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Commit 7dc8cf88 authored by Pierre Cazenave's avatar Pierre Cazenave

Merge branch 'dev' of gitlab.ecosystem-modelling.pml.ac.uk:fvcom/fvcom-toolbox into dev

parents 79a41030 58b2201d
......@@ -5,7 +5,7 @@ function [Mobj] = add_sponge_nodes_list(Mobj,SpongeList,SpongeName,SpongeRadius
% [Mobj] = add_sponge_nodes(Mobj)
% Select using ginput the set of nodes comprising a sponge layer
% Add the sponge parameters at the given nodes.
% Mobj = Matlab mesh object
......@@ -164,8 +164,8 @@ nuts_long = {'nitrogen','phosphorus','nitrogen'}
nuts_units = {'mmol N/m^3','mmol P/m^3','mg C/m^3'}
river_Z4c_varid = netcdf.defVar(nc, 'Z4_c', 'NC_FLOAT', [rivers_dimid, time_dimid]);
netcdf.putAtt(nc, river_z4c_varid, 'long_name', 'mesozooplankton carbon');
netcdf.putAtt(nc, river_z4c_varid, 'units', 'mg C/m^3');
netcdf.putAtt(nc, river_Z4c_varid, 'long_name', 'mesozooplankton carbon');
netcdf.putAtt(nc, river_Z4c_varid, 'units', 'mg C/m^3');
for zz=1:length(zoo_vars)
for nn=1:length(zuu_nuts)
......@@ -194,16 +194,49 @@ netcdf.putVar(nc, river_names_varid, rString);
netcdf.putVar(nc, time_varid, 0, nTimes, time);
netcdf.putVar(nc, itime_varid, 0, nTimes, floor(time));
netcdf.putVar(nc, itime2_varid, 0, nTimes, mod(time, 1)*24*3600*1000);
if any(isnan(flux(:)))
error('NaNs in river flux varaible')
netcdf.putVar(nc, river_flux_varid, flux');
if any(isnan(temp(:)))
error('NaNs in river temp varaible')
netcdf.putVar(nc, river_temp_varid, temp');
if any(isnan(salt(:)))
error('NaNs in river salt varaible')
netcdf.putVar(nc, river_salt_varid, salt');
if any(isnan(n1p(:)))
error('NaNs in river n1p varaible')
netcdf.putVar(nc, river_n1p_varid, n1p');
if any(isnan(n3n(:)))
error('NaNs in river n3n varaible')
netcdf.putVar(nc, river_n3n_varid, n3n');
if any(isnan(n4n(:)))
error('NaNs in river n4n varaible')
netcdf.putVar(nc, river_n4n_varid, n4n');
if any(isnan(n5s(:)))
error('NaNs in river n5s varaible')
netcdf.putVar(nc, river_n5s_varid, n5s');
if any(isnan(dic(:)))
error('NaNs in river dic varaible')
netcdf.putVar(nc, river_dic_varid, dic');
if any(isnan(o2(:)))
error('NaNs in river o2 varaible')
netcdf.putVar(nc, river_O2_varid, o2');
if any(isnan(alkalinity(:)))
error('NaNs in river alkalinity varaible')
netcdf.putVar(nc, river_TA_varid, alkalinity');
if any(isnan(bioalk(:)))
error('NaNs in river bioalk varaible')
netcdf.putVar(nc, river_bioalk_varid,bioalk');
% add small zooplankton values
% taken to be 10^-6 of L4 initial conditions.
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