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DART Documentation Main Index |
NCOMMAS 7_1 may now be used with the
Data Assimilation Research Testbed (DART).
Since NCOMMAS uses netCDF files or their restart mechanisms, it was possible to
make a namelist-controlled set of variables to be included in the DART state vector.
Each variable must also correspond to a DART "KIND"; required for the DART
interpolate routines. For example,
&ncommas_vars_nml ncommas_state_variables = 'U', 'QTY_U_WIND_COMPONENT', 'V', 'QTY_V_WIND_COMPONENT', 'W', 'QTY_VERTICAL_VELOCITY', 'TH', 'QTY_POTENTIAL_TEMPERATURE', 'DBZ', 'QTY_RADAR_REFLECTIVITY', 'WZ', 'QTY_VERTICAL_VORTICITY', 'PI', 'QTY_EXNER_FUNCTION', 'QV', 'QTY_VAPOR_MIXING_RATIO', 'QC', 'QTY_CLOUDWATER_MIXING_RATIO', 'QR', 'QTY_RAINWATER_MIXING_RATIO', 'QI', 'QTY_ICE_MIXING_RATIO', 'QS', 'QTY_SNOW_MIXING_RATIO', 'QH', 'QTY_GRAUPEL_MIXING_RATIO' /
These variables are then adjusted to be consistent
with observations and stuffed back into the same netCDF restart files.
Since DART is an ensemble algorithm, there are multiple restart files for a
single restart time: one for each ensemble member. Creating the initial ensemble
of states is an area of active research.
DART reads the grid information for NCOMMAS from
the restart file specified in the DART
input.nml&model_nml:ncommas_restart_filename
and checks for the existence and shape of the desired state variables. This not
only determines the size of the DART state vector, but DART also inherits much
of the metadata for the variables from the NCOMMAS restart file.
When DART is responsible for starting/stopping NCOMMAS, the information is
conveyed through the command line arguments to NCOMMAS.
was compiled with the Intel 10.1 compilers and run on a linux cluster running SLES10.
Initially, DART simply runs 'end-to-end' at every assimilation time, while the NCOMMAS
ensemble mechanism is responsible for slicing and dicing the observation sequences
and running correct_ensemble at the desired times.
This is a complete role-reversal from the normal DART operation.
The DART components were built with the following settings:
MPIFC = mpif90 MPILD = mpif90 FC = ifort LD = ifort INCS = -I/coral/local/netcdf-3.6.3_intel-10.1-64/include LIBS = -L/coral/local/netcdf-3.6.3_intel-10.1-64/lib -lnetcdf FFLAGS = -pc64 -fpe0 -mp -O0 -vec-report0 $(INCS) LDFLAGS = $(FFLAGS) $(LIBS)
is blissfully straighforward. Given the namelist mechanism for
determining the state variables and the fact that the NCOMMAS netCDF
file has all the grid and time information in it - everything that is needed
can be readily determined.
There are two programs - both require the list of NCOMMAS variables to use in
the DART state vector: the
ncommas_vars_nml namelist in the
ncommas_vars.nml file.
ncommas_to_dart.f90 | converts the ncommas restart file ncommas_restart.nc into a DART-compatible file normally called dart_ics . We usually wind up linking the restart file to a static name that is used by DART. |
dart_to_ncommas.f90 | inserts the DART output into an existing ncommas restart netCDF file by overwriting the variables in the ncommas restart netCDF file. There are two different types of DART output files, so there is a namelist option to specify if the DART file has two time records or just one (if there are two, the first one is the 'advance_to' time, followed by the 'valid_time' of the ensuing state). dart_to_ncommas determines the ncommas restart file name from the input.nml model_nml:ncommas_restart_filename. If the DART file contains an 'advance_to' time, dart_to_ncommas creates a new &time_manager_nml for ncommas in a file called ncommas_in.DART which can be used to control the length of the ncommas integration. |
Creating the initial ensemble is an area of active research.
The ncommas model cannot take one single model state and generate its own
ensemble (typically done with pert_model_state).
The ensemble has to come from 'somewhere else'.
At present, it may be sufficient to use a climatological ensemble; e.g.,
using the ncommas restarts for '1 January 00Z' from 50 consecutive years
from a hindcast experiment.
There is not yet a
shell_scripts/MakeInitialEnsemble.csh
script to demonstrate how to convert a set of ncommas netCDF
restart files into a set of DART files that have a consistent timestamp.
If you simply convert each ncommas file to a DART file using
ncommas_to_dart, each DART file will have a 'valid time'
that reflects the ncommas time of that state - instead of an ensemble of states
reflecting one single time. The
restart_file_utility
can be used to overwrite the timestep in the header of each DART initial
conditions file. The namelist for this program must look something like:
&restart_file_tool_nml input_file_name = "dart_input", output_file_name = "dart_output", ens_size = 1, single_restart_file_in = .true., single_restart_file_out = .true., write_binary_restart_files = .true., overwrite_data_time = .true., new_data_days = 145731, new_data_secs = 0, input_is_model_advance_file = .false., output_is_model_advance_file = .false., overwrite_advance_time = .false., new_advance_days = -1, new_advance_secs = -1, gregorian_cal = .true. /
The time of days = 145731
seconds = 0 relates to 00Z 1 Jan 2000 in the DART world.
We adhere to the F90 standard of starting a namelist with an ampersand '&' and terminating with a slash '/' for all our namelist input. Consider yourself forewarned that character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.
namelist /model_nml/ ncommas_restart_filename, & assimilation_period_days, assimilation_period_seconds, & model_perturbation_amplitude, output_state_vector, calendar, debug
This namelist is read in a file called input.nml. This namelist provides control over the assimilation period for the model. All observations within (+/-) half of the assimilation period are assimilated. The assimilation period is the minimum amount of time the model can be advanced, and checks are performed to ensure that the assimilation window is a multiple of the model dynamical timestep.
Contents | Type | Description |
---|---|---|
output_state_vector | logical [default: .true.] | The switch to determine the form of the state vector in the output netCDF files. If .true. the state vector will be output exactly as DART uses it ... one long array. If .false., the state vector is parsed into prognostic variables and output that way -- much easier to use with 'ncview', for example. |
assimilation_period_days | integer [default: 1] | The number of days to advance the model for each assimilation. |
assimilation_period_seconds | integer [default: 0] | In addition to assimilation_period_days, the number of seconds to advance the model for each assimilation. |
model_perturbation_amplitude | real(r8) [default: 0.2] | Reserved for future use. |
calendar | character(len=32) [default: 'Gregorian'] |
Character string specifying the calendar being used by NCOMMAS. |
debug | integer [default: 0] | The switch to specify the run-time verbosity. 0 is as quiet as it gets. > 1 provides more run-time messages. > 5 provides ALL run-time messages. All values above 0 will also write a netCDF file of the grid information and perform a grid interpolation test. |
&model_nml ncommas_restart_filename = 'ncommas_restart.nc'; assimilation_period_days = 1, assimilation_period_seconds = 0, model_perturbation_amplitude = 0.2, output_state_vector = .true., calendar = 'Gregorian', debug = 0 /
namelist /ncommas_vars_nml/ ncommas_state_variables
This namelist is read in a file called ncommas_vars.nml and contains the list of NCOMMAS variables that make up the DART state vector.
Contents | Type | Description |
---|---|---|
ncommas_state_variables | character(len=NF90_MAX_NAME):: dimension(160) [default: see example] |
The table that relates the NCOMMAS variables to use to build the DART state vector, and the corresponding DART kinds for those variables. |
&ncommas_vars_nml ncommas_state_variables = 'U', 'QTY_U_WIND_COMPONENT', 'V', 'QTY_V_WIND_COMPONENT', 'W', 'QTY_VERTICAL_VELOCITY', 'TH', 'QTY_POTENTIAL_TEMPERATURE', 'DBZ', 'QTY_RADAR_REFLECTIVITY', 'WZ', 'QTY_VERTICAL_VORTICITY', 'PI', 'QTY_EXNER_FUNCTION', 'QV', 'QTY_VAPOR_MIXING_RATIO', 'QC', 'QTY_CLOUDWATER_MIXING_RATIO', 'QR', 'QTY_RAINWATER_MIXING_RATIO', 'QI', 'QTY_ICE_MIXING_RATIO', 'QS', 'QTY_SNOW_MIXING_RATIO', 'QH', 'QTY_GRAUPEL_MIXING_RATIO' /
types_mod time_manager_mod threed_sphere/location_mod utilities_mod obs_kind_mod mpi_utilities_mod random_seq_mod
Only a select number of interfaces used are discussed here. Each module has its own discussion of their routines.
use model_mod, only : | get_gridsize |
restart_file_to_sv | |
sv_to_restart_file | |
get_ncommas_restart_filename | |
get_base_time | |
get_state_time |
use location_mod, only : | get_close_obs |
A note about documentation style. Optional arguments are enclosed in brackets [like this].
integer :: get_model_size
Returns the length of the model state vector. Required.
model_size | The length of the model state vector. |
real(r8), dimension(:), intent(inout) :: x type(time_type), intent(in) :: time
adv_1step is not used for the ncommas model. Advancing the model is done through the advance_model script. This is a NULL_INTERFACE, provided only for compatibility with the DART requirements.
x | State vector of length model_size. |
time | Specifies time of the initial model state. |
integer, intent(in) :: index_in type(location_type), intent(out) :: location integer, optional, intent(out) :: var_type
get_state_meta_data returns metadata about a given element of the DART representation of the model state vector. Since the DART model state vector is a 1D array and the native model grid is multidimensional, get_state_meta_data returns information about the native model state vector representation. Things like the location, or the type of the variable (for instance: temperature, u wind component, ...). The integer values used to indicate different variable types in var_type are themselves defined as public interfaces to model_mod if required.
index_in | Index of state vector element about which information is requested. |
location | Returns the 3D location of the indexed state variable. The location_ type comes from DART/assimilation_code/location/threed_sphere/location_mod.f90. Note that the lat/lon are specified in degrees by the user but are converted to radians internally. |
var_type | Returns the type of the indexed state variable as an optional argument. The type is one of the list of supported observation types, found in the block of code starting ! Integer definitions for DART TYPES in DART/assimilation_code/modules/observations/obs_kind_mod.f90 |
The list of supported variables in DART/assimilation_code/modules/observations/obs_kind_mod.f90 is created by preprocess.
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 model state, model_interpolate returns the value of
the desired observation type (which could be a state variable) that would be
observed at the desired location. The interpolation method is either
completely specified by the model, or uses some standard 2D or 3D scalar
interpolation routines.
Put another way, model_interpolate will apply the forward
operator H to the model state to create an observation at the desired
location.
If the interpolation is valid, istatus = 0.
In the case where the observation operator is not defined at the given
location (e.g. the observation is below the lowest model level, above the top
level, or 'dry'), interp_val is returned as 0.0 and istatus = 1.
x | A model state vector. |
location | Location to which to interpolate. |
itype | Integer indexing which type of observation is desired. |
obs_val | The interpolated value from the model. |
istatus | Integer flag indicating the success of the interpolation.
success == 0, failure == anything else |
type(time_type) :: get_model_time_step
get_model_time_step returns the forecast length to be used as the "model base time step" in the filter. This is the minimum amount of time the model can be advanced by filter. This is also the assimilation window. All observations within (+/-) one half of the forecast length are used for the assimilation. In the ncommas case, this is set from the namelist values for input.nml&model_nml:assimilation_period_days, assimilation_period_seconds.
var | Smallest time step of model. |
static_init_model
is called for runtime initialization of the model.
The namelists are read to determine runtime configuration of the model,
the grid coordinates, etc. There are no input arguments and no return values.
The routine sets module-local private attributes that can then be queried by the
public interface routines.
See the ncommas documentation for all namelists in ncommas_in .
Be aware that DART reads the ncommas &grid_nml namelist
to get the filenames for the horizontal and vertical grid information as well
as the topography information.
The namelists (all mandatory) are:
input.nml&model_mod_nml,
ncommas_in&time_manager_nml,
ncommas_in&io_nml,
ncommas_in&init_ts_nml,
ncommas_in&restart_nml,
ncommas_in&domain_nml, and
ncommas_in&grid_nml.
end_model is used to clean up storage for the model, etc. when the model is no longer needed. There are no arguments and no return values. The grid variables are deallocated.
type(time_type), intent(out) :: time
init_time returns the time at which the model will start if no input initial conditions are to be used. This is frequently used to spin-up models from rest, but is not meaningfully supported for the ncommas model. The only time this routine would get called is if the input.nml&perfect_model_obs_nml:start_from_restart is .false., which is not supported in the ncommas model.
time | the starting time for the model if no initial conditions are to be supplied. This is hardwired to 0.0 |
real(r8), dimension(:), intent(out) :: x
init_conditions returns default initial conditions for model; generally used for spinning up initial model states. For the ncommas model it is just a stub because the initial state is always provided by the input files.
x | Initial conditions for state vector. This is hardwired to 0.0 |
integer :: nc_write_model_atts integer, intent(in) :: ncFileID
nc_write_model_atts writes model-specific attributes to an opened netCDF file: In the ncommas case, this includes information like the coordinate variables (the grid arrays: ULON, ULAT, TLON, TLAT, ZG, ZC, KMT, KMU), information from some of the namelists, and either the 1D state vector or the prognostic variables (SALT,TEMP,UVEL,VVEL,PSURF). All the required information (except for the netCDF file identifier) is obtained from the scope of the model_mod module. Both the input.nml and ncommas_in files are preserved in the netCDF file as variables inputnml and ncommas_in, respectively.
ncFileID | Integer file descriptor to previously-opened netCDF file. |
ierr | Returns a 0 for successful completion. |
nc_write_model_atts is responsible for the model-specific attributes in the following DART-output netCDF files: true_state.nc, preassim.nc, and analysis.nc.
integer, intent(in) :: ncFileID real(r8), dimension(:), intent(in) :: statevec integer, intent(in) :: copyindex integer, intent(in) :: timeindex integer :: ierr
nc_write_model_vars writes a copy of the state variables to a NetCDF file. Multiple copies of the state for a given time are supported, allowing, for instance, a single file to include multiple ensemble estimates of the state. Whether the state vector is parsed into prognostic variables (SALT, TEMP, UVEL, VVEL, PSURF) or simply written as a 1D array is controlled by input.nml&model_mod_nml:output_state_vector. If output_state_vector = .true. the state vector is written as a 1D array (the simplest case, but hard to explore with the diagnostics). If output_state_vector = .false. the state vector is parsed into prognostic variables before being written.
ncFileID | file descriptor to previously-opened netCDF file. |
statevec | A model state vector. |
copyindex | Integer index of copy to be written. |
timeindex | The timestep counter for the given state. |
ierr | Returns 0 for normal completion. |
real(r8), dimension(:), intent(in) :: state real(r8), dimension(:), intent(out) :: pert_state logical, intent(out) :: interf_provided
Given a model state, pert_model_state produces a
perturbed model state. This is used to generate ensemble initial conditions
perturbed around some control trajectory state when one is preparing to
spin-up ensembles. Since the DART state vector for the ncommas model
contains both 'wet' and 'dry' cells, it is imperative to provide an
interface to perturb just the wet cells
(interf_provided == .true.).
The magnitude of the perturbation is wholly determined by
input.nml&model_mod_nml:model_perturbation_amplitude
and utterly, completely fails.
A more robust perturbation mechanism is needed.
Until then, avoid using this routine by using your own ensemble of initial conditions.
This is determined by setting
input.nml&filter_nml:start_from_restart = .false.
state | State vector to be perturbed. |
pert_state | The perturbed state vector. |
interf_provided | Because of the 'wet/dry' issue discussed above, this is always .true., indicating a model-specific perturbation is available. |
type(get_close_type), intent(inout) :: gc real(r8), intent(in) :: maxdist
Pass-through to the 3-D sphere locations module. See get_close_maxdist_init() for the documentation of this subroutine.
type(get_close_type), intent(inout) :: gc integer, intent(in) :: num type(location_type), intent(in) :: obs(num)
Pass-through to the 3-D sphere locations module. See get_close_obs_init() for the documentation of this subroutine.
type(get_close_type), intent(in ) :: gc type(location_type), intent(in ) :: base_obs_loc integer, intent(in ) :: base_obs_kind type(location_type), dimension(:), intent(in ) :: obs integer, dimension(:), intent(in ) :: obs_kind integer, intent(out) :: num_close integer, dimension(:), intent(out) :: close_ind real(r8), optional, dimension(:), intent(out) :: dist
Given a DART location (referred to as "base") and a set of locations, and a
definition of 'close' - return a subset of locations that are 'close', as well
as their distances to the DART location and their indices. This routine intentionally
masks a routine of the same name in location_mod because we
want to be able to discriminate against selecting 'dry land' locations.
Given a single location and a list of other locations, returns the indices
of all the locations close to the single one along with the number of
these and the distances for the close ones. The list of locations
passed in via the obs argument must be identical to
the list of obs passed into the most recent call
to get_close_obs_init(). If the list of locations
of interest changes, get_close_obs_destroy() must
be called and then the two initialization routines must be called
before using get_close_obs() again.
For vertical distance computations, the general philosophy is to convert all
vertical coordinates to a common coordinate. This coordinate type is defined
in the namelist with the variable "vert_localization_coord".
gc | Structure to allow efficient identification of locations 'close' to a given location. |
base_obs_loc | Single given location. |
base_obs_kind | Kind of the single location. |
obs | List of candidate locations. |
obs_kind | Kind associated with candidate locations. |
num_close | Number of locations close to the given location. |
close_ind | Indices of those locations that are close. |
dist | Distance between given location and the close ones identified in close_ind. |
real(r8), dimension(:), intent(in) :: ens_mean
ens_mean_for_model normally saves a copy of the ensemble mean to module-local storage. This is a NULL_INTERFACE for the ncommas model. At present there is no application which requires module-local storage of the ensemble mean. No storage is allocated.
ens_mean | State vector containing the ensemble mean. |
integer, intent(out) :: num_x, num_y, num_z
get_gridsize returns the dimensions of the compute domain. The horizontal gridsize is determined from ncommas_restart.nc.
num_x | The number of longitudinal gridpoints. |
num_y | The number of latitudinal gridpoints. |
num_z | The number of vertical gridpoints. |
character(len=*), intent(in) :: filename real(r8), dimension(:), intent(inout) :: state_vector type(time_type), intent(out) :: model_time
restart_file_to_sv Reads a NCOMMAS netCDF format restart file and packs the desired variables into a DART state vector. The desired variables are specified in the ncommas_vars_nml namelist.
filename | The name of the netCDF format NCOMMAS restart file. |
state_vector | the 1D array containing the concatenated NCOMMAS variables. |
model_time | the time of the model state. The last time in the netCDF restart file. |
real(r8), dimension(:), intent(in) :: state_vector character(len=*), intent(in) :: filename type(time_type), intent(in) :: statedate
sv_to_restart_file updates the variables in the NCOMMAS restart file with values from the DART vector state_vector. The last time in the file must match the statedate.
filename | the netCDF-format ncommas restart file to be updated. |
state_vector | the 1D array containing the DART state vector. |
statedate | the 'valid_time' of the DART state vector. |
character(len=*), intent(out) :: filename
get_ncommas_restart_filename returns the name of the NCOMMAS restart file - the filename itself is in private module storage.
filename | The name of the NCOMMAS restart file. |
integer, intent(in) :: filehandle -OR- character(len=*), intent(in) :: filehandle type(time_type), intent(out) :: time
get_base_time extracts the start time of the experiment as contained in the netCDF restart file. The file may be specified by either a character string or the integer netCDF fid.
integer, intent(in) :: filehandle -OR- character(len=*), intent(in) :: filehandle type(time_type), intent(out) :: time
get_state_time extracts the time of the model state as contained in the netCDF restart file. In the case of multiple times in the file, the last time is the time returned. The file may be specified by either a character string or the integer netCDF fid.
filename | purpose |
---|---|
input.nml | to read the model_mod namelist |
ncommas_vars.nml | to read the ncommas_vars_nml namelist |
ncommas_restart.nc | provides grid dimensions, model state, and 'valid_time' of the model state |
true_state.nc | the time-history of the "true" model state from an OSSE |
preassim.nc | the time-history of the model state before assimilation |
analysis.nc | the time-history of the model state after assimilation |
dart_log.out [default name] | the run-time diagnostic output |
dart_log.nml [default name] | the record of all the namelists actually USED - contains the default values |
Routine | Message | Comment |
---|---|---|
restart_file_to_sv | cannot open file "xxxx" for reading | The ncommas restart file "xxxx" does not exist. |
restart_file_to_sv | 'WARNING!!! year 0 not supported; setting to year 1 | year 0 ... is not supported in a Gregorian calendar. Our intent here is to do data assimilation, normally 'real' observations have 'real' dates. |
sv_to_restart_file | current time /= model time. FATAL error. | The DART time does not match the time of the ncommas restart file. This message is preceeded by several lines indicating the expected times of both DART and ncommas. |
none at this time
Provide a better mechanism for generating a set of perturbed initial conditions - pert_model_state()
N/A
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: | DART core group |
Revision: | $Revision$ |
Source: | $URL$ |
Change Date: | $Date$ |
Change history: | try "svn log" or "svn diff" |