Namelist

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.

INIT_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 ” “.

INIT_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.

INIT_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.

INIT_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.

INIT_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.

INIT_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.

INIT_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.

INIT_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).

INIT_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’.

INIT_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.

INIT_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.

INIT_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.

INIT_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.