5 files changed, 359 insertions, 13 deletions
diff --git a/doc/UsersGuide/Appendices.tex b/doc/UsersGuide/Appendices.tex
index 1d7078c1..09c95df8 100644
--- a/doc/UsersGuide/Appendices.tex
+++ b/doc/UsersGuide/Appendices.tex
@@ -831,6 +831,11 @@ Return to previous location before jump to tag (not widely implemented).
 \end{enumerate}
 
 
+\chapter{ThornLists}
+
+\label{chap:th}
+
+This section still needs to be written.
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/doc/UsersGuide/FunctionReference.tex b/doc/UsersGuide/FunctionReference.tex
index 59adfd4d..cf149818 100644
--- a/doc/UsersGuide/FunctionReference.tex
+++ b/doc/UsersGuide/FunctionReference.tex
@@ -67,7 +67,7 @@ available from C, not all are currently available from Fortran.
   Returns the Exponentiation of a complex number (only C) [not yet available]
 
 \item[CCTK\_CmplxImag]
-  [\pageref{CmplxReal}]
+  [\pageref{CmplxImag}]
   Returns the imaginary part of a complex number (only C)
 
 \item[CCTK\_CmplxLog]
@@ -291,9 +291,9 @@ available from C, not all are currently available from Fortran.
 \item[CCTK\_QueryGroupStorageI] 
   [\pageref{QueryGroupStorageI}] 
 
-\item[CCTK\_Reduce] 
-  [\pageref{Reduce}] 
-  Perform a reduction operation using a registered operator
+%\item[CCTK\_Reduce] 
+%  [\pageref{Reduce}] 
+%  Perform a reduction operation using a registered operator
 
 \item[CCTK\_ReductionHandle] 
   [\pageref{ReductionHandle}] 
@@ -507,6 +507,319 @@ available from C, not all are currently available from Fortran.
 % CCC
 %%%%%
 
+
+\begin{CCTKFunc}{CCTK\_Cmplx}{Turns two real numbers into a complex number}
+\label{Cmplx}
+\subroutine{CCTK\_COMPLEX}{}{cmpno}
+\argument{CCTK\_REAL}{}{realpart}
+\argument{CCTK\_REAL}{}{imagpart}
+\showcargs
+\begin{params}
+\parameter{cmpno}{The complex number}
+\parameter{realpart}{The real part of the complex number}
+\parameter{imagpart}{The imaginary part of the complex number}
+\end{params}
+\begin{discussion}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t cmpno = CCTK\_Cmplx(re,im)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+\begin{CCTKFunc}{CCTK\_CmplxAbs}{Absolute value of a complex number}
+\label{CmplxAbs}
+\subroutine{CCTK\_COMPLEX}{}{absval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{absval}{The computed absolute value}
+\parameter{realpart}{The complex number who absolute value is to be returned}
+\end{params}
+\begin{discussion}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t absval = CCTK\_CmplxAbs(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+\begin{CCTKFunc}{CCTK\_CmplxAdd}{Sum of two complex numbers}
+\label{CmplxAdd}
+\subroutine{CCTK\_COMPLEX}{}{addval}
+\argument{CCTK\_COMPLEX}{}{inval1}
+\argument{CCTK\_COMPLEX}{}{inval2}
+\showcargs
+\begin{params}
+\parameter{addval}{The computed added value}
+\parameter{inval1}{The first complex number to be summed}
+\parameter{inval2}{The second complex number to be summed}
+\end{params}
+\begin{discussion}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t addval = CCTK\_CmplxAdd(inval1,inval2)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxConjg}{Complex conjugate of a complex number}
+\label{CmplxConjg}
+\subroutine{CCTK\_COMPLEX}{}{conjgval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{conjval}{The computed conjugate}
+\parameter{inval}{The complex number to be conjugated}
+\end{params}
+\begin{discussion}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t conjgval = CCTK\_CmplxConjg(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxCos}{Cosine of a complex number}
+\label{CmplxCos}
+\subroutine{CCTK\_COMPLEX}{}{cosval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{cosval}{The computed cosine}
+\parameter{inval}{The complex number to be cosined}
+\end{params}
+\begin{discussion}
+{\bf NOT YET AVAILABLE}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t cosval = CCTK\_CmplxCos(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+\begin{CCTKFunc}{CCTK\_CmplxDiv}{Division of two complex numbers}
+\label{CmplxDiv}
+\subroutine{CCTK\_COMPLEX}{}{divval}
+\argument{CCTK\_COMPLEX}{}{inval1}
+\argument{CCTK\_COMPLEX}{}{inval2}
+\showcargs
+\begin{params}
+\parameter{divval}{The divided value}
+\parameter{inval1}{The enumerator}
+\parameter{inval1}{The denominator}
+\end{params}
+\begin{discussion}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t divval = CCTK\_CmplxDiv(inval1,inval2)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+\begin{CCTKFunc}{CCTK\_CmplxExp}{Exponent of a complex number}
+\label{CmplxExp}
+\subroutine{CCTK\_COMPLEX}{}{expval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{expval}{The computed exponent}
+\parameter{inval}{The complex number to be exponented}
+\end{params}
+\begin{discussion}
+{\bf NOT YET AVAILABLE}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t expval = CCTK\_CmplxExp(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxImag}{Imaginary part of a complex number}
+\label{CmplxImag}
+\subroutine{CCTK\_REAL}{}{imval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{imval}{The imaginary part}
+\parameter{inval}{The complex number}
+\end{params}
+\begin{discussion}
+The imaginary part of a complex number $z=a+bi$ is $b$.
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t imval = CCTK\_CmplxImag(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxLog}{Logarithm of a complex number}
+\label{CmplxLog}
+\subroutine{CCTK\_COMPLEX}{}{logval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{logval}{The computed logarithm}
+\parameter{inval}{The complex number}
+\end{params}
+\begin{discussion}
+{\bf NOT YET AVAILABLE}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t logval = CCTK\_CmplxLog(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxMul}{Multiplication of two complex numbers}
+\label{CmplxMul}
+\subroutine{CCTK\_COMPLEX}{}{mulval}
+\argument{CCTK\_COMPLEX}{}{inval1}
+\argument{CCTK\_COMPLEX}{}{inval2}
+\showcargs
+\begin{params}
+\parameter{mulval}{The product}
+\parameter{inval1}{First complex number to be multiplied}
+\parameter{inval2}{Second complex number to be multiplied}
+\end{params}
+\begin{discussion}
+The product of two complex numbers $z_1=a_1+b_1 i$ and $z_2=a_2+b_2 i$ is
+$z=(a_1 a_2 - b_1 b_2) + (a_1 b_2 + a_2 b_1)i$.
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t mulval = CCTK\_CmplxMul(inval1,inval2)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+
+\begin{CCTKFunc}{CCTK\_CmplxReal}{Real part of a complex number}
+\label{CmplxReal}
+\subroutine{CCTK\_REAL}{}{reval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{reval}{The real part}
+\parameter{inval}{The complex number}
+\end{params}
+\begin{discussion}
+The real part of a complex number $z=a+bi$ is $a$.
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t reval = CCTK\_CmplxReal(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxSin}{Sine of a complex number}
+\label{CmplxSin}
+\subroutine{CCTK\_COMPLEX}{}{sinval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{sinval}{The computed sine}
+\parameter{inval}{The complex number to be Sined}
+\end{params}
+\begin{discussion}
+{\bf NOT YET AVAILABLE}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t sinval = CCTK\_CmplxSin(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+\begin{CCTKFunc}{CCTK\_CmplxSub}{Subtraction of two complex numbers}
+\label{CmplxSub}
+\subroutine{CCTK\_COMPLEX}{}{subval}
+\argument{CCTK\_COMPLEX}{}{inval1}
+\argument{CCTK\_COMPLEX}{}{inval2}
+\showcargs
+\begin{params}
+\parameter{addval}{The computed subtracted value}
+\parameter{inval1}{The complex number to be subtracted from}
+\parameter{inval2}{The complex number to subtract}
+\end{params}
+\begin{discussion}
+If $z_1=a_1 + b_1 i$ and $z_2 = a_2+ b_2 i$ then 
+$$
+z_1-z_2 = (a_1-a_2)+ (b_1 - b_2)i
+$$
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t subval = CCTK\_CmplxSub(inval1,inval2)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+\begin{CCTKFunc}{CCTK\_CmplxSqrt}{Square root of a complex number}
+\label{CmplxSqrt}
+\subroutine{CCTK\_COMPLEX}{}{sqrtval}
+\argument{CCTK\_COMPLEX}{}{inval}
+\showcargs
+\begin{params}
+\parameter{expval}{The computed square root}
+\parameter{inval}{The complex number to be square rooted}
+\end{params}
+\begin{discussion}
+{\bf NOT YET AVAILABLE}
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t sqrtval = CCTK\_CmplxSqrt(inval)};
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
+
 \begin{CCTKFunc}{CCTK\_CoordSystemDim}{Give the dimension for a given coordinate system.}
 \label{CoordDim}
 \subroutine{int}{integer}{dim}
@@ -2051,8 +2364,35 @@ checked.
 % RRR
 %%%%%
 
+\begin{CCTKFunc}{CCTK\_ReductionHandle}{Handle for given reduction method}
+\label{ReductionHandle}
+\function{int}{integer}{handle}
+\argument{const char *}{character*(*)}{reduction}
+\showargs
+\begin{params}
+\parameter{handle}{handle returned for this method}
+\parameter{name}{name of the reduction method required}
+\end{params}
+\begin{discussion}
+Reduction methods should be registered at {\t CCTK\_STARTUP}. Note that
+integer reduction handles are used to call {\t CCTK\_Reduce} to avoid
+problems with passing Fortran strings. Note that the name of the reduction
+operator is case dependent.
+\end{discussion}
+\begin{examples}
+\begin{tabular}{@{}p{3cm}cp{11cm}}
+\hfill {\bf C} && {\t handle = CCTK\_ReductionHandle("maximum") };
+\\
+\hfill {\bf Fortran} && {\t call CCTK\_ReductionHandle(handle,"maximum")}
+\\
+\end{tabular}
+\end{examples}
+\begin{errorcodes}
+\end{errorcodes}
+\end{CCTKFunc}
+
+
 
-% cctk_IOMethods.h
 \begin{CCTKFunc}{CCTK\_RegisterIOMethod}{}
 \label{RegisterIOMethod}
 \function{int}{integer}{handle}
diff --git a/doc/UsersGuide/Infrastructure.tex b/doc/UsersGuide/Infrastructure.tex
index 841c2845..d6049de3 100644
--- a/doc/UsersGuide/Infrastructure.tex
+++ b/doc/UsersGuide/Infrastructure.tex
@@ -82,6 +82,7 @@ the schedule tree.
 \end{itemize}
 
 \chapter{IO Methods}
+\label{chap:iome}
 
 \chapter{Overloadable and Registerable Functions in Main}
 
diff --git a/doc/UsersGuide/RunningCactus.tex b/doc/UsersGuide/RunningCactus.tex
index 3934c5e8..de602b32 100644
--- a/doc/UsersGuide/RunningCactus.tex
+++ b/doc/UsersGuide/RunningCactus.tex
@@ -139,7 +139,7 @@ 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.
 
-CVS experts who want to use raw CVS commands are directed to Appendix~\ref{uscv}
+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.
 
@@ -158,10 +158,10 @@ that is a list of thorns with the syntax
 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{thsy}.
+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 same script can be used to checkout additional thorns.
+The same script can be used to checkout additional thorns.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
diff --git a/doc/UsersGuide/ThornWriters.tex b/doc/UsersGuide/ThornWriters.tex
index c6c97a58..068c9b9f 100644
--- a/doc/UsersGuide/ThornWriters.tex
+++ b/doc/UsersGuide/ThornWriters.tex
@@ -889,7 +889,7 @@ have stencil size 2, etc.
 Now, if you evolve the above scheme, it becomes apparent that at each iteration the number
 of grid points you can evolve decreases by one at each edge (see figure \ref{fig:noghost}).
 
-\begin{figure}[h]
+\begin{figure}[ht]
 \begin{center}
 \includegraphics[angle=0,width=8cm]{1dnoghost.eps}
 \end{center}
@@ -957,7 +957,7 @@ staggering each direction ({\tt stagger=CC}) is shown in (C). The full
 staggering in (D) ({\tt stagger=PP}) obeyes the same rules, but is
 rather unusual; included here for completeness. 
 
-\begin{figure}[h]
+\begin{figure}[ht]
   \def\epsfsize#1#2{0.45#1}
 \begin{center}
 \includegraphics[angle=0,width=8cm]{staggering1.eps}
@@ -968,7 +968,7 @@ staggerings. (a) : {\tt MC}, (b): {\tt CM}, (c): {\tt CC}, (d): {\tt
 PP}. Note that the staggering of gridfunctions does change its
 index. The staggered gridpoints and the corresponding unstaggered
 points (arrows) are accessed by the same indices.} 
-\label{fig:stagger2}
+\label{fig:stagger1}
 \end{figure}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -1480,7 +1480,7 @@ x-direction: {\em directional staggerindex} = CCTK\_STAGGER\_C (value 1).
 \end{Lentry}
 
 
-\begin{figure}[h]
+\begin{figure}[ht]
   \def\epsfsize#1#2{0.45#1}
 \begin{center}
 \includegraphics[angle=0,width=10cm]{staggering2.eps}
@@ -1949,7 +1949,7 @@ Provides the local range of a coordinate on a processor for
 
 To allow flexible IO, the flesh itself does not provide 
 any output routines, however it provides a mechanism for 
-thorns to register different routines as IO methods (see chapter \ref{chap:io_methods}).
+thorns to register different routines as IO methods (see chapter \ref{chap:iome}).
 Application thorns can interact with the different IO methods through the
 following function calls: