= Auxiliary Routines = 

[[PageOutline(2-3,Contents of this page)]]

PDAF provide a number of auxiliary routines. They provide access to PDAF-internal data, which is not available through the regular interface of PDAF.

== Interface specifications ==

=== Module PDAF ===

Starting with PDAF V3.0 the module `PDAF` is provided. It has to be included with
{{{ 
  USE PDAF
}}}
in all routines that call PDAF routines (i.e `PDAF_*`, `PDAFomi_*`, `PDAFlocal*`). 

The module `PDAF` replaces the former module `PDAF_interfaces_module` of PDAF2. In PDAF releases V2.3.1 and earlier, this module provides interface definitions for the routines of PDAF. Its use was optional. It can be included with `use PDAF_interfaces_module`.


== Set or reset PDAF parameters ==

=== PDAF_set_iparam ===

This routine is used to set integer parameters for PDAF. It was introduced with PDAF V3.0. 

The integer parameters specific to a DA method can be set in the array `filter_param_i` that is an argument of `PDAF_init` (see the [wiki:InitPdaf page on initializing PDAF]). `PDAF_set_iparam` provides an alternative way. Instead of providing all parameters in the call to `PDAF_init`, one can provide only the required minimum for this call. Afterwards, one can then call `PDAF_set_iparam` for each integer parameter that one intends to specify differently from the default value. An advantage of using `PDAF_set_iparam` is that one only needs to call it for parameters that one intends to change, while in the call to `PDAF_init` all parameters up to the index one intends to change have to be specified, even if one does not want to change a parameter value. The tutorials and templates show the use of `PDAF_set_iparam`.

Full documentation: [wiki:PDAF_set_iparam]

=== PDAF_set_rparam ===

This routine is used to set real-valued (floating-point) parameters for PDAF. It was introduced with PDAF V3.0. 

The real-value parameters specific to a DA method can be set in the array `filter_param_r` that is an argument of `PDAF_init` (see the [wiki:InitPdaf page on initializing PDAF]). `PDAF_set_rparam` provides an alternative way. Instead of providing all parameters in the call to `PDAF_init`, one can provide only the required minimum for this call. Afterwards, one can then call `PDAF_set_rparam` for each integer parameter that one intends to specify differently from the default value. An advantage of using `PDAF_set_rparam` is that one only needs to call it for parameters that one intends to change, while in the call to `PDAF_init`, all parameters up to the index one intends to change have to be specified, even if one does not want to change a parameter value. The tutorials and templates show the use of `PDAF_set_rparam`.

Full documentation: [wiki:PDAF_set_rparam]

== Get information for forecast phase ==

=== PDAF_get_fcst_info ===

This routine was introduced with PDAF V3.0.

This routine returns the number of time steps to be computed int he current forecast phase. It also returns an exit flag to control the termination of ensemble forecasting and a value of the model time at the beginning of the forecast.

This routine is required in the setup of the [wiki:OnlineFlexible_PDAF3 flexible parallelization variant] in the form introduced with PDAF V3.0. However it can balso be useful for the fully parallel case.

Full documentation: [wiki:PDAF_get_fcst_info]



== Access to PDAF-internal arrays ==

=== PDAF_get_smootherens ===

A smoother is available for several filters (ESTKF/LESTKF/ETKF/LETKF/EnKF/NETF/LNETF). 

This routine is called to set a Fortran pointer to the array in PDAF that stores the ensembles for smoothing. In addition, the routine returns the available lag of the smoothing. Using this routine is required to aassess the smoother array, e.g. to write the smoother ensemble or its mean into a file.

Full documentation: [wiki:PDAF_get_smootherens] 

 
=== PDAF_set_smootherens ===

A smoother is available for several filters (ESTKF/LESTKF/ETKF/LETKF/EnKF/NETF/LNETF). 

This routine is called to set a Fortran pointer to the array in PDAF that stores the ensembles for smoothing. In addition, it sets the available lag of the smoothing. This routine is called in the offline mode of PDAF. While in the online mode, the smoother ensemble array is filled automatically by PDAF, one has to fill it manually in the offline mode. `PDAF_set_smootherens` gives access to the smoother array to fill it. 

Full documentation: [wiki:PDAF_set_smootherens] 


=== PDAF_set_ens_pointer ===

This routine allows a program to get a Fortran pointer to the internal ensemble array of PDAF. This provides direct access to the ensemble array.

`PDAF_set_ens_pointer` is a special routine that is never needed when the standard online or offline modes of the implementation are used. However, the routine allows to build a code that uses each column of the ensemble array to store the model fields. Thus, one can avoid allocating additional memory for the model fields. 

Full documentation: [wiki:PDAF_set_ens_pointer] 

== Access to index information ==

=== PDAF_get_memberid ===

The routine returns the value of the ensemble member ID. It can be called during the ensemble integration, if a program needs this information, e.g. if ensemble-specific forcing is applied. Also it can be used in the routines `collect_state_pdaf` and `distribute_state_pdaf`. 

Full documentation: [wiki:PDAF_get_memberid] 


=== PDAF_get_obsmemberid ===

The routine returns the value of the ensemble member ID for the application of the observation operator. The routine can be called in the observation-operator routine `obs_op_OBSTYPE` in an PDAF_OMI observation module or in the user-supplied routine `obs_op_pdaf` if PDAF-OMI is not used. 

The routine an be useful if the observation operator does not actually operate on the state vector that is provided by PDAF. For the special situation where one, e.g., reads the observed state vector from a file (because it might be initialized separately). There might also be cases in which one likes to read model state information from a file (e.g. if the observation operator performs an averaging over time, while the state vector for the analysis step only contains a single time instance). Inthese cases one need to member index as provided by `PDAF_get_obsmemberid`.

Full documentation: [wiki:PDAF_get_obsmemberid] 



== Incremental analysis updates ==

See page on [wiki:IncrementalAnalysisUpdates Incremental Analysis Updates in PDAF3].


== Controlling the MPI communicator for PDAF ==

=== PDAF_set_comm_pdaf ===

This routime allows to specify the MPI communicator on which the overall PDAF communication bases.

By default, PDAF bases on `MPI_COMM_WORLD`, thus all processes in a program. This routine allows to set a different communicator. This can be useful if a model is e.g. run with an OI-server so that the world communicator is split into processes for the file (I/O) operations and other processes for the actual model run. In this case, the model would run using a communicator distinct from `MPI_COMM_WORLD` and PDAF should operate only with this communicator. `PDAF_set_comm_pdaf` allows the user to specify this communicator for PDAF. 

Full documentation: [wiki:PDAF_set_comm_pdaf] 

== Debugging ==

=== PDAF_set_debug_flag ===

This routine was introduced with PDAF V2.1.

The routine allows to activate debugging output. 

Full documentation: [wiki:PDAF_debugging PDAF debuggging].

== Information on localization ==

=== PDAF_localfilter ===

This is a Fortran function that was introduced with PDAF V3.0

The function is an alternative to the subroutine `PDAF_get_localfilter`. In PDAF_localfilter the return value of the function is directly used, while for PDAF_get_localfilter the return value is an argument of the routine.

The function returns the information whether the chosen filter is a domain-localized filter (LESTKF, LETKF, LSEIK, LNETF). It also indicates the ENSRF since these filters use the same observation handling of the domain-localized filters. 

Full documentation: [wiki:PDAF_localfilter]

There is also a variant in the form of a subroutine: [wiki:PDAF_get_localfilter]

=== PDAF_local_type ===

This is a Fortran function that was introduced with PDAF V3.0

The function returns the information on the localization type of the filter set in the call to `PDAF_init`. With this one can distinguish filters using domain localization (LESTKF, LETKF, LSEIK, LNETF), covariance localization (LEnKF), or covariance localization with observation handling like domain localization (ENSRF/EAKF). This information is more detailed than what is returned by `PDAF_localfilter`.

Full documentation: [wiki:PDAF_local_type]

There is also a variant in the form of a subroutine: [wiki:PDAF_get_local_type]


== Additional (advanced) functionality ==

=== PDAF_print_DA_types ===

This routine was introduced with PDAF V3.0.

`PDAF_print_DA_types` can be called to show a list of IDs of the DA methods in PDAF. It will list the integer values of `filtertype` that can be specified in the call to `PDAF_init`. In addition, it will list the pre-defined parameter values `PDAF_DA_X` which are set to these values. These pre-define parameter values allow the user to specify e.g. the LESTKF with `PDAF_DA_LESTKF` as filtertype argument in the call to `PDAF_init`.

Full documentation: [wiki:PDAF_print_DA_types]


=== PDAF_set_seedset ===

This routine was introduced with PDAF V2.1.

This routine can be called to choose a seedset for the random number generator used in PDAF. With this one can perform experiments using different random numbers.

Full documentation: [wiki:PDAF_set_seedset]


=== PDAF_reset_forget ===

This routine was introduced with PDAF V2.0

The routine allows a user to reset the forgetting factor manually during the assimilation process. 

Full documentation: [wiki:PDAF_reset_forget]

Note: Starting from PDAF V.30 one can also use `PDAF_set_rparam` to reset the value of the forgetting factor.



=== PDAF_force_analysis === 

This routine was introduced with PDAF 2.0.

The routine allows a user to enforce the execution of the analysis step at the next call to `PDAF*_put_state` or `PDAF*_assimilate`. 

In particular for `PDAF*_assimilate`, the number of time steps is set before the forecast phase is entered. However, one might not know the actual length of the forecast phase, e.g. the time when new observations arrive. In this case, one can set for number of time steps to a large value and then check for new observations during the time stepping and call `PDAF_force_analysis` just before `PDAF*_assimilate` is called to enforce that the analysis step is executed.

Full documentation: [wiki:PDAF_force_analysis]



=== PDAF_set_memberid === 

This routine was introduced with PDAF 2.0.

The routine allows a user to reset the ensemble member counter inside PDAF. This routine should only be used in the flexible parallelization mode. Resetting the member counter, allows e.g. to enforce the execution of the analysis step in the case, when according to the PDAF-internal counter, the ensemble integration is not yet complete. For this, one has to specify the member-ID to be the ensemble size.

To just enforce an analysis step, we recommend to use the routine [wiki:PDAF_force_analysis]. This routine is also compatible with `PDAF_assimilate_X`.

Full documentation: [wiki:PDAF_set_memberid]