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Re: [ESPResSo] analyze pressure and energy problems

From: Axel Arnold
Subject: Re: [ESPResSo] analyze pressure and energy problems
Date: Tue, 16 Jun 2009 11:19:13 +0200
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On Monday 15 June 2009 19:45, Markus Deserno wrote:
> Dear İbrahim,
> without having looked too much at your specific problem...
> ...but: In "natural" simulation units, assuming all masses are
> essentially the same, the integration time step should not
> be 1, rather maybe 0.01.  How many seconds that represents
> is a whole different question.  This requires mapping and
> depends not only on your masses but also the hard-to-guess
> speedup factor which you get from coarse-graining.  It seems
> to me that your system might just blow up.


just to add to that: if you look carefully at the error message, you see that 
Tcl complains that the result of "analyze energy kinetic" is not a valid 
floating point number. And indeed, if you would print the value directly, 
without enclosing in with "expr", you would see that in your case the result 
is "nan", i.e. "not a number", after the first step, i.e. that some particle 
velocities are completely out of range. This actually applies to most 
energies in your system, btw... So, Markus is definitely right that your 
timestep is about 2 orders of magnitude too large.

This also explains the signal 7 you received: if particle velocities are NaN, 
the positions also become NaN, and the domain decomposition runs into 

Finally, regarding the warning from P3M: it is a bit misleading: P3M cannot 
calculate the pressure tensor, however, it can calculate the scalar pressure. 
The warning is only regarding the tensorial pressure, which for 
electrostatics is a bit more cumbersome to calculate.


Dr. Axel Arnold 
Fraunhofer SCAI
Schloss Birlinghoven, 53754 Sankt Augustin, Germany
Tel: +49 2241 14 2575

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