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- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) For now, only in pkgs used in verification/hs94.1x64x5. - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage which are specific to TAF/TAMC).
Add TAF option "kind" (or adjust "byte") to enable real*4 common blocks
replace calls to "FIND_RHO" with recent version "FIND_RHO_2D"
More stores probably for NLFS.
iMin,iMax,jMin,jMax are set within convective_adjustment S/R instead of passed as argument ; fix uninitialized variable Pb by computing rhoK & rhoKm1 over the full domain.
add diagnostics for Convective Adjusment.
remove MINIMAL_TAVE_OUTPUT option.
"rkSign" replaces "-rkFac" (<- removed)
remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE and rename it: DIFFERENT_MULTIPLE
use baseTime as time origin ; DIFF_BASE_MULTIPLE replaces DIFFERENT_MULTIPLE
Added CPP option MINIMAL_TAVE_OUTPUT for minimal time-averaged output: S, T, U, V, W, ETA, and phiHydLow.
use flags: fluidIsAir/Water, usingP/ZCoords instead of buoyancyRelation
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) (adjoint stuff still has some tr1 names, but all use ptracer arrays)
o limit timeave output for hi-res integrations
Patrick says: "we should remove those lines" and I agree.
o first check-in for the "branch-genmake2" merge
o verification suite as run on shelley (gcc 3.2.2):
Wed Oct 8 23:42:29 EDT 2003
T S U V
G D M c m s m s m s m s
E p a R g m m e . m m e . m m e . m m e .
N n k u 2 i a a d i a a d i a a d i a a d
2 d e n d n x n . n x n . n x n . n x n .
OPTFILE=NONE
Y Y Y Y 13 16 16 16 0 16 16 16 16 16 16 16 16 13 12 0 0 pass adjustment.128x64x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 0 0 16 16 0 0 pass adjustment.cs-32x32x1
Y Y Y Y 16 16 16 16 0 16 16 16 16 16 16 22 0 16 16 22 0 pass adjust_nlfs.cs-32x32x1
Y Y Y Y -- 13 13 16 16 13 13 13 13 16 16 16 16 16 16 16 16 N/O advect_cs
Y Y Y Y -- 22 16 16 16 16 16 16 13 16 16 16 16 16 16 16 16 N/O advect_xy
Y Y Y Y -- 13 16 13 16 16 16 16 16 16 16 22 16 16 16 16 16 N/O advect_xz
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass aim.5l_cs
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 16 16 16 16 13 16 pass aim.5l_Equatorial_Channel
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 13 16 16 13 13 16 pass aim.5l_LatLon
Y Y Y Y 13 16 16 16 16 16 16 16 16 16 13 12 13 13 16 13 16 pass exp0
Y Y Y Y 14 16 16 16 16 16 16 16 22 16 16 16 13 16 16 22 16 pass exp1
Y Y Y Y 13 13 16 13 16 16 16 16 16 13 13 16 16 13 13 13 13 pass exp2
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass exp4
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 22 16 16 16 22 16 pass exp5
Y Y Y Y 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 pass front_relax
Y Y Y Y 14 16 16 13 13 16 16 13 13 16 13 13 16 12 13 13 16 pass global_ocean.90x40x15
Y Y Y Y 10 16 16 13 13 16 13 16 16 13 13 13 13 16 16 13 16 FAIL global_ocean.cs32x15
Y Y Y Y 6 11 12 13 13 12 13 16 13 9 9 9 9 10 9 9 11 FAIL global_ocean_pressure
Y Y Y Y 14 16 16 13 16 16 16 13 13 13 13 13 16 12 16 13 16 pass global_with_exf
Y Y Y Y 14 16 16 16 16 16 16 16 16 11 13 22 13 16 16 9 16 pass hs94.128x64x5
Y Y Y Y 13 16 16 16 16 16 16 16 16 11 16 16 16 13 16 22 13 pass hs94.1x64x5
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 16 13 13 16 16 22 13 pass hs94.cs-32x32x5
Y Y Y Y 10 10 16 13 13 16 16 16 22 16 13 13 13 13 13 22 13 FAIL ideal_2D_oce
Y Y Y Y 8 16 16 16 16 16 16 16 16 13 13 8 16 16 16 16 16 FAIL internal_wave
Y Y Y Y 14 16 16 16 16 16 16 16 16 13 13 22 13 13 13 22 16 pass inverted_barometer
Y Y Y Y 12 16 16 16 16 16 16 16 16 16 13 12 13 13 13 13 13 FAIL lab_sea
Y Y Y Y 11 16 16 16 16 16 16 16 13 13 13 12 13 16 13 12 13 FAIL natl_box
Y Y Y Y 16 16 16 16 16 16 16 16 22 16 16 16 16 16 16 16 16 pass plume_on_slope
Y Y Y Y 13 16 16 16 16 13 16 16 16 16 16 16 16 13 16 16 16 pass solid-body.cs-32x32x1
o included PACKAGES_CONFIG.h in all files where the ALLOW_${PKG_NAME}
defines are used
o added comments where IF ( use${PKG_NAME} ) statements will probably
be needed -- or need to be edited
Merging from c51
fix bug in convective adj. diagnostic (ConvectCount is a local array !) and add time-average diagnostic of U*V and diff_Kr*theta
merging c49 and e27
differentiable version of checkpoint46n_post o external_fields_load now part of differentiation list o pressure needs multiple storing; would be nice to have store_pressure at beginning or end of forward_step, e.g. by having phiHyd global (5-dim.) (NB: pressure is needed for certain cases in find_rho, which is also invoked through convective_adjustment). o recomputations in find_rho for cases 'JMD95'/'UNESCO' or 'MDJWF' are OK. o #define ATMOSPHERIC_LOADING should be differentiable o ini_forcing shifted to begining of initialise_varia
o fixed the k-loop range for pressure coordinates: goes backwards from Nr to 2 (instead of Nr-1 to 1)
made convective adjustment work with pressure coordinates: - changed the direction of k-loop in convective_adjustment.F for the case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) - adjusted the reference pressure k-index in convective_adjustment.F - adjusted the convection condition in convect.F (in analogy to calc_ivdc.F) - convective_adjustment no longer computes anything on the halos - removed the warnings about negative salinity from find_rho.F and find_alpha.F; instead the new routine look_for_neg_salinity, called at the beginning of find_rho, find_alpha, and find_beta, does a check of the entire slice, if CPP-option CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
o Include a new diagnostic variable phiHydLow for the ocean model
- in z-coordinates, it is the bottom pressure anomaly
- in p-coordinates, it is the sea surface elevation
- in both cases, these variable have global drift, reflecting the mass
drift in z-coordinates and the volume drift in p-coordinates
- included time averaging for phiHydLow, be aware of the drift!
o depth-dependent computation of Bo_surf for pressure coordinates
in the ocean (buoyancyRelation='OCEANICP')
- requires a new routine (FIND_RHO_SCALAR) to compute density with only
Theta, Salinity, and Pressure in the parameter list. This routine is
presently contained in find_rho.F. This routine does not give the
correct density for 'POLY3', which would be a z-dependent reference
density.
o cleaned up find_rho
- removed obsolete 'eqn' from the parameter list.
o added two new verification experiments: gop and goz
(4x4 degree global ocean, 15 layers in pressure and height coordinates)
removed some f90 comments ("!")
Removed f90 comments ("!")
Removed f90 comment (!)
Moving call packages_init_variables before convecti_adjustment_ini in initialise_varia for better consistency.
These changes constitute a patch to release1. They were made on a development branch called "release1_final" and are on the main trunk between chkpt44d_post and checkpoint44h_post along with other changes. This code is equivalent to chkpt44d_post with the following patches: - AD-related changes for GMRedi - fixes i KPP (delZ -> drF) - hook to OBCS songe layer code in external_forcing - errorMessageUnit non-zero in eeboot.F - modified test cost function and carbon verif.
Merged changes to enable stable adjoint of GM from release1_final.
Merged AD-related changes into release1_final
Header file TR1.h was missing for case ALLOW_PASSIVE_TRACER.
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.
Re-wrote the convective mixing algorithm to use pre-calculated weights. Uses two new routines: - convective_weights() calculates mixing factors A and B, called once - convectively_mixtracers() mixes a tracer (argument) using A and B and is called for each tracer The old call to convect() is simply commented out for the time-being. Similarly, convect.F still exists. I thought it prudent to leave them around until the TAF/TAMC related bits are added.
Merging changes on MAIN between checkpoint43 and checkpoint43a-release1mods
Command: cvs -q update -jcheckpoint43 -jcheckpoint43a-release1mods -d -P
These changes are most of the changes between c43 and c44 except those
that occured after "12:45 11 Jan 2002". As far as I can tell it is
checkpoint43 with the following mods:
o fix bug in mom_vi_del2uv
o select when filters are applied ; add options to zonal_filter (data.zonfilt) o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
o Jamar wet-points
This update does not contain the following mods that are in checkpoint44
o bug fix in pkg/generic_advdiff/
- thread related bug, bi,bj arguments in vertical advection routines
o some changes to pkg/autodiff, pkg/cost, pkg/exf, pkg/ecco,
verification/carbon and model/src/ related to adjoint
o some new Matlab scripts for diagnosing model density
- utils/matlab/dens_poly3.m and ini_poly3.m
The list of exclusions is accurate based on a "cvs diff". The list of
inclusions is based on the record in doc/tag-index which may not be complete.
Updating ecco-branch-mod1 to checkpoint44. Will be tagged ecco-branch-mod2.
Minor cleanup.
Bringing comments up to data and formatting for document extraction.
Modifications/fixes to support TAMC differentiability (mostly missing or wrong directives).
Modifications and additions to enable automatic differentiation. Detailed info's in doc/notes_c37_adj.txt
change Time-Average routine names (new package)
recover (after checkpoint35) time average output
Made sure each .F and .h file had the CVS keywords Header and Name at its start. Most had header but very few currently have Name, so lots of changes!
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Re-wrote calc_phi_hyd() - use theta and salt as arguments (necessary for staggered time-step) - calls find_rho() from inside - find_rho() also takes theta,salt as arguments - uses different formulation for 'OCEANIC' and 'ATMOSPHERIC' modes - "finite volume" (non-energy conserving) form supplied in comments
Tentative step towards "phase 2" o added wVel array to DYNVARS.h o re-arranged dynamics() substantially
Moved "correction" phase of algorithm from top of dynamcs() to end of forward_step(). - allows deletion of ini_predictor - need convective adjustment of initial conditions for backward compatibility. - exchange fields instead of tendancies, called in forward_step() - encapsulated convective adjustment for convenience: convective_adjustment()
file convective_adjustment.F was initially added on branch branch-atmos-merge.
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