python
compile.py

python
runM2R.py

    def __init__(self):
    logging.info('\n--------------------------\n')
    logging.info('Started ' + time.ctime(time.time()))
    os.environ['WRAP_STDERR'] = 'true'

    # EDIT ===================================================================
    # Set show_progress to "False" if you do not want to see the progress
    # indicator for horizontal interpolation.
    self.show_progress = True

    # Set compileAll to True if you want automatic re-compilation of all the
    # fortran files necessary to run model2roms. Options are "gfortran" or "ifort". Edit
    # compile.py to add other Fortran compilers.
    self.compile_all = False

    # Extract time-series of data for given longitude/latitude
    self.extract_stations = False

    # Define a set of longitude/latitude positions with names to extract into
    # station files (using extractStations)
    if self.extract_stations:
        #  stationNames = ['NorthSea', 'Iceland', 'EastandWestGreenland', 'Lofoten', 'Georges Bank']
        #  lonlist = [2.4301, -22.6001, -47.0801, 13.3801, -67.2001]
        #  latlist = [54.5601, 63.7010, 60.4201, 67.5001, 41.6423]

        self.station_names = ["Ytre Utsira", "Indre Utsira", "Lista"]
        self.latlist = [59.316667, 59.316667, 58.016667]
        self.lonlist = [4.800000, 4.983333, 6.533333]
        self.numberofpoints = 4  # Number of points around lat/lon to extract and average as output

    # Create the bry, init, and clim files for a given grid and input data
    self.create_ocean_forcing = True

    # Create atmospheric forcing for the given grid
    self.create_atmos_forcing = False  # currently in beta stages

    # Create a smaller resolution grid based on your original. Decimates every second for
    # each time run
    self.decimate_gridfile = False

    # Write ice values to file (for Arctic regions)
    self.write_ice = False

    # Write biogeochemistry values to file
    self.write_bcg = False

    # ROMS sometimes requires input of ice and ssh, but if you dont have these write files containing zeros to file
    self.set_2d_vars_to_zero = False

    # Apply filter to smooth the 2D fields after interpolation (time consuming but enhances results)
    self.use_filter = True

    # Format to write the ouput to: 'NETCDF4', 'NETCDF4_CLASSIC', 'NETCDF3_64BIT', or 'NETCDF3_CLASSIC'
    # Using NETCDF4 automatically turns on compression of files (ZLIB)
    self.output_format = 'NETCDF4'
    self.use_zlib = True

    # Frequency of the input data: usually monthly
    self.time_frequency_inputdata = "month"  # Possible options: "month", "hour", "5days"

    # Path to where results files should be stored
    self.outdir = "../oceanography/NAUTILOS/"
    if not os.path.exists(self.outdir):
        os.makedirs(self.outdir, exist_ok=True)

    # IN GRIDTYPES ------------------------------------------------------------------------------
    # Define what grid type you want to interpolate from (input MODEL data)
    # Currently supported options:
    # 1. NORESM, 2. GLORYS, 3. SODA3, 4. SODA3_5DAY
    self.ocean_indata_type = 'GLORYS'
    self.atmos_indata_type = 'ERA5'

    # Define contact info for final NetCDF files
    self.author_name = "Trond Kristiansen"
    self.author_email = "trond.kristiansen (at) niva.no"

    # Define what grid type you wnat to interpolate from: Can be Z for SIGMA for ROMS
    # vertical coordinate system or ZLEVEL. also define the name of the dimensions in the input files.
    # Options:
    # 1. SIGMA (not properly implemented yet), 2. ZLEVEL
    self.ingrid_type = "ZLEVEL"  # "ZLEVEL"

    # Define the names of the geographical variables in the input files. These may
    # differ depending how the variable is located in a grid (e.g. Arakawa C grid - ROMS). In
    # SODA 3.3.1 the u and v location is defined by xu_ocean,  yu_ocean while temperature is
    # located in xt_ocean, yt_ocean.
    self.grd_type = 'regular'
    self.lon_name = "longitude"
    self.lat_name = "latitude"
    self.depth_name = "depth"
    self.lon_name_u = "longitude"
    self.lat_name_u = "latitude"
    self.lon_name_v = "longitude"
    self.lat_name_v = "latitude"

    if self.ocean_indata_type == 'SODA3_5DAY':
        self.lon_name = "xt_ocean"
        self.lat_name = "yt_ocean"
        self.depth_name = "st_ocean"
        self.lon_name_u = "xu_ocean"
        self.lat_name_u = "yu_ocean"
        self.lon_name_v = "xu_ocean"
        self.lat_name_v = "yu_ocean"
        self.time_object = []

    self.time_name = "time"
    self.realm = "ocean"
    self.fillvaluein = -32767

    # OUT GRIDTYPES ------------------------------------------------------------------------------
    # Define what grid type you want to interpolate to
    # Options: This is just the name of your grid used to identify your selection later
    self.outgrid_name = 'ROHO160'  # "ROHO800", "A20"
    self.outgrid_type = "ROMS"

    # Subset input data. If you have global data you may want to seubset these to speed up reading. Make
    # sure that your input data are cartesian (0-360 or -180:180, -90:90)
    self.subset_indata = False
    if self.subset_indata:
        self.subset = self.define_subset_for_indata()

    # Define nmber of output depth levels
    self.nlevels = 40
    # Define the grid stretching properties (leave default if uncertain what to pick)
    self.vstretching = 4
    self.vtransform = 2
    self.theta_s = 7.0
    self.theta_b = 0.1
    self.tcline = 250.0
    self.hc = 250

    # PATH TO FORCING DATA --------------------------------------------------------------------
    # Define the path to the input data
    self.ocean_forcing_path = self.define_ocean_forcing_data_path()
    self.atmospheric_forcing_path = self.define_atmospheric_forcing_path()

    # PATH TO GRID -----------------------------------------------------------------------------
    # Define the path to the grid file
    self.roms_grid_path = self.define_roms_grid_path()

    # Climatology is only monthly and model2roms needs to know this
    self.isclimatology = False

    # DATE AND TIME DETAILS ---------------------------------------------------------
    # Define the period to create forcing for
    self.start_year = 2017
    self.end_year = 2019
    self.start_month = 1
    self.end_month = 11
    self.start_day = 15
    self.end_day = 31