path: root/doc/UsersGuide/ThornWriters.tex

% /*@@
%   @file      ThornWriters.tex
%   @date      27 Jan 1999
%   @author    Gabrielle Allen, Tom Goodale, Gerd Lanfermann
%   @desc 
%   Thorn writer's guide part of the Cactus User's Guide
%   @enddesc 
%   @version $Header$      
% @@*/

\begin{cactuspart}{2}{Application thorn writing}{$RCSfile$}{$Revision$}

\renewcommand{\thepage}{\Alph{part}\arabic{page}}

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\chapter{Overview}

This chapter goes into the nitty-gritty of writing a thorn. 
It introduces key concepts for thorns, then goes on to give
a brief outline of how to configure a thorn.
There is then some detail about concepts introduced by the configuration
step, followed by discussion of code which you must put into your files
in order to use Cactus functionality, and details of utility functions
you may use to gain extra functionality.


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\chapter{Thorn concepts} 


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\section{Thorns}

A thorn is the basic working module within Cactus.  All user-supplied
code goes into thorns, which are, by and large, independent of each other.
Thorns communicate with each other via calls to the flesh API, plus, more
rarely, custom APIs of other thorns.

The connection from a thorn to the flesh or to other thorns is specified in
configuration files which are parsed at compile time and used to generate
glue code which encapsulates the external appearence of a thorn.

Thorn names must be (case independently) unique, must start with a letter, 
and can only contain 
letters, numbers or underscores. 
In addition, a thorn cannot have the name {\t doc}, this is reserved 
for arrangement documentation. Arrangement names which start with a 
`\#', or finish with `\~{}' or `.bak' will be ignored.



\section{Arrangements}

Thorns are grouped into {\em arrangements}.  This is a logical grouping of
thorns which is purely for organisational purposes. For example, 
you might wish to keep all your initial data thorns in one arrangement,
and all your evolution thorns in another arrangement, or you may want 
to have separate arrangements for your developments, private and shared 
thorns. 

The arrangements live in the {\tt arrangements} directory off the main 
Cactus directory.  Arrangement names must be (case independently) unique, 
must start with a letter, 
and can only contain 
letters, numbers or underscores. Arrangement names which start with a 
`\#', or finish with `\~{}' or `.bak' will be ignored.

Inside an arrangement directory there are directories for each thorn 
belonging to the arrangement.  

\section{Implementations}

\label{sec:im}

One of the key concepts for thorns is the concept of the {\bf implementation}.
Relationships between thorns are all based upon relationship between the
{\bf implementations} they provide. 
In principle it should be possible to swap one thorn providing an 
implementation with another thorn providing that implementation,
without affecting any other thorn.

An {\bf implementation} defines a group of variables and parameters which
are used to implement some functionality.  For example the thorn 
{\tt CactusPUGH/PUGH} provides the implementation {\it driver}.  This 
implementation is responsible for providing memory for grid variables and
for communication.  Another thorn can also implement {\tt driver}, 
and both thorns can be compiled in {\em at the same time}.  
At runtime, the user can decide which thorn providing {\tt driver} is used.  
No other thorn should be affected by this choice.

When a thorn decides it needs access to a variable or a parameter provided by 
another thorn, it defines a relationship between itself and the other thorn's
{\bf implementation}, not explicitly with the other {\bf thorn}.  
This allows the transparent replacement, at compile or runtime, of one 
thorn with another thorn providing the same functionality as seen by 
the other thorns.


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\chapter{Anatomy of a thorn}
\label{sec:anofath}

\section{Thorns}
\label{sec:th}

A thorn consists of a subdirectory of an arrangement containing three 
administrative files

\begin{Lentry}
\item[{\tt interface.ccl}] the cactus interface, which defines the grid 
functions, variables, etc. See \ref{sec:in}.
\item[{\tt param.ccl}] the parameters introduced by this thorn, and the
parameters needed from other thorns. See
\ref{sec:pa}.
\item[{\tt schedule.ccl}] scheduling information for routines called by
the flesh. See \ref{sec:sc}
\end{Lentry}

Thorns can also contain  
\begin{itemize}
\item a subdirectory called {\tt src}, which should hold source files
        and compilation instructions for the thorn
\item a subdirectory {\tt src/include} for include files 
\item a {\tt README} containing a brief description of the thorn
\item a {\tt doc} directory for documentation
\item a {\tt par} directory for example parameter files
\item a {\tt test} subdirectory may also be added, to hold the thorn's
    testsuite. See \ref{sec:adatesu} for details.
\end{itemize}

\section{Creating a thorn}


To simplify the creation of a thorn, a make target {\tt
gmake newthorn} has been provided. When this is run:

\begin{enumerate} 
\item{} You will be prompted for the name of the new thorn.
\item{} You will be prompted for the name of the arrangement you would
like to include your thorn in. Either enter a new arrangement name or pick 
one from the list of available arrangements that are shown.
\end{enumerate}


\section{Configuring your thorn}

The interaction of a thorn with the flesh and other thorns is controlled
by various configuration files.

These consist of:

\begin{Lentry}

\item [{\tt interface.ccl}]
This defines the {\bf implementation} (Section~\ref{sec:im}) the thorn 
provides, and the variables the thorn needs, along with their 
visibility to other implementations.

\item [{\tt param.ccl}]
This defines the parameters that are used to control the thorn, along
with their visibility to other implementations.

\item [{\tt schedule.ccl}]
This defines which functions from the thorn are called and when they are 
called. It also handles memory and communication assignment for grid variables.

\end{Lentry}

\subsection{General syntax of CCL files}

CCL {\bf Cactus Configuration Language} files are simple text files
used to define configuration information for a thorn.  CCL files are
case independent, and may contain comments introduced by the `\#' character,
which indicates that the rest of the line is a comment. If the last non-blank character of a line in a CCL file is a backslash {\tt $\backslash$}, the following line is treated as a continuation of the current line.

\subsection{The {\tt interface.ccl}}

The {\tt interface.ccl} file is used to declare

\begin{itemize}
\item the implementation provided by the thorn, 
\item the variables provided by the thorn
\item the include files provided by the thorn
\item the functions provided by the thorn (in development)
\end{itemize}


The implementation is declared by a single line at the top of the file
\begin{verbatim}
implements: <name>
\end{verbatim}
Where {\tt <name>} can be any combination of alphanumeric 
characters and underscores, and is case independent.
There are three different access levels available for variables

\begin{Lentry}
\item[{\tt Public}]
Can be `inherited' by other implementations (see below).
\item[{\tt Protected}]
Can be shared with other implementations which declare themselves to
be friends of this one (see below).
\item[{\tt Private}]
Can only be seen by this thorn.
\end{Lentry}

Corresponding to the first two access levels there are two relationship
statements that can be used to get variables from other thorns.

\begin{Lentry}
\item [{\tt Inherits: <name>}]
This gets all {\tt Public} variables from implementation {\tt <name>}, and all
variables that {\tt <name>} has in turn inherited.  
An implementation may inherit from any number of other implementations.
\item [{\tt Friend: <name>}]
This gets all {\tt Protected} variables from implementation {\tt <name>}, but, 
unlike {\tt inherits} it also pushes its own implementations {\tt Protected}
variables onto implementation {\tt <name>}.  This keyword is used to define
a group of implementations which all end up with the same {\tt Protected}
variables.
\end{Lentry}

So, for example, an {\tt interface.ccl} starting
\begin{verbatim}
implements: wavetoy
inherits:   grid
friend:     wave_extract
\end{verbatim}
declares that the thorn provides an implementation called `wavetoy', gets
all the {\tt public} variables declared by an implementation called `grid', and
shares all {\tt protected} variables with {\tt wave\_extract} and its friends.

Cactus variables, described in Section~\ref{sec:cava} are placed
in groups with homogeneous attributes, where
the attributes describe properties such as the data type, group type, 
dimenension, ghostsize, number of timelevels, type of staggering and 
distribution. 

For example, a group, called {\tt realfields} of 5 real grid 
functions ({\tt phi}, {\tt a}, 
{\tt b}, {\tt c}, {\tt d}), on a 3D grid, would be defined by
\begin{verbatim}
CCTK_REAL realfields type=GF TimeLevels=3 Dim=3 
{
  phi
  a,b,c,d
} "Example grid functions"\end{verbatim}
or, for a group called {\tt intfields} consisting of just one 
distributed 2D array of integers, 
\begin{verbatim}
CCTK_INT intfields type=ARRAY size=xsize,ysize ghostsize=gxsize,gysize
{
 anarray
} "My 2D arrays"
\end{verbatim}
where {\tt xsize}, {\tt ysize}, {\tt gxsize}, {\tt gysize} are all 
parameters defined in the thorns {\tt param.ccl}.


By default all groups are {\tt private}, to change this an access
specification of the form {\tt public:} or {\tt protected:} (or 
{\tt private:} to change it back) may be placed on a line by itself.  This
changes the access level for any group defined in the file from that point on.

All variables seen by any one thorn must have distinct names.

\subsection{The {\tt param.ccl}}

Users control the operation of thorns via parameters given in a file
at runtime.  The {\tt param.ccl}
is used to specify the parameters used to control an individual thorn, and
to specify the values these parameters are allowed to take.  When the code
is run it reads a parameter file and sets the parameters if they fall
within the allowed values. If a parameter is not assigned in a parameter
file, it is given its default value.

There are three access levels available for parameters:

\begin{Lentry}
\item [{\tt Global}]
These parameters are seen by all thorns.
\item [{\tt Restricted}]
These parameters may be used by other implementations if they so desire.
\item [{\tt Private}]
These are only seen by this thorn.
\end {Lentry}

A parameter specification consists of:
\begin{itemize}

\item the parameter type (each may have an optional {\t CCTK\_} in front)
\begin{Lentry}
\item [{\tt REAL}]
\item [{\tt INT}]
\item [{\tt KEYWORD}]
A distinct string with only a few known allowed values.
\item [{\tt STRING}]
An arbitrary string, which must conform to a given regular expression.
\item [{\tt BOOLEAN}]
A boolean type which can take values 1, `t', `true', `yes' or 
0, `f', `false', `no'.
\end{Lentry}

\item the parameter name

\item a {\tt description} of the parameter

\item an allowed value block ---
This consists of a brace delimited block of lines
describing the allowed values of the parameter.  Each range may
have a description associated with it by placing a :: on the line and
putting the description afterwards.

\item the default value ---
This must be one of the allowed values.

\end{itemize}

For the numeric types {\tt INT} and {\tt REAL}, a range consists 
of a string of the
forms lower-bound:upper-bound:step where a missing number or a * denotes
anything (i.e. infinite bounds or an infinitesimal step).

For example 
\begin{verbatim}
REAL Coeff "Important coefficient"
{
0:3.14 :: "Range has to be from zero to Pi, default is zero"
} 0.0

#No need to define a range for BOOLEAN
BOOLEAN nice "Nice weather ?"
{
}"yes"

# A example for a set of keywords and its default (which has to be
# defined in the body)
KEYWORD confused "Are we getting confused ?"
{
  "yes"    :: "absolutely positively"
  "perhaps" :: "we are not sure"
  "never"   :: "never"
} "never"
\end{verbatim}
defines a REAL parameter, a BOOLEAN parameter, and a KEYWORD.

By default all parameters are {\tt private}, to change this an access
specification of the form {\tt global:} or {\tt restricted:} (or 
{\tt private:} to change it back) may be placed on a line by itself.  This
changes the access level for any parameter defined in the file from that point on.

To access {\tt restricted} parameters from another implementation, a line
containing {\tt shares: <name>} declares that all parameters mentioned in
the file from now until the next access specification originate in 
implementation {\tt <name>}. Each of these parameters must be qualified by the initial token {\tt USES} or {\tt EXTENDS}, where
\begin{Lentry}
\item[{\tt USES}] indicates that the parameters range remains unchanged.
\item[{\tt EXTENDS}] indicates that the parameters range is going to be extended.
\end{Lentry}

In contrast to parameter declarations in other access blocks, the default
value must be omitted - it is impossible to set the default value of any
parameter not originating in this thorn.
For example, the following block adds possible values to the keyword
{\tt initial\_data} originally defined in the implementation {\tt einstein}, 
and uses the real parameter {\tt speed}.

\begin{verbatim}
shares:einstein

EXTENDS KEYWORD initial_data
{
  "bl_bh"         :: "Brill Lindquist black holes"
  "misner_bh"     :: "Misner black holes"
  "schwarzschild" :: "One Schwarzschild black hole"
}

USES CCTK_REAL speed

\end{verbatim}

Note that you must compile at least one thorn which implements {\tt einstein}.


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\subsection{The {\tt schedule.ccl}}
\label{subsec:schedule_ccl}
By default no routine of a thorn will be run.  The {\tt schedule.ccl} file
defines those that should be run and when they should be run.

The specification of this is via a schedule block which consists of
 lines of the form

\begin{verbatim}
schedule <name> at <time bin> [other options] 
{
  LANG:     <FORTRAN|C>
  STORAGE:  [group list]
  TRIGGERS: [group list]
  SYNC:     [group list]
} "A description"
\end{verbatim}
where {\tt <name>} is the name of the routine, and 

\begin{Lentry}

\item[{\tt <time bin>}] is one of
(in the following the initial {\tt CCTK\_} is optional):

\begin{Lentry}

\item [{\tt CCTK\_STARTUP}]
For routines run before the grid hierachy is set up, for example function
registration.

\item [{\tt CCTK\_PARAMCHECK}]
For routines which check parameter combinations, routines registered here
only have access to the grid size and the parameters.

\item [{\tt CCTK\_BASEGRID}]
Responsible for setting up coordinates etc.

\item [{\tt CCTK\_RECOVER}]
For recovery from checkpoint.

\item [{\tt CCTK\_INITIAL}]

For generating initial data.

\item [{\tt CCTK\_POSTINITIAL}]

Tasks which must be applied after initial data is created.

\item [{\tt CCTK\_CPINITIAL}]
For recovery of initial data from a checkpoint file.

\item [{\tt CCTK\_PRESTEP}]
Stuff done before the evolution step.

\item [{\tt CCTK\_EVOL}]      

The evolution step.

\item [{\tt CCTK\_POSTSTEP}]

Stuff done after the evolution step.

\item [{\tt CCTK\_CHECKPOINT}]
For checkpointing data

\item [{\tt CCTK\_ANALYSIS}]
For analysing data.

\item [{\tt CCTK\_TERMINATE}]
Called when cactus terminates.

\item [{\tt CCTK\_CONVERGENCE}]
Convergence stuff.

\end{Lentry}

%These time bins can be given in the {\tt schedule.ccl} file with
%or without the initial {\tt CCTK\_}, and in any case.
%[[ This is redundant. ]]

\item[{\tt STORAGE}] The {\tt STORAGE} keyword specifies any groups for 
which  memory should be
allocated for the duration of the routine.
The storage status reverts to its previous status after the 
routine returns.

\item[{\tt TRIGGERS}] {\tt TRIGGERS} is used when the routine is registered at {\tt ANALYSIS} --- 
this is a 
special time bin, a routine registered here will only be called if one of
the variables from a group in {\tt TRIGGERS} is due for output.

\item[{\tt SYNC}] 
The keyword {\tt SYNC} specifies groups of variables which should be
synchronised (that is, their ghostzones should be exchanged between 
processors) on exit from the routine. Specifying synchonisation of 
grid variables in {\tt schedule.ccl} is an alternative to calling the
function {\tt CCTK\_SyncGroup} from inside a routine. Using the {\tt SYNC}
keyword in the {\tt schedule.ccl} is the preferred method, since it 
provides the Flesh with more information about the behaviour of your code,
and in particular is a requirement for using a driver with adaptive mesh
refinement.

\item[{\tt other options}]
The `other options' allow finer grained control of the scheduling.  It is
possible to state that the routine must run {\tt BEFORE} or {\tt AFTER} 
another routine. It is also possible to schedule the routine under an
alias name by using {\tt AS <alias\_name>}.

\end{Lentry}

The {\tt LANG} keyword specifies the linkage of the scheduled routine
which determines how to call it from the scheduler.
C and Fortran linkage are possible here. C++ routines should be defined as
{\tt extern "C"} and registered as {\tt LANG: C}.

As well as schedule blocks it's possible to embed C style {\tt if/else} 
statements in the schedule.ccl.
These can be used to schedule things based upon the value of a parameter.

\vskip .5cm
{\bf Example I:}

The routine {\tt hydro\_predictor} is scheduled at {\em evolution}, after the 
routine {\tt metric\_predictor} and before {\tt metric\_corrector}, if
the parameter {\tt evolve\_hydro} has been set.
\begin{verbatim}

if(CCTK_Equals(evolve_hydro,''yes''))
{
  SCHEDULE hydro_predictor AT evol AFTER metric_predictor BEFORE metric_corrector 
  {
    LANG:     FORTRAN
    STORAGE:  hydro_variables
  } "Do a predictor step on the hydro variables"
}
\end{verbatim}

\vskip .5cm
{\bf Example II:}

The thorns {\tt WaveToy77} and {\tt WaveToyC} each provide a
routine to evolve the 3D wave equation: {\tt WaveToyF77\_Evolution} and
{\tt WaveToyC\_Evolution}. The routine names have to be different, so
that both thorns can be compiled at the same time, their functionlity
is identical though. Either one of them can then be activated at run
time  in the parameter file via {\tt ActiveThorns}.  

Since each evolution routine provides the same
functionality, it makes sense to schedule them under the common alias {\tt
WaveToy\_Evolution} to allow relative scheduling ({\tt
BEFORE/AFTER}) independent of the actual routine name (which may
change depending on the activation in the parameter file).

In both cases the group of variables {\tt scalarfield} are synchronised
across processes when the routine is exited.

\begin{verbatim}
schedule WaveToyF77\_Evolution AS WaveToy\_Evolution AT evol \\
{ \\
  LANG: Fortran \\
  STORAGE: scalartmps \\
  SYNC: scalarfield \\
} "Evolution of 3D wave equation" \\

schedule WaveToyC_Evolution AS WaveToy_Evolution AT evol
{
  LANG: C
  STORAGE: scalartmps
  SYNC: scalarfield
} "Evolution of 3D wave equation"
\end{verbatim}

The thorn {\tt IDScalarWave} schedules the routine {\tt WaveBinary}
after the alias {\em WaveToy\_Evolution}. It is scheduled independently of
the C or Fortran routine name.

\begin{verbatim}
schedule WaveBinary AT evol AFTER WaveToy_Evolution
{
  STORAGE: wavetoy::scalarevolve
  LANG:    Fortran
} "Provide binary source during evolution" 
\end{verbatim}

\subsubsection{Storage Outside of Schedule Blocks}

The keyword {\tt STORAGE} can also be used outside
of the schedule blocks to indicate that storage for these
groups should be switched on at the start of the run. Note that
the storage is only allocated in this way at the start,
a thorn could explicitly switch the storage off.




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\section{Naming Conventions for Source Files}
\label{nacofosofi}

The make system uses file extensions
to designate coding language. The following extensions can be handled:

\begin{center}
\begin{tabular}{|c|c|}
\hline
Extension & Coding Language \\
\hline
{\t .F} & Fortran90 fixed form \\
{\t .f} & (no preprocessing) Fortran90 fixed form\\
{\t .F90} & Fortran90 free form form\\
{\t .f90} & (no preprocessing) Fortran90 free form\\
{\t .F77} & Fortran77 \\
{\t .f77} & (no preprocessing) Fortran77\\
{\t .c} & C \\
{\t .cc} or {\t .C} & C++ \\
\hline
\end{tabular}
\end{center}

The following restrictions apply to file names:
\begin{itemize}
\item Currently all source files in different subroutines within a 
thorn must have distinct names.  We hope
to relax this in future.  Different thorns can have files with the same names. 
\end{itemize}

\section{Adding source files}

By default the CCTK looks in the {\tt src} directory of the thorn for source
files.

There are two ways in which to specify the sources.  The easiest is to use the 
{\tt make.code.defn} based method in which the CCTK does all the work, but you
may instead put a {\tt Makefile} in the {\tt src} directory and do everything
yourself.

\subsection{{\tt make.code.defn} based thorn building}
\label{sec:mabathbu}

This is the standard way to do compile your thorn's source files.
The Cactus make system looks for a file called {\tt make.code.defn} in that
directory (if there is no file called {\tt Makefile} in the {\tt src} directory).  At its simplest, this file contains two lines

\begin{itemize}
\item {\t SRCS = <list of all source files in this directory>}

\item {\t SUBDIRS = <list of all subdirectories, including subdirectories of subdirectories>}

\end{itemize}

Each subdirectory listed should then have a {\tt make.code.defn} file 
containing just a {\tt SRCS = } line, a {\tt SUBDIRS = } line will
be ignored.

In addition, each directory can have a {\tt make.code.deps} file, which,
for files in that directory, can contain additional make rules and dependencies
for files in that directory.  See the GNU Make documentation for complete details of the
syntax.

\subsection{{\tt Makefile} based thorn building}

This method gives you the ultimate responsibility.  
The only requirement is that
a library called {\tt \$NAME} be created by the {\tt Makefile}.

The makefile is passed the following variables
\begin{Lentry}

\item [{\tt \$(CCTK\_HOME)}]  the main Cactus directory

\item [{\tt \$(TOP)}] the configuration directory

\item [{\tt \$(SRCDIR)}] the directory in which the source files can be found

\item [{\tt \$(CONFIG)}]  the directory containing the configuration files

\item [{\tt \$(THORN)}]   the thorn name

\item [{\tt \$(SCRATCH\_BUILD)}]  the scratch directory where Fortran90 module
files should end up if they need to be seen by other thorns.

\item [{\tt \$(NAME)}]

\end{Lentry}

and has a working directory of {\tt <config>/build/<thorn\_name>} .

\subsection{Other makefile variables}

\begin{itemize}
\item CC
\item CXX
\item F90
\item F77
\item CFLAGS
\item CXXFLAGS
\item F90FLAGS
\item F77FLAGS
\item LD
\end{itemize}

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\chapter{Cactus Variables}
\label{sec:cava}

Cactus variables are sorted into {\tt groups}.  All variables in a group 
are of the same type, and have
the same attributes, and most Cactus operations act on a group as a whole.

Cactus variables are used instead of local variables for a number of reasons
\begin{itemize}
\item Cactus variables can be made visable to other thorns, allowing 
thorns to communicate and share data, 
\item Cactus  variables can be distributed and communicated
        between processors, allowing parallel computation, 
\item A database of Cactus variables, and their attributes, is held by
      the Flesh, and this information is used by thorns, for example for
      obtaining a list of variables for checkpointing, 
\item Many Cactus APIs and tools can only be used with Cactus variables,
\item Cactus provides features for error checking based on Cactus variables
      and their attributes.
\end{itemize}

The specification for a group declaration 
(fully described in Section~\ref{sec:in}) is, 

\begin{verbatim}
<data_type> <group_name> [TYPE=<group_type>] [DIM=<dim>] [TIMELEVELS=<num>] \
   [SIZE=<size in each direction>] [DISTRIB=<distribution_type>] \
   [GHOSTSIZE=<ghostsize>] [STAGGER=<stagger-specification>]
[{
   <variable_name>[,]<variable_name>
   <variable_name>
}] ["<group_description>"]
\end{verbatim}

Currently, the names of groups and variables must be distinct.

\section{Data Type}

Cactus supports integer, real, complex and character variables, in 
various different sizes.  (Sizes in the following refer to the number of 
bytes the type takes).

\begin{Lentry}
\item[INTEGER]
CCTK\_INT, CCTK\_INT2, CCTK\_INT4, CCTK\_INT8.  (CCTK\_INT defaults to being CCTK\_INT4).
\item[REAL]
CCTK\_REAL, CCTK\_REAL4, CCTK\_REAL8, CCTK\_INT16.  (CCTK\_REAL defaults to being CCTK\_REAL8).
\item[COMPLEX]
CCTK\_COMPLEX, CCTK\_COMPLEX8, CCTK\_COMPLEX16, CCTK\_COMPLEX32.  
(CCTK\_COMPLEX defaults to being CCTK\_COMPLEX16).
\item[BYTE]
This is a 1 byte data type.
\end{Lentry}

Normally a thorn should use the default types --- 
CCTK\_INT, CCTK\_REAL, CCTK\_COMPLEX --- rather than explicitly setting the size, as this gives maximum 
portability. Also, the defaults can be changed at configuration time,  and 
this allows people to compile the code with different precisions to test 
for round-off effects, or to run more quickly with a lower accuracy.

\section{Group Types}

Groups can be either {\tt scalars}, {\tt grid functions (GFs)}, or {\tt grid arrays}. Different attributes are relevant for the different group types.

\begin{Lentry}
\item[SCALAR] 
This is just a single number, e.g. the total energy of some field.  These
variables aren't communicated between processors --- what would be the
result of such communication ?
\item[GF]
This is the most common group type.  A GF is a an array with a 
specific size, set at run-time in the parameter file, which is distributed 
across processors.  All GFs have the same size, and the same number of 
ghostzones. Groups of GFs can also specify a dimension, 
number of timelevels, and stagger type.
\item[ARRAY]
This is a more general form of the GF.  Each group of arrays can have 
a distinct size and number of ghostzones, in addition to dimension, 
number of timelevels and stagger type.  
The drawback of using an array over a GF is that a lot of data about the
array can only be determined by function calls, rather than the 
quicker methods available for GFs.
\end{Lentry}

\section{Timelevels}

These are best introduced by an example using finite differencing, 
take the 1-D wave equation
\begin{equation}
\frac{\partial^2 \phi}{\partial t^2} = \frac{\partial^2 \phi}{\partial x^2} 
\end{equation}
To solve this by partial differences, one discretises the derivatives, to get
an equation relating the solution at different times.  There are many ways
to do this, one of which produces the following difference equation
\begin{equation}
\label{equation:difference}
\phi(t+\Delta t,x) -2\phi(t,x) +\phi(t-\Delta t,x) = \frac{\Delta t}{\Delta x^2} \lbrace{\phi(t,x+\Delta x) -2\phi(t,x) +\phi(t,x-\Delta x)}\rbrace
\end{equation}
which relates the three timelevels $t+\Delta t$, $t$, and $t-\Delta t$.  

Obviously the code could just use three variables, one for each timelevel.  
This turns out, however, to be inefficient as, as soon as the time is 
incremented to $t+\Delta t$, it would be necessary to copy data from the 
$t$ variable to the $t-\Delta t$ variable and from the $t+\Delta t$ variable 
to the $t$ variable.

To remove this extraneous copy, Cactus allows you to specify the number 
of timelevels used by your numerical scheme.  It then generates variables 
with the base name (e.g. {\tt phi}) suffixed by a qualifier for 
which timelevel is being referred to --- no suffix for the 
next timelevel, and {\tt \_p} for each previous timelevel.

The timelevels are rotated (by the driver thorn) at the start
of each evolution step, that is:
\begin{verbatim}
initial
poststep
analysis

loop:
  rotate timelevels
  t = t + dt
  it = it + 1
  prestep
  evolve
  poststep 
  analysis
\end{verbatim}

Timelevel rotation means that, for example,
{\tt phi\_p} now holds the values of the former {\tt phi},
and {\tt phi\_p\_p} the values of the former {\tt phi\_p}, etc.
Note that after rotation {\tt phi} is  undefined, and it's values should 
not be used until they have been updated.

All timelevels, except the current level, should be considered {\bf read-only} during evolution, that is their values should not be changed by thorns. 
The exception to this rule is for function initialisation, when the
values at the previous timelevels do need to be explicately filled out.



\section{Size and Distrib}

A Cactus array has a size set at runtime by parameters.  
This size can either be the global size of the array across all processors
({\tt DISTRIB=DEFAULT}), 
or, if {\tt DISTRIB=CONSTANT} the specified
size on {\bf each} processor.  
If the size is split across processors, the driver thorn is
responsible for assigning the size on each processor.

\section{Ghost Size}

Cactus is based upon a {\tt distributed computing} paradigm.  That is
the problem domain is split into blocks, each of which is assigned to a 
processor.  For 
hyperbolic and parabolic problems the blocks only need to communicate at the edges.

To illustrate this, take the example of the wave equation again, equation \ref{equation:difference}  
describes a possible time-evolution scheme.  On examination you can see that to
generate the data at the point ($t+\Delta t$, $x$) we need data from the four points
($t$, $x$), ($t-\Delta t$, $x$), ($t$, $x+\Delta x$) and ($t$, $x-\Delta x$) only.
Ignoring the points at $x$, which are obviously always available, you can see that the
algorithm requires a point on either side of the point $x$, i.e. this algorithm
has {\tt stencil size} 1.  Similarly algorithms requiring two points on either side
have stencil size 2, etc.  

Now, if you evolve the above scheme, it becomes apparent that at each iteration the number
of grid points you can evolve decreases by one at each edge (see figure \ref{fig:noghost}).

\begin{figure}[ht]
\begin{center}
\ifpdf
\else
\includegraphics[angle=0,width=8cm]{1dnoghost.eps}
\fi
\end{center}
%\caption[]{} 
% I know this figure is rubbish, but it's after 2am and I'll fix it up later.
\label{fig:noghost}
\end{figure}

At the outer boundary of the physical domain the data for the boundary point can be
generated by the boundary conditions, however at internal boundaries the data has to
be copied from the adjacent processor.  It would be inefficient to copy each point 
individually, so instead, a number of {\tt ghostzones} are created at the internal boundaries.
A ghostzone consists of a copy of the whole plane (in 3d, line in 2d, point in 1d) of the data 
from the adjacent processor.  I.e. the array on each processor is augmented with copies of
points from the adjacent processors, thus allowing the algorithm to proceed {\tt on the 
points owned by this processor} without having to worry about copying data.  Once the
data has been evolved one step, the data in the ghostzones can be exchanged (or 
{\tt synchronised}) between processors in one fell swoop before the next evolution step.
(See figure \ref{fig:withghost}.)  Note that you should have at least as many ghostzones as
your stencil-size requires.

\section{Staggering}

The staggering of a gridfunction or array describes the {\em physical} 
placement of that gridfunction relative to the supporting grid
structure. For example, a gridfunction does not have to 
be placed at the intersection 
of the ``grid lines''. It can moved by half a grid spacing in
any or all dimensions. In the latter case, it will be placed in
the center of a cell.  

The staggering of grid function is a pure {\em physical} property: 
the values will be calculated at a different position in physical
space. Still the indexing (or bookeeping)  is kept the same for all
types of staggerings: the indexing of the default unstaggered grids is 
used.

\vskip .25cm

{\bf Specifying the staggertype}

The type of staggering applied to a gridfunction can be specified in
the {\tt interface.ccl} file by the attribute {\tt stagger} (see
\ref{sec:in}). Cactus supports three kind of staggering
per dimension. The physical location of a gridfunction is shifted 
relative to the default position by adding the following values to the 
stagger attribute:
\begin{Lentry}
\item[{\tt M}] no staggering, default. Refers to the ``minus'' face
relative to  the default gridpoint. 
\item[{\tt C}] centre staggering. The physical location is offset by
half of the grid spacing in the positive direction (or to the right).
\item[{\tt P}] full staggerd. P refers to plus. The physical location
is offset by a full gridspacing in the positive direction (or the
right).
\end{Lentry}
For multi dimensional gridfunctions you concatenate the code
characters in xyz order. In picture xy we show four different
staggerings of a two dimensional grid functions. The solid black grid
circles show the default location of the grid functions at the
intersections of the grid lines. In (A) we show an additional grid
function of type {\tt stagger=MC}: no staggering in x direction,
center staggered in y direction. In (B) we have  {\tt stagger=CM} and
staggering each direction ({\tt stagger=CC}) is shown in (C). The full
staggering in (D) ({\tt stagger=PP}) obeyes the same rules, but is
rather unusual; included here for completeness. 

\begin{figure}[ht]
  \def\epsfsize#1#2{0.45#1}
\begin{center}
\ifpdf
\else
\includegraphics[angle=0,width=8cm]{staggering1.eps}
\fi
%  \centerline{\epsfbox{./staggering1.eps}}
\end{center}
\caption[]{\small {\bf Staggered gridpoints in 2D} for several
staggerings. (a) : {\tt MC}, (b): {\tt CM}, (c): {\tt CC}, (d): {\tt
PP}. Note that the staggering of gridfunctions does change its
index. The staggered gridpoints and the corresponding unstaggered
points (arrows) are accessed by the same indices.} 
\label{fig:stagger1}
\end{figure}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\chapter{Cactus Parameters}

Parameters are the means by which the user specifies the run-time behaviour of
the code.  The user specifies values for parameters in the parameter file, and
then the flesh validates these values against the ranges the thorn writers have
specified to be valid.  Once validated, parameters values are fixed, and cannot
be changed (unless the parameter is specified to be steerable, see below).

The full specification for a parameter decalaration is
\begin{verbatim}
[EXTENDS|USES] <parameter_type> <parameter name> "<parameter description>" 
{
  <PARAMETER_RANGES>
} <default value>
\end{verbatim}

\section{Types and Ranges}

Parameters can be of several types:

\begin{Lentry}
\item[Integer]  Can take any integral value
\item[Real] Can take any floating point value
\item[Keyword] Can have a value consisting of one of a choice of strings
\item[Boolean] Can be true or false (1, `t', `true', or 0, `f', `false').
\item[String] Can have any string value
\end{Lentry}

Each parameter can be validated against a set of allowed values or ranges, each 
of which has a description associated with it.  The type of range is determined 
by the type of parameter.

\subsection{Integer}

The range specification is of the form 

\begin{verbatim}

lower:upper:stride

\end{verbatim}

where {\em lower} and {\em upper} specify the lower and upper allowed
range, and {\em stride} allows numbers to be be missed out.

e.g.

\begin{verbatim}

1:21:2

\end{verbatim}

means the value must be between one and twenty-one (inclusive), and
must be of the form $1+2n$ where $n$ is an integer.

A missing end of range (or a `\*') implies negative or positive
infinity, and the default stride is one.
 
\subsection{Real}

The range specification is of the form 

\begin{verbatim}

lower:upper

\end{verbatim}

where {\em lower} and {\em upper} specify the lower and upper allowed
range.  A missing end of range (or a `\*') implies negative or positive
infinity.  The above is inclusive of the end-points.  A '(' (or ')')
before (or after) the lower (or upper) range specifies an open end-point.

\subsection{Keyword}

The range specification consists of a string, which will be matched in 
a case-insensitive manner.

\subsection{Boolean}

There is no range specification for this type of parameter.

\subsection{String}

The range is a POSIX regular expression.  On some machines you may be
able to use extended regular expressions, but this is not guaranteed
to be portable.

\section{Scope}

Parameters can be {\em GLOBAL}, {\em RESTRICTED}, or {\em PRIVATE}.
Global parameters are visible to all thorns.  A restricted parameters
are visible to any thorn which chooses to {\em USE} or {\em EXTEND}
it.  A private parameter is only visible to the thorn which declares
it.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\chapter{Scheduling}

Cactus contains a rule-based scheduling system, which determines which
routines from which thorn are run in which order.  The scheduler 
determines if the specifications are inconsistent, but does allow the
user to schedule a routine with respect to another routine which may not
exist.

The full specification for a schedule declaration is
\begin{verbatim}
schedule [GROUP] <function|schedule group name> AT|IN <time|schedule group name> \
                 [BEFORE|AFTER <item>] [WHILE <variable>] [AS <alias>]
{
  LANG: <language>
  [STORAGE:       <group>,<group>...]
  [TRIGGER:       <group>,<group>...]
  [SYNC:          <group>,<group>...]
  [OPTIONS:       <option>,<option>...]
} "Description of function| schedule group"
\end{verbatim}

This consists of a mandatory part, a set of options, and the main
body, referred to as the {\tt schedule block}.

Each schedule item is scheduled either {\em AT} a particular {\em
scheduling bin}, or {\em IN} a schedule {\em group}.

\section{Schedule Bins}

These are the main points at which scheduled functions are run.
These are listed in \ref{subsec:schedule_ccl}.

\section{Groups}

If the optional {\tt GROUP} specifier is used, the item is a schedule
group rather than a normal function.  Schedule groups are effectively
new, user-defined, schedule bins.  Functions or groups may be
scheduled {\em IN} these in the same way as they are scheduled {\em
AT} the main schedule bins.  (I.e. groups may be nested.)

\section{Schedule Options}
The options define various charactertics of the schedule item.

\begin{Lentry}
\item[BEFORE or AFTER]
These specify a function or group before or after which this item will 
be scheduled.
\item[WHILE]
This specifies a {\em CCTK\_INT} grid scalar which is used to control
the execution of this item.  If the grid scalar has a non-zero value
the schedule item will be executed, otherwise the item will be
ignored.  This allows iteration within the scheduler.
\item[AS]
This assigns a new name to a function for scheduling purposes.  This
is used, for instance, to allow a thorn to schedule something before
or after a routine from another implementation;  two thorns providing this
implementation can schedule a routine {\em AS} the same thing, thus
allowing other thorns to operate independently of which one is active.
\end{Lentry}

\section{The Schedule Block}

The schedule block specifies further details of the scheduled function or group.

\begin{Lentry}
\item[LANG]
This specifies the language of the routine.  Currently this is either
C or Fortran.
\item[{\tt STORAGE}] The {\tt STORAGE} keyword specifies groups for 
which  memory should be
allocated for the duration of the routine or schedule group.
The storage status reverts to its previous status after the 
\item[TRIGGER]
This is only used for items scheduled at {\em CCTK\_ANALYSIS}.  The
item will only be executed if output is due for at least one
variable in one of the listed groups.
\item[SYNC]
On exit from this item the ghost zones of the listed groups will be
exchanged.
\item[OPTIONS]
This is for miscellaneous options.  The only currently supported
option is {\em GLOBAL} which tells the driver that this routine does
not use a local grid, but instead uses global operations to process
data;  such a routine should only be called once however many
sub-grids the driver may have broken the problem into.
\end{Lentry}

\section{How Cactus Calls Scheduled Functions}

For each scheduled function called, the flesh performs a variety of jobs at entry and exit. 

On entry to a scheduled routine, if the routine is being called at the ANALYSIS timebin first a check is made to see if the routine should actually be called on this timestep. For this, all grid variables in the trigger groups for the routine are checked with all registered output methods to determine if it is time to output any triggers. The routine will only be called if at least one is due to be output. Routines from all other timebins are always called.

Next storage is assigned for any required variables, remembering the original state of storage.

The routine is then called, and on exit, any required grid variables are 
first synchronised. Following synchronization, any required output methods are called for the triggers. Finally, the storage of grid variables is returned to the original state.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\chapter{Writing a Thorn}

\section{Thorn Programming Languages}

When you start writing a new thorn, the first decision to make is
which programming language to use? The source code in Cactus thorns
can be written in any mixture of {\tt FORTRAN77}, {\tt FORTRAN90}, 
{\tt C} or {\tt C++}. The following points should be considered when 
choosing a language to work in
\begin{itemize}

\item All functions designed for application thorn writers are available
      in all languages, however some of interfaces for infrastructure 
      thorn writing are only available from {\tt C} or {\tt C++}.

\item If you are writing in {\tt FORTRAN}, use {\tt F77} is you want
      to distribute your code to people who may not be able to afford 
      to buy proprietory {\tt F90} compilers.

\item Stick to {\tt C} rather than {\tt C++}, unless you really need 
      features from {\tt C++}, this will help you with portability.

\end{itemize}

Whatever language you choose, if you want your thorn to be portable, and
compile and run on multiple platforms, stick to the standards and don't 
use machine dependent extensions.


\section{What the Flesh provides}

The flesh provides for thorns.
\begin{Lentry}
\item [{\tt Variables}]
\item [{\tt Parameters}]
\item [{\tt Cactus Functions}]

\begin{itemize}
  \item{} driver (parallelisation) utilities
  \item{} IO utilities
  \item{} Coordinates utilities
  \item{} Reduction utilities
  \item{} Interpolation utilities
  \item{} Information utilities
\end{itemize}
\end{Lentry}


\subsection{Fortran Routines}

Any source file using Cactus infrastructure should include 
the header file {\tt cctk.h} using the line
\begin{verbatim}
#include "cctk.h"
\end{verbatim}
(Fortran programmers should not be put of by this being a C style
header file, most Cactus files are run through a C preprocessor
before compilation)

\subsubsection{Variables}

Any routine using Cactus argument lists (for example all 
routines called from the scheduler) should include at the
top of the file the header
\begin{verbatim}
#include "cctk_Arguments.h"
\end{verbatim}

A Cactus macro {\tt CCTK\_ARGUMENTS} is defined for each thorn
to contain
\begin{itemize}
\item General information about the grid hierarchy, for example
      the number of grid points used. See Section \ref{sec:cava2} for a 
      complete list.
\item All the grid variables defined in the thorns {\tt interface.ccl}
\item All the grid variables required from other thorns as requested by
      the {\tt inherits} and {\tt friend} lines in the {\tt interface.ccl}
\end{itemize}
These variables must be declared at the start of the routine using
the macro {\tt DECLARE\_CCTK\_ARGUMENTS}. 

To pass the arguments to another routine in the same thorn use the macro 
{\tt CCTK\_PASS\_FTOF} in the calling routine, and again the macro 
{\tt CCTK\_ARGUMENTS} in the receiving routine.


\subsubsection{Parameters}

All parameters defined in a thorn's {\tt param.ccl} and all {\tt global} 
parameters appear as local variables in a thorn.  These variables are 
{\tt read only} and {\em changes should not be made to them}.  The effect of
changing a parameter is undefined (at best).

The parameters should be declared at the start of the routine
using them with the macro {\tt DECLARE\_CCTK\_PARAMETERS}

Any routine using Cactus parameters should include at
the top of the file the header
\begin{verbatim}
#include "cctk_Parameters.h"
\end{verbatim}

In Fortran, special care should be taken with string valued parameters.
This parameters are passed as C pointers, and can not be treated as
normal Fortran strings. To compare a string valued parameter and Fortran
string use the function {\tt CCTK\_Equals}. To print the value of a string 
valued parameter to screen, use the subroutine {\tt CCTK\_PrintString}.

\subsubsection{Fortran Example}

The Fortran routine {\tt MyFRoutine} is scheduled in the {\tt schedule.ccl} file,
doesn't use Cactus parameters, and calls another routine, in the same thorn,  
{\tt MyNewRoutine} which does use parameters. 
This routine needs to be passed an integer flag as 
well as the standard Cactus variables. The source file should look like

\begin{verbatim}
#include "cctk.h"
#include "cctk_Arguments.h"
#include "cctk_Parameters.h"

      subroutine MyFRoutine(CCTK_ARGUMENTS)

c     I'm very cautious, so I want to declare all variables
      implicit none 

      DECLARE_CCTK_ARGUMENTS

      integer flag

      flag = 1
      call MyNewRoutine(CCTK_PASS_FTOF,flag)

      return 
      end

      subroutine MyNewRoutine(CCTK_ARGUMENTS,flag)

      implicit none 

      DECLARE_CCTK_ARGUMENTS
      DECLARE_CCTK_PARAMETERS
      integer flag

c     Main code goes here

      return
      end
      
\end{verbatim}

\subsubsection{Cactus Fortran Functions}

Cactus Fortran functions, for example {\tt CCTK\_MyProc}, can
all be declared by adding before any executable code, the declaration

\begin{verbatim}
DECLARE_CCTK_FUNCTIONS
\end{verbatim}

\subsubsection{Fortran 90 Modules}

Fortran 90 modules should be included in a thorn's {\tt make.code.deps} file
(\ref{sec:mabathbu}) to ensure they are compiled before the
routines which use them. This is especially important for parallel 
building. For example, if a routine in {\tt MyRoutine.F} uses a module
in {\tt MyModule.F} add the line:
{\tt
\begin{verbatim}
$(SYS_OBJD)/MyRoutine.F.o:         $(SYS_OBJD)/MyModule.F.o  
\end{verbatim}
}

\subsubsection{The {\tt MOD} function}

The intrinsic function {\tt MOD} in Fortran takes two integer 
arguments, which should both be of the same type. This means
that it may be necessary to cast the arguements to {\it e.g}
{\tt INT} for some architectures. This can occur in particular
when a {\tt CCTK\_INT} parameter and the Cactus variable {\tt cctk\_iteration}
(which is declared to be {\tt INTEGER}) are used, 
in which case the correct code is
{\tt
\begin{verbatim}
MOD(cctk_iteration,INT(MyParameter))
\end{verbatim}
}

\subsection{C Routines}

Any source file using Cactus infrastructure should include 
the header file {\tt cctk.h} using the line
\begin{verbatim}
#include "cctk.h"
\end{verbatim}

\subsubsection{Variables}

Any routine using Cactus argument lists (for example all 
routines called from the scheduler) should include at the
top of the file the header
\begin{verbatim}
#include "cctk_Arguments.h"
\end{verbatim}

A Cactus macro {\tt CCTK\_ARGUMENTS} is defined for each thorn
to contain
\begin{itemize}
\item General information about the grid hierachy, for example
      the number of grid points on the processor. See Section \ref{sec:cava2} for a 
      complete list.
\item All the grid variables defined in the thorns {\tt interface.ccl}
\item All the grid variables required from other thorns as requested by
      the {\tt inherits} and {\tt friend} lines in the {\tt interface.ccl}
\end{itemize}
These variables must be declared at the start of the routine using
the macro {\tt DECLARE\_CCTK\_ARGUMENTS}. This macro should always be the
first line of the routine.

To pass the arguments to another routine in the same thorn use the macro 
{\tt CCTK\_PASS\_CTOC} in the calling routine, and again the macro 
{\tt CCTK\_ARGUMENTS} in the receiving routine.


\subsubsection{Parameters}

All parameters defined in a thorn's {\tt param.ccl} and all {\tt global} 
parameters appear as local variables in a thorn.  These variables are 
{\tt read only} and {\em changes should not be made to them}.  The effect of
changing a parameter is undefined (at best).

Any routine using Cactus parameters should include at
the top of the file the header
\begin{verbatim}
#include "cctk_Parameters.h"
\end{verbatim}

The parameters should be declared at the start of the routine
using them with the macro {\tt DECLARE\_CCTK\_PARAMETERS}

\subsubsection{Example}

The C routine "MyCRoutine" is scheduled in the {\tt schedule.ccl} file,
and uses Cactus parameters. The source file should look like
\begin{verbatim}
#include "cctk.h"
#include "cctk_Arguments.h"
#include "cctk_Parameters.h"

void MyCRoutine(CCTK_ARGUMENTS)
{
  DECLARE_CCTK_ARGUMENTS
  DECLARE_CCTK_PARAMETERS

  /* Here goes your code */
}
\end{verbatim}

\subsubsection{Complex variables}

Cactus supports complex grid variables, and since there is no 
complex data type in C, Cactus provides a number
of functions for manipulating complex numbers to mirror the 
functionality available in Fortran. These functions are {\tt CCTK\_Cmplx},
{\tt CCTK\_CmplxReal}, {\tt CCTK\_CmplxImag}, {\tt CCTK\_CmplxConjg},
{\tt CCTK\_CmplxAdd}, {\tt CCTK\_CmplxSub}, {\tt CCTK\_CmplxMul},
{\tt CCTK\_CmplxDiv}, {\tt CCTK\_CmplxExp}, {\tt CCTK\_CmplSin},
{\tt CCTK\_CmplxAbs}, {\tt CCTK\_CmplxLog}, {\tt CCTK\_CmplSqrt}. 


\subsubsection{Specifically for C Programmers}

Grid functions are held in memory as 1D C arrays. These are laid
out in memory as in Fortran. This means that the first index should
be incremented through most rapidly. As can be seen in the example
below.


Cactus provides
macros to find the 1D index which is needed from the multidimensional
indices which are usually used. There is a macro for each dimension of
grid function.  Below is an articifial example to demonstrate this
using the 3D macro {\tt CCTK\_GFINDEX3D}:
\begin{verbatim}
for (k=0; k<cctk_lsh[2]; k++)
{
  for (j=0; j<cctk_lsh[1]; j++)
  {
    for (i=0; i<cctk_lsh[0]; i++)
    {
      My3D_GF[CCTK_GFINDEX3D(cctkGH,i,j,k)] = i*j*k;
    }
  }
}
\end{verbatim}

Here, {\tt CCTK\_GFINDEX3D(cctkGH,i,j,k)]} expands to 

\begin{verbatim}
((i) + cctkGH->cctk_lsh[0]*((j)+cctkGH->cctk_lsh[1]*(k)))
\end{verbatim}

\subsection{Cactus Variables}
\label{sec:cava2}

The Cactus variables which are passed through the macros
{\tt CCTK\_ARGUMENTS}, etc are
\begin{Lentry}
\item [{\tt cctk\_dim}] An integer with the number of dimensions
      used for this grid hierarchy
\item [{\tt cctk\_lsh}] An array of {\tt cctk\_dim} integers
      with the local grid size on this processor
\item [{\tt cctk\_gsh}] An array of {\tt cctk\_dim} integers
      with the {\it global} grid size. 
\item [{\tt cctk\_delta\_time}] A {\tt CCTK\_REAL} with the timestep 
\item [{\tt cctk\_time}] A {\tt CCTK\_REAL} with the current time
\item [{\tt cctk\_delta\_space}] An array of {\tt cctk\_dim} {\tt CCTK\_REAL}s with
         the grid spacing in each direction
\item [{\tt cctk\_nghostzones}] An array of {\tt cctk\_dim} integers with
         the number of ghostzones used in each direction
\item [{\tt cctkGH}] A C pointer identifying the grid hierachy
\end{Lentry}

The following variables describe the location of the local
grid (e.g. the grid treated on a given processor) within 
the global grid.
\begin{itemize}
\item {\tt cctk\_lbnd} 
      An array of {\tt cctk\_dim} integers 
      containing the lowest index (in each direction) 
      of the local grid, as seen on the global grid. Note that these indices
      start from zero, so you need to add one when using them in
      Fortran thorns.
\item {\tt cctk\_ubnd} 
      An array of {\tt cctk\_dim} integers 
      containing the largest index (in each direction) 
      of the local grid, as seen on the global grid.  Note that these indices
      start from zero, so you need to add one when using them in
      Fortran thorns.
\item {\tt cctk\_bbox} 
      An array of 2*{\tt cctk\_dim} integers (in the order
	$[{\mbox{dim}}_0^{\mbox{min}}, \mbox{dim}_0^{\mbox{max}}, 
	{\mbox dim}_1^{\mbox{min}}, {\mbox dim}_1^{\mbox{max}}, \ldots]$),
      which indicate whether the boundaries are internal boundaries
      (e.g. between processors), or physical boundaries. A value of 1 indicates
      a physical (outer) boundary at the edge of the computational grid, 
      and 0 indicates an internal boundary. 
\end{itemize}

The following variable is needed for grid refinement methods
\begin{itemize}
\item {\tt cctk\_levfac} The factor by which the local grid is refined
        with respect to the base grid.
\end{itemize}

The following variable is used for identifing convergence levels. {\tt NOTE:} Convergence is not currently implemented by Cactus, so that {\tt cctk\_convlevel} is currently always 0.
\begin{itemize}
\item {\tt cctk\_convlevel} The convergence level of this grid hierachy. 
 	The base level is 0, and every level above that is currently coarsened 	       by a factor of 2.
\end{itemize}
 
The variables {\tt cctk\_delta\_space} and {\tt cctk\_delta\_time}
denote the grid spacings on the {\em base} grid. If you are using 
a grid refinement method, you need yo calculate the grid spacings
on the grid you are on. There are Cactus macros provided for this,
with the syntax {\tt CCTK\_DELTA\_SPACE(dir)} and {\tt CCTK\_DELTA\_TIME}
for both C and Fortran. It is recommended that these macros are
always used to provide the grid spacings in your thorns. 

\subsection{Cactus Data Types}

The Cactus grid variables and parameters are defined and
declared using Cactus data types, to provide portability 
across platforms. The most important of 
these data types are described below, for a full description
see Section~\ref{sec:datyansi}. These data types should 
be used to declare local variables where needed, and to
declare Cactus grid variables or parameters that need 
declarations. 

\begin{Lentry}

\item[{\tt CCTK\_INT}] default size 4 bytes
\item[{\tt CCTK\_REAL}] default size 8 bytes

\end{Lentry}

\subsubsection{Example}

In the following example {\tt MyScalar} is a grid scalar which
is declared in the {\tt interface.ccl} as {\tt CCTK\_REAL}.

\begin{verbatim}
      subroutine InitialData(CCTK_ARGUMENTS)

      DECLARE_CCTK_ARGUMENTS

      CCTK_REAL local_var
      
      local_var = 1.0/3.0      
      MyScalar = local_var

      return
      end 
\end{verbatim}

Declaring {\tt local\_var} to have a non-Cactus data type, e.g.
{\tt REAL*4}, or using one of the other Cactus real data types
described in Section~\ref{sec:datyansi} could give problems for 
different architectures or configurations.

\subsection{Staggering}
\label{sec:st}


{\bf Indexing, ghostzones, etc.}
Note that staggering does not make any changes to the indexing of a
gridfunction: the black solid circles in diagramm \ref{fig:stagger2} and their
associated staggered gridfunctions (connected by arrows) have the same index!

Since the gridfunction does not ``know'' anything about the physical
location (it's only addressed by indeces) why add staggering if the
indexing is the same ?  

Indeed, you could roll your own, but there compelling reasons:
Readabilty and you are able to query the staggertype of a
gridfunction. More important: in the way the grid is laid out, there is one grid
point {\em less} for {\tt M} and {\tt P} staggered grid functions. This is
illustrated in picture \ref{fig:stagger2}, which shows 15 gridpoints distributed
across 3 processors. The solid black cirlces show the default
location of the gridfunctions, the grey circles depict the ghostzones.
Note that the number of center staggered gridpoints (fat crosses)
corresponds to the number of default gridpoint on all processors but
the last one. (Same is true for full staggered gridpoints).

{\bf Staggertypes}
The string specifying the staggering is encoded in a number called
the {\em staggerindex}. With the 3 supported staggerings, the string
is converted into a base-3 number. Several routines exist, to extract the
staggering in a specific direction, called {\em directional
staggerindex}. E.g. {\tt stagger = MCM}: {\em staggerindex} = 3, in the 
x-direction: {\em directional staggerindex} = CCTK\_STAGGER\_M (value 0),  in the 
x-direction: {\em directional staggerindex} = CCTK\_STAGGER\_C (value 1).

\begin{Lentry}
\item[{\tt CCTK\_STAGGER\_M}]  value used for M-type staggering
\item[{\tt CCTK\_STAGGER\_C}]  value used for C-type staggering
\item[{\tt CCTK\_STAGGER\_P}]  value used for P-type staggering
\item[{\tt CCTK\_NO\_STAGGER}] value to indicate no staggering
\item[{\tt CCTK\_STAGGER}]    value to indicate staggering
\item[{\tt CCTK\_NSTAGGER}]   number of coded staggerings (3)
\item[{\tt CCTK\_STAGGER\_ERROR}] failed stagger operation , negative
\end{Lentry}


\begin{figure}[ht]
  \def\epsfsize#1#2{0.45#1}
\begin{center}
\ifpdf
\else
\includegraphics[angle=0,width=10cm]{staggering2.eps}
\fi
%  \centerline{\epsfbox{./staggering2.eps}}
\end{center}
\caption[]{\small {\bf Unstaggered and center-staggered gridpoints} with
ghostzone size of one (above) and two (below). The points are
distributed across three processors. Note that the number of  
center staggered gridpoints (fat crosses) is one less on the outermost grid. How to
treat this case in a easy way is explained below. }
\label{fig:stagger2}
\end{figure}

When a thorn programmer uses staggered gridpoints, he has to be aware
of this gridpoint anomaly. This can be done easiest by using the {\tt
CCTL\_LSSH(<dir\_staggertype>,<direction>)} macro. For a given staggertype
and direction, this 2d array returns the local number of gridpoints,
including  ghostzones and the necessary change for the staggering on
the outermost processor. 

\begin{Lentry}
\item[{\tt CCTL\_LSSH(<dir\_staggertype>,<direction>)}]
for a given staggertype and a direction this macro returns the number
of processor local gridpoints, including ghostzones. 

\begin{itemize}
\item{macro has to be in capital letters}
\item{This macro is C/Fortran indexing aware:
can specify the dimension in C ranging from $0 \ldots$ and in Fortan
ranging from $1 \ldots$.}
\end{itemize}
\end{Lentry}

\vskip .25cm

Several functions exist to derive the staggertype for a given group
and for a certain direction.
\begin{Lentry}
\item[{\tt int CCTK\_GroupStaggerIndexGI(int group\_index)}] returns the
{\em staggerindex} for a given group index. 
\item[{\tt call CCTK\_GroupStaggerIndexGI(int staggerindex, int
group\_index)}]  returns the {\em staggerindex} for a given group index. 
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_GroupStaggerIndexGN(char *group\_name)}] returns the
{\em staggerindex} for a given group name. 
\item[{\tt call CCTK\_GroupStaggerIndexGN(int staggerindex, char *group\_name)}] returns the
{\em staggerindex} for a given group name. \vskip .25cm
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_GroupStaggerIndexVI(int variable\_index)}] returns the
{\em staggerindex} for a given variable index. 
\item[{\tt call CCTK\_GroupStaggerIndexVI(int staggerindex, int variable\_index)}] returns the
{\em staggerindex} for a given variable index. 
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_GroupStaggerIndexVN(char *variable\_name)}] returns the
{\em staggerindex} for a given variable name. 
\item[{\tt call CCTK\_GroupStaggerIndexVN(int staggerindex, char *variable\_name)}] returns the
{\em staggerindex} for a given variable name. 
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_StaggerIndex(char *stagger\_string)}] return the {\em
staggerindex} for a given stagger string.
\item[{\tt call CCTK\_StaggerIndex(int staggerindex, char *stagger\_string)}] return the {\em
staggerindex} for a given stagger string. 
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_StaggerIndex(char *stagger\_string)}] return the {\em
staggerindex} for a given stagger string.
\item[{\tt call CCTK\_StaggerIndex(int staggerindex, char *stagger\_string)}] return the {\em
staggerindex} for a given stagger string.
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_DirStaggerIndex(int direction, char *stagger\_string)}] 
returns the {\em directional staggerindex} for a given direction and
stagger string.
\item[{\tt call CCTK\_DirStaggerIndex(int dir\_staggerindex, int direction, char *stagger\_string)}] 
returns the {\em directional staggerindex} for a given direction and
stagger string.
\end{Lentry}
\vskip .45cm

\begin{Lentry}
\item[{\tt int CCTK\_DirStaggerIndexI(int direction, char *stagger\_type)}]
returns the {\em directional staggerindex} for a given direction and 
staggerindex.
\item[{\tt call CCTK\_DirStaggerIndexI(int dir\_direction, char *stagger\_type)}]
returns the {\em directional staggerindex} for a given direction and 
staggerindex.

\end{Lentry}


\section{Parallelisation}
\label{seap}

The flesh itself does not actually set up grid variables. This 
is done by a {\it driver} thorn. To allow the distribution of 
a grid over a number of processors, the driver thorn must 
also provide the grid decomposition, and routines to enable 
parallelisation. The method used to provide this parallelisation
(e.g. MPI, PVM) is not usually important for the thorn writer since
the driver thorn provides routines which are called by standard interfaces
from the flesh. Here we describe briefly the most important of these routines
for the application thorn writer. A more detailed description
of these interfaces with their arguments, is given in the Function Reference
Guide.
A complete description of the
routines a driver thorn must provide will be provided in the 
Interface Thorn Writers guide. The standard driver thorn is 
currently {\tt PUGH} in the {\tt CactusPUGH} package, which 
is a parallel unigrid driver. 

\begin{Lentry}
\item[{\tt CCTK\_nProcs}] Returns the number of processors being used
\item[{\tt CCTK\_MyProc}] Returns the processor number (this starts at
  processor number zero
\item[{\tt CCTK\_SyncGroup}] Synchronises a group of variables by 
  exchanging the values held in each processor ghostzones with the
  physical values of their neighbours
\item[{\tt CCTK\_Barrier}] Waits for all processors to reach this point
  before proceeding
\end{Lentry}

\chapter{Cactus Application Interfaces}


\section{Coordinates}
\label{sec:co}

The flesh provides utility routines for registering and querying coordinate 
information. The flesh does not provide any coordinates itself, these must be
supplied by a thorn. Thorns are not required to register coordinates to the
flesh, but registering coordinates provides a means for infrastructure thorns,
to make use of coordinate information.

Coordinate support is still being developed in the Cactus flesh. At the moment,
it is assumed that coordinates will usually be grid functions. 

Coordinates are grouped into {\it coordinate systems}, which have a specified
dimension. Any number of coordinate systems can be registered with the flesh,
and a coordinate system must be registered before any coordinates can be
registered, since they must be associated with their corresponding system. 
Coordinates can be registered, with any chosen name, with an existing coordinate
system, along with their direction or index in the coordinate system.
Optionally, the coordinate can also be associated with a given grid variable.
A separate call can register the global range for a coordinate on a given grid
hierachy. 

A registered coordinate system can be refered to by both its name and an
associated handle. Passing such an integer handle instead of the name string
is necessary for calling C routines from Fortran.\\

The registration utilities for thorns providing coordinates are:
\begin{Lentry}

\item[{\tt CCTK\_CoordRegisterSystem}]

Assigns a coordinate system with a chosen name and dimension

\item[{\tt CCTK\_CoordRegisterData}]

Defines a coordinate in a given coordinate system, with a given 
	direction and name, and optionally associates it to a grid variable.

\item[{\tt CCTK\_CoordRegisterRange}]

Assigns the global maximum and minimum for a coordinate 
            	on a grid hierachy, that is in a {\tt cctkGH}.

\end{Lentry}

The utilities for thorns using coordinates are:

\begin{Lentry}

\item[{\tt CCTK\_CoordSystemDim}]

Provides the dimension of a coordinate system

\item[{\tt CCTK\_CoordSystemHandle}]

Provides the integer handle for a given coordinate system name

\item[{\tt CCTK\_CoordSystemName}]

Provides the name string for a given coordinate system handle

\item[{\tt CCTK\_CoordIndex}]

Provides the grid variable index for a given coordinate

\item[{\tt CCTK\_CoordDir}]

Provides the direction for a given coordinate

\item[{\tt CCTK\_CoordRange}]

Provides the global range of a coordinate on a given grid hierachy

\item[{\tt CCTK\_CoordLocalRange}]

Provides the local range of a coordinate on a processor for 
	a given grid hierachy. WARNING: This utility only currently works for regular cartesian grids!!

\end{Lentry}


\section{IO}
\label{sec:io}

To allow flexible IO, the flesh itself does not provide any output
routines, however it provides a mechanism for thorns to register
different routines as IO methods (see chapter \ref{chap:io_methods}).
Application thorns can interact with the different IO methods through
the following function calls:

\begin{Lentry}

\item[{\tt CCTK\_OutputGH (cGH *GH)}]

This call loops over all registered IO methods, calling the routine
that each method has registered for {\t OutputGH}.  The expected
behaviour of any {\t OutputGH} routine is to loop over all GH
variables outputting them if the IO method contains appropriate
routines (that is, not all methods will supply routines to output all
different types of variables) and if the method decides it is an
appropriate time to output.

\item[{\tt CCTK\_OutputVar (cGH *GH, const char *varname)}]

Output a variable {\t varname} looping over all registered IO methods.
The output should take place if at all possible.  If output goes into
a file and the appropriate file exists the data is appended, otherwise
a new file is created.

\item[{\tt CCTK\_OutputVarAs (cGH *GH, const char *varname, const char *alias)}]

Output a variable {\t varname} looping over all registered IO methods.
The output should take place if at all possible.  If output goes into
a file and the appropriate file exists the data is appended, otherwise
a new file is created.  Uses {\t alias} as the name of the variable
for the purpose of constructing a filename.

\item[{\tt CCTK\_OutputVarByMethod (cGH *GH, const char *varname, const char *methodname)}]

Output a variable {\t varname} using the IO method {\t methodname} if
it is registered. The output should take place if at all possible.  If
output goes into a file and the appropriate file exists the data is
appended, otherwise a new file is created.

\item[{\tt CCTK\_OutputVarAsByMethod (cGH *GH,
                                     const char *varname,
                                     const char *methodname,
                                     const char *alias)}]

Output a variable {\t varname} using the IO method {\t methodname} if
it is registered.  The output should take place if at all possible.
If output goes into a file and the appropriate file exists the data is
appended, otherwise a new file is created.  Uses {\t alias} as the
name of the variable for the purpose of constructing a filename.

\end{Lentry}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Interpolation Operators}
\label{sec:inop}

The flesh does not provide interpolation routines by itself. Instead
it offers a general function API to thorns for the registration and
invocation of interpolation operators.

Interpolation is done on arrays which can be either processor-local or
distributed among all processors in the computational domain. Thorns
can register an interpolation operator under a unique name as a set of
2 routines -- one for every array type. If an operator cannot handle
both types, the corresponding routine may be left unregistered. At
registration every interpolation operator gets assigned a unique
integer number which is used as a handle to refer to the operator
later on.

Separate flesh routines exist to invoke an interpolation operator for
either one of these types. The number of points to interpolate along
with their coordinates are passed in as well as necessary information
about the coordinate system to use for interpolation.  The flesh
routines take a variable list of input and output arrays as arguments
thus allowing operators to be optimized for interpolating multiple
arrays at the same coordinate points.\\

The flesh registration routines for interpolation operators are:
\begin{Lentry}
  \item[{\tt CCTK\_InterpRegisterOperatorGV}]
    Registers a user-supplied routine as an interpolation operator for
    distributed CCTK variables
  \item[{\tt CCTK\_InterpRegisterOperatorLocal}]
    Registers a user-supplied routine as an interpolation operator for
    processor-local arrays
\end{Lentry}

The flesh routines for invoking an interpolation operator are:
\begin{Lentry}
  \item[{\tt CCTK\_InterpHandle}]
    Provides the handle for a given interpolation operator
  \item[{\tt CCTK\_InterpGV}]
    Calls the operator associated with the given handle
    for interpolating a list of distributed CCTK variables
  \item[{\tt CCTK\_InterpLocal}]
    Calls the operator associated with the given handle
    for interpolating a list of processor-local arrays
\end{Lentry}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Reduction Operators}
\label{sec:reop}

A reduction operation can be defined as an operation on variables
distributed  across multiple processor resulting in a single number.
Typical reduction operations are: sum, minimum/maximum value, boolean
operations. A typical application is, for example, 
finding the maximum reduction from processor local error estimates, 
therefor making the previous processor local error known to all processors. 

The exchange of
information across processors needs the functionality of a
communication layer eg. {\tt CactusPUGH/PUGH}. For this reason, the
reduction operation itself is not part of the flesh, instead Cactus (again)
provides a registration mechanism for thorns to register routines they 
provide as reduction operators. The different operators are
identified by their name and/or a unique number, called a {\em handle}.

The registration mechanism gives the advantage of a common
interface while hiding the individual communication calls in the
layer.

In Cactus, reduction operators can in principle be applied to 
grid functions, arrays and scalars, as well as to local arrays. Note that 
different implementations of reduction operators may be limited in 
the objects they can be applied to.
There is a fundamental difference between the reduction operation on
grid functions and quantities as arrays.

\vskip .25cm

{\bf Obtaining the reduction handle}

Before calling the routine which performs the reduction operation,
the handle, which indentifies the operation must be derived from its
registered name.

\begin{verbatim}

int CCTK_ReductionHandle(const char *reduction_name);

integer       reduction_handle
character*(*) reduction_name
call CCTK_ReductionHandle(reduction_handle, reduction_name)


int CCTK_ReductionArrayHandle(const char *reduction_name);

integer       reduction_handle
character*(*) reduction_name
call CCTK_ReductionArrayHandle(reduction_handle, reduction_name)

\end{verbatim}


\vskip .25cm

\begin{Lentry}
\item[{\tt reduction\_handle}] 
In Fortran the name of the variable will
contain the handle value after the call. In C this value is the
function value.
\item[{\tt reduction\_name}] 
is the name under which the operator has
been registered by the providing thorn. The only thorn in the standard
Computational Toolkit release which provides reduction operators is
{\tt CactusPUGH/PUGHReduce}.
\item[{\bf error checking}] 
negative handle value indicates failure to
identify the correct operator. 
\end{Lentry}

Get a integer handle corresponding to a given reduction operator.
The operator is identified by the name it was registered with.
(Note that although it would appear to be far more convenient to 
pass the name of the reduction operator directly to the following
function call to {\t CCTK\_Reduce} this causes problems with the
translation of strings from {\t FORTRAN} to {\t C} with variable
argument lists).

\vskip 0.25cm


{\bf The general reduction interface}
The main interfaces for reduction operations are quite powerful (and
hence rather complicated) To ease the use of these main interfaces, wrappers
designed for specific and more restricted use are described below. If 
uncertain, you should use these.

{\t
\begin{verbatim}

int CCTK_Reduce(  cGH *GH, 
                  int proc,
                  int operation_handle,
                  int num_out_vals,
                  int type_out_vals,
                  void *out_vals,
                  int num_in_fields,
                  ...);


call CCTK_Reduce( int returnvalue, 
                  cctkGH, 
                  int processor,
                  int operation_handle,
                  int num_out_vals,
                  int type_out_vals,
                  out_vals,
                  int num_in_fields,
                  ... )

int CCTK_ReduceArray(  cGH *GH,
                       int proc,
                       int operation_handle,
                       int num_out_vals,
                       int type_out_vals,
                       void *out_vals,
                       int num_dims,
                       int num_in_arrays,
                       int type_in_arrays,
                       ... )

call CCTK_ReduceArray(int returnvalue,
                      cctkGH,
                      int processor,
                      int operation_handle,
                      int num_out_vals,
                      int type_out_arrays,
                      void out_vals,
                      int num_dims,
                      int num_in_arrays,
                      int type_in_arrays,
                      ... )
\end{verbatim}
}

\begin{Lentry}
\item[{\tt int returnvalue}] 
the return value of the operation. negative
value indicates failure to perform reduction.
Zero indicates successfull operation.
\item[{\tt cctkGH}]
in fortran the pointer to the grid hierachy
structure. Cannot be used within Fortran but
can be used from within 
C. Since this name is fixed write it out shown
above.
\item[{\tt cGH *GH}]
 in the C the pointer to the grid hierarchy.
\item[{\tt int processor}] 
the processor which collects the
information, negative value ($-1$) will distribute the data to all
processors.
\item[{\tt int operation\_handle}] the number of the reduction operation
                handle, needs to be found by calling {\tt CCTK\_ReductionHandle} or
                {\tt CCTK\_ReductionArrayHandle}.
\item[{\tt int num\_out\_vals}] integer defining the number of ??
\item[{\tt int type\_out\_arrays}, {\tt type\_in\_arrays}] 
specifies the type of the gridfunction 
you are communicating. Use the values as specified in
\ref{sec:datyansi}. Note: do not {\em mix} datatypes: e.g. in
Fortran do not declare a variable as {\tt integer} and then specify  
the type {\tt CCTK\_VARIABLE\_INT} in the reduction command. These
types need not be the same on some architectures and will conflict.
\item[{\tt out\_vals}]
\item[{\tt int num\_in\_fields}] specifies the number of  to follow
\item[{\tt ...}] indicates a varible argument list: specify the size
of the array in each dimension, comma separated numbers or integer
variables. Specify the arrays which will be reduced, the number of
specified arrays must be the same as the value of the {\tt
num\_in\_fields} variable.
\item[{\bf error checking}] a return value other than zero indicates
failure to perform the operation.
\end{Lentry}

\vskip 0.25cm


{\bf Special reduction interfaces}

The routines are designed for the purpose of reducing scalars, arrays
and grid functions. They hide many of the options of the generic
interface described above.\\

{\bf Reduction of local scalars} across multiple processors, the result of 
the reduction operation will be on the specified processor or on all processors.

{\t
\begin{verbatim}
int CCTK_ReduceLocScalar (cGH *GH, 
                          int processor, 
                          int operation_handle,
                          void *in_scalar, 
                          void *out_scalar, 
                          int data_type)

call CCTK_ReduceLocScalar(int returnvalue,
                          cctkGH,
                          int processor,
                          int operation_handle,
                          in_scalar,
                          out_scalar,
                          int data_type)
\end{verbatim}
}
\begin{Lentry}
\item[{\tt in\_scalar}] the processor local variable with local value to be reduced
\item[{\tt out\_scalar}] the reduction result: a processor local variable 
with the global value (same on all procs) if {\tt processor} has been
set to $-1$. Otherwise {\tt processor} will hold the reduction result.
\item[{\tt data\_type}]
specifies the type of the gridfunction 
you are communicating. Use the values as specified in
\ref{sec:datyansi}.
\end{Lentry}

\vskip 0.25cm

{\bf Reduction of local 1d arrays} to a local arrays, this reduction is carried
out element by element. The arrays need to have the same size on all
processors.
{\t
\begin{verbatim}
int CCTK_ReduceLocArrayToArray1D( cGH *GH, 
                                  int processor,
                                  int operation_handle,
                                  void *in_array1d, 
                                  void *out_array1d, 
                                  int xsize)
                                  int data_type)

call CCTK_ReduceLocArrayToArray1D( int returnvalue
                                  cctkGH,
                                  int processor,
                                  int operation_handle,
                                  in_array1d,
                                  out_array1d,
                                  int xsize,
                                  int data_type)
\end{verbatim}
}

\begin{Lentry}
\item[{\tt in\_array1d}] one dimensional local arrays, to be reduced across a 
processors, element by element. 
\item[{\tt out\_array1d}] array holding the reduction result. out\_array1d[1]
= Reduction(in\_array[1]).
\item[{\tt xsize}] the size of the one dimensional array.
\end{Lentry}

\vskip 0.25cm

{\bf Reduction of local 2d arrays} to a local 2d array, this reduction is carried
out element by element. The arrays need to have the same size on all
processors.
{\t
\begin{verbatim}
int CCTK_ReduceLocArrayToArrayD( cGH *GH,
                                 int processor,
                                 int opertaion_handle,
                                 in_array_2d,
                                 out_array2d,
                                 int xsize,
                                 int ysize,
                                 int data_type)
                                 

call CCTK_ReduceLocArrayToArray2D( int returnvalue
                                   cctkGH,
                                   int processor,
                                   int operation_handle,
                                   in_array2d,
                                   out_array2d,
                                   int xsize,
                                   int ysize,
                                   int data_type)
                                 
\end{verbatim}
}

\begin{Lentry}
\item[{\tt in\_array1d}] two dimensional local arrays, to be reduced across a 
processors, element by element. 
\item[{\tt out\_array1d}] two dimensional array holding the reduction
result. out\_array2d[i,j]= Reduction(in\_array2d[i,j]).
\item[{\tt xsize}] the size of the one dimensional array in x direction.
\item[{\tt ysize}] the size of the one dimensional array in y direction.
\end{Lentry}

\vskip 0.25cm

{\bf Reduction of local 3d arrays} to a local 3d array, this reduction is carried
out element by element. The arrays need to have the same size on all
processors.
{\t
\begin{verbatim}
int CCTK_ReduceLocArrayToArray3D(cGH *GH,
                                 int processor,
                                 int opertaion_handle,
                                 in_array_3d,
                                 out_array3d,
                                 int xsize,
                                 int ysize,
                                 int zsize,
                                 int data_type)

call CCTK_ReduceLocArrayToArray3D(int returnvalue
                                 cctkGH,
                                 int processor,
                                 int operation_handle,
                                 in_array3d,
                                 out_array3d,
                                 int xsize,
                                 int ysize,
                                 int zsize,
                                 int data_type)
\end{verbatim}
}

\begin{Lentry}
\item[{\tt in\_array3d}] two dimensional local arrays, to be reduced across a 
processors, element by element. 
\item[{\tt out\_array3d}] two dimensional array holding the reduction
result. out\_array3d[i,j,k]= Reduction(in\_array3d[i,j,k]).
\item[{\tt xsize}] the size of the one dimensional array in x direction.
\item[{\tt ysize}] the size of the one dimensional array in y direction.
\item[{\tt ysize}] the size of the one dimensional array in z direction.
\end{Lentry}

\vskip .25cm

{\bf Some brief examples:}

{\bf Reduction of a local scalars:} a local error is reduced across all
processors wiht the maximum operation. The variable {\tt tmp} will
hold the maximum of the error and  is the same on all
processors. This quantity can then be reassigned to {\tt normerr}.
\begin{verbatim}
         CCTK_REAL normerr, tmp
         integer   ierr, reduction_handle

         call CCTK_ReductionArrayHandle(reduction_handle,"maximum")

         if (reduction_handle.lt.0) then
            call CCTK_WARN(1,"Cannot get reduction handle for maximum operation.")
         endif

         call CCTK_ReduceLocScalar(ierr, cctkGH, -1, 
     .             reduction_handle,
     .             normerr, tmp, CCTK_VARIABLE_REAL)
         if (ierr.ne.0) then
            call CCTK_WARN(1,"Reduction of norm failed!");
         endif
         normerr = tmp
\end{verbatim}


{\bf Reduction of a local 2d array:} a two dimensional array $(2x3)$ is 
rdeuced, reduction results (aray of same size: {\tt bla\_tmp}) is seen
on all processors ($-1$ entry as the thid argument); also demonstrates
some simple error checking with the {\tt CCTKi\_EXPECTOK} macro.
\begin{verbatim}
      CCTK_REAL bla(2,3),bla_tmp(2,3);
      integer   ierr, sum_handle

      call CCTK_ReductionArrayHandle(sum_handle,"sum")
      bla         =  1.0d0
      write (*,*) "BLA ",bla

      call CCTK_ReduceLocArrayToArray2D(ierr, cctkGH, -1, sum_handle,
     .     bla, bla_tmp, 2, 3, CCTK_VARIABLE_REAL)
      call CCTKi_EXPECTOK(ierr, 0, 1, "2D Reduction failed")

      bla = bla_tmp
      write (*,*) "BLA ",bla
\end{verbatim}

Note that the memory for the returned values must be allocated before
the reduction call is made.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\chapter{Completing a Thorn}

\section{Commenting Source Code}

Note that since most source files (see Section~\ref{nacofosofi} for
exceptions) pass through a C preprocessor, C style comments can be
used in Fortran code. (Note that C++ comments (that is //), 
should only be used in C++ source code).

The Flesh and the Cactus thorns use the {\tt grdoc} Code Documenting System
({\tt http://jean-luc.aei.mpg.de/Codes/grdoc/} to document source code.


\section{Providing Run Time Information}
\label{sec:prrutiin}

To write from thorns to standard output ({\it i.e.} the screen) 
at runtime, use the function {\tt CCTK\_INFO}. 
For example, from the Fortran thorn {\tt MyThorn},

{\tt 
call CCTK\_INFO("Starting Tricky Calculation")
}

will write the line:

{\tt
INFO (MyThorn): Starting Tricky Calculation
}

For a multiprocessor run, only information from processor zero 
will appear, unless the "{\tt -r"} command line option is used 
(Section~\ref{sec:coliop}).

To output a variable using {\tt CCTK\_INFO} is currently more tricky,
since you need to build the string to be output. For example, from Fortran,

{\tt
character*200 infoline\\
write(infoline,'(A,1X,I)') 'The integer was ',inum\\
call CCTK\_INFO(infoline)
}

and from C

{\tt
char *infoline;\\
infoline = (char *)malloc(18*sizeof(char));\\
sprintf(infoline,'The integer was \%d',inum);\\
CCTK\_INFO(infoline);\\
free(infoline);
}

Note that:
\begin{itemize}
\item{} {\tt CCTK\_INFO} is actually a macro for the function
        {\tt CCTK\_Info(<thorn name>,<message>)} which automatically
        includes the thorn name.

\item{} {\tt CCTK\_INFO} should be used rather than print statements,
       since it will give consistent behaviour on multiprocessors, and
       also provides a mechanism for switching the output to screen on 
       and off, even on a thorn-by-thorn basis. (Although this is 
       not yet implemented).

\item{}  The function {\tt CCTK\_VInfo}, available in C only,
         can be used to output a list of variables, using a C format string.
         For example, the above example becomes

{\tt
CCTK\_VInfo(CCTK\_THORNSTRING,'The integer was \%d',inum);
}

\end{itemize}



\section{Error handling, warnings and code termination}
\label{sec:erhawancote}
The Cactus function {\tt CCTK\_WARN} should be used to provide
warning messages during code execution. Along with the
warning message, an integer is given to indicate the severity
of the warning. The warning severity indicates whether the
message is printed to standard output and whether the code
should be stopped. A level 0 warning indicates the highest
severity, with higher numbers indicating lower severity.

By default, a Cactus run will abort on a level 0 warning
and will report level 1 and severer warnings to screen. 
This behaviour can be amended using command line arguments,
as described in Section~\ref{sec:coliop}.

For example, to provide a warning which will be printed to standard
output but which will not terminate the code for a run with default
options, a level 1 warning should be used. The syntax from Fortran is
{\tt
\begin{verbatim}
call CCTK_WARN(1,"Your warning message")
\end{verbatim}
}
or from C,
{\tt
\begin{verbatim}
CCTK_WARN(1,"Your warning message");
\end{verbatim}
}

Note that {\tt CCTK\_WARN} is actually a macro which automatically 
expands to include the name of the thorn, the source file name and line 
number of the error. (For this reason it is important that capital letters are
always used for the function). If the flesh parameter {\tt cctk\_full\_warnings} is
set to true, then the source file name and line number will be printed to
standard output along with the thorn name and warning.

To include variables in warning messages is more troublesome. From C, the
variable argument list
function {\tt CCTK\_VWarn} can be used to include variables using standard printf format strings. Unfortunately, a macro can no
longer be provided to automatically include the origin details of the warning,
and the syntax is for example,
{\tt
\begin{verbatim}
CCTK_VWarn(1,__LINE__,__FILE__,CCTK_THORNNAME,
  "Your warning message, including %f and %d",
  myreal,myint);
\end{verbatim}
}
To include variables from Fortran, a string must be constructed and passed
to the standard function {\tt CCTK\_WARN}, for example
{\tt
\begin{verbatim}
 character*200 warnline
 write(warnline,'(A32,G12.7,A5,I8)') 
&  'Your warning message, including ',myreal,' and ',myint
 call CCTK_WARN(1,warnline)
\end{verbatim}
}

The flesh will be implementing standard error return codes
which can be used by the thorns, although this is not 
yet ready. In general, thorns should attempt to handle errors
without terminating, and warning messages should be liberally
used.
      



\section{Adding documentation}

To include documentation from your thorn into the {\tt ThornGuide}
(obtained from using {\tt gmake <config>-ThornGuide} or 
{\tt gmake ThornGuide}), include a {\tt LaTeX} file called {\tt documentation.tex}
in the {\tt doc} directory as your thorn. Your thorn configuration 
files will be automatically parsed to create documentation for 
Cactus parameters, variables and scheduling. The format 
for the thorn documentation isn't standardized yet, for now please use
the following format:
\begin{verbatim}
\documentclass{article}

\begin{document}

\title{<Thorn Name>}
\author{<Authors>}
\date{<Date>}
\maketitle

\abstract{<The Abstract>}

\section{Purpose}

\section{<Whatever You Want}

<Thorn Documentation>

% Automatically created from the ccl files by using gmake ThornGuide
\include{interface}
\include{param}
\include{schedule}

\end{document}
\end{verbatim}

\section{Adding a test suite}
\label{sec:adatesu}

To add a test suite to your thorn, devise a series of parameter
files which use as many aspects of your thorn as possible. 
Make sure that the parameter files produce ascii output to files,
and that these files are in the directory 
{\tt ./<parameter file base name>}.

Run Cactus on each of the parameter files, and move the parameter files,
and the output directories they produced, to the {\tt test} directory
in your thorn. 

Document carefully any situations or architectures in which your test 
suite does not give the correct answers. 

For details on running the test suites, see Section~\ref{sec:te}.




\chapter{Advanced Thorn Writing}

\section{Using Cactus Timers}

\subsection{What are timers?}

Cactus Timers can only currently be used in C or C++ source code,
although the API's for Fortran code are currently being added [FIXME].

The standard timing information available during a simulation was
described in Section~\ref{????}. [FIXME: This isn't filled in yet
because it is being reworked] Cactus provides a flexible mechanism for
timing different sections of your thorns using various clocks which
have been registered with the Flesh.  By default, the Flesh provides a
set of clocks (if they are available), measuring for
example wall clock time and CPU time. Additional clocks can be 
implemented by thorns and registered with the Flesh (see
Section~\ref{????} [FIXME: clock registration to be added]
on how to write and register your own clock).

You can add any number of timers to your thorn source code, providing
each with a chosen name, for example {\tt TimeMyRoutine}, {\tt TimeNextCalculation}, and then use Cactus functions to switch on the
timers, stop or reset them, and recover timing information.

Note that we use the word {\it Clock} to describe the timing instrument
itself, for example the hardware counters on a machine, and the word
{\it Timer} to describe the calls in your code which collect results
from the different {\it Clocks}.

\subsection{Timing calls}

\begin{Lentry}

\item[{\t CCTK\_TimerCreate}, {\t CCTK\_TimerCreateI}]

Create a timer with a given name ({\t CCTK\_TimerCreate}), or with no name
({\tt CCTK\_TimerCreateI})  and give back a timer index. 
If no name is provided for the timer, future calls 
should be made using the returned timer index.

\item[{\t CCTK\_TimerDestroy}, {\t CCTK\_TimerDestroyI}]

Destroy a timer using either the timer name or timer index. 

\item[{\t CCTK\_TimerStart}, {\t CCTK\_TimerStartI}]

Start the given timer (identified by name or index), using all registered
clocks. 

\item[{\t CCTK\_TimerStop}, {\t CCTK\_TimerStopI}]

Stop the given timer (identified by name or index) on all registered clocks.

\item[{\t CCTK\_TimerReset}, {\t CCTK\_TimerResetI}]

Reset the given timer on all registered clocks.

\item[{\t CCTK\_TimerCreateData}, {\t CCTK\_Timer}, {\t CCTK\_TimerI}, {\t CCTK\_TimerDestroyData}]

Access the actual timing results, which are passed back as a 
structure, {\t cTimerData} described below, in {\t CCTK\_Timer}. 
Since the timing data is dynamic, before it can be assessed, the structure 
must be allocated with a call to {\t CCTK\_TimerCreateData}. A similar function
is provided to destroy the stucture

\item[{\t CCTK\_NumTimers}]

Return the number of created timers

\item[{\t CCTK\_TimerName}]

Provide the name of the timer for a given timer index

\end{Lentry}

\subsection{The {\tt cTimerData} Structure}

The structure holding the timing data, {\tt cTimerData}, contains
the number of collected times (one measurement for each registered clock),
and the measured time for each clock. The measured time is held in 
a structure of type {\tt cTimerVal} which contains the data type 
of the measured value, a description of the clock, and the units used
for the measurements. Hopefully additional interfaces will soon be added
to avoid detailed knowledge of these structures, but for now here are
the gory details:

{\tt
\begin{verbatim}
typedef enum {val_none, val_int, val_long, val_double} cTimerValType;

typedef struct
{
  cTimerValType type;
  const char *heading;
  const char *units;
  union
  {
    int        i;
    long int   l;
    double     d;
  } val;
} cTimerVal;

typedef struct
{
  int n_vals;
  cTimerVal *vals;
} cTimerData;
\end{verbatim}
}

\subsection{How to insert timers in your code}

The function prototypes and structure definitions are contained in the
include file {\tt cctk\_Timers.h}, which is included in the standard
thorn header file {\tt cctk.h}. At the moment the timer calls are only
available from C.

The following example, which uses a timer called {\t TimeMyStuff} to
instrument a section of code, illustrates how timers are used by
application thorns. A working example is available in the thorn {\tt
CactusTest/TestTimers}.

{\bf Creating the {\t TimeMyStuff} timer}

The first action for any timer is to create it, using {\t
CCTK\_TimerCreate}.  This can be performed at any time, as long as it
precedes using the timer: 
{\tt
\begin{verbatim}
#include "cctk_Timers.h"
ierr = CCTK_TimerCreate(`TimeMyStuff`);
\end{verbatim}
}

{\bf Instrumenting a section of code}

Code sections are instrumented using the Start, Stop and Reset functions. These
functions are applied to the chosen timer using all the registered clocks.
{\tt
\begin{verbatim}
#include "cctk_Timers.h"
ierr = CCTK_TimerStart(`TimeMyStuff`);
\* Piece of code to time *\
y = CalculateNewValue(y);
ierr = CCTK_TimerStop(`TimeMyStuff`);
\end{verbatim}
}

{\bf Accessing the timer results}

This is a little bit cumbersome at the moment, since the timer data can be
of different types.

{\tt
\begin{verbatim}
#include "cctk_Timers.h"
cTimerData *info;

info = CCTK_TimerCreateData();
ierr = CCTK_Timer('TimeMyStuff',info);

for (i = 0; i < info->n_vals; i++)
{
  switch (info->vals[i].type)
  {
    case val_int:
    printf("%s: %d %s", info->vals[i].heading,info->vals[i].val.i, 
                        info->vals[i].units);
    break;

    case val_long:
    printf("%s: %d %s", info->vals[i].heading,(int) info->vals[i].val.l, 
                        info->vals[i].units);
    break;

    case val_double:
    printf("%s: %.3f %s", info->vals[i].heading,info->vals[i].val.d, 
                          info->vals[i].units);
    break;

    default:
    CCTK_WARN(1, "Unknown data type for timer info");
    break;
  }
}
ierr = CCTK_TimerDestroyData(info);
\end{verbatim}
}  


\section{Include Files}

Cactus provides a mechanism for thorns to add code to 
include files which can be used by any other thorn.
Such include files can contain executable source code, or header/declaration
information. A difference is made between these two cases, since included
executable code is protected from being run if a thorn is compiled but
not active by being wrapped by a call to {\tt CCTK\_IsThornActive}. 


Any thorn 
which uses the include file must declare this in its 
{\tt interface.ccl} with the line

\begin{verbatim}
USES INCLUDE [SOURCE|HEADER]: <file_name>
\end{verbatim}

Any thorn which wishes to add to this include file, 
declares in its own {\tt interface.ccl}

\begin{verbatim}
INCLUDE [SOURCE|HEADER]: <file_to_include> in <file_name>
\end{verbatim}

\subsubsection{Example}

For an example of this in practice, for the case of Fortran code, 
consider thorn A which
wants to gather terms for a calculation from any thorn
which wishes to provide them. Thorn A could have
the lines in its source code

\begin{verbatim}
c Get source code from other thorns
      allterms = 0d0
#include "AllSources.inc"
\end{verbatim}
and would then add to {\tt interface.ccl} the line
\begin{verbatim}
USES INCLUDE SOURCE: AllSources.inc
\end{verbatim}

If thorn B wants to add terms for the calculation, it would
create a file, say {\tt Bterms.inc} with the lines
\begin{verbatim}
c Add this to AllSources.inc
      allterms = allterms + 1d0
\end{verbatim}
and would add to its own {\tt interface.ccl}

\begin{verbatim}
INCLUDE SOURCE: Bterms.inc in AllSources.inc
\end{verbatim}

The final file for thorn A  which is compiled will contain the code
\begin{verbatim}
c Get source code from other thorns
      allterms = 0d0
      if (CCTK_IsThornActive("B").eq.0) then
c Add this to AllSources.inc
        allterms = allterms + 1d0       
      end if
\end{verbatim}

Any Fortran thorn routines which include source code must include 
the declaration {\tt DECLARE\_CCTK\_FUNCTIONS}.


\section{Memory Tracing}
\label{sec:metr}

Cactus provides a mechanism for overriding the standard C memory
allocation routines ({\tt malloc, free,} \ldots) with Cactus specific
routines, that track the amount of memory allocated and from where the
allocation call was made. This information can be accessed by the user
to provide an understanding of the memory consumption between two
instances and to track down possible memory leaks. This feature is
available in C only.

\subsection{Activating Memory Tracing}
\label{sec:acmetr}

Memory tracing has to be activated at configure time. The standard
malloc statements are overriden with macros ({\tt CCTK\_MALLOC}).  To
activate memory tracing use either

\begin{Lentry}
\item[{\tt DEBUG=all}]  Enables all debug options (compiler debug
flags, redefines malloc)
\item[{\tt DEBUG=memory}] Redefine malloc only.
\end{Lentry}

The {\tt CCTK\_MALLOC} statements can also be used directly in the C
code. But by employing them this way, only a fraction of the total
memory consumption is traced. Also, they cannot be turned off at
configure time. (this behavior might change). For example:
\begin{verbatim}
machine> gmake bigbuild DEBUG=yes
 
machine> gmake bigbuild-config DEBUG=memory
\end{verbatim}
The new configuration {\tt bigbuild} is configured with all debugging
features turned on. The already existing configuration {\tt bigbuild}
is reconfigured with memory tracing only.

\subsection{Using Memory Tracing}
\label{sec:usmetr}

You can  request Cactus to store the memory consumption at a certain
instance in the program flow and return the difference in memory
allocation some time later.

\begin{Lentry}
\item[{\tt int CCTK\_MemTicketRequest(void)}]
	Request a ticket: save the current total memory to a database.
	Return an integer (ticket). Use the ticket to calculate the
	difference in memory allocation between the two instances in
 	CCTK\_MemTicketCash.	
 
\item[{\tt long int CCTK\_MemTicketCash(int your\_ticket)}]
	Cash in your ticket: return the memory difference between now and the
     	time the ticket was requested. Tickets can be cashed in
	several times. See Example below.
     	This only tracks the real data memory, which is the same as in
     	undebug mode. It does not keep track of the internal allocations
     	done to provide the database, motivation is that this is not
 	allocated either if you compile undebugged.

\item[{\tt int CCTK\_MemTicketDelete(int your\_ticket)}]
	Delete the memory ticket. The ticket-id will not be reused, since
        it's incremented with every ticket request, but the memory of
	the memory datastructure is deallocated.

\item[{\tt unsigned long int CCTK\_TotalMemory(void)}]
	Returns the total allocated memory (not including the tracing
        data structures). 

\item[{\tt void CCTK\_MemStat}] Prints an info string, stating the current, 
 	past and total memory (in bytes) allocation between two
	successive calls to this routine, as well as the difference. 
\end{Lentry}

Sample C Code demonstrating the ticket handling. Two tickets are
requested during malloc operations. The {\tt CCTK\_MALLOC} statement is 
used directly. They are cashed in and the memory
difference is printed. Ticket 1 is cashed twice. The tickets are
deleted at the end.
\begin{verbatim}

int ticket1;
int ticket2;

/* store current memstate, ticket: t1*/
t1 = CCTK_MemTicketRequest();

/* allocate data */	
hi = (int*) CCTK_MALLOC(10*sizeof(int));

/* store current memstate, ticket: t2*/
t2 = CCTK_MemTicketRequest();      
	
/* cash ticket t1, print mem difference */	
printf("NOW1a: %+d \n",CCTK_MemTicketCash(t1)); 

/* allocte some more data */
wo = (CCTK_REAL*)CCTK_MALLOC(10*sizeof(CCTK_REAL));
	
/* cash ticket t1 and t2, print mem difference */	
printf("NOW1b: %+d \n",CCTK_MemTicketCash(t1));  
printf("NOW2 : %+d \n",CCTK_MemTicketCash(t2));    

/* delete the tickets from the database */
CCTK_MemTicketDelete(t1);
CCTK_MemTicketDelete(t2);

\end{verbatim}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Calls between different programming languages}

\subsection{Calling C routines from FORTRAN}
\label{sec:cacrofr}

To make the following C routine,

{\tt
int <routine name>(<argument list>)\\
{\\
...\\
}
}

also callable from Fortran, a new routine must added, which is
declared using the {\tt CCTK\_FCALL} and {\tt CCTK\_FNAME} macros:

{\tt
void CCTK\_FCALL CCTK\_FNAME(<routine name>)(int *ierr, <argument list>)\\
<rewrite routine code, or call C routine itself>
}

The convention used in Cactus is that {\tt <routine name>} be the same as any
C-callable routine name, and that this is mixed-case.  The macros change
the case and number of underscores of the routine name to match that expected
by Fortran.

All arguments passed by Fortran to the routine (except strings) are
pointers in C, e.g. a call from Fortran

\begin{verbatim}
CCTK_INT arg1
CCTK_REAL arg2
CCTK_REAL arg3(30,30,30)

...

call MyCRoutine(arg1,arg2,arg3)
\end{verbatim}

should appear in C as

\begin{verbatim}
void CCTK_FCALL CCTK_FNAME(MyCRoutine)(CCTK_INT *arg1,
                                       CCTK_REAL *arg2,
                                       CCTK_REAL *arg3)
{
...
}
\end{verbatim}

\subsection{String Arguments from Fortran}

Fortran passes string arguments in a special, compiler-dependent, way.
To facilitate this, the CCTK provides a set of macros to enable the
translation to C strings.
The macros are defined in {\tt cctk\_FortranString.h} which
should be included in your C file.

String arguments {\em must always come last} in the argument list for
these macros to be effective (some Fortran compilers automatically
migrate the strings to the end so there is no portable workaround).

The macros to use depends upon the number of string arguments -- we
currently support up to three.  The macros are 
{\tt <ONE|TWO|THREE>\_FORTSTRING\_ARG}.  
Corresponding to each of these are two macros 
{\tt <ONE|TWO|THREE>\_FORTSTRING\_CREATE} and 
{\tt <ONE|TWO|THREE>\_FORTSTRING\_PTR} 
which take one,two,or three arguments depending on the number of strings.  
The latter set is only necessary if a string is to be modified. 
In more detail:

\begin{Lentry}

\item[{\tt <ONE|TWO|THREE>\_FORTSTRING\_ARG}]
	Used in the argument list of the C routine to which the Fortran
	strings are passed. 

\item[{\tt <ONE|TWO|THREE>\_FORTSTRING\_CREATE}]
	Used in the declaration section of the C routine to which the Fortran
	strings are passed. These macros have one, two or three arguments 
	which are the variable names you choose to use for the strings in 
	the C routine, created
	by null-terminating the passed-in Fortran strings. The {\tt CREATE}
	macros create new strings with the names you provide, and thus should 
	be treated as read-only and freed after use.

\item[{\tt <ONE|TWO|THREE>\_FORTSTRING\_PTR}]
	These macros, used in the declaration section of the C routine 
	{\em after} the {\tt CREATE} macro,
	should be used if you need to modify one of the passed-in strings.
	They declare and define pointers to the passed-in strings.
	
\item[{\tt cctk\_strlen<1|2|3>}] these integer variables, 
	automatically defined by
	the {\tt CREATE} macro, hold the lengths of the passed in 
	Fortran strings.
\end{Lentry}

The use of the macros is probably best explained with examples.
For read-only access to the strings, only the first two macros are needed,
the following example compares two strings passed in from Fortran. 

\begin{verbatim}
#include <stdlib.h>
#include <string.h>
#include <cctk_FortranString.h>

int CCTK_FCALL CCTK_FNAME(CompareStrings)(TWO_FORTSTRING_ARG)
{
  int retval;

  /* Allocate and create C strings with \0 at end. */
  /* This makes variable declarations so must be before
     any executable statements.*/

  TWO_FORTSTRING_CREATE(arg1,arg2)

  /* Do some work with the strings */
  retval = strcmp(arg1,arg2);

  /* Important, these must be freed after use */
  free(arg1); 
  free(arg2); 

  return retval;
}

\end{verbatim}

Since the null terminated strings may be copies of the strings passed
from Fortran, they should be treated as read-only.

To change the data in a string passed from Fortran, you need to use
the {\tt FORTSTRING\_PTR} macros, which declare and set up pointers 
to the strings passed from C. Note that this macro must be used 
{\em after} the {\tt FORTSTRING\_CREATE} macro. For example, the 
following routine copies the contents of the second string to the 
first string. 

\begin{verbatim}
#include <stdlib.h>
#include <string.h>
#include <cctk_FortranString.h>

int CCTK_FCALL CCTK_FNAME(CopyStrings)(TWO_FORTSTRING_ARG)
{
  int retval;

  /* Allocate and create C strings with \0 at end. */
  /* This makes variable declarations so must be before
     any executable statements. */

  TWO_FORTSTRING_CREATE(arg1,arg2)
  TWO_FORTSTRING_PTR(farg1,farg2)

  /* Do some work with the strings */

  retval = strncpy(farg1,arg2,cctk_strlen1);

  /* Important, these must be freed after use */
  free(arg1); 
  free(arg2); 

  return retval;
}

\end{verbatim}

Note that in the example above two new variables, pointers to the
Fortran strings, were created.  These are just pointers and {\em
should not be freed}.  The example also illustrates the
automatically-created variables (e.g. {\tt cctk\_strlen1} 
which hold the sizes of original Fortran strings.  
When writing to a string its length should never be exceeded.

\subsection{Calling FORTRAN routines from C}
\label{sec:caforofr}

To call a utility Fortran routine from C use

{\tt
void CCTK\_FCALL CCTK\_FNAME(<Fortran routine name>)(<argument list>)
}

Note that Fortran expects all arguments (apart from strings) to be
pointers, so any non-array data should be passed by address.

Currently we have no support for calling Fortran routines which expect 
strings from C.


\section{Naming conventions}

\begin{itemize}

\item{} Thorn names must not start with the word "Cactus" (in
        any case).
\item{} Arrangements will be ignored if their names start with \# or .
        or end in \~{} .bak or .BAK 
\item{} Thorns will be ignored if they are called doc or start with
        \# or . or end in \~{} .bak or .BAK
\item{} Routine names have to be unique among all thorns. 

\end{itemize}


\section{General Naming Conventions}

The following naming conventions are followed by the flesh and the
supported Cactus arrangements. They are not compulsory, but if followed
allow for a homogeneous code.

\begin{itemize}

\item Parameters: lower case (except for acronyms) with words separated
  by an underscore. Examples: {\tt my\_first\_parameter}, 
  {\tt solve\_PDE\_equation}.

\item Filenames and routine names: Prefixed by thorn name with an underscore, then capitalised words, with no spaces.
    Examples: {\tt MyThorn\_StartUpRoutine}, {\tt BestSolver\_InitialDataForPDE}.

\end{itemize}

\section{Data Types and Sizes}
\label{sec:datyansi}

Cactus supports the following fixed size data types

\begin{center}
\begin{tabular}{|c|c|c|c|}
\hline
Data Type & Size (bytes) & Variable Type & Fortran Equivalent\\
\hline
{\t CCTK\_INT2}      & 2  & {\t CCTK\_VARIABLE\_INT2}      & {\t integer*2}\\
{\t CCTK\_INT4}      & 4  & {\t CCTK\_VARIABLE\_INT4}      & {\t integer*4}\\
{\t CCTK\_INT8}      & 8  & {\t CCTK\_VARIABLE\_INT8}      & {\t integer*8}\\
{\t CCTK\_REAL4}     & 4  & {\t CCTK\_VARIABLE\_REAL4}     & {\t real*4}\\
{\t CCTK\_REAL8}     & 8  & {\t CCTK\_VARIABLE\_REAL8}     & {\t real*8}\\
{\t CCTK\_REAL16}    & 16 & {\t CCTK\_VARIABLE\_REAL16}    & {\t real*16}\\
{\t CCTK\_COMPLEX8}  & 8  & {\t CCTK\_VARIABLE\_COMPLEX8}  & {\t complex*8}\\
{\t CCTK\_COMPLEX16} & 16 & {\t CCTK\_VARIABLE\_COMPLEX16} & {\t complex*16}\\
{\t CCTK\_COMPLEX32} & 32 & {\t CCTK\_VARIABLE\_COMPLEX32} & {\t complex*32}\\
{\t CCTK\_CHAR}      & 1  & {\t CCTK\_VARIABLE\_CHAR}      & {\t character} \\ \hline
\end{tabular}
\end{center}

In addition Cactus provides three data types whose size is chosen
during the compilation process (at configuration time). This is to
allow the code to be easily run at different precisions. Note that
the effectiveness of running the code at a lower or higher precision
depends crucially on all thorns being used making consistent use
of the following data types:


\begin{center}
\begin{tabular}{|c|c|c|c|}
\hline
Data Type          & Default Size (bytes) & Variable Type & Configuration Option\\
\hline
{\t CCTK\_INT}     & 4 & {\t CCTK\_VARIABLE\_INT} & {\t INTEGER\_PRECISION}\\
{\t CCTK\_REAL}    & 8 & {\t CCTK\_VARIABLE\_REAL} & {\t REAL\_PRECISION}\\
{\t CCTK\_COMPLEX} & (8,8) & {\t CCTK\_VARIABLE\_COMPLEX} & Same as real precision\\
\hline
\end{tabular}
\end{center}

These variable types must be used by thorn writers to declare variables
 in the thorn interface files, and may be used to declare
variables in the thorn routines. Note that variable declarations in 
thorns should obviously match with definitions in the interface files
where appropriate.

Also provided, are a set of macros which
are interpreted by the preprocessor at compile time to signify which
data size is being used:

\begin{center}
\begin{tabular}{|c|c|}
\hline
Data Type & {\t \#define}\\
{\t CCTK\_INT2}      & {\t CCTK\_INT\_PRECISION\_2}      \\
{\t CCTK\_INT4}      & {\t CCTK\_INT\_PRECISION\_4}      \\
{\t CCTK\_INT8}      & {\t CCTK\_INT\_PRECISION\_8}      \\
{\t CCTK\_REAL4}     & {\t CCTK\_REAL\_PRECISION\_4}     \\
{\t CCTK\_REAL8}     & {\t CCTK\_REAL\_PRECISION\_8}     \\
{\t CCTK\_REAL16}    & {\t CCTK\_REAL\_PRECISION\_16}    \\
{\t CCTK\_COMPLEX8}  & {\t CCTK\_COMPLEX\_PRECISION\_8}  \\
{\t CCTK\_COMPLEX16} & {\t CCTK\_COMPLEX\_PRECISION\_16} \\
{\t CCTK\_COMPLEX32} & {\t CCTK\_COMPLEX\_PRECISION\_32} \\
\hline 
\end{tabular}
\end{center}

Note that the availability of these types, and the corresponding 
C data types are platform dependent.

\subsection{Fortran Thorn Writers}

Cactus provides a further data type {\tt CCTK\_POINTER} 
for use in Fortran code to declare a pointer passed from C. 
For example, the variable {\tt cctkGH} is of this type.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\chapter{Telling the makesystem what to do}

\section{Basic Recipe}

\section{Make Concepts}

\section{The Four Files}

\section{How your code is built}

\end{cactuspart}