Annotated Matlab diary

Load the files and reshape the matrices

>> cd Na24
>> ls

ans =

1.jpg
2.jpg
3.jpg
4.jpg
5.jpg
6way.jpg
6wayplot.ps
Na24.grd
Na24noH.grd
na
nalog
nalogold
naorg
tf1.jpg


>> load naorg
>> naorg_sq24 = reshape(naorg',140,140);
>> surf(naorg_sq24)
>> cd ..
>> ls

ans =

Na24
Na32
sub


>> cd Na32
>> ls

ans =

Na32.grd
na32
na32.jpg
na32surfl.jpg
na32surflclipped.jpg


>> load na32
>> size(na32)

ans =

        4900           4

>> naorg_sq32 = reshape(na32',140,140);
>> xstep = (4.75- -4.75)/139

xstep =

    0.0683

>> x = [-4.75:xstep:4.75];
>> size(x)

ans =

     1   140

>> y = x;

Make the surface plot figure

Na24 electron density surface

>> subplot(3,1,1)
>> surfl(x,y,naorg_sq24);
>> shading interp
>> colormap pink
>> title('Na24 electron density')
>> xlabel('distance, angstrom'),ylabel('distance, angstrom'),zlabel('e^-/angstrom^3')

Na32 electron density surface

>> subplot(3,1,2)
>> surfl(x,y,naorg_sq32);
>> shading interp
>> colormap pink
>> title('Na32 electron density')
>> xlabel('distance, angstrom'),ylabel('distance, angstrom'),zlabel('e^-/angstrom^3')

Na24 - Na32 electron density surface

Here is the operation to subtract the one density matrix from the other:

>> naorg_diff=(naorg_sq24-naorg_sq32);

Plot it:

>> subplot(3,1,3)
>> surfl(x,y,naorg_diff)
>> shading interp
>> title('Na24 - Na32 electron density difference')
>> xlabel('distance, angstrom'),ylabel('distance, angstrom'),zlabel('e^-/angstrom^3')

Make the contour plot figure

Plot the contours from 0 to 0.5 electrons/angstrom^3.

>> v = (0:0.1:0.5);

Na24 electron density contour

>> subplot(3,1,1)
>> contour(x,y,naorg_sq24,v)
>> axis square
>> title('Na24 electron density')
>> xlabel('distance, angstrom'),ylabel('distance, angstrom')
>> colormap jet

Na32 electron density contour

>> subplot(3,1,2)
>> contour(x,y,naorg_sq32,v)
>> axis square
>> title('Na32 electron density')
>> xlabel('distance, angstrom'),ylabel('distance, angstrom')

Na24 - Na32 electron density contours

Plot the contours from -0.5 to 0.5 electrons/angstrom^3.

>> vv = (-.5:.01:0.5);
>> subplot(3,1,3)
>> contour(x,y,naorg_diff,vv)
>> axis square 
>>  title('Na24 - Na32 electron density difference') 
>> xlabel('distance, angstrom'),ylabel('distance, angstrom')

Pages maintained by
Prof. Ramón Arrowsmith

Last modified November 18, 1999