s_outp_pkgs/text/grid_gen.tex

% $Header:  $
% $Name:  $

\section{Grid Generation}
\label{sec:pkg:grid_gen}
\begin{rawhtml}
<!-- CMIREDIR:package_grid_gen: -->
\end{rawhtml}


The horizontal discretizations within MITgcm have been written to work
with many different grid types including:
\begin{itemize}
\item cartesian coordinates
\item spherical polar (``latitude-longitude'') coordinates
\item general curvilinear orthogonal coordinates
\end{itemize}
The last of these, especially when combined with the domain
decomposition capabilities of MITgcm, allows a great degree of grid
flexibility.  To date, general curvilinear orthogonal coordinates have
been used primarily (in fact, almost exclusively) in conjunction with
so-called ``cube-sphere'' grids.  However, it is important to observe
that cube-sphere arrangements are only one example of what is possible
with domain-decomposed logically rectangular tiles each containing
curvilinear orthogonal coordinate systems.  Much more sophisticated 
domains can be imagined and constructed.

In order to explore the possibilities of domain-decomposed curvilinear
orthogonal coordinate systems, a suite of grid generation software
called ``SPGrid'' (for SPherical Gridding) has developed.  SPGrid is a
relatively new facility and papers detailing its algorithms are in
preparation.  Althogh SPGrid is new and still rapidly developing, it
has already demonstrated the ability to generate some useful and
interesting grids.

This section provides a very brief introduction to SPGrid and shows
some early results.  For further information, please contact the
MITgcm support list:
\begin{center}
  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
\end{center}


\subsection{Using SPGrid}

The SPGrid software is not a single program.  Rather, it is a
collection of \CC code and MatLAB scripts that can be used as a
framework or library for grid generation.  Currently, grid creation is
accomplished by writing a \CC ``driver'' program that specifies the
shape and connectivity of tiles and the preferred grid sizes (in the
sense of the number of grid cells) and edge locations of the cells at
the edges of grid faces.  The driver program then passes this
information to the SPGrid library which generates the actual grid and
produces the output files that describe it.

Currently, driver programs are available for a few examples including
cubes, ``lat-lon caps'' (cube topologies that have conformal caps at
the poles and are exactly lat-lon channels for the remainder of the
domain), and some simple ``embedded'' regions that are meant to be
used within typical cubes or traditional lat-lon grids.

To create new grids, one may start with an existing driver program and
modify it to describe a domain that has a different arrangement.  The
number, location, size, and connectivity of grid ``faces'' (the name
used for the logically rectangular regions) can be readily changed.
Further, the number of grid cells within faces and the location of
the grid cells at the face edges can also be specified.


\subsubsection{SPGrid Requirements}

The following programs and libraries are required to build and/or run
the SPGrid suite:
\begin{itemize}
\item MatLAB is a run-time requirement since many of the generation
  algorithms have been written as MatLAB scripts: \\
  \begin{rawhtml} <A href="http://www.mathworks.com"> \end{rawhtml}
  \texttt{http://www.mathworks.com}
  \begin{rawhtml} </A> \end{rawhtml}

\item the Wild Magic graphics engine (a \CC library) is needed for the
  main ``driver'' code: \\
  \begin{rawhtml} <A href="http://geometrictools.com/"> \end{rawhtml}
  \texttt{http://geometrictools.com/}
  \begin{rawhtml} </A> \end{rawhtml}

\item the NetCDF library is needed for file I/O: \\
  \begin{rawhtml} <A href="http://www.mathworks.com"> \end{rawhtml}
  \texttt{http://www.mathworks.com}
  \begin{rawhtml} </A> \end{rawhtml}

\item the BOOST Serialization library is used for I/O: \\
  \begin{rawhtml} <A href="http://www.boost.org"> \end{rawhtml}
  \texttt{http://www.boost.org}
  \begin{rawhtml} </A> \end{rawhtml}

\item a typical Unix/Linux build environment including the make
  utility (preferably Gnu Make) and a \CC compiler (SPGrid was
  developed with g++ v3.x and v4.x).
\end{itemize}


\subsubsection{Obtaining SPGrid}

The latest version can be obtained from:
\begin{center}
  \begin{rawhtml} <A href="http://mitgcm.org/eh3/grids/spgrid_releases/>
  \end{rawhtml}
  \texttt{http://mitgcm.org/eh3/grids/spgrid\_releases/}
  \begin{rawhtml} </A> \end{rawhtml}
\end{center}


\subsubsection{Building SPGrid}

The procedure for building is similar to many open source projects:
\begin{verbatim}
     tar -xf spgrid-0.9.4.tar.gz
     cd spgrid-0.9.4
     export CPPFLAGS="-I/usr/include/netcdf-3"
     export LDFLAGS="-L/usr/lib/netcdf-3"
     ./configure
     make
\end{verbatim}
where the \texttt{CPPFLAGS} and\texttt{LDFLAGS} environment variables
can be edited to reflect the locations of all the necessary
dependencies.  SPGrid is known to work on Fedora Core Linux and is
likely to work on most any Linux distribution that provides the needed
dependencies.


\subsubsection{Using SPGrid}

Within the \texttt{src} sub-directory, various example programs
exist.  These example programs describe small but complete domains and
can generate the input (formatted as either binary ``mitgrid'' or
netCDF) files required by MITgcm.

One such example is called ``SpF\_test\_cube\_cap'' and it can be run
with the following sequence of commands:
\begin{verbatim}
     cd spgrid-0.9.4/src
     mkdir SpF_test_cube_cap.d
     ( cd SpF_test_cube_cap.d && ln -s ../../scripts/*.m . )
     ./SpF_test_cube_cap
\end{verbatim}
which should create a series of output files of the form
\begin{verbatim}
     SpF_test_cube_cap.d/grid_*.mitgrid
     SpF_test_cube_cap.d/grid_*.nc
     SpF_test_cube_cap.d/std_topology.nc
\end{verbatim}
which describe each face of the domain and how the faces are
connected.


\subsection{Example Grids}

The following grids are various examples created with SPGrid. 
1	% $Header: $
2	% $Name: $
3
4	\section{Grid Generation}
5	\label{sec:pkg:grid_gen}
6	\begin{rawhtml}
7	<!-- CMIREDIR:package_grid_gen: -->
8	\end{rawhtml}
9
10
11	The horizontal discretizations within MITgcm have been written to work
12	with many different grid types including:
13	\begin{itemize}
14	\item cartesian coordinates
15	\item spherical polar (``latitude-longitude'') coordinates
16	\item general curvilinear orthogonal coordinates
17	\end{itemize}
18	The last of these, especially when combined with the domain
19	decomposition capabilities of MITgcm, allows a great degree of grid
20	flexibility. To date, general curvilinear orthogonal coordinates have
21	been used primarily (in fact, almost exclusively) in conjunction with
22	so-called ``cube-sphere'' grids. However, it is important to observe
23	that cube-sphere arrangements are only one example of what is possible
24	with domain-decomposed logically rectangular tiles each containing
25	curvilinear orthogonal coordinate systems. Much more sophisticated
26	domains can be imagined and constructed.
27
28	In order to explore the possibilities of domain-decomposed curvilinear
29	orthogonal coordinate systems, a suite of grid generation software
30	called ``SPGrid'' (for SPherical Gridding) has developed. SPGrid is a
31	relatively new facility and papers detailing its algorithms are in
32	preparation. Althogh SPGrid is new and still rapidly developing, it
33	has already demonstrated the ability to generate some useful and
34	interesting grids.
35
36	This section provides a very brief introduction to SPGrid and shows
37	some early results. For further information, please contact the
38	MITgcm support list:
39	\begin{center}
40	\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
41	MITgcm-support@mitgcm.org
42	\begin{rawhtml} </A> \end{rawhtml}
43	\end{center}
44
45
46	\subsection{Using SPGrid}
47
48	The SPGrid software is not a single program. Rather, it is a
49	collection of \CC code and MatLAB scripts that can be used as a
50	framework or library for grid generation. Currently, grid creation is
51	accomplished by writing a \CC ``driver'' program that specifies the
52	shape and connectivity of tiles and the preferred grid sizes (in the
53	sense of the number of grid cells) and edge locations of the cells at
54	the edges of grid faces. The driver program then passes this
55	information to the SPGrid library which generates the actual grid and
56	produces the output files that describe it.
57
58	Currently, driver programs are available for a few examples including
59	cubes, ``lat-lon caps'' (cube topologies that have conformal caps at
60	the poles and are exactly lat-lon channels for the remainder of the
61	domain), and some simple ``embedded'' regions that are meant to be
62	used within typical cubes or traditional lat-lon grids.
63
64	To create new grids, one may start with an existing driver program and
65	modify it to describe a domain that has a different arrangement. The
66	number, location, size, and connectivity of grid ``faces'' (the name
67	used for the logically rectangular regions) can be readily changed.
68	Further, the number of grid cells within faces and the location of
69	the grid cells at the face edges can also be specified.
70
71
72	\subsubsection{SPGrid Requirements}
73
74	The following programs and libraries are required to build and/or run
75	the SPGrid suite:
76	\begin{itemize}
77	\item MatLAB is a run-time requirement since many of the generation
78	algorithms have been written as MatLAB scripts: \\
79	\begin{rawhtml} <A href="http://www.mathworks.com"> \end{rawhtml}
80	\texttt{http://www.mathworks.com}
81	\begin{rawhtml} </A> \end{rawhtml}
82
83	\item the Wild Magic graphics engine (a \CC library) is needed for the
84	main ``driver'' code: \\
85	\begin{rawhtml} <A href="http://geometrictools.com/"> \end{rawhtml}
86	\texttt{http://geometrictools.com/}
87	\begin{rawhtml} </A> \end{rawhtml}
88
89	\item the NetCDF library is needed for file I/O: \\
90	\begin{rawhtml} <A href="http://www.mathworks.com"> \end{rawhtml}
91	\texttt{http://www.mathworks.com}
92	\begin{rawhtml} </A> \end{rawhtml}
93
94	\item the BOOST Serialization library is used for I/O: \\
95	\begin{rawhtml} <A href="http://www.boost.org"> \end{rawhtml}
96	\texttt{http://www.boost.org}
97	\begin{rawhtml} </A> \end{rawhtml}
98
99	\item a typical Unix/Linux build environment including the make
100	utility (preferably Gnu Make) and a \CC compiler (SPGrid was
101	developed with g++ v3.x and v4.x).
102	\end{itemize}
103
104
105	\subsubsection{Obtaining SPGrid}
106
107	The latest version can be obtained from:
108	\begin{center}
109	\begin{rawhtml} <A href="http://mitgcm.org/eh3/grids/spgrid_releases/>
110	\end{rawhtml}
111	\texttt{http://mitgcm.org/eh3/grids/spgrid\_releases/}
112	\begin{rawhtml} </A> \end{rawhtml}
113	\end{center}
114
115
116	\subsubsection{Building SPGrid}
117
118	The procedure for building is similar to many open source projects:
119	\begin{verbatim}
120	tar -xf spgrid-0.9.4.tar.gz
121	cd spgrid-0.9.4
122	export CPPFLAGS="-I/usr/include/netcdf-3"
123	export LDFLAGS="-L/usr/lib/netcdf-3"
124	./configure
125	make
126	\end{verbatim}
127	where the \texttt{CPPFLAGS} and\texttt{LDFLAGS} environment variables
128	can be edited to reflect the locations of all the necessary
129	dependencies. SPGrid is known to work on Fedora Core Linux and is
130	likely to work on most any Linux distribution that provides the needed
131	dependencies.
132
133
134	\subsubsection{Using SPGrid}
135
136	Within the \texttt{src} sub-directory, various example programs
137	exist. These example programs describe small but complete domains and
138	can generate the input (formatted as either binary ``mitgrid'' or
139	netCDF) files required by MITgcm.
140
141	One such example is called ``SpF\_test\_cube\_cap'' and it can be run
142	with the following sequence of commands:
143	\begin{verbatim}
144	cd spgrid-0.9.4/src
145	mkdir SpF_test_cube_cap.d
146	( cd SpF_test_cube_cap.d && ln -s ../../scripts/*.m . )
147	./SpF_test_cube_cap
148	\end{verbatim}
149	which should create a series of output files of the form
150	\begin{verbatim}
151	SpF_test_cube_cap.d/grid_*.mitgrid
152	SpF_test_cube_cap.d/grid_*.nc
153	SpF_test_cube_cap.d/std_topology.nc
154	\end{verbatim}
155	which describe each face of the domain and how the faces are
156	connected.
157
158
159	\subsection{Example Grids}
160
161	The following grids are various examples created with SPGrid.