3D Visualization of electron density in VESTA

Vitaliy Romaka - 2012-10-26

Hello everybody,
So, I have successfully plotted 3D electron density obtained from RHO3D.OUT file in program VESTA.
Step-by-step:
1. Generate RHO3D.OUT File, appropriate flags are required in elk.in (see Elk Manual) with some k-grid
In the file you will have something like this:

    20    20    20 : grid size
   0.000000000       0.000000000       0.000000000      0.1643019997E-01
0.4478461620       0.000000000       0.000000000      0.1747919287E-01
0.8956923241       0.000000000       0.000000000      0.2061542978E-01
   1.343538486       0.000000000       0.000000000      0.2528383332E-01
   1.791384648       0.000000000       0.000000000      0.2966042854E-01
…..
2. Note somewhere the first line (20 20 20) you will need it later. Now delete the first line, you should have only 4 columns. From these 4 columns we will need to have only the last one, so delete first 3 columns. (I usually open the file in Origin, and re-export only last column)
3. Change file name to something XXXXXX.LED and open the file. Now you should add at the beginning of your file:
Compound name, (something like - super-duper solid AxByCz)
Cell parameters separated by space, or TAB (a b c alpha beta gamma) (4.154 2.564 7.896 90 90 90) in Angstrems A.
I have found that with this method you may have probably to play with "a b c", to try them like "c b a". I used this method for tetragonal structure, so "c a a" were used, and of course remember alpha beta gamma.
And finally k-grid separated by space or TAB (kx ky kz). Remember, this k-grid we have already noted somewhere, it was 20 20 20.
Finally the file should looks like this:

super-duper solid AxByCz
4.154 2.564 7.896 90 90 90
20 20 20
0.1643019997E-01
0.1747919287E-01
0.2061542978E-01
0.2528383332E-01
0.2966042854E-01
…

Now save it. Run VESTA and open this file
Ta-dam!

P.S.
Use it, improve it, have fun, and don't forget to post your solutions here.

Vitaliy Romaka - 2012-10-26

Vitaliy Romaka - 2012-10-26

Same method was also successfully applied to visualize ELF (electron localization function) from ELF3D.OUT

Anton F. - 2012-10-27

Hi!
Thank you for this useful information on plotting 3d-data from Elk with Vesta! I've performed the algorythm and it worked out. So I think Elk developers should consider to add it to Elk's FAQ or user's guide.

Best wishes,
Anton F.

Vitaliy Romaka - 2012-10-27

Don't forget, that ou can open GEOMETRY.OUT file directly in VESTA. This is a new feature of the newest VESTA 3.x version

Hello.

Thanks to your work I could update my igor procedure for converting Rho2VESTA. I just tested it with Bi2Se3 and the result looks convincing, if compared with the output of GEOMETRY.OUT (see image). I have been using the GRD dataformat before so for this it seems that the plot3d vectors in elk have to look like this:
plot3d
0 0 0
0 0 1
0 1 0
1 0 0

So for those of you that have igor, here my procedure. Feel free to comment on points to improve.

And for those of you who do not like to dive to much into the code:
- The lattice constant remains in bohr for compatibility with loading GEOMETRY.OUT in VESTA.
- You can change the valueof aB in the 3. line if you want Angstroem.

Convert it with VESTA orIt leaves the lattice constant in bohr, but you can change the value of aB if you like A better.

function elk_3Dplot2VESTA() // (plot3dFile, title)

    string plot3dFile = "RHO3D.OUT" // string plot3dFile
    string title = "generic name" // string title
    variable aB = 1//0.52917720859 // stay in bohr for VESTA compatibility with GEOMETRY.OUT

    close/A
    //  pathInfo importPath 
    NewPath/O importPath
    
    
    // ################################################
    // BEGIN - read GEOMETRY.OUT
    // ################################################
    
    variable refGeo
    
    variable a1, a2, a3 // components of 1. lattice vector
    variable b1, b2, b3 // components of 2. lattice vector
    variable c1, c2, c3 // components of 3. lattice vector
    
    string GEOfile = "GEOMETRY.OUT"
    Open/R/Z=2/P=importPath refGeo as GEOfile
    string line

    variable g
    for(g=0;g>-1;g+=0)

        FReadLine refGeo, line
        if(strlen(line)==0)
            break
        endif
        if(strsearch(line, "avec", 0)>=0)
            FReadLine refGeo, line
            sscanf line, "%f  %f  %f " , a1, a2, a3
            FReadLine refGeo, line
            sscanf line, "%f  %f  %f " , b1, b2, b3
            FReadLine refGeo, line
            sscanf line, "%f  %f  %f " , c1, c2, c3
        endif
    endfor          
    close/A
  
    // ################################################
    // BEGIN - read "3D data".OUT
    // ################################################
    
    string exportLine
    string dumpStr
    variable dumpVar
    variable ref3dIN, ref3dOUT
    string numX, numy, numZ
    string intensity

    string fileName = plot3dFile
    Open /R/P=importPath ref3dIN as fileName

    FReadLine ref3dIN, line
    sscanf line ,"%s %s %s %s %s", numX, numy, numZ, dumpStr, dumpStr // get number of grid points in the x,y and z direction of plot 3D
    string exportName = plot3dFile[0,strlen(plot3dFile)-5] + ".GRD"
    print exportName
    Open/P=importPath ref3dOUT as exportName
    exportLine = title
    exportLine += "\n"
    fprintf ref3dOUT, exportLine
    exportLine = num2str(sqrt(a1^2+a2^2+a3^2)*aB) + " " + num2str(sqrt(b1^2+b2^2+b3^2)*aB) + " " + num2str(sqrt(c1^2+c2^2+c3^2)*aB) + " "
    exportLine += num2str(elk_vec2ang(b1,b2,b3,c1,c2,c3)) + " " + num2str(elk_vec2ang(a1,a2,a3,c1,c2,c3)) + " " + num2str(elk_vec2ang(a1,a2,a3,b1,b2,b3)) + " "
    exportLine += "\n"
    fprintf ref3dOUT, exportLine

    exportLine = numX + " " + numY + " " + numZ + " "
    exportLine += "\n"
    fprintf ref3dOUT, exportLine

    variable r
    for(r=0;r>-1;r+=0)

        FReadLine ref3dIN, line
        if(strlen(line)==0)
            break
        endif
        sscanf line ,"%f %f %f %s", dumpVar,dumpVar,dumpVar, intensity
        exportLine = intensity
        exportLine += "\n"
        fprintf ref3dOUT, exportLine

    endfor
        close/a

end
function elk_vec2ang(x1,x2,x3,y1,y2,y3)

    variable x1,x2,x3,y1,y2,y3

    return (360/2/pi)*acos( ( x1*y1 + x2*y2 + x3*y3 ) / ( sqrt(x1^2+x2^2+x3^2) * sqrt(y1^2+y2^2+y3^2) ) )
end

Also thank you Anton for the information about VESTA and the GEOMETRY.OUT file. This is a nice feature.

best wishes,
Eike

Vitaliy Romaka - 2012-11-19

Eike
Are you sure Anton wrote something about GEOMETRY.OUT and VESTA? ;-)
For additional information on volumteric and strucuture data formats, take a look on VESTA manual, probably you will find it useful for your programs.

Ups, sorry. It was in fact you who added the comment about VESTA and GEOMETRY.OUT after Antons post. Seems I missed the little dotted line separating your two posts. So after all, all thanks to you ;)
Actually I did read the manual on volumetric data, but I find the formats are not very well described or only described via links to external pages that did not seem to describe the formats either. So for someone who just wanted a converter that was kind of tough. But luckily, that is not the case anymore.

https://sourceforge.net/p/elk/discussion/897820/thread/0979b76b/