Adding matlab function for IC generation

SCRIPTS/nemo_IC_salinity.m

+clear all
+clc
+addpath('/projectsa/ETI/Tracer_work/Matlab_progs')
+
+fname = 'initcd_vosaline.nc';
+fname_data = 'Sal_16_0000.nc';
+z_data = 'domain_cfg.nc';
+
+Sin=ncread(fname_data,'so');
+xin=double(ncread(fname_data,'longitude'));
+yin=double(ncread(fname_data,'latitude'));
+zin=double(ncread(fname_data,'depth'));
+Sin=permute(Sin,[2 1 3]);
+
+Sout=double(ncread(fname,'vosaline'));
+xout=double(ncread(fname,'x'));
+yout=double(ncread(fname,'y'));
+dzout=ncread(z_data,'e3t_0');
+
+xout=repmat(xout,1,1,size(Sout,3));
+yout=repmat(yout,1,1,size(Sout,3));
+
+
+
+
+z=zeros(size(Sout,1),size(Sout,2),size(Sout,3));
+
+for i=1:size(Sout,3)
+    
+    
+    if i==1
+        z(:,:,i)=dzout(:,:,i);
+    else
+        z(:,:,i)=z(:,:,i-1)+dzout(:,:,i);
+    end
+    
+    
+    
+end
+
+zin(1)=0;
+zin(end)=max(z(:))+1;
+
+
+% 
+% parfor i=1:size(Sin,3)
+%     i
+% Sin(:,:,i)=smooth2(Sin(:,:,i),100,100);
+% 
+% end
+
+
+
+
+Sinterp=interp3(xin,yin,zin,Sin,xout,yout,z);
+
+
+
+
+
+ncid=netcdf.open(fname,'WRITE');
+varid = netcdf.inqVarID(ncid,'vosaline');
+
+netcdf.putVar(ncid,varid,Sinterp)
+
+

SCRIPTS/nemo_IC_temperature.m

+clear all
+clc
+
+fname = 'initcd_votemper.nc';
+fname_data = 'Temp_16_0000.nc';
+z_data = 'domain_cfg.nc';
+
+Tin=ncread(fname_data,'thetao');
+xin=double(ncread(fname_data,'longitude'));
+yin=double(ncread(fname_data,'latitude'));
+zin=double(ncread(fname_data,'depth'));
+Tin=permute(Tin,[2 1 3]);
+
+Tout=double(ncread(fname,'votemper'));
+xout=double(ncread(fname,'x'));
+yout=double(ncread(fname,'y'));
+dzout=ncread(z_data,'e3t_0');
+
+xout=repmat(xout,1,1,size(Tout,3));
+yout=repmat(yout,1,1,size(Tout,3));
+
+
+
+
+z=zeros(size(Tout,1),size(Tout,2),size(Tout,3));
+
+for i=1:size(Tout,3)
+    
+    
+    if i==1
+        z(:,:,i)=dzout(:,:,i);
+    else
+        z(:,:,i)=z(:,:,i-1)+dzout(:,:,i);
+    end
+    
+    
+    
+end
+
+zin(1)=0;
+zin(end)=max(z(:))+1;
+
+
+
+% parfor i=1:size(Tin,3)
+%     i
+% Tin(:,:,i)=smooth2(Tin(:,:,i),100,100);
+% 
+% end
+
+
+
+Tinterp=interp3(xin,yin,zin,Tin,xout,yout,z);
+
+
+
+
+
+ncid=netcdf.open(fname,'WRITE');
+varid = netcdf.inqVarID(ncid,'votemper');
+
+netcdf.putVar(ncid,varid,Tinterp)
+
+

SCRIPTS/smooth2.m

+function [mat_new] = smooth2(mat_old,stencilx,stencily)
+
+
+%stencil = 2;
+
+% check matrix in each direction
+
+% mat(x,y)
+
+%mat_new=nan(size(mat_old,1),size(mat_old,2));
+
+mat_new = mat_old;
+
+for i=1:size(mat_old,1)
+    for j=1:size(mat_old,2)
+        
+        if isnan(mat_old(i,j))
+            
+            type1=(i-1);
+            type2=abs(i-size(mat_old,1));
+            type3=(j-1);
+            type4=abs(j-size(mat_old,2));
+            
+            
+            %adj_stencil=min([stencil type1 type2 type3 type4]);
+            
+            
+            
+            
+            
+            x_min=(i-min([stencilx type1]));
+            x_max=(i+min([stencilx type2]));
+            y_min=(j-min([stencily type3]));
+            y_max=(j+min([stencily type4]));
+            
+            sub_mat = mat_old(x_min:x_max,y_min:y_max);
+            
+            
+            mat_new(i,j) = nanmean(sub_mat(:));
+            
+            %end
+            
+            %         if isnan(mat_old(i,j))
+            %             mat_new(i,j)=NaN;
+            %         end
+            
+            
+        end
+    end
+end
+
+
+end
+