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Commit 94d29e9f authored by Gildas Cambon's avatar Gildas Cambon
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Merge branch... 

Merge branch '46-add-make_ini-in-make_clim_pisces-to-correct-dic-alk-missing-values-at-bottom-in-hr-configuration' into 'master'

Resolve "Add make_ini in make_clim_pisces to correct DIC/ALK missing values at bottom in HR configuration"

Closes #46

See merge request !16
parents b0a8a875 d605c48e
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1 merge request!16Resolve "Add make_ini in make_clim_pisces to correct DIC/ALK missing values at bottom in HR configuration"
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Preprocessing_tools/Bio/add_dic.m
+ 15
− 13
View file @ 94d29e9f
function add_dic(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,dic]=add_dic(climfile,gridfile,...
......@@ -124,21 +124,23 @@ if (makeclim)
end
%
% Same thing for the Initial file
if (makeini)
%
%disp('Add_no3: creating variables and attributes for the Initial file')
disp('Add_dic: creating variables and attributes for the Initial file')
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'NO3'}.long_name = ncchar('Nitrate');
%nc{'NO3'}.long_name = 'Nitrate';
%nc{'NO3'}.units = ncchar('mMol N m-3');
%nc{'NO3'}.units = 'mMol N m-3';
%
%endef(nc);
%close(nc)
nc=netcdf(inifile,'write');
redef(nc);
nc{'DIC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
nc{'DIC'}.long_name = ncchar('DIC');
nc{'DIC'}.long_name = 'DIC';
nc{'DIC'}.units = ncchar('mMol C m-3');
nc{'DIC'}.units = 'mMol C m-3';
end
endef(nc);
close(nc)
return
Preprocessing_tools/Bio/add_doc.m
+ 13
− 11
View file @ 94d29e9f
function add_doc(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
......@@ -125,20 +125,22 @@ end
%
% Same thing for the Initial file
%
%disp('Add_doc: creating variables and attributes for the Initial file')
if (makeini)
disp('Add_doc: creating variables and attributes for the Initial file')
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc=netcdf(inifile,'write');
redef(nc);
nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'DOC'}.long_name = ncchar('Nitrate');
%nc{'DOC'}.long_name = 'Nitrate';
%nc{'DOC'}.units = ncchar('mMol N m-3');
%nc{'DOC'}.units = 'mMol N m-3';
nc{'DOC'}.long_name = ncchar('DOC');
nc{'DOC'}.long_name = 'DOC';
nc{'DOC'}.units = ncchar('mMol C m-3');
nc{'DOC'}.units = 'mMol C m-3';
%
%endef(nc);
%close(nc)
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_don.m
+ 13
− 11
View file @ 94d29e9f
function add_don(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim,makequota);
ann_datafile,cycle,makeoa,makeclim,makequota,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
......@@ -166,20 +166,22 @@ end
%
% Same thing for the Initial file
%
%disp('Add_doc: creating variables and attributes for the Initial file')
if (makeini)
disp('Add_don: creating variables and attributes for the Initial file')
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc=netcdf(inifile,'write');
redef(nc);
nc{'DON'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'DOC'}.long_name = ncchar('Nitrate');
%nc{'DOC'}.long_name = 'Nitrate';
%nc{'DOC'}.units = ncchar('mMol N m-3');
%nc{'DOC'}.units = 'mMol N m-3';
nc{'DON'}.long_name = ncchar('DON');
nc{'DON'}.long_name = 'DON';
nc{'DON'}.units = ncchar('mMol C m-3');
nc{'DON'}.units = 'mMol C m-3';
%
%endef(nc);
%close(nc)
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_dop.m
+ 14
− 15
View file @ 94d29e9f
function add_dop(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim,makequota);
ann_datafile,cycle,makeoa,makeclim,makequota,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,dop]=add_dop(climfile,gridfile,...
......@@ -163,23 +163,22 @@ if (makeclim)
nc{'dop_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
if (makeini)
disp('Add_dop: creating variables and attributes for the Initial file')
%
% Same thing for the Initial file
% open the clim file
%
%disp('Add_dop: creating variables and attributes for the Initial file')
nc=netcdf(inifile,'write');
redef(nc);
nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'DOP'}.long_name = ncchar('Nitrate');
%nc{'DOP'}.long_name = 'Nitrate';
%nc{'DOP'}.units = ncchar('mMol N m-3');
%nc{'DOP'}.units = 'mMol N m-3';
nc{'DOP'}.long_name = ncchar('DOP');
nc{'DOP'}.long_name = 'DOP';
nc{'DOP'}.units = ncchar('mMol C m-3');
nc{'DOP'}.units = 'mMol C m-3';
%
%endef(nc);
%close(nc)
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_fer.m
+ 18
− 1
View file @ 94d29e9f
function add_fer(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,fer]=add_fer(climfile,gridfile,...
......@@ -122,4 +122,21 @@ if (makeclim)
nc{'fer_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
if (makeini)
disp('Add_fer: creating variables and attributes for the Initial file')
%
% open the clim file
%
nc=netcdf(inifile,'write');
redef(nc);
nc{'FER'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
nc{'FER'}.long_name = ncchar('FER');
nc{'FER'}.long_name = 'FER';
nc{'FER'}.units = ncchar('uMol Fe m-3');
nc{'FER'}.units = 'uMol Fe m-3';
%
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_no3.m
+ 16
− 14
View file @ 94d29e9f
function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,no3]=add_no3(climfile,gridfile,...
......@@ -164,22 +164,24 @@ if (makeclim)
close(nc)
end
%
if (makeini)
% Same thing for the Initial file
%
%disp('Add_no3: creating variables and attributes for the Initial file')
disp('Add_no3: creating variables and attributes for the Initial file')
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'NO3'}.long_name = ncchar('Nitrate');
%nc{'NO3'}.long_name = 'Nitrate';
%nc{'NO3'}.units = ncchar('mMol N m-3');
%nc{'NO3'}.units = 'mMol N m-3';
%
%endef(nc);
%close(nc)
nc=netcdf(inifile,'write');
redef(nc);
nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'NO3'}.long_name = ncchar('Nitrate');
nc{'NO3'}.long_name = 'Nitrate';
nc{'NO3'}.units = ncchar('mMol N m-3');
nc{'NO3'}.units = 'mMol N m-3';
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_o2.m
+ 20
− 1
View file @ 94d29e9f
function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,o2]=add_o2(climfile,gridfile,...
......@@ -122,5 +122,24 @@ if (makeclim)
nc{'o2_time'}(:,:)=t*30; % if time in month in the dataset !!!
close(nc)
end
if (makeini)
% Same thing for the Initial file
%
disp('Add_o2: creating variables and attributes for the Initial file')
%
% open the clim file
nc=netcdf(inifile,'write');
redef(nc);
nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'O2'}.long_name = ncchar('Oxygen');
nc{'O2'}.long_name = 'Oxygen';
nc{'O2'}.units = ncchar('mMol O m-3');
nc{'O2'}.units = 'mMol O m-3';
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_po4.m
+ 20
− 1
View file @ 94d29e9f
function add_po4(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,po4]=add_po4(climfile,gridfile,...
......@@ -122,4 +122,23 @@ if (makeclim)
nc{'po4_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
if (makeini)
% Same thing for the Initial file
%
disp('Add_po4: creating variables and attributes for the Initial file')
%
% open the clim file
nc=netcdf(inifile,'write');
redef(nc);
nc{'PO4'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'PO4'}.long_name = ncchar('Phosphate');
nc{'PO4'}.long_name = 'Phosphate';
nc{'PO4'}.units = ncchar('mMol P m-3');
nc{'PO4'}.units = 'mMol P m-3';
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_sio3.m
+ 20
− 1
View file @ 94d29e9f
function add_sio3(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,sio3]=add_sio3(climfile,gridfile,...
......@@ -122,4 +122,23 @@ if (makeclim)
nc{'si_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
if (makeini)
% Same thing for the Initial file
%
disp('Add_si: creating variables and attributes for the Initial file')
%
% open the clim file
nc=netcdf(inifile,'write');
redef(nc);
nc{'Si'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc{'Si'}.long_name = ncchar('Silicate');
nc{'Si'}.long_name = 'Silicate';
nc{'Si'}.units = ncchar('mMol Si m-3');
nc{'Si'}.units = 'mMol Si m-3';
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/add_talk.m
+ 13
− 11
View file @ 94d29e9f
function add_talk(oafile,climfile,inifile,gridfile,seas_datafile,...
ann_datafile,cycle,makeoa,makeclim);
ann_datafile,cycle,makeoa,makeclim,makeini);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,talk]=add_talk(climfile,gridfile,...
......@@ -125,20 +125,22 @@ end
%
% Same thing for the Initial file
%
%disp('Add_no3: creating variables and attributes for the Initial file')
if (makeini)
disp('Add_talk: creating variables and attributes for the Initial file')
%
% open the clim file
%
%nc=netcdf(inifile,'write');
%redef(nc);
%nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
nc=netcdf(inifile,'write');
redef(nc);
nc{'TALK'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
%
%nc{'NO3'}.long_name = ncchar('Nitrate');
%nc{'NO3'}.long_name = 'Nitrate';
%nc{'NO3'}.units = ncchar('mMol N m-3');
%nc{'NO3'}.units = 'mMol N m-3';
nc{'TALK'}.long_name = ncchar('TALK');
nc{'TALK'}.long_name = 'TALK';
nc{'TALK'}.units = ncchar('mMol C m-3');
nc{'TALK'}.units = 'mMol C m-3';
%
%endef(nc);
%close(nc)
endef(nc);
close(nc)
end
return
Preprocessing_tools/Bio/make_biol.m
+ 6
− 11
View file @ 94d29e9f
......@@ -62,6 +62,12 @@ if (makeclim)
disp('========================')
disp('Climatology for PISCES variables')
make_clim_pisces
disp('------------------------')
disp('Iron deposition file')
make_dust
disp('------------------------')
disp('Nitrogen deposition')
make_ndepo
end
if (makebioebus)
disp('========================')
......@@ -106,17 +112,6 @@ if (makeini)
disp('Initial NPZD variables')
make_ini_npzd
end
if (makepisces)
disp('========================')
disp('Initial PISCES variables')
make_ini_pisces
disp('------------------------')
disp('Iron deposition file')
make_dust
disp('------------------------')
disp('Nitrogen deposition')
make_ndepo
end
if (makebioebus)
disp('========================')
disp('Initial BioEBUS variables')
......
Preprocessing_tools/Bio/make_clim_pisces.m
+ 101
− 12
View file @ 94d29e9f
......@@ -63,35 +63,35 @@ disp('=> You need the croco_oa.nc file created by make_clim.m ')
disp('=> with makeoa=1 from crocotools_param.m ')
disp('====================================================== ')
add_no3(oaname,clmname,ininame,grdname,no3_seas_data,...
no3_ann_data,cycle,makeoa,makeclim)
no3_ann_data,cycle,makeoa,makeclim,makeini)
add_dic(oaname,clmname,ininame,grdname,dic_seas_data,...
dic_ann_data,cycle,makeoa,makeclim,makeini)
add_po4(oaname,clmname,ininame,grdname,po4_seas_data,...
po4_ann_data,cycle,makeoa,makeclim)
po4_ann_data,cycle,makeoa,makeclim,makeini)
add_sio3(oaname,clmname,ininame,grdname,sio3_seas_data,...
sio3_ann_data,cycle,makeoa,makeclim)
sio3_ann_data,cycle,makeoa,makeclim,makeini)
add_o2(oaname,clmname,ininame,grdname,o2_seas_data,...
o2_ann_data,cycle,makeoa,makeclim)
add_dic(oaname,clmname,ininame,grdname,dic_seas_data,...
dic_ann_data,cycle,makeoa,makeclim)
o2_ann_data,cycle,makeoa,makeclim,makeini)
add_talk(oaname,clmname,ininame,grdname,talk_seas_data,...
talk_ann_data,cycle,makeoa,makeclim)
talk_ann_data,cycle,makeoa,makeclim,makeini)
add_doc(oaname,clmname,ininame,grdname,doc_seas_data,...
doc_ann_data,cycle,makeoa,makeclim)
doc_ann_data,cycle,makeoa,makeclim,makeini)
if makequota
add_don(oaname,clmname,ininame,grdname,doc_seas_data,...
doc_ann_data,cycle,makeoa,makeclim)
doc_ann_data,cycle,makeoa,makeclim,makequota,makeini)
add_dop(oaname,clmname,ininame,grdname,doc_seas_data,...
doc_ann_data,cycle,makeoa,makeclim)
doc_ann_data,cycle,makeoa,makeclim,makequota,makeini)
end
add_fer(oaname,clmname,ininame,grdname,fer_seas_data,...
fer_ann_data,cycle,makeoa,makeclim)
fer_ann_data,cycle,makeoa,makeclim,makeini)
%
% Horizontal extrapolation
......@@ -218,6 +218,95 @@ end
vinterp_clm(clmname,grdname,oaname,'FER','fer_time','Zfer',0,'r');
end
%----------------------------------------------------------------------------
% Initial file
%----------------------------------------------------------------------------
if (makeini)
%
% NO3
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' NO3...')
vinterp_clm(ininame,grdname,oaname,'NO3','no3_time','Zno3',tini,'r',1);
%
% DIC
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' DIC...')
vinterp_clm(ininame,grdname,oaname,'DIC','dic_time','Zdic',tini,'r',1);
%
% PO4
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' PO4...')
vinterp_clm(ininame,grdname,oaname,'PO4','po4_time','Zpo4',tini,'r',1);
%
% Si
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' Si...')
vinterp_clm(ininame,grdname,oaname,'Si','si_time','Zsi',tini,'r',1);
%
% O2
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' O2...')
vinterp_clm(ininame,grdname,oaname,'O2','o2_time','Zo2',tini,'r',1);
%
% TALK
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' TALK...')
vinterp_clm(ininame,grdname,oaname,'TALK','talk_time','Ztalk',tini,'r',1);
%
% DOC
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' DOC...')
vinterp_clm(ininame,grdname,oaname,'DOC','doc_time','Zdoc',tini,'r',1);
if makequota
%
% DON
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' DON...')
vinterp_clm(ininame,grdname,oaname,'DON','don_time','Zdon',tini,'r',1);
%
% DOP
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' DOP...')
vinterp_clm(ininame,grdname,oaname,'DOP','dop_time','Zdop',tini,'r',1);
end
%
% FER
%
disp(' ')
disp(' Vertical interpolations')
disp(' ')
disp(' FER...')
vinterp_clm(ininame,grdname,oaname,'FER','fer_time','Zfer',tini,'r',1);
end
if (makeplot)
disp(' ')
......
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