[ESPResSo-users] The myth of checkpointing

[Axel Arnold]

Hi all,

please note that checkpointing never really worked in ESPResSo, even 
when using invalidate_system or similar. Actually I removed 
invalidate_system, as neither the name was reasonable nor was it doing 
anything useful. There are now two replacements:
- a command sort_particles, which should work for checkpointing, but 
there are more caveats to that, see below.
- a flag recalc_forces to integrate which enforces force recalculation. 
This you should use for timing purposes, when you want to recompute the 
very same forces several times.

As for checkpointing, you should consider the following:
- the order of particles is important, as the random numbers are 
distributed sequentially. The new sort_particles command really sorts 
the particles not only across nodes as invalidate_system did, but
also on each node, which was missing.
- blockfile floats are not binarily exact, as they can be stored with at 
most 17 digits precision. Therefore, you need to write binary 
checkpoints. There is since ages a command for that, writemd, and now it 
even has documentation. However, it can only store positions, velocities 
and forces at present.
- other _integer_ information like type or bonds can be stored in a 
blockfile safely, but interaction parameters, time step and all other 
float information should be restored by the very same Tcl command in the 
same order that you used to create them the first time. Only by that all 
internal values will be binary equal.
- You don't have to write out forces. If you do and want to reuse them, 
then you need to specify "reuse_forces" to the very first integrate 
command after reading the checkpoint. If you don't write them, they will 
be recalculated, which can lead to wrong results with LB.
- LB has its own checkpointing, but implies that you should write out 
forces.

For more details, see the updated user's guide.

Best,
Axel


--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609