cd /nas/edl/OFES_UV_KOE/matlib
matlab2012 -nodesktop -nosplash

clear
YEAR=1979;
exp_name='SB';

for YEAR=1966:1974
    [Pstore, Ptime, grd]=ADVOFF_main_fwd(YEAR, exp_name);
end

exp_name='SB';
for YEAR=1975:1982
    [Pstore, Ptime, grd]=ADVOFF_main_fwd(YEAR, exp_name);
end


exp_name='SB';
for YEAR=1983:1991
    [Pstore, Ptime, grd]=ADVOFF_main_fwd(YEAR, exp_name);
end


exp_name='SB';
for YEAR=1993:1999
    [Pstore, Ptime, grd]=ADVOFF_main_fwd(YEAR, exp_name);
end

%% Process Forward tracer output
clear
load KOE_GRD.mat
grd.L=399;
grd.P=249;


for yr=1966:2000
    str=['pstore_mat/',num2str(yr),'_Pstore_SB.mat'];
    load (str);
    grd.T=length(Ptime);
    Ptime(1)=Ptime(2)-5;
    filename=['pstore_nc/pstore_SB_',num2str(yr),'.nc'];
    disp(filename);
    Convert2NC_tracer(grd,filename);
    nc=netcdf(filename, 'w');
    nc{'time'}(:)=Ptime;
    nc{'P'}(:,:,:)=perm(Pstore);
    close(nc)
end


%% Running the inverse Adjoint Calculations
clear
YEAR=1979;
exp_name='TR';

for YEAR=1966:1969
    [Pstore, Ptime, grd]=ADVOFF_main_adj(YEAR, exp_name);
end


exp_name='OY';

for YEAR=1966:2000
    [Pstore, Ptime, grd]=ADVOFF_main_adj(YEAR, exp_name);
end

%% Process Inverse tracer output
clear
load KOE_GRD.mat
grd.L=399;
grd.P=249;


for yr=1966:2000
    str=['pstore_mat/',num2str(yr),'_Pstore_TR.mat'];
    load (str);
    grd.T=length(Ptime);
    Ptime(1)=Ptime(2)+5;
    filename=['pstore_nc/pstore_TR_',num2str(yr),'.nc'];
    disp(filename);
    Convert2NC_tracer(grd,filename);
    nc=netcdf(filename, 'w');
    nc{'time'}(:)=Ptime(end:-1:1);
    nc{'P'}(:,:,:)=perm(Pstore(:,:,end:-1:1));
    close(nc)
end


for yr=1966:2000
    str=['pstore_mat/',num2str(yr),'_Pstore_OY.mat'];
    load (str);
    grd.T=length(Ptime);
    Ptime(1)=Ptime(2)+5;
    filename=['pstore_nc/pstore_OY_',num2str(yr),'.nc'];
    disp(filename);
    Convert2NC_tracer(grd,filename);
    nc=netcdf(filename, 'w');
    nc{'time'}(:)=Ptime(end:-1:1);
    nc{'P'}(:,:,:)=perm(Pstore(:,:,end:-1:1));
    close(nc)
end

%% Functions

% ADVOFF_GetGrid_DataStruct.m
[grd, ctl]=ADVOFF_GetGrid_DataStruct(); 
% Load grid and velocity ctl
% The ctl are stored in matrix 
load load KOE_GRD.mat
% if you add more velocity data open the function and update ctl.

% Process.m
% This function contains code to re-write mat files into netcdf. To apply
% both for the tracers and velocity data