Welcome to CHEEREIO!
Welcome to the CHEEREIO website and documentation! This site provides a manual for the installation, use, and modification of CHEEREIO for a variety of scientific applications. You can download CHEEREIO from the Github page and install by following the instructions on the Installing CHEEREIO page later in the documentation.
The GEOS-Chem CHEmistry and Emissions REanalysis Interface with Observations (CHEEREIO) is a set of Python and shell scripts that support data assimilation and emissions inversions for arbitrary runs of the GEOS-Chem chemical transport model via an ensemble approach (i.e. without the model adjoint). CHEEREIO follows five design principles:
Easy to customize: Assimilate anything, in any GEOS-Chem configuration or simulation.
Easy to maintain: Science automatically aligned with latest model version.
Easy to deploy: One configuration file controls installation and settings
Easy to link observations: Object-oriented observation operator implementation in Python allows the user to rapidly add new kinds of data with minimal programming required.
Quick to run: Wall runtime should be comparable to vanilla GEOS-Chem assuming resources are available.
This manual assumes that you are familiar with setting up and running the GEOS-Chem chemical transport model. For more information and background, please see the GEOS-Chem Wiki. Although this manual offers an intuitive explanation of CHEEREIO’s data assimilation algorithm in the How CHEEREIO works section, you should probably consider the original algorithm paper Hunt. et. al.,  as a prerequisite to using CHEEREIO. Don’t worry, it’s quite readable!
I am more than happy to collaborate with you, however you choose to use CHEEREIO: just send an email to me at pendergrass [AT] g [DOT] harvard [DOT] edu. Questions of any kind are also more than welcome. This can be on anything from interpreting results to getting the ensemble installed on your machine. Bugs should be reported by opening an issue on Github, as this will allow all users to see the solution.
- The ensemble configuration file
- The setup ensemble script
- The structure of the ensemble directory
- Running the ensemble
- Field guide to all core CHEEREIO scripts
- Installation and spinup scripts
- Run management scripts
- Assimilation scripts
- Observation scripts
- Deprecated scripts
- The LETKF Utility module