MODULE filter_mod
Overview
Main module for driving ensemble filter assimilations. Used by filter.f90, perfect_model_obs.f90, model_mod_check.f90, and a variety of test programs. See the PROGRAM filter for a general description of filter capabilities and controls.
filter_mod
is a Fortran 90 module, and provides a large number of options for controlling execution behavior and
parameter configuration that are driven from its namelist. See the namelist section below for more details. The number
of assimilation steps to be done is controlled by the input observation sequence and by the time-stepping capabilities
of the model being used in the assimilation.
See Welcome to the Data Assimilation Research Testbed for more documentation, including a discussion of the capabilities of the assimilation system, a diagram of the entire execution cycle, the options and features.
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.
&filter_nml
single_file_in = .false.,
input_state_files = '',
input_state_file_list = '',
init_time_days = 0,
init_time_seconds = 0,
perturb_from_single_instance = .false.,
perturbation_amplitude = 0.2,
stages_to_write = 'output'
single_file_out = .false.,
output_state_files = '',
output_state_file_list = '',
output_interval = 1,
output_members = .true.,
num_output_state_members = 0,
output_mean = .true.,
output_sd = .true.,
write_all_stages_at_end = .false.,
compute_posterior = .true.
ens_size = 20,
num_groups = 1,
distributed_state = .true.,
async = 0,
adv_ens_command = "./advance_model.csh",
tasks_per_model_advance = 1,
obs_sequence_in_name = "obs_seq.out",
obs_sequence_out_name = "obs_seq.final",
num_output_obs_members = 0,
first_obs_days = -1,
first_obs_seconds = -1,
last_obs_days = -1,
last_obs_seconds = -1,
obs_window_days = -1,
obs_window_seconds = -1,
inf_flavor = 0, 0,
inf_initial_from_restart = .false., .false.,
inf_sd_initial_from_restart = .false., .false.,
inf_deterministic = .true., .true.,
inf_initial = 1.0, 1.0,
inf_lower_bound = 1.0, 1.0,
inf_upper_bound = 1000000.0, 1000000.0,
inf_damping = 1.0, 1.0,
inf_sd_initial = 0.0, 0.0,
inf_sd_lower_bound = 0.0, 0.0,
inf_sd_max_change = 1.05, 1.05,
trace_execution = .false.,
output_timestamps = .false.,
output_forward_op_errors = .false.,
write_obs_every_cycle = .false.,
allow_missing_clm = .false.,
silence = .false.,
/
Particular options to be aware of are: ens_size, cutoff (localization radius), inflation flavor, outlier_threshold, input and output state filenames, obs_sequence_in_name, horiz_dist_only, and the binary or ascii controls for observation sequence file formats. Some of these important items are located in other namelists, but all are in the same input.nml file.
The inflation control variables are all dimensioned 2, the first value controls the prior inflation and the second controls the posterior inflation.
Item |
Type |
Description |
---|---|---|
single_file_in |
logical |
|
input_state_files |
character(len=256), dimension(MAXFILES) |
A list of the NetCDF files to open to read the state vectors. Models using multiple domains must put the domain and ensemble numbers in the file names. The order and format of those is to be determined. NOT SUPPORTED as of March, 2017. |
input_state_file_list |
character(len=256), dimension(MAXFILES) |
A list of files, one per domain. Each file must be a text file containing the names of the NetCDF files to open, one per ensemble member, one per line. |
init_time_days |
integer |
If negative, use the initial days read from the state data restart file. If positive, override the initial days read from state data restart files. Days since 1 Jan 1601. |
init_time_seconds |
integer |
If negative use the initial seconds read from the state data restart file. If positive, override the initial seconds read from state data restart files. Seconds since midnight. |
perturb_from_single_instance |
logical |
|
perturbation_amplitude |
real(r8) |
Standard deviation for the noise model
used when generating ensemble members.
This value is available to the model_mod
for use in the required interface
|
stages_to_write |
character(len=10), dimension(6) |
Controls diagnostic and restart output. Valid values are: ‘input’, ‘forecast’, ‘preassim’, ‘postassim’, ‘analysis’, ‘output’, and ‘null’. Input is case-insensitive. |
single_file_out |
logical |
|
output_state_files |
character(len=256), dimension(MAXFILES) |
A list of the netCDF files to open for writing updated state vectors. Not supported when using multiple domains. |
output_state_file_list |
character(len=256), |
A list of files, one per domain. Each file must be a text file containing the names of the netCDF files to open, one per ensemble member, one per line. |
output_interval |
integer |
Output state and observation diagnostics every ‘N’th assimilation time, N is output_interval. |
output_members |
logical |
|
num_output_state_members |
integer |
Number of ensemble members to be included
in the state diagnostic output for stages
‘forecast’, ‘preassim’, ‘postassim’ and
‘analysis’. |
output_mean |
logical |
|
output_sd |
logical |
|
write_all_stages_at_end |
logical |
For most cases this should be
|
compute_posterior |
logical |
If |
ens_size |
integer |
Size of ensemble. |
num_groups |
integer |
Number of groups for hierarchical filter. It should evenly divide ens_size. |
distributed_state |
logical |
|
async |
integer |
Controls method for advancing model:
Ignored if filter is not controlling the model advance, e.g. in CESM, WRF, etc |
adv_ens_command |
character(len=256) |
Command sent to shell if async is 2. |
tasks_per_model_advance |
integer |
Number of tasks to assign to each ensemble member advance. |
obs_sequence_in_name |
character(len=256) |
File name from which to read an observation sequence. |
obs_sequence_out_name |
character(len=256) |
File name to which to write output observation sequence. |
num_output_obs_members |
integer |
Number of ensemble members to be included in the output observation sequence file. |
first_obs_days |
integer |
If negative, don’t use. If non-negative, ignore all observations before this time. |
first_obs_seconds |
integer |
If negative, don’t use. If non-negative, ignore all observations before this time. |
last_obs_days |
integer |
If negative, don’t use. If non-negative, ignore all observations after this time. |
last_obs_seconds |
integer |
If negative, don’t use. If non-negative, ignore all observations after this time. |
obs_window_days |
integer |
Assimilation window days; defaults to model timestep size. |
obs_window_seconds |
integer |
Assimilation window seconds; defaults to model timestep size. |
All variables named inf_* are arrays of length 2. The first element controls the prior, the second element controls the posterior inflation. See PROGRAM filter for a discussion of inflation and effective strategies. |
||
inf_flavor |
character(len=32), dimension(2) |
Inflation flavor [prior, posterior] see Inflation Options below. |
inf_initial_from_restart |
logical, dimension(2) |
If |
inf_sd_initial_from_restart |
logical, dimension(2) |
If |
inf_deterministic |
logical, dimension(2) |
|
inf_initial |
real(r8), dimension(2) |
Initial value of inflation if not read from restart file. |
inf_lower_bound |
real(r8), dimension(2) |
Lower bound for inflation value. |
inf_upper_bound |
real(r8), dimension(2) |
Upper bound for inflation value. |
inf_damping |
real(r8), dimension(2) |
Damping factor for inflation mean values. The difference between the current inflation value and 1.0 is multiplied by this factor and added to 1.0 to provide the next inflation mean. The value should be between 0.0 and 1.0. Setting a value of 0.0 is full damping, which in fact turns off all inflation by fixing the inflation value at 1.0. A value of 1.0 turns inflation damping off leaving the original inflation value unchanged. |
inf_sd_initial |
real(r8) dimension(2) |
Initial value of inflation standard deviation if not read from restart file. If ≤ 0, do not update the inflation values, so they are time-constant. If positive, the inflation values will adapt through time. |
inf_sd_lower_bound |
real(r8), dimension(2) |
Lower bound for inflation standard deviation. If using a negative value for inf_sd_initial this should also be negative to preserve the setting. |
inf_sd_max_change |
real(r8), dimension(2) |
For |
trace_execution |
logical |
|
output_timestamps |
logical |
|
output_forward_op_errors |
logical |
|
write_obs_every_cycle |
logical |
For debug use; this option can significantly slow the execution of filter. True means to write the entire output observation sequence diagnostic file each time through the main filter loop even though only observations with times up to and including the current model time will have been assimilated. Unassimilated observations have the value -888888.0 (the DART “missing value”). If filter crashes before finishing it may help to see the forward operator values of observations that have been assimilated so far. |
allow_missing_clm |
logical |
Some models are allowed to have MISSING_R8
values in the DART state. If |
silence |
logical |
|
Inflation Options
The value for the inf_flavor
is a character string. For backwards compatiblity
(it was an integer code), the specification of the integer is still supported.
Inflation values (for flavors other than 0) will be time-varying
only if inf_sd_initial
> 0.
inflation option |
description |
---|---|
0
‘0’
‘NO_INFLATION’
|
no inflation |
2
‘2’
‘VARYING_SS_INFLATION’
|
spatially-varying state-space (gaussian) |
3
‘3’
‘SINGLE_SS_INFLATION’
|
spatially-fixed state-space (gaussian) |
4
‘4’
‘RELAXATION_TO_PRIOR_SPREAD’
‘RTPS
|
Relaxation To Prior Spread (Posterior inflation only) |
5
‘5’
‘ENHANCED_SS_INFLATION’
|
Enhanced spatially-varying state-space (inverse gamma).
Refer to |
Create an initial ensemble from a single file
If the default pert_model_copies
routine is used, random noise values drawn from a
gaussian distribution with the standard deviation specified by perturbation_amplitude
will be added to the data in a single
initial ensemble member to generate the rest of the members. This option is more frequently
used in the low order models and less frequently used in large models. This is in part due
to the different scales of real geophysical variable values, and the resulting inconsistencies
between related field values. A more successful initial condition generation strategy is to
generate climatological distributions from long model runs which have internally consistent
structures and values and then use observations with a ‘spin-up’ period of assimilation to
shape the initial states into a set of members with enough spread and which match the current
set of observations. Each model_mod is required to provide a pert_model_copies routine
which can be used to either pass-through to the default routine or can be customized for
that specific model.
Modules used
types_mod
obs_sequence_mod
obs_def_mod
obs_def_utilities_mod
time_manager_mod
utilities_mod
assim_model_mod
assim_tools_mod
obs_model_mod
ensemble_manager_mod
adaptive_inflate_mod
mpi_utilities_mod
smoother_mod
random_seq_mod
state_vector_io_mod
io_filenames_mod
forward_operator_mod
quality_control_mod
Files
See the filter overview for the list of files.
Error codes and conditions
Routine |
Message |
Comment |
---|---|---|
filter_main |
ens_size in namelist is ###: Must be > 1 |
Ensemble size must be at least 2. |
filter_main |
inf_flavor= ### Must be 0, 2, 3. |
Observation Inflation is no longer supported (i.e flavor 1). |
filter_main |
Posterior observation space inflation (type 1) not supported. |
Posterior observation space inflation doesn’t work. |
filter_main |
Number of processes > model size. |
Number of processes can’t exceed model size for now. |
filter_generate_copy_meta_data |
output metadata in filter needs state ensemble size < 10000, not ###. |
Only up to 10000 ensemble members with state output for now. |
filter_generate_copy_meta_data |
output metadata in filter needs obs ensemble size < 10000, not ###. |
Only up to 10000 ensemble members with obs space output for now. |
filter_setup_obs_sequence |
input obs_seq file has ### qc fields; must be < 2. |
Only 0 or 1 qc fields in input obs sequence for now. |
get_obs_copy_index |
Did not find observation copy with metadata observation. |
Only 0 or 1 qc fields in input obs sequence for now. |