[Dart-dev] [4522] DART/trunk: Using the new header style that Kevin, Nancy and I agreed on.

nancy at ucar.edu nancy at ucar.edu
Wed Oct 13 11:05:42 MDT 2010


Revision: 4522
Author:   thoar
Date:     2010-10-13 11:05:42 -0600 (Wed, 13 Oct 2010)
Log Message:
-----------
Using the new header style that Kevin, Nancy and I agreed on.
Makes the pages more 'documentation-like'. Where appropriate,
I also moved the namelist sections to be the first thing
after the Overview - as this is the most-oft used portion.

Modified Paths:
--------------
    DART/trunk/assim_model/assim_model_mod.html
    DART/trunk/assim_tools/assim_tools_mod.html
    DART/trunk/doc/html/boilerplate.html
    DART/trunk/ensemble_manager/ensemble_manager_mod.html
    DART/trunk/filter/filter.html
    DART/trunk/index.html
    DART/trunk/integrate_model/integrate_model.html
    DART/trunk/location/oned/location_mod.html
    DART/trunk/location/threed_sphere/location_mod.html
    DART/trunk/models/POP/dart_pop_mod.html
    DART/trunk/models/POP/dart_to_pop.html
    DART/trunk/models/POP/model_mod.html
    DART/trunk/models/POP/pop_to_dart.html
    DART/trunk/models/lorenz_63/model_mod.html
    DART/trunk/models/model_mod.html
    DART/trunk/models/wrf/model_mod.html
    DART/trunk/obs_def/DEFAULT_obs_def_mod.html
    DART/trunk/obs_sequence/obs_seq_to_netcdf.html
    DART/trunk/obs_sequence/obs_sequence_tool.html
    DART/trunk/utilities/PrecisionCheck.html

-------------- next part --------------
Modified: DART/trunk/assim_model/assim_model_mod.html
===================================================================
--- DART/trunk/assim_model/assim_model_mod.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/assim_model/assim_model_mod.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -3,24 +3,37 @@
 <HTML>
 <HEAD>
 <TITLE>module assim_model_mod</TITLE>
-<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link rel="stylesheet" type="text/css" href="../doc/html/doc.css" />
 </HEAD>
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>MODULE assim_model_mod</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>
+    <img src="../doc/html/Dartboard9.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 assim_model_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
 
 <P>
    This module acts as an intermediary between DART compliant models
@@ -36,10 +49,75 @@
    to the model_mod.
 </P>
 
+
+<H3 class=indent1>NOTES</H3>
+
+<P>
+Optional namelist interface
+<A HREF="#Namelist"> <em class=code>&#38;assim_model_nml</em> </A>
+may be read from file <em class=file>input.nml</em>.
+</P>
+
+<P>
+   A note about documentation style. 
+   Optional arguments are enclosed in brackets 
+   <em class=optionalcode>[like this]</em>.
+</P>
+
 <!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
+<!--==================================================================-->
 
-<A NAME="OtherModulesUsed"></A>
+<A NAME="Namelist"></A>
 <HR>
+<H2>NAMELIST</H2>
+<P>We adhere to the F90 standard of starting a namelist with an ampersand
+'&amp;' 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 / assim_model_nml / </em> &#38;
+    write_binary_restart_files,
+    netCDF_large_file_support
+</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%>
+<TR><TH align=left>Contents</TH>
+    <TH align=left>Type</TH>
+    <TH align=left>Description</TH></TR>
+<TR><!--contents--><TD valign=top><em class="code">write_binary_restart_files</em></TD>
+    <!--  type  --><TD valign=top>logical</TD>
+    <!--descript--><TD> Are output state restart files ascii (false) or 
+                        unformatted (true)? Default is .true.</TD></TR>
+<TR><!--contents--><TD valign=top><em class="code">netCDF_large_file_support</em></TD>
+    <!--  type  --><TD valign=top>logical</TD>
+    <!--descript--><TD> Use the netCDF LFS format that enables individual records
+        (i.e. all the information that has the same 'unlimited' record value) 
+        to exceed 2GB?  The only downside to using this flag is compatibility 
+        with some netCDF software. Some (but not all) software is not built 
+        with 'LFS' support.  Note it is, and has been, possible to create netCDF 
+        <strong>files</strong> larger than 2GB with a value of 
+        <em>.false</em> - which is compatible with the historical netCDF format. 
+        It is only necessary to use a value of <em>.true.</em> if the state vector 
+        is very large and you are outputting a large number of ensembles. 
+        Default is .false.</TD></TR>
+</TABLE>
+
+</div>
+<br>
+
+<!--==================================================================-->
+
+<A NAME="Interface"></A>
+<HR>
 <H2>OTHER MODULES USED</H2>
 <PRE>
 types_mod
@@ -59,7 +137,6 @@
 <!-- make sure you replace all yyyroutine?? strings                   -->
 <!--==================================================================-->
 
-<A NAME="Interface"></A>
 <HR>
 <H2>PUBLIC INTERFACES</H2>
 
@@ -108,20 +185,6 @@
 <TR><TD>&nbsp;</TD><TD><A HREF="#write_state_restart">write_state_restart</A></TD></TR>
 </TABLE>
 
-<H3 class=indent1>NOTES</H3>
-
-<P>
-Optional namelist interface
-<A HREF="#Namelist"> <em class=code>&#38;assim_model_nml</em> </A>
-may be read from file <em class=file>input.nml</em>.
-</P>
-
-<P>
-   A note about documentation style. 
-   Optional arguments are enclosed in brackets 
-   <em class=optionalcode>[like this]</em>.
-</P>
-
 <!--===================== DESCRIPTION OF A ROUTINE =====================-->
 
 <A NAME="assim_model_type"></A>
@@ -1441,56 +1504,6 @@
 <br>
 
 <!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
-<!--==================================================================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&amp;' 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 / assim_model_nml / </em> &#38;
-    write_binary_restart_files,
-    netCDF_large_file_support
-</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%>
-<TR><TH align=left>Contents</TH>
-    <TH align=left>Type</TH>
-    <TH align=left>Description</TH></TR>
-<TR><!--contents--><TD valign=top><em class="code">write_binary_restart_files</em></TD>
-    <!--  type  --><TD valign=top>logical</TD>
-    <!--descript--><TD> Are output state restart files ascii (false) or 
-                        unformatted (true)? Default is .true.</TD></TR>
-<TR><!--contents--><TD valign=top><em class="code">netCDF_large_file_support</em></TD>
-    <!--  type  --><TD valign=top>logical</TD>
-    <!--descript--><TD> Use the netCDF LFS format that enables individual records
-        (i.e. all the information that has the same 'unlimited' record value) 
-        to exceed 2GB?  The only downside to using this flag is compatibility 
-        with some netCDF software. Some (but not all) software is not built 
-        with 'LFS' support.  Note it is, and has been, possible to create netCDF 
-        <strong>files</strong> larger than 2GB with a value of 
-        <em>.false</em> - which is compatible with the historical netCDF format. 
-        It is only necessary to use a value of <em>.true.</em> if the state vector 
-        is very large and you are outputting a large number of ensembles. 
-        Default is .false.</TD></TR>
-</TABLE>
-
-</div>
-<br>
-
-<!--==================================================================-->
 <!-- Describe the Files Used by this module.                          -->
 <!--==================================================================-->
 

Modified: DART/trunk/assim_tools/assim_tools_mod.html
===================================================================
--- DART/trunk/assim_tools/assim_tools_mod.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/assim_tools/assim_tools_mod.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -3,24 +3,37 @@
 <HTML>
 <HEAD>
 <TITLE>module assim_tools_mod</TITLE>
-<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link rel="stylesheet" type="text/css" href="../doc/html/doc.css" />
 </HEAD>
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>MODULE assim_tools_mod</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>
+    <img src="../doc/html/Dartboard9.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 assim_tools_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
 
 <P>
 This module provides subroutines that implement the 'parallel' versions
@@ -34,9 +47,121 @@
 </P>
 
 <!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
+<!--==================================================================-->
 
-<A NAME="OtherModulesUsed"></A>
+<A NAME="Namelist"></A>
 <HR>
+<H2>NAMELIST</H2>
+<P>We adhere to the F90 standard of starting a namelist with an ampersand
+'&amp;' and terminating with a slash '/' for all our namelist input.
+The namelist declaration (i.e. what follows) has a different syntax, naturally.
+</P>
+<div class=namelist>
+<pre>
+<em class=call>namelist / assim_tools_nml / </em> &amp;
+filter_kind, cutoff, sort_obs_inc, print_every_nth_obs, &amp;
+spread_restoration, sampling_error_correction, adaptive_localization_threshold, &amp;
+output_localization_diagnostics, localization_diagnostics_file
+</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%>
+<TR><TH align=left>Contents    </TH>
+    <TH align=left>Type        </TH>
+    <TH align=left>Description </TH></TR>
+
+<TR><!--contents--><TD valign=top>filter_kind  </TD>
+    <!--  type  --><TD valign=top>integer      </TD>
+    <!--descript--><TD>Selects the variant of filter 
+        to be used. 1=EAKF, 2=ENKF, 3=Kernel filter, 
+        4=particle filter.  7=Boxcar kernel filter Default: 1.</TD></TR>
+
+<TR><!--contents--><TD valign=top>cutoff     </TD>
+    <!--  type  --><TD valign=top>real(r8)   </TD>
+    <!--descript--><TD>Cutoff controls a distance dependent weight that modulates
+                       the impact of an observation on a state variable. The units depend
+                       both on the location module being used and on the covariance cutoff
+                       module options selected. Default is 0.2.</TD></TR>
+
+<TR><!--contents--><TD valign=top>sort_obs_inc </TD>
+    <!--  type  --><TD valign=top>logical      </TD>
+    <!--descript--><TD> If true, the final increments from obs_increment are
+                        sorted so that the mean increment value is as small
+                        as possible. This minimizes regression errors when
+                        non-deterministic filter or error correction algorithms
+                        are applied. Default: false.</TD></TR>
+ 
+<TR><!--contents--><TD valign=top>spread_restoration </TD>
+    <!--  type  --><TD valign=top>logical            </TD>
+    <!--descript--><TD> True turns on algorithm to restore amount of spread that would be
+             expected to be lost if underlying obs/state variable correlation were really
+             0.  Default: false </TD></TR>
+
+<TR><!--contents--><TD valign=top>sampling_error_correction</TD>
+    <!--  type  --><TD valign=top>logical                  </TD>
+    <!--descript--><TD> True uses special input files generated by correl_error.f90
+     in system_simulation to reduce errors in the regression step. Special input
+     files corresponding with the ensemble size being used are required. This 
+     option is not yet fully supported. Contact the DART developers group if you 
+     have questions. 
+               Default: false </TD></TR>
+
+<TR><!--contents--><TD valign=top>adaptive_localization_threshold</TD>
+    <!--  type  --><TD valign=top>integer</TD>
+    <!--descript--><TD> Used to reduce the impact of observations in densely observed
+     regions. If the number of observations close to a given observation is greater
+     than the threshold number, the cutoff radius for localization is adjusted to
+     try to make the number of observations close to the given observation be
+     the threshold number. This should be dependent on the location module and
+     is tuned for a three_dimensional spherical implementation for numerical
+     weather prediction models at present.
+               Default: -1 </TD></TR>
+
+<TR><!--contents--><TD valign=top>output_localization_diagnostics</TD>
+    <!--  type  --><TD valign=top>logical</TD>
+    <!--descript--><TD> Setting this to .TRUE. will output an additional text
+     file that contains the obs key, the obs time, the obs location, the 
+     cutoff distance and the number of other obs which are within that radius.
+     If adaptive localization is enabled, the output also contains the updated 
+     cutoff distance and the number of other obs within that new radius.  Without
+     adaptive localization there will be a text line for each observation,
+     so this file could get very large.  With adaptive localization enabled,
+     there will only be one line per observation where the radius is changed,
+     so the size of the file will depend on the number of changed cutoffs.
+               Default: .false. </TD></TR>
+
+<TR><!--contents--><TD valign=top>localization_diagnostics_file</TD>
+    <!--  type  --><TD valign=top>character(len=129)</TD>
+    <!--descript--><TD> Filename for the localization diagnostics information.
+     This file will be opened in append mode, so new information will be written
+     at the end of any existing data.
+
+<TR><!--contents--><TD valign=top>print_every_nth_obs </TD>
+    <!--  type  --><TD valign=top>integer             </TD>
+    <!--descript--><TD> If set to a value <em class=code>N</em> greater than 0, 
+             the observation assimilation loop prints out a progress message 
+             every <em class=code>N</em>th observations.  This can be useful to
+             estimate the expected run time for a large observation file, 
+             or to verify progress is being made in cases with suspected problems.
+             Default: 0 </TD></TR>
+
+</TABLE>
+
+</div>
+<br>
+
+<!--==================================================================-->
+
+<A NAME="Interface"></A>
+<HR>
 <H2>OTHER MODULES USED</H2>
 <PRE>
 types_mod
@@ -63,7 +188,6 @@
 <!--Note to authors. The first row of the table is different.         -->
 <!--==================================================================-->
 
-<A NAME="Interface"></A>
 <HR>
 <H2>PUBLIC INTERFACES</H2>
 
@@ -179,118 +303,6 @@
 <br>
 
 <!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
-<!--==================================================================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&amp;' and terminating with a slash '/' for all our namelist input.
-The namelist declaration (i.e. what follows) has a different syntax, naturally.
-</P>
-<div class=namelist>
-<pre>
-<em class=call>namelist / assim_tools_nml / </em> &amp;
-filter_kind, cutoff, sort_obs_inc, print_every_nth_obs, &amp;
-spread_restoration, sampling_error_correction, adaptive_localization_threshold, &amp;
-output_localization_diagnostics, localization_diagnostics_file
-</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%>
-<TR><TH align=left>Contents    </TH>
-    <TH align=left>Type        </TH>
-    <TH align=left>Description </TH></TR>
-
-<TR><!--contents--><TD valign=top>filter_kind  </TD>
-    <!--  type  --><TD valign=top>integer      </TD>
-    <!--descript--><TD>Selects the variant of filter 
-        to be used. 1=EAKF, 2=ENKF, 3=Kernel filter, 
-        4=particle filter.  7=Boxcar kernel filter Default: 1.</TD></TR>
-
-<TR><!--contents--><TD valign=top>cutoff     </TD>
-    <!--  type  --><TD valign=top>real(r8)   </TD>
-    <!--descript--><TD>Cutoff controls a distance dependent weight that modulates
-                       the impact of an observation on a state variable. The units depend
-                       both on the location module being used and on the covariance cutoff
-                       module options selected. Default is 0.2.</TD></TR>
-
-<TR><!--contents--><TD valign=top>sort_obs_inc </TD>
-    <!--  type  --><TD valign=top>logical      </TD>
-    <!--descript--><TD> If true, the final increments from obs_increment are
-                        sorted so that the mean increment value is as small
-                        as possible. This minimizes regression errors when
-                        non-deterministic filter or error correction algorithms
-                        are applied. Default: false.</TD></TR>
- 
-<TR><!--contents--><TD valign=top>spread_restoration </TD>
-    <!--  type  --><TD valign=top>logical            </TD>
-    <!--descript--><TD> True turns on algorithm to restore amount of spread that would be
-             expected to be lost if underlying obs/state variable correlation were really
-             0.  Default: false </TD></TR>
-
-<TR><!--contents--><TD valign=top>sampling_error_correction</TD>
-    <!--  type  --><TD valign=top>logical                  </TD>
-    <!--descript--><TD> True uses special input files generated by correl_error.f90
-     in system_simulation to reduce errors in the regression step. Special input
-     files corresponding with the ensemble size being used are required. This 
-     option is not yet fully supported. Contact the DART developers group if you 
-     have questions. 
-               Default: false </TD></TR>
-
-<TR><!--contents--><TD valign=top>adaptive_localization_threshold</TD>
-    <!--  type  --><TD valign=top>integer</TD>
-    <!--descript--><TD> Used to reduce the impact of observations in densely observed
-     regions. If the number of observations close to a given observation is greater
-     than the threshold number, the cutoff radius for localization is adjusted to
-     try to make the number of observations close to the given observation be
-     the threshold number. This should be dependent on the location module and
-     is tuned for a three_dimensional spherical implementation for numerical
-     weather prediction models at present.
-               Default: -1 </TD></TR>
-
-<TR><!--contents--><TD valign=top>output_localization_diagnostics</TD>
-    <!--  type  --><TD valign=top>logical</TD>
-    <!--descript--><TD> Setting this to .TRUE. will output an additional text
-     file that contains the obs key, the obs time, the obs location, the 
-     cutoff distance and the number of other obs which are within that radius.
-     If adaptive localization is enabled, the output also contains the updated 
-     cutoff distance and the number of other obs within that new radius.  Without
-     adaptive localization there will be a text line for each observation,
-     so this file could get very large.  With adaptive localization enabled,
-     there will only be one line per observation where the radius is changed,
-     so the size of the file will depend on the number of changed cutoffs.
-               Default: .false. </TD></TR>
-
-<TR><!--contents--><TD valign=top>localization_diagnostics_file</TD>
-    <!--  type  --><TD valign=top>character(len=129)</TD>
-    <!--descript--><TD> Filename for the localization diagnostics information.
-     This file will be opened in append mode, so new information will be written
-     at the end of any existing data.
-
-<TR><!--contents--><TD valign=top>print_every_nth_obs </TD>
-    <!--  type  --><TD valign=top>integer             </TD>
-    <!--descript--><TD> If set to a value <em class=code>N</em> greater than 0, 
-             the observation assimilation loop prints out a progress message 
-             every <em class=code>N</em>th observations.  This can be useful to
-             estimate the expected run time for a large observation file, 
-             or to verify progress is being made in cases with suspected problems.
-             Default: 0 </TD></TR>
-
-</TABLE>
-
-</div>
-<br>
-
-<!--==================================================================-->
 <!-- Describe the Files Used by this module.                          -->
 <!--==================================================================-->
 

Modified: DART/trunk/doc/html/boilerplate.html
===================================================================
--- DART/trunk/doc/html/boilerplate.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/doc/html/boilerplate.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -4,24 +4,37 @@
 <HEAD>
 <TITLE>module xxxxxxx</TITLE>
 <!-- note ... DART/doc/html/doc.css is the true location -->
-<link rel="stylesheet" type="text/css" href="doc.css">
+<link rel="stylesheet" type="text/css" href="doc.css" />
 </HEAD>
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>MODULE xxxxxxx</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>
+    <img src="../../doc/html/Dartboard9.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 xxxxxxx</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
 
 <P>
    This is the place for the general description of the module
@@ -34,9 +47,91 @@
 </P>
 
 <!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
+<!--==================================================================-->
 
-<A NAME="OtherModulesUsed"></A>
+<A NAME="Namelist"></A>
 <HR>
+<H2>NAMELIST</H2>
+<P>We adhere to the F90 standard of starting a namelist with an ampersand
+'&amp;' and terminating with a slash '/' for all our namelist input.
+Consider yourself forewarned that character strings that contain a '/' must be
+enclosed in quotes to prevent them from prematurely terminating the namelist.
+The namelist declaration (i.e. what follows) has a different syntax, naturally.
+</P>
+<div class=namelist>
+<pre>
+<em class=call>namelist / model_nml / </em> &amp;
+    ens_size, spin_up_steps, num_steps, output_start, ens_spin_up_steps, &amp;
+    obs_freq, cov_inflate, mean_inflate, restart, add_on, noise_amp
+</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%>
+<TR><TH align=left>Contents    </TH>
+    <TH align=left>Type        </TH>
+    <TH align=left>Description </TH></TR>
+<TR><!--contents--><TD valign=top>ens_size             </TD>
+    <!--  type  --><TD valign=top>integer <em class="unit">[default: 0]</em></TD>
+    <!--descript--><TD>The number of "i" and "j" rows processed each time the 
+                       modular physics is called.      </TD></TR>
+
+<TR><!--contents--><TD valign=top>spin_up_steps        </TD>
+    <!--  type  --><TD valign=top>integer              </TD>
+    <!--descript--><TD>the month                       </TD></TR>
+
+<TR><!--contents--><TD valign=top>num_steps            </TD>
+    <!--  type  --><TD valign=top>real(r8)             </TD>
+    <!--descript--><TD>the day-of-month                </TD></TR>
+
+<TR><!--contents--><TD valign=top>output_start         </TD>
+    <!--  type  --><TD valign=top>real(r4)             </TD>
+    <!--descript--><TD>the hour-of-day                 </TD></TR>
+
+<TR><!--contents--><TD valign=top>ens_spin_up_steps    </TD>
+    <!--  type  --><TD valign=top>real(r4)             </TD>
+    <!--descript--><TD>the minute                      </TD></TR>
+
+<TR><!--contents--><TD valign=top>obs_freq,            </TD>
+    <!--  type  --><TD valign=top>real(r4)             </TD>
+    <!--descript--><TD>the second                      </TD></TR>
+
+<TR><!--contents--><TD valign=top>cov_inflate          </TD>
+    <!--  type  --><TD valign=top>real(r8)             </TD>
+    <!--descript--><TD>uniformly monotonic time        </TD></TR>
+
+<TR><!--contents--><TD valign=top>mean_inflate         </TD>
+    <!--  type  --><TD valign=top>character(len=80)    </TD>
+    <!--descript--><TD>the type of calendar being used </TD></TR>
+
+<TR><!--contents--><TD valign=top>restart              </TD>
+    <!--  type  --><TD valign=top>integer              </TD>
+    <!--descript--><TD>the type of calendar being used </TD></TR>
+
+<TR><!--contents--><TD valign=top>add_on               </TD>
+    <!--  type  --><TD valign=top>integer              </TD>
+    <!--descript--><TD>the type of calendar being used </TD></TR>
+
+<TR><!--contents--><TD valign=top>noise_amp            </TD>
+    <!--  type  --><TD valign=top>integer              </TD>
+    <!--descript--><TD>the type of calendar being used </TD></TR>
+
+</TABLE>
+
+</div>
+<br>
+
+
+<!--==================================================================-->
+
+<A NAME="Interface"></A>
+<HR>
 <H2>OTHER MODULES USED</H2>
 <PRE>
 types_mod
@@ -54,7 +149,6 @@
 <!--Note to authors. The first row of the table is different.         -->
 <!--==================================================================-->
 
-<A NAME="Interface"></A>
 <HR>
 <H2>PUBLIC INTERFACES</H2>
 
@@ -284,87 +378,6 @@
 <br>
 
 <!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
-<!--==================================================================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&amp;' and terminating with a slash '/' for all our namelist input.
-Consider yourself forewarned that character strings that contain a '/' must be
-enclosed in quotes to prevent them from prematurely terminating the namelist.
-The namelist declaration (i.e. what follows) has a different syntax, naturally.
-</P>
-<div class=namelist>
-<pre>
-<em class=call>namelist / model_nml / </em> &amp;
-    ens_size, spin_up_steps, num_steps, output_start, ens_spin_up_steps, &amp;
-    obs_freq, cov_inflate, mean_inflate, restart, add_on, noise_amp
-</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%>
-<TR><TH align=left>Contents    </TH>
-    <TH align=left>Type        </TH>
-    <TH align=left>Description </TH></TR>
-<TR><!--contents--><TD valign=top>ens_size             </TD>
-    <!--  type  --><TD valign=top>integer <em class="unit">[default: 0]</em></TD>
-    <!--descript--><TD>The number of "i" and "j" rows processed each time the 
-                       modular physics is called.      </TD></TR>
-
-<TR><!--contents--><TD valign=top>spin_up_steps        </TD>
-    <!--  type  --><TD valign=top>integer              </TD>
-    <!--descript--><TD>the month                       </TD></TR>
-
-<TR><!--contents--><TD valign=top>num_steps            </TD>
-    <!--  type  --><TD valign=top>real(r8)             </TD>
-    <!--descript--><TD>the day-of-month                </TD></TR>
-
-<TR><!--contents--><TD valign=top>output_start         </TD>
-    <!--  type  --><TD valign=top>real(r4)             </TD>
-    <!--descript--><TD>the hour-of-day                 </TD></TR>
-
-<TR><!--contents--><TD valign=top>ens_spin_up_steps    </TD>
-    <!--  type  --><TD valign=top>real(r4)             </TD>
-    <!--descript--><TD>the minute                      </TD></TR>
-
-<TR><!--contents--><TD valign=top>obs_freq,            </TD>
-    <!--  type  --><TD valign=top>real(r4)             </TD>
-    <!--descript--><TD>the second                      </TD></TR>
-
-<TR><!--contents--><TD valign=top>cov_inflate          </TD>
-    <!--  type  --><TD valign=top>real(r8)             </TD>
-    <!--descript--><TD>uniformly monotonic time        </TD></TR>
-
-<TR><!--contents--><TD valign=top>mean_inflate         </TD>
-    <!--  type  --><TD valign=top>character(len=80)    </TD>
-    <!--descript--><TD>the type of calendar being used </TD></TR>
-
-<TR><!--contents--><TD valign=top>restart              </TD>
-    <!--  type  --><TD valign=top>integer              </TD>
-    <!--descript--><TD>the type of calendar being used </TD></TR>
-
-<TR><!--contents--><TD valign=top>add_on               </TD>
-    <!--  type  --><TD valign=top>integer              </TD>
-    <!--descript--><TD>the type of calendar being used </TD></TR>
-
-<TR><!--contents--><TD valign=top>noise_amp            </TD>
-    <!--  type  --><TD valign=top>integer              </TD>
-    <!--descript--><TD>the type of calendar being used </TD></TR>
-
-</TABLE>
-
-</div>
-<br>
-
-<!--==================================================================-->
 <!-- Describe the Files Used by this module.                          -->
 <!--==================================================================-->
 

Modified: DART/trunk/ensemble_manager/ensemble_manager_mod.html
===================================================================
--- DART/trunk/ensemble_manager/ensemble_manager_mod.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/ensemble_manager/ensemble_manager_mod.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -8,19 +8,32 @@
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>MODULE ensemble_manager_mod</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>
+    <img src="../doc/html/Dartboard9.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 ensemble_manager_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
 
 <P>
 Manages storage and a number of operations for multiple copies of a vector.
@@ -40,9 +53,73 @@
 </P>
 
 <!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
+<!--==================================================================-->
 
-<A NAME="OtherModulesUsed"></A>
+<A NAME="Namelist"></A>
 <HR>
+<H2>NAMELIST</H2>
+<P>We adhere to the F90 standard of starting a namelist with an ampersand
+'&amp;' and terminating with a slash '/' for all our namelist input.
+Consider yourself forewarned that character strings that contain a '/' must be
+enclosed in quotes to prevent them from prematurely terminating the namelist.
+The namelist declaration (i.e. what follows) has a different syntax, naturally.
+</P>
+<div class=namelist>
+<pre>
+<em class=call>namelist / ensemble_manager_nml / </em>
+   single_restart_file_in, single_restart_file_out, perturbation_amplitude
+</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%>
+<TR><TH align=left>Contents    </TH>
+    <TH align=left>Type        </TH>
+    <TH align=left>Description </TH></TR>
+<TR><!--contents--><TD valign=top>single_restart_file_in</TD>
+    <!--  type  --><TD>logical</TD>
+    <!--descript--><TD>True if all copies read from a single file.
+      False for one file per copy. Default: .true.</TD></TR>
+<TR><!--contents--><TD valign=top>single_restart_file_out</TD>
+    <!--  type  --><TD>logical</TD>
+    <!--descript--><TD>True if all copies written to a single file.
+      False for one file per copy. Default: .true.</TD></TR>
+<TR><!--contents--><TD valign=top>perturbation_amplitude</TD>
+    <!--  type  --><TD valign=top>real(r8)</TD>
+    <!--descript--><TD>Perturbation standard deviation for generating 
+      ensemble member initial conditions if the model's model_mod does 
+      not provide code in a pert_model_state() routine to generate them
+      another way.
+      <br />Random noise values drawn from a gaussian distribution with this 
+      standard deviation will be added to the data in a single initial 
+      ensemble member to generate the rest of the members.
+      <br />This option is more frequently used in the low order models 
+      and less frequently used in large models.  This is in part due
+      to the different scales of real geophysical variable values, and the
+      resulting inconsistencies between related field values.  
+      A more successful initial condition generation
+      strategy is to generate climatological distributions from long model
+      runs which have internally consistent structures and values and then
+      use observations with a 'spin-up' period of assimilation to shape
+      the initial states into a set of members with enough spread and which
+      match the current set of observations.
+      Default: 0.2_r8</TD></TR>
+</TABLE>
+
+</div>
+<br>
+
+<!--==================================================================-->
+
+<A NAME="Interface"></A>
+<HR>
 <H2>OTHER MODULES USED</H2>
 <PRE>
 types_mod
@@ -61,7 +138,6 @@
 <!--Note to authors. The first row of the table is different.         -->
 <!--==================================================================-->
 
-<A NAME="Interface"></A>
 <HR>
 <H2>PUBLIC INTERFACES</H2>
 
@@ -804,70 +880,6 @@
 <br>
 
 <!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST  ===================-->
-<!--==================================================================-->
-
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>We adhere to the F90 standard of starting a namelist with an ampersand
-'&amp;' and terminating with a slash '/' for all our namelist input.
-Consider yourself forewarned that character strings that contain a '/' must be
-enclosed in quotes to prevent them from prematurely terminating the namelist.
-The namelist declaration (i.e. what follows) has a different syntax, naturally.
-</P>
-<div class=namelist>
-<pre>
-<em class=call>namelist / ensemble_manager_nml / </em>
-   single_restart_file_in, single_restart_file_out, perturbation_amplitude
-</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%>
-<TR><TH align=left>Contents    </TH>
-    <TH align=left>Type        </TH>
-    <TH align=left>Description </TH></TR>
-<TR><!--contents--><TD valign=top>single_restart_file_in</TD>
-    <!--  type  --><TD>logical</TD>
-    <!--descript--><TD>True if all copies read from a single file.
-      False for one file per copy. Default: .true.</TD></TR>
-<TR><!--contents--><TD valign=top>single_restart_file_out</TD>
-    <!--  type  --><TD>logical</TD>
-    <!--descript--><TD>True if all copies written to a single file.
-      False for one file per copy. Default: .true.</TD></TR>
-<TR><!--contents--><TD valign=top>perturbation_amplitude</TD>
-    <!--  type  --><TD valign=top>real(r8)</TD>
-    <!--descript--><TD>Perturbation standard deviation for generating 
-      ensemble member initial conditions if the model's model_mod does 
-      not provide code in a pert_model_state() routine to generate them
-      another way.
-      <br />Random noise values drawn from a gaussian distribution with this 
-      standard deviation will be added to the data in a single initial 
-      ensemble member to generate the rest of the members.
-      <br />This option is more frequently used in the low order models 
-      and less frequently used in large models.  This is in part due
-      to the different scales of real geophysical variable values, and the
-      resulting inconsistencies between related field values.  
-      A more successful initial condition generation
-      strategy is to generate climatological distributions from long model
-      runs which have internally consistent structures and values and then
-      use observations with a 'spin-up' period of assimilation to shape
-      the initial states into a set of members with enough spread and which
-      match the current set of observations.
-      Default: 0.2_r8</TD></TR>
-</TABLE>
-
-</div>
-<br>
-
-<!--==================================================================-->
 <!-- Describe the Files Used by this module.                          -->
 <!--==================================================================-->
 

Modified: DART/trunk/filter/filter.html
===================================================================
--- DART/trunk/filter/filter.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/filter/filter.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -8,43 +8,36 @@
 <BODY>
 <A NAME="TOP"></A>
 
-<div>
-<center>
-<strong><big><big><big>DART Project Documentation</big></big></big></strong> <br />
-<table width=80% border=0 summary="" cellpadding=0>
+<H1>PROGRAM <em class=program>filter</em></H1>
+
+<table border=0 summary="" cellpadding=5>
 <tr>
-<td align=center valign=middle>
-<a href="../index.html">DART Documentation Main Index</a> </td>
-<td align=center valign=middle>
-<img src="../doc/html/Dartboard9.png" alt="DART project logo" height=50 width=100> </td>
-<td align=center valign=middle>
-<small><small>Subversion info for this html file: <br />
-<!-- version tag follows, do not edit -->$Id$ 
-</small></small> </td>
+    <td valign=middle>
+    <img src="../doc/html/Dartboard9.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> <br />
-<A HREF="#Overview">OVERVIEW</A> / 
-<A HREF="#Namelist">NAMELIST</A> / 
+</table>
+
+<A HREF="#Namelist">NAMELIST</A> /
 <A HREF="#Modules">MODULES</A> /
 <A HREF="#FilesUsed">FILES</A> /
 <A HREF="#References">REFERENCES</A> /
 <A HREF="#Errors">ERRORS</A> /
 <A HREF="#FuturePlans">PLANS</A> /
 <A HREF="#Legalese">TERMS OF USE</A>
-</center>
-</div>
 
-<!--==================================================================-->
+<H2>Overview</H2>
 
-<H1>PROGRAM filter</H1>
 <P>
    Main program for driving ensemble filter assimilations. 
 </P>
 
-<A NAME="Overview"></A>
-<HR>
-<H2>OVERVIEW</H2>
-
 <P>
    <em class=program>filter</em> is a Fortran 90 program, and provides a large
    number of options for controlling execution behavior and parameter configuration

Modified: DART/trunk/index.html
===================================================================
--- DART/trunk/index.html	2010-10-13 17:02:19 UTC (rev 4521)
+++ DART/trunk/index.html	2010-10-13 17:05:42 UTC (rev 4522)
@@ -3,12 +3,27 @@
 <HTML>
 <HEAD>
 <TITLE>DART Documentation Index</TITLE>
-<link rel="stylesheet" type="text/css" href="doc/html/doc.css">
+<link rel="stylesheet" type="text/css" href="doc/html/doc.css" />
 </HEAD>
 <BODY>
 <A NAME="TOP"></A>
 
-<center>
+<H1>DART Documentation Index</H1>
+
+<table border=0 summary="" cellpadding=5>
+<tr>
+    <td valign=middle>

@@ Diff output truncated at 40000 characters. @@


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