List of commands and keywords for an ADAO calculation case
----------------------------------------------------------
-.. index:: single: Algorithm
-.. index:: single: AlgorithmParameters
-.. index:: single: ControlInput
-.. index:: single: Debug
-.. index:: single: InputVariables
-.. index:: single: Observer
-.. index:: single: Observers
-.. index:: single: Observer Template
-.. index:: single: OutputVariables
-.. index:: single: StudyName
-.. index:: single: StudyRepertory
-.. index:: single: UserDataInit
-.. index:: single: UserPostAnalysis
-.. index:: single: UserPostAnalysis Template
-
This set of commands is related to the description of a calculation case,
that is a *Data Assimilation* procedure or an *Optimization* procedure. The
terms are ordered in alphabetical order, except the first, which describes
The different commands are the following:
- **ASSIMILATION_STUDY**
- *Required command*. This is the general command describing the data
- assimilation or optimization case. It hierarchically contains all the other
- commands.
-
- AlgorithmParameters
- *Required command*. This indicates the data assimilation or optimization
- algorithm chosen by the keyword "*Algorithm*", and its potential optional
- parameters. The algorithm choices are available through the GUI. There
- exists for example "3DVAR", "Blue"... Each algorithm is defined, below, by a
- specific subsection. Optionally, the command allows also to add some
- parameters to control the algorithm. Their values are defined either
- explicitly or in a "*Dict*" type object. See the
- :ref:`section_ref_options_Algorithm_Parameters` for the detailed use of this
- command part.
-
- .. include:: snippets/Background.rst
-
- .. include:: snippets/BackgroundError.rst
-
- ControlInput
- *Optional command*. This indicates the control vector used to force the
- evolution model at each step, usually noted as :math:`\mathbf{U}`. Its value
- is defined as a "*Vector*" or a *VectorSerie* type object. When there is no
- control, it has to be a void string ''.
-
- Debug
- *Optional command*. This define the level of trace and intermediary debug
- information. The choices are limited between 0 (for False) and 1 (for
- True).
-
- .. include:: snippets/EvolutionError.rst
-
- .. include:: snippets/EvolutionModel.rst
-
- InputVariables
- *Optional command*. This command allows to indicates the name and size of
- physical variables that are bundled together in the state vector. This
- information is dedicated to data processed inside an algorithm.
-
- .. include:: snippets/Observation.rst
-
- .. include:: snippets/ObservationError.rst
-
- .. include:: snippets/ObservationOperator.rst
-
- Observers
- *Optional command*. This command allows to set internal observers, that are
- functions linked with a particular variable, which will be executed each
- time this variable is modified. It is a convenient way to monitor variables
- of interest during the data assimilation or optimization process, by
- printing or plotting it, etc. Common templates are provided to help the user
- to start or to quickly make his case.
-
- OutputVariables
- *Optional command*. This command allows to indicates the name and size of
- physical variables that are bundled together in the output observation
- vector. This information is dedicated to data processed inside an algorithm.
-
- StudyName
- *Required command*. This is an open string to describe the ADAO study by a
- name or a sentence.
-
- StudyRepertory
- *Optional command*. If available, this directory is used as base name for
- calculation, and used to find all the script files, given by name without
- path, that can be used to define some other commands by scripts.
-
- UserDataInit
- *Optional command*. This commands allows to initialize some parameters or
- data automatically before algorithm input processing. It indicates a script
- file name to be executed before entering in initialization phase of chosen
- variables.
-
- UserPostAnalysis
- *Optional command*. This commands allows to process some parameters or data
- automatically after data assimilation or optimization algorithm processing.
- Its value is defined as a script file or a string, allowing to put
- post-processing code directly inside the ADAO case. Common templates are
- provided to help the user to start or to quickly make his case.
+.. include:: snippets/ASSIMILATION_STUDY.rst
+
+.. include:: snippets/AlgorithmParameters.rst
+
+.. include:: snippets/Background.rst
+
+.. include:: snippets/BackgroundError.rst
+
+.. include:: snippets/ControlInput.rst
+
+.. include:: snippets/Debug.rst
+
+.. include:: snippets/EvolutionError.rst
+
+.. include:: snippets/EvolutionModel.rst
+
+.. include:: snippets/InputVariables.rst
+
+.. include:: snippets/Observation.rst
+
+.. include:: snippets/ObservationError.rst
+
+.. include:: snippets/ObservationOperator.rst
+
+.. include:: snippets/Observers.rst
+
+.. include:: snippets/OutputVariables.rst
+
+.. include:: snippets/StudyName.rst
+
+.. include:: snippets/StudyRepertory.rst
+
+.. include:: snippets/UserDataInit.rst
+
+.. include:: snippets/UserPostAnalysis.rst
List of commands and keywords for an ADAO checking case
-------------------------------------------------------
-.. index:: single: Algorithm
-.. index:: single: AlgorithmParameters
-.. index:: single: Debug
-.. index:: single: Observer
-.. index:: single: Observers
-.. index:: single: Observer Template
-.. index:: single: StudyName
-.. index:: single: StudyRepertory
-.. index:: single: UserDataInit
-
This set of commands is related to the description of a checking case, that is a
procedure to check required properties on information, used somewhere else by a
calculation case. The terms are ordered in alphabetical order, except the first,
The different commands are the following:
- **CHECKING_STUDY**
- *Required command*. This is the general command describing the checking
- case. It hierarchically contains all the other commands.
-
- AlgorithmParameters
- *Required command*. This indicates the checking algorithm chosen by the
- keyword "*Algorithm*", and its potential optional parameters. The algorithm
- choices are available through the GUI. There exists for example
- "FunctionTest", "GradientTest"... Each algorithm is defined, below, by a
- specific subsection. Optionaly, the command allows also to add some
- parameters to control the algorithm. Their values are defined either
- explicitly or in a "*Dict*" type object. See the
- :ref:`section_ref_options_Algorithm_Parameters` for the detailed use of this
- command part.
-
- .. include:: snippets/CheckingPoint.rst
-
- .. include:: snippets/BackgroundError.rst
-
- Debug
- *Optional command*. This define the level of trace and intermediary debug
- information. The choices are limited between 0 (for False) and 1 (for
- True).
-
- .. include:: snippets/Observation.rst
-
- .. include:: snippets/ObservationError.rst
-
- .. include:: snippets/ObservationOperator.rst
-
- Observers
- *Optional command*. This command allows to set internal observers, that are
- functions linked with a particular variable, which will be executed each
- time this variable is modified. It is a convenient way to monitor variables
- of interest during the data assimilation or optimization process, by
- printing or plotting it, etc. Common templates are provided to help the user
- to start or to quickly make his case.
-
- StudyName
- *Required command*. This is an open string to describe the ADAO study by a
- name or a sentence.
-
- StudyRepertory
- *Optional command*. If available, this directory is used as base name for
- calculation, and used to find all the script files, given by name without
- path, that can be used to define some other commands by scripts.
-
- UserDataInit
- *Optional command*. This commands allows to initialize some parameters or
- data automatically before algorithm input processing. It indicates a script
- file name to be executed before entering in initialization phase of chosen
- variables.
+.. include:: snippets/CHECKING_STUDY.rst
+
+.. include:: snippets/AlgorithmParameters.rst
+
+.. include:: snippets/CheckingPoint.rst
+
+.. include:: snippets/BackgroundError.rst
+
+.. include:: snippets/Debug.rst
+
+.. include:: snippets/Observation.rst
+
+.. include:: snippets/ObservationError.rst
+
+.. include:: snippets/ObservationOperator.rst
+
+.. include:: snippets/Observers.rst
+
+.. include:: snippets/StudyName.rst
+
+.. include:: snippets/StudyRepertory.rst
+
+.. include:: snippets/UserDataInit.rst
--- /dev/null
+.. index:: single: ASSIMILATION_STUDY
+
+**ASSIMILATION_STUDY**
+ *Required command*. This is the general command describing the data
+ assimilation or optimization case. It hierarchically contains all the other
+ commands.
--- /dev/null
+.. index:: single: Algorithm
+.. index:: single: AlgorithmParameters
+
+AlgorithmParameters
+ *Required command*. This indicates the data assimilation or optimization
+ algorithm chosen by the keyword "*Algorithm*", and its potential optional
+ parameters. The algorithm choices are available through the GUI. There
+ exists for example "3DVAR", "Blue"... Each algorithm is defined, below, by a
+ specific subsection. Optionally, the command allows also to add some
+ parameters to control the algorithm. Their values are defined either
+ explicitly or in a "*Dict*" type object. See the
+ :ref:`section_ref_options_Algorithm_Parameters` for the detailed use of this
+ command part.
--- /dev/null
+.. index:: single: CHECKING_STUDY
+
+**CHECKING_STUDY**
+ *Required command*. This is the general command describing the checking
+ case. It hierarchically contains all the other commands.
--- /dev/null
+.. index:: single: ControlInput
+
+ControlInput
+ *Optional command*. This indicates the control vector used to force the
+ evolution model at each step, usually noted as :math:`\mathbf{U}`. Its value
+ is defined as a "*Vector*" or a *VectorSerie* type object. When there is no
+ control, it has to be a void string ''.
--- /dev/null
+.. index:: single: Debug
+
+Debug
+ *Optional command*. This define the level of trace and intermediary debug
+ information. The choices are limited between 0 (for False) and 1 (for
+ True).
--- /dev/null
+.. warning::
+
+ in its present version, this algorithm is experimental, and so changes can be
+ required in forthcoming versions.
--- /dev/null
+Description
++++++++++++
--- /dev/null
+Optional and required commands
+++++++++++++++++++++++++++++++
+
+The general required commands, available in the editing user graphical or
+textual interface, are the following:
--- /dev/null
+The general optional commands, available in the editing user graphical or
+textual interface, are indicated in :ref:`section_ref_assimilation_keywords`.
+Moreover, the parameters of the command "*AlgorithmParameters*" allows to
+choose the specific options, described hereafter, of the algorithm. See
+:ref:`section_ref_options_Algorithm_Parameters` for the good use of this
+command.
+
+The options of the algorithm are the following:
--- /dev/null
+The general optional commands, available in the editing user graphical or
+textual interface, are indicated in :ref:`section_ref_checking_keywords`.
+Moreover, the parameters of the command "*AlgorithmParameters*" allow to choose
+the specific options, described hereafter, of the algorithm. See
+:ref:`section_ref_options_Algorithm_Parameters` for the good use of this
+command.
+
+The options of the algorithm are the following:
--- /dev/null
+Information and variables available at the end of the algorithm
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+At the output, after executing the algorithm, there are information and
+variables originating from the calculation. The description of
+:ref:`section_ref_output_variables` show the way to obtain them by the method
+named ``get``, of the variable "*ADD*" of the post-processing in graphical
+interface, or of the case in textual interface. The input variables, available
+to the user at the output in order to facilitate the writing of post-processing
+procedures, are described in the :ref:`subsection_r_o_v_Inventaire`.
+
+The unconditional outputs of the algorithm are the following:
--- /dev/null
+The conditional outputs of the algorithm are the following:
--- /dev/null
+See also
+++++++++
+
+References to other sections:
--- /dev/null
+Bibliographical references:
--- /dev/null
+References to other SALOME modules:
--- /dev/null
+.. index:: single: InputVariables
+
+InputVariables
+ *Optional command*. This command allows to indicates the name and size of
+ physical variables that are bundled together in the state vector. This
+ information is dedicated to data processed inside an algorithm.
--- /dev/null
+.. index:: single: JacobianMatrixAtBackground
+
+JacobianMatrixAtBackground
+ *List of matrices*. Each element is the jacobian matrix of partial
+ derivatives of the output of the observation operator with respect to the
+ input parameters, one column of derivatives per parameter. It is calculated
+ at the initial state.
+
+ Example:
+ ``GradH = ADD.get("JacobianMatrixAtBackground")[-1]``
--- /dev/null
+.. index:: single: JacobianMatrixAtCurrentState
+
+JacobianMatrixAtCurrentState
+ *List of matrices*. Each element is the jacobian matrix of partial
+ derivatives of the output of the observation operator with respect to the input
+ parameters, one column of derivatives per parameter. It is calculated at the
+ current state.
+
+ Example:
+ ``GradH = ADD.get("JacobianMatrixAtCurrentState")[-1]``
--- /dev/null
+.. index:: single: JacobianMatrixAtOptimum
+
+JacobianMatrixAtOptimum
+ *List of matrices*. Each element is the jacobian matrix of partial
+ derivatives of the output of the observation operator with respect to the
+ input parameters, one column of derivatives per parameter. It is calculated
+ at the optimal state.
+
+ Example:
+ ``GradH = ADD.get("JacobianMatrixAtOptimum")[-1]``
--- /dev/null
+.. index:: single: KalmanGainAtOptimum
+
+KalmanGainAtOptimum
+ *List of matrices*. Each element is a standard Kalman gain matrix, evaluated
+ using the linearized observation operator. It is calculated at the optimal
+ state.
+
+ Example:
+ ``KG = ADD.get("KalmanGainAtOptimum")[-1]``
--- /dev/null
+.. index:: single: OutputVariables
+
+OutputVariables
+ *Optional command*. This command allows to indicates the name and size of
+ physical variables that are bundled together in the output observation
+ vector. This information is dedicated to data processed inside an algorithm.
--- /dev/null
+.. index:: single: StudyName
+
+StudyName
+ *Required command*. This is an open string to describe the ADAO study by a
+ name or a sentence.
--- /dev/null
+.. index:: single: StudyRepertory
+
+StudyRepertory
+ *Optional command*. If available, this directory is used as base name for
+ calculation, and used to find all the script files, given by name without
+ path, that can be used to define some other commands by scripts.
--- /dev/null
+.. index:: single: UserDataInit
+
+UserDataInit
+ *Optional command*. This commands allows to initialize some parameters or
+ data automatically before algorithm input processing. It indicates a script
+ file name to be executed before entering in initialization phase of chosen
+ variables.
--- /dev/null
+.. index:: single: UserPostAnalysis
+.. index:: single: UserPostAnalysis Template
+
+UserPostAnalysis
+ *Optional command*. This commands allows to process some parameters or data
+ automatically after data assimilation or optimization algorithm processing.
+ Its value is defined as a script file or a string, allowing to put
+ post-processing code directly inside the ADAO case. Common templates are
+ provided to help the user to start or to quickly make his case.
