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%   @file      documentation.tex
%   @date      23 April 2002
%   @author    Denis Pollney
%   @desc 
%              LegoExcision users guide.
%   @enddesc 
%   @version $Header$      
% @@*/

\documentclass{article}

% Use the Cactus ThornGuide style file
% (Automatically used from Cactus distribution, if you have a 
%  thorn without the Cactus Flesh download this from the Cactus
%  homepage at www.cactuscode.org)
\usepackage{../../../../doc/latex/cactus}

\begin{document}

\title{Using LegoExcision}
\author{Denis Pollney}
\date{$ $Date$ $}

\maketitle

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\begin{abstract}
  LegoExcision implements excision on a Cactus grid. It uses a mask
  function to determine which grid points are to be excised, then
  applies a simple boundary condition to points on the edge of the
  mask.
\end{abstract}

\section{Background}

The \texttt{LegoExcision} thorn was originally written spring 2001 by
Miguel Alcubierre, Eric Schnetter and Deirdre Shoemaker. It extends
the functionality of Miguel's \texttt{SimpleExcision} thorn (described
in \cite{alcubierre-bruegmann:2001}) by allowing arbitrary shapes and
number of holes to be excised.

\section{Implementing excision in a thorn}

\texttt{LegoExcision} is not scheduled. It simply provides three
functions (\texttt{excision\_findboundary()},
\texttt{excision\_findnormals()} and 
\texttt{excision\_extrapolate()}) which are used to apply the excision
boundary condition to a grid function. This functions must be called at
the appropriate time (eg. whenever boundary conditions are applied)
within the source code of any thorn that wishes to use excision.
The functions are written in Fortran90, and no C wrappers exist as of
yet.

The first function, \texttt{excision\_findboundary()}, can be used to
mark the boundaries of an excision region in the mask function. It
is passed the mask in the form of a Cactus gridfunction which has
interior points marked appropriately (see Section \ref{sec:mask},
below). It then passes over the mask and marks any point which is on
the boundary of an excision region. Boundary points are any point
which has at least one neighbour that is not excised.
\\\vspace{\baselineskip}

\parbox{.9\linewidth}{
\texttt{excision\_findboundary (\emph{ierr}, \emph{mask}, \emph{ni},
  \emph{nj}, \emph{nk})}

\begin{description}
\item{\texttt{\emph{ierr}}} \texttt{(integer)}
  Holds the return value, 0 for success.
\item{\texttt{\emph{mask}}} \texttt{(CCTK\_REAL(ni,nj,nk))}
  A Cactus gridfunction (array of \texttt{CCTK\_REAL} whose
  dimensions are given by the \texttt{cctk\_lsh} variables)
  which contians the excision mask.
\item{\texttt{\emph{ni}}, \texttt{\emph{nj}}, \texttt{\emph{nk}}} (integer)
  Dimensions of the grid, corresponding to \texttt{cctk\_lsh(1...3)}.
\end{description}
}\\\vspace{\baselineskip}

Next, the function \texttt{excision\_findnormals()} can be used to
determine normal directions from each point on the excision boundary.
The normals are stored in three grid functions (\texttt{dirx},
\texttt{diry} and \texttt{dirz}) which contain the $(x,y,z)$
components of the normal vector for points on the boundary. The normal
is determined as a sum of the relative components of each active
(non-excised) neighbour,
\begin{equation}
n^i = \sum_{x^\prime\in\{\text{neighbours of} x\}} x^{\prime i} - x^i,
\end{equation}
which is then normalised. For points which are not on the excision
boundary, the normal is set to $0$.\\\vspace{\baselineskip}

\parbox{.9\linewidth}{
\texttt{excision\_findnormals (\emph{ierr}, \emph{mask}, \emph{dirx},
  \emph{diry}, \emph{dirz}, \emph{ni}, \emph{nj}, \emph{nk})}
\begin{description}
  \item[\texttt{\emph{ierr}}] (\texttt{integer})
    Holds the return value, 0 for success.
  \item[\texttt{\emph{mask}}] (\texttt{CCTK\_REAL(ni,nj,nk)})
    A Cactus gridfunction which contians the excision mask.
  \item[\texttt{\emph{dirx}}, \texttt{\emph{diry}},
    \texttt{\emph{dirz}}] (\texttt{CCTK\_REAL(ni,nj,nk)})
    Grid functions describing the normal directions to the excision
    boundary. These are determined by \texttt{excision\_findnormals()}.
  \item[\texttt{\emph{ni}}, \texttt{\emph{nj}}, \texttt{\emph{nk}}]
    (\texttt{integer}) Dimensions of the grid, corresponding to
    \texttt{cctk\_lsh(1...3)}.
\end{description}
}\\\vspace{\baselineskip}

Finally, the \texttt{excision\_extrapolate()} routine applies the a
boundary condition to a grid function at each point that the mask has
identified as an excision boundary. At present, only one boundary
condition is implemented, which corresponds to the `time derivative
copy' which was successfully used in
\cite{alcubierre-bruegmann:2001}. Namely, the time derivative $dv/dt$
of the variable is determined at one point away from the excision
boundary, and copied to the excision boundary where it is used as a
source. This determines a new value on the boundary at the next
timeslice.\\\vspace{\baselineskip}

\parbox{.9\linewidth}{
\texttt{excision\_extrapolate (\emph{ierr}, \emph{var}, \emph{oldvar},
  \emph{mask}, \emph{dirx}, \emph{diry}, \emph{dirz}, \emph{ni},
  \emph{nj}, \emph{nk}, \emph{var0})}
\begin{description}
  \item[\texttt{\emph{ierr}}] (\texttt{integer})
    Holds the return value, 0 for success.
  \item[\texttt{\emph{var}}] (\texttt{CCTK\_REAL(ni,nj,nk)})
    A Cactus gridfunction (array of \texttt{CCTK\_REAL} whose
    dimensions are given by the \texttt{cctk\_lsh} variables)
    corresponding the the variable to which excision is to be applied.
  \item[\texttt{\emph{oldvar}}] (\texttt{CCTK\_REAL(ni,nj,nk)})
    A Cactus gridfunction holding the values of the variable
    to be excised on the previous slice (ie. previous time).
  \item[\texttt{\emph{mask}}] (\texttt{CCTK\_REAL(ni,nj,nk)})
    A Cactus gridfunction which contians the excision mask.
  \item[\texttt{\emph{dirx}}, \texttt{\emph{diry}},
    \texttt{\emph{dirz}}] (\texttt{CCTK\_REAL(ni,nj,nk)}]
    Grid functions describing the normal directions to the excision
    boundary. These are determined by \texttt{excision\_findnormals()}.
  \item[\texttt{\emph{ni}}, \texttt{\emph{nj}}, \texttt{\emph{nk}}]
    (\texttt{integer}) Dimensions of the grid, corresponding to
    \texttt{cctk\_lsh(1...3)}.
  \item[\texttt{\emph{var0}}] (\texttt{CCTK\_REAL})
    A constant value which will be written to all points of the grid
    function within the excision mask.
\end{description}
}\\ \vspace{\baselineskip}

For example, given an excision mask \texttt{ex\_mask}, excision can
be applied to the grid functions \texttt{fn0}, \texttt{fn1}
and \texttt{fn2} using the following code:

\begin{verbatim}
       call excision_findboundary (ierr, ex_mask, nx, ny, nz)
       call excision_findnormals (ierr, ex_mask, normx, normy, normz, nx,
     +   ny, nz)

       call excision_extrapolate (ierr, fn0, fn0_p, ex_mask, normx,
     +   normy, normz, nx, ny, nz, 0.d0)
       call excision_extrapolate (ierr, fn1, fn1_p, ex_mask, normx,
     +   normy, normz, nx, ny, nz, 0.d0)
       call excision_extrapolate (ierr, fn2, fn2_p, ex_mask, normx,
     +   normy, normz, nx, ny, nz, 1.d0)
\end{verbatim}

Since  the excision  mask  is the  same  for each  grid function,  the
boundary  and normals  only  needed  to be  determined  once. In  this
example, \texttt{normx}, \texttt{normy}  and \texttt{normz} are cactus
grid functions which should have been declared as, for instance,
\begin{verbatim}
  real ex_norm type=GF
  {
    normx,
    normy,
    normz
  } "Excision boundary normals"
\end{verbatim}
in the \texttt{param.ccl} of the thorn implementing this code, or one
from which it inherits. The same is true of the excision mask.  The
\texttt{fn0\_p} grid function should hold the value of \texttt{fn0} on
the previous timestep.

The final argument which is passed is a value which is used to
overwrite grid function values within the excision region. Thus,
though boundary points have a value applied by
\texttt{excision\_extrapolate()}, points of \texttt{fn0} within the
boundary are overwritten by the value $0$, while for \texttt{fn2} the
value $1$ is used instead.

Finally, note that any thorn which uses code as in the example above
will depend on the \texttt{LegoExcision} thorn, and thus should
declare
\begin{verbatim}
  inherits: legoexcision
\end{verbatim}
in its \texttt{interface.ccl}, otherwise it will not compile unless
\texttt{LegoExcision} is also included. This can be avoided through
use of an \texttt{\#ifdef} clause around any section of code which
refers directly to \texttt{LegoExcision}:
\begin{verbatim}
  #ifdef EXCISION_LEGOEXCISION
  ...
  #endif
\end{verbatim}
This is, however, considered to be dubious form.

\section{The mask function}
\label{sec:mask}

The mask should be declared as a real-valued grid function, thus
something like
\begin{verbatim}
  real legoexcision_mask type=GF
  {
    ex_mask
  } "Excision mask"
\end{verbatim}
in the calling thorn, or one which it inherits. Each point of the mask
should take one of the following values, defined in
\texttt{maskvalues.h}:

\begin{description}
  \item[\texttt{MASK\_EXCISED}] points which are within the excision region;
  \item[\texttt{MASK\_BOUNDARY}] points on the excision boundary;
  \item[\texttt{MASK\_ACTIVE}] normal (non-excised) grid points.
\end{description}

The \texttt{LegoExcision} thorn does not specify any criteria for how
these points should be set (ie. which points should be marked as
excision points), but rather assumes that they have already been set by
the calling thorn, or at some other point in the schedule. Thus, for
instance for black hole evolutions, a horizon finder could be used to
set an excision mask which would then be passed to an evolution thorn
to ensure that points within horizon are not evolved. Note also that the
mask function does not need to have boundary points identified, as the
\texttt{excision\_findboundary()} function can be used to locate them.

The \texttt{CactusEinstein/Einstein} thorn defines a generic mask
function \texttt{einstein::emask} whose values are not defined, and
can be used for this purpose. Storage for this grid function is turned
on based on the value of the \texttt{einstein::use\_mask} parameter.

Note that as of the time of writing, the
\texttt{Einstein} heirarchy is undergoing a revision and the details
of this description are likely to be modified. In particular, the use
of the \texttt{Einstein} mask function is being formalised, so that at
least the above definitions will change in the near future.

\section{Boundary conditions}

As mentioned above, the \texttt{LegoExcision} thorn applies a copying
condition to points on the excision boundary. Namely, the time
derivative is determined at one point away from the boundary in the
direction determined by the normal. This time derivative is then
applied to evolve the variable on the excision boundary.

For black hole spacetimes, it is possible that this condition is
sufficient, since it is usually assumed that excision is only applied
within an event horizon so that errors are causally propogated into
the excision region. This particular condition has the advantage that
if the spacetime is stationary, or evolves to a stationary state,
outside of the excision region then the boundary respects this.

\section{Using excision}

The \texttt{LegoExcision} thorn has no parameters. To activate
excision, include \texttt{LegoExcision} in the \texttt{ActiveThorns}
any parameter file:
\begin{verbatim}
  ActiveThorns = "... LegoExcision ..."
\end{verbatim}
This will ensure that the functions described above are available
to any thorn which has implemented them.

\section{Thorns which use \texttt{LegoExcision}}

A number of the existing physic thorns can be used in conjunction with
\texttt{LegoExcision}. In particular, the horizon finder can be used
to set the mask to excise regions within the horizon so that they are
not evolved by the BSSN evolution system.\\

The apparent horizon finder, \texttt{CactusEinstein/AHFinder},
includes a number of parameters which can be used to set a mask:
\begin{description}
  \item[\texttt{ahf\_mask}] By setting this to either
    ``\texttt{strong}'' or ``\texttt{weak}'', the mask will be set to
    excise points within any detected horizon. The difference between
    the two is that if ``\texttt{weak}'' is specified then the mask
    will be set even if only a probable marginally trapped surface is
    found, while ``\texttt{strong}'' will only set the mask if a
    horizon is definitely found. Usually it is fine to set
    \texttt{ahfinder::ahf\_mask="weak"}.
  \item[\texttt{ahf\_masktype}] This parameter sets the shape of the
    mask which is set. If set to ``\texttt{cube}'', then a region the
    shape of a cube will be used. The largest cube which fits entirely
    within the horizon will be used. This option was used for
    comparison with earlier results using \texttt{SimpleExcision}.
  \item[\texttt{ahf\_mask\_0, ahf\_mask\_1, ahf\_mask\_2}]
    These parameters determine whether the mask should be set for the
    respective horizons.
  \item[\texttt{ahf\_maskbuffer}] This fixes the minimum number of
    points which must exist between the apparent horizon and the
    excision region. Thus, the masked region will sit within a 
    ``buffer'' region of the specified width from the horizon.
  \item[\texttt{ahf\_maskshrink}] The region which is masked will be
    smaller than the actual horizon by a factor which is specified by
    this parameter. As with the \texttt{ahf\_maskbuffer} parameter,
    this can be used to control the size of the buffer region between
    the horizon and the region to be excised.
\end{description}

If the apparent horizon finder is called with \texttt{ahf\_mask} set
to either ``\texttt{weak}'' or ``\texttt{strong}'', then the grid
function \texttt{einstein::emask} will be initialised according to the
horizon locations, and can then be passed to the \texttt{LegoExcision}
functions.\\

The \texttt{AEIThorns/ADM\_BSSN} thorn can make use of a
\texttt{LegoExcision} mask for evolutions. In order to turn on
excision for an evolution, the parameters
\begin{verbatim}
  adm_bssn::excise = "yes"
  adm_bssn::excisiontype = "lego"
\end{verbatim}
should be set. The same holds for the \texttt{BSSN\_MoL} thorn.\\

The \texttt{Einstein/ADMConstraints} thorn also respects the
\texttt{einstein::emask}, so that the constraints will not be
calculated within the excision region. To enable this feature,
set
\begin{verbatim}
  admconstraints::excise = "yes"
\end{verbatim}
\vspace{\baselineskip}

In summary, to use \texttt{LegoExcision} in a BSSN evolution using the
horizon finder to set the mask, modifications along the following
lines need to be made to a parameter file:
\begin{verbatim}
  activethorns = "... einstein adm_bssn ahfinder legoexcision ..."

  einstein::use_mask = "yes"

  adm_bssn::excise = "yes"
  adm_bssn::excisiontype = "lego"

  ahfinder::ahf_mask = "weak"
  ahfinder::ahf_maskbuffer = 0.9
\end{verbatim}

\begin{thebibliography}{9}
  \bibitem{alcubierre-bruegmann:2001}
    Miguel Alcubierre and Bernd Br\"ugmann (2001)
    \emph{Simple excision of a black hole in (3+1)d numerical
    relativity},
    Phys. Rev. \textbf{D63}, 104006 (gr-qc/0008067).
\end{thebibliography}


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