! ******************************* LTRANS Input Data File ******************************* !---- This is the file that contains input values for LTRANS with parameters grouped --- !---- (Previously LTRANS.inc) !*** NUMBER OF PARTICLES *** $numparticles numpar = 1612 ! Number of particles (total number for whole simulation) ! numpar should equal the number of rows in the particle ! locations input file $end !*** TIME PARAMETERS *** $timeparam days = 120 ! Number of days to run the model iprint = 3600 ! Print interval for LTRANS output (s); 3600 = every hour dt = 3600 ! External time step (duration between hydro model predictions) (s) idt = 3600 ! Internal (particle tracking) time step (s) $end !*** ROMS HYDRODYNAMIC MODULE PARAMETERS *** $hydroparam us = 8 ! Number of Rho grid s-levels in ROMS hydro model ws = 9 ! Number of W grid s-levels in ROMS hydro model tdim = 10 ! Number of time steps per ROMS hydro predictions file hc = 100 ! Min Depth - used in ROMS S-level transformations z0 = 0.02 ! ROMS bottom roughness parameter (Zob) Vtransform = 2 ! 1-WikiRoms Eq. 1, 2-WikiRoms Eq. 2, 3-Song/Haidvogel 1994 Eq. ! readZeta = .TRUE. ! If .TRUE. read in sea-surface height (zeta) from NetCDF file, else use constZeta constZeta = 0.0 ! Constant value for Zeta if readZeta is .FALSE. readSalt = .TRUE. ! If .TRUE. read in salinity (salt) from NetCDF file, else use constSalt constSalt = 0.0 ! Constant value for Salt if readSalt is .FALSE. readTemp = .TRUE. ! If .TRUE. read in temperature (temp) from NetCDF file, else use constTemp constTemp = 0.0 ! Constant value for Temp if readTemp is .FALSE. readU = .TRUE. ! If .TRUE. read in u-momentum component (U ) from NetCDF file, else use constU constU = 0.0 ! Constant value for U if readU is .FALSE. readV = .TRUE. ! If .TRUE. read in v-momentum component (V ) from NetCDF file, else use constV constV = 0.0 ! Constant value for V if readV is .FALSE. readW = .TRUE. ! If .TRUE. read in w-momentum component (W ) from NetCDF file, else use constW constW = 0.0 ! Constant value for W if readW is .FALSE. readAks = .TRUE. ! If .TRUE. read in salinity vertical diffusion coefficient (Aks ) from NetCDF file, else ! use constAks constAks = 0.0 ! Constant value for Aks if readAks is .FALSE. readDens = .FALSE. constDens = 1025.0 $end !*** TURBULENCE MODULE PARAMETERS *** $turbparam HTurbOn = .TRUE. ! Horizontal Turbulence on (.TRUE.) or off (.FALSE.) VTurbOn = .TRUE. ! Vertical Turbulence on (.TRUE.) or off (.FALSE.) ConstantHTurb = 1.0 ! Constant value of horizontal turbulence (m2/s) $end !*** BEHAVIOR MODULE PARAMETERS *** $behavparam Behavior = 0 ! Behavior type (specify a number) ! Note: The behavior types numbers are: ! 0 Passive, 1 near-surface, 2 near-bottom, 3 DVM, ! 4 C.virginica oyster larvae, 5 C.ariakensis oyster larvae, ! 6 constant, 7 Tidal Stream Transport OpenOceanBoundary = .TRUE. ! Note: If you want to allow particles to "escape" via open ocean ! boundaries, set this to TRUE; Escape means that the particle ! will stick to the boundary and stop moving mortality = .FALSE. ! TRUE if particles can die; else FALSE deadage = 17280000 ! Age at which a particle stops moving (i.e., dies) (s) ! Note: deadage stops particle motion for all behavior types pediage = 17280000 ! Age when particle reaches max swim speed and can settle (s) ! Note: for oyster larvae behavior types (4 & 5), ! pediage = age at which a particle becomes a pediveliger ! Note: pediage does not cause particles to settle if ! the Settlement module is not on swimstart = 0.0 ! Age that swimming or sinking begins (s) 1 day = 1.*24.*3600. swimslow = 0.0 ! Swimming speed when particle begins to swim (m/s) swimfast = 0.0 ! Maximum swimming speed (m/s) 0.05 m/s for 5 mm/s ! Note: for constant swimming speed for behavior types 1,2 & 3, ! set swimslow = swimfast = constant speed Sgradient = 1.0 ! Salinity gradient threshold that cues larval behavior (psu/m) ! Note: This parameter is only used if Behavior = 4 or 5. sink = -0.0003 ! Sinking velocity for behavior type 6 ! Note: This parameter is only used if Behavior = 6. ! Tidal Stream Transport behavior type: Hswimspeed = 0.9 ! Horizontal swimming speed (m/s) Swimdepth = 2 ! Depth at which fish swims during flood time ! in meters above bottom (this should be a positive value ! Note: this formulation may need some work $end !*** DVM. The following are parameters for the Diurnal Vertical Migration (DVM) behavior type *** ! Note: These values were calculated for September 1 at the latitude of 37.0 (Chesapeake Bay mouth) ! Note: Variables marked with ** were calculated with light_v2BlueCrab.f (not included in LTRANS yet) ! Note: These parameters are only used if Behavior = 3 $dvmparam twistart = 4.801821 ! Time of twilight start (hr) ** twiend = 19.19956 ! Time of twilight end (hr) ** daylength = 14.39774 ! Length of day (hr) ** Em = 1814.328 ! Irradiance at solar noon (microE m^-2 s^-1) ** Kd = 1.07 ! Vertical attenuation coefficient thresh = 0.0166 ! Light threshold that cues behavior (microE m^-2 s^-1) $end !*** SETTLEMENT MODULE PARAMETERS *** $settleparam settlementon = .FALSE. ! settlement module on (.TRUE.) or off (.FALSE.) ! Note: If settlement is off: set minholeid, maxholeid, minpolyid, ! maxpolyid, pedges, & hedges to 1 ! to avoid both wasted variable space and errors due to arrays of size 0. ! If settlement is on and there are no holes: set minholeid, ! maxholeid, and hedges to 1 holesExist = .FALSE. ! Are there holes in habitat? yes(TRUE) no(FALSE) minpolyid = 1 ! Lowest habitat polygon id number maxpolyid = 1 ! Highest habitat polygon id number minholeid = 1 ! Lowest hole id number maxholeid = 1 ! Highest hole id number pedges = 1 ! Number of habitat polygon edge points (# of rows in habitat polygon file) hedges = 1 ! Number of hole edge points (number of rows in holes file) $end !*** CONVERSION MODULE PARAMETERS *** $convparam PI = 3.14159265358979 ! Pi Earth_Radius = 6378000 ! Equatorial radius of Earth (m) SphericalProjection = .TRUE. ! Spherical Projection from ROMS if TRUE. If FALSE, mercator projection is used. latmin = 29.0954 ! Minimum longitude value, only used if SphericalProjection is .TRUE. lonmin = -90.3958 ! Minimum latitude value, only used if SphericalProjection is .TRUE. $end !*** INPUT FILE NAME AND LOCATION PARAMETERS ***; ! ** ROMS NetCDF Model Grid file ** !Note: the path to the file is necessary if the file is not in the same folder as the code !Note: if .nc file in separate folder in Linux, then include path. For example: ! NCgridfile = '/share/enorth/CPB_GRID_wUV.nc' !Note: if .nc file in separate folder in Windows, then include path. For example: ! NCgridfile = 'D:\ROMS\CPB_GRID_wUV.nc' $romsgrid NCgridfile='/project/zxue/you3/Barataria_20yr/inpdata/grid/Barataria_grid_minh1.5_hanning_smooth2_deep_barataria_pass.nc' $end ! ** ROMS Predictions NetCDF Input (History) File ** !Filename = prefix + filenum + suffix !Note: the path to the file is necessary if the file is not in the same folder as the code !Note: if .nc file in separate folder in Windows, then include path in prefix. For example: ! prefix='D:\ROMS\y95hdr_' ! if .nc file in separate folder in Linux, then include path in prefix. For example: ! prefix='/share/lzhong/1995/y95hdr_' $romsoutput prefix='/work/you3/output/Barataria/exp24_6/ocean_avg_' ! NetCDF Input Filename prefix suffix='.nc' ! NetCDF Input Filename suffix filenum = 1385 ! Number in first NetCDF input filename numdigits = 5 ! Number of digits in number portion of file name (with leading zeros) startfile = .FALSE. ! Is it the first file, i.e. does the file have an additional time step? $end ! ** Particle Location Input File ** !Note: the path to the file is necessary if the file is not in the same folder as the code $parloc parfile = '/project/zxue/you3/Barataria_20yr/inpdata/float/BRT_float_LTRANS.csv' !Particle locations $end ! ** Habitat Polygon Location Input Files ** !Note: the path to the file is necessary if the file is not in the same folder as the code $habpolyloc habitatfile = '' !Habitat polygons holefile = '' !Holes in habitat polygons $end ! ** Output Related Variables ** $output !NOTE: Full path must already exist. Model can create files, but not directories. outpath = '/work/you3/output/Barataria/LTRANS_floats/' ! Location to write output .csv and/or .nc files ! Use outpath = './' to write in same folder as the executable NCOutFile = 'LTRANS_floatsOUT' ! Name of the NetCDF output files (do not include .nc) outpathGiven = .TRUE. ! If TRUE files are written to the path given in outpath writeCSV = .FALSE. ! If TRUE write CSV output files writeNC = .TRUE. ! If TRUE write .NC output files NCtime = 0 ! Time interval between creation of new NetCDF output files (seconds) ! Note: setting this to 0 will result in just one large output file !NetCDF Model Metadata (these will be stale unless you edit them): SVN_Version = 'https://cmgsoft.repositoryhosting.com/svn/cmgsoft_ltrans/trunk' RunName = 'LTRANS v.2 test case' ExeDir = '/project/zxue/you3/Barataria_20yr/runscript/exp28_LTRANS1/' OutDir = '/work/you3/output/Barataria/exp24_62/LTRANS_floats/' RunBy = 'Dan Ou' Institution = 'DOCS LSU' StartedOn = 'Aug 2019' $end !*** OTHER PARAMETERS *** $other seed = 0 ! Seed value for random number generator (Mersenne Twister) ErrorFlag = 3 ! What to do if an error is encountered: 0=stop, 1=return particle to previous location, ! 2=kill particle & stop tracking that particle, 3=set particle out of bounds & ! stop tracking that particle ! Note: Options 1-3 will output information to ErrorLog.txt ! Note: This is only for particles that travel out of bounds illegally BoundaryBLNs = .FALSE. ! Create Surfer Blanking Files of boundaries? .TRUE.=yes, .FALSE.=no SaltTempOn = .FALSE. ! Calculate salinity and temperature at particle ! location: yes (.TRUE.) or no (.FALSE.) TrackCollisions = .FALSE. ! Write Bottom and Land Hit Files? .TRUE.=yes, .FALSE.=no WriteHeaders = .FALSE. ! Write .txt files with column headers? .TRUE.=yes, .FALSE.=no WriteModelTiming = .FALSE. ! Write .csv file with model timing data? .TRUE.=yes, .FALSE.=no ijbuff = 4 ! number of extra elements to read in on every side of the particles FreeSlip = .TRUE. ! enable the use of the free slip condition $end