function add_ini_no3(ininame,grdname,oaname,cycle,NO3min); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % function [longrd,latgrd,no3]=add_ini_no3(ininame,grdname,... % seas_datafile,ann_datafile,... % cycle); % % Add nitrate (mMol N m-3) in a CROCO initial file. % take seasonal data for the upper levels and annual data for the % lower levels. % do a temporal interpolation to have values at initial % time. % % input: % % ininame : croco initial file to process (netcdf) % grdname : croco grid file (netcdf) % seas_datafile : regular longitude - latitude - z seasonal data % file used for the upper levels (netcdf) % ann_datafile : regular longitude - latitude - z annual data % file used for the lower levels (netcdf) % cycle : time length (days) of climatology cycle (ex:360 for % annual cycle) - 0 if no cycle. % % output: % % [longrd,latgrd,no3] : surface field to plot (as an illustration) % % Further Information: % http://www.croco-ocean.org % % This file is part of CROCOTOOLS % % CROCOTOOLS is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the License, % or (at your option) any later version. % % CROCOTOOLS is distributed in the hope that it will be useful, but % WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License for more details. % % You should have received a copy of the GNU General Public License % along with this program; if not, write to the Free Software % Foundation, Inc., 59 Temple Place, Suite 330, Boston, % MA 02111-1307 USA % % Copyright (c) 2001-2006 by Pierrick Penven % e-mail:Pierrick.Penven@ird.fr % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % disp('Add_ini_no3: creating variable and attribute') % % open the grid file % nc=netcdf(grdname,'r'); h=nc{'h'}(:); close(nc); % % open the initial file % nc=netcdf(ininame,'write'); theta_s = nc{'theta_s'}(:); if isempty(theta_s) disp('Restart file') theta_s=nc.theta_s(:); theta_b=nc.theta_b(:); hc=nc.hc(:); else theta_b = nc{'theta_b'}(:); hc = nc{'hc'}(:); vtransform = nc{'Vtransform'}(:); if ~exist('vtransform') vtransform=1; %Old Vtransform disp([' NO VTRANSFORM parameter found']) disp([' USE TRANSFORM default value vtransform = 1']) end end N = length(nc('s_rho')); % % open the oa file % noa=netcdf(oaname,'r'); z=-noa{'Zno3'}(:); oatime=noa{'no3_time'}(:); tlen=length(oatime); % % Get the sigma depths % zcroco=zlevs(h,0.*h,theta_s,theta_b,hc,N,'r',vtransform); zmin=min(min(min(zcroco))); zmax=max(max(max(zcroco))); % % Check if the min z level is below the min sigma level % (if not add a deep layer) % %addsurf=max(z)zmin; if addsurf z=[100;z]; end if addbot z=[z;-100000]; end Nz=min(find(zmodeltime)); time2=oatime(l2); if isempty(l2) if cycle~=0 l2=1; time2=oatime(l2)+cycle; else error('No posterious time in the dataset') end end disp(['Initialisation time: ',num2str(modeltime),... ' - Time 1: ',num2str(time1),... ' - Time 2: ',num2str(time2)]) cff1=(modeltime-time2)/(time1-time2); cff2=(time1-modeltime)/(time1-time2); else cff1=1; l2=l1; cff2=0; end % % interpole the seasonal dataset on the horizontal croco grid % disp(['Add_ini_no3: vertical interpolation']) var=squeeze(noa{'NO3'}(l1,:,:,:)); if addsurf var=cat(1,var(1,:,:),var); end if addbot var=cat(1,var,var(end,:,:)); end var2=squeeze(noa{'NO3'}(l2,:,:,:)); if addsurf var2=cat(1,var2(1,:,:),var2); end if addbot var2=cat(1,var2,var2(end,:,:)); end var=cff1*var + cff2*var2; zeta = squeeze(nc{'zeta'}(l,:,:)); zcroco=zlevs(h,zeta,theta_s,theta_b,hc,N,'r',vtransform); nc{'NO3'}(l,:,:,:)=ztosigma(flipdim(var,1),zcroco,flipud(z)); end close(noa); % % Remove low values for oligotrophic areas % for l=1:tinilen NO3=nc{'NO3'}(l,:,:,:); NO3(NO3