Fixed numerous spelling errors, some grammatical boo-boos, formatting flaws

(inlcuding gratuitous hyphenation and un-dotted 'e.g.' and 'i.e')

Made more consistent use of italics (using \emph and \textit,
which are just better than \it for formatting)
	1) emphasis using \emph
	2) definitions, etc using \textit

Made capitalization more consistent and in-line with common usage
	1) Acronyms: MPI, MPICH, CVS
	2) Languages as proper nouns: Fortran, Perl
	3) Special capitalizations: LaTeX, PostScript
	4) Flesh seems best as a proper name, so capitalize
	5) thorn is a generic term, so capitalize accordingly
	6) 'tags' appears to be generic (TAGS is name of emacs database)

Made use of teletype font more consistent: ONLY for
	1) directory/file names
	2) typed commands and program names
	3) code
	4) URL's


git-svn-id: http://svn.cactuscode.org/flesh/trunk@3485 17b73243-c579-4c4c-a9d2-2d5706c11dac

1 files changed, 178 insertions, 177 deletions

diff --git a/doc/UsersGuide/RunningCactus.tex b/doc/UsersGuide/RunningCactus.tex
index 4319d76d..575a2414 100644
--- a/doc/UsersGuide/RunningCactus.tex
+++ b/doc/UsersGuide/RunningCactus.tex
@@ -24,26 +24,26 @@
 \section{Required software}
 \label{sec:reqo}
 
-In general, Cactus {\em requires} the following set of software to function
+In general, Cactus \emph{requires} the following set of software to function
 in single processor mode. Please refer to the architecture section
 \ref{sec:suar} for architecture specific items.
 \begin{Lentry}
-\item[{\tt Perl5.0}] Perl is used extensively during the Cactus
+\item[Perl5.0] Perl is used extensively during the Cactus
   thorn configuration phase. Perl is available for nearly all
   operating systems known to man and can be obtained at
   \url{http://www.perl.org}
-\item[{\tt GNU make}] The make
-  process works with the GNU make utility (referred to as {\bf gmake}
+\item[GNU make] The make
+  process works with the GNU make utility (referred to as {\tt gmake}
   henceforth). While other make utilities may also work, this is not
   guaranteed. Gmake can be obtained from your favorite GNU site or
   from \url{http://www.gnu.org}
-\item[{\tt C}] C compiler. For example, the GNU compiler. This
+\item[C] C compiler. For example, the GNU compiler. This
  is available for most supported platforms.  Platform specific compilers
  should also work.
-\item[{\tt CPP}] C Pre-processor. For example, the GNU CPP.  These are
-normally provided on most platforms, and many C compilers have an option
-to just run as a preprocessor.
-\item[{\tt CVS}] The {\em ``Concurrent Versioning System''} is not needed
+\item[CPP] C Preprocessor. For example, the GNU {\tt cpp}.  These are
+  normally provided on most platforms, and many C compilers have an option
+  to just run as a preprocessor.
+\item[CVS] The \textit{Concurrent Versions System} is not needed
   to run/compile Cactus, but you are strongly encourage to install
   this software to take advantage of the update procedures. It can be
   downloaded from your favorite GNU site.  Tar files of each release are
@@ -54,45 +54,45 @@ to just run as a preprocessor.
 To use Cactus, with the default driver\footnote{For help with unfamiliar terms, please consult the glossary, Appendix \ref{sec:glossary}.} ({\tt CactusPUGH/PUGH}) on multiple
 processors you also need:
 \begin{Lentry}
-\item[{\tt MPI}] the {\it Message Passing Interface (MPI)}
+\item[MPI] The \textit{Message Passing Interface} 
 which provides inter-processor communication.
-Supercomputing sites often supply a native {\tt MPI} implementation with
+Supercomputing sites often supply a native MPI implementation with
 which Cactus is very likely to be compatible. Otherwise there are
-various freely available ones available, e.g. the {\tt MPICH}
-version of {\tt MPI} is available for various architectures and operating
+various freely available ones available, e.g. the MPICH
+version of MPI is available for various architectures and operating
 systems at \url{http://www-unix.mcs.anl.gov/mpi/}.
 \end{Lentry}
 
 \noindent
 If you are using any thorns containing routines
-written in {\tt C++} you also need
+written in C++ you also need
 \begin{Lentry}
-\item[{\tt C++}] C++ compiler. For example, the GNU compiler. This
+\item[C++] C++ compiler. For example, the GNU compiler. This
  is available for most supported platforms.  Platform specific compilers
  should also work.  Note that if a C++ compiler is available then the
- {\em main} routine in the flesh is compiled with C++ to allow static
+ {\tt main} routine in the Flesh is compiled with C++ to allow static
  class initialisations.
 \end{Lentry}
 
 \noindent
 If you are using any thorns containing routines
-written in {\tt FORTRAN} you also need
+written in Fortran you also need
 \begin{Lentry}
-\item[{\tt F90/F77}] For routines written in F77, either an F90 or an F77
- compiler can be used. For routines written in F90 a F90 compiler is
- obviously
- required. There is a very limited set of free F90 compilers available
- for the different architectures.
+\item[F90/F77] For routines written in Fortran 77, either an Fortran 90 or
+ a Fortran 77 compiler can be used. For routines written in Fortran 90
+ a Fortran 90 compiler is obviously required. There is a very limited set of
+ free Fortran 90 compilers available for the different architectures.
 \end{Lentry}
 
 \noindent
 While not required for compiling or running Cactus, for thorn development
 it is useful to install
 \begin{Lentry}
-\item[{\tt ctags/etags}] The program Tags enables you browse through the calling structure
-  of a program by help of a function call database. Navigating the flesh and
-  arrangements becomes very easy. Emacs and vi both support this method. See
-  \ref{sec:usta} for a short guide to ``tags''.
+\item[{\tt ctags/etags}] These programs enable you browse through the
+  calling structure of a program by help of a function call database.
+  Navigating the Flesh and arrangements becomes very easy. Emacs and
+  {\tt vi} both support this method. See \ref{sec:usta} for a short guide
+  to ``tags''.
 \end{Lentry}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -110,39 +110,39 @@ be found at
 \end{center}
 
 \begin{Lentry}
-\item[{\bf SGI}] 32 or 64 bit running Irix.
-\item[{\bf Cray T3E}]
-\item[{\bf Compaq Alpha}]  Compaq operating system and Linux.  Single processor
-  mode and {\tt MPI} supported. The Alphas need to have the GNU {\tt C/C++}
+\item[\textbf{SGI}] 32 or 64 bit running Irix.
+\item[\textbf{Cray T3E}]
+\item[\textbf{Compaq Alpha}]  Compaq operating system and Linux.  Single processor
+  mode and MPI supported. The Alphas need to have the GNU C/C++
   compilers installed.
 \item[\textbf{IA32}] running Linux or Windows 2000/NT.  Single
-processor mode and MPI ({\tt MPICH} and {\tt LAM}) supported.\\On
+processor mode and MPI (MPICH and LAM) supported.\\On
 Windows Cactus compiles with Cygwin.  MPI
-({\tt WMPI}, {\tt HPVM}, and {\tt MPIPro}) supported.  Please read
-doc/README.NT for details.
+(WMPI, HPVM, and MPIPro) supported.  Please read
+{\tt doc/README.NT} for details.
 \item[\textbf{IA64}]  running Linux.
-\item[{\bf Macintosh PowerPC}] (MacOS X and Linux PPC)
-\item[{\bf IBM SP2}] 32 or 64 bit running AIX.
-\item[{\bf Hitachi SR8000-F1}]
-\item[{\bf Sun} Solaris]
-\item[{\bf Fujitsu}]
+\item[\textbf{Macintosh PowerPC}] (MacOS X and Linux PPC)
+\item[\textbf{IBM SP2}] 32 or 64 bit running AIX.
+\item[\textbf{Hitachi SR8000-F1}]
+\item[\textbf{Sun} Solaris]
+\item[\textbf{Fujitsu}]
 \end{Lentry}
 
 %\begin{Lentry}
 %\item[{\bf SGI Origin 2000} running Irix]
 %\item[{\bf SGI} 32 or 64 bit running Irix]
 %\item[{\bf Cray T3E}]
-%\item[{\bf Dec Alpha}]  Dec operating system and Linux. Single processor
-%  mode and {\tt MPI} supported. The Decs need to have the GNU {\tt C/C++}
+%\item[{\bf DEC Alpha}]  Dec operating system and Linux. Single processor
+%  mode and MPI supported. The DECs need to have the GNU C/C++
 %  compilers installed
 %\item[{\bf Linux (ia32, ia64, ppc, alpha)}] There is a
 %  free Linux F90 compiler available from  \url{http://www.psrv.com}
 %  -- the only free we know of; please note the comment about installing this in
 %the FAQ.
-%  Single processor mode and MPI ({\tt MPICH} and {\tt LAM}) supported.
+%  Single processor mode and MPI (MPICH and LAM) supported.
 %\item[{\bf Windows NT}] Compiles with Cygwin. Single processor mode and MPI ({\t
 %t WMPI},
-%{\tt HPVM}, and {\tt MPIPro}) supported.  Please read doc/README.NT for details.
+%{\tt HPVM}, and MPIPro) supported.  Please read doc/README.NT for details.
 %\item[{\bf Macintosh PowerPC (MacOS X)}]
 %\item[{\bf IBM SP2}]
 %\item[{\bf Hitachi SR8000-F1}]
@@ -151,8 +151,8 @@ doc/README.NT for details.
 
 The following machines are only partially supported
 \begin{Lentry}
-\item[{\bf HP Exemplar}]
-\item[{\bf NEC SX-5}]
+\item[\textbf{HP Exemplar}]
+\item[\textbf{NEC SX-5}]
 \end{Lentry}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -161,39 +161,39 @@ The following machines are only partially supported
 \label{sec:chpr}
 
 Cactus is distributed, extended, and maintained using the free CVS
-software ({\it Concurrent Versioning System}: \url{http://www.cvshome.org}).
+software (\textit{Concurrent Versions System}: \url{http://www.cvshome.org}).
 CVS  allows many people to work on a large software project
 together without getting into a tangle.
 Since Cactus thorns are distributed from several repositories on the
 main CVS site, and from a growing number of user sites, we provide a
-script, described below,  on our website for checking out the flesh and thorns.
-The Cactus website also provides a form interface for direct download.
+script, described below,  on our web site for checking out the Flesh and thorns.
+The Cactus web site also provides a form interface for direct download.
 
 CVS experts who want to use raw CVS commands are directed to Appendix~\ref{sec:uscv}
 for full instructions. For CVS novices, we also summarize in this
 appendix basic CVS commands.
 
 The space required for an installation depends on the arrangements and
-thorns used. The flesh on its own requires less than 5 MB.
+thorns used. The Flesh on its own requires less than 5 MB.
 
-The script for checking out the flesh and thorns, {\tt GetCactus}, is available
-from the website at
+The script for checking out the Flesh and thorns, {\tt GetCactus}, is available
+from the web site at
 
 \url{http://www.cactuscode.org/Download/GetCactus}
 
 The
-script takes as an argument the name of a file containing a {\it ThornList},
+script takes as an argument the name of a file containing a \textit{ThornList},
 that is a list of thorns with the syntax
 {\tt
 \begin{verbatim}
 <arrangement name>/<thorn name>
 \end{verbatim}
 }
-If no filename is given, only the flesh is checked out.
+If no filename is given, only the Flesh is checked out.
 Optional directives in the ThornList indicate which CVS repository to fetch
 thorns from. The default is to take the thorns from the same repository as
-the flesh. A full description of ThornList syntax is provided in Appendix~\ref{chap:th}.
-ThornLists for example applications are provided on the Cactus website.
+the Flesh. A full description of ThornList syntax is provided in Appendix~\ref{chap:th}.
+ThornLists for example applications are provided on the Cactus web site.
 
 The same script can be used to checkout additional thorns.
 
@@ -207,7 +207,7 @@ following subdirectories:
 
 \begin{Lentry}
 
-\item[{\tt CVS}] the CVS book-keeping directory, present in every subdirectory
+\item[{\tt CVS}] the CVS bookkeeping directory, present in every subdirectory
 
 \item[{\tt doc}] Cactus documentation
 
@@ -238,7 +238,7 @@ or
 \begin{itemize}
 \item{}  soft link this directory ({\tt ln -s
 scratch/cactus\_configs Cactus/configs/}) to the Cactus directory, if your
-file-system supports soft-links.
+filesystem supports soft links.
 \end{itemize}
 
 Configurations are described in detail in section \ref{sec:coaco}.
@@ -248,7 +248,7 @@ Configurations are described in detail in section \ref{sec:coaco}.
 \section{Getting help}
 \label{sec:gehe}
 
-For tracking problem reports and bugs we use GNATS, which is a bugtracking
+For tracking problem reports and bugs we use GNATS, which is a bug tracking
 system published under the GNU license. We have set up a web interface at
 \url{http://www.cactuscode.org} which allows easy submission and browsing
 of problem reports.
@@ -258,7 +258,7 @@ A description of the GNATS categories which we use is provided in the appendix
 
 % OK, there is NO emacs at the moment, because the GNATS setup is really stupid
 % and sendpr handles like c.... besides the fact, that the user has to go
-% through a make-process which installs stuff somewhere on his HD. gerd.
+% through a make process which installs stuff somewhere on his HD. gerd.
 % BUT, we could distribute our own, either copy cvsbug, or write a perl
 % version.  Tom
 % \begin{itemize}
@@ -281,14 +281,14 @@ the source files, and these different configurations coexist in the
  this can be useful:
 
 \begin{enumerate}
-\item{}Different configurations can be for {\em different
+\item{}Different configurations can be for \emph{different
 architectures}. You can keep executables for multiple architectures
 based on a single copy of source code, shared on a common file
 system.
-\item{} You can compare different {\em compiler options, debug-modes}.
+\item{} You can compare different \textit{compiler options, debug-modes}.
   You might want to compile different communication protocols
-  (e.g. {\tt MPI} or {\tt GLOBUS}) or leave them out all together.
-\item{} You can have different configurations for {\em different thorn
+  (e.g. MPI or Globus) or leave them out all together.
+\item{} You can have different configurations for \textit{different thorn
     collections} compiled into your executable.
 \end{enumerate}
 
@@ -305,7 +305,7 @@ At its simplest, this is done by {\tt gmake <config>}\footnote
 %
 {A note on the Cactus make system --- if at any point it prompts you
 to enter something, the default value, which will be assumed if you
-simply press enter, is shown in parantheses.}
+simply press enter, is shown in parentheses.}
 %
 .  This generates a
 configuration with the name {\tt config}, doing its best to
@@ -360,7 +360,7 @@ There is a plethora of available options.
 
 \begin{itemize}
 
-\item {\tt Compiled Thorns}
+\item {Compiled Thorns}
 
 These specify the chosen set of thorns for compilation. If the thorn choice is not provided
 during configuration, a list containing all thorns in the {\tt arrangements} directory
@@ -370,7 +370,7 @@ is automatically created, and the users prompted for any changes.
 
 \item [{\tt THORNLIST}] Name of file containing a list of thorns with
 the syntax {\tt <arrangement name>/<thorn name>}, lines beginning with
-\# or ! are ignored.
+{\tt \#} or {\tt !} are ignored.
 
 \item [{\tt THORNLIST\_DIR}] Location of directory containing {\tt THORNLIST}.
 This defaults to the current working directory.
@@ -378,7 +378,7 @@ This defaults to the current working directory.
 
 \end{Lentry}
 
-\item {\tt Compiler and tool specification}
+\item {Compiler and tool specification}
 
 These are used to specify which compilers and other tools to use. Entries followed
 by * may be specified on the command line.
@@ -387,16 +387,16 @@ by * may be specified on the command line.
 \item [{\tt CC}]   * The C compiler.
 \item [{\tt CXX}]    The C++ compiler.
 \item [{\tt F90}]  * The Fortran 90 compiler.
-\item [{\tt F77}]  * The FORTRAN 77 compiler.
+\item [{\tt F77}]  * The Fortran 77 compiler.
 \item [{\tt CPP}]    The preprocessor used to generate dependencies and to preprocess Fortran code.
 \item [{\tt LD}]   * The linker.
 \item [{\tt AR}]     The archiver used for generating libraries.
 \item [{\tt RANLIB}] The archive indexer to use.
 \item [{\tt MKDIR}]  The program to use to create a directory.
-\item [{\tt PERL}]   The name of the perl executable.
+\item [{\tt PERL}]   The name of the Perl executable.
 \end{Lentry}
 
-\item {\tt Compilation and tool flags}
+\item {Compilation and tool flags}
 
 Flags which are passed to the compilers and the tools.
 
@@ -411,14 +411,14 @@ Flags for the C++ compiler.
 * Flags for the Fortran 90 compiler.
 
 \item [{\tt F77FLAGS}]
-* Flags for the FORTRAN 77 compiler.
+* Flags for the Fortran 77 compiler.
 
 \item [{\tt CPPFLAGS}]
 Flags for the preprocessor (used to generate compilation dependencies
 and preprocess Fortran code).
 
 \item [{\tt MKDIRFLAGS}]
-  Flags for MKDIR so that no error is given if the directory exists.
+  Flags for {\tt MKDIR} so that no error is given if the directory exists.
 \item [{\tt LDFLAGS}]
 * Flags for the linker.
 
@@ -448,11 +448,11 @@ Optimisation flags for the C++ compiler, their use depends on the type of
 optimisation being used.
 
 \item [{\tt F90\_OPTIMISE\_FLAGS}]
-Optimisation flags for the FORTRAN 90 compiler, their use depends on the
+Optimisation flags for the Fortran 90 compiler, their use depends on the
 type of optimisation being used.
 
 \item [{\tt F77\_OPTIMISE\_FLAGS}]
-Optimisation flags for the FORTRAN 77 compiler, their use depends on the
+Optimisation flags for the Fortran 77 compiler, their use depends on the
 type of optimisation being used.
 
 \item [{\tt C\_WARN\_FLAGS}]
@@ -464,7 +464,7 @@ Warning flags for the C++ compiler, their use depends on the type of
 warnings used during compilation (\ref{sec:gmopfobuco}).
 
 \item [{\tt F90\_WARN\_FLAGS}]
-Warning flags for the FORTRAN 90 compiler, their use depends on the type of
+Warning flags for the Fortran 90 compiler, their use depends on the type of
 warnings used during compilation (\ref{sec:gmopfobuco}).
 
 \item [{\tt F77\_WARN\_FLAGS}]
@@ -473,7 +473,7 @@ warnings used during compilation (\ref{sec:gmopfobuco}).
 
 \end{Lentry}
 
-\item {\tt Architecture-specific flags}
+\item {Architecture-specific flags}
 
 \begin{Lentry}
 \item [{\tt IRIX\_BITS=32|64}] For Irix SGI systems: whether to build a 32- or 64-bit configuration.
@@ -483,7 +483,7 @@ warnings used during compilation (\ref{sec:gmopfobuco}).
 \item [{\tt AIX\_BITS=32|64}] For IBM SP systems: whether to build a 32- or 64-bit configuration.
 \end{Lentry}
 
-\item {\tt Library flags}
+\item {Library flags}
 
 Used to specify auxiliary libraries and directories to find them in.
 
@@ -492,7 +492,7 @@ Used to specify auxiliary libraries and directories to find them in.
 \item [{\tt LIBDIRS}] Any other library directories.
 \end{Lentry}
 
-\item {\tt Extra include directories}
+\item {Extra include directories}
 
 \begin{Lentry}
 \item [{\tt SYS\_INC\_DIRS}]
@@ -500,7 +500,7 @@ Used to specify any additional directories for system include files.
 \end{Lentry}
 
 
-\item {\tt Precision options}
+\item {Precision options}
 
 Used to specify the precision of the default real and integer data types,
 specified as the number of bytes the data takes up.  Note that not all
@@ -509,50 +509,50 @@ values will be valid on all architectures.
 \begin{Lentry}
 
 \item [{\tt REAL\_PRECISION}]
-* Allowed values are 16, 8, 4.
+* Allowed values are {\tt 16, 8, 4}.
 
 \item [{\tt INTEGER\_PRECISION}]
-* Allowed values are 8, 4 and 2.
+* Allowed values are {\tt 8, 4} and {\tt 2}.
 
 \end{Lentry}
 
-\item {\tt Executable name}
+\item {Executable name}
 
 \begin{Lentry}
 \item [{\tt EXEDIR}] The directory in which to place the executable.
 \item [{\tt EXE}] The name of the executable.
 \end{Lentry}
 
-\item{\tt Extra packages}
+\item{Extra packages}
 
 Compiling with extra packages is described fully in
 Section \ref{sec:cowiexpa},
 which should be consulted for the full range of configuration options.
 
 \begin{Lentry}
-\item [{\tt MPI} *] The {\tt MPI} package to use, if required. Supported values are
+\item [{\tt MPI}] * The MPI package to use, if required. Supported values are
         {\tt CUSTOM}, {\tt NATIVE}, {\tt MPICH} or {\tt LAM}.
 
 \item [{\tt HDF5}]
-Supported values are {\it yes, no}. A blank value is taken as {\it no}.
+Supported values are {\tt yes, no}. A blank value is taken as {\tt no}.
 
 \item [{\tt LAPACK}]
-Supported values are {\it yes, no}. A blank value is taken as {\it no}.
+Supported values are {\tt yes, no}. A blank value is taken as {\tt no}.
 
 \item [{\tt PETSC}]
-Supported values are {\it yes, no}. A blank value is taken as {\it no}.
+Supported values are {\tt yes, no}. A blank value is taken as {\tt no}.
 
 \item [{\tt PTHREADS}]
-Supported values are {\it yes}.
+Supported values are {\tt yes}.
 
 \end{Lentry}
 
-\item{\tt Miscellaneous}
+\item{Miscellaneous}
 
 \begin{Lentry}
-\item [{\tt PROMPT}] Setting this to 'no' turns off all prompts from the
+\item [{\tt PROMPT}] Setting this to {\tt no} turns off all prompts from the
 make system.
-\item [{\tt SILENT}] Setting this to 'no' instructs {\tt gmake} to print the
+\item [{\tt SILENT}] Setting this to {\tt no} instructs {\tt gmake} to print the
 commands that it is executing.
 \end{Lentry}
 
@@ -568,10 +568,10 @@ commands that it is executing.
 
 \subsubsection{MPI: Message Passing Interface}
 
-{\tt MPI} (the {\it Message Passing Interface}) provides inter-processor
+The \textit{Message Passing Interface} (MPI) provides inter-processor
 communication. It can either be implemented natively on a machine
 (this is usual on most supercomputers), or through a standard package
-such as {\tt MPICH}, {\tt LAM}, {WMPI}, or {PACX}.
+such as MPICH, LAM, WMPI, or PACX.
 
 To compile with MPI, the configure option is
 
@@ -582,14 +582,14 @@ may be specified on the configuration command line):
 
 \begin{Lentry}
 
-\item[{\tt CUSTOM}] For a custom {\tt MPI} configuration set the variables
+\item[{\tt CUSTOM}] For a custom MPI configuration set the variables
   \begin{Lentry}
-  \item [{\tt MPI\_LIBS} *] libraries.
-  \item [{\tt MPI\_LIB\_DIRS} *] library directories.
-  \item [{\tt MPI\_INC\_DIRS} *] include file directories.
+  \item [{\tt MPI\_LIBS}] * libraries.
+  \item [{\tt MPI\_LIB\_DIRS}] * library directories.
+  \item [{\tt MPI\_INC\_DIRS}] * include file directories.
   \end{Lentry}
 
-\item[{\tt NATIVE}] Use the native {\tt MPI} for this machine, as indicated in
+\item[{\tt NATIVE}] Use the native MPI for this machine, as indicated in
         the {\tt known-architectures} directory
         ({\tt lib/make/known-architectures}).
 
@@ -597,10 +597,10 @@ may be specified on the configuration command line):
 Use MPICH (\url{http://www-unix.mcs.anl.gov/mpi/mpich}). This is controlled
 by the options
   \begin{Lentry}
-  \item [{\tt MPICH\_ARCH} *] machine architecture.
-  \item [{\tt MPICH\_DIR} *] directory in which {\tt MPICH} is installed.
+  \item [{\tt MPICH\_ARCH}] * machine architecture.
+  \item [{\tt MPICH\_DIR} ] * directory in which MPICH is installed.
         If this option is not defined it will be searched for.
-  \item [{\tt MPICH\_DEVICE} *] the device used by {\tt MPICH}. If not
+  \item [{\tt MPICH\_DEVICE}] * the device used by MPICH. If not
         defined, the configuration process will search for this in a
         few defined places.
         Supported devices are currently {\tt ch\_p4}, {\tt ch\_shmem},
@@ -613,54 +613,54 @@ by the options
 If {\tt MPICH\_DEVICE} is chosen to be {\tt globus},
 (\url{http://www.globus.org}), an additional variable must be set
   \begin{Lentry}
-  \item[{\tt GLOBUS\_LIB\_DIR} *] directory in which Globus libraries are installed.
+  \item[{\tt GLOBUS\_LIB\_DIR}] * directory in which Globus libraries are installed.
   \end{Lentry}
 
 If {\tt MPICH\_DEVICE} is chosen to be {\tt ch\_gm},
 (\url{http://www.myri.com}), an additional variable must be set
   \begin{Lentry}
-  \item[{\tt MYRINET\_DIR} *] directory in which Myrinet libraries are installed.
+  \item[{\tt MYRINET\_DIR}] * directory in which Myrinet libraries are installed.
   \end{Lentry}
 
 \item[{\tt LAM}]
-Use {\tt LAM} (Local Area Multicomputer, \url{http://www.lam-mpi.org/}).
+Use {\tt LAM} (\textit{Local Area Multicomputer}, \url{http://www.lam-mpi.org/}).
 This is controlled by the variables
   \begin{Lentry}
-  \item[{\tt LAM\_DIR} *] directory in which {\tt LAM} is installed. This
+  \item[{\tt LAM\_DIR} ] * directory in which LAM is installed. This
      will be searched for in a few provided places if not given.
   \end{Lentry}
 if the {\tt LAM} installation splits libraries and include files into different
 directories, instead of setting {\tt LAM\_DIR} set the two variables
   \begin{Lentry}
-  \item[{\tt LAM\_LIB\_DIR} *] directory in which {\tt LAM} libraries are installed.
-  \item[{\tt LAM\_INC\_DIR} *] directory in which {\tt LAM} include files are installed.
+  \item[{\tt LAM\_LIB\_DIR}] * directory in which LAM libraries are installed.
+  \item[{\tt LAM\_INC\_DIR}] * directory in which LAM include files are installed.
   \end{Lentry}
 
 
 \item[{\tt WMPI}]
-Use WMPI (Win32 Message Passing Interface, \url{http://dsg.dei.uc.pt/w32mpi/intro.html}). This is controlled by the variable
+Use WMPI (\textit{Win32 Message Passing Interface}, \url{http://dsg.dei.uc.pt/w32mpi/intro.html}). This is controlled by the variable
   \begin{Lentry}
-  \item[{\tt WMPI\_DIR} *] directory in which {\tt WMPI} is installed.
+  \item[{\tt WMPI\_DIR}] * directory in which WMPI is installed.
   \end{Lentry}
 
 \item[{\tt HPVM}]
-Use HPVM (High Performance Virtual Machine,
+Use HPVM (\textit{High Performance Virtual Machine},
 (\url{http://www-csag.ucsd.edu/projects/hpvm.html}).
 This is controlled by the variable
   \begin{Lentry}
-  \item[{\tt HPVM\_DIR} *] directory in which {\tt HPVM} is installed.
+  \item[{\tt HPVM\_DIR}] * directory in which HPVM is installed.
   \end{Lentry}
 
 \item[{\tt MPIPro}]
 Use MPIPro (\url{http://www.mpi-softtech.com/}).
 
 \item[{\tt PACX}]
-Use the PACX Metacomputing package (PArallel Computer eXtension,\\
+Use the PACX Metacomputing package (\textit{PArallel Computer eXtension},\\
 \url{http://www.hlrs.de/structure/organisation/par/projects/pacx-mpi/}). This is controlled by the variables
   \begin{Lentry}
-  \item[{\tt PACX\_DIR} *] directory in which {\tt PACX} is installed.
+  \item[{\tt PACX\_DIR}] * directory in which PACX is installed.
         If this option is not defined it will be searched for.
-  \item[{\tt PACX\_MPI} *] the MPI package {\tt PACX} uses for node-local
+  \item[{\tt PACX\_MPI}] * the MPI package PACX uses for node-local
         communication. This can be any of the above MPI packages.
   \end{Lentry}
 
@@ -676,17 +676,17 @@ the configure options are
 
 {\tt HDF5 = yes/no [HDF5\_DIR = <dir>] [LIBZ\_DIR = <dir>] [LIBSZ\_DIR = <dir>]}
 
-If HDF5\_DIR is not given the configuration process will search for an
+If {\tt HDF5\_DIR} is not given the configuration process will search for an
 installed HDF5 package in some standard places (defined in
 {\tt lib/make/extras/HDF5}).
 If the found HDF5 library was built with the external deflate I/O filter,
 the configuration process also searches for the {\tt libz} library and adds it
 to the linker flags. You may also point directly to the location of
-{\tt libz.a} by setting LIBZ\_DIR.
-If the found HDF5 library was built with the external szlib I/O filter,
+{\tt libz.a} by setting {\tt LIBZ\_DIR}.
+If the found HDF5 library was built with the external {\tt szlib} I/O filter,
 the configuration process also searches for the {\tt szlib} library and adds it
 to the linker flags. You may also point directly to the location of
-{\tt libsz.a} by setting LIBSZ\_DIR.
+{\tt libsz.a} by setting {\tt LIBSZ\_DIR}.
 
 
 \subsubsection{LAPACK: Linear Algebra PACKage}
@@ -703,10 +703,10 @@ LAPACK = yes | no | <blank>
 \end{verbatim}
 
 If {\t LAPACK\_DIR} is not given the configuration process will search for a
-LAPACK library {\it liblapack.[\{a,so\}]} in some standard places (defined in
-{\tt lib/make/extras/LAPACK}). If {\t LAPACK\_DIR} is set to {\it no} the
+LAPACK library {\tt liblapack.[\{a,so\}]} in some standard places (defined in
+{\tt lib/make/extras/LAPACK}). If {\t LAPACK\_DIR} is set to {\tt no} the
 LAPACK library path is assumed to be installed in a standard system location
-(eg. {\i /usr/lib/}) and thus the library path will not be added to the linker's
+(e.g. {\tt /usr/lib/}) and thus the library path will not be added to the linker's
 command line.
 
 Because LAPACK doesn't come as a standardized system installation, there are
@@ -738,16 +738,16 @@ architecture-specific libraries as required by a PETSc configuration (usually
 PETSc needs the LAPACK library).
 
 
-\subsubsection{PTHREADS: POSIX threads}
+\subsubsection{Pthreads: POSIX threads}
 
 To enable multithreading support within Cactus using POSIX threads
 the configure option is
 
 {\tt PTHREADS = yes}
 
-The configuration process will check if a re-entrant C library is available
+The configuration process will check if a reentrant C library is available
 and adds it to the linker flags. It will also search for the system's Pthreads
-library (either libpthread or libpthreads) and set preprocessor
+library (either {\tt libpthread} or {\tt libpthreads}) and set preprocessor
 defines necessary for compiling multithreaded code.
 
 
@@ -788,7 +788,7 @@ In addition the following files may be informative:
 
 \begin{Lentry}
 \item [{\tt fortran\_name.pl}]
-A perl script used to determine how the Fortran compiler names subroutines.
+A Perl script used to determine how the Fortran compiler names subroutines.
 This is used to make some C routines callable from Fortran, and Fortran
 routines callable from C.
 
@@ -797,22 +797,22 @@ Initially empty.  Can be edited to add extra architecture specific dependencies
 needed to generate the executable.
 
 \item [{\tt make.config.rule}]
-Make rules for generating object files from source files.
+The {\tt make} rules for generating object files from source files.
 
 \end{Lentry}
 
-Finally, autoconf generates the following files.
+Finally, {\tt autoconf} generates the following files.
 
 \begin{Lentry}
 
 \item [{\tt config.log}]
-A log of the autoconf process.
+A log of the {\tt autoconf} process.
 
 \item [{\tt config.status}]
 A script which may be used to regenerate the configuration.
 
 \item [{\tt config.cache}]
-An internal file used by autoconf.
+An internal file used by {\tt autoconf}.
 
 \end{Lentry}
 
@@ -830,7 +830,7 @@ A file containing information about the configuration.
 generated by the CST from the \texttt{.ccl} files.
 
 \item [{\tt scratch}]
-A scratch directory which is used to accomodate Fortran 90 modules.
+A scratch directory which is used to accommodate Fortran 90 modules.
 
 \end{Lentry}
 
@@ -843,7 +843,7 @@ Once you have created a new configuration, the command
 {\tt gmake <configuration name>}
 \\ \\
 will build an executable, prompting you along the way for the
-thorns which should be included. There is a range of  gmake
+thorns which should be included. There is a range of {\tt gmake}
 targets and options which are detailed in the following sections.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -852,7 +852,7 @@ targets and options which are detailed in the following sections.
 
 A target for {\tt gmake} can be naively thought of as an argument
 that tells it which of several things listed in the {\tt Makefile} it
-is to do. The command {\tt gmake help} lists all gmake targets:
+is to do. The command {\tt gmake help} lists all {\tt gmake} targets:
 % colon clarifies that all (config) targets are listed here
 
 \begin{Lentry}
@@ -872,7 +872,7 @@ is to do. The command {\tt gmake help} lists all gmake targets:
 
 \item [{\tt gmake <config>-config}] creates a new configuration or reconfigures an old one.
 
-\item [{\tt gmake <config>-cvsupdate}] update the Flesh and Thorns for a configuration using CVS
+\item [{\tt gmake <config>-cvsupdate}] updates the Flesh and thorns for a configuration using CVS
 
 \item [{\tt gmake <config>-delete}] deletes a configuration ({\tt rm -r configs/<config>}).
 
@@ -882,9 +882,9 @@ is to do. The command {\tt gmake help} lists all gmake targets:
 
 \item [{\tt gmake <config>-realclean}] removes from a configuration
 all object and dependency files, as well as files generated from the
-CST (stands for Cactus Specification Tool, which is the perl scripts
+CST (stands for \textit{Cactus Specification Tool}, which is the set of Perl scripts
 which parse the thorn configuration files).  Only the files generated
-by configure and the ThornList file remain.
+by configure and the {\tt ThornList} file remain.
 
 \item [{\tt gmake <config>-rebuild}] rebuilds a configuration (reruns the CST).
 
@@ -892,7 +892,7 @@ by configure and the ThornList file remain.
  each thorn in the configuration. See section \ref{sec:te} for information about the
  testsuite mechanism.
 
-\item [{\tt gmake <config>-thornlist}] regenerates the ThornList for a configuration.
+\item [{\tt gmake <config>-thornlist}] regenerates the {\tt ThornList} for a configuration.
 
 \item [{\tt gmake <config>-utils [UTILS$=$<list>]}] builds all utility programs provided by the thorns of a configuration. Individual utilities can be selected by giving their names in the {\tt UTILS} variable.
 
@@ -901,7 +901,7 @@ in this configuration.
 
 \item[{\tt gmake <config>-configinfo}] displays the options used to build the configuration.
 
-\item[{\tt gmake <config>-cvsupdate}] updates the Flesh and this configuration's Thorns from the CVS repositories.
+\item[{\tt gmake <config>-cvsupdate}] updates the Flesh and this configuration's thorns from the CVS repositories.
 
 \end{Lentry}
 
@@ -913,7 +913,8 @@ in this configuration.
 Cactus will try to compile all thorns listed in
 {\tt configs/<config>/ThornList}.
 The {\tt ThornList} file is simply a list of the form
-{\t <arrangement>/<thorn>}.  All text after a \# or ! sign
+{\tt <arrangement>/<thorn>}.  All text after a pound sign `{\tt \#}' or 
+exclamation mark `{\tt !}' 
 on a line is treated as a comment and ignored.
 The first time that you compile a configuration, if you did
 not specify a ThornList already during configuration,
@@ -932,17 +933,17 @@ gmake <config>-editthorns
 \end{verbatim}
 
 Instead of using the editor to specify the thorns you want to
-  have compiled, you can {\em edit} the {\em ThornList} outside
+  have compiled, you can \emph{edit} the {\tt ThornList} outside
   the make process. It is located in {\tt configs/<config>/ThornList},
   where {\tt <config>} refers to the name of your configuration.
-  The directory, {\tt ./configs}, exists {\em
-    after} the very first  make phase for the first configuration.
+  The directory, {\tt ./configs}, exists \emph{ after} the very first 
+  make phase for the first configuration.
 
 \subsection{Notes and Caveats}
 \begin{itemize}
 \item{} If during the build you see the error ``{\tt missing
     separator}'' you are probably not using GNU make.
-\item{} {\em The EDITOR environment variable}. You may not be aware of
+\item{} \textit{The EDITOR environment variable}. You may not be aware of
   this, but this thing very often exists and may be set  by default to
   something scary like {\tt vi}. If you don't know how to use {\tt vi}
   or wish to
@@ -950,11 +951,11 @@ Instead of using the editor to specify the thorns you want to
   (To exit {\tt vi} type {\tt <ESC> :q!})
 \end{itemize}
 
-\subsection{gmake options for building configurations}
+\subsection{{\tt gmake} options for building configurations}
 \label{sec:gmopfobuco}
 
-An {\it option} for gmake can be thought of as an argument which tells
-it how it should make a {\tt target}. Note that the final result is always
+An \textit{option} for {\tt gmake} can be thought of as an argument which tells
+it how it should make a \textit{target}. Note that the final result is always
 the same.
 
 \begin{Lentry}
@@ -987,27 +988,27 @@ arrangements and thorns.  For example it can checkout all the thorns
 in any thornlist file found in the \texttt{thornlists} subdirectory of
 the Cactus root directory. % (usually \texttt{Cactus}).
 
-\item [{\tt gmake cvsdiff}] differences between checked out version of Cactus and that in the CVS repositories.
+\item [{\tt gmake cvsdiff}] shows differences between checked out version of Cactus and that in the CVS repositories.
 
-\item [{\tt gmake cvsstatus}] status of checked out version of Cactus, reporting which files have been modified or need updating.
+\item [{\tt gmake cvsstatus}] shows status of checked out version of Cactus, reporting which files have been modified or need updating.
 
-\item [{\tt gmake cvsupdate}] update Flesh and all Thorns from CVS repositories.
+\item [{\tt gmake cvsupdate}] updates Flesh and all thorns from CVS repositories.
 
 \item [{\tt gmake default}] creates a new configuration with a default name.
 
-\item [{\tt gmake distclean}] delete your {\tt configs} directory and hence all your configurations.
+\item [{\tt gmake distclean}] deletes your {\tt configs} directory and hence all your configurations.
 
 \item [{\tt gmake downsize}] removes non-essential files as documents
-  and testsuites to allow for minimal installation size.
+  and test suites to allow for minimal installation size.
 
 \item [{\tt gmake newthorn}] creates a new thorn, prompting for the necessary
   information and creating template files.
 
 \item [{\tt gmake TAGS}] creates an Emacs style TAGS file. See section
-  \ref{sec:usta} for using TAGS within Cactus.
+  \ref{sec:usta} for using tags within Cactus.
 
 \item [{\tt gmake tags}] creates a {\tt vi} style tags file. See section
-  \ref{sec:usta} for using TAGS within Cactus.
+  \ref{sec:usta} for using tags within Cactus.
 
 \item [{\tt gmake UsersGuide}] runs LaTeX to produce a copy of the Users' Guide.
 
@@ -1025,16 +1026,16 @@ configuration found in user's \texttt{configs} subdirectory.
 \label{sec:te}
 
 Some thorns come with a testsuite, consisting of example parameter files
-and the output files generated by running these. To run the testsuites
+and the output files generated by running these. To run the testsuite
 for the thorns you have compiled use
 
 {\tt gmake <configuration>-testsuite}
 
-These testsuites serve the dual purpose of
+These testsuite serve the dual purpose of
 
 \begin{Lentry}
 \item [Regression testing]
-i.e. making sure that changes to the thorn or the flesh don't affect the
+i.e. making sure that changes to the thorn or the Flesh don't affect the
 output from a known parameter file.
 \item [Portability testing]
 i.e. checking that the results are independent of the architecture --- this
@@ -1048,12 +1049,12 @@ is also of use when trying to get Cactus to work on a new architecture.
 
 Cactus executables always run from a parameter file (which may be a
 physical file or taken from standard input), which specifies which
-Thorns to use and set the values of any parameters which are different
+thorns to use and sets the values of any parameters which are different
 from the default values. Any accepted filename can be used for the name
 of the parameter file, although standard convention is to use the file
 extension {\tt .par}.  Optional command line arguments can be used
 to customise runtime behaviour, and to provide information about the
-Thorns used in the executable. The general syntax for running Cactus from
+thorns used in the executable. The general syntax for running Cactus from
 a physical parameter file is
 then
 
@@ -1126,7 +1127,7 @@ Produces version information of the code.
 %Runs the code far enough to check the consistency of the parameters.  If
 %given a numeric argument it will attempt to simulate being on that number
 %of processors. [To be implemented.]
-\item [{\tt -W<level>} or {\tt -waring-level=<level>}]
+\item [{\tt -W<level>} or {\tt -warning-level=<level>}]
 Sets the warning level of the code.  All warning messages are given a level ---
 the lower the level the greater the severity.  This parameter controls the
 level of messages to be seen, with all warnings of level $\le$ {\tt <level>}
@@ -1163,20 +1164,20 @@ Set the level of parameter checking to be used, either {\tt strict}, {\tt normal
 
 The parameter file is used to control the behaviour of the code at runtime.
 It is a text file with lines which are either comments, denoted
-by a `\#' or `!', or parameter statements. A parameter statement consists
-of one or more parameter names, followed by
-an `=', followed by the value(s) for this (these) parameter(s).
+by a `{\tt \#}' or `{\tt !}', or parameter statements. A parameter statement
+consists of one or more parameter names, followed by
+an `{\tt =}', followed by the value(s) for this (these) parameter(s).
 Note that all string parameters are case insensitive.
 
 The {\tt first parameter} in any parameter file should be {\tt ActiveThorns}.
 This is a special parameter  which tells the
-code which {\em thorns} are to be activated.  Only parameters from active
-thorns can be set  (and only those routines {\it scheduled} by active thorns
+code which \textit{thorns} are to be activated.  Only parameters from active
+thorns can be set  (and only those routines \textit{scheduled} by active thorns
 are run).  By default all thorns are inactive. For example, the first
 entry in a parameter file which is using just the two thorns
 {\tt CactusPUGH/PUGH} and {\tt CactusBase/CartGrid3D} should be
 
-{\tt ActiveThorns = ``PUGH CartGrid3D''}
+{\tt ActiveThorns = "PUGH CartGrid3D"}
 
 Parameters following the {\tt ActiveThorns} parameter all have names
 whose syntax depends on the scope of the parameter:
@@ -1185,20 +1186,20 @@ whose syntax depends on the scope of the parameter:
 Just the name of the parameter itself. Global parameters are avoided, and
 there are none in the Flesh and Cactus Toolkits.
 \item [{\tt Restricted parameters}]
-The name of the {\em implementation} which defined the parameter, two colons,
+The name of the \textit{implementation} which defined the parameter, two colons,
 and the name of the parameter --- e.g. {\tt driver::global\_nx}.
 \item [{\tt Private parameters}]
-The name of the {\em thorn} which defined the parameter, two colons,
+The name of the \textit{thorn} which defined the parameter, two colons,
 and the name of the parameter --- e.g. {\tt wavetoyF77::amplitude}.
 \end{Lentry}
 
-This notation is not strictly enforced currently in the code. It is
+This notation is not currently strictly enforced in the code. It is
 sufficient to specify the first part of the parameter name using either
 the implementation name, or the thorn name. However, it is suggested
 that the convention above is followed.
 
-The Cactus Flesh performs checks for consistency and range of parameters,
-the severity of these checks is controlled by the command line argument
+The Cactus Flesh performs checks for consistency and range of parameters.
+The severity of these checks is controlled by the command line argument
 {\tt -parameter-level} which can take the following values
 \begin{Lentry}
 \item[{\tt relaxed}] Cactus will issue a level 0 warning (that is the
@@ -1235,12 +1236,12 @@ Notes:
 each thorn using the command line options {\tt -o} and {\tt -O}
 (Section~\ref{sec:coliop}).
 
-\item{} The parameter file is read {\it sequentially} from top to bottom,
+\item{} The parameter file is read \textit{sequentially} from top to bottom,
         this means that if you set the value of a parameter twice in
         the parameter file, the second value will be used. (This is
         why the {\tt ActiveThorns} parameter is always first in the file).
 
-\item{} Some parameters are {\it steerable} and can be changed during
+\item{} Some parameters are \textit{steerable} and can be changed during
         the execution of a code using parameter steering interfaces
         (for example, thorn {\tt CactusConnect/HTTPD}, or using a
         parameter file when recovering from a checkpoint file.
@@ -1253,9 +1254,9 @@ each thorn using the command line options {\tt -o} and {\tt -O}
 \section{Thorn Documentation}
 \label{sec:thdo}
 
-The Cactus make system provides a mechanism for generating a {\it
-Thorn Guide} containing separate chapters for each thorn and
-arrangement in your configuration. The provided documentation for an
+The Cactus make system provides a mechanism for generating a
+\textit{Thorn Guide} containing separate chapters for each thorn and
+arrangement in your configuration. The documentation provided for an
 individual thorn obviously depends on what the thorn authors added,
 but the Thorn Guide is a good place to first look for special
 instructions on how to run and interpret the output from a Thorn.
@@ -1285,7 +1286,7 @@ or to make a Thorn Guide for all the thorns in the {\tt arrangements} directory
 As your Cactus executable runs, standard output and standard error
 are usually written to the screen. Standard output provides you
 with information about the run, and standard error reports warnings
-and errors from the flesh and thorns.
+and errors from the Flesh and thorns.
 
 As the program runs, the normal output provides the following information:
 
@@ -1370,8 +1371,8 @@ standard arrangements are described in those thorns' documentation.
 
 In general, these thorns decide what to output by parsing a string parameter
 containing the names of those grid variables, or groups of variables, for which
-output is required. The names should be fully qualified with the {\tt
-implementation} and {\tt group} or {\tt variable} names.
+output is required. The names should be fully qualified with the
+{\tt implementation} and {\tt group} or {\tt variable} names.
 
 There is usually a parameter for each method to denote how often, in evolution
 iterations, this output should be performed.  There is also usually a parameter
@@ -1391,7 +1392,7 @@ all the data from the checkpoint file.
 Checkpointing/recovery methods in Cactus are provided by thorns.
 
 In general, these thorns decide how often to generate a checkpoint. They also
-register their recovery routines with the flesh which then get called during
+register their recovery routines with the Flesh which then get called during
 initialization to perform the recovery of parameters and grid variables if
 requested in the parameter file.