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1  <!doctype html public "-//w3c//dtd html 4.0 transitional//en">  <!doctype html public "-//w3c//dtd html 4.0 transitional//en">
2  <html>  <html>
3  <head>  <head>
4     <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">     <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
5     <meta name="GENERATOR" content="Mozilla/4.75 [en] (X11; U; Linux 2.2.14-5.0 i686) [Netscape]">     <meta name="GENERATOR" content="Mozilla/4.74 [en]C-CCK-MCD   (Win98; U) [Netscape]">
6     <title>manual</title>     <title>manual</title>
7  </head>  </head>
8  <body bgcolor="#FFFFFF">  <body bgcolor="#FFFFFF">
9  <font size=+1>Documentation of MITgcm takes several forms:</font>  <font size=+1>Documentation of MITgcm takes several forms:</font>
10  <ul>  <ul>
11  <li>  <li>
12  <font size=+1>a <a href="manual/node3.html">manual</a></font></li>  <font size=+1>a <a href="manual/node3.html">manual</a></font></li>
13    
14  <li>  <li>
15  <font size=+1>a hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable  <font size=+1>a hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable
16  code</a></font></li>  code</a></font></li>
17    
18  <li>  <li>
19  <font size=+1>in-source documentation (<a href="#prologues">subroutine  <font size=+1>in-source documentation (<a href="#prologues">subroutine
20  descriptions</a>)</font></li>  descriptions</a>)</font></li>
21  </ul>  </ul>
22    
23  <center>  <center>
24  <h2>  <h2>
25  The manual</h2></center>  The Manual</h2></center>
26  The manual, documenting the formulation, descretization and implementation,  The manual, documenting the formulation, descretization and implementation,
27  can be accessed by following the links on the left. These take you to the  can be accessed by following the links on the left. These take you to the
28  main sections of the document:  main sections of the document:
29  <ol>  <ol>
30  <li>  <li>
31  <b><font size=+1><a href="manual/overview.html">Overview of MITgcm</a></font></b></li>  <b><font size=+1><a href="manual/overview.html">Overview of MITgcm</a></font></b></li>
32    
33  <br>Discusses the  <br>Discusses the
34  <a href="manual/continuous.html">  <a href="manual/continuous.html">continuous formulation
35  continuous formulation  </a>of
36  </a>  the model and illustrates some
37  of the model and illustrates some  <a href="manual/illustrations.html">applications</a>
38  <a href="manual/illustrations.html">applications</a>  <li>
39  <li>  <b><font size=+1><a href="manual/discrete.html">Discretization and Algorithm</a></font></b></li>
40  <b><font size=+1><a href="manual/discrete.html">Discretization and Algorithm</a></font></b></li>  
41    <br>describes the spatial and temporal discretization of the model equations
42  <br>describes the integration algorithm for the various formulations and  <li>
43  gives the spatial discretization of the model equations  <b><font size=+1><a href="manual/getting.html">Getting started and using
44  <li>  the MITgcm</a></font></b></li>
45  <b><font size=+1><a href="manual/getting.html">Getting started and using  
46  the MITgcm</a></font></b></li>  <br>describes how to <a href="manual/obtaining.html">download</a>,
47    <a href="manual/compiling.html">compile</a>,
48  <br>describes how to download, compile, run and modify the model  <a href="manual/running.html">run</a>
49  <li>  and <a href="manual/doing.html">modify</a> the model.
50  <b><font size=+1><a href="manual/sarch.html">Software Architecture</a></font></b></li>  <li>
51    <b><font size=+1><a href="manual/sarch.html">Software Architecture</a></font></b></li>
52  <br><font size=-1>describes the software used for implementing of the model  
53  on many different machines</font>  <br>describes the software <a href="manual/wrapper.html">infrastructure</a>
54  <li>  for
55  <b><font size=+1><a href="manual/autodiff.html">Automatic Differentiation</a></font></b></li>  <a href="manual/using_wrapper.html">running on parallel systems</a>.
56    <li>
57  <br>describes how to generate the adjoint and tangent linear forms of the  <b><font size=+1><a href="manual/autodiff.html">Automatic Differentiation</a></font></b></li>
58  model  
59  <li>  <br>describes how to generate the adjoint and tangent linear forms of the
60  <b><font size=+1><a href="manual/packages.html">Physical Parameterizations  model.
61  and Packages</a></font></b></li>  <li>
62    <b><font size=+1><a href="manual/packages.html">Physical Parameterizations
63  <br>describes the optional parameterizations and features supplied in the  and Packages</a></font></b></li>
64  model  
65  <li>  <br>describes the optional parameterizations and features available in
66  <b><font size=+1><a href="manual/diags.html">Diagnostics and other tools</a></font></b></li>  the model.
67    <li>
68  <br>off-line tools used in conjuction with the model  <b><font size=+1><a href="manual/diags.html">Diagnostics and other tools</a></font></b></li>
69  <li>  
70  <b><font size=+1><a href="manual/ecco.html">Interface with ECCO</a></font></b></li>  <br>details of off-line tools used in conjuction with the model.
71    <li>
72  <br>describes the relationship to the ECCO NOPP node project</ol>  <b><font size=+1><a href="manual/ecco.html">Interface with ECCO</a></font></b></li>
73  or jump to the full <a href="manual/contents.html">table of contents</a>.The  
74  manual is also downloadable in <a href="manual.ps.gz">PostScript</a> and  <br>describes the interface of MITgcm in the <a href="http://www.ecco-group.org" target="idontexist">ECCO</a>
75  <a href="manual.pdf">PDF</a>.  suite of optimization software tailored to large-scale ocean state-estimation</ol>
76  <br>&nbsp;  Jump to the full <a href="manual/contents.html">table of contents</a>.
77  <center>  <p>The manual is also downloadable in <a href="manual.ps.gz">PostScript</a>
78  <h2>  and
79  <font size=+1>The hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable  <a href="manual.pdf">PDF</a>.
80  code</a></font></h2></center>  <br>&nbsp;
81  This allows you to peruse the source code by following hyper-links for  <center>
82  variables, subroutines and functions. It allows you to find instances of  <h2>
83  variables, find where subroutines and functions are called from and see  <font size=+1>The hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable
84  the actual fortran.  code</a></font></h2></center>
85  <center>  This allows you to peruse the source code by following hyper-links for
86  <h2>  variables, subroutines and functions. It allows you to find instances of
87  <a NAME="prologues"></a>In-source documentation</h2></center>  variables, find where subroutines and functions are called from and inspect
88  This takes the form of comments in the source code and has been formatted  full model code.
89  to render subroutine descriptions (written as prologues at the top of each  <center>
90  routine). It is downloadable as:  <h2>
91  <ul>  <a NAME="prologues"></a>In-source documentation</h2></center>
92  <li>  Comments in the source code itself have been formatted to render subroutine
93  <a href="prologues.ps.gz">PostScript</a></li>  descriptions (written as prologues at the top of each routine). It is downloadable
94    as:
95  <li>  <ul>
96  <a href="prologues.pdf">PDF</a></li>  <li>
97  </ul>  <a href="prologues.ps.gz">PostScript</a></li>
98    
99  </body>  <li>
100  </html>  <a href="prologues.pdf">PDF</a></li>
101    </ul>
102    
103    </body>
104    </html>
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