Compiling problem in book class

Question

I am writing a book and I split it in to several files using \include{} and \includeonly{} commands. The chapter "chapterThomae" has the Thomae's function from here.

If I use the \includeonly{} command (like the code below) everything is OK. No one chapter has any problem.

\documentclass{book}
\includeonly{chapter1} % or chapter2 or chapter3 or chapterThomae etc
\begin{document}
\include{chapter1}
\include{chapter2}
\include{chapter3}
\include{chapterThomae}
%etc
\end{document}

If I disable \includeonly{} command (to have the whole book - see the code below) I get this error report.

\documentclass{book}
 %\includeonly{chapter1}
\begin{document}
\include{chapter1}
\include{chapter2}
\include{chapter3}
\include{chapterThomae}
%etc
\end{document}

Also the pdf-view (and the pdf file) is deleted.

I think something goes wrong with the chapter that includes Thomae's function. If I disable this chapter (like the code below) everything is OK again.

\documentclass{book}
 %\includeonly{chapter1}
\begin{document}
\include{chapter1}
\include{chapter2}
\include{chapter3}
 %\include{chapterThomae}
%etc
\end{document}

What is the problem? How can I fix it?

PS: I am sorry if the title is not correct. I cannot even imagine what is the problem, so I couldn't find a proper title.

Answer 1

There is a missunderstanding here: You can not have two commands \documentclass{} in one TeX document.

Please see the following MWE I created from your given codes (package filecontents is only used to have three tex code in one MWE; this is only for testing purpose here, you can use your original codes of course):

\RequirePackage{filecontents}
\begin{filecontents}{\jobname-chapter1.tex}
\chapter{Chapter One}

Text for chapter one ...
\end{filecontents}

\begin{filecontents}{\jobname-chapterThomae.tex}
\documentclass{article}
\usepackage{tikz}

\makeatletter
\pgfmathdeclarefunction*{gcd}{2}{%
  \begingroup
    \pgfmathcontinuelooptrue
    \pgfmath@xa=#1pt\relax % <-
    \pgfmath@xb=#2pt\relax % <-
    \ifdim\pgfmath@xa=0pt\relax
      \pgfmathcontinueloopfalse
      \pgfmath@xa=\pgfmath@xb
    \fi
    \ifdim\pgfmath@xb=0pt\relax
      \pgfmathcontinueloopfalse
      \pgfmath@xb=\pgfmath@xa
    \fi
    \ifdim\pgfmath@xa<0pt\relax
      \pgfmath@xa=-\pgfmath@xa
    \fi
    \ifdim\pgfmath@xb<0pt\relax
      \pgfmath@xb=-\pgfmath@xb
    \fi
    \loop
      \ifpgfmathcontinueloop
      \ifdim\pgfmath@xa=\pgfmath@xb
        \pgfmathcontinueloopfalse
      \else
        \ifdim\pgfmath@xa>\pgfmath@xb
          \advance\pgfmath@xa by-\pgfmath@xb\relax
        \else
          \advance\pgfmath@xb by-\pgfmath@xa\relax
        \fi
      \fi
    \repeat
    \pgfmathparse{int(\pgfmath@xa)}%
    \pgfmath@smuggleone\pgfmathresult
  \endgroup}
\makeatother

\begin{document}
\begin{center}
    \begin{tikzpicture}[scale=8]
    \draw [-stealth] (-0.1,0) -- (1.1,0);
    \draw [-stealth] (0,-0.1) -- (0,0.6);
    \foreach \X in {1,...,7}
    {\ifnum\X=1
        \else
        \draw (0.02,1/\X) -- (-0.02,1/\X) node[left,xshift={(-(1+pow(-1,\X)))*3pt}]{$\frac{1}{\X}$};
        \fi
    }
    \foreach \X [evaluate=\X as \Ymax using {int(\X-1)}]in {95,94,...,2}%Το μέγεθος του πρώτου όρου καθορίζει το πλήθος των κουκκίδων, άρα και την απόσταση του «τριγώνου» από τον χ'χ.
    {\foreach \Y in {1,...,\Ymax}
        {\ifnum\X<6
            \draw (\Y/\X,0.02) -- (\Y/\X,-0.02) node[below,fill=white]{$\frac{\Y}{\X}$};
            \else
            \draw[ultra thin] (\Y/\X,0.01) -- (\Y/\X,-0.01);
            \fi
            \pgfmathtruncatemacro{\TST}{gcd(\X,\Y)}
            \ifnum\TST=1
            \fill ({\Y/\X},1/\X) circle(0.05pt); %μέγεθος κουκκίδων
            \fi
        }
    }
    \foreach \X in {0,1,...,80}
    {\fill (\X/80,0) circle(0.05pt); } %μέγεθος κουκκίδων
    \end{tikzpicture}
\end{center}
\end{document}
\end{filecontents}


\documentclass{book}

%\includeonly{\jobname-chapter1} % or chapter2 or chapter3 or chapterThomae etc
\begin{document}
\include{\jobname-chapter1}
\include{\jobname-chapterThomae}
\end{document}

Copy this code to mwe.tex in a new directory of your computer and compile it with pdflatex mwe.tex. Then you will see the following error messages (and others more):

 (mwe-chapter1.tex
Chapter 1.
) [1
{C:/Users/User/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
\openout2 = `mwe-chapterThomae.aux'.
(mwe-chapterThomae.tex
! LaTeX Error: Can be used only in preamble.
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...
l.5 \documentclass
                  {article}
Your command was ignored.
Type  I <command> <return>  to replace it with another command,
or  <return>  to continue without it.

The error message ! LaTeX Error: Can be used only in preamble. tells you that you can not call \documentclass{article in your tex code for the document as you did with \include{\jobname-chapterThomae}, because this file contains that second call of command \documentclass ...

Now let us rework the given MWE above and delete \documentclass, \begin{document) and \end{document) in your file \jobname-chapterThomae.tex and move the call for tikz and the correcting code into the correct preamble of your code. Please see that file \jobname-chapterThomae.tex starts now with \begin{center}:

\RequirePackage{filecontents}
\begin{filecontents}{\jobname-chapter1.tex}
\chapter{Chapter One}

Text for chapter one ...
\end{filecontents}

\begin{filecontents}{\jobname-chapterThomae.tex}
\begin{center}
    \begin{tikzpicture}[scale=8]
    \draw [-stealth] (-0.1,0) -- (1.1,0);
    \draw [-stealth] (0,-0.1) -- (0,0.6);
    \foreach \X in {1,...,7}
    {\ifnum\X=1
        \else
        \draw (0.02,1/\X) -- (-0.02,1/\X) node[left,xshift={(-(1+pow(-1,\X)))*3pt}]{$\frac{1}{\X}$};
        \fi
    }
    \foreach \X [evaluate=\X as \Ymax using {int(\X-1)}]in {95,94,...,2}%Το μέγεθος του πρώτου όρου καθορίζει το πλήθος των κουκκίδων, άρα και την απόσταση του «τριγώνου» από τον χ'χ.
    {\foreach \Y in {1,...,\Ymax}
        {\ifnum\X<6
            \draw (\Y/\X,0.02) -- (\Y/\X,-0.02) node[below,fill=white]{$\frac{\Y}{\X}$};
            \else
            \draw[ultra thin] (\Y/\X,0.01) -- (\Y/\X,-0.01);
            \fi
            \pgfmathtruncatemacro{\TST}{gcd(\X,\Y)}
            \ifnum\TST=1
            \fill ({\Y/\X},1/\X) circle(0.05pt); %??????? ?????????
            \fi
        }
    }
    \foreach \X in {0,1,...,80}
    {\fill (\X/80,0) circle(0.05pt); } %??????? ?????????
    \end{tikzpicture}
\end{center}
\end{filecontents}


\documentclass{book}

\usepackage{tikz} % <===================================================

\makeatletter% <========================================================
\pgfmathdeclarefunction*{gcd}{2}{%
  \begingroup
    \pgfmathcontinuelooptrue
    \pgfmath@xa=#1pt\relax % <-
    \pgfmath@xb=#2pt\relax % <-
    \ifdim\pgfmath@xa=0pt\relax
      \pgfmathcontinueloopfalse
      \pgfmath@xa=\pgfmath@xb
    \fi
    \ifdim\pgfmath@xb=0pt\relax
      \pgfmathcontinueloopfalse
      \pgfmath@xb=\pgfmath@xa
    \fi
    \ifdim\pgfmath@xa<0pt\relax
      \pgfmath@xa=-\pgfmath@xa
    \fi
    \ifdim\pgfmath@xb<0pt\relax
      \pgfmath@xb=-\pgfmath@xb
    \fi
    \loop
      \ifpgfmathcontinueloop
      \ifdim\pgfmath@xa=\pgfmath@xb
        \pgfmathcontinueloopfalse
      \else
        \ifdim\pgfmath@xa>\pgfmath@xb
          \advance\pgfmath@xa by-\pgfmath@xb\relax
        \else
          \advance\pgfmath@xb by-\pgfmath@xa\relax
        \fi
      \fi
    \repeat
    \pgfmathparse{int(\pgfmath@xa)}%
    \pgfmath@smuggleone\pgfmathresult
  \endgroup}
\makeatother % <========================================================

%\includeonly{\jobname-chapter1} % or chapter2 or chapter3 or chapterThomae etc
\begin{document}
\include{\jobname-chapter1}
\include{\jobname-chapterThomae}
\end{document}

Now it compiles without errors and two warnings (okay, resulting from filecontents!) to the following result: