Fix some phrases that were not appearing in manual

Some phrases were in the index tag in the manual and not being
actually displayed. For example, "\index{potential function}s" only
displayed the letter "s". This should be "potential
functions\index{potential function}". This adds the appropriate
phrases next to the index tag.

Change-Id: Ia8e308f00a2542c1ee8c52fb017ba38926407876

diff --git a/docs/manual/analyse.tex b/docs/manual/analyse.tex
index 42038f5c395206aa376902e8f8324ab1a20a1dd4..21adb7460d7f0821b7815ed7072a5aa0497916f5 100644 (file)
--- a/docs/manual/analyse.tex
+++ b/docs/manual/analyse.tex
@@ -348,7 +348,8 @@ up to $r_{max}$, so angle dependent, see \figref{rdfex}D.
 The theory of correlation functions is well established~\cite{Allen87}.
 We describe here the implementation of the various 
 \normindex{correlation} function flavors in the {\gromacs} code.
-The definition of the \index{autocorrelation function} (ACF)
+The definition of the autocorrelation function\index{autocorrelation function} 
+(ACF)
 $C_f(t)$ for a property $f(t)$ is:
 \beq
 C_f(t)  ~=~     \left\langle f(\xi) f(\xi+t)\right\rangle_{\xi}
@@ -591,7 +592,8 @@ This is implemented in {\tt gmx viscosity}.
 \section{Mean Square Displacement}
 \label{sec:msd}
 {\tt gmx msd}\\
-To determine the self \index{diffusion coefficient} $D_A$ of
+To determine the self diffusion coefficient\index{diffusion coefficient} $D_A$ 
+of
 particles of type $A$, one can use the \normindex{Einstein
 relation}~\cite{Allen87}:
 \beq 

diff --git a/docs/manual/forcefield.tex b/docs/manual/forcefield.tex
index 7cffdd3b288ce3e6caa5accf890fbe688a274589..dc4b41834a9df83607dc14885245edafed53e8c9 100644 (file)
--- a/docs/manual/forcefield.tex
+++ b/docs/manual/forcefield.tex
@@ -2796,7 +2796,7 @@ improve upon the automatic load-balancing used by {\tt mdrun}.
 A force field is built up from two distinct components:
 \begin{itemize}
 \item The set of equations (called the {\em
-    \index{potential function}s}) used to generate the potential
+potential functions}\index{potential function}) used to generate the potential
   energies and their derivatives, the forces. These are described in
   detail in the previous chapter.
 \item The parameters used in this set of equations. These are not

diff --git a/docs/manual/implement.tex b/docs/manual/implement.tex
index 2d70c6b625fd76de80102adeb6f2c1d07ae984c7..fee86de639bd708278cadd2395d492973eb50c3b 100644 (file)
--- a/docs/manual/implement.tex
+++ b/docs/manual/implement.tex
@@ -1,7 +1,7 @@
 %
 % This file is part of the GROMACS molecular simulation package.
 %
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 % and including many others, as listed in the AUTHORS file in the
 % top-level source directory and at http://www.gromacs.org.
@@ -53,7 +53,8 @@ Here it is shown how it is possible to extract the virial calculation
 from the inner loop~\cite{Bekker93b}.
 
 \subsection{Virial}
-In a system with \index{periodic boundary conditions}, the
+In a system with periodic boundary conditions\index{periodic boundary 
+conditions}, the
 periodicity must be taken into account for the virial:
 \beq
 \Xi~=~-\half~\sum_{i < j}^{N}~\rnij\otimes\Fvij

diff --git a/docs/manual/special.tex b/docs/manual/special.tex
index 045f5a4dbcf7e208e2dd07a095e79b388696000d..0d2823d9dbc9b3b70afb3a339913f6dba0117c35 100644 (file)
--- a/docs/manual/special.tex
+++ b/docs/manual/special.tex
@@ -1602,9 +1602,9 @@ program.
 
 \subsection{User-specified potential functions}
 \label{subsec:userpot}
-You can also use your own \index{potential function}s 
-without editing the {\gromacs} code. 
-The potential function should be according to the following equation
+You can also use your own potential functions\index{potential function} without 
+editing the {\gromacs} code.  The potential function should be according to the 
+following equation
 \beq
 V(r_{ij}) ~=~ \frac{q_i q_j}{4 \pi\epsilon_0} f(r_{ij}) + C_6 \,g(r_{ij}) + C_{12} \,h(r_{ij})
 \eeq