Many variables at TRACMASS can be modified using the namelist without the need to recompile the program. Each project has a namelist_CASE.in in the project folder. When TRACMASS is compiled a copy of the namelist (namelist.in) can be found in the main TRACMASS directory.

This is a list of all the variables that can be changed in the namelist and their corresponding group.

CopyINIT_GRID_DESCRIPTION

Here you can set the paths and variable names to define the volume/mass fluxes.

  • griddir [integer, array]: the direction of the input data indexes referenced to the TRACMASS reference system. It’s a three element array; the first element corresponds to the zonal direction, the second one to the meridional direction and the third one to the vertical direction. Two possible values are possible (1) eastward/northward/upward or (-1) westward/southward/downward. The default values are [1,1,1].

  • zeroindx [logical]: the first index in the original dataset is given by zero instead of one. The default value is FALSE.

  • trunit [real]: constant to scale the TRACMASS transports.

  • l_onestep [logical]: read one time step per input file. The default value is FALSE.

  • physDataDir [character]: path to the input data directory.

  • physPrefixForm [character]: prefix of the input data file name.

  • dateFormat [character]: part of the input data name that will be corrected by the subroutine filledFileName.

  • tGridName [character]: the suffix for T grid files.

  • uGridName [character]: the suffix for U grid files.

  • vGridName [character]: the suffix for V grid files.

  • wGridName [character]: the suffix for W grid files.

  • fileSuffix [character]: describes the file format of the input files such as ‘nc’ or ‘nc4’.

  • hs_name [character]: variable name for surface height/pressure, etc.

  • ueul_name [character]: variable name for zonal velocity.

  • veul_name [character]: variable name for meridional velocity.

  • usgs_name [character]: variable name for subgrid zonal velocity. The default value is ” “.

  • vsgs_name [character]: variable name for subgrid meridional velocity. The default value is ” “.

  • usub_name [character]: variable name for secondary subgrid zonal velocity. The default value is ” “.

  • vsub_name [character]: variable name for secondary subgrid meridional velocity. The default value is ” “.

  • w_name [character]: variable name for vertical velocity. The default value is ” “.

CopyINIT_GRID_SIZE

Here you can set the paths to the files that contain the mesh grid as well as defined the size or the domain or the type of boundary conditions.

  • imt [integer]: number of global i points.

  • jmt [integer]: number of global j points.

  • km [integer]: number of global k points.

  • iperio [integer]: zonal boundary conditions. Two possible values: (0) no zonal boundary condition or (1) zonal conditions is on. The default values is 0.

  • jperio [integer]: meridional boundary conditions. Two possible values: (0) no meridional boundary condition or (1) meridional condition is on. The default values is 0.

  • topoDataDir [character]: path to the directory that contains mesh or topography data.

  • hgridFile [character]: name of the file that contains variables linked to horizontal grid data.

  • dy_name [character]: variable name for dy in T points.

  • dyu_name [character]: variable name for dy in U points.

  • dx_name [character]: variable name for dx in T points.

  • dxv_name [character]: variable name for dx in V points.

  • zgridFile [character]: name of the file that contains variables linked to vertical grid data.

  • dzt_name [character]: variable name for dz in T points.

  • dzu_name [character]: variable name for dz in U points.

  • dzv_name [character]: variable name for dz in V points.

  • dep_name [character]: variable name for total depth.

  • bathyFile [character]: name of the file that contains variables linked to bathymetry/topography.

  • kmt_name [character]: variable name for bathymetry.

CopyINIT_GRID_SUBDOMAIN

Here you can activate and define a subdomain in TRACMASS (more info can be found here).

  • l_subdom [logical]: activate a subdomain. Default value is FALSE.

  • imindom [integer]: index that represents the western boundary of the subdomain.

  • imaxdom [integer]: index that represents the eastern boundary of the subdomain.

  • jmindom [integer]: index that represents the southern boundary of the subdomain.

  • jmaxdom [integer]: index that represents the northern boundary of the subdomain.

CopyINIT_GRID_TIME

Here you can set the time step and unit at which the input data is stored, as well as define the number of subcycles use in TRACMASS.

  • ngcm_step [integer]: number of time steps between two time levels.

  • ngcm_unit [integer]: unit of the time step: (1) seconds, (2) minutes, (3) hours, (4) days, (5) months, and (6) years.

  • iter [integer]: number of subcycles between time levels.

CopyINIT_START_DATE

Here you can define the starting date of the simulation.

  • startSec [integer]: starting second.

  • startMin [integer]: starting minute.

  • startHour [integer]: starting hour.

  • startDay [integer]: starting day.

  • startMonth [integer]: starting month.

  • startYear [integer]: starting year.

  • noleap [logical]: if FALSE a calendar with leap years is used. Default value is TRUE.

  • mon30day [logical]: if TRUE a calendar with 360 days is used (30 days per month). Default value is FALSE.

CopyINIT_RUN_TIME

Here you can define the number of time steps that TRACMASS will be run as well as define a loop between two dates (more info can be found here).

  • loopYears [logical]: make a loop over two dates to run. Default value is FALSE.

  • loopStartYear [integer]: starting year of the loop.

  • loopEndYear [integer]: last year of the loop.

  • log_level [integer]: level of verbose.

  • intrun [integer]: number of time steps to run.

CopyINIT_WRITE_TRAJ

Here you can define all the parameters and paths linked to the output data (more info can be found here).

  • write_frec [integer]: output writing frequency: (1) write at time intervals of gcm datasets (each ints), (2) write at each time iteration, (3) write each spatial grid-crossing, (4) write at all time steps, and (5) write only start and end positions.

  • write_form [integer]: output writing format: (0) two decimals, (1) five decimals. Default values is zero.

  • outDataDir [character]: path to the directory where the output files are stored.

  • outDataFile [character]: prefix of the output file.

  • timeformat [integer]: format of the time array: (0) seconds from the starting date, (1) time fraction, or (2) date and time format.

CopyINIT_SEEDING

Here you can define all the parameters to seed trajectories in TRACMASS (more info can be found here).

  • nff [integer]: time arrow of TRACMASS: (1) run forward trajectories and (-1) backward trajectories.

  • isec [integer]: seeding section (1) zonal wall, (2) meridional wall, and (3) vertical wall.

  • idir [integer]: direction of initial fluxes (1) only positive fluxes are seeded, and (-1) only negative fluxes are seeded.

  • nqua [integer]: defines how many particles are initiliased per grid cell (1) constant number set by partQuant, (2) all trajectories reflect the same transport set by partQuant.

  • partQuant [integer]: number of trajectories per grid cell (if nqua is one) or the mass/volume transport per trajectory (if nqua is two).

  • loneparticle [integer]: trajectory number to run a lonely trajectory. The default value is set to zero (run all trajectories).

  • SeedType [integer]: defines the seeding type (1) using a seeding box defined by ist,jst,kst, or (2) using indexes from a file.

  • ist1 and ist2 [integer]: define the first and last zonal index of the seeding box (seedType=1)

  • jst1 and jst2 [integer]: define the first and last meridional index of the seeding box (seedType=1)

  • kst1 and kst2 [integer]: define the first and last vertical index of the seeding box (seedType=1)

  • seeddir [character]: path to the directory where the seeding file is stored (seedType=2).

  • seedfile [character]: name of the seeding file (seedType=2).

  • maskfile [character]: name of the masking file (seedType=1).

  • seedTime [integer]: defines the time seeding type (1) using a time range, or (2) using indexes from a file.

  • tst1 and tst2 [integer]: defines the first and last time steps to seed trajectories (seedTime=1).

  • timeFile [character]: name of the time seeding file (seedTime=2).

CopyINIT_TRACERS

Here you can activate tracers, define their names and properties, as well as set some modifications (more info can be found here).

  • l_tracers [logical]: activate tracers. Default value is FALSE.

  • l_swtraj [logical]: activate salt/water trajectories. Default value is FALSE.

  • tracertrajscale [real]: scale factor applied on the tracer which is used to compute salt/water trajectories. Default value is one.

  • tracername [character, array]: name of the tracers.

  • tracershift [real, array]: add a shift value to the tracer array. Default values is zero.

  • tracerscale [real, array]: multiple the tracer value by a scale factor. Default values is one.

  • tracerunit [character, array]: tracer units.

  • tracervarname [character, array]: variable name of the tracer.

  • traceraction [character, array]: action associated to the variable ‘read’ or ‘compute’.

  • tracermin [real, array]: minimum value of the tracer used to define the tracer coordinate space when stream functions are computed.

  • tracermax [real, array]: maximum value of the tracer used to define the tracer coordinate space when stream functions are computed.

  • tracerdimension [character, array]: defines the number of dimensions of the tracer, ‘2D’ or ‘3D’.

CopyINIT_TRACERS_SEEDING

Here you can define the maximum and mimimum tracer values when particles are seeded (an example can be found here).

  • tracer0min [real, array]: minimum value of the tracer to be seeded. The default values is -9999.

  • tracer0max [real, array]: maximum value of the tracer to be seeded. The default values is 9999.

CopyINIT_KILLZONES

Here you can define the maximum time limit, as well as define the regions where trajectories are terminated (some examples are shown here and here). For a detail description on how the kill zones work check the projets folder) section.

  • timax [real]: time limit before trajectories are terminated, calculated in days.

  • l_nosurface [logical]: prevent trajectories from reaching the last vertical level (sea surface/ land surface). Default value is .FALSE..

  • exitype [integer]: selects the type of killing zones (1) defined by a regular box, (2) defined by a tracer value, (3) a combined tracer-geographical zone, and (4) hard coded killing zone.

  • ienw and iene [integer, array]: define the western and eastern index of the killing zone (exitType=1).

  • jens and jenn [integer, array]: define the southern and northern index of the killing zone (exitType=1).

  • tracerchoice [integer, array]: defines the tracers that are used to defined the killing zone (exitType=2 or exitType=3). The index is given by the order of the tracer in tracername.

  • tracere [real, array]: value of the tracer that defines the killing zone (exitType=2 or exitType=3).

  • maxormin [integer, array]: sets the value of tracere to a (1) maximum or (-1) minimum value.

CopyINIT_POSTPROCESS

Here you can activate the stream function and/or the tracer divergence calculation (some examples are shown here and here). For a detail description on how the stream functions are computed check the mod_stream.F90) section. For information about the divergence calculation check mod_divergence.F90) section instead.

  • l_psi [logical]: activate stream function calculation.

  • l_offline [logical]: compute the stream functions offline. Default value is TRUE.

  • dirpsi [integer, array]: direction of integration of streamfunctions.

  • xyflux [integer]: compute barotropic fluxes using uflux (1) or vflux (2). Default value is 1.

  • l_divergence [logical]: activate the calculation tracer divergence.

  • divcons [real, array]: constants applied to the tracer divergence.

CopyINIT_ACTIVE

Here you can activate the Lagrangian diffusion scheme (for more information check here).

  • l_diffusion [logical]: activates the addition of a random displacement to trajectories. Default values is FALSE.

  • ah [real]: horizontal diffusion constant.

  • av [real]: vertical diffusion constant.