In case it matters, I'm using win edit as editor.
\documentclass[12pt,a4paper]{article}
\usepackage{amsmath}\usepackage{amssymb}
\textwidth=16.5cm \oddsidemargin=-0.10cm \evensidemargin=-0.10cm \topmargin=-1.0cm \textheight=24.5cm
\newcommand{\piRsquare}{\pi r^2}
\title{The small amplitude expansion: The class of theoritical considered}
\author{xyz }
\date{January 26, 2013}
\begin{document} \baselineskip=18pt
\section{Reconstruction of the article equation(15)}
Given, $$\phi_1= p_1\cos(\tau+\alpha)$$
$$\nabla\phi_1= -p_1\sin(\tau+\alpha) \nabla \alpha+\nabla p_1cos(\tau+\alpha)$$
$$\Delta\phi_1= -p_1 \nabla \alpha \cos(\tau+\alpha) \nabla \alpha-p_1 \sin(\tau+\alpha) \Delta\alpha -\nabla \alpha \sin(\tau+\alpha)\nabla p_1-\nabla p_1 \nabla \alpha \sin(\tau+ \alpha)+\Delta p_1\cos(\tau+\alpha)$$
$$\Delta\phi_1= \cos(\tau+\alpha) [-p_1 \Delta \alpha + \Delta p_1]- \sin(\tau+\alpha) [p_1\Delta \alpha+2\nabla \alpha \nabla p_1]$$
Differentiating $\phi_1$,
$$\phi_1= p_1cos(\tau+\alpha)$$
$$\dot\phi_1= -p_1 sin(\tau+\alpha)$$
$$\ddot\phi_1= -p_1cos(\tau+\alpha)$$
Again,
$$\phi_2 = p_2\cos(\tau + \alpha) + q_2\sin(\tau + \alpha) + \frac{g_2}{6}p_1^2[\cos(2\tau + 2\alpha) - 3] $$
$\omega_1=0$ for the bounding conditions.
$$\dot\phi_2 = -p_2\sin(\tau + \alpha) + q_2\cos(\tau + \alpha) + \frac{g_2}{6}p_1^2[-2 \sin(2\tau + 2\alpha) ] $$
$$\ddot\phi_2 = -p_2\cos(\tau + \alpha)- q_2\sin(\tau + \alpha) - \frac{4g_2}{6}p_1^2[\cos(2\tau + 2\alpha) ] $$
Putting these values in equation,
\begin{align}
\ddot\phi_3+\phi_3+2g_2\phi_1\phi_2+g_3\phi_1^3-\ddot\phi_1-\Delta\phi_1+\omega_1\ddot\phi_2+\omega_2\ddot\phi_1 =0 \\
\ddot\phi_3+\phi_3+2g_2p_1 \cos(\tau+\alpha)[p_2\cos(\tau + \alpha) + q_2\sin(\tau + \alpha) + \frac{g_2}{6}p_1^2[\cos(2\tau + 2\alpha) - 3]] +g_3p^3_1\cos^3(\tau+\alpha)-\cos(\tau+\alpha) [-p_1 \Delta \alpha+\Delta p_1] -\sin(\tau+\alpha) [p_1\Delta \alpha+2\nabla \alpha \nabla p_1] +\omega_2p_1\cos(\tau+\alpha)=0
\end{align}
\begin{align}
\ddot\phi_3+\phi_3+g_2p_1 p_2 [1+\cos2(\tau+\alpha)] + g_2p_1 q_2\sin2(\tau+\alpha) + \frac{2 g_2^2 p_1^3}{6} \cos(\tau +\alpha)[2\cos^2(\tau+\alpha)-4]
+ g_3p_1^3[\frac{1}{4}(3\cos(\tau +\alpha)+\cos3(\tau+\alpha))]+ p_1\cos(\tau+\alpha) -\cos(\tau+\alpha)[\Delta p_1-p_1 \Delta\alpha] +\sin(\tau+\alpha)[p_1\Delta \alpha+2 \nabla p_1 \nabla \alpha]+ \omega_2p_1\cos(\tau+\alpha) =0
\end{align}
\begin{align}
\ddot\phi_3+\phi_3+g_2p_1 p_2 + g_2p_1 p_2 \cos2(\tau+\alpha)] + g_2p_1 q_2\sin2(\tau+\alpha) + \frac{2 g_2^2 p_1^3}{3} \cos^3(\tau +\alpha)-\frac{8 g_2^2 p_1^3}{6} \cos(\tau +\alpha)+g_3p_1^3[\frac{1}{4}(3\cos(\tau +\alpha)+\cos3(\tau+\alpha))]+p_1\cos(\tau+\alpha)-\cos(\tau+\alpha)[\Delta p_1-p_1 \Delta \alpha]+\sin(\tau+\alpha)[p_1\Delta \alpha+2 \nabla p_1 \nabla \alpha]+\omega_2p_1\cos(\tau+\alpha)=0
\end{align}
\begin{align}
\ddot\phi_3+\phi_3+g_2p_1 p_2 + g_2p_1 p_2 cos2(\tau+\alpha)] + g_2p_1 q_2sin2(\tau+\alpha) + \frac{2 g_2^2 p_1^3}{3}[\frac{1}{4}(3cos(\tau +\alpha)+cos3(\tau+\alpha))] -\frac{8 g_2^2 p_1^3}{6} \cos(\tau +\alpha)+g_3p_1^3[\frac{1}{4}(3\cos(\tau +\alpha)+\cos3(\tau+\alpha))] +p_1\cos(\tau+\alpha)-\cos(\tau+\alpha)[\Delta p_1-p_1 \Delta \alpha]+\sin(\tau+\alpha)[p_1\Delta \alpha+2 \nabla p_1 \nabla \alpha]+\omega_2p_1\cos(\tau+\alpha)=0
\end{align}
\begin{align}
\ddot\phi_3+\phi_3+sin(\tau+\alpha)[p_1\Delta \alpha+2 \nabla p_1 \nabla \alpha] -\cos(\tau+ \alpha)[\Delata p_1 - p_1\Delata\alpha+\frac{5}{6}g_2^2p_1^3- \frac{3}{4}g_3p_1^3-p_1 +\omega_2 p_1] +\frac{ p_1^3}{12}(2g_2^2+3g_3)\cos3(\tau + \alpha)+g_2 p_1 [p_2+ p_2 cos2(\tau +\alpha)+q_2 \sin2(\tau+\alpha)] =0
\end{align}
\begin{align}
\ddot\phi_3+\phi_3+sin(\tau+\alpha)[p_1\Delta \alpha+2 \nabla p_1 \nabla \alpha] -\cos(\tau+ \alpha)[\Delta p_1-p_1\Delta \alpha \\ + \lambda p_1^3-p_1+\omega_2 p_1] +\frac{p_1^3}{12}(2g_2^2+3g_3)\cos3(\tau + \alpha)+g_2 p_1 [p_2+ p_2 \cos2(\tau +\alpha)+q_2 \sin2(\tau+\alpha)]=0
\end{align}
\end{document}


\Delatainstead of\Delta). – Jubobs Mar 1 at 8:53\documentclass{...}and ending with\end{document}. – texenthusiast Mar 1 at 8:57\Delatainstead of\Delta. About multiline: you have examples in theamslatexmanual (online here for example). See section 3.3 or 3.4 – JLDiaz Mar 1 at 8:57.texdocument and compile to diagnose the error,later start developing from simple example. – texenthusiast Mar 1 at 9:00geometry-package for setting the page margins; (2) If you want to set lengths manually (baselineskipfor example), use the LaTeX\setlength{\<command name>}{<length>}– the way you did could cause errors in combination with other packages; (3) use a 'real' environment likealign,gather, etc. instead of$$– ralfix Mar 1 at 9:21