Steps to check out codes, and driving/preprocessing/analysis scripts used in the FATES Logging Manuscript
---scripts
We provide detailed notes on running the logging experiments on PNNL's CONSTANCE cluster.
setenv BASE_DIR <dir-of-choice>
cd $BASE_DIR
git clone [email protected]: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
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
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
cd $BASE_DIR/scripts/shell
bash create_fates-clm_1x1pt_km83_intact_spinup.sh
bash create_fates-clm_1x1pt_km83_intact_sim.sh
bash create_fates-clm_1x1pt_km83_logging.sh
cd $BASE_DIR/scripts/ncl/postproc
ncl extract_outputs.ncl
ncl plot_Carbonflux_km83_bg.ncl
ncl plot_Carbonpools_km83_bg.ncl
ncl plot_energywater_km83_bg.ncl
ncl check_PFTcomposition_sim_ts4sc_bg.ncl
Maoyi Huang (huangmy at gmail.com)
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.
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.