Crystal structures with gOpenMol Caspar Fall October 2000

Warning: This information is provided primarily for users at the University of Exeter!

Three-dimensional crystal structures can be conveniently rendered in 3D using gOpenMol. There is a copy of the PDF manual kept locally and an HTML manual online.

gOpenMol HowTo:

• Launch gOpenMol using:        ~fall/bin/gom

• Read a crystal structure in XYZ format using:        File/Import/Coords...
• Select the Xmol format, not XYZ, as the latter does not support a comment on the second line of the file.
• Apply

 
• To plot balls and sticks:    View/Atom_Type...
• Click:    Licorice                       then     Apply
• Set:        Cyl_rad to 0.1         then     Apply

 
• To plot wavefunction isosurfaces:
• Generate the 3D grid of points (with AIMPRO, of course :-) If you are using AIMPRO, be warned of two things that are essential:
• The three vectors describing the grid edges must be parallel to z, y, & x (otherwise you will not easily be able to display the atoms too)!
• These vectors must be in the order z, y, and x! This is what gOpenmol expects as input.
• Edit the wavefunction/charge density file and add at the top the following information:

3 2
nz ny nx
zmin zmax ymin ymax xmin xmax

where nz, ny and nx are the numerical grid sizes and xmin, xmax, ymin, ymax, zmin, zmax are the physical grid extrema. Two important points to be warned about:

• Note that because the XYZ file is in Angstroms, these lengths should also be in Angstroms!
• The number of points in each dimension of the grid (nz,ny,nx) is one greater than the number of points requested in the AIMPRO dat file!

 
• The 3D-data file should now look similar to this:

3 2
52 52 52
-3.175063 3.175063 -3.175063 3.175063 -3.175063 3.175063
  -.00000315
  -.00000658
  -.00001166
  -.00001883
  -.00002850
  etc...
 
• The data file must now be converted into a binary format (*.plt file). To do this, run in gOpenMol:

Run/pltfile (conversion)
• Set the input (*.xyzi) and output files (*.plt)
• Click:    Formatted ==> Unformatted
• Apply

• Plot the contour using:        View/Contour...
• Import the *.plt file you have generated
• Set the isosurface contour level, colour and transparency (under Details...)
• Apply

• Under Edit/Display_properties...
• You can change the background colour.
• Try setting the bond_display_type to Smooth to get rid of two-coloured bonds.

• Printing can be done with:    File/Hardcopy...

Example:

C6H12 molecule:


 

Caspar Fall              email: C.J.Fall@exeter.ac.uk
University of Exeter     phone: +44 (1392) 264198
Exeter EX4 4QL, UK       fax  : +44 (1392) 264111

1st October 2000