MODULE smoother_mod

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$Id: smoother_mod.html 6382 2013-08-07 20:45:16Z nancy $

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

Overview

Implements a fixed lag ensemble smoother as part of the filter. For now, this is done inefficiently with a separate call to assim_tools_mod:filter_assim() for each lag.

To enable the smoother, set the number of lags (num_lags) to something larger than 0 in the smoother_nml section of your input.nml file and run filter as before.

&smoother_nml
   num_lags              = 10,
   start_from_restart    = .false.,
   output_restart        = .true.,
   restart_in_file_name  = "ics",
   restart_out_file_name = "restart"  /

In the low order models, 10 is a plausible number.

In addition to generating Prior_Diag.nc and Posterior_Diag.nc files, files of the form Lag_NNNNN_Diag.nc will be generated. Each of these has N fewer timesteps than the lag=0 run, starting at the same time but ending N timesteps sooner. The obs_seq.final file and the Prior_Diag.nc and Posterior_Diag.nc files will be the same as the non-lagged version; the new output will be in each of the Lag_NNNNN_Diag.nc files.

EXAMPLE

If you have a True_State.nc file and want to use the plot_total_err matlab function to plot the error, you must do the following steps to generate analogs of lagged True_State.nc files to use as a comparison. (The logic is not currently implemented in the matlab scripts to be able to compare netCDF files with unequal time coordinates.)

Make N separate versions of the True_State.nc with the last N timesteps removed. Using the netCDF NCO operator program 'ncks' is one way. If the True_State.nc file has 1000 time steps, then this command removes the last one:

ncks -d time,0,998 True_State.nc True_Lag01.nc

Note that the first time is at index 0, so the last timestep is index 999 in the full file, and 998 in the truncated file. Repeat this step for all N lags. Here are NCO commands to generate 10 truth files for num_lags = 10, 1000 time steps in True_State.nc:

ncks -d time,0,998 True_State.nc True_Lag01.nc
ncks -d time,0,997 True_State.nc True_Lag02.nc
ncks -d time,0,996 True_State.nc True_Lag03.nc
ncks -d time,0,995 True_State.nc True_Lag04.nc
ncks -d time,0,994 True_State.nc True_Lag05.nc
ncks -d time,0,993 True_State.nc True_Lag06.nc
ncks -d time,0,992 True_State.nc True_Lag07.nc
ncks -d time,0,991 True_State.nc True_Lag08.nc
ncks -d time,0,990 True_State.nc True_Lag09.nc
ncks -d time,0,989 True_State.nc True_Lag10.nc

Here is an example matlab session which plots the lag=0 results and then odd numbered lags from 1 to 9. It uses the plot_total_err function from the $DART/matlab directory:

datadir    = '.';
truth_file = fullfile(datadir,'True_State.nc');
diagn_file = fullfile(datadir,'Prior_Diag.nc');
plot_total_err
reply = input('original data.  hit enter to continue ');

truth_file = fullfile(datadir,'True_Lag01.nc');
diagn_file = fullfile(datadir,'Lag_00001_Diag.nc');
plot_total_err
reply = input('Lag 01.  hit enter to continue ');

truth_file = fullfile(datadir,'True_Lag03.nc');
diagn_file = fullfile(datadir,'Lag_00003_Diag.nc');
plot_total_err
reply = input('Lag 03.  hit enter to continue ');

truth_file = fullfile(datadir,'True_Lag05.nc');
diagn_file = fullfile(datadir,'Lag_00005_Diag.nc');
plot_total_err
reply = input('Lag 05.  hit enter to continue ');

truth_file = fullfile(datadir,'True_Lag07.nc');
diagn_file = fullfile(datadir,'Lag_00007_Diag.nc');
plot_total_err
reply = input('Lag 07.  hit enter to continue ');

truth_file = fullfile(datadir,'True_Lag09.nc');
diagn_file = fullfile(datadir,'Lag_00009_Diag.nc');
plot_total_err
reply = input('Lag 09.  hit enter to continue ');
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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.

&smoother_nml
   num_lags              = 0,
   start_from_restart    = .false.,
   output_restart        = .false.,
   restart_in_file_name  = 'ics',
   restart_out_file_name = 'restart'  
/


Item Type Description
num_lags integer Number of smoother lags; < 1 means no smoother.
start_from_restart logical True if smoother states are to come from restart file(s). False if they are to be spun up from scratch.
output_restart logical True if restart file(s) are to be written, else false.
restart_in_file_name character(len=129) String used to construct the file name from which to read restart data. 'Lag_NNNNN_' will be prepended to the specified value to create the actual filename. If each ensemble is to be read from a separate file, the .NNNN ensemble number will also be appended. e.g. specifying 'ics' here results in 'Lag_00001_ics' if all ensemble members are read from a single file, 'Lag_00001_ics.0001', 'Lag_00001_ics.0002', etc for multiples.
restart_out_file_name    character(len=129) String used to construct the file name to which to write restart data. 'Lag_NNNNN_' will be prepended to the specified value to create the actual filename. If each ensemble is to be written to a separate file, the .NNNN ensemble number will also be appended. e.g. specifying 'restart' here results in 'Lag_00001_restart' if all ensemble members are written to a single file, 'Lag_00001_restart.0001', 'Lag_00001_restart.0002', etc for multiples.


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OTHER MODULES USED

types_mod
mpi_utilities_mod
utilities_mod
ensemble_manager_mod
time_manager_mod
assim_model_mod
assim_tools_mod
obs_sequence_mod
adaptive_inflate_mod
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PUBLIC INTERFACES

use smoother_mod, only : smoother_read_restart
 advance_smoother
 smoother_gen_copy_meta_data
 smoother_write_restart
 init_smoother
 do_smoothing
 smoother_mean_spread
 smoother_assim
 filter_state_space_diagnostics
 smoother_ss_diagnostics
 smoother_end

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


call smoother_read_restart(ens_handle, ens_size, model_size, time1, init_time_days)
type(ensemble_type), intent(inout) :: ens_handle
integer, intent(in)                :: ens_size
integer, intent(in)                :: model_size
type(time_type), intent(inout)     :: time1
integer, intent(in)                :: init_time_days

Reads in ensemble of states for all lag estimates from a restart file.

ens_handle   Handle of ensemble manager structure of single state; copied into all lags for startup.
ens_size   Size of the ensemble.
model_size   Size of the model state vector.
time1   Overwrite the time in the restart file with this value if init_time_days is non-negative.
init_time_days   If non-negative, use time1 instead of time in restart file.


call advance_smoother(ens_handle)
type(ensemble_type), intent(in) :: ens_handle

Advances smoother state estimates at all lags forward in time. This entails copying the most recent smoother state, contained in ens_handle, into the lag 1 smoother state and pushing back all other lags by 1 (i.e. lag 1 becomes lag 2, etc.).

ens_handle   Ensemble handle with most recent filtered state.


call smoother_gen_copy_meta_data(num_output_state_members, output_inflation)
integer, intent(in) :: num_output_state_members
logical, intent(in) :: output_inflation

Initializes the metadata required for the smoother state space diagnostic files.

num_output_state_members   Number of copies of smoother state vector that should be in state space diagnostic output.
output_inflation   True if smoother state space output should include inflation values.


call smoother_write_restart(start_copy, end_copy)
integer, intent(in) :: start_copy
integer, intent(in) :: end_copy

Outputs restart files for all lags of smoother state. Integer arguments specify the start and end global indices of a continguous set of copies that contain the ensemble members.

start_copy   Global index of ensemble copy that starts the actual ensemble members for smoother.
end_copy   Global index of ensemble copy that ends the actual ensemble members for smoother.


call init_smoother(ens_handle, POST_INF_COPY, POST_INF_SD_COPY)
type(ensemble_type), intent(inout) :: ens_handle
integer, intent(in)                :: POST_INF_COPY
integer, intent(in)                :: POST_INF_SD_COPY

Initializes the storage needed for a smoother. Also initializes an adaptive inflation type that does NO inflation (not currently supported for smoothers).

ens_handle   An ensemble handle for the filter that contains information about ensemble and model size.
POST_INF_COPY   Global index of ensemble copy that holds posterior state space inflation values.
POST_INF_SD_COPY   Global index of ensemble copy that holds posterior inflation standard deviation values.


var = do_smoothing()
logical, intent(out) :: do_smoothing

Returns true if smoothing is to be done, else false.

do_smoothing   Returns true if smoothing is to be done.


call smoother_mean_spread(ens_size,ENS_MEAN_COPY,ENS_SD_COPY, output_state_ens_mean,output_state_ens_spread)
integer, intent(in) :: ens_size
integer, intent(in) :: ENS_MEAN_COPY
integer, intent(in) :: ENS_SD_COPY
logical, intent(in) :: output_state_ens_mean
logical, intent(in) :: output_state_ens_spread

Computes the ensemble mean (and spread if required) of all state variables for all lagged ensembles. Spread is only computed if it is required for output.

ens_size   Size of ensemble.
ENS_MEAN_COPY   Global index of copy that stores ensemble mean.
ENS_SD_COPY   Global index of copy that stores ensemble spread.
output_state_ens_mean   True if the ensemble mean is to be output to state diagnostic file.
output_state_ens_spread   True if ensemble spread is to be output to state diagnostic file.


call smoother_assim(obs_ens_handle, seq, keys, ens_size, num_groups, obs_val_index, ENS_MEAN_COPY, ENS_SD_COPY, PRIOR_INF_COPY, PRIOR_INF_SD_COPY, OBS_KEY_COPY, OBS_GLOBAL_QC_COPY, OBS_PRIOR_MEAN_START, OBS_PRIOR_MEAN_END, OBS_PRIOR_VAR_START, OBS_PRIOR_VAR_END)
type(ensemble_type), intent(inout)  :: obs_ens_handle
type(obs_sequence_type), intent(in) :: seq
integer, dimension(:), intent(in)   :: keys
integer, intent(in)                 :: ens_size
integer, intent(in)                 :: num_groups
integer, intent(in)                 :: obs_val_index
integer, intent(in)                 :: ENS_MEAN_COPY
integer, intent(in)                 :: ENS_SD_COPY
integer, intent(in)                 :: PRIOR_INF_COPY
integer, intent(in)                 :: PRIOR_INF_SD_COPY
integer, intent(in)                 :: OBS_KEY_COPY
integer, intent(in)                 :: OBS_GLOBAL_QC_COPY
integer, intent(in)                 :: OBS_PRIOR_MEAN_START
integer, intent(in)                 :: OBS_PRIOR_MEAN_END
integer, intent(in)                 :: OBS_PRIOR_VAR_START
integer, intent(in)                 :: OBS_PRIOR_VAR_END

Does assimilation of a set of observations for each smoother lag.

obs_ens_handle   Handle for ensemble manager holding prior estimates of observations.
seq   Observation sequence being assimilated.
keys   A one dimensional array containing indices in seq of observations to as similate at current time.
ens_size   Ensemble size.
num_groups   Number of groups in filter.
obs_val_index   Integer index of copy of data in seq that contains the observed value from instruments.
ENS_MEAN_COPY   Global index in smoother's state ensemble that holds ensemble mean.
ENS_SD_COPY   Global index in smoother's state ensemble that holds ensemble standard deviation.
PRIOR_INF_COPY   Global index in obs_ens_handle that holds inflation values (not used for smoother).
PRIOR_INF_SD_COPY   Global index in obs_ens_handle that holds inflation sd values (not used for smoother).
OBS_KEY_COPY   Global index in obs_ens_handle that holds the key for the observation.
OBS_GLOBAL_QC_COPY   Global index in obs_ens_handle that holds the quality control value.
OBS_PRIOR_MEAN_START   Global index in obs_ens_handle that holds the first group's prior mean.
OBS_PRIOR_MEAN_END   Global index in obs_ens_handle that holds the last group's prior mean.
OBS_PRIOR_VAR_START   Global index in obs_ens_handle that holds the first group's prior variance.
OBS_PRIOR_VAR_END   Global index in obs_ens_handle that holds the last group's prior variance.


call filter_state_space_diagnostics(out_unit, ens_handle, model_size, num_output_state_members, output_state_mean_index, output_state_spread_index, output_inflation, temp_ens, ENS_MEAN_COPY, ENS_SD_COPY, inflate, INF_COPY, INF_SD_COPY)
type(netcdf_file_type), intent(inout)   :: out_unit
type(ensemble_type), intent(inout)      :: ens_handle
integer, intent(in)                     :: model_size
integer, intent(in)                     :: num_output_state_members
integer, intent(in)                     :: output_state_mean_index
integer, intent(in)                     :: output_state_spread_index
logical, intent(in)                     :: output_inflation
real(r8), intent(out)                   :: temp_ens(model_size)
integer, intent(in)                     :: ENS_MEAN_COPY
integer, intent(in)                     :: ENS_SD_COPY
type(adaptive_inflate_type), intent(in) :: inflate
integer, intent(in)                     :: INF_COPY
integer, intent(in)                     :: INF_SD_COPY

Writes state space diagnostic values including ensemble members, mean and spread, and inflation mean and spread to a netcdf file.

out_unit   Descriptor for the netcdf file being written.
ens_handle   Ensemble handle whose state space values are to be written.
model_size   Size of the model state vector.
num_output_state_members   Number of individual state members to be output.
output_state_mean_index   Index in netcdf file for ensemble mean.
output_state_spread_index   Index in netcdf file for ensemble spread.
output_inflation   True if the inflation values are to be output. Default is .TRUE.
temp_ens   Storage passed in to avoid having to allocate extra space.
ENS_MEAN_COPY   Global index in ens_handle for ensemble mean.
ENS_SD_COPY   Global index in ens_handle for ensemble spread.
inflate   Contains description and values of state space inflation.
INF_COPY   Global index in ens_handle of inflation values.
INF_SD_COPY   Global index in ens_handle of inflation standard deviation values.


call smoother_ss_diagnostics(model_size, num_output_state_members, output_inflation, temp_ens, ENS_MEAN_COPY, ENS_SD_COPY, POST_INF_COPY, POST_INF_SD_COPY)
integer, intent(in)   :: model_size
integer, intent(in)   :: num_output_state_members
logical, intent(in)   :: output_inflation
real(r8), intent(out) :: temp_ens(model_size)
integer, intent(in)   :: ENS_MEAN_COPY
integer, intent(in)   :: ENS_SD_COPY
integer, intent(in)   :: POST_INF_COPY
integer, intent(in)   :: POST_INF_SD_COPY

Outputs state space diagnostics files for all smoother lags.

model_size   Size of the model state vector.
num_output_state_members   Number of state copies to be output in the state space diagnostics file.
output_inflation   True if the inflation values are to be output. Default is .TRUE.
temp_ens   Storage passed in to avoid having to allocate extra space.
ENS_MEAN_COPY   Global index of the ensemble mean in the lag smoother ensemble handles.
ENS_SD_COPY   Global index of the ensemble spread in the lag smoother ensemble handles.
POST_INF_COPY   Global index of the inflation value in the lag smoother ensemble handles (not currently used).
POST_INF_SD_COPY   Global index of the inflation spread in the lag smoother ensemble handles (not currently used).


call smoother_end()

Releases storage allocated for smoother.



call smoother_inc_lags()

Increments the number of lags that are in use for smoother. Used when a smoother is being started up and there have not been enough times to propagate the state to all requested lags.


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FILES

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REFERENCES

  1. none
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ERROR CODES and CONDITIONS

RoutineMessageComment
smoother_gen_copy_meta_data output metadata in smoother needs ensemble size < 10000, not ### Can't output more than 9999 copies.

KNOWN BUGS

none at this time

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FUTURE PLANS

none at this time

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PRIVATE COMPONENTS

N/A

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Terms of Use

DART software - Copyright 2004 - 2013 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: 6382 $
Source: $URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Lanai/smoother/smoother_mod.html $
Change Date: $Date: 2013-08-07 14:45:16 -0600 (Wed, 07 Aug 2013) $
Change history:  try "svn log" or "svn diff"