Isothermal layers volume budget with OCCA


Introduction


This is a set of matlab and fortran routines to compute a thermally defined layer volume budget over a subdomain of the global ocean from the OCCA state estimate.

This package was developed by Guillaume Maze and Gael Forget at MIT (Cambridge, USA) for the ECCO group and the CLIMODE project.

You can browse the package here: http://code.google.com/p/guillaumemaze/source/browse/trunk/OCCA/Tlayer_budget
(See below for downloading)

Requirements


To perform this analysis you'll need:
  • From the OCCA state estimate release 0 or 1 the fields:
    File name Z levels Grid Unit Definition
    THETA 50 SM degC Potential Temperature
    TENDT 50 SM degC/d Tendency of Potential Temperature
    ZADVT 51 WM degC.m^3/s Vertical Advective Flux of Pot.Temp
    XADVT 50 UU degC.m^3/s Zonal Advective Flux of Pot.Temp
    YADVT 50 VV degC.m^3/s Meridional Advective Flux of Pot.Temp
    XDIFT 51 WM degC.m^3/s Vertical Diffusive Flux of Pot.Temp (Explicit part)
    ZDIFTI 51 WM degC.m^3/s Vertical Diffusive Flux of Pot.Temp (Implicit part)
    XDIFT 50 UU degC.m^3/s Zonal Diffusive Flux of Pot.Temp
    YDIFT 50 VV degC.m^3/s Meridional Diffusive Flux of Pot.Temp
    GTABT 50 SM degC/s Tendency of Potential Temp. added by the Adams Bashforth Scheme
    GTFT 50 SM degC/s Tendency of Potential Temp. due to air-sea heat fluxes
    GHATT 51 WM degC.m^3/s Non-local transport term of KPP as a temperature flux
    DSSHT 51 WM degC.m^3/s Vertical flux of Pot.temp due to Sea Level Change

These are normally defined on a 360x160x50 grid points, daily from 2003/11/1 to 2006/11/3 (1099 days). You can download OCCA here: http://www.ecco-group.org/products.htm or email Gael Forget.
  • All the grid files of OCCA.
  • This package. To download it, go to your working directory and type:
svn checkout http://guillaumemaze.googlecode.com/svn/trunk/OCCA/Tlayer_budget Tlayer_budget

Help


There are 2 steps in the computation. Step 1 extracts a subdomain of the Atlas, Step 2 computes the budget with a 3D interpolation of all fields.

Step 1

  • Into Tlayer_budget/step1 you have to tune the header of the function extract_subdomain.m to match your environment.
Variables that need to be tuned are:
  • pathi: this is where we find input fields (original theta and flux of temp. fields)
  • patho: this is where we print out fields restricted to the subdomain.
  • subdomain: this table defines the subdomain. It has the format: [ixWest ixEast iySouth iyNorth izTop izBottom]. For example: subdomain = [122 200 90 130 1 25]; extract the Kuroshio region.

You may want to tune the subfunction wherearewe to match your machine. You may also want to use a special mask for your domain of analysis. You can do so by looking at the subfunction extract. Finally, if you have a fancy OCCA dataset, you may have to tune how the routine name the input files. Check at variables prefi, suffi and the subfunction open_files. Last, the function extract_subdomain.m takes as an argument a number which correspond to a particular set of fields to extract:
Argument Fields processed
1 Theta and volume elements
2 Tendency Native
3 Tendency Artificial
4 Air-sea heat flux
5 All other terms (ssh, gtabt, ghatt)
6 Total and individual advection terms
7 Total and individual diffusion terms

  • The routine create_queue_scripts.m creates a set of script files to submit the function to a SGE queuing system. It also create a shell script to submit all in one command. What you have to tune in create_queue_scripts.m are the variables: workdir (this is where the extract_subdomain.m routine is located) and matlabpath (this is where the job has to look for to find Matlab).

Step 2

  • Under Tlayer_budget/step2, you first have to create a set of time line files to indicate the fortran routine when you want the budget to be computed (the full time serie, only januaries, etc ...). This is done with the create_timeline.m routine where you only have to tune the variable patho to indicate where the time line files will be created.
  • Next, you have to create the parameters files for the fortran code with: create_param_files.m. There are several variables to be tuned here:
  • patho: This is where we print the param files
  • homedir: This is what we replace with the ~ into paths in order to deal with absolute paths.
  • tmp_path: This is where the fortan code will print out the results
  • lrf_path: This is where the fortran code looks for input fields (coming from step 1)
  • time_path: This is where the fortran code looks for the time line.
Then you have to select parameters for klist and tlist variables. They select what are the field(s) you want to compute the budget of and the time lines to use.
The variable klist can contain one of the following:
klist Subdomain file analysed (default name)
1 LRvol.3yV2adv.bin
2 LRtheta.3yV2adv.bin (NOT OK !)
3 LRadvTOT.3yV2adv.bin
4 LRdiffTOT.3yV2adv.bin
5 LRairsea3D.3yV2adv.bin
6 LRtendNATIVE.3yV2adv.bin
7 LRtendARTIF.3yV2adv.bin
8 LRallotherTOT.3yV2adv.bin
9 LRadvX.3yV2adv.bin
10 LRadvY.3yV2adv.bin
11 LRadvZ.3yV2adv.bin
12 LRdifX.3yV2adv.bin
13 LRdifY.3yV2adv.bin
14 LRdifZ.3yV2adv.bin
15 LRdifIZ.3yV2adv.bin
16 LRghat.3yV2adv.bin

and tlist can contain:
tlist Time line (default name)
1 Annual
2 JFM
3 JJA
4 Jan
5 Feb
... ...

  • Next, you may need to create scripts to launch the fortran routine with a SGE queuing system. Use the create_launch_scripts.m routine to do it. You need to tune the variables:
  • patho: This is where we print the queue files
  • prog_to_compile: This is the fortran code to compute the budget terms. If you didn't changed it from this package it is: interpBudgetallinonceS.F90
  • prog_to_run: This is compiled name of the code (by default: intBdgS_ifort)
  • workdir: This is the root dir, ie where the fortran code is and where are directories of parameters and queue scripts.
  • klist and tlist: Set up them as in create_param_files.m.
  • Last but not least, you need to tune the domain size and interpolation parameters in the fortran code: interpBudgetallinonceS.F90. The domain size (number of grid points in each directions) is fixed in the module mysizes. You must have:
jpi = diff(subdomain(1:2))+1;
jpj = diff(subdomain(3:4))+1;
jpk = diff(subdomain(5:6))+1;


Interpolation parameters are nb_in and nbIn2Out. nb_in is the factor by which the program will multiply the number of grid points. Starting from the 1x1 degree Atlas, nb_in=12 will interpolate the field to a 1/12 deg grid. The other parameter nbIn2Out sets the factor by which the interpolated fields are scaled for the output fields. nbIn2Out=3 will produce records on a 12/3=4, ie 1/4 degree grid. IMPORTANT: both nb_in and the result of nb_in/nbIn2Out must be even numbers (multiple of 2).
  • I almost forgot, you have to define the temperatures embedding the layer you're budgeting. Tune the parameters THETAlow and THETAhig in the fortran code.
  • You finally need to be sure your machine has the Intel fortran compiler. Otherwise you'll need to tune the compilation line in the queue script files.

Extra

This is a bunch of routines to look at the results in the subfolder Tlayer_budget/extra. If you want to do it on your own, you should know what the output files are.

For each field, you have two output files: the one with 'timeseries' in the name corresponds to the time serie of the domain integrated field, the other the 3D map of the field (time serie cumulated).

For example in Matlab, you can try:

% Your parameters here:
iter0 = 1;
iter1 = 1099;
nt = iter1 - iter0 + 1;
THETAlow = 16;
THETAhigh = 19;
nb_in = 12;
nbIn2Out = 3;
nb_out = nb_in/nbIn2Out;
dirtofiles = '~/my_outputs_are_here/';

% If you used the default set up of file names, this should be ok:
prefi = sprintf('%s/InterpALLonce_%4.4d_%4.4d_%2.0f.m%2.0f._timeseries_',dirtofiles,iter0,iter1,THETAlow,THETAhig);
sg = -1/3; % This is because fields are cumulated over 3 years and on the other side of the temperature tendency equation
t = datenum(2003,11,1,0,0,0); t = t(1):t(1)+nt-1; % Time axis

% Read outputs:

fid = fopen(strcat(prefi,'LRvol.3yV2adv.bin'),'r','ieee-be');
Vvol = fread(fid,[1 nt],'float32'); % Contains the layer volume time serie

fid = fopen(strcat(prefi,'LRvol.3yV2adv.bin'),'r','ieee-be');
M = fread(fid,[jpi*jpj*nb_out*nb_out jpk*nb_out],'float32');fclose(fid);
M = reshape(M,[jpi*nb_out jpj*nb_out jpk*nb_out]);
Mvol = permute(M*sg,[3 2 1]); clear M
% Mvol(x,y,z) contains the ''concentration'' of the layer

fid = fopen(strcat(prefi,'LRairsea3D.3yV2adv.bin'),'r','ieee-be');
Vq = fread(fid,[1 nt],'float32'); % Contains the air-sea heat flux formation rate time serie

fid = fopen(strcat(prefi,'LRairsea3D.3yV2adv.bin'),'r','ieee-be');
M = fread(fid,[jpi*jpj*nb_out*nb_out jpk*nb_out],'float32');fclose(fid);
M = reshape(M,[jpi*nb_out jpj*nb_out jpk*nb_out]);
Mq = permute(M*sg,[3 2 1]); clear M
% Mq contains the map of formation rate due to air-sea heat fluxes.

% Note that the total integral of Mq must match the last value of Vq.
% For all fields, the unit is Sv.y = 10^6*86400*365 ~ 3.15x10^13 m^3

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