From e28f8f5105c72073c0d4ec4b9f2b42ea22fa5fe1 Mon Sep 17 00:00:00 2001
From: Gildas Cambon <gildas.cambon@ird.fr>
Date: Wed, 19 Mar 2025 16:44:23 +0100
Subject: [PATCH] Resolve #51 #57 #58 #59 #60 "issues with time unit attribute
in inputs file for USE_CALENDAR" + Preprocessing/Bio + Nesting_tools +
various things
---
Aforc_ECMWF/make_bry_wkb_ECMWF.m | 12 +-
Aforc_ERA5/ERA5_convert.py | 7 +-
Aforc_ERA5/era5_crocotools_param.py | 8 +-
Aforc_ERA5/interp_ERA5.m | 22 +-
Aforc_ERA5/make_ERA5.m | 174 ++---
Aforc_ERA5/make_bry_wkb_ERA5.m | 14 +-
CHANGELOG.md | 15 +
Nesting_tools/create_nestedbulk.m | 20 +-
Nesting_tools/create_nestedclim.m | 73 +-
Nesting_tools/create_nesteddust.m | 50 +-
Nesting_tools/create_nestedforcing.m | 45 +-
Nesting_tools/create_nestedinitial.m | 23 +-
Nesting_tools/create_nestedndepo.m | 113 ++++
Nesting_tools/interp_dust.m | 1 +
Nesting_tools/nested_clim.m | 192 +++---
Nesting_tools/nested_dust.m | 4 +
Nesting_tools/nested_ndepo.m | 118 ++++
Nesting_tools/nestgui.fig | Bin 43757 -> 48005 bytes
Nesting_tools/plot_nestndepo.m | 83 +++
Oforc_OGCM/create_OGCM.m | 88 +--
Oforc_OGCM/make_OGCM_SODA.m | 222 +++---
Oforc_OGCM/make_OGCM_mercator.m | 635 +++++++++---------
Preprocessing_tools/Bio/add_bry_pisces.m | 347 +++++-----
Preprocessing_tools/Bio/add_bry_pisces_Z.m | 347 ++++++----
Preprocessing_tools/Bio/add_dic.m | 122 ++--
Preprocessing_tools/Bio/add_doc.m | 120 ++--
Preprocessing_tools/Bio/add_don.m | 69 +-
Preprocessing_tools/Bio/add_dop.m | 63 +-
Preprocessing_tools/Bio/add_fer.m | 117 ++--
Preprocessing_tools/Bio/add_no3.m | 150 +++--
Preprocessing_tools/Bio/add_o2.m | 114 ++--
Preprocessing_tools/Bio/add_po4.m | 111 +--
Preprocessing_tools/Bio/add_sio3.m | 112 +--
Preprocessing_tools/Bio/add_talk.m | 119 ++--
Preprocessing_tools/Bio/make_biol.m | 137 ++--
Preprocessing_tools/Bio/make_bry_pisces.m | 152 ++---
Preprocessing_tools/Bio/make_clim_pisces.m | 178 ++---
Preprocessing_tools/Bio/make_dust.m | 22 +-
Preprocessing_tools/Bio/make_ini_pisces.m | 3 +-
Preprocessing_tools/Bio/make_n2o_bioebus.m | 317 ---------
Preprocessing_tools/Bio/make_ndepo.m | 18 +-
.../{ => npzd-bioebus}/add_Sphyto_Lphyto.m | 26 +-
.../Bio/{ => npzd-bioebus}/add_Szoo_Lzoo.m | 26 +-
.../Bio/{ => npzd-bioebus}/add_bry_bioebus.m | 47 +-
.../{ => npzd-bioebus}/add_bry_bioebus_Z.m | 48 +-
.../Bio/{ => npzd-bioebus}/add_bry_npzd.m | 45 +-
.../Bio/{ => npzd-bioebus}/add_bry_npzd_Z.m | 39 +-
.../Bio/{ => npzd-bioebus}/add_chla.m | 0
.../add_ini_Sphyto_Lphyto.m | 0
.../{ => npzd-bioebus}/add_ini_Szoo_Lzoo.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_bioebus.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_chla.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_no3.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_npzd.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_o2.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_phyto.m | 0
.../Bio/{ => npzd-bioebus}/add_ini_zoo.m | 0
.../Bio/{ => npzd-bioebus}/add_phyto.m | 19 +-
.../Bio/{ => npzd-bioebus}/add_zoo.m | 20 +-
.../Bio/{ => npzd-bioebus}/bry_interp_bgc.m | 0
.../bry_interp_bgc_chloro.m | 0
.../Bio/{ => npzd-bioebus}/make_bry_bioebus.m | 2 +-
.../Bio/{ => npzd-bioebus}/make_bry_npzd.m | 4 +-
.../{ => npzd-bioebus}/make_clim_bioebus.m | 0
.../Bio/{ => npzd-bioebus}/make_clim_npzd.m | 4 +-
.../Bio/{ => npzd-bioebus}/make_ini_bioebus.m | 0
.../Bio/{ => npzd-bioebus}/make_ini_npzd.m | 0
.../Bio/npzd-bioebus/make_n2o_bioebus.m | 322 +++++++++
.../Bio/{ => npzd-bioebus}/nevis_2003.m | 0
.../Bio/{ => npzd-bioebus}/vinterp_bry_bgc.m | 1 -
Preprocessing_tools/create_bry_Z.m | 18 +-
Preprocessing_tools/create_bryfile.m | 104 ++-
Preprocessing_tools/create_bryfile_wkb.m | 31 +-
Preprocessing_tools/create_bulk.m | 21 +-
Preprocessing_tools/create_climfile.m | 190 +++---
Preprocessing_tools/create_forcing.m | 51 +-
Preprocessing_tools/create_inifile.m | 35 +-
Preprocessing_tools/create_oafile.m | 54 +-
Preprocessing_tools/get_time_attributes.m | 29 +
Preprocessing_tools/make_bry.m | 8 +-
Preprocessing_tools/make_clim.m | 46 +-
Preprocessing_tools/nc_add_globatt.m | 4 +-
Preprocessing_tools/vinterp_bry.m | 64 +-
Preprocessing_tools/write_time_attributes.m | 29 +
Rivers/create_runoff.m | 53 +-
Rivers/make_runoff.m | 6 +-
crocotools_param.m | 3 +
oct_start.m | 1 +
start.m | 1 +
89 files changed, 3318 insertions(+), 2570 deletions(-)
create mode 100644 Nesting_tools/create_nestedndepo.m
create mode 100644 Nesting_tools/nested_ndepo.m
create mode 100644 Nesting_tools/plot_nestndepo.m
delete mode 100644 Preprocessing_tools/Bio/make_n2o_bioebus.m
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_Sphyto_Lphyto.m (85%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_Szoo_Lzoo.m (84%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_bry_bioebus.m (92%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_bry_bioebus_Z.m (91%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_bry_npzd.m (90%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_bry_npzd_Z.m (91%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_chla.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_Sphyto_Lphyto.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_Szoo_Lzoo.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_bioebus.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_chla.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_no3.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_npzd.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_o2.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_phyto.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_ini_zoo.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_phyto.m (85%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/add_zoo.m (85%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/bry_interp_bgc.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/bry_interp_bgc_chloro.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_bry_bioebus.m (99%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_bry_npzd.m (98%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_clim_bioebus.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_clim_npzd.m (97%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_ini_bioebus.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/make_ini_npzd.m (100%)
create mode 100644 Preprocessing_tools/Bio/npzd-bioebus/make_n2o_bioebus.m
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/nevis_2003.m (100%)
rename Preprocessing_tools/Bio/{ => npzd-bioebus}/vinterp_bry_bgc.m (98%)
create mode 100644 Preprocessing_tools/get_time_attributes.m
create mode 100644 Preprocessing_tools/write_time_attributes.m
diff --git a/Aforc_ECMWF/make_bry_wkb_ECMWF.m b/Aforc_ECMWF/make_bry_wkb_ECMWF.m
index 6793a878..ddae7b73 100644
--- a/Aforc_ECMWF/make_bry_wkb_ECMWF.m
+++ b/Aforc_ECMWF/make_bry_wkb_ECMWF.m
@@ -75,6 +75,10 @@ result=close(nc);
grid_angle=mean(mean(angle(mask==1)));
[M L]=size(h);
%
+wkb_prefix=[wkb_prefix,'_ECMWF_'];
+frc_prefix=[frc_prefix,'_ECMWF_'];
+%
+%
% Loop over monthly files
%
for Y=Ymin:Ymax
@@ -92,20 +96,18 @@ for Y=Ymin:Ymax
%
% Forcing file name
%
- frc_prefix=[frc_prefix,'_ECMWF_'];
if level==0
nc_suffix='.nc';
else
nc_suffix=['.nc.',num2str(level)];
end
frcname=[frc_prefix,'Y',num2str(Y),...
- 'M',num2str(M),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
%
% WKB file name
%
- wkb_prefix=[wkb_prefix,'_ECMWF_'];
brywkbname=[wkb_prefix,'Y',num2str(Y),...
- 'M',num2str(M),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
disp(' ')
disp([' Making file: ',brywkbname])
disp([' from: ',frcname])
@@ -125,7 +127,7 @@ for Y=Ymin:Ymax
% Create the boundary file
%
create_bryfile_wkb(brywkbname,grdname,CROCO_title,wkb_obc,...
- wkb_time,wkb_cycle,'clobber');
+ wkb_time,wkb_cycle,'clobber',Yorig);
disp(' ')
%
%
diff --git a/Aforc_ERA5/ERA5_convert.py b/Aforc_ERA5/ERA5_convert.py
index 76def899..d3a7ff72 100755
--- a/Aforc_ERA5/ERA5_convert.py
+++ b/Aforc_ERA5/ERA5_convert.py
@@ -95,7 +95,7 @@ for iyear in range(year_start,year_end+1):
data[np.where(data==mvalue)]=9999.
#
-# Convert time from seconds since 1970-1-1 0:0:0 into days since Yorig-1-1 0:0:0
+# Convert time from seconds since 1970-1-1 0:0:0 into days since Yorig-01-01 00:00:00
#
time = time / 86400.
@@ -115,7 +115,7 @@ for iyear in range(year_start,year_end+1):
# Create and write output netcdf file
#
- fname_out = era5_dir_processed + '/' + vname.upper() + '_Y' + str(iyear) + 'M' + str(imonth) + '.nc'
+ fname_out = era5_dir_processed + '/' + vname.upper() + '_Y' + str(iyear) + 'M' + str(imonth).zfill(2) + '.nc'
nw = netcdf(fname_out,mode='w',format='NETCDF4')
@@ -132,7 +132,8 @@ for iyear in range(year_start,year_end+1):
vartime.long_name = 'Time'
varlon.units = 'degree_east'
varlat.units = 'degree_north'
- vartime.units = 'days since '+str(Yorig)+'-1-1'
+ vartime.units = 'days since '+str(Yorig)+'-01-01 00:00:00'
+ vartime.calendar = 'proleptic_gregorian'
vardata.missing_value = 9999.
vardata.units = units[k]
vardata.long_name = vlong
diff --git a/Aforc_ERA5/era5_crocotools_param.py b/Aforc_ERA5/era5_crocotools_param.py
index fd3630ea..a6872712 100644
--- a/Aforc_ERA5/era5_crocotools_param.py
+++ b/Aforc_ERA5/era5_crocotools_param.py
@@ -21,14 +21,15 @@ era5_dir_processed = config_dir + 'DATA/ERA5_' + config_name
#
# extraction wave variables
#
-wave_extract=False # True to extract wave variables
+#wave_extract=False # True to extract wave variables
+wave_extract=True # True to extract wave variables
#
# Dates limits
#
year_start = 2005
month_start = 1
year_end = 2005
-month_end = 3
+month_end = 4
#
# Year origin of time
#
@@ -40,7 +41,8 @@ n_overlap = 0
#
# Request time (daily hours '00/01/.../23')
#
-time = '00/01/02/03/04/05/06/07/08/09/10/11/12/13/14/15/16/17/18/19/20/21/22/23'
+time = '00/06/12/18'
+#time = '00/01/02/03/04/05/06/07/08/09/10/11/12/13/14/15/16/17/18/19/20/21/22/23'
#
# Request variables (see available at ERA5_variables.json)
variables = ['lsm','tp','strd','ssr','t2m','q','u10','v10'] #note lsm is land_sea_mask
diff --git a/Aforc_ERA5/interp_ERA5.m b/Aforc_ERA5/interp_ERA5.m
index 0c1364e5..568175a1 100644
--- a/Aforc_ERA5/interp_ERA5.m
+++ b/Aforc_ERA5/interp_ERA5.m
@@ -1,6 +1,6 @@
function interp_ERA5(ATMO_dir,Y,M,Roa,interp_method,...
lon1,lat1,lonwave1,latwave1,mask1,maskwave1,maskwave2,tin,...
- nc_frc, nc_blk,lon,lat,angle,tout, add_waves)
+ nc_frc, nc_blk,lon,lat,angle,tout, add_waves)
%
% Read the local ERA5 files and perform the space interpolations
%
@@ -12,7 +12,7 @@ function interp_ERA5(ATMO_dir,Y,M,Roa,interp_method,...
% 1: Air temperature: Convert from Kelvin to Celsius
%
vname='T2M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
tair=squeeze(nc{vname}(tin,:,:));
close(nc);
tair=get_missing_val(lon1,lat1,mask1.*tair,nan,Roa,nan);
@@ -25,7 +25,7 @@ tair=interp2(lon1,lat1,tair,lon,lat,interp_method);
% Get Specific Humidity [Kg/Kg]
%
vname='Q';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
shum=squeeze(nc{vname}(tin,:,:));
close(nc);
shum=get_missing_val(lon1,lat1,mask1.*shum,nan,Roa,nan);
@@ -40,7 +40,7 @@ rhum=shum./qsat(tair);
% 3: Precipitation rate: Convert from [kg/m^2/s] to cm/day
%
vname='TP';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
prate=squeeze(nc{vname}(tin,:,:));
close(nc);
prate=get_missing_val(lon1,lat1,mask1.*prate,nan,Roa,nan);
@@ -54,7 +54,7 @@ prate(prate<1.e-4)=0;
% Solar shortwave
%
vname='SSR';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
dswrf=squeeze(nc{vname}(tin,:,:));
close(nc);
radsw=get_missing_val(lon1,lat1,mask1.*dswrf,nan,Roa,nan);
@@ -77,7 +77,7 @@ radsw(radsw<1.e-10)=0;
% 5.2 get the downward longwave flux [W/m^2]
%
vname='STRD';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
dlwrf_in=squeeze(nc{vname}(tin,:,:));
close(nc);
radlw_in=get_missing_val(lon1,lat1,mask1.*dlwrf_in,nan,Roa,nan);
@@ -87,7 +87,7 @@ radlw_in=interp2(lon1,lat1,radlw_in,lon,lat,interp_method);
% 6: Wind [m/s]
%
vname='U10M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
uwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
uwnd=get_missing_val(lon1,lat1,mask1.*uwnd,nan,Roa,nan);
@@ -95,7 +95,7 @@ uwnd=interp2(lon1,lat1,uwnd,lon,lat,interp_method);
%
%
vname='V10M';
-nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
vwnd=squeeze(nc{vname}(tin,:,:));
close(nc)
vwnd=get_missing_val(lon1,lat1,mask1.*vwnd,nan,Roa,nan);
@@ -149,7 +149,7 @@ if add_waves == 1
% 8: Surface wave amplitude: convert from SWH to Amp
%
vname='SWH';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
awave=1/(2*sqrt(2))*squeeze(nc{vname}(tin,:,:));
close(nc);
%[ATMO_DIR,vname,'_Y',num2str(Y),'M',num2str(M),'.nc']
@@ -159,7 +159,7 @@ if add_waves == 1
% 9: Surface wave direction
%
vname='MWD';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
dwave=squeeze(nc{vname}(tin,:,:));
close(nc);
dwave=get_missing_val(lonwave1,latwave1,maskwave1.*dwave,nan,Roa,nan);
@@ -168,7 +168,7 @@ if add_waves == 1
% 10: Surface wave peak period
%
vname='PP1D';
- nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+ nc=netcdf([ATMO_dir,vname,'_Y',num2str(Y),'M',num2str(sprintf('%02d',M)),'.nc'],'r');
pwave=squeeze(nc{vname}(tin,:,:));
close(nc);
pwave=get_missing_val(lonwave1,latwave1,maskwave2.*pwave,nan,Roa,nan);
diff --git a/Aforc_ERA5/make_ERA5.m b/Aforc_ERA5/make_ERA5.m
index faee3873..b5d4c25b 100644
--- a/Aforc_ERA5/make_ERA5.m
+++ b/Aforc_ERA5/make_ERA5.m
@@ -1,13 +1,13 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% make_ERA5.m
-%
+%
% Create and fill frc and bulk files with ERA5 data.
% (ERA-5 Reanalysis)
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -25,7 +25,7 @@
% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
% MA 02111-1307 USA
%
-% Updated D. Donoso, G. Cambon. P. Penven (Oct 2021)
+% Updated D. Donoso, G. Cambon. P. Penven (Oct 2021)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear all
close all
@@ -33,8 +33,8 @@ close all
%
% Common parameters
%
-crocotools_param
-isoctave=exist('octave_config_info');
+crocotools_param
+isoctave=exist('octave_config_info');
frc_prefix=[frc_prefix,'_ERA5_'];
blk_prefix=[blk_prefix,'_ERA5_'];
%
@@ -68,8 +68,8 @@ close(nc);
%
% Get the ERA5 horizontal grids (it should be the same for every month)
%
-nc=netcdf([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'],'r');
-disp(['Use this land file :',char([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'])])
+nc=netcdf([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),'.nc'],'r');
+disp(['Use this land file :',char([ERA5_dir,'LSM_Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),'.nc'])])
lon1=nc{'lon'}(:);
lat1=nc{'lat'}(:);
@@ -85,10 +85,10 @@ close(nc);
if add_waves == 1
%
% get horizontal grid for ocean waves
- % for ERA5 wave variables, resolution change to 0.5° instead of 0.25°
+ % for ERA5 wave variables, resolution change to 0.5° instead of 0.25°
% for the atmo variable (0.25° x 0.25° (atmosphere) vs 0.5° x 0.5° (ocean waves))
%
- filein=[ERA5_dir,'SWH_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'];
+ filein=[ERA5_dir,'SWH_Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),'.nc'];
nc=netcdf(filein,'r');
lonwave=nc{'lon'}(:);
latwave=nc{'lat'}(:);
@@ -100,7 +100,7 @@ if add_waves == 1
close(nc);
% fix: PP1D doesn t have the same mask than SWH
- filein2=[ERA5_dir,'PP1D_Y',num2str(Ymin),'M',num2str(Mmin),'.nc'];
+ filein2=[ERA5_dir,'PP1D_Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),'.nc'];
nc=netcdf(filein2);
maskwave2=squeeze(nc{'PP1D'}(1,:,:));
missvalue_wave2 = ncreadatt(filein2,'PP1D','missing_value');
@@ -126,7 +126,7 @@ disp(['Loop on the years and the months'])
%
for Y=Ymin:Ymax
- if Y==Ymin
+ if Y==Ymin
mo_min=Mmin;
else
mo_min=1;
@@ -139,14 +139,14 @@ for Y=Ymin:Ymax
for M=mo_min:mo_max
disp(' ')
disp(['Processing year ',num2str(Y),...
- ' - month ',num2str(M)])
+ ' - month ',num2str(sprintf(Mth_format,M))])
disp(' ')
%-------------------------------------------------------------------%
%
% Process time (here in days), with SST file (minimum time step)
%
%-------------------------------------------------------------------%
- nc=netcdf([ERA5_dir,'T2M_Y',num2str(Y),'M',num2str(M),'.nc'],'r');
+ nc=netcdf([ERA5_dir,'T2M_Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),'.nc'],'r');
ERA5_time=nc{'time'}(:);
close(nc);
dt=mean(gradient(ERA5_time));
@@ -160,9 +160,9 @@ for Y=Ymin:Ymax
itolap=freq*itolap_era5;
tlen=tlen0+2*itolap;
disp(['tlen=',num2str(tlen)])
- disp(['Overlap is ',num2str(itolap_era5),' records before and after'])
+ disp(['Overlap is ',num2str(itolap_era5),' records before and after'])
time=0*(1:tlen);
- time(itolap+1:tlen0+itolap)=ERA5_time;
+ time(itolap+1:tlen0+itolap)=ERA5_time;
disp(['====================='])
disp('Compute time for croco file')
disp(['====================='])
@@ -178,59 +178,61 @@ for Y=Ymin:Ymax
%
% ------------------------------------------------------------------%
%
- disp(['====================='])
+ disp(['====================='])
disp('Create the frc/blk netcdf file')
disp(['====================='])
blkname=[blk_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
frcname=[frc_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
if makeblk==1
- disp(['Create a new bulk file: ' blkname])
- create_bulk(blkname,grdname,CROCO_title,time,0);
- nc_add_globatt(blkname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,'ERA5');
- disp([' '])
+ disp(['Create a new bulk file: ' blkname])
+ create_bulk(blkname,grdname,CROCO_title,time,0,Yorig);
+ nc_add_globatt(blkname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,'ERA5');
+ disp([' '])
end
if makefrc==1
- disp(['Create a new forcing file: ' frcname])
- disp([' '])
- create_forcing(frcname,grdname,CROCO_title,...
- time,0,0,...
- 0,0,0,...
- 0,0,0,0,0,0)
+ disp(['Create a new forcing file: ' frcname])
+ disp([' '])
+ create_forcing(frcname,grdname,CROCO_title,...
+ time,0,0,...
+ 0,0,0,...
+ 0,0,0,0,0,0,Yorig)
end
% %
% % Add the waves
% %
- if makefrc==1 && add_waves==1
- disp(['Add waves data'])
- disp(['=============='])
+ if makefrc==1 && add_waves==1
+ disp(['-> Add waves data previously downloaded'])
+ disp([' using Aforc_ERA5/ERA5_request.py'])
end
- % %
+ % %
% %
% % Add the tides
% %
if makefrc==1 && add_tides==1
- pot_tides=1;
- add_tidal_data(tidename,grdname,frcname,Ntides,tidalrank,...
+ disp([' '])
+ disp(['-> Add tidal data'])
+ pot_tides=1;
+ add_tidal_data(tidename,grdname,frcname,Ntides,tidalrank,...
Yorig,Y,M,coastfileplot,makeplot,pot_tides)
end
%
%
% Open the CROCO forcing files
if makefrc==1
- nc_frc=netcdf(frcname,'write');
+ nc_frc=netcdf(frcname,'write');
else
- nc_frc=[];
+ nc_frc=[];
end
- % Open the CROCO bulk files
+ % Open the CROCO bulk files
if makeblk==1
- nc_blk=netcdf(blkname,'write');
+ nc_blk=netcdf(blkname,'write');
else
- nc_blk=[];
+ nc_blk=[];
end
- %
+ %
% Check if there are ERA5 files for the previous Month
Mm=M-1;
Ym=Y;
@@ -239,12 +241,12 @@ for Y=Ymin:Ymax
Ym=Y-1;
end
%
- fname = [ERA5_dir,'TP_Y',num2str(Ym),'M',num2str(Mm),'.nc'];
+ fname = [ERA5_dir,'TP_Y',num2str(Ym),'M',num2str(sprintf(Mth_format,Mm)),'.nc'];
%nc=netcdf([ERA5_dir,'TP_Y',num2str(Ym),'M',num2str(Mm),'.nc']);
%
disp(' ')
disp('======================================================')
- disp('Perform interpolations for the previous month')
+ disp('Perform interpolations for the previous month')
disp('======================================================')
disp(' ')
if exist(fname)==0
@@ -256,16 +258,16 @@ for Y=Ymin:Ymax
nc=netcdf(fname,'r');
tndx=length(nc('time'));
if makefrc==1
- for aa=1:itolap
- nc_frc{'sms_time'}(aa)=nc{'time'}(tndx-(itolap-aa));
- end
+ for aa=1:itolap
+ nc_frc{'sms_time'}(aa)=nc{'time'}(tndx-(itolap-aa));
+ end
end
%
- if makeblk==1
- for aa=1:itolap
- nc_blk{'bulk_time'}(aa)=nc{'time'}(tndx-(itolap-aa));
- end
- end
+ if makeblk==1
+ for aa=1:itolap
+ nc_blk{'bulk_time'}(aa)=nc{'time'}(tndx-(itolap-aa));
+ end
+ end
close(nc)
end
%
@@ -279,29 +281,29 @@ for Y=Ymin:Ymax
end
interp_ERA5(ERA5_dir,Ym,Mm,Roa,interp_method,lon1,lat1,lon1wave,lat1wave, ...
mask,maskwave,maskwave2,aa0,nc_frc,nc_blk,lon,lat,angle,aa,add_waves)
- end
- %######################################################################
- %
+ end
+ %######################################################################
+ %
disp(' ')
disp('======================================================')
disp('Perform interpolations for the current month')
disp('======================================================')
disp(' ')
-
+
% Perform interpolations for the current month
%
-
+
for tndx=1:tlen0
if mod(tndx,6)==0
disp(['Step: ',num2str(tndx),' of ',num2str(tlen0)])
end
interp_ERA5(ERA5_dir,Y,M,Roa,interp_method,lon1,lat1,lon1wave,lat1wave,...
- mask,maskwave,maskwave2,tndx,nc_frc,nc_blk,lon,lat,angle,tndx+itolap,add_waves)
+ mask,maskwave,maskwave2,tndx,nc_frc,nc_blk,lon,lat,angle,tndx+itolap,add_waves)
end
-
- disp(' ')
+
+ disp(' ')
disp('======================================================')
- disp('Perform interpolations for next month')
+ disp('Perform interpolations for next month')
disp('======================================================')
disp(' ')
%######################################################################
@@ -313,9 +315,9 @@ for Y=Ymin:Ymax
Mp=1;
Yp=Y+1;
end
-
+
fname=[ERA5_dir,'TP_Y',num2str(Yp),'M',num2str(Mp),'.nc'];
-
+
if exist(fname)==0
disp(['No data for the next month: using current month'])
tndx=tlen0;
@@ -325,18 +327,18 @@ for Y=Ymin:Ymax
nc=netcdf(fname,'r');
if makefrc==1
- disp('sms_time')
- for tndx=tlen0+itolap+1:tlen;
- nc_frc{'sms_time'}(tndx)=nc{'time'}(tndx-tlen0-(itolap));
- end;
+ disp('sms_time')
+ for tndx=tlen0+itolap+1:tlen;
+ nc_frc{'sms_time'}(tndx)=nc{'time'}(tndx-tlen0-(itolap));
+ end;
end
- if makeblk==1
- disp('bulk_time')
- for tndx=tlen0+itolap+1:tlen;
- nc_blk{'bulk_time'}(tndx)=nc{'time'}(tndx-tlen0-(itolap));
- end
- end
+ if makeblk==1
+ disp('bulk_time')
+ for tndx=tlen0+itolap+1:tlen;
+ nc_blk{'bulk_time'}(tndx)=nc{'time'}(tndx-tlen0-(itolap));
+ end
+ end
close(nc)
end
%
@@ -349,23 +351,23 @@ for Y=Ymin:Ymax
disp(['tout=tndx ',num2str(tndx)])
if Mp==M
%tin=tlen0; % persistency if current month is used
- tin=tndx-2*itolap
+ tin=tndx-2*itolap;
disp(['tin=',num2str(tin)])
else
tin=tndx-tlen0-itolap;
disp(['tin=',num2str(tin)])
end
interp_ERA5(ERA5_dir,Yp,Mp,Roa,interp_method,lon1,lat1,lon1wave,lat1wave,...
- mask,maskwave,maskwave2,tin,nc_frc,nc_blk,lon,lat,angle,tout,add_waves)
+ mask,maskwave,maskwave2,tin,nc_frc,nc_blk,lon,lat,angle,tout,add_waves)
end;
%
% Close the CROCO forcing files
%
if ~isempty(nc_frc)
- close(nc_frc);
+ close(nc_frc);
end
if ~isempty(nc_blk)
- close(nc_blk);
+ close(nc_blk);
end
end
end
@@ -375,13 +377,13 @@ end
%
disp('======================================================')
if SPIN_Long>0
-disp('Add spin up phase')
+ disp('Add spin up phase')
M=Mmin-1;
Y=Ymin-SPIN_Long;
for month=1:12*SPIN_Long
M=M+1;
if M==13
- M=1;
+ M=1;
Y=Y+1;
end
%
@@ -392,22 +394,22 @@ disp('Add spin up phase')
%
blkname=[blk_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
blkname2=[blk_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',blkname2])
+ disp(['Create ',blkname2])
if (isoctave == 0)
eval(['!cp ',blkname,' ',blkname2])
else
system(['cp ',blkname,' ',blkname2])
- end
+ end
%
% Change the time
%
nc=netcdf(blkname2,'write');
time=nc{'bulk_time'}(:)-365.*(Ymin-Y);%+datenum(Yorig,1,1);
- %[y,m,d,h,mi,s]=datevec(time);
- %dy=Ymin-Y;
- %y=y-dy;
- %time=datenum(y,m,d,h,mi,s)-datenum(Yorig,1,1);
+ %[y,m,d,h,mi,s]=datevec(time);
+ %dy=Ymin-Y;
+ %y=y-dy;
+ %time=datenum(y,m,d,h,mi,s)-datenum(Yorig,1,1);
nc{'bulk_time'}(:)=time;
close(nc)
end
@@ -420,7 +422,7 @@ if makeplot==1
disp('======================================================')
disp(' Make a few plots...')
slides=[1 12 24 36];
-
+
test_forcing(blkname,grdname,'tair',slides,3,coastfileplot)
figure
test_forcing(blkname,grdname,'rhum',slides,3,coastfileplot)
diff --git a/Aforc_ERA5/make_bry_wkb_ERA5.m b/Aforc_ERA5/make_bry_wkb_ERA5.m
index b9c163c8..7d4097fe 100644
--- a/Aforc_ERA5/make_bry_wkb_ERA5.m
+++ b/Aforc_ERA5/make_bry_wkb_ERA5.m
@@ -75,6 +75,10 @@ result=close(nc);
grid_angle=mean(mean(angle(mask==1)));
[M L]=size(h);
%
+wkb_prefix=[wkb_prefix,'_ERA5_'];
+frc_prefix=[frc_prefix,'_ERA5_'];
+%
+%
% Loop over monthly files
%
for Y=Ymin:Ymax
@@ -92,20 +96,18 @@ for Y=Ymin:Ymax
%
% Forcing file name
%
- frc_prefix=[frc_prefix,'_ERA5_'];
if level==0
nc_suffix='.nc';
else
nc_suffix=['.nc.',num2str(level)];
end
frcname=[frc_prefix,'Y',num2str(Y),...
- 'M',num2str(M),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
%
% WKB file name
%
- wkb_prefix=[wkb_prefix,'_ERA5_'];
brywkbname=[wkb_prefix,'Y',num2str(Y),...
- 'M',num2str(M),nc_suffix];
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
disp(' ')
disp([' Making file: ',brywkbname])
disp([' from: ',frcname])
@@ -120,12 +122,12 @@ for Y=Ymin:Ymax
close(nc)
wkb_time=time;
- wkb_cycle=wkb_time(end);
+ wkb_cycle=0;
%
% Create the boundary file
%
create_bryfile_wkb(brywkbname,grdname,CROCO_title,wkb_obc,...
- wkb_time,wkb_cycle,'clobber');
+ wkb_time,wkb_cycle,'clobber',Yorig);
disp(' ')
%
%
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e62c6b3a..74e9ee83 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,8 +6,21 @@ Release changelog are available here : https://gitlab.inria.fr/croco-ocean/croco
### Added
+- Issue 57 : update croco_frcbio creation with make_dust.m and make_ndepo.m (Thanks to C. Ethee and R. Person)
+
+
## Fixed
+- Issue 60 : fix overlaps problems with mercator daily and monthly forcing starting the first days of the month at 00:00h
+- Issue 59 :
+ - propagate time unit, cycle_length and calendar attribute updates
+ - updates and fixes for bio into nestgui (interp_ini, interp_frcbio, interp_clim)
+
+- Issue 51 :
+ - various fixes, cleaning and indentation in croco_tools
+ - add time unit, cycle_length and calendar attribute update
+ - refactorization for time unit, cycle_length and calendar attributea
+
- Issue 50 : fix in mexcdf functionality for matlab 20xx versions (in particular matlab 2024)
- Issue 49, 43 : add GSHHS coastline dataset in m_map private directory
- Issue 44 : fix problem in editmask with longitude in 0-360° convention
@@ -15,6 +28,8 @@ Release changelog are available here : https://gitlab.inria.fr/croco-ocean/croco
## Changed
+- Issue 58 : cleaning and update in Preprocessing_tools/Bio
+
## Removed
### Deprecated
diff --git a/Nesting_tools/create_nestedbulk.m b/Nesting_tools/create_nestedbulk.m
index bb5b8ed6..cfb377fd 100644
--- a/Nesting_tools/create_nestedbulk.m
+++ b/Nesting_tools/create_nestedbulk.m
@@ -1,4 +1,4 @@
-function create_bulk(blkname,parentname,grdname,title,bulkt,bulkc)
+function create_bulk(blkname,parentname,grdname,title,bulkt,bulkc,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf heat flux bulk bulk file
@@ -38,7 +38,18 @@ M=length(nc('eta_psi'));
result=close(nc);
Lp=L+1;
Mp=M+1;
-
+%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
nw = netcdf(blkname, 'clobber');
%result = redef(nw);
@@ -60,9 +71,8 @@ nw('bulk_time') = length(bulkt);
nw{'bulk_time'} = ncdouble('bulk_time');
nw{'bulk_time'}.long_name = ncchar('bulk formulation execution time');
nw{'bulk_time'}.long_name = 'bulk formulation execution time';
-nw{'bulk_time'}.units = ncchar('days');
-nw{'bulk_time'}.units = 'days';
-nw{'bulk_time'}.cycle_length = bulkc;
+write_time_attributes(nc,'bulk_time',bulkc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'tair'} = ncdouble('bulk_time', 'eta_rho', 'xi_rho');
nw{'tair'}.long_name = ncchar('surface air temperature');
diff --git a/Nesting_tools/create_nestedclim.m b/Nesting_tools/create_nestedclim.m
index 9f38043d..bdea5542 100644
--- a/Nesting_tools/create_nestedclim.m
+++ b/Nesting_tools/create_nestedclim.m
@@ -4,8 +4,8 @@ function ncclim=create_nestedclim(climfile,gridfile,parentfile,title,...
tcycle,scycle,ucycle,vcycle,sshcycle,...
tbiol, cbiol,tpisces,cpisces,...
clobber,...
- biol,pisces,timebiol,cyclebiol,timepisces,cyclepisce, ...
- namebiol,namepisces,unitbiol,unitpisces,hc,vtransform)
+ biol,pisces,timebiol,cyclebiol,timepisces,cyclepisces, ...
+ namebiol,namepisces,unitbiol,unitpisces,hc,vtransform,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function ncclim=create_climfile(climfile,gridfile,theta_s,...
@@ -62,6 +62,18 @@ function ncclim=create_nestedclim(climfile,gridfile,parentfile,title,...
% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp(' ')
disp(['Creating the file : ',climfile])
@@ -95,11 +107,11 @@ ncclim('eta_rho') = Mp;
ncclim('s_rho') = N;
ncclim('s_w') = Np;
ncclim('tracer') = 2;
-ncclim('tclm_time') = size(ttime);
-ncclim('sclm_time') = size(stime);
-ncclim('uclm_time') = size(utime);
-ncclim('vclm_time') = size(vtime);
-ncclim('ssh_time') = size(sshtime);
+ncclim('tclm_time') = length(ttime);
+ncclim('sclm_time') = length(stime);
+ncclim('uclm_time') = length(utime);
+ncclim('vclm_time') = length(vtime);
+ncclim('ssh_time') = length(sshtime);
if biol
for k=1:length(timebiol)
@@ -152,13 +164,13 @@ ncclim{'Vstretching'}.long_name = 'vertical terrain-following stretching functio
%
ncclim{'tstart'}.long_name = ncchar('start processing day');
ncclim{'tstart'}.long_name = 'start processing day';
-ncclim{'tstart'}.units = ncchar('day');
-ncclim{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart',tcycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
ncclim{'tend'}.long_name = ncchar('end processing day');
ncclim{'tend'}.long_name = 'end processing day';
-ncclim{'tend'}.units = ncchar('day');
-ncclim{'tend'}.units = 'day';
+write_time_attributes(nc,'tend',tcycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
ncclim{'theta_s'}.long_name = ncchar('S-coordinate surface control parameter');
ncclim{'theta_s'}.long_name = 'S-coordinate surface control parameter';
@@ -200,43 +212,39 @@ ncclim{'Cs_rho'}.field = 'Cs_rho, scalar';
%
ncclim{'tclm_time'}.long_name = ncchar('time for temperature climatology');
ncclim{'tclm_time'}.long_name = 'time for temperature climatology';
-ncclim{'tclm_time'}.units = ncchar('day');
-ncclim{'tclm_time'}.units = 'day';
-ncclim{'tclm_time'}.cycle_length = tcycle;
ncclim{'tclm_time'}.field = ncchar('tclm_time, scalar, series');
ncclim{'tclm_time'}.field = 'tclm_time, scalar, series' ;
+write_time_attributes(nc,'tclm_time',tcycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
ncclim{'sclm_time'}.long_name = ncchar('time for salinity climatology');
ncclim{'sclm_time'}.long_name = 'time for salinity climatology';
-ncclim{'sclm_time'}.units = ncchar('day');
-ncclim{'sclm_time'}.units = 'day';
-ncclim{'sclm_time'}.cycle_length = scycle;
ncclim{'sclm_time'}.field = ncchar('sclm_time, scalar, serie');
ncclim{'sclm_time'}.field = 'sclm_time, scalar, serie';
+write_time_attributes(nc,'sclm_time',scycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
ncclim{'uclm_time'}.long_name = ncchar('time climatological u');
ncclim{'uclm_time'}.long_name = 'time climatological u';
-ncclim{'uclm_time'}.units = ncchar('day');
-ncclim{'uclm_time'}.units = 'day';
-ncclim{'uclm_time'}.cycle_length = ucycle;
ncclim{'uclm_time'}.field = ncchar('uclm_time, scalar, serie');
ncclim{'uclm_time'}.field = 'uclm_time, scalar, serie';
+write_time_attributes(nc,'uclm_time',ucycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
ncclim{'vclm_time'}.long_name = ncchar('time climatological v');
ncclim{'vclm_time'}.long_name = 'time climatological v';
-ncclim{'vclm_time'}.units = ncchar('day');
-ncclim{'vclm_time'}.units = 'day';
-ncclim{'vclm_time'}.cycle_length = vcycle;
ncclim{'vclm_time'}.field = ncchar('vclm_time, scalar, serie');
ncclim{'vclm_time'}.field = 'vclm_time, scalar, serie';
+write_time_attributes(nc,'vclm_time',vcycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
%
ncclim{'ssh_time'}.long_name = ncchar('time for sea surface height');
ncclim{'ssh_time'}.long_name = 'time for sea surface height';
-ncclim{'ssh_time'}.units = ncchar('day');
-ncclim{'ssh_time'}.units = 'day';
-ncclim{'ssh_time'}.cycle_length = sshcycle;
ncclim{'ssh_time'}.field = ncchar('ssh_time, scalar, serie');
ncclim{'ssh_time'}.field = 'ssh_time, scalar, serie';
+write_time_attributes(nc,'ssh_time',sshcycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
if biol
for k=1:length(timebiol)
@@ -244,12 +252,12 @@ if biol
ncclim{char(timebiol(k))} = ncdouble(char(timebiol(k,:)));
ncclim{char(timebiol(k))}.long_name = ncchar(char(timebiol(k)));
ncclim{char(timebiol(k))}.long_name = char(timebiol(k));
- ncclim{char(timebiol(k))}.units = ncchar('day');
- ncclim{char(timebiol(k))}.units = 'day';
- ncclim{char(timebiol(k))}.cycle_length = char(timebiol(k));
ncclim{char(timebiol(k))}.field = ncchar([char(timebiol(k)),', scalar, series']);
ncclim{char(timebiol(k))}.field = [char(timebiol(k)),', scalar, series'] ;
-%
+ write_time_attributes(nc,char(timebiol(k)),cbiol,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
% disp(char(namebiol(k)))
ncclim{char(namebiol(k))} = ncdouble(char(timebiol(k,:)),'s_rho','eta_rho','xi_rho');
ncclim{char(namebiol(k))}.long_name = ncchar(char(namebiol(k)));
@@ -269,11 +277,10 @@ if pisces
ncclim{char(timepisces(k))} = ncdouble(char(timepisces(k,:)));
ncclim{char(timepisces(k))}.long_name = ncchar(char(timepisces(k)));
ncclim{char(timepisces(k))}.long_name = char(timepisces(k));
- ncclim{char(timepisces(k))}.units = ncchar('day');
- ncclim{char(timepisces(k))}.units = 'day';
- ncclim{char(timepisces(k))}.cycle_length = ncchar([char(namepisces(k)),', scalar, series']);
ncclim{char(timepisces(k))}.field = ncchar([char(timepisces(k)), ',scalar, series']);
ncclim{char(timepisces(k))}.field = [char(timepisces(k)), ',scalar, series'] ;
+ write_time_attributes(nc,char(timepisces(k)),cpisces,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
%disp(char(namepisces(k)))
ncclim{char(namepisces(k))} = ncdouble(char(timepisces(k,:)),'s_rho','eta_rho','xi_rho');
diff --git a/Nesting_tools/create_nesteddust.m b/Nesting_tools/create_nesteddust.m
index ffb0ac73..e8ee205a 100644
--- a/Nesting_tools/create_nesteddust.m
+++ b/Nesting_tools/create_nesteddust.m
@@ -30,6 +30,17 @@ function create_nesteddust(dustname,parentname,grdname,title,dustt,dustc)
% e-mail:Pierrick.Penven@ird.fr
% Update : Gildas Cambon 13 Oct 2009
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
nc=netcdf(grdname);
L=length(nc('xi_psi'));
M=length(nc('eta_psi'));
@@ -56,11 +67,10 @@ nw('dust_time') = length(dustt);
nw{'dust_time'} = ncdouble('dust_time');
nw{'dust_time'}.long_name = ncchar('dust time');
nw{'dust_time'}.long_name = 'dust time';
-nw{'dust_time'}.units = ncchar('days');
-nw{'dust_time'}.units = 'days';
-nw{'dust_time'}.cycle_length = dustc;
nw{'dust_time'}.field = ncchar('time, scalar, series');
nw{'dust_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'dust_time',dustc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'dust'} = ncdouble('dust_time', 'eta_rho', 'xi_rho');
nw{'dust'}.long_name = ncchar('Fe Dust Deposition');
@@ -70,7 +80,39 @@ nw{'dust'}.units = 'nmol Fe m-3';
nw{'dust'}.field = ncchar('Fe Dust Deposition, scalar, series');
nw{'dust'}.field = 'Fe Dust Deposition, scalar, series';
-%endef(nw);
+nw{'dustfer'} = ncdouble('dust_time', 'eta_rho', 'xi_rho');
+nw{'dustfer'}.long_name = ncchar('Fe Dust Deposition');
+nw{'dustfer'}.long_name = 'Fe Dust Deposition';
+nw{'dustfer'}.units = ncchar('Kg m-2 s-1');
+nw{'dustfer'}.units = 'Kg m-2 s-1';
+nw{'dustfer'}.field = ncchar('dustfer, scalar, series');
+nw{'dustfer'}.field = 'dustfer, scalar, series';
+%
+nw{'dustpo4'} = ncdouble('dust_time', 'eta_rho', 'xi_rho');
+nw{'dustpo4'}.long_name = ncchar('PO4 Dust Deposition');
+nw{'dustpo4'}.long_name = 'PO4 Dust Deposition';
+nw{'dustpo4'}.units = ncchar('Kg m-2 s-1');
+nw{'dustpo4'}.units = 'Kg m-2 s-1';
+nw{'dustpo4'}.field = ncchar('dustpo4, scalar, series');
+nw{'dustpo4'}.field = 'dustpo4, scalar, series';
+%
+nw{'dustsi'} = ncdouble('dust_time', 'eta_rho', 'xi_rho');
+nw{'dustsi'}.long_name = ncchar('Si Dust Deposition');
+nw{'dustsi'}.long_name = 'Si Dust Deposition';
+nw{'dustsi'}.units = ncchar('Kg m-2 s-1');
+nw{'dustsi'}.units = 'Kg m-2 s-1';
+nw{'dustsi'}.field = ncchar('dustsi, scalar, series');
+nw{'dustsi'}.field = 'dustsi, scalar, series';
+%
+nw{'solubility2'} = ncdouble('dust_time', 'eta_rho', 'xi_rho');
+nw{'solubility2'}.long_name = ncchar('Fe solubility from Mahowald');
+nw{'solubility2'}.long_name = 'Fe solubility from Mahowald';
+nw{'solubility2'}.units = ncchar('%');
+nw{'solubility2'}.units = '%';
+nw{'solubility2'}.field = ncchar('solubility2, scalar, series');
+nw{'solubility2'}.field = 'solubility2, scalar, series';
+
+endef(nw);
%
% Create global attributes
diff --git a/Nesting_tools/create_nestedforcing.m b/Nesting_tools/create_nestedforcing.m
index 2a7c37ce..dfc2d432 100644
--- a/Nesting_tools/create_nestedforcing.m
+++ b/Nesting_tools/create_nestedforcing.m
@@ -1,6 +1,6 @@
function create_nestedforcing(frcname,parentname,grdname,title,smst,...
shft,swft,srft,sstt,ssst,smsc,...
- shfc,swfc,srfc,sstc,sssc)
+ shfc,swfc,srfc,sstc,sssc,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf forcing file
@@ -38,6 +38,18 @@ M=length(nc('eta_psi'));
close(nc);
Lp=L+1;
Mp=M+1;
+%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
nw = netcdf(frcname, 'clobber');
%redef(nw);
%
@@ -63,57 +75,52 @@ nw('sss_time') = length(ssst);
nw{'sms_time'} = ncdouble('sms_time');
nw{'sms_time'}.long_name = ncchar('surface momentum stress time');
nw{'sms_time'}.long_name = 'surface momentum stress time';
-nw{'sms_time'}.units = ncchar('days');
-nw{'sms_time'}.units = 'days';
-nw{'sms_time'}.cycle_length = smsc;
nw{'sms_time'}.field = ncchar('time, scalar, series');
nw{'sms_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'sms_time',smsc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'shf_time'} = ncdouble('shf_time');
nw{'shf_time'}.long_name = ncchar('surface heat flux time');
nw{'shf_time'}.long_name = 'surface heat flux time';
-nw{'shf_time'}.units = ncchar('days');
-nw{'shf_time'}.units = 'days';
-nw{'shf_time'}.cycle_length =shfc ;
nw{'shf_time'}.field = ncchar('time, scalar, series');
nw{'shf_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'shf_time',shfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'swf_time'} = ncdouble('swf_time');
nw{'swf_time'}.long_name = ncchar('surface freshwater flux time');
nw{'swf_time'}.long_name = 'surface freshwater flux time';
-nw{'swf_time'}.units = ncchar('days');
-nw{'swf_time'}.units = 'days';
-nw{'swf_time'}.cycle_length = swfc;
nw{'swf_time'}.field = ncchar('time, scalar, series');
nw{'swf_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'swf_time',swfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'sst_time'} = ncdouble('sst_time');
nw{'sst_time'}.long_name = ncchar('sea surface temperature time');
nw{'sst_time'}.long_name = 'sea surface temperature time';
-nw{'sst_time'}.units = ncchar('days');
-nw{'sst_time'}.units = 'days';
-nw{'sst_time'}.cycle_length = sstc;
nw{'sst_time'}.field = ncchar('time, scalar, series');
nw{'sst_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'sst_time',sstc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
nw{'sss_time'} = ncdouble('sss_time');
nw{'sss_time'}.long_name = ncchar('sea surface salinity time');
nw{'sss_time'}.long_name = 'sea surface salinity time';
-nw{'sss_time'}.units = ncchar('days');
-nw{'sss_time'}.units = 'days';
-nw{'sss_time'}.cycle_length = sssc;
nw{'sss_time'}.field = ncchar('time, scalar, series');
nw{'sss_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'sss_time',sssc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'srf_time'} = ncdouble('srf_time');
nw{'srf_time'}.long_name = ncchar('solar shortwave radiation time');
nw{'srf_time'}.long_name = 'solar shortwave radiation time';
-nw{'srf_time'}.units = ncchar('days');
-nw{'srf_time'}.units = 'days';
-nw{'srf_time'}.cycle_length = srfc;
nw{'srf_time'}.field = ncchar('time, scalar, series');
nw{'srf_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'srf_time',srfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'sustr'} = ncdouble('sms_time', 'eta_u', 'xi_u');
nw{'sustr'}.long_name = ncchar('surface u-momentum stress');
diff --git a/Nesting_tools/create_nestedinitial.m b/Nesting_tools/create_nestedinitial.m
index 7bb1e37e..6fb41bfb 100644
--- a/Nesting_tools/create_nestedinitial.m
+++ b/Nesting_tools/create_nestedinitial.m
@@ -1,7 +1,7 @@
function ncini=create_nestedinitial(inifile,gridfile,parentfile,title,...
theta_s,theta_b,Tcline,N,time,clobber,...
biol,pisces,namebiol,namepisces,...
- unitbiol,unitpisces,hc,vtransform)
+ unitbiol,unitpisces,hc,vtransform,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function ncini=create_inifile(inifile,gridfile,theta_s,...
@@ -68,6 +68,17 @@ elseif nargin <18
vtransform = 1;
end
%
+% options for write_time_attributes
+insecond = 1 ;
+add_cycle = 0 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Read the grid file
%
nc=netcdf(gridfile, 'nowrite');
@@ -143,11 +154,13 @@ ncini{'tstart'}.long_name = ncchar('start processing day');
ncini{'tstart'}.long_name = 'start processing day';
ncini{'tstart'}.units = ncchar('day');
ncini{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
ncini{'tend'}.long_name = ncchar('end processing day');
ncini{'tend'}.long_name = 'end processing day';
-ncini{'tend'}.units = ncchar('day');
-ncini{'tend'}.units = 'day';
+write_time_attributes(nc,'tend','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
ncini{'theta_s'}.long_name = ncchar('S-coordinate surface control parameter');
ncini{'theta_s'}.long_name = 'S-coordinate surface control parameter';
@@ -189,10 +202,10 @@ ncini{'Cs_rho'}.field = 'Cs_rho, scalar';
%
ncini{'scrum_time'}.long_name = ncchar('time since initialization');
ncini{'scrum_time'}.long_name = 'time since initialization';
-ncini{'scrum_time'}.units = ncchar('second');
-ncini{'scrum_time'}.units = 'second';
ncini{'scrum_time'}.field = ncchar('time, scalar, series');
ncini{'scrum_time'}.field = 'time, scalar, series';
+write_time_attributes(nc,'scrum_time','',time_unit_att,time_second_unit_att,...
+ calendar_att,1,0);
%
ncini{'u'}.long_name = ncchar('u-momentum component');
ncini{'u'}.long_name = 'u-momentum component';
diff --git a/Nesting_tools/create_nestedndepo.m b/Nesting_tools/create_nestedndepo.m
new file mode 100644
index 00000000..b1b0128e
--- /dev/null
+++ b/Nesting_tools/create_nestedndepo.m
@@ -0,0 +1,113 @@
+function create_nestedndepo(ndeponame,parentname,grdname,title,ndepot,ndepoc)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Create an empty netcdf ndepo forcing file (for PISCES)
+% ndeponame: name of the ndepo file
+% grdname: name of the grid file
+% title: title in the netcdf file
+%
+% 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) 2004-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
+% Update : Gildas Cambon 13 Oct 2009
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+nc=netcdf(grdname);
+L=length(nc('xi_psi'));
+M=length(nc('eta_psi'));
+close(nc);
+Lp=L+1;
+Mp=M+1;
+nw = netcdf(ndeponame, 'write');
+%redef(nw);
+%
+% Create dimensions
+%
+nw('xi_u') = L;
+nw('eta_u') = Mp;
+nw('xi_v') = Lp;
+nw('eta_v') = M;
+nw('xi_rho') = Lp;
+nw('eta_rho') = Mp;
+nw('xi_psi') = L;
+nw('eta_psi') = M;
+nw('ndepo_time') = length(ndepot);
+%
+% Create variables and attributes
+%
+nw{'ndepo_time'} = ncdouble('ndepo_time');
+nw{'ndepo_time'}.long_name = ncchar('ndepo time');
+nw{'ndepo_time'}.long_name = 'ndepo time';
+nw{'ndepo_time'}.units = ncchar('days');
+nw{'ndepo_time'}.units = 'days';
+nw{'ndepo_time'}.cycle_length = ndepoc;
+nw{'ndepo_time'}.field = ncchar('time, scalar, series');
+nw{'ndepo_time'}.field = 'time, scalar, series';
+
+%
+nw{'ndepo'} = ncdouble('ndepo_time', 'eta_rho', 'xi_rho');
+nw{'ndepo'}.long_name = ncchar('Nitrogen Deposition');
+nw{'ndepo'}.long_name = 'Nitrogen Deposition';
+nw{'ndepo'}.units = ncchar('KgN m-2 s-1');
+nw{'ndepo'}.units = 'KgN m-2 s-1';
+nw{'ndepo'}.field = ncchar('ndepo, scalar, series');
+nw{'ndepo'}.field = 'ndepo, scalar, series';
+%
+nw{'noyndepo'} = ncdouble('ndepo_time', 'eta_rho', 'xi_rho');
+nw{'noyndepo'}.long_name = ncchar('NOy Deposition');
+nw{'noyndepo'}.long_name = 'NOy Deposition';
+nw{'noyndepo'}.units = ncchar('KgN m-2 s-1');
+nw{'noyndepo'}.units = 'KgN m-2 s-1';
+nw{'noyndepo'}.field = ncchar('noyndepo, scalar, series');
+nw{'noyndepo'}.field = 'noyndepo, scalar, series';
+%
+nw{'nhxndepo'} = ncdouble('ndepo_time', 'eta_rho', 'xi_rho');
+nw{'nhxndepo'}.long_name = ncchar('NHx Deposition');
+nw{'nhxndepo'}.long_name = 'NHx Deposition';
+nw{'nhxndepo'}.units = ncchar('KgN m-2 s-1');
+nw{'nhxndepo'}.units = 'KgN m-2 s-1';
+nw{'nhxndepo'}.field = ncchar('nhxndepo, scalar, series');
+nw{'nhxndepo'}.field = 'nhxndepo, scalar, series';
+%
+%endef(nw);
+
+%
+% Create global attributes
+%
+
+nw.title = ncchar(title);
+nw.title = title;
+nw.date = ncchar(date);
+nw.date = date;
+nw.grd_file = ncchar(grdname);
+nw.grd_file = grdname;
+nw.parent_file = ncchar(parentname);
+nw.parent_file = parentname;
+
+%
+% Write time variables
+%
+
+nw{'ndepo_time'}(:) = ndepot;
+
+
+close(nw);
+return
diff --git a/Nesting_tools/interp_dust.m b/Nesting_tools/interp_dust.m
index cf9305e8..31cdf89b 100644
--- a/Nesting_tools/interp_dust.m
+++ b/Nesting_tools/interp_dust.m
@@ -50,4 +50,5 @@ switch Answer
handles.childdust=childname;
end
nested_dust(handles.childgrid,handles.parentdust,handles.childdust)
+nested_ndepo(handles.childgrid,handles.parentdust,handles.childdust)
return
diff --git a/Nesting_tools/nested_clim.m b/Nesting_tools/nested_clim.m
index b3847285..96bdf80a 100644
--- a/Nesting_tools/nested_clim.m
+++ b/Nesting_tools/nested_clim.m
@@ -1,12 +1,12 @@
function nested_clim(child_grd,parent_clim,child_clim,...
- vertical_correc,extrapmask,biol,bioebus,pisces)
+ vertical_correc,extrapmask,biol,bioebus,pisces)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% compute the climatology of the embedded grid
%
-% Further Information:
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -24,8 +24,8 @@ function nested_clim(child_grd,parent_clim,child_clim,...
% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
% MA 02111-1307 USA
%
-% Copyright (c) 2004-2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
+% Copyright (c) 2004-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -46,9 +46,8 @@ tpisces=[];cpisces=[];
% Check type of clim file
-%
-if nvar <= 31
-elseif (nvar <= 41 & biol)
+if biol
+ if (bioebus~=1) %% for biol + npzd
timebiol={'no3_time';'o2_time';'chla_time';'phyto_time';'zoo_time'};
cyclebiol={'no3_cyle';'o2_cycle';'chla_cycle';'phyto_cycle';'zoo_cycle'};
namebiol={'NO3';'O2';'CHLA';'PHYTO';'ZOO'};
@@ -57,30 +56,27 @@ elseif (nvar <= 41 & biol)
disp(['Compute Biogeochemical variables type NPZD : '])
disp(['NChlPZD or N2ChlPZD2 '])
disp('==========================')
-elseif (46 <= nvar <=47 & biobus)
+ else % for biol + bioebus)
timebiol={'no3_time';'o2_time';'chla_time';'sphyto_time';'lphyto_time';'szoo_time';'lzoo_time';'n2o_time'};
cyclebiol={'no3_cyle';'o2_cycle';'chla_cycle';'sphyto_cycle';'lphyto_cycle';'szoo_cycle';'lzoo_cycle';'n2o_cycle'};
namebiol={'NO3';'O2';'CHLA';'SPHYTO';'LPHYTO';'SZOO';'LZOO';'N2O'};
unitbiol={'mMol N m-3';'mMol O m-3';'mg C l-1';'mMol N m-3';'mMol N m-3';'mMol N m-3';'mMol N m-3';'mMol N m-3'};
disp(['Compute Biological variables for BIOEBUS : '])
disp('==========================')
-elseif (pisces & nvar>=47)
- timepisces={'no3_time';'po4_time';'si_time';'o2_time';'dic_time';'talk_time';'doc_time';'fer_time'};
- cyclepisces={'no3_cycle';'po4_cycle';'si_cycle';'o2_cycle';'dic_cycle';'talk_cycle';'doc_cycle';'fer_cycle'};
- namepisces={'NO3';'PO4';'Si';'O2';'DIC';'TALK';'DOC';'FER'};
- unitpisces={'mMol N m-3';'mMol P m-3';'mMol Si m-3';'mMol O m-3';'mMol C m-3';'mMol C m-3';'mMol C m-3';'uMol Fe m-3'};
- disp('Compute Biogeochemical variables for PISCES')
- disp('=========================')
-else
- error(sprintf(['You don''t have the neccesary variables in the clim file. \n',...
- 'or you didn''t choose the right bio. model. \n',...
- 'Check croco_ini.nc parent file and make_clim.m']))
+ end
+elseif (pisces)
+ timepisces={'no3_time';'po4_time';'si_time';'o2_time';'dic_time';'talk_time';'doc_time';'fer_time'};
+ cyclepisces={'no3_cycle';'po4_cycle';'si_cycle';'o2_cycle';'dic_cycle';'talk_cycle';'doc_cycle';'fer_cycle'};
+ namepisces={'NO3';'PO4';'Si';'O2';'DIC';'TALK';'DOC';'FER'};
+ unitpisces={'mMol N m-3';'mMol P m-3';'mMol Si m-3';'mMol O m-3';'mMol C m-3';'mMol C m-3';'mMol C m-3';'uMol Fe m-3'};
+ disp('Compute Biogeochemical variables for PISCES')
+ disp('=========================')
end
-%
+
% Title
%
title=['Climatology file for the embedded grid :',child_clim,...
- ' using parent forcing file: ',parent_clim];
+ ' using parent forcing file: ',parent_clim];
disp(' ')
disp(title)
if extrapmask==1
@@ -93,7 +89,7 @@ if vertical_correc==1
disp('===============')
end
%
-if pisces & biol
+if pisces & biol
error(['Both Biol NPZD and Pisces are ON, no possible yet...!'])
end
%
@@ -132,9 +128,9 @@ vtransform=nc{'Vtransform'}(:);
hc = nc{'hc'}(:);
disp([' Use parent VTRANSFORM = ',num2str(vtransform)])
if ~exist('vtransform') | isempty(vtransform)
- disp([' No VTRANSFORM parameter found'])
- disp([' Use the default one VTRANSFORM = 1'])
- vtransform=1;
+ disp([' No VTRANSFORM parameter found'])
+ disp([' Use the default one VTRANSFORM = 1'])
+ vtransform=1;
end
ttime = nc{'tclm_time'}(:);
tcycle = nc{'tclm_time'}.cycle_length(:);
@@ -148,23 +144,30 @@ sshtime = nc{'ssh_time'}(:);
sshcycle = nc{'ssh_time'}.cycle_length(:);
%
if biol==1
- for k=1:length(namebiol)
- eval([char(timebiol(k)),'=nc{''',char(timebiol(k)),'''}(:);']);
- eval([char(cyclebiol(k)),'=nc{''',char(timebiol(k)),'''}.cycle_length(:);']);
- %
- eval(['tbiol(k,:)=',char(timebiol(k)),';']);
- eval(['cbiol(k,:)=',char(cyclebiol(k)),';']);
-end
+ for k=1:length(namebiol)
+ if strcmp(char(namebiol{k}), 'NO3') || strcmp(char(namebiol{k}), 'O2') || strcmp(char(namebiol{k}), 'N2O')
+ skip = 3; % for no3_time + o2_time + n2o_time % a bit sloppy
+ % wa tale value every 3 month to have kinf of seasonal ...
+ else
+ skip = 1;
+ end
+
+ eval([char(timebiol(k)),'=nc{''',char(timebiol(k)),'''}(1:skip:end,:);']);
+ eval([char(cyclebiol(k)),'=nc{''',char(timebiol(k)),'''}.cycle_length(:);']);
+
+ eval(['tbiol(k,:)=',char(timebiol(k)),';']);
+ eval(['cbiol(k,:)=',char(cyclebiol(k)),';']);
+ end
end
%
if pisces==1
- for k=1:length(namepisces)
- eval([char(timepisces(k)),'=nc{''',char(timepisces(k)),'''}(:);']);
- eval([char(cyclepisces(k)),'=nc{''',char(timepisces(k)),'''}.cycle_length(:);']);
- %
- eval(['tpisces(k,:)=',char(timepisces(k)),';']);
- eval(['cpisces(k,:)=',char(cyclepisces(k)),';']);
- end
+ for k=1:length(namepisces)
+ eval([char(timepisces(k)),'=nc{''',char(timepisces(k)),'''}(:);']);
+ eval([char(cyclepisces(k)),'=nc{''',char(timepisces(k)),'''}.cycle_length(:);']);
+ %
+ eval(['tpisces(k,:)=',char(timepisces(k)),';']);
+ eval(['cpisces(k,:)=',char(cyclepisces(k)),';']);
+ end
end
%
result=close(nc);
@@ -178,15 +181,16 @@ end
%
disp(' ')
disp(' Create the climatology file...')
+%
ncclim=create_nestedclim(child_clim,child_grd,parent_clim,title,...
- theta_s,theta_b,Tcline,N,...
- ttime,stime,utime,vtime,sshtime,...
- tcycle,scycle,ucycle,vcycle,sshcycle,...
- tbiol,cbiol,tpisces, cpisces, ...
- 'clobber',...
- biol,pisces,...
- timebiol, cyclebiol,timepisces,cyclepisces,...
- namebiol,namepisces,unitbiol,unitpisces,hc,vtransform);
+ theta_s,theta_b,Tcline,N,...
+ ttime,stime,utime,vtime,sshtime,...
+ tcycle,scycle,ucycle,vcycle,sshcycle,...
+ tbiol,cbiol,tpisces, cpisces, ...
+ 'clobber',...
+ biol,pisces,...
+ timebiol, cyclebiol,timepisces,cyclepisces,...
+ namebiol,namepisces,unitbiol,unitpisces,hc,vtransform);
%
% parent indices
%
@@ -207,66 +211,66 @@ jrchild=(jmin+0.5-0.5/refinecoeff:1/refinecoeff:jmax+0.5+0.5/refinecoeff);
[ichildgrd_v,jchildgrd_v]=meshgrid(irchild,jpchild);
%
% interpolations
-%
+%
disp(' ')
-disp(' Do the interpolations...')
+disp(' Do the interpolations...')
np=netcdf(parent_clim);
disp('u...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar4d(np,ncclim,igrd_u,jgrd_u,ichildgrd_u,jchildgrd_u,'u',mask,tindex,N)
end
disp('v...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar4d(np,ncclim,igrd_v,jgrd_v,ichildgrd_v,jchildgrd_v,'v',mask,tindex,N)
end
disp('zeta...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar3d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'SSH',mask,tindex)
end
disp('ubar...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar3d(np,ncclim,igrd_u,jgrd_u,ichildgrd_u,jchildgrd_u,'ubar',mask,tindex)
end
disp('vbar...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar3d(np,ncclim,igrd_v,jgrd_v,ichildgrd_v,jchildgrd_v,'vbar',mask,tindex)
end
disp('temp...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'temp',mask,tindex,N)
end
disp('salt...')
for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'salt',mask,tindex,N)
end
%
%%
%
if biol
- for k=1:length(namebiol)
- disp(char(namebiol(k)))
- for tindex=1:length(tbiol(k,:))
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(tbiol(k,:)))])
- interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,char(namebiol(k)),mask,tindex,N)
- end
+ for k=1:length(namebiol)
+ disp(char(namebiol(k)))
+ for tindex=1:length(tbiol(k,:))
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(tbiol(k,:)))])
+ interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,char(namebiol(k)),mask,tindex,N)
end
+ end
end
%
if pisces
- for k=1:length(namepisces)
- disp(char(namepisces(k)))
- for tindex=1:length(tpisces(k,:))
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(tpisces(k,:)))])
- interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,char(namepisces(k)),mask,tindex,N)
- end
+ for k=1:length(namepisces)
+ disp(char(namepisces(k)))
+ for tindex=1:length(tpisces(k,:))
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(tpisces(k,:)))])
+ interpvar4d(np,ncclim,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,char(namepisces(k)),mask,tindex,N)
end
+ end
end
close(np);
close(ncclim);
@@ -274,33 +278,33 @@ close(ncclim);
% Vertical corrections
%
if (vertical_correc==1)
- disp('Process variable physical variables')
- for tindex=1:length(climtime)
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
- vert_correc(child_clim,tindex,0,0,namebiol,namepisces)
- end
- %%
- if biol
- disp('Process variable NPZD')
- for k=1:length(namebiol)
- disp(char(namebiol(k)))
- for tindex=1:length(tbiol(k,:))
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(tbiol(k,:)))])
- vert_correc_onefield(child_clim,tindex,char(namebiol(k)))
- end
- end
+ disp('Process variable physical variables')
+ for tindex=1:length(climtime)
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(climtime))])
+ vert_correc(child_clim,tindex,0,0,namebiol,namepisces)
+ end
+ %%
+ if biol
+ disp('Process variable NPZD')
+ for k=1:length(namebiol)
+ disp(char(namebiol(k)))
+ for tindex=1:length(tbiol(k,:))
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(tbiol(k,:)))])
+ vert_correc_onefield(child_clim,tindex,char(namebiol(k)))
+ end
end
- %%
- if pisces
- disp('Process variable PISCES')
- for k=1:length(namepisces)
- disp(char(namepisces(k)))
- for tindex=1:length(tpisces(k,:))
- disp([' Time index : ',num2str(tindex),' of ',num2str(length(tpisces(k,:)))])
- vert_correc_onefield(child_clim,tindex,char(namepisces(k)))
- end
- end
+ end
+ %%
+ if pisces
+ disp('Process variable PISCES')
+ for k=1:length(namepisces)
+ disp(char(namepisces(k)))
+ for tindex=1:length(tpisces(k,:))
+ disp([' Time index : ',num2str(tindex),' of ',num2str(length(tpisces(k,:)))])
+ vert_correc_onefield(child_clim,tindex,char(namepisces(k)))
+ end
end
+ end
end
%
% Make a plot
diff --git a/Nesting_tools/nested_dust.m b/Nesting_tools/nested_dust.m
index 98a94db7..10d34370 100644
--- a/Nesting_tools/nested_dust.m
+++ b/Nesting_tools/nested_dust.m
@@ -102,6 +102,10 @@ nc=netcdf(child_dust,'write');
disp('dust...')
for tindex=1:length(dustt)
interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'dust',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'dustfer',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'dustpo4',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'dustsi',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'solubility2',mask,tindex)
end
result=close(np);
result=close(nc);
diff --git a/Nesting_tools/nested_ndepo.m b/Nesting_tools/nested_ndepo.m
new file mode 100644
index 00000000..63d6f102
--- /dev/null
+++ b/Nesting_tools/nested_ndepo.m
@@ -0,0 +1,118 @@
+function nested_ndepo(child_grd,parent_ndepo,child_ndepo)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% compute the ndepo file (PISCES biogeochemical model)
+% of the embedded grid
+%
+% 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) 2004-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
+% Update : Gildas Cambon: 13 Nov 2009
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+extrapmask=0;
+%
+% Title
+%
+title=['ndepo file for the embedded grid :',child_ndepo,...
+ ' using parent ndepo file: ',parent_ndepo];
+disp(' ')
+disp(title)
+%
+% Read in the embedded grid
+%
+disp(' ')
+disp(' Read in the embedded grid...')
+nc=netcdf(child_grd);
+parent_grd=nc.parent_grid(:);
+imin=nc{'grd_pos'}(1);
+imax=nc{'grd_pos'}(2);
+jmin=nc{'grd_pos'}(3);
+jmax=nc{'grd_pos'}(4);
+refinecoeff=nc{'refine_coef'}(:);
+result=close(nc);
+nc=netcdf(parent_grd);
+Lp=length(nc('xi_rho'));
+Mp=length(nc('eta_rho'));
+if extrapmask==1
+ mask=nc{'mask_rho'}(:);
+else
+ mask=[];
+end
+result=close(nc);
+%
+% Read in the parent ndepo file
+%
+disp(' ')
+disp(' Read in the parent ndepo file...')
+nc = netcdf(parent_ndepo);
+ndepot = nc{'ndepo_time'}(:);
+ndepoc = nc{'ndepo_time'}.cycle_length(:);
+result=close(nc);
+%
+% Create the ndepo file
+%
+disp(' ')
+disp(' Create the ndepo file...')
+create_nestedndepo(child_ndepo,parent_ndepo,child_grd,title,...
+ ndepot,ndepoc)
+%
+% parent indices
+%
+[igrd_r,jgrd_r]=meshgrid((1:1:Lp),(1:1:Mp));
+[igrd_p,jgrd_p]=meshgrid((1:1:Lp-1),(1:1:Mp-1));
+[igrd_u,jgrd_u]=meshgrid((1:1:Lp-1),(1:1:Mp));
+[igrd_v,jgrd_v]=meshgrid((1:1:Lp),(1:1:Mp-1));
+%
+% the children indices
+%
+ipchild=(imin:1/refinecoeff:imax);
+jpchild=(jmin:1/refinecoeff:jmax);
+irchild=(imin+0.5-0.5/refinecoeff:1/refinecoeff:imax+0.5+0.5/refinecoeff);
+jrchild=(jmin+0.5-0.5/refinecoeff:1/refinecoeff:jmax+0.5+0.5/refinecoeff);
+[ichildgrd_p,jchildgrd_p]=meshgrid(ipchild,jpchild);
+[ichildgrd_r,jchildgrd_r]=meshgrid(irchild,jrchild);
+[ichildgrd_u,jchildgrd_u]=meshgrid(ipchild,jrchild);
+[ichildgrd_v,jchildgrd_v]=meshgrid(irchild,jpchild);
+%
+% interpolations
+%
+disp(' ')
+disp(' Do the interpolations...')
+np=netcdf(parent_ndepo);
+nc=netcdf(child_ndepo,'write');
+disp('ndepo...')
+for tindex=1:length(ndepot)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'ndepo',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'noyndepo',mask,tindex)
+ interpvar3d(np,nc,igrd_r,jgrd_r,ichildgrd_r,jchildgrd_r,'nhxndepo',mask,tindex)
+end
+result=close(np);
+result=close(nc);
+disp(' ')
+disp(' Done ')
+%
+% Make a plot
+%
+disp(' ')
+disp(' Make a plot...')
+figure(1)
+plot_nestndepo(child_ndepo,'ndepo',[1 6],1)
diff --git a/Nesting_tools/nestgui.fig b/Nesting_tools/nestgui.fig
index b6a22c1684e145f76caa30e670a28dcfc8018a03..4f5c4b92d7fd0473e92ea098b8dde0bf487acec2 100644
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diff --git a/Nesting_tools/plot_nestndepo.m b/Nesting_tools/plot_nestndepo.m
new file mode 100644
index 00000000..111a655a
--- /dev/null
+++ b/Nesting_tools/plot_nestndepo.m
@@ -0,0 +1,83 @@
+function plot_nestndepo(child_ndepo,thefield,thetime,skip)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Test the embedded ndepo forcing file.
+%
+% 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) 2004-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+npts=[0 0 0 0];
+i=0;
+for time=thetime
+ i=i+1;
+
+ subplot(2,length(thetime),i)
+
+
+ nc=netcdf(child_ndepo);
+ parent_ndepo=nc.parent_file(:);
+ child_grd=nc.grd_file(:);
+ fieldc=nc{thefield}(time,:,:);
+ fieldname=nc{thefield}.long_name(:);
+ result=close(nc);
+
+ nc=netcdf(child_grd);
+ parent_grd=nc.parent_grid(:);
+ refinecoeff=nc{'refine_coef'}(:);
+ lonc=nc{'lon_rho'}(:);
+ latc=nc{'lat_rho'}(:);
+ mask=nc{'mask_rho'}(:);
+ result=close(nc);
+ mask(mask==0)=NaN;
+ pcolor(lonc,latc,mask.*fieldc)
+ shading flat
+ axis image
+ caxis([min(min(fieldc)) max(max(fieldc))])
+ colorbar
+ axis([min(min(lonc)) max(max(lonc)) min(min(latc)) max(max(latc))])
+ title(['\bf ',fieldname,' CHILD'])
+
+ subplot(2,length(thetime),i+length(thetime))
+ nc=netcdf(parent_ndepo);
+ field=nc{thefield}(time,:,:);
+ fieldname=nc{thefield}.long_name(:);
+ result=close(nc);
+
+ nc=netcdf(parent_grd);
+ lon=nc{'lon_rho'}(:);
+ lat=nc{'lat_rho'}(:);
+ mask=nc{'mask_rho'}(:);
+ result=close(nc);
+ mask(mask==0)=NaN;
+ pcolor(lon,lat,mask.*field)
+ shading flat
+ axis image
+ caxis([min(min(fieldc)) max(max(fieldc))])
+ colorbar
+ axis([min(min(lonc)) max(max(lonc)) min(min(latc)) max(max(latc))])
+ title(['\bf ',fieldname,' PARENT'])
+end
+
+
+return
diff --git a/Oforc_OGCM/create_OGCM.m b/Oforc_OGCM/create_OGCM.m
index 88f04690..c4428922 100644
--- a/Oforc_OGCM/create_OGCM.m
+++ b/Oforc_OGCM/create_OGCM.m
@@ -1,12 +1,12 @@
function create_OGCM(fname,lonT,latT,lonU,latU,lonV,latV,depth,time,...
- temp,salt,u,v,ssh,Yorig)
+ temp,salt,u,v,ssh,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create the OGCM file
%
-% Further Information:
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -24,8 +24,8 @@ function create_OGCM(fname,lonT,latT,lonU,latU,lonV,latV,depth,time,...
% 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
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
% Updated 6-Sep-2006 by Pierrick Penven
% Updated 7-Oct-2013 by Gildas Cambon
@@ -120,8 +120,10 @@ nc{'depth'}=ncdouble('depth') ;
nc{'depth'}.units=ncchar('meters');
nc{'depth'}.units='meters';
nc{'time'}=ncdouble('time') ;
-eval(['nc{''time''}.units = ncchar(''days since 1-Jan-',num2str(Yorig),' 00:00:0.0'');'])
-eval(['nc{''time''}.units = ''days since 1-Jan-',num2str(Yorig),' 00:00:0.0'';'])
+eval(['nc{''time''}.units = ncchar(''days since ',sprintf('%04d', Yorig),'-01-01 00:00:00'');'])
+eval(['nc{''time''}.units = ''days since ',sprintf('%04d', Yorig),'-01-01 00:00:00'';'])
+nc{'time'}.calendar = ncchar('proleptic_gregorian');
+nc{'time'}.calendar = 'proleptic_gregorian';
endef(nc);
%
% File the file
@@ -136,13 +138,13 @@ nc{'latV'}(:)=latV;
nc{'lonV'}(:)=lonV;
%
for tndx=1:length(time)
-%
-nc{'time'}(tndx)=time(tndx);
-%
+ %
+ nc{'time'}(tndx)=time(tndx);
+ %
if length(time)==1
nc{'ssh'}(tndx,:,:)=ssh;
-% nc{'taux'}(tndx,:,:)=taux;
-% nc{'tauy'}(tndx,:,:)=tauy;
+ % nc{'taux'}(tndx,:,:)=taux;
+ % nc{'tauy'}(tndx,:,:)=tauy;
u1=u;
v1=v;
nc{'u'}(tndx,:,:,:)=u1;
@@ -151,8 +153,8 @@ nc{'time'}(tndx)=time(tndx);
nc{'salt'}(tndx,:,:,:)=salt;
else
nc{'ssh'}(tndx,:,:)=squeeze(ssh(tndx,:,:));
-% nc{'taux'}(tndx,:,:)=squeeze(taux(tndx,:,:));
-% nc{'tauy'}(tndx,:,:)=squeeze(tauy(tndx,:,:));
+ % nc{'taux'}(tndx,:,:)=squeeze(taux(tndx,:,:));
+ % nc{'tauy'}(tndx,:,:)=squeeze(tauy(tndx,:,:));
u1=squeeze(u(tndx,:,:,:));
v1=squeeze(v(tndx,:,:,:));
nc{'u'}(tndx,:,:,:)=u1;
@@ -160,35 +162,35 @@ nc{'time'}(tndx)=time(tndx);
nc{'temp'}(tndx,:,:,:)=squeeze(temp(tndx,:,:,:));
nc{'salt'}(tndx,:,:,:)=squeeze(salt(tndx,:,:,:));
end
-%
-% Compute the barotropic velocities
-%
-masku=isfinite(u1);
-maskv=isfinite(v1);
-u1(isnan(u1))=0;
-v1(isnan(v1))=0;
-dz=gradient(depth);
-NZ=length(depth);
-du=0*squeeze(u1(1,:,:));
-zu=du;
-dv=0*squeeze(v1(1,:,:));
-zv=dv;
-for k=1:NZ
- du=du+dz(k)*squeeze(u1(k,:,:));
- zu=zu+dz(k)*squeeze(masku(k,:,:));
- dv=dv+dz(k)*squeeze(v1(k,:,:));
- zv=zv+dz(k)*squeeze(maskv(k,:,:));
-end
-du(zu==0)=NaN;
-dv(zv==0)=NaN;
-zu(zu==0)=NaN;
-zv(zv==0)=NaN;
-ubar=du./zu;
-vbar=dv./zv;
-%
-nc{'ubar'}(tndx,:,:)=ubar;
-nc{'vbar'}(tndx,:,:)=vbar;
-%
+ %
+ % Compute the barotropic velocities
+ %
+ masku=isfinite(u1);
+ maskv=isfinite(v1);
+ u1(isnan(u1))=0;
+ v1(isnan(v1))=0;
+ dz=gradient(depth);
+ NZ=length(depth);
+ du=0*squeeze(u1(1,:,:));
+ zu=du;
+ dv=0*squeeze(v1(1,:,:));
+ zv=dv;
+ for k=1:NZ
+ du=du+dz(k)*squeeze(u1(k,:,:));
+ zu=zu+dz(k)*squeeze(masku(k,:,:));
+ dv=dv+dz(k)*squeeze(v1(k,:,:));
+ zv=zv+dz(k)*squeeze(maskv(k,:,:));
+ end
+ du(zu==0)=NaN;
+ dv(zv==0)=NaN;
+ zu(zu==0)=NaN;
+ zv(zv==0)=NaN;
+ ubar=du./zu;
+ vbar=dv./zv;
+ %
+ nc{'ubar'}(tndx,:,:)=ubar;
+ nc{'vbar'}(tndx,:,:)=vbar;
+ %
end
%
close(nc)
diff --git a/Oforc_OGCM/make_OGCM_SODA.m b/Oforc_OGCM/make_OGCM_SODA.m
index f59e5e54..31a2f33e 100644
--- a/Oforc_OGCM/make_OGCM_SODA.m
+++ b/Oforc_OGCM/make_OGCM_SODA.m
@@ -6,10 +6,10 @@
% http://iridl.ldeo.columbia.edu./SOURCES/.CARTON-GIESE/.SODA/
% The on-line reference to ECCO is at
% http://ecco.jpl.nasa.gov/cgi-bin/nph-dods/datasets/
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -27,8 +27,8 @@
% 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
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
% Contributions of P. Marchesiello (IRD), J. Lefevre (IRD),
% and F. Colberg (UCT)
@@ -46,18 +46,18 @@ close all
%
crocotools_param
- %
- % SODA DODS URL
- %
- % SODA_2.2.4/ [ C20R-2 1871-2008 / POP2.1 ]
- %%url='http://iridl.ldeo.columbia.edu/SOURCES/.CARTON-GIESE/.SODA/.v2p2p4' ;
- url='http://apdrc.soest.hawaii.edu:80/dods/public_data/SODA/soda_pop2.2.4' ;
+%
+% SODA DODS URL
+%
+% SODA_2.2.4/ [ C20R-2 1871-2008 / POP2.1 ]
+%%url='http://iridl.ldeo.columbia.edu/SOURCES/.CARTON-GIESE/.SODA/.v2p2p4' ;
+url='http://apdrc.soest.hawaii.edu:80/dods/public_data/SODA/soda_pop2.2.4' ;
%
itolap_tot=itolap_a + itolap_p;
disp(['Overlap before =',num2str(itolap_a)])
disp(['Overlap after =',num2str(itolap_p)])
disp(['Total overlap =',num2str(itolap_tot)])
-disp(['...'])
+disp(['...'])
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% end of user input parameters
@@ -81,6 +81,10 @@ lat=nc{'lat_rho'}(:);
angle=nc{'angle'}(:);
h=nc{'h'}(:);
close(nc)
+
+if ~strcmp(OGCM, 'SODA')
+ error('Error: OGCM must be "SODA" in crocotools_param.m. Exiting script.');
+end
%
% Extract data over the internet
%
@@ -94,16 +98,16 @@ if Download_data==1
latmax=max(max(lat));
%
% Download data with DODS (the download matlab routine depends on the OGCM)
- %
+ %
disp('Download data...')
- download_SODA(Ymin,Ymax,Mmin,Mmax,lonmin,lonmax,latmin,latmax,...
- OGCM_dir,OGCM_prefix,url,Yorig)
+ download_SODA(Ymin,Ymax,Mmin,Mmax,lonmin,lonmax,latmin,latmax,...
+ OGCM_dir,OGCM_prefix,url,Yorig)
end
%
%------------------------------------------------------------------------------------
%
-% Get the OGCM grid
-%
+% Get the OGCM grid
+%
nc=netcdf([OGCM_dir,OGCM_prefix,'Y',num2str(Ymin),'M',num2str(Mmin),'.cdf'],'r');
lonT=nc{'lonT'}(:);
latT=nc{'latT'}(:);
@@ -117,18 +121,18 @@ NZ=NZ-rmdepth;
Z=Z(1:NZ);
close(nc)
%
-% Initial file
+% Initial file
% (the strategy is to start at the begining of a month)
-% it is possible to do some temporal interpolation...
+% it is possible to do some temporal interpolation...
% but I am too lazy. lets start the first day of
% month Mmin of year Ymin... with the first data available.
%
if makeini==1
- if ~exist('vtransform')
- vtransform=1; %Old Vtransform
- disp([' NO VTRANSFORM parameter found'])
- disp([' USE vtransform default value Vtransfor = 1'])
- end
+ if ~exist('vtransform')
+ vtransform=1; %Old Vtransform
+ disp([' NO VTRANSFORM parameter found'])
+ disp([' USE vtransform default value Vtransfor = 1'])
+ end
ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
%
% Process the time in Yorig time (i.e days since Yorig-01-01)
@@ -136,29 +140,29 @@ if makeini==1
tini=datenum(Ymin,Mmin,1)-datenum(Yorig,1,1);
disp(['Create an initial file for ',datestr(tini+datenum(Yorig,1,1));])
create_inifile(ininame,grdname,CROCO_title,...
- theta_s,theta_b,hc,N,...
- tini,'clobber', vtransform);
- nc_add_globatt(ininame,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ theta_s,theta_b,hc,N,...
+ tini,'clobber', vtransform,Yorig);
+ nc_add_globatt(ininame,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
nc_ini=netcdf(ininame,'write');
interp_OGCM(OGCM_dir,OGCM_prefix,Ymin,Mmin,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,1,...
- nc_ini,[],lon,lat,angle,h,1,obc,vtransform)
+ lonU,latU,lonV,latV,lonT,latT,Z,1,...
+ nc_ini,[],lon,lat,angle,h,1,obc,vtransform)
close(nc_ini)
end
%
-% Clim and Bry files
+% Clim and Bry files
%
if makeclim==1 | makebry==1
- if ~exist('vtransform')
- vtransform=1; %Old Vtransform
- disp([' NO VTRANSFORM parameter found'])
- disp([' USE vtransform default value Vtransfor = 1'])
- end
+ if ~exist('vtransform')
+ vtransform=1; %Old Vtransform
+ disp([' NO VTRANSFORM parameter found'])
+ disp([' USE vtransform default value Vtransfor = 1'])
+ end
%
% Loop on the years and the months
%
for Y=Ymin:Ymax
- if Y==Ymin
+ if Y==Ymin
mo_min=Mmin;
else
mo_min=1;
@@ -171,100 +175,100 @@ if makeclim==1 | makebry==1
for M=mo_min:mo_max
disp(' ')
disp(['Processing year ',num2str(Y),...
- ' - month ',num2str(sprintf(Mth_format,M))])
+ ' - month ',num2str(sprintf(Mth_format,M))])
disp(' ')
%
Mm=M-1;Ym=Y;
if Mm==0
- Mm=12;
- Ym=Y-1;
+ Mm=12;
+ Ym=Y-1;
end
Mp=M+1;Yp=Y;
if Mp==13
- Mp=1;
- Yp=Y+1;
+ Mp=1;
+ Yp=Y+1;
end
%
- % Add 2 times step in the CROCO files: 1 at the beginning and 1 at the end
+ % Add 2 times step in the CROCO files: 1 at the beginning and 1 at the end
%
nc=netcdf([OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf'],'r');
OGCM_time=nc{'time'}(:);
ntimes=length(OGCM_time);
if ntimes==1
- dt=30; % monthly files (SODA..)
+ dt=30; % monthly files (SODA..)
itolap_a=1; itolap_p=1;
itolap_tot=itolap_a + itolap_p;
disp(['Reduced overlap for monthly SODA files'])
disp(['...'])
else
- dt=max(gradient(OGCM_time));
+ dt=max(gradient(OGCM_time));
end
%
%% Fill the time axis
%
croco_time=0*(1:ntimes+itolap_tot);
- %Current month
+ %Current month
croco_time(itolap_a+1:end-itolap_p)=OGCM_time;
%
%Previous month
%
disp(['==================================='])
for aa= 1:itolap_a
- disp(['Compute beginning overlap, time index:',num2str(aa)])
- disp(['Add ',num2str(-(itolap_a + 1 - aa)), ' timestep dt'])
- disp(['--------'])
- croco_time(aa) = croco_time(itolap_a+1) - ((itolap_a + 1 - aa).* dt);
+ disp(['Compute beginning overlap, time index:',num2str(aa)])
+ disp(['Add ',num2str(-(itolap_a + 1 - aa)), ' timestep dt'])
+ disp(['--------'])
+ croco_time(aa) = croco_time(itolap_a+1) - ((itolap_a + 1 - aa).* dt);
end
%
- %Next month
+ %Next month
%
- disp(['==================================='])
+ disp(['==================================='])
for aa= 1:itolap_p
- disp(['Compute end overlap, time index:',num2str(ntimes+itolap_tot - itolap_p + aa)])
- disp(['Add ',num2str(aa), ' timestep dt'])
- disp(['--------'])
- croco_time(end - itolap_p + aa ) = croco_time(end - itolap_p) + aa.* dt;
+ disp(['Compute end overlap, time index:',num2str(ntimes+itolap_tot - itolap_p + aa)])
+ disp(['Add ',num2str(aa), ' timestep dt'])
+ disp(['--------'])
+ croco_time(end - itolap_p + aa ) = croco_time(end - itolap_p) + aa.* dt;
end
disp(['==================================='])
close(nc)
- %-----------------------------------------------------
+ %-----------------------------------------------------
%
% Create and open the CROCO files
%
if makebry==1
- bryname=[bry_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
- theta_s,theta_b,hc,N,...
- croco_time,0,'clobber',vtransform);
- nc_add_globatt(bryname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
- nc_bry=netcdf(bryname,'write');
+ bryname=[bry_prefix,'Y',num2str(Y),...
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
+ theta_s,theta_b,hc,N,...
+ croco_time,0,'clobber',vtransform,Yorig);
+ nc_add_globatt(bryname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ nc_bry=netcdf(bryname,'write');
else
- nc_bry=[];
+ nc_bry=[];
end
if makeclim==1
- clmname=[clm_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- create_climfile(clmname,grdname,CROCO_title,...
- theta_s,theta_b,hc,N,croco_time,0,'clobber',vtransform);
- nc_add_globatt(clmname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
- nc_clm=netcdf(clmname,'write');
+ clmname=[clm_prefix,'Y',num2str(Y),...
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ create_climfile(clmname,grdname,CROCO_title,...
+ theta_s,theta_b,hc,N,croco_time,0,'clobber',vtransform,Yorig);
+ nc_add_globatt(clmname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ nc_clm=netcdf(clmname,'write');
else
- nc_clm=[];
+ nc_clm=[];
end
%
% Check if there are OGCM files for the previous Month
%
fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Ym),'M',num2str(Mm),'.cdf'];
if exist(fname)==0
- disp([' No data for the previous month: using current month'])
- Mm=M;
- Ym=Y;
- tndx_OGCM=ones(itolap_a,1);
+ disp([' No data for the previous month: using current month'])
+ Mm=M;
+ Ym=Y;
+ tndx_OGCM=ones(itolap_a,1);
else
- nc=netcdf(fname,'r');
- tndx_OGCM=[(length(nc('time'))- (itolap_a -1) ):1: (length(nc('time')))];
- close(nc)
+ nc=netcdf(fname,'r');
+ tndx_OGCM=[(length(nc('time'))- (itolap_a -1) ):1: (length(nc('time')))];
+ close(nc)
end
%
% Perform the interpolations for the previous month
@@ -272,11 +276,11 @@ if makeclim==1 | makebry==1
disp(' Previous month :')
disp('=================')
for aa=1:itolap_a
- disp(['Beg overlap # ', num2str(aa),' -> tindex ',num2str(aa)])
- disp(['It. of prev month used for it= ',num2str(tndx_OGCM(aa))])
- interp_OGCM(OGCM_dir,OGCM_prefix,Ym,Mm,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
- nc_clm,nc_bry,lon,lat,angle,h,aa,obc,vtransform)
+ disp(['Beg overlap # ', num2str(aa),' -> tindex ',num2str(aa)])
+ disp(['It. of prev month used for it= ',num2str(tndx_OGCM(aa))])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Ym,Mm,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
+ nc_clm,nc_bry,lon,lat,angle,h,aa,obc,vtransform)
end
%
% Perform the interpolations for the current month
@@ -285,26 +289,26 @@ if makeclim==1 | makebry==1
disp(' Current month :')
disp('================')
for tndx_OGCM=1:ntimes
- disp([' Time step : ',num2str(tndx_OGCM),' of ',num2str(ntimes),' :'])
- interp_OGCM(OGCM_dir,OGCM_prefix,Y,M,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM,...
- nc_clm,nc_bry,lon,lat,angle,h,tndx_OGCM+itolap_a,obc,vtransform)
+ disp([' Time step : ',num2str(tndx_OGCM),' of ',num2str(ntimes),' :'])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Y,M,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM,...
+ nc_clm,nc_bry,lon,lat,angle,h,tndx_OGCM+itolap_a,obc,vtransform)
end
%
% Read the OGCM file for the next month
%
fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Yp),'M',num2str(Mp),'.cdf'];
if exist(fname)==0
- disp([' No data for the next month: using current month'])
- Mp=M;
- Yp=Y;
- for aa=1:itolap_p
- tndx_OGCM(aa)=ntimes;
- end
+ disp([' No data for the next month: using current month'])
+ Mp=M;
+ Yp=Y;
+ for aa=1:itolap_p
+ tndx_OGCM(aa)=ntimes;
+ end
else
- for aa=1:itolap_p
- tndx_OGCM(aa)=aa;
- end;
+ for aa=1:itolap_p
+ tndx_OGCM(aa)=aa;
+ end;
end
%
% Perform the interpolations for the next month
@@ -312,20 +316,20 @@ if makeclim==1 | makebry==1
disp(' Next month :')
disp('=============')
for aa=1:itolap_p
- disp(['End Overlap #',num2str(aa),' -> tindex ',num2str(ntimes+itolap_a+aa)])
- disp(['It. of next month used for it= ',num2str(tndx_OGCM(aa))])
- interp_OGCM(OGCM_dir,OGCM_prefix,Yp,Mp,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
- nc_clm,nc_bry,lon,lat,angle,h,ntimes+itolap_a+aa,obc,vtransform)
+ disp(['End Overlap #',num2str(aa),' -> tindex ',num2str(ntimes+itolap_a+aa)])
+ disp(['It. of next month used for it= ',num2str(tndx_OGCM(aa))])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Yp,Mp,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
+ nc_clm,nc_bry,lon,lat,angle,h,ntimes+itolap_a+aa,obc,vtransform)
end
%
% Close the CROCO files
%
if ~isempty(nc_clm)
- close(nc_clm);
+ close(nc_clm);
end
if ~isempty(nc_bry)
- close(nc_bry);
+ close(nc_bry);
end
%
end
@@ -345,7 +349,7 @@ if SPIN_Long>0
%
ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
ininame2=[ini_prefix,'Y',num2str(Ymin-SPIN_Long),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',ininame2])
+ disp(['Create ',ininame2])
eval(['!cp ',ininame,' ',ininame2])
%
% Change the time
@@ -361,7 +365,7 @@ if SPIN_Long>0
for month=1:12*SPIN_Long
M=M+1;
if M==13
- M=1;
+ M=1;
Y=Y+1;
end
%
@@ -373,8 +377,8 @@ if SPIN_Long>0
%
clmname=[clm_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
clmname2=[clm_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',clmname2])
- eval(['!cp ',clmname,' ',clmname2])
+ disp(['Create ',clmname2])
+ eval(['!cp ',clmname,' ',clmname2])
%
% Change the time
%
@@ -401,8 +405,8 @@ if SPIN_Long>0
%
bryname=[bry_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
bryname2=[bry_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',bryname2])
- eval(['!cp ',bryname,' ',bryname2])
+ disp(['Create ',bryname2])
+ eval(['!cp ',bryname,' ',bryname2])
%
% Change the time
%
diff --git a/Oforc_OGCM/make_OGCM_mercator.m b/Oforc_OGCM/make_OGCM_mercator.m
index 687dcdbf..f7243368 100644
--- a/Oforc_OGCM/make_OGCM_mercator.m
+++ b/Oforc_OGCM/make_OGCM_mercator.m
@@ -1,6 +1,6 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Create and fill CROCO clim and bry files with OGCM
+% Create and fill CROCO clim and bry files with OGCM
% MERCATOR data.
%
% On crocotools_param.m, available datasets:
@@ -17,10 +17,10 @@
% (more than 15days from now : Best analysis)
%
% Online reference to MERCATOR is at http://marine.copernicus.eu
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -38,8 +38,8 @@
% 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
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
% Contributions of P. Marchesiello (IRD), J. Lefevre (IRD),
% and F. Colberg (UCT)
@@ -68,7 +68,7 @@ itolap_tot=itolap_a + itolap_p;
disp(['Overlap before =',num2str(itolap_a)])
disp(['Overlap after =',num2str(itolap_p)])
disp(['Total overlap =',num2str(itolap_tot)])
-disp(['...'])
+disp(['...'])
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% end of user input parameters
@@ -78,10 +78,10 @@ disp(['==================='])
disp([' Compute time axis '])
disp(['==================='])
if level==0
- nc_suffix='.nc';
+ nc_suffix='.nc';
else
- nc_suffix=['.nc.',num2str(level)];
- grdname=[grdname,'.',num2str(level)];
+ nc_suffix=['.nc.',num2str(level)];
+ grdname=[grdname,'.',num2str(level)];
end
%
% Get the model grid
@@ -93,6 +93,10 @@ angle=nc{'angle'}(:);
h=nc{'h'}(:);
close(nc)
%
+if ~strcmp(OGCM, 'mercator')
+ error('Error: OGCM must be "mercator" in crocotools_param.m. Exiting script.');
+ end
+%
% Extract data over the internet
%
if Download_data==1
@@ -105,7 +109,7 @@ if Download_data==1
latmax=max(max(lat));
%
% Download data with DODS (the download matlab routine depends on the OGCM)
- %
+ %
disp('Download data...')
% Loop on the years
%
@@ -122,20 +126,20 @@ if Download_data==1
mo_max=12;
end
for M=mo_min:mo_max
- thedatemonth=['Y',num2str(Y),'M',num2str(M)];
+ thedatemonth=['Y',num2str(Y),'M',num2str(M)];
download_mercator_python(pathCMC,user,password,mercator_type,...
- product_id, ...
- Y,M, ...
- lonmin,lonmax,latmin,latmax,hmax, ...
- OGCM_dir,OGCM_prefix,thedatemonth,Yorig)
+ product_id, ...
+ Y,M, ...
+ lonmin,lonmax,latmin,latmax,hmax, ...
+ OGCM_dir,OGCM_prefix,thedatemonth,Yorig)
end
- end %End loop over month and years for the downloading with python/motu client
+ end %End loop over month and years for the downloading with python/motu client
end %End loop for Download_data
%
%------------------------------------------------------------------------------------
%
-% Get the OGCM grid
-%
+% Get the OGCM grid
+%
nc=netcdf([OGCM_dir,OGCM_prefix,'Y',num2str(Ymin),'M',num2str(Mmin),'.cdf']);
lonT=nc{'lonT'}(:);
latT=nc{'latT'}(:);
@@ -149,9 +153,9 @@ NZ=NZ-rmdepth;
Z=Z(1:NZ);
close(nc)
%
-% Initial file
+% Initial file
% (the strategy is to start at the begining of a month)
-% it is possible to do some temporal interpolation...
+% it is possible to do some temporal interpolation...
% but I am too lazy. lets start the first day of
% month Mmin of year Ymin... with the first data available.
%
@@ -161,25 +165,25 @@ if makeini==1
disp([' NO VTRANSFORM parameter found'])
disp([' USE vtransform default value Vtransfor = 1'])
end
- ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
- %
- % Process the time in Yorig time (i.e days since Yorig-01-01)
- %
- tini=datenum(Ymin,Mmin,1)-datenum(Yorig,1,1);
- disp([' '])
- disp(['=> Create an initial file for ',datestr(tini+datenum(Yorig,1,1));])
- create_inifile(ininame,grdname,CROCO_title,...
- theta_s,theta_b,hc,N,...
- tini,'clobber', vtransform);
- nc_ini=netcdf(ininame,'write');
- interp_OGCM(OGCM_dir,OGCM_prefix,Ymin,Mmin,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,1,...
- nc_ini,[],lon,lat,angle,h,1,obc,vtransform)
- nc_add_globatt(ininame,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
- close(nc_ini)
+ ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
+ %
+ % Process the time in Yorig time (i.e days since Yorig-01-01)
+ %
+ tini=datenum(Ymin,Mmin,1)-datenum(Yorig,1,1);
+ disp([' '])
+ disp(['=> Create an initial file for ',datestr(tini+datenum(Yorig,1,1));])
+ create_inifile(ininame,grdname,CROCO_title,...
+ theta_s,theta_b,hc,N,...
+ tini,'clobber', vtransform,Yorig);
+ nc_ini=netcdf(ininame,'write');
+ interp_OGCM(OGCM_dir,OGCM_prefix,Ymin,Mmin,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,1,...
+ nc_ini,[],lon,lat,angle,h,1,obc,vtransform)
+ nc_add_globatt(ininame,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ close(nc_ini)
end
%
-% Clim and Bry files
+% Clim and Bry files
%
if makeclim==1 | makebry==1
if ~exist('vtransform')
@@ -187,297 +191,302 @@ if makeclim==1 | makebry==1
disp([' NO VTRANSFORM parameter found'])
disp([' USE vtransform default value Vtransfor = 1'])
end
- %
- % Loop on the years and the months
- %
- for Y=Ymin:Ymax
- if Y==Ymin
- mo_min=Mmin;
- else
- mo_min=1;
- end
- if Y==Ymax
- mo_max=Mmax;
- else
- mo_max=12;
- end
- for M=mo_min:mo_max
- disp(' ')
- disp(['Processing year ',num2str(Y),...
- ' - month ',num2str(M)])
- disp(' ')
- %
- Mm=M-1;Ym=Y;
- if Mm==0
- Mm=12;
- Ym=Y-1;
- end
- Mp=M+1;Yp=Y;
- if Mp==13
- Mp=1;
- Yp=Y+1;
- end
- %
- % Add 2 times step in the CROCO files: 1 at the beginning and 1 at the end
- %
- nc=netcdf([OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf']);
- OGCM_time=nc{'time'}(:);
- ntimes=length(OGCM_time);
- if ntimes==1
- dt=30; % monthly files
- itolap_a=1; itolap_p=1;
- itolap_tot=itolap_a + itolap_p;
- disp(['Reduced overlap for monthly files'])
- disp(['...'])
- else
- dt=max(gradient(OGCM_time));
- end
- %
- %% Fill the time axis
- %
- croco_time=0*(1:ntimes+itolap_tot);
- %Current month
- croco_time(itolap_a+1:end-itolap_p)=OGCM_time;
- %
- %Previous month
- %
- disp(['==================================='])
- for aa= 1:itolap_a
- disp(['Compute beginning overlap, time index:',num2str(aa)])
- disp(['Add ',num2str(-(itolap_a + 1 - aa)), ' timestep dt'])
- disp(['--------'])
- croco_time(aa) = croco_time(itolap_a+1) - ((itolap_a + 1 - aa).* dt);
- end
- %
- %Next month
- %
- disp(['==================================='])
- for aa= 1:itolap_p
- disp(['Compute end overlap, time index:',num2str(ntimes+itolap_tot - itolap_p + aa)])
- disp(['Add ',num2str(aa), ' timestep dt'])
- disp(['--------'])
- croco_time(end - itolap_p + aa ) = croco_time(end - itolap_p) + aa.* dt;
- end
- disp(['==================================='])
- close(nc)
- %-----------------------------------------------------
- %
- % Create and open the CROCO files
- %
- if makebry==1
- bryname=[bry_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp([' '])
- disp(['=> Create bry file : ', bryname ])
- create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
- theta_s,theta_b,hc,N,...
- croco_time,0,'clobber',vtransform);
- nc_add_globatt(bryname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
- nc_bry=netcdf(bryname,'write');
- else
- nc_bry=[];
- end
- if makeclim==1
- clmname=[clm_prefix,'Y',num2str(Y),...
- 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- create_climfile(clmname,grdname,CROCO_title,...
- theta_s,theta_b,hc,N,...
- croco_time,0,'clobber',vtransform);
- nc_add_globatt(clmname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
- nc_clm=netcdf(clmname,'write');
- else
- nc_clm=[];
- end
- %
- % Check if there are OGCM files for the previous Month
- %
- fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Ym),'M',num2str(Mm),'.cdf'];
- if exist(fname)==0
- disp([' No data for the previous month: using current month'])
- Mm=M;
- Ym=Y;
- tndx_OGCM=ones(itolap_a,1);
- else
- nc=netcdf(fname);
- tndx_OGCM=[(length(nc('time'))- (itolap_a -1) ):1: (length(nc('time')))];
- close(nc)
- end
- %
- % Perform the interpolations for the previous month
- %
- disp(' Previous month :')
- disp('=================')
- for aa=1:itolap_a
- disp(['Beg overlap # ', num2str(aa),' -> tindex ',num2str(aa)])
- disp(['It. of prev month used for it= ',num2str(tndx_OGCM(aa))])
- interp_OGCM(OGCM_dir,OGCM_prefix,Ym,Mm,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
- nc_clm,nc_bry,lon,lat,angle,h,aa,obc,vtransform)
- end
- %
- % Perform the interpolations for the current month
- %
+ %
+ % Loop on the years and the months
+ %
+ for Y=Ymin:Ymax
+ if Y==Ymin
+ mo_min=Mmin;
+ else
+ mo_min=1;
+ end
+ if Y==Ymax
+ mo_max=Mmax;
+ else
+ mo_max=12;
+ end
+ for M=mo_min:mo_max
+ disp(' ')
+ disp(['Processing year ',num2str(Y),...
+ ' - month ',num2str(M)])
+ disp(' ')
+ %
+ Mm=M-1;Ym=Y;
+ if Mm==0
+ Mm=12;
+ Ym=Y-1;
+ end
+ Mp=M+1;Yp=Y;
+ if Mp==13
+ Mp=1;
+ Yp=Y+1;
+ end
+ %
+ % Add 2 times step in the CROCO files: 1 at the beginning and 1 at the end
+ %
+ nc=netcdf([OGCM_dir,OGCM_prefix,'Y',num2str(Y),'M',num2str(M),'.cdf']);
+ OGCM_time=nc{'time'}(:);
+ ntimes=length(OGCM_time);
+ if ntimes==1
+ dt = eomday(Y, M); % monthly files
+ %disp(['Number of days of the given month: ',num2str(dt)]);
+ if strcmp(OGCM, 'mercator')
+ dt = eomday(Y, M) + 1 ; % add +1 days to avoid problems
+ % with mercator starting at first days month
+ end
+ itolap_a=1; itolap_p=1;
+ itolap_tot=itolap_a + itolap_p;
+ disp(['Reduced overlap for monthly files'])
+ disp(['...'])
+ else
+ dt=max(gradient(OGCM_time));
+ end
+ %
+ %Fill the time axis
+ %
+ croco_time=0*(1:ntimes+itolap_tot);
+ %Current month
+ croco_time(itolap_a+1:end-itolap_p)=OGCM_time;
+ %
+ %Previous month
+ %
+ disp(['==================================='])
+ for aa= 1:itolap_a
+ disp(['Compute beginning overlap, time index:',num2str(aa)])
+ disp(['Add ',num2str(-(itolap_a + 1 - aa)), ' timestep dt'])
+ disp(['--------'])
+ croco_time(aa) = croco_time(itolap_a+1) - ((itolap_a + 1 - aa).* dt);
+ end
+ %
+ %Next month
+ %
+ disp(['==================================='])
+ for aa= 1:itolap_p
+ disp(['Compute end overlap, time index:',num2str(ntimes+itolap_tot - itolap_p + aa)])
+ disp(['Add ',num2str(aa), ' timestep dt'])
+ disp(['--------'])
+ croco_time(end - itolap_p + aa ) = croco_time(end - itolap_p) + aa.* dt;
+ end
+ disp(['==================================='])
+ close(nc)
+ %-----------------------------------------------------
+ %
+ % Create and open the CROCO files
+ %
+ if makebry==1
+ bryname=[bry_prefix,'Y',num2str(Y),...
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ disp([' '])
+ disp(['=> Create bry file : ', bryname ])
+ create_bryfile(bryname,grdname,CROCO_title,[1 1 1 1],...
+ theta_s,theta_b,hc,N,...
+ croco_time,0,'clobber',vtransform,Yorig);
+ nc_add_globatt(bryname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ nc_bry=netcdf(bryname,'write');
+ else
+ nc_bry=[];
+ end
+ if makeclim==1
+ clmname=[clm_prefix,'Y',num2str(Y),...
+ 'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ create_climfile(clmname,grdname,CROCO_title,...
+ theta_s,theta_b,hc,N,...
+ croco_time,0,'clobber',vtransform,Yorig);
+ nc_add_globatt(clmname,Yorig,Mmin,Dmin,Hmin,Min_min,Smin,OGCM);
+ nc_clm=netcdf(clmname,'write');
+ else
+ nc_clm=[];
+ end
+ %
+ % Check if there are OGCM files for the previous Month
+ %
+ fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Ym),'M',num2str(Mm),'.cdf'];
+ if exist(fname)==0
+ disp([' No data for the previous month: using current month'])
+ Mm=M;
+ Ym=Y;
+ tndx_OGCM=ones(itolap_a,1);
+ else
+ nc=netcdf(fname);
+ tndx_OGCM=[(length(nc('time'))- (itolap_a -1) ):1: (length(nc('time')))];
+ close(nc)
+ end
+ %
+ % Perform the interpolations for the previous month
+ %
+ disp(' Previous month :')
+ disp('=================')
+ for aa=1:itolap_a
+ disp(['Beg overlap # ', num2str(aa),' -> tindex ',num2str(aa)])
+ disp(['It. of prev month used for it= ',num2str(tndx_OGCM(aa))])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Ym,Mm,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
+ nc_clm,nc_bry,lon,lat,angle,h,aa,obc,vtransform)
+ end
+ %
+ % Perform the interpolations for the current month
+ %
- disp(' Current month :')
- disp('================')
- for tndx_OGCM=1:ntimes
- disp([' Time step : ',num2str(tndx_OGCM),' of ',num2str(ntimes),' :'])
- interp_OGCM(OGCM_dir,OGCM_prefix,Y,M,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM,...
- nc_clm,nc_bry,lon,lat,angle,h,tndx_OGCM+itolap_a,obc,vtransform)
- end
- %
- % Read the OGCM file for the next month
- %
- fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Yp),'M',num2str(Mp),'.cdf'];
- if exist(fname)==0
- disp([' No data for the next month: using current month'])
- Mp=M;
- Yp=Y;
- for aa=1:itolap_p
- tndx_OGCM(aa)=ntimes;
- end
- else
- for aa=1:itolap_p
- tndx_OGCM(aa)=aa;
- end;
- end
- %
- % Perform the interpolations for the next month
- %
- disp(' Next month :')
- disp('=============')
- for aa=1:itolap_p
- disp(['End Overlap #',num2str(aa),' -> tindex ',num2str(ntimes+itolap_a+aa)])
- disp(['It. of next month used for it= ',num2str(tndx_OGCM(aa))])
- interp_OGCM(OGCM_dir,OGCM_prefix,Yp,Mp,Roa,interp_method,...
- lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
- nc_clm,nc_bry,lon,lat,angle,h,ntimes+itolap_a+aa,obc,vtransform)
- end
- %
- % Close the CROCO files
- %
- if ~isempty(nc_clm)
- close(nc_clm);
- end
- if ~isempty(nc_bry)
- close(nc_bry);
- end
- %
+ disp(' Current month :')
+ disp('================')
+ for tndx_OGCM=1:ntimes
+ disp([' Time step : ',num2str(tndx_OGCM),' of ',num2str(ntimes),' :'])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Y,M,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM,...
+ nc_clm,nc_bry,lon,lat,angle,h,tndx_OGCM+itolap_a,obc,vtransform)
+ end
+ %
+ % Read the OGCM file for the next month
+ %
+ fname=[OGCM_dir,OGCM_prefix,'Y',num2str(Yp),'M',num2str(Mp),'.cdf'];
+ if exist(fname)==0
+ disp([' No data for the next month: using current month'])
+ Mp=M;
+ Yp=Y;
+ for aa=1:itolap_p
+ tndx_OGCM(aa)=ntimes;
+ end
+ else
+ for aa=1:itolap_p
+ tndx_OGCM(aa)=aa;
+ end;
+ end
+ %
+ % Perform the interpolations for the next month
+ %
+ disp(' Next month :')
+ disp('=============')
+ for aa=1:itolap_p
+ disp(['End Overlap #',num2str(aa),' -> tindex ',num2str(ntimes+itolap_a+aa)])
+ disp(['It. of next month used for it= ',num2str(tndx_OGCM(aa))])
+ interp_OGCM(OGCM_dir,OGCM_prefix,Yp,Mp,Roa,interp_method,...
+ lonU,latU,lonV,latV,lonT,latT,Z,tndx_OGCM(aa),...
+ nc_clm,nc_bry,lon,lat,angle,h,ntimes+itolap_a+aa,obc,vtransform)
+ end
+ %
+ % Close the CROCO files
+ %
+ if ~isempty(nc_clm)
+ close(nc_clm);
+ end
+ if ~isempty(nc_bry)
+ close(nc_bry);
+ end
+ %
+ end
end
- end
end
%
% Spin-up: (reproduce the first year 'SPIN_Long' times)
% just copy the files for the first year and change the time
%
if SPIN_Long>0
- %
- % Initial file
- %
- if makeini==1
%
- % Copy the file
- %
- ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
- ininame2=[ini_prefix,'Y',num2str(Ymin-SPIN_Long),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
- disp(['Create ',ininame2])
- eval(['!cp ',ininame,' ',ininame2])
+ % Initial file
%
- % Change the time
- %
- nc=netcdf(ininame2,'write');
- time=nc{'scrum_time'}(:)-365.*SPIN_Long*(24*3600);
- nc{'scrum_time'}(:)=time;
- close(nc)
- end
- %
- M=Mmin-1;
- Y=Ymin-SPIN_Long;
- for month=1:12*SPIN_Long
- M=M+1;
- if M==13
- M=1;
- Y=Y+1;
+ if makeini==1
+ %
+ % Copy the file
+ %
+ ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
+ ininame2=[ini_prefix,'Y',num2str(Ymin-SPIN_Long),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
+ disp(['Create ',ininame2])
+ eval(['!cp ',ininame,' ',ininame2])
+ %
+ % Change the time
+ %
+ nc=netcdf(ininame2,'write');
+ time=nc{'scrum_time'}(:)-365.*SPIN_Long*(24*3600);
+ nc{'scrum_time'}(:)=time;
+ close(nc)
end
%
- % Climatology files
- %
- if makeclim==1
- %
- % Copy the file
- %
- clmname=[clm_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- clmname2=[clm_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',clmname2])
- eval(['!cp ',clmname,' ',clmname2])
- %
- % Change the time
- %
- nc=netcdf(clmname2,'write');
- time=nc{'tclm_time'}(:)-365.*(Ymin-Y);
- nc{'tclm_time'}(:)=time;
- nc{'temp_time'}(:)=time;
- nc{'sclm_time'}(:)=time;
- nc{'salt_time'}(:)=time;
- nc{'uclm_time'}(:)=time;
- nc{'vclm_time'}(:)=time;
- nc{'v2d_time'}(:)=time;
- nc{'v3d_time'}(:)=time;
- nc{'ssh_time'}(:)=time;
- nc{'zeta_time'}(:)=time;
- close(nc)
- end
- %
- % Boundary files
- %
- if makebry==1
- %
- % Copy the file
- %
- bryname=[bry_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- bryname2=[bry_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- disp(['Create ',bryname2])
- eval(['!cp ',bryname,' ',bryname2])
- %
- % Change the time
- %
- nc=netcdf(bryname2,'write');
- time=nc{'bry_time'}(:)-365.*(Ymin-Y);
- nc{'bry_time'}(:)=time;
- close(nc)
+ M=Mmin-1;
+ Y=Ymin-SPIN_Long;
+ for month=1:12*SPIN_Long
+ M=M+1;
+ if M==13
+ M=1;
+ Y=Y+1;
+ end
+ %
+ % Climatology files
+ %
+ if makeclim==1
+ %
+ % Copy the file
+ %
+ clmname=[clm_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ clmname2=[clm_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ disp(['Create ',clmname2])
+ eval(['!cp ',clmname,' ',clmname2])
+ %
+ % Change the time
+ %
+ nc=netcdf(clmname2,'write');
+ time=nc{'tclm_time'}(:)-365.*(Ymin-Y);
+ nc{'tclm_time'}(:)=time;
+ nc{'temp_time'}(:)=time;
+ nc{'sclm_time'}(:)=time;
+ nc{'salt_time'}(:)=time;
+ nc{'uclm_time'}(:)=time;
+ nc{'vclm_time'}(:)=time;
+ nc{'v2d_time'}(:)=time;
+ nc{'v3d_time'}(:)=time;
+ nc{'ssh_time'}(:)=time;
+ nc{'zeta_time'}(:)=time;
+ close(nc)
+ end
+ %
+ % Boundary files
+ %
+ if makebry==1
+ %
+ % Copy the file
+ %
+ bryname=[bry_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ bryname2=[bry_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ disp(['Create ',bryname2])
+ eval(['!cp ',bryname,' ',bryname2])
+ %
+ % Change the time
+ %
+ nc=netcdf(bryname2,'write');
+ time=nc{'bry_time'}(:)-365.*(Ymin-Y);
+ nc{'bry_time'}(:)=time;
+ close(nc)
+ end
end
- end
end
%---------------------------------------------------------------
% Make a few plots
%---------------------------------------------------------------
if makeplot==1
- disp(' ')
- disp(' Make a few plots...')
- if makeini==1
- ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
- figure
- test_clim(ininame,grdname,'temp',1,coastfileplot)
- figure
- test_clim(ininame,grdname,'salt',1,coastfileplot)
- end
- if makeclim==1
- clmname=[clm_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- figure
- test_clim(clmname,grdname,'temp',1,coastfileplot)
- figure
- test_clim(clmname,grdname,'salt',1,coastfileplot)
- end
- if makebry==1
- bryname=[bry_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
- figure
- test_bry(bryname,grdname,'temp',1,obc)
- figure
- test_bry(bryname,grdname,'salt',1,obc)
- figure
- test_bry(bryname,grdname,'u',1,obc)
- figure
- test_bry(bryname,grdname,'v',1,obc)
- end
+ disp(' ')
+ disp(' Make a few plots...')
+ if makeini==1
+ ininame=[ini_prefix,'Y',num2str(Ymin),'M',num2str(sprintf(Mth_format,Mmin)),nc_suffix];
+ figure
+ test_clim(ininame,grdname,'temp',1,coastfileplot)
+ figure
+ test_clim(ininame,grdname,'salt',1,coastfileplot)
+ end
+ if makeclim==1
+ clmname=[clm_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ figure
+ test_clim(clmname,grdname,'temp',1,coastfileplot)
+ figure
+ test_clim(clmname,grdname,'salt',1,coastfileplot)
+ end
+ if makebry==1
+ bryname=[bry_prefix,'Y',num2str(Y),'M',num2str(sprintf(Mth_format,M)),nc_suffix];
+ figure
+ test_bry(bryname,grdname,'temp',1,obc)
+ figure
+ test_bry(bryname,grdname,'salt',1,obc)
+ figure
+ test_bry(bryname,grdname,'u',1,obc)
+ figure
+ test_bry(bryname,grdname,'v',1,obc)
+ end
end
diff --git a/Preprocessing_tools/Bio/add_bry_pisces.m b/Preprocessing_tools/Bio/add_bry_pisces.m
index 966f7527..96550928 100644
--- a/Preprocessing_tools/Bio/add_bry_pisces.m
+++ b/Preprocessing_tools/Bio/add_bry_pisces.m
@@ -1,25 +1,26 @@
-function add_bry_pisces(bryname,obc,time,cycle,makequota,clobber);
+function add_bry_pisces(bryname,obc,time,cycle,...
+ makequota,clobber,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% 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:
+%
+% 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
@@ -37,14 +38,26 @@ function add_bry_pisces(bryname,obc,time,cycle,makequota,clobber);
% 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
+% 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. %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp([' Adding PISCES data into file : ',bryname])
disp(' ')
@@ -65,8 +78,8 @@ nc('si_time') = length(time);
nc('fer_time') = length(time);
nc('o2_time') = length(time);
if makequota
- nc('dop_time') = length(time);
- nc('don_time') = length(time);
+ nc('dop_time') = length(time);
+ nc('don_time') = length(time);
end
nc('one') = 1;
%
@@ -75,346 +88,344 @@ nc('one') = 1;
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;%
+write_time_attributes(nc,'dic_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'talk_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'po4_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'si_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'doc_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'fer_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
%
if makequota
- nc{'dop_time'} = ncdouble('dop_time') ;
- nc{'dop_time'}.long_name = ncchar('time for DOP climatology');
- nc{'dop_time'}.long_name = 'time for DOP climatology';
- nc{'dop_time'}.units = ncchar('day');
- nc{'dop_time'}.units = 'day';
- nc{'dop_time'}.cycle_length = cycle;%
-%
- nc{'don_time'} = ncdouble('don_time') ;
- nc{'don_time'}.long_name = ncchar('time for DON climatology');
- nc{'don_time'}.long_name = 'time for DON climatology';
- nc{'don_time'}.units = ncchar('day');
- nc{'don_time'}.units = 'day';
- nc{'don_time'}.cycle_length = cycle;%
+ nc{'dop_time'} = ncdouble('dop_time') ;
+ nc{'dop_time'}.long_name = ncchar('time for DOP climatology');
+ nc{'dop_time'}.long_name = 'time for DOP climatology';
+ write_time_attributes(nc,'dop_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
+ nc{'don_time'} = ncdouble('don_time') ;
+ nc{'don_time'}.long_name = ncchar('time for DON climatology');
+ nc{'don_time'}.long_name = 'time for DON climatology';
+ write_time_attributes(nc,'don_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
end
%
%
if obc(1)==1
-%
-% Southern boundary
-%
+ %
+ % 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';
-%
+ %
if makequota
- nc{'DOP_south'} = ncdouble('dop_time','s_rho','xi_rho') ;
- nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
- nc{'DOP_south'}.long_name = 'southern boundary DOP';
- nc{'DOP_south'}.units = ncchar('mMol N m-3');
- nc{'DOP_south'}.units = 'mMol N m-3';
-%
- nc{'DON_south'} = ncdouble('don_time','s_rho','xi_rho') ;
- nc{'DON_south'}.long_name = ncchar('southern boundary DON');
- nc{'DON_south'}.long_name = 'southern boundary DON';
- nc{'DON_south'}.units = ncchar('mMol N m-3');
- nc{'DON_south'}.units = 'mMol N m-3';
- end
-%
+ nc{'DOP_south'} = ncdouble('dop_time','s_rho','xi_rho') ;
+ nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
+ nc{'DOP_south'}.long_name = 'southern boundary DOP';
+ nc{'DOP_south'}.units = ncchar('mMol N m-3');
+ nc{'DOP_south'}.units = 'mMol N m-3';
+ %
+ nc{'DON_south'} = ncdouble('don_time','s_rho','xi_rho') ;
+ nc{'DON_south'}.long_name = ncchar('southern boundary DON');
+ nc{'DON_south'}.long_name = 'southern boundary DON';
+ nc{'DON_south'}.units = ncchar('mMol N m-3');
+ nc{'DON_south'}.units = 'mMol N m-3';
+ end
+ %
end
%
if obc(2)==1
-%
-% Eastern boundary
-%
+ %
+ % 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';
-%
+ %
if makequota
- nc{'DOP_east'} = ncdouble('dop_time','s_rho','eta_rho') ;
- nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
- nc{'DOP_east'}.long_name = 'eastern boundary DOP';
- nc{'DOP_east'}.units = ncchar('mMol N m-3');
- nc{'DOP_east'}.units = 'mMol N m-3';
-%
- nc{'DON_east'} = ncdouble('don_time','s_rho','eta_rho') ;
- nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
- nc{'DON_east'}.long_name = 'eastern boundary DON';
- nc{'DON_east'}.units = ncchar('mMol N m-3');
- nc{'DON_east'}.units = 'mMol N m-3';
+ nc{'DOP_east'} = ncdouble('dop_time','s_rho','eta_rho') ;
+ nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
+ nc{'DOP_east'}.long_name = 'eastern boundary DOP';
+ nc{'DOP_east'}.units = ncchar('mMol N m-3');
+ nc{'DOP_east'}.units = 'mMol N m-3';
+ %
+ nc{'DON_east'} = ncdouble('don_time','s_rho','eta_rho') ;
+ nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
+ nc{'DON_east'}.long_name = 'eastern boundary DON';
+ nc{'DON_east'}.units = ncchar('mMol N m-3');
+ nc{'DON_east'}.units = 'mMol N m-3';
end
-%
+ %
end
%
if obc(3)==1
-%
-% Northern boundary
-%
+ %
+ % 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';
-%
+ %
if makequota
- nc{'DOP_north'} = ncdouble('dop_time','s_rho','xi_rho') ;
- nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
- nc{'DOP_north'}.long_name = 'northern boundary DOP';
- nc{'DOP_north'}.units = ncchar('mMol N m-3');
- nc{'DOP_north'}.units = 'mMol N m-3';
-%
- nc{'DON_north'} = ncdouble('don_time','s_rho','xi_rho') ;
- nc{'DON_north'}.long_name = ncchar('northern boundary DON');
- nc{'DON_north'}.long_name = 'northern boundary DON';
- nc{'DON_north'}.units = ncchar('mMol N m-3');
- nc{'DON_north'}.units = 'mMol N m-3';
+ nc{'DOP_north'} = ncdouble('dop_time','s_rho','xi_rho') ;
+ nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
+ nc{'DOP_north'}.long_name = 'northern boundary DOP';
+ nc{'DOP_north'}.units = ncchar('mMol N m-3');
+ nc{'DOP_north'}.units = 'mMol N m-3';
+ %
+ nc{'DON_north'} = ncdouble('don_time','s_rho','xi_rho') ;
+ nc{'DON_north'}.long_name = ncchar('northern boundary DON');
+ nc{'DON_north'}.long_name = 'northern boundary DON';
+ nc{'DON_north'}.units = ncchar('mMol N m-3');
+ nc{'DON_north'}.units = 'mMol N m-3';
end
-%
+ %
end
%
if obc(4)==1
-%
-% Western boundary
-%
+ %
+ % 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';
-%
+ %
if makequota
- nc{'DOP_west'} = ncdouble('dop_time','s_rho','eta_rho') ;
- nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
- nc{'DOP_west'}.long_name = 'western boundary DOP';
- nc{'DOP_west'}.units = ncchar('mMol N m-3');
- nc{'DOP_west'}.units = 'mMol N m-3';
-%
- nc{'DON_west'} = ncdouble('don_time','s_rho','eta_rho') ;
- nc{'DON_west'}.long_name = ncchar('western boundary DON');
- nc{'DON_west'}.long_name = 'western boundary DON';
- nc{'DON_west'}.units = ncchar('mMol N m-3');
- nc{'DON_west'}.units = 'mMol N m-3';
+ nc{'DOP_west'} = ncdouble('dop_time','s_rho','eta_rho') ;
+ nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
+ nc{'DOP_west'}.long_name = 'western boundary DOP';
+ nc{'DOP_west'}.units = ncchar('mMol N m-3');
+ nc{'DOP_west'}.units = 'mMol N m-3';
+ %
+ nc{'DON_west'} = ncdouble('don_time','s_rho','eta_rho') ;
+ nc{'DON_west'}.long_name = ncchar('western boundary DON');
+ nc{'DON_west'}.long_name = 'western boundary DON';
+ nc{'DON_west'}.units = ncchar('mMol N m-3');
+ nc{'DON_west'}.units = 'mMol N m-3';
end
-%
+ %
end
%
% Leave define mode
@@ -432,8 +443,8 @@ nc{'si_time'}(:) = time;
nc{'fer_time'}(:) = time;
nc{'o2_time'}(:) = time;
if makequota
- nc{'dop_time'}(:) = time;
- nc{'don_time'}(:) = time;
+ nc{'dop_time'}(:) = time;
+ nc{'don_time'}(:) = time;
end
if obc(1)==1
nc{'NO3_south'}(:) = 0;
@@ -445,10 +456,10 @@ if obc(1)==1
nc{'DOC_south'}(:) = 0;
nc{'FER_south'}(:) = 0;
if makequota
- nc{'DOP_south'}(:) = 0;
- nc{'DON_south'}(:) = 0;
+ nc{'DOP_south'}(:) = 0;
+ nc{'DON_south'}(:) = 0;
end
-end
+end
if obc(2)==1
nc{'NO3_east'}(:) = 0;
nc{'PO4_east'}(:) = 0;
@@ -459,10 +470,10 @@ if obc(2)==1
nc{'DOC_east'}(:) = 0;
nc{'FER_east'}(:) = 0;
if makequota
- nc{'DOP_east'}(:) = 0;
- nc{'DON_east'}(:) = 0;
+ nc{'DOP_east'}(:) = 0;
+ nc{'DON_east'}(:) = 0;
end
-end
+end
if obc(3)==1
nc{'NO3_north'}(:) = 0;
nc{'PO4_north'}(:) = 0;
@@ -473,10 +484,10 @@ if obc(3)==1
nc{'DOC_north'}(:) = 0;
nc{'FER_north'}(:) = 0;
if makequota
- nc{'DOP_north'}(:) = 0;
- nc{'DON_north'}(:) = 0;
+ nc{'DOP_north'}(:) = 0;
+ nc{'DON_north'}(:) = 0;
end
-end
+end
if obc(4)==1
nc{'NO3_west'}(:) = 0;
nc{'PO4_west'}(:) = 0;
@@ -487,10 +498,10 @@ if obc(4)==1
nc{'DOC_west'}(:) = 0;
nc{'FER_west'}(:) = 0;
if makequota
- nc{'DOP_west'}(:) = 0;
- nc{'DON_west'}(:) = 0
+ nc{'DOP_west'}(:) = 0;
+ nc{'DON_west'}(:) = 0
end
-end
+end
close(nc)
return
diff --git a/Preprocessing_tools/Bio/add_bry_pisces_Z.m b/Preprocessing_tools/Bio/add_bry_pisces_Z.m
index 69bde9cd..97667243 100644
--- a/Preprocessing_tools/Bio/add_bry_pisces_Z.m
+++ b/Preprocessing_tools/Bio/add_bry_pisces_Z.m
@@ -1,4 +1,5 @@
-function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,makequota,clobber);
+function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,makequota,...
+ clobber,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% function add_bry_pisces_Z(zbryname,obc,... %
@@ -23,6 +24,19 @@ function add_bry_pisces_Z(zbryname,obc,Z,time,cycle,makequota,clobber);
% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+
disp(' ')
disp([' Adding PISCES data into file : ',zbryname])
disp(' ')
@@ -35,59 +49,118 @@ nc = netcdf(zbryname,clobber);
% Create dimensions
%
nc('dic_time') = length(time);
+nc{'dic_time'} = ncdouble('dic_time') ;
+nc{'dic_time'}.long_name = 'time for DIC';
+write_time_attributes(nc,'dic_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('doc_time') = length(time);
+nc{'doc_time'} = ncdouble('doc_time') ;
+nc{'doc_time'}.long_name = 'time for DOC';
+write_time_attributes(nc,'doc_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('no3_time') = length(time);
+nc{'no3_time'} = ncdouble('no3_time') ;
+nc{'no3_time'}.long_name = 'time for NO3';
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('po4_time') = length(time);
+nc{'po4_time'} = ncdouble('po4_time') ;
+nc{'po4_time'}.long_name = 'time for PO4';
+write_time_attributes(nc,'po4_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('talk_time') = length(time);
+nc{'talk_time'} = ncdouble('talk_time') ;
+nc{'talk_time'}.long_name = 'time for TALK';
+write_time_attributes(nc,'talk_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('si_time') = length(time);
+nc{'si_time'} = ncdouble('si_time') ;
+nc{'si_time'}.long_name = 'time for silicate';
+write_time_attributes(nc,'si_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+%
nc('fer_time') = length(time);
+nc{'fer_time'} = ncdouble('fer_time') ;
+nc{'fer_time'}.long_name = 'time for iron';
+write_time_attributes(nc,'fer_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+% %
nc('o2_time') = length(time);
+nc{'o2_time'} = ncdouble('o2_time') ;
+nc{'o2_time'}.long_name = 'time for oxygen';
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+
if makequota
- nc('dop_time') = length(time);
- nc('don_time') = length(time);
+ nc('dop_time') = length(time);
+ nc{'dop_time'} = ncdouble('dop_time') ;
+ nc{'dop_time'}.long_name = 'time for dop';
+ write_time_attributes(nc,'dop_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
+ nc('don_time') = length(time);
+ nc{'don_time'} = ncdouble('don_time') ;
+ nc{'don_time'}.long_name = 'time for don';
+ write_time_attributes(nc,'don_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
end
nc('one') = 1;
%
if obc(1)==1
-%
-% Southern boundary
-%
+ %
+ % 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';
@@ -99,225 +172,225 @@ if obc(1)==1
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';
-%
- if makequota
- nc{'DOP_south'} = ncdouble('dop_time','Z','xi_rho') ;
- nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
- nc{'DOP_south'}.long_name = 'southern boundary DOP';
- nc{'DOP_south'}.units = ncchar('mMol N m-3');
- nc{'DOP_south'}.units = 'mMol N m-3';
-%
- nc{'DON_south'} = ncdouble('don_time','Z','xi_rho') ;
- nc{'DON_south'}.long_name = ncchar('southern boundary DON');
- nc{'DON_south'}.long_name = 'southern boundary DON';
- nc{'DON_south'}.units = ncchar('mMol N m-3');
- nc{'DON_south'}.units = 'mMol N m-3';
- end
-%
+ %
+ if makequota
+ nc{'DOP_south'} = ncdouble('dop_time','Z','xi_rho') ;
+ nc{'DOP_south'}.long_name = ncchar('southern boundary DOP');
+ nc{'DOP_south'}.long_name = 'southern boundary DOP';
+ nc{'DOP_south'}.units = ncchar('mMol N m-3');
+ nc{'DOP_south'}.units = 'mMol N m-3';
+ %
+ nc{'DON_south'} = ncdouble('don_time','Z','xi_rho') ;
+ nc{'DON_south'}.long_name = ncchar('southern boundary DON');
+ nc{'DON_south'}.long_name = 'southern boundary DON';
+ nc{'DON_south'}.units = ncchar('mMol N m-3');
+ nc{'DON_south'}.units = 'mMol N m-3';
+ end
+ %
end
%
if obc(2)==1
-%
-% Eastern boundary
-%
+ %
+ % 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';
-%
- if makequota
- nc{'DOP_east'} = ncdouble('dop_time','Z','eta_rho') ;
- nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
- nc{'DOP_east'}.long_name = 'eastern boundary DOP';
- nc{'DOP_east'}.units = ncchar('mMol N m-3');
- nc{'DOP_east'}.units = 'mMol N m-3';
-%
- nc{'DON_east'} = ncdouble('don_time','Z','eta_rho') ;
- nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
- nc{'DON_east'}.long_name = 'eastern boundary DON';
- nc{'DON_east'}.units = ncchar('mMol N m-3');
- nc{'DON_east'}.units = 'mMol N m-3';
- end
-%
+ %
+ if makequota
+ nc{'DOP_east'} = ncdouble('dop_time','Z','eta_rho') ;
+ nc{'DOP_east'}.long_name = ncchar('eastern boundary DOP');
+ nc{'DOP_east'}.long_name = 'eastern boundary DOP';
+ nc{'DOP_east'}.units = ncchar('mMol N m-3');
+ nc{'DOP_east'}.units = 'mMol N m-3';
+ %
+ nc{'DON_east'} = ncdouble('don_time','Z','eta_rho') ;
+ nc{'DON_east'}.long_name = ncchar('eastern boundary DON');
+ nc{'DON_east'}.long_name = 'eastern boundary DON';
+ nc{'DON_east'}.units = ncchar('mMol N m-3');
+ nc{'DON_east'}.units = 'mMol N m-3';
+ end
+ %
end
%
if obc(3)==1
-%
-% Northern boundary
-%
+ %
+ % 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';
-%
- if makequota
- nc{'DOP_north'} = ncdouble('dop_time','Z','xi_rho') ;
- nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
- nc{'DOP_north'}.long_name = 'northern boundary DOP';
- nc{'DOP_north'}.units = ncchar('mMol N m-3');
- nc{'DOP_north'}.units = 'mMol N m-3';
-%
- nc{'DON_north'} = ncdouble('don_time','Z','xi_rho') ;
- nc{'DON_north'}.long_name = ncchar('northern boundary DON');
- nc{'DON_north'}.long_name = 'northern boundary DON';
- nc{'DON_north'}.units = ncchar('mMol N m-3');
- nc{'DON_north'}.units = 'mMol N m-3';
- end
-%
+ %
+ if makequota
+ nc{'DOP_north'} = ncdouble('dop_time','Z','xi_rho') ;
+ nc{'DOP_north'}.long_name = ncchar('northern boundary DOP');
+ nc{'DOP_north'}.long_name = 'northern boundary DOP';
+ nc{'DOP_north'}.units = ncchar('mMol N m-3');
+ nc{'DOP_north'}.units = 'mMol N m-3';
+ %
+ nc{'DON_north'} = ncdouble('don_time','Z','xi_rho') ;
+ nc{'DON_north'}.long_name = ncchar('northern boundary DON');
+ nc{'DON_north'}.long_name = 'northern boundary DON';
+ nc{'DON_north'}.units = ncchar('mMol N m-3');
+ nc{'DON_north'}.units = 'mMol N m-3';
+ end
+ %
end
%
if obc(4)==1
-%
-% Western boundary
-%
+ %
+ % 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';
-%
- if makequota
- nc{'DOP_west'} = ncdouble('dop_time','Z','eta_rho') ;
- nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
- nc{'DOP_west'}.long_name = 'western boundary DOP';
- nc{'DOP_west'}.units = ncchar('mMol N m-3');
- nc{'DOP_west'}.units = 'mMol N m-3';
-%
- nc{'DON_west'} = ncdouble('don_time','Z','eta_rho') ;
- nc{'DON_west'}.long_name = ncchar('western boundary DON');
- nc{'DON_west'}.long_name = 'western boundary DON';
- nc{'DON_west'}.units = ncchar('mMol N m-3');
- nc{'DON_west'}.units = 'mMol N m-3';
- end
-%
+ %
+ if makequota
+ nc{'DOP_west'} = ncdouble('dop_time','Z','eta_rho') ;
+ nc{'DOP_west'}.long_name = ncchar('western boundary DOP');
+ nc{'DOP_west'}.long_name = 'western boundary DOP';
+ nc{'DOP_west'}.units = ncchar('mMol N m-3');
+ nc{'DOP_west'}.units = 'mMol N m-3';
+ %
+ nc{'DON_west'} = ncdouble('don_time','Z','eta_rho') ;
+ nc{'DON_west'}.long_name = ncchar('western boundary DON');
+ nc{'DON_west'}.long_name = 'western boundary DON';
+ nc{'DON_west'}.units = ncchar('mMol N m-3');
+ nc{'DON_west'}.units = 'mMol N m-3';
+ end
+ %
end
%
% Leave define mode
@@ -326,18 +399,18 @@ end
%
% 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 makequota
- nc('dop_time') = time;
- nc('don_time') = time;
- end
+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 makequota
+ nc{'dop_time'}(:) = time;
+ nc{'don_time'}(:) = time;
+end
if obc(1)==1
nc{'NO3_south'}(:) = 0;
nc{'PO4_south'}(:) = 0;
@@ -347,12 +420,12 @@ if obc(1)==1
nc{'TALK_south'}(:) = 0;
nc{'DOC_south'}(:) = 0;
nc{'FER_south'}(:) = 0;
- if makequota
- nc{'DOP_south'}(:) = 0;
- nc{'DON_south'}(:) = 0;
- end
-end
-if obc(2)==1
+ if makequota
+ nc{'DOP_south'}(:) = 0;
+ nc{'DON_south'}(:) = 0;
+ end
+end
+if obc(2)==1
nc{'NO3_east'}(:) = 0;
nc{'PO4_east'}(:) = 0;
nc{'Si_east'}(:) = 0;
@@ -361,12 +434,12 @@ if obc(2)==1
nc{'TALK_east'}(:) = 0;
nc{'DOC_east'}(:) = 0;
nc{'FER_east'}(:) = 0;
- if makequota
- nc{'DOP_east'}(:) = 0;
- nc{'DON_east'}(:) = 0;
- end
-end
-if obc(3)==1
+ if makequota
+ nc{'DOP_east'}(:) = 0;
+ nc{'DON_east'}(:) = 0;
+ end
+end
+if obc(3)==1
nc{'NO3_north'}(:) = 0;
nc{'PO4_north'}(:) = 0;
nc{'Si_north'}(:) = 0;
@@ -375,12 +448,12 @@ if obc(3)==1
nc{'TALK_north'}(:) = 0;
nc{'DOC_north'}(:) = 0;
nc{'FER_north'}(:) = 0;
- if makequota
- nc{'DOP_north'}(:) = 0;
- nc{'DON_north'}(:) = 0;
- end
-end
-if obc(4)==1
+ if makequota
+ nc{'DOP_north'}(:) = 0;
+ nc{'DON_north'}(:) = 0;
+ end
+end
+if obc(4)==1
nc{'NO3_west'}(:) = 0;
nc{'PO4_west'}(:) = 0;
nc{'Si_west'}(:) = 0;
@@ -389,11 +462,11 @@ if obc(4)==1
nc{'TALK_west'}(:) = 0;
nc{'DOC_west'}(:) = 0;
nc{'FER_west'}(:) = 0;
- if makequota
- nc{'DOP_west'}(:) = 0;
- nc{'DON_west'}(:) = 0;
- end
-end
+ if makequota
+ nc{'DOP_west'}(:) = 0;
+ nc{'DON_west'}(:) = 0;
+ end
+end
close(nc)
return
diff --git a/Preprocessing_tools/Bio/add_dic.m b/Preprocessing_tools/Bio/add_dic.m
index 7796c218..fd3edaac 100644
--- a/Preprocessing_tools/Bio/add_dic.m
+++ b/Preprocessing_tools/Bio/add_dic.m
@@ -1,5 +1,5 @@
function add_dic(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,dic]=add_dic(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_dic(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -29,13 +29,25 @@ function add_dic(oafile,climfile,inifile,gridfile,seas_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +58,37 @@ kmax=max(find(zdic<hmax))-1;
zdic=zdic(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_dic: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'dic_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
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
-%
+ %
+ %% 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)
@@ -91,56 +98,55 @@ end
%
if (makeclim)
disp('Add_dic: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'dic_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% 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
-if (makeini)
-%
-disp('Add_dic: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'DIC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'DIC'}.long_name = ncchar('DIC');
-nc{'DIC'}.long_name = 'DIC';
-nc{'DIC'}.units = ncchar('mMol C m-3');
-nc{'DIC'}.units = 'mMol C m-3';
-end
+% %
+% % Same thing for the Initial file
+% if (makeini)
+% %
+% disp('Add_dic: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'DIC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'DIC'}.long_name = ncchar('DIC');
+% nc{'DIC'}.long_name = 'DIC';
+% nc{'DIC'}.units = ncchar('mMol C m-3');
+% nc{'DIC'}.units = 'mMol C m-3';
+% endef(nc);
+% close(nc)
+% end
+
+
-endef(nc);
-close(nc)
return
diff --git a/Preprocessing_tools/Bio/add_doc.m b/Preprocessing_tools/Bio/add_doc.m
index 2a101b7a..5362a137 100644
--- a/Preprocessing_tools/Bio/add_doc.m
+++ b/Preprocessing_tools/Bio/add_doc.m
@@ -1,5 +1,5 @@
function add_doc(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_doc(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -29,13 +29,24 @@ function add_doc(oafile,climfile,inifile,gridfile,seas_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +57,40 @@ kmax=max(find(zdoc<hmax))-1;
zdoc=zdoc(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_doc: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'doc_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
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
-%
+ %
+ %% 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)
@@ -91,56 +100,53 @@ end
%
if (makeclim)
disp('Add_doc: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'doc_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% 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
-%
-if (makeini)
-disp('Add_doc: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'DOC'}.long_name = ncchar('DOC');
-nc{'DOC'}.long_name = 'DOC';
-nc{'DOC'}.units = ncchar('mMol C m-3');
-nc{'DOC'}.units = 'mMol C m-3';
-%
-endef(nc);
-close(nc)
-end
+% %
+% % Same thing for the Initial file
+% %
+% if (makeini)
+% disp('Add_doc: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'DOC'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'DOC'}.long_name = ncchar('DOC');
+% nc{'DOC'}.long_name = 'DOC';
+% nc{'DOC'}.units = ncchar('mMol C m-3');
+% nc{'DOC'}.units = 'mMol C m-3';
+% %
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_don.m b/Preprocessing_tools/Bio/add_don.m
index 4d769193..005b6f03 100644
--- a/Preprocessing_tools/Bio/add_don.m
+++ b/Preprocessing_tools/Bio/add_don.m
@@ -1,5 +1,5 @@
function add_don(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makequota,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makequota,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,doc]=add_doc(climfile,gridfile,...
@@ -50,6 +50,18 @@ function add_don(oafile,climfile,inifile,gridfile,seas_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
@@ -100,11 +112,9 @@ if (makeoa)
nc{'don_time'}.long_name = ncchar('time for don');
nc{'don_time'}.long_name = 'time for don';
- nc{'don_time'}.units = ncchar('day');
- nc{'don_time'}.units = 'day';
- if cycle~=0
- nc{'don_time'}.cycle_length = cycle;
- end
+ write_time_attributes(nc,'don_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
%%
nc{'Zdon'}.long_name = ncchar('Depth for DON');
nc{'Zdon'}.long_name = 'Depth for DON';
@@ -143,11 +153,8 @@ if (makeclim)
%
nc{'don_time'}.long_name = ncchar('time for don');
nc{'don_time'}.long_name = 'time for don';
- nc{'don_time'}.units = ncchar('day');
- nc{'don_time'}.units = 'day';
- if cycle~=0
- nc{'don_time'}.cycle_length = cycle;
- end
+ write_time_attributes(nc,'don_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'DON'}.long_name = ncchar('DON');
nc{'DON'}.long_name = 'DON';
@@ -163,25 +170,25 @@ if (makeclim)
nc{'don_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-%
-% Same thing for the Initial file
-%
-if (makeini)
-disp('Add_don: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'DON'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'DON'}.long_name = ncchar('DON');
-nc{'DON'}.long_name = 'DON';
-nc{'DON'}.units = ncchar('mMol C m-3');
-nc{'DON'}.units = 'mMol C m-3';
-%
-endef(nc);
-close(nc)
-end
+% %
+% % Same thing for the Initial file
+% %
+% if (makeini)
+% disp('Add_don: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'DON'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'DON'}.long_name = ncchar('DON');
+% nc{'DON'}.long_name = 'DON';
+% nc{'DON'}.units = ncchar('mMol C m-3');
+% nc{'DON'}.units = 'mMol C m-3';
+% %
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_dop.m b/Preprocessing_tools/Bio/add_dop.m
index 8c990087..5010f40d 100644
--- a/Preprocessing_tools/Bio/add_dop.m
+++ b/Preprocessing_tools/Bio/add_dop.m
@@ -1,5 +1,5 @@
function add_dop(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makequota,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makequota,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,dop]=add_dop(climfile,gridfile,...
@@ -49,6 +49,18 @@ function add_dop(oafile,climfile,inifile,gridfile,seas_datafile,...
% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
%
% Read in the grid
%
@@ -100,11 +112,8 @@ if (makeoa)
nc{'dop_time'}.long_name = ncchar('time for dop');
nc{'dop_time'}.long_name = 'time for dop';
- nc{'dop_time'}.units = ncchar('day');
- nc{'dop_time'}.units = 'day';
- if cycle~=0
- nc{'dop_time'}.cycle_length = cycle;
- end
+ write_time_attributes(nc,'dop_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'Zdop'}.long_name = ncchar('Depth for DOP');
nc{'Zdop'}.long_name = 'Depth for DOP';
@@ -143,11 +152,8 @@ if (makeclim)
%
nc{'dop_time'}.long_name = ncchar('time for dop');
nc{'dop_time'}.long_name = 'time for dop';
- nc{'dop_time'}.units = ncchar('day');
- nc{'dop_time'}.units = 'day';
- if cycle~=0
- nc{'dop_time'}.cycle_length = cycle;
- end
+ write_time_attributes(nc,'dop_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'DOP'}.long_name = ncchar('DOP');
nc{'DOP'}.long_name = 'DOP';
@@ -163,22 +169,23 @@ if (makeclim)
nc{'dop_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-if (makeini)
-disp('Add_dop: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'DOP'}.long_name = ncchar('DOP');
-nc{'DOP'}.long_name = 'DOP';
-nc{'DOP'}.units = ncchar('mMol C m-3');
-nc{'DOP'}.units = 'mMol C m-3';
-%
-endef(nc);
-close(nc)
-end
+% %
+% if (makeini)
+% disp('Add_dop: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'DOP'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'DOP'}.long_name = ncchar('DOP');
+% nc{'DOP'}.long_name = 'DOP';
+% nc{'DOP'}.units = ncchar('mMol C m-3');
+% nc{'DOP'}.units = 'mMol C m-3';
+% %
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_fer.m b/Preprocessing_tools/Bio/add_fer.m
index 086a1879..6ae7633c 100644
--- a/Preprocessing_tools/Bio/add_fer.m
+++ b/Preprocessing_tools/Bio/add_fer.m
@@ -1,5 +1,5 @@
function add_fer(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,fer]=add_fer(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_fer(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -29,13 +29,25 @@ function add_fer(oafile,climfile,inifile,gridfile,seas_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +58,40 @@ kmax=max(find(zfer<hmax))-1;
zfer=zfer(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_fer: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'fer_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
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
-%
+ %
+ %% 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)
@@ -91,52 +101,49 @@ end
%
if (makeclim)
disp('Add_fer: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
- nc('fer_time') = length(t);;
+ %% 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
-%
+ write_time_attributes(nc,'fer_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% endef(nc);
+ %
+ % record the time and close
+ %
nc{'fer_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-if (makeini)
-disp('Add_fer: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'FER'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'FER'}.long_name = ncchar('FER');
-nc{'FER'}.long_name = 'FER';
-nc{'FER'}.units = ncchar('uMol Fe m-3');
-nc{'FER'}.units = 'uMol Fe m-3';
-%
-endef(nc);
-close(nc)
-end
+% if (makeini)
+% disp('Add_fer: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'FER'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'FER'}.long_name = ncchar('FER');
+% nc{'FER'}.long_name = 'FER';
+% nc{'FER'}.units = ncchar('uMol Fe m-3');
+% nc{'FER'}.units = 'uMol Fe m-3';
+% %
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_no3.m b/Preprocessing_tools/Bio/add_no3.m
index ac708dae..8a528bde 100644
--- a/Preprocessing_tools/Bio/add_no3.m
+++ b/Preprocessing_tools/Bio/add_no3.m
@@ -1,5 +1,5 @@
function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,no3]=add_no3(climfile,gridfile,...
@@ -11,12 +11,12 @@ function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -24,10 +24,10 @@ function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
% output:
%
% [longrd,latgrd,no3] : surface field to plot (as an illustration)
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -45,18 +45,30 @@ function add_no3(oafile,climfile,inifile,gridfile,seas_datafile,...
% 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
+% Copyright (c) 2001-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -70,59 +82,56 @@ zno3=zno3(1:kmax);
size(zno3);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_no3: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
- % redef(nc);
-
+ % redef(nc);
+
%Create Dimensions
nc('no3_time') = length(t);
%Create Variable
nc{'no3_time'} = ncdouble('no3_time') ;
-%
-%%
-%
+ %
+ %%
+ %
%Create Dimensions
- nc('Zno3') = length(zno3);
+ 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
-%%%
+ write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %%%
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
-%
+ %%%
+ %% 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)
@@ -132,56 +141,59 @@ end
%
if (makeclim)
disp('Add_no3: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
- % redef(nc);
+ % 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';
+ nc{'no3_time'}.units = ncchar(time_unit_att);
+ nc{'no3_time'}.units = time_unit_att;
+ nc{'no3_time'}.calendar = calendar_att;
if cycle~=0
nc{'no3_time'}.cycle_length = cycle;
end
-%
+ write_time_attributes(nc,'tclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% endef(nc);
+ %
+ % record the time and close
+ %
nc{'no3_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-%
-if (makeini)
-% 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') ;
+% %
+% if (makeini)
+% % Same thing for the Initial file
+% %
+% disp('Add_no3: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
-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=netcdf(inifile,'write');
+% redef(nc);
+% nc{'NO3'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-endef(nc);
-close(nc)
-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';
+
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_o2.m b/Preprocessing_tools/Bio/add_o2.m
index 7a266525..febe5c29 100644
--- a/Preprocessing_tools/Bio/add_o2.m
+++ b/Preprocessing_tools/Bio/add_o2.m
@@ -1,5 +1,5 @@
function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,o2]=add_o2(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% month_datafile : regular longitude - latitude - z monthly data
+% month_datafile : regular longitude - latitude - z monthly data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -29,13 +29,25 @@ function add_o2(oafile,climfile,inifile,gridfile,month_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(month_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +58,40 @@ kmax=max(find(zo2<hmax))-1;
zo2=zo2(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_o2: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
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
-%
+ %
+ %% 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)
@@ -91,55 +101,53 @@ end
%
if (makeclim)
disp('Add_o2: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
- %% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% endef(nc);
+ %
+ % record the time and close
+ %
nc{'o2_time'}(:,:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-if (makeini)
-% Same thing for the Initial file
-%
-disp('Add_o2: creating variables and attributes for the Initial file')
-%
-% open the clim file
+% %
+% if (makeini)
+% % Same thing for the Initial file
+% %
+% disp('Add_o2: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'O2'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'O2'}.long_name = ncchar('Oxygen');
-nc{'O2'}.long_name = 'Oxygen';
-nc{'O2'}.units = ncchar('mMol O m-3');
-nc{'O2'}.units = 'mMol O m-3';
+% nc{'O2'}.long_name = ncchar('Oxygen');
+% nc{'O2'}.long_name = 'Oxygen';
+% nc{'O2'}.units = ncchar('mMol O m-3');
+% nc{'O2'}.units = 'mMol O m-3';
-endef(nc);
-close(nc)
-end
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_po4.m b/Preprocessing_tools/Bio/add_po4.m
index b495f53f..16f4c6ec 100644
--- a/Preprocessing_tools/Bio/add_po4.m
+++ b/Preprocessing_tools/Bio/add_po4.m
@@ -1,5 +1,5 @@
function add_po4(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,po4]=add_po4(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_po4(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -28,6 +28,17 @@ function add_po4(oafile,climfile,inifile,gridfile,seas_datafile,...
% [longrd,latgrd,po4] : surface field to plot (as an illustration)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
%
% Read in the grid
%
@@ -35,7 +46,7 @@ nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +57,39 @@ kmax=max(find(zpo4<hmax))-1;
zpo4=zpo4(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_po4: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'po4_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% 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)
@@ -91,54 +99,51 @@ end
%
if (makeclim)
disp('Add_po4: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'po4_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% endef(nc);
+ %
+ % record the time and close
+ %
nc{'po4_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-if (makeini)
-% Same thing for the Initial file
-%
-disp('Add_po4: creating variables and attributes for the Initial file')
-%
-% open the clim file
+% if (makeini)
+% % Same thing for the Initial file
+% %
+% disp('Add_po4: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'PO4'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'PO4'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'PO4'}.long_name = ncchar('Phosphate');
-nc{'PO4'}.long_name = 'Phosphate';
-nc{'PO4'}.units = ncchar('mMol P m-3');
-nc{'PO4'}.units = 'mMol P m-3';
+% nc{'PO4'}.long_name = ncchar('Phosphate');
+% nc{'PO4'}.long_name = 'Phosphate';
+% nc{'PO4'}.units = ncchar('mMol P m-3');
+% nc{'PO4'}.units = 'mMol P m-3';
-endef(nc);
-close(nc)
-end
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_sio3.m b/Preprocessing_tools/Bio/add_sio3.m
index b7ad5053..9708ce01 100644
--- a/Preprocessing_tools/Bio/add_sio3.m
+++ b/Preprocessing_tools/Bio/add_sio3.m
@@ -1,5 +1,5 @@
function add_sio3(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,sio3]=add_sio3(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_sio3(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -29,13 +29,25 @@ function add_sio3(oafile,climfile,inifile,gridfile,seas_datafile,...
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read in the grid
%
nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +58,39 @@ kmax=max(find(zsi<hmax))-1;
zsi=zsi(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_sio3: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'si_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% 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)
@@ -91,54 +100,51 @@ end
%
if (makeclim)
disp('Add_sio3: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'si_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% endef(nc);
+ %
+ % record the time and close
+ %
nc{'si_time'}(:)=t*30; % if time in month in the dataset !!!
close(nc)
end
-if (makeini)
-% Same thing for the Initial file
-%
-disp('Add_si: creating variables and attributes for the Initial file')
-%
-% open the clim file
+% if (makeini)
+% % Same thing for the Initial file
+% %
+% disp('Add_si: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'Si'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'Si'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'Si'}.long_name = ncchar('Silicate');
-nc{'Si'}.long_name = 'Silicate';
-nc{'Si'}.units = ncchar('mMol Si m-3');
-nc{'Si'}.units = 'mMol Si m-3';
+% nc{'Si'}.long_name = ncchar('Silicate');
+% nc{'Si'}.long_name = 'Silicate';
+% nc{'Si'}.units = ncchar('mMol Si m-3');
+% nc{'Si'}.units = 'mMol Si m-3';
-endef(nc);
-close(nc)
-end
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/add_talk.m b/Preprocessing_tools/Bio/add_talk.m
index 41f56e0c..5a4757c4 100644
--- a/Preprocessing_tools/Bio/add_talk.m
+++ b/Preprocessing_tools/Bio/add_talk.m
@@ -1,5 +1,5 @@
function add_talk(oafile,climfile,inifile,gridfile,seas_datafile,...
- ann_datafile,cycle,makeoa,makeclim,makeini);
+ ann_datafile,cycle,makeoa,makeclim,makeini,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function [longrd,latgrd,talk]=add_talk(climfile,gridfile,...
@@ -13,12 +13,12 @@ function add_talk(oafile,climfile,inifile,gridfile,seas_datafile,...
% lower levels
%
% input:
-%
+%
% climfile : croco climatology file to process (netcdf)
% gridfile : croco grid file (netcdf)
-% seas_datafile : regular longitude - latitude - z seasonal data
+% seas_datafile : regular longitude - latitude - z seasonal data
% file used for the upper levels (netcdf)
-% ann_datafile : regular longitude - latitude - z annual data
+% 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.
@@ -28,6 +28,16 @@ function add_talk(oafile,climfile,inifile,gridfile,seas_datafile,...
% [longrd,latgrd,talk] : surface field to plot (as an illustration)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
%
% Read in the grid
%
@@ -35,7 +45,7 @@ nc=netcdf(gridfile,'r');
hmax=max(max(nc{'h'}(:)));
close(nc);
%
-% read in the datafiles
+% read in the datafiles
%
nc=netcdf(seas_datafile,'r');
t=nc{'T'}(:);
@@ -46,42 +56,40 @@ kmax=max(find(ztalk<hmax))-1;
ztalk=ztalk(1:kmax);
close(nc)
%
-% open the OA file
-%
+% open the OA file
+%
if (makeoa)
disp('Add_talk: creating variables and attributes for the OA file')
nc=netcdf(oafile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'talk_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
+ %
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
-%
+ %
+ %% 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)
@@ -91,56 +99,53 @@ end
%
if (makeclim)
disp('Add_talk: creating variables and attributes for the Climatology file')
-%
-% open the clim file
-%
+ %
+ % open the clim file
+ %
nc=netcdf(climfile,'write');
-%% redef(nc);
+ %% 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
-%
+ write_time_attributes(nc,'talk_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+ %
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
-%
+ %
+ %% 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
-%
-if (makeini)
-disp('Add_talk: creating variables and attributes for the Initial file')
-%
-% open the clim file
-%
-nc=netcdf(inifile,'write');
-redef(nc);
-nc{'TALK'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-%
-nc{'TALK'}.long_name = ncchar('TALK');
-nc{'TALK'}.long_name = 'TALK';
-nc{'TALK'}.units = ncchar('mMol C m-3');
-nc{'TALK'}.units = 'mMol C m-3';
-%
-endef(nc);
-close(nc)
-end
+% %
+% % Same thing for the Initial file
+% %
+% if (makeini)
+% disp('Add_talk: creating variables and attributes for the Initial file')
+% %
+% % open the clim file
+% %
+% nc=netcdf(inifile,'write');
+% redef(nc);
+% nc{'TALK'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+% %
+% nc{'TALK'}.long_name = ncchar('TALK');
+% nc{'TALK'}.long_name = 'TALK';
+% nc{'TALK'}.units = ncchar('mMol C m-3');
+% nc{'TALK'}.units = 'mMol C m-3';
+% %
+% endef(nc);
+% close(nc)
+% end
return
diff --git a/Preprocessing_tools/Bio/make_biol.m b/Preprocessing_tools/Bio/make_biol.m
index 32968ef0..a226e7dd 100644
--- a/Preprocessing_tools/Bio/make_biol.m
+++ b/Preprocessing_tools/Bio/make_biol.m
@@ -4,9 +4,9 @@ close all
%
% Add biological parameters to CROCO input files
%
-% Further Information:
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -24,8 +24,8 @@ close all
% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
% MA 02111-1307 USA
%
-% Copyright (c) 2003-2006 by Pierrick Penven
-% e-mail:Pierrick.Penven@ird.fr
+% Copyright (c) 2003-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
% Contributions of P. Marchesiello (IRD)
%
@@ -50,54 +50,60 @@ crocotools_param
% Climatological file
%----------------------------------------------------------------------
if (makeclim)
- disp('===========================================================')
- disp('Climatology for the biogeochemical model')
- if (makenpzd)
- disp('========================')
- disp('Climatology for NPZD variables')
- % disp('already done in make_ini_npzd')
- make_clim_npzd
- end
- if (makepisces)
- disp('========================')
- disp('Climatology for PISCES variables')
- make_clim_pisces
- disp('------------------------')
- disp('Iron deposition file')
- make_dust
- disp('------------------------')
- disp('Nitrogen deposition')
- make_ndepo
- end
- if (makebioebus)
- disp('========================')
- disp('Climatology for BioEBUS variables')
- %disp('already done in make_ini_bioebus')
- make_clim_bioebus
- end
+ disp('===========================================================')
+ disp('Climatology for the biogeochemical model')
+ if (makenpzd)
+ disp('========================')
+ disp('Climatology for NPZD variables')
+ make_clim_npzd
+ end
+ if (makebioebus)
+ disp('========================')
+ disp('Climatology for BioEBUS variables')
+ make_clim_bioebus
+ end
+ if (makepisces)
+ disp('========================')
+ disp('Climatology for PISCES variables')
+ make_clim_pisces
+ disp('------------------------')
+ disp('Iron deposition file')
+ make_dust
+ disp('------------------------')
+ disp('Nitrogen deposition')
+ make_ndepo
+ end
+
end
%----------------------------------------------------------------------
% Bry file
%----------------------------------------------------------------------
if (makebry)
- disp('===========================================================')
- disp('Bry for the biogeochemical model')
- if (makenpzd)
- disp('========================')
- disp('Bry for NPZD variables')
- make_bry_npzd
- end
- if (makepisces)
- disp('========================')
- disp('Bry for PISCES variables')
- make_bry_pisces
- end
- if (makebioebus)
- disp('========================')
- disp('Bry for BioEBUS variables')
- make_bry_bioebus
- end
+ disp('===========================================================')
+ disp('Bry for the biogeochemical model')
+ if (makenpzd)
+ disp('========================')
+ disp('Bry for NPZD variables')
+ make_bry_npzd
+ end
+ if (makebioebus)
+ disp('========================')
+ disp('Bry for BioEBUS variables')
+ make_bry_bioebus
+ end
+ if (makepisces)
+ disp('========================')
+ disp('Bry for PISCES variables')
+ make_bry_pisces
+ disp('------------------------')
+ disp('Iron deposition file')
+ make_dust
+ disp('------------------------')
+ disp('Nitrogen deposition')
+ make_ndepo
+ end
+
end
%----------------------------------------------------------------------
@@ -105,29 +111,34 @@ end
%----------------------------------------------------------------------
if (makeini)
- disp('===========================================================')
- disp('Initial variables for the biogeochemical model')
- if (makenpzd)
- disp('========================')
- disp('Initial NPZD variables')
- make_ini_npzd
- end
- if (makebioebus)
- disp('========================')
- disp('Initial BioEBUS variables')
- make_ini_bioebus
- end
+ disp('===========================================================')
+ disp('Initial variables for the biogeochemical model')
+ if (makenpzd)
+ disp('========================')
+ disp('Initial NPZD variables')
+ make_ini_npzd
+ end
+ if (makebioebus)
+ disp('========================')
+ disp('Initial BioEBUS variables')
+ make_ini_bioebus
+ end
+ if (makepisces)
+ disp('========================')
+ disp('Initial PISCES variables')
+ make_ini_pisces
+ end
end
%----------------------------------------------------------------------
% N2O in BioEBUS
%----------------------------------------------------------------------
- if (makebioebus)
- disp('========================')
- disp('Input values for N2O in BioEBUS')
- make_n2o_bioebus
- end
+if (makebioebus)
+ disp('========================')
+ disp('Input values for N2O in BioEBUS')
+ make_n2o_bioebus
+end
diff --git a/Preprocessing_tools/Bio/make_bry_pisces.m b/Preprocessing_tools/Bio/make_bry_pisces.m
index bb9d5406..406a8be9 100644
--- a/Preprocessing_tools/Bio/make_bry_pisces.m
+++ b/Preprocessing_tools/Bio/make_bry_pisces.m
@@ -5,7 +5,7 @@
% Extrapole and interpole temperature and salinity from a
% climatology to get boundary conditions for
% CROCO (boundary netcdf file) .
-% Get the velocities and sea surface elevation via a
+% Get the velocities and sea surface elevation via a
% geostrophic computation.
%
% Data input format (netcdf):
@@ -18,10 +18,10 @@
% 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/
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -39,8 +39,8 @@
% 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
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
% Updated 1-Sep-2006 by Pierrick Penven
% Pierrick Penven, IRD, 2005. %
@@ -64,8 +64,8 @@ Roa;
%
% Set times and cycles: monthly climatology for all data
%
-time=woa_time; % time
-cycle=woa_cycle; % cycle
+time=woa_time; % time
+cycle=woa_cycle; % cycle
%
% Data climatologies file names:
%
@@ -89,9 +89,9 @@ fer_ann_data = [woapisces_dir,'fer_ann.cdf'];
dust_seas_data = [woapisces_dir,'dust_seas.cdf'];
dust_ann_data = [woapisces_dir,'dust_ann.cdf'];
if strcmp(climato_dir,cars2009_dir);
- err_msg=sprintf(['Error : you need to use woadir when creating the croco_oa.nc (Z) \n'...
- 'file to be compatible with PISCES'])
- error(err_msg)
+ err_msg=sprintf(['Error : you need to use woadir when creating the croco_oa.nc (Z) \n'...
+ 'file to be compatible with PISCES'])
+ error(err_msg)
end
%
%
@@ -109,7 +109,7 @@ disp([' Title: ',CROCO_title])
%
disp(' ')
disp(' Read in the grid...')
- nc=netcdf(grdname,'r');
+nc=netcdf(grdname,'r');
lon=nc{'lon_rho'}(:);
lat=nc{'lat_rho'}(:);
Lp=length(nc('xi_rho'));
@@ -134,10 +134,10 @@ end
if (makeZbry)
disp(' ')
disp(' Redefine the boundary Z-file...')
-%
-% get Z
-%
- nc=netcdf(no3_ann_data,'r');
+ %
+ % get Z
+ %
+ nc=netcdf(no3_ann_data,'r');
Z=nc{'Z'}(:);
kmax=max(find(Z<hmax))-1;
Z=Z(1:kmax);
@@ -145,82 +145,82 @@ if (makeZbry)
add_bry_pisces_Z(Zbryname,obc,Z,time,cycle,makequota,'write');
disp(' ')
disp(' Horizontal extrapolations')
-%
-% Loop on the lateral boundaries
-%
+ %
+ % Loop on the lateral boundaries
+ %
for obcndx=1:4
if obc(obcndx)==1
if obcndx==1
disp(' Processing southern boundary...')
- suffix='_south';
+ suffix='_south';
elseif obcndx==2
disp(' Processing eastern boundary...')
- suffix='_east';
+ suffix='_east';
elseif obcndx==3
disp(' Processing northern boundary...')
- suffix='_north';
+ suffix='_north';
elseif obcndx==4
disp(' Processing western boundary...')
- suffix='_west';
+ suffix='_west';
end
disp(' Nitrate...')
bry_interp_pisces(Zbryname,lon,lat,no3_seas_data,no3_ann_data,...
- 'nitrate',['NO3',suffix],obcndx,Roa);
+ 'nitrate',['NO3',suffix],obcndx,Roa);
disp(' Phosphate...')
bry_interp_pisces(Zbryname,lon,lat,po4_seas_data,po4_ann_data,...
- 'phosphate',['PO4',suffix],obcndx,Roa);
+ 'phosphate',['PO4',suffix],obcndx,Roa);
disp(' Silicate...')
bry_interp_pisces(Zbryname,lon,lat,sio3_seas_data,sio3_ann_data,...
- 'silicate',['Si',suffix],obcndx,Roa);
+ 'silicate',['Si',suffix],obcndx,Roa);
disp(' Oxygen...')
bry_interp_pisces(Zbryname,lon,lat,o2_seas_data,o2_ann_data,...
- 'oxygen',['O2',suffix],obcndx,Roa);
+ 'oxygen',['O2',suffix],obcndx,Roa);
disp(' Dissolved Inorganic Carbon...')
bry_interp_pisces(Zbryname,lon,lat,dic_seas_data,dic_ann_data,...
- 'dic',['DIC',suffix],obcndx,Roa);
+ 'dic',['DIC',suffix],obcndx,Roa);
disp(' Total Alkalinity...')
bry_interp_pisces(Zbryname,lon,lat,talk_seas_data,talk_ann_data,...
- 'talk',['TALK',suffix],obcndx,Roa);
+ 'talk',['TALK',suffix],obcndx,Roa);
disp(' Dissolved Organic Carbon...')
bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
- 'doc',['DOC',suffix],obcndx,Roa);
- if makequota
- disp(' Dissolved Organic Nitrogen...')
- bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
- 'doc',['DON',suffix],obcndx,Roa);
- disp(' Dissolved Organic Phosphorus...')
- bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
- 'doc',['DOP',suffix],obcndx,Roa);
+ 'doc',['DOC',suffix],obcndx,Roa);
+ if makequota
+ disp(' Dissolved Organic Nitrogen...')
+ bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
+ 'doc',['DON',suffix],obcndx,Roa);
+ disp(' Dissolved Organic Phosphorus...')
+ bry_interp_pisces(Zbryname,lon,lat,doc_seas_data,doc_ann_data,...
+ 'doc',['DOP',suffix],obcndx,Roa);
end
disp(' Iron...')
bry_interp_pisces(Zbryname,lon,lat,fer_seas_data,fer_ann_data,...
- 'fer',['FER',suffix],obcndx,Roa);
+ 'fer',['FER',suffix],obcndx,Roa);
end
end
end
%
-% Vertical interpolations
+% Vertical interpolations
%
if (makebry)
disp(' ')
disp(' Vertical interpolations')
-%
-% Loop on the lateral boundaries
-%
+ %
+ % Loop on the lateral boundaries
+ %
for obcndx=1:4
if obc(obcndx)==1
if obcndx==1
disp(' Processing southern boundary...')
- suffix='_south';
+ suffix='_south';
elseif obcndx==2
disp(' Processing eastern boundary...')
- suffix='_east';
+ suffix='_east';
elseif obcndx==3
disp(' Processing northern boundary...')
- suffix='_north';
+ suffix='_north';
elseif obcndx==4
disp(' Processing western boundary...')
- suffix='_west';
+ suffix='_west';
end
disp(' ')
disp(' Nitrate...')
@@ -244,12 +244,12 @@ if (makebry)
disp(' Dissolved Organic Carbon...')
vinterp_bry(bryname,grdname,Zbryname,['DOC',suffix],obcndx);
if makequota
- disp(' ')
- disp(' Dissolved Organic Nitrogen...')
- vinterp_bry(bryname,grdname,Zbryname,['DON',suffix],obcndx);
- disp(' ')
- disp(' Dissolved Organic Phosphorus...')
- vinterp_bry(bryname,grdname,Zbryname,['DOP',suffix],obcndx);
+ disp(' ')
+ disp(' Dissolved Organic Nitrogen...')
+ vinterp_bry(bryname,grdname,Zbryname,['DON',suffix],obcndx);
+ disp(' ')
+ disp(' Dissolved Organic Phosphorus...')
+ vinterp_bry(bryname,grdname,Zbryname,['DOP',suffix],obcndx);
end
disp(' ')
disp(' Iron...')
@@ -261,30 +261,30 @@ end
% Make a few plots
%
if makeplot==1
-disp(' ')
-disp(' Make a few plots...')
-test_bry(bryname,grdname,'NO3',1,obc)
-figure
-test_bry(bryname,grdname,'PO4',1,obc)
-figure
-test_bry(bryname,grdname,'Si',1,obc)
-figure
-test_bry(bryname,grdname,'O2',1,obc)
-figure
-test_bry(bryname,grdname,'DIC',6,obc)
-figure
-test_bry(bryname,grdname,'TALK',6,obc)
-figure
-test_bry(bryname,grdname,'DOC',6,obc)
-figure
-test_bry(bryname,grdname,'FER',6,obc)
-figure
- if makequota
- test_bry(bryname,grdname,'DON',6,obc)
- figure
- test_bry(bryname,grdname,'DOP',6,obc)
- figure
- end
+ disp(' ')
+ disp(' Make a few plots...')
+ test_bry(bryname,grdname,'NO3',1,obc)
+ figure
+ test_bry(bryname,grdname,'PO4',1,obc)
+ figure
+ test_bry(bryname,grdname,'Si',1,obc)
+ figure
+ test_bry(bryname,grdname,'O2',1,obc)
+ figure
+ test_bry(bryname,grdname,'DIC',6,obc)
+ figure
+ test_bry(bryname,grdname,'TALK',6,obc)
+ figure
+ test_bry(bryname,grdname,'DOC',6,obc)
+ figure
+ test_bry(bryname,grdname,'FER',6,obc)
+ figure
+ if makequota
+ test_bry(bryname,grdname,'DON',6,obc)
+ figure
+ test_bry(bryname,grdname,'DOP',6,obc)
+ figure
+ end
end
%
% End
diff --git a/Preprocessing_tools/Bio/make_clim_pisces.m b/Preprocessing_tools/Bio/make_clim_pisces.m
index 51342d1a..0198dcb3 100644
--- a/Preprocessing_tools/Bio/make_clim_pisces.m
+++ b/Preprocessing_tools/Bio/make_clim_pisces.m
@@ -218,95 +218,95 @@ end
vinterp_clm(clmname,grdname,oaname,'FER','fer_time','Zfer',0,'r');
end
-%----------------------------------------------------------------------------
-% Initial file
-%----------------------------------------------------------------------------
-if (makeini)
-%
-% NO3
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' NO3...')
- vinterp_clm(ininame,grdname,oaname,'NO3','no3_time','Zno3',tini,'r',1);
-%
-% DIC
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DIC...')
- vinterp_clm(ininame,grdname,oaname,'DIC','dic_time','Zdic',tini,'r',1);
-%
-% PO4
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' PO4...')
- vinterp_clm(ininame,grdname,oaname,'PO4','po4_time','Zpo4',tini,'r',1);
- %
- % Si
- %
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' Si...')
- vinterp_clm(ininame,grdname,oaname,'Si','si_time','Zsi',tini,'r',1);
-%
-% O2
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' O2...')
- vinterp_clm(ininame,grdname,oaname,'O2','o2_time','Zo2',tini,'r',1);
-%
-% TALK
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' TALK...')
- vinterp_clm(ininame,grdname,oaname,'TALK','talk_time','Ztalk',tini,'r',1);
-%
-% DOC
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DOC...')
- vinterp_clm(ininame,grdname,oaname,'DOC','doc_time','Zdoc',tini,'r',1);
-
-if makequota
-%
-% DON
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DON...')
- vinterp_clm(ininame,grdname,oaname,'DON','don_time','Zdon',tini,'r',1);
-%
-% DOP
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' DOP...')
- vinterp_clm(ininame,grdname,oaname,'DOP','dop_time','Zdop',tini,'r',1);
-end
-
-%
-% FER
-%
- disp(' ')
- disp(' Vertical interpolations')
- disp(' ')
- disp(' FER...')
- vinterp_clm(ininame,grdname,oaname,'FER','fer_time','Zfer',tini,'r',1);
-end
+% %----------------------------------------------------------------------------
+% % Initial file
+% %----------------------------------------------------------------------------
+% if (makeini)
+% %
+% % NO3
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' NO3...')
+% vinterp_clm(ininame,grdname,oaname,'NO3','no3_time','Zno3',tini,'r',1);
+% %
+% % DIC
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' DIC...')
+% vinterp_clm(ininame,grdname,oaname,'DIC','dic_time','Zdic',tini,'r',1);
+% %
+% % PO4
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' PO4...')
+% vinterp_clm(ininame,grdname,oaname,'PO4','po4_time','Zpo4',tini,'r',1);
+% %
+% % Si
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' Si...')
+% vinterp_clm(ininame,grdname,oaname,'Si','si_time','Zsi',tini,'r',1);
+% %
+% % O2
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' O2...')
+% vinterp_clm(ininame,grdname,oaname,'O2','o2_time','Zo2',tini,'r',1);
+% %
+% % TALK
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' TALK...')
+% vinterp_clm(ininame,grdname,oaname,'TALK','talk_time','Ztalk',tini,'r',1);
+% %
+% % DOC
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' DOC...')
+% vinterp_clm(ininame,grdname,oaname,'DOC','doc_time','Zdoc',tini,'r',1);
+
+% if makequota
+% %
+% % DON
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' DON...')
+% vinterp_clm(ininame,grdname,oaname,'DON','don_time','Zdon',tini,'r',1);
+% %
+% % DOP
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' DOP...')
+% vinterp_clm(ininame,grdname,oaname,'DOP','dop_time','Zdop',tini,'r',1);
+% end
+
+% %
+% % FER
+% %
+% disp(' ')
+% disp(' Vertical interpolations')
+% disp(' ')
+% disp(' FER...')
+% vinterp_clm(ininame,grdname,oaname,'FER','fer_time','Zfer',tini,'r',1);
+% end
if (makeplot)
disp(' ')
diff --git a/Preprocessing_tools/Bio/make_dust.m b/Preprocessing_tools/Bio/make_dust.m
index bfcf43b8..6ba5f98c 100644
--- a/Preprocessing_tools/Bio/make_dust.m
+++ b/Preprocessing_tools/Bio/make_dust.m
@@ -26,6 +26,18 @@
clear all
close all
%%%%%%%%%%%%%%%%%%%%% USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp('Creating biology forcing file')
%
@@ -86,13 +98,9 @@ nc{'dustpo4'} = ncdouble('dust_time','eta_rho','xi_rho') ;
nc{'dustsi'} = ncdouble('dust_time','eta_rho','xi_rho') ;
nc{'solubility2'} = ncdouble('dust_time','eta_rho','xi_rho') ;
%
-nc{'dust_time'}.long_name = ncchar('time for dust');
-nc{'dust_time'}.long_name = 'time for dust';
-nc{'dust_time'}.units = ncchar('day');
-nc{'dust_time'}.units = 'day';
-if cycle~=0
- nc{'dust_time'}.cycle_length = cycle;
-end
+write_time_attributes(nc,'dust_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
%
nc{'dust'}.long_name = ncchar('Dust Deposition');
nc{'dust'}.long_name = 'Dust Deposition';
diff --git a/Preprocessing_tools/Bio/make_ini_pisces.m b/Preprocessing_tools/Bio/make_ini_pisces.m
index 80a3afa4..29199244 100644
--- a/Preprocessing_tools/Bio/make_ini_pisces.m
+++ b/Preprocessing_tools/Bio/make_ini_pisces.m
@@ -115,7 +115,8 @@ disp(' ')
disp('Iron ...')
ext_tracers_ini(ininame,grdname,fer_month_data,fer_ann_data,...
'fer','FER','r',tini);
-if (makeplot == 1)disp(' ')
+if (makeplot == 1)
+ disp(' ')
%
% Make a few plots
%
diff --git a/Preprocessing_tools/Bio/make_n2o_bioebus.m b/Preprocessing_tools/Bio/make_n2o_bioebus.m
deleted file mode 100644
index c8805312..00000000
--- a/Preprocessing_tools/Bio/make_n2o_bioebus.m
+++ /dev/null
@@ -1,317 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Add N2O data in input CROCO files from Global Atlas (WOA or CARS)
-%
-% N2O distribution from Nevison et al. (2003) formulation
-%
-% Data input format (netcdf):
-% variable(T, Z, Y, X)
-% T : time [Months]
-% Z : Depth [m]
-% Y : Latitude [degree north]
-% X : Longitude [degree east]
-%
-%
-% Elodie Gutknecht, 2013
-% Gildas Cambon, 2013
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clear all
-close all
-%
-% Title
-%
-crocotools_param
-%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
-
-%
-%=========
-
-if makeini
- nc=netcdf(grdname,'r');
-h = nc{'h'}(:);
-close(nc)
-% O2 initial conditions
-nc=netcdf(ininame,'r');
-theta_s = nc{'theta_s'}(:);
-theta_b = nc{'theta_b'}(:);
-Tcline = nc{'Tcline'}(:);
-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
-O2_ini = nc{'O2'}(:);
-close(nc)
-type = 'initial conditions file' ;
-history = 'CROCO' ;
-[KK,LL,MM]=size(O2_ini);
-%
-zw_ini=zlevs(h,0.,theta_s,theta_b,Tcline,N,'w',vtransform);
-N2O_ini=zeros(KK,LL,MM);N2O_ini=NaN;
-for k=1:KK
- for j=1:LL
- for i=1:MM
- N2O_ini(k,j,i)=nevis_2003(squeeze(zw_ini(k,j,i)),squeeze(O2_ini(k,j,i)));
- end
- end
-end
-% Find NaN
-find(isnan(N2O_ini)==1);%
-%
-% open the ini file
-nc = netcdf(ininame,'write');
-% new variable
-%%redef(nc);
-nc('n2o_time') = 1;
-nc{'n2o_time'} = ncdouble('time') ;
-nc{'N2O'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
-nc{'N2O'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O'}.long_name = 'Nitrous oxide';
-nc{'N2O'}.units = ncchar('mMol N2O m-3');
-nc{'N2O'}.units = 'mMol N2O m-3';
-nc{'N2O'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O'}.fields = 'NO2, scalar, series';
-%%endef(nc);
-% write new variable
-nc{'N2O'}(:,:,:) = N2O_ini;
-% Synchronize on disk
-close(nc);
-end
-
-%==========
-if makeclim
- nc=netcdf(grdname,'r');
-h = nc{'h'}(:);
-close(nc)
-% O2 climatological conditions
-nc=netcdf(clmname,'r');
-theta_s = nc{'theta_s'}(:);
-theta_b = nc{'theta_b'}(:);
-Tcline = nc{'Tcline'}(:);
-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
-O2_clm = nc{'O2'}(:);
-O2_time = nc{'o2_time'}(:);
-O2_cycle = nc{'o2_time'}.cycle_length(:);
-zeta = nc{'zeta'}(:);
-close(nc)
-[TT,KK,LL,MM]=size(O2_clm);
-for itps=1:length(O2_time)
- zw_clm(itps,:,:,:)=zlevs(h,squeeze(zeta(itps,:,:)),theta_s,theta_b,Tcline,N,'w',vtransform);
-end
-N2O_clm=zeros(TT,KK,LL,MM); N2O_clm(:)=NaN;
-for t=1:TT
- for k=1:KK
- for j=1:LL
- for i=1:MM
- zw= squeeze(zw_clm(t,k,j,i));
- O2=squeeze(O2_clm(t,k,j,i));
- N2O_clm(t,k,j,i)=nevis_2003(zw,02);
- end
- end
- end
-end
-% Find NaN
-find(isnan(N2O_clm)==1);
-%
-% add N20 in climatological file
-type = 'climatological conditions file' ;
-history = 'CROCO' ;
-%
-% open the clm file
-%
-nc = netcdf(clmname,'write');
-%
-% new variable
-%
-%%redef(nc);
-nc('n2o_time') = TT;
-nc{'n2o_time'} = ncdouble('n2o_time') ;
-nc{'n2o_time'}.long_name = ncchar('time climatological N2O');
-nc{'n2o_time'}.long_name = 'time climatological N2O';
-nc{'n2o_time'}.units = ncchar('day');
-nc{'n2o_time'}.units = 'day';
-nc{'n2o_time'}.cycle_length = O2_cycle;
-
-nc{'N2O'} = ncdouble('n2o_time','s_rho','eta_rho','xi_rho') ;
-nc{'N2O'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O'}.long_name = 'Nitrous oxide';
-nc{'N2O'}.units = ncchar('mMol N2O m-3');
-nc{'N2O'}.units = 'mMol N2O m-3';
-nc{'N2O'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O'}.fields = 'NO2, scalar, series';
-%%endef(nc);
-%
-% write new variable
-%
-nc{'n2o_time'}(:) = O2_time(:);
-nc{'N2O'}(:,:,:,:) = N2O_clm(:);
-%
-% Synchronize on disk
-%
-close(nc);
-end
-
-%==========
-if makebry
-% O2 boundary conditions
- nc=netcdf(grdname,'r');
-h = nc{'h'}(:);
-close(nc)
-
-nc=netcdf(bryname,'r');
-theta_s = nc{'theta_s'}(:);
-theta_b = nc{'theta_b'}(:);
-Tcline = nc{'Tcline'}(:);
-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
-O2_bry_west = nc{'O2_west'}(:);
-O2_bry_east = nc{'O2_east'}(:);
-O2_bry_south = nc{'O2_south'}(:);
-O2_bry_north = nc{'O2_north'}(:);
-O2_time = nc{'o2_time'}(:);
-O2_cycle = nc{'o2_time'}.cycle_length(:);
-zeta_west = nc{'zeta_west'}(:);
-zeta_east = nc{'zeta_east'}(:);
-zeta_south = nc{'zeta_south'}(:);
-zeta_north = nc{'zeta_north'}(:);
-close(nc)
-
-% BRY
-[TT,KK,MM]=size(O2_bry_south); [TT,KK,LL]=size(O2_bry_west);
-type='w';
-zw_bry_west = zeros(TT,KK+1);
-zw_bry_east = zeros(TT,KK+1);
-zw_bry_south = zeros(TT,KK+1);
-zw_bry_north = zeros(TT,KK+1);
-
-N2O_bry_east = zeros(TT,KK,LL); N2O_bry_east(:)=NaN ;
-N2O_bry_west = zeros(TT,KK,LL); N2O_bry_west(:)=NaN ;
-N2O_bry_south = zeros(TT,KK,MM); N2O_bry_south(:)=NaN ;
-N2O_bry_north = zeros(TT,KK,MM); N2O_bry_north(:)=NaN ;
-for t=1:TT
- for j=1:LL
- h_west = squeeze(h(j,1));
- h_east = squeeze(h(j,end));
- zw_bry_west(t,:,j) = zlevs_1d(h_west , squeeze(zeta_west(t,j)) , theta_s, theta_b, hc, N, type, vtransform);
- zw_bry_east(t,:,j)= zlevs_1d(h_east , squeeze(zeta_east(t,j)) , theta_s, theta_b, hc, N, type, vtransform);
- end
-end
-for t=1:TT
- for i=1:MM
- h_south = squeeze(h(1,i));
- h_north = squeeze(h(end,i));
- zw_bry_south(t,:,i)= zlevs_1d(h_south , squeeze(zeta_south(t,i)) , theta_s, theta_b, hc, N, type, vtransform);
- zw_bry_north(t,:,i)= zlevs_1d(h_north , squeeze(zeta_north(t,i)) , theta_s, theta_b, hc, N, type, vtransform);
- end
-end
-for t=1:TT
- for k=1:KK
- for j=1:LL
- zw_east=zw_bry_east(t,k,j);
- zw_west=zw_bry_west(t,k,j);
- O2_east=O2_bry_east(t,k,j);
- O2_west=O2_bry_west(t,k,j);
- N2O_bry_east(t,k,j)= nevis_2003(zw_east,O2_east);
- N2O_bry_west(t,k,j)= nevis_2003(zw_west,O2_west);
- end
- end
-end
-for t=1:TT
- for k=1:KK
- for i=1:MM
- zw_north=zw_bry_north(t,k,i);
- zw_south=zw_bry_south(t,k,i);
- O2_north=O2_bry_north(t,k,i);
- O2_south=O2_bry_south(t,k,i);
- N2O_bry_north(t,k,i)=nevis_2003(zw_north,O2_north);
- N2O_bry_south(t,k,i)=nevis_2003(zw_south,O2_south);
- end
- end
-end
-T= O2_time ;% time in days
-cycle=O2_cycle;
-
-%
-% add N20 in bryfile file
-%
-type = 'boundary conditions file' ;
-history = 'CROCO' ;
-%
-% open the bry file
-%
-nc = netcdf(bryname,'write');
-% new variable
-%
-%%redef(nc);
-nc('n2o_time') = length(T);
-nc{'n2o_time'} = ncdouble('n2o_time') ;
-nc{'n2o_time'}.long_name = ncchar('time climatological N2O');
-nc{'n2o_time'}.long_name = 'time climatological N2O';
-nc{'n2o_time'}.units = ncchar('day');
-nc{'n2o_time'}.units = 'day';
-nc{'n2o_time'}.cycle_length = O2_cycle;
-
-nc{'N2O_east'} = ncdouble('n2o_time','s_rho','eta_rho') ;
-nc{'N2O_east'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O_east'}.long_name = 'Nitrous oxide';
-nc{'N20_east'}.units = ncchar('mMol N2O m-3');
-nc{'N2O_east'}.units = 'mMol N2O m-3';
-nc{'N2O_east'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O_east'}.fields = 'NO2, scalar, series';
-
-nc{'N2O_west'} = ncdouble('n2o_time','s_rho','eta_rho') ;
-nc{'N2O_west'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O_west'}.long_name = 'Nitrous oxide';
-nc{'N2O_west'}.units = ncchar('mMol N2O m-3');
-nc{'N2O_west'}.units = 'mMol N2O m-3';
-nc{'N2O_west'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O_west'}.fields = 'NO2, scalar, series';
-
-nc{'N2O_south'} = ncdouble('n2o_time','s_rho','xi_rho') ;
-nc{'N2O_south'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O_south'}.long_name = 'Nitrous oxide';
-nc{'N20_south'}.units = ncchar('mMol N2O m-3');
-nc{'N2O_south'}.units = 'mMol N2O m-3';
-nc{'N2O_south'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O_south'}.fields = 'NO2, scalar, series';
-
-nc{'N2O_north'} = ncdouble('n2o_time','s_rho','xi_rho') ;
-nc{'N2O_north'}.long_name = ncchar('Nitrous oxide');
-nc{'N2O_north'}.long_name = 'Nitrous oxide';
-nc{'N20_north'}.units = ncchar('mMol N2O m-3');
-nc{'N2O_north'}.units = 'mMol N2O m-3';
-nc{'N2O_north'}.fields = ncchar('NO2, scalar, series');
-nc{'N2O_north'}.fields = 'NO2, scalar, series';
-
-%
-% write new variable
-%
-nc{'n2o_time'}(:) = T;
-nc{'N2O_east'}(:,:,:,:) = N2O_bry_east;
-nc{'N2O_west'}(:,:,:,:) = N2O_bry_west;
-nc{'N2O_south'}(:,:,:,:) = N2O_bry_south;
-nc{'N2O_north'}(:,:,:,:) = N2O_bry_north;
-%
-% Synchronize on disk
-%
-close(nc);
-end
-
-
-
-
-
-
diff --git a/Preprocessing_tools/Bio/make_ndepo.m b/Preprocessing_tools/Bio/make_ndepo.m
index 1c2c35bb..1571c796 100644
--- a/Preprocessing_tools/Bio/make_ndepo.m
+++ b/Preprocessing_tools/Bio/make_ndepo.m
@@ -29,6 +29,17 @@ close all
disp(' ')
disp('Creating biology forcing file')
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Title - Grid file name - Forcing file name
%
crocotools_param
@@ -84,11 +95,8 @@ nc{'nhxndepo'} = ncdouble('ndepo_time','eta_rho','xi_rho') ;
%
nc{'ndepo_time'}.long_name = ncchar('time for nitrogen deposition');
nc{'ndepo_time'}.long_name = 'time for nitrogen deposition';
-nc{'ndepo_time'}.units = ncchar('day');
-nc{'ndepo_time'}.units = 'day';
-if cycle~=0
- nc{'ndepo_time'}.cycle_length = cycle;
-end
+write_time_attributes(nc,'ndepo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'ndepo'}.long_name = ncchar('Nitrogen Deposition');
nc{'ndepo'}.long_name = 'Nitrogen Deposition';
diff --git a/Preprocessing_tools/Bio/add_Sphyto_Lphyto.m b/Preprocessing_tools/Bio/npzd-bioebus/add_Sphyto_Lphyto.m
similarity index 85%
rename from Preprocessing_tools/Bio/add_Sphyto_Lphyto.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_Sphyto_Lphyto.m
index 95a2eade..ed04cf5e 100644
--- a/Preprocessing_tools/Bio/add_Sphyto_Lphyto.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_Sphyto_Lphyto.m
@@ -41,6 +41,18 @@ function add_Sphyto_Lphyto(climfile);
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
theta1=0.1;
theta2=0.4;
%
@@ -61,11 +73,8 @@ 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
+write_time_attributes(nc,'sphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc('lphyto_time') = tlen;
nc{'lphyto_time'} = ncdouble('lphyto_time') ;
@@ -73,11 +82,8 @@ 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
+write_time_attributes(nc,'lphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'SPHYTO'}.long_name = ncchar('Small Phytoplankton');
nc{'SPHYTO'}.long_name = 'Small Phytoplankton';
diff --git a/Preprocessing_tools/Bio/add_Szoo_Lzoo.m b/Preprocessing_tools/Bio/npzd-bioebus/add_Szoo_Lzoo.m
similarity index 84%
rename from Preprocessing_tools/Bio/add_Szoo_Lzoo.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_Szoo_Lzoo.m
index 96bc091c..1015c3a3 100644
--- a/Preprocessing_tools/Bio/add_Szoo_Lzoo.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_Szoo_Lzoo.m
@@ -41,6 +41,18 @@ function add_Szoo_Lzoo(climfile);
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
theta1=0.2;
theta2=0.3;
%
@@ -61,11 +73,8 @@ 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
+write_time_attributes(nc,'szoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc('lzoo_time') = tlen;
nc{'lzoo_time'} = ncdouble('lzoo_time') ;
@@ -73,11 +82,8 @@ 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
+write_time_attributes(nc,'lzoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'SZOO'}.long_name = ncchar('Small Zooplankton');
nc{'SZOO'}.long_name = 'Small Zooplankton';
diff --git a/Preprocessing_tools/Bio/add_bry_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus.m
similarity index 92%
rename from Preprocessing_tools/Bio/add_bry_bioebus.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus.m
index 6938dafe..ab69dbd2 100644
--- a/Preprocessing_tools/Bio/add_bry_bioebus.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus.m
@@ -46,6 +46,18 @@ function add_bry_bioebus(bryname,obc,time_no3,time_o2,time_zoo,time_phyto,time_c
% Gildas Cambon, IRD, 2011 %
% Gildas Cambon, IRD, 2013 : Add oxygen processing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp([' Adding BIOEBUS BGC data into file : ',bryname])
disp(' ')
@@ -71,51 +83,44 @@ nc('one') = 1;
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;%
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'chla_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'sphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'lphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'szoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'lzoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
%
if obc(1)==1
diff --git a/Preprocessing_tools/Bio/add_bry_bioebus_Z.m b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus_Z.m
similarity index 91%
rename from Preprocessing_tools/Bio/add_bry_bioebus_Z.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus_Z.m
index 4a953a06..d643aa40 100644
--- a/Preprocessing_tools/Bio/add_bry_bioebus_Z.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_bioebus_Z.m
@@ -23,6 +23,18 @@ function add_bry_bioebus_Z(zbryname,obc,Z,time_no3,time_o2,time_zoo,time_phyto,t
% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
% Gildas Cambon, IRD/LEGOS, 2013 : Add O2 processing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp([' Adding BioEBUS data into file : ',zbryname])
disp(' ')
@@ -48,51 +60,45 @@ nc('one') = 1;
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;
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'chla_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'sphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'lphyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'szoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'lzoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
if obc(1)==1
diff --git a/Preprocessing_tools/Bio/add_bry_npzd.m b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd.m
similarity index 90%
rename from Preprocessing_tools/Bio/add_bry_npzd.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd.m
index 9cd49e6b..a46c0111 100644
--- a/Preprocessing_tools/Bio/add_bry_npzd.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd.m
@@ -46,6 +46,22 @@ function add_bry_npzd(bryname,obc,time_no3,time_o2,time_zoo,time_phyto,time_chla
% Gildas Cambon, IRD, 2011 %
% Gildas Cambon, IRD, 2013 : Add oxygen processing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+disp(' ')
+disp([' Adding PISCES data into file : ',bryname])
+disp(' ')
+%
disp(' ')
disp([' Adding NPZD BGC data into file : ',bryname])
disp(' ')
@@ -67,39 +83,34 @@ 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 = 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;%
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'o2_time'} = ncdouble('o2_time') ;
-nc{'o2_time'}.long_name = ncchar('time for O2 climatology')
+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;
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'chla_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'phyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'zoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
%
if obc(1)==1
diff --git a/Preprocessing_tools/Bio/add_bry_npzd_Z.m b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd_Z.m
similarity index 91%
rename from Preprocessing_tools/Bio/add_bry_npzd_Z.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd_Z.m
index c1755f6a..29b60a6b 100644
--- a/Preprocessing_tools/Bio/add_bry_npzd_Z.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_bry_npzd_Z.m
@@ -23,6 +23,18 @@ function add_bry_npzd_Z(zbryname,obc,Z,time_no3,time_o2,time_zoo,time_phyto,time
% Christophe Eugene Raoul Menkes, the slave, IRD, 2007. %
% Gildas Cambon, IRD/LEGOS, 2013 : Add O2 processing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
disp(' ')
disp([' Adding NPZD data into file : ',zbryname])
disp(' ')
@@ -46,37 +58,32 @@ nc('one') = 1;
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;
+write_time_attributes(nc,'no3_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'o2_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'chla_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;%
+write_time_attributes(nc,'phyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_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;
+write_time_attributes(nc,'zoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
if obc(1)==1
@@ -89,7 +96,7 @@ if obc(1)==1
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'} = 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');
diff --git a/Preprocessing_tools/Bio/add_chla.m b/Preprocessing_tools/Bio/npzd-bioebus/add_chla.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_chla.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_chla.m
diff --git a/Preprocessing_tools/Bio/add_ini_Sphyto_Lphyto.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_Sphyto_Lphyto.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_Sphyto_Lphyto.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_Sphyto_Lphyto.m
diff --git a/Preprocessing_tools/Bio/add_ini_Szoo_Lzoo.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_Szoo_Lzoo.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_Szoo_Lzoo.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_Szoo_Lzoo.m
diff --git a/Preprocessing_tools/Bio/add_ini_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_bioebus.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_bioebus.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_bioebus.m
diff --git a/Preprocessing_tools/Bio/add_ini_chla.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_chla.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_chla.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_chla.m
diff --git a/Preprocessing_tools/Bio/add_ini_no3.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_no3.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_no3.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_no3.m
diff --git a/Preprocessing_tools/Bio/add_ini_npzd.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_npzd.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_npzd.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_npzd.m
diff --git a/Preprocessing_tools/Bio/add_ini_o2.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_o2.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_o2.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_o2.m
diff --git a/Preprocessing_tools/Bio/add_ini_phyto.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_phyto.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_phyto.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_phyto.m
diff --git a/Preprocessing_tools/Bio/add_ini_zoo.m b/Preprocessing_tools/Bio/npzd-bioebus/add_ini_zoo.m
similarity index 100%
rename from Preprocessing_tools/Bio/add_ini_zoo.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_ini_zoo.m
diff --git a/Preprocessing_tools/Bio/add_phyto.m b/Preprocessing_tools/Bio/npzd-bioebus/add_phyto.m
similarity index 85%
rename from Preprocessing_tools/Bio/add_phyto.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_phyto.m
index c38091ca..cbcc07cc 100644
--- a/Preprocessing_tools/Bio/add_phyto.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_phyto.m
@@ -39,6 +39,18 @@ function add_phyto(climfile);
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
theta=0.5;
%
disp('Add_phyto: creating variable and attribute')
@@ -56,11 +68,8 @@ 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
+write_time_attributes(nc,'phyto_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'PHYTO'}.long_name = ncchar('Phytoplankton');
nc{'PHYTO'}.long_name = 'Phytoplankton';
diff --git a/Preprocessing_tools/Bio/add_zoo.m b/Preprocessing_tools/Bio/npzd-bioebus/add_zoo.m
similarity index 85%
rename from Preprocessing_tools/Bio/add_zoo.m
rename to Preprocessing_tools/Bio/npzd-bioebus/add_zoo.m
index 597a1c10..cf14cdaf 100644
--- a/Preprocessing_tools/Bio/add_zoo.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/add_zoo.m
@@ -41,6 +41,19 @@ function add_zoo(climfile);
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
theta=0.2;
%
disp('Add_zoo: creating variable and attribute')
@@ -58,11 +71,8 @@ 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
+write_time_attributes(nc,'zoo_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'ZOO'}.long_name = ncchar('Zooplankton');
nc{'ZOO'}.long_name = 'Zooplankton';
diff --git a/Preprocessing_tools/Bio/bry_interp_bgc.m b/Preprocessing_tools/Bio/npzd-bioebus/bry_interp_bgc.m
similarity index 100%
rename from Preprocessing_tools/Bio/bry_interp_bgc.m
rename to Preprocessing_tools/Bio/npzd-bioebus/bry_interp_bgc.m
diff --git a/Preprocessing_tools/Bio/bry_interp_bgc_chloro.m b/Preprocessing_tools/Bio/npzd-bioebus/bry_interp_bgc_chloro.m
similarity index 100%
rename from Preprocessing_tools/Bio/bry_interp_bgc_chloro.m
rename to Preprocessing_tools/Bio/npzd-bioebus/bry_interp_bgc_chloro.m
diff --git a/Preprocessing_tools/Bio/make_bry_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/make_bry_bioebus.m
similarity index 99%
rename from Preprocessing_tools/Bio/make_bry_bioebus.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_bry_bioebus.m
index 7e7ad426..9bea5deb 100644
--- a/Preprocessing_tools/Bio/make_bry_bioebus.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/make_bry_bioebus.m
@@ -72,7 +72,7 @@ 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'];
-chla_ann_data=[chla_dir,'chla_seas.cdf'];
+chla_ann_data=[chla_dir,'chla_ann.cdf'];
%
%
%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Preprocessing_tools/Bio/make_bry_npzd.m b/Preprocessing_tools/Bio/npzd-bioebus/make_bry_npzd.m
similarity index 98%
rename from Preprocessing_tools/Bio/make_bry_npzd.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_bry_npzd.m
index 11b9b01a..0dd9b10b 100644
--- a/Preprocessing_tools/Bio/make_bry_npzd.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/make_bry_npzd.m
@@ -67,9 +67,9 @@ Roa;
% Data climatologies file names:
%
%
-no3_seas_data=[climato_dir,'no3_seas.cdf'];
+no3_seas_data=[climato_dir,'no3_month.cdf'];
no3_ann_data=[climato_dir,'no3_ann.cdf'];
-o2_seas_data=[climato_dir,'o2_seas.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'];
chla_ann_data=[chla_dir,'chla_ann.cdf'];
diff --git a/Preprocessing_tools/Bio/make_clim_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/make_clim_bioebus.m
similarity index 100%
rename from Preprocessing_tools/Bio/make_clim_bioebus.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_clim_bioebus.m
diff --git a/Preprocessing_tools/Bio/make_clim_npzd.m b/Preprocessing_tools/Bio/npzd-bioebus/make_clim_npzd.m
similarity index 97%
rename from Preprocessing_tools/Bio/make_clim_npzd.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_clim_npzd.m
index 0f31acb2..65edff43 100644
--- a/Preprocessing_tools/Bio/make_clim_npzd.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/make_clim_npzd.m
@@ -34,9 +34,9 @@ crocotools_param
%
% Data climatologies file names:
%
-no3_seas_data=[climato_dir,'no3_seas.cdf'];
+no3_seas_data=[climato_dir,'no3_month.cdf'];
no3_ann_data=[climato_dir,'no3_ann.cdf'];
-o2_seas_data=[climato_dir,'o2_seas.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'];
diff --git a/Preprocessing_tools/Bio/make_ini_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/make_ini_bioebus.m
similarity index 100%
rename from Preprocessing_tools/Bio/make_ini_bioebus.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_ini_bioebus.m
diff --git a/Preprocessing_tools/Bio/make_ini_npzd.m b/Preprocessing_tools/Bio/npzd-bioebus/make_ini_npzd.m
similarity index 100%
rename from Preprocessing_tools/Bio/make_ini_npzd.m
rename to Preprocessing_tools/Bio/npzd-bioebus/make_ini_npzd.m
diff --git a/Preprocessing_tools/Bio/npzd-bioebus/make_n2o_bioebus.m b/Preprocessing_tools/Bio/npzd-bioebus/make_n2o_bioebus.m
new file mode 100644
index 00000000..ea0677a5
--- /dev/null
+++ b/Preprocessing_tools/Bio/npzd-bioebus/make_n2o_bioebus.m
@@ -0,0 +1,322 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Add N2O data in input CROCO files from Global Atlas (WOA or CARS)
+%
+% N2O distribution from Nevison et al. (2003) formulation
+%
+% Data input format (netcdf):
+% variable(T, Z, Y, X)
+% T : time [Months]
+% Z : Depth [m]
+% Y : Latitude [degree north]
+% X : Longitude [degree east]
+%
+%
+% Elodie Gutknecht, 2013
+% Gildas Cambon, 2013
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+clear all
+close all
+%
+% Title
+%
+crocotools_param
+%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
+%
+% options for write_time_attributes
+insecond = 0 ;
+add_cycle = 1 ;
+Yorig='';
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
+%=========
+
+if makeini
+ nc=netcdf(grdname,'r');
+ h = nc{'h'}(:);
+ close(nc)
+ % O2 initial conditions
+ nc=netcdf(ininame,'r');
+ theta_s = nc{'theta_s'}(:);
+ theta_b = nc{'theta_b'}(:);
+ Tcline = nc{'Tcline'}(:);
+ 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
+ O2_ini = nc{'O2'}(:);
+ close(nc)
+ type = 'initial conditions file' ;
+ history = 'CROCO' ;
+ [KK,LL,MM]=size(O2_ini);
+ %
+ zw_ini=zlevs(h,0.,theta_s,theta_b,Tcline,N,'w',vtransform);
+ N2O_ini=zeros(KK,LL,MM);N2O_ini=NaN;
+ for k=1:KK
+ for j=1:LL
+ for i=1:MM
+ N2O_ini(k,j,i)=nevis_2003(squeeze(zw_ini(k,j,i)),squeeze(O2_ini(k,j,i)));
+ end
+ end
+ end
+ % Find NaN
+ find(isnan(N2O_ini)==1);%
+ %
+ % open the ini file
+ nc = netcdf(ininame,'write');
+ % new variable
+ %%redef(nc);
+ %
+ nc{'N2O'} = ncdouble('time','s_rho','eta_rho','xi_rho') ;
+ nc{'N2O'}.long_name = 'Nitrous oxide';
+ nc{'N2O'}.fields = 'NO2, scalar, series';
+ %%endef(nc);
+ % write new variable
+ nc{'N2O'}(:,:,:) = N2O_ini;
+ % Synchronize on disk
+ close(nc);
+end
+
+%==========
+if makeclim
+ nc=netcdf(grdname,'r');
+ h = nc{'h'}(:);
+ close(nc)
+ % O2 climatological conditions
+ nc=netcdf(clmname,'r');
+ theta_s = nc{'theta_s'}(:);
+ theta_b = nc{'theta_b'}(:);
+ Tcline = nc{'Tcline'}(:);
+ 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
+ O2_clm = nc{'O2'}(:);
+ O2_time = nc{'o2_time'}(:);
+ O2_cycle = nc{'o2_time'}.cycle_length(:);
+ zeta = nc{'zeta'}(:);
+ close(nc)
+ [TT,KK,LL,MM]=size(O2_clm);
+ for itps=1:length(O2_time)
+ zw_clm(itps,:,:,:)=zlevs(h,squeeze(zeta(itps,:,:)),theta_s,theta_b,Tcline,N,'w',vtransform);
+ end
+ N2O_clm=zeros(TT,KK,LL,MM); N2O_clm(:)=NaN;
+ for t=1:TT
+ for k=1:KK
+ for j=1:LL
+ for i=1:MM
+ zw= squeeze(zw_clm(t,k,j,i));
+ O2=squeeze(O2_clm(t,k,j,i));
+ N2O_clm(t,k,j,i)=nevis_2003(zw,02);
+ end
+ end
+ end
+ end
+ % Find NaN
+ find(isnan(N2O_clm)==1);
+ %
+ % add N20 in climatological file
+ type = 'climatological conditions file' ;
+ history = 'CROCO' ;
+ %
+ % open the clm file
+ %
+ nc = netcdf(clmname,'write');
+ %
+ % new variable
+ %
+ %%redef(nc);
+ nc('n2o_time') = TT;
+ nc{'n2o_time'} = ncdouble('n2o_time') ;
+ nc{'n2o_time'}.long_name = ncchar('time climatological N2O');
+ nc{'n2o_time'}.long_name = 'time climatological N2O';
+ write_time_attributes(nc,'n2o_time',O2_cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,1);
+
+ nc{'N2O'} = ncdouble('n2o_time','s_rho','eta_rho','xi_rho') ;
+ nc{'N2O'}.long_name = ncchar('Nitrous oxide');
+ nc{'N2O'}.long_name = 'Nitrous oxide';
+ nc{'N2O'}.units = ncchar('mMol N2O m-3');
+ nc{'N2O'}.units = 'mMol N2O m-3';
+ nc{'N2O'}.fields = ncchar('NO2, scalar, series');
+ nc{'N2O'}.fields = 'NO2, scalar, series';
+ %%endef(nc);
+ %
+ % write new variable
+ %
+ nc{'n2o_time'}(:) = O2_time(:);
+ nc{'N2O'}(:,:,:,:) = N2O_clm(:);
+ %
+ % Synchronize on disk
+ %
+ close(nc);
+end
+
+%==========
+if makebry
+ % O2 boundary conditions
+ nc=netcdf(grdname,'r');
+ h = nc{'h'}(:);
+ close(nc)
+
+ nc=netcdf(bryname,'r');
+ theta_s = nc{'theta_s'}(:);
+ theta_b = nc{'theta_b'}(:);
+ Tcline = nc{'Tcline'}(:);
+ 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
+ O2_bry_west = nc{'O2_west'}(:);
+ O2_bry_east = nc{'O2_east'}(:);
+ O2_bry_south = nc{'O2_south'}(:);
+ O2_bry_north = nc{'O2_north'}(:);
+ O2_time = nc{'o2_time'}(:);
+ O2_cycle = nc{'o2_time'}.cycle_length(:);
+ zeta_west = nc{'zeta_west'}(:);
+ zeta_east = nc{'zeta_east'}(:);
+ zeta_south = nc{'zeta_south'}(:);
+ zeta_north = nc{'zeta_north'}(:);
+ close(nc)
+
+ % BRY
+ [TT,KK,MM]=size(O2_bry_south); [TT,KK,LL]=size(O2_bry_west);
+ type='w';
+ zw_bry_west = zeros(TT,KK+1);
+ zw_bry_east = zeros(TT,KK+1);
+ zw_bry_south = zeros(TT,KK+1);
+ zw_bry_north = zeros(TT,KK+1);
+
+ N2O_bry_east = zeros(TT,KK,LL); N2O_bry_east(:)=NaN ;
+ N2O_bry_west = zeros(TT,KK,LL); N2O_bry_west(:)=NaN ;
+ N2O_bry_south = zeros(TT,KK,MM); N2O_bry_south(:)=NaN ;
+ N2O_bry_north = zeros(TT,KK,MM); N2O_bry_north(:)=NaN ;
+ for t=1:TT
+ for j=1:LL
+ h_west = squeeze(h(j,1));
+ h_east = squeeze(h(j,end));
+ zw_bry_west(t,:,j) = zlevs_1d(h_west , squeeze(zeta_west(t,j)) , theta_s, theta_b, hc, N, type, vtransform);
+ zw_bry_east(t,:,j)= zlevs_1d(h_east , squeeze(zeta_east(t,j)) , theta_s, theta_b, hc, N, type, vtransform);
+ end
+ end
+ for t=1:TT
+ for i=1:MM
+ h_south = squeeze(h(1,i));
+ h_north = squeeze(h(end,i));
+ zw_bry_south(t,:,i)= zlevs_1d(h_south , squeeze(zeta_south(t,i)) , theta_s, theta_b, hc, N, type, vtransform);
+ zw_bry_north(t,:,i)= zlevs_1d(h_north , squeeze(zeta_north(t,i)) , theta_s, theta_b, hc, N, type, vtransform);
+ end
+ end
+ for t=1:TT
+ for k=1:KK
+ for j=1:LL
+ zw_east=zw_bry_east(t,k,j);
+ zw_west=zw_bry_west(t,k,j);
+ O2_east=O2_bry_east(t,k,j);
+ O2_west=O2_bry_west(t,k,j);
+ N2O_bry_east(t,k,j)= nevis_2003(zw_east,O2_east);
+ N2O_bry_west(t,k,j)= nevis_2003(zw_west,O2_west);
+ end
+ end
+ end
+ for t=1:TT
+ for k=1:KK
+ for i=1:MM
+ zw_north=zw_bry_north(t,k,i);
+ zw_south=zw_bry_south(t,k,i);
+ O2_north=O2_bry_north(t,k,i);
+ O2_south=O2_bry_south(t,k,i);
+ N2O_bry_north(t,k,i)=nevis_2003(zw_north,O2_north);
+ N2O_bry_south(t,k,i)=nevis_2003(zw_south,O2_south);
+ end
+ end
+ end
+ T= O2_time ;% time in days
+ cycle=O2_cycle;
+
+ %
+ % add N20 in bryfile file
+ %
+ type = 'boundary conditions file' ;
+ history = 'CROCO' ;
+ %
+ % open the bry file
+ %
+ nc = netcdf(bryname,'write');
+ % new variable
+ %
+ %%redef(nc);
+ nc('n2o_time') = length(T);
+ nc{'n2o_time'} = ncdouble('n2o_time') ;
+ nc{'n2o_time'}.long_name = ncchar('time climatological N2O');
+ nc{'n2o_time'}.long_name = 'time climatological N2O';
+ write_time_attributes(nc,'n2o_time',O2_cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,1);
+
+ nc{'N2O_east'} = ncdouble('n2o_time','s_rho','eta_rho') ;
+ nc{'N2O_east'}.long_name = ncchar('Nitrous oxide');
+ nc{'N2O_east'}.long_name = 'Nitrous oxide';
+ nc{'N20_east'}.units = ncchar('mMol N2O m-3');
+ nc{'N2O_east'}.units = 'mMol N2O m-3';
+ nc{'N2O_east'}.fields = ncchar('NO2, scalar, series');
+ nc{'N2O_east'}.fields = 'NO2, scalar, series';
+
+ nc{'N2O_west'} = ncdouble('n2o_time','s_rho','eta_rho') ;
+ nc{'N2O_west'}.long_name = ncchar('Nitrous oxide');
+ nc{'N2O_west'}.long_name = 'Nitrous oxide';
+ nc{'N2O_west'}.units = ncchar('mMol N2O m-3');
+ nc{'N2O_west'}.units = 'mMol N2O m-3';
+ nc{'N2O_west'}.fields = ncchar('NO2, scalar, series');
+ nc{'N2O_west'}.fields = 'NO2, scalar, series';
+
+ nc{'N2O_south'} = ncdouble('n2o_time','s_rho','xi_rho') ;
+ nc{'N2O_south'}.long_name = ncchar('Nitrous oxide');
+ nc{'N2O_south'}.long_name = 'Nitrous oxide';
+ nc{'N20_south'}.units = ncchar('mMol N2O m-3');
+ nc{'N2O_south'}.units = 'mMol N2O m-3';
+ nc{'N2O_south'}.fields = ncchar('NO2, scalar, series');
+ nc{'N2O_south'}.fields = 'NO2, scalar, series';
+
+ nc{'N2O_north'} = ncdouble('n2o_time','s_rho','xi_rho') ;
+ nc{'N2O_north'}.long_name = ncchar('Nitrous oxide');
+ nc{'N2O_north'}.long_name = 'Nitrous oxide';
+ nc{'N20_north'}.units = ncchar('mMol N2O m-3');
+ nc{'N2O_north'}.units = 'mMol N2O m-3';
+ nc{'N2O_north'}.fields = ncchar('NO2, scalar, series');
+ nc{'N2O_north'}.fields = 'NO2, scalar, series';
+
+ %
+ % write new variable
+ %
+ nc{'n2o_time'}(:) = T;
+ nc{'N2O_east'}(:,:,:,:) = N2O_bry_east;
+ nc{'N2O_west'}(:,:,:,:) = N2O_bry_west;
+ nc{'N2O_south'}(:,:,:,:) = N2O_bry_south;
+ nc{'N2O_north'}(:,:,:,:) = N2O_bry_north;
+ %
+ % Synchronize on disk
+ %
+ close(nc);
+end
+
+
+
+
+
+
diff --git a/Preprocessing_tools/Bio/nevis_2003.m b/Preprocessing_tools/Bio/npzd-bioebus/nevis_2003.m
similarity index 100%
rename from Preprocessing_tools/Bio/nevis_2003.m
rename to Preprocessing_tools/Bio/npzd-bioebus/nevis_2003.m
diff --git a/Preprocessing_tools/Bio/vinterp_bry_bgc.m b/Preprocessing_tools/Bio/npzd-bioebus/vinterp_bry_bgc.m
similarity index 98%
rename from Preprocessing_tools/Bio/vinterp_bry_bgc.m
rename to Preprocessing_tools/Bio/npzd-bioebus/vinterp_bry_bgc.m
index 154fb011..ea3c42dc 100644
--- a/Preprocessing_tools/Bio/vinterp_bry_bgc.m
+++ b/Preprocessing_tools/Bio/npzd-bioebus/vinterp_bry_bgc.m
@@ -93,7 +93,6 @@ 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
diff --git a/Preprocessing_tools/create_bry_Z.m b/Preprocessing_tools/create_bry_Z.m
index ffd60b91..10e06c66 100644
--- a/Preprocessing_tools/create_bry_Z.m
+++ b/Preprocessing_tools/create_bry_Z.m
@@ -1,5 +1,5 @@
function create_bry_Z(zbryname,grdname,title,obc,...
- Z,time,cycle,clobber);
+ Z,time,cycle,clobber,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function create the header of a Netcdf boundary
@@ -44,6 +44,17 @@ disp(' ')
disp([' Creating the file : ',zbryname])
disp(' ')
%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Read the grid file and check the topography
%
nc = netcdf(grdname, 'nowrite');
@@ -81,9 +92,8 @@ nc{'Z'}.units = 'm';
nc{'bry_time'} = ncdouble('bry_time') ;
nc{'bry_time'}.long_name = ncchar('time for temperature climatology');
nc{'bry_time'}.long_name = 'time for temperature climatology';
-nc{'bry_time'}.units = ncchar('day');
-nc{'bry_time'}.units = 'day';
-nc{'bry_time'}.cycle_length = cycle;%
+write_time_attributes(nc,'bry_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
if obc(1)==1
%
diff --git a/Preprocessing_tools/create_bryfile.m b/Preprocessing_tools/create_bryfile.m
index e36dde8a..0c24858a 100644
--- a/Preprocessing_tools/create_bryfile.m
+++ b/Preprocessing_tools/create_bryfile.m
@@ -1,6 +1,6 @@
function create_bryfile(bryname,grdname,title,obc,...
theta_s,theta_b,hc,N,...
- time,cycle,clobber,vtransform);
+ time,cycle,clobber,vtransform,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function create_bryfile(bryname,grdname,title,obc...
@@ -60,6 +60,19 @@ if nargin < 12
end
disp([' VTRANSFORM = ',num2str(vtransform)])
%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read the grid file and check the topography
%
nc = netcdf(grdname, 'nowrite');
@@ -130,14 +143,14 @@ nc{'Vstretching'}.long_name = 'vertical terrain-following stretching function';
nc{'tstart'} = ncdouble('one') ;
nc{'tstart'}.long_name = ncchar('start processing day');
nc{'tstart'}.long_name = 'start processing day';
-nc{'tstart'}.units = ncchar('day');
-nc{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'tend'} = ncdouble('one') ;
nc{'tend'}.long_name = ncchar('end processing day');
nc{'tend'}.long_name = 'end processing day';
-nc{'tend'}.units = ncchar('day');
-nc{'tend'}.units = 'day';
+write_time_attributes(nc,'tend','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'theta_s'} = ncdouble('one') ;
nc{'theta_s'}.long_name = ncchar('S-coordinate surface control parameter');
@@ -214,103 +227,70 @@ nc{'Cs_w'}.valid_min = -1;
nc{'Cs_w'}.valid_max = 0;
%
nc{'bry_time'} = ncdouble('bry_time') ;
-nc{'bry_time'}.long_name = ncchar('time for boundary climatology');
-nc{'bry_time'}.long_name = 'time for boundary climatology';
-nc{'bry_time'}.units = ncchar('day');
-nc{'bry_time'}.units = 'day';
-nc{'bry_time'}.calendar = ncchar('360.0 days in every year');
-nc{'bry_time'}.calendar = '360.0 days in every year';
-nc{'bry_time'}.cycle_length = cycle;
+nc{'bry_time'}.long_name = ncchar('time for boundary');
+nc{'bry_time'}.long_name = 'time for boundary';
+write_time_attributes(nc,'bry_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'tclm_time'} = ncdouble('tclm_time') ;
nc{'tclm_time'}.long_name = ncchar('time for temperature climatology');
nc{'tclm_time'}.long_name = 'time for temperature climatology';
-nc{'tclm_time'}.units = ncchar('day');
-nc{'tclm_time'}.units = 'day';
-nc{'tclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'tclm_time'}.calendar = '360.0 days in every year';
-nc{'tclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'tclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'temp_time'} = ncdouble('temp_time') ;
nc{'temp_time'}.long_name = ncchar('time for temperature climatology');
nc{'temp_time'}.long_name = 'time for temperature climatology';
-nc{'temp_time'}.units = ncchar('day');
-nc{'temp_time'}.units = 'day';
-nc{'temp_time'}.calendar = ncchar('360.0 days in every year');
-nc{'temp_time'}.calendar = '360.0 days in every year';
-nc{'temp_time'}.cycle_length = cycle;
+write_time_attributes(nc,'temp_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'sclm_time'} = ncdouble('sclm_time') ;
nc{'sclm_time'}.long_name = ncchar('time for salinity climatology');
nc{'sclm_time'}.long_name = 'time for salinity climatology';
-nc{'sclm_time'}.units = ncchar('day');
-nc{'sclm_time'}.units = 'day';
-nc{'sclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'sclm_time'}.calendar = '360.0 days in every year';
-nc{'sclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'sclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'salt_time'} = ncdouble('salt_time') ;
nc{'salt_time'}.long_name = ncchar('time for salinity climatology');
nc{'salt_time'}.long_name = 'time for salinity climatology';
-nc{'salt_time'}.units = ncchar('day');
-nc{'salt_time'}.units = 'day';
-nc{'salt_time'}.calendar = ncchar('360.0 days in every year');
-nc{'salt_time'}.calendar = '360.0 days in every year';
-nc{'salt_time'}.cycle_length = cycle;
+write_time_attributes(nc,'salt_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'uclm_time'} = ncdouble('uclm_time') ;
nc{'uclm_time'}.long_name = ncchar('time climatological u');
nc{'uclm_time'}.long_name = 'time climatological u';
-nc{'uclm_time'}.units = ncchar('day');
-nc{'uclm_time'}.units = 'day';
-nc{'uclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'uclm_time'}.calendar = '360.0 days in every year';
-nc{'uclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'sclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'vclm_time'} = ncdouble('vclm_time') ;
nc{'vclm_time'}.long_name = ncchar('time climatological v');
nc{'vclm_time'}.long_name = 'time climatological v';
-nc{'vclm_time'}.units = ncchar('day');
-nc{'vclm_time'}.units = 'day';
-nc{'vclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'vclm_time'}.calendar = '360.0 days in every year';
-nc{'vclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'vclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v2d_time'} = ncdouble('v2d_time') ;
nc{'v2d_time'}.long_name = ncchar('time for 2D velocity climatology');
nc{'v2d_time'}.long_name = 'time for 2D velocity climatology';
-nc{'v2d_time'}.units = ncchar('day');
-nc{'v2d_time'}.units = 'day';
-nc{'v2d_time'}.calendar = ncchar('360.0 days in every year');
-nc{'v2d_time'}.calendar = '360.0 days in every year';
-nc{'v2d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v2d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v3d_time'} = ncdouble('v3d_time') ;
nc{'v3d_time'}.long_name = ncchar('time for 3D velocity climatology');
nc{'v3d_time'}.long_name = 'time for 3D velocity climatology';
-nc{'v3d_time'}.units = ncchar('day');
-nc{'v3d_time'}.units = 'day';
-nc{'v3d_time'}.calendar = ncchar('360.0 days in every year');
-nc{'v3d_time'}.calendar = '360.0 days in every year';
-nc{'v3d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v3d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'ssh_time'} = ncdouble('ssh_time') ;
nc{'ssh_time'}.long_name = ncchar('time for sea surface height');
nc{'ssh_time'}.long_name = 'time for sea surface height';
-nc{'ssh_time'}.units = ncchar('day');
-nc{'ssh_time'}.units = 'day';
-nc{'ssh_time'}.calendar = ncchar('360.0 days in every year');
-nc{'ssh_time'}.calendar = '360.0 days in every year';
-nc{'ssh_time'}.cycle_length = cycle;
+write_time_attributes(nc,'ssh_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'zeta_time'} = ncdouble('zeta_time') ;
nc{'zeta_time'}.long_name = ncchar('time for sea surface height');
nc{'zeta_time'}.long_name = 'time for sea surface height';
-nc{'zeta_time'}.units = ncchar('day');
-nc{'zeta_time'}.units = 'day';
-nc{'zeta_time'}.calendar = ncchar('360.0 days in every year');
-nc{'zeta_time'}.calendar = '360.0 days in every year';
-nc{'zeta_time'}.cycle_length = cycle;
+write_time_attributes(nc,'zeta_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
if obc(1)==1
%
diff --git a/Preprocessing_tools/create_bryfile_wkb.m b/Preprocessing_tools/create_bryfile_wkb.m
index 1320ede3..b7729550 100644
--- a/Preprocessing_tools/create_bryfile_wkb.m
+++ b/Preprocessing_tools/create_bryfile_wkb.m
@@ -1,5 +1,5 @@
function create_bryfile(brywkbname,grdname,title,wkb_obc,...
- time,cycle,clobber);
+ time,cycle,clobber,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function create_bryfile(brywkbname,grdname,title,wkb_obc...
@@ -46,6 +46,17 @@ disp(' ')
disp([' Creating the file : ',brywkbname])
disp(' ')
%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+ %
+ % Get time attributes
+ [time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
% Read the grid file
%
nc = netcdf(grdname, 'nowrite');
@@ -78,25 +89,21 @@ nc('one') = 1;
nc{'tstart'} = ncdouble('one') ;
nc{'tstart'}.long_name = ncchar('start processing day');
nc{'tstart'}.long_name = 'start processing day';
-nc{'tstart'}.units = ncchar('day');
-nc{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'tend'} = ncdouble('one') ;
nc{'tend'}.long_name = ncchar('end processing day');
nc{'tend'}.long_name = 'end processing day';
-nc{'tend'}.units = ncchar('day');
-nc{'tend'}.units = 'day';
-%
+write_time_attributes(nc,'tend','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'brywkb_time'} = ncdouble('brywkb_time') ;
nc{'brywkb_time'}.long_name = ncchar('time for boundary climatology');
nc{'brywkb_time'}.long_name = 'time for boundary climatology';
-nc{'brywkb_time'}.units = ncchar('day');
-nc{'brywkb_time'}.units = 'day';
-nc{'brywkb_time'}.calendar = ncchar('360.0 days in every year');
-nc{'brywkb_time'}.calendar = '360.0 days in every year';
-nc{'brywkb_time'}.cycle_length = cycle;
-%
+write_time_attributes(nc,'brywkb_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
+
if wkb_obc(1)==1
%
% Southern boundary
diff --git a/Preprocessing_tools/create_bulk.m b/Preprocessing_tools/create_bulk.m
index 1ef47816..e7783e5c 100644
--- a/Preprocessing_tools/create_bulk.m
+++ b/Preprocessing_tools/create_bulk.m
@@ -1,4 +1,4 @@
-function create_bulk(frcname,grdname,title,bulkt,bulkc)
+function create_bulk(frcname,grdname,title,bulkt,bulkc,Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf heat flux bulk forcing file
@@ -39,10 +39,20 @@ M=length(nc('eta_psi'));
close(nc);
Lp=L+1;
Mp=M+1;
-
+%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
nw = netcdf(frcname, 'clobber');
%result = redef(nw);
-
%
% Create dimensions
%
@@ -61,9 +71,8 @@ nw('bulk_time') = 0;
nw{'bulk_time'} = ncdouble('bulk_time');
nw{'bulk_time'}.long_name = ncchar('bulk formulation execution time');
nw{'bulk_time'}.long_name = 'bulk formulation execution time';
-nw{'bulk_time'}.units = ncchar('days');
-nw{'bulk_time'}.units = 'days';
-nw{'bulk_time'}.cycle_length = bulkc;
+write_time_attributes(nc,'bulk_time',bulkc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'tair'} = ncdouble('bulk_time', 'eta_rho', 'xi_rho');
nw{'tair'}.long_name = ncchar('surface air temperature');
diff --git a/Preprocessing_tools/create_climfile.m b/Preprocessing_tools/create_climfile.m
index 7e2bee7a..617d1de9 100644
--- a/Preprocessing_tools/create_climfile.m
+++ b/Preprocessing_tools/create_climfile.m
@@ -1,39 +1,39 @@
function create_climfile(clmname,grdname,title,...
- theta_s,theta_b,hc,N,...
- time,cycle,clobber,vtransform);
+ theta_s,theta_b,hc,N,...
+ time,cycle,clobber,vtransform, Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function create_climfile(clmname,grdname,title,...
% theta_s,theta_b,hc,N,...
% time,cycle,clobber);
%
-% This function create the header of a Netcdf climatology
+% This function create the header of a Netcdf climatology
% file.
%
% Input:
%
% clmname Netcdf climatology file name (character string).
% grdname Netcdf grid file name (character string).
-% theta_s S-coordinate surface control parameter.(Real)
+% theta_s S-coordinate surface control parameter.(Real)
% theta_b S-coordinate bottom control parameter.(Real)
% hc Width (m) of surface or bottom boundary layer
% where higher vertical resolution is required
-% during stretching.(Real)
-% N Number of vertical levels.(Integer)
-% time Temperature climatology time.(vector)
+% during stretching.(Real)
+% N Number of vertical levels.(Integer)
+% time Temperature climatology time.(vector)
% time Salinity climatology time.(vector)
% time Velocity climatology time.(vector)
% cycle Length (days) for cycling the climatology.(Real)
-% clobber Switch to allow or not writing over an existing
+% clobber Switch to allow or not writing over an existing
% file.(character string)
%
% Output
%
% nc Output netcdf object.
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -51,20 +51,32 @@ function create_climfile(clmname,grdname,title,...
% 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
+% Copyright (c) 2001-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp(' ')
disp([' Creating the file : ',clmname])
disp(' ')
if nargin < 11
- disp([' NO VTRANSFORM parameter found'])
- disp([' USE TRANSFORM default value vtransform = 1'])
- vtransform = 1;
+ disp([' NO VTRANSFORM parameter found'])
+ disp([' USE TRANSFORM default value vtransform = 1'])
+ vtransform = 1;
end
disp([' VTRANSFORM = ',num2str(vtransform)])
%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read the grid file
%
nc = netcdf(grdname, 'nowrite');
@@ -75,9 +87,9 @@ Mp=length(nc('eta_rho'));
close(nc);
hmin=min(min(h(maskr==1)));
if vtransform ==1;
- if hc > hmin
- error([' hc (',num2str(hc),' m) > hmin (',num2str(hmin),' m)'])
- end
+ if hc > hmin
+ error([' hc (',num2str(hc),' m) > hmin (',num2str(hmin),' m)'])
+ end
end
L=Lp-1;
M=Mp-1;
@@ -85,7 +97,7 @@ Np=N+1;
%
% Create the climatology file
%
-type = 'CLIMATOLOGY file' ;
+type = 'CLIMATOLOGY file' ;
history = 'CROCO' ;
nc = netcdf(clmname,clobber);
% result = redef(nc);
@@ -164,13 +176,13 @@ nc{'spherical'}.flag_meanings = 'spherical Cartesian';
%
nc{'tstart'}.long_name = ncchar('start processing day');
nc{'tstart'}.long_name = 'start processing day';
-nc{'tstart'}.units = ncchar('day');
-nc{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'tend'}.long_name = ncchar('end processing day');
nc{'tend'}.long_name = 'end processing day';
-nc{'tend'}.units = ncchar('day');
-nc{'tend'}.units = 'day';
+write_time_attributes(nc,'tend',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'theta_s'}.long_name = ncchar('S-coordinate surface control parameter');
nc{'theta_s'}.long_name = 'S-coordinate surface control parameter';
@@ -203,7 +215,7 @@ if (vtransform ==1)
nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g1';
elseif (vtransform ==2)
nc{'s_rho'}.standard_name = ncchar('ocean_s_coordinate_g2');
- nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g2';
+ nc{'s_rho'}.standard_name = 'ocean_s_coordinate_g2';
end
nc{'s_rho'}.formula_terms = ncchar('s: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc');
nc{'s_rho'}.formula_terms = 's: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc';
@@ -240,83 +252,53 @@ nc{'Cs_w'}.valid_max = 0;
%
nc{'tclm_time'}.long_name = ncchar('time for temperature climatology');
nc{'tclm_time'}.long_name = 'time for temperature climatology';
-nc{'tclm_time'}.units = ncchar('day');
-nc{'tclm_time'}.units = 'day';
-nc{'tclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'tclm_time'}.calendar = '360.0 days in every year';
-nc{'tclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'tclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'temp_time'}.long_name = ncchar('time for temperature climatology');
nc{'temp_time'}.long_name = 'time for temperature climatology';
-nc{'temp_time'}.units = ncchar('day');
-nc{'temp_time'}.units = 'day';
-nc{'temp_time'}.calendar = ncchar('360.0 days in every year');
-nc{'temp_time'}.calendar = '360.0 days in every year';
-nc{'temp_time'}.cycle_length = cycle;
+write_time_attributes(nc,'temp_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'sclm_time'}.long_name = ncchar('time for salinity climatology');
nc{'sclm_time'}.long_name = 'time for salinity climatology';
-nc{'sclm_time'}.units = ncchar('day');
-nc{'sclm_time'}.units = 'day';
-nc{'sclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'sclm_time'}.calendar = '360.0 days in every year';
-nc{'sclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'sclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'salt_time'}.long_name = ncchar('time for salinity climatology');
nc{'salt_time'}.long_name = 'time for salinity climatology';
-nc{'salt_time'}.units = ncchar('day');
-nc{'salt_time'}.units = 'day';
-nc{'salt_time'}.calendar = ncchar('360.0 days in every year');
-nc{'salt_time'}.calendar = '360.0 days in every year';
-nc{'salt_time'}.cycle_length = cycle;
+write_time_attributes(nc,'salt_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'uclm_time'}.long_name = ncchar('time climatological u');
nc{'uclm_time'}.long_name = 'time climatological u';
-nc{'uclm_time'}.units = ncchar('day');
-nc{'uclm_time'}.units = 'day';
-nc{'uclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'uclm_time'}.calendar = '360.0 days in every year';
-nc{'uclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'uclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'vclm_time'}.long_name = ncchar('time climatological v');
nc{'vclm_time'}.long_name = 'time climatological v';
-nc{'vclm_time'}.units = ncchar('day');
-nc{'vclm_time'}.units = 'day';
-nc{'vclm_time'}.calendar = ncchar('360.0 days in every year');
-nc{'vclm_time'}.calendar = '360.0 days in every year';
-nc{'vclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'vclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v2d_time'}.long_name = ncchar('time for 2D velocity climatology');
nc{'v2d_time'}.long_name = 'time for 2D velocity climatology';
-nc{'v2d_time'}.units = ncchar('day');
-nc{'v2d_time'}.units = 'day';
-nc{'v2d_time'}.calendar = ncchar('360.0 days in every year');
-nc{'v2d_time'}.calendar = '360.0 days in every year';
-nc{'v2d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v2d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v3d_time'}.long_name = ncchar('time for 3D velocity climatology');
nc{'v3d_time'}.long_name = 'time for 3D velocity climatology';
-nc{'v3d_time'}.units = ncchar('day');
-nc{'v3d_time'}.units = 'day';
-nc{'v3d_time'}.calendar = ncchar('360.0 days in every year');
-nc{'v3d_time'}.calendar = '360.0 days in every year';
-nc{'v3d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v3d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'ssh_time'}.long_name = ncchar('time for sea surface height');
nc{'ssh_time'}.long_name = 'time for sea surface height';
-nc{'ssh_time'}.units = ncchar('day');
-nc{'ssh_time'}.units = 'day';
-nc{'ssh_time'}.calendar = ncchar('360.0 days in every year');
-nc{'ssh_time'}.calendar = '360.0 days in every year';
-nc{'ssh_time'}.cycle_length = cycle;
+write_time_attributes(nc,'ssh_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'zeta_time'}.long_name = ncchar('time for sea surface height');
nc{'zeta_time'}.long_name = 'time for sea surface height';
-nc{'zeta_time'}.units = ncchar('day');
-nc{'zeta_time'}.units = 'day';
-nc{'zeta_time'}.calendar = ncchar('360.0 days in every year');
-nc{'zeta_time'}.calendar = '360.0 days in every year';
-nc{'zeta_time'}.cycle_length = cycle;
+write_time_attributes(nc,'zeta_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'temp'}.long_name = ncchar('potential temperature');
nc{'temp'}.long_name = 'potential temperature';
@@ -412,52 +394,40 @@ nc.history = history;
% Set S-Curves in domain [-1 < sc < 0] at vertical W- and RHO-points.
%
[s_rho,Cs_rho,s_w,Cs_w] = scoordinate(theta_s,theta_b,N,hc,vtransform);
-%disp(['vtransform=',num2str(vtransform)])
-
-% cff1=1./sinh(theta_s);
-% cff2=0.5/tanh(0.5*theta_s);
-% s_rho=((1:N)-N-0.5)/N;
-% Cs_rho=(1.-theta_b)*cff1*sinh(theta_s*s_rho)...
-% +theta_b*(cff2*tanh(theta_s*(s_rho+0.5))-0.5);
-% s_w=((0:N)-N)/N;
-% Cs_w=(1.-theta_b)*cff1*sinh(theta_s*s_w)...
-% +theta_b*(cff2*tanh(theta_s*(s_w+0.5))-0.5);
-
-
%
% Write variables
%
nc{'spherical'}(:)='T';
nc{'Vtransform'}(:)=vtransform;
nc{'Vstretching'}(:)=1;
-nc{'tstart'}(:) = min([min(time) min(time) min(time)]);
-nc{'tend'}(:) = max([max(time) max(time) max(time)]);
-nc{'theta_s'}(:) = theta_s;
-nc{'theta_b'}(:) = theta_b;
-nc{'Tcline'}(:) = hc;
-nc{'hc'}(:) = hc;
+nc{'tstart'}(:) = min([min(time) min(time) min(time)]);
+nc{'tend'}(:) = max([max(time) max(time) max(time)]);
+nc{'theta_s'}(:) = theta_s;
+nc{'theta_b'}(:) = theta_b;
+nc{'Tcline'}(:) = hc;
+nc{'hc'}(:) = hc;
nc{'s_rho'}(:) = s_rho;
nc{'s_w'}(:) = s_w;
-nc{'Cs_rho'}(:) = Cs_rho;
+nc{'Cs_rho'}(:) = Cs_rho;
nc{'Cs_w'}(:) = Cs_w;
-nc{'tclm_time'}(:) = time;
-nc{'temp_time'}(:) = time;
-nc{'sclm_time'}(:) = time;
-nc{'salt_time'}(:) = time;
-nc{'uclm_time'}(:) = time;
-nc{'vclm_time'}(:) = time;
-nc{'v2d_time'}(:) = time;
-nc{'v3d_time'}(:) = time;
+nc{'tclm_time'}(:) = time;
+nc{'temp_time'}(:) = time;
+nc{'sclm_time'}(:) = time;
+nc{'salt_time'}(:) = time;
+nc{'uclm_time'}(:) = time;
+nc{'vclm_time'}(:) = time;
+nc{'v2d_time'}(:) = time;
+nc{'v3d_time'}(:) = time;
nc{'ssh_time'}(:) = time;
nc{'zeta_time'}(:) = time;
-nc{'u'}(:) = 0;
-nc{'v'}(:) = 0;
-nc{'ubar'}(:) = 0;
-nc{'vbar'}(:) = 0;
-nc{'SSH'}(:) = 0;
-nc{'zeta'}(:) = 0;
-nc{'temp'}(:) = 0;
-nc{'salt'}(:) = 0;
+nc{'u'}(:) = 0;
+nc{'v'}(:) = 0;
+nc{'ubar'}(:) = 0;
+nc{'vbar'}(:) = 0;
+nc{'SSH'}(:) = 0;
+nc{'zeta'}(:) = 0;
+nc{'temp'}(:) = 0;
+nc{'salt'}(:) = 0;
close(nc)
return
diff --git a/Preprocessing_tools/create_forcing.m b/Preprocessing_tools/create_forcing.m
index 624c2de9..f56963d0 100644
--- a/Preprocessing_tools/create_forcing.m
+++ b/Preprocessing_tools/create_forcing.m
@@ -1,6 +1,6 @@
function create_forcing(frcname,grdname,title,smst,...
shft,swft,srft,sstt,ssst,smsc,...
- shfc,swfc,srfc,sstc,sssc)
+ shfc,swfc,srfc,sstc,sssc, Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf forcing file
@@ -38,7 +38,18 @@ M=length(nc('eta_psi'));
close(nc);
Lp=L+1;
Mp=M+1;
-
+%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
nw = netcdf(frcname, 'clobber');
%result = redef(nw);
@@ -67,52 +78,44 @@ nw('wwv_time') = length(smst);
nw{'sms_time'} = ncdouble('sms_time');
nw{'sms_time'}.long_name = ncchar('surface momentum stress time');
nw{'sms_time'}.long_name = 'surface momentum stress time';
-nw{'sms_time'}.units = ncchar('days');
-nw{'sms_time'}.units = 'days';
-nw{'sms_time'}.cycle_length = smsc;
+write_time_attributes(nc,'sms_time',smsc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'shf_time'} = ncdouble('shf_time');
nw{'shf_time'}.long_name = ncchar('surface heat flux time');
nw{'shf_time'}.long_name = 'surface heat flux time';
-nw{'shf_time'}.units = ncchar('days');
-nw{'shf_time'}.units = 'days';
-nw{'shf_time'}.cycle_length =shfc ;
+write_time_attributes(nc,'shf_time',shfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'swf_time'} = ncdouble('swf_time');
nw{'swf_time'}.long_name = ncchar('surface freshwater flux time');
nw{'swf_time'}.long_name = 'surface freshwater flux time';
-nw{'swf_time'}.units = ncchar('days');
-nw{'swf_time'}.units = 'days';
-nw{'swf_time'}.cycle_length = swfc;
+write_time_attributes(nc,'swf_time',swfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'sst_time'} = ncdouble('sst_time');
nw{'sst_time'}.long_name = ncchar('sea surface temperature time');
nw{'sst_time'}.long_name = 'sea surface temperature time';
-nw{'sst_time'}.units = ncchar('days');
-nw{'sst_time'}.units = 'days';
-nw{'sst_time'}.cycle_length = sstc;
+write_time_attributes(nc,'sst_time',sstc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'sss_time'} = ncdouble('sss_time');
nw{'sss_time'}.long_name = ncchar('sea surface salinity time');
nw{'sss_time'}.long_name = 'sea surface salinity time';
-nw{'sss_time'}.units = ncchar('days');
-nw{'sss_time'}.units = 'days';
-nw{'sss_time'}.cycle_length = sssc;
+write_time_attributes(nc,'sss_time',sssc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'srf_time'} = ncdouble('srf_time');
nw{'srf_time'}.long_name = ncchar('solar shortwave radiation time');
nw{'srf_time'}.long_name = 'solar shortwave radiation time';
-nw{'srf_time'}.units = ncchar('days');
-nw{'srf_time'}.units = 'days';
-nw{'srf_time'}.cycle_length = srfc;
+write_time_attributes(nc,'srf_time',srfc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'wwv_time'} = ncdouble('wwv_time');
nw{'wwv_time'}.long_name = ncchar('surface wave fields time');
nw{'wwv_time'}.long_name = 'surface wave fields time';
-nw{'wwv_time'}.units = ncchar('days');
-nw{'wwv_time'}.units = 'days';
-nw{'wwv_time'}.cycle_length = smsc;
-
+write_time_attributes(nc,'wwv_time',smsc,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
nw{'sustr'} = ncdouble('sms_time', 'eta_u', 'xi_u');
nw{'sustr'}.long_name = ncchar('surface u-momentum stress');
diff --git a/Preprocessing_tools/create_inifile.m b/Preprocessing_tools/create_inifile.m
index acdc9abc..265bb410 100644
--- a/Preprocessing_tools/create_inifile.m
+++ b/Preprocessing_tools/create_inifile.m
@@ -1,5 +1,6 @@
function create_inifile(inifile,gridfile,title,...
- theta_s,theta_b,hc,N,time,clobber,vtransform)
+ theta_s,theta_b,hc,N,time,clobber,vtransform,...
+ Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function nc=create_inifile(inifile,gridfile,theta_s,...
@@ -53,12 +54,24 @@ function create_inifile(inifile,gridfile,title,...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp(' ')
disp([' Creating the file : ',inifile])
+
if nargin < 10
disp([' NO VTRANSFORM parameter found'])
disp([' USE TRANSFORM default value vtransform = 1'])
vtransform = 1;
+ disp([' VTRANSFORM = ',num2str(vtransform)])
end
-disp([' VTRANSFORM = ',num2str(vtransform)])
+%
+% options for write_time_attributes
+insecond = 1 ;
+add_cycle = 0 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = []; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
%
% Read the grid file
%
@@ -131,13 +144,13 @@ nc{'Vstretching'}.long_name = 'vertical terrain-following stretching function';
%
nc{'tstart'}.long_name = ncchar('start processing day');
nc{'tstart'}.long_name = 'start processing day';
-nc{'tstart'}.units = ncchar('day');
-nc{'tstart'}.units = 'day';
+write_time_attributes(nc,'tstart','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'tend'}.long_name = ncchar('end processing day');
nc{'tend'}.long_name = 'end processing day';
-nc{'tend'}.units = ncchar('day');
-nc{'tend'}.units = 'day';
+write_time_attributes(nc,'tend','',time_unit_att,time_second_unit_att,...
+ calendar_att,0,0);
%
nc{'theta_s'}.long_name = ncchar('S-coordinate surface control parameter');
nc{'theta_s'}.long_name = 'S-coordinate surface control parameter';
@@ -175,13 +188,13 @@ nc{'Cs_rho'}.valid_max = 0;
%
nc{'ocean_time'}.long_name = ncchar('time since initialization');
nc{'ocean_time'}.long_name = 'time since initialization';
-nc{'ocean_time'}.units = ncchar('second');
-nc{'ocean_time'}.units = 'second';
-%
+write_time_attributes(nc,'ocean_time','',time_unit_att,time_second_unit_att,...
+ calendar_att,1,0);
+
nc{'scrum_time'}.long_name = ncchar('time since initialization');
nc{'scrum_time'}.long_name = 'time since initialization';
-nc{'scrum_time'}.units = ncchar('second');
-nc{'scrum_time'}.units = 'second';
+write_time_attributes(nc,'scrum_time','',time_unit_att,time_second_unit_att,...
+ calendar_att,1,0);
%
nc{'u'}.long_name = ncchar('u-momentum component');
nc{'u'}.long_name = 'u-momentum component';
diff --git a/Preprocessing_tools/create_oafile.m b/Preprocessing_tools/create_oafile.m
index 875e1cd8..7b765817 100644
--- a/Preprocessing_tools/create_oafile.m
+++ b/Preprocessing_tools/create_oafile.m
@@ -1,5 +1,5 @@
function create_oafile(oaname,grdname,title,Z,...
- time,cycle,clobber);
+ time,cycle,clobber,Yorig);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% function nc=create_oafile(oaname,grdname,title,Z,...
@@ -49,6 +49,18 @@ disp(' ')
disp([' Creating the file : ',oaname])
disp(' ')
%
+% options for write_time_attributes
+insecond = 0;
+add_cycle = 1 ;
+%
+% Initialize Yorig if not provided
+if ~exist('Yorig', 'var') , Yorig = [] ; , end
+%
+% Get time attributes
+[time_unit_att,time_second_unit_att,calendar_att]=...
+ get_time_attributes(Yorig);
+%
+%
% Read the grid file
%
nc = netcdf(grdname, 'nowrite');
@@ -153,51 +165,43 @@ nc{'Z'}.units = 'm';
%
nc{'tclm_time'}.long_name = ncchar('time for temperature climatology');
nc{'tclm_time'}.long_name = 'time for temperature climatology';
-nc{'tclm_time'}.units = ncchar('day');
-nc{'tclm_time'}.units = 'day';
-nc{'tclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'tclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'sclm_time'}.long_name = ncchar('time for salinity climatology');
nc{'sclm_time'}.long_name = 'time for salinity climatology';
-nc{'sclm_time'}.units = ncchar('day');
-nc{'sclm_time'}.units = 'day';
-nc{'sclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'sclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'uclm_time'}.long_name = ncchar('time for u climatology');
nc{'uclm_time'}.long_name = 'time for u climatology';
-nc{'uclm_time'}.units = ncchar('day');
-nc{'uclm_time'}.units = 'day';
-nc{'uclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'uclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'vclm_time'}.long_name = ncchar('time for v climatology');
nc{'vclm_time'}.long_name = 'time for v climatology';
-nc{'vclm_time'}.units = ncchar('day');
-nc{'vclm_time'}.units = 'day';
-nc{'vclm_time'}.cycle_length = cycle;
+write_time_attributes(nc,'vclm_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v2d_time'}.long_name = ncchar('time for 2D velocity climatology');
nc{'v2d_time'}.long_name = 'time for 2D velocity climatology';
-nc{'v2d_time'}.units = ncchar('day');
-nc{'v2d_time'}.units = 'day';
-nc{'v2d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v2d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'v3d_time'}.long_name = ncchar('time for 3D velocity climatology');
nc{'v3d_time'}.long_name = 'time for 3D velocity climatology';
-nc{'v3d_time'}.units = ncchar('day');
-nc{'v3d_time'}.units = 'day';
-nc{'v3d_time'}.cycle_length = cycle;
+write_time_attributes(nc,'v3d_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'ssh_time'}.long_name = ncchar('time for sea surface height');
nc{'ssh_time'}.long_name = 'time for sea surface height';
-nc{'ssh_time'}.units = ncchar('day');
-nc{'ssh_time'}.units = 'day';
-nc{'ssh_time'}.cycle_length = cycle;
+write_time_attributes(nc,'ssh_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'zeta_time'}.long_name = ncchar('time for zeta climatology');
nc{'zeta_time'}.long_name = 'time for zeta climatology';
-nc{'zeta_time'}.units = ncchar('day');
-nc{'zeta_time'}.units = 'day';
-nc{'zeta_time'}.cycle_length = cycle;
+write_time_attributes(nc,'zeta_time',cycle,time_unit_att,time_second_unit_att,...
+ calendar_att,insecond,add_cycle);
%
nc{'temp'}.long_name = ncchar('potential temperature');
nc{'temp'}.long_name = 'potential temperature';
diff --git a/Preprocessing_tools/get_time_attributes.m b/Preprocessing_tools/get_time_attributes.m
new file mode 100644
index 00000000..5d1ca468
--- /dev/null
+++ b/Preprocessing_tools/get_time_attributes.m
@@ -0,0 +1,29 @@
+function [time_unit_att, time_second_unit_att, calendar_att] = ...
+ get_time_attributes(Yorig) ;
+
+ % GET_TIME_ATTRIBUTES Get time and calendar attributes for CROCO NetCDF files
+ %
+ % Inputs:
+ % Yorig - Reference year (optional) for time origin
+ %
+ % Outputs:
+ % time_unit_att - Time unit attribute string
+ % calendar_att - Calendar type attribute string
+
+ % Initialize default values
+ time_unit_att = 'days';
+ time_second_unit_att = 'seconds';
+ calendar_att = 'none';
+
+ % Check if valid Yorig is provided
+ % if nargin >= 1 && ~isempty(Yorig)
+ if ~isempty(Yorig)
+ disp([' Time reference is ', sprintf('%04d', Yorig), '-01-01 00:00:00'])
+ time_unit_att = ['days since ', sprintf('%04d', Yorig), '-01-01 00:00:00'];
+ time_second_unit_att = ['seconds since ',sprintf('%04d', Yorig),'-01-01 00:00:00'];
+ calendar_att = 'proleptic_gregorian';
+ else
+ disp(' No time reference')
+ end
+
+end
\ No newline at end of file
diff --git a/Preprocessing_tools/make_bry.m b/Preprocessing_tools/make_bry.m
index 92b8dfa4..709a88e3 100644
--- a/Preprocessing_tools/make_bry.m
+++ b/Preprocessing_tools/make_bry.m
@@ -60,10 +60,10 @@ crocotools_param
% salt_month_data : monthly salinity climatology
% salt_ann_data : annual salinity climatology
%
-temp_month_data=[climato_dir,'temp_month.cdf']
-temp_ann_data=[climato_dir,'temp_ann.cdf']
-salt_month_data=[climato_dir,'salt_month.cdf']
-salt_ann_data=[climato_dir,'salt_ann.cdf']
+temp_month_data=[climato_dir,'temp_month.cdf'];
+temp_ann_data=[climato_dir,'temp_ann.cdf'];
+salt_month_data=[climato_dir,'salt_month.cdf'];
+salt_ann_data=[climato_dir,'salt_ann.cdf'];
%
%
%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Preprocessing_tools/make_clim.m b/Preprocessing_tools/make_clim.m
index daf515f5..6709dd1f 100644
--- a/Preprocessing_tools/make_clim.m
+++ b/Preprocessing_tools/make_clim.m
@@ -169,29 +169,29 @@ end
-%----------------------------------------------------------------------------
-% Initial file
-%----------------------------------------------------------------------------
-if (makeini)
-
- disp('======================== ')
- disp('Initial')
- create_inifile(ininame,grdname,CROCO_title,...
- theta_s,theta_b,hc,N,...
- tini,'clobber',vtransform);
- disp(' ')
- disp(' Temperature...')
- vinterp_clm(ininame,grdname,oaname,'temp','tclm_time','Z',tini,'r',1);
- disp(' ')
- disp(' Salinity...')
- vinterp_clm(ininame,grdname,oaname,'salt','sclm_time','Z',tini,'r',1);
- if (insitu2pot)
- disp(' ')
- disp(' Compute potential temperature from in-situ...')
- getpot(ininame,grdname)
- end
-
-end
+% %----------------------------------------------------------------------------
+% % Initial file
+% %----------------------------------------------------------------------------
+% if (makeini)
+
+% disp('======================== ')
+% disp('Initial')
+% create_inifile(ininame,grdname,CROCO_title,...
+% theta_s,theta_b,hc,N,...
+% tini,'clobber',vtransform);
+% disp(' ')
+% disp(' Temperature...')
+% vinterp_clm(ininame,grdname,oaname,'temp','tclm_time','Z',tini,'r',1);
+% disp(' ')
+% disp(' Salinity...')
+% vinterp_clm(ininame,grdname,oaname,'salt','sclm_time','Z',tini,'r',1);
+% if (insitu2pot)
+% disp(' ')
+% disp(' Compute potential temperature from in-situ...')
+% getpot(ininame,grdname)
+% end
+
+% end
diff --git a/Preprocessing_tools/nc_add_globatt.m b/Preprocessing_tools/nc_add_globatt.m
index 1b244761..67d800c6 100644
--- a/Preprocessing_tools/nc_add_globatt.m
+++ b/Preprocessing_tools/nc_add_globatt.m
@@ -30,7 +30,9 @@ if nargin < 8
product = 'unknown'
end
%
-origin_date = datestr(datenum(Yorig,Mmin,Dmin,Hmin,Min_min,Smin),0);
+%origin_date = datestr(datenum(Yorig,Mmin,Dmin,Hmin,Min_min,Smin),0);
+origin_date = char(datetime(Yorig,Mmin,Dmin,Hmin,Min_min,Smin, 'Format', 'yyyy-MM-dd HH:mm:ss'));
+
%
nc=netcdf(filename,'write');
nc.origin_date = origin_date;
diff --git a/Preprocessing_tools/vinterp_bry.m b/Preprocessing_tools/vinterp_bry.m
index de614f7d..3606af22 100644
--- a/Preprocessing_tools/vinterp_bry.m
+++ b/Preprocessing_tools/vinterp_bry.m
@@ -3,10 +3,10 @@ function vinterp_bry(bryname,grdname,Zbryname,vname,obcndx)
%
% Vertical interpolation from a Z-grid to a sigma-grid in the
% case of boundary (bry) files.
-%
-% Further Information:
+%
+% Further Information:
% http://www.croco-ocean.org
-%
+%
% This file is part of CROCOTOOLS
%
% CROCOTOOLS is free software; you can redistribute it and/or modify
@@ -24,13 +24,13 @@ function vinterp_bry(bryname,grdname,Zbryname,vname,obcndx)
% 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
+% Copyright (c) 2005-2006 by Pierrick Penven
+% e-mail:Pierrick.Penven@ird.fr
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% open the grid file
-%
+% open the grid file
+%
ng=netcdf(grdname,'r');
L=length(ng('xi_rho'));
M=length(ng('eta_rho'));
@@ -45,8 +45,8 @@ elseif obcndx==4
end
close(ng);
%
-% open the boundary file
-%
+% open the boundary file
+%
nc=netcdf(bryname,'write');
theta_s = nc{'theta_s'}(:);
theta_b = nc{'theta_b'}(:);
@@ -54,14 +54,14 @@ 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 VTRANSFORM default value vtransform = 1'])
+ vtransform=1; %Old Vtransform
+ disp([' NO VTRANSFORM parameter found'])
+ disp([' USE VTRANSFORM default value vtransform = 1'])
end
%
-% open the oa file
-%
- noa=netcdf(Zbryname,'r');
+% open the oa file
+%
+noa=netcdf(Zbryname,'r');
z=-noa{'Z'}(:);
t=noa{'bry_time'}(:);
tlen=length(t);
@@ -73,16 +73,16 @@ 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
+% 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];
+ z=[100;z];
end
if addbot
- z=[z;-100000];
+ z=[z;-100000];
end
Nz=min(find(z<zmin));
z=z(1:Nz);
@@ -90,10 +90,9 @@ z=z(1:Nz);
% loop on time
%
for l=1:tlen
-%for l=1:1
-% disp([' Time index: ',num2str(l),' of total: ',num2str(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
@@ -105,27 +104,4 @@ for l=1:tlen
end
close(nc);
close(noa);
-
-
-%DEBUG
-%
-%size(var)
-%var
-%
-%size(flipdim(var,1))
-%flipdim(var,1)
-%
-%size(z)
-%z
-%
-%size(flipud(z))
-%flipud(z)
-%
-%size(zcroco)
-%zcroco
-%
-%size(ztosigma_1d(flipdim(var,1),zcroco,flipud(z)))
-%
-%
-%%
return
diff --git a/Preprocessing_tools/write_time_attributes.m b/Preprocessing_tools/write_time_attributes.m
new file mode 100644
index 00000000..cdd646b7
--- /dev/null
+++ b/Preprocessing_tools/write_time_attributes.m
@@ -0,0 +1,29 @@
+function write_time_attributes(nc,time_name,cycle,...
+ time_unit_att,...
+ time_second_unit_att, ...
+ calendar_att, ...
+ insecond,...
+ add_cycle) ;
+ %-----------------------------------------------------------------------
+ % Inputs:
+ % time_unit_att : Time unit attribute string,
+ % used by default for time units
+ % time_second_unit_att : Time unit attribute string
+ % calendar_att : Calendar type attribute string
+ % insecond : optional, switch to have time units in seconds
+ %-----------------------------------------------------------------------
+
+ nc{time_name}.calendar = calendar_att;
+ %
+ if exist('insecond', 'var') && insecond == 1
+ nc{time_name}.units = time_second_unit_att;
+ else
+ nc{time_name}.units = time_unit_att;
+ end
+ %
+ %Add cycle attribute
+ if exist('add_cycle', 'var') && add_cycle == 1
+ nc{time_name}.cycle_length = cycle ;
+ end
+
+end
\ No newline at end of file
diff --git a/Rivers/create_runoff.m b/Rivers/create_runoff.m
index 4cedbe46..878a083b 100644
--- a/Rivers/create_runoff.m
+++ b/Rivers/create_runoff.m
@@ -1,6 +1,7 @@
function create_runoff(runoffname,grdname,title,...
qbart,qbarc,rivername,rivernumber,...
- runoffname_StrLen,dir,psource_ncfile_ts,biol,pisces,quota)
+ runoffname_StrLen,dir,psource_ncfile_ts,...
+ biol,pisces,quota, Yorig)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Create an empty netcdf runoff file
@@ -27,14 +28,25 @@ function create_runoff(runoffname,grdname,title,...
% MA 02111-1307 USA
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+timeref = 1 ;
+if nargin < 14
+ disp([' Yorig parameter found'])
+ disp([' No time reference'])
+ timeref = 0 ;
+end
+if timeref == 1
+ time_unit_att = ['days since ',sprintf('%04d', Yorig),'-01-01 00:00:00'];
+ calendar_att = 'proleptic_gregorian' ;
+else
+ time_unit_att = ['days'];
+ calendar_att = 'climatological year' ;
+end
+%
nw=netcdf(runoffname,'clobber');
%%%result = redef(nw);
-
-
%
% Create dimensions
%
-
nw('qbar_time') = length(qbart);
nw('n_qbar') = rivernumber;
nw('runoffname_StrLen') = runoffname_StrLen;
@@ -45,18 +57,21 @@ nw('two') = 2;
%
nw{'qbar_time'} = ncdouble('qbar_time');
nw{'qbar_time'}.long_name = ncchar('runoff time');
-nw{'qbar_time'}.units = ncchar('days');
+nw{'qbar_time'}.units = ncchar(time_unit_att);
+nw{'qbar_time'}.calendar = calendar_att;
nw{'qbar_time'}.cycle_length = qbarc;
if psource_ncfile_ts
nw{'temp_src_time'} = ncdouble('qbar_time');
nw{'temp_src_time'}.long_name = ncchar('runoff time');
- nw{'temp_src_time'}.units = ncchar('days');
+ nw{'temp_src_time'}.units = ncchar(time_unit_att);
+ nw{'temp_src_time'}.calendar = calendar_att;
nw{'temp_src_time'}.cycle_length = qbarc;
nw{'salt_src_time'} = ncdouble('qbar_time');
nw{'salt_src_time'}.long_name = ncchar('runoff time');
- nw{'salt_src_time'}.units = ncchar('days');
+ nw{'salt_src_time'}.units = ncchar(time_unit_att);
+ nw{'salt_src_time'}.calendar = calendar_att;
nw{'salt_src_time'}.cycle_length = qbarc;
end
nw{'runoff_name'} = ncchar('n_qbar','runoffname_StrLen');
@@ -86,7 +101,8 @@ if psource_ncfile_ts
if biol
nw{'no3_src_time'} = ncdouble('qbar_time');
nw{'no3_src_time'}.long_name = ncchar('runoff time');
- nw{'no3_src_time'}.units = ncchar('days');
+ nw{'no3_src_time'}.units = ncchar(time_unit_att);
+ nw{'no3_src_time'}.calendar = calendar_att;
nw{'no3_src_time'}.cycle_length = 360;
nw{'NO3_src'} = ncdouble('n_qbar','qbar_time');
@@ -95,7 +111,8 @@ if psource_ncfile_ts
if pisces
nw{'po4_src_time'} = ncdouble('qbar_time');
nw{'po4_src_time'}.long_name = ncchar('runoff time');
- nw{'po4_src_time'}.units = ncchar('days');
+ nw{'po4_src_time'}.units = ncchar(time_unit_att);
+ nw{'po4_src_time'}.calendar = calendar_att;
nw{'po4_src_time'}.cycle_length = 360;
nw{'PO4_src'} = ncdouble('n_qbar','qbar_time');
@@ -104,7 +121,8 @@ if psource_ncfile_ts
nw{'si_src_time'} = ncdouble('qbar_time');
nw{'si_src_time'}.long_name = ncchar('runoff time');
- nw{'si_src_time'}.units = ncchar('days');
+ nw{'si_src_time'}.units = ncchar(time_unit_att);
+ nw{'si_src_time'}.calendar = calendar_att;
nw{'si_src_time'}.cycle_length = 360;
nw{'Si_src'} = ncdouble('n_qbar','qbar_time');
@@ -113,7 +131,8 @@ if psource_ncfile_ts
nw{'dic_src_time'} = ncdouble('qbar_time');
nw{'dic_src_time'}.long_name = ncchar('runoff time');
- nw{'dic_src_time'}.units = ncchar('days');
+ nw{'dic_src_time'}.units = ncchar(time_unit_att);
+ nw{'dic_src_time'}.calendar = calendar_att;
nw{'dic_src_time'}.cycle_length = 360;
nw{'DIC_src'} = ncdouble('n_qbar','qbar_time');
@@ -122,7 +141,8 @@ if psource_ncfile_ts
nw{'doc_src_time'} = ncdouble('qbar_time');
nw{'doc_src_time'}.long_name = ncchar('runoff time');
- nw{'doc_src_time'}.units = ncchar('days');
+ nw{'doc_src_time'}.units = ncchar(time_unit_att);
+ nw{'doc_src_time'}.calendar = calendar_att;
nw{'doc_src_time'}.cycle_length = 360;
nw{'DOC_src'} = ncdouble('n_qbar','qbar_time');
@@ -131,7 +151,8 @@ if psource_ncfile_ts
nw{'talk_src_time'} = ncdouble('qbar_time');
nw{'talk_src_time'}.long_name = ncchar('runoff time');
- nw{'talk_src_time'}.units = ncchar('days');
+ nw{'talk_src_time'}.units = ncchar(time_unit_att);
+ nw{'talk_src_time'}.calendar = calendar_att;
nw{'talk_src_time'}.cycle_length = 360;
nw{'TALK_src'} = ncdouble('n_qbar','qbar_time');
@@ -140,7 +161,8 @@ if psource_ncfile_ts
if quota
nw{'don_src_time'} = ncdouble('qbar_time');
nw{'don_src_time'}.long_name = ncchar('runoff time');
- nw{'don_src_time'}.units = ncchar('days');
+ nw{'don_src_time'}.units = ncchar(time_unit_att);
+ nw{'don_src_time'}.calendar = calendar_att;
nw{'don_src_time'}.cycle_length = 360;
nw{'DON_src'} = ncdouble('n_qbar','qbar_time');
@@ -149,7 +171,8 @@ if psource_ncfile_ts
nw{'dop_src_time'} = ncdouble('qbar_time');
nw{'dop_src_time'}.long_name = ncchar('runoff time');
- nw{'dop_src_time'}.units = ncchar('days');
+ nw{'dop_src_time'}.units = ncchar(time_unit_att);
+ nw{'dop_src_time'}.calendar = calendar_att;
nw{'dop_src_time'}.cycle_length = 360;
nw{'DOP_src'} = ncdouble('n_qbar','qbar_time');
diff --git a/Rivers/make_runoff.m b/Rivers/make_runoff.m
index edef1e76..226b185e 100644
--- a/Rivers/make_runoff.m
+++ b/Rivers/make_runoff.m
@@ -104,7 +104,7 @@ plotting_zoom=0;
%
%=========================================================================================
% Add biogeochemical variables
-if (makenpzd | makepisces | makebioebus | makequota) makebio = 1;
+if (makenpzd | makepisces | makebioebus | makequota) makebio = 1;
else
makebio = 0;
end
@@ -390,7 +390,9 @@ else
disp(' Create the runoff file...')
create_runoff(rivname,grdname,title_name,...
qbar_time,qbar_cycle, ...
- rivername,number_rivertoprocess,rivname_StrLen,dir,psource_ncfile_ts,makebio,makepisces,makequota)
+ rivername,number_rivertoprocess,...
+ rivname_StrLen,dir,psource_ncfile_ts,...
+ makebio,makepisces,makequota)
%%
%% Adjust the rivers positions relative to the mask
%%
diff --git a/crocotools_param.m b/crocotools_param.m
index 8b310ce1..e1a593e8 100644
--- a/crocotools_param.m
+++ b/crocotools_param.m
@@ -490,6 +490,9 @@ end
rmdepth = 2;
%
% Overlap parameters : nb of records around each sequence
+% => for SODA put itolap_a = itolap_p = 1
+% => for mercator daily put itolap_a = itolap_p = 2
+% (due to date of the month first day of month)
%
itolap_a = 1; % before
itolap_p = 1; % after
diff --git a/oct_start.m b/oct_start.m
index d16ae96d..5fb8b9ed 100644
--- a/oct_start.m
+++ b/oct_start.m
@@ -59,6 +59,7 @@ addpath([tools_path,'Forecast_tools'])
addpath([tools_path,'Nesting_tools'])
addpath([tools_path,'Preprocessing_tools'])
addpath([tools_path,'Preprocessing_tools/Bio'])
+addpath([tools_path,'Preprocessing_tools/Bio/npzd-bioebus'])
addpath([tools_path,'Oforc_OGCM'])
addpath([tools_path,'Tides'])
addpath([tools_path,'Tides/T_TIDE'])
diff --git a/start.m b/start.m
index 52509619..df81a16a 100644
--- a/start.m
+++ b/start.m
@@ -55,6 +55,7 @@ addpath([tools_path,'Forecast_tools'])
addpath([tools_path,'Nesting_tools'])
addpath([tools_path,'Preprocessing_tools'])
addpath([tools_path,'Preprocessing_tools/Bio'])
+addpath([tools_path,'Preprocessing_tools/Bio/npzd-bioebus'])
addpath([tools_path,'Oforc_OGCM'])
addpath([tools_path,'Tides'])
addpath([tools_path,'Tides/T_TIDE'])
--
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