Working with Directories

Directories (or folders) form the backbone of your project organization. When working in Linux, WSL, or macOS, it’s essential to know how to create, rename, move, and manage directories efficiently using terminal commands. This becomes especially important for simulation workflows, where you’ll organize geometries, meshes, scripts, and results across multiple folders.

Understanding Directories

In Linux-based systems, everything — from files to devices — is organized inside a directory tree, starting from the root (/). Your workspace for simulations usually resides inside your home directory (~), or inside your mounted drive (e.g., /mnt/d/ in WSL).

Example path structure:

/mnt/d/fenics-projects/
 ├── beam/
 │   ├── geometry/
 │   ├── mesh/
 │   ├── solver/
 │   └── results/
 └── logs/

Having such a structured approach keeps your work organized and reproducible.

Creating Directories

To create new folders:

Command	Description	Example
mkdir folder_name	Creates a single new directory	mkdir simulations
mkdir -p path/folder/subfolder	Creates nested directories (parent + child)	mkdir -p beam_project/mesh/outputs

Tip: Use descriptive names like mesh_files, solver_scripts, or results_2025 to make your directory structure self-explanatory.

Viewing Directory Contents

To see what’s inside a directory:

Command	Description	Example
ls	Lists all files and folders	ls
ls -l	Displays details like permissions, size, and date	ls -l
ls -a	Shows hidden files (those starting with a dot .)	ls -a
ls -lh	Lists contents with human-readable sizes	ls -lh

Navigating Between Directories

Move through directories with these basic commands:

Command	Description	Example
cd folder_name	Move into a directory	cd mesh
cd ..	Move one level up	cd ..
cd ../..	Move two levels up	cd ../..
cd ~	Jump back to your home directory	cd ~
cd \	Jump to the root directory	cd \
cd /mnt/d/fenics-projects	Move directly to an absolute path	cd /mnt/d/fenics-projects

Tip: Press Tab for auto-completion while typing directory names.

Renaming and Moving Directories

You can rename or relocate folders using the mv (move) command:

Command	Description	Example
mv old_name new_name	Rename a folder	mv test_mesh final_mesh
mv folder1 /new/location/	Move a folder to another location	mv mesh /mnt/d/archives/

Copying and Removing Directories

Sometimes, you may want to duplicate a directory or remove one completely.

Command	Description	Example
cp -r source destination	Copy a directory and its contents	cp -r mesh mesh_backup
rm -r folder_name	Delete a folder and all files inside it	rm -r old_results
rm -rf folder_name	Force delete without confirmation (use with caution)	rm -rf temp_files

Always double-check before using rm -rf, as it permanently deletes data without recovery.

Checking Your Current Location

You can always confirm your current directory path using:

pwd

Example output:

/mnt/d/fenics-projects/beam/mesh

This helps you keep track of where you are before executing file or folder operations.

Summary

Working confidently with directories allows you to stay organized and efficient — an essential habit for scientific computing and simulation work.

You’ve learned how to:

• Create, rename, move, and remove directories
• Navigate between different levels of your workspace
• Maintain clean and structured project folders

In the next section, we’ll explore file permissions and ownership, which determine who can access, modify, or execute files within your Linux environment.