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$Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.103 2002/11/12 20:59:27 heimbach Exp $ |
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|
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Notes on tags used in MITgcmUV |
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============================== |
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|
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checkpoint47 |
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differentiable version of checkpoint46n_post |
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o bug fix in quasihydrostaticterms |
9 |
o * "clean" adjoint code (in terms of extensive recomputations) |
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can now be obtained for all GMREDI options (i.e. for |
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- GM_VISBECK_VARIABLE_K |
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- GM_NON_UNITY_DIAGONAL |
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- GM_EXTRA_DIAGONAL |
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- GM_BOLUS_ADVEC ) |
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* However, wrong gradient check problem remains unsolved. |
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* New CPP options have been introduced for different |
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tapering schemes |
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o external_fields_load now part of differentiation list |
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o pressure needs multiple storing; |
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would be nice to have store_pressure at beginning or |
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end of forward_step, e.g. by having phiHyd global (5-dim.) |
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(NB: pressure is needed for certain cases in find_rho, |
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which is also invoked through convective_adjustment). |
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o recomputations in find_rho for cases |
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'JMD95'/'UNESCO' or 'MDJWF' are OK. |
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o #define ATMOSPHERIC_LOADING should be differentiable |
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o ini_forcing shifted to begining of initialise_varia |
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o Incorporating QNVS line search routines into MITgcm |
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(this is separate code, and therefore not under pkg) |
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lsopt/, optim/ |
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o Updated verification/carbon/ |
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- #define GM_VISBECK_VARIABLE_K |
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- GM_taper_scheme = 'ldd97' |
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|
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checkpoint46n_post |
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Merging from release1_p8: |
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o verification/natl_box: |
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updating new external_fields_load routine |
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o New package: pkg/seaice |
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Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
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The sea-ice code is based on Hibler (1979-1980). |
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Two sea-ice dynamic solvers, ADI and LSR, are included. |
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In addition to computing prognostic sea-ice variables and diagnosing |
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the forcing/external data fields that drive the ocean model, |
45 |
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
46 |
The implied surface heat flux is then stored in variable |
47 |
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
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kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
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non-local transport term. Because this call precedes model |
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thermodynamics, temperature under sea-ice may not be "exactly" at |
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the freezing point by the time theta is dumped or time-averaged. |
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N.B.: fairly large differences in accuracy occur across |
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different platforms/compilers; comparison between |
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g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
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generated output gives: |
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T S U V |
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C D M c m s m s m s m s |
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n p a R g m m e . m m e . m m e . m m e . |
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f n k u 2 i a a d i a a d i a a d i a a d |
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g d e n d n x n . n x n . n x n . n x n . |
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|
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Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
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o GAD: |
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- generated new common blocks to account for call of |
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same gad routines with differing traceridentities |
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(needed to modify tracerIdentity indices in GAD.h) |
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- generated separate common blocks for case useCubedSphereExchange |
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(Department of Futurology) |
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- parameter lists to gmredi_?transport: added tracerIdentity |
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- added new key indices to tamc.h |
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o external_fields_load: |
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- added this routine to TAF list |
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- needed to make some common blocks global and additional storing |
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along the same lines as exf package (checkpoint_lev?_directives.h) |
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o exf: |
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updated external forcing package |
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- bug fixes carried over from ecco-branch |
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(missing OBCS_OPTIONS.h in two routines) |
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- enable easy to use "no forcing". |
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- added exf I/O for atmospheric loading |
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- added exf I/O for runoff data |
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- transfered scaling between exf <-> MITgcm to exf namelist |
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o Adding new verification experiment global_with_exf. |
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This verification experiment is almost identical to the |
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global_ocean.90x40x15 experiment, except that it uses |
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the exf (and cal) package instead of the |
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external_fields_load routine (cf README file). |
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|
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checkpoint46m_post |
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o modified testscript to return -- when there are no lines of "%MON" output |
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o added new flag "quasiHydrostatic" for QH mode |
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and new routine quasihydrostaticterms() |
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o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
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New routine: mom_u_coriolis_nh() |
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o fixed sign of non-hydrostatic metric terms in u and v equations. |
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Depend on correct sign of gravitySign. |
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o added work.pc* to .cvsignore in aim directories using ifc |
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o introduced flag for controllin non-hydrostatic metric terms |
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o removed gravitySign from PARM04 |
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o switched to g77/ifc from pgf77 in aim experiments |
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|
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checkpoint46l_post |
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o made convective adjustment work with pressure coordinates: |
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- changed the direction of k-loop in convective_adjustment.F for the |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
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- adjusted the reference pressure k-index in convective_adjustment.F |
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- adjusted the convection condition in convect.F (in analogy to |
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calc_ivdc.F) |
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- convective_adjustment no longer computes anything on the halos |
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- removed the warnings about negative salinity from find_rho.F and |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
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check of the entire slice, if CPP-option |
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CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
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checkpoint46l_pre |
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|
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checkpoint46k_post |
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o fixed the verification/global_ocean.90x40x15 experiment: |
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- new bathymetry (the world according to A., JMC, and M.) |
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- new initial fields and forcing fields (*.bin files) |
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- new POLY3.COEFFS (for the next release one should switch to a full |
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equation of state: JMD95P or MDJWF) |
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- fixed several errors and redundancies in the data file |
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- experiment uses looped cells |
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- added matlab directory with diagnostic scripts for plotting of output |
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|
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
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- read AIM physics parameters from a file (data.aimphys) |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
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|
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checkpoint46j_post |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
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o update timeave pkg for wVel diagnostic. |
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checkpoint46j_pre |
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|
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checkpoint46i_post |
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o Clean up AIM package (and keep the results unchanged): |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
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|
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checkpoint46h_post |
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o cleaned up the use of rhoNil and rhoConst. |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
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and the dynamical equations are all divided by rhoConst |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
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value is 999.8 kg/m^3 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
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- can now be used by both OCEANIC and OCEANICP |
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checkpoint46h_pre |
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|
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Added code to convert surface volume flux (fresh water) into |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
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|
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checkpoint46g_post |
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o Include a new diagnostic variable phiHydLow for the ocean model |
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- in z-coordinates, it is the bottom pressure anomaly |
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- in p-coordinates, it is the sea surface elevation |
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- in both cases, these variable have global drift, reflecting the mass |
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drift in z-coordinates and the volume drift in p-coordinates |
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- included time averaging for phiHydLow, be aware of the drift! |
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o depth-dependent computation of Bo_surf for pressure coordinates |
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in the ocean (buoyancyRelation='OCEANICP') |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
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presently contained in find_rho.F. This routine does not give the |
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correct density for 'POLY3', which would be a z-dependent reference |
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density. |
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o cleaned up find_rho |
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- removed obsolete 'eqn' from the parameter list. |
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o added two new verification experiments: gop and goz |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
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checkpoint46g_pre |
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|
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checkpoint46f_post |
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o Enable tangent linear (forward mode) gradient checks: |
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- extended active file handling to g_... files |
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- added TANGENT_SIMULATION to theSimulationMode |
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- extended grdchk package accordingly |
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o added tangent linear setup in verification/carbon/code_ftl |
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o added adjoint setup in verification/front_relax/code_ad |
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|
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checkpoint46e_post |
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o Added new equation of state -> MDJWF |
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- EOS of McDougall et al., 2002, JAOT, submitted |
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- caveat: the equation of state is only valid for a smaller (more |
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realistic?) range of values than JMD95P/Z and UNESCO |
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- added masks to the calculation of pressure in store_pressure |
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- added more check values for density in check_eos (ini_eos.F), some of |
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the old check values are out of the range of the MDJWF-eos, so don't |
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expect perfect matches for those |
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checkpoint46e_pre |
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|
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checkpoint46d_post |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
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case of pressure coordinates. eosType='JMD95Z' in |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
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in find_alpha/beta. |
206 |
checkpoint46d_pre |
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|
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
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|
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checkpoint46c_post |
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o Changes necessary for ocean in p-coordinates |
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- Added new buoyancy relation = 'OCEANICP' |
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- Added new parameters = gravitySign (this used to be contained inside |
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the factor dRdZ which I added when we first switched to R coordinates). |
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X GM/Redi is not compatible (yet) |
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X bottom drag and no-slip need to be debugged. |
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checkpoint46c_pre |
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|
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checkpoint46b_post |
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o Added new equation of state -> JMD95Z and JMD95P |
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- EOS of Jackett and McDougall, 1995, JAOT |
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- moved all EOS parameters into EOS.h |
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- new routines ini_eos.F, store_pressure.F |
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o Added UNESCO EOS, but not recommended because it requires |
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in-situ temperature (see JMD95) |
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o Modified formatting for knudsen2.f in utils/knudsen2 and added |
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unesco.f to be used with POLY3 |
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checkpoint46b_pre |
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|
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checkpoint46a_post |
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o Added (atmospheric) pressure loading |
233 |
- new field in FFIELDS.h, etc... |
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- new cpp flag ATMOSPHERIC_LOADING |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
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o Added SHORTWAVE_HEATING to some files for consistency |
237 |
checkpoint46a_pre |
238 |
|
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checkpoint46 |
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further merges from release1_p5 |
241 |
o new ctrl package |
242 |
- adopted from ECCO environment to enable optimization |
243 |
- added Eliassen Palm fluxes to controls |
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o added Eliassen Palm flux controls to gradient check package |
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o cost package |
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- Compatible with new ctrl package |
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- added Eliassen Palm cost hooks |
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- modif's of existing cost functions |
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o Adjoint-related bug fixes in kpp: |
250 |
- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
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o autodiff package |
253 |
- flow directives: |
254 |
+ new for S/R do_the_model_io |
255 |
+ enhanced for S/R checkpoint |
256 |
+ new gmredi.flow |
257 |
- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
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disable adcommon.h/g_common.h by default. |
259 |
- fixed problem for adjoint of global_max |
260 |
o modified verification/carbon/ |
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o New setup for adjoint of global_ocean |
262 |
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
264 |
o incorporated hooks for sponge layer code (external_forcing.F) |
265 |
|
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checkpoint45d_post |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
268 |
o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
269 |
(affects plume_on_slope "cg2d" output) |
270 |
o add new parameter deltaTfreesurf for free-surface time stepping |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
272 |
o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
273 |
o change phiMin in exp1 (to agree with documentation) |
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o add new flags: |
275 |
- T,S forcing inside/outside Adams-Bashforth |
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- turn off temp,salt advection and/or forcing |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
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o monitor: change definition of KE to check conservation of Energy |
279 |
|
280 |
checkpoint45c_post |
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o Removed f90 comments ("!") |
282 |
o Modified initialisations to enable exf package for MITgcm |
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(without invoking ECCO_PACKAGE). |
284 |
o modifications to gradient check package (Martin Losch) |
285 |
- enable centered differences |
286 |
- modified format of standard output |
287 |
|
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checkpoint45b_post |
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o cleaned exchange calls in cg2d |
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o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
291 |
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
292 |
to configure barotropic setup (Martin Losch) |
293 |
o moved some initialisations within bi,bj loop in dynamics |
294 |
(TAF flow dependency) |
295 |
o in initialise_varia, moved call packages_init_variables |
296 |
before convective_adjustment_init |
297 |
(corresponding adjustment of TAF tape initialisation). |
298 |
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
299 |
|
300 |
checkpoint45a_post |
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o compute Rho over the whole domain (extend iMin,jMin indices) |
302 |
o specific exchange for X-slice domain (case Ny=1) |
303 |
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
304 |
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
305 |
|
306 |
checkpoint44h_post = checkpoint45 |
307 |
o Fix to restore differentiability: |
308 |
place at which packages_init_variables is called in |
309 |
initialise_varia is crucial for reverse control flow. |
310 |
o modifications in GMRedi to enable stable adjoint |
311 |
(corresponding modif's in thermodynamics, dynamics) |
312 |
o added missing hook for sponge layer code in external_forcing |
313 |
o modified test cost functions |
314 |
o storing in gad_advection (plus removal of write(0,*)! |
315 |
o missing headers TR1.h added in convective_adjustment routines |
316 |
o errorMessageUnit set non-equal zero in eeboot |
317 |
(conflict on some platforms, e.g. IBM SP3) |
318 |
o modified carbon verif. |
319 |
|
320 |
checkpoint44h_pre |
321 |
o vertical grid option: allow to put the Interface at the middle between |
322 |
2 cell-centers ; replace delZ in pkg/kpp by drF. |
323 |
o GM Advective form: Tracers are advected using the residual transport (= |
324 |
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
325 |
|
326 |
checkpoint44g_post |
327 |
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
328 |
results) ; ifdef missing in thermodynamics.F |
329 |
|
330 |
checkpoint44f_pre,checkpoint44f_post |
331 |
o added PTRACERS package |
332 |
This allows an arbitrary number of passive tracers to be integrated |
333 |
forward simultaneously with the dynamicaly model. |
334 |
+ Implemented so far: |
335 |
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
336 |
- I/O and checkpointing |
337 |
- GM/Redi *but* using the GM/Redi coefficient of Salt |
338 |
+ Not implemented so far: |
339 |
- KPP |
340 |
- OBCS |
341 |
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
342 |
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
343 |
line in data.pkg. |
344 |
+ This package is disabled by default since it increases storage. |
345 |
|
346 |
|
347 |
o testscript: added -cleanup option |
348 |
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
349 |
b) enable to filter 2D fields. |
350 |
|
351 |
checkpoint44e_pre,post |
352 |
o re-wrote convective adjustment to use pre-calculated weights |
353 |
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
354 |
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
355 |
Original calls to convect() still in place. |
356 |
|
357 |
chkpt44d_pre,post |
358 |
o added missing EXCLUDE_MONITOR flags |
359 |
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
360 |
(incompatible typ in MIN/MAX expressions caused problems |
361 |
on IBM SP3) |
362 |
o in genmake added variable MAKEDEPEND |
363 |
plus resetting for case SunOS |
364 |
o added timer_stats.c routine for IBM SP3 |
365 |
o removed variables in dynamics |
366 |
!!! I forgot to create tag chkpt44d_pre !!! |
367 |
!!! But chkpt44d_pre = chkpt44c_post !!! |
368 |
|
369 |
o real fresh water flux implemented with non-linear free-surface. |
370 |
|
371 |
chkpt44c_pre,post |
372 |
o few fix (mask in shap_s2, EmPmR in external_field_load, |
373 |
USE_NATURAL_BCS in solve_for_P); |
374 |
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
375 |
|
376 |
checkpoint44b_pre/_post |
377 |
o merge of relevant stuff from the ecco-branch: |
378 |
- genmake: removed $S64 overwrite for case SunOS |
379 |
- pkg/exf: update and corrections for field swapping and obcs |
380 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
381 |
harmonized between ECCO and MITgcm |
382 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
383 |
updated checkpointing_lev... lists for obcs |
384 |
- model/src: minor changes in forward_step, plot_field |
385 |
added directive for divided adjoint in the_main_loop |
386 |
- pkg/mdsio: added mdsio_gl_slice |
387 |
|
388 |
o check parameters & config (chkpt44a_pre,post) |
389 |
o OBC and NonLin_FrSurf. |
390 |
|
391 |
checkpoint44 |
392 |
o fix bug in mom_vi_del2uv |
393 |
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
394 |
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
395 |
o update AIM experiments (NCEP input files) |
396 |
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
397 |
o added some stuff for AD |
398 |
|
399 |
checkpoint43 |
400 |
o added two new advection tests |
401 |
o added global 4x4 degree ocean test |
402 |
o added test of H&S94 with free surface on cube |
403 |
o some final mods for gradient check, adjoint,... |
404 |
|
405 |
checkpoint42 |
406 |
Fixed AD-related problems: |
407 |
o Store directives up-to-date with re-arranged Adams-Bashforth |
408 |
(mainly thermodynamics.F) |
409 |
o New store directives for multi-dim. advection schemes |
410 |
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
411 |
* new common block and key passkey |
412 |
(mainly gad_advection.F) |
413 |
o Modified store directives for split of dynamics/thermodynamics |
414 |
for the case ALLOW_KPP |
415 |
o Cleaned argument list for timestep_tracer.F |
416 |
|
417 |
checkpoint41 |
418 |
o re-formatted/added comments in prologues of key subroutines |
419 |
to work with protex |
420 |
|
421 |
checkpoint40 |
422 |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
423 |
o added FLT (floats) package from Arne along with demo. experiment |
424 |
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
425 |
implementation of forward-in-time forcing terms |
426 |
o more mods for non-linear free-surface including new variable |
427 |
o modified multi-dim method to work on cube |
428 |
o bug fix in KPP (from DM) |
429 |
|
430 |
checkpoint40pre9 |
431 |
o added DST advection schemes |
432 |
o fix MPI bug on SGI's |
433 |
o modifications for non-linear free-surface |
434 |
o fixed conditionals for fixed flow/passive tracer only mode |
435 |
o added tension/strain form of stress tensor |
436 |
o changes to commenting of arguments for TAF/TAMC |
437 |
o added/updated many matlab scripts |
438 |
o added multi-dimensional advection method for tracers |
439 |
|
440 |
checkpoint40pre8 |
441 |
o new package rw/ |
442 |
Added method for dumping intermediate local arrays: |
443 |
mdsio_writetile - same as mdsio_writefield except works from inside |
444 |
bi,bj loop |
445 |
mdsio_writelocal - same as mdsio_writetile except works for local |
446 |
arrays |
447 |
write_local_r? - higher-level wrapper for mdsio_writelocal |
448 |
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
449 |
Example given at end of mom_vecinv.F that dumps some local arrays. |
450 |
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
451 |
control flux-form versus vector invariant code. |
452 |
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
453 |
or genmake -DISABLE ... |
454 |
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
455 |
(additional storing is now needed for case vecinv; |
456 |
currently nothing implemented to switch this storing off |
457 |
in case fluxform is used since no CPP flag available). |
458 |
|
459 |
checkpoint40pre7 |
460 |
o bug fix in dynamics.F |
461 |
calc_viscosity called before k=1,Nr loop. |
462 |
o added some #ifdef's ALLOW_PASSIVE_TRACER |
463 |
o cleaned initialisations in ctrl_map_ini |
464 |
related to TAF |
465 |
|
466 |
checkpoint40pre6 |
467 |
o split dynamics into thermodynamics & dynamics |
468 |
o corresponding split of calc_diffusivity into |
469 |
calc_diffusivity, calc_viscosity |
470 |
(kpp_calc_diff, kpp_calc_visc). |
471 |
o Added diffkr, kapgm to control variables |
472 |
o bug fix in gmredi_slope_limit for ldd97 |
473 |
|
474 |
checkpoint40pre5 |
475 |
o proper initialization of Adams-Bashforth time stepping |
476 |
+ uses forward step for very first step of model (iter=0) |
477 |
o re-generated *all* output since almost all output is modified by this |
478 |
change (sorry but we've been putting this one off for about 2 years) |
479 |
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
480 |
*not* regenerated since they are already out of date and I don't |
481 |
want to create the impression that they are suddenly working. |
482 |
o removed KAP stuff for DEC's |
483 |
o modified/added many .cvsignore files in */code and */input |
484 |
o added new expt "solid-body.cs-32x32x1" |
485 |
+ this uses an alternative form of ini_curvilinear_grid.F which |
486 |
is not necessarily any better than the current one... |
487 |
|
488 |
checkpoint40pre4 |
489 |
o added re-initialisations of utrans,vtrans,rtrans in |
490 |
calc_common_factors which are crucial for TAF. |
491 |
o extended iMin,jMin range for calc_common_factors, |
492 |
calc_diffusivity |
493 |
o added option ALLOW_PASSIVE_TRACER |
494 |
o a few minor updates and fixes |
495 |
|
496 |
checkpoint40pre3 |
497 |
o created calc_gtr1.F for gad package |
498 |
o split the_main_loop and re-introduced forward_step |
499 |
o some recomputations of nIter0 for TAMC |
500 |
|
501 |
checkpoint40pre2 |
502 |
o Updated to latest branch of AJA, JMC |
503 |
o Added gradient check package |
504 |
o Added routines for passive tracer handling |
505 |
o Added carbon sequestration sensitivity experiment |
506 |
|
507 |
checkpoint39 |
508 |
o Modifications and fixes to support TAMC |
509 |
(mainly missing or wrong directives) |
510 |
o Corrected common blocks when fooling TAMC to produce adjoint I/O |
511 |
in addummy_in_stepping |
512 |
o Updated verification/vero/ (bug fixes in code/, correct pickups in input/) |
513 |
o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs. |
514 |
o Included following packages: |
515 |
cal: calendar |
516 |
exf: external forcing |
517 |
ecco: essential routines to control use of cal, exf |
518 |
(NB: this is not the full ECCO environment) |
519 |
o disabled some packages by default in genmake |
520 |
|
521 |
checkpoint38 |
522 |
o see notes_c37_adj.txt |
523 |
o corrected wrong layer index in external_forcing_t |
524 |
o replaced the_main_loop/forward_step by the_main_loop |
525 |
o removed forceoutput from write_state |
526 |
(replaced criteria for initial/final state) |
527 |
o added runtime flag for pre-C35 pickups: usePickupBeforeC35 |
528 |
|
529 |
checkpoint37 |
530 |
o mdsio.F routine split and packaged in pkg/mdsio |
531 |
(mdsio.F and mdsio_gl.F still exist in eesupp/src but are not |
532 |
used unless genmake -disable=mdsio) |
533 |
o allow a more precise surface-geopotential gradient for the atmosphere |
534 |
taking into account the change in space of Alpha (=1/rho) at the surface. |
535 |
o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit] |
536 |
(ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa]) |
537 |
o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and |
538 |
Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential |
539 |
[m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere). |
540 |
o Time-Average diagnostics defined as a pseudo package "timeave". |
541 |
o pickup files : old pickup (before c35) did not work with new code (c35 |
542 |
and after) unless activating 2 commented lines in initialise-varia. |
543 |
o Non-Hydrostatic pickup file Pb fixed. |
544 |
o bug with Rigid-lid version (since c35) fixed. |
545 |
|
546 |
checkpoint36 |
547 |
o implement Crank-Nickelson barotropic time-stepping |
548 |
o recover Time-Average diagnostics |
549 |
o fix Pb in checkpoint (PR#19) |
550 |
o AIM become a standard package ; clean unused CPP_kees |
551 |
|
552 |
checkpoint35 |
553 |
o subtantial rewrite of dynamics.f |
554 |
o allows staggered time-stepping |
555 |
o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt |
556 |
o added bottom drag (linear + quadratic) |
557 |
|
558 |
checkpoint34 |
559 |
o Modified exchange routines for correct reverse simulation. |
560 |
o Added verification output to comply with bug fix in impldiff.F |
561 |
as of c33 (exp2, natl_box). |
562 |
o Corrected store directives in dynamics.F |
563 |
o Corrected array boundaries in impldiff.F |
564 |
o Corrected array dimensions in gmredi. |
565 |
Added temporary scalars to avoid storage by TAMC (gmredi, kpp). |
566 |
o Added routine GLOBAL_SUM_INT to global_sum.F |
567 |
o Added mdsio_gl.F for ECCO purposes. |
568 |
|
569 |
checkpoint33 |
570 |
o Fixed bug in lower BC in impldiff.F |
571 |
o Fixed confusion about units of forcing arrays in FFIELDS.h |
572 |
namely Fu,Fv,Qnet,Qsw,EmPmR: |
573 |
- Removed verification/natl_box/code/external_fields_scale.F |
574 |
(did not differ from that in model/src) |
575 |
- Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units |
576 |
(see FFIELDS.h for description) |
577 |
- Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F, |
578 |
kpp_calc.F and kpp_transport_t.F |
579 |
- Removed model/src/external_fields_scale.F and calls to it |
580 |
- verification/natl_box uses flux data with "atmospheric" sign so |
581 |
a special version of external_fields_load.F is used to |
582 |
change the data as it's read in. This way, the arrays |
583 |
have the right units and signs at all times tha a user could |
584 |
possibly use them. |
585 |
o Corrected genmake to delete a temporary file during configuration |
586 |
|
587 |
checkpoint32 |
588 |
o Scaling of forcing fields moved from external_forcing.F to |
589 |
external_fields_scale.F, called directly after loading fields. |
590 |
o Surface relaxation terms added to surface tendency fields in |
591 |
extra subroutine. |
592 |
o impldiff.F changed to avoid storing by TAMC of huge intermediate |
593 |
fields. |
594 |
o Changes in GMRedi to comply with packaging structure. |
595 |
o Modifications and bug fixes in KPP package. |
596 |
o Verification experiment for KPP added (verification/nat_box/) |
597 |
|
598 |
checkpoint31 |
599 |
o Packages interface brought in line with defined standard |
600 |
-> new routines packages_...F |
601 |
-> changes in initialise_fixed.F, initialise_varia.F |
602 |
-> enables initialisation interface for ECCO package |
603 |
o Rescaling of external forcing fields immediately after read |
604 |
(removed from external_forcing.F) |
605 |
-> new: surface_fields_scale.F |
606 |
-> affects ini_foorcing.F, external_fields_load.F |
607 |
o Computation of surface tendencies before tendency updates. |
608 |
-> new: external_forcing_surf.F |
609 |
o Change of variable names useGMRedi, useKPP, useECCO |
610 |
o Further changes in dynamics.F, impldiff.F for TAMC |
611 |
o Tested for experiments 0, 2, 4. |
612 |
- not yet tested for GMRedi. |
613 |
- not yet tested for KPP. |
614 |
|
615 |
checkpoint30 |
616 |
o Updates for OBCs |
617 |
o New experiment for test OBCs (internal_wave) |
618 |
o New output.txt in verification/exp4/results/ |
619 |
o Updates for KPP: calculation of viscosity corrected, new variables |
620 |
kpp_dumpFreq and kpp_taveFreq |
621 |
o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.) |
622 |
and entry for T90 in genmake |
623 |
|
624 |
checkpoint29 |
625 |
o packaged KPP and GM/Redi |
626 |
|
627 |
checkpoint28 |
628 |
o Corrected initialization of hFacMin for difference vertical coordinates |
629 |
o Modified calculation of partial cell thickness to more robust algorithm |
630 |
o config_summary.F: replaced write_1D_... by write_0D_... |
631 |
read_write.F: added subroutines write_0D_... |
632 |
o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho: |
633 |
included some initialisations required for TAMC. |
634 |
o routine calc_isoslopes: modified sqrt computation to make it |
635 |
differentiable for zero argument. |
636 |
o routines dynamics, impldiff: |
637 |
included store directives and tape key computations required for TAMC. |
638 |
o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC |
639 |
|
640 |
checkpoint27 |
641 |
o fixed calc_isoslopes() to so that cancellation of terms in tensor |
642 |
formulation works properly with variable resolution. |
643 |
o restructured the calling tree between the_model_main() and dynamics() |
644 |
o split initialise() into initialise_fixed() and initialise_varia() |
645 |
o introduced initialization file pSurfInitFile for free surface (cg2d_x) |
646 |
in new routine ini_psurf() |
647 |
|
648 |
checkpoint26 |
649 |
o moved some #ifdef in optional routines to encompass everything |
650 |
except the argument declarations. This was using up some memory. |
651 |
o fixed macros like _ADT to work with both versions of Linux cpp |
652 |
o cleaned up some unused and uninitialized variables |
653 |
(helps when debugging with strict compile options) |
654 |
o split up CPP_EEOPTIONS.h into options and macros |
655 |
(macros are now in eesupp/inc/CPP_EEMACROS.h) |
656 |
o patch for 2 processor JAM mode |
657 |
|
658 |
checkpoint25 |
659 |
o updates for OBCs and NH |
660 |
o dramatically reduced memory usage |
661 |
o added "JAM" routines for use on Artic network |
662 |
o parameterization of convection by implicit vertical diffusion |
663 |
o added a diagnostic of convective index |
664 |
o moved call to calc_divg_hat() from dynamics() to solve_for_pressure() |
665 |
(this is was partly for OBCs and NH but also in anticipation of |
666 |
an explicit free-surface option) |
667 |
o initial state input files for U and V |
668 |
|
669 |
checkpoint24 |
670 |
o Removed some spurious "REAL"s |
671 |
o Updated KPP to latest version from JPL |
672 |
o Added a COS(latitude) in horizontal viscosity |
673 |
|
674 |
checkpoint23 |
675 |
o Added del^4 diffusion for salt and temperature |
676 |
o Multiple minor fixes (implicit none's, arguments to global_sum, etc.) |
677 |
|
678 |
checkpoint22 |
679 |
o Made many small changes: implicit none, format(i5), etc... |
680 |
o Introduced KPP mixing scheme (compiles and runs but *not* tested) |
681 |
|
682 |
checkpoint21 |
683 |
o Introduced new I/O package that supports direct-access records (mdsio.F) |
684 |
o Split-up mid-level I/O routines |
685 |
o Updated input data for experiments 0,1,2,4 and 5 |
686 |
o Finally removed the genmake.* scripts (everyone seems happy with genmake) |
687 |
|
688 |
checkpoint20 |
689 |
o Tidied up open-boundaries some more |
690 |
o Added non-hydrostatic code |
691 |
o Fixed some input data |
692 |
o Modified MPI start-up to work in "coupled" context. |
693 |
|
694 |
checkpoint19 |
695 |
o Tidied up directory structure for verification experiments. |
696 |
o Added new code for open boundaries. |
697 |
o Corrected advective terms near boundaries. |
698 |
o Added CPP flag for "old UV" geometry and corrected spherical geometry. |
699 |
o Implemented free-slip/no-slip BCs and del^4 dissipation. |
700 |
o Split default parameters out of ini_parms.F into set_defaults.F. |
701 |
|
702 |
checkpoint18 |
703 |
o Further changes for optional code generation with |
704 |
CPP - ugh! |
705 |
|
706 |
checkpoint17 |
707 |
o Beginning to incorporating modularity |
708 |
for supporting atmos. and ocean configs. |
709 |
o Small changes for TAMC complinace |
710 |
o New ultra simple test case. Barotropic box |
711 |
configuration "exp0". |
712 |
|
713 |
checkpoint16 |
714 |
o Minor changes to exchange routines to support |
715 |
accumulation in reverse mode. Adjoint of an |
716 |
assignment is an addition. |
717 |
o Changes to support compilation by TAMC (LR(1) |
718 |
syntax) and by g77 under Linux ( 72 character |
719 |
limit ). |
720 |
|
721 |
checkpoint15 |
722 |
Rewrote exchange routines to allow |
723 |
o General tile <-> tile connectivity. |
724 |
o TAMC reverse mode flag ( is this really needed? ) |
725 |
o Variable width overlap and exchange region widths. |
726 |
o Hooks for sharing data via DMA, Arctic, Memory Channel, |
727 |
shmput/shmget, VIA, SYSV shmem and every other cool |
728 |
communication method. |
729 |
|
730 |
checkpoint14 |
731 |
Consistent isomorphism chages made. These allow dynamical core |
732 |
to support both pressure and meters as a vertical coordinate. |
733 |
|
734 |
checkpoint13 |
735 |
Release which corrects global_max problem and a couple |
736 |
of KGM time-averaging diagnostic errors. Also contains |
737 |
a double-gyre experiment setup as well as the baseline |
738 |
4 degree global template. The double gyre template is |
739 |
organised to allow it to be applied automatically to |
740 |
the baseline configuration. |
741 |
|
742 |
branch-point-rdot |
743 |
A few tidy-ups have been made bt the real point of this |
744 |
check-point (excuse the pun) is to allow a branch to be |
745 |
made for the purposes of adding the rDot alterations. |
746 |
I don't want to commit the rDot to the main-trunk until |
747 |
we've actually tested it... |
748 |
|
749 |
checkpoint12 |
750 |
Tidy up and added generic genmake script (formerly |
751 |
configure script). |
752 |
Released to testers. |
753 |
|
754 |
checkpoint11 |
755 |
Re-arranged initialise() and introduced ini_vertical_grid() |
756 |
and ini_masks_etc(). |
757 |
|
758 |
checkpoint10 |
759 |
Introduced the configure script. |
760 |
Separated out the diags package. |
761 |
Added template for writing time-averages of tile/intermediate quantities. |
762 |
Updated SIZE.h in exp2 and made the data big-endian. |
763 |
|
764 |
checkpoint9 |
765 |
MPI fix. Filename changes (meta/data). salbin*y stuff. |
766 |
General tidy-up. |
767 |
SST.bin SSS.bin added to verification/exp2 |
768 |
|
769 |
checkpoint8 |
770 |
Inludes time-dependant forcing and time-averaging. |
771 |
Works at 4x4 and 2.8125x2.8125 global |
772 |
|
773 |
checkpoint7-4degree-ref |
774 |
Branch from checkpoint7. Released for application to |
775 |
global modeling and general modeling - process studies, regional |
776 |
model etc.. |
777 |
Configured for verification/exp2 - 4 degree global, two process. |
778 |
|
779 |
checkpoint7 |
780 |
Created by cnh |
781 |
Simple 4 degree global simulation |
782 |
configuration. |
783 |
Includes climatological wind, |
784 |
hydrography, bathymetry etc |
785 |
Does not include Heat Flux and E-P |
786 |
|
787 |
checkpoint6 |
788 |
Created by cnh |
789 |
merged checkpoint5 with CD and |
790 |
spherical polar code. |
791 |
Still some problems with GM Redi |
792 |
abd full topography. |
793 |
|
794 |
checkpoint5 |
795 |
Created by AJA |
796 |
contains updates to GM Redi |
797 |
and reordered timestepping loop |
798 |
for Implicit Diffusion. |
799 |
|
800 |
checkpoint4 |
801 |
Created by cnh |
802 |
Contains memory saving macros ( _rdxc etc..) for when |
803 |
grid variations are limited. |
804 |
Contains polynomial coeffs for EOS and knudsen program |
805 |
for generation. |
806 |
|
807 |
checkpoint3 |
808 |
Created by cnh |
809 |
Added extra flags for runtime options |
810 |
Added this file |
811 |
Added implicit free-surface |
812 |
Added pre-conditioner |
813 |
Put compare01 into repository ( compare01/... ) |
814 |
Put data and eedata into repository ( verification/exp1 ) |
815 |
|
816 |
checkpoint2 |
817 |
Created by AJA |
818 |
Added GM/Redi |
819 |
|
820 |
checkpoint1 |
821 |
Created by AJA |
822 |
Restructured kloop in dynamics.F |
823 |
Added non-linear EOS |
824 |
|
825 |
baseline |
826 |
Original checked in code |