From 251292b1df66aba76516d533f8e28c5f9f4a5172 Mon Sep 17 00:00:00 2001
From: Gildas Cambon <gildas.cambon@ird.fr>
Date: Thu, 27 Oct 2022 21:12:58 +0200
Subject: [PATCH] BIOLOGY
Again ... Still cleaning to put routines for preprocessing bgc (npzd,
bioebus, pisces) input files into a subdirectory Bio of Preprocessing_tools/
---
Preprocessing_tools/Bio/add_chla.m | 303 ++++++++-------
Preprocessing_tools/Bio/add_dic.m | 19 +
Preprocessing_tools/Bio/add_doc.m | 19 +
Preprocessing_tools/Bio/add_no3.m | 344 +++++++++--------
Preprocessing_tools/Bio/add_o2.m | 255 ++++++-------
Preprocessing_tools/{ => Bio}/make_biol.m | 0
Preprocessing_tools/{ => Bio}/nevis_2003.m | 0
Preprocessing_tools/add_Sphyto_Lphyto.m | 112 ------
Preprocessing_tools/add_Szoo_Lzoo.m | 112 ------
Preprocessing_tools/add_bry_bioebus.m | 372 ------------------
Preprocessing_tools/add_bry_bioebus_Z.m | 341 -----------------
Preprocessing_tools/add_bry_npzd.m | 298 ---------------
Preprocessing_tools/add_bry_npzd_Z.m | 267 -------------
Preprocessing_tools/add_bry_pisces.m | 399 --------------------
Preprocessing_tools/add_bry_pisces_Z.m | 319 ----------------
Preprocessing_tools/add_chla.m | 151 --------
Preprocessing_tools/add_dic.m | 144 -------
Preprocessing_tools/add_doc.m | 144 -------
Preprocessing_tools/add_fer.m | 144 -------
Preprocessing_tools/add_ini_Sphyto_Lphyto.m | 82 ----
Preprocessing_tools/add_ini_Szoo_Lzoo.m | 84 -----
Preprocessing_tools/add_ini_bioebus.m | 52 ---
Preprocessing_tools/add_ini_chla.m | 202 ----------
Preprocessing_tools/add_ini_no3.m | 204 ----------
Preprocessing_tools/add_ini_npzd.m | 63 ----
Preprocessing_tools/add_ini_o2.m | 205 ----------
Preprocessing_tools/add_ini_phyto.m | 68 ----
Preprocessing_tools/add_ini_pisces.m | 117 ------
Preprocessing_tools/add_ini_zoo.m | 70 ----
Preprocessing_tools/add_no3.m | 185 ---------
Preprocessing_tools/add_o2.m | 126 -------
Preprocessing_tools/add_phyto.m | 85 -----
Preprocessing_tools/add_po4.m | 144 -------
Preprocessing_tools/add_sio3.m | 144 -------
Preprocessing_tools/add_talk.m | 144 -------
Preprocessing_tools/add_zoo.m | 87 -----
Preprocessing_tools/make_clim_bioebus.m | 159 --------
Preprocessing_tools/make_clim_npzd.m | 152 --------
Preprocessing_tools/make_clim_pisces.m | 221 -----------
Preprocessing_tools/vinterp_bry_bgc.m | 109 ------
40 files changed, 496 insertions(+), 5950 deletions(-)
rename Preprocessing_tools/{ => Bio}/make_biol.m (100%)
rename Preprocessing_tools/{ => Bio}/nevis_2003.m (100%)
delete mode 100644 Preprocessing_tools/add_Sphyto_Lphyto.m
delete mode 100644 Preprocessing_tools/add_Szoo_Lzoo.m
delete mode 100644 Preprocessing_tools/add_bry_bioebus.m
delete mode 100644 Preprocessing_tools/add_bry_bioebus_Z.m
delete mode 100644 Preprocessing_tools/add_bry_npzd.m
delete mode 100644 Preprocessing_tools/add_bry_npzd_Z.m
delete mode 100644 Preprocessing_tools/add_bry_pisces.m
delete mode 100644 Preprocessing_tools/add_bry_pisces_Z.m
delete mode 100644 Preprocessing_tools/add_chla.m
delete mode 100644 Preprocessing_tools/add_dic.m
delete mode 100644 Preprocessing_tools/add_doc.m
delete mode 100644 Preprocessing_tools/add_fer.m
delete mode 100644 Preprocessing_tools/add_ini_Sphyto_Lphyto.m
delete mode 100644 Preprocessing_tools/add_ini_Szoo_Lzoo.m
delete mode 100644 Preprocessing_tools/add_ini_bioebus.m
delete mode 100644 Preprocessing_tools/add_ini_chla.m
delete mode 100644 Preprocessing_tools/add_ini_no3.m
delete mode 100644 Preprocessing_tools/add_ini_npzd.m
delete mode 100644 Preprocessing_tools/add_ini_o2.m
delete mode 100644 Preprocessing_tools/add_ini_phyto.m
delete mode 100644 Preprocessing_tools/add_ini_pisces.m
delete mode 100644 Preprocessing_tools/add_ini_zoo.m
delete mode 100644 Preprocessing_tools/add_no3.m
delete mode 100644 Preprocessing_tools/add_o2.m
delete mode 100644 Preprocessing_tools/add_phyto.m
delete mode 100644 Preprocessing_tools/add_po4.m
delete mode 100644 Preprocessing_tools/add_sio3.m
delete mode 100644 Preprocessing_tools/add_talk.m
delete mode 100644 Preprocessing_tools/add_zoo.m
delete mode 100644 Preprocessing_tools/make_clim_bioebus.m
delete mode 100644 Preprocessing_tools/make_clim_npzd.m
delete mode 100644 Preprocessing_tools/make_clim_pisces.m
delete mode 100644 Preprocessing_tools/vinterp_bry_bgc.m
diff --git a/Preprocessing_tools/Bio/add_chla.m b/Preprocessing_tools/Bio/add_chla.m
index abc0a6f1..a5ecdd22 100644
--- a/Preprocessing_tools/Bio/add_chla.m
+++ b/Preprocessing_tools/Bio/add_chla.m
@@ -1,156 +1,151 @@
-function add_chla(climfile, gridfile, seas_datafile, cycle, Roa);
+function add_chla(climfile,gridfile,seas_datafile,cycle,Roa);
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- %
- % function add_chla(climfile,gridfile,seas_datafile,cycle);
- %
- % Add chlorophyll (mg C) in a CROCO climatology file.
- % take seasonal data for the surface levels and extrapole
- % using Morel and Berthon (1989) parameterization for the
- % lower levels. warning ! the unit is (micro mole/l) in the
- % dataset.
- % ref: Morel and Berthon, Surface pigments, algal biomass
- % profiles, and potential production of the euphotic layer:
- % Relationships reinvestigated in view of remote-sensing
- % applications. Limnol. Oceanogr., 34, 1989, 1545-1562.
- %
- % input:
- %
- % climfile : croco climatology file to process (netcdf)
- % gridfile : 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.
- %
- % 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_chla: creating variable and attribute')
- default = NaN;
- %
- % read in the datafile
- %
- ncseas = netcdf(seas_datafile, 'r');
- x = ncseas{'X'}(:);
- y = ncseas{'Y'}(:);
- t = ncseas{'T'}(:);
- tlen = length(t);
- %
- % open the grid file
- %
- ng = netcdf(gridfile, 'r');
- lon = ng{'lon_rho'}(:);
- %lon(lon<0)=lon(lon<0)+360;
- lat = ng{'lat_rho'}(:);
- h = ng{'h'}(:);
- close(ng);
- [M, L] = size(lon);
- dl = 2.;
- minlon = min(min(lon)) - dl;
- maxlon = max(max(lon)) + dl;
- minlat = min(min(lat)) - dl;
- maxlat = max(max(lat)) + dl;
- imin = max(find(x <= minlon));
- imax = min(find(x >= maxlon));
- jmin = max(find(y <= minlat));
- jmax = min(find(y >= maxlat));
- x = x(imin:imax);
- y = y(jmin:jmax);
- %
- % open the clim file
- %
- nc = netcdf(climfile, 'write');
- theta_s = nc{'theta_s'}(:);
- theta_b = nc{'theta_b'}(:);
- Tcline = nc{'Tcline'}(:);
- vtransform = nc{'Vtransform'}(:);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% function add_chla(climfile,gridfile,seas_datafile,cycle);
+%
+% Add chlorophyll (mg C) in a CROCO climatology file.
+% take seasonal data for the surface levels and extrapole
+% using Morel and Berthon (1989) parameterization for the
+% lower levels. warning ! the unit is (micro mole/l) in the
+% dataset.
+% ref: Morel and Berthon, Surface pigments, algal biomass
+% profiles, and potential production of the euphotic layer:
+% Relationships reinvestigated in view of remote-sensing
+% applications. Limnol. Oceanogr., 34, 1989, 1545-1562.
+%
+% input:
+%
+% climfile : croco climatology file to process (netcdf)
+% gridfile : 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.
+%
+% 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_chla: creating variable and attribute')
+default=NaN;
+%
+% read in the datafile
+%
+ncseas=netcdf(seas_datafile,'r');
+x=ncseas{'X'}(:);
+y=ncseas{'Y'}(:);
+t=ncseas{'T'}(:);
+tlen=length(t);
+%
+% open the grid file
+%
+ng=netcdf(gridfile,'r');
+lon=ng{'lon_rho'}(:);
+%lon(lon<0)=lon(lon<0)+360;
+lat=ng{'lat_rho'}(:);
+h=ng{'h'}(:);
+close(ng);
+[M,L]=size(lon);
+dl=2.;
+minlon=min(min(lon))-dl;
+maxlon=max(max(lon))+dl;
+minlat=min(min(lat))-dl;
+maxlat=max(max(lat))+dl;
+imin=max(find(x<=minlon));
+imax=min(find(x>=maxlon));
+jmin=max(find(y<=minlat));
+jmax=min(find(y>=maxlat));
+x=x(imin:imax);
+y=y(jmin:jmax);
+%
+% open the clim file
+%
+nc=netcdf(climfile,'write');
+theta_s = nc{'theta_s'}(:);
+theta_b = nc{'theta_b'}(:);
+Tcline = nc{'Tcline'}(:);
+vtransform=nc{'Vtransform'}(:);
+if ~exist('vtransform')
+ vtransform=1; %Old Vtransform
+ disp([' NO VTRANSFORM parameter found'])
+end
+N = length(nc('s_rho'));
- if ~exist('vtransform')
- vtransform = 1; %Old Vtransform
- disp([' NO VTRANSFORM parameter found'])
- end
-
- N = length(nc('s_rho'));
-
- %redef(nc);
- nc('chla_time') = tlen;
- nc{'chla_time'} = ncdouble('chla_time');
- nc{'CHLA'} = ncdouble('chla_time', 's_rho', 'eta_rho', 'xi_rho');
- %
- nc{'chla_time'}.long_name = ncchar('time for chlorophyll');
- nc{'chla_time'}.long_name = 'time for chlorophyll';
- nc{'chla_time'}.units = ncchar('day');
- nc{'chla_time'}.units = 'day';
-
- if cycle ~= 0
- nc{'chla_time'}.cycle_length = cycle;
- end
-
- %
- nc{'CHLA'}.long_name = ncchar('Chlorophyll');
- nc{'CHLA'}.long_name = 'Chlorophyll';
- nc{'CHLA'}.units = ncchar('mg C');
- nc{'CHLA'}.units = 'mg C';
- nc{'CHLA'}.fields = ncchar('CHLA, scalar, series');
- nc{'CHLA'}.fields = 'CHLA, scalar, series';
- %
- %endef(nc);
- %
- % Record the time
- %
- nc{'chla_time'}(:) = t * 30; % if time in month in the dataset !!!
- %
- % Get the missing values
- %
- missval = ncseas{'chlorophyll'}.missing_value(:);
- %
- % loop on time
- %
- for l = 1:tlen
- disp(['time index: ', num2str(l), ' of total: ', num2str(tlen)])
- %
- % extrapole the annual dataset on the horizontal croco grid
- %
- disp('Add_chla: horizontal interpolation of surface data')
- surfchla = squeeze(ncseas{'chlorophyll'}(l, jmin:jmax, imin:imax));
- surfchla = get_missing_val(x, y, surfchla, missval, Roa, default);
- surfchlacroco = interp2(x, y, surfchla, lon, lat);
- %
- % extrapole the chlorophyll on the vertical
- %
- zcroco = zlevs(h, 0 .* h, theta_s, theta_b, Tcline, N, 'r', vtransform);
- disp(['Add_chla: vertical ', ...
- 'extrapolation of chlorophyll'])
- chlacroco = extr_chlo(surfchlacroco, zcroco);
- nc{'CHLA'}(l, :, :, :) = chlacroco;
- end
-
- close(nc);
- close(ncseas);
- chla = squeeze(chlacroco(N, :, :));
- return
+%redef(nc);
+nc('chla_time') = tlen;
+nc{'chla_time'} = ncdouble('chla_time') ;
+nc{'CHLA'} = ncdouble('chla_time','s_rho','eta_rho','xi_rho') ;
+%
+nc{'chla_time'}.long_name = ncchar('time for chlorophyll');
+nc{'chla_time'}.long_name = 'time for chlorophyll';
+nc{'chla_time'}.units = ncchar('day');
+nc{'chla_time'}.units = 'day';
+if cycle~=0
+ nc{'chla_time'}.cycle_length = cycle;
+end
+%
+nc{'CHLA'}.long_name = ncchar('Chlorophyll');
+nc{'CHLA'}.long_name = 'Chlorophyll';
+nc{'CHLA'}.units = ncchar('mg C');
+nc{'CHLA'}.units = 'mg C';
+nc{'CHLA'}.fields = ncchar('CHLA, scalar, series');
+nc{'CHLA'}.fields = 'CHLA, scalar, series';
+%
+%endef(nc);
+%
+% Record the time
+%
+nc{'chla_time'}(:)=t*30; % if time in month in the dataset !!!
+%
+% Get the missing values
+%
+missval=ncseas{'chlorophyll'}.missing_value(:);
+%
+% loop on time
+%
+for l=1:tlen
+disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
+%
+% extrapole the annual dataset on the horizontal croco grid
+%
+ disp('Add_chla: horizontal interpolation of surface data')
+ surfchla=squeeze(ncseas{'chlorophyll'}(l,jmin:jmax,imin:imax));
+ surfchla=get_missing_val(x,y,surfchla,missval,Roa,default);
+ surfchlacroco=interp2(x,y,surfchla,lon,lat);
+%
+% extrapole the chlorophyll on the vertical
+%
+ zcroco=zlevs(h,0.*h,theta_s,theta_b,Tcline,N,'r',vtransform);
+ disp(['Add_chla: vertical ',...
+ 'extrapolation of chlorophyll'])
+ chlacroco=extr_chlo(surfchlacroco,zcroco);
+ nc{'CHLA'}(l,:,:,:)=chlacroco;
+end
+close(nc);
+close(ncseas);
+chla=squeeze(chlacroco(N,:,:));
+return
diff --git a/Preprocessing_tools/Bio/add_dic.m b/Preprocessing_tools/Bio/add_dic.m
index 9864ee62..88cace3b 100644
--- a/Preprocessing_tools/Bio/add_dic.m
+++ b/Preprocessing_tools/Bio/add_dic.m
@@ -122,4 +122,23 @@ if (makeclim)
nc{'dic_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
+%
+% Same thing 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)
+
return
diff --git a/Preprocessing_tools/Bio/add_doc.m b/Preprocessing_tools/Bio/add_doc.m
index e6374601..d8c3e30f 100644
--- a/Preprocessing_tools/Bio/add_doc.m
+++ b/Preprocessing_tools/Bio/add_doc.m
@@ -122,4 +122,23 @@ if (makeclim)
nc{'doc_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
+%
+% Same thing for the Initial file
+%
+%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{'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';
+%
+%endef(nc);
+%close(nc)
+
return
diff --git a/Preprocessing_tools/Bio/add_no3.m b/Preprocessing_tools/Bio/add_no3.m
index d8b53361..1670583b 100644
--- a/Preprocessing_tools/Bio/add_no3.m
+++ b/Preprocessing_tools/Bio/add_no3.m
@@ -1,161 +1,185 @@
-function add_no3(oafile, climfile, inifile, gridfile, seas_datafile, ...
- ann_datafile, cycle, makeoa, makeclim);
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- %
- % function [longrd,latgrd,no3]=add_no3(climfile,gridfile,...
- % seas_datafile,ann_datafile,...
- % cycle);
- %
- % Add nitrate (mMol N m-3) in a CROCO climatology file
- % take seasonal data for the upper levels and annual data for the
- % lower levels
- %
- % input:
- %
- % climfile : croco climatology file to process (netcdf)
- % gridfile : 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
- %
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- %
- % Read in the grid
- %
- nc = netcdf(gridfile, 'r');
- hmax = max(max(nc{'h'}(:)));
- close(nc);
- %
- % read in the datafiles
- %
- nc = netcdf(seas_datafile, 'r');
- t = nc{'T'}(:);
- t;
- close(nc)
- nc = netcdf(ann_datafile, 'r');
- zno3 = nc{'Z'}(:);
- kmax = max(find(zno3 < hmax)) - 1;
- zno3 = zno3(1:kmax);
- size(zno3);
- close(nc)
- %
- % open the OA file
- %
- if (makeoa)
- disp('Add_no3: creating variables and attributes for the OA file')
- nc = netcdf(oafile, 'write');
- % redef(nc);
+function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
+ ann_datafile,cycle,makeoa,makeclim);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% function [longrd,latgrd,no3]=add_no3(climfile,gridfile,...
+% seas_datafile,ann_datafile,...
+% cycle);
+%
+% Add nitrate (mMol N m-3) in a CROCO climatology file
+% take seasonal data for the upper levels and annual data for the
+% lower levels
+%
+% input:
+%
+% climfile : croco climatology file to process (netcdf)
+% gridfile : 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
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Read in the grid
+%
+nc=netcdf(gridfile,'r');
+hmax=max(max(nc{'h'}(:)));
+close(nc);
+%
+% read in the datafiles
+%
+nc=netcdf(seas_datafile,'r');
+t=nc{'T'}(:);
+t;
+close(nc)
+nc=netcdf(ann_datafile,'r');
+zno3=nc{'Z'}(:);
+kmax=max(find(zno3<hmax))-1;
+zno3=zno3(1:kmax);
+%disp('Size zno3=')
+size(zno3);
+close(nc)
+%
+% open the OA file
+%
+if (makeoa)
+ disp('Add_no3: creating variables and attributes for the OA file')
+ nc=netcdf(oafile,'write');
+ % redef(nc);
+
+ %Create Dimensions
+ nc('no3_time') = length(t);
+ %Create Variable
+ nc{'no3_time'} = ncdouble('no3_time') ;
+%
+%%
+%
+ %Create Dimensions
+ nc('Zno3') = length(zno3);
+ %Create Variable
+ nc{'Zno3'} = ncdouble('Zno3') ;
+%
+%%
+%
+ %Create Variable
+ nc{'NO3'} = ncdouble('no3_time','Zno3','eta_rho','xi_rho') ;
+%
+%%
+%
+ %Create Attribute
+
+ nc{'no3_time'}.long_name = ncchar('time for nitrate');
+ nc{'no3_time'}.long_name = 'time for nitrate';
+ nc{'no3_time'}.units = ncchar('day');
+ nc{'no3_time'}.units = 'day';
+ if cycle~=0
+ nc{'no3_time'}.cycle_length = cycle;
+ end
+%%%
+ nc{'Zno3'}.long_name = ncchar('Depth for NO3');
+ nc{'Zno3'}.long_name = 'Depth for NO3';
+ nc{'Zno3'}.units = ncchar('m');
+ nc{'Zno3'}.units = 'm';
+%%%
+ 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{'NO3'}.fields = ncchar('NO3, scalar, series');
+ nc{'NO3'}.fields = 'NO3, scalar, series';
+%%%
+%% endef(nc);
+%
+%% Write variables
+%% record depth and time and close
+%
+ nc{'no3_time'}(:)=t*30; % if time in month in the dataset !!!
+ nc{'Zno3'}(:)=zno3;
+ close(nc)
+end
+%
+% Same thing for the Clim file
+%
+if (makeclim)
+ disp('Add_no3: creating variables and attributes for the Climatology file')
+%
+% open the clim file
+%
+ nc=netcdf(climfile,'write');
+ % redef(nc);
+ nc('no3_time') = length(t);;
+ nc{'no3_time'} = ncdouble('no3_time') ;
+ nc{'NO3'} = ncdouble('no3_time','s_rho','eta_rho','xi_rho') ;
+%
+ nc{'no3_time'}.long_name = ncchar('time for nitrate');
+ nc{'no3_time'}.long_name = 'time for nitrate';
+ nc{'no3_time'}.units = ncchar('day');
+ nc{'no3_time'}.units = 'day';
+ if cycle~=0
+ nc{'no3_time'}.cycle_length = cycle;
+ end
+%
+ 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{'NO3'}.fields = ncchar('NO3, scalar, series');
+ nc{'NO3'}.fields = 'NO3, scalar, series';
+%
+%% endef(nc);
+%
+% record the time and close
+%
+ nc{'no3_time'}(:)=t*30; % if time in month in the dataset !!!
+ close(nc)
+end
+%
+% Same thing 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)
- %Create Dimensions
- nc('no3_time') = length(t);
- %Create Variable
- nc{'no3_time'} = ncdouble('no3_time');
- %
- %Create Dimensions
- nc('Zno3') = length(zno3);
- %Create Variable
- nc{'Zno3'} = ncdouble('Zno3');
- %
- %Create Variable
- nc{'NO3'} = ncdouble('no3_time', 'Zno3', 'eta_rho', 'xi_rho');
- %
- %Create Attribute
- nc{'no3_time'}.long_name = ncchar('time for nitrate');
- nc{'no3_time'}.long_name = 'time for nitrate';
- nc{'no3_time'}.units = ncchar('day');
- nc{'no3_time'}.units = 'day';
-
- if cycle ~= 0
- nc{'no3_time'}.cycle_length = cycle;
- end
-
- %%%
- nc{'Zno3'}.long_name = ncchar('Depth for NO3');
- nc{'Zno3'}.long_name = 'Depth for NO3';
- nc{'Zno3'}.units = ncchar('m');
- nc{'Zno3'}.units = 'm';
- %%%
- 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{'NO3'}.fields = ncchar('NO3, scalar, series');
- nc{'NO3'}.fields = 'NO3, scalar, series';
- %%%
- %% endef(nc);
- %
- %% Write variables record depth and time and close
- %
- nc{'no3_time'}(:) = t * 30; % if time in month in the dataset !!!
- nc{'Zno3'}(:) = zno3;
- close(nc)
- end
-
- %
- % Same thing for the Clim file
- %
- if (makeclim)
- disp('Add_no3: creating variables and attributes for the Climatology file')
- %
- % open the clim file
- %
- nc = netcdf(climfile, 'write');
- % redef(nc);
- nc('no3_time') = length(t);;
- nc{'no3_time'} = ncdouble('no3_time');
- nc{'NO3'} = ncdouble('no3_time', 's_rho', 'eta_rho', 'xi_rho');
- %
- nc{'no3_time'}.long_name = ncchar('time for nitrate');
- nc{'no3_time'}.long_name = 'time for nitrate';
- nc{'no3_time'}.units = ncchar('day');
- nc{'no3_time'}.units = 'day';
-
- if cycle ~= 0
- nc{'no3_time'}.cycle_length = cycle;
- end
- %
- 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{'NO3'}.fields = ncchar('NO3, scalar, series');
- nc{'NO3'}.fields = 'NO3, scalar, series';
- %
- %% endef(nc);
- %
- % record the time and close
- %
- nc{'no3_time'}(:) = t * 30; % if time in month in the dataset !!!
- close(nc)
- end
- return
+return
diff --git a/Preprocessing_tools/Bio/add_o2.m b/Preprocessing_tools/Bio/add_o2.m
index 0ac3e045..86321ce1 100644
--- a/Preprocessing_tools/Bio/add_o2.m
+++ b/Preprocessing_tools/Bio/add_o2.m
@@ -1,131 +1,126 @@
-function add_o2(oafile, climfile, inifile, gridfile, month_datafile, ...
- ann_datafile, cycle, makeoa, makeclim);
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- %
- % function [longrd,latgrd,o2]=add_o2(climfile,gridfile,...
- % month_datafile,ann_datafile,...
- % cycle);
- %
- % pierrick 2001
- %
- % Add oxygen (mMol 0 m-3) in a CROCO climatology file
- % take monthly data for the upper levels and annual data for the
- % lower levels
- %
- % input:
- %
- % climfile : croco climatology file to process (netcdf)
- % gridfile : croco grid file (netcdf)
- % month_datafile : regular longitude - latitude - z monthly 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,o2] : surface field to plot (as an illustration)
- %
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- %
- % Read in the grid
- %
- nc = netcdf(gridfile, 'r');
- hmax = max(max(nc{'h'}(:)));
- close(nc);
- %
- % read in the datafiles
- %
- nc = netcdf(month_datafile, 'r');
- t = nc{'T'}(:);
- close(nc)
- nc = netcdf(ann_datafile, 'r');
- zo2 = nc{'Z'}(:);
- kmax = max(find(zo2 < hmax)) - 1;
- zo2 = zo2(1:kmax);
- close(nc)
- %
- % open the OA file
- %
- if (makeoa)
- disp('Add_o2: creating variables and attributes for the OA file')
- nc = netcdf(oafile, 'write');
- %% redef(nc);
- nc('o2_time') = length(t);
- nc{'o2_time'} = ncdouble('o2_time');
- nc('Zo2') = length(zo2);
- nc{'Zo2'} = ncdouble('Zo2');
- nc{'O2'} = ncdouble('o2_time', 'Zo2', 'eta_rho', 'xi_rho');
- %
- nc{'o2_time'}.long_name = ncchar('time for oxygen');
- nc{'o2_time'}.long_name = 'time for oxygen';
- nc{'o2_time'}.units = ncchar('day');
- nc{'o2_time'}.units = 'day';
+function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
+ ann_datafile,cycle,makeoa,makeclim);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% function [longrd,latgrd,o2]=add_o2(climfile,gridfile,...
+% month_datafile,ann_datafile,...
+% cycle);
+%
+% pierrick 2001
+%
+% Add oxygen (mMol 0 m-3) in a CROCO climatology file
+% take monthly data for the upper levels and annual data for the
+% lower levels
+%
+% input:
+%
+% climfile : croco climatology file to process (netcdf)
+% gridfile : croco grid file (netcdf)
+% month_datafile : regular longitude - latitude - z monthly 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,o2] : surface field to plot (as an illustration)
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Read in the grid
+%
+nc=netcdf(gridfile,'r');
+hmax=max(max(nc{'h'}(:)));
+close(nc);
+%
+% read in the datafiles
+%
+nc=netcdf(month_datafile,'r');
+t=nc{'T'}(:);
+close(nc)
+nc=netcdf(ann_datafile,'r');
+zo2=nc{'Z'}(:);
+kmax=max(find(zo2<hmax))-1;
+zo2=zo2(1:kmax);
+close(nc)
+%
+% open the OA file
+%
+if (makeoa)
+ disp('Add_o2: creating variables and attributes for the OA file')
+ nc=netcdf(oafile,'write');
+%% redef(nc);
+ nc('o2_time') = length(t);
+ nc{'o2_time'} = ncdouble('o2_time') ;
+ nc('Zo2') = length(zo2);
+ nc{'Zo2'} = ncdouble('Zo2') ;
+ nc{'O2'} = ncdouble('o2_time','Zo2','eta_rho','xi_rho') ;
+%
+ nc{'o2_time'}.long_name = ncchar('time for oxygen');
+ nc{'o2_time'}.long_name = 'time for oxygen';
+ nc{'o2_time'}.units = ncchar('day');
+ nc{'o2_time'}.units = 'day';
+ if cycle~=0
+ nc{'o2_time'}.cycle_length = cycle;
+ end
+%
+ nc{'Zo2'}.long_name = ncchar('Depth for O2');
+ nc{'Zo2'}.long_name = 'Depth for O2';
+ nc{'Zo2'}.units = ncchar('m');
+ nc{'Zo2'}.units = 'm';
+%
+ 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';
+ nc{'O2'}.fields = ncchar('O2, scalar, series');
+ nc{'O2'}.fields = 'O2, scalar, series';
+%
+%% endef(nc);
+%
+% record depth and time and close
+%
+ nc{'o2_time'}(:)=t*30; % ojo aqui quite *30 % if time in month in the dataset !!!
+ nc{'Zo2'}(:)=squeeze(zo2);
+ close(nc)
+end
+%
+% Same thing for the Clim file
+%
+if (makeclim)
+ disp('Add_o2: creating variables and attributes for the Climatology file')
+%
+% open the clim file
+%
+ nc=netcdf(climfile,'write');
+ %% redef(nc);
+ nc('o2_time') = length(t);
+ nc{'o2_time'} = ncdouble('o2_time') ;
+ nc{'O2'} = ncdouble('o2_time','s_rho','eta_rho','xi_rho') ;
+%
+ nc{'o2_time'}.long_name = ncchar('time for oxygen');
+ nc{'o2_time'}.long_name = 'time for oxygen';
+ nc{'o2_time'}.units = ncchar('day');
+ nc{'o2_time'}.units = 'day';
+ if cycle~=0
+ nc{'o2_time'}.cycle_length = cycle;
+ end
+%
+ 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';
+ nc{'O2'}.fields = ncchar('O2, scalar, series');
+ nc{'O2'}.fields = 'O2, scalar, series';
+%
+%% endef(nc);
+%
+% record the time and close
+%
+ nc{'o2_time'}(:,:)=t*30; % if time in month in the dataset !!!
+ close(nc)
+end
- if cycle ~= 0
- nc{'o2_time'}.cycle_length = cycle;
- end
-
- %
- nc{'Zo2'}.long_name = ncchar('Depth for O2');
- nc{'Zo2'}.long_name = 'Depth for O2';
- nc{'Zo2'}.units = ncchar('m');
- nc{'Zo2'}.units = 'm';
- %
- 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';
- nc{'O2'}.fields = ncchar('O2, scalar, series');
- nc{'O2'}.fields = 'O2, scalar, series';
- %
- %% endef(nc);
- %
- % record depth and time and close
- %
- nc{'o2_time'}(:) = t * 30; % ojo aqui quite *30 % if time in month in the dataset !!!
- nc{'Zo2'}(:) = squeeze(zo2);
- close(nc)
- end
-
- %
- % Same thing for the Clim file
- %
- if (makeclim)
- disp('Add_o2: creating variables and attributes for the Climatology file')
- %
- % open the clim file
- %
- nc = netcdf(climfile, 'write');
- %% redef(nc);
- nc('o2_time') = length(t);
- nc{'o2_time'} = ncdouble('o2_time');
- nc{'O2'} = ncdouble('o2_time', 's_rho', 'eta_rho', 'xi_rho');
- %
- nc{'o2_time'}.long_name = ncchar('time for oxygen');
- nc{'o2_time'}.long_name = 'time for oxygen';
- nc{'o2_time'}.units = ncchar('day');
- nc{'o2_time'}.units = 'day';
-
- if cycle ~= 0
- nc{'o2_time'}.cycle_length = cycle;
- end
-
- %
- 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';
- nc{'O2'}.fields = ncchar('O2, scalar, series');
- nc{'O2'}.fields = 'O2, scalar, series';
- %
- %% endef(nc);
- %
- % record the time and close
- %
- nc{'o2_time'}(:, :) = t * 30; % if time in month in the dataset !!!
- close(nc)
- end
-
- return
+return
diff --git a/Preprocessing_tools/make_biol.m b/Preprocessing_tools/Bio/make_biol.m
similarity index 100%
rename from Preprocessing_tools/make_biol.m
rename to Preprocessing_tools/Bio/make_biol.m
diff --git a/Preprocessing_tools/nevis_2003.m b/Preprocessing_tools/Bio/nevis_2003.m
similarity index 100%
rename from Preprocessing_tools/nevis_2003.m
rename to Preprocessing_tools/Bio/nevis_2003.m
diff --git a/Preprocessing_tools/add_Sphyto_Lphyto.m b/Preprocessing_tools/add_Sphyto_Lphyto.m
deleted file mode 100644
index 95a2eade..00000000
--- a/Preprocessing_tools/add_Sphyto_Lphyto.m
+++ /dev/null
@@ -1,112 +0,0 @@
-function add_Sphyto_Lphyto(climfile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_phyto(climfile);
-%
-% Add phytoplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the climatology file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations.
-%
-% phyto = 0.5 * chla
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-%
-% 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
-%
-% Updated 14/10/14 Andres Sepulveda (DGEO) Octave compatibility
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta1=0.1;
-theta2=0.4;
-%
-disp('Add_Sphyto_Lphyto: creating variable and attribute')
-%
-% open the clim file
-%
-nc=netcdf(climfile,'write');
-time= nc{'chla_time'}(:);
-cycle= nc{'chla_time'}.cycle_length(:);
-tlen=length(time);
-%
-%%redef(nc);
-%
-nc('sphyto_time') = tlen;
-nc{'sphyto_time'} = ncdouble('sphyto_time') ;
-nc{'SPHYTO'} = ncdouble('sphyto_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'sphyto_time'}.long_name = ncchar('time for Small Phytoplankton');
-nc{'sphyto_time'}.long_name = 'time for Small Phytoplankton';
-nc{'sphyto_time'}.units = ncchar('day');
-nc{'sphyto_time'}.units = 'day';
-if cycle~=0
- nc{'sphyto_time'}.cycle_length = cycle;
-end
-%
-nc('lphyto_time') = tlen;
-nc{'lphyto_time'} = ncdouble('lphyto_time') ;
-nc{'LPHYTO'} = ncdouble('lphyto_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'lphyto_time'}.long_name = ncchar('time for Large Phytoplankton');
-nc{'lphyto_time'}.long_name = 'time for Large Phytoplankton';
-nc{'lphyto_time'}.units = ncchar('day');
-nc{'lphyto_time'}.units = 'day';
-if cycle~=0
- nc{'lphyto_time'}.cycle_length = cycle;
-end
-%
-nc{'SPHYTO'}.long_name = ncchar('Small Phytoplankton');
-nc{'SPHYTO'}.long_name = 'Small Phytoplankton';
-nc{'SPHYTO'}.units = ncchar('mMol N m-3');
-nc{'SPHYTO'}.units = 'mMol N m-3';
-nc{'SPHYTO'}.fields = ncchar('SPHYTO, scalar, series');
-nc{'SPHYTO'}.fields = 'SPHYTO, scalar, series';
-%
-nc{'LPHYTO'}.long_name = ncchar('Large Phytoplankton');
-nc{'LPHYTO'}.long_name = 'Large Phytoplankton';
-nc{'LPHYTO'}.units = ncchar('mMol N m-3');
-nc{'LPHYTO'}.units = 'mMol N m-3';
-nc{'LPHYTO'}.fields = ncchar('LPHYTO, scalar, series');
-nc{'LPHYTO'}.fields = 'LPHYTO, scalar, series';
-%
-%%endef(nc);
-%
-% record the time
-%
-nc{'sphyto_time'}(:)=time;
-nc{'lphyto_time'}(:)=time;
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'SPHYTO'}(l,:,:,:)=theta1*squeeze(nc{'CHLA'}(l,:,:,:));
- nc{'LPHYTO'}(l,:,:,:)=theta2*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
-
diff --git a/Preprocessing_tools/add_Szoo_Lzoo.m b/Preprocessing_tools/add_Szoo_Lzoo.m
deleted file mode 100644
index 96bc091c..00000000
--- a/Preprocessing_tools/add_Szoo_Lzoo.m
+++ /dev/null
@@ -1,112 +0,0 @@
-function add_Szoo_Lzoo(climfile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_zoo(climfile);
-%
-% Add zooplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the climatology file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations (Gruber et al., 2005)
-%
-% zoo = 0.2 * chla
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-%
-% 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
-%
-% Updated 2005 by Patrick Marchesiello (IRD)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta1=0.2;
-theta2=0.3;
-%
-disp('Add_Szoo_Lzoo: creating variable and attribute')
-%
-% open the clim file
-%
-nc=netcdf(climfile,'write');
-time= nc{'chla_time'}(:);
-cycle= nc{'chla_time'}.cycle_length(:);
-tlen=length(time);
-%
-%%redef(nc);
-%
-nc('szoo_time') = tlen;
-nc{'szoo_time'} = ncdouble('szoo_time') ;
-nc{'SZOO'} = ncdouble('szoo_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'szoo_time'}.long_name = ncchar('time for Small Zooplankton');
-nc{'szoo_time'}.long_name = 'time for Small Zooplankton';
-nc{'szoo_time'}.units = ncchar('day');
-nc{'szoo_time'}.units = 'day';
-if cycle~=0
- nc{'szoo_time'}.cycle_length = cycle;
-end
-%
-nc('lzoo_time') = tlen;
-nc{'lzoo_time'} = ncdouble('lzoo_time') ;
-nc{'LZOO'} = ncdouble('lzoo_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'lzoo_time'}.long_name = ncchar('time for Large Zooplankton');
-nc{'lzoo_time'}.long_name = 'time for Large Zooplankton';
-nc{'lzoo_time'}.units = ncchar('day');
-nc{'lzoo_time'}.units = 'day';
-if cycle~=0
- nc{'lzoo_time'}.cycle_length = cycle;
-end
-%
-nc{'SZOO'}.long_name = ncchar('Small Zooplankton');
-nc{'SZOO'}.long_name = 'Small Zooplankton';
-nc{'SZOO'}.units = ncchar('mMol N m-3');
-nc{'SZOO'}.units = 'mMol N m-3';
-nc{'SZOO'}.fields = ncchar('SZOO, scalar, series');
-nc{'SZOO'}.fields = 'SZOO, scalar, series';
-%
-nc{'LZOO'}.long_name = ncchar('Large Zooplankton');
-nc{'LZOO'}.long_name = 'Large Zooplankton';
-nc{'LZOO'}.units = ncchar('mMol N m-3');
-nc{'LZOO'}.units = 'mMol N m-3';
-nc{'LZOO'}.fields = ncchar('LZOO, scalar, series');
-nc{'LZOO'}.fields = 'LZOO, scalar, series';
-%
-%%endef(nc);
-%
-% record the time
-%
-nc{'szoo_time'}(:)=time;
-nc{'lzoo_time'}(:)=time;
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'SZOO'}(l,:,:,:)=theta1*squeeze(nc{'CHLA'}(l,:,:,:));
- nc{'LZOO'}(l,:,:,:)=theta2*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
-
diff --git a/Preprocessing_tools/add_bry_bioebus.m b/Preprocessing_tools/add_bry_bioebus.m
deleted file mode 100644
index 6938dafe..00000000
--- a/Preprocessing_tools/add_bry_bioebus.m
+++ /dev/null
@@ -1,372 +0,0 @@
-function add_bry_bioebus(bryname,obc,time_no3,time_o2,time_zoo,time_phyto,time_chla,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_bry_bioebus(bryname,grdname,title,obc...
-% theta_s,theta_b,hc,N,...
-% time,cycle,clobber);
-%
-% This function create the header of a Netcdf climatology
-% file.
-%
-% Input:
-%
-% bryname Netcdf climatology file name (character string).
-% obc open boundaries flag (1=open , [S E N W]).
-% time time.(vector)
-% cycle Length (days) for cycling the climatology.(Real)
-% clobber Switch to allow or not writing over an existing
-% file.(character string)
-%
-% 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
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% Gildas Cambon, IRD, 2011 %
-% Gildas Cambon, IRD, 2013 : Add oxygen processing %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding BIOEBUS BGC data into file : ',bryname])
-disp(' ')
-%
-% Redefine the boundary file
-%
-nc = netcdf(bryname,clobber);
-%%result = redef(nc);
-%
-% Create dimenPHYTOons
-%
-nc('no3_time') = length(time_no3);
-nc('o2_time') = length(time_o2);
-nc('chla_time') = length(time_chla);
-nc('sphyto_time') = length(time_phyto);
-nc('lphyto_time') = length(time_phyto);
-nc('szoo_time') = length(time_zoo);
-nc('lzoo_time') = length(time_zoo);
-nc('one') = 1;
-%
-% Create variables and attributes
-%
-nc{'no3_time'} = ncdouble('no3_time') ;
-nc{'no3_time'}.long_name = ncchar('time for NO3 climatology')
-nc{'no3_time'}.long_name = 'time for NO3 climatology';
-nc{'no3_time'}.units = ncchar('day');
-nc{'no3_time'}.units = 'day';
-nc{'no3_time'}.cycle_length = cycle;%
-%
-nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology')
-nc{'o2_time'}.long_name = 'time for O2 climatology';
-nc{'o2_time'}.units = ncchar('day');
-nc{'o2_time'}.units = 'day';
-nc{'o2_time'}.cycle_length = cycle;
-%
-nc{'chla_time'} = ncdouble('chla_time') ;
-nc{'chla_time'}.long_name = ncchar('time for CHLA climatology');
-nc{'chla_time'}.long_name = 'time for CHLA climatology';
-nc{'chla_time'}.units = ncchar('day');
-nc{'chla_time'}.units = 'day';
-nc{'chla_time'}.cycle_length = cycle;%
-%
-nc{'sphyto_time'} = ncdouble('sphyto_time') ;
-nc{'sphyto_time'}.long_name = ncchar('time for SPHYTO climatology');
-nc{'sphyto_time'}.long_name = 'time for SPHYTO climatology';
-nc{'sphyto_time'}.units = ncchar('day');
-nc{'sphyto_time'}.units = 'day';
-nc{'sphyto_time'}.cycle_length = cycle;%
-%
-nc{'lphyto_time'} = ncdouble('lphyto_time') ;
-nc{'lphyto_time'}.long_name = ncchar('time for LPHYTO climatology');
-nc{'lphyto_time'}.long_name = 'time for LPHYTO climatology';
-nc{'lphyto_time'}.units = ncchar('day');
-nc{'lphyto_time'}.units = 'day';
-nc{'lphyto_time'}.cycle_length = cycle;%
-%
-nc{'szoo_time'} = ncdouble('szoo_time') ;
-nc{'szoo_time'}.long_name = ncchar('time for SZOO climatology');
-nc{'szoo_time'}.long_name = 'time for SZOO climatology';
-nc{'szoo_time'}.units = ncchar('day');
-nc{'szoo_time'}.units = 'day';
-nc{'szoo_time'}.cycle_length = cycle;%
-%
-nc{'lzoo_time'} = ncdouble('lzoo_time') ;
-nc{'lzoo_time'}.long_name = ncchar('time for LZOO climatology');
-nc{'lzoo_time'}.long_name = 'time for LZOO climatology';
-nc{'lzoo_time'}.units = ncchar('day');
-nc{'lzoo_time'}.units = 'day';
-nc{'lzoo_time'}.cycle_length = cycle;%
-%
-%
-if obc(1)==1
-%
-% Southern boundary
-%
- disp('Process Southern boundary')
-
- nc{'NO3_south'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol O m-3');
- nc{'O2_south'}.units = 'mMol N m-3';
- %
- nc{'CHLA_south'} = ncdouble('chla_time','s_rho','xi_rho') ;
- nc{'CHLA_south'}.long_name = ncchar('southern boundary CHLA');
- nc{'CHLA_south'}.long_name = 'southern boundary CHLA';
- nc{'CHLA_south'}.units = ncchar('mMol N m-3');
- nc{'CHLA_south'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_south'} = ncdouble('sphyto_time','s_rho','xi_rho') ;
- nc{'SPHYTO_south'}.long_name = ncchar('southern boundary SPHYTO');
- nc{'SPHYTO_south'}.long_name = 'southern boundary SPHYTO';
- nc{'SPHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_south'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_south'} = ncdouble('lphyto_time','s_rho','xi_rho') ;
- nc{'LPHYTO_south'}.long_name = ncchar('southern boundary LPHYTO');
- nc{'LPHYTO_south'}.long_name = 'southern boundary LPHYTO';
- nc{'LPHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_south'}.units = 'mMol N m-3';
-%
- nc{'SZOO_south'} = ncdouble('szoo_time','s_rho','xi_rho') ;
- nc{'SZOO_south'}.long_name = ncchar('southern boundary SZOO');
- nc{'SZOO_south'}.long_name = 'southern boundary SZOO';
- nc{'SZOO_south'}.units = ncchar('mMol N m-3');
- nc{'SZOO_south'}.units = 'mMol N m-3';
-%
- nc{'LZOO_south'} = ncdouble('lzoo_time','s_rho','xi_rho') ;
- nc{'LZOO_south'}.long_name = ncchar('southern boundary LZOO');
- nc{'LZOO_south'}.long_name = 'southern boundary LZOO';
- nc{'LZOO_south'}.units = ncchar('mMol N m-3');
- nc{'LZOO_south'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- disp('Process Eastern boundary')
-
- nc{'NO3_east'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol O m-3');
- nc{'O2_east'}.units = 'mMol N m-3';
- %
- nc{'CHLA_east'} = ncdouble('chla_time','s_rho','eta_rho') ;
- nc{'CHLA_east'}.long_name = ncchar('eastern boundary CHLA');
- nc{'CHLA_east'}.long_name = 'eastern boundary CHLA';
- nc{'CHLA_east'}.units = ncchar('mMol N m-3');
- nc{'CHLA_east'}.units = 'mMol N m-3';
-%
- nc{'SZOO_east'} = ncdouble('szoo_time','s_rho','eta_rho') ;
- nc{'SZOO_east'}.long_name = ncchar('eastern boundary SZOO');
- nc{'SZOO_east'}.long_name = 'eastern boundary SZOO';
- nc{'SZOO_east'}.units = ncchar('mMol N m-3');
- nc{'SZOO_east'}.units = 'mMol N m-3';
-%
- nc{'LZOO_east'} = ncdouble('lzoo_time','s_rho','eta_rho') ;
- nc{'LZOO_east'}.long_name = ncchar('eastern boundary LZOO');
- nc{'LZOO_east'}.long_name = 'eastern boundary LZOO';
- nc{'LZOO_east'}.units = ncchar('mMol N m-3');
- nc{'LZOO_east'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_east'} = ncdouble('sphyto_time','s_rho','eta_rho') ;
- nc{'SPHYTO_east'}.long_name = ncchar('eastern boundary SPHYTO');
- nc{'SPHYTO_east'}.long_name = 'eastern boundary SPHYTO';
- nc{'SPHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_east'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_east'} = ncdouble('lphyto_time','s_rho','eta_rho') ;
- nc{'LPHYTO_east'}.long_name = ncchar('eastern boundary LPHYTO');
- nc{'LPHYTO_east'}.long_name = 'eastern boundary LPHYTO';
- nc{'LPHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- disp('Process Northern boundary')
-
- nc{'NO3_north'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol O m-3');
- nc{'O2_north'}.units = 'mMol N m-3';
-%
- nc{'CHLA_north'} = ncdouble('chla_time','s_rho','xi_rho') ;
- nc{'CHLA_north'}.long_name = ncchar('northern boundary CHLA');
- nc{'CHLA_north'}.long_name = 'northern boundary CHLA';
- nc{'CHLA_north'}.units = ncchar('mMol N m-3');
- nc{'CHLA_north'}.units = 'mMol N m-3';
-%
- nc{'SZOO_north'} = ncdouble('szoo_time','s_rho','xi_rho') ;
- nc{'SZOO_north'}.long_name = ncchar('northern boundary SZOO');
- nc{'SZOO_north'}.long_name = 'northern boundary SZOO';
- nc{'SZOO_north'}.units = ncchar('mMol N m-3');
- nc{'SZOO_north'}.units = 'mMol N m-3';
-%
- nc{'LZOO_north'} = ncdouble('lzoo_time','s_rho','xi_rho') ;
- nc{'LZOO_north'}.long_name = ncchar('northern boundary LZOO');
- nc{'LZOO_north'}.long_name = 'northern boundary LZOO';
- nc{'LZOO_north'}.units = ncchar('mMol N m-3');
- nc{'LZOO_north'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_north'} = ncdouble('sphyto_time','s_rho','xi_rho') ;
- nc{'SPHYTO_north'}.long_name = ncchar('northern boundary SPHYTO');
- nc{'SPHYTO_north'}.long_name = 'northern boundary SPHYTO';
- nc{'SPHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_north'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_north'} = ncdouble('lphyto_time','s_rho','xi_rho') ;
- nc{'LPHYTO_north'}.long_name = ncchar('northern boundary LPHYTO');
- nc{'LPHYTO_north'}.long_name = 'northern boundary LPHYTO';
- nc{'LPHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- disp('Process Western boundary')
-
- nc{'NO3_west'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol O m-3');
- nc{'O2_west'}.units = 'mMol N m-3';
-%
- nc{'CHLA_west'} = ncdouble('chla_time','s_rho','eta_rho') ;
- nc{'CHLA_west'}.long_name = ncchar('western boundary CHLA');
- nc{'CHLA_west'}.long_name = 'western boundary CHLA';
- nc{'CHLA_west'}.units = ncchar('mMol N m-3');
- nc{'CHLA_west'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_west'} = ncdouble('sphyto_time','s_rho','eta_rho') ;
- nc{'SPHYTO_west'}.long_name = ncchar('western boundary SPHYTO');
- nc{'SPHYTO_west'}.long_name = 'western boundary SPHYTO';
- nc{'SPHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_west'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_west'} = ncdouble('lphyto_time','s_rho','eta_rho') ;
- nc{'LPHYTO_west'}.long_name = ncchar('western boundary LPHYTO');
- nc{'LPHYTO_west'}.long_name = 'western boundary LPHYTO';
- nc{'LPHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_west'}.units = 'mMol N m-3';
-%
- nc{'SZOO_west'} = ncdouble('szoo_time','s_rho','eta_rho') ;
- nc{'SZOO_west'}.long_name = ncchar('western boundary SZOO');
- nc{'SZOO_west'}.long_name = 'western boundary SZOO';
- nc{'SZOO_west'}.units = ncchar('mMol N m-3');
- nc{'SZOO_west'}.units = 'mMol N m-3';
-%
- nc{'LZOO_west'} = ncdouble('lzoo_time','s_rho','eta_rho') ;
- nc{'LZOO_west'}.long_name = ncchar('western boundary LZOO');
- nc{'LZOO_west'}.long_name = 'western boundary LZOO';
- nc{'LZOO_west'}.units = ncchar('mMol N m-3');
- nc{'LZOO_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'szoo_time'}(:) = time_zoo;
-nc{'lzoo_time'}(:) = time_zoo;
-nc{'sphyto_time'}(:) = time_phyto;
-nc{'lphyto_time'}(:) = time_phyto;
-nc{'no3_time'}(:) = time_no3;
-nc{'o2_time'}(:) = time_o2;
-nc{'chla_time'}(:) = time_chla;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'CHLA_south'}(:) = 0;
- nc{'SPHYTO_south'}(:) = 0;
- nc{'LPHYTO_south'}(:) = 0;
- nc{'SZOO_south'}(:) = 0;
- nc{'LZOO_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'CHLA_east'}(:) = 0;
- nc{'SPHYTO_east'}(:) = 0;
- nc{'LPHYTO_east'}(:) = 0;
- nc{'SZOO_east'}(:) = 0;
- nc{'LZOO_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'CHLA_north'}(:) = 0;
- nc{'SPHYTO_north'}(:) = 0;
- nc{'LPHYTO_north'}(:) = 0;
- nc{'SZOO_north'}(:) = 0;
- nc{'LZOO_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'CHLA_west'}(:) = 0;
- nc{'SPHYTO_west'}(:) = 0;
- nc{'LPHYTO_west'}(:) = 0;
- nc{'SZOO_west'}(:) = 0;
- nc{'LZOO_west'}(:) = 0;
-end
-close(nc)
-return
-
diff --git a/Preprocessing_tools/add_bry_bioebus_Z.m b/Preprocessing_tools/add_bry_bioebus_Z.m
deleted file mode 100644
index 4a953a06..00000000
--- a/Preprocessing_tools/add_bry_bioebus_Z.m
+++ /dev/null
@@ -1,341 +0,0 @@
-function add_bry_bioebus_Z(zbryname,obc,Z,time_no3,time_o2,time_zoo,time_phyto,time_chla,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% function add_bry_bioebus_Z(zbryname,obc,... %
-% Z,time,cycle,clobber); %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% zbryname Netcdf climatology file name (character string). %
-% obc open boundaries flag (1=open , [S E N W]). %
-% Z Depth of vertical levels.(Vector) %
-% time time.(vector) %
-% cycle Length (days) for cycling the climatology.(Real) %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% Gildas Cambon, IRD/LEGOS, 2013 : Add O2 processing %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding BioEBUS data into file : ',zbryname])
-disp(' ')
-%
-% Create the boundary file
-%
-nc = netcdf(zbryname,clobber);
-%%result = redef(nc);
-%
-% Create dimensions
-%
-nc('no3_time') = length(time_no3);
-nc('o2_time') = length(time_o2);
-nc('chla_time') = length(time_chla);
-nc('szoo_time') = length(time_zoo);
-nc('lzoo_time') = length(time_zoo);
-nc('sphyto_time') = length(time_phyto);
-nc('lphyto_time') = length(time_phyto);
-nc('one') = 1;
-%
-% Create variables and attributes
-%
-nc{'no3_time'} = ncdouble('no3_time') ;
-nc{'no3_time'}.long_name = ncchar('time for NO3 climatology')
-nc{'no3_time'}.long_name = 'time for NO3 climatology';
-nc{'no3_time'}.units = ncchar('day');
-nc{'no3_time'}.units = 'day';
-nc{'no3_time'}.cycle_length = cycle;
-%
-nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology')
-nc{'o2_time'}.long_name = 'time for O2 climatology';
-nc{'o2_time'}.units = ncchar('day');
-nc{'o2_time'}.units = 'day';
-nc{'o2_time'}.cycle_length = cycle;
-%
-nc{'chla_time'} = ncdouble('chla_time') ;
-nc{'chla_time'}.long_name = ncchar('time for CHLA climatology');
-nc{'chla_time'}.long_name = 'time for CHLA climatology';
-nc{'chla_time'}.units = ncchar('day');
-nc{'chla_time'}.units = 'day';
-nc{'chla_time'}.cycle_length = cycle;%
-%
-nc{'sphyto_time'} = ncdouble('sphyto_time') ;
-nc{'sphyto_time'}.long_name = ncchar('time for SPHYTO climatology');
-nc{'sphyto_time'}.long_name = 'time for SPHYTO climatology';
-nc{'sphyto_time'}.units = ncchar('day');
-nc{'sphyto_time'}.units = 'day';
-nc{'sphyto_time'}.cycle_length = cycle;%
-%
-nc{'lphyto_time'} = ncdouble('lphyto_time') ;
-nc{'lphyto_time'}.long_name = ncchar('time for LPHYTO climatology');
-nc{'lphyto_time'}.long_name = 'time for LPHYTO climatology';
-nc{'lphyto_time'}.units = ncchar('day');
-nc{'lphyto_time'}.units = 'day';
-nc{'lphyto_time'}.cycle_length = cycle;%
-%
-nc{'szoo_time'} = ncdouble('szoo_time') ;
-nc{'szoo_time'}.long_name = ncchar('time for SZOO climatology');
-nc{'szoo_time'}.long_name = 'time for SZOO climatology';
-nc{'szoo_time'}.units = ncchar('day');
-nc{'szoo_time'}.units = 'day';
-nc{'szoo_time'}.cycle_length = cycle;
-%
-nc{'lzoo_time'} = ncdouble('lzoo_time') ;
-nc{'lzoo_time'}.long_name = ncchar('time for LZOO climatology');
-nc{'lzoo_time'}.long_name = 'time for LZOO climatology';
-nc{'lzoo_time'}.units = ncchar('day');
-nc{'lzoo_time'}.units = 'day';
-nc{'lzoo_time'}.cycle_length = cycle;
-%
-
-if obc(1)==1
-%
-% Southern boundary
-%
- nc{'NO3_south'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('o2_time','Z','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol O m-3');
- nc{'O2_south'}.units = 'mMol O m-3';
-%
- nc{'CHLA_south'} = ncdouble('chla_time','Z','xi_rho') ;
- nc{'CHLA_south'}.long_name = ncchar('southern boundary CHLA');
- nc{'CHLA_south'}.long_name = 'southern boundary CHLA';
- nc{'CHLA_south'}.units = ncchar('mMol N m-3');
- nc{'CHLA_south'}.units = 'mMol N m-3';
-%
- nc{'SZOO_south'} = ncdouble('szoo_time','Z','xi_rho') ;
- nc{'SZOO_south'}.long_name = ncchar('southern boundary SZOO');
- nc{'SZOO_south'}.long_name = 'southern boundary SZOO';
- nc{'SZOO_south'}.units = ncchar('mMol N m-3');
- nc{'SZOO_south'}.units = 'mMol N m-3';
-%
- nc{'LZOO_south'} = ncdouble('lzoo_time','Z','xi_rho') ;
- nc{'LZOO_south'}.long_name = ncchar('southern boundary LZOO');
- nc{'LZOO_south'}.long_name = 'southern boundary LZOO';
- nc{'LZOO_south'}.units = ncchar('mMol N m-3');
- nc{'LZOO_south'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_south'} = ncdouble('sphyto_time','Z','xi_rho') ;
- nc{'SPHYTO_south'}.long_name = ncchar('southern boundary SPHYTO');
- nc{'SPHYTO_south'}.long_name = 'southern boundary SPHYTO';
- nc{'SPHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_south'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_south'} = ncdouble('lphyto_time','Z','xi_rho') ;
- nc{'LPHYTO_south'}.long_name = ncchar('southern boundary LPHYTO');
- nc{'LPHYTO_south'}.long_name = 'southern boundary LPHYTO';
- nc{'LPHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_south'}.units = 'mMol N m-3';
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- nc{'NO3_east'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','Z','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol O m-3');
- nc{'O2_east'}.units = 'mMol O m-3';
-%
- nc{'CHLA_east'} = ncdouble('chla_time','Z','eta_rho') ;
- nc{'CHLA_east'}.long_name = ncchar('eastern boundary CHLA');
- nc{'CHLA_east'}.long_name = 'eastern boundary CHLA';
- nc{'CHLA_east'}.units = ncchar('mMol N m-3');
- nc{'CHLA_east'}.units = 'mMol N m-3';
-%
- nc{'SZOO_east'} = ncdouble('szoo_time','Z','eta_rho') ;
- nc{'SZOO_east'}.long_name = ncchar('eastern boundary SZOO');
- nc{'SZOO_east'}.long_name = 'eastern boundary SZOO';
- nc{'SZOO_east'}.units = ncchar('mMol N m-3');
- nc{'SZOO_east'}.units = 'mMol N m-3';
-%
- nc{'LZOO_east'} = ncdouble('lzoo_time','Z','eta_rho') ;
- nc{'LZOO_east'}.long_name = ncchar('eastern boundary LZOO');
- nc{'LZOO_east'}.long_name = 'eastern boundary LZOO';
- nc{'LZOO_east'}.units = ncchar('mMol N m-3');
- nc{'LZOO_east'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_east'} = ncdouble('sphyto_time','Z','eta_rho') ;
- nc{'SPHYTO_east'}.long_name = ncchar('eastern boundary SPHYTO');
- nc{'SPHYTO_east'}.long_name = 'eastern boundary SPHYTO';
- nc{'SPHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_east'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_east'} = ncdouble('lphyto_time','Z','eta_rho') ;
- nc{'LPHYTO_east'}.long_name = ncchar('eastern boundary LPHYTO');
- nc{'LPHYTO_east'}.long_name = 'eastern boundary LPHYTO';
- nc{'LPHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- nc{'NO3_north'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','Z','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol O m-3');
- nc{'O2_north'}.units = 'mMol O m-3';
-%
- nc{'CHLA_north'} = ncdouble('chla_time','Z','xi_rho') ;
- nc{'CHLA_north'}.long_name = ncchar('northern boundary CHLA');
- nc{'CHLA_north'}.long_name = 'northern boundary CHLA';
- nc{'CHLA_north'}.units = ncchar('mMol N m-3');
- nc{'CHLA_north'}.units = 'mMol N m-3';
-%
- nc{'SZOO_north'} = ncdouble('szoo_time','Z','xi_rho') ;
- nc{'SZOO_north'}.long_name = ncchar('northern boundary SZOO');
- nc{'SZOO_north'}.long_name = 'northern boundary SZOO';
- nc{'SZOO_north'}.units = ncchar('mMol N m-3');
- nc{'SZOO_north'}.units = 'mMol N m-3';
-%
- nc{'LZOO_north'} = ncdouble('lzoo_time','Z','xi_rho') ;
- nc{'LZOO_north'}.long_name = ncchar('northern boundary LZOO');
- nc{'LZOO_north'}.long_name = 'northern boundary LZOO';
- nc{'LZOO_north'}.units = ncchar('mMol N m-3');
- nc{'LZOO_north'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_north'} = ncdouble('sphyto_time','Z','xi_rho') ;
- nc{'SPHYTO_north'}.long_name = ncchar('northern boundary SPHYTO');
- nc{'SPHYTO_north'}.long_name = 'northern boundary SPHYTO';
- nc{'SPHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_north'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_north'} = ncdouble('lphyto_time','Z','xi_rho') ;
- nc{'LPHYTO_north'}.long_name = ncchar('northern boundary LPHYTO');
- nc{'LPHYTO_north'}.long_name = 'northern boundary LPHYTO';
- nc{'LPHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- nc{'NO3_west'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol O m-3');
- nc{'O2_west'}.units = 'mMol O m-3';
-%
- nc{'CHLA_west'} = ncdouble('chla_time','Z','eta_rho') ;
- nc{'CHLA_west'}.long_name = ncchar('western boundary CHLA');
- nc{'CHLA_west'}.long_name = 'western boundary CHLA';
- nc{'CHLA_west'}.units = ncchar('mMol N m-3');
- nc{'CHLA_west'}.units = 'mMol N m-3';
-%
- nc{'SZOO_west'} = ncdouble('szoo_time','Z','eta_rho') ;
- nc{'SZOO_west'}.long_name = ncchar('western boundary SZOO');
- nc{'SZOO_west'}.long_name = 'western boundary SZOO';
- nc{'SZOO_west'}.units = ncchar('mMol N m-3');
- nc{'SZOO_west'}.units = 'mMol N m-3';
-%
- nc{'LZOO_west'} = ncdouble('lzoo_time','Z','eta_rho') ;
- nc{'LZOO_west'}.long_name = ncchar('western boundary LZOO');
- nc{'LZOO_west'}.long_name = 'western boundary LZOO';
- nc{'LZOO_west'}.units = ncchar('mMol N m-3');
- nc{'LZOO_west'}.units = 'mMol N m-3';
-%
- nc{'SPHYTO_west'} = ncdouble('sphyto_time','Z','eta_rho') ;
- nc{'SPHYTO_west'}.long_name = ncchar('western boundary SPHYTO');
- nc{'SPHYTO_west'}.long_name = 'western boundary SPHYTO';
- nc{'SPHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'SPHYTO_west'}.units = 'mMol N m-3';
-%
- nc{'LPHYTO_west'} = ncdouble('lphyto_time','Z','eta_rho') ;
- nc{'LPHYTO_west'}.long_name = ncchar('western boundary LPHYTO');
- nc{'LPHYTO_west'}.long_name = 'western boundary LPHYTO';
- nc{'LPHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'LPHYTO_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'no3_time'}(:) = time_no3;
-nc{'o2_time'}(:) = time_no3;
-nc{'chla_time'}(:) = time_chla;
-nc{'szoo_time'}(:) = time_zoo;
-nc{'lzoo_time'}(:) = time_zoo;
-nc{'sphyto_time'}(:) = time_phyto;
-nc{'lphyto_time'}(:) = time_phyto;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'CHLA_south'}(:) = 0;
- nc{'SZOO_south'}(:) = 0;
- nc{'LZOO_south'}(:) = 0;
- nc{'SPHYTO_south'}(:) = 0;
- nc{'LPHYTO_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'CHLA_east'}(:) = 0;
- nc{'SZOO_east'}(:) = 0;
- nc{'LZOO_east'}(:) = 0;
- nc{'SPHYTO_east'}(:) = 0;
- nc{'LPHYTO_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'CHLA_north'}(:) = 0;
- nc{'SZOO_north'}(:) = 0;
- nc{'LZOO_north'}(:) = 0;
- nc{'SPHYTO_north'}(:) = 0;
- nc{'LPHYTO_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'CHLA_west'}(:) = 0;
- nc{'SZOO_west'}(:) = 0;
- nc{'LZOO_west'}(:) = 0;
- nc{'SPHYTO_west'}(:) = 0;
- nc{'LPHYTO_west'}(:) = 0;
-end
-close(nc)
-return
-
-
diff --git a/Preprocessing_tools/add_bry_npzd.m b/Preprocessing_tools/add_bry_npzd.m
deleted file mode 100644
index 9cd49e6b..00000000
--- a/Preprocessing_tools/add_bry_npzd.m
+++ /dev/null
@@ -1,298 +0,0 @@
-function add_bry_npzd(bryname,obc,time_no3,time_o2,time_zoo,time_phyto,time_chla,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_bry_bgc(bryname,grdname,title,obc...
-% theta_s,theta_b,hc,N,...
-% time,cycle,clobber);
-%
-% This function create the header of a Netcdf climatology
-% file.
-%
-% Input:
-%
-% bryname Netcdf climatology file name (character string).
-% obc open boundaries flag (1=open , [S E N W]).
-% time time.(vector)
-% cycle Length (days) for cycling the climatology.(Real)
-% clobber Switch to allow or not writing over an existing
-% file.(character string)
-%
-% 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
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% Gildas Cambon, IRD, 2011 %
-% Gildas Cambon, IRD, 2013 : Add oxygen processing %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding NPZD BGC data into file : ',bryname])
-disp(' ')
-%
-% Redefine the boundary file
-%
-nc = netcdf(bryname,clobber);
-%%result = redef(nc);
-%
-% Create dimensions
-%
-nc('no3_time') = length(time_no3);
-nc('o2_time') = length(time_o2);
-nc('chla_time') = length(time_chla);
-nc('phyto_time') = length(time_phyto);
-nc('zoo_time') = length(time_zoo);
-nc('one') = 1;
-%
-% Create variables and attributes
-%
-nc{'no3_time'} = ncdouble('no3_time') ;
-nc{'no3_time'}.long_name = ncchar('time for NO3 climatology')
-nc{'no3_time'}.long_name = 'time for NO3 climatology';
-nc{'no3_time'}.units = ncchar('day');
-nc{'no3_time'}.units = 'day';
-nc{'no3_time'}.cycle_length = cycle;%
-%
-nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology')
-nc{'o2_time'}.long_name = 'time for O2 climatology';
-nc{'o2_time'}.units = ncchar('day');
-nc{'o2_time'}.units = 'day';
-nc{'o2_time'}.cycle_length = cycle;
-%
-nc{'chla_time'} = ncdouble('chla_time') ;
-nc{'chla_time'}.long_name = ncchar('time for CHLA climatology');
-nc{'chla_time'}.long_name = 'time for CHLA climatology';
-nc{'chla_time'}.units = ncchar('day');
-nc{'chla_time'}.units = 'day';
-nc{'chla_time'}.cycle_length = cycle;%
-%
-nc{'phyto_time'} = ncdouble('phyto_time') ;
-nc{'phyto_time'}.long_name = ncchar('time for PHYTO climatology');
-nc{'phyto_time'}.long_name = 'time for PHYTO climatology';
-nc{'phyto_time'}.units = ncchar('day');
-nc{'phyto_time'}.units = 'day';
-nc{'phyto_time'}.cycle_length = cycle;%
-%
-nc{'zoo_time'} = ncdouble('zoo_time') ;
-nc{'zoo_time'}.long_name = ncchar('time for ZOO climatology');
-nc{'zoo_time'}.long_name = 'time for ZOO climatology';
-nc{'zoo_time'}.units = ncchar('day');
-nc{'zoo_time'}.units = 'day';
-nc{'zoo_time'}.cycle_length = cycle;%
-%
-%
-if obc(1)==1
-%
-% Southern boundary
-%
- disp('Process Southern boundary')
-
- nc{'NO3_south'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol O m-3');
- nc{'O2_south'}.units = 'mMol N m-3';
- %
- nc{'CHLA_south'} = ncdouble('chla_time','s_rho','xi_rho') ;
- nc{'CHLA_south'}.long_name = ncchar('southern boundary CHLA');
- nc{'CHLA_south'}.long_name = 'southern boundary CHLA';
- nc{'CHLA_south'}.units = ncchar('mMol N m-3');
- nc{'CHLA_south'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_south'} = ncdouble('phyto_time','s_rho','xi_rho') ;
- nc{'PHYTO_south'}.long_name = ncchar('southern boundary PHYTO');
- nc{'PHYTO_south'}.long_name = 'southern boundary PHYTO';
- nc{'PHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_south'}.units = 'mMol N m-3';
-%
- nc{'ZOO_south'} = ncdouble('zoo_time','s_rho','xi_rho') ;
- nc{'ZOO_south'}.long_name = ncchar('southern boundary ZOO');
- nc{'ZOO_south'}.long_name = 'southern boundary ZOO';
- nc{'ZOO_south'}.units = ncchar('mMol N m-3');
- nc{'ZOO_south'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- disp('Process Esater boundary')
-
- nc{'NO3_east'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol O m-3');
- nc{'O2_east'}.units = 'mMol N m-3';
- %
- nc{'CHLA_east'} = ncdouble('chla_time','s_rho','eta_rho') ;
- nc{'CHLA_east'}.long_name = ncchar('eastern boundary CHLA');
- nc{'CHLA_east'}.long_name = 'eastern boundary CHLA';
- nc{'CHLA_east'}.units = ncchar('mMol N m-3');
- nc{'CHLA_east'}.units = 'mMol N m-3';
-%
- nc{'ZOO_east'} = ncdouble('zoo_time','s_rho','eta_rho') ;
- nc{'ZOO_east'}.long_name = ncchar('eastern boundary ZOO');
- nc{'ZOO_east'}.long_name = 'eastern boundary ZOO';
- nc{'ZOO_east'}.units = ncchar('mMol N m-3');
- nc{'ZOO_east'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_east'} = ncdouble('phyto_time','s_rho','eta_rho') ;
- nc{'PHYTO_east'}.long_name = ncchar('eastern boundary PHYTO');
- nc{'PHYTO_east'}.long_name = 'eastern boundary PHYTO';
- nc{'PHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- disp('Process Northern boundary')
-
- nc{'NO3_north'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol O m-3');
- nc{'O2_north'}.units = 'mMol N m-3';
-%
- nc{'CHLA_north'} = ncdouble('chla_time','s_rho','xi_rho') ;
- nc{'CHLA_north'}.long_name = ncchar('northern boundary CHLA');
- nc{'CHLA_north'}.long_name = 'northern boundary CHLA';
- nc{'CHLA_north'}.units = ncchar('mMol N m-3');
- nc{'CHLA_north'}.units = 'mMol N m-3';
-%
- nc{'ZOO_north'} = ncdouble('zoo_time','s_rho','xi_rho') ;
- nc{'ZOO_north'}.long_name = ncchar('northern boundary ZOO');
- nc{'ZOO_north'}.long_name = 'northern boundary ZOO';
- nc{'ZOO_north'}.units = ncchar('mMol N m-3');
- nc{'ZOO_north'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_north'} = ncdouble('phyto_time','s_rho','xi_rho') ;
- nc{'PHYTO_north'}.long_name = ncchar('northern boundary PHYTO');
- nc{'PHYTO_north'}.long_name = 'northern boundary PHYTO';
- nc{'PHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- disp('Process Western boundary')
-
- nc{'NO3_west'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol O m-3');
- nc{'O2_west'}.units = 'mMol N m-3';
-%
- nc{'CHLA_west'} = ncdouble('chla_time','s_rho','eta_rho') ;
- nc{'CHLA_west'}.long_name = ncchar('western boundary CHLA');
- nc{'CHLA_west'}.long_name = 'western boundary CHLA';
- nc{'CHLA_west'}.units = ncchar('mMol N m-3');
- nc{'CHLA_west'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_west'} = ncdouble('phyto_time','s_rho','eta_rho') ;
- nc{'PHYTO_west'}.long_name = ncchar('western boundary PHYTO');
- nc{'PHYTO_west'}.long_name = 'western boundary PHYTO';
- nc{'PHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_west'}.units = 'mMol N m-3';
-%
- nc{'ZOO_west'} = ncdouble('zoo_time','s_rho','eta_rho') ;
- nc{'ZOO_west'}.long_name = ncchar('western boundary ZOO');
- nc{'ZOO_west'}.long_name = 'western boundary ZOO';
- nc{'ZOO_west'}.units = ncchar('mMol N m-3');
- nc{'ZOO_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'zoo_time'}(:) = time_zoo;
-nc{'phyto_time'}(:) = time_phyto;
-nc{'no3_time'}(:) = time_no3;
-nc{'o2_time'}(:) = time_o2;
-nc{'chla_time'}(:) = time_chla;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'CHLA_south'}(:) = 0;
- nc{'PHYTO_south'}(:) = 0;
- nc{'ZOO_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'CHLA_east'}(:) = 0;
- nc{'PHYTO_east'}(:) = 0;
- nc{'ZOO_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'CHLA_north'}(:) = 0;
- nc{'PHYTO_north'}(:) = 0;
- nc{'ZOO_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'CHLA_west'}(:) = 0;
- nc{'PHYTO_west'}(:) = 0;
- nc{'ZOO_west'}(:) = 0;
-end
-close(nc)
-return
-
diff --git a/Preprocessing_tools/add_bry_npzd_Z.m b/Preprocessing_tools/add_bry_npzd_Z.m
deleted file mode 100644
index c1755f6a..00000000
--- a/Preprocessing_tools/add_bry_npzd_Z.m
+++ /dev/null
@@ -1,267 +0,0 @@
-function add_bry_npzd_Z(zbryname,obc,Z,time_no3,time_o2,time_zoo,time_phyto,time_chla,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% function add_bry_npzd_Z(zbryname,obc,... %
-% Z,time,cycle,clobber); %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% zbryname Netcdf climatology file name (character string). %
-% obc open boundaries flag (1=open , [S E N W]). %
-% Z Depth of vertical levels.(Vector) %
-% time time.(vector) %
-% cycle Length (days) for cycling the climatology.(Real) %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% Gildas Cambon, IRD/LEGOS, 2013 : Add O2 processing %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding NPZD data into file : ',zbryname])
-disp(' ')
-%
-% Create the boundary file
-%
-nc = netcdf(zbryname,clobber);
-%%result = redef(nc);
-%
-% Create dimensions
-%
-nc('no3_time') = length(time_no3);
-nc('o2_time') = length(time_o2);
-nc('chla_time') = length(time_chla);
-nc('zoo_time') = length(time_zoo);
-nc('phyto_time') = length(time_phyto);
-nc('one') = 1;
-%
-% Create variables and attributes
-%
-nc{'no3_time'} = ncdouble('no3_time') ;
-nc{'no3_time'}.long_name = ncchar('time for NO3 climatology')
-nc{'no3_time'}.long_name = 'time for NO3 climatology';
-nc{'no3_time'}.units = ncchar('day');
-nc{'no3_time'}.units = 'day';
-nc{'no3_time'}.cycle_length = cycle;
-%
-nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology')
-nc{'o2_time'}.long_name = 'time for O2 climatology';
-nc{'o2_time'}.units = ncchar('day');
-nc{'o2_time'}.units = 'day';
-nc{'o2_time'}.cycle_length = cycle;
-%
-nc{'chla_time'} = ncdouble('chla_time') ;
-nc{'chla_time'}.long_name = ncchar('time for CHLA climatology');
-nc{'chla_time'}.long_name = 'time for CHLA climatology';
-nc{'chla_time'}.units = ncchar('day');
-nc{'chla_time'}.units = 'day';
-nc{'chla_time'}.cycle_length = cycle;%
-%
-nc{'phyto_time'} = ncdouble('phyto_time') ;
-nc{'phyto_time'}.long_name = ncchar('time for PHYTO climatology');
-nc{'phyto_time'}.long_name = 'time for PHYTO climatology';
-nc{'phyto_time'}.units = ncchar('day');
-nc{'phyto_time'}.units = 'day';
-nc{'phyto_time'}.cycle_length = cycle;%
-%
-nc{'zoo_time'} = ncdouble('zoo_time') ;
-nc{'zoo_time'}.long_name = ncchar('time for ZOO climatology');
-nc{'zoo_time'}.long_name = 'time for ZOO climatology';
-nc{'zoo_time'}.units = ncchar('day');
-nc{'zoo_time'}.units = 'day';
-nc{'zoo_time'}.cycle_length = cycle;
-%
-
-if obc(1)==1
-%
-% Southern boundary
-%
- nc{'NO3_south'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol O m-3');
- nc{'O2_south'}.units = 'mMol O m-3';
-%
- nc{'CHLA_south'} = ncdouble('chla_time','Z','xi_rho') ;
- nc{'CHLA_south'}.long_name = ncchar('southern boundary CHLA');
- nc{'CHLA_south'}.long_name = 'southern boundary CHLA';
- nc{'CHLA_south'}.units = ncchar('mMol N m-3');
- nc{'CHLA_south'}.units = 'mMol N m-3';
-%
- nc{'ZOO_south'} = ncdouble('zoo_time','Z','xi_rho') ;
- nc{'ZOO_south'}.long_name = ncchar('southern boundary ZOO');
- nc{'ZOO_south'}.long_name = 'southern boundary ZOO';
- nc{'ZOO_south'}.units = ncchar('mMol N m-3');
- nc{'ZOO_south'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_south'} = ncdouble('phyto_time','Z','xi_rho') ;
- nc{'PHYTO_south'}.long_name = ncchar('southern boundary PHYTO');
- nc{'PHYTO_south'}.long_name = 'southern boundary PHYTO';
- nc{'PHYTO_south'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_south'}.units = 'mMol N m-3';
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- nc{'NO3_east'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','Z','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol O m-3');
- nc{'O2_east'}.units = 'mMol O m-3';
-%
- nc{'CHLA_east'} = ncdouble('chla_time','Z','eta_rho') ;
- nc{'CHLA_east'}.long_name = ncchar('eastern boundary CHLA');
- nc{'CHLA_east'}.long_name = 'eastern boundary CHLA';
- nc{'CHLA_east'}.units = ncchar('mMol N m-3');
- nc{'CHLA_east'}.units = 'mMol N m-3';
-%
- nc{'ZOO_east'} = ncdouble('zoo_time','Z','eta_rho') ;
- nc{'ZOO_east'}.long_name = ncchar('eastern boundary ZOO');
- nc{'ZOO_east'}.long_name = 'eastern boundary ZOO';
- nc{'ZOO_east'}.units = ncchar('mMol N m-3');
- nc{'ZOO_east'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_east'} = ncdouble('phyto_time','Z','eta_rho') ;
- nc{'PHYTO_east'}.long_name = ncchar('eastern boundary PHYTO');
- nc{'PHYTO_east'}.long_name = 'eastern boundary PHYTO';
- nc{'PHYTO_east'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- nc{'NO3_north'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','Z','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol O m-3');
- nc{'O2_north'}.units = 'mMol O m-3';
-%
- nc{'CHLA_north'} = ncdouble('chla_time','Z','xi_rho') ;
- nc{'CHLA_north'}.long_name = ncchar('northern boundary CHLA');
- nc{'CHLA_north'}.long_name = 'northern boundary CHLA';
- nc{'CHLA_north'}.units = ncchar('mMol N m-3');
- nc{'CHLA_north'}.units = 'mMol N m-3';
-%
- nc{'ZOO_north'} = ncdouble('zoo_time','Z','xi_rho') ;
- nc{'ZOO_north'}.long_name = ncchar('northern boundary ZOO');
- nc{'ZOO_north'}.long_name = 'northern boundary ZOO';
- nc{'ZOO_north'}.units = ncchar('mMol N m-3');
- nc{'ZOO_north'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_north'} = ncdouble('phyto_time','Z','xi_rho') ;
- nc{'PHYTO_north'}.long_name = ncchar('northern boundary PHYTO');
- nc{'PHYTO_north'}.long_name = 'northern boundary PHYTO';
- nc{'PHYTO_north'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- nc{'NO3_west'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol O m-3');
- nc{'O2_west'}.units = 'mMol O m-3';
-%
- nc{'CHLA_west'} = ncdouble('chla_time','Z','eta_rho') ;
- nc{'CHLA_west'}.long_name = ncchar('western boundary CHLA');
- nc{'CHLA_west'}.long_name = 'western boundary CHLA';
- nc{'CHLA_west'}.units = ncchar('mMol N m-3');
- nc{'CHLA_west'}.units = 'mMol N m-3';
-%
- nc{'ZOO_west'} = ncdouble('zoo_time','Z','eta_rho') ;
- nc{'ZOO_west'}.long_name = ncchar('western boundary ZOO');
- nc{'ZOO_west'}.long_name = 'western boundary ZOO';
- nc{'ZOO_west'}.units = ncchar('mMol N m-3');
- nc{'ZOO_west'}.units = 'mMol N m-3';
-%
- nc{'PHYTO_west'} = ncdouble('phyto_time','Z','eta_rho') ;
- nc{'PHYTO_west'}.long_name = ncchar('western boundary PHYTO');
- nc{'PHYTO_west'}.long_name = 'western boundary PHYTO';
- nc{'PHYTO_west'}.units = ncchar('mMol N m-3');
- nc{'PHYTO_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'no3_time'}(:) = time_no3;
-nc{'o2_time'}(:) = time_no3;
-nc{'chla_time'}(:) = time_chla;
-nc{'zoo_time'}(:) = time_zoo;
-nc{'phyto_time'}(:) = time_phyto;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'CHLA_south'}(:) = 0;
- nc{'ZOO_south'}(:) = 0;
- nc{'PHYTO_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'CHLA_east'}(:) = 0;
- nc{'ZOO_east'}(:) = 0;
- nc{'PHYTO_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'CHLA_north'}(:) = 0;
- nc{'ZOO_north'}(:) = 0;
- nc{'PHYTO_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'CHLA_west'}(:) = 0;
- nc{'ZOO_west'}(:) = 0;
- nc{'PHYTO_west'}(:) = 0;
-end
-close(nc)
-return
-
-
diff --git a/Preprocessing_tools/add_bry_pisces.m b/Preprocessing_tools/add_bry_pisces.m
deleted file mode 100644
index c170f967..00000000
--- a/Preprocessing_tools/add_bry_pisces.m
+++ /dev/null
@@ -1,399 +0,0 @@
-function add_bry_pisces(bryname,obc,time,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_bry_pisces(bryname,grdname,title,obc...
-% theta_s,theta_b,hc,N,...
-% time,cycle,clobber);
-%
-% This function create the header of a Netcdf climatology
-% file.
-%
-% Input:
-%
-% bryname Netcdf climatology file name (character string).
-% obc open boundaries flag (1=open , [S E N W]).
-% time time.(vector)
-% cycle Length (days) for cycling the climatology.(Real)
-% clobber Switch to allow or not writing over an existing
-% file.(character string)
-%
-% 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
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding PISCES data into file : ',bryname])
-disp(' ')
-%
-% Redefine the boundary file
-%
-nc = netcdf(bryname,clobber);
-%%result = redef(nc);
-%
-% Create dimensions
-%
-nc('dic_time') = length(time);
-nc('doc_time') = length(time);
-nc('no3_time') = length(time);
-nc('po4_time') = length(time);
-nc('talk_time') = length(time);
-nc('si_time') = length(time);
-nc('fer_time') = length(time);
-nc('o2_time') = length(time);
-nc('one') = 1;
-%
-% Create variables and attributes
-%
-nc{'dic_time'} = ncdouble('dic_time') ;
-nc{'dic_time'}.long_name = ncchar('time for DIC climatology');
-nc{'dic_time'}.long_name = 'time for DIC climatology';
-nc{'dic_time'}.units = ncchar('day');
-nc{'dic_time'}.units = 'day';
-nc{'dic_time'}.cycle_length = cycle;%
-%
-nc{'talk_time'} = ncdouble('talk_time') ;
-nc{'talk_time'}.long_name = ncchar('time for TALK climatology');
-nc{'talk_time'}.long_name = 'time for TALK climatology';
-nc{'talk_time'}.units = ncchar('day');
-nc{'talk_time'}.units = 'day';
-nc{'talk_time'}.cycle_length = cycle;%
-%
-nc{'no3_time'} = ncdouble('no3_time') ;
-nc{'no3_time'}.long_name = ncchar('time for NO3 climatology');
-nc{'no3_time'}.long_name = 'time for NO3 climatology';
-nc{'no3_time'}.units = ncchar('day');
-nc{'no3_time'}.units = 'day';
-nc{'no3_time'}.cycle_length = cycle;%
-%
-nc{'po4_time'} = ncdouble('po4_time') ;
-nc{'po4_time'}.long_name = ncchar('time for PO4 climatology');
-nc{'po4_time'}.long_name = 'time for PO4 climatology';
-nc{'po4_time'}.units = ncchar('day');
-nc{'po4_time'}.units = 'day';
-nc{'po4_time'}.cycle_length = cycle;%
-%
-nc{'si_time'} = ncdouble('si_time') ;
-nc{'si_time'}.long_name = ncchar('time for Si climatology');
-nc{'si_time'}.long_name = 'time for Si climatology';
-nc{'si_time'}.units = ncchar('day');
-nc{'si_time'}.units = 'day';
-nc{'si_time'}.cycle_length = cycle;%
-%
-nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology');
-nc{'o2_time'}.long_name = 'time for O2 climatology';
-nc{'o2_time'}.units = ncchar('day');
-nc{'o2_time'}.units = 'day';
-nc{'o2_time'}.cycle_length = cycle;%
-%
-nc{'doc_time'} = ncdouble('doc_time') ;
-nc{'doc_time'}.long_name = ncchar('time for DOC climatology');
-nc{'doc_time'}.long_name = 'time for DOC climatology';
-nc{'doc_time'}.units = ncchar('day');
-nc{'doc_time'}.units = 'day';
-nc{'doc_time'}.cycle_length = cycle;%
-%
-nc{'fer_time'} = ncdouble('fer_time') ;
-nc{'fer_time'}.long_name = ncchar('time for FER climatology');
-nc{'fer_time'}.long_name = 'time for FER climatology';
-nc{'fer_time'}.units = ncchar('day');
-nc{'fer_time'}.units = 'day';
-nc{'fer_time'}.cycle_length = cycle;%
-%
-if obc(1)==1
-%
-% Southern boundary
-%
- nc{'NO3_south'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'PO4_south'} = ncdouble('po4_time','s_rho','xi_rho') ;
- nc{'PO4_south'}.long_name = ncchar('southern boundary PO4');
- nc{'PO4_south'}.long_name = 'southern boundary PO4';
- nc{'PO4_south'}.units = ncchar('mMol N m-3');
- nc{'PO4_south'}.units = 'mMol N m-3';
-%
- nc{'Si_south'} = ncdouble('si_time','s_rho','xi_rho') ;
- nc{'Si_south'}.long_name = ncchar('southern boundary Si');
- nc{'Si_south'}.long_name = 'southern boundary Si';
- nc{'Si_south'}.units = ncchar('mMol N m-3');
- nc{'Si_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol N m-3');
- nc{'O2_south'}.units = 'mMol N m-3';
-%
- nc{'DIC_south'} = ncdouble('dic_time','s_rho','xi_rho') ;
- nc{'DIC_south'}.long_name = ncchar('southern boundary DIC');
- nc{'DIC_south'}.long_name = 'southern boundary DIC';
- nc{'DIC_south'}.units = ncchar('mMol N m-3');
- nc{'DIC_south'}.units = 'mMol N m-3';
-%
- nc{'TALK_south'} = ncdouble('talk_time','s_rho','xi_rho') ;
- nc{'TALK_south'}.long_name = ncchar('southern boundary TALK');
- nc{'TALK_south'}.long_name = 'southern boundary TALK';
- nc{'TALK_south'}.units = ncchar('mMol N m-3');
- nc{'TALK_south'}.units = 'mMol N m-3';
-%
- nc{'DOC_south'} = ncdouble('doc_time','s_rho','xi_rho') ;
- nc{'DOC_south'}.long_name = ncchar('southern boundary DOC');
- nc{'DOC_south'}.long_name = 'southern boundary DOC';
- nc{'DOC_south'}.units = ncchar('mMol N m-3');
- nc{'DOC_south'}.units = 'mMol N m-3';
-%
- nc{'FER_south'} = ncdouble('fer_time','s_rho','xi_rho') ;
- nc{'FER_south'}.long_name = ncchar('southern boundary Iron');
- nc{'FER_south'}.long_name = 'southern boundary Iron';
- nc{'FER_south'}.units = ncchar('mMol N m-3');
- nc{'FER_south'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- nc{'NO3_east'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'PO4_east'} = ncdouble('po4_time','s_rho','eta_rho') ;
- nc{'PO4_east'}.long_name = ncchar('eastern boundary PO4');
- nc{'PO4_east'}.long_name = 'eastern boundary PO4';
- nc{'PO4_east'}.units = ncchar('mMol N m-3');
- nc{'PO4_east'}.units = 'mMol N m-3';
-%
- nc{'Si_east'} = ncdouble('si_time','s_rho','eta_rho') ;
- nc{'Si_east'}.long_name = ncchar('eastern boundary Si');
- nc{'Si_east'}.long_name = 'eastern boundary Si';
- nc{'Si_east'}.units = ncchar('mMol N m-3');
- nc{'Si_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol N m-3');
- nc{'O2_east'}.units = 'mMol N m-3';
-%
- nc{'DIC_east'} = ncdouble('dic_time','s_rho','eta_rho') ;
- nc{'DIC_east'}.long_name = ncchar('eastern boundary DIC');
- nc{'DIC_east'}.long_name = 'eastern boundary DIC';
- nc{'DIC_east'}.units = ncchar('mMol N m-3');
- nc{'DIC_east'}.units = 'mMol N m-3';
-%
- nc{'TALK_east'} = ncdouble('talk_time','s_rho','eta_rho') ;
- nc{'TALK_east'}.long_name = ncchar('eastern boundary TALK');
- nc{'TALK_east'}.long_name = 'eastern boundary TALK';
- nc{'TALK_east'}.units = ncchar('mMol N m-3');
- nc{'TALK_east'}.units = 'mMol N m-3';
-%
- nc{'DOC_east'} = ncdouble('doc_time','s_rho','eta_rho') ;
- nc{'DOC_east'}.long_name = ncchar('eastern boundary DOC');
- nc{'DOC_east'}.long_name = 'eastern boundary DOC';
- nc{'DOC_east'}.units = ncchar('mMol N m-3');
- nc{'DOC_east'}.units = 'mMol N m-3';
-%
- nc{'FER_east'} = ncdouble('fer_time','s_rho','eta_rho') ;
- nc{'FER_east'}.long_name = ncchar('eastern boundary Iron');
- nc{'FER_east'}.long_name = 'eastern boundary Iron';
- nc{'FER_east'}.units = ncchar('mMol N m-3');
- nc{'FER_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- nc{'NO3_north'} = ncdouble('no3_time','s_rho','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'PO4_north'} = ncdouble('po4_time','s_rho','xi_rho') ;
- nc{'PO4_north'}.long_name = ncchar('northern boundary PO4');
- nc{'PO4_north'}.long_name = 'northern boundary PO4';
- nc{'PO4_north'}.units = ncchar('mMol N m-3');
- nc{'PO4_north'}.units = 'mMol N m-3';
-%
- nc{'Si_north'} = ncdouble('si_time','s_rho','xi_rho') ;
- nc{'Si_north'}.long_name = ncchar('northern boundary Si');
- nc{'Si_north'}.long_name = 'northern boundary Si';
- nc{'Si_north'}.units = ncchar('mMol N m-3');
- nc{'Si_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','s_rho','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol N m-3');
- nc{'O2_north'}.units = 'mMol N m-3';
-%
- nc{'DIC_north'} = ncdouble('dic_time','s_rho','xi_rho') ;
- nc{'DIC_north'}.long_name = ncchar('northern boundary DIC');
- nc{'DIC_north'}.long_name = 'northern boundary DIC';
- nc{'DIC_north'}.units = ncchar('mMol N m-3');
- nc{'DIC_north'}.units = 'mMol N m-3';
-%
- nc{'TALK_north'} = ncdouble('talk_time','s_rho','xi_rho') ;
- nc{'TALK_north'}.long_name = ncchar('northern boundary TALK');
- nc{'TALK_north'}.long_name = 'northern boundary TALK';
- nc{'TALK_north'}.units = ncchar('mMol N m-3');
- nc{'TALK_north'}.units = 'mMol N m-3';
-%
- nc{'DOC_north'} = ncdouble('doc_time','s_rho','xi_rho') ;
- nc{'DOC_north'}.long_name = ncchar('northern boundary DOC');
- nc{'DOC_north'}.long_name = 'northern boundary DOC';
- nc{'DOC_north'}.units = ncchar('mMol N m-3');
- nc{'DOC_north'}.units = 'mMol N m-3';
-%
- nc{'FER_north'} = ncdouble('fer_time','s_rho','xi_rho') ;
- nc{'FER_north'}.long_name = ncchar('northern boundary Iron');
- nc{'FER_north'}.long_name = 'northern boundary Iron';
- nc{'FER_north'}.units = ncchar('mMol N m-3');
- nc{'FER_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- nc{'NO3_west'} = ncdouble('no3_time','s_rho','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'PO4_west'} = ncdouble('po4_time','s_rho','eta_rho') ;
- nc{'PO4_west'}.long_name = ncchar('western boundary PO4');
- nc{'PO4_west'}.long_name = 'western boundary PO4';
- nc{'PO4_west'}.units = ncchar('mMol N m-3');
- nc{'PO4_west'}.units = 'mMol N m-3';
-%
- nc{'Si_west'} = ncdouble('si_time','s_rho','eta_rho') ;
- nc{'Si_west'}.long_name = ncchar('western boundary Si');
- nc{'Si_west'}.long_name = 'western boundary Si';
- nc{'Si_west'}.units = ncchar('mMol N m-3');
- nc{'Si_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('o2_time','s_rho','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol N m-3');
- nc{'O2_west'}.units = 'mMol N m-3';
-%
- nc{'DIC_west'} = ncdouble('dic_time','s_rho','eta_rho') ;
- nc{'DIC_west'}.long_name = ncchar('western boundary DIC');
- nc{'DIC_west'}.long_name = 'western boundary DIC';
- nc{'DIC_west'}.units = ncchar('mMol N m-3');
- nc{'DIC_west'}.units = 'mMol N m-3';
-%
- nc{'TALK_west'} = ncdouble('talk_time','s_rho','eta_rho') ;
- nc{'TALK_west'}.long_name = ncchar('western boundary TALK');
- nc{'TALK_west'}.long_name = 'western boundary TALK';
- nc{'TALK_west'}.units = ncchar('mMol N m-3');
- nc{'TALK_west'}.units = 'mMol N m-3';
-%
- nc{'DOC_west'} = ncdouble('doc_time','s_rho','eta_rho') ;
- nc{'DOC_west'}.long_name = ncchar('western boundary DOC');
- nc{'DOC_west'}.long_name = 'western boundary DOC';
- nc{'DOC_west'}.units = ncchar('mMol N m-3');
- nc{'DOC_west'}.units = 'mMol N m-3';
-%
- nc{'FER_west'} = ncdouble('fer_time','s_rho','eta_rho') ;
- nc{'FER_west'}.long_name = ncchar('western boundary Iron');
- nc{'FER_west'}.long_name = 'western boundary Iron';
- nc{'FER_west'}.units = ncchar('mMol N m-3');
- nc{'FER_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'dic_time'}(:) = time;
-nc{'doc_time'}(:) = time;
-nc{'no3_time'}(:) = time;
-nc{'po4_time'}(:) = time;
-nc{'talk_time'}(:) = time;
-nc{'si_time'}(:) = time;
-nc{'fer_time'}(:) = time;
-nc{'o2_time'}(:) = time;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'PO4_south'}(:) = 0;
- nc{'Si_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'DIC_south'}(:) = 0;
- nc{'TALK_south'}(:) = 0;
- nc{'DOC_south'}(:) = 0;
- nc{'FER_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'PO4_east'}(:) = 0;
- nc{'Si_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'DIC_east'}(:) = 0;
- nc{'TALK_east'}(:) = 0;
- nc{'DOC_east'}(:) = 0;
- nc{'FER_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'PO4_north'}(:) = 0;
- nc{'Si_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'DIC_north'}(:) = 0;
- nc{'TALK_north'}(:) = 0;
- nc{'DOC_north'}(:) = 0;
- nc{'FER_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'PO4_west'}(:) = 0;
- nc{'Si_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'DIC_west'}(:) = 0;
- nc{'TALK_west'}(:) = 0;
- nc{'DOC_west'}(:) = 0;
- nc{'FER_west'}(:) = 0;
-end
-close(nc)
-return
-
diff --git a/Preprocessing_tools/add_bry_pisces_Z.m b/Preprocessing_tools/add_bry_pisces_Z.m
deleted file mode 100644
index 7aa1b507..00000000
--- a/Preprocessing_tools/add_bry_pisces_Z.m
+++ /dev/null
@@ -1,319 +0,0 @@
-function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,clobber);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% function add_bry_pisces_Z(zbryname,obc,... %
-% Z,time,cycle,clobber); %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% zbryname Netcdf climatology file name (character string). %
-% obc open boundaries flag (1=open , [S E N W]). %
-% Z Depth of vertical levels.(Vector) %
-% time time.(vector) %
-% cycle Length (days) for cycling the climatology.(Real) %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont the master, IRD, 2006. %
-% Patricio Marchesiello, chief, IRD, 2007. %
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
-% %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding PISCES data into file : ',zbryname])
-disp(' ')
-%
-% Create the boundary file
-%
-nc = netcdf(zbryname,clobber);
-%%result = redef(nc);
-%
-% Create dimensions
-%
-nc('dic_time') = length(time);
-nc('doc_time') = length(time);
-nc('no3_time') = length(time);
-nc('po4_time') = length(time);
-nc('talk_time') = length(time);
-nc('si_time') = length(time);
-nc('fer_time') = length(time);
-nc('o2_time') = length(time);
-nc('one') = 1;
-%
-if obc(1)==1
-%
-% Southern boundary
-%
- nc{'NO3_south'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_south'}.long_name = ncchar('southern boundary NO3');
- nc{'NO3_south'}.long_name = 'southern boundary NO3';
- nc{'NO3_south'}.units = ncchar('mMol N m-3');
- nc{'NO3_south'}.units = 'mMol N m-3';
-%
- nc{'PO4_south'} = ncdouble('po4_time','Z','xi_rho') ;
- nc{'PO4_south'}.long_name = ncchar('southern boundary PO4');
- nc{'PO4_south'}.long_name = 'southern boundary PO4';
- nc{'PO4_south'}.units = ncchar('mMol N m-3');
- nc{'PO4_south'}.units = 'mMol N m-3';
-%
- nc{'Si_south'} = ncdouble('si_time','Z','xi_rho') ;
- nc{'Si_south'}.long_name = ncchar('southern boundary Si');
- nc{'Si_south'}.long_name = 'southern boundary Si';
- nc{'Si_south'}.units = ncchar('mMol N m-3');
- nc{'Si_south'}.units = 'mMol N m-3';
-%
- nc{'O2_south'} = ncdouble('o2_time','Z','xi_rho') ;
- nc{'O2_south'}.long_name = ncchar('southern boundary O2');
- nc{'O2_south'}.long_name = 'southern boundary O2';
- nc{'O2_south'}.units = ncchar('mMol N m-3');
- nc{'O2_south'}.units = 'mMol N m-3';
-%
- nc{'DIC_south'} = ncdouble('dic_time','Z','xi_rho') ;
- nc{'DIC_south'}.long_name = ncchar('southern boundary DIC');
- nc{'DIC_south'}.long_name = 'southern boundary DIC';
- nc{'DIC_south'}.units = ncchar('mMol N m-3');
- nc{'DIC_south'}.units = 'mMol N m-3';
-%
- nc{'TALK_south'} = ncdouble('talk_time','Z','xi_rho') ;
- nc{'TALK_south'}.long_name = ncchar('southern boundary TALK');
- nc{'TALK_south'}.long_name = 'southern boundary TALK';
- nc{'TALK_south'}.units = ncchar('mMol N m-3');
- nc{'TALK_south'}.units = 'mMol N m-3';
-%
- nc{'DOC_south'} = ncdouble('doc_time','Z','xi_rho') ;
- nc{'DOC_south'}.long_name = ncchar('southern boundary DOC');
- nc{'DOC_south'}.long_name = 'southern boundary DOC';
- nc{'DOC_south'}.units = ncchar('mMol N m-3');
- nc{'DOC_south'}.units = 'mMol N m-3';
-%
- nc{'FER_south'} = ncdouble('fer_time','Z','xi_rho') ;
- nc{'FER_south'}.long_name = ncchar('southern boundary Iron');
- nc{'FER_south'}.long_name = 'southern boundary Iron';
- nc{'FER_south'}.units = ncchar('mMol N m-3');
- nc{'FER_south'}.units = 'mMol N m-3';
-end
-%
-if obc(2)==1
-%
-% Eastern boundary
-%
- nc{'NO3_east'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_east'}.long_name = ncchar('eastern boundary NO3');
- nc{'NO3_east'}.long_name = 'eastern boundary NO3';
- nc{'NO3_east'}.units = ncchar('mMol N m-3');
- nc{'NO3_east'}.units = 'mMol N m-3';
-%
- nc{'PO4_east'} = ncdouble('po4_time','Z','eta_rho') ;
- nc{'PO4_east'}.long_name = ncchar('eastern boundary PO4');
- nc{'PO4_east'}.long_name = 'eastern boundary PO4';
- nc{'PO4_east'}.units = ncchar('mMol N m-3');
- nc{'PO4_east'}.units = 'mMol N m-3';
-%
- nc{'Si_east'} = ncdouble('si_time','Z','eta_rho') ;
- nc{'Si_east'}.long_name = ncchar('eastern boundary Si');
- nc{'Si_east'}.long_name = 'eastern boundary Si';
- nc{'Si_east'}.units = ncchar('mMol N m-3');
- nc{'Si_east'}.units = 'mMol N m-3';
-%
- nc{'O2_east'} = ncdouble('o2_time','Z','eta_rho') ;
- nc{'O2_east'}.long_name = ncchar('eastern boundary O2');
- nc{'O2_east'}.long_name = 'eastern boundary O2';
- nc{'O2_east'}.units = ncchar('mMol N m-3');
- nc{'O2_east'}.units = 'mMol N m-3';
-%
- nc{'DIC_east'} = ncdouble('dic_time','Z','eta_rho') ;
- nc{'DIC_east'}.long_name = ncchar('eastern boundary DIC');
- nc{'DIC_east'}.long_name = 'eastern boundary DIC';
- nc{'DIC_east'}.units = ncchar('mMol N m-3');
- nc{'DIC_east'}.units = 'mMol N m-3';
-%
- nc{'TALK_east'} = ncdouble('talk_time','Z','eta_rho') ;
- nc{'TALK_east'}.long_name = ncchar('eastern boundary TALK');
- nc{'TALK_east'}.long_name = 'eastern boundary TALK';
- nc{'TALK_east'}.units = ncchar('mMol N m-3');
- nc{'TALK_east'}.units = 'mMol N m-3';
-%
- nc{'DOC_east'} = ncdouble('doc_time','Z','eta_rho') ;
- nc{'DOC_east'}.long_name = ncchar('eastern boundary DOC');
- nc{'DOC_east'}.long_name = 'eastern boundary DOC';
- nc{'DOC_east'}.units = ncchar('mMol N m-3');
- nc{'DOC_east'}.units = 'mMol N m-3';
-%
- nc{'FER_east'} = ncdouble('fer_time','Z','eta_rho') ;
- nc{'FER_east'}.long_name = ncchar('eastern boundary Iron');
- nc{'FER_east'}.long_name = 'eastern boundary Iron';
- nc{'FER_east'}.units = ncchar('mMol N m-3');
- nc{'FER_east'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(3)==1
-%
-% Northern boundary
-%
- nc{'NO3_north'} = ncdouble('no3_time','Z','xi_rho') ;
- nc{'NO3_north'}.long_name = ncchar('northern boundary NO3');
- nc{'NO3_north'}.long_name = 'northern boundary NO3';
- nc{'NO3_north'}.units = ncchar('mMol N m-3');
- nc{'NO3_north'}.units = 'mMol N m-3';
-%
- nc{'PO4_north'} = ncdouble('po4_time','Z','xi_rho') ;
- nc{'PO4_north'}.long_name = ncchar('northern boundary PO4');
- nc{'PO4_north'}.long_name = 'northern boundary PO4';
- nc{'PO4_north'}.units = ncchar('mMol N m-3');
- nc{'PO4_north'}.units = 'mMol N m-3';
-%
- nc{'Si_north'} = ncdouble('si_time','Z','xi_rho') ;
- nc{'Si_north'}.long_name = ncchar('northern boundary Si');
- nc{'Si_north'}.long_name = 'northern boundary Si';
- nc{'Si_north'}.units = ncchar('mMol N m-3');
- nc{'Si_north'}.units = 'mMol N m-3';
-%
- nc{'O2_north'} = ncdouble('o2_time','Z','xi_rho') ;
- nc{'O2_north'}.long_name = ncchar('northern boundary O2');
- nc{'O2_north'}.long_name = 'northern boundary O2';
- nc{'O2_north'}.units = ncchar('mMol N m-3');
- nc{'O2_north'}.units = 'mMol N m-3';
-%
- nc{'DIC_north'} = ncdouble('dic_time','Z','xi_rho') ;
- nc{'DIC_north'}.long_name = ncchar('northern boundary DIC');
- nc{'DIC_north'}.long_name = 'northern boundary DIC';
- nc{'DIC_north'}.units = ncchar('mMol N m-3');
- nc{'DIC_north'}.units = 'mMol N m-3';
-%
- nc{'TALK_north'} = ncdouble('talk_time','Z','xi_rho') ;
- nc{'TALK_north'}.long_name = ncchar('northern boundary TALK');
- nc{'TALK_north'}.long_name = 'northern boundary TALK';
- nc{'TALK_north'}.units = ncchar('mMol N m-3');
- nc{'TALK_north'}.units = 'mMol N m-3';
-%
- nc{'DOC_north'} = ncdouble('doc_time','Z','xi_rho') ;
- nc{'DOC_north'}.long_name = ncchar('northern boundary DOC');
- nc{'DOC_north'}.long_name = 'northern boundary DOC';
- nc{'DOC_north'}.units = ncchar('mMol N m-3');
- nc{'DOC_north'}.units = 'mMol N m-3';
-%
- nc{'FER_north'} = ncdouble('fer_time','Z','xi_rho') ;
- nc{'FER_north'}.long_name = ncchar('northern boundary Iron');
- nc{'FER_north'}.long_name = 'northern boundary Iron';
- nc{'FER_north'}.units = ncchar('mMol N m-3');
- nc{'FER_north'}.units = 'mMol N m-3';
-%
-end
-%
-if obc(4)==1
-%
-% Western boundary
-%
- nc{'NO3_west'} = ncdouble('no3_time','Z','eta_rho') ;
- nc{'NO3_west'}.long_name = ncchar('western boundary NO3');
- nc{'NO3_west'}.long_name = 'western boundary NO3';
- nc{'NO3_west'}.units = ncchar('mMol N m-3');
- nc{'NO3_west'}.units = 'mMol N m-3';
-%
- nc{'PO4_west'} = ncdouble('po4_time','Z','eta_rho') ;
- nc{'PO4_west'}.long_name = ncchar('western boundary PO4');
- nc{'PO4_west'}.long_name = 'western boundary PO4';
- nc{'PO4_west'}.units = ncchar('mMol N m-3');
- nc{'PO4_west'}.units = 'mMol N m-3';
-%
- nc{'Si_west'} = ncdouble('si_time','Z','eta_rho') ;
- nc{'Si_west'}.long_name = ncchar('western boundary Si');
- nc{'Si_west'}.long_name = 'western boundary Si';
- nc{'Si_west'}.units = ncchar('mMol N m-3');
- nc{'Si_west'}.units = 'mMol N m-3';
-%
- nc{'O2_west'} = ncdouble('o2_time','Z','eta_rho') ;
- nc{'O2_west'}.long_name = ncchar('western boundary O2');
- nc{'O2_west'}.long_name = 'western boundary O2';
- nc{'O2_west'}.units = ncchar('mMol N m-3');
- nc{'O2_west'}.units = 'mMol N m-3';
-%
- nc{'DIC_west'} = ncdouble('dic_time','Z','eta_rho') ;
- nc{'DIC_west'}.long_name = ncchar('western boundary DIC');
- nc{'DIC_west'}.long_name = 'western boundary DIC';
- nc{'DIC_west'}.units = ncchar('mMol N m-3');
- nc{'DIC_west'}.units = 'mMol N m-3';
-%
- nc{'TALK_west'} = ncdouble('talk_time','Z','eta_rho') ;
- nc{'TALK_west'}.long_name = ncchar('western boundary TALK');
- nc{'TALK_west'}.long_name = 'western boundary TALK';
- nc{'TALK_west'}.units = ncchar('mMol N m-3');
- nc{'TALK_west'}.units = 'mMol N m-3';
-%
- nc{'DOC_west'} = ncdouble('doc_time','Z','eta_rho') ;
- nc{'DOC_west'}.long_name = ncchar('western boundary DOC');
- nc{'DOC_west'}.long_name = 'western boundary DOC';
- nc{'DOC_west'}.units = ncchar('mMol N m-3');
- nc{'DOC_west'}.units = 'mMol N m-3';
-%
- nc{'FER_west'} = ncdouble('fer_time','Z','eta_rho') ;
- nc{'FER_west'}.long_name = ncchar('western boundary Iron');
- nc{'FER_west'}.long_name = 'western boundary Iron';
- nc{'FER_west'}.units = ncchar('mMol N m-3');
- nc{'FER_west'}.units = 'mMol N m-3';
-%
-end
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc('dic_time') = time;
-nc('doc_time') = time;
-nc('no3_time') = time;
-nc('po4_time') = time;
-nc('talk_time') = time;
-nc('si_time') = time;
-nc('fer_time') = time;
-nc('o2_time') = time;
-if obc(1)==1
- nc{'NO3_south'}(:) = 0;
- nc{'PO4_south'}(:) = 0;
- nc{'Si_south'}(:) = 0;
- nc{'O2_south'}(:) = 0;
- nc{'DIC_south'}(:) = 0;
- nc{'TALK_south'}(:) = 0;
- nc{'DOC_south'}(:) = 0;
- nc{'FER_south'}(:) = 0;
-end
-if obc(2)==1
- nc{'NO3_east'}(:) = 0;
- nc{'PO4_east'}(:) = 0;
- nc{'Si_east'}(:) = 0;
- nc{'O2_east'}(:) = 0;
- nc{'DIC_east'}(:) = 0;
- nc{'TALK_east'}(:) = 0;
- nc{'DOC_east'}(:) = 0;
- nc{'FER_east'}(:) = 0;
-end
-if obc(3)==1
- nc{'NO3_north'}(:) = 0;
- nc{'PO4_north'}(:) = 0;
- nc{'Si_north'}(:) = 0;
- nc{'O2_north'}(:) = 0;
- nc{'DIC_north'}(:) = 0;
- nc{'TALK_north'}(:) = 0;
- nc{'DOC_north'}(:) = 0;
- nc{'FER_north'}(:) = 0;
-end
-if obc(4)==1
- nc{'NO3_west'}(:) = 0;
- nc{'PO4_west'}(:) = 0;
- nc{'Si_west'}(:) = 0;
- nc{'O2_west'}(:) = 0;
- nc{'DIC_west'}(:) = 0;
- nc{'TALK_west'}(:) = 0;
- nc{'DOC_west'}(:) = 0;
- nc{'FER_west'}(:) = 0;
-end
-close(nc)
-return
-
-
diff --git a/Preprocessing_tools/add_chla.m b/Preprocessing_tools/add_chla.m
deleted file mode 100644
index a5ecdd22..00000000
--- a/Preprocessing_tools/add_chla.m
+++ /dev/null
@@ -1,151 +0,0 @@
-function add_chla(climfile,gridfile,seas_datafile,cycle,Roa);
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_chla(climfile,gridfile,seas_datafile,cycle);
-%
-% Add chlorophyll (mg C) in a CROCO climatology file.
-% take seasonal data for the surface levels and extrapole
-% using Morel and Berthon (1989) parameterization for the
-% lower levels. warning ! the unit is (micro mole/l) in the
-% dataset.
-% ref: Morel and Berthon, Surface pigments, algal biomass
-% profiles, and potential production of the euphotic layer:
-% Relationships reinvestigated in view of remote-sensing
-% applications. Limnol. Oceanogr., 34, 1989, 1545-1562.
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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.
-%
-% 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_chla: creating variable and attribute')
-default=NaN;
-%
-% read in the datafile
-%
-ncseas=netcdf(seas_datafile,'r');
-x=ncseas{'X'}(:);
-y=ncseas{'Y'}(:);
-t=ncseas{'T'}(:);
-tlen=length(t);
-%
-% open the grid file
-%
-ng=netcdf(gridfile,'r');
-lon=ng{'lon_rho'}(:);
-%lon(lon<0)=lon(lon<0)+360;
-lat=ng{'lat_rho'}(:);
-h=ng{'h'}(:);
-close(ng);
-[M,L]=size(lon);
-dl=2.;
-minlon=min(min(lon))-dl;
-maxlon=max(max(lon))+dl;
-minlat=min(min(lat))-dl;
-maxlat=max(max(lat))+dl;
-imin=max(find(x<=minlon));
-imax=min(find(x>=maxlon));
-jmin=max(find(y<=minlat));
-jmax=min(find(y>=maxlat));
-x=x(imin:imax);
-y=y(jmin:jmax);
-%
-% open the clim file
-%
-nc=netcdf(climfile,'write');
-theta_s = nc{'theta_s'}(:);
-theta_b = nc{'theta_b'}(:);
-Tcline = nc{'Tcline'}(:);
-vtransform=nc{'Vtransform'}(:);
-if ~exist('vtransform')
- vtransform=1; %Old Vtransform
- disp([' NO VTRANSFORM parameter found'])
-end
-N = length(nc('s_rho'));
-
-%redef(nc);
-nc('chla_time') = tlen;
-nc{'chla_time'} = ncdouble('chla_time') ;
-nc{'CHLA'} = ncdouble('chla_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'chla_time'}.long_name = ncchar('time for chlorophyll');
-nc{'chla_time'}.long_name = 'time for chlorophyll';
-nc{'chla_time'}.units = ncchar('day');
-nc{'chla_time'}.units = 'day';
-if cycle~=0
- nc{'chla_time'}.cycle_length = cycle;
-end
-%
-nc{'CHLA'}.long_name = ncchar('Chlorophyll');
-nc{'CHLA'}.long_name = 'Chlorophyll';
-nc{'CHLA'}.units = ncchar('mg C');
-nc{'CHLA'}.units = 'mg C';
-nc{'CHLA'}.fields = ncchar('CHLA, scalar, series');
-nc{'CHLA'}.fields = 'CHLA, scalar, series';
-%
-%endef(nc);
-%
-% Record the time
-%
-nc{'chla_time'}(:)=t*30; % if time in month in the dataset !!!
-%
-% Get the missing values
-%
-missval=ncseas{'chlorophyll'}.missing_value(:);
-%
-% loop on time
-%
-for l=1:tlen
-disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
-%
-% extrapole the annual dataset on the horizontal croco grid
-%
- disp('Add_chla: horizontal interpolation of surface data')
- surfchla=squeeze(ncseas{'chlorophyll'}(l,jmin:jmax,imin:imax));
- surfchla=get_missing_val(x,y,surfchla,missval,Roa,default);
- surfchlacroco=interp2(x,y,surfchla,lon,lat);
-%
-% extrapole the chlorophyll on the vertical
-%
- zcroco=zlevs(h,0.*h,theta_s,theta_b,Tcline,N,'r',vtransform);
- disp(['Add_chla: vertical ',...
- 'extrapolation of chlorophyll'])
- chlacroco=extr_chlo(surfchlacroco,zcroco);
- nc{'CHLA'}(l,:,:,:)=chlacroco;
-end
-close(nc);
-close(ncseas);
-chla=squeeze(chlacroco(N,:,:));
-return
diff --git a/Preprocessing_tools/add_dic.m b/Preprocessing_tools/add_dic.m
deleted file mode 100644
index 88cace3b..00000000
--- a/Preprocessing_tools/add_dic.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_dic(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,dic]=add_dic(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add DIC (mMol C m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,dic] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zdic=nc{'Z'}(:);
-kmax=max(find(zdic<hmax))-1;
-zdic=zdic(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_dic: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('dic_time') = length(t);
- nc{'dic_time'} = ncdouble('dic_time') ;
- nc('Zdic') = length(zdic);
- nc{'Zdic'} = ncdouble('Zdic') ;
- nc{'DIC'} = ncdouble('dic_time','Zdic','eta_rho','xi_rho') ;
-%
- nc{'dic_time'}.long_name = ncchar('time for DIC');
- nc{'dic_time'}.long_name = 'time for DIC';
- nc{'dic_time'}.units = ncchar('day');
- nc{'dic_time'}.units = 'day';
- if cycle~=0
- nc{'dic_time'}.cycle_length = cycle;
- end
-%
- nc{'Zdic'}.long_name = ncchar('Depth for DIC');
- nc{'Zdic'}.long_name = 'Depth for DIC';
- nc{'Zdic'}.units = ncchar('m');
- nc{'Zdic'}.units = 'm';
-%
- 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';
- nc{'DIC'}.fields = ncchar('DIC, scalar, series');
- nc{'DIC'}.fields = 'DIC, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'dic_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zdic'}(:)=zdic;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_dic: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('dic_time') = length(t);;
- nc{'dic_time'} = ncdouble('dic_time') ;
- nc{'DIC'} = ncdouble('dic_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'dic_time'}.long_name = ncchar('time for DIC');
- nc{'dic_time'}.long_name = 'time for DIC';
- nc{'dic_time'}.units = ncchar('day');
- nc{'dic_time'}.units = 'day';
- if cycle~=0
- nc{'dic_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'DIC'}.fields = ncchar('DIC, scalar, series');
- nc{'DIC'}.fields = 'DIC, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'dic_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing 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)
-
-return
diff --git a/Preprocessing_tools/add_doc.m b/Preprocessing_tools/add_doc.m
deleted file mode 100644
index d8c3e30f..00000000
--- a/Preprocessing_tools/add_doc.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_doc(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add DOC (mMol C m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,doc] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zdoc=nc{'Z'}(:);
-kmax=max(find(zdoc<hmax))-1;
-zdoc=zdoc(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_doc: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('doc_time') = length(t);
- nc{'doc_time'} = ncdouble('doc_time') ;
- nc('Zdoc') = length(zdoc);
- nc{'Zdoc'} = ncdouble('Zdoc') ;
- nc{'DOC'} = ncdouble('doc_time','Zdoc','eta_rho','xi_rho') ;
-%
- nc{'doc_time'}.long_name = ncchar('time for doc');
- nc{'doc_time'}.long_name = 'time for doc';
- nc{'doc_time'}.units = ncchar('day');
- nc{'doc_time'}.units = 'day';
- if cycle~=0
- nc{'doc_time'}.cycle_length = cycle;
- end
-%
- nc{'Zdoc'}.long_name = ncchar('Depth for DOC');
- nc{'Zdoc'}.long_name = 'Depth for DOC';
- nc{'Zdoc'}.units = ncchar('m');
- nc{'Zdoc'}.units = 'm';
-%
- 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';
- nc{'DOC'}.fields = ncchar('DOC, scalar, series');
- nc{'DOC'}.fields = 'DOC, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'doc_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zdoc'}(:)=zdoc;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_doc: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('doc_time') = length(t);;
- nc{'doc_time'} = ncdouble('doc_time') ;
- nc{'DOC'} = ncdouble('doc_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'doc_time'}.long_name = ncchar('time for doc');
- nc{'doc_time'}.long_name = 'time for doc';
- nc{'doc_time'}.units = ncchar('day');
- nc{'doc_time'}.units = 'day';
- if cycle~=0
- nc{'doc_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'DOC'}.fields = ncchar('DOC, scalar, series');
- nc{'DOC'}.fields = 'DOC, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'doc_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing for the Initial file
-%
-%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{'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';
-%
-%endef(nc);
-%close(nc)
-
-return
diff --git a/Preprocessing_tools/add_fer.m b/Preprocessing_tools/add_fer.m
deleted file mode 100644
index f8d7cf89..00000000
--- a/Preprocessing_tools/add_fer.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_fer(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,fer]=add_fer(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add iron (mMol Fe m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,fer] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zfer=nc{'Z'}(:);
-kmax=max(find(zfer<hmax))-1;
-zfer=zfer(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_fer: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('fer_time') = length(t);
- nc{'fer_time'} = ncdouble('fer_time') ;
- nc('Zfer') = length(zfer);
- nc{'Zfer'} = ncdouble('Zfer') ;
- nc{'FER'} = ncdouble('fer_time','Zfer','eta_rho','xi_rho') ;
-%
- nc{'fer_time'}.long_name = ncchar('time for iron');
- nc{'fer_time'}.long_name = 'time for iron';
- nc{'fer_time'}.units = ncchar('day');
- nc{'fer_time'}.units = 'day';
- if cycle~=0
- nc{'fer_time'}.cycle_length = cycle;
- end
-%
- nc{'Zfer'}.long_name = ncchar('Depth for FER');
- nc{'Zfer'}.long_name = 'Depth for FER';
- nc{'Zfer'}.units = ncchar('m');
- nc{'Zfer'}.units = 'm';
-%
- nc{'FER'}.long_name = ncchar('Iron');
- nc{'FER'}.long_name = 'Iron';
- nc{'FER'}.units = ncchar('uMol Fe m-3');
- nc{'FER'}.units = 'uMol Fe m-3';
- nc{'FER'}.fields = ncchar('FER, scalar, series');
- nc{'FER'}.fields = 'FER, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'fer_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zfer'}(:)=zfer;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_fer: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('fer_time') = length(t);;
- nc{'fer_time'} = ncdouble('fer_time') ;
- nc{'FER'} = ncdouble('fer_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'fer_time'}.long_name = ncchar('time for iron');
- nc{'fer_time'}.long_name = 'time for iron';
- nc{'fer_time'}.units = ncchar('day');
- nc{'fer_time'}.units = 'day';
- if cycle~=0
- nc{'fer_time'}.cycle_length = cycle;
- end
-%
- nc{'FER'}.long_name = ncchar('Iron');
- nc{'FER'}.long_name = 'Iron';
- nc{'FER'}.units = ncchar('uMol Fe m-3');
- nc{'FER'}.units = 'uMol Fe m-3';
- nc{'FER'}.fields = ncchar('FER, scalar, series');
- nc{'FER'}.fields = 'FER, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'fer_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing for the Initial file
-%
-%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('Nitrate');
-%nc{'FER'}.long_name = 'Nitrate';
-%nc{'FER'}.units = ncchar('mMol N m-3');
-%nc{'FER'}.units = 'mMol N m-3';
-%
-%endef(nc);
-%close(nc)
-
-return
diff --git a/Preprocessing_tools/add_ini_Sphyto_Lphyto.m b/Preprocessing_tools/add_ini_Sphyto_Lphyto.m
deleted file mode 100644
index e6354de5..00000000
--- a/Preprocessing_tools/add_ini_Sphyto_Lphyto.m
+++ /dev/null
@@ -1,82 +0,0 @@
-function add_ini_Sphyto_Lphyto(inifile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_ini_phyto(inifile);
-%
-% Add phytoplancton (mMol N m-3) in a CROCO initial file.
-% take the chlorophyll (mg C) from the initial file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations.
-%
-% phyto = theta * chla
-%
-% input:
-%
-% inifile : croco initial file to process (netcdf)
-%
-% 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
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta1=0.1;
-theta2=0.4;
-%
-disp('Add_ini_Sphyto_Lphyto: creating variable and attribute')
-%
-% open the initial file
-%
-nc=netcdf(inifile,'write');
-time= nc{'scrum_time'}(:);
-tlen=length(time);
-%
-%redef(nc);
-%
-nc{'SPHYTO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'SPHYTO'}.long_name = ncchar('Small Phytoplankton');
-nc{'SPHYTO'}.long_name = 'Small Phytoplankton';
-nc{'SPHYTO'}.units = ncchar('mMol N m-3');
-nc{'SPHYTO'}.units = 'mMol N m-3';
-nc{'SPHYTO'}.fields = ncchar('SPHYTO, scalar, series');
-nc{'SPHYTO'}.fields = 'SPHYTO, scalar, series';
-%
-nc{'LPHYTO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'LPHYTO'}.long_name = ncchar('Large Phytoplankton');
-nc{'LPHYTO'}.long_name = 'Large Phytoplankton';
-nc{'LPHYTO'}.units = ncchar('mMol N m-3');
-nc{'LPHYTO'}.units = 'mMol N m-3';
-nc{'LPHYTO'}.fields = ncchar('LPHYTO, scalar, series');
-nc{'LPHYTO'}.fields = 'LPHYTO, scalar, series';
-%
-%endef(nc);
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'SPHYTO'}(l,:,:,:)=theta1*squeeze(nc{'CHLA'}(l,:,:,:));
- nc{'LPHYTO'}(l,:,:,:)=theta2*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
-
diff --git a/Preprocessing_tools/add_ini_Szoo_Lzoo.m b/Preprocessing_tools/add_ini_Szoo_Lzoo.m
deleted file mode 100644
index 8a65476c..00000000
--- a/Preprocessing_tools/add_ini_Szoo_Lzoo.m
+++ /dev/null
@@ -1,84 +0,0 @@
-function add_ini_Szoo_Lzoo(inifile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_ini_zoo(inifile);
-%
-% Add zooplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the initial file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations (Gruber et al., 2005)
-%
-% zoo = theta * chla
-
-% input:
-%
-% inifile : croco initial file to process (netcdf)
-%
-% 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
-%
-% Updated in 2005 by Patrick Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta1=0.2;
-theta2=0.3;
-%
-disp('Add_ini_Szoo_Lzoo: creating variable and attribute')
-%
-% open the initial file
-%
-nc=netcdf(inifile,'write');
-time= nc{'scrum_time'}(:);
-tlen=length(time);
-%
-%redef(nc);
-%
-nc{'SZOO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'SZOO'}.long_name = ncchar('Small Zooplankton');
-nc{'SZOO'}.long_name = 'Small Zooplankton';
-nc{'SZOO'}.units = ncchar('mMol N m-3');
-nc{'SZOO'}.units = 'mMol N m-3';
-nc{'SZOO'}.fields = ncchar('SZOO, scalar, series');
-nc{'SZOO'}.fields = 'SZOO, scalar, series';
-%
-nc{'LZOO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'LZOO'}.long_name = ncchar('Large Zooplankton');
-nc{'LZOO'}.long_name = 'Large Zooplankton';
-nc{'LZOO'}.units = ncchar('mMol N m-3');
-nc{'LZOO'}.units = 'mMol N m-3';
-nc{'LZOO'}.fields = ncchar('LZOO, scalar, series');
-nc{'LZOO'}.fields = 'LZOO, scalar, series';
-%
-%endef(nc);
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'SZOO'}(l,:,:,:)=theta1*squeeze(nc{'CHLA'}(l,:,:,:));
- nc{'LZOO'}(l,:,:,:)=theta2*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
-
diff --git a/Preprocessing_tools/add_ini_bioebus.m b/Preprocessing_tools/add_ini_bioebus.m
deleted file mode 100644
index a1c6ec60..00000000
--- a/Preprocessing_tools/add_ini_bioebus.m
+++ /dev/null
@@ -1,52 +0,0 @@
-function add_ini_bioebus(inifile,clobber)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Copyright (c) 2014 IRD %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% %
-% function nc=add_ini_bioebus(inifile,clobber) %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% inifile Netcdf initial file name (character string). %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Output %
-% %
-% nc Output netcdf object. %
-% %
-% Gildas Cambon, IRD 2014 %
-% %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding BIOEBUS data in file : ',inifile])
-%
-% Create the initial file
-%
-nc = netcdf(inifile,clobber);
-%%result = redef(nc);
-%
-% Create variables
-%
-nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-% Create attributes
-%
-nc{'NO3'}.long_name = ncchar('NO3');
-nc{'NO3'}.long_name = 'NO3';
-nc{'NO3'}.units = ncchar('mMol N m-3');
-nc{'NO3'}.units = 'mMol N m-3';
-%
-nc{'O2'}.long_name = ncchar('O2');
-nc{'O2'}.long_name = 'O2';
-nc{'O2'}.units = ncchar('mMol O m-3');
-nc{'O2'}.units = 'mMol O m-3';
-%
-% Leave define mode
-%
-%%result = endef(nc);
\ No newline at end of file
diff --git a/Preprocessing_tools/add_ini_chla.m b/Preprocessing_tools/add_ini_chla.m
deleted file mode 100644
index 9df8a5fc..00000000
--- a/Preprocessing_tools/add_ini_chla.m
+++ /dev/null
@@ -1,202 +0,0 @@
-function add_ini_chla(inifile,gridfile,seas_datafile,cycle,Roa);
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,chla]=add_ini_chla(inifile,gridfile,...
-% seas_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add chlorophyll in a CROCO initial file.
-% take seasonal data for the surface levels and extrapole
-% using Morel and Berthon (1989) parameterization for the
-% lower levels. warning ! the unit is (micro mole/l) in the
-% dataset.
-% do a temporal interpolation to have values at initial
-% time.
-%
-% ref: Morel and Berthon, Surface pigments, algal biomass
-% profiles, and potential production of the euphotic layer:
-% Relationships reinvestigated in view of remote-sensing
-% applications. Limnol. Oceanogr., 34, 1989, 1545-1562.
-%
-% input:
-%
-% inifile : croco initial file to process (netcdf)
-% gridfile : 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,chla] : 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
-%
-% Updated August-2006 by Pierrick Penven
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-disp('Add_ini_chla: creating variable and attribute')
-default=NaN;
-%
-% read in the datafile
-%
-ncseas=netcdf(seas_datafile,'r');
-x=ncseas{'X'}(:);
-y=ncseas{'Y'}(:);
-datatime=ncseas{'T'}(:);
-datatime=datatime*30; % !!! if the time in the dataset is in months !!!
-tlen=length(datatime);
-%
-% open the grid file
-%
-%
-% open the grid file
-%
-ng=netcdf(gridfile,'r');
-lon=ng{'lon_rho'}(:);
-%lon(lon<0)=lon(lon<0)+360;
-lat=ng{'lat_rho'}(:);
-h=ng{'h'}(:);
-close(ng);
-[M,L]=size(lon);
-dl=0.5;
-minlon=min(min(lon))-dl;
-maxlon=max(max(lon))+dl;
-minlat=min(min(lat))-dl;
-maxlat=max(max(lat))+dl;
-imin=max(find(x<=minlon));
-imax=min(find(x>=maxlon));
-jmin=max(find(y<=minlat));
-jmax=min(find(y>=maxlat));
-x=x(imin:imax);
-y=y(jmin:jmax);
-%
-% open the initial file
-%
-nc=netcdf(inifile,'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'}(:);
-end
-N = length(nc('s_rho'));
-scrum_time = nc{'scrum_time'}(:);
-scrum_time = scrum_time / (24*3600);
-tinilen = length(scrum_time);
-%redef(nc);
-nc{'CHLA'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'CHLA'}.long_name = ncchar('Chlorophyll');
-nc{'CHLA'}.long_name = 'Chlorophyll';
-nc{'CHLA'}.units = ncchar('mg C');
-nc{'CHLA'}.units = 'mg C';
-nc{'CHLA'}.fields = ncchar('CHLA, scalar, series');
-nc{'CHLA'}.fields = 'CHLA, scalar, series';
-%
-%endef(nc);
-%
-% Get the missing values
-%
-missval=ncseas{'chlorophyll'}.missing_value(:);
-%
-% loop on time
-%
-for l=1:tinilen
- disp(['time index: ',num2str(l),' of total: ',num2str(tinilen)])
-%
-% get data time indices and weights for temporal interpolation
-%
- if cycle~=0
- modeltime=mod(scrum_time(l),cycle);
- else
- modeltime=scrum_time;
- end
- l1=find(modeltime==datatime);
- if isempty(l1)
- disp('temporal interpolation')
- l1=max(find(datatime<modeltime));
- time1=datatime(l1);
- if isempty(l1)
- if cycle~=0
- l1=tlen;
- time1=datatime(l1)-cycle;
- else
- error('No previous time in the dataset')
- end
- end
- l2=min(find(datatime>modeltime));
- time2=datatime(l2);
- if isempty(l2)
- if cycle~=0
- l2=1;
- time2=datatime(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 annual dataset on the horizontal croco grid
-%
- disp('Add_ini_chla: horizontal extrapolation of surface data')
- surfchla=squeeze(ncseas{'chlorophyll'}(l1,jmin:jmax,imin:imax));
- surfchla=get_missing_val(x,y,surfchla,missval,Roa,default);
- surfchla2=squeeze(ncseas{'chlorophyll'}(l2,jmin:jmax,imin:imax));
- surfchla2=get_missing_val(x,y,surfchla2,missval,Roa,default);
- surfchla=cff1*surfchla + cff2*surfchla2;
- surfchlacroco=interp2(x,y,surfchla,lon,lat);
-%
-% extrapole the chlorophyll on the vertical
-%
- zeta = squeeze(nc{'zeta'}(l,:,:));
- zcroco=zlevs(h,zeta,theta_s,theta_b,hc,N,'r',vtransform);
- disp(['Add_ini_chla: vertical ',...
- 'extrapolation of chlorophyll'])
- chlacroco=extr_chlo(surfchlacroco,zcroco);
- nc{'CHLA'}(l,:,:,:)=chlacroco;
-end
-close(nc);
-close(ncseas);
-return
diff --git a/Preprocessing_tools/add_ini_no3.m b/Preprocessing_tools/add_ini_no3.m
deleted file mode 100644
index b3573181..00000000
--- a/Preprocessing_tools/add_ini_no3.m
+++ /dev/null
@@ -1,204 +0,0 @@
-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)<zmax;
-addsurf=1;
-addbot=min(z)>zmin;
-if addsurf
- z=[100;z];
-end
-if addbot
- z=[z;-100000];
-end
-Nz=min(find(z<zmin));
-z=z(1:Nz);
-%
-% read in the initial file
-%
-scrum_time = nc{'scrum_time'}(:);
-scrum_time = scrum_time / (24*3600);
-tinilen = length(scrum_time);
-%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';
-nc{'NO3'}.fields = ncchar('NO3, scalar, series');
-nc{'NO3'}.fields = 'NO3, scalar, series';
-%endef(nc);
-%
-% loop on initial time
-%
-for l=1:tinilen
- disp(['time index: ',num2str(l),' of total: ',num2str(tinilen)])
-%
-% get data time indices and weights for temporal interpolation
-%
- if cycle~=0
- modeltime=mod(scrum_time(l),cycle);
- else
- modeltime=scrum_time;
- end
- l1=find(modeltime==oatime);
- if isempty(l1)
- disp('temporal interpolation')
- l1=max(find(oatime<modeltime));
- time1=oatime(l1);
- if isempty(l1)
- if cycle~=0
- l1=tlen;
- time1=oatime(l1)-cycle;
- else
- error('No previous time in the dataset')
- end
- end
- l2=min(find(oatime>modeltime));
- 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<NO3min)=0;
- nc{'NO3'}(l,:,:,:)=NO3;
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/add_ini_npzd.m b/Preprocessing_tools/add_ini_npzd.m
deleted file mode 100644
index d89cbc20..00000000
--- a/Preprocessing_tools/add_ini_npzd.m
+++ /dev/null
@@ -1,63 +0,0 @@
-function add_ini_npzd(inifile,clobber)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Copyright (c) 2014 IRD %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% %
-% function nc=add_ini_npzd(inifile,clobber) %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% inifile Netcdf initial file name (character string). %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Output %
-% %
-% nc Output netcdf object. %
-% %
-% Gildas Cambon, IRD, 20123 %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding NPZD data in file : ',inifile])
-%
-% Create the initial file
-%
-nc = netcdf(inifile,clobber);
-%%result = redef(nc);
-%
-% Create variables
-%
-nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-% Create attributes
-%
-nc{'NO3'}.long_name = ncchar('NO3');
-nc{'NO3'}.long_name = 'NO3';
-nc{'NO3'}.units = ncchar('mMol N m-3');
-nc{'NO3'}.units = 'mMol N m-3';
-%
-nc{'O2'}.long_name = ncchar('O2');
-nc{'O2'}.long_name = 'O2';
-nc{'O2'}.units = ncchar('mMol O m-3');
-nc{'O2'}.units = 'mMol O m-3';
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'NO3'}(:) = 0;
-nc{'O2'}(:) = 0;
-%
-% Synchronize on disk
-%
-close(nc);
-return
-
-
diff --git a/Preprocessing_tools/add_ini_o2.m b/Preprocessing_tools/add_ini_o2.m
deleted file mode 100644
index 8212a904..00000000
--- a/Preprocessing_tools/add_ini_o2.m
+++ /dev/null
@@ -1,205 +0,0 @@
-function add_ini_o2(ininame,grdname,oaname,cycle,O2min);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,o2]=add_ini_o2(ininame,grdname,...
-% month_datafile,ann_datafile,...
-% cycle);
-%
-% Add oxygen (mMol O2 m-3) in a CROCO initial file.
-% take monthly 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)
-% month_datafile : regular longitude - latitude - z monthly 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,o2] : 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_o2: 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{'Zo2'}(:);
-oatime=noa{'o2_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)<zmax;
-addsurf=1;
-addbot=min(z)>zmin;
-if addsurf
- z=[100;z];
-end
-if addbot
- z=[z;-100000];
-end
-Nz=min(find(z<zmin));
-z=z(1:Nz);
-%
-% read in the initial file
-%
-scrum_time = nc{'scrum_time'}(:);
-scrum_time = scrum_time / (24*3600);
-tinilen = length(scrum_time);
-%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';
-nc{'O2'}.fields = ncchar('O2, scalar, series');
-nc{'O2'}.fields = 'O2, scalar, series';
-%endef(nc);
-%
-% loop on initial time
-%
-for l=1:tinilen
- disp(['time index: ',num2str(l),' of total: ',num2str(tinilen)])
-%
-% get data time indices and weights for temporal interpolation
-%
- if cycle~=0
- modeltime=mod(scrum_time(l),cycle);
- else
- modeltime=scrum_time;
- end
- l1=find(modeltime==oatime);
- if isempty(l1)
- disp('temporal interpolation')
- l1=max(find(oatime<modeltime));
- time1=oatime(l1);
- if isempty(l1)
- if cycle~=0
- l1=tlen;
- time1=oatime(l1)-cycle;
- else
- error('No previous time in the dataset')
- end
- end
- l2=min(find(oatime>modeltime));
- 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 monthly dataset on the horizontal croco grid
-%
- disp(['Add_ini_o2: vertical interpolation'])
- var=squeeze(noa{'O2'}(l1,:,:,:));
-
- if addsurf
- var=cat(1,var(1,:,:),var);
- end
- if addbot
- var=cat(1,var,var(end,:,:));
- end
- var2=squeeze(noa{'O2'}(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{'O2'}(l,:,:,:)=ztosigma(flipdim(var,1),zcroco,flipud(z));
-end
-close(noa);
-%
-% Remove low values for oligotrophic areas
-%
-for l=1:tinilen
- O2=nc{'O2'}(l,:,:,:);
- O2(O2<O2min)=O2min;
- nc{'O2'}(l,:,:,:)=O2;
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/add_ini_phyto.m b/Preprocessing_tools/add_ini_phyto.m
deleted file mode 100644
index 6c811b9b..00000000
--- a/Preprocessing_tools/add_ini_phyto.m
+++ /dev/null
@@ -1,68 +0,0 @@
-function add_ini_phyto(inifile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_ini_phyto(inifile);
-%
-% Add phytoplancton (mMol N m-3) in a CROCO initial file.
-% take the chlorophyll (mg C) from the initial file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations.
-%
-% phyto = 0.5 * chla
-%
-% input:
-%
-% inifile : croco initial file to process (netcdf)
-%
-% 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
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta=0.5;
-%
-disp('Add_ini_phyto: creating variable and attribute')
-%
-% open the initial file
-%
-nc=netcdf(inifile,'write');
-time= nc{'scrum_time'}(:);
-tlen=length(time);
-%%redef(nc);
-nc{'PHYTO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'PHYTO'}.long_name = ncchar('Phytoplankton');
-nc{'PHYTO'}.long_name = 'Phytoplankton';
-nc{'PHYTO'}.units = ncchar('mMol N m-3');
-nc{'PHYTO'}.units = 'mMol N m-3';
-nc{'PHYTO'}.fields = ncchar('PHYTO, scalar, series');
-nc{'PHYTO'}.fields = 'PHYTO, scalar, series';
-%%endef(nc);
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'PHYTO'}(l,:,:,:)=theta*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/add_ini_pisces.m b/Preprocessing_tools/add_ini_pisces.m
deleted file mode 100644
index c25cbb61..00000000
--- a/Preprocessing_tools/add_ini_pisces.m
+++ /dev/null
@@ -1,117 +0,0 @@
-function add_ini_pisces(inifile,clobber)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Copyright (c) 2000 IRD %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %
-% %
-% function nc=add_ini_pisces(inifile,clobber) %
-% %
-% This function create the header of a Netcdf climatology %
-% file. %
-% %
-% Input: %
-% %
-% inifile Netcdf initial file name (character string). %
-% clobber Switch to allow or not writing over an existing %
-% file.(character string) %
-% %
-% Output %
-% %
-% nc Output netcdf object. %
-% %
-% Pierrick Penven, IRD, 2005. %
-% Olivier Aumont, IRD, 2006. %
-% Patricio Marchesiello, IRD 2007 %
-% Christophe Eugene Raoul Menkes, IRD 2007 %
-% %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp([' Adding PISCES data in file : ',inifile])
-%
-% Create the initial file
-%
-nc = netcdf(inifile,clobber);
-%%result = redef(nc);
-%
-% Create variables
-%
-nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'PO4'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'Si'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'DIC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'TALK'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'FER'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-
-%
-% Create attributes
-%
-nc{'NO3'}.long_name = ncchar('NO3');
-nc{'NO3'}.long_name = 'NO3';
-nc{'NO3'}.units = ncchar('mMol N m-3');
-nc{'NO3'}.units = 'mMol N m-3';
-%
-%
-nc{'PO4'}.long_name = ncchar('PO4');
-nc{'PO4'}.long_name = 'PO4';
-nc{'PO4'}.units = ncchar('mMol P m-3');
-nc{'PO4'}.units = 'mMol P m-3';
-%
-%
-nc{'Si'}.long_name = ncchar('Si');
-nc{'Si'}.long_name = 'Si';
-nc{'Si'}.units = ncchar('mMol Si m-3');
-nc{'Si'}.units = 'mMol Si m-3';
-%
-%
-nc{'O2'}.long_name = ncchar('O2');
-nc{'O2'}.long_name = 'O2';
-nc{'O2'}.units = ncchar('mMol O m-3');
-nc{'O2'}.units = 'mMol O m-3';
-%
-%
-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';
-%
-%
-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';
-%
-%
-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';
-%
-%
-nc{'FER'}.long_name = ncchar('FER');
-nc{'FER'}.long_name = 'FER';
-nc{'FER'}.units = ncchar('mMol Fe m-3');
-nc{'FER'}.units = 'mMol Fe m-3';
-%
-% Leave define mode
-%
-%%result = endef(nc);
-%
-% Write variables
-%
-nc{'NO3'}(:) = 0;
-nc{'PO4'}(:) = 0;
-nc{'Si'}(:) = 0;
-nc{'O2'}(:) = 0;
-nc{'DIC'}(:) = 0;
-nc{'TALK'}(:) = 0;
-nc{'DOC'}(:) = 0;
-nc{'FER'}(:) = 0;
-%
-% Synchronize on disk
-%
-close(nc);
-return
-
-
diff --git a/Preprocessing_tools/add_ini_zoo.m b/Preprocessing_tools/add_ini_zoo.m
deleted file mode 100644
index aed5c31e..00000000
--- a/Preprocessing_tools/add_ini_zoo.m
+++ /dev/null
@@ -1,70 +0,0 @@
-function add_ini_zoo(inifile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_ini_zoo(inifile);
-%
-% Add zooplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the initial file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations (Gruber et al., 2005)
-%
-% zoo = 0.2 * chla
-
-% input:
-%
-% inifile : croco initial file to process (netcdf)
-%
-% 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
-%
-% Updated in 2005 by Patrick Marchesiello
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta=0.2;
-%
-disp('Add_ini_zoo: creating variable and attribute')
-%
-% open the initial file
-%
-nc=netcdf(inifile,'write');
-time= nc{'scrum_time'}(:);
-tlen=length(time);
-%%redef(nc);
-nc{'ZOO'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'ZOO'}.long_name = ncchar('Zooplankton');
-nc{'ZOO'}.long_name = 'Zooplankton';
-nc{'ZOO'}.units = ncchar('mMol N m-3');
-nc{'ZOO'}.units = 'mMol N m-3';
-nc{'ZOO'}.fields = ncchar('ZOO, scalar, series');
-nc{'ZOO'}.fields = 'ZOO, scalar, series';
-%%endef(nc);
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'ZOO'}(l,:,:,:)=theta*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/add_no3.m b/Preprocessing_tools/add_no3.m
deleted file mode 100644
index 1670583b..00000000
--- a/Preprocessing_tools/add_no3.m
+++ /dev/null
@@ -1,185 +0,0 @@
-function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,no3]=add_no3(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% Add nitrate (mMol N m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-t;
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zno3=nc{'Z'}(:);
-kmax=max(find(zno3<hmax))-1;
-zno3=zno3(1:kmax);
-%disp('Size zno3=')
-size(zno3);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_no3: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
- % redef(nc);
-
- %Create Dimensions
- nc('no3_time') = length(t);
- %Create Variable
- nc{'no3_time'} = ncdouble('no3_time') ;
-%
-%%
-%
- %Create Dimensions
- nc('Zno3') = length(zno3);
- %Create Variable
- nc{'Zno3'} = ncdouble('Zno3') ;
-%
-%%
-%
- %Create Variable
- nc{'NO3'} = ncdouble('no3_time','Zno3','eta_rho','xi_rho') ;
-%
-%%
-%
- %Create Attribute
-
- nc{'no3_time'}.long_name = ncchar('time for nitrate');
- nc{'no3_time'}.long_name = 'time for nitrate';
- nc{'no3_time'}.units = ncchar('day');
- nc{'no3_time'}.units = 'day';
- if cycle~=0
- nc{'no3_time'}.cycle_length = cycle;
- end
-%%%
- nc{'Zno3'}.long_name = ncchar('Depth for NO3');
- nc{'Zno3'}.long_name = 'Depth for NO3';
- nc{'Zno3'}.units = ncchar('m');
- nc{'Zno3'}.units = 'm';
-%%%
- 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{'NO3'}.fields = ncchar('NO3, scalar, series');
- nc{'NO3'}.fields = 'NO3, scalar, series';
-%%%
-%% endef(nc);
-%
-%% Write variables
-%% record depth and time and close
-%
- nc{'no3_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zno3'}(:)=zno3;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_no3: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
- % redef(nc);
- nc('no3_time') = length(t);;
- nc{'no3_time'} = ncdouble('no3_time') ;
- nc{'NO3'} = ncdouble('no3_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'no3_time'}.long_name = ncchar('time for nitrate');
- nc{'no3_time'}.long_name = 'time for nitrate';
- nc{'no3_time'}.units = ncchar('day');
- nc{'no3_time'}.units = 'day';
- if cycle~=0
- nc{'no3_time'}.cycle_length = cycle;
- end
-%
- 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{'NO3'}.fields = ncchar('NO3, scalar, series');
- nc{'NO3'}.fields = 'NO3, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'no3_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing 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)
-
-return
diff --git a/Preprocessing_tools/add_o2.m b/Preprocessing_tools/add_o2.m
deleted file mode 100644
index 86321ce1..00000000
--- a/Preprocessing_tools/add_o2.m
+++ /dev/null
@@ -1,126 +0,0 @@
-function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,o2]=add_o2(climfile,gridfile,...
-% month_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add oxygen (mMol 0 m-3) in a CROCO climatology file
-% take monthly data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : croco grid file (netcdf)
-% month_datafile : regular longitude - latitude - z monthly 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,o2] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(month_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zo2=nc{'Z'}(:);
-kmax=max(find(zo2<hmax))-1;
-zo2=zo2(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_o2: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('o2_time') = length(t);
- nc{'o2_time'} = ncdouble('o2_time') ;
- nc('Zo2') = length(zo2);
- nc{'Zo2'} = ncdouble('Zo2') ;
- nc{'O2'} = ncdouble('o2_time','Zo2','eta_rho','xi_rho') ;
-%
- nc{'o2_time'}.long_name = ncchar('time for oxygen');
- nc{'o2_time'}.long_name = 'time for oxygen';
- nc{'o2_time'}.units = ncchar('day');
- nc{'o2_time'}.units = 'day';
- if cycle~=0
- nc{'o2_time'}.cycle_length = cycle;
- end
-%
- nc{'Zo2'}.long_name = ncchar('Depth for O2');
- nc{'Zo2'}.long_name = 'Depth for O2';
- nc{'Zo2'}.units = ncchar('m');
- nc{'Zo2'}.units = 'm';
-%
- 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';
- nc{'O2'}.fields = ncchar('O2, scalar, series');
- nc{'O2'}.fields = 'O2, scalar, series';
-%
-%% endef(nc);
-%
-% record depth and time and close
-%
- nc{'o2_time'}(:)=t*30; % ojo aqui quite *30 % if time in month in the dataset !!!
- nc{'Zo2'}(:)=squeeze(zo2);
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_o2: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
- %% redef(nc);
- nc('o2_time') = length(t);
- nc{'o2_time'} = ncdouble('o2_time') ;
- nc{'O2'} = ncdouble('o2_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'o2_time'}.long_name = ncchar('time for oxygen');
- nc{'o2_time'}.long_name = 'time for oxygen';
- nc{'o2_time'}.units = ncchar('day');
- nc{'o2_time'}.units = 'day';
- if cycle~=0
- nc{'o2_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'O2'}.fields = ncchar('O2, scalar, series');
- nc{'O2'}.fields = 'O2, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'o2_time'}(:,:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-
-return
diff --git a/Preprocessing_tools/add_phyto.m b/Preprocessing_tools/add_phyto.m
deleted file mode 100644
index c38091ca..00000000
--- a/Preprocessing_tools/add_phyto.m
+++ /dev/null
@@ -1,85 +0,0 @@
-function add_phyto(climfile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_phyto(climfile);
-%
-% Add phytoplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the climatology file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations.
-%
-% phyto = 0.5 * chla
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-%
-% 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
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta=0.5;
-%
-disp('Add_phyto: creating variable and attribute')
-%
-% open the clim file
-%
-nc=netcdf(climfile,'write');
-time= nc{'chla_time'}(:);
-cycle= nc{'chla_time'}.cycle_length(:);
-tlen=length(time);
-%%redef(nc);
-nc('phyto_time') = tlen;
-nc{'phyto_time'} = ncdouble('phyto_time') ;
-nc{'PHYTO'} = ncdouble('phyto_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'phyto_time'}.long_name = ncchar('time for phytoplankton');
-nc{'phyto_time'}.long_name = 'time for phytoplankton';
-nc{'phyto_time'}.units = ncchar('day');
-nc{'phyto_time'}.units = 'day';
-if cycle~=0
- nc{'phyto_time'}.cycle_length = cycle;
-end
-%
-nc{'PHYTO'}.long_name = ncchar('Phytoplankton');
-nc{'PHYTO'}.long_name = 'Phytoplankton';
-nc{'PHYTO'}.units = ncchar('mMol N m-3');
-nc{'PHYTO'}.units = 'mMol N m-3';
-nc{'PHYTO'}.fields = ncchar('PHYTO, scalar, series');
-nc{'PHYTO'}.fields = 'PHYTO, scalar, series';
-%
-%%endef(nc);
-%
-% record the time
-%
-nc{'phyto_time'}(:)=time;
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'PHYTO'}(l,:,:,:)=theta*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/add_po4.m b/Preprocessing_tools/add_po4.m
deleted file mode 100644
index 0c442009..00000000
--- a/Preprocessing_tools/add_po4.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_po4(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,po4]=add_po4(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add phosphate (mMol P m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,po4] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zpo4=nc{'Z'}(:);
-kmax=max(find(zpo4<hmax))-1;
-zpo4=zpo4(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_po4: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('po4_time') = length(t);
- nc{'po4_time'} = ncdouble('po4_time') ;
- nc('Zpo4') = length(zpo4);
- nc{'Zpo4'} = ncdouble('Zpo4') ;
- nc{'PO4'} = ncdouble('po4_time','Zpo4','eta_rho','xi_rho') ;
-%
- nc{'po4_time'}.long_name = ncchar('time for phosphate');
- nc{'po4_time'}.long_name = 'time for phosphate';
- nc{'po4_time'}.units = ncchar('day');
- nc{'po4_time'}.units = 'day';
- if cycle~=0
- nc{'po4_time'}.cycle_length = cycle;
- end
-%
- nc{'Zpo4'}.long_name = ncchar('Depth for PO4');
- nc{'Zpo4'}.long_name = 'Depth for PO4';
- nc{'Zpo4'}.units = ncchar('m');
- nc{'Zpo4'}.units = 'm';
-%
- 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';
- nc{'PO4'}.fields = ncchar('PO4, scalar, series');
- nc{'PO4'}.fields = 'PO4, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'po4_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zpo4'}(:)=zpo4;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_po4: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('po4_time') = length(t);;
- nc{'po4_time'} = ncdouble('po4_time') ;
- nc{'PO4'} = ncdouble('po4_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'po4_time'}.long_name = ncchar('time for phosphate');
- nc{'po4_time'}.long_name = 'time for phosphate';
- nc{'po4_time'}.units = ncchar('day');
- nc{'po4_time'}.units = 'day';
- if cycle~=0
- nc{'po4_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'PO4'}.fields = ncchar('PO4, scalar, series');
- nc{'PO4'}.fields = 'PO4, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'po4_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing 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)
-
-return
diff --git a/Preprocessing_tools/add_sio3.m b/Preprocessing_tools/add_sio3.m
deleted file mode 100644
index b5be4d2d..00000000
--- a/Preprocessing_tools/add_sio3.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_sio3(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,sio3]=add_sio3(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add silicate (mMol Si m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,SiO3] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-zsi=nc{'Z'}(:);
-kmax=max(find(zsi<hmax))-1;
-zsi=zsi(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_sio3: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('si_time') = length(t);
- nc{'si_time'} = ncdouble('si_time') ;
- nc('Zsi') = length(zsi);
- nc{'Zsi'} = ncdouble('Zsi') ;
- nc{'Si'} = ncdouble('si_time','Zsi','eta_rho','xi_rho') ;
-%
- nc{'si_time'}.long_name = ncchar('time for silicate');
- nc{'si_time'}.long_name = 'time for silicate';
- nc{'si_time'}.units = ncchar('day');
- nc{'si_time'}.units = 'day';
- if cycle~=0
- nc{'si_time'}.cycle_length = cycle;
- end
-%
- nc{'Zsi'}.long_name = ncchar('Depth for Si');
- nc{'Zsi'}.long_name = 'Depth for Si';
- nc{'Zsi'}.units = ncchar('m');
- nc{'Zsi'}.units = 'm';
-%
- 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';
- nc{'Si'}.fields = ncchar('Si, scalar, series');
- nc{'Si'}.fields = 'Si, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'si_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Zsi'}(:)=zsi;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_sio3: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('si_time') = length(t);;
- nc{'si_time'} = ncdouble('si_time') ;
- nc{'Si'} = ncdouble('si_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'si_time'}.long_name = ncchar('time for silicate');
- nc{'si_time'}.long_name = 'time for silicate';
- nc{'si_time'}.units = ncchar('day');
- nc{'si_time'}.units = 'day';
- if cycle~=0
- nc{'si_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'Si'}.fields = ncchar('Si, scalar, series');
- nc{'Si'}.fields = 'Si, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'si_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing 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)
-
-return
diff --git a/Preprocessing_tools/add_talk.m b/Preprocessing_tools/add_talk.m
deleted file mode 100644
index 1bdf16b7..00000000
--- a/Preprocessing_tools/add_talk.m
+++ /dev/null
@@ -1,144 +0,0 @@
-function add_talk(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function [longrd,latgrd,talk]=add_talk(climfile,gridfile,...
-% seas_datafile,ann_datafile,...
-% cycle);
-%
-% pierrick 2001
-%
-% Add talk (mMol P m-3) in a CROCO climatology file
-% take seasonal data for the upper levels and annual data for the
-% lower levels
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-% gridfile : 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,talk] : surface field to plot (as an illustration)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Read in the grid
-%
-nc=netcdf(gridfile,'r');
-hmax=max(max(nc{'h'}(:)));
-close(nc);
-%
-% read in the datafiles
-%
-nc=netcdf(seas_datafile,'r');
-t=nc{'T'}(:);
-close(nc)
-nc=netcdf(ann_datafile,'r');
-ztalk=nc{'Z'}(:);
-kmax=max(find(ztalk<hmax))-1;
-ztalk=ztalk(1:kmax);
-close(nc)
-%
-% open the OA file
-%
-if (makeoa)
- disp('Add_talk: creating variables and attributes for the OA file')
- nc=netcdf(oafile,'write');
-%% redef(nc);
- nc('talk_time') = length(t);
- nc{'talk_time'} = ncdouble('talk_time') ;
- nc('Ztalk') = length(ztalk);
- nc{'Ztalk'} = ncdouble('Ztalk') ;
- nc{'TALK'} = ncdouble('talk_time','Ztalk','eta_rho','xi_rho') ;
-%
- nc{'talk_time'}.long_name = ncchar('time for TALK');
- nc{'talk_time'}.long_name = 'time for TALK';
- nc{'talk_time'}.units = ncchar('day');
- nc{'talk_time'}.units = 'day';
- if cycle~=0
- nc{'talk_time'}.cycle_length = cycle;
- end
-%
- nc{'Ztalk'}.long_name = ncchar('Depth for TALK');
- nc{'Ztalk'}.long_name = 'Depth for TALK';
- nc{'Ztalk'}.units = ncchar('m');
- nc{'Ztalk'}.units = 'm';
-%
- 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';
- nc{'TALK'}.fields = ncchar('TALK, scalar, series');
- nc{'TALK'}.fields = 'TALK, scalar, series';
-%
-%% endef(nc);
-%
-% record deth and time and close
-%
- nc{'talk_time'}(:)=t*30; % if time in month in the dataset !!!
- nc{'Ztalk'}(:)=ztalk;
- close(nc)
-end
-%
-% Same thing for the Clim file
-%
-if (makeclim)
- disp('Add_talk: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
- nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('talk_time') = length(t);;
- nc{'talk_time'} = ncdouble('talk_time') ;
- nc{'TALK'} = ncdouble('talk_time','s_rho','eta_rho','xi_rho') ;
-%
- nc{'talk_time'}.long_name = ncchar('time for TALK');
- nc{'talk_time'}.long_name = 'time for TALK';
- nc{'talk_time'}.units = ncchar('day');
- nc{'talk_time'}.units = 'day';
- if cycle~=0
- nc{'talk_time'}.cycle_length = cycle;
- end
-%
- 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';
- nc{'TALK'}.fields = ncchar('TALK, scalar, series');
- nc{'TALK'}.fields = 'TALK, scalar, series';
-%
-%% endef(nc);
-%
-% record the time and close
-%
- nc{'talk_time'}(:)=t*30; % if time in month in the dataset !!!
- close(nc)
-end
-%
-% Same thing 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)
-
-return
diff --git a/Preprocessing_tools/add_zoo.m b/Preprocessing_tools/add_zoo.m
deleted file mode 100644
index 597a1c10..00000000
--- a/Preprocessing_tools/add_zoo.m
+++ /dev/null
@@ -1,87 +0,0 @@
-function add_zoo(climfile);
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% function add_zoo(climfile);
-%
-% Add zooplancton (mMol N m-3) in a CROCO climatology file.
-% take the chlorophyll (mg C) from the climatology file and
-% multiply by the ratio chlorophyll / phytoplancton derived
-% from previous simulations (Gruber et al., 2005)
-%
-% zoo = 0.2 * chla
-%
-% input:
-%
-% climfile : croco climatology file to process (netcdf)
-%
-% 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
-%
-% Updated 2005 by Patrick Marchesiello (IRD)
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-theta=0.2;
-%
-disp('Add_zoo: creating variable and attribute')
-%
-% open the clim file
-%
-nc=netcdf(climfile,'write');
-time= nc{'chla_time'}(:);
-cycle= nc{'chla_time'}.cycle_length(:);
-tlen=length(time);
-%%redef(nc);
-nc('zoo_time') = tlen;
-nc{'zoo_time'} = ncdouble('zoo_time') ;
-nc{'ZOO'} = ncdouble('zoo_time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'zoo_time'}.long_name = ncchar('time for zooplankton');
-nc{'zoo_time'}.long_name = 'time for zooplankton';
-nc{'zoo_time'}.units = ncchar('day');
-nc{'zoo_time'}.units = 'day';
-if cycle~=0
- nc{'zoo_time'}.cycle_length = cycle;
-end
-%
-nc{'ZOO'}.long_name = ncchar('Zooplankton');
-nc{'ZOO'}.long_name = 'Zooplankton';
-nc{'ZOO'}.units = ncchar('mMol N m-3');
-nc{'ZOO'}.units = 'mMol N m-3';
-nc{'ZOO'}.fields = ncchar('ZOO, scalar, series');
-nc{'ZOO'}.fields = 'ZOO, scalar, series';
-%
-%%endef(nc);
-%
-% record the time
-%
-nc{'zoo_time'}(:)=time;
-%
-% loop on time
-%
-for l=1:tlen
- disp(['time index: ',num2str(l),' of total: ',num2str(tlen)])
- nc{'ZOO'}(l,:,:,:)=theta*squeeze(nc{'CHLA'}(l,:,:,:));
-end
-close(nc);
-return
diff --git a/Preprocessing_tools/make_clim_bioebus.m b/Preprocessing_tools/make_clim_bioebus.m
deleted file mode 100644
index b9a9f2fa..00000000
--- a/Preprocessing_tools/make_clim_bioebus.m
+++ /dev/null
@@ -1,159 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Build a CROCO initial file from Global Atlas (WOA or CARS)
-%
-% Extrapole and interpole fields from a
-% Climatology to get initial conditions for
-% CROCO (initial netcdf files) .
-%
-% Data input format (netcdf):
-% variable(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 2013
-% Elodie Gutknecht, 2013
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clear all
-close all
-%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Title
-%
-crocotools_param
-%
-% Data climatologies file names:
-%
-
-no3_seas_data = [climato_dir,'no3_month.cdf'];
-no3_ann_data = [climato_dir,'no3_ann.cdf'];
-o2_seas_data = [climato_dir,'o2_month.cdf'];
-o2_ann_data = [climato_dir,'o2_ann.cdf'];
-chla_seas_data = [chla_dir,'chla_seas.cdf'];
-
-NO3min=0.01;
-O2min=0.01;
-%
-%
-%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
-disp('')
-disp('====================================================== ')
-disp('=> You need the croco_oa.nc file created by make_clim.m ')
-disp('=> with makeoa=1 from crocotools_param.m ')
-disp('====================================================== ')
-
-%
-% Add variables in the files
-%
-add_no3(oaname,clmname,ininame,grdname,no3_seas_data,...
- no3_ann_data,woa_cycle,makeoa,makeclim)
-
-add_o2(oaname,clmname,ininame,grdname,o2_seas_data,...
- o2_ann_data,woa_cycle,makeoa,makeclim)
-
-
-%
-% Horizontal extrapolation
-%
-if (makeoa)
-
- ext_tracers(oaname,no3_seas_data,no3_ann_data,...
- 'nitrate','NO3','no3_time','Zno3',Roa);
-
- ext_tracers(oaname,o2_seas_data,o2_ann_data,...
- 'oxygen','O2','o2_time','Zo2',Roa);
-
-end
-
-
-%
-% Vertical interpolations
-%
-if (makeclim)
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' O2...')
- vinterp_clm(clmname,grdname,oaname,'O2','o2_time','Zo2',0,'r');
- disp(' ')
- disp(' NO3...')
- vinterp_clm(clmname,grdname,oaname,'NO3','no3_time','Zno3',0,'r');
-%
-% Remove low values for oligotrophic areas
-%
- nc=netcdf(clmname,'write');
- tlen=length(nc('no3_time'));
- for l=1:tlen
- NO3=nc{'NO3'}(l,:,:,:);
- NO3(NO3<NO3min)=NO3min;
- nc{'NO3'}(l,:,:,:)=NO3;
- end
- close(nc)
-
- nc=netcdf(clmname,'write');
- tlen=length(nc('o2_time'));
- for l=1:tlen
- O2=nc{'O2'}(l,:,:,:);
- O2(O2<O2min)=O2min;
- nc{'O2'}(l,:,:,:)=O2;
- end
- close(nc)
-
-
-%
-% CHla
- disp(' ')
- disp(' CHla...')
- add_chla(clmname,grdname,chla_seas_data,woa_cycle,Roa);
-%
-% Phyto
- disp(' ')
- disp(' SPhyto and LPhyto...')
- add_Sphyto_Lphyto(clmname);
-%
-% Zoo
- disp(' ')
- disp(' SZoo and LZoo...')
- add_Szoo_Lzoo(clmname);
-
-end
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%
-% Make a few plots
-%
-
-if (makeplot)
- disp(' ')
- disp(' Make a few plots...')
- test_clim(clmname,grdname,'O2',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'NO3',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'CHLA',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'SPHYTO',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'LPHYTO',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'SZOO',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'LZOO',1,coastfileplot)
-end
-
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
diff --git a/Preprocessing_tools/make_clim_npzd.m b/Preprocessing_tools/make_clim_npzd.m
deleted file mode 100644
index 0f31acb2..00000000
--- a/Preprocessing_tools/make_clim_npzd.m
+++ /dev/null
@@ -1,152 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Build a CROCO initial file from Global Atlas (WOA or CARS)
-%
-% Extrapole and interpole fields from a
-% Climatology to get initial conditions for
-% CROCO (initial netcdf files) .
-%
-% Data input format (netcdf):
-% variable(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 2013
-% Elodie Gutknecht, 2013
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clear all
-close all
-%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Title
-%
-crocotools_param
-%
-% Data climatologies file names:
-%
-no3_seas_data=[climato_dir,'no3_seas.cdf'];
-no3_ann_data=[climato_dir,'no3_ann.cdf'];
-o2_seas_data=[climato_dir,'o2_seas.cdf'];
-o2_ann_data=[climato_dir,'o2_ann.cdf'];
-chla_seas_data=[chla_dir,'chla_seas.cdf'];
-
-NO3min=0.01;
-O2min=0.01;
-%
-%
-%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
-disp('')
-disp('====================================================== ')
-disp('=> You need the croco_oa.nc file created by make_clim.m ')
-disp('=> with makeoa=1 from crocotools_param.m ')
-disp('====================================================== ')
-%
-% Add variables in the files
-%
-add_no3(oaname,clmname,ininame,grdname,no3_seas_data,...
- no3_ann_data,woa_cycle,makeoa,makeclim)
-
-add_o2(oaname,clmname,ininame,grdname,o2_seas_data,...
- o2_ann_data,woa_cycle,makeoa,makeclim)
-
-
-%
-% Horizontal extrapolation
-%
-if (makeoa)
-
- ext_tracers(oaname,no3_seas_data,no3_ann_data,...
- 'nitrate','NO3','no3_time','Zno3',Roa);
-
- ext_tracers(oaname,o2_seas_data,o2_ann_data,...
- 'oxygen','O2','o2_time','Zo2',Roa);
-
-end
-
-
-%
-% Vertical interpolations
-%
-if (makeclim)
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' O2...')
- vinterp_clm(clmname,grdname,oaname,'O2','o2_time','Zo2',0,'r');
- disp(' ')
- disp(' NO3...')
- vinterp_clm(clmname,grdname,oaname,'NO3','no3_time','Zno3',0,'r');
-%
-% Remove low values for oligotrophic areas
-%
- nc=netcdf(clmname,'write');
- tlen=length(nc('no3_time'));
- for l=1:tlen
- NO3=nc{'NO3'}(l,:,:,:);
- NO3(NO3<NO3min)=NO3min;
- nc{'NO3'}(l,:,:,:)=NO3;
- end
- close(nc)
-
- nc=netcdf(clmname,'write');
- tlen=length(nc('o2_time'));
- for l=1:tlen
- O2=nc{'O2'}(l,:,:,:);
- O2(O2<O2min)=O2min;
- nc{'O2'}(l,:,:,:)=O2;
- end
- close(nc)
-
-
-%
-% CHla
- disp(' ')
- disp(' CHla...')
- add_chla(clmname,grdname,chla_seas_data,woa_cycle,Roa);
-%
-% Phyto
- disp(' ')
- disp(' Phyto...')
- add_phyto(clmname);
-%
-% Zoo
- disp(' ')
- disp(' Zoo...')
- add_zoo(clmname);
-
-end
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%
-% Make a few plots
-%
-
-if (makeplot)
- disp(' ')
- disp(' Make a few plots...')
- test_clim(clmname,grdname,'O2',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'NO3',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'CHLA',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'PHYTO',1,coastfileplot)
-end
-
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
diff --git a/Preprocessing_tools/make_clim_pisces.m b/Preprocessing_tools/make_clim_pisces.m
deleted file mode 100644
index a3bc593a..00000000
--- a/Preprocessing_tools/make_clim_pisces.m
+++ /dev/null
@@ -1,221 +0,0 @@
-clear all
-close all
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Extrapole and interpole biology data and write in climatology file
-%
-% Data source : IRI/LDEO Climate Data Library (World Ocean Atlas 1998)
-% http://ingrid.ldgo.columbia.edu/
-% http://iridl.ldeo.columbia.edu/SOURCES/.NOAA/.NODC/.WOA2001/
-%
-% Pierrick Penven, IRD, 2005.
-% Olivier Aumont the master, IRD, 2006.
-% Patricio Marchesiello, chief, IRD, 2007.
-% Christophe Eugene Raoul Menkes, the slave, IRD, 2007.
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clear all
-close all
-%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Switches for selecting what to process (1=ON)
-%
-crocotools_param
-%
-% Climatology files
-%
-%
-no3_seas_data = [woapisces_dir,'no3_seas.cdf'];
-no3_ann_data = [woapisces_dir,'no3_ann.cdf'];
-po4_seas_data = [woapisces_dir,'po4_seas.cdf'];
-po4_ann_data = [woapisces_dir,'po4_ann.cdf'];
-o2_seas_data = [woapisces_dir,'o2_seas.cdf'];
-o2_ann_data = [woapisces_dir,'o2_ann.cdf'];
-sio3_seas_data = [woapisces_dir,'sio3_seas.cdf'];
-sio3_ann_data = [woapisces_dir,'sio3_ann.cdf'];
-dic_seas_data = [woapisces_dir,'dic_seas.cdf'];
-dic_ann_data = [woapisces_dir,'dic_ann.cdf'];
-talk_seas_data = [woapisces_dir,'talk_seas.cdf'];
-talk_ann_data = [woapisces_dir,'talk_ann.cdf'];
-doc_seas_data = [woapisces_dir,'doc_seas.cdf'];
-doc_ann_data = [woapisces_dir,'doc_ann.cdf'];
-fer_seas_data = [woapisces_dir,'fer_seas.cdf'];
-fer_ann_data = [woapisces_dir,'fer_ann.cdf'];
-dust_seas_data = [woapisces_dir,'dust_seas.cdf'];
-dust_ann_data = [woapisces_dir,'dust_ann.cdf'];
-%
-cycle=woa_cycle;
-NO3min=1;
-if strcmp(climato_dir,cars2009_dir);
- err_msg=sprintf(['Error : you need to use woadir when creating the croco_oa.nc (Z) \n'...
- 'files to be compatible with PISCES'])
- error(err_msg)
-end
-
-%
-%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
-%
-% Add variables in the files
-%
-disp('')
-disp('====================================================== ')
-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)
-
-add_po4(oaname,clmname,ininame,grdname,po4_seas_data,...
- po4_ann_data,cycle,makeoa,makeclim)
-
-add_sio3(oaname,clmname,ininame,grdname,sio3_seas_data,...
- sio3_ann_data,cycle,makeoa,makeclim)
-
-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)
-
-add_talk(oaname,clmname,ininame,grdname,talk_seas_data,...
- talk_ann_data,cycle,makeoa,makeclim)
-
-add_doc(oaname,clmname,ininame,grdname,doc_seas_data,...
- doc_ann_data,cycle,makeoa,makeclim)
-
-add_fer(oaname,clmname,ininame,grdname,fer_seas_data,...
- fer_ann_data,cycle,makeoa,makeclim)
-
-%
-% Horizontal extrapolation
-%
-if (makeoa)
- ext_tracers(oaname,no3_seas_data,no3_ann_data,...
- 'nitrate','NO3','no3_time','Zno3',Roa);
-
- ext_tracers(oaname,po4_seas_data,po4_ann_data,...
- 'phosphate','PO4','po4_time','Zpo4',Roa);
-
- ext_tracers(oaname,sio3_seas_data,sio3_ann_data,...
- 'silicate','Si','si_time','Zsi',Roa);
-
- ext_tracers(oaname,o2_seas_data,o2_ann_data,...
- 'oxygen','O2','o2_time','Zo2',Roa);
-
- ext_tracers(oaname,dic_seas_data,dic_ann_data,...
- 'dic','DIC','dic_time','Zdic',Roa);
-
- ext_tracers(oaname,talk_seas_data,talk_ann_data,...
- 'talk','TALK','talk_time','Ztalk',Roa);
-
- ext_tracers(oaname,doc_seas_data,doc_ann_data,...
- 'doc','DOC','doc_time','Zdoc',Roa);
-
- ext_tracers(oaname,fer_seas_data,fer_ann_data,...
- 'fer','FER','fer_time','Zfer',Roa);
-end
-%
-% Vertical interpolations
-%
-if (makeclim)
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' NO3...')
- vinterp_clm(clmname,grdname,oaname,'NO3','no3_time','Zno3',0,'r');
-%
-% PO4
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' PO4...')
- vinterp_clm(clmname,grdname,oaname,'PO4','po4_time','Zpo4',0,'r');
- %
- % Si
- %
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' Si...')
- vinterp_clm(clmname,grdname,oaname,'Si','si_time','Zsi',0,'r');
-%
-% O2
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' O2...')
- vinterp_clm(clmname,grdname,oaname,'O2','o2_time','Zo2',0,'r');
-
-%
-% DIC
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DIC...')
- vinterp_clm(clmname,grdname,oaname,'DIC','dic_time','Zdic',0,'r');
-%
-% TALK
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' TALK...')
- vinterp_clm(clmname,grdname,oaname,'TALK','talk_time','Ztalk',0,'r');
-
-%
-% DOC
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DOC...')
- vinterp_clm(clmname,grdname,oaname,'DOC','doc_time','Zdoc',0,'r');
-%
-% FER
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' FER...')
- vinterp_clm(clmname,grdname,oaname,'FER','fer_time','Zfer',0,'r');
-end
-
-
-if (makeplot)
-disp(' ')
-disp(' Make a few plots...')
-test_clim(clmname,grdname,'NO3',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'PO4',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'Si',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'O2',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'DIC',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'TALK',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'DOC',1,coastfileplot)
-figure
-test_clim(clmname,grdname,'FER',1,coastfileplot)
-end
-%
-% End
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/Preprocessing_tools/vinterp_bry_bgc.m b/Preprocessing_tools/vinterp_bry_bgc.m
deleted file mode 100644
index 154fb011..00000000
--- a/Preprocessing_tools/vinterp_bry_bgc.m
+++ /dev/null
@@ -1,109 +0,0 @@
-function vinterp_bry_bgc(bryname,grdname,Zbryname,time,vname,obcndx)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Vertical interpolation from a Z-grid to a sigma-grid in the
-% case of boundary (bry) files.
-%
-% 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) 2005-2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% open the grid file
-%
-ng=netcdf(grdname,'r');
-L=length(ng('xi_rho'));
-M=length(ng('eta_rho'));
-if obcndx==1
- h=ng{'h'}(1,:);
-elseif obcndx==2
- h=ng{'h'}(:,L);
-elseif obcndx==3
- h=ng{'h'}(M,:);
-elseif obcndx==4
- h=ng{'h'}(:,1);
-end
-close(ng);
-%
-% open the boundary file
-%
-nc=netcdf(bryname,'write');
-theta_s = nc{'theta_s'}(:);
-theta_b = nc{'theta_b'}(:);
-hc = nc{'hc'}(:);
-N = length(nc('s_rho'));
-vtransform = nc{'Vtransform'}(:);
-if ~exist('vtransform')
- vtransform=1; %Old Vtransform
- disp([' NO VTRANSFORM parameter found'])
- disp([' USE TRANSFORM default value vtransform = 1'])
-end
-% open the oa file
-%
-noa=netcdf(Zbryname,'r');
-z=-noa{'Z'}(:);
-t=noa{time}(:);
-tlen=length(t);
-Nz0=length(z);
-%
-% Get the sigma depths
-%
-zcroco=squeeze(zlevs(h,0.*h,theta_s,theta_b,hc,N,'r',vtransform));
-zmin=min(min(zcroco));
-zmax=max(max(zcroco));
-%
-% Check if the min z level is below the min sigma level
-% (if not add a deep layer)
-%
-addsurf=max(z)<zmax;
-addbot=min(z)>zmin;
-if addsurf
- z=[100;z];
-end
-if addbot
- z=[z;-100000];
-end
-Nz=min(find(z<zmin));
-z=z(1:Nz);
-%
-% loop on time
-%
-
-for l=1:tlen
-%for l=1:1
- disp([' Time index: ',num2str(l),' of total: ',num2str(tlen)])
- var=squeeze(noa{vname}(l,:));
-% disp(['SIZE VAR=',num2str(size(var))])
- if addsurf
- var=cat(1,var(1,:),var);
- end
- if addbot
- var=cat(1,var,var(end,:));
- end
- var=var(1:Nz,:);
- nc{vname}(l,:,:)=ztosigma_1d(flipdim(var,1),zcroco,flipud(z));
-end
-close(nc);
-close(noa);
-
-return
--
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