= Implementation of the analysis step =

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<div class="wiki-toc">
<h4>Implementation Guide</h4>
<ol><li><a href="ImplementationGuide">Main page</a></li>
<li><a href="AdaptParallelization">Adaptation of the parallelization</a></li>
<li><a href="InitPdaf">Initialization of PDAF</a></li>
<li><a href="ModifyModelforEnsembleIntegration">Modifications for ensemble integration</a></li>
<li>Implementation of the analysis step</li>
<ol>
<li><a href="ImplementAnalysisestkf">Implementation for ESTKF</a></li>
<li><a href="ImplementAnalysislestkf">Implementation for LESTKF</a></li>
<li><a href="ImplementAnalysisetkf">Implementation for ETKF</a></li>
<li><a href="ImplementAnalysisletkf">Implementation for LETKF</a></li>
<li><a href="ImplementAnalysisseik">Implementation for SEIK</a></li>
<li><a href="ImplementAnalysislseik">Implementation for LSEIK</a></li>
<li><a href="ImplementAnalysisseek">Implementation for SEEK</a></li>
<li><a href="ImplementAnalysisenkf">Implementation for EnKF</a></li>
<li><a href="ImplementAnalysislenkf">Implementation for LEnKF</a></li>
<li><a href="ImplementAnalysisnetf">Implementation for NETF</a></li>
<li><a href="ImplementAnalysislnetf">Implementation for LNETF</a></li>
<li><a href="ImplementAnalysislpf">Implementation for PF</a></li>
</ol>
<li><a href="AddingMemoryandTimingInformation">Memory and timing information</a></li>
</ol>
</div>
}}}

The implementation of the analysis step requires that the user-supplied routines whose names are given in the call to the filter-specific put-state routine are implemented with full functionality. 

Several of the routines are general and hence usable for all filter algorithms. There are some differences between the available local and global filters. The routines are described in separate pages for each filter algorithm. The general routines will be repeated, but they are marked as general.

Filter-specific implementations for global filters:
 * [ImplementAnalysisestkf Implementation of the analysis for the ESTKF]
 * [ImplementAnalysisetkf Implementation of the analysis for the ETKF]
 * [ImplementAnalysisseik Implementation of the analysis for the SEIK filter]
 * [ImplementAnalysisseek Implementation of the analysis for the SEEK filter]
 * [ImplementAnalysisenkf Implementation of the analysis for the EnKF]
 * [ImplementAnalysisnetf Implementation of the analysis for the NETF]
 * [ImplementAnalysispf Implementation of the analysis for the PF]

Filter-specific implementations for domain-local filters:
 * [ImplementAnalysislestkf Implementation of the analysis for the LESTKF]
 * [ImplementAnalysisletkf Implementation of the analysis for the LETKF]
 * [ImplementAnalysislseik Implementation of the analysis for the LSEIK filter]
 * [ImplementAnalysislnetf Implementation of the analysis for the LNETF]

Filter-specific implementation for filter with covariance localization:
 * [ImplementAnalysislenkf Implementation of the analysis for the LEnKF]

(The filters ESTKF and LESTKF have been added with PDAF version 1.8; the filters LEnKF, NETF and LNETF have been addid with PDAF version 1.12)

== Testing the full implementation ==

After the implementation of the user-supplied routines for the analysis step, the data assimilation system is fully implemented. In order to test the program one has to compile it without setting 'PDAF_NO_UPDATE'. 

To speed up the testing it can be useful to comment out the time stepping part. In that case only the model initialization and the assimilation cycle would be executed, without the usually costly time integration of the ensemble. One should then check if all user-supplied routines perform as they should.