FATES_Logging_Manuscript

Steps to check out codes, and driving/preprocessing/analysis scripts used in the FATES Logging Manuscript

Repository structure

---scripts

Tutorial to configure the CLM(FATES)-logging experiments on CONSTANCE

We provide detailed notes on running the logging experiments on PNNL's CONSTANCE cluster.

Download script repository

setenv BASE_DIR <dir-of-choice>
cd $BASE_DIR
git clone git@github.com:huangmy/FATES_Logging_Manuscript.git

Check out CLM and FATES codes, please check http://www.cesm.ucar.edu/models/cesm2.0/land and https://fates-docs.readthedocs.io/en/latest/index.html for CLM5 and FATES documentations

CLM codes with fates api capatible with https://github.com/NGEET/fates/releases/tag/sci.1.27.2_api.7.3.0

cd $BASE_DIR
git clone -b fates_next_api https://github.com/ESCOMP/ctsm.git clm5.0
setenv CLM_SRC_DIR $BASE_DIR/clm5.0
cd $CLM_SRC_DIR

Update CLM externals to the fates branch used

cp -f $BASE_DIR/scripts/shell/user_machines/Externals_CLM.cfg .

Check out FATES codes, specific branch used is https://github.com/huangmy/fates/tree/fix_export_frac, with minor update from M. Huang to fates release tag sci.1.27.2_api.7.3.0. The update has been integrated to newer fates releases

./manage_externals/checkout_externals

Download input and output datasets

Click the link: https://drive.google.com/drive/folders/1ufnxkE2aw6bueLG7LttR-N8UrStLgCqZ?usp=sharing
Unzip and untar inputdata.tar.gz and outputdata.tar.gz in $BASE_DIR

Configure a user_defined single point CLM5 simulation

cd $BASE_DIR/scripts/shell

Spin up the intact forest

bash create_fates-clm_1x1pt_km83_intact_spinup.sh

Intact Simulation

bash create_fates-clm_1x1pt_km83_intact_sim.sh 

Logging Experiments

bash create_fates-clm_1x1pt_km83_logging.sh

Extract and analyze your simulations

cd $BASE_DIR/scripts/ncl/postproc

Extract ouputs

ncl extract_outputs.ncl

Plotting carbon cycle variables

ncl plot_Carbonflux_km83_bg.ncl
ncl plot_Carbonpools_km83_bg.ncl

Plotting energy and water variables

ncl plot_energywater_km83_bg.ncl

Plotting forest structure variables

ncl check_PFTcomposition_sim_ts4sc_bg.ncl 

Who do I talk to?

Maoyi Huang (huangmy at gmail.com)

Reference

Huang, M., Xu, Y., Longo, M., Keller, M., Knox, R., Koven, C., and Fisher, R.: Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator, Biogeosciences, Biogeosciences, 17, 1–25, 2020, https://doi.org/10.5194/bg-17-1-2020.

Acknowledgment

This research was supported by The Next-Generation Ecosystem Experiments – Tropics project through the Terrestrial Ecosystem Science (TES) program within US Department of Energy’s Office of Biological and Environmental Research (BER). The Pacific Northwest National Laboratory is operated by the DOE and by the Battelle Memorial Institute under contract DE-AC05-76RL01830. LBNL is managed and operated by the Regents of the University of California under prime contract no. DE-AC02-05CH11231. The research carried out at the Jet Propulsion Laboratory, California Institute of Technology, was under a contract with the National Aeronautics and Space Administration (80NM0018D004). Marcos Longo was supported by the Sa˜o Paulo State Research Foundation (FAPESP, grant 2015/07227-6) and by the NASA Postdoctoral Program, administered by the Universities Space Research Association under contract with NASA (80NM0018D004). Rosie A. Fisher acknowledges the National Science Foundation via their support of the National Center for Atmospheric Research.