|Subject:||Re: [ESPResSo-users] different simulation scenario on desktop or cluster|
|Date:||Wed, 07 Aug 2013 23:01:08 +0200|
|User-agent:||Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20130620 Thunderbird/17.0.7|
Bonded interactions are only computed for particles that are located on the same CPU. If you increase the number of cores, the range over which a bond can be computed, gets shorted. However, any reasonable bond is much shorter than your box dimensions, so that bond broken errors definitely point to excessive forces. That it "works" on your desktop probably simply means that on that machine, the long bonds can still be accommodated, but it is very likely that your simulation is still aphysical. In particular, I doubt that the problem is due to MPI or the machine, but rather a problem of your setup. An easy check would be to run just with 6 cores or even one core on the cluster, just as on your desktop.
To check the physics of your simulation, just write out the energies, and check that in particular the kinetic energy fluctuates around 1/2 N k_BT, where N is the number of degrees of freedom. Although, there should be no other strong energy drift.
Under most circumstances, it is very likely that you actually need a warmup phase. However, when combined with walls, capping the wall forces is usually not a good idea, since particles are then not hindered from penetrating the hard core of the wall constraint. Therefore, you should use the individual force cap feature, and only set a cap radius for the particle-particle interactions, see the User's guide for details on "inter forcecap individual".
On 07.08.13 12:36, Arash Azari wrote:
-- JP Dr. Axel Arnold ICP, Universität Stuttgart Allmandring 3 70569 Stuttgart, Germany Email: address@hidden Tel: +49 711 685 67609
|[Prev in Thread]||Current Thread||[Next in Thread]|