Jmol and c2x

The natural environment of Jmol is displaying molecules. This site has an example of Jmol with ethene. However, it can cope with periodic systems too.

The most convenient form for volumetric data is the .cube format. However, Jmol does not read unit cell dimensions from this format, so two input files are required for this example, a structure in FeO.cell and the volumetric data in FeO.spin.cube.gz. Like XCrysDen, it can open gzipped files directly.

After starting Jmol, its console needs to be opened (File, Console), and then the following typed:

  load "FeO.cell" packed
  connect delete
  isosurface pos cutoff 0.06 "FeO.spin.cube.gz"
  isosurface neg cutoff -0.06 "FeO.spin.cube.gz"

The "connect delete" command removes the bonds (which jmol finds too many of), and, after the above, one should see:

Jmol with spin density

If one wishes to tile multiple cells, this can be achieved with

  load "FeO.cell" {1 2 2} packed
  connect delete
  isosurface spin sign cutoff 0.06 "FeO.spin.cube.gz" lattice {1 2 2}

where here the use of "sign" produces a single isosurface with positive and negative sheets. This leads to

Jmol tiled with spin density

This looks very confused, as the isosurfaces do not quite join correctly cleanly at the cell edges. However, rotation produces

Jmol tiled and rotated with spin density

which looks correct.