Add AlphaThorns_MoL_ in front of every reference in sight.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusNumerical/MoL/trunk@27 578cdeb0-5ea1-4b81-8215-5a3b8777ee0b

1 files changed, 22 insertions, 22 deletions

diff --git a/doc/documentation.tex b/doc/documentation.tex
index 4934e84..3558990 100644
--- a/doc/documentation.tex
+++ b/doc/documentation.tex
@@ -136,20 +136,20 @@
 % \subsection{Acknowledgements}
 
 \section{Purpose}
-\label{sec:purpose}
+\label{AlphaThorns_MoL_sec:purpose}
 
 The Method of Lines (MoL) converts a (system of) partial differential
 equation(s) into an ordinary differential equation containing some
 spatial differential operator. As an example, consider writing the
 hyperbolic system of PDE's
 \begin{equation}
-  \label{eq:mol1}
+  \label{AlphaThorns_MoL_eq:mol1}
   \partial_t {\bf q} + {\bf A}^i({\bf q}) \partial_i {\bf B}({\bf q})
   = {\bf s}({\bf q})
 \end{equation}
 in the alternative form
 \begin{equation}
-  \label{eq:mol2}
+  \label{AlphaThorns_MoL_eq:mol2}
   \partial_t {\bf q} = {\bf L}({\bf q}),
 \end{equation}
 which (assuming a given discretization of space) is an ODE.
@@ -165,7 +165,7 @@ coupling different physical models.
 MoL can be used for hyperbolic, parabolic and even elliptic problems
 (although I definitely don't recommend the latter). As it currently
 stands it is set up for systems of equations in the first order type
-form of equation~(\ref{eq:mol2}). If you want to implement a
+form of equation~(\ref{AlphaThorns_MoL_eq:mol2}). If you want to implement a
 multilevel scheme such as leapfrog it is not obvious to me that MoL is
 the thing to use. However if you have lots of thorns that you want to
 interact, for example ADM\_BSSN and a hydro code plus maybe EM or a
@@ -192,11 +192,11 @@ Choptuik~\cite{AlphaThorns_MoL_Neilsen00} is also quite good. For Ian
 Hawke's viewpoint either see below or contact by email.
 
 \section{How to use}
-\label{sec:use}
+\label{AlphaThorns_MoL_sec:use}
 
 
 \subsection{Thorn users}
-\label{sec:useruse}
+\label{AlphaThorns_MoL_sec:useruse}
 
 For those who used the old version of MoL, this version is
 unfortunately slightly more effort to use. That is, for most methods
@@ -235,7 +235,7 @@ are likely to be limited unless you're doing something very memory
 intensive at initialization or analysis.
 
 \subsection{Thorn writers}
-\label{sec:writeruse}
+\label{AlphaThorns_MoL_sec:writeruse}
 
 To port an existing thorn using the method of lines, or to write a new
 thorn using it, should hopefully be relatively simple. As an example,
@@ -323,9 +323,9 @@ evolved (in ADM) or constrained (in ADM\_BSSN), both of which have
 precedence. To register your GFs with MoL schedule a routine in the
 bin {\tt MoL\_Register} which just contains the relevant function
 calls.  For an evolved variable the GF corresponding to the update
-term (${\bf L}({\bf q})$ in equation~(\ref{eq:mol2})) should be
+term (${\bf L}({\bf q})$ in equation~(\ref{AlphaThorns_MoL_eq:mol2})) should be
 registered at the same time. The appropriate functions are given in
-section~\ref{sec:molfns}.
+section~\ref{AlphaThorns_MoL_sec:molfns}.
 
 These functions are provided using function aliasing. For details on
 using function aliasing, see sections B10.5 and F2.2.3 of the
@@ -366,7 +366,7 @@ USES FUNCTION MoLChangeToNone
 
 Note that the list of paramters not complete; see the section on
 parameters for the use of arrays or complex variables. However, the
-list of functions is, and is expanded on in section~\ref{sec:molfns}.
+list of functions is, and is expanded on in section~\ref{AlphaThorns_MoL_sec:molfns}.
 MoL will check whether a group or variable is a GF or an array and
 whether it is real or complex. Note that currently complex variable
 support is disabled.
@@ -414,7 +414,7 @@ MoL thorn and the flesh. Also the synchronization of grids across
 separate processors will be dealt with by the MoL thorn and the flesh.
 
 \section{Example}
-\label{sec:example}
+\label{AlphaThorns_MoL_sec:example}
 
 As a fairly extended example of how to use MoL I'll outline how
 ADM\_BSSN works in this context. The actual implementation of this is
@@ -520,7 +520,7 @@ variables back to the standard ADM variables in {\tt
 of the lapse in {\tt ADM\_BSSN\_LapseChange}.
 
 \section{Functions provided by MoL}
-\label{sec:molfns}
+\label{AlphaThorns_MoL_sec:molfns}
 
 All the functions listed below return error codes in theory. However
 at this current point in time they always return 0 (success). Any
@@ -533,7 +533,7 @@ directly through header files, but this feature may be phased
 out. Using function aliasing is the recommended method.
 
 \begin{FunctionDescription}{MoLRegisterEvolved}
-  \label{MoLRegisterEvolved}
+  \label{AlphaThorns_MoL_MoLRegisterEvolved}
   
   Tells MoL that the given GF is in the evolved category with the
   associated update GF.
@@ -612,7 +612,7 @@ ierr = MoLRegisterEvolved(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterConstrained}
-  \label{MoLRegisterConstrained}
+  \label{AlphaThorns_MoL_MoLRegisterConstrained}
   
   Tells MoL that the given GF is in the constrained category.
 
@@ -683,7 +683,7 @@ ierr = MoLRegisterConstrained(ConstrainedIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterSaveAndRestore}
-  \label{MoLRegisterSaveAndRestore}
+  \label{AlphaThorns_MoL_MoLRegisterSaveAndRestore}
   
   Tells MoL that the given GF is in the Save and Restore category.
 
@@ -754,7 +754,7 @@ ierr = MoLRegisterSaveAndRestore(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterEvolvedGroup}
-  \label{MoLRegisterEvolvedGroup}
+  \label{AlphaThorns_MoL_MoLRegisterEvolvedGroup}
   
   Tells MoL that the given group is in the evolved category with the
   associated update group.
@@ -830,7 +830,7 @@ ierr = MoLRegisterEvolvedGroup(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterConstrainedGroup}
-  \label{MoLRegisterConstrainedGroup}
+  \label{AlphaThorns_MoL_MoLRegisterConstrainedGroup}
   
   Tells MoL that the given group is in the constrained category.
 
@@ -901,7 +901,7 @@ ierr = MoLRegisterConstrainedGroup(ConstrainedIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterSaveAndRestoreGroup}
-  \label{MoLRegisterSaveAndRestoreGroup}
+  \label{AlphaThorns_MoL_MoLRegisterSaveAndRestoreGroup}
   
   Tells MoL that the given group is in the Save and Restore category.
 
@@ -969,7 +969,7 @@ ierr = MoLRegisterSaveAndRestoreGroup(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToEvolved}
-  \label{MoLChangeToEvolved}
+  \label{AlphaThorns_MoL_MoLChangeToEvolved}
 
   Sets a GF to belong to the evolved category, with the associated
   update GF. Not used for the initial setting.
@@ -1051,7 +1051,7 @@ ierr = MoLChangeToEvolved(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToConstrained}
-  \label{MoLChangeToConstrained}
+  \label{AlphaThorns_MoL_MoLChangeToConstrained}
   
   Sets a GF to belong to the constrained category. Not used for the
   initial setting.
@@ -1126,7 +1126,7 @@ ierr = MoLChangeToConstrained(EvolvedIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToSaveAndRestore}
-  \label{MoLChangeToSaveAndRestore}
+  \label{AlphaThorns_MoL_MoLChangeToSaveAndRestore}
   
   Sets a GF to belong to the Save and Restore category. Not used for the
   initial setting.
@@ -1201,7 +1201,7 @@ ierr = MoLChangeToSaveAndRestore(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToNone}
-  \label{MoLChangeToNone}
+  \label{AlphaThorns_MoL_MoLChangeToNone}
   
   Sets a GF to belong to the ``unknown'' category. Not used for the
   initial setting.