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    Metadata details:
    filename: d_mercator2roms.m
    path of file: ./repos/tracacode/1911-COAWST/script/mfiles/rutgers/initial
    
    the code of the file until where you have to start completion: %
%  D_MERCATOR2ROMS:  Driver script to create a ROMS initial conditions
%
%  This a user modifiable script that can be used to prepare ROMS
%  initial conditions NetCDF file from Mercator dataset. It sets-up
%  all the necessary parameters and variables. USERS can use this
%  as a prototype for their application.
%

% svn $Id: d_mercator2roms.m 938 2019-01-28 06:35:10Z arango $
%=========================================================================%
%  Copyright (c) 2002-2019 The ROMS/TOMS Group                            %
%    Licensed under a MIT/X style license                                 %
%    See License_ROMS.txt                           Hernan G. Arango      %
%=========================================================================%

% Set file names.

OPR_Dir = '/home/arango/ocean/toms/repository/Projects/philex/Mercator/OPR';
RTR_Dir = '/home/arango/ocean/toms/repository/Projects/philex/Mercator/RTR';

Tfile = 'ext-PSY3V2R2_1dAV_20070101_20070102_gridT_R20070110.nc.gz';
Ufile = 'ext-PSY3V2R2_1dAV_20070101_20070102_gridU_R20070110.nc.gz';
Vfile = 'ext-PSY3V2R2_1dAV_20070101_20070102_gridV_R20070110.nc.gz';

 GRDname = 'philex_grd_b.nc';
 INIname = 'philex_ini_mercator_b.nc';

CREATE = true;                   % logical switch to create NetCDF
report = false;                  % report vertical grid information

% Get number of grid points.

[Lr,Mr]=size(nc_read(GRDname,'h'));

Lu = Lr-1;   Lv = Lr;
Mu = Mr;     Mv = Mr-1;

%--------------------------------------------------------------------------
%  Create initial conditions NetCDF file.
%--------------------------------------------------------------------------

% Set full path of Mercator files assigned as initial conditions.

fileT=fullfile(RTR_Dir,Tfile); lenT=length(fileT)-3;
fileU=fullfile(RTR_Dir,Ufile); lenU=length(fileU)-3;
fileV=fullfile(RTR_Dir,Vfile); lenV=length(fileV)-3;

%--------------------------------------------------------------------------
%  Set application parameters in structure array, S.
%--------------------------------------------------------------------------

S.ncname      = INIname;     % output NetCDF file

S.spherical   = 1;           % spherical grid

S.Lm          = Lr-2;        % number of interior RHO-points, X-direction
S.Mm          = Mr-2;        % number of interior RHO-po
    
function

S.theta_s     = 7.0;         % S-coordinate surface control parameter
S.theta_b     = 0.1;         % S-coordinate bottom control parameter
S.Tcline      = 150.0;       % S-coordinate surface/bottom stretching width
S.hc          = S.Tcline;    % S-coordinate stretching width

%--------------------------------------------------------------------------
%  Set grid variables.
%--------------------------------------------------------------------------

S.h           = nc_read(GRDname, 'h');            % bathymetry

S.lon_rho     = nc_read(GRDname, 'lon_rho');      % RHO-longitude
S.lat_rho     = nc_read(GRDname, 'lat_rho');      % RHO-latitude

S.lon_u       = nc_read(GRDname, 'lon_u');        % U-longitude
S.lat_u       = nc_read(GRDname, 'lat_u');        % U-latitude

S.lon_v       = nc_read(GRDname, 'lon_v');        % V-longitude
S.lat_v       = nc_read(GRDname, 'lat_v');        % V-latitude

S.mask_rho    = nc_read(GRDname, 'mask_rho');     % RHO-mask
S.mask_u      = nc_read(GRDname, 'mask_u');       % U-mask
S.mask_v      = nc_read(GRDname, 'mask_v');       % V-mask

S.angle       = nc_read(GRDname, 'angle');        % curvilinear angle

%  Set vertical grid variables.

kgrid=0;                                          % RHO-points

[S.s_rho, S.Cs_r]=stretching(S.Vstretching, ...
                             S.theta_s, S.theta_b, S.hc, S.N,         ...
                             kgrid, report);

kgrid=1;                                          % W-points			 

[S.s_w,   S.Cs_w]=stretching(S.Vstretching, ...
                             S.theta_s, S.theta_b, S.hc, S.N,         ...
                             kgrid, report);

%--------------------------------------------------------------------------
%  Interpolate initial conditions from Mercator data to application grid.
%--------------------------------------------------------------------------

disp(' ')
disp(['Interpolating from Mercator to ROMS grid ...']);
disp(' ')

%  Uncompress input Mercator files.

s=unix(['gunzip ',fileT]);
s=unix(['gunzip ',fileU]);
s=unix(['gunzip ',fileV]);

%  Read Mercator data has a time coordinate counter (seconds) that
%  starts on 11-Oct-2006.

time=nc_read(fileT(1:lenT),'time_counter');
mydate=datestr(datenum('11-Oct-2006')+time/86400-0.5,0);

disp([ '    Processing: ', mydate]);
disp(' ')
  
%  Get Mercator grid.

Tlon=nc_read(fileT(1:lenT),'nav_lon');
Tlat=nc_read(fileT(1:lenT),'nav_lat');
Tdepth=nc_read(fileT(1:lenT),'deptht');

Ulon=nc_read(fileU(1:lenU),'nav_lon');
Ulat=nc_read(fileU(1:lenU),'nav_lat');
Udepth=nc_read(fileU(1:lenU),'depthu');

Vlon=nc_read(fileV(1:lenV),'nav_lon');
Vlat=nc_read(fileV(1:lenV),'nav_lat');
Vdepth=nc_read(fileV(1:lenV),'depthv');

%  In the western Pacific, the level 50 (z=5727.9 m) of the Mercator data
%  is all zeros. Our grid needs depth of Zr=-5920 m.  Therefore, the depths
%  are modified in level 49 (z=5274.7 m) to bound the vertical interpolation.

Tdepth(49)=6000; Udepth(49)=6000; Vdepth(49)=6000;
Tdepth(50)=6100; Udepth(50)=6100; Vdepth(50)=6100;

%  Read in initial conditions fields.

Zeta=nc_read(fileT(1:lenT),'sossheig');
Temp=nc_read(fileT(1:lenT),'votemper');
Salt=nc_read(fileT(1:lenT),'vosaline');
Uvel=nc_read(fileU(1:lenU),'vozocrtx');
Vvel=nc_read(fileV(1:lenV),'vomecrty');

%  Determine Mercator Land/Sea mask.  Since Mercator is a Z-level
%  model, the mask is 3D.

Rmask3d=ones(size(Temp));
ind=find(Temp == 0);
Rmask3d(ind)=0;

clear ind

%  Compress input Mercator files.

s=unix(['gzip ',fileT(1:lenT)]);
s=unix(['gzip ',fileU(1:lenU)]);
s=unix(['gzip ',fileV(1:lenV)]);

%  Set initial conditions time (seconds). The time coordinate for this
%  ROMS application is "seconds since 2007-01-01 00:00:00". The 0.5
%  coefficient here is to account Mecator daily average.

MyTime=time/86400-(datenum('1-Jan-2007')-datenum('11-Oct-2006'))-0.5;

%S.ocean_time = MyTime*86400;
 S.ocean_time = 86400;               % set to Jan 1, because of forcing

%  Interpolate free-surface initial conditions.

zeta=mercator2roms('zeta',S,Zeta,Tlon,Tlat,Rmask3d(:,:,1));

%  Compute ROMS model depths.  Ignore free-sruface contribution
%  so interpolation is bounded below mean sea level.

ssh=zeros(size(zeta));

igrid=1;
[S.z_r]=set_depth(S.Vtransform, S.Vstretching,                        ...
                  S.theta_s, S.theta_b, S.hc, S.N,                    ...
		  igrid, S.h, ssh, report);
	      
igrid=3;
[S.z_u]=set_depth(S.Vtransform, S.Vstretching,                        ...
                  S.theta_s, S.theta_b, S.hc, S.N,                    ...
		  igrid, S.h, ssh, report);

igrid=4;
[S.z_v]=set_depth(S.Vtransform, S.Vstretching,                        ...
                  S.theta_s, S.theta_b, S.hc, S.N,                    ...
		  igrid, S.h, ssh, report);

%  Compute ROMS vertical level thicknesses (m).
	      
N=S.N;
igrid=5;
[S.z_w]=set_depth(S.Vtransform, S.Vstretching,                        ...
                  S.theta_s, S.theta_b, S.hc, S.N,                    ...
		  igrid, S.h, zeta, report);

S.Hz=S.z_w(:,:,2:N+1)-S.z_w(:,:,1:N);
	      
%  Interpolate temperature and salinity.

temp=mercator2roms('temp',S,Temp,Tlon,Tlat,Rmask3d,Tdepth);
salt=mercator2roms('salt',S,Salt,Tlon,Tlat,Rmask3d,Tdepth);
Urho=mercator2roms('u'   ,S,Uvel,Ulon,Ulat,Rmask3d,Udepth);
Vrho=mercator2roms('v'   ,S,Vvel,Vlon,Vlat,Rmask3d,Vdepth);

%  Process velocity: rotate and/or average to staggered C-grid locations.

[u,v]=roms_vectors(Urho,Vrho,S.angle,S.mask_u,S.mask_v);

%  Compute barotropic velocities by vertically integrating (u,v).

[ubar,vbar]=uv_barotropic(u,v,S.Hz);

%--------------------------------------------------------------------------
%  Create initial condition Netcdf file.
%--------------------------------------------------------------------------

if (CREATE),
  [status]=c_initial(S);

%  Set attributes for "ocean_time".

  avalue='seconds since 2007-01-01 00:00:00';
  [status]=nc_attadd(INIname,'units',avalue,'ocean_time');
  
  avalue='gregorian';
  [status]=nc_attadd(INIname,'calend