I'm having problems (errors) in writing the advection-diffusion equation in tex.

$\frac{\partial C}{\partial t} -\frac{\partial }{\partial x} \left[D_{x} \frac{\partial c}{\partial x} -u_{x} c\right]-\frac{\partial }{\partial y} \left[D_{y} \frac{\partial c}{\partial y} -u_{y} c\right]-\frac{\partial }{\partial z} \left[D_{z} \frac{\partial c}{\partial z} -u_{z} c\right]=F\left[c,t\right]$


It should work out as

Document splitted in various sections:

Main document

\documentclass[oneside,12pt]{Classes/CUEDthesisPSnPDF}
\usepackage{amsmath}
\begin{document}
\tableofcontents
\listoffigures
\listoftables
\printnomenclature  %% Print the nomenclature
\include{Introduction/introduction}
\include{Chapter2/chapter2}
\include{Chapter3/chapter3}
\include{Chapter4/chapter4}
\include{Chapter5/chapter5}
\include{Conclusions/conclusions}
\bibliographystyle{plainnat}
\renewcommand{\bibname}{References} % changes default name Bibliography to References
\bibliography{References/references} % References file
\backmatter % book mode only
\appendix
\include{Appendix1/appendix1}
\end{document}


The appendix document has nothing different from other sections really...but there are no problems in the other when I write equations...

Help?

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Welcome to TeX.SX! @cmhughes, indeed, it gives the expected output even without amsmath. – Paul Gessler Apr 28 '14 at 18:35
this code works for me (even without amsmath) could you specify what you want different? – romeovs Apr 28 '14 at 18:36
You are right...strange, but inside the Appendix section (where it should be in the thesis) doesn't work :S – user17653 Apr 28 '14 at 18:37
@user17653, please edit your question to include a complete minimal working example (MWE) that illustrates your problem. This will make it much easier for us to help you. :-) – Paul Gessler Apr 28 '14 at 18:40
@user17653 this is not a MWE. We do not have any of your included files, and the LoF, LoT, nomenclature, and friends should be removed (unless removing them causes the problem to go away). Please review my previous link and post a complete, self-contained document that exhibits the issue you're seeing. – Paul Gessler Apr 28 '14 at 19:23