NOAH, NOAH-MP
Overview
The Manhattan-compliant version of the NOAH (technically NOAH-MP) supports NOAH-MP V3.6 and was largely updated in support of the data assimilation efforts with wrf_hydro. Experiments to perform data assimilation strictly with the NOAH-MP model have been run at the University of Texas at Austin by Jingjing Liang. We know other people are using DART and NOAH-MP. however, we have not had the chance to update the documentation for the Manhattan release. Consequently, we readily welcome any advice on how to improve the documentation and heartily encourage participation.
The NOAH Land Surface Model and Data Assimilation Research Testbed (DART) may now be used for assimilation experiments. The Classic or Lanai version should be considered an ‘alpha’ release – the code has only been tested for a single column configuration of NOAH.
Any of the variables in the NOAH restart file are available to be adjusted by the assimilation. The list of variables is set though a simple namelist interface. Since we are testing in a column configuration, there is no practical reason not to include all the variables necessary for a bit-for-bit restart: SOIL_T, SOIL_M, SOIL_W, SKINTEMP, SNODEP, WEASD, CANWAT, and QFX. These variables are then adjusted to be consistent with real observations and stuffed back into the same netCDF restart files. Since DART is an ensemble algorithm there are multiple restart files for a single restart time; one for each ensemble member. Creating the initial ensemble of land surface states is an area of active research. At present, it may be sufficient to use a climatological ensemble; e.g., using the restarts for ‘1 January 00Z’ from 50 consecutive years.
There is reason to believe that the ensemble system will benefit from having unique atmospheric forcing for each ensemble member. A reasonable ensemble size is 50 or 80 or so.
DART reads the NOAH namelist &NOAHLSM_OFFLINE from a file called
namelist.hrldas for several pieces of information. DART is responsible for
starting/stopping NOAH; the restart information is conveyed through the NOAH
namelist. Unpleasant Reality #1 : managing the tremendous number of hourly
forcing files for every ensemble member is tedious. To facilitate matters, the
DART/NOAH system uses a single netCDF file for each ensemble member that
contains ALL of the forcing for that ensemble member.
updates some or all of a NOAH restart file with the posterior DART state vector. There is the ability to selectively avoid updating the NOAH variables. This allows one to include NOAH variables in the DART state vector to aid in the application of observation operators, etc., without having to modify those variables in the NOAH restart file. [dart_to_noah.html] |
Running a “Perfect Model” experiment … OSSE
The example requires a basic knowledge of running NOAH. Four scripts are provided to demonstrate how to set up and run a perfect model experiment for a single site - with one caveat. You must provide your own initial ensemble for the experiment. The scripts are not intended to be black boxes. You are expected to read them and modify them to your own purpose.
The scripts assume the directory containing the DART executables is
${DARTDIR}/work, and assume that the directory containing the NOAH
executables is ${NOAHDIR}/Run.
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This script stages the run of
program perfect_model_obs.
The directory where you run the script is called |
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very simply - it advances NOAH and applies the observation operator to put the “perfect” observations in an observation sequence file that can then be used for an assimilation. |
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builds upon the work of |
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Actually runs the filtering (assimilation) experiment. |
Generating the initial ensemble
Creating the initial ensemble of soil moisture states is an area of active research. The ensemble must come from ‘somewhere else’. At present, it may be sufficient to use a climatological ensemble; e.g., using the NOAH restarts for ‘1 January 00Z’ from 50 consecutive years from a hindcast experiment. It may also be sufficient to take a single model state, replicate it N times and force each of the N instances with different atmospheric conditions for ‘a long time’.
By The Way
Experience has shown that having a paired (unique) atmospheric forcing maintains the ensemble spread during an assimilation better than simply forcing all the ensemble members with one single atmospheric state.
DART has routines to perturb a single NOAH state and generate its own ensemble
(typically done with pert_model_state), but this produces model states that
are incompatible with NOAH. We are interested in adopting/adapting strategies
to create sensible initial conditions for NOAH.
If you have an algorithm you believe will be useful, please contact us!
Observations
Some novel observations come from the Cosmic-ray Soil Moisture Observing System:
COSMOS and are processed by DART routines
in the $DARTROOT/observations/COSMOS directory.
DART has a very object-oriented approach to observation support. All
observations that are intended to be supported must be preprocessed (see
$DARTROOT/preprocess/ into a single obs_def_mod.f90 and
obs_kind_mod.f90 in the standard DART way.
Exploring the Output
There are Matlab® scripts for exploring the performance of the assimilation in
observation-space (after running obs_diag). See $DARTROOT/diagnostics/threed_sphere/obs_diag.html
to explore the obs_seq.final file) - use the scripts starting with plot_,
i.e. $DARTROOT/diagnostics/matlab/plot_*.m*. As always, there are some
model-specific items Matlab® will need to know about in
$DARTROOT/models/NOAH/matlab.
The Prior_Diag.nc and Posterior_Diag.nc (and possibly True_State.nc)
netCDF files have the model prognostic variables before and after the
assimilation. The ./matlab scripts for NOAH are under development.
It is also worthwhile to convert your obs_seq.final file to a netCDF format
obs_sequence file with obs_seq_to_netcdf. See
$DARTROOT/obs_sequence/obs_seq_to_netcdf.html and use any of the standard
plots. Be aware that the COSMOS site-specific metadata will not get conveyed to
the netCDF file.
Namelist
The &model_nml namelist is read from the input.nml file. 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. The standard values are shown below:
&model_nml
lsm_model_choice = 'noahMP_36'
domain_shapefiles = 'RESTART.2003051600_DOMAIN1_01'
assimilation_period_days = 0
assimilation_period_seconds = 3600
model_perturbation_amplitude = 0.2
perturb_distribution = 'gaussian'
debug = 0
polar = .false.
periodic_x = .false.
periodic_y = .false.
lsm_variables = 'SOIL_T', 'QTY_SOIL_TEMPERATURE', '0.0', 'NA', 'UPDATE',
'SMC', 'QTY_SOIL_MOISTURE', '0.0', '1.0', 'UPDATE',
'WA', 'QTY_AQUIFER_WATER', '0.0', 'NA', 'UPDATE',
'SNEQV', 'QTY_SNOW_WATER', '0.0', 'NA', 'UPDATE',
'FSNO', 'QTY_SNOWCOVER_FRAC', '0.0', '1.0', 'UPDATE'
/
This namelist is read from a file called input.nml. This namelist provides
control over the assimilation period for the model. All observations within
(+/-) half of the assimilation period are assimilated. The assimilation period
is the minimum amount of time the model can be advanced, and checks are
performed to ensure that the assimilation window is a multiple of the NOAH
model dynamical timestep.
Item |
Type |
Description |
|---|---|---|
lsm_model_choice |
character(len=256) |
The version of the NOAH namelist to read |
domain_shapefiles |
an array of character(len=256) |
The name of the NOAH RESTART files to use to specify the shape of the variables and geographic metadata. One per domain. |
assimilation_period_days |
integer |
The number of days to advance the model for each assimilation. |
assimilation_period_seconds |
integer |
In addition to
|
model_perturbation_amplitude |
real(r8) |
The amount of noise to add when trying
to perturb a single state vector to
create an ensemble. Only used when
|
perturb_distribution |
character(len=256) |
The switch to determine the distribution
of the perturbations used to create an
initial ensemble from a single model
state. Valid values are :
|
periodic_x |
logical |
Switch to determine if the configuration has periodicity in the X direction. |
periodic_y |
logical |
Switch to determine if the configuration has periodicity in the Y direction. |
lsm_variables |
character(len=32):: dimension(5,40) |
The list of variable names in the NOAH restart file to use to create the DART state vector and their corresponding DART kind. [default: see example below] |
The columns of lsm_variables needs some explanation. Starting with the column 5,
UPDATE denotes whether or not to replace the variable with the Posterior (i.e.
assimilated) value. Columns 3 and 4 denote lower and upper bounds that should be
enforced when writing to the files used to restart the model. These limits are not
enforced for the DART diagnostic files. Column 2 specifies the relationship between
the netCDF variable name for the model and the corresponding DART QUANTITY.
The DART ‘QTY’s match what the model_mod knows how to interpolate, so you can’t
just add a new quantity and expect it to work. There is a complex interplay between
obs_def_mod and preprocess, and model_mod that defines what QUANTITIES
are supported. There is only a single QUANTITY that works with each variable and
the example shows the current QUANTITYs. Support for these QUANTITYs was provided by
running preprocess with the following namelist settings:
&preprocess_nml
input_obs_kind_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90'
output_obs_kind_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90'
input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90'
output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90'
input_files = '../../../observations/forward_operators/obs_def_land_mod.f90',
'../../../observations/forward_operators/obs_def_COSMOS_mod.f90',
'../../../observations/forward_operators/obs_def_GRACE_mod.f90'
/
NOAHLSM_OFFLINE NAMELIST
namelist /NOAHLSM_OFFLINE/
hrldas_constants_file, &
indir, outdir, &
restart_filename_requested, &
khour, kday, &
forcing_timestep, &
noah_timestep, &
output_timestep, &
restart_frequency_hours, &
split_output_count, &
nsoil, &
zsoil
The remaining variables are not used by DART - but are used by NOAH. Since DART verifies namelist accuracy, any namelist entry in NOAHLSM_OFFLINE that is not in the following list will cause a FATAL DART ERROR.
zlvl, zlvl_wind, iz0tlnd, sfcdif_option, update_snow_from_forcing,
start_year, start_month, start_day, start_hour, start_min,
external_fpar_filename_template, external_lai_filename_template,
subwindow_xstart, subwindow_xend, subwindow_ystart, subwindow_yend
This namelist is read from a file called namelist.hrldas. This namelist is
the same one that is used by NOAH. The values are explained in full in the NOAH
documentation. Only the namelist variables of interest to DART are discussed.
All other namelist variables are ignored by DART - but mean something to NOAH.
Item |
Type |
Description |
|---|---|---|
hrldas_constants_file |
character(len=256) |
The name of the netCDF file containing
the grid information. [default:
|
indir |
character(len=256) |
The DART/NOAH environment requires all
the input files to be in the current
working directory. [default: |
outdir |
character(len=256) |
The DART/NOAH environment requires all
output files are in the current working
directory. [default: |
restart_filename_requested |
character(len=256) |
The name of the file containing the grid
information. The default value is
implicitly used by the scripting
examples. Change at your own risk.
[default: |
khour |
integer |
The duration (in hours) of the model
integration. [default: |
kday |
integer |
The duration (in days) of the model
integration. [default: |
forcing_timestep |
integer |
The timestep (in seconds) of the
atmospheric forcing. [default: |
noah_timestep |
integer |
The internal (dynamical) timestep (in
seconds). [default: |
output_timestep |
integer |
The output interval (in seconds).
[default: |
restart_frequency_hours |
integer |
How often the NOAH restart files get
written. [default: |
split_output_count |
integer |
should be 1 or bad things happen.
[default: |
nsoil |
integer |
The number of soil interfaces. As I
understand it, NOAH requires this to be
4. [default: |
zsoil |
integer(NSOLDX) |
The depth (in meters) of the soil
interfaces. [default: |
Example
Note: the FORCING_FILE_DIRECTORY line is not required by NOAH but IS required
by DART - specifically in the advance_model.csh script.
### THIS IS FOR DART ###
FORCING_FILE_DIRECTORY = "/path/to/your/forcing/files"
&NOAHLSM_OFFLINE
HRLDAS_CONSTANTS_FILE = "wrfinput"
INDIR = "."
OUTDIR = "."
RESTART_FILENAME_REQUESTED = "restart.nc"
KHOUR = 1
FORCING_TIMESTEP = 3600
NOAH_TIMESTEP = 3600
OUTPUT_TIMESTEP = 3600
RESTART_FREQUENCY_HOURS = 1
SPLIT_OUTPUT_COUNT = 1
NSOIL=4
ZSOIL(1) = -0.10
ZSOIL(2) = -0.40
ZSOIL(3) = -1.00
ZSOIL(4) = -2.00
/
Input Files
filename |
purpose |
|---|---|
input.nml |
to read the model_mod namelist |
namelist.hrldas |
to read the NOAHLSM_OFLINE namelist |
wrfinput |
provides NOAH grid information |
&model_nml:noah_netcdf_filename |
the RESTART file containing the NOAH model state. |