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A few more wording adjustments and typo corrections for the DISPERSIO…
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…N case
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jsauer-NCAR committed Aug 9, 2024
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Expand Up @@ -48,12 +48,12 @@ Note that this example requires customization of the initial condition file. Fol
4. Execute the Jupyter notebook provided in **tutorials/notebooks/Dispersion_Prep1.ipynb** to create the topography file *Topography_504x498.dat*, which will be written to the **Example07_DISPERSION_SBL** subdirectory. Users will need to set code:`path_case` in the "Generate the WOA hill terrain file" section to specify the full path to and including the **Example07_DISPERSION_SBL** subdirectory. Be sure to include the trailing slash :code:`/`.
5. The FastEddy code will write its output to an **output** subdirectory. Create an **output** directory, if one does not already exist.
6. Run FastEddy for 1 timestep using the default state of the (*Example07_DISPERSION_SBL.in*) and required binary terrain file generated in the previous step, specified as input through the FastEddy parameter file (:code:`topoFile`). This step creates an output file *FE_DISPERSION.0* that includes the topography and establishes a terrain-following vertical coordinate grid.
7. Execute the Jupyter notebook provided in **tutorial/notebooks/Dispersion_Prep2.ipynb** to modify the surface roughness distribution over the hill. This run of the Jupyter notebook in the next step will write an *FE_DISPERSION.0* file in an **initial** subdirectory. Create an **initial** subdirectory, if one does not already exist. Users will need to set code:`path_case` in the "Modify z0 after terrain has been incorporated" section to specify the full path to and including the **Example07_DISPERSION_SBL** directory. Be sure to include the trailing slash :code:`/`.
8. Execute the Jupyter notebook provided in **/tutorial/notebooks/Dispersion_Prep3.ipynb** to create the source specification input file. Users will need to set :code:`path_base` in the "Create the input file with AuxScalar information" section to specify the full path to and including the **Example07_DISPERSION_SBL** subdirectory. Be sure to include the trailing slash :code:`/`. This run will produce a *Example07_sources.nc* file in the **Example07_DISPERSION_SBL** subdirectory.
7. Create an **initial** subdirectory under **Example07_DISPERSION_SBL**, if one does not already exist. Execute the Jupyter notebook provided in **tutorial/notebooks/Dispersion_Prep2.ipynb** to modify the surface roughness distribution over the hill. Running this Jupyter notebook will create a new *FE_DISPERSION.0* file in the **initial** subdirectory. Users will need to set code:`path_case` in the "Modify z0 after terrain has been incorporated" section to specify the full path to and including the **Example07_DISPERSION_SBL** directory. Be sure to include the trailing slash :code:`/`.
8. Execute the Jupyter notebook provided in **/tutorial/notebooks/Dispersion_Prep3.ipynb** to create the source specification input file. Users will need to set :code:`path_base` in the "Create the input file with AuxScalar information" section to specify the full path to and including the **Example07_DISPERSION_SBL** subdirectory. Be sure to include the trailing slash :code:`/`. Executing this notebook will produce a *Example07_sources.nc* file in the **Example07_DISPERSION_SBL** subdirectory.
9. Adjust the *Example07_DISPERSION_SBL.in* file to specify the targeted initial condition file (:code:`inPath`, :code:`inFile`) by removing the :code:`#` just to the right of the equal sign to uncomment these parameters values. Uncomment the pre-formed passive tracer source file (:code:`srcAuxScFile`). Remove the value of :math:`0` and uncomment the value of :math:`2` for the number of source emissions (:code:`NhydroAuxScalars`). Run FastEddy for :math:`1` h of the simulation by changing :code:`frqOutput`, :code:`Nt`, and :code:`NtBatch` removing the values of :math:`1` for each and the (:code:`#`) to uncomment appropriate full-simulation parameters values. The emissions begin :math:`45` min into the simulation.

Two FastEddy simulation setups are provided for this tutorial, corresponding to weakly stable (*Example07_DISPERSION_SBL.in*) and convective conditions (*Example07_DISPERSION_CBL.in*). The initial condition and terrain preparation steps only need to be carried out once for the stable case, then can be reused directly in the convective stability case. Additionally, the CBL case is set up to demonstrate the use of N-to-N binary outputs.
To run the convective case and exercise the binary output functionality, create a **Example07_DISPERSION_CBL** subdirectory and change to that directory. Create an **initial** sub-directory and copy the initial condition file from **Example07_DISPERSION_SBL/initial/** into the **Example07_DISPERSION_CBL/initial/** subdirectory. Create an **output_binary** sub-directory where binary files will be written during the simulation. Then personalize and use the batch submission script **/scripts/batch_jobs/fasteddy_convert_pbs_script_casper.sh** which will invoke a python script (**/scripts//python_utilities/post-processing/FEbinaryToNetCDF.py**) to convert the per-rank binary files from each output timestep into a single aggregate NetCDF output file per timestep analogous to those resulting from the SBL case.
Two FastEddy simulation setups are provided for this tutorial, corresponding to weakly stable (*Example07_DISPERSION_SBL.in*) and convective conditions (*Example07_DISPERSION_CBL.in*). The initial condition and terrain preparation steps only need to be carried out once for the stable case, then can be reused directly in the convective stability case. Additionally, the CBL case is set up to demonstrate the use of a rank-wise binary output mode in FastEddy for efficient dumping of the model state to file.
To run the convective case and exercise the binary output functionality, create a **Example07_DISPERSION_CBL** subdirectory and change to that directory. Create an **initial** subdirectory and copy the initial condition file from **Example07_DISPERSION_SBL/initial/** into the **Example07_DISPERSION_CBL/initial/** subdirectory. Create an **output_binary** subdirectory where binary files will be written during the simulation. Then personalize and use the batch submission script **/scripts/batch_jobs/fasteddy_convert_pbs_script_casper.sh** which will invoke a python script (**/scripts//python_utilities/post-processing/FEbinaryToNetCDF.py**) to convert the rank-wise binary files from each output timestep into a single aggregate NetCDF output file per timestep analogous to those resulting from the SBL case.

Visualize the output
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