Description of swan2netcdf

0001 function swan2netcdf(matfile,ncfile,basename,first_time,last_time,increment,isforcing,kn)
0002 %matfile = 'c4.mat';
0003 %ncfile = 'case_s0004.nc';
0004 %basename = 'skg4.3';
0005 %first_time = '20090618_000000';
0006 %last_time = '20090621_000000';
0007 %increment = 3600;
0008 %isforcing = true;
0009 %kn = .003;
0010 % Convert a SWAN output file (Matlab) into a NetCDF file
0011 %
0012 % function swan2netcdf(matfile,ncfile,basename,first_time,last_time,increment);
0013 %
0014 % DESCRIPTION:
0015 %    read output from unstructured SWAN model (currently 40.82) and
0016 %    dump to a NetCDF file which is far more useful than a Matlab file.
0017 %
0018 % INPUT
0019 %   matfile  = Unstructured SWAN Matlab file
0020 %   ncfile   = NetCDF file for output
0021 %   basename = prefix for SWAN mesh, bathymetry, connectivity files
0022 %   first_time:  first time frame in Matlab object frame time
0023 %   last_time:   last time frame in Matlab object frame time
0024 %   increment:   increment in seconds
0025 %   isforcing:   converts NaNs from .mat file to 1.0's or 0.0's
0026 %   kn:          Nikuradse roughness in meters  [OPTIONAL, default = .01]
0027 % OUTPUT:
0028 %    NetCDF file containing:
0029 %      a.) time in modified Julian day
0030 %      b.) significant wave height (hs)
0031 %      c.) wave direction
0032 %      d.) mesh
0033 %      e.) peak period
0034 %      f.) U10
0035 %      g.) V10
0036 %      h.) bottom orbital velocity
0037 %      i.) bottom period
0038 %      j.) H/h ratio
0039 %      k.) wave-induced bed stress
0040 %
0041 % EXAMPLE USAGE
0042 %   swan2netcdf('gom1.mat','gom1.nc','gom1','20070101_000000','20070131_000000',3600,true,.045)
0043 %     this converts gom1.mat to gom1.nc using SWAN grid files gom1.ele, gom1.bot
0044 %     and gom1.node from Jan 1, 2007 00:00:00 to Jan 31, 2007 00:00:00 in increments
0045 %     of 1 hour.
0046 %
0047 % NOTE
0048 %    routine is not refined, e.g. will not check if files exist and will
0049 %    probably crash if you do not have the variables above in the SWAN
0050 %    output file.
0051 %    You will need approximately the following BLOCK command in your SWAN runfile
0052 %
0053 %    BLOCK 'COMPGRID' NOHEAD 'gom1.mat' LAY 3 XP YP DEP HS RTP TPS DIR WLEN &
0054 %                WINDV OUTPUT 20070101_000000 3600 SEC
0055 %
0056 % Author(s):
0057 %    Geoff Cowles (University of Massachusetts Dartmouth)
0058 %    Eric Holmes (University of Massachusetts Dartmouth)
0059 %
0060 % Revision history
0061 %    09-29-2010 -Now warns you if variable was not found in SWAN output
0062 %    .mat file and added two variables from SWAN output Ubot and TmBot.
0063 %    12-01-2010 Added 'isforcing' option
0064 %==============================================================================
0065 
0066 % set Nikaradse roughness to 1 cm if user does not specify
0067 if(~exist('kn'))
0068   kn = .01;
0069 end;
0070 z0 = kn/30.;  %hydraulic roughness
0071 
0072 eval(['load ' matfile]);              % load binary file containing SWAN results
0073 % obtained using BLOCK command with COMPGRID-set
0074 % load the connectivity
0075 elefile=[basename '.ele'];
0076 fid = fopen(elefile);                 % load TRIANGLE element based connectivity file
0077 [nele] = fscanf(fid,'%i',[1 3]);     % get number of triangles
0078 jnk = fscanf(fid,'%i',[4 nele(1)])'; % get connectivity table
0079 tri = jnk(:,2:4);
0080 
0081 % load the bathymetry
0082 bathfile=[basename '.bot'];
0083 h = textread(bathfile,'%f\n');
0084 node = prod(size(h));
0085 
0086 % check if variable range exists
0087 f = first_time;
0088 l = last_time;
0089 tbeg = datenum(str2num(f(1:4)),str2num(f(5:6)),str2num(f(7:8)),str2num(f(10:11)),str2num(f(12:13)),str2num(f(14:15)));
0090 tend = datenum(str2num(l(1:4)),str2num(l(5:6)),str2num(l(7:8)),str2num(l(10:11)),str2num(l(12:13)),str2num(l(14:15)));
0091 tinc  = increment/(24*3600);
0092 times = tbeg:tinc:tend;
0093 ntimes = prod(size(times));
0094 for i=1:ntimes;
0095     %  datestr(times(i))
0096     date = datestr(times(i),30);
0097     vname = ['Hsig_',date(1:8),'_',date(10:15)];
0098     if(exist(vname) == 0)
0099         error('variable frame %s\n does not exist',vname)
0100     end;
0101 end;
0102 
0103 
0104 % dump the netcdf file
0105 nc = netcdf(ncfile, 'clobber');
0106 nc.info = 'created from SWAN unstructured grid output file';
0107 nc.source = 'fvcom grid (unstructured) surface forcing';
0108 
0109 % dimensions
0110 nc('nele') = nele;
0111 nc('node') = node;
0112 nc('three') = 3;
0113 nc('time') = 0;
0114 
0115 % variables
0116 date = datestr(times(1),30);
0117 
0118 
0119 
0120 nc{'x'} = ncfloat('node');
0121 nc{'x'}.long_name = 'nodal x-coordinate';
0122 nc{'x'}.units     = 'm';
0123 
0124 nc{'y'} = ncfloat('node');
0125 nc{'y'}.long_name = 'nodal y-coordinate';
0126 nc{'y'}.units     = 'm';
0127 
0128 nc{'h'} = ncfloat('node');
0129 nc{'h'}.long_name = 'Bathymetry';
0130 nc{'h'}.units     = 'm';
0131 
0132 nc{'d'} = ncfloat('time','node');
0133 nc{'d'}.long_name = 'Depth';
0134 nc{'d'}.units     = 'm';
0135 
0136 nc{'nv'} = ncint('three','nele');
0137 nc{'nv'}.long_name = 'nodes surrounding element';
0138 
0139 
0140 nc{'time'} = ncfloat('time');
0141 nc{'time'}.long_name = 'time';
0142 nc{'time'}.units = 'days since 1858-11-17 00:00:00';
0143 nc{'time'}.format = 'modified julian day (MJD)';
0144 nc{'time'}.time_zone = 'UTC';
0145 
0146 nc{'Itime'} = ncint('time');
0147 nc{'Itime'}.units = 'days since 1858-11-17 00:00:00';
0148 nc{'Itime'}.format = 'modified julian day (MJD)';
0149 nc{'Itime'}.time_zone = 'UTC';
0150 
0151 nc{'Itime2'} = ncint('time');
0152 nc{'Itime2'}.units = 'msec since 00:00:00';
0153 nc{'Itime2'}.time_zone = 'UTC';
0154 
0155 vname = ['Hsig_',date(1:8),'_',date(10:15)];
0156 if(exist(vname) == 0)
0157     warning('Variable Hsig does not exist not being added to netCDF output')
0158 else
0159     nc{'hs'} = ncfloat('time','node');
0160     nc{'hs'}.long_name = 'Significant Wave Height';
0161     nc{'hs'}.units     = 'm';
0162 end;
0163 
0164 vname = ['Dir_',date(1:8),'_',date(10:15)];
0165 if(exist(vname) == 0)
0166     warning('Variable Dir does not exist not being added to netCDF output')
0167 else
0168     nc{'wdir'} = ncfloat('time','node');
0169     nc{'wdir'}.long_name = 'Wave  Direction';
0170     nc{'wdir'}.units     = 'degree';
0171 end;
0172 
0173 vname = ['RTpeak_',date(1:8),'_',date(10:15)];
0174 if(exist(vname) == 0)
0175     warning('Variable RTpeak does not exist not being added to netCDF output')
0176 else
0177     nc{'tpeak'} = ncfloat('time','node');
0178     nc{'tpeak'}.long_name = 'Relative Peak Period';
0179     nc{'tpeak'}.units     = 's';
0180 end;
0181 
0182 vname = ['Windv_x_',date(1:8),'_',date(10:15)];
0183 if(exist(vname) == 0)
0184     warning('Variable WindV_x_ does not exist not being added to netCDF output')
0185 else
0186     nc{'U10'} = ncfloat('time','node');
0187     nc{'U10'}.long_name = 'Wind Velocity x-direction';
0188     nc{'U10'}.units     = 'm/s';
0189 end;
0190 
0191 vname = ['Windv_y_',date(1:8),'_',date(10:15)];
0192 if(exist(vname) == 0)
0193     warning('Variable WindV_y_ does not exist not being added to netCDF output')
0194 else
0195     nc{'V10'} = ncfloat('time','node');
0196     nc{'V10'}.long_name = 'Wind Velocity y-direction';
0197     nc{'V10'}.units     = 'm/s';
0198 end;
0199 
0200 vname = ['Wlen_',date(1:8),'_',date(10:15)];
0201 if(exist(vname) == 0)
0202     warning('Variable Wlen does not exist not being added to netCDF output')
0203 else
0204     nc{'wlen'} = ncfloat('time','node');
0205     nc{'wlen'}.long_name = 'wavelength';
0206     nc{'wlen'}.units     = 'm';
0207 end;
0208 
0209 vname = ['Ubot_',date(1:8),'_',date(10:15)];
0210 if(exist(vname) == 0)
0211     warning('Variable Ubot does not exist not being added to netCDF output')
0212 else
0213     nc{'Ubot'} = ncfloat('time','node');
0214     nc{'Ubot'}.long_name = 'Bottom Orbital Velocity';
0215     nc{'Ubot'}.units     = 'm/s';
0216 end;
0217 
0218 
0219 vname = ['TmBot_',date(1:8),'_',date(10:15)];
0220 if(exist(vname) == 0)
0221     warning('Variable TmBot does not exist not being added to netCDF output')
0222 else
0223     nc{'TmBot'} = ncfloat('time','node');
0224     nc{'TmBot'}.long_name = 'Bottom Wave Period';
0225     nc{'TmBot'}.units     = 's';
0226 end;
0227 
0228 vname1 = ['Hsig_',date(1:8),'_',date(10:15)];
0229 vname2 = ['Depth_',date(1:8),'_',date(10:15)];
0230 if(exist(vname1) == 0 | exist(vname2)==0)
0231     warning('Bot Hsig and Depth do not exist so will not dump H/h')   
0232 else
0233     nc{'H_over_h'} = ncfloat('time','node');
0234     nc{'H_over_h'}.long_name = 'Ratio of Hsig to depth';
0235     nc{'H_over_h'}.units     = '-';
0236 end;
0237 
0238 vname1 = ['TmBot_',date(1:8),'_',date(10:15)];
0239 vname2 = ['Ubot_',date(1:8),'_',date(10:15)];
0240 if(exist(vname1) == 0 | exist(vname2)==0)
0241     warning('Bot TmBot and Ubot do not exist so will not dump bed stress')
0242 else
0243     nc{'tau_w'} = ncfloat('time','node');
0244     nc{'tau_w'}.long_name = 'wave-induced bed stress'; 
0245     nc{'tau_w'}.units     = 'm^2/s^2';
0246 end;
0247 
0248 % static vars
0249 nc{'x'}(:) = Xp;
0250 nc{'y'}(:) = Yp;
0251 nc{'h'}(:) = h;
0252 nc{'nv'}(:,:) = tri';
0253 
0254 badpts = [];
0255 % dump dynamic vars
0256 for i=1:ntimes;
0257     
0258     fprintf('processing time %s\n',datestr(times(i)));
0259     
0260     if(isforcing==1)
0261         date = datestr(times(i),30);
0262         vname = ['Hsig_',date(1:8),'_',date(10:15)]; var1 = eval(vname)';
0263         vname = ['RTpeak_',date(1:8),'_',date(10:15)];var2 = eval(vname)';
0264         var3  = var1+var2;
0265         badpts = find(isnan(var3));
0266         clear var1;
0267         clear var2;
0268         clear var3;
0269     end; 
0270     
0271     %time
0272     shift = 678942.;  % datenum(2010,1,1,0,0,0)-greg2mjulian(2010,1,1,0,0,0);
0273     time  = times(i) - shift;
0274     nc{'time'}(i) = time;
0275     nc{'Itime'}(i) = floor(time);
0276     nc{'Itime2'}(i) = mod(time,1)*24*3600*1000.;
0277     
0278     
0279     %hs
0280     date = datestr(times(i),30);
0281     vname = ['Hsig_',date(1:8),'_',date(10:15)];
0282     if(exist(vname) == 0)
0283         %fprintf('variable frame %s\n does not exist',vname)
0284     else
0285         var = eval(vname)';
0286         if (isforcing == 1); var(badpts) = 0.; end;
0287         nc{'hs'}(i,:) = var;
0288     end;
0289     
0290     %tp
0291     date = datestr(times(i),30);
0292     vname = ['RTpeak_',date(1:8),'_',date(10:15)];
0293     if(exist(vname) == 0)
0294         %fprintf('variable frame %s\n does not exist',vname)
0295     else
0296         var = eval(vname)';
0297         if (isforcing == 1);  var(badpts) = 1.; end;
0298         nc{'tpeak'}(i,:) = var;
0299     end;
0300     
0301     
0302     %depth
0303     date = datestr(times(i),30);
0304     vname = ['Depth_',date(1:8),'_',date(10:15)];
0305     if(exist(vname) == 0)
0306         %fprintf('variable frame %s\n does not exist',vname)
0307     else
0308         nc{'d'}(i,:) = eval(vname)';
0309     end;
0310     
0311     % wave dir
0312     date = datestr(times(i),30);
0313     vname = ['Dir_',date(1:8),'_',date(10:15)];
0314     if(exist(vname) == 0)
0315         %fprintf('variable frame %s\n does not exist',vname)
0316     else
0317         var = eval(vname)';
0318         if (isforcing == 1); var(badpts) = 0.; end;
0319         nc{'wdir'}(i,:) = var;
0320     end;
0321     
0322     % U10
0323     date = datestr(times(i),30);
0324     vname = ['Windv_x_',date(1:8),'_',date(10:15)];
0325     if(exist(vname) == 0)
0326         %fprintf('variable frame %s\n does not exist',vname)
0327     else
0328         var = eval(vname)';
0329         nc{'U10'}(i,:) = var;
0330     end;
0331     
0332     % V10
0333     date = datestr(times(i),30);
0334     vname = ['Windv_y_',date(1:8),'_',date(10:15)];
0335     if(exist(vname) == 0)
0336         %fprintf('variable frame %s\n does not exist',vname)
0337     else
0338         var = eval(vname)';
0339         if (isforcing == 1)
0340             var(isnan(var)) = 0.0;
0341         end
0342         nc{'V10'}(i,:) = var';
0343     end;
0344     
0345     % orbital velocity
0346     date = datestr(times(i),30);
0347     vname = ['Ubot_',date(1:8),'_',date(10:15)];
0348     if(exist(vname) == 0)
0349         %fprintf('variable frame %s\n does not exist',vname)
0350     else
0351         var = eval(vname)';
0352         if (isforcing == 1); var(badpts) = 0.; end;
0353         nc{'Ubot'}(i,:) = var';
0354     end;
0355     
0356     % wavelength
0357     date = datestr(times(i),30);
0358     vname = ['Wlen_',date(1:8),'_',date(10:15)];
0359     if(exist(vname) == 0)
0360         %fprintf('variable frame %s\n does not exist',vname)
0361     else
0362         var = eval(vname)';
0363         if (isforcing == 1); var(badpts) = 1.; end;
0364         nc{'wlen'}(i,:) = var';
0365     end;
0366     
0367     % bottom wave period
0368     date = datestr(times(i),30);
0369     vname = ['TmBot_',date(1:8),'_',date(10:15)];
0370     if(exist(vname) == 0)
0371         %fprintf('variable frame %s\n does not exist',vname)
0372     else
0373         var = eval(vname)';
0374         if (isforcing == 1); var(badpts) = 1.; end;
0375         nc{'TmBot'}(i,:) = var';
0376     end;
0377 
0378     % hsig/depth
0379     date = datestr(times(i),30);
0380     vname1 = ['Hsig_',date(1:8),'_',date(10:15)];
0381     vname2 = ['Depth_',date(1:8),'_',date(10:15)];
0382     if(exist(vname1) == 0 | exist(vname2)==0)
0383         %fprintf('variable frame %s\n does not exist',vname)
0384     else
0385         var1 = eval(vname1)';
0386         var2 = eval(vname2)';
0387         var  = var1./var2;
0388         if (isforcing == 1); var(badpts) = 0.; end;
0389         nc{'H_over_h'}(i,:) = var';
0390     end;
0391     
0392     % wave-induced bed stress
0393     date = datestr(times(i),30);
0394     vname1 = ['TmBot_',date(1:8),'_',date(10:15)];
0395     vname2 = ['Ubot_',date(1:8),'_',date(10:15)];
0396     if(exist(vname1) == 0 | exist(vname2)==0)
0397         %fprintf('variable frame %s\n does not exist',vname)
0398     else
0399         %compute wave induced bed stress using Soulsby formulas
0400         %friction factor (fw) is eq 62A
0401         %tau_w = 0.5*fw*Ubot^2
0402         var1 = eval(vname1)';
0403         var2 = eval(vname2)';
0404         omega_wave = (2.0*pi./max(var1,.05))'; %wave-orbital frequency
0405         var=0.5*1.39*((omega_wave*z0).^.52)'.*(var2.^(2.0-.52));
0406         if (isforcing == 1); var(badpts) = 0.; end;
0407         nc{'tau_w'}(i,:) = var';
0408     end;
0409     %error('hog')
0410 
0411 end;
0412 
0413 
0414 nc = close(nc);
swan2netcdf

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
