[Dart-dev] [6336] DART/trunk/models: doc updates - add standard header to the model docs
nancy at ucar.edu
nancy at ucar.edu
Tue Jul 30 17:01:32 MDT 2013
Revision: 6336
Author: nancy
Date: 2013-07-30 17:01:31 -0600 (Tue, 30 Jul 2013)
Log Message:
-----------
doc updates - add standard header to the model docs
which were missing them. fix some namelists, change
the things that the 'tidy' tool complained about.
Modified Paths:
--------------
DART/trunk/models/9var/model_mod.html
DART/trunk/models/CESM/model_mod.html
DART/trunk/models/MITgcm_ocean/create_ocean_obs.html
DART/trunk/models/MITgcm_ocean/model_mod.html
DART/trunk/models/NCOMMAS/model_mod.html
DART/trunk/models/POP/model_mod.html
DART/trunk/models/cam/model_mod.html
DART/trunk/models/coamps/model_mod.html
DART/trunk/models/forced_lorenz_96/model_mod.html
DART/trunk/models/gitm/model_mod.html
DART/trunk/models/ikeda/model_mod.html
DART/trunk/models/lorenz_04/model_mod.html
DART/trunk/models/lorenz_63/model_mod.html
DART/trunk/models/lorenz_84/model_mod.html
DART/trunk/models/lorenz_96/model_mod.html
DART/trunk/models/mpas_atm/model_mod.html
DART/trunk/models/mpas_ocn/model_mod.html
DART/trunk/models/noah/dart_to_noah.html
DART/trunk/models/noah/noah_to_dart.html
DART/trunk/models/null_model/model_mod.html
DART/trunk/models/pe2lyr/model_mod.html
DART/trunk/models/simple_advection/model_mod.html
DART/trunk/models/sqg/model_mod.html
DART/trunk/models/wrf/model_mod.html
-------------- next part --------------
Modified: DART/trunk/models/9var/model_mod.html
===================================================================
--- DART/trunk/models/9var/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/9var/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module model_mod (9-variable)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (9-variable)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (9-variable)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the 9-variable model. The 17 public interfaces
Modified: DART/trunk/models/CESM/model_mod.html
===================================================================
--- DART/trunk/models/CESM/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/CESM/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,16 +4,17 @@
<HEAD>
<TITLE>module model_mod (POP)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<H1>MODULE model_mod (POP)</H1>
+<H1>MODULE model_mod (CESM)</H1>
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
@@ -35,38 +36,43 @@
<H2>Overview</H2>
-<P>The <strong>Parallel Ocean Program (POP)</strong> may now be used with the
- <strong>Data Assimilation Research Testbed (DART)</strong>.
- Both main variants - <a href="http://climate.lanl.gov/Models/POP/">LANL POP</a> and
- <a href="http://www.cesm.ucar.edu/models/cesm1.0/pop2/">CESM1.0 POP2</a> have been
- tested. At present (July 2010), we are assimilating salinity and temperature
- observations from the World Ocean Database (2005) with the intention of switching
- to the World Ocean Database (2009) as needed.
- <br />
- <br />
- The following POP variables are extracted from the POP netCDF restart files and
- are conveyed to DART:
- <em class=code>SALT_CUR</em>,
- <em class=code>TEMP_CUR</em>,
- <em class=code>UVEL_CUR</em>,
- <em class=code>VVEL_CUR</em>, and
- <em class=code>PSURF_CUR</em>. These variables are then adjusted to be consistent
- with real observations and stuffed back into the same netCDF restart files.
- Since DART is an ensemble algorithm, there are multiple restart files for a
- single restart time: one for each ensemble member. Creating the initial ensemble
- of ocean states is an area of active research. At present, it may be sufficient
- to use a climatological ensemble; e.g., using the restarts for '1 January 00Z'
- from 50 consecutive years. Experience has shown that having a paired (unique)
- atmospheric forcing maintains the ensemble spread better than simply forcing
- all the ocean ensemble members with one single atmospheric state.
- <br />
- <br />
- DART reads the grid information for POP from the files specified in
- POP's <em class=code>&grid_nml</em>.
- When DART is responsible for starting/stopping POP, the information is
- conveyed through POP's <em class=code>&time_manager_nml</em>.
+<P>
+The current interface to the CESM climate modeling system does assimilation
+into CAM, POP, and CLM separately. Therefore at this point there is NOT
+a single CESM model_mod that is compiled into a single filter. However, there
+exists a beta version of a unified model_mod that redirects forward operator
+calls to the proper component-specific model_mod, and works around the
+conflicts between the naming of the model_mod at the module level. It would
+require a single state vector to fit into the memory space of one process,
+which means it would be limited in resolution. cesm_to_dart and dart_to_cesm
+converter prototypes also exist, which pack the data from each model
+end-to-end in the state vector.
</P>
+<P>
+For now, see each of the component specific model_mod documentation for information
+on the namelists and requirements:
+</P>
+<UL>
+<LI><a href="../cam/model_mod.html">CAM</a>
+<LI><a href="../POP/model_mod.html">POP</a>
+<LI><a href="../clm/model_mod.html">CLM</a>
+</UL>
+
+<P>
+There are scripts in the CESM/shell_scripts directory which are intended to
+build the 3 filter programs for each of the components, copy the right files
+into the CESM caseroot directory, build CESM, and stage files to run an experiment.
+</P>
+
+<pre>
+FIXME: add info about
+byte swap flag
+-fp-model precise
+</pre>
+
+
+
<div class=indent1>
<h2><a href="http://www.cesm.ucar.edu/models/cesm1.0/pop2/">CESM1.0 POP2</a></h2>
<P>
@@ -1652,7 +1658,7 @@
<TR><TD valign=top>Revision: </TD><TD> $Revision$ </TD></TR>
<TR><TD valign=top>Source: </TD><TD> $URL$ </TD></TR>
<TR><TD valign=top>Change Date: </TD><TD> $Date$ </TD></TR>
-<TR><TD valign=top>Change history: </TD><TD> try "svn log" or "svn diff" </TD></TR>
+<TR><TD valign=top>Change history:</TD><TD> try "svn log" or "svn diff" </TD></TR>
</TABLE>
<!--==================================================================-->
Modified: DART/trunk/models/MITgcm_ocean/create_ocean_obs.html
===================================================================
--- DART/trunk/models/MITgcm_ocean/create_ocean_obs.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/MITgcm_ocean/create_ocean_obs.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -98,7 +98,7 @@
<P>
It is always possible to combine observation sequence files with the program
-<a href="../../obs_sequence/merge_obs_seq.html">merge_obs_seq</a>, so
+<a href="../../obs_sequence/obs_sequence_tool.html">obs_sequence_tool</a>, so
it was simply convenient to generate a separate file for each observation
platform and type ('GLIDER' and 'TEMPERATURE'), however it is by no means
required.
Modified: DART/trunk/models/MITgcm_ocean/model_mod.html
===================================================================
--- DART/trunk/models/MITgcm_ocean/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/MITgcm_ocean/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,24 +4,39 @@
<HEAD>
<TITLE>module MITgcm_ocean model_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE MITgcm_ocean</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE MITgcm_ocean</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
+
<P>
The <a href="http://mitgcm.org/">MIT ocean GCM</a> version 'checkpoint59a'
is the foundation of this directory. It was modified by Ibrahim Hoteit
Modified: DART/trunk/models/NCOMMAS/model_mod.html
===================================================================
--- DART/trunk/models/NCOMMAS/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/NCOMMAS/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -5,14 +5,17 @@
<HEAD>
<TITLE>module model_mod (NCOMMAS)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
+<H1>MODULE model_mod (NCOMMAS)</H1>
+
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P><a href="../../index.html">DART Documentation Main Index</a><br />
@@ -32,7 +35,7 @@
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-<H1>MODULE model_mod (NCOMMAS)</H1>
+<H2>Overview</H2>
<P><strong>NCOMMAS 7_1</strong> may now be used with the
<strong>Data Assimilation Research Testbed (DART)</strong>.
Modified: DART/trunk/models/POP/model_mod.html
===================================================================
--- DART/trunk/models/POP/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/POP/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>module model_mod (POP)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
@@ -13,7 +14,7 @@
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
Modified: DART/trunk/models/cam/model_mod.html
===================================================================
--- DART/trunk/models/cam/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/cam/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,7 +4,7 @@
<HEAD>
<TITLE>module model_mod (CAM)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
-<link href="../../doc/html/dart.ico" rel="shortcut icon" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
@@ -14,7 +14,7 @@
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
Modified: DART/trunk/models/coamps/model_mod.html
===================================================================
--- DART/trunk/models/coamps/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/coamps/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module model_mod (COAMPS)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (COAMPS)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (COAMPS)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the
Modified: DART/trunk/models/forced_lorenz_96/model_mod.html
===================================================================
--- DART/trunk/models/forced_lorenz_96/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/forced_lorenz_96/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module model_mod (forced_lorenz_96)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (Lorenz_96, forced)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (Lorenz_96, forced)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the forced_lorenz-96 model. The 17 public interfaces
Modified: DART/trunk/models/gitm/model_mod.html
===================================================================
--- DART/trunk/models/gitm/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/gitm/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -5,14 +5,17 @@
<HEAD>
<TITLE>module model_mod (GITM)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
+<H1>MODULE model_mod (GITM)</H1>
+
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P><a href="../../index.html">DART Documentation Main Index</a><br />
@@ -32,7 +35,7 @@
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-<H1>MODULE model_mod (GITM)</H1>
+<H2>Overview</H2>
<P>The <strong>GITM </strong> interface for
<strong>Data Assimilation Research Testbed (DART)</strong> is under development.
Modified: DART/trunk/models/ikeda/model_mod.html
===================================================================
--- DART/trunk/models/ikeda/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/ikeda/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module model_mod (Ikeda)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (Ikeda)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (Ikeda)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the Ikeda model. The 17 public interfaces
Modified: DART/trunk/models/lorenz_04/model_mod.html
===================================================================
--- DART/trunk/models/lorenz_04/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/lorenz_04/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,40 @@
<HEAD>
<TITLE>module model_mod (Lorenz_04)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
+<H1>MODULE model_mod (Lorenz_04)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A NAME="TOP"></A>
+
<center>
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
-<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
</center>
-<H1>MODULE model_mod (Lorenz_04)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the Lorenz-05 models II and III.
@@ -33,7 +50,7 @@
<P>The reference for these models is Lorenz, E.N., 2005: Designing
chaotic models. <span style="font-style: italic;">J. Atmos. Sci.</span>,
-<span style="font-weight: bold;">62</span>, 1574-1587.<br>
+<span style="font-weight: bold;">62</span>, 1574-1587.
</P>
<P>Model II is a single-scale model, similar to Lorenz 96, but with
@@ -46,13 +63,119 @@
and thus model II is a deficient form of model III. The basic
equations are documented in Lorenz (2005) and also in the model_mod.f90
code. The user is free to choose model II or III with a Namelist
-variable.<br>
+variable.
</P>
+<br />
+<br />
+
+<!--===================== DESCRIPTION OF A NAMELIST =====================-->
+
+<A NAME="Namelist"></A>
+<div class="top">[<a href="#">top</a>]</div><hr />
+<H2>NAMELIST</H2>
+<P>
+This namelist is read from the file <em class=file>input.nml</em>.
+Namelists start with an ampersand
+'&' and terminate with a slash '/'.
+Character strings that contain a '/' must be
+enclosed in quotes to prevent them from
+prematurely terminating the namelist.
+</P>
+
+<div class=namelist>
+<pre>
+&model_nml
+ model_size = 960,
+ forcing = 15.00,
+ delta_t = 0.001,
+ space_time_scale = 10.00,
+ coupling = 3.00,
+ K = 32,
+ smooth_steps = 12,
+ time_step_days = 0,
+ time_step_seconds = 3600,
+ model_number = 3
+/
+</pre>
+</div>
+
+<br />
+
+<div>
+<TABLE border=0 cellpadding=3 width=100% summary='namelist description'>
+<THEAD align=left>
+<TR><TH>Contents </TH>
+ <TH>Type </TH>
+ <TH>Description </TH></TR>
+</THEAD>
+
+<TBODY valign=top>
+<TR><TD>model_size </TD>
+ <TD>integer </TD>
+ <TD>Number of variables in model
+ </TD></TR>
+
+<TR><TD>forcing </TD>
+ <TD>real(r8) </TD>
+ <TD>Forcing, F, for model
+ </TD></TR>
+
+<TR><TD>delta_t </TD>
+ <TD>real(r8) </TD>
+ <TD>Non-dimensional timestep
+ </TD></TR>
+
+<TR><TD>space_time_scale </TD>
+ <TD>real(r8) </TD>
+ <TD>Determines temporal and spatial relationship between
+ fast and slow variables (model III)
+ </TD></TR>
+
+<TR><TD>coupling </TD>
+ <TD>real(r8) </TD>
+ <TD>Linear coupling between fast and slow variables (model III)
+ </TD></TR>
+
+<TR><TD>K </TD>
+ <TD>integer </TD>
+ <TD>Determines the wavenumber of the slow variables
+ (K=1, smooth_steps=0 reduces model II to Lorenz 96)
+ </TD></TR>
+
+<TR><TD>smooth_steps </TD>
+ <TD>integer </TD>
+ <TD>Determines filter length to separate fast and slow scales
+ </TD></TR>
+
+<TR><TD>time_step_days </TD>
+ <TD>integer </TD>
+ <TD>Arbitrary real time step days
+ </TD></TR>
+
+<TR><TD>time_step_seconds </TD>
+ <TD>integer </TD>
+ <TD>Arbitrary real time step seconds
+ (could choose this for proper scaling)
+ </TD></TR>
+
+<TR><TD>model_number </TD>
+ <TD>integer </TD>
+ <TD>2 = single-scale, 3 = 2-scale.
+ (This follows the notation in the paper.)
+ </TD></TR>
+
+</TBODY>
+</TABLE>
+</div>
+
+<br />
+<br />
+
<!--==================================================================-->
<A NAME="OtherModulesUsed"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>OTHER MODULES USED</H2>
<PRE>
types_mod
@@ -61,6 +184,9 @@
utilities_mod
</PRE>
+<br />
+<br />
+
<!--==================================================================-->
<!-- Declare all public entities ... -->
<!-- duplicate public routines template as many times as necessary -->
@@ -70,7 +196,7 @@
<!--==================================================================-->
<A NAME="Interface"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>PUBLIC INTERFACES</H2>
<TABLE>
@@ -109,7 +235,7 @@
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_model_size"></A>
-<br>
+<br />
<div class=routine>
<em class=call>model_size = get_model_size( )</em>
<pre>
@@ -133,12 +259,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="adv_1step"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call adv_1step(x, time)</em>
<pre>
@@ -166,12 +292,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_state_meta_data"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call get_state_meta_data (index_in, location,
<em class=optionalcode>[, var_type]</em> )</em>
@@ -209,12 +335,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="model_interpolate"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call model_interpolate(x, location, itype, obs_val, istatus)</em>
<pre>
@@ -257,12 +383,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_model_time_step"></A>
-<br>
+<br />
<div class=routine>
<em class=call>var = get_model_time_step()</em>
<pre>
@@ -286,12 +412,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="static_init_model"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call static_init_model()</em>
</div>
@@ -308,12 +434,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="end_model"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call end_model()</em>
</div>
@@ -329,12 +455,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="init_time"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call init_time(time)</em>
<pre>
@@ -360,12 +486,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="init_conditions"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call init_conditions(x)</em>
<pre>
@@ -389,12 +515,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="nc_write_model_atts"></A>
-<br>
+<br />
<div class=routine>
<em class=call>ierr = nc_write_model_atts(ncFileID)</em>
<pre>
@@ -425,12 +551,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="nc_write_model_vars"></A>
-<br>
+<br />
<div class=routine>
<em class=call>ierr = nc_write_model_vars(ncFileID, statevec, copyindex, timeindex)</em>
<pre>
@@ -471,12 +597,12 @@
</TABLE>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="nc_read_model_vars"></A>
-<br>
+<br />
<div class="routine">
<em class="call"> ierr = nc_read_model_vars(ncFileID, statevec, copyindex, timeindex)</em>
<pre>
@@ -515,12 +641,12 @@
</P>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="pert_model_state"></A>
-<br>
+<br />
<div class="routine">
<em class="call">call pert_model_state(state, pert_state, interf_provided)</em>
<pre>
@@ -561,12 +687,12 @@
</P>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_close_maxdist_init"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call get_close_maxdist_init(gc, maxdist)</em>
<pre>
@@ -585,12 +711,12 @@
</P>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_close_obs_init"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call get_close_obs_init(gc, num, obs)</em>
<pre>
@@ -610,12 +736,12 @@
</P>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="get_close_obs"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call get_close_obs(gc, base_obs_loc, base_obs_kind,
obs, obs_kind, num_close, close_ind
@@ -642,12 +768,12 @@
</P>
</div>
-<br>
+<br />
<!--===================== DESCRIPTION OF A ROUTINE =====================-->
<A NAME="ens_mean_for_model"></A>
-<br>
+<br />
<div class=routine>
<em class=call>call ens_mean_for_model(ens_mean)</em>
<pre>
@@ -670,97 +796,16 @@
</TABLE>
</div>
-<br>
-<!--===================== DESCRIPTION OF A NAMELIST =====================-->
+<br />
+<br />
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&' and terminating with a slash '/' for all our namelist input.
-The declarations have a different syntax, naturally.
-</P>
-<div class=namelist>
-<pre>
-<em class=call>namelist / model_nml / </em> &
- model_size, forcing, delta_t, space_time_scale, &
- coupling, K, smooth_steps, &
- time_step_days, time_step_seconds, model_number
-</pre>
-</div>
-
-<div class=indent1>
-<!-- Description -->
-
-<P>
-This namelist is read in a file called <em class=file>input.nml</em>
-</P>
-
-<TABLE border=0 cellpadding=3 width=100%>
-<tbody>
-<TR><th align="left">Contents </th>
- <th align="left">Type </th>
- <th align="left">Description </th></TR>
-
-<TR><!--contents--><TD valign="top">model_size </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>Number of variables in model, default is 960. </TD></TR>
-
-<TR><!--contents--><TD valign="top">forcing </TD>
- <!-- type --><TD valign="top">real(r8) </TD>
- <!--descript--><TD>Forcing, F, for model, default 15.0 </TD> </TR>
-
-<TR><!--contents--><TD valign="top">delta_t </TD>
- <!-- type --><TD valign="top">real(r8) </TD>
- <!--descript--><TD>Non-dimensional timestep, default 0.001</TD> </TR>
-
-<TR><!--contents--><TD valign="top">space_time_scale </TD>
- <!-- type --><TD valign="top">real(r8) </TD>
- <!--descript--><TD>Determines temporal and spatial relationship between
- fast and slow variables (model III), default 10.0 </TD></TR>
-
-<TR><!--contents--><TD valign="top">coupling </TD>
- <!-- type --><TD valign="top">real(r8) </TD>
- <!--descript--><TD>Linear coupling between fast and slow variables
- (model III), default 3.0 </TD></TR>
-
-<TR><!--contents--><TD valign="top">K </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>Determines the wavenumber of the slow variables
- (K=1, smooth_steps=0 reduces model II to Lorenz 96), default 32</TD></TR>
-
-<TR><!--contents--><TD valign="top">smooth_steps </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>Determines filter length to separate fast and
- slow scales, default 12 </TD></TR>
-
-<TR><!--contents--><TD valign="top">time_step_days </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>Arbitrary real time step days, default 0</TD></TR>
-
-<TR><!--contents--><TD valign="top">time_step_seconds </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>Arbitrary real time step seconds (could choose this
- for proper scaling), default 3600 </TD></TR>
-
-<TR><!--contents--><TD valign="top">model_number </TD>
- <!-- type --><TD valign="top">integer </TD>
- <!--descript--><TD>2 = single-scale, 3 = 2-scale.
- (This follows the notation in the paper.) default 3</TD></TR>
-
-</tbody>
-</TABLE>
-
-</div>
-<br>
-
<!--==================================================================-->
<!-- Describe the Files Used by this module. -->
<!--==================================================================-->
<A NAME="FilesUsed"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>FILES</H2>
<TABLE border=0 >
@@ -779,12 +824,15 @@
contains the default values</TD></TR>
</TABLE>
+<br />
+<br />
+
<!--==================================================================-->
<!-- Cite references, if need be. -->
<!--==================================================================-->
<A NAME="References"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>REFERENCES</H2>
<ol>
<li>Lorenz, E.N., 2005: Designing chaotic models.
@@ -792,12 +840,15 @@
<span style="font-weight: bold;">62</span>, 1574-1587.</li>
</ol>
+<br />
+<br />
+
<!--==================================================================-->
<!-- Describe all the error conditions and codes. -->
<!--==================================================================-->
<A NAME="Errors"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>ERROR CODES and CONDITIONS</H2>
<div class=errors>
<TABLE border=1 cellspacing=1 cellpadding=10 width=100%>
@@ -817,40 +868,35 @@
none at this time
</P>
+<br />
+<br />
+
<!--==================================================================-->
<!-- Describe Future Plans. -->
<!--==================================================================-->
<A NAME="FuturePlans"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>FUTURE PLANS</H2>
<P>
none at this time
</P>
-<!--==================================================================-->
-<!-- PrivateComponents -->
-<!--==================================================================-->
+<br />
+<br />
-<A NAME="PrivateComponents"></A>
-<HR>
-<H2>PRIVATE COMPONENTS</H2>
-<P>
-N/A
-</P>
-
<!--==================================================================-->
<!-- Legalese & Metadata -->
<!--==================================================================-->
<A NAME="Legalese"></A>
-<HR>
+<div class="top">[<a href="#">top</a>]</div><hr />
<H2>Terms of Use</H2>
<P>
-DART software - Copyright 2004 - 2013 UCAR.<br>
-This open source software is provided by UCAR, "as is",<br>
-without charge, subject to all terms of use at<br>
+DART software - Copyright 2004 - 2013 UCAR.<br />
+This open source software is provided by UCAR, "as is",<br />
+without charge, subject to all terms of use at<br />
<a href="http://www.image.ucar.edu/DAReS/DART/DART_download">
http://www.image.ucar.edu/DAReS/DART/DART_download</a>
</P>
@@ -860,7 +906,7 @@
<TR><TD valign=top>Revision: </TD><TD> $Revision$ </TD></TR>
<TR><TD valign=top>Source: </TD><TD> $URL$ </TD></TR>
<TR><TD valign=top>Change Date: </TD><TD> $Date$ </TD></TR>
-<TR><TD valign=top>Change history: </TD><TD> try "svn log" or "svn diff" </TD></TR>
+<TR><TD valign=top>Change history: </TD><TD> try "svn log" or "svn diff" </TD></TR>
</TABLE>
<!--==================================================================-->
Modified: DART/trunk/models/lorenz_63/model_mod.html
===================================================================
--- DART/trunk/models/lorenz_63/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/lorenz_63/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>module model_mod (Lorenz_63)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
@@ -13,7 +14,7 @@
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
Modified: DART/trunk/models/lorenz_84/model_mod.html
===================================================================
--- DART/trunk/models/lorenz_84/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/lorenz_84/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module model_mod (Lorenz_84)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (Lorenz_84)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (Lorenz_84)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
DART interface module for the Lorenz-84 model. The 17 public interfaces
Modified: DART/trunk/models/lorenz_96/model_mod.html
===================================================================
--- DART/trunk/models/lorenz_96/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/lorenz_96/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -4,24 +4,39 @@
<HEAD>
<TITLE>module model_mod (Lorenz_96)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css">
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE model_mod (Lorenz_96)</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+ <td valign=middle>
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
+ </td>
+ <td>
+ <P>Jump to <a href="../../index.html">DART Documentation Main Index</a><br />
+ <small><small>version information for this file: <br />
+ <!-- version tag follows, do not edit -->
+ $Id$</small></small>
+ </P></td>
+</tr>
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
<A HREF="#References">REFERENCES</A> /
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE model_mod (Lorenz_96)</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
+
<P>
DART interface module for the Lorenz-96 model. The 17 public interfaces
are standardized for all DART compliant models. These interfaces allow
Modified: DART/trunk/models/mpas_atm/model_mod.html
===================================================================
--- DART/trunk/models/mpas_atm/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/mpas_atm/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -5,14 +5,17 @@
<HEAD>
<TITLE>module model_mod (MPAS ATM)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
+<H1>MODULE model_mod (MPAS ATM)</H1>
+
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P><a href="../../index.html">DART Documentation Main Index</a><br />
@@ -32,7 +35,7 @@
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-<H1>MODULE model_mod (MPAS ATM)</H1>
+<H2>Overview</H2>
<P>The <strong>MPAS ATM </strong> interface for
<strong>Data Assimilation Research Testbed (DART)</strong> is under development.
Modified: DART/trunk/models/mpas_ocn/model_mod.html
===================================================================
--- DART/trunk/models/mpas_ocn/model_mod.html 2013-07-30 22:40:17 UTC (rev 6335)
+++ DART/trunk/models/mpas_ocn/model_mod.html 2013-07-30 23:01:31 UTC (rev 6336)
@@ -3,16 +3,19 @@
<HTML>
<HEAD>
-<TITLE>module model_mod (MPAS ATM)</TITLE>
+<TITLE>module model_mod (MPAS OCN)</TITLE>
<link rel="stylesheet" type="text/css" href="../../doc/html/doc.css" />
+<link href="../../doc/images/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
+<H1>MODULE model_mod (MPAS OCN)</H1>
+
<table border=0 summary="" cellpadding=5>
<tr>
<td valign=middle>
- <img src="../../doc/html/Dartboard7.png" alt="DART project logo" height=70 />
+ <img src="../../doc/images/Dartboard7.png" alt="DART project logo" height=70 />
</td>
<td>
<P><a href="../../index.html">DART Documentation Main Index</a><br />
@@ -32,13 +35,13 @@
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-<H1>MODULE model_mod (MPAS ATM)</H1>
+<H2>Overview</H2>
-<P>The <strong>MPAS ATM </strong> interface for
@@ Diff output truncated at 40000 characters. @@
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