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

[Abderrahmane Reggad]

Thank you for all for the rich discussion

If I introduce the Ni atom and I change the Z number to 27 or 26 it still
nickel because the atom is ont only Z and I change Z the number of neutrons
and protons still inchanged.As I mentionned when I have changed Z I have
observed that the total energy changes.

An other question: We suppose that the ionic state of NiO is a result from
the electron density , can we force this ionic state to be Ni+3S-3 and it's
yes how?

Best regards



2017-08-24 0:43 GMT+01:00 Abderrahmane Reggad :

> Hello
>
> 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.
>
> Thank you for contribution to clarify the picture.
>
> Best regards
>
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Re: [Wien] How to simulate the ionic state of a compound?

[Abderrahmane Reggad]

Hello

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.

Thank you for contribution to clarify the picture.

Best regards
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Re: [Wien] Bugs : related to nlvdw calculations

[tran]

1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F

the error : Insufficient virtual memory

to Fix : After the line 41 in SRC_nlvdw/calc_vvdw.F add :
            lmtmp =0
and recompile a selected package :  nlvdw


Thanks for the bug fix.


2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h  ( for 
example : if we use rev-vdW-DF2 correction ) :
the errors :
stop in lapw1 with : SELECT - error
no energy limits found for atom ..
E-Bottom ...

to Fix : just add to SRC_lapw0/xc_funcs.h this line :

#define  XC_GGA_X_B86_R    41 


This is due to an error (we were not aware of it) in the Makefile of
SRC_lapw0 for WIEN2k_16 and WIEN2k_17: LIBXCDIR has to be replaced by
LIBXCROOT such that the file xc_funcs.h of the version of libxc that
you use (it's probably 3.0.0) is copied in SRC_lapw0 when lapw0 is
compiled. The file xc_funcs.h that is provided by WIEN2k_16/17
is, for some strange reason, the old one from libxc version 2.1.2.
Thus, modify Makefile and recompile lapw0.


3- The parallel run with nlvdw correction doesn't work for me
with the errors:

lapw5 : command not found


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Re: [Wien] Bugs : related to nlvdw calculations

[zanat]

i will try to trace back the errors, and i will see what i will find. 
Thank yo 



From: "Laurence Marks"  
To: "A Mailing list for WIEN2k users"  
Sent: Wednesday, August 23, 2017 6:15:38 PM 
Subject: Re: [Wien] Bugs : related to nlvdw calculations 

lapw5 is being launched by prepare_xsw using python (which I am not good with). 
On my cluster I could find an indicator in /var/log/messages that the python 
command was failing, and intuit from there. 
N.B. prepare_xsw should, like the rest of Wien2k, crash gracefully if something 
goes wrong and stop further execution -- it does not appear to. 

On Wed, Aug 23, 2017 at 12:06 PM, zanat < zanat.ka...@univ-guelma.dz > wrote: 



Thank you for your reading. 
The problem in the parallel is in a nlvdw level because i run the wien2k 
normally without nlvdw option (i run it locally on multi-cores PC), there is my 
.machines file : 
- 
lapw0: localhost:4 
nlvdw: localhost:4 

1:localhost:1 
1:localhost:1 
1:localhost:1 
1:localhost:1 

granularity:1 
extrafine:1 
--- 
and the errors : 

kamel@kamel-MS-7915:~/WIEN2k/nlvdw_test/t$ run_lapw -I -fc 1.0 -i 90 -nlvdw -p 
bash: lapw5: command not found 
... 
... 
... 
bash: lapw5: command not found 
PREPARE_XSF END 
NLVDW END 
LAPW0 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW2 - FERMI; weights written 
LAPW2 END 
LAPW2 END 
LAPW2 END 
LAPW2 END 
SUMPARA END 
CORE END 
MIXER END 
ec cc and fc_conv 1 1 0 
in cycle 2 ETEST: 6.43407905 CTEST: .652549 
hup: Command not found. 
bash: lapw5: command not found 
 
bash: lapw5: command not found 
PREPARE_XSF END 
NLVDW END 
LAPW0 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW2 - FERMI; weights written 
LAPW2 END 
LAPW2 END 
LAPW2 END 
LAPW2 END 
SUMPARA END 
CORE END 
MIXER END 
ec cc and fc_conv 1 1 0 
in cycle 3 ETEST: 3.23042138 CTEST: .604975 
 
... 
-
 

with the errors repeated as many as : t.output5_1 to t.output5_152, I mean 152 
times . 
So, is lapw5: command not found is an error or something is wrong as the lapw5 
command not executed. 


From: "Laurence Marks" < l-ma...@northwestern.edu > 
To: "A Mailing list for WIEN2k users" < wien@zeus.theochem.tuwien.ac.at > 
Sent: Wednesday, August 23, 2017 5:36:40 PM 
Subject: Re: [Wien] Bugs : related to nlvdw calculations 

The third one is connected to prepare_xsw, and may have two sources: 

a) The .machines file. In the parallel case, prepare_xsw reads the lapw1 lines 
and can have problems because it makes assumptions about the format. You can 
use a format such as 
1:node1:4 

If you make it more than 4 you may have a problem, and 16 certainly fails. I 
got it to work by trial and error. 

b) Something else such as $WIENROOT not being exported to the python command 
that is launched. (This is a guess.) 

On Wed, Aug 23, 2017 at 11:30 AM, zanat < zanat.ka...@univ-guelma.dz > wrote: 

BQ_BEGIN

Dear all, 
Recently, I found this bugs related to inclusion of the nlvdw corrention to the 
calculation of band structure of some material in WIEN2k 17.1 running at Linux 
system (intel Xeon Processor) with intel compilers. In the following I report 
the bugs with their errors and my proposed fixed bugs, if found. 
-
 
1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F 

the error : Insufficient virtual memory 

to Fix : After the line 41 in SRC_nlvdw/calc_vvdw.F add : 
lmtmp =0 
and recompile a selected package : nlvdw 
-
 
2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h ( for 
example : if we use rev-vdW-DF2 correction ) : 
the errors : 
stop in lapw1 with : SELECT - error 
no energy limits found for atom .. 
E-Bottom ... 

to Fix : just add to SRC_lapw0/xc_funcs.h this line : 

#define XC_GGA_X_B86_R 41 

---
 
3- The parallel run with nlvdw correction doesn't work for me 
with the errors : 

lapw5 : command not found 

any suggestions. 

Thanks in advance 






-- 
Professor Laurence Marks 
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi 
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu 
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent 
Co-Editor, Acta Cryst A 

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Re: [Wien] Bugs : related to nlvdw calculations

[Laurence Marks]

lapw5 is being launched by prepare_xsw using python (which I am not good
with). On my cluster I could find an indicator in /var/log/messages that
the python command was failing, and intuit from there.

N.B. prepare_xsw should, like the rest of Wien2k, crash gracefully if
something goes wrong and stop further execution -- it does not appear to.

On Wed, Aug 23, 2017 at 12:06 PM, zanat  wrote:

> Thank you for your reading.
> The problem in the parallel is in a nlvdw level because i run the wien2k
> normally without nlvdw option (i run it locally on multi-cores PC), there
> is my .machines file :
> -
> lapw0: localhost:4
> nlvdw: localhost:4
>
> 1:localhost:1
> 1:localhost:1
> 1:localhost:1
> 1:localhost:1
>
> granularity:1
> extrafine:1
> ---
> and the errors :
>
> kamel@kamel-MS-7915:~/WIEN2k/nlvdw_test/t$ run_lapw -I -fc 1.0 -i 90
> -nlvdw -p
> bash: lapw5: command not found
> ...
> ...
> ...
> bash: lapw5: command not found
> PREPARE_XSF END
> NLVDW END
> LAPW0 END
> LAPW1 END
> LAPW1 END
> LAPW1 END
> LAPW1 END
> LAPW2 - FERMI; weights written
> LAPW2 END
> LAPW2 END
> LAPW2 END
> LAPW2 END
> SUMPARA END
> CORE END
> MIXER END
> ec cc and fc_conv 1 1 0
> in cycle 2 ETEST: 6.43407905 CTEST: .652549
> hup: Command not found.
> bash: lapw5: command not found
> 
> bash: lapw5: command not found
> PREPARE_XSF END
> NLVDW END
> LAPW0 END
> LAPW1 END
> LAPW1 END
> LAPW1 END
> LAPW1 END
> LAPW2 - FERMI; weights written
> LAPW2 END
> LAPW2 END
> LAPW2 END
> LAPW2 END
> SUMPARA END
> CORE END
> MIXER END
> ec cc and fc_conv 1 1 0
> in cycle 3 ETEST: 3.23042138 CTEST: .604975
> 
> ...
> 
> -
>
> with the errors repeated as many as : t.output5_1 to t.output5_152, I mean
> 152 times .
> So, is lapw5: command not found is an error or something is wrong as the
> lapw5 command not executed.
>
> --
> *From: *"Laurence Marks" 
> *To: *"A Mailing list for WIEN2k users" 
> *Sent: *Wednesday, August 23, 2017 5:36:40 PM
> *Subject: *Re: [Wien] Bugs : related to nlvdw calculations
>
> The third one is connected to prepare_xsw, and may have two sources:
>
> a) The .machines file. In the parallel case, prepare_xsw reads the lapw1
> lines and can have problems because it makes assumptions about the format.
> You can use a format such as
> 1:node1:4
>
> If you make it more than 4 you may have a problem, and 16 certainly fails.
> I got it to work by trial and error.
>
> b) Something else such as $WIENROOT not being exported to the python
> command that is launched. (This is a guess.)
>
> On Wed, Aug 23, 2017 at 11:30 AM, zanat 
> wrote:
>
>> Dear all,
>> Recently, I found this bugs related to inclusion of the nlvdw corrention
>> to the calculation of band structure of some material in WIEN2k 17.1
>> running at Linux system (intel Xeon Processor) with intel compilers. In the
>> following I report the bugs with their errors and my proposed* fixed
>> bugs, *if found.
>> 
>> -
>> 1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F
>>
>> * the error : *Insufficient virtual memory
>>
>> *to Fix :* After the line 41 in SRC_nlvdw/calc_vvdw.F add :
>>   *  lmtmp =0*
>> and recompile a selected package :  nlvdw
>> 
>> -
>> 2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h  ( for
>> example : if we use rev-vdW-DF2 correction ) :
>> *the errors :*
>> stop in lapw1 with : SELECT - error
>> no energy limits found for atom ..
>> E-Bottom ...
>>
>> *to Fix : *just add to SRC_lapw0/xc_funcs.h this line :
>>
>> #define  XC_GGA_X_B86_R41
>>
>> 
>> ---
>> 3- The parallel run with nlvdw correction doesn't work for me
>> with the *errors*:
>>
>> lapw5 : command not found
>>
>> any suggestions.
>>
>> Thanks in advance
>>
>
>
>
> --
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu
> Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> 
> Co-Editor, Acta Cryst A
>
> ___
> 

Re: [Wien] Bugs : related to nlvdw calculations

[zanat]

Thank you for your reading. 
The problem in the parallel is in a nlvdw level because i run the wien2k 
normally without nlvdw option (i run it locally on multi-cores PC), there is my 
.machines file : 
- 
lapw0: localhost:4 
nlvdw: localhost:4 

1:localhost:1 
1:localhost:1 
1:localhost:1 
1:localhost:1 

granularity:1 
extrafine:1 
--- 
and the errors : 

kamel@kamel-MS-7915:~/WIEN2k/nlvdw_test/t$ run_lapw -I -fc 1.0 -i 90 -nlvdw -p 
bash: lapw5: command not found 
... 
... 
... 
bash: lapw5: command not found 
PREPARE_XSF END 
NLVDW END 
LAPW0 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW2 - FERMI; weights written 
LAPW2 END 
LAPW2 END 
LAPW2 END 
LAPW2 END 
SUMPARA END 
CORE END 
MIXER END 
ec cc and fc_conv 1 1 0 
in cycle 2 ETEST: 6.43407905 CTEST: .652549 
hup: Command not found. 
bash: lapw5: command not found 
 
bash: lapw5: command not found 
PREPARE_XSF END 
NLVDW END 
LAPW0 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW1 END 
LAPW2 - FERMI; weights written 
LAPW2 END 
LAPW2 END 
LAPW2 END 
LAPW2 END 
SUMPARA END 
CORE END 
MIXER END 
ec cc and fc_conv 1 1 0 
in cycle 3 ETEST: 3.23042138 CTEST: .604975 
 
... 
-
 

with the errors repeated as many as : t.output5_1 to t.output5_152, I mean 152 
times . 
So, is lapw5: command not found is an error or something is wrong as the lapw5 
command not executed. 


From: "Laurence Marks"  
To: "A Mailing list for WIEN2k users"  
Sent: Wednesday, August 23, 2017 5:36:40 PM 
Subject: Re: [Wien] Bugs : related to nlvdw calculations 

The third one is connected to prepare_xsw, and may have two sources: 

a) The .machines file. In the parallel case, prepare_xsw reads the lapw1 lines 
and can have problems because it makes assumptions about the format. You can 
use a format such as 
1:node1:4 

If you make it more than 4 you may have a problem, and 16 certainly fails. I 
got it to work by trial and error. 

b) Something else such as $WIENROOT not being exported to the python command 
that is launched. (This is a guess.) 

On Wed, Aug 23, 2017 at 11:30 AM, zanat < zanat.ka...@univ-guelma.dz > wrote: 



Dear all, 
Recently, I found this bugs related to inclusion of the nlvdw corrention to the 
calculation of band structure of some material in WIEN2k 17.1 running at Linux 
system (intel Xeon Processor) with intel compilers. In the following I report 
the bugs with their errors and my proposed fixed bugs, if found. 
-
 
1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F 

the error : Insufficient virtual memory 

to Fix : After the line 41 in SRC_nlvdw/calc_vvdw.F add : 
lmtmp =0 
and recompile a selected package : nlvdw 
-
 
2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h ( for 
example : if we use rev-vdW-DF2 correction ) : 
the errors : 
stop in lapw1 with : SELECT - error 
no energy limits found for atom .. 
E-Bottom ... 

to Fix : just add to SRC_lapw0/xc_funcs.h this line : 

#define XC_GGA_X_B86_R 41 

---
 
3- The parallel run with nlvdw correction doesn't work for me 
with the errors : 

lapw5 : command not found 

any suggestions. 

Thanks in advance 






-- 
Professor Laurence Marks 
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi 
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu 
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent 
Co-Editor, Acta Cryst A 

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Re: [Wien] Bugs : related to nlvdw calculations

[Laurence Marks]

The third one is connected to prepare_xsw, and may have two sources:

a) The .machines file. In the parallel case, prepare_xsw reads the lapw1
lines and can have problems because it makes assumptions about the format.
You can use a format such as
1:node1:4

If you make it more than 4 you may have a problem, and 16 certainly fails.
I got it to work by trial and error.

b) Something else such as $WIENROOT not being exported to the python
command that is launched. (This is a guess.)

On Wed, Aug 23, 2017 at 11:30 AM, zanat  wrote:

> Dear all,
> Recently, I found this bugs related to inclusion of the nlvdw corrention
> to the calculation of band structure of some material in WIEN2k 17.1
> running at Linux system (intel Xeon Processor) with intel compilers. In the
> following I report the bugs with their errors and my proposed* fixed
> bugs, *if found.
> 
> -
> 1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F
>
> * the error : *Insufficient virtual memory
>
> *to Fix :* After the line 41 in SRC_nlvdw/calc_vvdw.F add :
>   *  lmtmp =0*
> and recompile a selected package :  nlvdw
> 
> -
> 2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h  ( for
> example : if we use rev-vdW-DF2 correction ) :
> *the errors :*
> stop in lapw1 with : SELECT - error
> no energy limits found for atom ..
> E-Bottom ...
>
> *to Fix : *just add to SRC_lapw0/xc_funcs.h this line :
>
> #define  XC_GGA_X_B86_R41
>
> 
> ---
> 3- The parallel run with nlvdw correction doesn't work for me
> with the *errors*:
>
> lapw5 : command not found
>
> any suggestions.
>
> Thanks in advance
>



-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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[Wien] Bugs : related to nlvdw calculations

[zanat]

Dear all, 
Recently, I found this bugs related to inclusion of the nlvdw corrention to the 
calculation of band structure of some material in WIEN2k 17.1 running at Linux 
system (intel Xeon Processor) with intel compilers. In the following I report 
the bugs with their errors and my proposed fixed bugs, if found. 
-- -- 
- 
1- the initialisation of lmtmp integer array in SRC_nlvdw/calc_vvdw.F 

the error : Insufficient virtual memory 

to Fix : After the line 41 in SRC_nlvdw/calc_vvdw.F add : 
lmtmp =0 
and recompile a selected package : nlvdw 
-- -- 
- 
2- missing of XC_GGA_X_B86_R xc functional in SRC_lapw0/xc_funcs.h ( for 
example : if we use rev-vdW-DF2 correction ) : 
the errors : 
stop in lapw1 with : SELECT - error 
no energy limits found for atom .. 
E-Bottom ... 

to Fix : just add to SRC_lapw0/xc_funcs.h this line : 

#define XC_GGA_X_B86_R 41 

-- -- 
-- - 
3- The parallel run with nlvdw correction doesn't work for me 
with the errors : 

lapw5 : command not found 

any suggestions. 

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

[Laurence Marks]

I am not sure where this discussion is wandering. There is one general
point of some importance: the " Charge" or "Ionic State" is not an absolute
number, it changes with the property/experiment:

1) Bader charge: a measure of the ionicity.
2) Valence charge, as normally used this is the charge measured in an
electrochemical experiment. This corresponds to a purely ionic model.
3) Spectroscopies charge, what is measured using XPS and many other
Spectroscopies, and is close to the bond valence sum.
4) Born charge, the dynamic charge, for instance the effective charge of a
moving atom that one can get from a Berry phase calculation.

1)-4) are all different, and if you use them inappropriately GIGO. For
instance, there is the infamous polar catastrophy at surfaces/interfaces
that arises when people nievely use 2).

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
Co-Editor, Acta Cryst A


On Aug 23, 2017 06:58, "pieper"  wrote:

> Not knowing what your average Fe knows I still would guess it probably
> doesn't. Maybe thats why nothing else changes when you relabel atoms in
> xcrysden. However, upon adding two protons (and some neutrons) in
> Wien2k, Fe seems to know it became Ni - we learned from the initial
> question that it says so through ETOT. ;-)
>
> Best regards,
>
> Martin Pieper
>
> ---
> Dr. Martin Pieper
> Karl-Franzens University
> Institute of Physics
> Universitätsplatz 5
> A-8010 Graz
> Austria
> Tel.: +43-(0)316-380-8564
>
>
> Am 23.08.2017 11:16, schrieb Fecher, Gerhard:
> > Funny discussion,
> > I wonder wether iron (Z=26) knows that it is Nickel just if one gives
> > it a new name ?
> >
> >
> > Ciao
> > Gerhard
> >
> > DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> > "I think the problem, to be quite honest with you,
> > is that you have never actually known what the question is."
> >
> > 
> > Dr. Gerhard H. Fecher
> > Institut of Inorganic and Analytical Chemistry
> > Johannes Gutenberg - University
> > 55099 Mainz
> > and
> > Max Planck Institute for Chemical Physics of Solids
> > 01187 Dresden
> > 
> > Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
> > Víctor Luaña Cabal [vic...@fluor.quimica.uniovi.es]
> > Gesendet: Mittwoch, 23. August 2017 00:33
> > An: A Mailing list for WIEN2k users
> > Cc: Victor Luaña
> > Betreff: Re: [Wien] How to simulate the ionic state of a compound?
> >
> > 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
> > 

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

[pieper]

Not knowing what your average Fe knows I still would guess it probably 
doesn't. Maybe thats why nothing else changes when you relabel atoms in 
xcrysden. However, upon adding two protons (and some neutrons) in 
Wien2k, Fe seems to know it became Ni - we learned from the initial 
question that it says so through ETOT. ;-)


Best regards,

Martin Pieper

---
Dr. Martin Pieper
Karl-Franzens University
Institute of Physics
Universitätsplatz 5
A-8010 Graz
Austria
Tel.: +43-(0)316-380-8564


Am 23.08.2017 11:16, schrieb Fecher, Gerhard:

Funny discussion,
I wonder wether iron (Z=26) knows that it is Nickel just if one gives
it a new name ?


Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
Víctor Luaña Cabal [vic...@fluor.quimica.uniovi.es]
Gesendet: Mittwoch, 23. August 2017 00:33
An: A Mailing list for WIEN2k users
Cc: Victor Luaña
Betreff: Re: [Wien] How to simulate the ionic state of a compound?

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

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

[Fecher, Gerhard]

Funny discussion,
I wonder wether iron (Z=26) knows that it is Nickel just if one gives it a new 
name ?


Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Víctor Luaña 
Cabal [vic...@fluor.quimica.uniovi.es]
Gesendet: Mittwoch, 23. August 2017 00:33
An: A Mailing list for WIEN2k users
Cc: Victor Luaña
Betreff: Re: [Wien] How to simulate the ionic state of a compound?

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 !
++
 GroupPage: 
 Articles:  

Re: [Wien] Regarding electron numbers

[tran]

In case.scf :NEC02 and :CHA are the total and valence
electrons, respectively.

On Wednesday 2017-08-23 09:11, mandeep hooda wrote:


Date: Wed, 23 Aug 2017 09:11:00
From: mandeep hooda 
Reply-To: A Mailing list for WIEN2k users 
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Regarding electron numbers

Dear Wien2k users,                                 The total number of 
electrons are usually given in scf file. Is there any file containing  number 
of core
electrons or valence electrons ?. If not, can we calculate the number of core 
electrons from the total number  by any formula or other means ?. Your comments
will be appreciable. Thanking you in advance

Mandeep Kumar Hooda
Physics Scholar

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[Wien] Regarding electron numbers

[mandeep hooda]

Dear Wien2k users,
 The total number of electrons are usually
given in scf file. Is there any file containing  number of core electrons
or valence electrons ?. If not, can we calculate the number of core
electrons from the total number  by any formula or other means ?. Your
comments will be appreciable. Thanking you in advance

Mandeep Kumar Hooda
Physics Scholar
___
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Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html