Numerical Ocean Modeling

Welcome to an Introduction to Ocean Modeling!

This resource is designed to be a practical guide to introduce the construction, implementation, and analysis of ocean models. Here, we investigate 3D numerical models constructed by solving equations of motion and thermodynamics in a time-stepping scheme. The primary tool used in this book is the MIT General Circulation model - a versitile, open-sourced framework used widely in oceanography. Many of the the examples use output from the Estimating the Circulation and Climate of the Ocean (ECCO) state estimates which are generated with MITgcm.

Note

This book is currently being updated for a graduate-level course at the Moss Landing Marine Labs, San José State University. It is a work in progress and will continue to be updated through Fall 2025 and beyond. If you have any feedback or constructive suggestions, feel free to submit an issue on the Github repository for this book.

This book is for people new to ocean modeling although it will hopefully also serve as a convenient reference for those who have been at it for a while. People with an introductory background in coding, some knowledge of calculus, and an understanding of Earth science topics will be most suited to leverage these resources.

The book is organized into six main sections:

1. Getting Started - instructions for installing tools used throughout this book

2. Oceanography - a short background in various oceanographic topics

3. Numerical Modeling - introduction to some aspects of ocean modeling

4. ECCO - overview of the Estimating the Circulation and Climate of the Ocean state estimates

5. MITgcm - instructions for constructing and running models using MIT General Circulation Model

6. Computing Clusters - instructions for running models on a computing cluster

7. A Regional Model Example - a step-by-step guide to creating a simple regional model with MITgcm

8. MITgcm Special Topics - other packages and procedures specific to MITgcm

9. State Estimation - an introduction to some approaches to generate estate estimates

None of these sections is intended to be exhaustive - rather, the aim is to generate a practical introduction to the topic. Additional references are provided at the end of each section.

Table of Contents

Getting Started

• Installing Python and Jupyter
• Setting up a Github Repository
• Getting Familiar with Jupyter Notebooks
• Installing a compiler with MPI
• Getting Familiar with Unix Environments

Oceanography

• Overview
• Wind-Driven Circulation
• Thermohaline Circulation
• Primitive Equations
• Momentum
• Thermodynamics
• Equation of State

Numerical Modeling

• Exploring Time Stepping
• Time Stepping Schemes for ODEs
• Difference Methods
• From ODEs to PDEs
• Model Grids

ECCO

• Overview
• Visualizing ECCO Model Output
• Computing Trends in ECCO Output
• Understanding the ECCO Lat-Lon-Cap grid

MITgcm

• Overview
• Getting Started with MITgcm
• File Layout
• Choosing an optfile
• Defining the Model Grid
• Initial Conditions
• External Forcing
• Boundary Conditions
• Diagnosing Issues

Computing Clusters

• Navigating an HPC
• Running jobs on an HPC
• conda Environments

MITgcm Special Topics

• Diagnostics_vec
• Volume Budgets
• Heat Budgets
• Salt Budgets

State Estimation

• Green’s Functions

Documentation

• Contributions
• References

This book was initially created for an undergraduate CS 185C Special Topics course at San José State University. It has subsequently updated with graduate-level material for the MS 274 Special Topics course at the Moss Landing Marine Labs.