.. |eficas_new| image:: images/eficas_new.png
:align: middle
+ :scale: 50%
.. |eficas_save| image:: images/eficas_save.png
:align: middle
+ :scale: 50%
+.. |eficas_saveas| image:: images/eficas_saveas.png
+ :align: middle
+ :scale: 50%
.. |eficas_yacs| image:: images/eficas_yacs.png
:align: middle
+ :scale: 50%
+.. |yacs_compile| image:: images/yacs_compile.png
+ :align: middle
+ :scale: 50%
This section presents the usage of the ADAO module in SALOME. It is complemented
-by advanced usage procedures in the section :ref:`section_advanced`, and by
-examples in the section :ref:`section_examples`.
+by the detailed description of all the commands and keywords in the section
+:ref:`section_reference`, by advanced usage procedures in the section
+:ref:`section_advanced`, and by examples in the section :ref:`section_examples`.
Logical procedure to build an ADAO test case
--------------------------------------------
Each step will be detailed in the next section.
-Detailed procedure to build an ADAO test case
----------------------------------------------
-
-Activate the ADAO module and use the editor GUI
-+++++++++++++++++++++++++++++++++++++++++++++++
+STEP: Activate the ADAO module and use the editor GUI
+-----------------------------------------------------
As always for a module, it has to be activated by choosing the appropriate
module button (or menu) in the toolbar of SALOME. If there is no SALOME study
.. centered::
**The EFICAS editor for cases definition in module ADAO**
-It is a good habit to save the ADAO case now, by pushing the "*Save*" button
-|eficas_save| or by choosing the "*Save/Save as*" entry in the "*ADAO*" menu.
-You will be prompted for a location in your file tree and a name, that will be
-completed by a "*.comm*" extension used for JDC EFICAS files.
+STEP: Build and modify the ADAO case and save it
+------------------------------------------------
-Build and modify the ADAO case and save it
-++++++++++++++++++++++++++++++++++++++++++
-
-To build a case using EFICAS, you have to go through a series of steps, by
-selecting a keyword and then filling in its value.
+To build a case using EFICAS, you have to go through a series of substeps, by
+selecting, at each substep, a keyword and then filling in its value.
The structured editor indicates hierarchical types, values or keywords allowed.
Incomplete or incorrect keywords are identified by a visual error red flag.
Possible values are indicated for keywords defined with a limited list of
-values, and adapted entries are given for the other keywords. All the mandatory
-command or keyword are already present, and optionnal commands can be added.
+values, and adapted entries are given for the other keywords. Some help messages
+are contextually provided in the editor reserved places.
-A new case is set up with the minimal list of commands. No mandatory command can
-be suppressed, but others can be added as allowed keywords for an
-"*ASSIMILATION_STUDY*" command. As an example, one can add an
-"*AlgorithmParameters*" keyword, as described in the last part of the section
-:ref:`section_examples`.
+A new case is set up with the minimal list of commands. All the mandatory
+commands or keywords are already present, none of them can be suppressed.
+Optionnal keywords can be added by choosing them in a list of suggestions of
+allowed ones for the main command, for example the "*ASSIMILATION_STUDY*"
+command. As an example, one can add an "*AlgorithmParameters*" keyword, as
+described in the last part of the section :ref:`section_examples`.
At the end, when all fields or keywords have been correctly defined, each line
of the commands tree must have a green flag. This indicates that the whole case
-is valid and completed.
+is valid and completed (and can be saved).
.. _adao_jdcexample00:
.. image:: images/adao_jdcexample01.png
:align: center
- :width: 50%
+ :scale: 75%
.. centered::
**Example of a valid ADAO case**
Finally, you have to save your ADAO case by pushing the "*Save*" button
-|eficas_save| or by choosing the "*Save/Save as*" entry in the "*ADAO*" menu.
+|eficas_save|, or the "*Save as*" button |eficas_saveas|, or by choosing the
+"*Save/Save as*" entry in the "*ADAO*" menu. You will be prompted for a location
+in your file tree and a name, that will be completed by a "*.comm*" extension
+used for JDC EFICAS files. This will generate a pair of files describing the
+ADAO case, with the same base name, the first one being completed by a "*.comm*"
+extension and the second one by a "*.py*" extension [#]_.
-Export the ADAO case as a YACS scheme
-+++++++++++++++++++++++++++++++++++++
+STEP: Export the ADAO case as a YACS scheme
+-------------------------------------------
When the ADAO case is completed, you have to export it as a YACS scheme [#]_ in
order to execute the data assimilation calculation. This can be easily done by
.. centered::
**"Export to YACS" sub-menu to generate the YACS scheme from the ADAO case**
-This will lead to automatically generate an XML file for the YACS scheme, and
-open YACS module on this file. The YACS file will be stored in the same
-directory and with the same name as the ADAO saved case, only changing its
-extension from "*.comm*" to "*.xml*". *Be careful, if the name already exist, it
-will overwrite it without prompting for replacing the file*. In the same time,
-an intermediary python file is also stored in the same place, with a "*.py*"
-extension replacing the "*.comm*" one [#]_.
+This will lead to automatically generate a YACS scheme, and open the YACS module
+on this scheme. The YACS file, associated with the scheme, will be stored in the
+same directory and with the same base name as the ADAO saved case, only changing
+its extension to "*.xml*". Be careful, *if the XML file name already exist, it
+will be overwriten without prompting for replacing the file*.
-Modify and supplement the YACS scheme and save it
-+++++++++++++++++++++++++++++++++++++++++++++++++
+STEP: Supplement and modify the YACS scheme and save it
+-------------------------------------------------------
.. index:: single: Analysis
When the YACS scheme is generated and opened in SALOME through the YACS module
-GUI, you can modify or supplement the scheme like any YACS scheme. It is
-recommended to save the modified scheme with a new name, in order to preserve in
-the case you re-export to YACS the ADAO case.
+GUI, you can modify or supplement the scheme like any YACS scheme. Nodes or
+blocs can be added, copied or modified to elaborate complex analysis, or to
+insert data assimilation or optimization capabilities into more complex YACS
+calculation schemes. It is recommended to save the modified scheme with a new
+name, in order to preserve the XML file in the case you re-export the ADAO case
+to YACS.
The main supplement needed in the YACS scheme is a postprocessing step. The
evaluation of the results has to be done in the physical context of the
-simulation used by the data assimilation procedure.
+simulation used by the data assimilation procedure. The postprocessing can be
+provided throught the "*UserPostAnalysis*" ADAO keyword as a script, or can be
+build as YACS nodes using all SALOME possibilities.
The YACS scheme has an "*algoResults*" output port of the computation bloc,
-which gives access to a "*pyobj*" containing all the results. These results can
-be obtained by retrieving the named variables stored along the calculation. The
-main is the "*Analysis*" one, that can be obtained by the python command (for
-example in an in-line script node)::
+which gives access to a "*pyobj*" named hereafter "*ADD*", containing all the
+processing results. These results can be obtained by retrieving the named
+variables stored along the calculation. The main is the "*Analysis*" one, that
+can be obtained by the python command (for example in an in-line script node or
+a script provided throught the "*UserPostAnalysis*" keyword)::
- Analysis = results.ADD.get("Analysis").valueserie(-1)
+ ADD = algoResults.getAssimilationStudy()
+ Analysis = ADD.get("Analysis").valueserie()
-This is a complex object, similar to a list of values calculated at each step of
-data assimilation calculation. In order to get the last data assimilation
-analysis, one can use::
+"*Analysis*" is a complex object, similar to a list of values calculated at each
+step of data assimilation calculation. In order to get and print the optimal
+data assimilation state evaluation, in script provided throught the
+"*UserPostAnalysis*" keyword, one can use::
- Xa = results.ADD.get("Analysis").valueserie(-1)
+ Xa = ADD.get("Analysis").valueserie(-1)
+ print "Optimal state:", Xa
+ print
This ``Xa`` is a vector of values, that represents the solution of the data
-assimilation evaluation problem, noted as :math:`\mathbf{x}^a` in the section
-:ref:`section_theory`.
+assimilation or optimization evaluation problem, noted as :math:`\mathbf{x}^a`
+in the section :ref:`section_theory`.
Such command can be used to print results, or to convert these ones to
structures that can be used in the native or external SALOME postprocessing. A
simple example is given in the section :ref:`section_examples`.
-Execute the YACS case and obtain the results
-++++++++++++++++++++++++++++++++++++++++++++
-
-.. index:: single: Analysis
-.. index:: single: Innovation
-.. index:: single: APosterioriCovariance
-.. index:: single: OMB (Observation minus Background)
-.. index:: single: BMA (Background minus Analysis)
-.. index:: single: OMA (Observation minus Analysis)
-.. index:: single: CostFunctionJ
-.. index:: single: CostFunctionJo
-.. index:: single: CostFunctionJb
+STEP: Execute the YACS case and obtain the results
+--------------------------------------------------
The YACS scheme is now complete and can be executed. Parametrisation and
execution of a YACS case is fully compliant with the standard way to deal with a
YACS scheme, and is described in the *YACS module User's Guide*.
-Results can be obtained, through the "*algoResults*" output port, using YACS
-nodes to retrieve all the informations in the "*pyobj*" object, to transform
-them, to convert them, to save part of them, etc.
-
-The data assimilation results and complementary calculations can be retrieved
-using the "*get*" method af the "*algoResults.ADD*" object. This method pick the
-different output variables identified by their name. Indicating in parenthesis
-their availability as automatic (for every algorithm) or optional (depending on
-the algorithm), and their notation coming from section :ref:`section_theory`,
-the main available output variables are the following:
-
-#. "Analysis" (automatic): the control state evaluated by the data assimilation
- procedure, noted as :math:`\mathbf{x}^a`.
-#. "Innovation" (automatic): the difference between the observations and the
- control state transformed by the observation operator, noted as
- :math:`\mathbf{y}^o - \mathbf{H}\mathbf{x}^b`.
-#. "APosterioriCovariance" (optional): the covariance matrix of the *a
- posteriori* analysis errors, noted as :math:`\mathbf{A}`.
-#. "OMB" (optional): the difference between the observations and the
- background, similar to the innovation.
-#. "BMA" (optional): the difference between the background and the analysis,
- noted as :math:`\mathbf{x}^b - \mathbf{x}^a`.
-#. "OMA" (optional): the difference between the observations and the analysis,
- noted as :math:`\mathbf{y}^o - \mathbf{H}\mathbf{x}^a`.
-#. "CostFunctionJ" (optional): the minimisation function, noted as :math:`J`.
-#. "CostFunctionJo" (optional): the observation part of the minimisation
- function, noted as :math:`J^o`.
-#. "CostFunctionJb" (optional): the background part of the minimisation
- function, noted as :math:`J^b`.
-
-Input variables are also available as output in order to gather all the
-information at the end of the procedure.
-
-All the variables are list of typed values, each item of the list
-corresponding to the value of the variable at a time step or an iteration step
-in the data assimilation optimization procedure. The variable value at a given
-"*i*" step can be obtained by the method "*valueserie(i)*". The last one
-(consisting in the solution of the evaluation problem) can be obtained using the
-step "*-1*" as in a standard list.
+To recall the simplest way to proceed, the YACS scheme has to be compiled using
+the button |yacs_compile|, or the equivalent YACS menu entry, to prepare the
+scheme to run. Then the compiled scheme can be started, executed step by step or
+using breakpoints, etc.
+
+The standard output will be pushed into the "*YACS Container Log*", obtained
+through the right click menu of the "*proc*" window in the YACS GUI. The errors
+are shown either in the "*YACS Container Log*", or at the command line in the
+shell window (if SALOME has been launched by its explicit command and not by
+menu). As an example, the output of the above simple case is the following::
+
+ Entering in the assimilation study
+ Name is set to........: Test
+ Algorithm is set to...: Blue
+ Debug is set to.......: False
+ Launching the analyse
+
+ Optimal state: [0.5, 0.5, 0.5]
+
+shown in the "*YACS Container Log*".
+
+The execution can also be done using a shell script, as described in the section
+:ref:`section_advanced`.
.. [#] For more information on EFICAS, see the *EFICAS module* available in SALOME GUI.
.. [#] For more information on YACS, see the *YACS module User's Guide* available in the main "*Help*" menu of SALOME GUI.
-.. [#] This intermediary python file can be safely removed after YACS export, but can also be used as described in the section :ref:`section_advanced`.
+.. [#] This intermediary python file can also be used as described in the section :ref:`section_advanced`.
