DART supported models:
Hints for porting a new model to DART:
Copy the contents of the
DART/models/xxx directory for your new model.
If your model is closer to the simpler examples (e.g. lorenz), the existing model_mod.f90 is a good place to start. If your model is a full 3d geophysical one (e.g. like cam, pop, etc) then rename full_model_mod.f90 to model_mod.f90 and start there.
LOCATION in quickbuild.sh to
full 3d geophysical models.
./quickbuild.sh and everything should compile at this point.
The required subroutines are these:
public :: get_model_size, & get_state_meta_data, & model_interpolate, & shortest_time_between_assimilations, & static_init_model, & init_conditions, & adv_1step, & nc_write_model_atts, & pert_model_copies, & nc_write_model_vars, & init_time, & get_close_obs, & get_close_state, & end_model, & convert_vertical_obs, & convert_vertical_state, & read_model_time, & write_model_time
If needed, model_mod can contain additional subroutines that are used for any model-specific utility programs. No routines other than these will be called by programs in the DART distribution.
Edit the model_mod and fill in these routines:
static_init_model()- make it read in any grid information and the number of variables that will be in the state vector. Fill in the model_size variable. Now
get_model_time_step()from the template should be ok as-is.
get_state_meta_data()- given an index number into the state vector return the location and kind.
model_interpolate()- given a location (lon/lat/vert in 3d, x in 1d) and a state QTY_xxx kind, return the interpolated value the field has at that location. this is probably one of the routines that will take the most code to write.
For now, ignore these routines:
nc_write_model_vars() get_close_obs() get_close_state() end_model() convert_vertical_obs() convert_vertical_state() read_model_time() write_model_time()
If you have data in a dart initial condition/restart file, then you can ignore these routines:
Otherwise, have them return an initial time and an initial default ensemble state.
If your model is NOT subroutine callable, you can ignore this routine:
Otherwise have it call the interface to your model and add the files necessary to build your model to all the work/path_names_* files. Add any needed model source files to a src/ directory.
If you want to let filter add gaussian noise to a single state vector to generate an ensemble, you can ignore this routine:
Otherwise fill in code that does whatever perturbation makes sense to have an initial ensemble of states. in some cases that means adding a different range of values to each different field in the state vector.
At this point you should have enough code to start testing with
model_mod_check program. It is a stand-alone utility
that calls many of the model_mod interface routines and should
be easier to debug than some of the other DART programs.
Once you have that program working you should have enough code to test and run simple experiments.
The general flow is:
./create_obs_sequence- make a file with a single observation in it
./perfect_model_obs- should interpolate a value for the obs
generate an ensemble of states, or set ‘perturb_from_single_instance’ to .true.
./filterwith the single observation
Look at the preassim.nc and analysis.nc files Diff them with
ncdiff analysis.nc preassim.nc Innov.nc
plot it, with
The difference between the two is the impact of that single observation see if it’s at the right location and if the differences seem reasonable
If your model data cannot be output in NetCDF file format, or cannot be directly converted to NetCDF file format with the ncgen program, there are 2 additional steps:
model_to_dart- read your native format and output data in NetCDF format
dart_to_model- write the updated data back to the native file format
More details on each of these 5 steps follows.
model_to_dart if needed
If your model data is not stored in NetCDF file format, a program to convert your data from the model to NetCDF is needed. It needs to read your model data in whatever format it uses and create NetCDF variables with the field names, and appropriate dimensions if these are multi-dimensional fields (e.g. 2d or 3d). If the data is ASCII, the generic NetCDF utility ncgen may be helpful.
You can make a synthetic observation (or a series of them) with this interactive program and use them for testing. Before running make sure the observation types you want to use are in the input.nml file in the &obs_kind_nml section, either in the assimilate or evaluate lists.
Run the program. Give the total number of obs you want to create (start with 1). Answer 0 to number of data items and 0 to number of quality control items. Answer 0 when it says enter -1 to quit. You will be prompted for an observation number to select what type of observation you are going to test.
Give it a location that should be inside your domain, someplace where you can compute (by hand) what the correct value should be. When it asks for time, give it a time that is the same as the time on your model data.
When it asks for error variance, at this point it doesn’t matter. give it something like 10% of the expected data value. Later on this is going to matter a lot, but for testing the interpolation of a single synthetic obs, this will do.
For an output filename, it suggests ‘set_def.out’ but in this case tell it ‘obs_seq.in’.
Make sure the NetCDF file with your input data matches the input name in the input.nml file, the &perfect_model_obs_nml namelist. Make sure the input obs_sequence is still set to ‘obs_seq.in’. run perfect_model_obs. Something bad will happen, most likely. Fix it.
Eventually it will run and you will get an ‘obs_seq.out’ file. For these tests, make sure &obs_sequence_nml : write_binary_obs_sequence = .false. in the input.nml file. The sequence files will be short and in ascii. You can check to see what the interpolated value is. if it’s right, congratulations. If not, debug the interpolation code in the model_mod.f90 file.
Using a single input state
In the &filter_nml namelist, set ‘perturb_from_single_instance’ to .true. this tells filter that you have not generated N initial conditions, that you are only going to supply one and it needs to perturb that one to generate an initial ensemble. Make sure the ‘input_state_files’ matches the name of the single state vector file you have. You can use the ‘obs_seq.out’ file from the perfect_model run because now it has data for that observation. Later on you will need to decide on how to generate a real set of initial states, and then you will set ‘perturb_from_single_instance’ back to .false. and supply N files instead of one. You may need to set the &ensemble_manager_nml : perturbation_amplitude down to something smaller than 0.2 for these tests - 0.00001 is a good first guess for adding small perturbations to a state.
Set the ens_size to something small for testing - between 4 and 10 is usually a good range. Make sure your observation type is in the ‘assimilate_these_obs_types’ list and not in the evaluate list. run filter. Find bugs and fix them until the output ‘obs_seq.final’ seems to have reasonable values. Running filter will generate NetCDF diagnostic files. The most useful for diagnosis will be comparing preassim.nc and analysis.nc.
Run ‘ncdiff analysis.nc preassim.nc differences.nc’ and use your favorite netcdf plotting tool to see if there are any differences between the 2 files. For modules using a regular lat/lon grid ‘ncview’ is a quick way to scan files. For something on an irregular grid a more complicated tool will have to be used. If the files are identical the assimilation didn’t do anything. Check to see if there is a non-zero DART quality control value in the obs_seq.final file. Check to see if there are errors in the dart_log.out file. Figure out why there’s no change. If there is a difference, it should be at the location of the observation and extend out from it for a short distance. If it isn’t in the right location, look at your get_state_meta_data() code. If it doesn’t have a reasonable value, look at your model_interpolate() code.
dart_to_model if needed
After you have run filter, the files named in the ‘output_state_files’ namelist item will contain the changed values. If your model is reading NetCDF format it can ingest these directly. If not, an additional step is needed to copy over the updated values for the next model run.