state_structure_mod is a module that holds all the domain, variable, dimension info about the model_mods in the state. Note it stores only metadata about the state, not the actual state variables themselves.
It is the foundation for two parts of the code:
Read/write state variables from/to netcdf files
Calculate DART index from x,y,z variable indices and the inverse: x,y,z, variable from DART index.
static_init_model a call is made to
add_domain. This call is required as it communicates to the state
structure that a new domain has been added to the state. The state structure keeps track of the number of domains in the
state. These may be multiple domains in one model_mod, e.g. nested domains in WRF, or multiple model_mods, e.g. POP
coupled with CAM. The minimum amount of information
add_domain needs is model size which means vector of length
model size has been added to the state. This equivalent to Lanai where the only information filter has is that the model
is a vector of length model_size. For models with netcdf restart files you supply
a netcdf file
the number of variables to read from the file
the name of the variables
the DART KINDS of the variables
clamping upper and lower bounds
update/not update this variable
For models that are spun up in perfect_model_obs you can manually describe the variables so you can create netcdf files containing the varibles in the model state, e.g. Temperature, Surface Pressure, etc. There are 3 steps to this process:
add_domainwith almost the same arguments as you would for a netcdf file, but skip the first arguement (netcdf filename).
For each variable, loop around the required number of dimensions and call
finished_adding_domainto let the state structure know that you have finished adding dimensions to variables.
get_dart_vector_index(i, j, k, dom_id, var_id)
get_model_variable_indices(dart_index, i, j, k, var_id, dom_id)
Note That (i,j,k) needs to be converted to (lon, lat, lev) or to whatever grid the variable is on.
can be used to get the dimension name from i,j,k if needed.
Unlimited dimensions: io vs model_mod routines
Some model restart files have an unlimited dimension. For IO purposes, e.g. creating netcdf files, the unlimited
dimension is used. For state structure accessor functions called be the model_mod the unlimited dimension is ignored. So
if you have a variable TEMPERATURE in your netcdf file, with dimensions (lon, lat, level, time) the IO routines will see
a 4D variable, but
get_num_dims used in model_mod will return 3D.