'ERROR: Domain too large for neighbor bins' with fix ave/time

Dear Users

I am trying to run a simulation of a 2d couette flow using NVT to thermostat the system with the compute temp/profile command with the option ‘out bin’.

When I try to get the the temperature profile through fix ave/time, the simulation runs fine for few timesteps and them:

ERROR: Domain too large for neighbor bins (…/neighbor.cpp:1494)

When I comment out the line with the fix ave/time everything runs smoothly.

Any ideas?

thanks,

best wishes

Marcio

test.lmp (1.13 KB)

As the Section_error doc page explains, that error occurs
b/c your box has become gigantic. Likely you are using shrink
wrap boundaries and an atom has blown out of the box.

Steve

Hi Steve,

thanks for your answer. Yes, that’s exactly what is happening. I tried the simulation with periodic and shrink wraped bc and got the same error in both cases. What I am curious about is that when I comment the following line in the input script:

fix 2 flow ave/time 2000 10 20000 c_put mode vector file test.dat

Everything works. It seems that this fix is messing with the temperature control…

Thanks again

It’s unlikely that diagnostic command has anything to do with why
your box is blowing up. You need to monitor the dynamics
and figure out why that is happening.

Steve

Hi again,

I followed your advice and checked the dynamics. Couldn’t find anything wrong and I am getting reasonable results as long as I don’t try to get the binned results from temp/profile and ‘fix ave/time’. I was able to get rid of some warnings once I started building the neighbor list more frequenty but besides that nothing else seems to be wrong.

However, I noticed that when I use the ‘bin out’ and ‘fix ave/time’ the pressure and the temperature of the system drops quickly to zero and the fluid solidifies. Then the error message ‘ERROR: Domain too large for neighbor bins’ appears if I continue to shear the system.

I know that this makes absolutelly no sense but it seems that the combination of ‘out bin’ and ‘fix ave/time’ is somehow preventing the calculation of the kinetic energy tensor used in the calclation of the pressure tensor.

I am giving up and will get the temperature profile by post processing the data. Some python scripting should do the trick.

Thanks again,

Best

Marcio

Hi again,

I followed your advice and checked the dynamics. Couldn't find anything
wrong and I am getting reasonable results as long as I don't try to get the
binned results from temp/profile and 'fix ave/time'. I was able to get rid
of some warnings once I started building the neighbor list more frequenty
but besides that nothing else seems to be wrong.

However, I noticed that when I use the 'bin out' and 'fix ave/time' the
pressure and the temperature of the system drops quickly to zero and the
fluid solidifies. Then the error message 'ERROR: Domain too large for
neighbor bins' appears if I continue to shear the system.

I know that this makes absolutelly no sense but it seems that the
combination of 'out bin' and 'fix ave/time' is somehow preventing the
calculation of the kinetic energy tensor used in the calclation of the
pressure tensor.

I am giving up and will get the temperature profile by post processing the
data. Some python scripting should do the trick.

don't give up yet. there is an explanation and hope.

first off, your test input is creating a *huge* amount of dangerous
builds. that is not good. you need to increase your neighbor list
skin.

with some experimenting i found that the root of your problem is that
there is some conflict arising using the temp/profile compute from
multiple places. if you'd create a _second_ temp/profile compute that
is only used by the fix ave/time, your simulation will continue as you
hope it to be. apparently, there is something in how fix ave/time
invokes the compute that massively throws off fix nvt which in turn
results in the unexpected behavior of your simulation.

not sure what is the real root of this issue, but at least you *do*
have a workaround now.

axel.

Hi Axel,

Thanks. It worked.

Best

Marcio