Update auto-generated code

6 files changed, 590 insertions, 0 deletions

diff --git a/doc/mclachlan.aux b/doc/mclachlan.aux
new file mode 100644
index 0000000..2db4105
--- /dev/null
+++ b/doc/mclachlan.aux
@@ -0,0 +1,67 @@
+\relax 
+\ifx\hyper@anchor\@undefined
+\global \let \oldcontentsline\contentsline
+\gdef \contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global \let \oldnewlabel\newlabel
+\gdef \newlabel#1#2{\newlabelxx{#1}#2}
+\gdef \newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\let \contentsline\oldcontentsline
+\let \newlabel\oldnewlabel}
+\else
+\global \let \hyper@last\relax 
+\fi
+
+\citation{ES-Brown2007b}
+\citation{ES-mclachlanweb}
+\citation{cvsweb}
+\citation{svnweb}
+\citation{gitweb}
+\citation{Goodale02a}
+\citation{ES-cactusweb}
+\newlabel{FirstPage}{{}{1}{\relax }{}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {I}McLachlan}{1}{section*.1}}
+\@writefile{toc}{\contentsline {section}{\numberline {II}Obtaining McLachlan}{1}{section*.2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {A}Tools}{1}{section*.3}}
+\citation{ES-Schnetter2003b}
+\citation{ES-Schnetter2006a}
+\citation{ES-carpetweb}
+\citation{ES-Brown2007b}
+\citation{ES-mclachlanweb}
+\@writefile{toc}{\contentsline {subsection}{\numberline {B}Cactus}{2}{section*.4}}
+\newlabel{sec:cactus}{{II\tmspace  +\thinmuskip {.1667em}B}{2}{\relax }{section*.4}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {C}Carpet}{2}{section*.5}}
+\citation{kranc04}
+\citation{Husa:2004ip}
+\citation{krancweb}
+\citation{ES-krancweb}
+\@writefile{toc}{\contentsline {subsection}{\numberline {D}McLachlan}{3}{section*.6}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {E}Other Thorns}{3}{section*.7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {F}Consistency Check}{3}{section*.8}}
+\citation{ES-simfactoryweb}
+\@writefile{toc}{\contentsline {section}{\numberline {III}Building McLachlan}{4}{section*.9}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {A}Documentation}{4}{section*.10}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {B}Option List}{4}{section*.11}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {C}Building}{4}{section*.12}}
+\bibdata{references,publications-schnetter}
+\bibcite{cvsweb}{{1}{}{{cvs}}{{}}}
+\bibcite{svnweb}{{2}{}{{svn}}{{}}}
+\bibcite{gitweb}{{3}{}{{git}}{{}}}
+\bibcite{Goodale02a}{{4}{2003}{{Goodale et~al.}}{{Goodale, Allen, Lanfermann, Mass{\'o}, Radke, Seidel, and Shalf}}}
+\bibcite{ES-cactusweb}{{5}{}{{Cactus}}{{}}}
+\bibcite{ES-Schnetter2003b}{{6}{2004}{{Schnetter et~al.}}{{Schnetter, Hawley, and Hawke}}}
+\bibcite{ES-Schnetter2006a}{{7}{2006}{{Schnetter et~al.}}{{Schnetter, Diener, Dorband, and Tiglio}}}
+\bibcite{ES-carpetweb}{{8}{}{{Carpet}}{{}}}
+\bibcite{ES-Brown2007b}{{9}{2009}{{Brown et~al.}}{{Brown, Diener, Sarbach, Schnetter, and Tiglio}}}
+\bibcite{ES-mclachlanweb}{{10}{}{{McLachlan}}{{}}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {D}Cleaning}{5}{section*.13}}
+\@writefile{toc}{\contentsline {section}{\numberline {IV}Running McLachlan}{5}{section*.14}}
+\@writefile{toc}{\contentsline {section}{\numberline {}References}{5}{section*.15}}
+\bibcite{kranc04}{{11}{2004}{{Lechner et~al.}}{{Lechner, Alic, and Husa}}}
+\bibcite{Husa:2004ip}{{12}{2006}{{Husa et~al.}}{{Husa, Hinder, and Lechner}}}
+\bibcite{krancweb}{{13}{}{{kra}}{{}}}
+\bibcite{ES-krancweb}{{14}{}{{Kranc}}{{}}}
+\bibcite{ES-simfactoryweb}{{15}{}{{SimFactory}}{{}}}
+\global \chardef \firstnote@num15\relax 
+\bibstyle{apsrev-titles-manyauthors}
+\newlabel{LastBibItem}{{15}{6}{\relax }{section*.15}{}}
+\newlabel{LastPage}{{}{6}}
diff --git a/doc/mclachlan.bbl b/doc/mclachlan.bbl
new file mode 100644
index 0000000..f89fc00
--- /dev/null
+++ b/doc/mclachlan.bbl
@@ -0,0 +1,123 @@
+\begin{thebibliography}{15}
+\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi
+\expandafter\ifx\csname bibnamefont\endcsname\relax
+  \def\bibnamefont#1{#1}\fi
+\expandafter\ifx\csname bibfnamefont\endcsname\relax
+  \def\bibfnamefont#1{#1}\fi
+\expandafter\ifx\csname citenamefont\endcsname\relax
+  \def\citenamefont#1{#1}\fi
+\expandafter\ifx\csname url\endcsname\relax
+  \def\url#1{\texttt{#1}}\fi
+\expandafter\ifx\csname urlprefix\endcsname\relax\def\urlprefix{URL }\fi
+\providecommand{\bibinfo}[2]{#2}
+\providecommand{\eprint}[2][]{\url{#2}}
+
+\bibitem[{cvs()}]{cvsweb}
+\bibinfo{note}{{CVS}: {Concurrent} {Versions} {System}},
+  \urlprefix\url{http://www.nongnu.org/cvs/}.
+
+\bibitem[{svn()}]{svnweb}
+\bibinfo{note}{{SVN}: {Subversion}},
+  \urlprefix\url{http://subversion.tigris.org/}.
+
+\bibitem[{git()}]{gitweb}
+\bibinfo{note}{Git: Fast version control system},
+  \urlprefix\url{http://www.git-scm.org/}.
+
+\bibitem[{\citenamefont{Goodale et~al.}(2003)\citenamefont{Goodale, Allen,
+  Lanfermann, Mass{\'o}, Radke, Seidel, and Shalf}}]{Goodale02a}
+\bibinfo{author}{\bibfnamefont{T.}~\bibnamefont{Goodale}},
+  \bibinfo{author}{\bibfnamefont{G.}~\bibnamefont{Allen}},
+  \bibinfo{author}{\bibfnamefont{G.}~\bibnamefont{Lanfermann}},
+  \bibinfo{author}{\bibfnamefont{J.}~\bibnamefont{Mass{\'o}}},
+  \bibinfo{author}{\bibfnamefont{T.}~\bibnamefont{Radke}},
+  \bibinfo{author}{\bibfnamefont{E.}~\bibnamefont{Seidel}}, \bibnamefont{and}
+  \bibinfo{author}{\bibfnamefont{J.}~\bibnamefont{Shalf}},
+  \emph{\bibinfo{title}{The {C}actus framework and toolkit: Design and
+  applications}}, in \emph{\bibinfo{booktitle}{Vector and Parallel Processing
+  -- VECPAR'2002, 5th International Conference, Lecture Notes in Computer
+  Science}} (\bibinfo{publisher}{Springer}, \bibinfo{address}{Berlin},
+  \bibinfo{year}{2003}).
+
+\bibitem[{Cactus()}]{ES-cactusweb}
+Cactus, \bibinfo{note}{{Cactus} Computational Toolkit},
+  \urlprefix\url{http://www.cactuscode.org/}.
+
+\bibitem[{\citenamefont{Schnetter et~al.}(2004)\citenamefont{Schnetter, Hawley,
+  and Hawke}}]{ES-Schnetter2003b}
+\bibinfo{author}{\bibfnamefont{E.}~\bibnamefont{Schnetter}},
+  \bibinfo{author}{\bibfnamefont{S.~H.} \bibnamefont{Hawley}},
+  \bibnamefont{and} \bibinfo{author}{\bibfnamefont{I.}~\bibnamefont{Hawke}},
+  \emph{\bibinfo{title}{Evolutions in {3D} numerical relativity using fixed
+  mesh refinement}}, \bibinfo{journal}{Class. Quantum Grav.}
+  \textbf{\bibinfo{volume}{21}}, \bibinfo{pages}{1465} (\bibinfo{year}{2004}),
+  \eprint{arXiv:gr-qc/0310042},
+  \urlprefix\url{http://arxiv.org/abs/gr-qc/0310042}.
+
+\bibitem[{\citenamefont{Schnetter et~al.}(2006)\citenamefont{Schnetter, Diener,
+  Dorband, and Tiglio}}]{ES-Schnetter2006a}
+\bibinfo{author}{\bibfnamefont{E.}~\bibnamefont{Schnetter}},
+  \bibinfo{author}{\bibfnamefont{P.}~\bibnamefont{Diener}},
+  \bibinfo{author}{\bibfnamefont{E.~N.} \bibnamefont{Dorband}},
+  \bibnamefont{and} \bibinfo{author}{\bibfnamefont{M.}~\bibnamefont{Tiglio}},
+  \emph{\bibinfo{title}{A multi-block infrastructure for three-dimensional
+  time-dependent numerical relativity}}, \bibinfo{journal}{Class. Quantum
+  Grav.} \textbf{\bibinfo{volume}{23}}, \bibinfo{pages}{S553}
+  (\bibinfo{year}{2006}), \eprint{arXiv:gr-qc/0602104},
+  \urlprefix\url{http://arxiv.org/abs/gr-qc/0602104}.
+
+\bibitem[{Carpet()}]{ES-carpetweb}
+Carpet, \bibinfo{note}{mesh Refinement with {Carpet}},
+  \urlprefix\url{http://www.carpetcode.org/}.
+
+\bibitem[{\citenamefont{Brown et~al.}(2009)\citenamefont{Brown, Diener,
+  Sarbach, Schnetter, and Tiglio}}]{ES-Brown2007b}
+\bibinfo{author}{\bibfnamefont{D.}~\bibnamefont{Brown}},
+  \bibinfo{author}{\bibfnamefont{P.}~\bibnamefont{Diener}},
+  \bibinfo{author}{\bibfnamefont{O.}~\bibnamefont{Sarbach}},
+  \bibinfo{author}{\bibfnamefont{E.}~\bibnamefont{Schnetter}},
+  \bibnamefont{and} \bibinfo{author}{\bibfnamefont{M.}~\bibnamefont{Tiglio}},
+  \emph{\bibinfo{title}{Turduckening black holes: an analytical and
+  computational study}}, \bibinfo{journal}{Phys. Rev. D}
+  \textbf{\bibinfo{volume}{79}}, \bibinfo{pages}{044023}
+  (\bibinfo{year}{2009}), \eprint{arXiv:0809.3533 [gr-qc]},
+  \urlprefix\url{http://arxiv.org/abs/0809.3533}.
+
+\bibitem[{McLachlan()}]{ES-mclachlanweb}
+McLachlan, \bibinfo{note}{{McLachlan}, a Public {BSSN} Code},
+  \urlprefix\url{http://www.cct.lsu.edu/~eschnett/McLachlan/}.
+
+\bibitem[{\citenamefont{Lechner et~al.}(2004)\citenamefont{Lechner, Alic, and
+  Husa}}]{kranc04}
+\bibinfo{author}{\bibfnamefont{C.}~\bibnamefont{Lechner}},
+  \bibinfo{author}{\bibfnamefont{D.}~\bibnamefont{Alic}}, \bibnamefont{and}
+  \bibinfo{author}{\bibfnamefont{S.}~\bibnamefont{Husa}},
+  \emph{\bibinfo{title}{From tensor equations to numerical code --- computer
+  algebra tools for numerical relativity}}, in \emph{\bibinfo{booktitle}{SYNASC
+  2004 --- 6th International Symposium on Symbolic and Numeric Algorithms for
+  Scientific Computing, Timisoara, Romania}} (\bibinfo{year}{2004}),
+  \eprint{cs.SC/0411063}, \urlprefix\url{http://arxiv.org/abs/cs.SC/0411063}.
+
+\bibitem[{\citenamefont{Husa et~al.}(2006)\citenamefont{Husa, Hinder, and
+  Lechner}}]{Husa:2004ip}
+\bibinfo{author}{\bibfnamefont{S.}~\bibnamefont{Husa}},
+  \bibinfo{author}{\bibfnamefont{I.}~\bibnamefont{Hinder}}, \bibnamefont{and}
+  \bibinfo{author}{\bibfnamefont{C.}~\bibnamefont{Lechner}},
+  \emph{\bibinfo{title}{Kranc: a {Mathematica} application to generate
+  numerical codes for tensorial evolution equations}},
+  \bibinfo{journal}{Comput. Phys. Comm.} \textbf{\bibinfo{volume}{174}},
+  \bibinfo{pages}{983} (\bibinfo{year}{2006}), \eprint{gr-qc/0404023}.
+
+\bibitem[{kra()}]{krancweb}
+\bibinfo{note}{{Kranc}: Automated Code Generation},
+  \urlprefix\url{http://numrel.aei.mpg.de/Research/Kranc/}.
+
+\bibitem[{Kranc()}]{ES-krancweb}
+Kranc, \bibinfo{note}{{Kranc}: Automated Code Generation},
+  \urlprefix\url{http://www.cct.lsu.edu/~eschnett/Kranc/}.
+
+\bibitem[{SimFactory()}]{ES-simfactoryweb}
+SimFactory, \bibinfo{note}{{SimFactory}: Herding Numerical Simulations},
+  \urlprefix\url{http://www.cct.lsu.edu/~eschnett/SimFactory/}.
+
+\end{thebibliography}
diff --git a/doc/mclachlan.blg b/doc/mclachlan.blg
new file mode 100644
index 0000000..2be77e4
--- /dev/null
+++ b/doc/mclachlan.blg
@@ -0,0 +1,47 @@
+This is BibTeX, Version 0.99c (Web2C 7.5.6)
+The top-level auxiliary file: mclachlan.aux
+The style file: apsrev-titles-manyauthors.bst
+Database file #1: references.bib
+Database file #2: publications-schnetter.bib
+Reallocated wiz_functions (elt_size=4) to 6000 items from 3000.
+You've used 15 entries,
+            3482 wiz_defined-function locations,
+            1245 strings with 12424 characters,
+and the built_in function-call counts, 7627 in all, are:
+= -- 456
+> -- 206
+< -- 25
++ -- 198
+- -- 50
+* -- 965
+:= -- 808
+add.period$ -- 15
+call.type$ -- 15
+change.case$ -- 68
+chr.to.int$ -- 15
+cite$ -- 23
+duplicate$ -- 710
+empty$ -- 694
+format.name$ -- 118
+if$ -- 1443
+int.to.chr$ -- 1
+int.to.str$ -- 16
+missing$ -- 103
+newline$ -- 60
+num.names$ -- 18
+pop$ -- 268
+preamble$ -- 1
+purify$ -- 60
+quote$ -- 0
+skip$ -- 286
+stack$ -- 0
+substring$ -- 250
+swap$ -- 460
+text.length$ -- 25
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 90
+warning$ -- 0
+while$ -- 16
+width$ -- 0
+write$ -- 164
diff --git a/doc/mclachlan.log b/doc/mclachlan.log
new file mode 100644
index 0000000..1250ee3
--- /dev/null
+++ b/doc/mclachlan.log
@@ -0,0 +1,338 @@
+This is pdfTeX, Version 3.141592-1.40.3 (Web2C 7.5.6) (format=pdflatex 2009.7.3)  9 SEP 2009 08:28
+entering extended mode
+**\nonstopmode \input{/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachl
+an.tex}
+(/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.tex
+(/opt/local/share/texmf-dist/tex/latex/revtex/revtex4.cls
+Document Class: revtex4 2001/08/02 v4.0 (http://publish.aps.org/revtex4/ for do
+cumentation)
+ Copyright (c) 2001 The American Physical Society.
+ mailto:revtex@aps.org
+ Licensed under the LPPL:
+http://www.ctan.org/tex-archive/macros/latex/base/lppl.txt
+ Arthur Ogawa <ogawa@teleport.com>
+ Based on work by David Carlisle <david@dcarlisle.demon.co.uk>.
+ltxutil: portions licensed from W. E. Baxter (web@superscript.com)
+Class revtex4 Info: Repairing broken LateX \@sect on input line 596.
+\intertabularlinepenalty=\count79
+\@tbpen=\count80
+\@arstrutbox@hline=\box26
+Class revtex4 Info: Repairing broken LaTeX \@xbitor on input line 1610.
+ltxgrid: portions licensed from W. E. Baxter (web@superscript.com)
+\c@linecount=\count81
+\output=\toks14
+\@protection@box=\box27
+\@topmark@saved=\toks15
+\footins@saved=\box28
+\pagesofar=\box29
+\footbox=\box30
+\pagegrid@col=\count82
+Class revtex4 Info: Incorporating package {textcase}  [1998/11/12 v0.06 Text on
+ly upper/lower case changing (DPC)]. on input line 3682.
+(/opt/local/share/texmf-local/tex/latex/html/url.sty
+Package: url 1999/03/02  ver 1.4  Verb mode for urls, email addresses, and file
+ names
+)
+\c@affil=\count83
+\absbox=\box31
+\c@part=\count84
+\c@section=\count85
+\c@subsection=\count86
+\c@subsubsection=\count87
+\c@paragraph=\count88
+\c@subparagraph=\count89
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\c@figure=\count90
+\c@table=\count91
+
+(/opt/local/share/texmf-dist/tex/latex/natbib/natbib.sty
+Package: natbib 2007/02/05 8.0 (PWD)
+\bibhang=\skip43
+\bibsep=\skip44
+LaTeX Info: Redefining \cite on input line 602.
+\c@NAT@ctr=\count92
+)
+\widetext@top=\box32
+\widetext@bot=\box33
+
+(/opt/local/share/texmf-dist/tex/latex/revtex/revsymb.sty
+Package: revsymb 2001/08/02 v4.0 (http://publish.aps.org/revtex4/ for documenta
+tion)
+LaTeX Info: Redefining \REV@mathfrak on input line 118.
+))
+
+Class revtex4 Warning: No Society specified, using generic APS style.
+
+(/opt/local/share/texmf-dist/tex/latex/revtex/aps.rtx
+File: aps.rtx 2001/08/02 v4.0 (http://publish.aps.org/revtex4/ for documentatio
+n)
+)
+(/opt/local/share/texmf-dist/tex/latex/revtex/11pt.rtx
+File: 11pt.rtx 2001/08/02 v4.0 (http://publish.aps.org/revtex4/ for documentati
+on)
+)
+(/opt/local/share/texmf-dist/tex/latex/amsmath/amsmath.sty
+Package: amsmath 2000/07/18 v2.13 AMS math features
+\@mathmargin=\skip45
+
+For additional information on amsmath, use the `?' option.
+(/opt/local/share/texmf-dist/tex/latex/amsmath/amstext.sty
+Package: amstext 2000/06/29 v2.01
+
+(/opt/local/share/texmf-dist/tex/latex/amsmath/amsgen.sty
+File: amsgen.sty 1999/11/30 v2.0
+\@emptytoks=\toks16
+\ex@=\dimen102
+))
+(/opt/local/share/texmf-dist/tex/latex/amsmath/amsbsy.sty
+Package: amsbsy 1999/11/29 v1.2d
+\pmbraise@=\dimen103
+)
+(/opt/local/share/texmf-dist/tex/latex/amsmath/amsopn.sty
+Package: amsopn 1999/12/14 v2.01 operator names
+)
+\inf@bad=\count93
+LaTeX Info: Redefining \frac on input line 211.
+\uproot@=\count94
+\leftroot@=\count95
+LaTeX Info: Redefining \overline on input line 307.
+\classnum@=\count96
+\DOTSCASE@=\count97
+LaTeX Info: Redefining \ldots on input line 379.
+LaTeX Info: Redefining \dots on input line 382.
+LaTeX Info: Redefining \cdots on input line 467.
+\Mathstrutbox@=\box34
+\strutbox@=\box35
+\big@size=\dimen104
+LaTeX Font Info:    Redeclaring font encoding OML on input line 567.
+LaTeX Font Info:    Redeclaring font encoding OMS on input line 568.
+\macc@depth=\count98
+\c@MaxMatrixCols=\count99
+\dotsspace@=\muskip10
+\c@parentequation=\count100
+\dspbrk@lvl=\count101
+\tag@help=\toks17
+\row@=\count102
+\column@=\count103
+\maxfields@=\count104
+\andhelp@=\toks18
+\eqnshift@=\dimen105
+\alignsep@=\dimen106
+\tagshift@=\dimen107
+\tagwidth@=\dimen108
+\totwidth@=\dimen109
+\lineht@=\dimen110
+\@envbody=\toks19
+\multlinegap=\skip46
+\multlinetaggap=\skip47
+\mathdisplay@stack=\toks20
+LaTeX Info: Redefining \[ on input line 2666.
+LaTeX Info: Redefining \] on input line 2667.
+)
+(/opt/local/share/texmf-dist/tex/latex/amsfonts/amssymb.sty
+Package: amssymb 2002/01/22 v2.2d
+
+(/opt/local/share/texmf-dist/tex/latex/amsfonts/amsfonts.sty
+Package: amsfonts 2001/10/25 v2.2f
+\symAMSa=\mathgroup4
+\symAMSb=\mathgroup5
+LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
+(Font)                  U/euf/m/n --> U/euf/b/n on input line 132.
+LaTeX Info: Redefining \frak on input line 135.
+LaTeX Info: Redefining \Bbb on input line 137.
+))
+(/opt/local/share/texmf-dist/tex/latex/graphics/color.sty
+Package: color 2005/11/14 v1.0j Standard LaTeX Color (DPC)
+
+(/opt/local/share/texmf/tex/latex/config/color.cfg
+File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
+)
+Package color Info: Driver file: pdftex.def on input line 130.
+
+(/opt/local/share/texmf-dist/tex/latex/pdftex-def/pdftex.def
+File: pdftex.def 2007/01/08 v0.04d Graphics/color for pdfTeX
+\Gread@gobject=\count105
+))
+(/opt/local/share/texmf-dist/tex/latex/float/float.sty
+Package: float 2001/11/08 v1.3d Float enhancements (AL)
+\c@float@type=\count106
+\float@exts=\toks21
+\float@box=\box36
+\@float@everytoks=\toks22
+\@floatcapt=\box37
+)
+(/opt/local/share/texmf-dist/tex/latex/graphics/graphicx.sty
+Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
+
+(/opt/local/share/texmf-dist/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV@toks@=\toks23
+)
+(/opt/local/share/texmf-dist/tex/latex/graphics/graphics.sty
+Package: graphics 2006/02/20 v1.0o Standard LaTeX Graphics (DPC,SPQR)
+
+(/opt/local/share/texmf-dist/tex/latex/graphics/trig.sty
+Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
+)
+(/opt/local/share/texmf/tex/latex/config/graphics.cfg
+File: graphics.cfg 2007/01/18 v1.5 graphics configuration of teTeX/TeXLive
+)
+Package graphics Info: Driver file: pdftex.def on input line 90.
+)
+\Gin@req@height=\dimen111
+\Gin@req@width=\dimen112
+)
+(/opt/local/share/texmf-dist/tex/latex/base/inputenc.sty
+Package: inputenc 2006/05/05 v1.1b Input encoding file
+\inpenc@prehook=\toks24
+\inpenc@posthook=\toks25
+
+(/opt/local/share/texmf-local/tex/latex/html/latin9.def
+File: latin1.def 1998/03/05 v0.97 Input encoding file(test version: still liabl
+e to change)
+))
+(/opt/local/share/texmf-dist/tex/latex/hyperref/hyperref.sty
+Package: hyperref 2007/02/07 v6.75r Hypertext links for LaTeX
+\@linkdim=\dimen113
+\Hy@linkcounter=\count107
+\Hy@pagecounter=\count108
+
+(/opt/local/share/texmf-dist/tex/latex/hyperref/pd1enc.def
+File: pd1enc.def 2007/02/07 v6.75r Hyperref: PDFDocEncoding definition (HO)
+)
+(/opt/local/share/texmf/tex/latex/config/hyperref.cfg
+File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
+)
+(/opt/local/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty
+Package: kvoptions 2006/08/22 v2.4 Connects package keyval with LaTeX options (
+HO)
+)
+Package hyperref Info: Option `bookmarks' set `true' on input line 2238.
+Package hyperref Info: Option `bookmarksopen' set `true' on input line 2238.
+Package hyperref Info: Option `bookmarksnumbered' set `true' on input line 2238
+.
+Package hyperref Info: Hyper figures OFF on input line 2288.
+Package hyperref Info: Link nesting OFF on input line 2293.
+Package hyperref Info: Hyper index ON on input line 2296.
+Package hyperref Info: Plain pages OFF on input line 2303.
+Package hyperref Info: Backreferencing OFF on input line 2308.
+
+Implicit mode ON; LaTeX internals redefined
+Package hyperref Info: Bookmarks ON on input line 2444.
+LaTeX Info: Redefining \url on input line 2599.
+\Fld@menulength=\count109
+\Field@Width=\dimen114
+\Fld@charsize=\dimen115
+\Choice@toks=\toks26
+\Field@toks=\toks27
+Package hyperref Info: Hyper figures OFF on input line 3102.
+Package hyperref Info: Link nesting OFF on input line 3107.
+Package hyperref Info: Hyper index ON on input line 3110.
+Package hyperref Info: backreferencing OFF on input line 3117.
+Package hyperref Info: Link coloring OFF on input line 3122.
+\Hy@abspage=\count110
+\c@Item=\count111
+\c@Hfootnote=\count112
+)
+*hyperref using default driver hpdftex*
+(/opt/local/share/texmf-dist/tex/latex/hyperref/hpdftex.def
+File: hpdftex.def 2007/02/07 v6.75r Hyperref driver for pdfTeX
+\Fld@listcount=\count113
+)
+(/opt/local/share/texmf-dist/tex/latex/oberdiek/hypcap.sty
+Package: hypcap 2006/02/20 v1.5 Adjusting anchors of captions (HO)
+)
+(/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.aux)
+\openout1 = `mclachlan.aux'.
+
+LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 26.
+LaTeX Font Info:    ... okay on input line 26.
+Class revtex4 Info: Patching LaTeX tabular. on input line 26.
+Class revtex4 Info: cite was not loaded (OK!) on input line 26.
+Class revtex4 Info: multicol was not loaded (OK!) on input line 26.
+
+(/opt/local/share/texmf-dist/tex/context/base/supp-pdf.tex
+[Loading MPS to PDF converter (version 2006.09.02).]
+\scratchcounter=\count114
+\scratchdimen=\dimen116
+\scratchbox=\box38
+\nofMPsegments=\count115
+\nofMParguments=\count116
+\MPscratchCnt=\count117
+\MPscratchDim=\dimen117
+\MPnumerator=\count118
+\everyMPtoPDFconversion=\toks28
+)
+Package hyperref Info: Link coloring OFF on input line 26.
+ (/opt/local/share/texmf-dist/tex/latex/hyperref/nameref.sty
+Package: nameref 2006/12/27 v2.28 Cross-referencing by name of section
+
+(/opt/local/share/texmf-dist/tex/latex/oberdiek/refcount.sty
+Package: refcount 2006/02/20 v3.0 Data extraction from references (HO)
+)
+\c@section@level=\count119
+)
+LaTeX Info: Redefining \ref on input line 26.
+LaTeX Info: Redefining \pageref on input line 26.
+
+(/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.out)
+(/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.out)
+\@outlinefile=\write3
+\openout3 = `mclachlan.out'.
+
+LaTeX Font Info:    Try loading font information for U+msa on input line 46.
+
+(/opt/local/share/texmf-dist/tex/latex/amsfonts/umsa.fd
+File: umsa.fd 2002/01/19 v2.2g AMS font definitions
+)
+LaTeX Font Info:    Try loading font information for U+msb on input line 46.
+
+(/opt/local/share/texmf-dist/tex/latex/amsfonts/umsb.fd
+File: umsb.fd 2002/01/19 v2.2g AMS font definitions
+) [1{/opt/local/share/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4]
+Underfull \hbox (badness 10000) in paragraph at lines 312--314
+[][]\OT1/cmtt/m/n/10.95 env OMP_NUM_THREADS=1 mpirun -np 1 ../exe/cactus_sim \
+ []
+
+(/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.bbl [5])
+
+Class revtex4 Warning: Command \address is obsolete;
+Use \affiliation instead.
+
+[6] (/Users/eschnett/Calpha/arrangements/McLachlan/doc/mclachlan.aux) ) 
+Here is how much of TeX's memory you used:
+ 5270 strings out of 94073
+ 69353 string characters out of 1164798
+ 140835 words of memory out of 1500000
+ 8414 multiletter control sequences out of 10000+50000
+ 13323 words of font info for 52 fonts, out of 1200000 for 2000
+ 648 hyphenation exceptions out of 8191
+ 41i,7n,28p,296b,461s stack positions out of 5000i,500n,6000p,200000b,5000s
+</opt/lo
+cal/share/texmf-dist/fonts/type1/bluesky/cm/cmbx10.pfb></opt/local/share/texmf-
+dist/fonts/type1/bluesky/cm/cmbx12.pfb></opt/local/share/texmf-dist/fonts/type1
+/bluesky/cm/cmmi10.pfb></opt/local/share/texmf-dist/fonts/type1/bluesky/cm/cmr1
+0.pfb></opt/local/share/texmf-dist/fonts/type1/bluesky/cm/cmr9.pfb></opt/local/
+share/texmf-dist/fonts/type1/bluesky/cm/cmsy6.pfb></opt/local/share/texmf-dist/
+fonts/type1/bluesky/cm/cmsy7.pfb></opt/local/share/texmf-dist/fonts/type1/blues
+ky/cm/cmsy8.pfb></opt/local/share/texmf-dist/fonts/type1/bluesky/cm/cmti10.pfb>
+</opt/local/share/texmf-dist/fonts/type1/bluesky/cm/cmtt10.pfb>
+Output written on mclachlan.pdf (6 pages, 107710 bytes).
+PDF statistics:
+ 251 PDF objects out of 1000 (max. 8388607)
+ 76 named destinations out of 1000 (max. 131072)
+ 137 words of extra memory for PDF output out of 10000 (max. 10000000)
+
diff --git a/doc/mclachlan.out b/doc/mclachlan.out
new file mode 100644
index 0000000..bd9a451
--- /dev/null
+++ b/doc/mclachlan.out
@@ -0,0 +1,15 @@
+\BOOKMARK [1][]{section*.1}{I McLachlan}{}
+\BOOKMARK [1][]{section*.2}{II Obtaining McLachlan}{}
+\BOOKMARK [2][]{section*.3}{A Tools}{section*.2}
+\BOOKMARK [2][]{section*.4}{B Cactus}{section*.2}
+\BOOKMARK [2][]{section*.5}{C Carpet}{section*.2}
+\BOOKMARK [2][]{section*.6}{D McLachlan}{section*.2}
+\BOOKMARK [2][]{section*.7}{E Other Thorns}{section*.2}
+\BOOKMARK [2][]{section*.8}{F Consistency Check}{section*.2}
+\BOOKMARK [1][]{section*.9}{III Building McLachlan}{}
+\BOOKMARK [2][]{section*.10}{A Documentation}{section*.9}
+\BOOKMARK [2][]{section*.11}{B Option List}{section*.9}
+\BOOKMARK [2][]{section*.12}{C Building}{section*.9}
+\BOOKMARK [2][]{section*.13}{D Cleaning}{section*.9}
+\BOOKMARK [1][]{section*.14}{IV Running McLachlan}{}
+\BOOKMARK [1][]{section*.15}{ References}{}
diff --git a/doc/mclachlan.pdf b/doc/mclachlan.pdf
new file mode 100644
index 0000000..b41275b
--- /dev/null
+++ b/doc/mclachlan.pdf