Output¶

SPECIFICATION OF RESULT FOLDER

RESULT_FOLDER: result folder name, e.g., RESULT_FOLDER = /Users/tmp/

SPECIFICATION OF OUTPUT VARIABLES

NumberStations: number of station for output. If NumberStations \(> 0\), need input i,j in STATIONS_FILE
OUTPUT_RES: integer parameter for output data resolution. e.g. 2 for print every 2 points
DEPTH_OUT: logical parameter for output depth. T or F.
U: logical parameter for output u. T or F.
V: logical parameter for output v. T or F.
ETA: logical parameter for output \(\eta\). T or F.
MASK: logical parameter for output wetting-drying MASK. T or F.
MASK9: logical parameter for output MASK9 (switch for Boussinesq/NSWE). T or F.
SourceX: logical parameter for output source terms in x direction. T or F.
SourceY: logical parameter for output source terms in y direction. T or F.
P: logical parameter for output of momentum flux in x direction. T or F.
Q: logical parameter for output of momentum flux in y direction. T or F.
Fx: logical parameter for output of numerical flux F in x direction. T or F.
Fy: logical parameter for output of numerical flux F in y direction. T or F.
Gx: logical parameter for output of numerical flux G in x direction. T or F.
Gy: logical parameter for output of numerical flux G in y direction. T or F.
AGE: logical parameter for output of breaking age. T or F.
HMAX: logical parameter for output of recorded maximum surface elevation . T or F.
HMIN: logical parameter for output of recorded minimum surface elevation . T or F.
UMAX: logical parameter for output of recorded maximum velocity . T or F.
VORMAX: logical parameter for output of recorded maximum vorticity . T or F.
MFMAX: logical parameter for output of recorded maximum momentum flux . T or F.
OUT_Time: logical parameter for output of recorded tsunami arrival time . T or F.
WaveHeight: logical parameter for output of wave height, Hsig, Hrms, Havg. T or F.
OUT_METEO: logical parameter for output of pressure field. T or F.
ROLLER: logical parameter for output of roller-induced flux. T or F.
UNDERTOW: logical parameter for output of undertow. T or F.
OUT_NU: logical parameter for output of breaking location. T or F.

OUTPUT FILES

The output files are saved in the result directory defined by RESULT_FOLDER in “input.txt”. Output file names are a combination of variable name and an output series number such as eta_00001, eta_00002, ..... The format and read/write algorithm are consistent with a depth file.

CENTRAL module

eta_xxxxx: surface elevation

u_xxxxx: velocity in the x direction

v_xxxxx: velocity in the y direction

mask_xxxxx: masks for wetting (1) and drying (0)

mask9_xxxxx: masks for wetting (1) and drying (0) defined in 9 points

hmax_xxxxx: maximum surface elevation

hmin_xxxxx: minimum surface elevation

umax_xxxxx: maximum velocity

MFmax_xxxxx: maximum momentum flux

VORmax_xxxxx: maximum vertical vorticiy

time_xxxxx: tsunami arrival time

p_xxxxx: volume flux in the x direction

q_xxxxx: volume flux in the y direction

nubrk_xxxxx: breaking induced eddy viscosity (when viscosity breaker is on)

etat_xxxxx: \(\eta_t\)

age_xxxxx: breaking age (in seconds)

roller_xxxxx: roller-induced mass flux

U_undertow_xxxxx: roller-induced extra undertow flux in the x direction

V_undertow_xxxxx: roller-induced extra undertow flux in the y direction

METEO module

Pstorm_xxxxx: air pressure

Ustorm_xxxxx: wind velocity in the x direction

Vstorm_xxxxx: wind velocity in the y direction

VESSEL module

Fves_xxxxx: gradient of mass flux induced by vessel (panel source)

Pves_xxxxx: pressure specified for the pressure source

SEDIMENT module

C_xxxxx: sediment concentration (g/l)

Pick_xxxxx: pickup rate

Depo_xxxxx: deposition rate

DchgS_xxxxx: depth change in suspended load

DchgB_xxxxx: depth change in bed load

BedFx_xxxxx: bedload flux in the x direction

BedFy_xxxxx: bedload flux in the y direction

dep_xxxxx: depth

Station files

To get time series of surface elevation, u and v at interested locations, you can specify a station file which includes the locations for output. Station input files (e.g., gauges.txt) have size (# of stations) x 2, where column 1 contains Mglob location (unit = grid points) and column 2 contains Nglob location (unit = grid points). In 1D cases, the Nglob location (second column) needs to be set to 1 for all gauges; if set to 0, station files will not be outputted.

in “input.txt”, add NumberStations = <integer number of stations>

in “input.txt”, STATIONS_FILE = <file name, e.g., gauges.txt>

format of STATIONS_FILE: two integers for grid points in x and y, respectively.

Example: refer to Example: station file

Output for stations is a series of numbered files such as sta_0001, sta_0002 .... (NOTE: four digit numbers here vs. five digit numbers for 2D output like eta_00001). The output file for stations contains four columns: time, eta, u, and v.

The version after 3.4 uses a buffer to write out stations to speed up the program on a large scale HPC. The array dimensions for the buffer are (StationOutputBuffer,NumberStations,4), where StationOutputBuffer = 1000 by default. You can also specify StationOutputBuffer in input.txt. An example to set StationOutputBuffer is in /simple_cases/tide_constant/.

TOTAL_TIME = 200.0
PLOT_INTV = 1.0
PLOT_INTV_STATION = 0.5
SCREEN_INTV = 1.0
StationOutputBuffer = 100

ASCII format

The default format is ASCII. The format and read algorithm are consistent with a depth file.

A station file contains four columns, which are values of time (s), eta (m), u (m/s) and v (m/s), respectively.

BINARY format

When FIELD_IO_TYPE = BINARY is specified in “input.txt”, the 2D output files such as eta_00001, ... are in the binary format. Here’s an example of reading in:

MATLAB:

fileID = fopen('eta_00001');

eta = fread(fileID,[Mglob Nglob],'*double');

fclose(fileID);

pcolor(eta),shading flat

PYTHON:

def readBathyData(outputDir, args):
   """Function that reads in FUNWAVE's bathy data from: dep.out in output directory."""

   bathyFileName = os.path.join(outputDir, 'dep.out')

   # read in and convert into 2D numpy array if binary fieldiotype
   fieldIOType = args.fieldiotype # 'ascii' or 'binary'

   if fieldIOType == 'ascii':
      bathy = np.loadtxt(bathyFileName)
      (Ny, Nx) = bathy.shape # [Nglob,Mglob]

   else:
      Ny = args.nglob    # if not included in args, manually set Nx, Ny
      Nx = args.mglob

      # option 1
      bathy = np.fromfile(bathyFileName).reshape(Ny,Nx)

      # option 2
      with open(bathyFileName, 'rb') as file: # 'rb' is used to read binary in windows, on linux you can use 'r'
      bathy_file = file.read()
      bathy = np.frombuffer(bathy_file, dtype=np.float32)
      bathy = bathy.reshape(Ny, Nx)

      # option 3
      fin = open(bathyFileName, mode='rb')
      dataType = np.dtype([('elev', '<f8', Ny*Nx)])
      bathyNotParsed = np.fromfile(fin, dtype=dataType)
      bathy = np.zeros([Ny,Nx])
      for j in range(Nx):
        for i in range(Ny):
          bathy[i,j] = bathyNotParsed[0][0][(j*Ny)+i]

   return bathy

Station files do not have Binary format.

Other format

Other formats such as NetCDF and HDF5 are also provided but not distributed in the master Github repository.