I am receiving the error bond atoms 8 9 missing on pro 0 step 10, does
this mean the bond is missing, or that the atoms themselves are
missing? The atoms are of type hybrid charge bond. I have a completely
bounded system, with boundary fff, and walls around each plane, does
this mean an atom is still escaping or that there is some fundamental
error in the data file? I checked atoms 8 and 9, and they are within
the bounds of the simulation, so I'm somewhat confused as to what is
causing this error.
thanks,
~Nickhil Rokkam
I am receiving the error bond atoms 8 9 missing on pro 0 step 10, does
this mean the bond is missing, or that the atoms themselves are
missing? The atoms are of type hybrid charge bond. I have a completely
bounded system, with boundary fff, and walls around each plane, does
this mean an atom is still escaping or that there is some fundamental
error in the data file? I checked atoms 8 and 9, and they are within
the bounds of the simulation, so I'm somewhat confused as to what is
causing this error.
lost atoms can also happen inside a system when atoms move too fast.
axel.
Hi Nickhil,
Your initial data file must have folded (to the central simulation
cell) co-ordinates. If you use that with boundary fff, then you are
basically starting with bonds far apart. That's the reason for 'bond
atoms missing' error. You have to unwrap the co-ordinates into the
central sim box before starting fff simulation.
Assuming you are using 'chain.f': Edit chain.f, comment out the PBC
part to generate data file for this run.
Monojoy
It means that an atom on a processor has a bond
to another atom. And it cannot find that 2nd atom,
typically b/c it is too far away from the processor.
Steve