Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[prasenjit roy]

Dear Prof Laurence Marks, Elias Assmann and Prof Víctor Luaña Cabal,

   Thank you very much for your responses. I Have carefully thought
about your suggestions.

   I completely agree with the fact that the integration of the charge
density is, and should be dependent on the density of the mesh. As I
understood, your suggestion is that the accuracy of integration increases
with a denser mesh. A proper weight factor might help, but I do not know
how it can be implemented during the integration of the charge density
file. According to my knowledge, the mesh is created to make tiny volumes
of equal size, within the unit cell. And the charge density is actually the
small charge within that tiny volume.

   If the above is true, I have two inquiries. First, what is the scale
of the charge density plot as drawn in Xcrysden. Secondly, as the
integration of the charge density mesh can not lead to the total charge
contained within the unit cell; what can be the size of a reasonably dense
mesh that produce an acceptable image of charge density plot {specially
around the core}. This is very much important for drawing the charge
density difference of almost exactly similar unitcell with a tiny shift of
a single atom in real space.

   P.S. As Alias Assmann predicted some scale factor, I think this is not
just the volume (the unitcell I used has volume 213.81 Å^3).

Thank you very much, with kind regards,
Prasenjit

Prasenjit Roy
Electronic Structures of Materials
Radboud University
Nijmegen
+31 (0) 24 36 52805

On Thu, Oct 8, 2015 at 7:34 PM, prasenjit roy 
wrote:

> Dear Prof. Laurence Marks and Dr. Gavin Abo,
>
>  I want to obtain the total number of electron in the
> unit cell, by summing over the total charge density within that unitcell
> and then match that number to the "atomic numbers times the respective
> multiplicity". Since WIen2K is full electron code, I expect these two be
> equal.
>
>  I actually used wien2venus.py and generated
> case.rho3d already (with -S option). The system I worked on is :
> Mn6Fe6Si2P4 (total electron 394 in unitcell). When I summed up all the
> densities over the mesh (I chose 74*74*80 points), I obtained ~257050. So,
> what exactly I need to do in order to get 394 electrons? The answer totally
> depends on how Wien2K (and in this case wien2venus.py) write this
> case.rho3d, in which format.
>
> I am copying the head of the case.rho3d file.
>
> --
>
> cell
>
> 11.577350  11.577350  12.430392
>
> 90.00  90.00  120.10
>
> 74  74  80 11.577350  11.577350  12.430392
>
>  1.53087370e+04  1.07070090e+02  1.59715700e+01  4.54635570e+00
> 3.16747870e+00
>
>  1.98851650e+00  1.10770850e+00  5.92331460e-01  3.20779160e-01
> 1.82854040e-01
>
>  1.12909070e-01  7.67608340e-02  5.74585830e-02  4.66722780e-02
> 4.02846880e-02
>
> ..
> It is a hexagonal unitcell, and the lattice parameters are given in Ry.
>
>  I hope, the problem is clear. Kindly help me solve it. Thank
> you again, with kind regards,
> Prasenjit Roy
> Electronic Structures of Materials
> Radboud University
> Nijmegen
> +31 (0) 24 36 52805
>
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[Laurence Marks]

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.

On Mon, Oct 12, 2015 at 3:39 AM, Elias Assmann 
wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> On 10/08/2015 07:34 PM, prasenjit roy wrote:
> > I want to obtain the total number of electron in the unit cell, by
> > summing over the total charge density within that unitcell and then
> > match that number to the "atomic numbers times the respective
> > multiplicity". Since WIen2K is full electron code, I expect these
> > two be equal.
>
> I have never tried that, but I would expect the number to depend quite
> sensitively on your mesh of r-points.  At least, this is what I saw
> when I looked at normalization of Wannier functions on an r-grid.
> Since you want also the core electrons, you could actually expect even
> larger spikes.
>
> > The system I worked on is : Mn6Fe6Si2P4 (total electron 394 in
> > unitcell). When I summed up all the densities over the mesh (I
> > chose 74*74*80 points), I obtained ~257050.
>
> However, this I would say sounds more like some missing factor …
> Units?  dV?
>
>
> Elias
>
>
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> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
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>



-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[Elias Assmann]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 10/08/2015 07:34 PM, prasenjit roy wrote:
> I want to obtain the total number of electron in the unit cell, by
> summing over the total charge density within that unitcell and then
> match that number to the "atomic numbers times the respective
> multiplicity". Since WIen2K is full electron code, I expect these
> two be equal.

I have never tried that, but I would expect the number to depend quite
sensitively on your mesh of r-points.  At least, this is what I saw
when I looked at normalization of Wannier functions on an r-grid.
Since you want also the core electrons, you could actually expect even
larger spikes.

> The system I worked on is : Mn6Fe6Si2P4 (total electron 394 in
> unitcell). When I summed up all the densities over the mesh (I
> chose 74*74*80 points), I obtained ~257050.

However, this I would say sounds more like some missing factor …
Units?  dV?


Elias


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=Gwas
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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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[Wien] CHARGE DENSITY --> TOTAL CHARGE

[prasenjit roy]

Dear Prof. Blaha and WIEN2K users.

 I want to obtain the total number of electrons within
the unitcell from charge density. So I think I have to sum up all the
charge density within the unit cell. How to do that?

 As far I understood from the Wien2K forum is that:
first plot the 3D charge density using XCRYSDEN or VESTA(using
wien2venus.py). Then save the file and sum up those values, and obtain the
total charge. I am interested in total charge, not the valence charge.

 The problem is, after seeing the isosurface plots
using xcrysden following a lapw5 run,  I dont know which file the 3D charge
density was written.

Kindly help me to solve the problems. Thank you very much, with kind regards

Prasenjit Roy
Electronic Structures of Materials
Radboud University
Nijmegen
+31 (0) 24 36 52805
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[Laurence Marks]

If you really just want to know the total number of electrons, it is the
sum of the atomic numbers times the respective multiplicity -- no need to
do anything more. It is printed out in mixer, do a grep on :NEC.

I suspect that you want to do something else.

On Thu, Oct 8, 2015 at 11:23 AM, Gavin Abo  wrote:

> For XCrySDen, you should be able to save the 3D density as an xsf file
> [1-3].  You should be able to change the Norm. Flag in XCrySDen from
> valence (VAL) to total (TOT) [4].
>
> If you use wien2venus.py:
>
> If you run "wien2venus.py -h" in a terminal, it should show you that the
> -S flag is needed for the total density.
>
> usage: venus.py [-h] [-v] [-p] [-S|V|C|R|T] nx ny nz
> -h print help.
> -c complex version of lapw5.
> -t trigonal case.
> -v verbose mode.
> -p preserve intermediate files
> -S generate total density map from case.clmsum (default)
> -V generate valence density map from case.clmval
> -C generate coulomb potential map from case.vcoul
> -R generate exchange-correlation potential map from case.r2v
> -T generate total potential map from case.vtotal
>
> The 3D density should be written to case.rho3d [5].
>
> [1]
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg07128.html
> [2] http://www.democritos.it/pipermail/xcrysden/2012-June/001208.html
> [3] http://www.xcrysden.org/doc/density.html
> [4] http://www.xcrysden.org/doc/wien.html#__toc__9
> [5]
> http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg09042.html
>
> On 10/8/2015 6:43 AM, prasenjit roy wrote:
>
> Dear Prof. Blaha and WIEN2K users.
>
>  I want to obtain the total number of electrons within
> the unitcell from charge density. So I think I have to sum up all the
> charge density within the unit cell. How to do that?
>
>  As far I understood from the Wien2K forum is that:
> first plot the 3D charge density using XCRYSDEN or VESTA(using
> wien2venus.py). Then save the file and sum up those values, and obtain the
> total charge. I am interested in total charge, not the valence charge.
>
>  The problem is, after seeing the isosurface plots
> using xcrysden following a lapw5 run,  I dont know which file the 3D charge
> density was written.
>
> Kindly help me to solve the problems. Thank you very much, with kind
> regards
>
> Prasenjit Roy
> Electronic Structures of Materials
> Radboud University
> Nijmegen
> +31 (0) 24 36 52805
>
>


-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[Gavin Abo]

For XCrySDen, you should be able to save the 3D density as an xsf file 
[1-3].  You should be able to change the Norm. Flag in XCrySDen from 
valence (VAL) to total (TOT) [4].


If you use wien2venus.py:

If you run "wien2venus.py -h" in a terminal, it should show you that the 
-S flag is needed for the total density.


usage: venus.py [-h] [-v] [-p] [-S|V|C|R|T] nx ny nz
-h print help.
-c complex version of lapw5.
-t trigonal case.
-v verbose mode.
-p preserve intermediate files
-S generate total density map from case.clmsum (default)
-V generate valence density map from case.clmval
-C generate coulomb potential map from case.vcoul
-R generate exchange-correlation potential map from case.r2v
-T generate total potential map from case.vtotal

The 3D density should be written to case.rho3d [5].

[1] 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg07128.html

[2] http://www.democritos.it/pipermail/xcrysden/2012-June/001208.html
[3] http://www.xcrysden.org/doc/density.html
[4] http://www.xcrysden.org/doc/wien.html#__toc__9
[5] 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg09042.html


On 10/8/2015 6:43 AM, prasenjit roy wrote:

Dear Prof. Blaha and WIEN2K users.

 I want to obtain the total number of electrons 
within the unitcell from charge density. So I think I have to sum up 
all the charge density within the unit cell. How to do that?


 As far I understood from the Wien2K forum is 
that: first plot the 3D charge density using XCRYSDEN or VESTA(using 
wien2venus.py). Then save the file and sum up those values, and obtain 
the total charge. I am interested in total charge, not the valence charge.


 The problem is, after seeing the isosurface plots 
using xcrysden following a lapw5 run,  I dont know which file the 3D 
charge density was written.


Kindly help me to solve the problems. Thank you very much, with kind 
regards


Prasenjit Roy
Electronic Structures of Materials
Radboud University
Nijmegen
+31 (0) 24 36 52805
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Re: [Wien] CHARGE DENSITY --> TOTAL CHARGE

[prasenjit roy]

Dear Prof. Laurence Marks and Dr. Gavin Abo,

 I want to obtain the total number of electron in the
unit cell, by summing over the total charge density within that unitcell
and then match that number to the "atomic numbers times the respective
multiplicity". Since WIen2K is full electron code, I expect these two be
equal.

 I actually used wien2venus.py and generated case.rho3d
already (with -S option). The system I worked on is : Mn6Fe6Si2P4 (total
electron 394 in unitcell). When I summed up all the densities over the mesh
(I chose 74*74*80 points), I obtained ~257050. So, what exactly I need to
do in order to get 394 electrons? The answer totally depends on how Wien2K
(and in this case wien2venus.py) write this case.rho3d, in which format.

I am copying the head of the case.rho3d file.
--

cell

11.577350  11.577350  12.430392

90.00  90.00  120.10

74  74  80 11.577350  11.577350  12.430392

 1.53087370e+04  1.07070090e+02  1.59715700e+01  4.54635570e+00
3.16747870e+00

 1.98851650e+00  1.10770850e+00  5.92331460e-01  3.20779160e-01
1.82854040e-01

 1.12909070e-01  7.67608340e-02  5.74585830e-02  4.66722780e-02
4.02846880e-02
..
It is a hexagonal unitcell, and the lattice parameters are given in Ry.

 I hope, the problem is clear. Kindly help me solve it. Thank
you again, with kind regards,
Prasenjit Roy
Electronic Structures of Materials
Radboud University
Nijmegen
+31 (0) 24 36 52805
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