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Commit 37fdb4ee authored by Pierre Cazenave's avatar Pierre Cazenave
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Add new function to export a nesting forcing file from external model output... 

Add new function to export a nesting forcing file from external model output (either interpolated from a regular model grid (type 3 nesting) or from a bigger FVCOM model (type 1 and 2)).
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fvcom_prepro/write_FVCOM_nested_forcing.m 0 → 100644
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function write_FVCOM_nested_forcing(nest, ncfile, nesttype)
% Creates an FVCOM nesting file.
%
% function write_nesting_struct_fvcom(Mobj, out_nesting, N)
%
% DESCRIPTION:
% Uses timeseries data from structured grid already interpolated into
% FVCOM nodes and elements and generates a netcdf file to drive FVCOM at
% boundaries
%
% Optionally specify nesting type:
% 1/2: DIRECT/INDIRECT nesting:
% - Full variables/no surface elevation respectively.
% 3: RELAXATION nestING:
% - Nesting with a relaxation method.
%
% INPUT:
% nest = struct whose field names are the variable names to be
% included in netCDF file. Additional required fields are:
% - time (in Modified Julian Days)
% - nv (triangulation table)
% - lon, lat, x, y - node coordinates (spherical and
% cartesian).
% - lonc, latc, xc, yc - element coordinates (spherical and
% cartesian).
% ncfile = full path to the nesting file to be created.
% nesttype = [optional] nesting type (defaults to 1 = direct nesting).
%
% OUTPUT:
% FVCOM nesting file.
%
% EXAMPLE USAGE:
% nest.temp = Temperature
% nest.salinity = Salinity
% nest.ua = Vertically averaged x velocity
% nest.va = Vertically averaged y velocity
% nest.u = Eastward Water Velocity
% nest.v = Northward Water Velocity
% nest.hyw = hydro static vertical velocity
% nest.weight_cell = weights see manual for explanation
% nest.weight_node = weights see manual for explanation
% nest.Itime = time in modified julian days
% nest.Itime2 = time milliseconds since midnight
%
% write_FVCOM_nested_forcing('/tmp/fvcom_restart.nc', ...
% '/tmp/fvcom_restart_interp.nc', N)
%
% Author(s):
% Ricardo Torres (Plymouth Marine Laboratory)
% Pierre Cazenave (Plymouth Marine Laboratory)
%
% Revision history:
% 2013-06-04 First version.
% 2015-02-19 Updated to use either weighted or non-weighted nesting. Also
% general tidy up.
%
%==========================================================================
% We need the following variables:
%
% zeta: Sea surface elevation [node, time]
% ua: Vertically averaged x velocity [node, time]
% va: Vertically averaged y velocity [nele, time]
% u: Eastward Water Velocity [nele, siglay, time]
% v: Northward Water Velocity [nele, siglay, time]
% temp: Temperature [node, siglay, time]
% salinity: Salinity [node, siglay, time]
% hyw: Hydro static vertical velocity [node, siglev, time]
% weight_cell: Weighting for elements [nele]
% weight_node: Weighting for nodes [node]
% Itime: Days since 1858-11-17 00:00:00 [time]
% Itime2: msec since 00:00:00 [time]
subname = 'write_FVCOM_nested_forcing';
global ftbverbose
if ftbverbose
fprintf('\nbegin : %s\n', subname)
end
if nargin == 2
nesttype = 1;
elseif nargin < 2 || nargin > 3
error(['Incorrect input arguments. Supply netCDF file path, ', ...
'nesting struct and optionally the nesting type (1, 2 or 3).'])
end
% Check we have all the data we need.
required = {'time', 'x', 'y', 'lon', 'lat', 'xc', 'yc', 'lonc', 'latc', ...
'nv', 'h', 'u', 'v', 'ua', 'va', 'temp', 'salinity', 'hyw', ...
'weight_cell', 'weight_node'};
fields = fieldnames(nest);
for f = required
if any(strcmpi(f{1}, {'weight_node', 'weight_cell'})) && nesttype == 3
assert(any(strcmpi(f, fields)), 'Missing %s struct field', f{1});
elseif any(strcmpi(f{1}, {'weight_node', 'weight_cell'})) && nesttype ~= 3
continue
end
end
[elems, nsiglay, ~] = size(nest.u);
nsiglev = nsiglay + 1;
[nodes, ~] = size(nest.zeta);
nc = netcdf.create(ncfile, 'clobber');
% define global attributes
netcdf.putAtt(nc, netcdf.getConstant('NC_GLOBAL'), 'type', ...
'FVCOM nestING TIME SERIES FILE')
netcdf.putAtt(nc, netcdf.getConstant('NC_GLOBAL'), 'title', ...
sprintf('FVCOM nestING TYPE %d TIME SERIES data for open boundary', ...
nesttype))
netcdf.putAtt(nc, netcdf.getConstant('NC_GLOBAL'), 'history', ...
['File created using write_FVCOM_nested_forcing.m', ...
'from the MATLAB fvcom-toolbox'])
netcdf.putAtt(nc, netcdf.getConstant('NC_GLOBAL'), 'filename', ncfile)
netcdf.putAtt(nc, netcdf.getConstant('NC_GLOBAL'), 'Conventions', 'CF-1.0')
% define dimensions
elem_dimid = netcdf.defDim(nc, 'nele', elems);
node_dimid = netcdf.defDim(nc, 'node', nodes);
three_dimid = netcdf.defDim(nc, 'three', 3);
time_dimid = netcdf.defDim(nc, 'time', netcdf.getConstant('NC_UNLIMITED'));
siglay_dimid = netcdf.defDim(nc, 'siglay', nsiglay);
siglev_dimid = netcdf.defDim(nc, 'siglev', nsiglev);
% define variables
% time_varid = netcdf.defVar(nc, 'time', 'NC_FLOAT', time_dimid);
% netcdf.putAtt(nc, time_varid, 'long_name', 'time');
% netcdf.putAtt(nc, time_varid, 'units', 'days since 1858-11-17 00:00:00');
% netcdf.putAtt(nc, time_varid, 'format', 'modified julian day (MJD)');
% netcdf.putAtt(nc, time_varid, 'time_zone', 'UTC');
itime_varid = netcdf.defVar(nc, 'Itime', 'NC_INT', ...
time_dimid);
netcdf.putAtt(nc, itime_varid, 'units', 'days since 1858-11-17 00:00:00');
netcdf.putAtt(nc, itime_varid, 'format', 'modified julian day (MJD)');
netcdf.putAtt(nc, itime_varid, 'time_zone', 'UTC');
itime2_varid = netcdf.defVar(nc, 'Itime2', 'NC_INT', ...
time_dimid);
netcdf.putAtt(nc, itime2_varid, 'units', 'msec since 00:00:00');
netcdf.putAtt(nc, itime2_varid, 'time_zone', 'UTC');
x_varid = netcdf.defVar(nc, 'x', 'NC_FLOAT', ...
node_dimid);
netcdf.putAtt(nc, x_varid, 'units', 'meters');
netcdf.putAtt(nc, x_varid, 'long_name', 'nodal x-coordinate');
y_varid = netcdf.defVar(nc, 'y', 'NC_FLOAT', ...
node_dimid);
netcdf.putAtt(nc, y_varid, 'units', 'meters');
netcdf.putAtt(nc, y_varid, 'long_name', 'nodal y-coordinate');
xc_varid = netcdf.defVar(nc, 'xc', 'NC_FLOAT', ...
elem_dimid);
netcdf.putAtt(nc, xc_varid, 'units', 'meters');
netcdf.putAtt(nc, xc_varid, 'long_name', 'zonal x-coordinate');
nv_varid = netcdf.defVar(nc, 'nv', 'NC_INT', ...
[elem_dimid, three_dimid]);
netcdf.putAtt(nc, xc_varid, 'units', 'no units');
netcdf.putAtt(nc, xc_varid, 'long_name', 'elements nodes indices');
yc_varid = netcdf.defVar(nc, 'yc', 'NC_FLOAT', ...
elem_dimid);
netcdf.putAtt(nc, yc_varid, 'units', 'meters');
netcdf.putAtt(nc, yc_varid, 'long_name', 'zonal y-coordinate');
lon_varid = netcdf.defVar(nc, 'lon', 'NC_FLOAT', ...
node_dimid);
netcdf.putAtt(nc, lon_varid, 'units', 'degrees_east');
netcdf.putAtt(nc, lon_varid, 'standard_name', 'longitude');
netcdf.putAtt(nc, lon_varid, 'long_name', 'nodal longitude');
lat_varid = netcdf.defVar(nc, 'lat', 'NC_FLOAT', ...
node_dimid);
netcdf.putAtt(nc, lat_varid, 'units', 'degrees_north');
netcdf.putAtt(nc, lat_varid, 'standard_name', 'latitude');
netcdf.putAtt(nc, lat_varid, 'long_name', 'nodal latitude');
lonc_varid = netcdf.defVar(nc, 'lonc', 'NC_FLOAT', ...
elem_dimid);
netcdf.putAtt(nc, lonc_varid, 'units', 'degrees_east');
netcdf.putAtt(nc, lonc_varid, 'standard_name', 'longitude');
netcdf.putAtt(nc, lonc_varid, 'long_name', 'zonal longitude');
latc_varid = netcdf.defVar(nc, 'latc', 'NC_FLOAT', ...
elem_dimid);
netcdf.putAtt(nc, latc_varid, 'units', 'degrees_north');
netcdf.putAtt(nc, latc_varid, 'standard_name', 'latitude');
netcdf.putAtt(nc, latc_varid, 'long_name', 'zonal latitude');
zeta_varid = netcdf.defVar(nc, 'zeta', 'NC_FLOAT', ...
[node_dimid, time_dimid]);
netcdf.putAtt(nc, zeta_varid, 'long_name', 'Water Surface Elevation');
netcdf.putAtt(nc, zeta_varid, 'units', 'meters');
netcdf.putAtt(nc, zeta_varid, 'positive', 'up');
netcdf.putAtt(nc, zeta_varid, 'standard_name', ...
'sea_surface_height_above_geoid');
netcdf.putAtt(nc, zeta_varid, 'grid', 'Bathymetry_Mesh');
netcdf.putAtt(nc, zeta_varid, 'coordinates', 'time lat lon');
netcdf.putAtt(nc, zeta_varid, 'type', 'data');
netcdf.putAtt(nc, zeta_varid, 'location', 'node');
ua_varid = netcdf.defVar(nc, 'ua', 'NC_FLOAT', ...
[elem_dimid, time_dimid]);
netcdf.putAtt(nc, ua_varid, 'long_name', 'Vertically Averaged x-velocity');
netcdf.putAtt(nc, ua_varid, 'units', 'meters s-1');
netcdf.putAtt(nc, ua_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, ua_varid, 'type', 'data');
va_varid = netcdf.defVar(nc, 'va', 'NC_FLOAT', ...
[elem_dimid, time_dimid]);
netcdf.putAtt(nc, va_varid, 'long_name', 'Vertically Averaged y-velocity');
netcdf.putAtt(nc, va_varid, 'units', 'meters s-1');
netcdf.putAtt(nc, va_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, va_varid, 'type', 'data');
u_varid = netcdf.defVar(nc, 'u', 'NC_FLOAT', ...
[elem_dimid, siglay_dimid, time_dimid]);
netcdf.putAtt(nc, u_varid, 'long_name', 'Eastward Water Velocity');
netcdf.putAtt(nc, u_varid, 'units', 'meters s-1');
netcdf.putAtt(nc, u_varid, 'standard_name', 'eastward_sea_water_velocity');
netcdf.putAtt(nc, u_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, u_varid, 'coordinates', 'time siglay latc lonc');
netcdf.putAtt(nc, u_varid, 'type', 'data');
netcdf.putAtt(nc, u_varid, 'location', 'face');
v_varid = netcdf.defVar(nc, 'v', 'NC_FLOAT', ...
[elem_dimid, siglay_dimid, time_dimid]);
netcdf.putAtt(nc, v_varid, 'long_name', 'Northward Water Velocity');
netcdf.putAtt(nc, v_varid, 'units', 'meters s-1');
netcdf.putAtt(nc, v_varid, 'standard_name', ...
'Northward_sea_water_velocity');
netcdf.putAtt(nc, v_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, v_varid, 'coordinates', 'time siglay latc lonc');
netcdf.putAtt(nc, v_varid, 'type', 'data');
netcdf.putAtt(nc, v_varid, 'location', 'face');
temp_varid = netcdf.defVar(nc, 'temp', 'NC_FLOAT', ...
[node_dimid, siglay_dimid, time_dimid]);
netcdf.putAtt(nc, temp_varid, 'long_name', 'Temperature');
netcdf.putAtt(nc, temp_varid, 'standard_name', 'sea_water_temperature');
netcdf.putAtt(nc, temp_varid, 'units', 'degrees Celcius');
netcdf.putAtt(nc, temp_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, temp_varid, 'coordinates', 'time siglay lat lon');
netcdf.putAtt(nc, temp_varid, 'type', 'data');
netcdf.putAtt(nc, temp_varid, 'location', 'node');
salinity_varid = netcdf.defVar(nc, 'salinity', 'NC_FLOAT', ...
[node_dimid, siglay_dimid, time_dimid]);
netcdf.putAtt(nc, salinity_varid, 'long_name', 'Salinity');
netcdf.putAtt(nc, salinity_varid, 'standard_name', 'sea_water_salinity');
netcdf.putAtt(nc, salinity_varid, 'units', '1e-3');
netcdf.putAtt(nc, salinity_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, salinity_varid, 'coordinates', 'time siglay lat lon');
netcdf.putAtt(nc, salinity_varid, 'type', 'data');
netcdf.putAtt(nc, salinity_varid, 'location', 'node');
hyw_varid = netcdf.defVar(nc, 'hyw', 'NC_FLOAT', ...
[node_dimid, siglev_dimid, time_dimid]);
netcdf.putAtt(nc, hyw_varid, 'long_name', ...
'hydro static vertical velocity');
netcdf.putAtt(nc, hyw_varid, 'units', 'meters s-1');
netcdf.putAtt(nc, hyw_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, hyw_varid, 'type', 'data');
netcdf.putAtt(nc, hyw_varid, 'coordinates', 'time siglay lat lon');
if nesttype > 2
cweights_varid = netcdf.defVar(nc, 'weight_cell', 'NC_FLOAT', ...
[elem_dimid, time_dimid]);
netcdf.putAtt(nc, cweights_varid, 'long_name', ...
'Weights for elements in relaxation zone');
netcdf.putAtt(nc, cweights_varid, 'units', 'no units');
netcdf.putAtt(nc, cweights_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, cweights_varid, 'type', 'data');
nweights_varid = netcdf.defVar(nc, 'weight_node', 'NC_FLOAT', ...
[node_dimid, time_dimid]);
netcdf.putAtt(nc, nweights_varid, 'long_name', ...
'Weights for nodes in relaxation zone');
netcdf.putAtt(nc, nweights_varid, 'units', 'no units');
netcdf.putAtt(nc, nweights_varid, 'grid', 'fvcom_grid');
netcdf.putAtt(nc, nweights_varid, 'type', 'data');
end
% end definitions
netcdf.endDef(nc);
% write data
netcdf.putVar(nc, itime_varid, 0, numel(nest.time), floor(nest.time));
netcdf.putVar(nc, itime2_varid, 0, numel(nest.time), ...
mod(nest.time, 1)*24*3600*1000);
% write grid information
netcdf.putVar(nc, nv_varid, nest.nv);
netcdf.putVar(nc, x_varid, nest.x);
netcdf.putVar(nc, y_varid, nest.y);
netcdf.putVar(nc, xc_varid, nest.xc);
netcdf.putVar(nc, yc_varid, nest.yc);
netcdf.putVar(nc, lon_varid, nest.lon);
netcdf.putVar(nc, lat_varid, nest.lat);
netcdf.putVar(nc, lonc_varid, nest.lonc);
netcdf.putVar(nc, latc_varid, nest.latc);
% dump data
netcdf.putVar(nc, zeta_varid, nest.zeta);
netcdf.putVar(nc, ua_varid, nest.ua);
netcdf.putVar(nc, va_varid, nest.va);
netcdf.putVar(nc, u_varid, nest.u);
netcdf.putVar(nc, v_varid, nest.v);
netcdf.putVar(nc, temp_varid, nest.temp);
netcdf.putVar(nc, salinity_varid, nest.salinity);
netcdf.putVar(nc, hyw_varid, nest.hyw);
if nesttype > 2
netcdf.putVar(nc, cweights_varid, nest.weight_cell);
netcdf.putVar(nc, nweights_varid, nest.weight_node);
end
% close file
netcdf.close(nc)
if ftbverbose
fprintf('end : %s\n', subname)
end
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