AlphaThorns -> CactusBase in document labels and references.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusNumerical/MoL/trunk@73 578cdeb0-5ea1-4b81-8215-5a3b8777ee0b

1 files changed, 43 insertions, 43 deletions

diff --git a/doc/documentation.tex b/doc/documentation.tex
index 56c03a6..b8ca497 100644
--- a/doc/documentation.tex
+++ b/doc/documentation.tex
@@ -136,20 +136,20 @@
 % \subsection{Acknowledgements}
 
 \section{Purpose}
-\label{AlphaThorns_MoL_sec:purpose}
+\label{CactusBase_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{AlphaThorns_MoL_eq:mol1}
+  \label{CactusBase_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{AlphaThorns_MoL_eq:mol2}
+  \label{CactusBase_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{AlphaThorns_MoL_eq:mol2}). If you want to implement a
+form of equation~(\ref{CactusBase_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
@@ -184,18 +184,18 @@ Mesh Refinement work.
 
 For more information on the Method of Lines the most comprehensive
 references are the works of Jonathan
-Thornburg~\cite{AlphaThorns_MoL_Thornburg93,AlphaThorns_MoL_Thornburg99}
+Thornburg~\cite{CactusBase_MoL_Thornburg93,CactusBase_MoL_Thornburg99}
 - see especially section 7.3 of the thesis. From the CFD viewpoint the
-review of ENO methods by Shu,~\cite{AlphaThorns_MoL_Shu99}, has some
+review of ENO methods by Shu,~\cite{CactusBase_MoL_Shu99}, has some
 information. For relativistic fluids the paper of Neilsen and
-Choptuik~\cite{AlphaThorns_MoL_Neilsen00} is also quite good.
+Choptuik~\cite{CactusBase_MoL_Neilsen00} is also quite good.
 
 \section{How to use}
-\label{AlphaThorns_MoL_sec:use}
+\label{CactusBase_MoL_sec:use}
 
 
 \subsection{Thorn users}
-\label{AlphaThorns_MoL_sec:useruse}
+\label{CactusBase_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
@@ -215,7 +215,7 @@ methods (first to fourth order) and {\tt ICN} for the implementation
 of the Iterative Crank Nicholson method in generic form.
 
 Full descriptions of the currently implemented methods are given in
-section~\ref{AlphaThorns_MoL_sec:methods}. 
+section~\ref{CactusBase_MoL_sec:methods}. 
 
 The parameter {\tt MoL\_Intermediate\_Steps} controls the number of
 intermediate steps for the ODE solver. For the generic Runge-Kutta
@@ -252,7 +252,7 @@ purely first order in space and time you may wish to set this to {\tt
   "no"}.
 
 \subsection{Thorn writers}
-\label{AlphaThorns_MoL_sec:writeruse}
+\label{CactusBase_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,
@@ -345,9 +345,9 @@ 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{AlphaThorns_MoL_eq:mol2}))
+term (${\bf L}({\bf q})$ in equation~(\ref{CactusBase_MoL_eq:mol2}))
 should be registered at the same time. The appropriate functions are
-given in section~\ref{AlphaThorns_MoL_sec:molfns}.
+given in section~\ref{CactusBase_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
@@ -389,7 +389,7 @@ 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{AlphaThorns_MoL_sec:molfns}.  MoL will check whether a
+section~\ref{CactusBase_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.
 
@@ -415,7 +415,7 @@ of boundary conditions\footnote{It is possible to alter the
   updated and do not need setting. This is slightly tricksy. For an
   example of how this would work see the new radiative boundary
   condition in ADM\_BSSN. For more on this see section 7.3.4
-  of~\cite{AlphaThorns_MoL_Thornburg93}.}, the solution of elliptic
+  of~\cite{CactusBase_MoL_Thornburg93}.}, the solution of elliptic
 equations (although this would be a very expensive place to solve
 them, some sets of equations might require the updating of some
 variables by constraints in this fashion). When applying boundary
@@ -437,7 +437,7 @@ separate processors will be dealt with by the MoL thorn, the driver
 the flesh.
 
 \subsection{Evolution method writers}
-\label{AlphaThorns_MoL_sec:evol-meth-writ}
+\label{CactusBase_MoL_sec:evol-meth-writ}
 
 If you want to try adding a new evolution method to MoL the simplest
 way is to use the generic table option to specify it completely in the
@@ -445,12 +445,12 @@ parameter file - no coding is required at all.
 
 All the generic methods evolve the equation
 \begin{equation}
-  \label{AlphaThorns_MoL_eq:mol3}
+  \label{CactusBase_MoL_eq:mol3}
   \partial_t {\bf q} = {\bf L}({\bf q})
 \end{equation}
 using the following algorithm for an $N$-step method:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:genrk1}
+  \label{CactusBase_MoL_eq:genrk1}
   {\bf q}^{(0)} & = & {\bf q}^n, \nonumber \\
   {\bf q}^{(i)} & = & \sum_{k=0}^{i-1} \left( \alpha_{ik} {\bf
   q}^{(k)} \right) + \Delta t \beta_{i-1} {\bf L} ( {\bf q}^{(i-1)} ),
@@ -467,7 +467,7 @@ will use. This table is created from the string parameter {\tt
 As an example, the standard TVD RK2 method that is implemented both in
 optimized and generic form is written as
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:rk2}
+  \label{CactusBase_MoL_eq:rk2}
   {\bf q}^{(1)} & = & {\bf q}^n + \Delta t {\bf L} ({\bf q}^n), \\
   {\bf q}^{n+1} & = & \frac{1}{2} \left( {\bf q}^n + {\bf q}^{(1)} +
   \Delta t {\bf L} ({\bf q}^{(1)}) \right). 
@@ -499,7 +499,7 @@ you are happy with the method. To do this you should
 \end{itemize}
 
 \section{Example}
-\label{AlphaThorns_MoL_sec:example}
+\label{CactusBase_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
@@ -605,14 +605,14 @@ variables back to the standard ADM variables in {\tt
 of the lapse in {\tt ADM\_BSSN\_LapseChange}.
 
 \section{Time evolution methods provided by MoL}
-\label{AlphaThorns_MoL_sec:methods}
+\label{CactusBase_MoL_sec:methods}
 
 The default method is Iterative Crank-Nicholson. There are many ways
 of implementing this. The standard {\tt "ICN"} and {\tt
   "Generic"}/{\tt"ICN"} methods both implement the following, assuming
 an $N$ iteration method:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:icn}
+  \label{CactusBase_MoL_eq:icn}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   {\bf q}^{(i)} & = & {\bf q}^{(0)} + \frac{\Delta t}{2} {\bf L}({\bf
     q}^{(i-1)}), \quad i = 1,\dots,N-1, \\
@@ -624,7 +624,7 @@ an $N$ iteration method:
 The ``averaging'' ICN method {\tt "ICN-avg"} instead calculates
 intermediate steps before averaging:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:icn-avg}
+  \label{CactusBase_MoL_eq:icn-avg}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   \tilde{{\bf q}}^{(i)} & = & \frac{1}{2}\left( {\bf q}^{(i)} + {\bf
       q}^{n} \right), \quad i = 0,\dots,N-1 \\
@@ -634,10 +634,10 @@ intermediate steps before averaging:
 \end{eqnarray}
 
 The Runge-Kutta methods are those typically used in hydrodynamics by,
-e.g., Shu and others - see~\cite{AlphaThorns_MoL_Shu99} for
+e.g., Shu and others - see~\cite{CactusBase_MoL_Shu99} for
 example. Explicitly the first order method is the Euler method:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:rk1}
+  \label{CactusBase_MoL_eq:rk1}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   {\bf q}^{(1)} & = & {\bf q}^{(0)} +  \Delta t {\bf L}(\tilde{{\bf
       q}}^{(0)}), \\
@@ -645,7 +645,7 @@ example. Explicitly the first order method is the Euler method:
 \end{eqnarray}
 The second order method is:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:rk2}
+  \label{CactusBase_MoL_eq:rk2}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   {\bf q}^{(1)} & = & {\bf q}^{(0)} + \Delta t {\bf L} ({\bf q}^{(0)}), \\
   {\bf q}^{(2)} & = & \frac{1}{2} \left( {\bf q}^{(0)} + {\bf q}^{(1)}
@@ -654,7 +654,7 @@ The second order method is:
 \end{eqnarray}
 The third order method is:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:rk3}
+  \label{CactusBase_MoL_eq:rk3}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   {\bf q}^{(1)} & = & {\bf q}^{(0)} + \Delta t {\bf L} ({\bf q}^{(0)}), \\
   {\bf q}^{(2)} & = & \frac{1}{4} \left( 3 {\bf q}^{(0)} + {\bf q}^{(1)} +
@@ -665,7 +665,7 @@ The third order method is:
 \end{eqnarray}
 The fourth order method, which is not strictly TVD, is:
 \begin{eqnarray}
-  \label{AlphaThorns_MoL_eq:rk4}
+  \label{CactusBase_MoL_eq:rk4}
   {\bf q}^{(0)} & = & {\bf q}^{n}, \\
   {\bf q}^{(1)} & = & {\bf q}^{(0)} + \frac{1}{2} \Delta t {\bf L}
   ({\bf q}^{(0)}), \\ 
@@ -680,7 +680,7 @@ The fourth order method, which is not strictly TVD, is:
 \end{eqnarray}
 
 \section{Functions provided by MoL}
-\label{AlphaThorns_MoL_sec:molfns}
+\label{CactusBase_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
@@ -693,7 +693,7 @@ directly through header files, but this feature may be phased
 out. Using function aliasing is the recommended method.
 
 \begin{FunctionDescription}{MoLRegisterEvolved}
-  \label{AlphaThorns_MoL_MoLRegisterEvolved}
+  \label{CactusBase_MoL_MoLRegisterEvolved}
   
   Tells MoL that the given GF is in the evolved category with the
   associated update GF.
@@ -772,7 +772,7 @@ ierr = MoLRegisterEvolved(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterConstrained}
-  \label{AlphaThorns_MoL_MoLRegisterConstrained}
+  \label{CactusBase_MoL_MoLRegisterConstrained}
   
   Tells MoL that the given GF is in the constrained category.
 
@@ -843,7 +843,7 @@ ierr = MoLRegisterConstrained(ConstrainedIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterSaveAndRestore}
-  \label{AlphaThorns_MoL_MoLRegisterSaveAndRestore}
+  \label{CactusBase_MoL_MoLRegisterSaveAndRestore}
   
   Tells MoL that the given GF is in the Save and Restore category.
 
@@ -914,7 +914,7 @@ ierr = MoLRegisterSaveAndRestore(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterEvolvedGroup}
-  \label{AlphaThorns_MoL_MoLRegisterEvolvedGroup}
+  \label{CactusBase_MoL_MoLRegisterEvolvedGroup}
   
   Tells MoL that the given group is in the evolved category with the
   associated update group.
@@ -990,7 +990,7 @@ ierr = MoLRegisterEvolvedGroup(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterConstrainedGroup}
-  \label{AlphaThorns_MoL_MoLRegisterConstrainedGroup}
+  \label{CactusBase_MoL_MoLRegisterConstrainedGroup}
   
   Tells MoL that the given group is in the constrained category.
 
@@ -1061,7 +1061,7 @@ ierr = MoLRegisterConstrainedGroup(ConstrainedIndex)
 
 
 \begin{FunctionDescription}{MoLRegisterSaveAndRestoreGroup}
-  \label{AlphaThorns_MoL_MoLRegisterSaveAndRestoreGroup}
+  \label{CactusBase_MoL_MoLRegisterSaveAndRestoreGroup}
   
   Tells MoL that the given group is in the Save and Restore category.
 
@@ -1129,7 +1129,7 @@ ierr = MoLRegisterSaveAndRestoreGroup(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToEvolved}
-  \label{AlphaThorns_MoL_MoLChangeToEvolved}
+  \label{CactusBase_MoL_MoLChangeToEvolved}
 
   Sets a GF to belong to the evolved category, with the associated
   update GF. Not used for the initial setting.
@@ -1211,7 +1211,7 @@ ierr = MoLChangeToEvolved(EvolvedIndex, RHSIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToConstrained}
-  \label{AlphaThorns_MoL_MoLChangeToConstrained}
+  \label{CactusBase_MoL_MoLChangeToConstrained}
   
   Sets a GF to belong to the constrained category. Not used for the
   initial setting.
@@ -1286,7 +1286,7 @@ ierr = MoLChangeToConstrained(EvolvedIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToSaveAndRestore}
-  \label{AlphaThorns_MoL_MoLChangeToSaveAndRestore}
+  \label{CactusBase_MoL_MoLChangeToSaveAndRestore}
   
   Sets a GF to belong to the Save and Restore category. Not used for the
   initial setting.
@@ -1361,7 +1361,7 @@ ierr = MoLChangeToSaveAndRestore(SandRIndex)
 
 
 \begin{FunctionDescription}{MoLChangeToNone}
-  \label{AlphaThorns_MoL_MoLChangeToNone}
+  \label{CactusBase_MoL_MoLChangeToNone}
   
   Sets a GF to belong to the ``unknown'' category. Not used for the
   initial setting.
@@ -1437,7 +1437,7 @@ ierr = MoLChangeToNone(RemoveIndex)
 
 \begin{thebibliography}{9}
 
-\bibitem{AlphaThorns_MoL_Thornburg93}
+\bibitem{CactusBase_MoL_Thornburg93}
 J. Thornburg.
 \newblock {N}umerical {R}elativity in {B}lack {H}ole {S}pacetimes. 
 \newblock Unpublished thesis, University of British Columbia.
@@ -1445,14 +1445,14 @@ J. Thornburg.
 \newblock Available from \mbox{\tt
   http://www.aei.mpg.de/\~{}jthorn/phd/html/phd.html}. 
 
-\bibitem{AlphaThorns_MoL_Thornburg99}
+\bibitem{CactusBase_MoL_Thornburg99}
 J. Thornburg.
 \newblock A {3+1} {C}omputational {S}cheme for {D}ynamic {S}pherically
 {S}ymmetric {B}lack {H}ole {S}pacetimes -- {II}: {T}ime {E}volution.
 \newblock Preprint {\tt gr-qc/9906022}, submitted to {\em Phys. Rev.}
 {\bf D}. 
 
-\bibitem{AlphaThorns_MoL_Shu99}
+\bibitem{CactusBase_MoL_Shu99}
 C. Shu.
 \newblock {H}igh {O}rder {ENO} and {WENO} {S}chemes for
 {C}omputational {F}luid {D}ynamics.
@@ -1463,7 +1463,7 @@ C. Shu.
   {S}chemes for {H}yperbolic {C}onservation {L}aws} at {\tt
   http://www.icase.edu/library/reports/rdp/97/97-65RDP.tex.refer.html}. 
 
-\bibitem{AlphaThorns_MoL_Neilsen00}
+\bibitem{CactusBase_MoL_Neilsen00}
 D.~W. Neilsen and M.~W. Choptuik.
 \newblock Ultrarelativistic fluid dynamics.
 \newblock {\em Class. Quantum Grav.}, {\bf 17}:\penalty0 733--759, 2000.