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- implement Adams-Bashforth on pTracers (instead of on tracer tendency), switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs).
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, and update corresponding calls in S/R temp/salt/ptracers_integrate.F
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T. - use local temperature/salinity/ptracer tendency array (without bi,bj) in S/R temp/salt/ptracers_integrate.F ;
pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
- push the k loop inside S/R TIMESTEP_TRACER (and call it outside the k loop). - call S/R DWNSLP_APPLY before TIMESTEP_TRACER;
move cycle_tracer calls from tracers_correction_step.F to temp/salt/ptracer_integrate.F so that theta,salt and pTracers arrays are already updated when leaving S/R THERMODYANMICS while adjustments (filters, conv.adjustment) are still applied later, in S/R TRACERS_CORRECTION_STEP.
change implemetation of AB on tracer (doAB_onGtGs=F, not AB on tendency): store AB(Tr)=Tr^(n+1/2) into gtNm(m2) instead of directly in theta,salt. This fix some forcing-term calculation (e.g., relaxation) that should not be computed from AB(Tr) but instead directly from Tr.
- collect forcing tendency into local 2-D array (passed as argument to apply_forcing S/R); add 3-D diagnostics for forcing tendency.
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; for NLFS case, use new recip_hFac value in order to conserve tracer.
- change argument list of all S/R called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) to pass, as argument, the current level dendency array to update (instead of a direct update of the common bloc array). - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
- move calls to GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from thermodynamics.F to inside ptracers_integrate.F - call MATRIX_STORE_TENDENCY_EXP for each tracer - add fZon & fMer as output argument of S/R GAD_CALC_RHS
move calls to GAD_ADVECTION (Multi-Dim advection) inside ptracers_integrate.F and remove ptracers_advection.F
remove storage dir for rTrans (no longer needed after changing calc_adv_flow.F)
add initialisation of sTrans (only for AD)
- remove k from thermodynamics.F and move it to ptracers_integrate.F (now done inside the tracer loop). - compute locally (in thermodynamics.F) 3-D velocity field that is used to advect tracers; pass it as argument to this routine
Add 3-D array 3rd dimension to argument list of S/R adams_bashforth2/3
change argument list of S/R GAD_CALC_RHS (for vertical biharmonic diffusion)
-rename PTRACERS_RESTART.h --> PTRACERS_START.h -only step forward tracer if PTRACERS_StepFwd(iTr)=T
- additional output argument for ADAMS_BASHFORTH2 S/R ; - add diagnostics for Adams-Bashforth tendency increment.
remove unused arguments from S/R TIMESTEP_TRACER interface
Bug fix.
using ptracers with NLFS adjoint.
always call OBCS_APLY_PTRACER from ptracers_implicit.F (and remove the previous call from ptracers_integrate.F)
longstep: fix tracer conservation with rstar/nonlinear free surface
add package longstep
fix syntax error from previous modif.
add internal parameter and flags: a) ptracer multi-Dim advection flag and AdamsBashforth flag b) starting AdamsBashforth flag (in new header file: PTRACERS_RESTART.h)
split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
add startAB parameter to argument list of S/R ADAMS_BASHFORTH2
add trUseGMRedi & trUseKPP to the argument list of S/R GAD_CALC_RHS
make a local copy of velocity to pass (like u,v,r_Trans) to tracer advection S/R
Fix ptracers adjoint o avoid extensive recomputatations o fix missing re-init. of gptr (missed by TAF)
change forcing_In_AB to affects both T,S forcing and Momentum forcing (allow to differentiate between forcing components using new integer flags: momForcingOutAB=1/0 & tracForcingOutAB=1/0) and add new flag to put Dissipation tendency out of Adams-Bashforth.
added 1 argument to S/R GAD_CALC_RHS
Bring call gad_calc_rhs parameter list up-to-date w.r.t. calc_gt, calc_gs
remove unused variables (reduces number of compiler warning)
updated since GAD_CALC_RHS has a new argument (for AB(T,S))
o OBCS and PTRACERS: add open boundary support for passive tracers
- either use homogenous (pseudo) v.Neumann conditions or prescribe
OB-values from file; this is not different from the way theta and salinity
are treated
- however, Orlanski-radiation conditions are not supported, and the model
will stop if you use pTracers and Orlanski at the same time.
- beefed up the rountine obcs_external_fields_load: now only those open
boundary values are overwritten with values from files for which there
are really files, otherwise the OB-fields remain untouched. This makes
it possible to use different OBs at different ends of the domain (as
with EXF)
- TODO: add support for OB?w and OB?eta, which can currently not be read
from a file.
Added support for pkg/matrix
updated after changing adams_bashforth2.F
implement Implicit Vertical advection for pTracers
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
this flag is now only visible within GCHEM-pkg routines.
- moved gchem_forcing_int temporarily into ptracers_forcing, this will
be replaced by a 3D array that is computed before thermodynamics; for
this, the tracer ID iTracer had to be included into the parameter list
of ptracers_forcing
- cleaning up
o GCHEM: introduced a useGCHEM runtime flag, add a check for gchem package
each ptracer uses its own background vertical diffusivity
Explicit vertical diffusivity: use a 2.D vertical diffusivity array
add myTime & myIter to argument list of GAD_CALC_RHS
replace surfaceTendencyPtr by surfaceForcingPtr
max number of passive tracers is now defined in PTRACERS_SIZE.h
T & S: separate Vert.Advec.Scheme from horizontal Advec.Scheme
rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) to work with implicit vertical advection and AB
cosmetic changes
o initialisation of rFlx extended to full array (required by TAF) and shifted to thermodynamics o removed PTRACERS.h in ptracers routine o added surfacetendencyPtr to S/R parameter list pracers_forcing
modifications so gchem pkg is more versatile
o Mods and bug fixes to pkg/cal, pkg/exf, etc. needed for computation of tracer Green's fucntions for ocean inversion project.
checkpoint51f_post
o Added on-the-fly spatial interpolation capability
"USE_EXF_INTERPOLATION" to pkg/exf.
This is a temporary Cartesian-grid hack until
the super-duper ESMF coupler becomes available.
Usage example is in verification/global_with_exf.
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
non-local transport term.
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM o made ptracers_forcing same as external_forcing_s
files needed for biogeochemistry package (gchem)
Added include of PARAMS.h which fixes broken compile of pkg/ptracers due to the recently added flag "forcing_In_AB".
apply rescaling (NONLIN_FRSURF) also to gNm1 to get a better conservation
* tracer forcing inside or outside Adams-Bashforh ; * modified after gad_calc_rhs changes ;
Bug fix: missing indices for argument. Reported by Stephanie way back before Christmas!
Added PTRACERS package
This allows an arbitrary number of passive tracers to be integrated
forward simultaneously with the dynamicaly model.
+ Implemented so far:
- basic forward algorithm (time-stepping, advection, diffusion, convection)
- I/O and checkpointing
- GM/Redi *but* using the GM/Redi coefficient of Salt
+ Not implemented so far:
- KPP
- OBCS
+ No specific example supplied (yet) but global_ocean.90x40x15 has the
necessary data.ptracer file. Simply use -enable=ptracers and uncomment
line in data.pkg. PTRACER01 then reproduces Salt exactly.
+ This package is disabled by default since it increases storage.
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