Re: matlab code: isovalues and isosurface

[Liam Groener]

On Jul 15, 2011, at 9:51 AM, Uwe Brauer wrote:

> 
> Hello
> 
> I would like to switch from matlab to octave.
> Most of the code in questions run flawlessly in octave.
> 
> However the following bit of code  is tougher. 
> 
> 
> The matlab code plots in, a more or less sophisticated way,
> levels of the atomic orbits.  The code I have attached
> below, it contains two commands  which are not defined in
> octave, namely camlight and daspect. Both make the plot look
> nicer but are not strictly necessary. All the other
> functions are in principle defined in octave. However the
> code does not run I obtain the following error
> 
> 
> Thanks in advance for any help
> 
> Uwe Brauer 
> ,----
> | error: number of columns must match (0 != 6)
> | error: called from:
> | error:   /usr/share/octave/3.2.3/m/plot/__patch__.m at line 46, column 12
> | error:   /usr/share/octave/3.2.3/m/plot/patch.m at line 55, column 5
> | error:   
> /home/oub/ALLES/tex/vorlesungen/11-12/Calculo-Comput_11_12/Cuantica/orbitales_auto.m
>  at line 13, column 12
> `----
> 
> 
> The code in question is 
> ,----
> | [x,y,z]=meshgrid(-20:.5:20);
> | Psi=FdOn320(x,y,z);
> | m=min(Psi(:));
> | M=max(Psi(:));
> | color=[1 1 0;1 0 1; 0 1 1;0 1 0;1 0 0; 0 0 1; 0 0 0];
> | n=5;
> | for i=1:n
> |     isovalue=m+i*(M-m)/n;
> |     fv = isosurface(x,y,z,Psi,isovalue);
> |     hpatch = patch(fv);
> |     isonormals(x,y,z,Psi,hpatch);
> |     Alphalevel=0.2+0.8*i/n;
> |      
> set(hpatch,'FaceAlpha',Alphalevel,'FaceColor',color(i,:),'EdgeColor','none')
> |      set(hpatch,'FaceColor',color(i,:),'EdgeColor','none')
> | %     daspect([1,1,1])
> |      view(3); 
> |      axis tight
> | %     camlight left; 
> | end

Hi,
I'm not knowledgeable enough to be of much help. However, a couple of 
observations may be useful clues to others:

(1) The failure comes because fv is computed to be empty when i = n, that is 
when isovalue = M (the maximum value in Psi).

(2) What I find very confusing is that the failure occurs almost instantly when 
the for loop is run from 1 to n, but the code runs for more than a minute 
(without failue) if the loop is run from 1 to n-1. It seems like it is actually 
running it from n to 1 in the former case?

I would attach the plot resulting from the 1:n-1 case but it is 11 MB long (in 
pdf form). The final graph is pretty uninteresting; it looks pretty much like 
three stacked disks, a central yellow one with smaller purple ones above and 
below. (Actually there is a bit of an even smaller disk showing too.) However, 
opening the file takes a few seconds and it builds like a movie. This 'movie' 
allows you to see more detail as the orbitals build.