PhD Dissertation: Contributions to Finite Element Analysis in Electromagnetics

LaTeX sources for a PhD dissertation ("Contributions to the Art of Finite Element Analysis in Electromagnetics", University of Florence, 2011–2013) and its defense presentation. Also includes annual progress reports, conference talks, and an external seminar handout.

Repository Layout

manuscript/                    Main dissertation document
├── dissertation.tex           Entry point (\documentclass{book})
├── title.tex                  Title page
├── pub.tex                    List of publications
├── abs.tex                    Italian + English abstract
├── ack.tex                    Acknowledgments
├── intro.tex                  Introduction
├── ch1.tex                    Finite elements for the wave equation
├── ch2.tex                    Domain decomposition methods
├── ch3.tex                    Nonlinear analysis (harmonic balance FE)
├── concl.tex                  Conclusion
├── dissertation.bib           Bibliography (BibLaTeX, biber)
├── cover/                     Cover page files
├── img/                       Figures by chapter
│   ├── ch1/
│   ├── ch2/
│   └── ch3/
├── reviews/                   Review comments
└── [dissertation.pdf]         Generated output

presentation/                 Defense Beamer presentation
├── defense.tex               Entry point
├── custom.tex                Theme and package config
├── img/                      Slide images and diagrams
└── [defense.pdf]             Generated output

notes/                        Supplementary PDFs (split from merged archive)
├── 01_Dissertation_Manuscript.pdf    Full dissertation (144 pp)
├── 02_PhD_Defense_Presentation.pdf   Defense slides (104 pp)
├── 03_Yearly_Reports.pdf             1st–3rd year reports (46 pp)
├── 04_CEM_Seminar.pdf                Prof. J.F. Lee CEM seminar (85 pp)
└── 05_MBDA.pdf                       MBDA presentation scans (10 pp)

archives/                     ZIP bundles of published/submitted papers
drafts/                       Earlier works (MEng thesis, journal articles)
Makefile                      Build orchestration
README.md                     This file
configure                     Automated dependency installer

Requirements

• make - build automation
• pdflatex - LaTeX engine (included in most TeX distributions)
• Optional: biber or bibtex for bibliography processing

Install dependencies on macOS, Debian/Ubuntu, Arch, Fedora/RHEL, and other supported systems:

./configure

This script automatically detects your system and installs required packages.

Quick Start

Build both documents:

make

Build only the thesis manuscript:

make manuscript

Build only the defense presentation:

make presentation

View results:

• manuscript/dissertation.pdf - Thesis PDF
• presentation/defense.pdf - Presentation PDF

Build Process

The build system compiles LaTeX documents in multiple passes to resolve cross-references and citations:

1. LaTeX compilation: Initial document processing
2. Bibliography (if configured): Process bibliography database (optional)
3. LaTeX compilation (pass 2): Update citations and references
4. LaTeX compilation (pass 3): Finalize all references

Three-pass compilation ensures:

• ✓ All cross-references are resolved
• ✓ Table of contents is accurate
• ✓ Citations and bibliography are properly formatted
• ✓ Page numbers in references reflect final layout

Cleaning Up

Remove temporary LaTeX files (keeps generated PDFs):

make clean

Remove temporary files AND generated PDFs:

make distclean

Temporary files cleaned: *.aux, *.log, *.toc, *.nav, *.out, *.bbl, etc.

Configuration

Override default settings from the command line:

make VAR=value target

Manuscript variables

• MS_FILE - Main source file without .tex extension (default: thesis)
• MS_TEX - LaTeX engine command (default: pdflatex)
• MS_TEXFLAGS - Compiler flags (default: -interaction=nonstopmode -file-line-error)
• MS_BIB - Bibliography processor: biber or leave empty for none (default: biber)

Presentation variables

• PR_FILE - Main source file without .tex extension (default: defense)
• PR_TEX - LaTeX engine command (default: pdflatex)
• PR_TEXFLAGS - Compiler flags (default: -shell-escape -interaction=nonstopmode -file-line-error)
• PR_BIB - Bibliography processor (default: biber)

Examples

Build manuscript with Biber bibliography:

make MS_BIB=biber manuscript

Build with different source file names:

make MS_FILE=mainThesis PR_FILE=presentation

List all available targets:

make help

Project Structure Details

Manuscript Organization

The main dissertation file (manuscript/dissertation.tex) uses \include commands to import chapters modularly:

\include{title}
\include{abs}
\include{ack}
\include{pub}
\include{intro}
\include{ch1}
\include{ch2}
\include{ch3}
\include{concl}

This modular structure allows:

• Selective compilation of individual chapters during editing
• Easy reordering of chapters
• Clean separation of concerns

Custom Commands

Both documents include custom.tex for:

• Common package imports
• Custom command definitions
• Document-specific configurations

Image Management

Images are organized by chapter to maintain clarity:

• Chapter-specific images in img/ch1/, img/ch2/, etc.
• Shared resources (logos) in img/
• All images use lowercase filenames for consistency across platforms

Troubleshooting

"Make: command not found"

• macOS: brew install make
• Ubuntu/Debian: apt install build-essential
• Other systems: See your package manager

"pdflatex: command not found"

• Install a TeX distribution: ./configure or manually install TeX Live

Bibliography not appearing

• Ensure MS_BIB or PR_BIB is set to biber or bibtex
• Example: make MS_BIB=biber manuscript

PDF not updating

• Run make distclean to remove all cache, then make to rebuild

Outputs

Generated files:

• manuscript/dissertation.pdf - Full dissertation document
• presentation/defense.pdf - Presentation slides