HW1: Terrestrial Carbon Cycle Modeling

EEPS 3230 Biogeochemistry — Spring 2026

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Quick Links

• Assignment Instructions — What to do
• Git & GitHub Guide — How to submit (start here if new to Git!)
• Grading — How you'll be evaluated

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Assignment Overview

In this homework, you will extend a three-box terrestrial carbon cycle model to explore how feedbacks shape the global carbon cycle. You will:

1. Calibrate the model against synthetic atmospheric CO2 data
2. Add a feedback mechanism (choose one of three options)
3. Design emission scenarios using the built-in scenario selector

See the full assignment handout (HW1_Terrestrial_Carbon.docx on Canvas) for detailed instructions.

Files in This Repository

File	Description
hw1_starter.stmx	Your starting model — make a copy with your name
README.md	This file

What to Submit

Your completed model file: hw1_yourname.stmx

Commit and push this file to your repository before the deadline.

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Git & GitHub Guide

If you're new to Git and GitHub, don't worry! This section walks you through everything step by step.

What is Git?

Git is a version control system that tracks changes to your files over time. Think of it like "track changes" in Word, but much more powerful:

• See the history of every change you've made
• Go back to earlier versions if something breaks
• Safely experiment without losing your work

GitHub is a website that hosts your Git repositories online, allowing you to:

• Submit assignments
• Back up your work
• Collaborate with others (in future courses)

Step 1: Create a GitHub Account

If you don't already have one:

1. Go to github.com
2. Click Sign up
3. Use your @wustl.edu email (you get free Pro features with a student account!)
4. Choose a professional username (employers may see this someday)

Step 2: Install Git

Mac:

1. Open Terminal (Applications → Utilities → Terminal)
2. Type git --version and press Enter
3. If not installed, you'll be prompted to install it (click Install)

Windows:

1. Download Git from git-scm.com
2. Run the installer (accept all defaults)
3. Use "Git Bash" for running Git commands

Step 3: Configure Git (One-Time Setup)

Open Terminal (Mac) or Git Bash (Windows) and run these commands, replacing with your info:

git config --global user.name "Your Name"
git config --global user.email "your.email@wustl.edu"

Step 4: Accept the Assignment

1. Click the GitHub Classroom assignment link (on Canvas)
2. Authorize GitHub Classroom if prompted
3. Find your name in the roster and click it
4. Click Accept this assignment
5. Wait for your personal repository to be created
6. Click the repository link to open it

Step 5: Clone Your Repository

"Cloning" downloads the repository to your computer.

1. On your repository page, click the green Code button
2. Copy the HTTPS URL
3. Open Terminal/Git Bash and navigate to where you want to work:

   cd ~/Documents

4. Clone the repository:

   git clone https://github.com/washu-eeps/hw1-yourname.git

5. Enter the folder:

   cd hw1-yourname

Step 6: Do Your Work

1. Open hw1_starter.stmx in Stella
2. Save As → hw1_yourname.stmx (use your actual name!)
3. Complete the assignment following the handout
4. Save your work frequently

Step 7: Track Your Changes (Optional but Recommended)

As you work, you can save "snapshots" of your progress. This is useful if you want to go back to an earlier version.

Check what's changed:

git status

Save a snapshot (commit):

git add hw1_yourname.stmx
git commit -m "Completed Part 1 calibration"

The message in quotes describes what you changed. Make it meaningful!

Example workflow:

# After completing calibration
git add hw1_yourname.stmx
git commit -m "Calibrated GPP_base to 110"

# After adding feedback mechanism
git add hw1_yourname.stmx
git commit -m "Added Q10 temperature feedback"

# After finishing scenarios
git add hw1_yourname.stmx
git commit -m "Implemented 3 emission scenarios"

Step 8: Submit Your Work (Push)

When you're ready to submit, "push" your commits to GitHub:

git push

You may be asked for your GitHub username and password. For the password, you'll need a Personal Access Token (GitHub no longer accepts regular passwords):

1. Go to GitHub → Settings → Developer settings → Personal access tokens → Tokens (classic)
2. Click Generate new token (classic)
3. Give it a name like "EEPS 3230"
4. Select the repo scope
5. Click Generate token
6. Copy the token immediately (you won't see it again!)
7. Use this token as your password when pushing

Tip: On Mac, you can store credentials in Keychain. On Windows, Git Credential Manager should handle this automatically after the first push.

Verifying Your Submission

After pushing:

1. Go to your repository on GitHub
2. Confirm your .stmx file is there
3. Click on Actions to see if the autograder ran
4. A green checkmark means all checks passed!

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Common Git Commands

Command	What it does
git status	Show what files have changed
git add filename	Stage a file for commit
git commit -m "message"	Save a snapshot with a description
git push	Upload your commits to GitHub
git pull	Download updates from GitHub
git log --oneline	See your commit history

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Troubleshooting

"Permission denied" when pushing

• Make sure you're using a Personal Access Token, not your password
• Check that you accepted the assignment and the repo is yours

"Your branch is ahead/behind"

• Run git pull first, then git push

Made a mistake?

• If you haven't committed yet: just fix the file and save
• If you committed but haven't pushed: ask for help (we can undo it)
• If you already pushed: make another commit with the fix (that's fine!)

Stella backup files cluttering your repo?

• The .gitignore file should prevent .stmx~ files from being tracked
• If you see them, don't add them to Git

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Grading

Your model will be automatically checked for required elements:

Component	Weight
Base model structure	20%
Calibration	25%
Feedback mechanism	25%
Scenario design	20%
Mass conservation	10%

Required Named Elements

All students:

• Stocks: Atmosphere, Vegetation, SOM
• Flows: GPP, Autotrophic_Respiration, Litterfall, Heterotrophic_Respiration, Emissions
• Converters: GPP_base, Scenario, Total_Carbon, RMSE

Plus one feedback set:

• Option A: Temperature, Q10, T_ref
• Option B: Available_N, Kn
• Option C: Deforestation_Rate + Deforestation flow

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Getting Help

• Office hours: Check Canvas for times
• Ed Discussion: Post questions there
• Git issues: Come to office hours — we'll help you debug!

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Due Date

Class 12 — Check Canvas for the exact date and time.

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EEPS 3230 Biogeochemistry — Washington University in St. Louis