[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>&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
+'&' 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> &
+ 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> </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>&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
-'&' 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> &
- 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
+'&' 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> &
+filter_kind, cutoff, sort_obs_inc, print_every_nth_obs, &
+spread_restoration, sampling_error_correction, adaptive_localization_threshold, &
+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
-'&' 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> &
-filter_kind, cutoff, sort_obs_inc, print_every_nth_obs, &
-spread_restoration, sampling_error_correction, adaptive_localization_threshold, &
-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
+'&' 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> &
+ ens_size, spin_up_steps, num_steps, output_start, ens_spin_up_steps, &
+ 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
-'&' 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> &
- ens_size, spin_up_steps, num_steps, output_start, ens_spin_up_steps, &
- 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
+'&' 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
-'&' 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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