Write a namelist for the timeseries extraction at specifc nodes.
write_FVCOM_probes(Mobj, nml_file, interval, varlist, locations)
DESCRIPTION:
Write a namelist of variables to extract at given positions with the
interval specified.
INPUT:
nml_file - full path to the output namelist file.
interval - output interval (in seconds)
probe - struct of structs with fields whose names are the probe title.
Each probe struct must have the following fields:
node - unstructured grid node ID (for all scalars except u
and v).
elem - unstructured grid element ID (for u and v only).
file - file name for the current probe's output. If the
'variable' field is a cell array of multiple variables, each
output file name will have the variable name appended (e.g.
'Newlyn.dat' becomes 'Newlyn_el.dat' for elevation time
series).
description - description of this output. If multiple variable are
specified in variable, the length of the description must match
the number of variables.
variable - variable name to extract from FVCOM. Define as a cell
array for multiple variables. Output file names in the namelist
will be appended with the variable name. Variable names are the
internal FVCOM variable names (which is not always the same as
the output file variable name). Check mod_probe.F in subroutine
PROBE_STORE for the full list of supported variables. I've
reproduced that list in the NOTES below.
longname - long name for the current variable. Must also match
the number of variables.
levels - start and end level for 3D variables (u, v, w, ww,
t1, s1, q2, l, q2l, km, kh, kq, rho1).
OUTPUT:
Namelist for inclusion in the main FVCOM namelist (PROBES_FILE).
EXAMPLE USAGE:
probes.newlyn.file = 'newlyn_elev.dat';
probes.newlyn.node = 1045;
probes.newlyn.elem = 467;
probes.newlyn.description = 'Elevation at Newlyn';
probes.newlyn.variable = 'el';
probes.newlyn.longname = 'Surface elevation (m)';
probes.newlyn.levels = [1, length(Mobj.siglay)];
write_FVCOM_river_nml(Mobj, 'casename_probes.nml', 600, probes)
NOTES:
Available output variables are currently (FVCOM v3.1.6) limited to:
- el - surface elevation
- t1, s1 - temperature and salinity
- rho1 - density
- u, v, ua, va - velocity and depth-averaged velocities
- ww - vertical water velocity
- w - vertical velocity in sigma system
- q2, l, q2l - turbulent kinetic energy (TKE), TKE lengthscale and
TKE times TKE lengthscale
- km, kh, kq - turbulent eddy viscosity for momentum, scalars and
q2/q2l
- aice, vice, uice2, vice2 - ice parameters
- csed - suspended sediment concentration
Author(s):
Pierre Cazenave (Plymouth Marine Laboratory)
Revision history:
2014-02-10 - First version.
2015-01-14 - Fix export of the u and v locations to use the closest
element instead of the node ID. Using the node ID for the u and v data
will yield velocity time series miles away from the actual location of
interest.
==========================================================================0001 function write_FVCOM_probes(nml_file, interval, probes) 0002 % Write a namelist for the timeseries extraction at specifc nodes. 0003 % 0004 % write_FVCOM_probes(Mobj, nml_file, interval, varlist, locations) 0005 % 0006 % DESCRIPTION: 0007 % Write a namelist of variables to extract at given positions with the 0008 % interval specified. 0009 % 0010 % INPUT: 0011 % nml_file - full path to the output namelist file. 0012 % interval - output interval (in seconds) 0013 % probe - struct of structs with fields whose names are the probe title. 0014 % Each probe struct must have the following fields: 0015 % node - unstructured grid node ID (for all scalars except u 0016 % and v). 0017 % elem - unstructured grid element ID (for u and v only). 0018 % file - file name for the current probe's output. If the 0019 % 'variable' field is a cell array of multiple variables, each 0020 % output file name will have the variable name appended (e.g. 0021 % 'Newlyn.dat' becomes 'Newlyn_el.dat' for elevation time 0022 % series). 0023 % description - description of this output. If multiple variable are 0024 % specified in variable, the length of the description must match 0025 % the number of variables. 0026 % variable - variable name to extract from FVCOM. Define as a cell 0027 % array for multiple variables. Output file names in the namelist 0028 % will be appended with the variable name. Variable names are the 0029 % internal FVCOM variable names (which is not always the same as 0030 % the output file variable name). Check mod_probe.F in subroutine 0031 % PROBE_STORE for the full list of supported variables. I've 0032 % reproduced that list in the NOTES below. 0033 % longname - long name for the current variable. Must also match 0034 % the number of variables. 0035 % levels - start and end level for 3D variables (u, v, w, ww, 0036 % t1, s1, q2, l, q2l, km, kh, kq, rho1). 0037 % 0038 % OUTPUT: 0039 % Namelist for inclusion in the main FVCOM namelist (PROBES_FILE). 0040 % 0041 % EXAMPLE USAGE: 0042 % probes.newlyn.file = 'newlyn_elev.dat'; 0043 % probes.newlyn.node = 1045; 0044 % probes.newlyn.elem = 467; 0045 % probes.newlyn.description = 'Elevation at Newlyn'; 0046 % probes.newlyn.variable = 'el'; 0047 % probes.newlyn.longname = 'Surface elevation (m)'; 0048 % probes.newlyn.levels = [1, length(Mobj.siglay)]; 0049 % write_FVCOM_river_nml(Mobj, 'casename_probes.nml', 600, probes) 0050 % 0051 % NOTES: 0052 % Available output variables are currently (FVCOM v3.1.6) limited to: 0053 % - el - surface elevation 0054 % - t1, s1 - temperature and salinity 0055 % - rho1 - density 0056 % - u, v, ua, va - velocity and depth-averaged velocities 0057 % - ww - vertical water velocity 0058 % - w - vertical velocity in sigma system 0059 % - q2, l, q2l - turbulent kinetic energy (TKE), TKE lengthscale and 0060 % TKE times TKE lengthscale 0061 % - km, kh, kq - turbulent eddy viscosity for momentum, scalars and 0062 % q2/q2l 0063 % - aice, vice, uice2, vice2 - ice parameters 0064 % - csed - suspended sediment concentration 0065 % 0066 % Author(s): 0067 % Pierre Cazenave (Plymouth Marine Laboratory) 0068 % 0069 % Revision history: 0070 % 2014-02-10 - First version. 0071 % 2015-01-14 - Fix export of the u and v locations to use the closest 0072 % element instead of the node ID. Using the node ID for the u and v data 0073 % will yield velocity time series miles away from the actual location of 0074 % interest. 0075 % 0076 %========================================================================== 0077 0078 subname = 'write_FVCOM_probes'; 0079 0080 global ftbverbose; 0081 if ftbverbose 0082 fprintf('\nbegin : %s\n', subname) 0083 end 0084 0085 fnames = fieldnames(probes); 0086 np = length(fnames); 0087 0088 f = fopen(nml_file, 'w'); 0089 assert(f >= 0, 'Error writing to %s. Check permissions and try again.', nml_file) 0090 0091 for p = 1:np 0092 if iscell(probes.(fnames{p}).variable) 0093 nv = length(probes.(fnames{p}).variable); 0094 assert(length(probes.(fnames{p}).description) == nv, 'Specify one description per output variable.') 0095 assert(length(probes.(fnames{p}).description) == nv, 'Specify one longname per output variable.') 0096 else 0097 nv = 1; 0098 vname = probes.(fnames{p}).variable; 0099 lname = probes.(fnames{p}).longname; 0100 desc = probes.(fnames{p}).description; 0101 end 0102 for v = 1:nv 0103 if nv > 1 0104 vname = probes.(fnames{p}).variable{v}; 0105 lname = probes.(fnames{p}).longname{v}; 0106 desc = probes.(fnames{p}).description{v}; 0107 end 0108 [pathstr, name, ext] = fileparts(probes.(fnames{p}).file); 0109 name = sprintf('%s_%s%s', name, vname, ext); 0110 file = fullfile(pathstr, name); 0111 fprintf(f, '&NML_PROBE\n'); 0112 fprintf(f, ' PROBE_INTERVAL = "seconds=%.1f",\n', interval); 0113 if any(strcmpi(vname, {'u', 'v'})) 0114 fprintf(f, ' PROBE_LOCATION = %i,\n', probes.(fnames{p}).elem); 0115 else 0116 fprintf(f, ' PROBE_LOCATION = %i,\n', probes.(fnames{p}).node); 0117 end 0118 fprintf(f, ' PROBE_TITLE = "%s",\n', file); 0119 % If we've got something which is vertically resolved, output the 0120 % vertical levels. 0121 switch vname 0122 case {'u', 'v', 'w', 'ww', 't1', 's1', 'km', 'kh', 'q2', 'l', 'q2l', 'kq', 'rho1'} 0123 fprintf(f, ' PROBE_LEVELS = %i %i,\n', probes.(fnames{p}).levels); 0124 end 0125 fprintf(f, ' PROBE_DESCRIPTION = "%s",\n', desc); 0126 fprintf(f, ' PROBE_VARIABLE = "%s",\n', vname); 0127 fprintf(f, ' PROBE_VAR_NAME = "%s"\n', lname); 0128 fprintf(f, '/\n'); 0129 end 0130 end 0131 0132 fclose(f); 0133 0134 if ftbverbose 0135 fprintf('end : %s\n', subname) 0136 end