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create_ini_vinz.m
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create_ini_vinz.m
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%
%=========================================================================%
% create_ini_vinz.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
% Created: 27 March 2018
% Last edit: 5.16.18 --> Changed LZOO, SZOO and ocean_time.
% 8.31.18 --> changed to absolute path name for fid.
% 9.17.18 --> resolved function name ambiguity (was create_ini).
% 11.5.18 --> added 3rd Fe pool, changed Fep to DetFe
% 12.31.18--> split fid into physics and biology files to
% use spun-up physics.
% --> removed NaN mask from restart file, since model
% requires mask to be 0 (blows up at first time
% step with -NaN everywhere if NaN mask present.
% --> changed ocean_time to reflect model spinup
% date (23 June 2006).
% --> updated pathnames to reflect new directory
% structure.
% 2.1.19 --> Allow ocean_time to start model run in April
% instead of June.
% --> Percent of total chlorophyll signal going
% to phyto and dia variable with depth.
% 2.5.19 --> Chlorophyll from spinup April -> June
%=========================================================================%
%
function create_ini_vinz(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','seconds 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_u' xi_u '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_v' eta_v '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_u' xi_u '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_v' eta_v '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');
% Detrital Iron
nccreate(fname,'DetFe', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'DetFe','long_name','Detrital iron concentration');
ncwriteatt(fname,'DetFe','units','umol Fe m-3');
% Large Detrital Iron
nccreate(fname,'LDetFe', ...
'Dimensions',{'xi_rho' xi_rho 'eta_rho' eta_rho 's_rho' s_rho 'time' time},...
'Datatype','double', ...
'Format','netcdf4');
ncwriteatt(fname,'LDetFe','long_name','Large detrital iron concentration');
ncwriteatt(fname,'LDetFe','units','umol Fe m-3');
%
%----------------------------------------------------------------------
% Read data into variables. Where data are unavailable, populate with
% analytical functions.
%----------------------------------------------------------------------
%
myroot = '/home/server/pi/homes/zwallace/ROMS/Project_Patagonia';
outroot = '/home/morrison/data2/zach';
biodir = 'orig/vinz_in_3-21-18';
%chldir = 'spinup';
%chldir= 'spinup_MY25_bio_tempArctic4_alphaLutz_scavDOC_graz0.05_thetamExud_dustx2M05_AprStart';
hdir = 'bulk';
fid_bio = fullfile(myroot,biodir,'rst_PHYSIQUE_NEMURO_CHLAseawif_2001Jun_WOA_VinzFeC_ini.nc'); % get name of Vincent's initial conditions file
% fid_phys= '/home/morrison/data2/zach/phys-QCORRBarnier-swradIcecorr-windminuscurr-emmiss-dqdtVar-rhumFrac-MY25/patagonia_rst.nc';
% fid_phys= '/home/morrison/data2/zach/phys-QCORRBarnier-swradIcecorr-windminuscurr-emmiss-dqdtVar-rhumFrac/patagonia_rst.nc';
fid_phys= fullfile(outroot,'phys-QCORRBarnier-swradIcecorr-windminuscurr-emmiss-dqdtVar-rhumFrac-MY25/patagonia_avg_0059.nc');
%fid_chl = fullfile(myroot,chldir,'chlo_grd_3D_April.mat');
%fid_chl1 = fullfile(outroot,chldir,'patagonia_avg_0002.nc');
%fid_chl2 = fullfile(outroot,chldir,'patagonia_avg_0003.nc');
fid_grd = fullfile(myroot,hdir,'roms_grd_rivers.nc');
%idx_end = 10; % last index in restart file
idx_end = 4; % 15 April 2006 from avg file
start_2D=[1,1,idx_end];
count_2D=[Inf,Inf,1];
start_3D=[1,1,1,idx_end];
count_3D=[Inf,Inf,Inf,1];
C2N = 6.625; % Redfield C:N ratio
% Time variables
% scrum_time = ncread(fid,'scrum_time');
% ocean_time = scrum_time-367*86400; % subtract a year to account for indexing difference
% ocean_time = (datenum('24-Jun-2001')-datenum('01-Jan-1900'))*86400.; % Model start: 24 June 0101
ocean_time = (datenum('23-Jun-2006')-datenum('01-Jan-1900'))*86400.; % Model start: 23 June 0106
% ocean_time = (datenum('15-Apr-2006')-datenum('01-Jan-1900'))*86400.; % Model start: 15 April 0106
% Read in bathymetery data for variable %chl going to biomass as a
% function of depth.
h = ncread(fid_grd,'h');
depth_le75 = zeros(xi_rho,eta_rho); % preallocate for speed
for i=1:xi_rho
for j=1:eta_rho
if h(i,j) <= 75
depth_le75(i,j) = 1;
else
depth_le75(i,j) = 0;
end
end
end
% Load in April chlorophyll data
% chl_tot = load(fid_chl,'chlo_grd_3D_April');
% chl_tot = chl_tot.chlo_grd_3D_April;
% chl_tot = chl_tot.chlo_grd_3D_April;
% Load in June spin-up data
% chl_tot1 = ncread(fid_chl1,'Chlorophyll',[1,1,1,5],[Inf,Inf,Inf,Inf]) + ...
% ncread(fid_chl1,'ChlD',[1,1,1,5],[Inf,Inf,Inf,Inf]);
% chl_tot2 = ncread(fid_chl2,'Chlorophyll',[1,1,1,1],[Inf,Inf,Inf,4]) + ...
% ncread(fid_chl2,'ChlD',[1,1,1,1],[Inf,Inf,Inf,4]);
% chl_tot = cat(4,chl_tot1,chl_tot2);
% chl_tot = mean(chl_tot,4);
chl_tot = 1.59*(ncread(fid_bio,'SPHY')+ncread(fid_bio,'LPHY'));
% Vary %Chl per phyto group with depth
chls = zeros(xi_rho,eta_rho,s_rho);
chld = zeros(xi_rho,eta_rho,s_rho);
for k = 1:s_rho
for j = 1:eta_rho
for i = 1:xi_rho
if depth_le75(i,j)
% 80% of total chl signal to diatoms
chls(i,j,k) = chl_tot(i,j,k)*0.2;
chld(i,j,k) = chl_tot(i,j,k)*0.8;
else
% 20% to diatoms
chls(i,j,k) = chl_tot(i,j,k)*0.8;
chld(i,j,k) = chl_tot(i,j,k)*0.2;
end
end
end
end
% Read into variables for writing
Chlorophyll = chls;
Chlorophyll(isnan(Chlorophyll)) = 0;
ChlD = chld;
ChlD(isnan(ChlD)) = 0;
% zeta
zeta = ncread(fid_phys,'zeta',start_2D,count_2D);
zeta(isnan(zeta)) = 0;
% ubar
ubar = ncread(fid_phys,'ubar',start_2D,count_2D);
ubar(isnan(ubar)) = 0;
% vbar
vbar = ncread(fid_phys,'vbar',start_2D,count_2D);
vbar(isnan(vbar)) = 0;
% u
u = ncread(fid_phys,'u',start_3D,count_3D);
u(isnan(u)) = 0;
% v
v = ncread(fid_phys,'v',start_3D,count_3D);
v(isnan(v)) = 0;
% temp
temp = ncread(fid_phys,'temp',start_3D,count_3D);
temp(isnan(temp)) = 0;
% salt
salt = ncread(fid_phys,'salt',start_3D,count_3D);
salt(isnan(salt)) = 0;
% NO3
NO3 = ncread(fid_bio,'NO3');
NO3(isnan(NO3)) = 0;
% NH4
% NH4 = ncread(fid,'NH4');
NH4 = NO3*0.01;
NH4(isnan(NH4)) = 0;
% Phytoplankton
%Phytoplankton = ncread(fid_bio,'SPHY');
Phytoplankton = Chlorophyll./1.59;
Phytoplankton(isnan(Phytoplankton)) = 0;
% Diatoms
%Diatoms = ncread(fid_bio,'LPHY');
Diatoms = ChlD./1.59;
Diatoms(isnan(Diatoms)) = 0;
% Bacteria
Bacteria = 0.1*Phytoplankton;
Bacteria(isnan(Bacteria)) = 0;
% Chlorophyll
% Chlorophyll = Phytoplankton*1.59;
% ChlD
%ChlD = Diatoms*1.59;
% DON
% DON = ncread(fid,'DON');
DON = NH4;
DON(isnan(DON)) = 0;
% DOC
DOC = C2N*DON;
% DetN
% DetN = ncread(fid,'PON');
DetN = DON;
DetN(isnan(DetN)) = 0;
% DetC
DetC = C2N*DetN;
% Silica
Silica = ncread(fid_bio,'SiOH');
Silica(isnan(Silica)) = 0;
% LDetN
LDetN = DetN;
LDetN(isnan(LDetN)) = 0;
% LDetC
LDetC = C2N*LDetN;
% LDetS
% LDetS = ncread(fid,'OPAL');
LDetS = Diatoms*0.1;
% Microzooplankton
% Microzooplankton = ncread(fid,'SZOO');
Microzooplankton= 0.01*Phytoplankton;
Microzooplankton(isnan(Microzooplankton)) = 0;
% Mesozooplankton
% Mesozooplankton = ncread(fid,'LZOO');
%Mesozooplankton(xi_rho,eta_rho,s_rho) = CONST_VAL;
Mesozooplankton= 0.01*Diatoms;
Mesozooplankton(isnan(Mesozooplankton)) = 0;
% Dissolved Iron
FeD = ncread(fid_bio,'FeD');
FeD(isnan(FeD)) = 0;
% Particulate Iron
% combine small and large particulate from NEMURO
% FeSp = ncread(fid,'FeSp');
% FeLp = ncread(fid,'FeLp');
%
% FeP = FeSp+FeLp;
DetFe = 0.1 * FeD;
DetFe(isnan(DetFe)) = 0;
% Large detrital iron
LDetFe = 0.1 * DetFe;
LDetFe(isnan(LDetFe)) = 0;
%
%----------------------------------------------------------------------
% 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);
% Detrital Iron
ncwrite(fname,'DetFe',DetFe);
% Large Detrital iron
ncwrite(fname,'LDetFe',LDetFe);
end % create_ini_vinz