AK K64G Demo Quick Start Guide 2b: C Cycle (adjusting Vcmax via flnr)

NGEE-Arctic: AK-K64G simulation example 2 - Parameterization

This example 2B runs a single-point, extracted from half-degree Global data, ELM v2 simulation, within which NGEE Kougarok Mile 64 study site located, Using user-tuned parameter, flnr, Fraction of Leaf Nitrogen in Rubisco, to adjust specific PFT's photosynthesis parameter Vcmax, namely VCMAX25TOP (top canopy Vcmax at 25 degree C ) in ELM.

(1) It will start from an initial restart file from after-final-spinup in regular run of a site, but with option --site_name=kougarok

(2) It will modify 'clm_params.nc', parameter file for ELM to read, in a temporary work directory.

(3) Re-run ELM, using newly-generated 'clm_params.nc'.

(4) Check specified PFT VCMAX25TOP (or GPP/NEP/NEE) output in jupyter notebook.

REPEAT (2)-(4), for purpose to obtain a reasonbly well GPP simulation for site, or Vcmax if observed.

NOTE that this demo is very similar to Leaf parameter SLA modification

I. Parametering ELM Demo Example B

STEP 1. Modifying ELM PFT's leaf rubisco N fraction, flnr, to adjust VCMAX25TOP

• Click Jupyter Notebook for visualizing's Left Panel Folder brower, and click open folder work/kougarok, and one file, clm_params.txt, like following,

OR, if clm_params.txt has already been opened, click the upper windows' tab:

NOTE that clm_params.txt is an ASCII file converted from clm_params.nc which actually read by ELM, and editable in juypter notebook text editor.

• Scrolling down the file clm_params.txt to Line 375-378 (shown in shade), where are the header information of parameter flnr.
  

• Further Scrolling down to Line 1104-1129 (shown in shade), where are the PFT names and order for current ELM model.

NOTE that Line 1116 and 1117 are two primary PFTs possibly exit in high-latitude region, including Arctic, in default ELM model. REMEMBER their orders, 12th and 13th respectively. NEXT we will try to edit the 13th (c3_arctic_grass) value of parameter flnr.

• Further Scrolling down to Line 1485-1487 (shown in shaded are the 12th and 13th values for what we're interested in this Demo).

• For an example, modify default value of 0.1365 of the 13th (c3_arctic_grass), to 0.2365.

NOTE that Jupyter Notebook text editor will automatically save this modified clm_params.txt file. For sure, you may click open menu File and chose save text to save your change(s).

AND, this modified clm_params.txt will be converted back to overwrite clm_params.nc when running OLMT example script in STEP 2 next.

STEP 2. Re-Run the model of 1 year transient simulation using OLMT

• In Terminal for running ELM docker container, Type the following command, OR, copy/paste it. NOTE the command line is appended one more option --case_prefix=MyFlnr so that this demo won't erase any previous same-site simulations.

docker run -t -i --hostname=docker --user=modeluser -v elmdata:/inputdata/ -v elmoutput:/output/ -v elmwork:/tmp/ fasstsimulation/elm-builds:elm_v2-for-ngee_multiarch /bin/bash /tools/OLMT/examples/site_fullrun_docker_transient_oneyear.sh --transient_years=1 --case_prefix=MyFlnr

OR, by pressing UP-ARROW key one time (to get the same command as used before), and append/edit NEW --case_prefix=MyFlnr, as following:

STEP 3. Visualizing new ELM output variable, VCMAX25TOP, and/or others.

• AFTER STEP 2 (re-run) finished, Click-open UPPER Tab Plot_ELM_variable_v2.ipynb file again.

• THEN, click that restart the kernel & run all cells button, , it will run script in all-steps at once, and will plot **GPP** by default. NOTE this rerun script is Needed to refresh simulations just finished.

• Scrolling up/down to move your mouse pointer to cell [3], and clicking the dropdown arrow, choose case name MyFlnr_...:

• Click the one-step advance button in the upper bar (OR CTRL+Enter) to move cursor down to cell [5], choose Individual PFTs:

• Scrolling up/down to move your mouse pointer to variable name dropdown box, and by clicking the dropdown arrow, it will show whole list of variables from ELM outputs, and Choose one, such as VCMAX25TOP, Canopy Top Vcmax at 25 degree C, like:

• AND, then Clicking one-step advance button, in the upper bar, until end of script,

OR, Clicking open menu Run, and clicking Run Selected Cell and All Below:

THEN, it will plot like following:

YOU may notice what have changed, comparing to default run shown in the previous default Demo.

REPEAT STEP 1 - 3, to obtain reasonably well VCMAX for this 13th (c3_arctic_grass) PFT. THEN changing other concerned PFT(s).

FINALLY, save modified clm_params.nc into your file systems, like following (back to Docker App)

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