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 ../../programs/filter/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 page for more documentation, including a discussion of the capabilities of the assimilation system, a diagram of the entire execution cycle, the options and features.
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 | .true. means all ensemble members are read from a single netCDF file (which can only be used with subroutine-callable models). .false. means each member is in a separate file. |
| 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 | .true. means perturb a single state vector from one restart file to create an ensemble. This may be done by model_mod, if model_mod provides subroutine pert_model_copies. .false. means an an ensemble-sized set of restart files is provided. |
| 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 pert_model_copies. For more, see pert_model_copies below. Ignored if perturb_from_single_instance = .false. |
| 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 | .true. means all ensemble members are written to a single netCDF file. .false. means each member is output in a separate file. Only subroutine-callable models may write a single output file. |
| 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 | .true. means output the ensemble members in any stage that is enabled. |
| 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_members must be .true. |
| output_mean | logical | .true. means output the ensemble mean in any stage that is enabled. |
| output_sd | logical | .true. means output the ensemble standard deviation (spread) in any stage that is enabled. |
| write_all_stages_at_end | logical | For most cases this should be .false.; data will be output as it is generated for the 'forecast', 'preassim', 'postassim', and 'analysis' diagnostics, and then restart data will be output at the end. However, if I/O time dominates the runtime, setting this to .true. will store the data and it can all be written in parallel at the end of the execution. This will require slightly more memory at runtime, but can lower the job cost significantly in some cases. |
| compute_posterior | logical | If .false., skip computing posterior forward operators and do not write posterior values in the obs_seq.final file. Those are rarely worth examining. Saves time and memory. Posterior inflation is not possible. For backwards compatibility the default .true. |
| ens_size | integer | Size of ensemble. |
| num_groups | integer | Number of groups for hierarchical filter. It should evenly divide ens_size. |
| distributed_state | logical | .true. means the ensemble data is distributed across all tasks as it is read in, so a single task never has to have enough memory to store the data for an ensemble member. Large models should always set this to .true., while for small models it may be faster to set this to .false. This is different from &assim_tools_mod :: distributed_mean. |
| 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 the second element controls th for a discussion of inflation | arrays of length 2. Th e posterior inflation. and effective strategi |
|
| inf_flavor | character(len=32), dimension(2) | Inflation flavor [prior, posterior] see Inflation Options below. |
| inf_initial_from_restart | logical, dimension(2) | If .true., get initial mean values for inflation from inflation file. If .false. , use the corresponding namelist value inf_initial. |
| inf_sd_initial_from_restart | logical, dimension(2) | If .true., get initial standard deviation values for inflation from file. If .false. , use the corresponding namelist value inf_sd_initial. |
| inf_deterministic | logical, dimension(2) | .true. means deterministic inflation, .false. means stochastic. |
| 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 inf_flavor 5 (enhanced inflation), controls the maximum change of the inflation standard deviation when adapting for the next assimilation cycle. The value should be between 1.0 and 2.0. 1.0 prevents any changes, while 2.0 allows 100% change. For the enhanced inflation option, if the standard deviation initial value is equal to the standard deviation lower bound, the standard deviation will not adapt in time. See ../../programs/filter/filter for a discussion of how the standard deviation adapts based on different types of inflation. |
| trace_execution | logical | .true. means output very detailed messages about what routines are being called in the main filter loop. Useful if a job hangs or otherwise doesn't execute as expected. |
| output_timestamps | logical | .true. means write timing information to the log before and after the model advance and the observation assimilation phases. |
| output_forward_op_errors | logical | .true. means output errors from forward observation operators. This is the 'istatus' error return code from the model_interpolate routine. An ascii text file prior_forward_op_errors and/or post_forward_op_errors will be created in the current directory. For each ensemble member which returns a non-zero return code, a line will be written to this file. Each line will list the following values: the ensemble member number, local observation number, the key for the observation, and then the istatus return code. Be cautious when turning this option on. The number of lines in this file can be up to the number of observations times the number of ensemble members times the number of assimilation cycles performed. This option is generally most useful when run with a small observation sequence file and a small number of ensemble members to diagnose forward operator problems. |
| 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 .true. extra caution is taken (at considerable computational cost) to allow missing values in the DART state. So far, only CLM requires this to be .true. |
| silence | logical | .true. means output almost no runtime messages. Not recommended for general use, but can speed long runs of the lower order models if the execution time becomes dominated by the volume of output. |
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 inf_sd_initial for how to set the time evolution options. |
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.
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
random_seq_mod
state_vector_io_mod
io_filenames_mod
forward_operator_mod
quality_control_modSee the filter overview for the list of files.
| 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. |