NOTICE: We’re in the process of migrating the NGEE-Tropics Data Archive to ESS-DIVE, the long-term data archive for BER/ESS. All public NGEE-Tropics datasets can be accessed in the new NGEE-Tropics Portal in ESS-DIVE, including after the NGEE-Tropics Data Archive is retired. Updates to NGEE-Tropics datasets should now be done via ESS-DIVE; please contact us at [email protected] if you need to edit an NGEE-Tropics dataset or if you have any questions about NGEE-Tropics datasets.
Login to download

Files and scripts to support manuscript Needham et al. Canopy Gradients of Respiration

Author(s): Needham J


Dataset Information

Site ID: XX-Glo

Site Name: Global

Variables: Model output

Date Range: Aug. 1, 2024 - Aug. 1, 2024

Description: This dataset includes the parameter files, relevant output files, and scripts to perform analysis with Jupyter notebooks that support the manuscript Needham et al 2025 “Canopy Gradients of Respiration Drive Plant Carbon Budgets and Leaf Area Index.” We add functionality to the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) to allow flexible vertical gradients of leaf maintenance respiration (Rdark) and maximum carboxylation rate (Vcmax) through the canopy. We test the sensitivity of FATES to canopy gradients in Rdark, both in global simulations to assess broad scale impacts on leaf area index (LAI) and vegetation carbon, and in single site simulations where we assess impacts on plant functional type (PFT) competitive dynamics. Parameter files are netcdf files that can be converted to human readable .cdl files using NCO tools. Analysis scripts are Jupyter notebook files. These can be opened and run using the open source Jupyter notebook software. Model outputs are netcdf files. (The data files for this version 2.0 were updated with new runs)

QA/QC: None

Methods Description: A total of eight global simulations were run at 4x5 degree resolution using GSWP3 climate forcing data. We used a 12 PFT parameter file and ran simulations in 'fixed-biogeography' and 'no-competition' mode meaning PFT distributions are prescribed and PFTs do not compete with one another on a patch. In each global run we changed the canopy gradient of Rdark. We also ran 12 single site simulations to explore how different canopy gradients of Rdark impact competitive dynamics. In these simulations we used a two PFT parameter file with a shade-tolerant and a light-demanding PFT. There are three parameterizations of the two PFTs, and for each parameterization we ran a simulation with four different canopy gradients of Rdark, giving 12 simulations in total. For global and single site simulations we analyzed outputs using Jupyter notebooks.

Access Level: Public

Originating Institution(s): Lawrence Berkeley National Laboratory

Sponsor Organization(s):

Contact: Needham, Jessica - Lawrence Berkeley National Laboratory ([email protected])


Data Download

Version: 2.0

Dataset Citation: Needham J (2025): Files and scripts to support manuscript Needham et al. Canopy Gradients of Respiration. 2.0. NGEE Tropics Data Collection. (dataset). https://doi.org/10.15486/ngt/2425967

Acknowledgement: This research was supported as part of the Next Generation Ecosystem Experiments-Tropics, funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research and as part of the Energy Exascale Earth System Model (E3SM) project, funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research Earth Systems Model Development Program area of Earth and Environmental System Modeling. LBNL is managed and operated by the Regents of the University of California under prime contract number DEAC02-05CH11231.

Data Link: Download Dataset

NGEE Tropics data policy.


Reference:

Needham, J. F., Dey, S., Koven, C., Fisher, R., Knox, R., Lamour, J., Lemieux, G., Longo, M., Rogers, A., & Holm, J. Canopy Gradients of Respiration Drive Plant Carbon Budgets and Leaf Area Index