Hello,
I'm posting my question in this thread since I am experiencing a similar problem. First, let me say that I'm fairly new to WRF but I've been consulting with a colleague with a good amount of experience and so far we've not been able to figure out the problem.
My setup:
The grid is 5 km and I'm trying to use thin vertical levels starting at about 50 m up to a height of ~42 km, where the layers have a thickness of ~600 m. The goal is to resolve orographic gravity waves in the Andes (i.e. complex terrain). I'm using the automatic levels configuration. The boundary conditions are from ERA-5 (obtained following this guide:
Initializing the WRF model with ERA5 (pressure level)). Following my colleague's suggestion, I'm not using 16pts interpolants to avoid problems with my tight levels (only using wt_average_4pt in METGRID.TBL). I've tried both highres and lowres in geogrid and I have the same problem. I'm attaching the relevant files.
My problem:
WRF crashes after the first time step. However, if I increase the dzbot from 50 to, say, 100, it works. Following a few online discussions, including this old post (
Extrapolation over complex terrain and propagation to real.exe), I was able to find this issue which might be what's causing the problem. I've generated a figure to explain what I've observed. I read the first met_* file and the wrfinput and calculated the dz over my domain. Then I analyzed one example where one of the dz values is < 0:

The top plot is the DZ from the wrfinput as a function of geopotential height [(phb + ph) ./ g] and the bottom plot is the met_ data from ERA-5 (after running metgrid) showing pressure (field PRES) as a function of geopotential height (field GHT). The red vertical lines show the terrain height obtained from the met_ and wfinput (variable HGT). I'm not sure if this is a problem, but my guess is that there should not be data below the terrain. It almost looks like real is interpolating and using data below the terrain which is causing the negative dz in the top plot.
Please let me know if I've missed anything that you need to better understand my problem. Any help that you can provide will be greatly appreciated!