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rwildermuth / omNEUS

Code to calibrate Atlantis NEUS as an operating model for Ch 4 MSE
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Wind energy forcing file #1

Open rwildermuth opened 3 years ago

rwildermuth commented 3 years ago

Hi @gavinfay,

I put together a template for the wind farm mortality scalar here, but I don't see how to connect this to the specific groups I want to force mortality on. Unless the mortsc is a global parameter that affects everything?

Please let me know if this is on the right track.

Thank you, Robert

rwildermuth commented 3 years ago

Hi @gavinfay,

I updated the code here, and tried to compare output from the test runs using the code in scenarioCalcs.R, but they still seem to be the same in both runs (i.e., the mort scenario doesn't have different N values for benthic groups).

I moved the AtlantisTesting directories to the storage1 lab file under rwildermuth/ATLANTIS, if you'd like to take a look there. They were too big to include on DropBox.

Also, in the general run_.nc file, there are the correct number of time points as I've calculated for the test, but the BiomIndx.txt file only has the initial and last time point, even though I said to report output every 1 day in the run.prm file. I'm not sure why those are different, and I'm not sure how to translate the time codes (column t) from the .nc file into days or model time. Do you know how to compare these?

Thank you, Robert

gavinfay commented 3 years ago

BiomIndx.txt is annual values so as you haven't run a full year, only the initial and final time step are output. Time in the .nc file is in seconds.

gavinfay commented 3 years ago

These scenarios look the same. Did you check your .ts file is being read in? You're not writing much output to the log, change the flag(s) in the run file so you get more information from Atlantis, and suggest also sinking what is being written to screen.