Thank you Dr. Kohlmeyer!
"Your 100s of calculations are an embarrassingly parallel problem and thus the time to solution can be easily reduced by a large factor. "
I did not realize this: it should be very useful if I can figure out how to parallelize the problem properly (I’m using my university’s Seawulf cluster).
as I mentioned, this is embarrassingly parallel. you can just write a python (or bash or other script language) script that will generate your 100s of inputs for the 100s of calculations and put each in a different folder. then you can write a script that generates the submission scripts for the cluster where each bundles multiple runs into a single script.
if your cluster supports job arrays, you can exploit that feature as well. in the simplest case you would run each calculation in serial then you would place as many calculations as you have CPU cores into a single submit script then have in it:
(cd job###; lmp_serial -in in.job### -log log.job### ) &
(cd job###; lmp_serial -in in.job### -log log.job### ) &
(cd job###; lmp_serial -in in.job### -log log.job### ) &
(cd job###; lmp_serial -in in.job### -log log.job### ) &
(cd job###; lmp_serial -in in.job### -log log.job### ) &
…
(cd job###; lmp_serial -in in.job### -log log.job### ) &
wait
submit and wait until all are done and collect the results.
“With shrink-wrapped BCs, you have to consider sample with sufficiently large dimension to minimum surface or finite geometry effects. Otherwise, you won’t get accurate bulk mechanical properties. I am guessing you are interested in structure and mechanical properties.”
“Tensile tests without periodic boundary conditions are a problem and more difficult”
I’m basing the boundary condition on the previous work done in the research group I’m in (it was actually fixed BC, not shrink-wrapped, although I imagine the problem would be the same). We are running these tests for samples of different sizes, seeing the effect of size on structural and mechanical properties. Our goal is to determine the properties of that size as opposed to the properties of a bulk sample.
However, the sizes are still less than the 10 nm length, with the smallest being 2 nm.
Would using non-periodic BC be an issue for what we are attempting?
with PBC you can use fix deform and easily deform the entire sample homogeneously (because of the PBC the system will pull/push itself when you change the box size). with fixed or shrinkwrap you don’t have this option (changing the box size does not at all impact the sample) but have to pull on each side explicitly, which means you have surface and boundary effects, need to wait until changes due to the pulling have properly propagated throughout the sample, and have different behavior due to the pulling in those faces. hence you need the larger sample size and have to be careful whether the results are really comparable i.e. you first need to do a series of test calculations to confirm which geometry will reproduce the results you are looking for.
at the length and time scales of atomic simulations the construction of the system always needs to be taken into account when planning simulations. things are not as straightforward as with physical experiments, while at the same time, you have more control and can do things that are impossible in the real world.
axel.