[Dart-dev] [4992] DART/trunk/filter/filter.html: Clean up tags.
nancy at ucar.edu
nancy at ucar.edu
Mon Jun 13 16:42:07 MDT 2011
Revision: 4992
Author: nancy
Date: 2011-06-13 16:42:07 -0600 (Mon, 13 Jun 2011)
Log Message:
-----------
Clean up tags.
Modified Paths:
--------------
DART/trunk/filter/filter.html
-------------- next part --------------
Modified: DART/trunk/filter/filter.html
===================================================================
--- DART/trunk/filter/filter.html 2011-06-13 22:34:13 UTC (rev 4991)
+++ DART/trunk/filter/filter.html 2011-06-13 22:42:07 UTC (rev 4992)
@@ -48,6 +48,7 @@
time-stepping capabilities of the model being used in the assimilation.
</P><P>
This overview includes these subsections:
+</P>
<UL><LI> <A href="#ProgramFlow">Program Flow</A> </LI>
<LI> <A href="#FilterTypes">Filter Types</A> </LI>
<LI> <A href="#GettingStarted">Getting Started</A> </LI>
@@ -58,6 +59,7 @@
<LI> <A href="#Inflation">Description of Inflation Options</A> </LI>
<LI> <A href="#DetailedProgramFlow">Detailed Program Flow</A> </LI>
</UL>
+<P>
See the <A href="http://www.image.ucar.edu/DAReS/DART">DART web site</A>
for more documentation, including a discussion of the capabilities of the
assimilation system, a diagram of the entire execution cycle, the options
@@ -69,7 +71,7 @@
<H4>Overview of Program Flow</H4>
<P>
The basic execution loop is:
-<br />
+</P>
<UL><LI>Read in model initial conditions, observations, set up and initialize</LI>
<LI>Until out of observations:
<UL><LI>Run multiple copies of the model to get forecasts of model state</LI>
@@ -79,6 +81,7 @@
<LI>Write out diagnostic files, restart files,
final observation sequence file</LI>
</UL>
+<P>
The time of the observations in the input observation sequence file
controls the length of execution of filter.
</P> <P>
@@ -151,8 +154,9 @@
</P> <P>
Suggestions for the most common namelist settings and features built
into DART for running a successful assimilation include:
+</P>
<ul>
-<li>Ensemble Size</li>
+<li>Ensemble Size
<P>
In practice, ensemble sizes between 20 and 100 seem to work best.
Fewer than 20-30 members leads to statistical errors which are too large.
@@ -165,8 +169,8 @@
once you have a set of baseline results to compare it with.
The namelist setting for ensemble size is
<em class="code">&filter_nml :: ens_size </em>
-</P>
-<li>Localization</li>
+</P></li>
+<li>Localization
<P>
There are two main advantages to using localization. One is it avoids
an observation impacting unrelated state variables because of spurious
@@ -177,8 +181,8 @@
using it usually results in a very large performance gain.
See <a href="../assim_tools/assim_tools_mod.html#Localization">here</a>
for a discussion of localization-related namelist items.
-</P>
-<li>Inflation</li>
+</P></li>
+<li>Inflation
<P>
Since the filter is being run with a fixed number of ensembles
which is usually small compared to the number of degrees of freedom
@@ -191,8 +195,8 @@
vary in density over time and location.
See <a href="#Inflation">here</a>
for a discussion of inflation-related namelist items.
-</P>
-<li>Outlier Rejection</li>
+</P></li>
+<li>Outlier Rejection
<P>
Outlier rejection can be used to avoid bad observations (ones
where the value was recorded in error or the processing has an
@@ -209,8 +213,8 @@
to include is
<em class="code">&filter_nml :: outlier_threshold </em>
and we typically suggest starting with a value of 3.0.
-</P>
-<li>Sampling Error</li>
+</P></li>
+<li>Sampling Error
<P>
For small ensemble sizes a table of expected statistical error
distributions can be generated before running DART. Corrections
@@ -229,10 +233,9 @@
for instructions on where to find (or how to generate)
the auxiliary file needed by this code.
See Anderson (2011).
-</P>
+</P></li>
</ul>
-</P>
<A NAME="FreeRun"></A>
<H4>Free run/Forecast After Assimilation</H4>
@@ -384,6 +387,7 @@
and the second is for Posterior inflation.
If 'flavor' is 0, all other settings for that
column are ignored.
+</P>
<dl>
<dt>
<em>&filter_nml :: flavor</em><br />
@@ -510,7 +514,7 @@
<br /> <br />
</dl>
-</P> <P>
+<P>
The suggested procedure for testing inflation options
is to start without
any (both 'flavor' values set to 0). Then enable Prior
@@ -533,6 +537,7 @@
<H4>Detailed Program Execution Flow</H4>
<P>
The detailed execution flow inside the filter program is:
+</P>
<ul>
<li>Read in observations. </li>
@@ -540,34 +545,35 @@
<li>Initialize inflation fields, possibly reading restart files. </li>
<li>Initialize output netcdf diagnostic files. </li>
<li>Trim off any observations if start/stop times specified. </li>
-<li>Begin main assimilation loop: </li>
+<li>Begin main assimilation loop:
<ul>
-<li>Check model time vs observation times: </li>
+<li>Check model time vs observation times:
<ul>
<li>If current assimilation window is earlier than model time, error. </li>
<li>If current assimilation window includes model time, begin assimilating. </li>
-<li>If current assimilation window is later than model time, advance model: </li>
+<li>If current assimilation window is later than model time, advance model:
<ul>
<li>Write out current state vectors for all ensemble members. </li>
-<li>Advance the model by subroutine call or by shell script: </li>
+<li>Advance the model by subroutine call or by shell script:
<ul>
<li>Convert the data into format suitable for model. </li>
<li>Tell the model to run up to the requested time. </li>
<li>Convert the new data back into DART format. </li>
</ul>
+</li>
<li>Read in new state vectors for all ensemble members. </li>
-</ul>
-</ul>
+</ul></li>
+</ul></li>
<li>Apply prior inflation if requested. </li>
<li>Compute ensemble of prior observation values with forward operators. </li>
<li>Compute and write out prior state space diagnostics. (Note this is AFTER
any prior inflation has been applied.)</li>
<li>Compute and write out prior observation space diagnostics. </li>
-<li>Assimilate all observations in this window: </li>
+<li>Assimilate all observations in this window:
<ul>
<li>Get all obs locations and kinds. </li>
<li>Get all state vector locations and kinds. </li>
-<li>For each observation: </li>
+<li>For each observation:
<ul>
<li>Compute the observation increments. </li>
<li>Find all other obs and states within localization radius. </li>
@@ -575,14 +581,14 @@
<li>Apply increments weighted by correlation values. </li>
<li>Apply increments to any remaining unassimilated observations. </li>
<li>Loop until all observations in window processed. </li>
-</ul>
-</ul>
+</ul></li>
+</ul></li>
<li>Apply posterior inflation if requested. </li>
<li>Compute ensemble of posterior observation values with forward operators. </li>
<li>Compute and write out posterior state space diagnostics. </li>
<li>Compute and write out posterior observation space diagnostics. </li>
<li>Loop until all observations in input file processed. </li>
-</ul>
+</ul></li>
<li>Close diagnostic files. </li>
<li>Write out final observation sequence file. </li>
<li>Write out inflation restart files if requested. </li>
@@ -590,8 +596,6 @@
<li>Release memory for state vector and observation ensemble members. </li>
</ul>
-</P>
-
<P>
Namelist
<A HREF="#Namelist"> <em class=code>&filter_nml</em> </A>
@@ -1066,24 +1070,27 @@
<span style="font-weight: bold;">129</span>, 2884-2903.<br />
<a href="http://dx.doi.org/10.1175/1520-0493%282001%29129%3C2884%3AAEAKFF%3E2.0.CO%3B2"
target="_blank" >
-doi: 10.1175/1520-0493(2001)129<2884:AEAKFF>2.0.CO;2</a> </li>
+doi: 10.1175/1520-0493(2001)129<2884:AEAKFF>2.0.CO;2</a>
<br />
+</li>
<li>Anderson, J. L., 2003:
A Local Least Squares Framework for Ensemble Filtering.
<span style="font-style: italic;">Mon. Wea. Rev.</span>,
<span style="font-weight: bold;">131</span>, 634-642.<br />
<a href="http://dx.doi.org/10.1175/1520-0493%282003%29131%3C0634%3AALLSFF%3E2.0.CO%3B2"
target="_blank" >
-doi: 10.1175/1520-0493(2003)131<0634:ALLSFF>2.0.CO;2</a></li>
+doi: 10.1175/1520-0493(2003)131<0634:ALLSFF>2.0.CO;2</a>
<br />
+</li>
<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>
+doi: 10.1111/j.1600-0870.2006.00216.x </a>
<br />
+</li>
<li>Anderson, J. L., 2007:
Exploring the need for localization in ensemble data
assimilation using a hierarchical ensemble filter.
@@ -1091,24 +1098,27 @@
<span style="font-weight: bold;">230</span>, 99-111.<br />
<a href="http://dx.doi.org/10.1016/j.physd.2006.02.011"
target="_blank" >
-doi:10.1016/j.physd.2006.02.011</a></li>
+doi:10.1016/j.physd.2006.02.011</a>
<br />
+</li>
<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/JTECH2049.1</a></li>
+doi: 10.1175/JTECH2049.1</a>
<br />
+</li>
<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>
+doi: 10.1111/j.1600-0870.2008.00361.x</a>
<br />
+</li>
<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.
@@ -1116,16 +1126,18 @@
<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>
+doi: 10.1175/2009BAMS2618.1</a>
<br />
+</li>
<li>Anderson, J. L., 2010:
A Non-Gaussian Ensemble Filter Update for Data Assimilation.
<span style="font-style: italic;">Mon. Wea. Rev.</span>,
<span style="font-weight: bold;">139</span>, 4186-4198.<br />
<a href="http://dx.doi.org/10.1175/2010MWR3253.1"
target="_blank" >
-doi: 10.1175/2010MWR3253.1</a></lI>
+doi: 10.1175/2010MWR3253.1</a>
<br />
+</li>
<li>Anderson, J. L., 2011:
Localization and Sampling Error Correction
in Ensemble Kalman Filter Data Assimilation.
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