NOTE: Postprocessors have been written for the following programs:
QChem is an area where terminology is important and the virtual consortium will be developing a hyperglossary to support the effort. Volunteers or contributions are welcome, especially for trying to normalise terms across the different programs.
Note also that Units are important here as a wide variety is used and many programs do not explicitly add units. Energies can be in calories, joules or hartrees and distances in meters, angstroms or bohrs. Markup can be very valuable here and application programs should be able to convert between units.
(The CML files output for these examples are NOT complete - this is because chunks of information have been omitted by the postprocessor. Some of the real numbers have also lost precision - this is simply due to the limitations of JDK1.0 in dealing with formats and not a problem with CML. These problems will disappear.)
This was a simple SCF convergence using Gaussian94. JUMBO has
postprocessed the output, and the TOC shows the convergence history.
The occupied energy levels are also shown, the most obvious effects being
the large difference in the energy for the different atoms.
This was a simple SCF convergence using GAMESS (US version). It's very
similar to the Gaussian document - it's simply a matter of writing a
In this example
MOPAC has been used to calculate the vibrational
eigenanalysis for a planar cyclohexane (a highly energetic
conformational transition state.) (No geometry optimisation was done
so the numbers shouldn't be taken too seriously).
The reader has selected one of the eigenvectors and asked JUMBO to interpret it as a set of atomic displacement vectors (a 'molecular object'). This has been added to the display and is shown as a series of atomic displacements (arbitrary scale) corresponding to the low energy B1g wagging mode. This can be animated if required :-).
In this example, VAMP has been used to calculate the 13C chemical
shifts for a medium-sized molecule. The first screenshot shows the
large number of calculated properties, including the 13C spectrum, displayed
as a BAR graph (all lines of equal intensity). Note also the Eigenvalues
which have been displayed as a graph, showing the gap between occupied and
The next shot shows a very powerful feature of CML which is worth inspecting
in the CML file
There is no restriction on the semantics of a RELATION, and in this case JUMBO shows them by highlighting the subaddress in each object. For atoms this is an increase in size, for peaks it is a different colour and background. Clicking on the "Peak"s in turn gives a hyperactive link between the two components, and this technology is very general.