] ELF calculation

[Víctor Luaña Cabal]

* Bon, Marta  [2018-06-11 10:09:37 +]:
> If I have understood correctly, critic2 uses tau.clmsum (obviously, kinetic 
> energy density).
> 
> Is there anyone that can tell me how to print this quantity out? (Wien2K v. 
> 13.1 PBE+U calculation).
> 
> This is the section in the Critic2 manual for the ELF calculation:
> 
> load rho.clmsum
> load tau.clmsum
> load as "0.348282306469781*$1^(-5/3)" n1 n2 n3
> load as "0.125 * $g1^2 / $1" n1 n2 n3
> load as "$1^(5/3) * ($2 - $4)" n1 n2 n3
> load as "1/(1+$5^2)" n1 n2 n3
> cube grid field 6 file elf.cube
> 
> where n1, n2 and n3 are the number of points in the new grid. 
> 
Marta,

The load orders in critic2 are exactly that: load the files written by
ither codes. In this case wien2k is the creator of data and critic2 uses
the data. In our jargon (QTAIM speak) rho is the electron density, but I
don't recognize right now what is tau for. Maybe are you trying to use
\eta (the ELF common designation)?

With the "load as" orders you are manipilating algrebraically the
properties. The $1 designates the data first read in (rho in your case)
and (n1,n2,n3) defines the new grid you want to create with your data.

Alberto Otero-de-la-Roza is the genial programmer of the new capacities
of critic2. He may add to my answer.

Good luck using critic,
  Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
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 Articles:  
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Re: [Wien] ELF calculation

[Víctor Luaña Cabal]

* t...@theochem.tuwien.ac.at  [2018-06-06 14:11:22 
+0200]:
> It seems that ELF was not yet implemented in WIEN2k 13.1.
> As suggested by Victor, critic2 is probably a better choice.
> In addition, the plotting of the ELF function (calculated in
> lapw0) shows really huge discontinuities at the atomic spheres
> boundaries.

Prof Tran is absolutelly right,

What happens at the boundaries of the atomic spheres has always been
a big issue for QTAIM studies with the wien code. The critic program
has needed including techniques to deal with the problem as better as
possible. Finnally, a technique by Yu and Trinkle was a big improvement
in critic2.  The details are in the critic1 and critic2 documentation,
plenty of examples and references.

On a topic related to chemical bonding remember we will
have a meeting in Oviedo 
and sending abstracts to Sagamore-2018 ends this friday:
.

Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
 GroupPage: 
 Articles:  
 git-hub:   
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Re: [Wien] ELF calculation

[Víctor Luaña Cabal]

* Bon, Marta  [2018-06-06 09:12:47 +]:
> Dear Wien2k users and developers,
> 
> I would like to calculate the electron localization function (ELF), after 
> having performed a PBE+U calculation with Wien2k.
> Is it possible (with lapw0)?
> If yes, can someone show me the case.in0 file for that?
> 

Marta,

Check the critic2 code. It can read wien2k data and performing QTAIM
related analysis of the electron density, the elf function and more.
The code is freely available. My signature provides you related
information. Current critc2 maintainer is Alberto Otero-le-la-Roza.

Cheers,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+ A person is slave of his words
! Dr.Víctor Luaña, in silico chemist & prof. ! and owner of his silences.
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! The collective intelligence of
! e-mail:! a comitee equals the CI of its
! phone: +34-984080927fax: +34-985103125 ! worst divided by the number
++ of members
 GroupPage: 
 Articles:  
 git-hub:   
 ORCID: -0003-4585-4627; RID: H-2045-2015
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Re: [Wien] Volume optimization to monoclinic structure

[Víctor Luaña Cabal]

On Tue, May 08, 2018 at 06:22:25AM -0600, Gavin Abo wrote:
> Currently, I believe parabolfit_lapw is the best way available at this  
> time.  I'm not currently aware of any better fitting methods. If you  
> find a better way, feel free to share.

I don't even know parabolfit_lapw, but I ever try the simplest tool
available, and the non linear fitting tool of gnuplot works for almost
anything. You create first a data file

# comment
# data description
# var1   var2   var3  function
#   a  b  c   E
  1.234  1.342  1.785  -764.456
.

then create in gnuplot the mathematical description of the f(v1,v2,v3)
and then, ggain in gnuplot
E(V,k1,k2,k3) = ..

fit f(x,y,z) 'datafile' using ($1*$2*$3):4 via  k1,k2,k3

whithin gnuplot a 'help fit' will provide you a detailed description
and examples.

It will not be the best method but an all-purpose tool.

Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. ! A person is slave of his words
! Departamento de Química Física y Analítica ! and owner of his silences.
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    ! What has been seen cannot
! phone: +34-984080927fax: +34-985103125 ! be unseen, ¿are you sure?
++
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Re: [Wien] SO in 3d and 4f elements

[Víctor Luaña Cabal]

On Tue, Mar 13, 2018 at 07:19:36AM +0100, Xavier Rocquefelte wrote:
> Dear Pablo
>
> It really depends on the property you are considering:
>
> 1. In terms of chemical bond, the effect of SO on 3d and 4f elements  
> will be negligeable.

In terms of chemical bond electrostatic interactions are the only terms
essential. There is a magnetochemistry, but it deals with properties
far more sophisticated to those that determine chemical bond.

> 2. In terms of spectroscopy it can be significant if you have access to  
> d3/2 and d5/2 states, but also p1/2 and p3/2 ... and similar for f states
>
> 3. In terms of magnetic properties, it will be negligeable for the  
> magnetic exchange couplings but not for the anisotropy and thus the easy  
> magnetization direction.
>
>
> Thus it really depends on the calculation you plan to do and the  
> property you are looking for.

This is *always* the most important element to consider. *Always*.
Xavier words are extremely important in this respect.

Best Regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sun, Feb 25, 2018 at 08:17:55AM +0100, William Lafargue-dit-Hauret wrote:
> Dear Victor,
> If you remove the space between « print » and the first parenthesis, you can 
> do it in python 3 ; this is the print function.

Before we enter in an interminable war of languages my

print (( 2.8*2)*2+(-0.31749*2)+( -0.98948))

can be used in "ANY" scripting language. In this case I had a window
in gnuplot close to my window for email. It could be bash, erl, python, ...

Best regards from coldy (today) northern Spain,
   Víctor Luaña
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sun, Feb 25, 2018 at 06:06:39AM +, Badis Bennecer wrote:
> Dear Victor,
> 
> 
> It is minus signs

Badis,

Sorry, but my main question was the language (computer language).
Otherwise

print (( 2.8*2)*2+(-0.31749*2)+( -0.98948))

the result is 6.82026

Maybe you were using some form of lisp? The odd number of parenthesis:
open 5, close 4, were my main trouble. I had to add an extra ")".  Of
course,  minus signs obtained from web pages may cause awful errors so
it is important to prevent that.

Best regards,
  Víctor Luaña
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sat, Feb 24, 2018 at 11:46:06PM +, Badis Bennecer wrote:
> Hi
> 
> It looks like the total magnetic moment in the cell, with Z=2 (unit cell 
> defined in your case.structure)
> 
> (( 2.8*2)*2+(-0.31749*2)+( -0.98948)= 8,4472-0,63498--0.98948=6,82274 
> (unity)

Dear Badis,

Sorry, but I don't even recognize the computer languaje in which your
answer is written.

Can you clarify that point for me?
Is the "--" a misprint? Same thing for the odd number of parenthesis?

Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-984080927fax: +34-985103125 !
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Re: [Wien] bash script to run initso_lapw for different M-axis

[Víctor Luaña Cabal]

On Tue, Sep 19, 2017 at 07:57:36AM +0800, venkatesh chandragiri wrote:
> Dear Prof. Gavin,
> 
> Thank you again for the script to create the input for initso_lapw  and it
> works fine now. However, the initso_lapw is asking to edit the following
> files.
> 
> 1. case.inso
> 
> 2. case.in1
> 
> 3. case.outsymso
> 
> 4. case.klist
> 
> Hence, kindly let me know (paste the script lines) to avoid the editing of
> those above files and continue the initso_lapw in background itself.

If you are going to iniciate running a program or script ending thw task with & 
sends it to the background and you have another task at hand to continue 
editing, for instance. So

$ script -options file &

or

run_code -options input_file output_file &

or

run_code -options < input_file > output_file &

will send the run_code to the background.

If the script or program is already running you can use crtl-Z to
interrupt it and gain a new  shell (cshell or bash shell, for instance)
Using bg will send the interrumped process to background and fg to
the fore ground.  > > thank you and looking forward to your reply.
> > with best regards, > > venkatesh


Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from doing
   / `' \ what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ 
|  \'`'`/  | 
|  |'`'`|  | 
 \/`'`'`'\/
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] How to know if the M+2 has a high spin from calculation?

[Víctor Luaña Cabal]

On Sat, Aug 26, 2017 at 12:20:19PM +0100, Abderrahmane Reggad wrote:
> Dear wien2k users
> 
> We know that the ion Fe+2 has a high spin configuration (3d6 (teg(4) eg(2))
> because the crystal field effect..
> 
> How to check that from calculation ?

Abderrahmane,

There are several questions implicit here.

1) By asking for a crystal field interpretation you are demanding the
   orbital population of a Fe(+2)L6 octahedral or tetrahedral cluster,
   because t2g and eg are the names of the O_h and T_h irreps (irreducible
   representations). You know tyhe population by examining the orbital
   energies of the irreps: the irreps with smaller energies are populated
   first. Given an open shell population symmetry lets you predict the
   total spin of the cluster, so you can check whether this agrees or
   not with the electronic state of your impurity.

2) By using a band structure code F(+2) levels contribute to a local band,
   that are labeled in the output with the indication of the irrep of
   the impurity contributing most.

Hope this helps you. Best reards,
 Víctor Luaña
--
.  ."Half of the US people use twitter to form its opinion and half
   / `' \   also elect the US president. I only hope they are not the same
  /(o)(o)\  half". --From a sentence by Gore Vidal
 /`. \/ .'\
/   '`'`   \ "[Technocrats, academics and journalists} are often motivated
|  \'`'`/  | by hope while the public at large tends to be more focused
|  |'`'`|  | on fear." -- Russell Mead (The Washington Post, 2017)
 \/`'`'`'\/
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] How to simulate the ionic state of a compound?

[Víctor Luaña Cabal]

On Thu, Aug 24, 2017 at 12:43:45AM +0100, Abderrahmane Reggad wrote:
> The reason for my question is that I don't how does a DFT code work and I
> want to know if the ionic state is a result or an assumption.

Abderrahmane,

In a wien2k calculation you provide the number of electrons assigned
to the core and to the valence regions of each chemical species in your
system.  However that is defining a population in orbital space. If the
calculations proceeds appropiatelryi (convergence of results, convergence
o basis set [k space], etc). The final distribution of the electrons
should not be determined by your assumptions, so obtaining an ionic,
covalent, metallic, magnetic, etc result should be a consecuence and
not an assumption. However, you must examine the correctness of the
calculation performing the analysis that is described in wien2k user
guide (muffin tin radius, k vectors, ...)

The analysis of the wien2k wavefunction and density can produce the
approximate picture of a very ionic system (NaCl and MgO, for instance),
a mostly covalent crystal (diamond and graphite, for instance), a
metallic one (alkali metals), and so on.


You can check all those examples in (sorry to describe my own
publications, but those are things that I know quite well ;-) )

* Ions in crystals: The topology of the electron density in ionic
  materials. II. The cubic alkali halide perovskites
  V Luaña, A Costales, AM Pendás
  Physical Review B 55 (7), 4285

* A classification of covalent, ionic, and metallic solids based on
  the electron density
  P Mori-Sánchez, AM Pendás, V Luaña
  Journal of the American Chemical Society 124 (49), 14721-14723

* Non-nuclear maxima of the electron density on alkaline metals
  V Luaña, P Mori-Sánchez, A Costales, MA Blanco, AM Pendás
  The Journal of chemical physics 119 (12), 6341-6350

* Topological characterization of the electron density laplacian in
  crystals. The case of the group IV elements
  A Otero-de-la-Roza, V Luaña
  Journal of Chemical Theory and Computation 6 (12), 3761-3779

* Ions in Crystals: The Topology of the Electron Density in Ionic
  Materials. 4. The Danburite (CaB2Si2O8) Case and the Occurrence of
  Oxide− Oxide Bond Paths in Crystals
  V Luana, A Costales, P Mori-Sanchez, AM Pendás
  The Journal of Physical Chemistry B 107 (21), 4912-4921


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Re: [Wien] How to simulate the ionic state of a compound?

[Víctor Luaña Cabal]

On Tue, Aug 22, 2017 at 11:41:53PM +0200, pieper wrote:
> my response to Abderrahmane Reggad appears perhaps a little harsh. It  
> was not meant that way. I wanted to emphasize that in my view the idea  
> of telling Wien2k (or any other DFT program) its result (where the  
> electrons are) and to simulate properties from there is completely  
> backwards.

Martin,

It was not harsh at all in my perception, but I canot say what
Abderrahmane thought about your words.

I perceived as a normal exchange of ideas in a subject that I love.

I agree that using a questionable populaton technique to obtain a number
of electrons associated to an ion from a expensive DFT calculation
is not neccesarily a good idea. Providing a number to say this is a
Ni(+1.98) O(-2.02) crystal should not be the main result from a good
article. However, a good physically based theory of chemical bonding in
molecules, solids and clusters provides far more that that.

Let me be very particular in describing QTAIM (quantum theory of atoms
in molecules, aka Richard F. W. Bader et al work) as a beautiful and
well founded physical teory on chemical bonding.

Bader's QTAIM can be used to partition every property into contributions
of a particular atom or functional group.

Then you can find an explanation why many perovskite oxides, for
instance, have a very similar bulk modulus, and the explanation comes
from the fact that the oxide is the major contribution, and that
contribution is common to the incumbent crystals.

> This is, however, what I wanted to point out: DFT (or Wien2k) tells you  
> where the electrons are. Thats its central result. It does not make any  
> sense (to me) to use a DFT program to - as A. Reggad put it - "simulate  
> the NiO compound in its ionic state". If NiO would be a ionic compound  
> then DFT would (hopefully, when set up properly) calculate an electron  
> density with a lot of weight at O and a lot less at Ni as a RESULT. The  
> simulation of any property one wishes to study can proceed from there.

I agree, of course. That should be the spirit of an ab initio calculation.
However, DFT sometimes separates from the ab initio family when the xc
functional is chosen not because of its properties or for exploring the
sensibility of the predictions to the functional but because a spurious
predictive agreement to whatever 'experiment'.

I believe finding explanations to peculiar facts is the real motive
of computational research, at least until the point is achieved at
which theoretical calculations become competitive with experimental
measurements in terms of precision, exactitude and cost.

> And if the electron density of NiO does not really resemble the ionic  
> picture, why use the ionic model to simulate things?

Yes, but having a predictive measurement of the ionicity lets you
examine how ionicity depends on thermodynamic conditions: is the effect
of pressure more important than the effect of temperature or pH ... on
a geological scale?

*Chemical bonding* can be at the core of geophysics, research on
materials, ... and many more fields. However, I'm a peculiar chemist and
I love Physical Review since I was working on my phd thesis, long ago.

Best regards from sunny north Spain,
Víctor
--
.  ."Half of the US people use twitter to form its opinion and half
   / `' \   also elect the US president. I only hope they are not the same
  /(o)(o)\  half". --From a sentence by Gore Vidal
 /`. \/ .'\
/   '`'`   \ "[Technocrats, academics and journalists] are often motivated
|  \'`'`/  | by hope while the public at large tends to be more focused
|  |'`'`|  | on fear." -- Russell Mead (The Washington Post, 2017)
 \/`'`'`'\/
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] Gap calculated with GGA+U, mBJ and HF

[Víctor Luaña Cabal]

On Mon, Aug 07, 2017 at 11:02:19AM +0200, Wien2k User wrote:
> But for my problem is what I have to say that the material is semimetalic
> since this result is obtained with GW, GGA+U and mBJ?.
> Or I have to present all the results even those obtained by HF and I would
> say that the calculations gave different results pending confirmation of
> the experiment?
> 

You adopt the position that theory is only justified if it is in
agreement with an experiment. There are many people adopting that point
of view, but it is *not* the only one. An excellent article can examine
deeply which are the factors that control the property you are interested
in, for instance. Or explaining why those factors are important. A
tinkertoy model can be the main contribution to an extraordinary Physical
Review Letters.

Remember that theory contributes to knowledge, and only when theory is
so well polished that it can compete in agreement and precision with
experimental measurements it can contribute to databases of properties.

Being realistic,  a careful examination of the articles published
lately (a few years) in the journal you want to send your research is
the best step in determining the orientation of your contribution.
Many contributions tend to use "results pending confirmation" and the
referee answer may be 'let us wait to the experiments' ... ;-)

Best regards,
 Víctor Luaña

--
.  ."Half of the US people use twitter to form its opinion and half
   / `' \   also elect the US president. I only hope they are not the same
  /(o)(o)\  half". --From a sentence by Gore Vidal
 /`. \/ .'\ 
/   '`'`   \
|  \'`'`/  |
|  |'`'`|  |
 \/`'`'`'\/ 
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
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Re: [Wien] Gap calculated with GGA+U, mBJ and HF

[Víctor Luaña Cabal]

On Mon, Aug 07, 2017 at 01:32:04AM +0200, Wien2k User wrote:
> I calculated the gap of a material whose experimental value is unknown.
> 
> With GGA+U, mBJ potential and GW, I found that this material is semimetal
> (a slight band overlap) but with HF i found it to be semiconductor of very
> small gap.
> 
> How can I know what is the real nature of the gap of this material?
> 
> This calculation is a part of a future paper so I have to put all found
>  results (GGA + U, mBJ, GW and HF) in spite of what give deferent nature or
> I have to adopt that of the HF since it is a more accurate method?

This is a very good question related to the nature and philosophy of
theoretical calculations.

Assuming that the role of a theoretical calculation is predicting or
duplicating the experimental results is a dead way when the theory is yet
imprecise or incompletely developed.

In fact, as theory matures it becomes a part of engineering and it
can be accepted that doing a calculation can sustitute performing an
experiment. When designing a building or a bridge. Nobody would accept
that a good resistence analysis is missed, but that means that materials
resistence is well known in advance.

Until theory reaches that point of development, the role of a good
calculation is determining how dependent are the obtained properties
to the inner parameters of the calculation. So, in your example,
I would give more value to exploring the effects and meaning of the
different methods.

Also the examination of families of compounds in looking for the most
promising candidates can be of great help, even in early stages of
a research.

Hope this helps,
Víctor Luaña
--
.  ."Half of the US people use twitter to form its opinion and half
   / `' \   also elect the US president. I only hope they are not the same
  /(o)(o)\  half". --From a sentence by Gore Vidal
 /`. \/ .'\ 
/   '`'`   \
|  \'`'`/  |
|  |'`'`|  |
 \/`'`'`'\/ 
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] change of lattice parameters while alloying

[Víctor Luaña Cabal]

On Tue, May 09, 2017 at 10:15:22PM +0530, Dr. K. C. Bhamu wrote:
> Thank you Prof. Peter for detailed reply,
> May be I still have some doubts on symmetries and need to read some
> literature.
> For meanwhile, from literature I came to know that the distortion in my
> doped structure "change in unit cell ("lattice parameters and angles")"
>  may occur depending on size effects, deviations from the ideal composition
> and the JTE etc.
> 
> So what I am doing is good and there is no way to preserve the same SG/unit
> cell.
> 
> I  tried to maintain the original structure and got below warnings which
> support my above understanding:
> 

Dr. Bhamu,

It is a cultural division, but crystalographers have a better
perspective, in my opinion, than solid state physicists on the
description of solids. Traditionally solid state teory has been very
much related to the treatement of simple structures and only recently
complex crystals have been affordable to quantum treatment.

You have an excellent test: "Fundamentals of crystallography" by C.
Giacovazzo et al.
"Chapter 1: symmetry of crystals" is a must reading if you want to master
the subject.

wien2k interface started from the perspective of treating simple solids,
but a crystallographicaly adapted code could be able to deal with
something like

crystal
   spacegroup  F m -3 m
   cell  a
   atom Cr 0 0 0
   atom B  0.5 0.5 0.5
   optimize a
end

So you should take account of: (a) the space group; (b) the celll parameters
compatible with the space group; (c) the Wyckoff positions occupied in
your structure. The Bilbao crystallographic server has a lot of tools:



In this case the WYCKPOS tool provides the starting information.

Alberto Otero-de-la-Roza developed some time ago a runwien interface for
wien2k that was able to do a restricted version of this approach. It was
part of his PhD thesis, in fact. One in 8 or 9 chapters. That interface
was published as

@article{OterodelaRoza2009RunwienAT,
  title={Runwien: a text-based interface for the WIEN package},
  author={A. Otero-de-la-Roza and V{\'i}ctor Lua{\~n}a},
  journal={Computer Physics Communications},
  year={2009},
  volume={180},
  pages={800-812}
}

The source can be found in



but some adaptation *may* be needed for the current wien2k.

Best regards,
  Dr. Víctor Luaña
--
.  ."De la cuna a la tumba es una escuela, por eso lo que llamas 
   / `' \   problemas son lecciones."
  /(o)(o)\  -- Facundo Cabral, Cuna
 /`. \/ .'\ 
/   '`'`   \
|  \'`'`/  | 
|  |'`'`|  | 
 \/`'`'`'\/  
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] SPACE GROUP DOES NOT CONTAIN INVERSION

[Víctor Luaña Cabal]

On Sat, Dec 31, 2016 at 08:36:56PM +0530, Dr. K. C. Bhamu wrote:
> Thank you Dr. Delamora
> 
> The parent compound is AB2 type with space group 194.
> 

Bhamu,

Using just that information and the Bilbao crystallographic server
(http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list)

Wyckoff Positions of Group 194 (P63/mmc):
There are positions of multiplicity 2, 4, 6, 12, and 24.

The 2/4, 6/12, and 12/24 are coherent with your specifications, and
there are several ways to select each.

Best regards and have joy and success in 2017,
  Víctor Luaña
--
.  ."De la cuna a la tumba es una escuela, por eso lo que llamas
   / `' \problemas son lecciones."
  /(o)(o)\   (From the cradle to the grave life is a school so, what you
 /`. \/ .'\  call trouble are lessons)
/   '`'`   \ -- Facundo Cabral, Cuna
|  \'`'`/  | "When are we ready to learn something? Motivation is the
|  |'`'`|  | is the most important step in education."
 \/`'`'`'\/  -- adapted from Adam Steltzner, 2016 (ElPaís)
==(((==)))===0===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] volume optimization

[Víctor Luaña Cabal]

On Tue, Dec 13, 2016 at 05:00:01PM +0530, Rajneesh Chaurasiya wrote:
> I have optimised the cubic structure by calculating the total energy with
> varying the lattice parameter size (%). In the optimised file, data has
> been plotted between the total energy and volume of cell. i found that the
> optimized lattice parameter is 8.19 angstrom and corresponding volume of
> cell is 928.34 (a.u3). now if i change the lattice parameter from angstrom
> to atomic unit and calculate the volume then i found 3702 (a.u3) approx. so
> i could not find how the conversion taken place. So can any one suggest
> what types of conversion are happened in the background.

Rajneesh,

1) 3702/928.34 approx 4 (3.9878)
2) The 4 factor agrees with a F structure. The rest is basic crystallography.
3) A cubic structures is not enough information. What cubic? A Pm-3m? A Im-3m?
   A Fm-3m? The three are correct cubic structures (different, of course).

Best,
 Dr. Víctor Luaña
--
.  ."De la cuna a la tumba es una escuela, por eso lo que llamas
   / `' \problemas son lecciones."
  /(o)(o)\   (From the cradle to the grave life is a school, ...)
 /`. \/ .'\  -- Facundo Cabral, Cuna
/   '`'`   \ 
|  \'`'`/  | "When are we ready to learn something? Motivation is the
|  |'`'`|  | Motivation is the most important step in education."
 \/`'`'`'\/  -- adapted from Adam Steltzner, 2016 (ElPaís)
==(((==)))==+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] [not solved] regarding permission of Wien2k commands

[Víctor Luaña Cabal]

On Thu, Nov 17, 2016 at 11:05:21PM +0530, Dr. K. C. Bhamu wrote:
> Thank you Dr. Víctor for suggestion.
> But, it could not helped me.
> I ran the chmod -R ugo+r,a+X *   command in the Wien2k dir and the problem
> is still same:
> 
>  -rwxrwxr-x for all files.

Do you mean that every file has those permissions? Including executabables,
inputs and uoutputs?

In that case you have to use the chmod ro remove permissions or set
exactly then to the ones you decide.

The permissions at the time of creation of a new file are decided by
the umask setting. For instance, if you are using bash your ~/.bashrc
shoud containg something like

umask 027

that will give you (the owner) rw permission and the x will be provided
after compilling and loading, or you can assing it with a chmod un the
case you are creating a text script (bash, pytho, awk, ...) and decide
to convert the script into a executable.

The umask gives also everybody in your group r permissions, and others
no permission whatever.

Try reading a good user guide on the shell you prefer. It pays the time
you dedicate at the beginning.

Best regards,
 V.
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Re: [Wien] regarding permission of Wien2k commands

[Víctor Luaña Cabal]

On Thu, Nov 17, 2016 at 01:03:48PM +0530, Dr. K. C. Bhamu wrote:
> Dear Users,
> 
> While playing with unix commands on my machine, I lost permission of all
> Wien2k commands. Because of this I am not able to run any Wien2k commands.
> 
> I am getting the following permissions for all commands:
> 
> -rwxrwxr-x" .
> 
> How to get rid off this problem?

1) Go to the directory where the wien2k codes are installed

2) If you are the owner of the files:

chmod -R ugo+r,a+X *
  
This gives reading permission to the owner (you) and sticky execution
permissions to anybody. Your "-rwxrwxr-x" refects that this is tour desire,
The -R option works recursibely on the directory you are in.

3) You can modify the owner:group propietary of the files with chown.
   Current linux installments tend to create ${USER} and ${GROUP} equivalent,
   but this is not the best decission if you have coworkers and students
   that could share your codes and scripts.
   You will need root permisions (or be a sudoer) to change owner:group
   of files.

Good luck,
  Víctor

--
 .  ."When are we ready to learn something? Motivation is the
/ `' \   most important step in education."
   /(o)(o)\  -- adapted from Adam Steltzner, 2016 (ElPaís)
  /`. \/ .'\ 
 /   '`'`   \ 
 |  \'`'`/  | "You educate a man, you educate a person. You
 |  |'`'`|  |  educate a woman, you educate a family."
  \/`'`'`'\/  -- Bárbara Valencia, 2016 (NYTimes)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
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Re: [Wien] 2D optimization

[Víctor Luaña Cabal]

On Wed, Nov 16, 2016 at 03:45:42PM +0100, boudiaf khadidja wrote:
> Dear wien2k user;
> whene i run the 2Doptimize.job
> i have this proplem:
> rm : No match.

This corresponds to a shell script
You need to identify what kind of script is used in the 2Doptimize:
¿bash? ¿cshell? ¿python?

> Too many ('s.
> what does it means?

An error in the script. This a bash code to check if the parentheses
of an expression do balance:

while [[ $string = *'()'* ]] ; do
string=${string//()/}
done

if [[ $string ]] ; then
echo Invalid
else
echo Valid
fi

Good luck!
  Víctor
--
 .  ."When are we ready to learn something? Motivation is the
/ `' \   most important step in education."
   /(o)(o)\  -- adapted from Adam Steltzner, 2016 (ElPaís)
  /`. \/ .'\ 
 /   '`'`   \ 
 |  \'`'`/  | "You educate a man, you educate a person. You
 |  |'`'`|  |  educate a woman, you educate a family."
  \/`'`'`'\/  -- Bárbara Valencia, 2016 (NYTimes)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
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! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] potential

[Víctor Luaña Cabal]

On Thu, Sep 01, 2016 at 11:15:32PM -0700, Yundi Quan wrote:
> What's the sign convention used in the output files of critic2? I notice
> that there are positive and negative values in both vcoul.cube and
> rho.cube. Maybe it is OK to have both positive and negative vcoul.cube. But
> what does it mean to have both positive and negative date in rho.cube? Or
> is it just numerical inaccuracy?

It should be, as rho >= 0. I should not worry if it is *quite* close to xero.
Otherwise, please, tell me the lowest value you find.

Best,
 Víctor Luaña
--
 .  ."Las mujeres suelen ser menos fanáticas que los hombres,
/ `' \más prácticas y más responsables." 
   /(o)(o)\   --John Carlin (ElPaís, 2016-07-03)
  /`. \/ .'\  Women USE to be less fanatical than men, more practical
 /   '`'`   \ and more responsible."
 |  \'`'`/  |
 |  |'`'`|  | "let's hope our world learns from UK what political lies
  \/`'`'`'\/   and false patrioterism can comdemn a generation to suffer"
===(((==)))==+=
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! Departamento de Química Física y Analítica !
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Re: [Wien] Volume of BP unit cell.

[Víctor Luaña Cabal]

On Mon, Jun 27, 2016 at 11:17:47AM +0200, Luciano Ortenzi wrote:
>
>
> is a*b*c=1002,09359 Bohr^3.
>
> Here is the struct file.
> Best!
>
> Title
> CXY LATTICE,NONEQUIV.ATOMS:  1 64_Cmca
> MODE OF CALC=RELA unit=ang
>   6.264445 19.558673  8.178738 90.00 90.00 90.00
 &&&

Be careful with the units:

#! /usr/bin/octave -f

format long
cell = [6.264445 19.558673  8.178738];
volume=prod(cell)
volume =  1002.09358630267 # ansgtrom**3 per ¿8 atoms?
volume = prod(cell*0.5291771)
volume =  148.494855591321 # bohr**3 ¿per 8 atoms?

Have a productive week,
   Víctor Luaña

--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
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Re: [Wien] [SPAM?] optical properties

[Víctor Luaña Cabal]

On Thu, Jun 16, 2016 at 01:40:17PM -0300, Dr Antonio Vanderlei dos Santos wrote:
>  
> 
> I wonder about the optical properties.
> It is not clear to me
> what it means

Antonio,

The interaction of light with a material (or a chemical). In chemistry
we should refer to spectroscopic properties. In physics it can be more
general and they prefer optical properties. After all, optics is a very
old part of physics as it includes from reflection and refraction to
lasers and much more. Remember Newton's Opticks.

> The results and figures.

What do you mean?

> Can someone help me?

There are LOTS of books on optics. It is so a vast subject that you
better select a small portion. ¿Want to know about the color of gems?
¿What gives color to a fruit or abutterfly? ¿What is the principle behind
a laser? You really need to select a narrower field!

Best regards,
Víctor Luaña
--
 .  ."Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought"-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
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Re: [Wien] How to simulate the spin reorientation in the magnetic study

[Víctor Luaña Cabal]

On Thu, Jun 16, 2016 at 05:49:54PM +0100, Abderrahmane Reggad wrote:
> Thanks Mr Victor for the advise, but right now I need a special workshop
> that talk about my interesting.

Mr. A,

Forgive me, but northern spaniards (like me) use to be quite informal
in our conversation. May I ask where the A. comes from?

I assume from your signature that you are working to get doctorship
or similar.

In  you find a
conference on magnetism. This corresponds to the talk by K. Schwarz
. Check it carefully.

Prof. Karlheinz Schwarz, apart from the founder of the wien2k group
was a postdoc with John C. Slater himself. May I provide you a better
recomendation?

Enjoy,
  Víctor Luaña
--
 .  ."The hardest part in solving a problem is recognizing
/ `' \   its existence. Learning the causes CAN be the road to
   /(o)(o)\  the solution."
  /`. \/ .'\  -- ¿?
 /   '`'`   \ "Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud"
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
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Re: [Wien] How to simulate the spin reorientation in the magnetic study

[Víctor Luaña Cabal]

On Thu, Jun 16, 2016 at 12:41:49PM +0100, Abderrahmane Reggad wrote:
> Thanks Mr Victor for your reply
> 
> I have learned from the literature that spin-orbit coupling is involved in
> the spin orientation .
> 
> Even for a ferromagnetic or a antiferromagnetic state , the spins have
> different orientations. How can we determine the orientation of the spins
> according to the use of the spin-orbit coupling ?

My best advise for you is: examine the tutorial materials
created for wien2k and try to learn from there. See
 where you have lots of
materials to learn. The ones for the 2016 school at McMaster is now
accessible. Next time perhaps you will be able to ask some very good
questions.

Have a good time studying,
  Dr. Víctor Luaña
--
 .  ."Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought"-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:   vic...@fluor.quimica.uniovi.es   !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] How to simulate the spin reorientation in the magnetic study

[Víctor Luaña Cabal]

On Wed, Jun 15, 2016 at 07:50:55PM +0100, Abderrahmane Reggad wrote:
> 
> we know that the spin reorientation in the magnetic structure has an effect
> on the physicak properties of materials.
> 
> How to simulate that using the wien2k code

That's not a particular issue on wien2k. That's a problem of coupling
spins in your system, be it a molecule, a crystal or any other type
of system.

In the case of a crystal you are interested in the type of magnetism,
which is the result of the coupling of spins. In wien2k you decide
the crystal cell to explore and define the type of magnetism for your
atructure.

Just to mention some simple sources to start:



Notice the vec{j}=\vec{l}+\vec{s}, so it includes the orbital and
spinorial moments of the electron.

In the case of light atoms and impurities on solids you will see
an independent coupling of \vec{l}'s to form \vec{L}, and \vec{s}'s
to form \vec{S} before finally \vec{L} and \vec{S} couple to form the
total \vec{J} momentum-



Best regards,
  Víctor Luaña

--
 .  ."El sabio siempre quiere aprender, el ignorante siempre
/ `' \   quiere enseñar" (-- refranero )
   /(o)(o)\  ~The wise always wants to learn, teach the ignorant always wants~
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | ~Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude~
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] Stress-Strain curve

[Víctor Luaña Cabal]

On Sun, May 29, 2016 at 05:47:27AM +0530, Murugan Sundareswari wrote:
> Dear All,
> Greetings from India.
> We are working on mechanical properties and ductility behavior of some
> refractory materials... How to plot stress-strain curve for a cubic
> intermetallic?

That's exactly the purpose of two open source codes: asturfit is written
in octave and I find it more useful for an user that likes scientific
programming. The gibbs2 software is written in fortran and it is more
powerful if you want to include information on the  phonon density
of states and examine the thermal effect on to the properties.

Alll codes hav been published on Comput. Phys Commun. The gibbs2 is
an improvement on the gibbs code published in

Comput Phys Commun 158 (2004) 57--72


The article is written with mastery by the late Miguel Álvarez Blanco
and it is useful to start here.

For the asturfit and gibbs2 code:

Comput Phys Commun 182 (2011) 1708--1720; 2232--2248

The codes are actively maintained and you can find the last versions
in github (see my signature below.

Best regards,
 Víctor Luaña

--
 .  ."El sabio siempre quiere aprender, el ignorante siempre
/ `' \   quiere enseñar" (-- refranero )
   /(o)(o)\  ~The wise always wants to learn, teach the ignorant always wants~
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | ~Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude~
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
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Re: [Wien] How to get lattice parameter as a function of pressure?

[Víctor Luaña Cabal]

On Fri, May 27, 2016 at 11:12:30AM -0400, Wangwei Lan wrote:
> Dear WIEN2K user,
> 
> Can you tell me how to extract lattice parameter as a function of pressure?
> I didn't find it in case.eosfit as mentioned here
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg04276.html

If you have the Energy versus volume data for your crystal you can euse
the gibbs2 free code to do all the analysis. You can learn about the
method in

MA Blanco, E francisco and V. Luaña, Comput. Phys. Commun. 158 (2004) 57--72


an improved version of the code was described in

A. Otero-de-la-Roza and V. Luaña, Comput. Phys. Commun. 182 (2011)
1708--1720; 2232--2248
doi:<10.1016/j.cpc.2011.04.016>
doi:<10.1016/j.cpc.2011.05.009>

The code is maintained and you can get the last version and a detailed
manual from



Best regards,
 Víctor Luaña

--
 .  ."El sabio siempre quiere aprender, el ignorante siempre
/ `' \   quiere enseñar" (-- refranero )
   /(o)(o)\  ~The wise always wants to learn, teach the ignorant always wants~
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | ~Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude~
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
++
 GroupPage: 
 Articles:  
 git-hub:   
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Re: [Wien] runsp_lapw in bash

[Víctor Luaña Cabal]

On Sun, Mar 27, 2016 at 11:11:25PM -0700, Yundi Quan wrote:
> Hi,
> I'm working on a supercomputer which doesn't have csh on their computing
> nodes. But they do have bash shell enabled. Is there a runsp_lapw and x
> script written in bash?

csh and bash are rather similar to convert yourself the tool, but it will need
some time to check that everything works perfectly. Here are some pages than can
help you:


This is a short description of both shells in comparison.


This short bash script does a useful transcription from csh to bash.
Start with the txt, non colored page.

Good luck,
   Víctor

--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-985-103491  fax: +34-985-103125 !
++
 GroupPage: 
 Articles:  
 git-hub:   
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Re: [Wien] Reg: Errors in the installation of Critic2 program

[Víctor Luaña Cabal]

On Thu, Feb 25, 2016 at 09:46:04AM +0530, Peram sreenivasa reddy wrote:
> Dear wien2k,
> 
> I facing some problem while the installation of criti2 program. I
> downloaded the program form
> 
> https://github.com/aoterodelaroza/critic2
> 
> At the time of installation i am facing error as given bellow. Any body
> have experience with these type of errors.
> 
> 
> ifort -DPACKAGE_NAME=\"critic2\" -DPACKAGE_TARNAME=\"critic2\"
> -DPACKAGE_VERSION=\"e7d44b3ee15876ac5dca5951c108a0689910200e\"

Peram,

The problems ptobably appear from using a version too old of the ifort
compiler As critic2 can be ompiled perfectly using even gfortran I
suggest you actualizing a little your S/O.

Better than using the wien2k list in this case is contacting directly
Dr. Alberto Otero-de-la-Roza (now in Canada) or myself (in Spain).

albe...@fluor.quimica.uniovi.es
vic...@fluor.quimica.uniovi.es
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[Víctor Luaña Cabal]

On Mon, Oct 12, 2015 at 04:43:24AM -0500, Laurence Marks wrote:
> Rather than giving the answer to the original question, I think it is
> better to try and encourage people to solve problems themselves -- perhaps
> I am being too much of an teacher, but that is my approach.
> 
> So, let me pose a question in response to the original question. What is
> the relationship between summing a set of values on a grid and the integral
> of a function sampled at a set of grid points. Think about this, and the
> reason why the numbers are very different will be obvious.
> 
> If they still do not completely agree (they wont), then think about the
> accuracy of numerical integration. It is quite important in DFT codes to
> remember that numerical integrations are never exact, and this leads to
> many small limitations.

Laurence,

I love your approach. May I continue?

There are two main strategies in doing a numerical integration. The
first is designing the geometry of the grid by simplicity and providing
each grid point an equal weight. The alternative approach is far more
complex, but it can also be more successful. The position and weight
of grid points can be used to improve the quality of the integration.

Best regards,
 Víctor Luaña
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Re: [Wien] query regarding opticplot

[Víctor Luaña Cabal]

On Mon, Sep 21, 2015 at 03:48:29PM +0530, Dr. K. C. Bhamu wrote:
> Thank you Prof Blaha
> I usually do same as you suggested. I extract these files in excel and then
> used to plot in another softwares.
> I wanted through terminal just for new learning and really it also gives
> good plots.

Bhamu,

gnuplot is excellent, but it has some limitations. The veusz
(http://home.gna.org/veusz) follows a line very familiar for gnuplot
users and it represents a clear improvement on flexibility. You may
enjoy giving it a look.

It is also GPL like gnuplot. I would not mention it otherwise.

Best regards,
  V'ictor Lua~na
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] Problem with aim.def

[Víctor Luaña Cabal]

On Fri, Sep 18, 2015 at 12:25:52PM -0500, Bruno Landeros wrote:
> Dear users:
> I'm having trouble when I try to run the aim module.

Bruno,

If you are interested in doing QTAIM or QCT you can try critic2.
It is free, works for solids and molecules and it is able to
understand many types of wavefunction inputs. It also does works
no many people have heard about yet.

Forgive me not repeating this message in spanish. Let me be
correct with the people in this firum ;-)

Good luck,
  Víctor Luaña
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] Problem with aim.def

[Víctor Luaña Cabal]

On Fri, Sep 18, 2015 at 06:16:04PM +, Bruno Landeros wrote:
> Dear Víctor:
> 
> 
> Thanks for the advisement! I'll try with critic2. This is from Oviedo’s group 
> right?

Yes. The first version was made by Angel Martin Pendas, with
contributions from myself.  Alberto Otero-de-la-Roza, now in the canadian
NINT was the one who cleaned the code used for decades and let it ready
for publishing the critic1 version. A portioon of his PhD project.. When
in Merced and working under Erin Johnson Alberto created an awesome new
version,which is critic2.  We are trying to improve the code even more.

Enjoy it and let us now of any problem you may found. I'm listening
from Manchester now and Alberto does the same from Kelowna.

Regards,
Víctor
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Re: [Wien] need your help please

[Víctor Luaña Cabal]

On Thu, Sep 10, 2015 at 03:48:01AM -0700, sikander Azam wrote:
> Resp. Prof. Víctor Luaña
> Thanks sir for your reply, but sir experimentally silcon dioxide has 8.0 eV
> band gap, but when I doped Nitrogen at Oxygen site then I get metallic
> nature. This is the confusion.

Sikander,

Then you are trying to simulate a N:SiO2 system.

You must explore the concentration of the N impurity in your SiO2 host
and how to model the charge compensation of replacing the original O(-2)
center by a N(-3) one. SiO2 is basically an ionic system, after all. No
doping at small concentrations will transform that.

Good luck,
  Víctor
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Re: [Wien] need your help please

[Víctor Luaña Cabal]

On Thu, Sep 10, 2015 at 03:07:41AM -0700, sikander Azam wrote:
> Dear user
> I am doing calculations on silicon dioxide, but When I make the supercell,
> and replace Oxygen by Nitrogen. This give me metalic nature,
>  Please help me in this regards

Sikander,

Silicon nitride, Si3N4, exists in nature as a ceramic and very hard
material. The description in your e-mail does not corresponds to this
compound. Try to revise your ideas on chemistry. The cif of Si3N4 can
be found in the "Crystallography Open Database"



Regards,
 Dr. Víctor Luaña
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] Energy vs Volume is linear!

[Víctor Luaña Cabal]

On Wed, Sep 09, 2015 at 10:49:57AM +0200, pieper wrote:
> I took the freedomn to use your data to test a little fitting procedure  
> I just wrote. I tried to fit parameters a, b, c of the function
> y=a(x-b)**2+c
> to your data.
>
> The fit crashed - probably like the one you may have used - when  
> presented the data and asked to fit the parabola from scratch. The  
> reason for such a behaviour of a fit procedure frequently is bad user  
> behaviour: The program is quite understandably unable to guess  
> reasonable starting values for the fit parameters from such data.
>
> Presented with starting values
> a=1.00e-06,   b=9.50e+03,  c=-8.857000e+04
>
> the fit finds without complaining a very good fit with
> a=5.687893e-07,  b=9.612186e+03,  c=-8.856770e+04
>
> So you should do your DFT volume optimization around a volume of 9612 -  
> and probably give a little thought to the problem of why you started so  
> far off the optimum at larger volumes.

Marzieh,

Martin description of your problem shows you perfectly what is happening.

May I indicate my practice in studying elastic properties and phase
transition problems?

If you know the equilibrium volume of your material (previous
calculations, experiments ...) try to use a +/- 10 or 15% for your
calculations. The contraction part is essential to determine bulk
modulus and high pressure properties. The expansion part approaches
linear behavior if the range is small enough.

Best regards,
 Víctor Luaña

--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] berryPI code

[Víctor Luaña Cabal]

>> grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}

Let me explain a little the command by Elias:

grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}
 --- -
  1 1

1: text to find
2: set of files to explore. Three files in this case.

A even improved serach would be

grep -B 5 -A 5 Id: SRC_w2w/{almgen.F,l2mmn.f,main.f}

that provides 5 lines of context before and after the pattern that
it is searched for. If you don't know much about the routines Elias
advise is *a minimal*. A search with some context would provide some
more datail, useful to a programmer.

Notice that Elias command corresponds to a bash shell, probably.

Regards,
  Víctor Luaña
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] crystal field splitting

[Víctor Luaña Cabal]

On Sun, Aug 23, 2015 at 07:51:33PM +, Lan, Wangwei wrote:
 Dear Wien2k user:
 
 
 I am very new in WIEN2k. Now I am running case on our crystal system
 which contains a transition metal Cr. I am particularly interested in
 the d orbital splitting, the energy levels of 5 d orbitals. Does anyone
 know how to calculate the orbital splitting using WIEN2k?

Wangwei,

The answer is not simple and there can be more than one opinion living
around. Let me express mu 0.02 euros.

Crystal field splitting parameters (delta-D, i.e. t2g-eg splitting, Racah
parameters, etc) is by fitting a model to the theoretical or experimental
true calculations of total energy diferences between correlated
electronic states. In other terms, there are no such a thing as
orbital splitting as a well defined element. The orbital approach is
a interpretative description, not a physical definition.

There are decades that I not contribute to this old subject and I
reccomend you to follow the more recent papers by Profs. Luis Seijo and
Zoila Barandiarán, from the UAM (Universidad Aotónoma de Madrid).
You will find in their work a good description of old and modern
treatments, laike MOLCAS calculations, relativity contributions, and
the huge importance of large correlation treatments. Both contribute
to the development of MOLCAS.

http://www.uam.es/personal_pdi/ciencias/lseijo/
http://www.uam.es/personal_pdi/ciencias/yara/

Notice that the field emerged from dealing with impurities within
crystals, so most of the evolution that I learned was releted to
the moleculartreatment of embedded impurities neighborhoods.

On a solid state perspective, and your mention of wannier functions
lets me thing you may prefer that, notice that d-d, d-s and d-p
transitions correspond to heavily correlated problems, and the wave
funcion perspective has a much longer tradition than TD-DFT ones,
but let me just say that I know less abiout them. The conferences
by  Stefano Baroni on the calculation of the color of natural dies
are simple awesome.

http://stefano.baroni.me/presentations.html

Best regards and good luck if you come new to this field,
Dr. Vñictor Luaña
--
 .  .In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! I hate the bureaucracy
! Departamento de Química Física y Analítica ! imposed by companies to
! Universidad de Oviedo, 33006-Oviedo, Spain ! which I owe nothing:
! e-mail:   vic...@fluor.quimica.uniovi.es   ! amazon, ResearchGATE and
! phone: +34-985-103491  fax: +34-985-103125 ! the like.
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] How to use the ElaStic1.0 package to calculate the elastic properties

[Víctor Luaña Cabal]

On Sat, May 30, 2015 at 04:01:25PM +0100, Abed Reg wrote:
 Thanks Dr Abo for your reply and for your interesting to my questions
 
 I have already read the readme file and i have found a problem with the
 first step :
 
 STEP 0.1:
  The ElaSticROOT shell variable must be set by the user. For
 instance, add the following line with the correct ElaStic path, in the
 .bashrc file:
  export ElaSticROOT=/home/dir1/dir2/ElaStic
 
 Can you explain more about :
 
 the elastROOT
 give me an example about how to set : ElaSticROOT=/home/dir1/dir2/ElaStic
 
 did export a command to execute in the reminal ?

You shold try to get some help from the Computer Science professionals
in your University. If you have none you need to read something on the
operating system and the shell you are using for your work.

You have installed wien2k in a linux or unix computer (the operating
system). Right now there are many distributions of the GNU/linux
environment. Having details on yours will help anyone that
takes the time to help you, so be prepared to learn a minimum
details on that. For instance I'm writing this at home using
an old Ubuntu distribution, but I have all my professional
machines on real Debian.

What Dr. Abo asks you to do is absolutely clear to anyone with
knowledge of the linux environment:

export ElaSticROOT=/home/dir1/dir2/ElaStic

This assumes you are using a bash sell or equivalent. You can do that
command averytime you enter in session in your machine. Better you can
include that order in the .bashrc file in your root directory.
As my user name is victor in all my machines my root directory
is ~victor or, equivalently /home/victor 

In other words, assuming your username in your computer is xxxyyyzzz
you can add Dr. Abo lines at the end of the /home/xxxyyyzzz/.bashrc
file. There are a number of books on the bash shell that you may read
to be more efficient in your work. Remember that an editor (vim, emacs,
...) and a shell (bash, csh, ...) are the imprescindible tools you
need to be efficient with.

Good luck,
  Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
 GroupPage : http://azufre.quimica.uniovi.es/
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Re: [Wien] Checking the effect of pressure on the bandstructure

[Víctor Luaña Cabal]

On Thu, May 07, 2015 at 10:01:15AM +0300, amit ribak wrote:
 ​Hello,
 
 I'm interested in checking the effect of pressure (uni-axial) on the band
 structure. I first calculated the band structure with and without
 spin-orbit interaction and was able to restore previous results.
 Now, I want to see how the pressure affects the band structure. How can I
 incorporate this into Wien2k?
 
 The c over a optimization is the way to do it or I simply need to change
 the lattice parameters of the initial structure?

Amit,

1) Use thermodynamics

2) Your wien2k calculation is giving you the internal energy:
   E = U(S,V), nominally at 0K, no zero temperature effect, and 0Pa.

3) To analyze pressure effects you can analyze the enthalpy or the
   Gibbs funcion:

   H(S,V) = U + pV
   G(T,p) = U + pV -TS

   If you have enough information on the vibrations of your system try
   to study G, clearly. The zero temperature effect (ZPE, zero point
   energy) has not been deeply studied in this field of solid state.
   It is an interesting subject to explore better.

4) Look for papers in Phys Rev B on this subject. I have mine
   available, so forgive me for citing mainly my publications on this
   subject. The most recent are articles by Alberto Otero-de-la-Roza
   and myself. For example:
   Phys. Rev. B 84 (2011) 184103

5) On Computer Phys Commun you have freeware codes to do this task.
   Look for the gibbs, asturfit and gibbs2 programs.

6) Notice that the codes in (5) are truly devoted to hydrostatic
   conditions, no uni-axial situations. For that I would recommend
   analyzing the grand potential

   \Omegai(T,p,\vec{\mu}) = U +pV -TS - \vec{n} \vec{\mu}

   (Sorry for the tex jargon)
   If you want to analyze a pure substance, remember that
   $\mu = g = G/n$, and \vec{n} = n.

Best regards,
 Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
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Re: [Wien] irrep and sg 204

[Víctor Luaña Cabal]

On Thu, May 07, 2015 at 11:51:37AM +0200, torsten weissbach wrote:
 my question regards the Irrep program. I am interested in a  
 representation analysis at Gamma point for a symmorphic space group (no. 
 204). The point group is identified as Th, but then the program crashes 
 saying trsym:cannot find class. The calculation is just PBE.

Torsten,

The gamma point (\vec{k} = [0,0,0]) is always the maximal symmetry
point. In space group 204 (Pa-3), the symmetry is m-3:

http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list

Examine the first Brillouin zone at

http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-kv-list?gnum=205fig=fm3qpwhat=data

In molecular symmetry parlance m-3 is the C_{3v}, but if we want
to obtain the character table for this group look at the answer
of the Bilbao cryst server:

#
Space Groups and Representations.
-

This program calculates irreducible representations of space
groups. Space group irreps are labeled by k-vector star and a symbol
for the little group representation. In this new version, thanks to
the collaboration of H. Stokes, the assigned irrep labels coincide
with the notation used in Cracknell-Davies-Miller-Love tables [1] and
ISOTROPY. The program is also linked to KVEC for an automatic choice
of the k-vector. The program is still under construction.

You have to introduce the space group number, you can give this number,
if you know it, or you can choose it from the table with the space
group numbers and symbols if you click on the button choose it. When
you click on the botton next you will find a form where you have to
introduce the k vector.

[1] Cracknell, A. P., Davies, B.L., Miller, S. C., and Love,
W. F. (1979). Kronecker Product Tables. Vol. 1. General Introduction
and Tables of Irreducible Representations of Space Groups. New York:
IFI/Plenum.


If you are using this program in the preparation of a paper, please
cite it in the following form:

M. I. Aroyo, A. Kirov, C. Capillas, J. M. Perez-Mato 
H. Wondratschek.Bilbao Crystallographic Server II: Representations
of crystallographic point groups and space groups. Acta Cryst. A62,
115-128 (2006).


So: be careful to determine if you are using a 

200 Pm-3
201 Pn-3
202 Fm-3
203 Fd-3
204 Im-3
205 Pa-3
206 Ia-3

space group in your calculations.

Regards,
   Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
 GroupPage : http://azufre.quimica.uniovi.es/
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Re: [Wien] Symmetry related

[Víctor Luaña Cabal]

On Sat, May 02, 2015 at 08:25:25AM +, Lawal Mohammed wrote:
 Dear Developers and Users
  Please what is wrong in having P1 symmetry? I got P1 when I
 initialized supercell calculations. In the mail archive P1 is regarded
 as less efficient. How can I improve the symmetry at the same time
 maintaining same structure? Could somebody elaborate please.

Lawal,

1) Nothing is wrong. P1 eans that there is no rotational symmetry
   available in your crystal. Rotattion, reflection, inversion, etc.

2) Unfortunately symmetry elements (other than traslation) are used
   by the codes to refuce the computationl cost so it may represent
   bad news. Traslation is also used, but that is implicit, as
   you are using solid state codes designed for crystals.

3) This computer experiment may help you to understand: Take a simple
   compund and reduce the symetry progressively. You will see how the
   computer time required for the calculation increases. The less
   symmetry operations available the higher the cpu involved.
   Bad news if your disponibility of computer resources is limited.

Best regards,
 Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
 GroupPage : http://azufre.quimica.uniovi.es/
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Re: [Wien] Position of Atoms in AFM calculation.

[Víctor Luaña Cabal]

On Fri, May 01, 2015 at 06:08:28PM +0530, Murugan Sundareswari wrote:
 Thanks a lot.its is not frustating, but it is confusing, each one of you
 have given different answer.it will take time for me to do calculation.i
 will definetly come back with some more doubts please help me like this
 thanks all

Pablo,

1) Lev Kantorovich (or Kantorovitch) from King's College London
   has a long tradition working on contact microscopies from
   a theoretical point of view.

2) His webpage is

https://www.kcl.ac.uk/nms/depts/physics/people/academicstaff/kantorovich.aspx

3) Some of the codes useful for your purpose can be found on
   http://www.mth.kcl.ac.uk/~lev/codes/index.html

Good international labor day,
 Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
 GroupPage : http://azufre.quimica.uniovi.es/
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Re: [Wien] Regarding electron density calculations

[Víctor Luaña Cabal]

On Fri, May 01, 2015 at 06:30:47PM +0200, Stefaan Cottenier wrote:

 Should I mention again that...

 imho: yes, you should.

 Why not feeling happy that you get the opportunity to advertise your  
 work to someone who can benefit from it?

Stefaan,

1) That's what I just did!

2) Maybe I'm a little hard to understand? Too opaque sense of humor?
   Do I need some training on communication abilities?

3) Our group has worked on electron density since 1987.
   Our first article on the subject was published on a french journal
   now disappeared. Better I should say that the J. Chim. Phys. (Paris)
   merged with other journals that I don't remember now. Probably is
   now in the Springer or Elsevier  net.

   J. Chim. Phys. (Paris) 84 (1987) 871--874
   Electronic deformation density maps for manganese and chromium
   hexafluoride ions

4) Maybe decades have passed by and methods have improved a lot but
   I like what we did on that old article with antediluvian methods.

   Antediluvian? you would ask.
   Yes, I would say. In my region of Spain it rains abundantly.

5) If you want to see the last creations on electron density from my
   group look for any article by Ángel Martín-Pendás.

6) My last publicacion on electron density in solids was on a molecular
   crystal too big to treat with wien2k, or so I guess:

   J. Chem. Theory Comput. 10 (2014) 5010--5019
   Unraveling Interactions in Molecular Crystals Using Dispersion
   Corrected Density Functional Theory:
   The Case of the Epoxydihydroarsanthrene Molecules

   For the ones not recently trained in the opaque names of chemists
   (myself?) that's an AsO2 or SbO2 central body with two benzene or
   hexa-fluoro bencene wings to form a butterfly shaped molecule. The
   crystals and the molecules could be in an art gallery.

7) By the way, my last fully trained PhD, Alberto Otero-de-la-Roza,
   implemented the XDM method in quantum espresso that made the
   calculations possible. I'm highly proud of his achievements in
   California and Alberta!

8) So, I feel happily on holiday, and working like I love doing at home.

9) I even released today the new banner for this month ;-)

Best regards,
 Víctor

--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought-- Albert Szent-Gyorgi
   /(o)(o)\  
  /`. \/ .'\  Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! 
! Departamento de Química Física y Analítica ! 
! Universidad de Oviedo, 33006-Oviedo, Spain ! 
! e-mail:   vic...@fluor.quimica.uniovi.es   ! 
! phone: +34-985-103491  fax: +34-985-103125 ! 
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)

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Re: [Wien] Regarding electron density calculations

[Víctor Luaña Cabal]

On Fri, May 01, 2015 at 12:30:43PM +0530, Mamta Chauhan wrote:
 I want to calculate the difference charge density. I can calculate the
 valence charge density. but don't know to calculate the difference density.
 Can anyone help me and suggest to calculate the difference density for
 example TiC (Titanium Carbide) in Wien2k? Is there any tutorial available
 for it?

Mamta,

1) Please, think a little ...

2) If you know how to obtain the electron density in a region (1D, 2D, 3D)
   what impedes you to do two calculations modifying anything in your
   system and obtain their difference?

3) Do you need that some slave provides you a script to do the difference?
   Paint it in nice colors? Anything else, bwana?

Sorry if my words disturb you, but today it is the international day of
workers. Did you realise? Did you even know?

Good luck in your adventure of learning some physics and mathematics,

Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought 
   /(o)(o)\  -- Albert Szent-Gyorgi
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)

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Re: [Wien] Regarding electron density calculations

[Víctor Luaña Cabal]

On Fri, May 01, 2015 at 11:11:02AM +0200, Michael Sluydts wrote:
 That being said, one should be able to ask questions without fear of  
 repercussions as to not unnecessarily reinvent the wheel.

Michael,

1) I absolutely agree.

2) Should I mention again that We have provided and published
   freeware codes that do exactly this kind of analisys?

3) Should I mention that wien2k, quantum espresso, crystal, elm,
   and any code able to provide the electron density or any electron
   density related property in the gaussian cube format can be
   analyzed and plotted with our critic family of codes?

4) Should I mention that the critic.f was already published in
   2009 and ritic2.f, an improved version in 2011? Both as freewares?
   Both still maintained and actualized regularly?

5) It is absolutely needed that I  cite the articles?

6) Can anyone interested look at my webpage?

7) There are other codes as well and some not from my group, so I will
   examine with interest anyone suggested or shown in this list.

Sorry if my first answer was a bit harsh but today it is really the
worldwide working holiday and I feel a little revindicative ;-)
I'm a worker in a country hardly affected by the crisis, after all!

Let me wish good day to all,
Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought 
   /(o)(o)\  -- Albert Szent-Gyorgi
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] (no subject)

[Víctor Luaña Cabal]

On Thu, Apr 23, 2015 at 05:56:00PM +0530, Shakeel Khandy wrote:
 I m a beginner and i want to study a compound of ABO3 type pervoskite with
 space group *pbnm*.I have got confused with the atomic positions of
 *pbnm *spacegroup.
 Although the experimental atomic positions are in my hand,but the problem
 lies in the negative atomic positions given by experimental data. Is there
 any other method to have the required atomic positions.

Shakeel,

1) The crystallographic description of coordinates assumes periodicity.
   So x=-0.12 is identical to 1+x=1-0.12. Any crystallographer is trained
   to do the operation quickly and the easy way is thinking

1 = 0.9(10)
  - as mant 9's as it is needed

2) ¿Don't have a professor to traing you? ¿Don't have books on
   crystallography available?

3) Assuming the answers are NO in both cases let me recommend
   you some materials appropriate to the level of your question

a) My own slides on the subject

   http://azufre.quimica.uniovi.es/DetEst/

   Sorry by the spanish. Use google translate as you need.

b) An excellent and recent manual by italian crystallographers:

   C. Giacovazzo, Ed. Fundamentals of crystallography, IUCr  Oxford Univ Press
   IUCR: 0198555784, 1992

   There is a new edition, but I don't have it al hand.

4) This type of question should be solved by your prof./teacher

Good luck,
  Dr. Víctor Luaña
--
 .  .DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
/ `' \   I think the problem, to be quite honest with you,
   /(o)(o)\  is that you have never actually known what the question is.
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] Phonon calculation

[Víctor Luaña Cabal]

On Thu, Apr 23, 2015 at 12:26:02PM +0300, Madesis Ioannis(John) wrote:
 This is why I specified that I work with phonopy. Phonopy, (if you don't  
 already know) requires all generated structures to be of P symmetry. To  
 be honest, this is not always possible since I cannot override Wien2K  
 algorith, which detects possible symmetries (initialization runs in  
 batch mode, inside a home-made script). For phonopy, all atoms must be  
 inequivalent, for proper results. Since I run FIRST all the  
 initializations, and keep a log file, I am in position to tell if the  
 spacegroup of all structures is P1, which again, is a primary target for  
 a good phonopy calculation.

John,

1) If you need to use P1 symmetry try a extremely small displacement
   of your atoms to force the reduction of symmetry you need.
2) Notice that symmetry is used by the codes to reduce the computational
   effort. The other route is better if you hace time, experience and
   the capacity to improve Phonopy: use symmetry in the analysis.

Regards,
   Dr. Víctor Luaña
--
 .  .DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
/ `' \   I think the problem, to be quite honest with you,
   /(o)(o)\  is that you have never actually known what the question is.
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] Parallel running in ubuntu

[Víctor Luaña Cabal]

On Tue, Apr 14, 2015 at 04:17:04PM +0400, Lyudmila Dobysheva wrote:
 On Fri, Apr 10, 2015 at 06:10:12PM +, delamora wrote:
 Excuse me for commenting very late, I haven't seen these letters in time.
 I want to give a voice pro UBUNTU. I am working under it without problems.
 So, Pablo de la Mora has something wrong not because of system.

Lyudmila,

1) My experience is also very good working with Ubuntu at home, don't
   believe otherwise. Ubuntu is a very practical version of a GNU/linux
   environment. The rest is just a very technical discussion about what
   distribution is more appropriate for any particular interest.

2) In that respect, with Debian you have more freedom, and the same
   can be said of redHat. Nowadays there is a huge disponibility of
   GNU/linux distributions.

Regards,
Dr. Víctor Luaña
--
 .  .DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
/ `' \   I think the problem, to be quite honest with you,
   /(o)(o)\  is that you have never actually known what the question is.
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
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Re: [Wien] Pressure and elastic constants

[Víctor Luaña Cabal]

On Tue, Apr 14, 2015 at 12:52:29PM +0530, Shakeel Khandy wrote:
 thanks sir for your suggession.I got c12 a negative quantity as given
 below.How can i calculate elastic constants at 0 pressure .what changes i
 have to make.

Shakeel,

1) Pressure and elastic constants ... You have started a question where
   there still is some debate about what is correct.

2) Some people would say that you must study the curvature of the
   internal energy (the total electronic energy of your solid) with
   respect to the strain deformations.

3) Some perople (myself) would say that it is better to examine the
   Gibbs energy and use whatever exact or aproximate treatment of
   the pressure and temperature of your system.

4) From the E(V) data you have a family of codes to determine the
   Bulk modulus and other elastic terms under a range of pressure and
   temperature.

Read the paper on the gibbs code (freeware) to know how to introduce
pressure and temperature under the QHA (quasi-harmonic, aka Debye,
approximation):

MA Blanco et al, Comput Phys Commun 158 (2004) 2004

The next two papers explain some improvements in the programming and
theory:

A. Otero-de-la-Roza and V.Luaña, Comput Phys Commun 182 (2011) 1708.
A. Otero-de-la-Roza and V.Luaña, Comput Phys Commun 182 (2011) 2232.

If you want to examine further applications on converting the internal
energy data en elastic constants I can provide you more articles in the
subject. You may be interested in

T. Ouahrani et al, Physica B: Condensed Matter 405 (2010) 3658

Best regards,
Dr. Víctor Luaña
--
 .  .Research is to see what everybody else has seen, and to
/ `' \   think what nobody else has thought 
   /(o)(o)\  -- Albert Szent-Gyorgi
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist  prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] t2g-eg splitting

[Víctor Luaña Cabal]

On Sat, Apr 11, 2015 at 11:52:11AM +0530, Vijeta Singh wrote:
 Dear Wien2k users,
 
 I have a question concerning t2g-eg splitting. Suppose we have an
 orthorhombic system LaMnO3 as example. It has both structure Pnma and
 Pbnm.  For an orthorhombic system dxy, dyz and dxz are in t2g states and
 dx2-y2 and dz2 are in eg states. By using Pnma symmetry i am getting dxy,
 dyz and dz2 in t2g states and dxz and dx2-y2 in eg states. What is the
 reason behind this?

Vijeta,

1) The reason is symmetry
2) t2g and eg are denominations of irreducible represetations (irreps)
   of the Oh (m-3m) symmetry group. When the crystal suffers deformations
   the Oh symmetry descends in the symmetry scale.
3) The subject is very deep and I love it.

Best regards,
 Dr. Víctor Luaña
--
 .  .DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
/ `' \   I think the problem, to be quite honest with you,
   /(o)(o)\  is that you have never actually known what the question is.
  /`. \/ .'\ 
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
!Dr.Víctor Luaña ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/
 (being reworked)
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Re: [Wien] Space group P4(2)/nmc (137)

[Víctor Luaña Cabal]

On Thu, Mar 26, 2015 at 02:51:13PM +0100, Ary Ferreira wrote:
 Please,
 
 I'm trying to use the makestruct script to build the structure of
 tetragonal zirconia. According to [Acta Cryst. (1962). 15, 1187], the space
 group is P4(2)/nmc (137), the parameters are a = 3.64 Ang., c =5.27 Ang.,
 and there are 6 atomic positions in the full cell:
 
 [symbol] [id] [WP] [x] [y] [z]
 Zr 1 2a 0. 0. 0.
 Zr 2 2a 0.5000 0.5000 0.5000
 O 1 4d 0. 0.5000 0.1850
 O 2 4d 0.5000 0. -0.1850
 O 3 4d 0. 0.5000 0.6850
 O 4 4d 0.5000 0. 0.3150

Ary,

Let's us forget programs. In the bilbao crystallographic server
you find:

space group P4(2)/nmc (137) , Wyckoff positions:

http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list

(2a) (3/4,1/4,3/4),(1/4,3/4,1/4)

Does not coincide with your positions, so the setting is not in the
same origin. However, the same page lets you displace the origen to the
reference of your data:

(2a) - (0.75,0.25,0.75) - (0,0,0)

Now continues ...

This page lets you decide any origin:

http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-chbasis?what=wposgnum=137gor=t

Best regards,
 Dr. Víctor Luaña
--
 .  .The hardest part in solving a problem is recognizing
/ `' \   its existence. Learning the causes CAN be the road to
   /(o)(o)\  the solution.
  /`. \/ .'\  -- ¿?
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
!Dr.Víctor Luaña ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)


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Re: [Wien] temparature calculation

[Víctor Luaña Cabal]

On Fri, Mar 06, 2015 at 09:08:45PM +0530, Murugan Sundareswari wrote:
 Dear wien 2k users,
 i have been  working on thermoelectric material DyPdBi.
 experimentalist have reported that the compound is anti ferromagnetic and
 resistivity shows two different regime ,metallic at low temperature and
 semiconductor at high temperature.  they have reported  energy gap at 300K.
 in such cases
 how do  i change temperature  for abinitio calculation in wien 2k 13.1.

Muragan,

1) What you are asking is a problem of thermodynamics. You clearly need
   to learn some thermodynamics (classical? statistical?, probably both).

2) wien 2k provides you the total energy of your system and the
   vibrational properties of your system. The total energy is basically
   the internal energy. With the vibrational properties you recover
   a big component of the temperture.

3) To resume a complex sybject: learn some thermodynamics.

Best regards,
 Dr. Víctor Luaña
--
 .  .The hardest part in solving a problem is recognizing
/ `' \   its existence. Learning the causes CAN be the road to
   /(o)(o)\  the solution.
  /`. \/ .'\  -- ¿?
 /   '`'`   \ Lo mediocre es peor que lo bueno, pero también es peor
 |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
 |  |'`'`|  | actitud
  \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
!Dr.Víctor Luaña ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)
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Re: [Wien] Vol optimization for BaRuO3, propose to change eosfit

[Víctor Luaña Cabal]

On Fri, Feb 27, 2015 at 01:56:56PM +0400, Lyudmila Dobysheva wrote:
 On 26.02.2015 00:28, delamora wrote:
 The fit for the Birch-Murnaghan is also not good: gives bad V0, though  
 on the plot it is clearly seen by eye.
 I have tried a fit of Murnaghan through simply gnuplot, and it gave  
 rather good answer:

The source codes for asturfit (octave/matlab) and gibbs2 (fortran77-90)
can be downloaded free in

http://azufre.quimica.uniovi.es/software.html

The technique implemented, codes and examples are described in

Comput Phys Commun Comput. Phys. Commun. 182 (2011) 1708-1720 
and
Comput. Phys. Commun. 182 (2011) 2232-2248 

The Birch-Murnaghan EOS to any order can be used, also the
Poirier-Tarantella and many other families of EOS, most in the
strain-stress superfamily, but not all. If your data points contain
problems the codes should detect them.

If you need fitting EOS to your data maybe the next document will
interest you:

http://azufre.quimica.uniovi.es/src/asturfit/asturfit.txt

Best regards,
Dr. Víctor Luaña

--
 .  . La suma de la mediocridad y de la creatividad es
/ `' \   constante: a más de la una menos de la otra
   /(o)(o)\ (Jorge Wasenberg, 2015)
  /`. \/ .'\  mediocrity+creativity=constant
 /   '`'`   \ (First Principle of thermodynamics,Universal version)
 |  \'`'`/  | Lo mediocre es peor que lo bueno, pero también es peor
 |  |'`'`|  | que lo malo, porque la mediocridad no es un grado, es una
  \/`'`'`'\/  actitud
===(((==)))==+=
!Dr.Víctor Luaña ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)
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Re: [Wien] inverse participation ratio

[Víctor Luaña Cabal]

Pavel,

If you can compute the electron density on a grid of points in
any region you can integrate it to get the total charge. You can
do the sampling of the grid using wien2k. For the integration
you can use critic2:

integration of the density:
Yu, M. and Trinkle, D., J. Chem. Phys. 134 (2011) 064111.

critic2:
Otero-de-la-Roza, A. et al., Comput. Phys. Commun. 180 (2009) 157–166.
Otero-de-la-Roza, A. et al., Comput. Phys. Commun. 185 (2014) 2232--2248.

critic2 is distributed free in source code by the CPC. If you
don't have access to the CPC ask for the code.

critic let's you analyze the electron density and integrate it.
With a good grid you can use vsd to plot the density in a 3D space.

Regards,
   Dr. Víctor Luaña
--
   \|/a Oh, The cheapness of mindless calculation in modern age
  |^.^|  (Roger Penrose, The Emperor's new mind)
+-!OO--\_/--OO!--+---
!Dr. Víctor Luaña  !
! Departamento de Química Física y Analítica   !
! Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491  fax: +34-985-103125   !
+--+
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Re: [Wien] Chemical potental

[Víctor Luaña Cabal]

On Fri, Jan 30, 2015 at 05:50:58PM +, Mohammed Abujafar wrote:
 Dear Wien2k users and developers,Hi,How can I calculate the chemical
 potential using WIEN2k code?Any help will be appreciated.With best
 regardsMohammed

Mohammed,

The chemical potential has MANY definitions so is kind of
ambiguous.

For your purpose the chem pot is the Gibbs function per mol, g=G/n.
This equation is your objective:

   G(N,p,T) = U(N,V,E) - pV + TS

where U is the internal energy, for our purpose equivalent to the
quantum mechanical energy of your crystal (computed wwith wien2k),
p is the pressure (a parameter in this description), T the absolute
temperature (also a parameter).

The pV is easy theoretically: the pressure is a parameter and the volume,
V, should be known for you to do a calculation. If you have problems with
that part learn some crystallography.

The TS is more complex. I will describe here a bit of the 0K quasiharmonic
model. To learn a bit more you can read the extraordinary article of my
late academic son: Miguel Álvarez Blanco:

   [1] MAB et al, Comput Phys Commun 158 (2004) 57

There you will know of a free code (GIBBS) to use this model.
The GIBBS code has a second version, more stable in the mathematical
analysis of data. Unfortunatelly Miguel was not ready at that moment
to publish the GIBBS2 code:

   [2] AOR and VLC, Comput Phys Commun 182 (2011) 1708
   [3] AOR and VLC, Comput Phys Commun 182 (2011) 2232

If you are interested in the big idea read carefully [1]. [2] is
devoted to the mathematical treatment of data, and [3] describes how
to use  wien2k to do this kind of analysis. Unfortunatelly we no longer
have acess to wien2k, so maybe its current output will need a bit of
work from your part ;-)

Regards,
Dr. Víctor Luaña
--
 .  . La suma de la mediocridad y de la creatividad es
/ `' \   constante: a más de la una menos de la otra
   /(o)(o)\ (Jorge Wasenberg, 2015)
  /`. \/ .'\  mediocrity+creativity=constant
 /   '`'`   \ (First Principle of thermodynamics,Universal version)
 |  \'`'`/  | Lo mediocre es peor que lo bueno, pero también es peor
 |  |'`'`|  | que lo malo, porque la mediocridad no es un grado, es una
  \/`'`'`'\/  actitud
===(((==)))==+=
!Dr.Víctor Luaña ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)
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Re: [Wien] The space groups C2/c and B2/b

[Víctor Luaña Cabal]

On Sat, Oct 25, 2014 at 12:18:14AM +0300, Osama Yassin wrote:
 By searching old posts, I found the answer..

Perfect. You might check to obtain the same solution using
the Bilbao crystallographic tools http://www.cryst.ehu.es/

Regards,
 Víctor Luaña

--
   \|/a  After years of working on a problem the genius shout:
  |^.^| what an idiot I am ... the solution is trivial!'
+-!OO--\_/--OO!--+---
!Dr.Víctor Luaña   !
! Departamento de Química Física y Analítica   !
! Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491  fax: +34-985-103125   !
+--+
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Re: [Wien] Wien Digest, Vol 107, Issue 6

[Víctor Luaña Cabal]

On Wed, Oct 22, 2014 at 02:31:15PM +0200, Salman Zarrini wrote:
 +
 Dear Victor,

 Thank you for your answer, I know the concepts one by one (at least I  
 think I know), however, my question is still about their equalization,  
 for example, when we run an Anti ferromagnetic calculation in Wien2k  
 for a bulk system, which one of the Closed shell, open shell,  

I guess that you are a chemist (may I ask your main subject?) trying to follow
a road to solid state physics. Wellcome to the road.

May be you will find useful the book by Roald Hoffmann that tries to introduce
chemists to solid state:

Roald Hoffmann,
Solid State Physics: An Introduction, 2nd ed
http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527412824.html

There is a book by Dronskowski devoted to computational methods:

Computational Chemistry of Solid State Materials: A Guide for Materials
Scientists, Chemists, Physicists and others
by Richard Dronskowski
http://eu.wiley.com/WileyCDA/Section/id-WILEYEUROPE2_SEARCH_RESULT.html?query=Dronskowski

Regards,
 Dr. Víctor Luaña

--
   \|/a  After years of working on a problem the genius shout:
  |^.^| what an idiot I am ... the solution is trivial!'
+-!OO--\_/--OO!--+---
!Dr.Víctor Luaña   !
! Departamento de Química Física y Analítica   !
! Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491  fax: +34-985-103125   !
+--+
 GroupPage : http://azufre.quimica.uniovi.es/  (being reworked)
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Re: [Wien] Bridging from Physics to Chemistry

[Víctor Luaña Cabal]

On Mon, Oct 20, 2014 at 03:17:48PM +0200, Salman Zarrini wrote:
 +++
 Dear Wien2k users,

 I get always confused while bridging from Physics to Chemistry in  
 explaining spin and Magnetism.
 So, I would be highly appreciated if anybody kindly equalized (if it is 
 possible)in DFT the concepts like Nonmagnetic, Paramagnetic,  
 Ferromagnetic, Anti-ferromagnetic and Ferrimagnetic in one hand  
 and Closed shell, Open shell, Spin restricted and Spin  
 unrestricted configurations in the another hand, specially in the case 
 of infinite system like an usual bulk (magnetic or nonmagnetic) which is 
 possible to be easily treated in a plane wave code like Wien2k.

 To start, I can just say:  doing a non-spin polarized calculation in for 
 example Wien2k (run_lapw) equals to a Closed shell calculation.

 And also, for me a Ferrimagnetic looks like a Spin unrestricted  
 configuration ... .

You are asking an impressive list of things and it is not easy
to answer them. You would need a complete master course for this.

1) Let me start from the electronic structure concept of closed and open
shell. A closed shell corresponds to have all orbital levels empty or
containing a complete collection of electrons. So a ns(2), np(6), nd(10)
or nf(14) are closed shells.  An open shell corresponds to have nl(N),
for 0N2*(2*l+1). Remember that in period n the nl orbitals are the
valence ones and the ones involved in chemical bonding.

Closed shells are electronic groups that belong to the fully symmetric
irreducible representation (irrep) for the local symetry group. So they
do not provide many energy levels to your system.

So, when you examine the optical properties of a Cr(+3) impurity in a
Al2O3 corundum crystal is the energy levels of the Cr(+3) open shell
the ones that produce the interesting optical properties. The Al(+3) and
O(-2) ions are closed shells and the provide the chemical ambient where
the 3d impurities do the nice things.

Similarly in the second and third transition metal atoms or in the nf
rare earths. All of them tend to produce rich open shell groups.

2) As for the cooperative magnetism of ferro, ferri, etc I advice you
to explore some good text on the subject: Tipler, Kittel, Ashcroft-Mermin.
The diffrent types of magnetism correspond to different couplings of the
m_s spins in neighbor unit cells of the crystal.

3) The spin restricted and unrestricted SCF techniques correspond
to force the alfa (m_s=+1/2) and beta (m_s=-1/2) electrons having
the same spacial description (restricted) or let the two groups
occupy different regions in space, i.e. different R_{nl}(r) and
R_{nl}^prime(r) orbitals. The unrestricted techniques are very important
as a first step in solving the correlation energy problem.

If you have been lost in this lengthy post don't worry. I told you that
your question was not easy.

Regards,
 Víctor Luaña

--
   \|/a  After years of working on a problem the genius shout:
  |^.^| what an idiot I am ... the solution is trivial!'
+-!OO--\_/--OO!--+---
!Dr.Víctor Luaña   !
! Departamento de Química Física y Analítica   !
! Universidad de Oviedo, 33006-Oviedo, Spain   !
! e-mail:   vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491  fax: +34-985-103125   !
+--+
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Re: [Wien] A problem with symmetry

[Víctor Luaña Cabal]

On Thu, Oct 16, 2014 at 12:25:22AM +0300, Osama Yassin wrote:
 In trying to generate the structure file of Sr2MnTiO6 in the space group
 I4/m (No 87), the Sr and the O positions do not split. The message
 Splitting of equivalent positions not available.
 To split you must select a lattice type
 
 I suspect some is corrupted because it was working well with Wien2k 13 and
 14.
 
 How do I recover this problem.

There are several options, but there are years since I do not work with wien2k.
In principle FP-LAPW techniques do not average the potentials from ions in 
fractional
occupy positions so you have to replicate the cell and move the ions to
the different cells. You can do a statistical treatment of the different
posibilities. Hard but not imposible.

Probably the wien2k current programmers have studied other possibilities.

Regards,
   Dr. Víctor Luaña
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Re: [Wien] Relaxation of already known structure

[Víctor Luaña Cabal]

On Mon, Jul 21, 2014 at 02:16:27PM -0500, Jihoon Park wrote:
 I am wondering if we must do the relaxation for all calculations.
 I have found some first principles studies with experimental lattice
 constants, including Dr. Novak's work PRB 71, 1844422 (2005).
 Therefore, I need to know if the first principles calculations with
 experimental lattice constants are reliable or in what case, it is good
 enough or somethings.
 Could anybody please give me some guidance?

It depends very much on your intention. Optimizing an structure can be
taken as a test of how appropriate is your calculation method for the
system you are trying to analyze. The experimental value is the thing
you are trying to reproduce, but not all experiments are done under
the same precision, nor all experiments provide a well defined result.

Remember that science is understanding, not only producing tables
of numbers. Very simple models have been fundamental in science.
For instance we owe our periodic table of the elements basically to
ideas and concepts generated before quantum mechanics.

It is not wrong, of course, the use a simple well defined recipe on a
large collection of compounds trying to get some systematic rule.

So, try to learn from the literature in your field and try to follow
an unexploited road from the best starting point. Not a simple way but
remember: It is easy to imagine a simple solution for a complex problem
... the pity is that most are wrong!

Best regards,
 Dr. Víctor Luaña

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Re: [Wien] Reg: AFM structure in 111, 110 and 100

[Víctor Luaña Cabal]

On Sat, May 31, 2014 at 03:05:15PM +, delamora wrote:
 What are the Heusler compounds, what are their crystal structure, otherwise 
 it is difficult to help you...

https://en.wikipedia.org/wiki/Heusler_alloy

wikipedia is not the most credible source but it can be used to start.

I'm sure there are more credible sources in the audience ;-)

Simple and nice material to study if you are interested in magnetism.

Regards,
Dr. Víctor Luaña
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Re: [Wien] gibbs calculation

[Víctor Luaña Cabal]

On Tue, May 20, 2014 at 12:43:04AM -0700, MAHDI SALMANI HIRMAND wrote:
 Is there a program for finding gibbs value and therefore
 pressure-induced phase transition with WIEN2k?

There is no M$oft-like code (a GUI) but there are three freeware tools:

1) Comput. Phys. Commun. 158 (2004) 57--72
2) Comput. Phys. Commun. 182 (2011) 1708--1720
3) Comput. Phys. Commun. 182 (2011) 2232--2248

(1) Is devoted to the the Debye-Gibbs model: how you can obtain the
thermodynamic properties fro the E(V) curve.
The fortran freeware in this paper is the first version of the gibbs code.

(2) Is devoted to the problem of obtaining the error estimation.
An octave tool is provided and described in this paper: asturfit.

(3) Is devoted to the building of an efficient fortran code to use all
the previous ideas. It is the second version of the gibbs code.

Best regards,
 Dr. Víctor Luaña
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Re: [Wien] possible pressure-induced transition(find DeltaG)

[Víctor Luaña Cabal]

On Thu, Mar 13, 2014 at 09:43:02PM -0700, MAHDI SALMANI HIRMAND wrote:
 Dear Prof. Blaha,
 I am studying possible pressure-induced transition for some compounds.
 stefaan guide me how i can calculate Gibbs energy and find the pressure.
 
 He told me you can easily calculated the enthalpy H=E+PV using
 case.eosfit and case.eosfitb. Repeat for the second phase, and see
 at which pressure the two enthalpy curves intersect.i did it
 but the two enthalpy  curves are almost the same and it is difficult
 finding the position  which two enthalpy curves intersect.   usually
 in paper they find difference of enthalpy energy from two phases and 
 therefore the pressure which in it DeltaG or DeltaH=0

This is appraching a tutorial. Mr. X, can you help me to do my
homework? I'm solving this difficult problem and there are not authomatic
tools. What can I do.

Answer: Try to learn a little.

QUESTION: how i can calculate Gibbs energy and find the pressure?

ASUMPTION: Do you already have The E(V) curve por several volumes.

POINTS: 1) In highly symmetrical phases the volume is directly related
to a lattice parameter and all internal positions of the atoms are fixed
by symmetry. Crystalographers would say the atoms are occupying Wykoff
positions of multiplicity 1.

2) In less symmetric phases there are other degrees of freedom. Let
us call them $\vec{x}$. If you have some formation on crystallography
(and the problem you are asking for is a crystallography problem). in
that systems you must solve the problem

$E(V) = \min_{\vec{x}}^{V=V_0} E(V,\vec{x})$

and build a table of E versus V. In all points keeping the SAME
crystallographic structure The same solid state phase.

Then introducing the effect of pressure is trivial. You decide it. If
p=10 GPa the Gibbs energy is:

G(p) = E(V) + pV

To reflect all the thermodynamic variables that influence the problem:

$G(p,T) = E(V(\vec{x})) + pV(\vec{x}) - TS(\vec{x})$

If you are interested in pressure-driven phase transitions you can assume
T=0~K. Of course, thermal effects are important. Peter Debje (Debye if
you follow the way he decided to write his name when travaling to US)
dis reseach on that and you can study the result of his research and
learn a little more looking for the seminal paper of the GIBBS code.
In fact, using the gibbs code you can transform the E(V) data in a
G(p,T) estimation. If you have the more complete E(V) + vibronic spectra
($\vec{x}$) you can use the gibbs2 code, ...

From the E(V) curve you can obtain parameters, like the bulk modulus.
Tn fact using the gibbs code you will have estimations of any
thermodynamic property for a single crystalline phase.

If the number of points you determine on the E(V) curve is large enough
you can even gain some knowledge on the statistical errors associated
to the thermodynamic properties.

Let me stop here. You can find about gibbs and gibbs2 in CPC (Comput Phys
Comm). An yoou can find some of the work done on the subject studying
a little about some of the PhD students that I've helped to form. In
the particular subject you want to transit:

Miguel Álvarez Blanco
(main person behind gibbs, death in his youth, but his work will live
for a LONG TIME)

in fact, the paper on the gibbs still code receive tens to hundreds of
citations every year since published in 2004.

Alberto Otero-de-la-Roza
(main person behind gibbs2, currently working in Canada)

If you are really interested on the subject of high pressure maybe the
activity of the Malta-Consolider project might be of your interest. The
project has ended the subvention of our government, but the activities
done are still visible in the web.

Regards,
 Dr: Víctor Luaña
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Re: [Wien] possible pressure-induced transition(find DeltaG)

[Víctor Luaña Cabal]

On Fri, Mar 14, 2014 at 09:29:27AM +0100, Stefaan Cottenier wrote:

 This is a typical numerical annoyance -- the enthalpy curves of both  
 phases are shallowly intersecting. And plotting the difference as a  
 function of pressure is tricky because you don't have the same pressure  
 grid for both phases.

 However, as you have all parameters of the (Birch-)Murnaghan equation at  
 this stage, you can find the volume and the energy at any given pressure  
 (for the Murnaghan equation, you even have the analytical expression at  
 Wikipedia -- http://en.wikipedia.org/wiki/Murnaghan_equation_of_state).  
 And therefore also the enthalpy at that pressure. Hence, you can  
 construct the enthalpies for both phases on the same pressure grid.

 Stefaan

Stefaan,

Murnaghan, Birch-Murnaghan, Poirier-Tarantola, ... There is a huge
unmber of EOS that can be analyzed simultaneously. This is examined
in the code named asturfit, an octave package published in CPC
(Comput. Phys. Commun. 182(2011)1708) doi:10.1016/j.cpc.2011.04.016.

Regards,
  Dr. Víctor Luaña
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Re: [Wien] possible pressure-induced transition

[Víctor Luaña Cabal]

On Thu, Feb 27, 2014 at 02:31:21AM -0800, MAHDI SALMANI HIRMAND wrote:
 Dear Dr. Stefaan,
 Thanks for your reply.
 Therefore, pressure-induced phases transition=(DeltaE)/(DeltaV) which 
 DeltaE=E2-E1 ( Energy of two phases at optimized Volume) and DeltaV=V2-V1( 
 Volume of two phases at optimized volume)
 Is it correct?
 
 usually in paper, they find possible pressure-induced phases transition by 
 using Gibbs data.
 they find difference of Gibbs energy (DeltaG) from two phases and find the 
 pressure which in it DeltaG=0.
 Can you guide me how i can do that?
 I know Gibbs=E + PV at zero-temperature.
 Can you guide me how i can find data (E,P,V) for gibbs calculations in WIEN2k.
 With best,
 Mahdi  

That road has already been explored. Check:

1: http://cpc.cs.qub.ac.uk/summaries/ADSY

and the more stable version of the same code

2: http://cpc.cs.qub.ac.uk/summaries/AEJI_v1_0.html
3: URL:http://cpc.cs.qub.ac.uk/summaries/AEIY_v1_0.html}

If you want to read the associated papers: 

1: http://dx.doi.org/10.1016/j.comphy.2003.12.001

2: doi:10.1016/j.cpc.2011.04.016
3: doi:10.1016/j.cpc.2011.05.009

Regards,
 Dr. Víctor Luaña
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Re: [Wien] error in plotting electron density

[Víctor Luaña Cabal]

On Wed, Feb 26, 2014 at 03:18:06PM -0500, Farshad Nejadsattari wrote:
 Dear Wien2k users and Developers,
 
   I am working on the compound FeNiSn and when I try to plot the electron
 density for spin up, at the x lapw -up stage I receive this error:
 

The route of examining the density, the Laplacian of the density and
so on has already been explored. You can check:

http://cpc.cs.qub.ac.uk/summaries/AECB_v1_0.html

and follow the line up or down.

Regards,
  Dr. Víctor Luaña

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Re: [Wien] electron density plot

[Víctor Luaña Cabal]

On Sat, Feb 08, 2014 at 11:51:41PM +0330, mohamadreza sahmani wrote:
 Dear Wien2k developers and users
 I want to plot electron density (2D) of a structure by XCrysDen.
 After following the procedure given in wien2k user guide, just a
 Thermometer Box appears. I want a plot like those depicted in Koller
 et al. (2011) [Merits and limits of mBJ exchange potential]
 Thanks
 Reza Sahmani, University of Mohaghegh, Iran

Dear Reza,

Electron density in crystals, QTAIM analysis, electron density laplacian,
Bader topology. maybe you will find useful the critic2 code. Look
http://gatsby.ucmerced.edu/wiki/Critic2.

Best regards,
Víctor Luaña
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Re: [Wien] Problem with plotting Electron Density

[Víctor Luaña Cabal]

On Mon, Feb 03, 2014 at 08:30:49PM +0330, Mojtaba AlaviSadr (Zareii) wrote:
 Dear wien2k users
 

Check the critic2 software and its examples:
http://gatsby.ucmerced.edu/wiki/Critic2 It can read wien2k output. For
how to do calculations of electron density using wien2k see the runwien
descriptions. You will find examples and descriptions about using wien2k
for QTAIM (aka Bader analysis) work. There are PhD thesis available on
the subject from the University of Oviedo QCG group.

Best regards,
 V. Luaña
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Re: [Wien] How to quantify charge density (as a single value of charge density) along certain bond length ?

[Víctor Luaña Cabal]

On Wed, Jan 15, 2014 at 09:44:58AM +0100, Georg Eickerling wrote:
 Hi,
 
 I guess you are asking for something like Baders QTAIM which will for
 example provide the density at the bond critical point (local mininum
 along the bond-path connecting to atoms) as a criterion? See the AIM
 module of WIEN2K and the external CRITIC program (listed on the wien
 page under software goodies) for details.

To complete a correct answer: It is also possible to integrate the
electron density and other escalar fields in the basin related to an
atom. A complete topological code should include such ability to perform
the complete QTAIM task. The critic (see critic2 for the most recent
public version) code is able to read wien2k outpput and provide you the
charges for the basin of different atoms. Even non nuclear maxima. See
details of the code in CPC (Computer Physics Communications).

Best regards,
   Dr Víctor Luaña
   University of Oviedo
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