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Tracmass for the isopycnic model MICOM #14

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4 changes: 4 additions & 0 deletions .gitignore
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# Build and statics
*.csv
*.mod
*.o
_build
docs/_build
docs/_static
docs/_templates
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22 changes: 22 additions & 0 deletions projects/MICOM/Makefile.prj
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# Makefile for BLOM run
#========================================================================

# Vertical velocities
#------------------------------------------------------------------------
#fl01 = -Dw_2dim # Turn off vertical velocities.
#fl01 = -Dw_3dim # Compute 3D vertical velocities.
fl01 = -Dw_explicit # Explicit 3D vertical velocities.


# Time integration scheme
#------------------------------------------------------------------------
#fl02 = -Dtime_analytical

# Isopycnic model
#------------------------------------------------------------------------
fl03 = -Disopycnic_model

#========================================================================

ORM_FLAGS= -D$(PROJECT) \
$(fl01)$(fl02)$(fl03)
86 changes: 86 additions & 0 deletions projects/MICOM/kill_zones.F90
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SUBROUTINE kill_zones
!==========================================================================
!
! Purpose
! -------
!
! Defines the limits of the domain.
! If a trajectory is outside the domain the subroutine will identify it
! with a flag (nend)
!
! nend = 0 is reserved to the time limit
! nend = 1 is reserved to trajectories reaching the surface
!
! ==========================================================================


USE mod_traj
USE mod_domain
USE mod_tracervars

IMPLICIT NONE

INTEGER :: nexit, itrac, numexit

nend = -1

SELECT CASE(exitType)

! Exit domain defined by the boxes [ienw, iene]x[jens, jenn]
! in the namelist
CASE(1)
DO nexit = 1, 10
IF(ienw(nexit) <= x1 .AND. x1 <= iene(nexit) .AND. &
jens(nexit) <= y1 .AND. y1 <= jenn(nexit) ) THEN
nend = nexit +1
END IF
END DO

! Exit domain defined by the value of tracers in the namelist tracere
CASE(2)

numexit = MINLOC(tracerchoice, DIM=1,MASK=(tracerchoice==999)) - 1

DO nexit = 1, numexit
itrac = tracerchoice(nexit)

IF ( maxormin(nexit)*tracervalue(itrac)>= maxormin(nexit)*tracere(nexit) ) THEN
nend = nexit +1
END IF

END DO

! Exit domain defined by the value of tracers in the namelist tracere and domain
CASE(3)

! First thermodynamic killing zone
numexit = MINLOC(tracerchoice, DIM=1,MASK=(tracerchoice==999)) - 1

DO nexit = 1, numexit
itrac = tracerchoice(nexit)

IF ( maxormin(nexit)*tracervalue(itrac)>= maxormin(nexit)*tracere(nexit) ) THEN
nend = nexit +1
END IF

END DO

! Next the geographical killing zone
DO nexit = 1, 10
IF(ienw(nexit) <= x1 .AND. x1 <= iene(nexit) .AND. &
jens(nexit) <= y1 .AND. y1 <= jenn(nexit) ) THEN
nend = nexit +1 + numexit
END IF
END DO

! If the exit domained is defined in a different way:
! - Read from a file
! - Defined by curve, no linear shape, ...
! This must be hard coded below.

CASE(4)
PRINT*, 'Hard coded limits of the domain'

END SELECT

END SUBROUTINE kill_zones
220 changes: 220 additions & 0 deletions projects/MICOM/namelist_MICOM.in
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&INIT_GRID_DESCRIPTION
! Direction of the grid (1 - E->W, S->N, B->U)
griddir = -1,1,1

! Does the netcdf data start with a zero index?
zeroindx = .FALSE.

l_onestep = .TRUE.

! Describe filenames
physDataDir = '/projects/NS9560K/noresm/cases/NHISTfrc2_f09_tn14_20191025/ocn/hist/'
physPrefixForm = 'NHISTfrc2_f09_tn14_20191025.micom.hm.',
dateformat = 'YYYY-MM'

fileSuffix = '.nc', ! suffix of files, e.g. ".nc"

! Describe variable names
ueul_name = 'uflx', ! name of resolved zonal velocity
veul_name = 'vflx', ! ---- " ------- meridional
w_name = 'wflx', ! name of diagnosed vertical velocity
usgs_name = '', ! name of eddy induced zonal velocity
vsgs_name = '', ! ---- " ------- meridional
/

&INIT_GRID_SIZE
! Size of global grid
imt = 360, ! number of global i points
jmt = 384, ! number of global j points
km = 53, ! number of global k points

iperio = 1, ! zonal periodic
jperio = 2, ! meridional boundary conditions

topoDataDir = './', ! directory of grid data

hgridFile = 'grid.nc', ! file with dx, dy etc
!dy_name = 'pdy', ! name of dy at T point
dyu_name = 'udy', ! dy at U point
!dx_name = 'pdx', ! name of dx at T point
dxv_name = 'vdx', ! dx at V point

dzt_name = 'dp' ! name of 3D dp at T point
!dzu_name = 'dp' ! --- " --- dp at U point
!dzv_name = 'dp' ! --- " --- dp at V point

/

&INIT_GRID_SUBDOMAIN
l_subdom = .FALSE. ! Initialise subdomain
imindom = 50 ! Eastern and western wall for subdomain
imaxdom = 100
jmindom = 50 ! Southern and northern wall for subdomain
jmaxdom = 100
/

&INIT_GRID_TIME
ngcm_step = 1, ! time between two time levels
! if ngcm_unit = 5, then ngcm_step = 3 means 3 months
ngcm_unit = 5, ! units of ngcm

iter = 120, ! number of subcycles between time levels stopped
/

&INIT_START_DATE
startsec = 0, ! start time
startmin = 0,
starthour = 0,
startday = 1, ! start date
startmon = 1,
startyear = 2000,
noleap = .TRUE., ! don't use leap years?
mon30day = .true.
/

&INIT_RUN_TIME
! Loop run
loopYears = .TRUE., ! make a time loop to run
! e.g. 1000 years using only 100 years of data
loopStartYear = 2000, ! year to start loop from
loopEndYear = 2000, ! last year of loop

! Verbose
log_level = 1 ! precise 1->3->5 verbose

! Information of run time
intrun = 121 ! number of time steps for run
/

&INIT_WRITE_TRAJ
write_frec = 1 ! 1 = write at time intervals of gcm datasets (each ints)
! 2 = write at each time iteration
! 3 = write each spatial grid-crossing
! 4 = write all the time steps
! 5 = write only start and end positions
!write_form = 1,
write_form = 0,
outDataDir = './output/MICOM/',
outDataFile = 'output',

timeformat = 1, ! Format of the time array
! 0 - tt / 1 - ts / 2 - YYYY, MM, DD, HH
l_compress = .FALSE. ! Compress _run.csv files on exceeding 2GB filesize using gzip
/

&INIT_SEEDING
nff = 1, ! = 1 run forward trajectories
! = -1 run backwards
isec = 1, ! = 1 start on zonal cell wall
! = 2 start on meridional cell wall
! = 3 start on vertical wall
idir = 1, ! = 1 start only when flux > 0
! = -1 only when flux < 0
nqua = 2, ! number of trajectories can be set by
! = 1 constant number of particles in all seeding cells
! set by partQuant (particles / gridcell)
! = 2 Each particle reflects mass transport at seeding.
! set by partQuant (m3/s or kg/s per particle)
! = 3 Each particle reflects air/water mass/volume at seeding.
! set by partQuant in m3 or kg per particle
nsdtraj = 10, ! number of trajectories to allocate per seeding cell (used for allocation if nqua > 1)
partquant = 5e6, ! particles/gridcell or m3s-1/particle or m3/particle
loneparticle = 0, ! start only one trajectory for debugging
seedtype = 1, ! = 1 seed using ist,jst,kst (below)
! = 2 seed using file with start positions

! when seedtype = 1
! gulf stream
ist1 = 30, ! seed in box in range i = [ist1,ist2]
ist2 = 35,
jst1 = 266, ! j = [jst1,jst2]
jst2 = 266,
kst1 = 1, ! k = [kst1,kst2]
kst2 = 53,
! when seedtype = 2
seeddir = '', ! directory for seed files
seedfile = '', ! name of seed file


seedtime = 1, ! = 1 seed only for specific times
! = 2 seed using file with start positions

! when seedtime = 1
tst1 = 1, ! seed only between tst1 and tst2
tst2 = 5,

! when seedtime = 2
timefile = '', ! name of seed file
/

&INIT_TRACERS
l_tracers = .True. ! Should we evaluate tracers along the trajectories?

! Tracer name (description)
tracername = 'temp','saln','depth'
! Tracer unit (description)
tracerunit = 'degC','PSU','m'

! Name of the variable in the netcdf (if it's read)
tracervarname = 'temp','saln','dz'

! Action (read or compute)
traceraction = 'read','read','read'

! Minimum and maximum value of the binning
tracermin = -3, 32, -11000
tracermax = 33, 38, 0

! Dimension of the tracer
tracerdimension = 3D, 3D, 3D
/

&INIT_TRACERS_SEEDING
! minimum and maximum value for seeding
! same order as in tracername
!tracer0min = 2, 34.9,
!tracer0max = 4, 35.0,
/

&INIT_KILLZONES
timax = 75000 ! time limit for traj [days]
l_nosurface = .TRUE.

exitType = 1
! If exitType = 1: killing zone defined by a box
! IMPORTANT -> The maximum number of boxes than can be defined are 10
! ienw,iene are western and eastern i indices of killzone
! jens,jenn are southern and northern j indices of killzone
! ienw = 0, 500,
! iene = 100, 1000,
! jens = 200, 450,
! jenn = 300, 470,
! sets up two killzones, the first i = [0,100], j = [200,300]
! the other i = [500,1000], j = [450,470]
ienw = 10,10, ! west indices of killzones
iene = 150,150, ! east indices of killzones
jens = 365, 365, ! south indices of killzones
jenn = 366, 366, ! north indices of killzones

! If exitType = 2: killing zone defined by tracer value
! Tracerchoice defines which tracer is used for the killing zone
! it could be different
!tracerchoice = 1, 2
!tracere = 25, 35
!maxormin = 1, -1
! This set up defines a killing zone by the 25C isotherm (maximum)
! and the 35psu isohaline (minimum)

/

&INIT_POSTPROCESS
l_psi = .FALSE. ! Compute stream Functions
dirpsi = -1,-1,-1,-1 ! Direction of integration
/

&INIT_ACTIVE
l_diffusion = .FALSE. ! Apply Stochastic diffusion along particle trajectories
Ah = 0 ! Horizontal diffusivity coefficient
Av = 0 ! Vertical diffusivity coefficient

/
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