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content/gsi/01-gsi.html

@@ -202,11 +202,12 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#available-observations-for-assimilation" id="toc-available-observations-for-assimilation" class="nav-link active" data-scroll-target="#available-observations-for-assimilation">Available observations for assimilation</a>
   <ul class="collapse">
-  <li><a href="#conventional-observations-including-satellite-retrievals" id="toc-conventional-observations-including-satellite-retrievals" class="nav-link" data-scroll-target="#conventional-observations-including-satellite-retrievals">Conventional observations (including satellite retrievals):</a></li>
-  <li><a href="#satellite-radiancebrightness-temperature-observations-instrumentsatellite-id" id="toc-satellite-radiancebrightness-temperature-observations-instrumentsatellite-id" class="nav-link" data-scroll-target="#satellite-radiancebrightness-temperature-observations-instrumentsatellite-id">Satellite radiance/brightness temperature observations (instrument/satellite ID):</a></li>
-  <li><a href="#others" id="toc-others" class="nav-link" data-scroll-target="#others">Others:</a></li>
+  <li><a href="#conventional-observations" id="toc-conventional-observations" class="nav-link" data-scroll-target="#conventional-observations">Conventional observations:</a></li>
+  <li><a href="#satellite-radiancebrightness-temperature-observations" id="toc-satellite-radiancebrightness-temperature-observations" class="nav-link" data-scroll-target="#satellite-radiancebrightness-temperature-observations">Satellite radiance/brightness temperature observations</a></li>
+  <li><a href="#other-observations" id="toc-other-observations" class="nav-link" data-scroll-target="#other-observations">Other observations</a></li>
   </ul></li>
   <li><a href="#running-gsi" id="toc-running-gsi" class="nav-link" data-scroll-target="#running-gsi">Running GSI</a></li>
+  <li><a href="#about-the-gsi-code" id="toc-about-the-gsi-code" class="nav-link" data-scroll-target="#about-the-gsi-code">About the GSI code</a></li>
   </ul>
 <div class="toc-actions"><ul><li><a href="https://github.com/paocorrales/DA-documentation/edit/main/content/gsi/01-gsi.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/paocorrales/DA-documentation/issues/new/choose" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
@@ -240,8 +241,8 @@ <h1 class="title">The GSI assimilation system</h1>
 <section id="available-observations-for-assimilation" class="level2">
 <h2 class="anchored" data-anchor-id="available-observations-for-assimilation">Available observations for assimilation</h2>
 <p>Here is the list of observations that can be assimilated by GSI. In bold are the observations for with I have experience and/or the ones <a href="https://github.com/paocorrales/comGSIv3.7_EnKFv1.3">I’ve adapted the code for it</a>.</p>
-<section id="conventional-observations-including-satellite-retrievals" class="level3">
-<h3 class="anchored" data-anchor-id="conventional-observations-including-satellite-retrievals">Conventional observations (including satellite retrievals):</h3>
+<section id="conventional-observations" class="level3">
+<h3 class="anchored" data-anchor-id="conventional-observations">Conventional observations:</h3>
 <ul>
 <li><strong>Radiosondes</strong></li>
 <li>Pilot ballon (PIBAL) winds</li>
@@ -269,8 +270,8 @@ <h3 class="anchored" data-anchor-id="conventional-observations-including-satelli
 <li>Tall tower wind</li>
 </ul>
 </section>
-<section id="satellite-radiancebrightness-temperature-observations-instrumentsatellite-id" class="level3">
-<h3 class="anchored" data-anchor-id="satellite-radiancebrightness-temperature-observations-instrumentsatellite-id">Satellite radiance/brightness temperature observations (instrument/satellite ID):</h3>
+<section id="satellite-radiancebrightness-temperature-observations" class="level3">
+<h3 class="anchored" data-anchor-id="satellite-radiancebrightness-temperature-observations">Satellite radiance/brightness temperature observations</h3>
 <ul>
 <li>SBUV: NOAA-17, NOAA-18, NOAA-19</li>
 <li><strong>High Resolution Infrared Radiation Sounder (HIRS): Meteorological Operational-A(MetOp-A), MetOp-B, NOAA-17, NOAA-19</strong></li>
@@ -296,8 +297,8 @@ <h3 class="anchored" data-anchor-id="satellite-radiancebrightness-temperature-ob
 <li><strong>GOES ABI</strong></li>
 </ul>
 </section>
-<section id="others" class="level3">
-<h3 class="anchored" data-anchor-id="others">Others:</h3>
+<section id="other-observations" class="level3">
+<h3 class="anchored" data-anchor-id="other-observations">Other observations</h3>
 <ul>
 <li>GPS Radio occultation (RO) refractivity and bending angle profiles</li>
 <li>Solar Backscatter Ultraviolet (SBUV) ozone profiles, Microwave Limb Sounder (MLS) (including NRT) ozone, * and Ozone Monitoring Instrument (OMI) total ozone</li>
@@ -400,6 +401,32 @@ <h2 class="anchored" data-anchor-id="running-gsi">Running GSI</h2>
 </tr>
 </tbody>
 </table>
+</section>
+<section id="about-the-gsi-code" class="level2">
+<h2 class="anchored" data-anchor-id="about-the-gsi-code">About the GSI code</h2>
+<p>GSI is writen in fortran and the code is separated in more than 5 hundred files. While GSI has 2 good user guides, not everything is documented and sometimes you will need to read the code.</p>
+<p>To swim around the code I found the <code>grep -r "key word"</code> command very useful. Each file and subroutine inside it has a header with information about what it does, changes and input and output arguments. It’s worth mentioning a few key files:</p>
+<ul>
+<li><code>gsimain.f90</code> and <code>gsimod.f90</code> are the main files that control the system. <code>gsimain.f90</code> has a list off code errors and the possible cause.</li>
+<li><code>*info.f90</code> like <code>convinfo.f90</code> and <code>radinfo.f90</code> are the routines that read the configuration files. Note that the <code>satinfo</code> file is read by the <code>radinfo.f90</code> subroutine.</li>
+<li><code>read_*.f90</code> are a family of routines every bufr file that GSI is prepared to work with. For example there is a <code>read_prepbufr.f90</code> and a <code>read_goesimg.f90</code> that read goes observations including ABI.</li>
+<li>Another important family of files is <code>setup*.f90</code>, these files process each variable to be assimilated. For example, <code>setupt.f90</code> will:
+<ul>
+<li>reads temperature obs assigned to given mpi task (geographic region),</li>
+<li>simulates obs from guess,</li>
+<li>apply some quality control to obs,</li>
+<li>load weight and innovation arrays used in minimization</li>
+<li>collects statistics for runtime diagnostic output</li>
+<li>writes additional diagnostic information to output file</li>
+</ul></li>
+<li><code>qcmod.f90</code> includes important routines for the quality control of radiance observations.</li>
+</ul>
+<p>The mail files associated to the enkf code are:</p>
+<ul>
+<li><code>enkf.f90</code> and <code>enkf_main.f90</code></li>
+<li><code>read*.f90</code> are the family of files that read the diag files generated by the observation operator.</li>
+<li><code>radbias.f90</code> manage the bias correction for radiance observation.</li>
+</ul>
 
 
 

content/gsi/02-convencionals.html

@@ -294,13 +294,13 @@ <h3 class="anchored" data-anchor-id="observation-errors-and-quality-control">Obs
 <p>The meaning of each column is described in the following table:</p>
 <table class="table">
 <colgroup>
+<col style="width: 16%">
 <col style="width: 14%">
-<col style="width: 14%">
-<col style="width: 14%">
-<col style="width: 14%">
-<col style="width: 14%">
-<col style="width: 14%">
-<col style="width: 14%">
+<col style="width: 13%">
+<col style="width: 17%">
+<col style="width: 7%">
+<col style="width: 7%">
+<col style="width: 22%">
 </colgroup>
 <thead>
 <tr class="header">
@@ -367,8 +367,13 @@ <h3 class="anchored" data-anchor-id="observation-errors-and-quality-control">Obs
 </tbody>
 </table>
 <p>You can find more details about the quality control flags in <a href="https://www.emc.ncep.noaa.gov/mmb/data_processing/prepbufr.doc/table_7.htm">Table 7</a>.</p>
-<p>GSI can also perform a thinning for conventional observations. You can activate that option for each type of observation changing <code>ithin = 1</code> in the <code>convinfo</code> file.</p>
-<p>For each observation GSI will check different things and change the observation error accordingly. The final observation error is recorded in the <code>diag</code> file and then used during the assimilation.</p>
+<p>GSI can also perform a thinning for conventional observations. You can activate that option for each type of observation changing <code>ithin = 1</code> in the <code>convinfo</code> file. There are other important columns, <code>rmesh</code>, <code>pmesh</code>, in the <code>convinfo</code> file to configure conventional data thinning:</p>
+<ul>
+<li><code>ithin</code>: 0 = no thinning; 1 = thinning with grid mesh decided by <code>rmesh</code> and <code>pmesh</code></li>
+<li><code>rmesh</code>: horizontal thinning grid size in km</li>
+<li><code>pmesh</code>: vertical thinning grid size in mb; if 0, then use background vertical grid</li>
+</ul>
+<p><strong>For each observation GSI will check different things and change the observation error accordingly.</strong> The final observation error is recorded in the <code>diag</code> file and then used during the assimilation.</p>
 
 
 </section>

content/gsi/03-radiances.html

@@ -406,7 +406,7 @@ <h2 class="anchored" data-anchor-id="observation-errors-and-quality-control">Obs
 <h3 class="anchored" data-anchor-id="thinning">Thinning</h3>
 <p>During the thinning process the observations to be assimilated are chosen based on their distance to the model grid points, the quality of the observation (based on available data quality information) and the number of available channels (for the same pixel and sensor). The thinning algorithm determines the quality of each observation based on the available information about the channels and their known errors, the type of surface below each pixel (preferring observations over the sea to those over land or snow) and predictors that give information about the quality of the observations <span class="citation" data-cites="hu2018">(<a href="#ref-hu2018" role="doc-biblioref">M. Hu et al. 2018</a>)</span>. By applying the thinning we avoid incorporating information from smaller scale processes than the model can not represent and to reduce the error correlation of the observations from the same sensor.</p>
 <p>The thinning resolution is configured in the GSI namelist:</p>
-<p>In this case we have 3 possible resolutions in kilometers: <code>dmesh(1)=120.0, dmesh(2)=60.0, dmesh(3)=10.0</code>. We define which resolution to use for each sensor in the <code>dthin</code> column. Here <code>amsua_n15</code> will use a thinning of 60 km and <code>abi_g16</code> a thinning of 10 km.</p>
+<p>In this case we have 3 possible mesh size in kilometers: <code>dmesh(1)=120.0, dmesh(2)=60.0, dmesh(3)=10.0</code>. We define which resolution to use for each sensor in the <code>dthin</code> column. Here <code>amsua_n15</code> will use a thinning of 60 km and <code>abi_g16</code> a thinning of 10 km.</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a> <span class="kw">&amp;</span><span class="ex">OBS_INPUT</span></span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>   <span class="ex">dmesh</span><span class="er">(</span><span class="ex">1</span><span class="kw">)</span><span class="ex">=120.0,</span> dmesh<span class="er">(</span><span class="ex">2</span><span class="kw">)</span><span class="ex">=60.0,</span> dmesh<span class="er">(</span><span class="ex">3</span><span class="kw">)</span><span class="ex">=10.0,</span> time_window_max=0.5,ext_sonde=.true.,</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="ex">/</span></span>
@@ -419,6 +419,11 @@ <h3 class="anchored" data-anchor-id="thinning">Thinning</h3>
 <span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>   <span class="ex">amsuabufr</span>      amsua       metop-b   amsua_metop-b       10.0     2     0</span>
 <span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>   <span class="ex">airsbufr</span>       amsua       aqua      amsua_aqua           5.0     2     0</span>
 <span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>   <span class="ex">abibufr</span>        abi         g16       abi_g16              1.0     3     0</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>If the value of <code>dthin</code> is:</p>
+<ul>
+<li>an integer less than or equal to zero, no thinning is needed</li>
+<li>an integer larger than zero, this kind of radiance data will be thinned using the mesh size defined as <code>dmesh</code> (<code>dthin</code>).</li>
+</ul>
 </section>
 <section id="sec-bias-correction" class="level3">
 <h3 class="anchored" data-anchor-id="sec-bias-correction">Bias correction</h3>