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I have some questions on some simulation details that I couldn't find from the manual.
macro, micro
In the manual, the number of outer and inner MC steps are defined by macro and micro, respectively. What is the exact difference between these parameter? Specific MC moves are only applied, for example micro move?
Potential form of slit simulation box.
What type of potential is applied to the slit geometry? I suspect that the upper and lower bound of the slit box might be charged. I notice that there are peaks of density profile of the charged molecules near the surface, but cannot be sure. It is not critical for my research, but would it be possible for make the wall interact with all of the particles in the system via WCA potential?
Using multiple cores to run faunus
I put export OMP_NUM_THREADS=4 on my bash environment file and run the Faunus, but fail to run it with 4 cores. I also tried bash script as follows, but also failed. I installed Faunus via miniconda. Do you have some idea what should I check for running multi-core simulation?
Thanks for the input; it's very useful for improving faunus and particular the documentation (or lack thereof!).
We discussed this just last week, Iet's ping @rc83. Indeed this is undocumented, and currently the only difference is that analysis is saved to disk every macro step. The total number of MC steps is micro*macro.
slit is like cuboid but there's no PBC in the z direction. Particles are never allowed outside the box in any container (infinite potential).
Again you've found lack of documentation. Currently OpenMP applies only to certain analysis routines and will generally not affect MC simulation speed. We're working on this and it can be hacked in for specific use-cases. If your system equilibrates fast, I can recommend to make multiple runs with different random seeds for now.
Dear Faunus team,
I have some questions on some simulation details that I couldn't find from the manual.
macro
,micro
In the manual, the number of outer and inner MC steps are defined by
macro
andmicro
, respectively. What is the exact difference between these parameter? Specific MC moves are only applied, for examplemicro
move?Potential form of
slit
simulation box.What type of potential is applied to the
slit
geometry? I suspect that the upper and lower bound of theslit
box might be charged. I notice that there are peaks of density profile of the charged molecules near the surface, but cannot be sure. It is not critical for my research, but would it be possible for make the wall interact with all of the particles in the system via WCA potential?Using multiple cores to run faunus
I put
export OMP_NUM_THREADS=4
on my bash environment file and run the Faunus, but fail to run it with 4 cores. I also tried bash script as follows, but also failed. I installed Faunus via miniconda. Do you have some idea what should I check for running multi-core simulation?As always, I appreciate your consideration.
Sincerely,
A user
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