[Dart-dev] [4743] DART/trunk: Minor updates, mostly to the headers of these files
nancy at ucar.edu
nancy at ucar.edu
Tue Feb 22 13:53:51 MST 2011
Revision: 4743
Author: nancy
Date: 2011-02-22 13:53:51 -0700 (Tue, 22 Feb 2011)
Log Message:
-----------
Minor updates, mostly to the headers of these files
but also fix minor things which were out-of-date or
were missing documentation.
Modified Paths:
--------------
DART/trunk/DART_LAB/DART_LAB.html
DART/trunk/adaptive_inflate/adaptive_inflate_mod.html
DART/trunk/assim_model/assim_model_mod.html
DART/trunk/common/types_mod.html
DART/trunk/cov_cutoff/cov_cutoff_mod.html
DART/trunk/doc/html/index.shtml
DART/trunk/ensemble_manager/ensemble_manager_mod.html
DART/trunk/filter/filter.html
DART/trunk/filter/wakeup_filter.html
DART/trunk/index.html
DART/trunk/integrate_model/integrate_model.html
DART/trunk/mkmf/mkmf.html
DART/trunk/models/model_mod.html
DART/trunk/mpi_utilities/mpi_utilities_mod.html
DART/trunk/obs_def/DEFAULT_obs_def_mod.html
DART/trunk/obs_def/obs_def_1d_state_mod.html
DART/trunk/obs_def/obs_def_dew_point_mod.html
DART/trunk/obs_def/obs_def_mod.html
DART/trunk/obs_def/obs_def_ocean_mod.html
DART/trunk/obs_def/obs_def_radar_mod.html
DART/trunk/obs_kind/DEFAULT_obs_kind_mod.html
DART/trunk/obs_kind/obs_kind_mod.html
DART/trunk/obs_model/obs_model_mod.html
DART/trunk/obs_sequence/create_fixed_network_seq.html
DART/trunk/obs_sequence/create_obs_sequence.html
DART/trunk/obs_sequence/obs_selection.html
DART/trunk/obs_sequence/obs_seq_to_netcdf.html
DART/trunk/obs_sequence/obs_sequence_mod.html
DART/trunk/obs_sequence/obs_sequence_tool.html
DART/trunk/observations/observations.html
DART/trunk/perfect_model_obs/perfect_model_obs.html
DART/trunk/preprocess/preprocess.html
DART/trunk/random_nr/random_nr_mod.html
DART/trunk/random_seq/random_seq_mod.html
DART/trunk/reg_factor/reg_factor_mod.html
DART/trunk/smoother/smoother_mod.html
DART/trunk/system_simulation/system_simulation.html
DART/trunk/time_manager/advance_time.html
DART/trunk/time_manager/schedule_mod.html
DART/trunk/time_manager/time_manager_mod.html
DART/trunk/utilities/PrecisionCheck.html
DART/trunk/utilities/restart_file_tool.html
DART/trunk/utilities/utilities_mod.html
-------------- next part --------------
Modified: DART/trunk/DART_LAB/DART_LAB.html
===================================================================
--- DART/trunk/DART_LAB/DART_LAB.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/DART_LAB/DART_LAB.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,20 +4,32 @@
<HEAD>
<TITLE>DART_LAB Tutorial</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>DART_LAB Tutorial</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="#Presentations">Presentations</A> /
<A HREF="#Matlab">Matlab Programs</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>DART_LAB Tutorial</H1>
-<small><P>Latest subversion revision tag:
-<!-- version tag follows, do not edit -->$Id$
-</P></small>
+<H2>Overview</H2>
<P>
The files in this directory contain PDF tutorial
Modified: DART/trunk/adaptive_inflate/adaptive_inflate_mod.html
===================================================================
--- DART/trunk/adaptive_inflate/adaptive_inflate_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/adaptive_inflate/adaptive_inflate_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,11 +4,27 @@
<HEAD>
<TITLE>module adaptive_inflate_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE adaptive_inflate_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="#Interface">INTERFACES</A> /
<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
@@ -17,21 +33,23 @@
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE adaptive_inflate_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
This module implements a variety of hierarchical Bayesian adaptive
inflation algorithms for use with ensemble filters. It can provide
-constant valued inflation in state or obsevation space, consistent with
+constant valued inflation in state or observation space, consistent with
previous DART releases. It can provide spatially-constant, time-varying
-spatial adaptive inflation. It can provide spatially-varying, time-varying
-spatial adaptive inflation and it can provide temporally-varying
-observation space inflation. Diagnostic output and restart files are
-available. Several papers on the NCAR/IMAGe/DAReS web page document the
-algorithms in detail. The <em class=file>DART/tutorial/section12</em>
+adaptive inflation. It can provide spatially-varying, time-varying
+adaptive inflation and it can provide temporally-varying
+observation space inflation. And finally, it can provide adaptive
+damped inflation, which decreases inflation through time when
+observation density varies.
+Diagnostic output and restart files are
+available. Several papers on the NCAR
+<a href="http://www.image.ucar.edu/DAReS">IMAGe/DAReS<a> web page document
+the algorithms in detail. The <em class=file>DART/tutorial/section12</em>
chapter has more information.
<BR>
<BR>
@@ -705,12 +723,24 @@
<A NAME="References"></A>
<HR>
<H2>REFERENCES</H2>
-<OL>
-<LI>Anderson, Jeffrey L., 2006: An adaptive covariance inflation error
- correction algorithm for ensemble filters.</LI>
-<LI>Anderson, Jeffrey L., 2006: Spatially-varying adaptive covariance
- inflation in an ensemble filter.</LI>
-</OL>
+<uL>
+<li>Anderson, J. L., 2007:
+An adaptive covariance inflation error correction algorithm for ensemble filters.
+<span style="font-style: italic;">Tellus A</span>,
+<span style="font-weight: bold;">59</span>, 210-224.<br />
+<a href="http://dx.doi.org/10.1111/j.1600-0870.2006.00216.x
+target="_blank" >
+doi: 10.1111/j.1600-0870.2006.00216.x </a></li>
+<br />
+<li>Anderson, J. L., 2009:
+Spatially and temporally varying adaptive covariance inflation for ensemble filters.
+<span style="font-style: italic;">Tellus A</span>,
+<span style="font-weight: bold;">61</span>, 72-83.<br />
+<a href="http://dx.doi.org/10.1111/j.1600-0870.2008.00361.x"
+target="_blank" >
+doi: 10.1111/j.1600-0870.2008.00361.x</a></li>
+<br />
+</uL>
<!--==================================================================-->
<!-- Describe all the error conditions and codes. -->
@@ -724,7 +754,7 @@
<TR><TH>Routine</TH><TH>Message</TH><TH>Comment</TH></TR>
<TR><!-- routine --><TD VALIGN=top>adaptive_inflate_init</TD>
- <!-- message --><TD VALIGN=top>Cannot have non-determisitic inflation and
+ <!-- message --><TD VALIGN=top>Cannot have non-deterministic inflation and
inf_lower_bound < 1.</TD>
<!-- comment --><TD VALIGN=top>Algorithm can't work in this case.<BR>
</TR>
Modified: DART/trunk/assim_model/assim_model_mod.html
===================================================================
--- DART/trunk/assim_model/assim_model_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/assim_model/assim_model_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>module assim_model_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css" />
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
Modified: DART/trunk/common/types_mod.html
===================================================================
--- DART/trunk/common/types_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/common/types_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,11 +4,27 @@
<HEAD>
<TITLE>module types_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>MODULE types_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="#Interface">INTERFACES</A> /
<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
@@ -17,11 +33,10 @@
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#PrivateComponents">PRIVATE COMPONENTS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>MODULE types_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
+
<P>
Provides some commonly used mathematical constants, and a set of
Fortran integer and real kinds, to be used to select the right
Modified: DART/trunk/cov_cutoff/cov_cutoff_mod.html
===================================================================
--- DART/trunk/cov_cutoff/cov_cutoff_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/cov_cutoff/cov_cutoff_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,23 +4,37 @@
<HEAD>
<TITLE>module cov_cutoff_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
-<A HREF="#Interface">INTERFACES</A> /
+<H1>MODULE cov_cutoff_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="#FilesUsed">FILES</A> /
+<A HREF="#Interface">INTERFACES</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 cov_cutoff_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
Computes the weight with which an observation should impact a state
@@ -29,7 +43,49 @@
</P>
<!--==================================================================-->
+<!--=================== 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.
+Filenames that contain a '/' must be
+enclosed in quotes to prevent them from prematurely terminating the namelist.
+</P>
+<div class=namelist>
+<pre>
+<em class=call>namelist / cov_cutoff_nml / </em> select_localization
+</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>select_localization</TD>
+ <!-- type --><TD valign=top>integer<br>
+ <em class="unit"> </em></TD>
+ <!--descript--><TD>Selects the localization function. [Default: 1] <BR>
+ 1 = Gaspari-Cohn 5th order polynomial with halfwidth c. <BR>
+ 2 = Boxcar with halfwidth c (goes to 0 for z_in < 2c). <BR>
+ 3 = ramped boxcar. Has value 1 for z_in < c and then
+ reduces linearly to 0 at z_in = 2c. </TD></TR>
+</TABLE>
+
+</div>
+<br>
+
+<!--==================================================================-->
+
<A NAME="OtherModulesUsed"></A>
<HR>
<H2>OTHER MODULES USED</H2>
@@ -128,49 +184,6 @@
<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 filenames 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 / cov_cutoff_nml / </em> select_localization
-</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>select_localization</TD>
- <!-- type --><TD valign=top>integer<br>
- <em class="unit"> </em></TD>
- <!--descript--><TD>Selects the localization function. [Default: 1] <BR>
- 1 = Gaspari-Cohn 5th order polynomial with halfwidth c. <BR>
- 2 = Boxcar with halfwidth c (goes to 0 for z_in < 2c). <BR>
- 3 = ramped boxcar. Has value 1 for z_in < c and then
- reduces linearly to 0 at z_in = 2c. </TD></TR>
-</TABLE>
-
-</div>
-<br>
-
-<!--==================================================================-->
<!-- Describe the Files Used by this module. -->
<!--==================================================================-->
Modified: DART/trunk/doc/html/index.shtml
===================================================================
--- DART/trunk/doc/html/index.shtml 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/doc/html/index.shtml 2011-02-22 20:53:51 UTC (rev 4743)
@@ -591,25 +591,30 @@
<h2>DART Contact list</h2>
<p>
We're a very small group, so the contact list is pretty short.
- We don't have a central contact email address, but we all know how
- to forward email to each other. So no matter who you send the email TO,
- it will find its way to the best person. Pretty cool, eh?
+ Our central email contact is <a href="mailto:dart at ucar.edu">dart at ucar.edu</a>.
+ Or if you want to contact us individually, here is our information:
</p>
<table width="95%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr><th align="left">general</th>
- <th align="left">general</th>
+ <th align="left">general/diagnostics</th>
<th align="left">platforms/mpi</th>
<th align="left">CAM</th>
+ <th align="left">WRF</th>
+ <th align="left">GPS Radio Occultation</th>
</tr>
<tr><td>Jeff Anderson</td>
<td>Tim Hoar</td>
<td>Nancy Collins</td>
<td>Kevin Raeder</td>
+ <td>Glen Romine</td>
+ <td>Hui Liu</td>
</tr>
<tr><td>jla @ ucar . edu</td>
<td>thoar @ ucar . edu</td>
<td>nancy @ ucar . edu</td>
<td>raeder @ ucar . edu</td>
+ <td>romine @ ucar . edu</td>
+ <td>hliu @ ucar . edu</td>
</tr>
</table>
Modified: DART/trunk/ensemble_manager/ensemble_manager_mod.html
===================================================================
--- DART/trunk/ensemble_manager/ensemble_manager_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/ensemble_manager/ensemble_manager_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>module ensemble_manager_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
Modified: DART/trunk/filter/filter.html
===================================================================
--- DART/trunk/filter/filter.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/filter/filter.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>program filter</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
@@ -990,7 +991,7 @@
An adaptive covariance inflation error correction algorithm for ensemble filters.
<span style="font-style: italic;">Tellus A</span>,
<span style="font-weight: bold;">59</span>, 210-224.<br />
-<a href="http://dx.doi.org/10.1111/j.1600-0870.2006.00216.x
+<a href="http://dx.doi.org/10.1111/j.1600-0870.2006.00216.x"
target="_blank" >
doi: 10.1111/j.1600-0870.2006.00216.x </a></li>
<br />
@@ -1003,14 +1004,13 @@
target="_blank" >
doi:10.1016/j.physd.2006.02.011</a></li>
<br />
-<li>Anderson, J., T. Hoar, K. Raeder, H. Liu,
-N. Collins, R. Torn, and A. Arellano, 2009:
-The Data Assimilation Research Testbed: A Community Facility.
-<span style="font-style: italic;">Bull. Amer. Meteor. Soc.</span>,
-<span style="font-weight: bold;">90</span>, 1283-1296.<br />
-<a href="http://dx.doi.org/10.1175/2009BAMS2618.1"
+<li>Anderson, J., Collins, N., 2007:
+Scalable Implementations of Ensemble Filter Algorithms for Data Assimilation.
+<span style="font-style: italic;">Journal of Atmospheric and Oceanic Technology</span>,
+<span style="font-weight: bold;">24</span>, 1452-1463.<br />
+<a href="http://dx.doi.org/10.1175/JTECH2049.1"
target="_blank" >
-doi: 10.1175/2009BAMS2618.1</a></li>
+doi: 10.1175/JTECH2049.1</a></li>
<br />
<li>Anderson, J. L., 2009:
Spatially and temporally varying adaptive covariance inflation for ensemble filters.
@@ -1020,6 +1020,15 @@
target="_blank" >
doi: 10.1111/j.1600-0870.2008.00361.x</a></li>
<br />
+<li>Anderson, J., T. Hoar, K. Raeder, H. Liu,
+N. Collins, R. Torn, and A. Arellano, 2009:
+The Data Assimilation Research Testbed: A Community Facility.
+<span style="font-style: italic;">Bull. Amer. Meteor. Soc.</span>,
+<span style="font-weight: bold;">90</span>, 1283-1296.<br />
+<a href="http://dx.doi.org/10.1175/2009BAMS2618.1"
+target="_blank" >
+doi: 10.1175/2009BAMS2618.1</a></li>
+<br />
<li>Anderson, J. L., 2010:
A Non-Gaussian Ensemble Filter Update for Data Assimilation.
<span style="font-style: italic;">Mon. Wea. Rev.</span>,
Modified: DART/trunk/filter/wakeup_filter.html
===================================================================
--- DART/trunk/filter/wakeup_filter.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/filter/wakeup_filter.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,11 +4,27 @@
<HEAD>
<TITLE>program wakeup_filter</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
+<H1>PROGRAM <em class=program>wakeup_filter</em></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="#Modules">MODULES</A> /
<A HREF="#Namelist">NAMELIST</A> /
<A HREF="#FilesUsed">FILES</A> /
@@ -16,10 +32,8 @@
<A HREF="#Errors">ERRORS</A> /
<A HREF="#FuturePlans">PLANS</A> /
<A HREF="#Legalese">TERMS OF USE</A>
-</center>
-<H1>PROGRAM <em class=program>wakeup_filter</em></H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
Small auxiliary program for use in the "async=4" case where
Modified: DART/trunk/index.html
===================================================================
--- DART/trunk/index.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/index.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,11 +4,12 @@
<HEAD>
<TITLE>DART Documentation Index</TITLE>
<link rel="stylesheet" type="text/css" href="doc/html/doc.css" />
+<link href="doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<H1>DART Documentation Index</H1>
+<H1>DART Documentation Main Index</H1>
<table border=0 summary="" cellpadding=5>
<tr>
@@ -16,7 +17,7 @@
<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 />
+ <P><!-- already here: 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>
@@ -25,17 +26,66 @@
</table>
<A HREF="#Programs">Programs</A> /
-<A HREF="#Models">MODELS</A> /
-<A HREF="#Namelists">NAMELIST</A> /
-<A HREF="#Modules">MODULES</A> /
-<A HREF="#OtherDocs">OTHER DOCUMENTATION</A> /
-<A HREF="#KitchenSink">ALL DOCUMENTS</A> /
-<A HREF="#Legalese">TERMS OF USE</A>
+<A HREF="#Models">Models</A> /
+<A HREF="#Namelists">Namelist</A> /
+<A HREF="#Modules">Modules</A> /
+<A HREF="#OtherDocs">Other Documentation</A> /
+<A HREF="#KitchenSink">All Documents</A> /
+<A HREF="#Legalese">Terms of Use</A>
<H2>Overview</H2>
<P>
-This page contains links to all the documentation for this DART release.
+The Data Assimilation Research Testbed (DART) is a public-domain,
+community facility for doing research on and applying ensemble
+data assimilation techniques over a variety of models and observation types.
+It includes many example models and support for
+common observation types and for different filter types.
+It also includes material for teaching and learning the basic
+principles of data assimilation.
+</P><P>
+DART strives to implement general solutions
+which work over a range of models and observation types,
+and to develop theory-based algorithms that solve the many
+real problems encountered when doing ensemble data assimilation.
+The algorithms in DART are tested on both simple one-dimensional
+models (e.g. the Lorenz series of models) as well as full-up
+3D NWP (Numerical Weather Prediction) models and GCMs (Global Climate Models).
+The basic Kalman filter code can be written in a few lines.
+In practice, however, there are a variety of difficulties
+resulting from sampling error, model bias, observation error,
+lack of model divergence, variations in observation density in
+space and time, etc.
+There are tools built into the DART framework to address
+many of these problems.
+</P> <P>
+To get started, look here:
+<ul>
+<li>Our extensive <a href="http://www.image.ucar.edu/DAReS/">web pages</a></li>
+<li>Documentation for the
+main assimilation program <a href="filter/filter.html">filter</a></li>
+<li>Documentation for the other related
+<a href="#Programs">programs</a> that come with DART</li>
+<li>Documentation for <a href="observations/observations.html">observation
+types</a> supported by DART</li>
+<li>Documentation for the Matlab <a href="#Diagnostics">diagnostic tools
+types</a></li>
+<li>Discussion of <a href="assim_tools/assim_tools_mod.html">localization</a>,
+<a href="filter/filter.html#Inflation">inflation</a></li>
+<li>The web pages specific to <a href="#Models">each model</a></li>
+<li>The web pages specific to <a href="#Observations">each observation type</a></li>
+</ul>
+</P>
+<P>
+The best way to get to know the DART software is to follow along while
+reading the tutorial documents in the <em class="file">DART_LAB</em>
+and then the <em class="file">DART/tutorial</em> directory.
+</P>
+<P>
+The remainder of this page
+contains links to all the documentation for this DART release.
+</P>
+<P>
The latest official release was named "Jamaica" but that was quite a
while ago. We have been making significant code improvements since then
and now recommend people check out the head of the trunk branch of the
@@ -44,17 +94,14 @@
<a href="doc/html/Jamaica_release.html">doc/html/Jamaica_release.html</a> and
the differences from the previous release are highlighted in
<a href="doc/html/Jamaica_diffs_from_I.html">doc/html/Jamaica_diffs_from_I.html</a>.
- General DART documentation can be found in the
+</P>
+<P>
+General DART documentation can be found in the
<em class="file">doc/html</em> directory.
Every source file has a corresponding .html file that contains
specifics for public interfaces in each of the DART
modules, for the executable programs which come with DART, and for
how to interface new models into the DART system.
-<br>
-<br>
-The best way to get to know the DART software is to follow along while
-reading the tutorial documents in the <em class="file">DART_LAB</em>
-and then the <em class="file">DART/tutorial</em> directory.
</P>
<!--==================================================================-->
@@ -122,6 +169,7 @@
<A HREF="filter/wakeup_filter.html">program wakeup_filter</A> - needed when running a parallel model advance
</pre>
+<A NAME="Diagnostics"></A>
<P>
The diagnostic programs that process observations after being assimilated
by DART include:
@@ -135,6 +183,7 @@
<A HREF="diagnostics/rms_diag.f90">program rms_diag</A> - example code to compute diagnostics
</pre>
+<A NAME="Observations"></A>
<P>
The executable programs that convert observations into DART format include:
</P>
Modified: DART/trunk/integrate_model/integrate_model.html
===================================================================
--- DART/trunk/integrate_model/integrate_model.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/integrate_model/integrate_model.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>program integrate_model</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
Modified: DART/trunk/mkmf/mkmf.html
===================================================================
--- DART/trunk/mkmf/mkmf.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/mkmf/mkmf.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -3,6 +3,7 @@
<head>
<!-- $Id$ -->
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
<title>mkmf user's guide</title>
</head>
Modified: DART/trunk/models/model_mod.html
===================================================================
--- DART/trunk/models/model_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/models/model_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,6 +4,7 @@
<HEAD>
<TITLE>module model_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css" />
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
Modified: DART/trunk/mpi_utilities/mpi_utilities_mod.html
===================================================================
--- DART/trunk/mpi_utilities/mpi_utilities_mod.html 2011-02-22 20:50:20 UTC (rev 4742)
+++ DART/trunk/mpi_utilities/mpi_utilities_mod.html 2011-02-22 20:53:51 UTC (rev 4743)
@@ -4,33 +4,218 @@
<HEAD>
<TITLE>module mpi_utilities_mod</TITLE>
<link rel="stylesheet" type="text/css" href="../doc/html/doc.css">
+<link href="../doc/html/dart.ico" rel="shortcut icon" />
</HEAD>
<BODY>
<A NAME="TOP"></A>
-<center>
-<A HREF="#Interface">INTERFACES</A> /
-<A HREF="#Namelist">NAMELIST</A> /
+<H1>MODULE mpi_utilities_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="#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 mpi_utilities_mod</H1>
-<!-- version tag follows, do not edit --><P>$Id$</P>
+<H2>Overview</H2>
<P>
-This module provides subroutines which access the MPI
-(message passing interface) parallel communications library.
-To compile without using MPI substitute the
-<em class="file">null_mpi_utilities_mod.f90</em> for this one.
+This module provides subroutines which utilize the MPI
+(Message Passing Interface) parallel communications library.
+DART does <strong>not</strong> require MPI;
+to compile without using MPI substitute the
+<em class="file">null_mpi_utilities_mod.f90</em> file for this one.
+That file contains the same module name and public entry points
+as this one but implements a serial version of all the routines.
+However, to be able to run most larger models with a reasonable
+number of ensemble members (e.g. 30-100) MPI will be needed.
+</P> <P>
+The main DART executable
+<em class="file">filter</em> can be compiled and run
+as either a serial program or a parallel program.
+Most work directories in the DART distribution source tree
+have a <em class="file">quickbuild.csh</em> script which can
+take a <em class="code">-mpi</em>
+or a <em class="code">-nompi</em> flag. This flag changes the list
+of files to be compiled to use either the module which uses
+the MPI library or the one which makes no MPI calls.
+No source code changes are required to switch between
+the two options.
+</P> <P>
+A parallel program generally runs faster and requires less memory
+per CPU than the serial code. It requires an implementation of
+the MPI library and run-time system to pass data between different
+nodes on a parallel cluster or supercomputer. There is a lot of
+information about MPI on the web. See here for
+<a href="http://www.lam-mpi.org/tutorials">
+an intro to MPI and parallel programming</a>, and here for
+<a href="http://www.open-mpi.org">downloads and technical help</a>.
+</P> <P>
+Most of the larger models need to be compiled and run with MPI
+because of limitations on total memory accessible by a single
+executable. The smaller models (e.g. any of the Lorenz models)
+can generally be run as a serial program without needing MPI.
+</P> <P>
+The MPI distributions usually include a module named <em class="file">mpi</em>
+which defines the public entry points and the types and
+names of the routine arguments. However there are build-time
+options and older distributions which only supply an
+<em class="file">mpi.h</em> include file. If you get a compile-time
+error about the mpi module being missing, edit the source code
+in <em class="code">mpi_utilities/mpi_utilities_mod.f90</em>
+and comment out the <em class="code">use mpi</em> line and
+comment in the <em class="code">include 'mpi.h'</em> line.
+</P> <P>
+If you get a compile-time error about the <em class="code">system()</em>
+function being undefined, try running the <em class=file>fixsystem</em>
+shell script in this directory. It comments out (or back in if you run
+it a second time) the interface block for the system() call. As of this
+writing, all compilers except gfortran require the block while
+gfortran fails if the block is defined. Go figure.
+</P> <P>
+To preserve backwards compatibility this code does not require
+a namelist. However there is a namelist defined in the source file
+which contains some useful run-time options.
+To enable it edit the source file
+in <em class="code">mpi_utilities/mpi_utilities_mod.f90</em>
+and set <em class="code">use_namelist</em>
+to .TRUE. and recompile. The code will then read the namelist described below.
+Messages printed to the nml output log file will confirm whether
+the defaults are being used or if the namelist is being read in.
</P>
<!--==================================================================-->
+<!--=================== DESCRIPTION OF A NAMELIST ===================-->
+<!--==================================================================-->
+<A NAME="Namelist"></A>
+<HR>
+<H2>NAMELIST</H2>
+<P>
+The source code defines a namelist, but for backwards compatibility
+it is not read in unless the source code
+in <em class="code">mpi_utilities/mpi_utilities_mod.f90</em>
+is edited, the module
+global variable <em class="code">use_namelist</em> is changed from
+.FALSE. to .TRUE., and then all executables must be recompiled.
+</P>
+
+<P>
+If the namelist is enabled, then the values in the namelist
+<A HREF="#Namelist"><em class=code>&mpi_utilities_nml</em> </A>
+will be read from file <em class=file>input.nml</em>.
+</P>
+
+<div class=namelist>
+<pre>
+<em class=call> namelist /mpi_utilities_nml/ </em>
+ reverse_task_layout, all_tasks_print, &
+ verbose, async2_verbose, async4_verbose, &
+ shell_name, separate_node_sync, &
+ create_local_comm /
+</pre>
+</div>
+
+<div class=indent1>
+<!-- Description -->
+
+
+<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>reverse_task_layout</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>If running async=4 mode (parallel filter
+ and parallel model advance) with the OpenMPI library,
+ this must be .TRUE. . The synchronizing
+ mechanism between the scripting and the filter executable will
+ fail otherwise. Default: .FALSE.</TD></TR>
+
+<TR><!--contents--><TD valign=top>all_tasks_print</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>In the parallel filter, informational messages only
+ print from task 0 to avoid N copies of the same messages. Error
+ messages and warnings print no matter which task they occur in.
+ If this variable is set to true, messages will print
+ from all tasks. Default: .FALSE. </TD></TR>
+
+<TR><!--contents--><TD valign=top>verbose</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>USE WITH CAUTION! This flag enables debugging
+ print messages for every MPI call - sends, receives, syncs - and
+ is very, very verbose. In most cases the size of the output file
+ will exceed the filesystem limits or will cause the executable to
+ run so slowly that it will not be useful. However in small
+ testcases this can be useful to trace problems. Default: .FALSE. </TD></TR>
+
+<TR><!--contents--><TD valign=top>async2_verbose</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>Print out messages about the handshaking
+ between filter and the advance model scripts when running
+ in async=2 mode. Not anywhere as verbose as the flag above;
+ in most cases the output volume is reasonable. Default: .FALSE. </TD></TR>
+
+<TR><!--contents--><TD valign=top>async4_verbose</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>Print out messages about the handshaking
+ between filter and the run script when running
+ in async=4 mode. Not anywhere as verbose as the flag above;
+ in most cases the output volume is reasonable. Default: .FALSE. </TD></TR>
+
+<TR><!--contents--><TD valign=top>shell_name</TD>
+ <!-- type --><TD valign=top>character(len=129)</TD>
+ <!--descript--><TD>If running on compute nodes which do not have the
+ expected default shell for async=2 or async=4 mode, specify the
+ full pathname of the shell to execute the script. Not normally
+ needed on most systems we run on (Cray execute nodes being an
+ exception.) Default: '' </TD></TR>
+
+<TR><!--contents--><TD valign=top>separate_node_sync</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>Not supported yet. Will use files to handshake between
+ the filter executable and the run script in async=4 mode when the
+ launch script is not running on any of the same nodes as the filter tasks.
+ Default: .FALSE.</TD></TR>
+
+<TR><!--contents--><TD valign=top>create_local_comm</TD>
+ <!-- type --><TD valign=top>logical</TD>
+ <!--descript--><TD>The DART MPI routines normally create a separate
+ local MPI communicator instead of using MPI_COMM_WORLD. This
+ keeps DART communications separate from any other user code.
+ To use the default world communicator set this to .FALSE. .
+ Normal use should leave this true.
+ Default: .TRUE.</TD></TR>
+
+
+</TABLE>
+
+
+</div>
+<br>
+
+<!--==================================================================-->
+<!--==================================================================-->
+<!--==================================================================-->
+
<A NAME="OtherModulesUsed"></A>
<HR>
<H2>OTHER MODULES USED</H2>
@@ -42,12 +227,8 @@
</PRE>
<!--==================================================================-->
-<!-- Declare all public entities ... -->
-<!-- duplicate public routines template as many times as necessary -->
-<!-- make sure you replace all yyyroutine?? strings -->
+<!-- Public entities -->
<!--==================================================================-->
-<!--Note to authors. The first row of the table is different. -->
-<!--==================================================================-->
<A NAME="Interface"></A>
<HR>
@@ -71,6 +252,7 @@
<TR><TD> </TD><TD><A HREF="#shell_execute">shell_execute</A></TD></TR>
<TR><TD> </TD><TD><A HREF="#sleep_seconds">sleep_seconds</A></TD></TR>
<TR><TD> </TD><TD><A HREF="#sum_across_tasks">sum_across_tasks</A></TD></TR>
+<TR><TD> </TD><TD><A HREF="#get_dart_mpi_comm">get_dart_mpi_comm</A></TD></TR>
<TR><TD> </TD><TD><A HREF="#exit_all">exit_all</A></TD></TR>
</TABLE>
@@ -425,14 +607,11 @@
<BR>
<P>
-It would generally be helpful to write out some kind of
-message before calling this routine, to indicate where in
-the code it is dying. The eventual intent is that this
-routine will be called by the standard error handler
-in the utilities module after writing out the
-pending error message, but right now that would create
-a circular reference in the modules since the mpi module
-uses the utilities module already for other services.
+This routine is now called from the standard error handler.
+To avoid circular references this is NOT a module routine.
+Programs which are compiled without the mpi code must now
+compile with the <em class="file">null_mpi_utilities_mod.f90</em>
+file to satisfy the call to this routine in the error handler.
</P>
</div>
@@ -930,31 +1109,35 @@
</div>
<br>
-<!--==================================================================-->
-<!--=================== DESCRIPTION OF A NAMELIST ===================-->
-<!--==================================================================-->
+<!--===================== DESCRIPTION OF FUNCTION =====================-->
-<A NAME="Namelist"></A>
-<HR>
-<H2>NAMELIST</H2>
-<P>
-No namelist interfaces are currently defined for this module,
-but at some point in the future an optional namelist interface
-<A HREF="#Namelist"><em class=code>&mpi_utilities_nml</em> </A>
-may be supported. It would be read from file <em class=file>input.nml</em>.
-</P>
+<A NAME="get_dart_mpi_comm"></A>
+<br>
+<div class=routine>
+<em class=call> comm = get_dart_mpi_comm()</em>
+<pre>
+integer :: <em class=code>get_dart_mpi_comm</em>
+</pre>
+</div>
+
<div class=indent1>
<!-- Description -->
<P>
-One anticipated addition
-would be a list of task numbers in which the default option is to print
-out all informational messages; the current default is that messages are
-only printed from task 0 and all others suppressed.
-(Warnings and Errors print in all cases.)
+This code creates a private communicator for DART MPI calls, in case
+other code in the executable is using the world communicator.
+This routine returns the private communicator. If it is called
+before the internal setup work is completed it
+returns MPI_COMM_WORLD. If it is called before MPI is initialized,
+it returns 0.
</P>
+<TABLE width=100% border=0 summary="" cellpadding=3>
+<TR><TD valign=top><em class=code>comm </em></TD>
+ <TD> The private DART communicator. </TD></TR>
+</TABLE>
+
</div>
<br>
@@ -1002,7 +1185,19 @@
with the numeric error code it received from MPI.
See any of the MPI references for an up-to-date list of error codes.
</P>
+<P>
+After printing to the standard output and log files, the DART error
+handler calls the <em class=code>exit_all()</em> routine which calls
+<em class=code>MPI_Abort()</em> to make sure all tasks exit and the
+entire job does not hang if only one task has an error.
+</P>
+<!--==================================================================-->
+<!-- Describe all known bugs -->
+<!--==================================================================-->
+
@@ Diff output truncated at 40000 characters. @@
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