I don't know why I wasn't seeing this problem with previous models (perhaps because I wasn't importing any CAD or STEP files), but my latest attempts at meshing and selecting specific domains of my model were being thwarted by inconsistent domain definitions. I was previously always manually selecting domains, which is confusing because all domains just get assigned a number when they are created. Worse, sometimes the numbers assigned to domains change when the model rebuilds, especially if there has been a significant change in the model geometry. This results in later steps selecting the wrong set of domains (or boundaries, etc).
To fix this problem, I created new selections (sets of domains, boundaries, or etc that receive their own label and can be selected as a group later in the model). The new selections include:
This is probably also a necessary step for getting reliable results when interfacing with MATLAB, and might explain some weird problems I was running in to a while ago and just made haphazard fixes for.
I use the following mesh steps to get what seems like a pretty reliable meshing:
Note on the skin depth: I defined the thickness of the surface layer by the parameter skin_depth. Since we are interested in how the energy in the surface layer changes with the radius of the fiber, and expect that the surface depth doesn't change much with fiber radius (a very thick fiber will have a few micron surface layer; so will a fiber half that diameter). I managed to get the mesh working with a 15um surface layer, but was having trouble getting a 10um layer. I wasn't completely sure how small a surface layer would be necessary, but for a test mass 1/100 the size of the aLIGO masses, the main part of the fiber would have a radius of 20um, so if we want to study the surface layer for masses down to that size I figure the skin depth should be at most around 10-15um. It would be better to be motivated by the actual scale of the physics going on at the surface--how deep to micro cracks and other lossy imperfections go?
I'm running the frequency study on a small number (2) of frequencies in each decade from 60Hz to 10kHz (so there should be 5-8 total frequencies in the study). I started it at 4:25pm on my local machine, and it hasn't gotten very far in 30 minutes, so I may abort the study and try to make the mesh coarser--especially the distribution settings, which are easy to change.