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create_ini.m
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create_ini.m
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%=========================================================================%
% create_ini.m
%
% Create initial conditions file for Biology Model.
%
% Initial conditions for the physics are monthly averages from 2000-2007
% taken from OFES.
% Initial conditions for the biology are monthly climatologies taken from
% WOA(09?)
%
% Author: Z. Wallace
% Last edit: 20 March 2018
%=========================================================================%
function create_ini(fname)
ncid = netcdf.create(fname,'NETCDF4'); % create and open new ini file
netcdf.close(ncid);
%
%----------------------------------------------------------------------
% Create dimensions
%----------------------------------------------------------------------
%
% grid dimensions
xi_rho = 482;
xi_u = 481;
eta_rho = 770;
eta_v = 769;
s_rho = 40;
s_w = 41;
time = 1;
%
%----------------------------------------------------------------------
% Create variables and add attributes
%----------------------------------------------------------------------
%
% Ocean time
nccreate(fname,'ocean_time', ...
'Dimensions',{'ocean_time' time}, ...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'ocean_time','long_name','Time since 1900-01-01 00:00:00');
ncwriteatt(fname,'ocean_time','units','seconds');
% Free-surface
nccreate(fname,'zeta', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'zeta','long_name','free-surface');
ncwriteatt(fname,'zeta','units','meter');
% 2D u-direction velocity
nccreate(fname,'ubar', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'ubar','long_name','Vertically integrated u-momentum component');
ncwriteatt(fname,'ubar','units','meter second-1');
% 2D v-direction velocity
nccreate(fname,'vbar', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'vbar','long_name','Vertically integrated v-momentum component');
ncwriteatt(fname,'vbar','units','meter second-1');
% 3D u-direction velocity
nccreate(fname,'u', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'u','long_name','u-momentum component');
ncwriteatt(fname,'u','units','meter second-1');
% 3D v-direction velocity
nccreate(fname,'v', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'v','long_name','v-momentum component');
ncwriteatt(fname,'v','units','meter second-1');
% temperature
nccreate(fname,'temp', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'temp','long_name','potential temperature');
ncwriteatt(fname,'temp','units','meter second-1');
% salinity
nccreate(fname,'salt', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'salt','long_name','salinity');
ncwriteatt(fname,'salt','units','PSU');
% NO3
nccreate(fname,'NO3', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'NO3','long_name','nitrate concentration');
ncwriteatt(fname,'NO3','units','mmol N m-3');
% NH4
nccreate(fname,'NH4', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'NH4','long_name','NH4 concentration');
ncwriteatt(fname,'NH4','units','mmol N m-3');
% Phytoplankton
nccreate(fname,'Phytoplankton', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Phytoplankton','long_name','Phytoplankton concentration');
ncwriteatt(fname,'Phytoplankton','units','mmol N m-3');
% Diatoms
nccreate(fname,'Diatoms', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Diatoms','long_name','Diatom concentration');
ncwriteatt(fname,'Diatoms','units','mmol N m-3');
% Bacteria
nccreate(fname,'Bacteria', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Bacteria','long_name','Bacteria concentration');
ncwriteatt(fname,'Bacteria','units','mmol N m-3');
% Chlorophyll-a
nccreate(fname,'Chlorophyll', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Chlorophyll','long_name','Chlorophyll concentration');
ncwriteatt(fname,'Chlorophyll','units','mg Chl m-3');
% Diatom Chlorophyll
nccreate(fname,'ChlD', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'ChlD','long_name','ChlD concentration');
ncwriteatt(fname,'ChlD','units','mg Chl m-3');
% DON
nccreate(fname,'DON', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'DON','long_name','DON concentration');
ncwriteatt(fname,'DON','units','mmol N m-3');
% DOC
nccreate(fname,'DOC', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'DOC','long_name','DOC concentration');
ncwriteatt(fname,'DOC','units','mmol C m-3');
% DetN
nccreate(fname,'DetN', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'DetN','long_name','DetN concentration');
ncwriteatt(fname,'DetN','units','mmol N m-3');
% DetC
nccreate(fname,'DetC', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'DetC','long_name','DetC concentration');
ncwriteatt(fname,'DetC','units','mmol C m-3');
% Silica
nccreate(fname,'Silica', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Silica','long_name','Silica concentration');
ncwriteatt(fname,'Silica','units','mmol Si m-3');
% LDetN
nccreate(fname,'LDetN', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'LDetN','long_name','LDetN concentration');
ncwriteatt(fname,'LDetN','units','mmol N m-3');
% LDetC
nccreate(fname,'LDetC', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'LDetC','long_name','LDetC concentration');
ncwriteatt(fname,'LDetC','units','mmol C m-3');
% LDetS
nccreate(fname,'LDetS', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'LDetS','long_name','LDetS concentration');
ncwriteatt(fname,'LDetS','units','mmol Si m-3');
% Microzooplankton
nccreate(fname,'Microzooplankton', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Microzooplankton','long_name','Microzooplankton concentration');
ncwriteatt(fname,'Microzooplankton','units','mmol N m-3');
% Mesozooplankton
nccreate(fname,'Mesozooplankton', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'Mesozooplankton','long_name','Mesozooplankton concentration');
ncwriteatt(fname,'Mesozooplankton','units','mmol N m-3');
% Dissolved Iron
nccreate(fname,'FeD', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'FeD','long_name','Dissolved iron concentration');
ncwriteatt(fname,'FeD','units','umol Fe m-3');
% Particulate Iron
nccreate(fname,'FeP', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'FeP','long_name','Particulate iron concentration');
ncwriteatt(fname,'FeP','units','umol Fe m-3');
%
%----------------------------------------------------------------------
% Read data into variables. Where data are unavailable, populate with
% analytical functions.
%----------------------------------------------------------------------
%
% fid = 'roms_ini_oceantime.nc'; % get name of Vincent's initial conditions file
fid_phys = 'roms_ini_1900.nc';
fid_bio = '../Project_Patagonia/roms_ini_oceantime.nc';
C2N = 6.625; % Redfield C:N ratio
% Time variables
ocean_time = ncread(fid_phys,'ocean_time'); % this value already corrected
% zeta
zeta = ncread(fid_phys,'zeta');
% ubar
ubar = ncread(fid_phys,'ubar');
% vbar
vbar = ncread(fid_phys,'vbar');
% u
u = ncread(fid_phys,'u');
% v
v = ncread(fid_phys,'v');
% temp
temp = ncread(fid_phys,'temp');
% salt
salt = ncread(fid_phys,'salt');
% NO3
NO3 = ncread(fid_bio,'NO3');
% NH4
NH4 = ncread(fid_bio,'NH4');
% Phytoplankton
Phytoplankton = ncread(fid_bio,'SPHY');
Phytoplankton = Phytoplankton*100; % set to 1 mmol m-3
% Diatoms
Diatoms = ncread(fid_bio,'LPHY');
Diatoms = Diatoms*100; % set to 1 mmol m-3
% Bacteria
Bacteria = 0.1*Phytoplankton;
% Chlorophyll
Chlorophyll = ncread(fid_bio,'CHLAS');
Chlorophyll = Chlorophyll*100; % keep in line w/phyto
% ChlD
ChlD = Chlorophyll;
ChlD = ChlD*100; % keep in line w/dia
% DON
DON = ncread(fid_bio,'DON');
% DOC
DOC = C2N*DON;
% DetN
DetN = ncread(fid_bio,'PON');
% DetC
DetC = C2N*DetN;
% Silica
Silica = ncread(fid_bio,'SiOH');
% LDetN
LDetN = 0.1*DetN;
% LDetC
LDetC = C2N*LDetN;
% LDetS
LDetS = ncread(fid_bio,'OPAL');
% Microzooplankton
Microzooplankton = ncread(fid_bio,'SZOO');
% Mesozooplankton
Mesozooplankton = ncread(fid_bio,'LZOO');
% Dissolved Iron
FeD = ncread(fid_bio,'FeD');
% Particulate Iron
% combine small and large particulate from NEMURO
FeSp = ncread(fid_bio,'FeSp');
FeLp = ncread(fid_bio,'FeLp');
FeP = FeSp+FeLp;
%
%----------------------------------------------------------------------
% Write data to variables.
%----------------------------------------------------------------------
%
% bry_time
ncwrite(fname,'ocean_time',ocean_time);
% zeta
ncwrite(fname,'zeta',zeta);
% ubar
ncwrite(fname,'ubar',ubar);
% vbar
ncwrite(fname,'vbar',vbar);
% u
ncwrite(fname,'u',u);
% v
ncwrite(fname,'v',v);
% temp
ncwrite(fname,'temp',temp);
% salt
ncwrite(fname,'salt',salt);
% NO3
ncwrite(fname,'NO3',NO3);
% NH4
ncwrite(fname,'NH4',NH4);
% Phytoplankton
ncwrite(fname,'Phytoplankton',Phytoplankton);
% Diatoms
ncwrite(fname,'Diatoms',Diatoms);
% Bacteria
ncwrite(fname,'Bacteria',Bacteria);
% Chlorophyll
ncwrite(fname,'Chlorophyll',Chlorophyll);
% ChlD
ncwrite(fname,'ChlD',ChlD);
% DON
ncwrite(fname,'DON',DON);
% DOC
ncwrite(fname,'DOC',DOC);
% DetN
ncwrite(fname,'DetN',DetN);
% DetC
ncwrite(fname,'DetC',DetC);
% Silica
ncwrite(fname,'Silica',Silica);
% LDetN
ncwrite(fname,'LDetN',LDetN);
% LDetC
ncwrite(fname,'LDetC',LDetC);
% LDetS
ncwrite(fname,'LDetS',LDetS);
% Microzooplankton
ncwrite(fname,'Microzooplankton',Microzooplankton);
% Mesozooplankton
ncwrite(fname,'Mesozooplankton',Mesozooplankton);
% Dissolved Iron
ncwrite(fname,'FeD',FeD);
% Particulate Iron
ncwrite(fname,'FeP',FeP);
end % create_ini