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12 fix subvol for cell volume seeding #13

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1838c56
Allow users to specify trajectory allocation (ntracmax) at seeding us…
oj-tooth Dec 18, 2025
8777157
Update example namelist files to include l_compress writw, nsdtraj se…
oj-tooth Dec 18, 2025
febe8b3
Use current time index to calculate grid cell volume.
oj-tooth Dec 18, 2025
c51a9f8
Update mod_seed.F90 unit tests to include nsdtraj def.
oj-tooth Dec 18, 2025
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13 changes: 9 additions & 4 deletions projects/AVISO/namelist_AVISO.in
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@

timeformat = 0 ! 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
Expand All @@ -93,10 +95,11 @@
! = 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 = 10, ! 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
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
ist1 = 135, ! seed in box in range i = [ist1,ist2]
Expand Down Expand Up @@ -163,5 +166,7 @@
/

&INIT_ACTIVE

l_diffusion = .FALSE. ! Apply Stochastic diffusion along particle trajectories
Ah = 0 ! Horizontal diffusivity coefficient
Av = 0 ! Vertical diffusivity coefficient
/
17 changes: 11 additions & 6 deletions projects/IFS/namelist_IFS.in
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Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,10 @@
outDataDir = '',
outDataFile = '',

timeformat = 0 ! Format of the time array
! 0 - tt / 1 - ts / 2 - YYYY, MM, DD, HH
timeformat = 0 ! 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
Expand All @@ -98,10 +100,11 @@
! = 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 = 1, ! 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
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
ist1 = 70, ! seed in box in range i = [ist1,ist2]
Expand Down Expand Up @@ -196,5 +199,7 @@
/

&INIT_ACTIVE

l_diffusion = .FALSE. ! Apply Stochastic diffusion along particle trajectories
Ah = 0 ! Horizontal diffusivity coefficient
Av = 0 ! Vertical diffusivity coefficient
/
45 changes: 25 additions & 20 deletions projects/NEMO/namelist_ORCA1.in
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Original file line number Diff line number Diff line change
Expand Up @@ -102,30 +102,33 @@
outDataDir = '',
outDataFile = '',

timeformat = 0 ! Format of the time array
! 0 - tt / 1 - ts / 2 - YYYY, MM, DD, HH
timeformat = 0 ! 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 = 2, ! = 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 = 1, ! 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

! = -1 run backwards
isec = 2, ! = 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 = 1, ! 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 = 1, ! 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
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
ist1 = 220, ! seed in box in range i = [ist1,ist2]
Expand Down Expand Up @@ -216,5 +219,7 @@
/

&INIT_ACTIVE

l_diffusion = .FALSE. ! Apply Stochastic diffusion along particle trajectories
Ah = 0 ! Horizontal diffusivity coefficient
Av = 0 ! Vertical diffusivity coefficient
/
17 changes: 11 additions & 6 deletions projects/ROMS/namelist_ROMS.in
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Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,10 @@
outDataDir = '',
outDataFile = '',

timeformat = 0 ! Format of the time array
! 0 - tt / 1 - ts / 2 - YYYY, MM, DD, HH
timeformat = 0 ! 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
Expand All @@ -123,10 +125,11 @@
! = 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 = 1, ! 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
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
ist1 = 65, ! seed in box in range i = [ist1,ist2]
Expand Down Expand Up @@ -218,5 +221,7 @@
/

&INIT_ACTIVE

l_diffusion = .FALSE. ! Apply Stochastic diffusion along particle trajectories
Ah = 0 ! Horizontal diffusivity coefficient
Av = 0 ! Vertical diffusivity coefficient
/
44 changes: 24 additions & 20 deletions projects/Theoretical/namelist_Theoretical.in
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Original file line number Diff line number Diff line change
Expand Up @@ -67,29 +67,33 @@

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 = 1, ! 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

partquant = 1, ! 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
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 = 1, ! 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 = 1, ! 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
ist1 = 150, ! seed in box in range i = [ist1,ist2]
Expand Down
2 changes: 2 additions & 0 deletions src/_funit/mod_seed.fun
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Original file line number Diff line number Diff line change
Expand Up @@ -348,6 +348,7 @@ TEST test_seed_7
!partQuant
partQuant = 10
nqua = 2
nsdtraj = 10

CALL init_seed
CALL seed
Expand Down Expand Up @@ -376,6 +377,7 @@ TEST test_seed_8
!partQuant
partQuant = 1
nqua = 2
nsdtraj = 10

CALL init_seed
CALL seed
Expand Down
6 changes: 3 additions & 3 deletions src/mod_init.F90
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Expand Up @@ -57,13 +57,13 @@ SUBROUTINE init_namelist()
namelist /INIT_RUN_TIME/ loopYears, loopStartYear, loopEndYear, &
log_level, intrun
namelist /INIT_WRITE_TRAJ/ write_frec, write_form, outDataDir, outDataFile, timeformat, l_compress
namelist /INIT_SEEDING/ nff, isec, idir, nqua, partQuant, &
namelist /INIT_SEEDING/ nff, isec, idir, nqua, partQuant, nsdtraj, &
loneparticle, SeedType, ist1, &
ist2, jst1, jst2, kst1, kst2, tst1, tst2,&
ist2, jst1, jst2, kst1, kst2, tst1, tst2, &
seedDir, seedFile, maskFile, seedTime, timeFile
namelist /INIT_TRACERS/ l_tracers, l_swtraj, tracertrajscale, &
tracername, tracershift, tracerscale, &
tracerunit, tracervarname,&
tracerunit, tracervarname, &
traceraction,tracermin, tracermax, &
tracerdimension
namelist /INIT_TRACERS_SEEDING/ tracer0min, tracer0max
Expand Down
7 changes: 4 additions & 3 deletions src/mod_seed.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,8 @@ SUBROUTINE init_seed()
IF (nqua == 1) THEN
ntracmax = nsdMax*nsdTim*INT(partQuant)
ELSE
ntracmax = nsdMax*nsdTim*10000
! Allocate trajectories using nsdtraj trajectories per seed cell.
ntracmax = nsdMax*nsdTim*nsdtraj
END IF

ALLOCATE ( trajectories(ntracmax) )
Expand Down Expand Up @@ -406,8 +407,8 @@ SUBROUTINE seed()
num = (INT(SQRT(FLOAT(num))) + 1)**2
END IF

CASE (3) ! particle reflects air/water mass/volume at seeding
vol = dzt(ib,jb,kb,1)
CASE (3) ! particle reflects air/water volume at seeding
vol = dxdy(ib,jb) * dzt(ib,jb,kb,nsp) * zstot(ib,jb,0)
num = INT(vol/partQuant)
END SELECT

Expand Down
1 change: 1 addition & 0 deletions src/mod_vars.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ MODULE mod_seedvars

REAL(DP) :: partQuant ! number of particles per grid to seed

INTEGER :: nsdtraj ! number of trajectories per seed cell
INTEGER :: ist1, ist2 ! Zonal seeding region
INTEGER :: jst1, jst2 ! Meridional seeding region
INTEGER :: kst1, kst2 ! Vertical seeding region
Expand Down