Creates an FVCOM nesting file.
function add_weights_FVCOM_nested_forcing(conf, ncfile)
DESCRIPTION:
Modifies in place the nested file to add weights for the number of levels
suitable for types 3.
INPUT:
conf = with either new_weights field or conf.nest.levels
ncfile2read = full path to the nesting file to be created.
OUTPUT:
FVCOM nesting file.
EXAMPLE USAGE:
conf.new_weight_cell = weights see manual for explanation [0-1]. It
only requires nlevel values, not spatial or temporal dimension is
expected.
conf.new_weight_node = weights see manual for explanation [0-1]. It
only requires nlevel values, not spatial or temporal dimension is
expected.
conf.nest.levels = [1]; The value reflect the inner most level to keep.
1 will keep the most external boundary, 4 will keep 1-4 levels.
modify_FVCOM_nested_forcing(conf, '/tmp/fvcom_nested.nc', 1)
Author(s):
Ricardo Torres (Plymouth Marine Laboratory)
Pierre Cazenave (Plymouth Marine Laboratory)
Revision history:
2017-01-17 First version based on Pierre's write_FVCOM_nested_forcing.m
script. Compress the time series data to save space. Requires
netCDF4 in FVCOM.
==========================================================================0001 function add_weights_FVCOM_nested_forcing(conf, ncfile2read) 0002 % Creates an FVCOM nesting file. 0003 % 0004 % function add_weights_FVCOM_nested_forcing(conf, ncfile) 0005 % 0006 % DESCRIPTION: 0007 % Modifies in place the nested file to add weights for the number of levels 0008 % suitable for types 3. 0009 % 0010 % 0011 % INPUT: 0012 % conf = with either new_weights field or conf.nest.levels 0013 % ncfile2read = full path to the nesting file to be created. 0014 % 0015 % OUTPUT: 0016 % FVCOM nesting file. 0017 % 0018 % EXAMPLE USAGE: 0019 % conf.new_weight_cell = weights see manual for explanation [0-1]. It 0020 % only requires nlevel values, not spatial or temporal dimension is 0021 % expected. 0022 % conf.new_weight_node = weights see manual for explanation [0-1]. It 0023 % only requires nlevel values, not spatial or temporal dimension is 0024 % expected. 0025 % conf.nest.levels = [1]; The value reflect the inner most level to keep. 0026 % 1 will keep the most external boundary, 4 will keep 1-4 levels. 0027 % 0028 % modify_FVCOM_nested_forcing(conf, '/tmp/fvcom_nested.nc', 1) 0029 % 0030 % Author(s): 0031 % Ricardo Torres (Plymouth Marine Laboratory) 0032 % Pierre Cazenave (Plymouth Marine Laboratory) 0033 % 0034 % Revision history: 0035 % 2017-01-17 First version based on Pierre's write_FVCOM_nested_forcing.m 0036 % script. Compress the time series data to save space. Requires 0037 % netCDF4 in FVCOM. 0038 % 0039 %========================================================================== 0040 0041 % The following variables are read from the file: 0042 % 0043 % lon, lat: Grid node positions [node] 0044 % lonc, latc: Grid element positions [nele] 0045 % h: Grid node depths [node] 0046 % hc: Grid element depth [nele] 0047 % nv: Triangulation table [nele, 3] 0048 % zeta: Sea surface elevation [node, time] 0049 % ua: Vertically averaged x velocity [node, time] 0050 % va: Vertically averaged y velocity [nele, time] 0051 % u: Eastward Water Velocity [nele, siglay, time] 0052 % v: Northward Water Velocity [nele, siglay, time] 0053 % temp: Temperature [node, siglay, time] 0054 % salinity: Salinity [node, siglay, time] 0055 % hyw: Hydrostatic vertical velocity [node, siglev, time] 0056 % weight_cell: Weighting for elements [nele] 0057 % weight_node: Weighting for nodes [node] 0058 % Itime: Days since 1858-11-17 00:00:00 [time] 0059 % Itime2: msec since 00:00:00 [time] 0060 % 0061 % We include these optional ones for humans: 0062 % time: Modified Julian Day [time] 0063 % Times: Gregorian dates [time, datestrlen] 0064 0065 [~, subname] = fileparts(mfilename('fullpath')); 0066 0067 global ftbverbose 0068 if ftbverbose 0069 fprintf('\nbegin : %s\n', subname) 0070 end 0071 0072 % Can't use CLOBBER and NETCDF4 at the same time (the bitwise or didn't 0073 % work). Fall back to a horrible delete and then create instead. 0074 if exist(ncfile2read, 'file') 0075 nc2read = netcdf.open(ncfile2read,'WRITE'); 0076 [PATHSTR,NAME,EXT] = fileparts(ncfile2read); 0077 if ftbverbose 0078 fprintf('\nProcessing file : %s\n', ncfile2read) 0079 end 0080 else 0081 sprintf('I am stoping. The nesting file %s doesn''t exist',ncfile2read); 0082 error(['Aborting the script ',subname]) 0083 end 0084 % List of data we need. 0085 required = {'weight_cell', 'weight_node'}; 0086 for f = required 0087 nest.(f{1})=[]; 0088 end 0089 % Read all variables from the existing file 0090 if ~isfield (conf,'nest') 0091 error('Missing conf.nest, aborting... ') 0092 end 0093 if ~isfield (conf.nest,'levels') 0094 error('Missing conf.nest.levels, aborting... ') 0095 end 0096 % define dimensions 0097 0098 timeid = netcdf.inqDimID(nc2read, 'time'); 0099 siglayid = netcdf.inqDimID(nc2read, 'siglay'); 0100 siglevid = netcdf.inqDimID(nc2read, 'siglev'); 0101 nodeid = netcdf.inqDimID(nc2read,'node'); 0102 neleid = netcdf.inqDimID(nc2read,'nele'); 0103 0104 [~,nsiglay] = netcdf.inqDim(nc2read, siglayid); 0105 [~,nsiglev] = netcdf.inqDim(nc2read, siglevid); 0106 [~,ntimes] = netcdf.inqDim(nc2read, timeid); 0107 [~,nodes] = netcdf.inqDim(nc2read, nodeid); 0108 [~,elems] = netcdf.inqDim(nc2read, neleid); 0109 0110 % Replicate weights in time 0111 0112 nest.weight_cell = repmat([conf.new_weight_cell{:}]',1,ntimes); 0113 nest.weight_node = repmat([conf.new_weight_node{:}]',1,ntimes) 0114 0115 [elem_nest] =size(nest.weight_cell,1); 0116 0117 if elem_nest ~= elems 0118 error('We have different elements in FVCOM nesting output file and our calculations') 0119 end 0120 try 0121 netcdf.reDef(nc2read); 0122 0123 cweights_varid = netcdf.defVar(nc2read, 'weight_cell', 'NC_FLOAT', ... 0124 [neleid, timeid]); 0125 netcdf.putAtt(nc2read, cweights_varid, 'long_name', ... 0126 'Weights for elements in relaxation zone'); 0127 netcdf.putAtt(nc2read, cweights_varid, 'units', 'no units'); 0128 netcdf.putAtt(nc2read, cweights_varid, 'grid', 'fvcom_grid'); 0129 netcdf.putAtt(nc2read, cweights_varid, 'type', 'data'); 0130 0131 nweights_varid = netcdf.defVar(nc2read, 'weight_node', 'NC_FLOAT', ... 0132 [nodeid, timeid]); 0133 netcdf.putAtt(nc2read, nweights_varid, 'long_name', ... 0134 'Weights for nodes in relaxation zone'); 0135 netcdf.putAtt(nc2read, nweights_varid, 'units', 'no units'); 0136 netcdf.putAtt(nc2read, nweights_varid, 'grid', 'fvcom_grid'); 0137 netcdf.putAtt(nc2read, nweights_varid, 'type', 'data'); 0138 0139 % end definitions 0140 netcdf.endDef(nc2read); 0141 0142 0143 netcdf.putVar(nc2read, cweights_varid, nest.weight_cell); 0144 netcdf.putVar(nc2read, nweights_varid, nest.weight_node); 0145 catch e 0146 fprintf(e.message) 0147 error('Adding variable %s failed - does the variable already exist?', 'weight_cell') 0148 end 0149 0150 0151 % close file 0152 netcdf.close(nc2read) 0153 0154 if ftbverbose 0155 fprintf('end : %s\n', subname) 0156 end