MODULE obs_def_mod

Overview

The DART Fortran90 derived type obs_def provide an abstraction of the definition of an observation. An observation sequence obs_seq at a higher level is composed of observation definitions associated with observed values. For now, the basic operations required to implement an observation definition are an ability to compute a forward operator given the model state vector, the ability to read/write the observation definition from/to a file, and a capability to do a standard input driven interactive definition of the observation definition.

DART makes a distinction between specific observation types and generic observation quantities. The role of the various obs_def input files is to define the mapping between the types and quantities, and optionally to provide type-specific processing routines.

A single obs_def output module is created by the program preprocess from two kinds of input files. First, a DEFAULT obs_def module (normally called DEFAULT_obs_def_mod.F90 and documented in this directory) is used as a template into which the preprocessor incorporates information from zero or more special obs_def modules (such as obs_def_1d_state_mod.f90 or obs_def_reanalysis_bufr_mod.f90, also documented in this directory). If no special obs_def files are included in the preprocessor namelist, a minimal obs_def_mod.f90 is created which can only support identity forward observation operators.

New Observation Types

To add a new observation type which does not fit into any of the already-defined obs_def files, a new file should be created in the obs_def directory. These files are usually named according the the pattern obs_def_X_mod.f90, where the X is either an instrument name, a data source, or a class of observations. See the existing filenames in that directory for ideas. Then this new filename must be listed in the input.nml namelist for the model, in the &preprocess_nml section, in the obs_type_files variable. This variable is a string list type which can contain multiple filenames. Running the preprocess program will then use the contents of the new file to generate the needed output files for use in linking to the rest of the DART system.

Simple observations

If the new observation type can be directly interpolated by a model_mod interpolation routine, and has no additional observation-specific code for reading, writing, or initializing the observation, then the entire contents of the new file is:

! BEGIN DART PREPROCESS TYPE DEFINITIONS
! type, quantity, COMMON_CODE
! (repeat lines for each type)
! END DART PREPROCESS TYPE DEFINITIONS

DART will automatically generate all interface code needed for these new observation types. For example, here is a real list:

! BEGIN DART PREPROCESS TYPE DEFINITIONS
!VELOCITY,                     QTY_VELOCITY,              COMMON_CODE
!TRACER_CONCENTRATION,         QTY_TRACER_CONCENTRATION,  COMMON_CODE
!TRACER_SOURCE,                QTY_TRACER_SOURCE,         COMMON_CODE
!MEAN_SOURCE,                  QTY_MEAN_SOURCE,           COMMON_CODE
!SOURCE_PHASE,                 QTY_SOURCE_PHASE,          COMMON_CODE
! END DART PREPROCESS TYPE DEFINITIONS

The first column is the specific observation type and should be unique. The second column is the generic observation quantity. The quantities available to DART are defined at compile time by preprocess via the option 'quantity_files' in the preprocess_nml namelist. The third column must be the keyword COMMON_CODE which tells the preprocess program to automatically generate all necessary interface code for this type.

Observations needing special handling

For observation types which have observation-specific routines, must interpolate using a combination of other generic quantities, or require additional observation-specific data to be stored, the following format is used:

! BEGIN DART PREPROCESS TYPE DEFINITIONS
! type, quantity
! (repeat lines for each type/quantity pair)
! END DART PREPROCESS TYPE DEFINITIONS

DART will need user-supplied interface code for each of the listed types. For example, here is a real list:

! BEGIN DART PREPROCESS TYPE DEFINITIONS
! DOPPLER_RADIAL_VELOCITY, QTY_VELOCITY
! RADAR_REFLECTIVITY,      QTY_RADAR_REFLECTIVITY
! END DART PREPROCESS TYPE DEFINITIONS

In this case, DART needs additional information for how to process these types. They include code sections delimited by precisely formatted comments, and possibly module code sections:

! BEGIN DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE
! END DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE

Any fortran use statements for public subroutines or variables from other modules should be placed between these lines, with comment characters in the first column.
For example, if the forward operator code includes a module with public routines then a "use" statement like:

use obs_def_1d_state_mod, only : write_1d_integral, read_1d_integral, &
                                 interactive_1d_integral, get_expected_1d_integral

needs to be added to the obs_def_mod so the listed subroutines are available to be called. This would look like:

! BEGIN DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE
! use obs_def_1d_state_mod, only : write_1d_integral, read_1d_integral, &
!                                  interactive_1d_integral, get_expected_1d_integral
! END DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE

! BEGIN DART PREPROCESS GET_EXPECTED_OBS_FROM_DEF
! END DART PREPROCESS GET_EXPECTED_OBS_FROM_DEF

These comments must enclose a case statement for each defined type that returns the expected observation value based on the current values of the state vector. The code must be in comments, with the comment character in the first column.
The variables available to be passed to subroutines or used in this section of code are:

`state`	the entire model state vector
`state_time`	the time of the state data
`ens_index`	the ensemble member number
`location`	the observation location
`obs_kind_ind`	the index of the specific observation type
`obs_time`	the time of the observation
`error_val`	the observation error variance

The routine must fill in the values of these variables:

`obs_val`	the computed forward operator value
`istatus`	return code: 0=ok, >0 is error, <0 reserved for system use

To call a model_mod interpolate routine directly, the argument list must match exactly:

interpolate(state, location, QTY_xxx, obs_val, istatus)

This can be useful if the forward operator needs to retrieve values for fields which are typically found in a model and then compute a derived value from them.

! BEGIN DART PREPROCESS READ_OBS_DEF
! END DART PREPROCESS READ_OBS_DEF

These comments must enclose a case statement for each defined type that reads any additional data associated with a single observation. If there is no information beyond that for the basic obs_def type, the case statement must still be provided, but the code can simply be continue. The code must be in comments, with the comment character in the first column.
The variables available to be passed to subroutines or used in this section of code are:

`ifile`	the open unit number positioned ready to read, read-only
`obs_def`	the rest of the obs_def derived type for this obs, read-write
`key`	the index observation number in this sequence, read-only
`obs_val`	the observation value, if needed. in general should not be changed
`is_ascii`	logical to indicate how the file was opened, formatted or unformatted

The usual use of this routine is to read in additional metadata per observation and to set the private key in the obs_def to indicate which index to use for this observation to look up the corresponding metadata in arrays or derived types. Do not confuse the key in the obs_def with the key argument to this routine; the latter is the global observation sequence number for this observation.

! BEGIN DART PREPROCESS WRITE_OBS_DEF
! END DART PREPROCESS WRITE_OBS_DEF

These comments must enclose a case statement for each defined type that writes any additional data associated with a single observation. If there is no information beyond that for the basic obs_def type, the case statement must still be provided, but the code can simply be continue. The code must be in comments, with the comment character in the first column.
The variables available to be passed to subroutines or used in this section of code are:

`ifile`	the open unit number positioned ready to write, read-only
`obs_def`	the rest of the obs_def derived type for this obs, read-only
`key`	the index observation number in this sequence, read-only
`is_ascii`	logical to indicate how the file was opened, formatted or unformatted

The usual use of this routine is to write the additional metadata for this observation based on the private key in the obs_def. Do not confuse this with the key in the subroutine call which is the observation number relative to the entire observation sequence file.

```
! BEGIN DART PREPROCESS INTERACTIVE_OBS_DEF
! END DART PREPROCESS INTERACTIVE_OBS_DEF
```
These comments must enclose a case statement for each defined type that prompts the user for any additional data associated with a single observation. If there is no information beyond that for the basic obs_def type, the case statement must still be provided, but the code can simply be continue. The code must be in comments, with the comment character in the first column.
The variables available to be passed to subroutines or used in this section of code are:

obs_def the rest of the obs_def derived type for this obs, read-write

key the index observation number in this sequence, read-only

The DART code will prompt for the rest of the obs_def values (location, type, value, error) but any additional metadata needed by this observation type should be prompted to, and read from, the console (e.g. write(*,*), and read(*, *)). The code will generally set the obs_def%key value as part of setting the metadata.
```
! BEGIN DART PREPROCESS MODULE CODE
! END DART PREPROCESS MODULE CODE
```
If the code to process this observation requires module data and/or subroutines, then these comments must surround the module definitions. Unlike all the other sections, this comment pair is optional, and if used, the code must not be in comments; it will be copied verbatim over to the output file.
Generally the code for a forward operator should be defined inside a module, to keep module variables and other private subroutines from colliding with unrelated routines and variables in other forward operator files.

It is possible to mix automatic code types and user-supplied code types in the same list. Simply add the COMMON_CODE keyword on the lines which need no special data or interfaces. For example, here is an extract from the 1d state obs_def module, where the raw state variable needs only autogenerated code, but the 1d integral has user-supplied processing code:

! BEGIN DART PREPROCESS TYPE LIST
! RAW_STATE_VARIABLE,    QTY_STATE_VARIABLE, COMMON_CODE
! RAW_STATE_1D_INTEGRAL, QTY_1D_INTEGRAL
! END DART PREPROCESS TYPE LIST


! BEGIN DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE
!   use obs_def_1d_state_mod, only : write_1d_integral, read_1d_integral, &
!                                    interactive_1d_integral, get_expected_1d_integral
! END DART PREPROCESS USE OF SPECIAL OBS_DEF MODULE

! BEGIN DART PREPROCESS GET_EXPECTED_OBS_FROM_DEF
!         case(RAW_STATE_1D_INTEGRAL)
!            call get_expected_1d_integral(state, location, obs_def%key, obs_val, istatus)
! END DART PREPROCESS GET_EXPECTED_OBS_FROM_DEF

! BEGIN DART PREPROCESS READ_OBS_DEF
!      case(RAW_STATE_1D_INTEGRAL)
!         call read_1d_integral(obs_def%key, ifile, fileformat)
! END DART PREPROCESS READ_OBS_DEF

! BEGIN DART PREPROCESS WRITE_OBS_DEF
!      case(RAW_STATE_1D_INTEGRAL)
!         call write_1d_integral(obs_def%key, ifile, fileformat)
! END DART PREPROCESS WRITE_OBS_DEF

! BEGIN DART PREPROCESS INTERACTIVE_OBS_DEF
!      case(RAW_STATE_1D_INTEGRAL)
!         call interactive_1d_integral(obs_def%key)
! END DART PREPROCESS INTERACTIVE_OBS_DEF

! BEGIN DART PREPROCESS MODULE CODE
module obs_def_1d_state_mod

use        types_mod, only : r8
use    utilities_mod, only : register_module, error_handler, E_ERR, E_MSG
use     location_mod, only : location_type, set_location, get_location
use  assim_model_mod, only : interpolate
use   cov_cutoff_mod, only : comp_cov_factor

implicit none

public :: write_1d_integral, read_1d_integral, interactive_1d_integral, &
          get_expected_1d_integral

...  (module code here)

end module obs_def_1d_state_mod
! END DART PREPROCESS MODULE CODE

See the ./obs_def_1d_state_mod documentation for more details and examples of each section. Also see obs_def_wind_speed_mod.f90 for an example of a 3D geophysical forward operator.
In addition to collecting and managing any additional observation type-specific code, this module provides the definition of the obs_def_type derived type, and a collection of subroutines for creating, accessing, and updating this type. The remainder of this document describes the subroutines provided by this module.

Other modules used

types_mod
utilities_mod
location_mod (depends on model choice)
time_manager_mod
assim_model_mod
obs_kind_mod
Other special obs_def_kind modules as required

Public interfaces

use obs_def_mod, only :	obs_def_type
	init_obs_def
	get_obs_def_location
	get_obs_def_type_of_obs
	get_obs_def_time
	get_obs_def_error_variance
	get_obs_def_key
	set_obs_def_location
	set_obs_def_type_of_obs
	set_obs_def_time
	set_obs_def_error_variance
	set_obs_def_key
	interactive_obs_def
	write_obs_def
	read_obs_def
	get_expected_obs_from_def
	destroy_obs_def
	copy_obs_def
	assignment(=)
	get_name_for_type_of_obs

A note about documentation style. Optional arguments are enclosed in brackets [like this].

type obs_def_type
   private
   type(location_type)  :: location
   integer              :: kind
   type(time_type)      :: time
   real(r8)             :: error_variance
   integer              :: key
end type obs_def_type

Models all that is known about an observation except for actual values. Includes a location, type, time and error variance.

Component	Description
location	Location of the observation.
kind	Despite the name, the specific type of the observation.
time	Time of the observation.
error_variance	Error variance of the observation.
key	Unique identifier for observations of a particular type.

call init_obs_def(obs_def, location, kind, time, error_variance) :

type(obs_def_type),  intent(out) :: obs_def
type(location_type), intent(in)  :: location
integer,             intent(in)  :: kind
type(time_type),     intent(in)  :: time
real(r8),            intent(in)  :: error_variance

Creates an obs_def type with location, type, time and error_variance specified.

`obs_def`	The obs_def that is created
`location`	Location for this obs_def
`kind`	Observation type for obs_def
`time`	Time for obs_def
`error_variance`	Error variance of this observation

call copy_obs_def(obs_def1, obs_def2) :

type(obs_def_type), intent(out) :: obs_def1
type(obs_def_type), intent(in)  :: obs_def2

Copies obs_def2 to obs_def1, overloaded as assignment (=).

`obs_def1`	obs_def to be copied into
`obs_def2`	obs_def to be copied from

var = get_obs_def_key(obs_def) :

integer                        :: get_obs_def_key
type(obs_def_type), intent(in) :: obs_def

Returns key from an observation definition.

`var`	Returns key from an obs_def
`obs_def`	An obs_def

var = get_obs_def_error_variance(obs_def) :

real(r8)                       :: get_obs_def_error_variance
type(obs_def_type), intent(in) :: obs_def

Returns error variance from an observation definition.

`var`	Error variance from an obs_def
`obs_def`	An obs_def

var = get_obs_def_location(obs_def) :

type(location_type)              :: get_obs_def_location
type(obs_def_type), intent(in)   :: obs_def

Returns the location from an observation definition.

`var`	Returns location from an obs_def
`obs_def`	An obs_def

var = get_obs_def_type_of_obs(obs_def) :

integer                         :: get_obs_def_type_of_obs
type(obs_def_type),  intent(in) :: obs_def

Returns an observation type from an observation definition.

`var`	Returns the observation type from an obs_def
`obs_def`	An obs_def

var = get_obs_def_time(obs_def) :

type(time_type)                :: get_obs_def_time
type(obs_def_type), intent(in) :: obs_def

Returns time from an observation definition.

`var`	Returns time from an obs_def
`obs_def`	An obs_def

obs_name = get_name_for_type_of_obs(obs_kind_ind) :

character(len = 32)            :: get_name_for_type_of_obs
integer, intent(in)            :: obs_kind_ind

Returns an observation name from an observation type.

`var`	Returns name from an observation type
`obs_kind_ind`	An observation type

call set_obs_def_location(obs_def, location) :

type(obs_def_type),  intent(inout) :: obs_def
type(location_type), intent(in)    :: location

Set the location in an observation definition.

`obs_def`	An obs_def
`location`	A location

call set_obs_def_error_variance(obs_def, error_variance) :

type(obs_def_type), intent(inout) :: obs_def
real(r8), intent(in)              :: error_variance

Set error variance for an observation definition.

`obs_def`	An obs_def
`error_variance`	Error variance

call set_obs_def_key(obs_def, key) :

type(obs_def_type), intent(inout) :: obs_def
integer,            intent(in)    :: key

Set the key for an observation definition.

`obs_def`	An obs_def
`key`	Unique identifier for this observation

call set_obs_def_type_of_obs(obs_def, kind) :

type(obs_def_type), intent(inout) :: obs_def
integer,            intent(in)    :: kind

Set the type of observation in an observation definition.

`obs_def`	An obs_def
`kind`	An integer observation type

call set_obs_def_time(obs_def, time) :

type(obs_def_type), intent(inout) :: obs_def
type(time_type), intent(in)       :: time

Sets time for an observation definition.

`obs_def`	An obs_def
`time`	Time to set

call get_expected_obs_from_def(key, obs_def, obs_kind_ind, ens_index, state, state_time, obs_val, istatus, assimilate_this_ob, evaluate_this_ob) :

integer,            intent(in)  :: key
type(obs_def_type), intent(in)  :: obs_def
integer,            intent(in)  :: obs_kind_ind
integer,            intent(in)  :: ens_index
real(r8),           intent(in)  :: state(:)
type(time_type),    intent(in)  :: state_time
real(r8),           intent(out) :: obs_val
integer,            intent(out) :: istatus
logical,            intent(out) :: assimilate_this_ob
logical,            intent(out) :: evaluate_this_ob

Compute the observation (forward) operator for a particular obs definition.

`key`	descriptor for observation type
`obs_def`	The input obs_def
`obs_kind_ind`	The obs type
`ens_index`	The ensemble member number of this state vector
`state`	Model state vector
`state_time`	Time of the data in the model state vector
`istatus`	Returned integer describing problems with applying forward operator (0 == OK, >0 == error, <0 reserved for sys use).
`assimilate_this_ob`	Indicates whether to assimilate this obs or not
`evaluate_this_ob`	Indicates whether to evaluate this obs or not

call read_obs_def(ifile, obs_def, key, obs_val [,fform]) :

integer,                    intent(in)    :: ifile
type(obs_def_type),         intent(inout) :: obs_def
integer,                    intent(in)    :: key
real(r8),                   intent(inout) :: obs_val
character(len=*), optional, intent(in)    :: fform

Reads an obs_def from file open on channel ifile. Uses format specified in fform or FORMATTED if fform is not present.

`ifile`	File unit open to output file
`obs_def`	Observation definition to be read
`key`	Present if unique identifier key is needed by some obs type. Unused by default code.
`obs_val`	Present if needed to perform operations based on value. Unused by default code.
`fform`	File format specifier: FORMATTED or UNFORMATTED; default FORMATTED (FORMATTED in this case is the human readable/text option as opposed to UNFORMATTED which is binary.)

call interactive_obs_def(obs_def, key) :

type(obs_def_type), intent(inout) :: obs_def
integer,            intent(in)    :: key

Creates an obs_def via input from standard in.

`obs_def`	An obs_def to be created
`key`	Present if unique identifier key is needed by some obs type. Unused by default code.

call write_obs_def(ifile, obs_def, key [,fform]) :

integer,                    intent(in) :: ifile
type(obs_def_type),         intent(in) :: obs_def
integer,                    intent(in) :: key
character(len=*), optional, intent(in) :: fform

Writes an obs_def to file open on channel ifile. Uses format specified in fform or FORMATTED if fform is not present.

`ifile`	File unit open to output file
`obs_def`	Observation definition to be written
`key`	Present if unique identifier key is needed by some obs type. Unused by default code.
`fform`	File format specifier: FORMATTED or UNFORMATTED; default FORMATTED

call destroy_obs_def(obs_def) :

type(obs_def_type), intent(inout) :: obs_def

Releases all storage associated with an obs_def and its subcomponents.

obs_def An obs_def to be released.

Files

The read_obs_def() and write_obs_def() routines are passed an already-opened file channel/descriptor and read to or write from it.

References

none

Error codes and conditions

Routine	Message	Comment
get_expected_obs_from_def	Attempt to evaluate undefined observation type	An observation type for which no forward operator has been defined is an error.
read_obs_def	Expected header "obdef" in input file	The format of the input file is not consistent.
read_obs_def	Expected kind header "kind " in input file	The format of the input file is not consistent.
read_obs_def	Attempt to read for undefined obs_kind index	Reading for an observation type for which no forward operator has been defined is an error.
write_obs_def	Attempt to write for undefined obs_kind index	Writing for an observation type for which no forward operator has been defined is an error.
interactive_obs_def	Attempt to interactively create undefined obs_kind index	Creating an observation type for which no forward operator has been defined is an error.

Private components

N/A

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obs_def_mod.rst

obs_def_mod.rst

MODULE obs_def_mod

Overview

New Observation Types

Simple observations

Observations needing special handling

Other modules used

Public interfaces

Files

References

Error codes and conditions

Private components

Files

obs_def_mod.rst

Latest commit

History

obs_def_mod.rst

File metadata and controls

MODULE obs_def_mod

Overview

New Observation Types

Simple observations

Observations needing special handling

Other modules used

Public interfaces

Files

References

Error codes and conditions

Private components