Welcome to the CARDAMOM documentation

Technical documentation of the CARbon DAta-MOdel fraMework C implemtation (CARDAMOM-C)

Authors: Paul A. Levine, A. Anthony Bloom, Matthew A. Worden, T. Eren Bilir, Gregory R. Quetin, Shuang Ma, Alexander J. Norton

This technical documentation is under construction. In due course, incremental versions will be designated with a digital object identifier (DOI). In the meantime, to make reference to this documentation, please use the following:

How to cite: Levine, Paul A., Bloom, A. Anthony, Worden, Matthew A., Bilir, T. Eren, Quetin, Gregory R., Ma, Shuang, Norton, Alexander J., Technical documentation of the CARbon DAta-MOdel fraMework C implemtation (CARDAMOM-C), in prep. https://cardamom-framework.github.io/CARDAMOM (last accessed insert date accessed)

The CARDAMOM documentation presented here is written specifically for the JPL, Stanford, UCSB and Caltech CARDAMOM framework implementation, publicly available under an Apache License v2.0. Copyright © 2024, California Institute of Technology (“Caltech”) and University of Washington. U.S. Government sponsorship acknowledged.

Getting Started:

• Getting Started with CARDAMOM

CARDAMOM Overview:

• CARDAMOM overview
• Forward model
• Model-data fusion

DALEC Model:

Select DALEC version DALEC 1100 DALEC 1101

• Show all DALEC versions

• DALEC 1100
Overview of DALEC 1100
Modules used by DALEC 1100
Variables in DALEC 1100

• DALEC 1101
Overview of DALEC 1101
Modules used by DALEC 1101
Variables in DALEC 1101

Model-data fusion framework:

• Cost function
• Observation operators
• MCMC

Using CARDAMOM:

• File formats
• Compilation
• Git hooks
  • What git hooks are
  • Hooks used by CARDAMOM
  • Why the compilation hook matters
  • Installing the hooks
  • Skipping the rebuild
• Stress Testing your CARDAMOM input (.nc) file
  • Overview
  • Location
  • Usage
  • What the Script Tests
  • Why These Tests Matter
  • File Naming Convention
  • Interpreting Results
  • Related Files
• Analyst checklist
• Contributing to this technical documentation
  • Structure of the DALEC technical documentation
  • Citing publications and other sources
  • Making edits/modifications locally
  • Making edits/modifications on the GitHub web interface
  • Interacting with our GitHub repository
• CARDAMOM.c governance structure

• Creating a New DALEC Model ID
  • Overview
  • Prerequisites
  • Step 1: Copy the Template Model Directory
  • Step 2: Rename Files in New Directories
  • Step 3: Update Internal Code References
  • Step 4: Register Models in CARDAMOM_MODEL_LIBRARY.c
  • Step 5: Update DALEC_MODEL_FIELD_REQUIREMENTS.txt
  • Step 6: Compile CARDAMOM
  • Step 7: Create Test Input Files
  • Step 8: Run Stress Tests
  • Verification Checklist
  • Troubleshooting
  • For AI Assistants
  • Summary
  • Additional Resources
• Adding new input variable type
  • Overview
  • Step-by-step procedure
  • Validation checklist
  • Important notes
  • See also

Old Markdown Manual:

• Adding new netcdf variables and attributes
• Diagnose and resolve memory leaks
• CARDAMOM C developer guide
  • Intro tips.
  • Make a new model.
  • Add more parameters to the model.
  • Add more pools to the model
  • Guidelines on comments and naming conventions
• CARDAMOM Netcdf input file
  • Summary
  • Variable names, definitions and conventions
  • FAQ
• CARDAMOM cost function
  • Editing LIKELIHOOD field in the output file (cbr)
• Debugging tips and FAQs
  • Test 1. Forward model mirroring test
• Getting Started with CARDAMOM
  • “Installing” CARDAMOM
  • Tips
  • FAQ
  • CARDAMOM Github User Must Read
  • CARDAMOM Matlab Demo and Setup Test
  • CARDAMOM Python Demo and Setup
• Using CARDAMOM’s github repository
  • Issues and labels
  • Github basics and tips
  • Delete branch remotely (e.g. “testonly”) and remote is “cardamom
  • Pull request recommendations
• MATLAB demo
  • Run Matlab Demo
• MCMC in CARDAMOM Overview
  • EDC Initial-Condition Search
  • MCMC Modes
  • Recommended CBF MCMCID Settings for Comparing Methods
  • Proposal Building Blocks and Hybrid Modes
  • Adding a new MCMC mode
  • FAQ
• DALEC model IDs
  • Appendix
• Output Data and Analysis
  • CARDAMOM state and flux conventions
  • Aggregation and uncertainty propagatation
• Parallelization
  • Step 1a (Personal Computer) Check how many cores you have
  • Step 1b (Server) Check how many cores you have access to
  • Quick and Dirty Method using Command Line/Terminal (For only a few runs)
  • Use the python script tutorial (For many runs)
  • Bash Script for Parallelizing
• Perturbation experiments using CARDAMOM outputs
  • ###Warning: ensure “reference_mean” attribute is either (a) the same value, and explicitly defined, in perturbed.cbf.nc and actual.cbf.nc, or (b) is definied in perturbed.cbf.nc as the time averaged values from actual.cbf.nc###
• Python demo
  • Compile code from Github
  • Tutorials

All of our old stuff is here. We can delete things once they are put into the RST manual, and eventually delete this entire section once it’s empty.

Miscellaneous

• Copyright

• Index

• Module Index

• Search Page