AK K64G Demo Quick Start Guide 2a: Modifying the vegetation parameter Specific Leaf Area

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-modified plant physiological parameter, slatop, Specific Leaf Area (SLA) at top canopy (unit: m2/gC).

(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, and Customize ELM outputs in user_nl_elm, in a temporary work directory.

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

(4) Check a couple of ELM output variables, e.g. TLAI, LEAFC, etc., in jupyter notebook.

I. Parametering ELM Demo Example A

NOTE, assuming that you've already done with AK-K64G Demo Quick Start Guide 2. one year simulation of transient run.

AND, you should have TWO (2) containers, one for running ELM model (but stopped), another for visualizing outputs in jupyter notebook which is active in your internet brower. Your laptop layout should be in some ways like following:

TWO Terminal windows:

ELM visualizing Jupyter notebook in internet brower:

STEP 1. Modifying ELM parameter, slatop, Specific Leaf Area at top canopy.

• If NOT YET, Click Jupyter Notebook for visualizing's Left Panel Folder brower, and Click open folder work/kougarok, and one of files for ELM parameters, clm_params.txt, like following:

NOTE that, in this Demo, we will aslo show how to customize user_nl_elm, for output variable LEAFN, leaf biomass N, which originally not meant to output in AK-K64G Demo Quick Start Guide 2. one year simulation of transient run.

• Scrolling down the file clm_params.txt to Line 170-172 (shown in shaded), where are the header information of parameter slatop.
  

• Further Scrolling down to Line 1327-1329 (shown in shaded are the 12th and 13th values for what we're interested in this Demo).

• For an example, modify default value of 0.03 of the 13th (c3_arctic_grass), to 0.0165 (m2/gC leaf), i.e. thicker leaf per biomass.

NOTE: this value here is totally assumed, implying USER should obtain its real value from field/lab works or literature studies.

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 3 of this Demo.

STEP 2. (OPTIONALLY) Add ELM output of LEAFN and other vegetation N varibles into user_nl_elm, which will control ELM's actual output variable list.

• Click-open file user_nl_elm in folder /work/kougarok, which had already customized but NO vegetation N variables output originally, as shown:

• Add TOTVEGN, LEAFN, etc. (separated by comma) into the list. NOTE again the file will be automactically saved, but you may manully save it for sure.

STEP 3. Re-Run the model of 1 year transient simulation using OLMT

• In the 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=MySLA so that this demo won't erase AK-K64G Demo Quick Start Guide 2. one year simulation of transient run:

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_nyears.sh --transient_years=1 --case_prefix=MySLA

STEP 4. Visualizing newly-simulated ELM output variable, TLAI, LEAFC, LEAFN, and/or others.

• AFTER STEP 3 (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 to move your mouse pointer to cell [3], and clicking the dropdown arrow, choose case name MySLA_...:

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

• • Click the one-step advance button (OR CTRL+Enter) and move cursor down further to Choose Variable Name dropdow, and clicking the dropdown arrow, it will show whole list of variables from ELM outputs, and Choose one, such as TLAI, total leaf area index:

• AND, then Clicking open menu Run, and clicking Run Selected Cell and All Below:

THEN, it will plot like following:

FOR LEAFC, we can do similarly to show as following:

REPEAT STEP 1 - 4, to obtain reasonably well LAI and leaf biomass 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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