MODULE model_mod

DART project logo

Jump to DART Documentation Main Index
version information for this file:
$Id: model_mod.html 11996 2017-10-17 22:19:25Z nancy@ucar.edu $

NAMELIST / INTERFACES / FILES / REFERENCES / ERRORS / PLANS / PRIVATE COMPONENTS / TERMS OF USE

Overview

Every model that is DART compliant must provide an interface as documented here. The file models/template/model_mod.f90 provides the fortran interfaces for a minimal implementation meeting these requirements. When adding a new model to DART you can either start by modifying a model_mod.f90 file from a similar model already in DART or start with the template file. Either way, the supplied interface must match these descriptions exactly; no details of the underlying model can impact the interface.

Several of the routines listed below are allowed to be a NULL INTERFACE. This means the subroutine or function name must exist in this file, but it is ok if it contains no executable code.

A few of the routines listed below are allowed to be a PASS-THROUGH INTERFACE. This means the subroutine or function name can be listed on the 'use' line from the location_mod, and no subroutine or function with that name is supplied in this file. Alternatively, this file can provide an implementation which calls the underlying routines from the location_mod and then alters or augments the results based on model-specific requirements.

The system comes with several types of location modules for computing distances appropriately. Two of the ones most commonly used are for data in a 1D system and for data in a 3D spherical coordinate system. Make the selection by listing the appropriate choice from location/*/location_mod.f90 in the corresponding path_names_* file at compilation time.

[top]

NAMELIST

This namelist is read from the file input.nml. Namelists start with an ampersand '&' and terminate with a slash '/'. Character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.

&model_nml 
 /


Models are free to include a model namelist which can be read when static_init_model is called. A good example can be found in the lorenz_96 model_mod.f90.

[top]

OTHER MODULES USED

types_mod
time_manager_mod
location_mod (multiple choices here)
utilities_mod
POSSIBLY MANY OTHERS DEPENDING ON MODEL DETAILS
[top]

PUBLIC INTERFACES

use model_mod, only : get_model_size
 adv_1step
 get_state_meta_data
 model_interpolate
 shortest_time_between_assimilations
 static_init_model
 init_time
 init_conditions
 nc_write_model_atts
 nc_write_model_vars
 pert_model_copies
 get_close_obs
 get_close_state
 convert_vertical_obs
 convert_vertical_state
 read_model_time
 write_model_time
 end_model

A namelist interface &model_nml may be defined by the module, in which case it will be read from file input.nml. The details of the namelist are always model-specific (there are no generic namelist values).

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


model_size = get_model_size( )
integer(i8) :: get_model_size

Returns the length of the model state vector. Required.

model_size The length of the model state vector.


call adv_1step(x, time)
real(r8), dimension(:), intent(inout) :: x
type(time_type),        intent(in)    :: time

Does a single timestep advance of the model. The input value of the vector x is the starting condition and x must be updated to reflect the changed state after a timestep. The time argument is intent in and is used for models that need to know the date/time to compute a timestep, for instance for radiation computations. This interface is only called if the namelist parameter async is set to 0 in perfect_model_obs or filter or if the program integrate_model is to be used to advance the model state as a separate executable. If one of these options is not going to be used (the model will only be advanced as a separate model-specific executable), this can be a NULL INTERFACE. (The subroutine name must still exist, but it can contain no code and it will not be called.)

x State vector of length model_size.
time    Specifies time of the initial model state.


call get_state_meta_data (index_in, location, [, var_type] )
integer,             intent(in)  :: index_in
type(location_type), intent(out) :: location
integer, optional,   intent(out) ::  var_type 

Given an integer index into the state vector, returns the associated location. An optional argument returns the generic quantity of this item, e.g. QTY_TEMPERATURE, QTY_DENSITY, QTY_SALINITY, QTY_U_WIND_COMPONENT. This interface is required to be functional for all applications.

index_in Index of state vector element about which information is requested.
location The location of state variable element.
var_type The generic quantity of the state variable element.


call model_interpolate(state_handle, x, location, itype, obs_val, istatus)
type(ensemble_type),    intent(in)  :: state_handle
real(r8), dimension(:), intent(in)  :: x
type(location_type),    intent(in)  :: location
integer,                intent(in)  :: itype
real(r8),               intent(out) :: obs_val
integer,                intent(out) :: istatus

Given a handle containing information for a state vector, a state vector, a location, and a model state variable kind interpolates the state variable field to that location and returns the value in obs_val. The istatus variable should be returned as 0 unless there is some problem in computing the interpolation in which case a positive value should be returned. The itype variable is one of the quantity (QTY) parameters defined in the obs_kind_mod.f90 file and maps the quantity to a model variable for the interpolation. In low-order models that have no notion of kinds of variables this argument may be ignored. For applications in which only perfect model experiments with identity observations (i.e. only the value of a particular state variable is observed), this can be a NULL INTERFACE. Otherwise it is required (which is the most common case).

state_handle    The handle to the state structure containing information about the state vector about which information is requested.
x A model state vector.
location    Location to which to interpolate.
itype Quantity of state field to be interpolated.
obs_val The interpolated value from the model.
istatus Integer value returning 0 for success. Other values can be defined for various failures.


var = shortest_time_between_assimilations()
type(time_type) :: shortest_time_between_assimilations

Returns the time step (forecast length) of the model; the smallest increment in time that the model is capable of advancing the state in a given implementation. The actual value may be set by the model_mod namelist (depends on the model). This interface is required for all applications.

var    Smallest time step of model.


call static_init_model()

Called to do one time initialization of the model. As examples, might define information about the model size or model timestep. In models that require pre-computed static data, for instance spherical harmonic weights, these would also be computed here. Can be a NULL INTERFACE for the simplest models.



call init_time(time)
type(time_type), intent(out) :: time

Companion interface to init_conditions. Returns a time that is somehow appropriate for starting up a long integration of the model. At present, this is only used if the perfect_model_obs namelist parameter read_input_state_from_file = .false. If this option should not be used in perfect_model_obs, calling this routine should issue a fatal error.

time    Initial model time.


call init_conditions(x)
real(r8), dimension(:), intent(out) :: x

Returns a model state vector, x, that is some sort of appropriate initial condition for starting up a long integration of the model. At present, this is only used if the perfect_model_obs namelist parameter read_input_state_from_file = .false. If this option should not be used in perfect_model_obs, calling this routine should issue a fatal error.

x    Initial conditions for state vector.


call nc_write_model_atts(ncFileID, domain_id)
integer, intent(in) :: ncFileID
integer, intent(in) :: domain_id

This routine writes the model-specific attributes to netCDF files that DART creates. This includes coordinate variables and any metadata, but NOT the actual model state vector. models/template/model_mod.f90 contains code that can be used for any model as-is.

The typical sequence for adding new dimensions, variables, attributes:

NF90_OPEN             ! open existing netCDF dataset               
   NF90_redef         ! put into define mode                       
   NF90_def_dim       ! define additional dimensions (if any)     
   NF90_def_var       ! define variables: from name, kind, and dims
   NF90_put_att       ! assign attribute values                    
NF90_ENDDEF           ! end definitions: leave define mode         
   NF90_put_var       ! provide values for variable                
NF90_CLOSE            ! close: save updated netCDF dataset        
ncFileID Integer file descriptor to previously-opened netCDF file.
domain_id integer describing the domain (which can be a nesting level, a component model ...) Models with nested grids are decomposed into 'domains' in DART. The concept is extended to refer to 'coupled' models where one model component may be the atmosphere, another component may be the ocean, or land, or ionosphere ... these would be referenced as different domains.


call nc_write_model_vars(ncFileID, domain_id, state_ens_handle [, memberindex] [, timeindex])
integer,             intent(in) :: ncFileID
integer,             intent(in) :: domain_id
type(ensemble_type), intent(in) :: state_ens_handle
integer, optional,   intent(in) :: memberindex
integer, optional,   intent(in) :: timeindex

This routine may be used to write the model-specific state vector (data) to a netCDF file. Only used if model_mod_writes_state_variables = .true.

Typical sequence for adding new dimensions,variables,attributes:

NF90_OPEN             ! open existing netCDF dataset               
   NF90_redef         ! put into define mode                       
   NF90_def_dim       ! define additional dimensions (if any)      
   NF90_def_var       ! define variables: from name, kind, and dims
   NF90_put_att       ! assign attribute values                    
NF90_ENDDEF           ! end definitions: leave define mode         
   NF90_put_var       ! provide values for variable                
NF90_CLOSE            ! close: save updated netCDF dataset         
ncFileID file descriptor to previously-opened netCDF file.
domain_id integer describing the domain (which can be a nesting level, a component model ...)
state_ens_handle The handle to the state structure containing information about the state vector about which information is requested.
memberindex Integer index of ensemble member to be written.
timeindex The timestep counter for the given state.


call pert_model_copies(state_ens_handle, ens_size, pert_amp, interf_provided)
type(ensemble_type), intent(inout) :: state_ens_handle
integer,             intent(in)    :: ens_size
real(r8),            intent(in)    :: pert_amp
logical,             intent(out)   :: interf_provided

Given an ensemble handle, the ensemble size, and a perturbation amplitude; perturb the ensemble. Used to generate initial conditions for spinning up ensembles. If the model_mod does not want to do this, instead allowing the default algorithms in filter to take effect, interf_provided =&nbps;.false. and the routine can be trivial. Otherwise, interf_provided must be returned as .true.

state_ens_handle The handle containing an ensemble of state vectors to be perturbed.
ens_size The number of ensemble members to perturb.
pert_amp the amplitude of the perturbations. The interpretation is based on the model-specific implementation.
interf_provided    Returns false if model_mod cannot do this, else true.


call get_close_obs(gc, base_loc, base_type, locs, loc_qtys, loc_types, num_close, close_ind [, dist] [, state_handle)
type(get_close_type),          intent(in)  :: gc
type(location_type),           intent(in)  :: base_loc
integer,                       intent(in)  :: base_type
type(location_type),           intent(in)  :: locs(:)
integer,                       intent(in)  :: loc_qtys(:)
integer,                       intent(in)  :: loc_types(:)
integer,                       intent(out) :: num_close
integer,                       intent(out) :: close_ind(:)
real(r8),            optional, intent(out) :: dist(:)
type(ensemble_type), optional, intent(in)  :: state_handle

Given a location and kind, compute the distances to all other locations in the obs list. The return values are the number of items which are within maxdist of the base, the index numbers in the original obs list, and optionally the distances. The gc contains precomputed information to speed the computations.

In general this is a PASS-THROUGH ROUTINE. It is listed on the use line for the locations_mod, and in the public list for this module, but has no subroutine declaration and no other code in this module:

use location_mod, only: get_close_obs

public :: get_close_obs

However, if the model needs to alter the values or wants to supply an alternative implementation it can intercept the call like so:

use location_mod, only: &
        lm_get_close_obs => get_close_obs
        
public :: get_close_obs

In this case a local get_close_obs() routine must be supplied. To call the original code in the location module use:

call lm_get_close_obs(gc, base_loc, ...)

This subroutine will be called after get_close_maxdist_init and get_close_obs_init.

In most cases the PASS-THROUGH ROUTINE will be used, but some models need to alter the actual distances depending on the observation or state vector kind, or based on the observation or state vector location. It is reasonable in this case to leave get_close_maxdist_init() and get_close_obs_init() as pass-through routines and intercept only get_close_obs(). The local get_close_obs() can first call the location mod routine and let it return a list of values, and then inspect the list and alter or remove any entries as needed. See the CAM and WRF model_mod files for examples of this use.

gc The get_close_type which stores precomputed information about the locations to speed up searching
base_loc Reference location. The distances will be computed between this location and every other location in the obs list
base_type    The DART quantity at the base_loc
locs(:) Compute the distance between the base_loc and each of the locations in this list
loc_qtys(:) The corresponding quantity of each item in the locs list
loc_types(:) The corresponding type of each item in the locs list. This is not available in the default implementation but may be used in custom implementations.
num_close The number of items from the locs list which are within maxdist of the base location
close_ind(:) The list of index numbers from the locs list which are within maxdist of the base location
dist(:) If present, return the distance between each entry in the close_ind list and the base location. If not present, all items in the obs list which are closer than maxdist will be added to the list but the overhead of computing the exact distances will be skipped.
state_handle    The handle to the state structure containing information about the state vector about which information is requested.


call get_close_state(gc, base_loc, base_type, state_loc, state_qtys, state_indx, num_close, close_ind, dist, state_handle)
type(get_close_type), intent(in)    :: gc
type(location_type),  intent(inout) :: base_loc
integer,              intent(in)    :: base_type
type(location_type),  intent(inout) :: state_loc(:)
integer,              intent(in)    :: state_qtys(:)
integer(i8),          intent(in)    :: state_indx(:)
integer,              intent(out)   :: num_close
integer,              intent(out)   :: close_ind(:)
real(r8),             intent(out)   :: dist(:)
type(ensemble_type),  intent(in)    :: state_handle

Given a location and kind, compute the distances to all other locations in the state_loc list. The return values are the number of items which are within maxdist of the base, the index numbers in the original state_loc list, and optionally the distances. The gc contains precomputed information to speed the computations.

In general this is a PASS-THROUGH ROUTINE. It is listed on the use line for the locations_mod, and in the public list for this module, but has no subroutine declaration and no other code in this module:

use location_mod, only: get_close_state

public :: get_close_state

However, if the model needs to alter the values or wants to supply an alternative implementation it can intercept the call like so:

use location_mod, only: &
        lm_get_close_state => get_close_state
        
public :: get_close_state

In this case a local get_close_state() routine must be supplied. To call the original code in the location module use:

call loc_get_close_state(gc, base_loc, ...)

This subroutine will be called after get_close_maxdist_init and get_close_state_init.

In most cases the PASS-THROUGH ROUTINE will be used, but some models need to alter the actual distances depending on the observation or state vector kind, or based on the observation or state vector location. It is reasonable in this case to leave get_close_maxdist_init() and get_close_state_init() as pass-through routines and intercept only get_close_state(). The local get_close_state() can first call the location mod routine and let it return a list of values, and then inspect the list and alter or remove any entries as needed. See the CAM and WRF model_mod files for examples of this use.

gc The get_close_type which stores precomputed information about the locations to speed up searching
base_loc Reference location. The distances will be computed between this location and every other location in the obs list
base_type    The DART quantity at the base_loc
state_loc(:) Compute the distance between the base_loc and each of the locations in this list
state_qtys(:) The corresponding quantity of each item in the state_loc list
state_indx(:) The corresponding DART index of each item in the state_loc list. This is not available in the default implementation but may be used in custom implementations.
num_close The number of items from the state_loc list which are within maxdist of the base location
close_ind(:) The list of index numbers from the state_loc list which are within maxdist of the base location
dist(:) If present, return the distance between each entry in the close_ind list and the base location. If not present, all items in the state_loc list which are closer than maxdist will be added to the list but the overhead of computing the exact distances will be skipped.
state_handle    The handle to the state structure containing information about the state vector about which information is requested.


call convert_vertical_obs(state_handle, num, locs, loc_qtys, loc_types, which_vert, status)
type(ensemble_type), intent(in)  :: state_handle
integer,             intent(in)  :: num
type(location_type), intent(in)  :: locs(:)
integer,             intent(in)  :: loc_qtys(:)
integer,             intent(in)  :: loc_types(:)
integer,             intent(in)  :: which_vert
integer,             intent(out) :: status(:)

Converts the observations to the desired vertical localization coordinate system. Some models (toy models with no 'real' observations) will not need this. Most (real) models have observations in one or more coordinate systems (pressure, height) and the model is generally represented in only one coordinate system. To be able to interpolate the model state to the observation location, or to compute the true distance between the state and the observation, it is necessary to convert everything to one coodinate system.

state_handle    The handle to the state.
num the number of observation locations
locs the array of observation locations
loc_qtys the array of observation quantities.
loc_types the array of observation types.
which_vert the desired vertical coordinate system. There is a table in the location_mod.f90 that relates integers to vertical coordinate systems.
status Specifies the success or failure of the vertical conversion. If istatus = 0, the conversion was a sucess. Any other value is a failure.


call convert_vertical_state(state_handle, num, locs, loc_qtys, loc_types, which_vert, status)
type(ensemble_type), intent(in)  :: state_handle
integer,             intent(in)  :: num
type(location_type), intent(in)  :: locs(:)
integer,             intent(in)  :: loc_qtys(:)
integer,             intent(in)  :: loc_types(:)
integer,             intent(in)  :: which_vert
integer,             intent(out) :: status(:)

Converts the state to the desired vertical localization coordinate system. Some models (toy models with no 'real' observations) will not need this. Most (real) models have observations in one or more coordinate systems (pressure, height) and the model is generally represented in only one coordinate system. To be able to interpolate the model state to the observation location, or to compute the true distance between the state and the observation, it is necessary to convert everything to one coodinate system.

state_handle    The handle to the state.
num the number of state locations
locs the array of state locations
loc_qtys the array of state quantities.
loc_types the array of state types.
which_vert the desired vertical coordinate system. There is a table in the location_mod.f90 that relates integers to vertical coordinate systems.
status Specifies the success or failure of the vertical conversion. If istatus = 0, the conversion was a sucess. Any other value is a failure.


model_time = read_model_time(filename)
character(len=*), intent(in) :: filename
type(time_type)              :: model_time

Reads the valid time of the model state in a netCDF file. There is a default routine in assimilation_code/modules/io/dart_time_io_mod.f90 that can be used as a pass-through. That routine will read the last timestep of a 'time' variable - which is the same strategy used for reading netCDF files that have multiple timesteps in them. If your model has some other representation of time (i.e. it does not use a netCDF variable named 'time') - you will have to write this routine.

ncid handle to an open netCDF file
dart_time    Specifies the (last) time of the model state.


call write_model_time(ncid, dart_time)
integer,          intent(in) :: ncid
type(time_type),  intent(in) :: dart_time

Writes the assimilation time to a netCDF file. There is a default routine in assimilation_code/modules/io/dart_time_io_mod.f90 that can be used as a pass-through. If your model has some other representation of time (i.e. it does not use a netCDF variable named 'time') - you will have to write this routine.

ncid handle to an open netCDF file
dart_time    Specifies the time of the assimilation (the current time step).


call end_model()

Does any shutdown and clean-up needed for model. Can be a NULL INTERFACE if the model has no need to clean up storage, etc.

[top]

FILES

[top]

REFERENCES

  1. none
[top]

ERROR CODES and CONDITIONS

KNOWN BUGS

none at this time

[top]

FUTURE PLANS

It is likely that a number of additional optional interfaces will be added to the model_mod structure. For instance, hints about how to divide the state vector into regions for parallel assimilation will need to be obtained from the model. It is planned that the interf_provided mechanism used in pert_model_copies will allow those who do not wish to support enhanced interfaces to add NULL interfaces by simply pasting in an interface block.

[top]

PRIVATE COMPONENTS

N/A

[top]

Terms of Use

DART software - Copyright UCAR. This open source software is provided by UCAR, "as is", without charge, subject to all terms of use at http://www.image.ucar.edu/DAReS/DART/DART_download

Contact: your_name_here
Revision: $Revision: 11996 $
Source: $URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/models/template/model_mod.html $
Change Date: $Date: 2017-10-17 16:19:25 -0600 (Tue, 17 Oct 2017) $
Change history:  try "svn log" or "svn diff"