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update API docs
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yumengch committed Oct 15, 2024
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Expand Up @@ -38,26 +38,46 @@ <h1>pyPDAF.PDAF.assimilate_3dvar<a class="headerlink" href="#pypdaf-pdaf-assimil
<dl class="py function">
<dt class="sig sig-object py" id="pyPDAF.PDAF.assimilate_3dvar">
<span class="sig-prename descclassname"><span class="pre">pyPDAF.PDAF.</span></span><span class="sig-name descname"><span class="pre">assimilate_3dvar</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pyPDAF.PDAF.assimilate_3dvar" title="Link to this definition"></a></dt>
<dd><p>It is recommended to use OMI functionalities for fewer user-supplied functions and improved efficiency.I.e., <cite>pyPDAF.PDAF.omi_assimilate_3dvar</cite> or <cite>pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR</cite>.
Using 3DVar for DA without OMI. This is a deterministic filtering scheme. This function should be called at each model time step.</p>
<p>The function is a combination of <cite>pyPDAF.PDAF.put_state_3dvar</cite> and <cite>pyPDAF.PDAF.get_state</cite>, and executes the user-supplied function in the following sequence:
1. py__collect_state_pdaf
2. py__prepoststep_state_pdaf
3. py__init_dim_obs_pdaf
4. py__obs_op_pdaf
5. py__init_obs_pdaf
Starting the iterative optimisation:
6. py__cvt_pdaf
7. py__obs_op_lin_pdaf
8. py__prodRinvA_pdaf
9. py__obs_op_adj_pdaf
10. py__cvt_adj_pdaf
11. core DA algorithm
After the iterations:
12. py__cvt_pdaf
13. py__prepoststep_state_pdaf
14. py__distribute_state_pdaf
15. py__next_observation_pdaf</p>
<dd><p>It is recommended to use <a class="reference internal" href="pyPDAF.PDAF.omi_assimilate_3dvar.html#pyPDAF.PDAF.omi_assimilate_3dvar" title="pyPDAF.PDAF.omi_assimilate_3dvar"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_assimilate_3dvar()</span></code></a>
or <a class="reference internal" href="pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR.html#pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR" title="pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR()</span></code></a>.</p>
<p>PDAF-OMI modules require fewer user-supplied functions and improved efficiency.</p>
<p>3DVar DA for a single step without OMI.
When 3DVar is used, the background error covariance matrix
has to be modelled for cotrol variable transformation.
This is a deterministic filtering scheme so no ensemble and parallelisation is needed.
This function should be called at each model time step.</p>
<p>The function is a combination of <a class="reference internal" href="pyPDAF.PDAF.put_state_3dvar.html#pyPDAF.PDAF.put_state_3dvar" title="pyPDAF.PDAF.put_state_3dvar"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.put_state_3dvar()</span></code></a>
and <a class="reference internal" href="pyPDAF.PDAF.get_state.html#pyPDAF.PDAF.get_state" title="pyPDAF.PDAF.get_state"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.get_state()</span></code></a>.</p>
<dl class="simple">
<dt>User-supplied functions are executed in the following sequence:</dt><dd><ol class="arabic simple">
<li><p>py__collect_state_pdaf</p></li>
<li><p>py__prepoststep_state_pdaf</p></li>
<li><p>py__init_dim_obs_pdaf</p></li>
<li><p>py__obs_op_pdaf</p></li>
<li><p>py__init_obs_pdaf</p></li>
<li><dl class="simple">
<dt>Iterative optimisation:</dt><dd><ol class="arabic simple">
<li><p>py__cvt_pdaf</p></li>
<li><p>py__obs_op_lin_pdaf</p></li>
<li><p>py__prodRinvA_pdaf</p></li>
<li><p>py__obs_op_adj_pdaf</p></li>
<li><p>py__cvt_adj_pdaf</p></li>
<li><p>core DA algorithm</p></li>
</ol>
</dd>
</dl>
</li>
<li><p>py__cvt_pdaf</p></li>
<li><p>py__prepoststep_state_pdaf</p></li>
<li><p>py__distribute_state_pdaf</p></li>
<li><p>py__next_observation_pdaf</p></li>
</ol>
</dd>
</dl>
<div class="deprecated">
<p><span class="versionmodified deprecated">Deprecated since version 1.0.0: </span>This function is replaced by <a class="reference internal" href="pyPDAF.PDAF.omi_assimilate_3dvar.html#pyPDAF.PDAF.omi_assimilate_3dvar" title="pyPDAF.PDAF.omi_assimilate_3dvar"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_assimilate_3dvar()</span></code></a>
and <a class="reference internal" href="pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR.html#pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR" title="pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR"><code class="xref py py-func docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_assimilate_3dvar_nondiagR()</span></code></a></p>
</div>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
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