Ticket #666: diff2francis

Index: changes_log_appendices.tex
===================================================================
--- changes_log_appendices.tex  (revision 6436)
+++ changes_log_appendices.tex  (working copy)
@@ -28,7 +28,7 @@
 
 At least three times are of relevance here.
 
-\textbf{UTC} = Coordinated Universal Time, a time which, since 0Z 01/07/1972, has been subjected to occasional leap second shifts to ensure that it keeps broadly in step with astronomical time.
+\textbf{UTC} = Coordinated Universal Time, a time which, since 0Z 01/07/1972, has been subjected to occasional leap second shifts to ensure that it k.pdf broadly in step with astronomical time.
 
 \textbf{TAI} = Temps Atomique International, the international atomic time scale based on a continuous counting of the SI second. TAI is currently ahead of UTC by 37 seconds, 27 of which are leap seconds and 10 of which were already in place before leap seconds started to be added in 1972.
 
@@ -40,7 +40,7 @@
 % leapsec_plot.ps
 \begin{figure}[tb]
   \centering
-  \includegraphics[width=0.95\textwidth]{figs/leapsec_plot.eps}
+  \includegraphics[width=0.95\textwidth]{figs/leapsec_plot.pdf}
   \caption{}
   \label{fig:change_log_fig1}
 \end{figure}
@@ -140,8 +140,8 @@
 % eci2eci.png
 \begin{figure}[tb]
   \centering
-%  \includegraphics[width=0.95\textwidth]{figs/eci2eci.eps}
-  \includegraphics[width=0.95\textwidth]{figs/eci2eci.eps}
+%  \includegraphics[width=0.95\textwidth]{figs/eci2eci.pdf}
+  \includegraphics[width=0.95\textwidth]{figs/eci2eci.pdf}
   \caption{}
   \label{fig:change_log_fig2}
 \end{figure}
@@ -179,7 +179,7 @@
 % ellipsoid.png
 \begin{figure}[tb]
   \centering
-  \includegraphics[width=0.99\textwidth]{figs/ellipsoid.eps}
+  \includegraphics[width=0.99\textwidth]{figs/ellipsoid.pdf}
   \caption{Radio occultation geometry. Shown are the bending angle
     $\alpha$, the GNSS and LEO side impact parameters ($p_G$ and
     $p_L$), the GNSS and LEO coordinate vectors ($\vr_G$, $\vr_L$),
@@ -199,7 +199,7 @@
 % plot_POD.ps
 \begin{figure}[tb]
   \centering
-  \includegraphics[height=0.8\textheight,width=0.8\textwidth]{figs/plot_POD.eps}
+  \includegraphics[height=0.8\textheight,width=0.8\textwidth]{figs/plot_POD.pdf}
   \caption{}
   \label{fig:change_log_fig4}
 \end{figure}
Index: coordinates.tex
===================================================================
--- coordinates.tex     (revision 6436)
+++ coordinates.tex     (working copy)
@@ -51,8 +51,8 @@
 % eci2eci.png
 \begin{figure}[tb]
   \centering
-%  \includegraphics[width=0.95\textwidth]{figs/eci2eci.eps}
-  \includegraphics[width=0.95\textwidth]{figs/eci2eci.eps}
+%  \includegraphics[width=0.95\textwidth]{figs/eci2eci.pdf}
+  \includegraphics[width=0.95\textwidth]{figs/eci2eci.pdf}
   \caption{Net of extended co-ordinate transformations available in ROPP}
   \label{fig:change_log_fig2}
 \end{figure}
@@ -91,7 +91,7 @@
 % ellipsoid.png
 \begin{figure}[tb]
   \centering
-  \includegraphics[width=0.99\textwidth]{figs/ellipsoid.eps}
+  \includegraphics[width=0.99\textwidth]{figs/ellipsoid.pdf}
   \caption{Radio occultation geometry. Shown are the bending angle
     $\alpha$, the GNSS and LEO side impact parameters ($p_G$ and
     $p_L$), the GNSS and LEO coordinate vectors ($\vr_G$, $\vr_L$),
@@ -109,7 +109,7 @@
 % plot_POD.ps
 \begin{figure}[tb]
   \centering
-  \includegraphics[height=0.8\textheight,width=0.8\textwidth]{figs/plot_POD.eps}
+  \includegraphics[height=0.8\textheight,width=0.8\textwidth]{figs/plot_POD.pdf}
   \caption{}
   \label{fig:change_log_fig4}
 \end{figure}
Index: datetime.tex
===================================================================
--- datetime.tex        (revision 6436)
+++ datetime.tex        (working copy)
@@ -43,7 +43,7 @@
 
 At least three times are of relevance here.
 
-\textbf{UTC} = Coordinated Universal Time, a time which, since 0Z 01/07/1972, has been subjected to occasional leap second shifts to ensure that it keeps broadly in step with astronomical time.
+\textbf{UTC} = Coordinated Universal Time, a time which, since 0Z 01/07/1972, has been subjected to occasional leap second shifts to ensure that it k.pdf broadly in step with astronomical time.
 
 \textbf{TAI} = Temps Atomique International, the international atomic time scale based on a continuous counting of the SI second. TAI is currently ahead of UTC by 37 seconds, 27 of which are leap seconds and 10 of which were already in place before leap seconds started to be added in 1972.
 
@@ -52,7 +52,7 @@
 % leapsec_plot.ps
 \begin{figure}[tb]
   \centering
-  \includegraphics[width=0.95\textwidth]{figs/leapsec_plot.eps}
+  \includegraphics[width=0.95\textwidth]{figs/leapsec_plot.pdf}
   \caption{This figure records the history of leap second insertions, and their effect on GPS vs UTC.}
   \label{fig:change_log_fig1}
 \end{figure}
Index: romsaf_ropp_ug_utils.tex
===================================================================
--- romsaf_ropp_ug_utils.tex    (revision 6436)
+++ romsaf_ropp_ug_utils.tex    (working copy)
@@ -45,7 +45,7 @@
 \usepackage{setspace}
 \usepackage{relsize}
 \usepackage[title,titletoc]{appendix}
-\usepackage[dvipdfm]{hyperref}
+%\usepackage[dvipdfm]{hyperref}
 \usepackage{varioref}
 \usepackage{bold-extra}
 
Index: ug_ropp_intro.tex
===================================================================
--- ug_ropp_intro.tex   (revision 6436)
+++ ug_ropp_intro.tex   (working copy)
@@ -1 +1,113 @@
-link ../common/ug_ropp_intro.tex
\ No newline at end of file
+%% $Id: ug_ropp_intro.tex 1431 2008-03-14 16:41:55Z idculv $
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%                                                                              %
+% ROPP User Guide: I/O                                                         %
+%                                                                              %
+% Met Office, Exeter                                                           %
+%                                                                              %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%---------------------------------------------------------------------------
+\chapter{ROPP}\label{ch:ropp}
+\section{ROPP introduction}
+
+The aim of ROPP is
+%
+\begin{quote}
+  \emph{\ldots{}to provide users with a comprehensive software package,
+  containing all necessary functionality to pre-process RO data from
+  Level 1a (Phase), Level 1b (Bending Angle) or Level 2 (Refractivity)
+  files, plus RO-specific components to assist with the assimilation
+  of these data in NWP systems.}
+\end{quote}
+%
+ROPP is a collection of software modules (provided as source code), supporting
+data files and documentation, which aids users wishing to assimilate radio
+occultation data into their NWP models. As far as is practical, the ROPP
+software is generic, in that it can handle any standard GNSS--LEO configuration
+radio occultation mission (Metop, COSMIC, CHAMP, GRACE, C/NOFS, SAC--C,
+TerraSAR--X, TanDEM--X, Megha-Tropiques, PAZ, KOMPSAT--5 etc).
+
+The software is distributed in the form of a source code library written in
+Fortran 90. ROPP is implemented using Fortran modules and derived types,
+enabling the use of object oriented techniques such as the overloading of
+routines. The software is split into several modules.
+Figure~\ref{fig:ropp_structure} illustrates the inter-relationships between each
+module. Users may wish to integrate a subset of ROPP code into their own
+software applications, individually linking modules to their own code. These
+users may not require the complete ROPP distribution package. Alternatively,
+users may wish to use the executable tools provided as part of each module as
+stand-alone applications for RO data processing. These users should download the
+complete ROPP release.
+
+\begin{figure}[htb]
+\centering
+\includegraphics[height=150mm]{../common/figs/structure_ropp.pdf}
+\caption{The \textbf{modules} and \emph{tools} within ROPP-10.0. The module at
+ the head of an arrow depends directly on the module at its tail.}
+\label{fig:ropp_structure}
+\end{figure}
+
+ROPP contains support for a generic data format for radio occultation data
+(\roppio), one- and two-dimensional forward models (\roppfm), routines for the
+implementation of 1D--Var retrievals, including quality control routines
+(\roppod), pre-processing and wave optics propagator routines (\ropppp), and
+various standalone applications (\roppapps). Utility routines used by some or
+all of the ROPP modules are provided in an additional module (\ropput). This
+structure (Figure~\ref{fig:ropp_structure}) reflects the various degrees of
+interdependence of the difference ROPP modules. For example, the subroutines and
+functions in \roppio{} and \roppfm{} modules are mutually indepdendent, whereas
+routines in \roppod{} depend on \roppfm. Sample standalone implementations of
+\ropppp{}, \roppfm{} and \roppod{} (which then require \roppio{} for file
+interfaces, reading and writing data) are provided with those modules and
+documented in the relevant User Guides.
+
+
+%---------------------------------------------------------------------------
+\section{User documentation}
+
+A full list of user documentation is provided in Tables~\ref{tab:docset},
+\ref{tab:gsr} and~\ref{tab:rsr}. These documents are available via the ROM SAF
+website at {\color{blue}http://www.romsaf.org}.
+
+The ROPP distribution website has a Release Notes file in the root directory
+which provides a `Quick Start' guide to the package. This should be read before
+downloading the package files. Detailed build and install instructions are
+contained in the release notes of the individual ROPP software modules.
+
+Module-specific user guides for the utilities \citep{romsaf_utils_ug},
+input/output \citep{romsaf_io_ug}, pre-processor \citep{romsaf_pp_ug}, forward
+model \citep{romsaf_fm_ug}, 1D--Var \citep{romsaf_1dvar_ug} and applications
+\citep{romsaf_apps_ug} modules describe the algorithms and routines used in
+those modules.  These provide the necessary background and descriptions of the
+ROPP software for users to process radio occultation data from excess phase to
+bending angle or refractivity, to forward model background fields to
+refractivity and bending angle profiles, to simulate the propagation of GNSS
+radio waves through idealised atmospheric refractivity structures, and to
+perform 1D--Var retrievals of radio occultation data, as well as advice on how
+to implement ROPP in their own applications.
+
+More detailed Reference Manuals are also available for each module for users
+wishing to write their own interfaces to the ROPP routines, or to modify the
+ROPP code. These are provided in the associated module distribution files.
+
+Further documentation can be downloaded from the ROPP section of the ROM SAF web
+site \linebreak {\color{blue}http://www.romsaf.org}. The full user documentation
+set is listed in Table~\ref{tab:docset}.
+
+In addition to these PDF documents, most of the stand-alone application programs
+have Unix-style `man page' help files which are installed during the build
+procedures. All such programs have summary help information which is available
+by running the command with the \texttt{-h} switch.
+
+Any comments on the ROPP software should in the first instance be raised via the
+ROM SAF Helpdesk at {\color{blue}http://www.romsaf.org}.
+
+
+%\bibliographystyle{romsaf}
+\bibliography{meteorology,rom_saf}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "romsaf_ropp_ug"
+%%% End:
Index: ug_utils.tex
===================================================================
--- ug_utils.tex        (revision 6436)
+++ ug_utils.tex        (working copy)
@@ -350,8 +350,8 @@
 \texttt{\ropput} must respect the same conditions in turn.
 
 
-\bibliographystyle{romsaf}
-\bibliography{meteorology,rom_saf}
+%\bibliographystyle{romsaf}
+%\bibliography{meteorology,rom_saf}
 
 %%% Local Variables:
 %%% mode: latex
Index: ug_utils_intro.tex
===================================================================
--- ug_utils_intro.tex  (revision 6436)
+++ ug_utils_intro.tex  (working copy)
@@ -49,7 +49,7 @@
 \end{itemize}
 \end{itemize}
 
-
+\newpage
 %---------------------------------------------------------------------------
 \input{../common/romsaf_acronyms}