Trouble Shooting
- What other kMC codes are there?
Kinetic Monte Carlo codes that I am currently aware of,
that are in some form released on the intertubes are
with no claim of completeness :
Though The Google might find you some more.
Please drop me a line if you find any information
inaccurate.
- When I run kmos the GUI way and close it, it seems to hang and I need to use the window manager to kill it.
- This is a bug waiting to be fixed. To avoid it close
the window showing the atoms object by clicking on its
close button or Alt-F4 or whichever shortcut your WM uses.
Running a model it sometimes prints
Warning: numerical precision too low, to resolve time-steps
This means that the kMC step of the current process was so
small compared to the current kMC time that for the processor
. This should under normal circumstances
only occur if you changed external conditions during a kMC run.
Otherwise it could mean that your rate constants vary over
12 or more orders of magnitude. If this is the case one needs
to wonder whether non-coarse graind kMC is actually the right
approach for the system. On the hand because the selection of
the next process will no longer be reliable and second because
reasonable sampling of all involved process may no longer happen.
- When running a model without GUI evaluation steps seem very slow.
- If you have a kmos.run.KMC_Model instance and call model.get_atoms()
the generation of the real-space geometry takes the longest time. If you
only have to evaluate coverages or turn-over frequencies you are
better off using model.get_atoms(geometry=False), which returns an
object with all numbers but without the actual geometry.
- What units is kmos using ?
- By default length are measured in angstrom, energies in eV, pressure
in bar, constants are taken from CODATA 2010. Note that the rate
expressions though contain explicit conversion factors like bar,
eV etc. If in doubt check the resulting rate constants by hand.
- When running the model I sometimes get mysterious infty or nan values!
- This most likely can be traced back to fact that some variable ran outside
its range and is caused by the fact that the wrong kind values are chosen
(Fortran stuff). Kind values are currently all hard-code in the the src
directory at /path-to-export/src/kind_values_f2py.f90 and set for ifort.
While I am working to have this set dynamically at compile time, you have
to figure out the right kind value for your compiler for now.
- How can I change the occupation of a model at runtime?
This is explained in detail at Manipulating the Model at Runtime though
the import bit is that you call
after changing the occupation and before doing the next kMC step.
More to follow.
Please post issues
here
or via email mjhoffmann .at. gmail .dot. com
or via twitter @maxjhoffmann
Todo
Explain post-mortem procedure
