Welcome to the NEON Tutorial 2023#
+ + +This tutorial will be used as a resource during the 2023 NEON Tutorial, Flux Course 2023 & ESA 2023 workshop.
+ +The materials and notebooks in this tutorial is published as a Jupyter book here.
+These tutorials are designed as an introduction to running the Community Terrestrial Systems Model (CTSM). Users can begin with the notebooks in the Getting Started
directory, which contains:
-
+
An introduction to CTSM, CESM-Lab, and Git
+Running CTSM simulations at NEON tower sites
+Evaluating CTSM at NEON tower sites
+
We’ll also have opportunities to explore more ProjectExamples
which describe how to:
-
+
Plot data
+Make simple code modifications
+Change simulated plant type
+Change model options (eg, FATES)
+Identify how to change model output
+
Quick Start#
+Step 1: Open up CESM-Lab#
+-
+
In your web browser go to https://neon2023.cesm.cloud
+It will automatically open up a portal to connect to the cloud:
+ + +
+Enter your username and password provided with your tutorial registration
+This should launch a JupyterLab window in your browser.
+
IF you need to update the tutorial repository, you can clone CTSM Tutorial Repository:#
+-
+
Click on the
Terminal
icon to open a terminal window.
+
-
+
If the directory does not already exist (everything should be pre-staged, so you shouldn’t have to do this), run the following command to clone this repository. (Just copy and paste the text below into the terminal window that opens in JupyterLab)
+
git clone -b NEON_Tutorial_2023 https://github.com/NCAR/CTSM-Tutorial
+
Then, run the following command from within CTSM-Tutorial to update.
+git pull
+
This gives you an updated local copy of the material you’ll need for the tutorial
+Can you see a new directory on your navigation sidebar called CTSM-Tutorial
? (See the left sidebar of your JupyterLab window)
+
Notebook Table of Contents#
+-
+
GettingStarted: These notebooks are the building blocks for all additional notebooks.
+-
+
1_NEON_Simulation_Tutorial.ipynb : This notebook shows how to run a NEON simulation
+2_NEON_Simulation_Visualization.ipynb : This notebook shows how to visualize NEON simulation output
+
+ProjectExamples: These notebooks are project-specific and build upon the GettingStarted notebooks
+-
+
Basic_CTSM-NEON_Plots.ipynb : This notebook shows how to create plots from NEON data, as well as perform time averaging, etc
+CTSMsp_NEON_fromScratch.ipynb : This notebook focuses on using CTSM with satellite phenology
+Clone_Case.ipynb : This notebook shares how to clone a case
+FATES_NEON_fromScratch.ipynb : This notebook works on creating a FATES case from scratch with NEON
+Plot_flux_climatology.ipynb : This notebook provides climatology plotting examples
+QuickPlot_CTSM-FATESsp.ipynb : This notebook provides plotting tools for use with FATES run with satellite phenology
+QuickPlot_CTSM_h0.ipynb : This plots monthly CTSM data
+QuickPlot_CTSM_spinup.ipynb : This plots CTSM cases that have been spun up
+customizeCase_PRISM.ipynb : This customizes a case to use PRISM precipitation input data
+customizeCase_modelFeatures.ipynb : This customizes various model features
+customizeCase_parameterModifications.ipynb : This notebook provides tools for parameter modifications and takes input that is generated from modifyParameterFile.ipynb
+modifyParameterFile.ipynb : This notebook modifies a parameter file that can then be used by customizeCase_parameterModifications.ipynb
+modifySurfdataFile.ipynb : This notebook modifies a surface data file that can then be used by customizeCase_modelFeatures.ipynb
+
+ContributedNotebooks: These notebooks are contributed by workshop participants who dove further into a particular project.
+
📚 Resources#
+CTSM Repository which includes the CTSM Wiki page that has lots of resources, including much of the following:
+-
+
- +
- +
- +
- +
Running NEON cases with a container – Running CTSM for NEON cases on a laptop
+
CLM5 Overview Paper Lawrence et al. 2019 JAMES
+CLM5 Diagnostic plots, from the overview paper.
+CLM5 ILAMB page, also from the overview paper.
+❓ Questions#
+For questions about running simulations, please use DiscussCESM Forums:
+ + +👍 Acknowledgements#
+A number of people have been critical to this effort, including:
+-
+
Adrianna Foster, Negin Sobhani, Danica Lombardozzi, Will Wieder, Gordon Bonan, & Teagan King who put together tutorial materials.
+Brian Dobbins, who put together the AWS configuration of CESM-Lab;
+Jackie Shuman, Polly Buotte, & Keith Oleson, who tested tutorial materials;
+Erik Kluzek & Bill Sacks, who made CTSM tags needed for running simulations.
+Elizabeth Faircloth and Ryan Johnson who helped with tutorial registration, logistics and webpages; and finally the rest of the
+TSS staff who provided lecture materials and helped answer questions during the tutorial.
+
This material is based upon work supported by the National Center for Atmospheric Research (NCAR), which is a major facility sponsored by the National Science Foundation (NSF) under Cooperative Agreement No. 1852977. Staff time on this project was also supported by NSF award numbers 2039932, 2031238, 1926413, and 2120804.
+