%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%  Build a CROCO initial file from Levitus Data
%
%  Extrapole and interpole temperature and salinity from a
%  Climatology to get initial conditions for
%  CROCO (initial netcdf files) .
%  Get the velocities and sea surface elevation via a 
%  geostrophic computation.
%
%  Data input format (netcdf):
%     temperature(T, Z, Y, X)
%     T : time [Months]
%     Z : Depth [m]
%     Y : Latitude [degree north]
%     X : Longitude [degree east]
%
%  Data source : IRI/LDEO Climate Data Library (World Ocean Atlas 1998)
%    http://ingrid.ldgo.columbia.edu/
%    http://iridl.ldeo.columbia.edu/SOURCES/.NOAA/.NODC/.WOA98/
%
%  Pierrick Penven, IRD, 2005.
%  Olivier Aumont, IRD, 2006.
%  Patricio Marchesiello, IRD 2007
%  Christophe Eugene Raoul Menkes, IRD 2007
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear all
close all
%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
%
%  Title 
%
crocotools_param
%
%  Data climatologies file names:
%
no3_month_data  = [woapisces_dir,'no3_seas.cdf'];
no3_ann_data   = [woapisces_dir,'no3_ann.cdf'];
po4_month_data  = [woapisces_dir,'po4_seas.cdf'];
po4_ann_data   = [woapisces_dir,'po4_ann.cdf'];
o2_month_data   = [woapisces_dir,'o2_seas.cdf'];
o2_ann_data    = [woapisces_dir,'o2_ann.cdf'];
sio3_month_data = [woapisces_dir,'sio3_seas.cdf'];
sio3_ann_data  = [woapisces_dir,'sio3_ann.cdf'];
dic_month_data  = [woapisces_dir,'dic_seas.cdf'];
dic_ann_data   = [woapisces_dir,'dic_ann.cdf'];
talk_month_data = [woapisces_dir,'talk_seas.cdf'];
talk_ann_data  = [woapisces_dir,'talk_ann.cdf'];
doc_month_data  = [woapisces_dir,'doc_seas.cdf'];
doc_ann_data   = [woapisces_dir,'doc_ann.cdf'];
fer_month_data  = [woapisces_dir,'fer_seas.cdf'];
fer_ann_data   = [woapisces_dir,'fer_ann.cdf'];
dust_month_data = [woapisces_dir,'dust_seas.cdf'];
dust_ann_data  = [woapisces_dir,'dust_ann.cdf'];
%
%
%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
%
% Title
%
if makeini
disp(' ')
disp([' Adding PISCES data into initial file: ',ininame])
%
% Initial file
%
add_ini_pisces(ininame,'write');
%
% Horizontal and vertical interp/extrapolations 
%
disp(' ')
disp(' Interpolations / extrapolations')
disp(' ')
disp('nitrate ...')
ext_tracers_ini(ininame,grdname,no3_month_data,no3_ann_data,...
             'nitrate','NO3','r',tini);
disp(' ')
disp('phosphate ...')
ext_tracers_ini(ininame,grdname,po4_month_data,po4_ann_data,...
             'phosphate','PO4','r',tini);
disp(' ')
disp('Silicate ...')
ext_tracers_ini(ininame,grdname,sio3_month_data,sio3_ann_data,...
             'silicate','Si','r',tini);
disp(' ')
disp(' Oxygen ...')
ext_tracers_ini(ininame,grdname,o2_month_data,o2_ann_data,...
             'oxygen','O2','r',tini);
disp(' ')
disp('Dissolved Inorganic Carbon ...')
ext_tracers_ini(ininame,grdname,dic_month_data,dic_ann_data,...
             'dic','DIC','r',tini);
disp(' ')
disp('Total alkalinity ...')
ext_tracers_ini(ininame,grdname,talk_month_data,talk_ann_data,...
             'talk','TALK','r',tini);
disp(' ')
disp('Dissolved Organic Carbon...')
ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
             'doc','DOC','r',tini);

if makequota
disp(' ')
disp('Dissolved Organic Nitrogen...')
ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
             'doc','DON','r',tini);
disp(' ')
disp('Dissolved Organic Phosphorus...')
ext_tracers_ini(ininame,grdname,doc_month_data,doc_ann_data,...
             'doc','DOP','r',tini);
end

disp(' ')
disp('Iron ...')
ext_tracers_ini(ininame,grdname,fer_month_data,fer_ann_data,...
             'fer','FER','r',tini);
if (makeplot == 1)disp(' ')
%
% Make a few plots
%
   disp(' Make a few plots...')
   test_clim(ininame,grdname,'NO3',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'PO4',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'Si',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'O2',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'DIC',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'TALK',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'DOC',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'DON',1,coastfileplot)
   figure
   test_clim(ininame,grdname,'FER',1,coastfileplot)
end

end %if makeini
%
% End
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%