function [inifile, ctli]=nepd_ex_init(sub_I, sub_J, grd, grdn, nameit, res, inittime, npzd, np)
% function [inifile, ctli]=nepd_ex_init(sub_I, sub_J, grd, grdn, nameit, res, inittime, npzd, np)
%   Extract a subgrid of GRD at resolution RES for the 
%   subdomain SUB_I, SUB_J.
%   RES=1  keep existing resolution
%   RES=2  double the resolution
%   INITTIME choosen date for initial condition in MATLAB datenum format
%   NP number of passive tracers to introduce in initial cond.
%   NPZD =1 to introduce NPZD variables, else =0 
%%
%   Requires RNT, RGRD, RNC, Opendap and netcdf
%   
%   GLOBEC Ocean Modeling Support 
%   - E. Di Lorenzo (globec_extract@o3d.org)
%


inifile=[nameit,'-init.nc'];
solution='http://dods.o3d.org:8080/thredds/dodsC/nepd/nepd_forc_full_monthly_avg.nc'; 
ctl=rnt_timectl({solution},'ocean_time','r');

% Compute dates and find index of selected initial condition
for i=1:length(ctl.time)
	mydate(i)=datenum(ctl.year(i)+1950, ctl.month(i),ctl.day(i));
end
ctl.mydate=mydate;
istr=find(inittime<=ctl.mydate); 
timeind=istr(1);

% Set options for initial condition file creation
optini.npzd=npzd;
optini.ptracer=np;
ex_vars={'salt' 'temp' 'u' 'v' 'ubar' 'vbar' 'zeta' };
%       'detritus' 'phytoplankton' 'zooplankton' 'NO3'};

% Create initial condition
disp (['Creating Sub INI file  ',inifile]);
rnc_CreateIniFile(grdn,inifile,optini);


nc=netcdf(inifile,'w'); nc{'ocean_time'}(1)=ctl.time(timeind); close(nc);
state=rnt_loadStateSub(ctl,timeind,ex_vars,grd,sub_I,sub_J);
ctli=rnt_timectl({inifile},'ocean_time','r');
rnt_saveState(ctli,1,ex_vars,state);

%/drive/edl/matlib-master/rnc/rnc_CreateIniFile.m

% Set passive tracers to zero
nc = netcdf(inifile, 'w');
for inert=1:optini.ptracer

if inert<10 
str=['dye_0',num2str(inert)];
else
str=['dye_',num2str(inert)];
end
nc{str}(:) = 0;

end
close(nc);