Shiny Pictures

Today, Felix introduced me to his new density analysis code and how he translates the resulting .cube-files into shiny 3D-pictures. 

His density analysis stuff comes in really handy for the characterization and interpretation of excited-states. There will be a paper out very soon, which you should definitely read (and cite)!

Transition densities of the bright
2 A1 (top), 1 B1 (middle), and
lowest 1 A2 singlet excited states
of nitrobenzene at the ADC2/
cc-pVDZ level of theory

What impressed me even more coming in even handier was the degree of automation he established for turning the .cube-files into pictures via VMD. He wrote a post about that some time ago and since then I guess I could have saved 2 or 3 days of work if I read and used it ever since. If you belong to the group of people using VMD to render MOs the manual way, you should really look into this his post or continue reading here.

After he showed me his work today, I basically stole his bash script, added options to render either two or three isosurfaces instead of just one and then spent the whole day adjusting the surface properties to make the pictures as shiny and informative as possible. If you like the results shown on the right side (using 3 isosurfaces with the standard isovalues of our script (0.0128, 0.0032, 0.0008), you might want to read on and learn how the script works:

If executed in a folder, it iterates over all .cube files present to write out 4 files:
load_all_plt.vmd
plot_all.vmd
convert.bash
vmd_plots.html.

Next, the user reads the geometry (e.g. from any xyz file) into vmd (vmd file.xyz), which needs to have the same orientation as in the job that created the cube files.

Afterwards, the vmd option "load visualization state" is used to read in the "load_all_plt.vmd" file. This script basically tells VMD to load all the .cube files and sets the options for the surfaces. At this point, the user can adapt the visualization and orientation of the molecule according to his wishes.

After selecting a reasonable orientation for the molecule in the usual way (with the mouse), the "plot_all.vmd" file is loaded, causing VMD to successively render all .cube files found in the folder yielding a bunch of .tga picture files.

Now, the convert.bash script is executed from the terminal to turn all those .tga files into .png files, which can be viewed in a very convenient way - by just opening the .html file with any browser. - DONE

Again, many thanks to Felix for this script! Thank him by (using his analysis tools and) citing is work!

And here is the script:
#!/bin/bash
# 0. $pointval mo 65-74 (Turbomole), plots (QChem), ...
# 1. call this script
# 2. open the molecular structure file in VMD
# 3. load the .plt/.cube files and some settings
#    - "Load state" load_all_plt.vmd
#    - click "Apply" in "Graphical Representations"
# 4. adjust perspective
# 5. "Load state" plot_all.vmd

###
ifmt=cube
ofmt=tga
out=load_all_plt.vmd
plot=plot_all.vmd
conv=convert.bash
html=vmd_plots.html
ncol=4
###

echo 'USAGE: $0 [<2 or 3 surfaces, STD = 3 >] [<highest iso, STD(2/3) = (0.1/0.128)>]'

isotemp=$2

if [ $1 -eq 2 ]
then
  isov=${isotemp:=0.01}
  isov2=`echo $isov'/8' | bc -l`
  isov3=0.99

#isovalue of 0.99 will produce no surface
  echo 'Using 2 surfaces for isovalues:'
  echo $isov $isov2
  echo "material change opacity Glass3 0.150000" > $out
  echo "material change diffuse Glass3 0.10000" >> $out
elif [ $1 -eq 3 ]
then
  isov=${isotemp:=0.0128}
  isov2=`echo $isov'/4' | bc -l`
  isov3=`echo $isov'/16' | bc -l`
  echo 'Using 3 surfaces for isovalues:'
  echo $isov $isov2 $isov3
  echo "material change opacity Glass3 0.400000" > $out
else
   echo "Please enter 2 or 3 for # of surfaces!"
   echo "Falling back to 3 surfaces with standard values"
   isov=0.0128
   isov2=0.0032
   isov3=0.0008
  echo "Using standard isovalues: "
  echo "Values: "$isov $isov2 $isov3
  echo "material change opacity Glass3 0.400000" > $out
fi

echo "axes location Off" >> $out
echo "display projection Orthographic" >> $out
echo "display rendermode GLSL" >> $out
echo "display depthcue off" >> $out
echo "color Display Background white" >> $out
echo "menu graphics on" >> $out
echo "material change diffuse Ghost 0.000000" >> $out
echo "material change ambient Ghost 0.300000" >> $out
echo "material change opacity Ghost 0.100000" >> $out
echo "material change shininess Ghost 0.000000" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol addrep 0" >> $out
echo "mol modmaterial 1 0 Opaque" >> $out
echo "mol modmaterial 2 0 Opaque" >> $out
echo "mol modmaterial 3 0 Glass3" >> $out
echo "mol modmaterial 4 0 Glass3" >> $out
echo "mol modmaterial 5 0 Ghost" >> $out
echo "mol modmaterial 6 0 Ghost" >> $out
echo "mol modstyle 1 0 Isosurface  $isov 0 0 0 1 1" >> $out
echo "mol modstyle 2 0 Isosurface -$isov 0 0 0 1 1" >> $out
echo "mol modstyle 3 0 Isosurface  $isov2 0 0 0 1 1" >> $out
echo "mol modstyle 4 0 Isosurface -$isov2 0 0 0 1 1" >> $out
echo "mol modstyle 5 0 Isosurface  $isov3 0 0 0 1 1" >> $out
echo "mol modstyle 6 0 Isosurface -$isov3 0 0 0 1 1" >> $out
echo "mol modcolor 1 0 ColorID 0" >> $out
echo "mol modcolor 2 0 ColorID 1" >> $out
echo "mol modcolor 3 0 ColorID 0" >> $out
echo "mol modcolor 4 0 ColorID 1" >> $out
echo "mol modcolor 5 0 ColorID 0" >> $out
echo "mol modcolor 6 0 ColorID 1" >> $out
echo "" > $plot

echo "#!/bin/bash" > $conv
chmod +x $conv

echo -e "<html>\n<head></head>\n<body>" > $html
echo -e "<table>\n<tr>" >> $html

N=0
for I in *$ifmt
do
   echo "mol addfile $I" >> $out
   echo "mol modstyle 1 0 Isosurface  $isov $N 0 0 1 1" >> $plot
   echo "mol modstyle 2 0 Isosurface -$isov $N 0 0 1 1" >> $plot
   echo "mol modstyle 3 0 Isosurface  $isov2 $N 0 0 1 1" >> $plot
   echo "mol modstyle 4 0 Isosurface -$isov2 $N 0 0 1 1" >> $plot
   echo "mol modstyle 5 0 Isosurface  $isov3 $N 0 0 1 1" >> $plot
   echo "mol modstyle 6 0 Isosurface -$isov3 $N 0 0 1 1" >> $plot
   echo "render TachyonInternal $I.$ofmt" >> $plot

   echo "convert $I.$ofmt $I.png" >> $conv
   echo "rm $I.$ofmt" >> $conv

   echo "<td><img src=\"$I.png\" border=\"1\" width=\"400\">" >> $html
   echo "$I<br></td>" >> $html

   N=$(($N+1))

   if [ $((N%$ncol)) -eq 0 ]; then
      echo "</tr><tr>" >> $html
   fi
done

echo -e "</tr></table>" >> $html
echo -e "</body>\n</html>" >> $html

echo "... finished."