[Wien] AIM: charge-integration

Sat Feb 5 19:36:26 CET 2005

Excellent!  I got it working in 2 minutes.
Maybe we should just clean it up a little bit (eg. not use file 20 for scratch, since the user may have 10 atoms or more ...), and then ask Peter to include it in the SRC_aim package.

Extensions we could think of :
Use case.struct also, and include in the plot :
* the 'structure' (i.e., unit cell box and dots for atom positions (though these will be invisible unless we make the atoms transparent)
* replications of the inequivalent atoms to all the equivalent ones

Thank you very much,

Kevin Jorissen

EMAT - Electron Microscopy for Materials Science   (http://webhost.ua.ac.be/emat/)
Dept. of Physics

UA - Universiteit Antwerpen
Groenenborgerlaan 171
B-2020 Antwerpen
Belgium

tel  +32 3 2653249
fax + 32 3 2653257
e-mail kevin.jorissen at ua.ac.be

-----Original Message-----
From: wien-admin at zeus.theochem.tuwien.ac.at on behalf of Antoine Villesuzanne
Sent: Sat 5-2-2005 1:39
To: wien at zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] AIM: charge-integration

Dear Kevin,

I use the "OFF" format for Geomview. Details and other formats can be found 
in the /doc/oogltour file in the Geomview subdirectories.

Basically the first (simple) problem is to convert from spherical 
coordinates in case.surf to cartesian in the Geomview input file.
Geomview will plot polyhedra (which can be smoothed, see Geomview box menu), 
and here comes the second (much more tedious) problem : Geomview needs as 
input, too,  each face of the polyhedra.
Each face is defined by 7 numbers : the first four are the indices of the 
points (or vertices) defining the face, the last three are the face color, 
in RGB mode.

But once that's done, the result is worth the headache. I have been through 
this, and I can propose you an automated procedure to plot Bader surfaces 
for one or more atoms, starting from the case.surf files. I simplified the 
problem by using theta : 0 to pi and phi : 0 to 2*pi in the case.inaim file, 
so I do not have to reconstruct the full atomic surface by symmetry.

The procedure is very "home-made" and crude. It is based on the attached 
mkgeomview.f program (fortran77), which builts the input file for Geomview.
You can modify or add atom colors in mkgeomview.f. The procedure is :
1) copy case.surf files, for every atom you want to plot on the same image, 
in fort.11, fort.12, fort.13... etc. One fort.1x file per atom.
2) write a file called "datgeo" (I join a template) First line : number of 
atoms to plot; second line : color for first atom ; third line : color for 
second atom; etc...
Colors indices are 1 : blue ; 2 : red ; 3 : purple.
3) run the shellscript mkgeo.e
4) Now you have a file called resgeo, ready to use in Geomview.

In all cases where I used this procedure, case.surf files were calculated 
with 20 theta directions between 0 and pi , and 40 phi directions between 0 
and 2*pi (case.inaim).
Therefore the mkgeomview.f program may have to be modified (for face 
indices) for other choices, maybe, maybe not.

Again, this is very home-made, sorry for that.

I hope we can send attached files to the wienlist. I not, I will send them 
to your email adress.

Regards

Antoine Villesuzanne
Department of Chemistry
North Carolina State University
Raleigh, NC 27695-8204
USA
Tel (+1) 919-515-8919
----- Original Message ----- 
From: "Jorissen Kevin" <Kevin.Jorissen at ua.ac.be>
To: <wien at zeus.theochem.tuwien.ac.at>
Sent: Friday, February 04, 2005 11:25 PM
Subject: RE: [Wien] AIM: charge-integration

Dear A. Villesuzanne,

could you please tell me in a little more detail how you use geomview to 
plot the Bader surface?
Which of the supported file formats do you use?  Any tricks for conversion 
from case.surf?

Thanks,

Kevin Jorissen

EMAT - Electron Microscopy for Materials Science 
(http://webhost.ua.ac.be/emat/)
Dept. of Physics

UA - Universiteit Antwerpen
Groenenborgerlaan 171
B-2020 Antwerpen
Belgium

tel  +32 3 2653249
fax + 32 3 2653257
e-mail kevin.jorissen at ua.ac.be

-----Original Message-----
From: wien-admin at zeus.theochem.tuwien.ac.at on behalf of Antoine 
Villesuzanne
Sent: Tue 1-2-2005 0:58
To: wien at zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] AIM: charge-integration

The case.outputaim file contains information on critical points, and the
electron density integrated in the atomic 'basin'.
 RHOTOT = RHOSPHE+RHOINTE, i.e. sum of the charge in the MT sphere and in
the interstitial.

The case.surf file contains all the positions of points delimiting the
atomic basin. You can use them to plot the atomic surface (using for example
a visualization tool as Geomview http://www.geomview.org ), calculate its
volume, ...

Antoine Villesuzanne
Department of Chemistry
North Carolina State University
Raleigh, NC 27695-8204
USA
Tel (+1) 919-515-8919
----- Original Message ----- 
From: "L. D. Marks" <L-marks at northwestern.edu>
To: <Wien at zeus.theochem.tuwien.ac.at>
Sent: Tuesday, February 01, 2005 12:05 AM
Subject: [Wien] AIM: charge-integration

> Can someone please provide a little explanation as to what are the
> relevant output parameters from case.outputaim. I assume that it is the
> :RHO terms, with :RHOTOT the total charge for the target atom. (The UG
> does not describe what anything is, and the notes on the web page about
> the method appear to be for an earlier version of the code.)
>
> -----------------------------------------------
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60201, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L - marks @ northwestern . edu
> http://www.numis.northwestern.edu
> -----------------------------------------------
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>

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