Hi,
I think it can also happen if you place your particles to far apart.
This way the bond is already broken, before any forces are applied.
In this case the particles are created with the polymer command, and
than later, in line 150, put to a random place. If this is avoided,
the simulation works just fine.
Kind Regards,
David
On 31/08/15 16:51, Peter Košovan wrote:
Hi all,
as already mentioned by Kai, the "bond broken" error
occurs when you initially put your particles too close (or
too far), such that huge forces occur and within one step
they move more than the bond length. Then the simulation
"explodes".
The generic Espresso solution to this problem is to use
force capping and gradually increase the cap until the
overlaps are gone - see UG and the pe_solution.tcl example
script. This is the primary purpose of the "warmup" phase.
You a cycle called "warmup" in your script, but the force
capping has been moved outside the warmup loop. For this
problem it does not matter whether you use the polymer
command or set particle positions manually.
Btw: perhaps this problem might be added to the Espresso FAQ.
Greetings,
peter
Pokud
je tento e-mail součástí obchodního jednání, Přírodovědecká
fakulta Univerzity Karlovy v Praze:
a)
si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení
důvodu,
b)
stanovuje, že smlouva musí mít písemnou formu,
c)
vylučuje přijetí nabídky s dodatkem či odchylkou,
d)
stanovuje, že smlouva je uzavřena teprve výslovným dosažením
shody na všech náležitostech smlouvy.
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