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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 <a href=../online_documents/manual/obtaining.html>  <a href="manual/running.html">run</a>
49  download</a>,  and <a href="manual/doing.html">modify</a> the model.
50  <a href=../online_documents/manual/compiling.html>compile</a>,  <li>
51  <a href=../online_documents/manual/running.html>run</a> and  <b><font size=+1><a href="manual/sarch.html">Software Architecture</a></font></b></li>
52  <a href=../online_documents/manual/doing.html>modify</a> the model.  
53  <li>  <br>describes the software <a href="manual/wrapper.html">infrastructure</a>
54  <b><font size=+1><a href="manual/sarch.html">Software Architecture</a></font></b></li>  for
55    <a href="manual/using_wrapper.html">running on parallel systems</a>.
56  <br><font >describes the software <a href=../online_documents/manual/wrapper.html>infrastructure</a> used for deploying the model  <li>
57  efficiently on a wide range of parallel and uniprocessor machines.  <b><font size=+1><a href="manual/autodiff.html">Automatic Differentiation</a></font></b></li>
58  <a href=../online_documents/manual/using_wrapper.html>Running on parallel  
59  systems</a> is discussed here.  <br>describes how to generate the adjoint and tangent linear forms of the
60  </font>  model.
61  <li>  <li>
62  <b><font size=+1><a href="manual/autodiff.html">Automatic Differentiation</a></font></b></li>  <b><font size=+1><a href="manual/packages.html">Physical Parameterizations
63    and Packages</a></font></b></li>
64  <br>describes how to generate the adjoint and tangent linear forms of the  
65  model.  <br>describes the optional parameterizations and features available in
66  <li>  the model.
67  <b><font size=+1><a href="manual/packages.html">Physical Parameterizations  <li>
68  and Packages</a></font></b></li>  <b><font size=+1><a href="manual/diags.html">Diagnostics and other tools</a></font></b></li>
69    
70  <br>describes the optional parameterizations and features supplied in the  <br>details of off-line tools used in conjuction with the model.
71  model.  <li>
72  <li>  <b><font size=+1><a href="manual/ecco.html">Interface with ECCO</a></font></b></li>
73  <b><font size=+1><a href="manual/diags.html">Diagnostics and other tools</a></font></b></li>  
74    <br>describes the interface of MITgcm in the <a href="http://www.ecco-group.org" target="idontexist">ECCO</a>
75  <br>details of off-line tools used in conjuction with the model.  suite of optimization software tailored to large-scale ocean state-estimation</ol>
76  <li>  Jump to the full <a href="manual/contents.html">table of contents</a>.
77  <b><font size=+1><a href="manual/ecco.html">Interface with ECCO</a></font></b></li>  <p>The manual is also downloadable in <a href="manual.ps.gz">PostScript</a>
78    and
79  <br>describes the interface to the  <a href="manual.pdf">PDF</a>.
80  <A href=http://www.ecco-group.org target=idontexist>ECCO</a> environment  <br>&nbsp;
81  (a custom suite of  <center>
82  optimization software tailored to large-scale ocean  <h2>
83  state-estimation). </ol>  <font size=+1>The hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable
84  or jump to the full <a href="manual/contents.html">table of contents</a>.The  code</a></font></h2></center>
85  manual is also downloadable in <a href="manual.ps.gz">PostScript</a> and  This allows you to peruse the source code by following hyper-links for
86  <a href="manual.pdf">PDF</a>.  variables, subroutines and functions. It allows you to find instances of
87  <br>&nbsp;  variables, find where subroutines and functions are called from and inspect
88  <center>  full model code.
89  <h2>  <center>
90  <font size=+1>The hyper-linked <a href="../code_reference/index.html" target="mainFrame">browsable  <h2>
91  code</a></font></h2></center>  <a NAME="prologues"></a>In-source documentation</h2></center>
92  This allows you to peruse the source code by following hyper-links for  Comments in the source code itself have been formatted to render subroutine
93  variables, subroutines and functions. It allows you to find instances of  descriptions (written as prologues at the top of each routine). It is downloadable
94  variables, find where subroutines and functions are called from and see  as:
95  the actual fortran.  <ul>
96  <center>  <li>
97  <h2>  <a href="prologues.ps.gz">PostScript</a></li>
98  <a NAME="prologues"></a>In-source documentation</h2></center>  
99  This takes the form of comments in the source code and has been formatted  <li>
100  to render subroutine descriptions (written as prologues at the top of each  <a href="prologues.pdf">PDF</a></li>
101  routine). It is downloadable as:  </ul>
102  <ul>  
103  <li>  </body>
104  <a href="prologues.ps.gz">PostScript</a></li>  </html>
   
 <li>  
 <a href="prologues.pdf">PDF</a></li>  
 </ul>  
   
 </body>  
 </html>  
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