redo bibtex bibliography

git-svn-id: http://svn.einsteintoolkit.org/cactus/EinsteinAnalysis/AHFinderDirect/trunk@1476 f88db872-0e4f-0410-b76b-b9085cfa78c5

2 files changed, 137 insertions, 23 deletions

diff --git a/doc/AHFinderDirect.bib b/doc/AHFinderDirect.bib
new file mode 100644
index 0000000..d948f1d
--- /dev/null
+++ b/doc/AHFinderDirect.bib
@@ -0,0 +1,112 @@
+% bibtex file for AHFinderDirect thorn guide
+% $Header$
+
+@article{AHFinderDirect/Diener03a,
+        author  = {P. Diener},
+        title   = {A New General Purpose Event Horizon Finder for {3D}
+                   Numerical Spacetimes},
+        journal = {Class. Quantum Grav.},
+        volume  = 20,
+        number  = 22,
+        year    = 2003,
+        pages   = {4901-4917},
+        eprint  = {gr-qc/0305039},
+	doi     = {10.1088/0264-9381/20/22/014},
+	url     = {http://stacks.iop.org/0264-9381/20/4901},
+}
+
+@article{AHFinderDirect/Dreyer-etal-2002-isolated-horizons,
+        author = "Olaf Dreyer and Badri Krishnan and Deirdre Shoemaker
+                  and Erik Schnetter",
+        title  = "Introduction to {Isolated} {Horizons} in {Numerical} {Relativity}",
+        journal = "Phys. Rev. D",
+        year   = 2003, volume = 67,
+        pages = 024018,
+        eprint = "gr-qc/0206008",
+        }
+
+@article{AHFinderDirect/Gundlach97a,
+        key     = {Gundlach97a},
+        author  = {Carsten Gundlach},
+        title   = {Pseudo-spectral apparent horizon finders: An efficient new
+                   algorithm},
+        journal = {Phys. Rev. D},
+        volume  = {57},
+        year    = {1998},
+        eprint  = {gr-qc/9707050},
+        pages   = {863-875}
+}
+
+@Book{AHFinderDirect/Schroeder86,
+  author    = {Manfred R. Schroeder},
+  title     = {Number Theory in Science and Communication},
+  edition   = {2nd enlarged},
+  publisher = {Springer-Verlag},
+  address   = {Berlin},
+  year      = 1986,
+  isbn      = {3-540-15800-6},
+  X-note    = {Minkowski's definition of a Strahlk\"{o}rper
+               is in section 7.9, page 108},
+}
+
+@unpublished{AHFinderDirect/Schnetter02a,
+        author = {Erik Schnetter},
+        title = "A fast apparent horizon algorithm",
+        year = {2002},
+        eprint = "gr-qc/0206003",
+        note   = "gr-qc/0206003",
+	snote  = "see \cite{Schnetter03a} for a substantially revised version",
+}
+
+@article{AHFinderDirect/Schnetter03a,
+  author =       {Erik Schnetter},
+  title =        {Finding Apparent Horizons and other Two-Surfaces of
+                  Constant Expansion},
+  journal =      {Class. Quantum Grav.},
+  year =         2003,
+  volume =       20,
+  number =       22,
+  pages =        {4719-4737},
+  eprint =       {gr-qc/0306006},
+  doi =          {10.1088/0264-9381/20/22/001},
+  url =          {http://stacks.iop.org/0264-9381/20/4719},
+}
+
+@article{AHFinderDirect/Thornburg95,
+  author = {Jonathan Thornburg},
+  title = {Finding apparent horizons in numerical relativity},
+  journal = {Phys. Rev. D},
+  volume = 54,
+  number = 8,
+  year = {1996},
+  month = {October 15},
+  pages = {4899--4918},
+  eprint = "gr-qc/9508014",
+}
+
+@article{AHFinderDirect/Thornburg2003:AH-finding,
+        author = "Jonathan Thornburg",
+        title  = "A Fast Apparent-Horizon Finder
+                  for 3-Dimensional {C}artesian Grids in Numerical Relativity",
+        journal = "Class. Quantum Grav.",
+        volume = 21, number = 2,
+        year   = "2004", month = "21 January",
+        pages  = "743--766",
+        doi    = "10.1088/0264-9381/21/2/026",
+        url    = "http://stacks.iop.org/0264-9381/21/743",
+        eprint = "gr-qc/0306056",
+}
+
+@incollection{AHFinderDirect/York89,
+        key     = {York89},
+        author  = {James W. York},
+        title   = {Initial Data for Collisions of Black Holes and
+                  Other Gravitational Miscellany},
+        editor  = {C. Evans and L. Finn and D. Hobill},
+        booktitle = {Frontiers in Numerical Relativity},
+        publisher = {Cambridge University Press},
+        address = {Cambridge, England},
+        year    = 1989,
+        pages   = {89-109},
+	isbn    = {0-521-36666-6},
+}
diff --git a/doc/documentation.tex b/doc/documentation.tex
index 2a1c401..018bd03 100644
--- a/doc/documentation.tex
+++ b/doc/documentation.tex
@@ -158,9 +158,8 @@ the equation
 \end{equation}
 where $n^i$ is the outward-pointing unit normal to the apparent horizon,
 and $\del_i$ is the covariant derivative operator associated with the
-3-metric $g_\ij$ in the slice.
-(See \cite{AEIThorns/AHFinderDirect/York-1989-in-Frontiers} for a
-derivation of equation~\eqref{AHFinderDirect/eqn-horizon}.)
+3-metric $g_\ij$ in the slice.  (See \cite{AHFinderDirect/York89}
+for a derivation of equation~\eqref{AHFinderDirect/eqn-horizon}.)
 (Optionally, you can replace the right hand side
 of~\eqref{AHFinderDirect/eqn-horizon} by any specified nonzero
 constant, \ie{} you can find a surface of constant
@@ -179,9 +178,8 @@ the irreducable mass associated with the area.
 
 Besides this thorn guide, the other main sources of information on
 \thorn{AHFinderDirect} are the comments in the \verb|param.ccl| file,
-the paper \cite{AEIThorns/AHFinderDirect/Thornburg2003:AH-finding},
-and to a lesser extent the paper
-\cite{AEIThorns/AHFinderDirect/Thornburg-1996-apparent-horizon-finding}.
+the paper \cite{AHFinderDirect/Thornburg2003:AH-finding},
+and to a lesser extent the paper \cite{AHFinderDirect/Thornburg95}.
 As a courtesy, I ask that both these papers be cited in any published
 research which uses this thorn, or which uses code from this thorn.
 
@@ -227,7 +225,7 @@ necessary in order for \thorn{AHFinderDirect} to work:
 	(literally ``ray body'', or more commonly ``star-shaped region'')
 	relative to some local coordinate origin (which you must specify).
 	A Strahlk\"{o}rper is defined by Minkowski
-(\cite[p.~108]{AEIThorns/AHFinderDirect/Schroeder-1986-number-theory})
+	(\cite[p.~108]{AHFinderDirect/Schroeder86})
 	as
 	   \begin{quote}
 	   a region in $n$-dimensional Euclidean space containing the
@@ -1304,7 +1302,7 @@ This is controlled by the following parameters:
 \item[%%%
      \begin{tabular}{@{}l@{}}
      \code{run\_at\_CCTK\_ANALYSIS}	\\
-     \code{run\_at\_CCTK\_POSTSTEP}	%%%\\
+     \code{run\_at\_CCTK\_POSTSTEP}	\\
      \code{run\_at\_CCTK\_POSTINITIAL}	%%%\\
      \end{tabular}
      ]
@@ -1316,6 +1314,8 @@ This is controlled by the following parameters:
 	still the default, but these parameters allow you to change this
 	so it runs in CCTK\_POSTSTEP and/or CCTK\_POSTINITIAL
 	instead.  (You can even run in all three bins if you want!)
+	\thorn{AHFinderDirect}'s scheculing is discussed in more detail
+	In section~\ref{AHFinderDirect/sect-scheduling}.
 
 \item[%%%
      \begin{tabular}{@{}l@{}}
@@ -1422,12 +1422,12 @@ This is controlled by the following parameters:
 	horizons.  With other settings of this parameter this thorn
 	can be used to find \defn{surfaces of constant expansion};
 	these may be useful for excision, wave extraction, or
-	other purposes (\cite{AEIThorns/AHFinderDirect/Schnetter03a}).
+	other purposes (\cite{AHFinderDirect/Schnetter03a}).
 
 	To help in choosing the value(s) of the
 	\verb|surface_expansion[|$n$\verb|]| parameter,
 	figure~\ref{AHFinderDirect/fig-Schwarzschild-EF-Theta(r)}
-(from \cite{AEIThorns/AHFinderDirect/Thornburg-1996-apparent-horizon-finding}),
+	(from \cite{AHFinderDirect/Thornburg95}),
 	shows the expansion of $r = \text{constant}$ surfaces
 	in an Eddington-Finkelsteon slice of the unit-mass
 	Schwarzschild spacetime.
@@ -1453,6 +1453,11 @@ This is controlled by the following parameters:
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+\section{Scheduling}
+\label{AHFinderDirect/sect-scheduling}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \section{Monitoring \thorn{AHFinderDirect}'s Status}
 
 There are two primary ways of monitoring what \thorn{AHFinderDirect}
@@ -1588,7 +1593,7 @@ in Kerr-Schild coordinates,
 $m_\text{irreducible}/m_\text{ADM} = 0.949$, $0.894$, and $0.723$
 for spin parameters $a \equiv J/m^2 = 0.6$, $0.8$, and $0.999$, respectively.
 It would be better to (also) use the ``isolated horizons'' formalism of
-\cite{AEIThorns/AHFinderDirect/Dreyer-etal-2002-isolated-horizons};
+\cite{AHFinderDirect/Dreyer-etal-2002-isolated-horizons};
 at some point this thorn may be enhanced to do this.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -1667,10 +1672,10 @@ AHFinderDirect::initial_guess__coord_sphere__radius[1] = 2.0
 
 \thorn{AHFinderDirect} uses the apparent horizon
 (henceforth \defn{horizon}) finding algorithm of
-\cite{AEIThorns/AHFinderDirect/Thornburg-1996-apparent-horizon-finding},
+\cite{AHFinderDirect/Thornburg95},
 modified slightly to work with $g_\ij$ and $K_\ij$ on a Cartesian ($xyz$)
 grid.  The algorithm is described in detail in
-\cite{AEIThorns/AHFinderDirect/Thornburg2003:AH-finding}.
+\cite{AHFinderDirect/Thornburg2003:AH-finding}.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -1697,8 +1702,7 @@ Computationally, this algorithm has 3 main parts:
 	solely on $S^2$ (\ie{} at the horizon-surface grid points).
 \item	Computation of the Jacobian matrix $\Jac[\Theta(h)]$ of $\Theta(h)$.
 	This thorn incorporates the \defn{symbolic differentiation} technique
-	described in
-\cite{AEIThorns/AHFinderDirect/Thornburg-1996-apparent-horizon-finding},
+	described in \cite{AHFinderDirect/Thornburg95},
 	so this computation is quite fast.  The Jacobian is a highly
 	sparse matrix; \thorn{AHFinderDirect} has code to store it
 	as either a dense matrix (for debugging purposes), or a sparse
@@ -1827,20 +1831,19 @@ interested in some other related thorns:
 \item[\thorn{EHFinder}] (in the \arrangement{AEIDevelopment} arrangement)
 	was written by Peter Diener, and finds the {\em event\/} horizon(s)
 	in a numerically computed spacetime.  It's described in detail in
-	the paper~\cite{AEIThorns/AHFinderDirect/Diener03a}.
+	the paper~\cite{AHFinderDirect/Diener03a}.
 \item[\thorn{AHFinder}] (in the \arrangement{CactusEinstein} arrangement)
 	was written by Miguel Alcubierre, and includes two different
 	algorithms for finding apparent horizons, a minimization method
-	and a ``fast flow'' method based on
-\cite{AEIThorns/AHFinderDirect/Gundlach-1998-apparent-horizon-finding}.
+	and a ``fast flow'' method based on \cite{AHFinderDirect/Gundlach97a}.
 	Unfortunately, both methods are very slow in practice.
 \item[\thorn{TGRapparentHorizon2D}] (in the \arrangement{TAT} arrangement)
 	was written by Erik Schnetter, and is another apparent horizon
 	finder.  It uses methods very similar to this thorn, and (like
 	this thorn) is very fast and accurate.  However, it's no longer
 	under active development.  It's described in detail in the
-	papers~\cite{AEIThorns/AHFinderDirect/Schnetter02a}
-	and~\cite{AEIThorns/AHFinderDirect/Schnetter03a}.
+	papers~\cite{AHFinderDirect/Schnetter02a}
+	and~\cite{AHFinderDirect/Schnetter03a}.
 \item[\thorn{AHFinderDirect} (\cvsplace{Erik} branch)]
       (in the \arrangement{AEIThorns} arrangement)\\
 	Erik Schnetter has added a number of new features to
@@ -1869,9 +1872,8 @@ and postdoctoral fellowships programs for financial support.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-% make LaTeX read in ahfinderdirect.bbl produced by bibtex
-% run 'make bib' in this directory to update this
-\bibliography{documentation}
+% make LaTeX read in AHFinderDirect.bbl produced by bibtex
+\bibliography{AHFinderDirect}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%