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I'm writing my phd thesis. In some chapters I simply begin the chapter with one or maybe two (at most) paragraphs that mostly gives the outline, and then I begin the sectioning. That is, this paragraph has no section, the sections start right afterwards. I'm wondering if this is normal and acceptable or should I put it in a separate section?

This is how it looks in latex:

\chapter{System Modeling}

A paragraph giving the outline of this chapter. Section ?? discusses this and that. ....

\section{Equation of Motion} %this is the first section of this chapter
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    Were you given style guide when you started your thesis? Did you ask your advisor this question? – scaaahu Feb 11 '16 at 9:28
  • In my University this is quite common to do, but like commented by @scaaahu I would ask first if there is a style guide. – agold Feb 11 '16 at 9:31
  • there is unfortunately no style guide. – Ehsan Feb 11 '16 at 9:37
  • What did your advisor say? You do have an advisor, don't you? – scaaahu Feb 11 '16 at 9:42
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In general, sections should be organized to create a chapter just like subsections are organized to create a section and subsubsection should be organized to create a subsection. In other words, the important unit is the largest one, and the smaller elements (sections, subsections, etc.) are used only the assist and guide the reader in their understanding of a large chunk of narrative.

As such, I would consider it the normal and preferred case to begin a chapter with prose, setting forth an introduction to the chapter before the first section heading. In fact, a particularly short chapter might have no section headings at all, as it is a good rule of thumb to note use any textual subdivision until you need two of them (e.g., don't divide a chapter into one section, or a section into one subsection).

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