| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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| 6 |
ecco_c44_e20 |
o fixed the verification/global_ocean.90x40x15 experiment: |
| 7 |
o before major merges from the Scripps setup |
- new bathymetry (the world according to A., JMC, and M.) |
| 8 |
here are two small updates: |
- new initial fields and forcing fields (*.bin files) |
| 9 |
- field swapping for surface flux controls enabled |
- new POLY3.COEFFS (for the next release one should switch to a full |
| 10 |
(remains t.b.d. for atmos. state plus obcs) |
equation of state: JMD95P or MDJWF) |
| 11 |
- bug fix in active_file.F for xz-/yz- routines |
- fixed several errors and redundancies in the data file |
| 12 |
- added missing xz-/yz- routines to active_file_ad.F |
- experiment uses looped cells |
| 13 |
|
- added matlab directory with diagnostic scripts for plotting of output |
| 14 |
ecco_c44_e19 |
|
| 15 |
o merged necessary patches: |
o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
| 16 |
- AD-related changes for GMRedi |
- read AIM physics parameters from a file (data.aimphys) |
| 17 |
- fixes i KPP (delZ -> drF) |
- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
| 18 |
- hook to OBCS songe layer code in external_forcing |
|
| 19 |
- errorMessageUnit non-zero in eeboot.F |
checkpoint46j_post |
| 20 |
- included GMREDI, EXACT_CONSERV to natl_box_adjoint verif. |
o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
| 21 |
|
o move wVel computation at the end of the time step, in S/R integr_continuity |
| 22 |
ecco_c44_e18 |
o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
| 23 |
o sponge layer code for obcs was missing |
o update timeave pkg for wVel diagnostic. |
| 24 |
- added hook in external_forcing.F |
checkpoint46j_pre |
| 25 |
- added storing for TAF |
|
| 26 |
o new routine cost_init_barfiles to initialise |
checkpoint46i_post |
| 27 |
adjoint fields adtbar, adsbar, adpsbar |
o Clean up AIM package (and keep the results unchanged): |
| 28 |
(needed in conjunction with corrected ladinit for active I/O) |
include CPP_OPTION and use IMPLICT NONE in all routines ; |
| 29 |
o cleaned up and corrected order in packages_readparms, ecco_readparms |
declare all the variables _RL ; use _d 0 for all numerical constants. |
| 30 |
o corrected and simplified weights for obcs controls |
use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
| 31 |
- weight fields simplified |
|
| 32 |
- bug fix in ctrl_pack |
checkpoint46h_post |
| 33 |
- no more write of control vector in ctrl_pack |
o cleaned up the use of rhoNil and rhoConst. |
| 34 |
o i/j index bug fixes in cost_ssh_mean |
- rhoNil should only appear in the LINEAR equation of state, everywhere |
| 35 |
|
else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
| 36 |
ecco_c44_e17 |
and the dynamical equations are all divided by rhoConst |
| 37 |
o bug fixes in cost package |
o introduced new parameter rhoConstFresh, a reference density of fresh |
| 38 |
* wrong identifier for active I/O of monthly mean psbar |
water, to remove the fresh water flux's dependence on rhoNil. The default |
| 39 |
(cost_averagesfields, cost_ssh) xx_psbar_dummy |
value is 999.8 kg/m^3 |
| 40 |
* cleaned all identifier for active I/O of monthly fields |
o cleanup up external_forcing.F and external_forcing_surf.F |
| 41 |
* wrong ladinit in various cost routines |
- can now be used by both OCEANIC and OCEANICP |
| 42 |
o merge with interval (chkpt44c_post - chkpt44d_post) |
checkpoint46h_pre |
| 43 |
* added missing EXCLUDE_MONITOR flags |
|
| 44 |
* changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
Added code to convert surface volume flux (fresh water) into |
| 45 |
(incompatible typ in MIN/MAX expressions caused problems |
a mass flux when using P coordinates in the ocean (OCEANICP). |
| 46 |
on IBM SP3) |
Note: It assumes you have set rho0=rhoConst=density of fresh water. |
| 47 |
* in genmake added variable MAKEDEPEND |
|
| 48 |
plus resetting for case SunOS |
checkpoint46g_post |
| 49 |
added timer_stats.c routine for IBM SP3 |
o Include a new diagnostic variable phiHydLow for the ocean model |
| 50 |
* removed variables in dynamics |
- in z-coordinates, it is the bottom pressure anomaly |
| 51 |
|
- in p-coordinates, it is the sea surface elevation |
| 52 |
ecco_c44_e16 |
- in both cases, these variable have global drift, reflecting the mass |
| 53 |
o new ECCO checkpoint, the first since ecco_c43_e15 |
drift in z-coordinates and the volume drift in p-coordinates |
| 54 |
which is branched from MITgcm. |
- included time averaging for phiHydLow, be aware of the drift! |
| 55 |
All changes were merged in between (see ecco-branch-mod? tags). |
o depth-dependent computation of Bo_surf for pressure coordinates |
| 56 |
o last changes: |
in the ocean (buoyancyRelation='OCEANICP') |
| 57 |
* assuming path for TAF and TAMC are known (e.g. in $path) |
- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
| 58 |
* genmake: |
Theta, Salinity, and Pressure in the parameter list. This routine is |
| 59 |
- added tools/xmakedepend to circumvene shortcoming of |
presently contained in find_rho.F. This routine does not give the |
| 60 |
SUN's makedepend (size too small) |
correct density for 'POLY3', which would be a z-dependent reference |
| 61 |
- invoking ../tools/xmakedepend instead of makedepend |
density. |
| 62 |
- changed compiler flags for case SunOS |
o cleaned up find_rho |
| 63 |
|
- removed obsolete 'eqn' from the parameter list. |
| 64 |
ecco-branch-mod5 |
o added two new verification experiments: gop and goz |
| 65 |
o mod's to reproduce open boundary run |
(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
| 66 |
o enable field swapping for OB's and climatology |
checkpoint46g_pre |
| 67 |
o update store directives for OB control |
|
| 68 |
o added option ALLOW_OBCS_PRESCRIBE |
checkpoint46f_post |
| 69 |
o call of getobcs now out of obcs_calc (param. list modified) |
o Enable tangent linear (forward mode) gradient checks: |
| 70 |
|
- extended active file handling to g_... files |
| 71 |
ecco-branch-mod4 |
- added TANGENT_SIMULATION to theSimulationMode |
| 72 |
o this is the second part of changes necessary to reconcile |
- extended grdchk package accordingly |
| 73 |
the natl_box_adjoint verification (with and without grdchk). |
o added tangent linear setup in verification/carbon/code_ftl |
| 74 |
>>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<< |
o added adjoint setup in verification/front_relax/code_ad |
| 75 |
>>>!!! AND ecco-branch-mod4 !!!<<< |
|
| 76 |
>>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK !!!<<< |
checkpoint46e_post |
| 77 |
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o Added new equation of state -> MDJWF |
| 78 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
| 79 |
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- caveat: the equation of state is only valid for a smaller (more |
| 80 |
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realistic?) range of values than JMD95P/Z and UNESCO |
| 81 |
|
- added masks to the calculation of pressure in store_pressure |
| 82 |
|
- added more check values for density in check_eos (ini_eos.F), some of |
| 83 |
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the old check values are out of the range of the MDJWF-eos, so don't |
| 84 |
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expect perfect matches for those |
| 85 |
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checkpoint46e_pre |
| 86 |
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| 87 |
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checkpoint46d_post |
| 88 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
| 89 |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
| 90 |
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case of pressure coordinates. eosType='JMD95Z' in |
| 91 |
|
combination with buoyancyRelation='OCEANICP' now causes an error. |
| 92 |
|
o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 93 |
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in find_alpha/beta. |
| 94 |
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checkpoint46d_pre |
| 95 |
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|
| 96 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
| 97 |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
| 98 |
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|
| 99 |
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checkpoint46c_post |
| 100 |
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o Changes necessary for ocean in p-coordinates |
| 101 |
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- Added new buoyancy relation = 'OCEANICP' |
| 102 |
|
- Added new parameters = gravitySign (this used to be contained inside |
| 103 |
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the factor dRdZ which I added when we first switched to R coordinates). |
| 104 |
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X GM/Redi is not compatible (yet) |
| 105 |
|
X bottom drag and no-slip need to be debugged. |
| 106 |
|
checkpoint46c_pre |
| 107 |
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|
| 108 |
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checkpoint46b_post |
| 109 |
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o Added new equation of state -> JMD95Z and JMD95P |
| 110 |
|
- EOS of Jackett and McDougall, 1995, JAOT |
| 111 |
|
- moved all EOS parameters into EOS.h |
| 112 |
|
- new routines ini_eos.F, store_pressure.F |
| 113 |
|
o Added UNESCO EOS, but not recommended because it requires |
| 114 |
|
in-situ temperature (see JMD95) |
| 115 |
|
o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 116 |
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unesco.f to be used with POLY3 |
| 117 |
|
checkpoint46b_pre |
| 118 |
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|
| 119 |
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checkpoint46a_post |
| 120 |
|
o Added (atmospheric) pressure loading |
| 121 |
|
- new field in FFIELDS.h, etc... |
| 122 |
|
- new cpp flag ATMOSPHERIC_LOADING |
| 123 |
|
o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 124 |
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o Added SHORTWAVE_HEATING to some files for consistency |
| 125 |
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checkpoint46a_pre |
| 126 |
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| 127 |
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checkpoint46 |
| 128 |
|
further merges from release1_p5 |
| 129 |
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o new ctrl package |
| 130 |
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- adopted from ECCO environment to enable optimization |
| 131 |
|
- added Eliassen Palm fluxes to controls |
| 132 |
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o added Eliassen Palm flux controls to gradient check package |
| 133 |
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o cost package |
| 134 |
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- Compatible with new ctrl package |
| 135 |
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- added Eliassen Palm cost hooks |
| 136 |
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- modif's of existing cost functions |
| 137 |
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o Adjoint-related bug fixes in kpp: |
| 138 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 139 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 140 |
|
o autodiff package |
| 141 |
|
- flow directives: |
| 142 |
|
+ new for S/R do_the_model_io |
| 143 |
|
+ enhanced for S/R checkpoint |
| 144 |
|
+ new gmredi.flow |
| 145 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 146 |
|
disable adcommon.h/g_common.h by default. |
| 147 |
|
- fixed problem for adjoint of global_max |
| 148 |
|
o modified verification/carbon/ |
| 149 |
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o New setup for adjoint of global_ocean |
| 150 |
|
o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 151 |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 152 |
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o incorporated hooks for sponge layer code (external_forcing.F) |
| 153 |
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| 154 |
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checkpoint45d_post |
| 155 |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 156 |
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o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 157 |
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(affects plume_on_slope "cg2d" output) |
| 158 |
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o add new parameter deltaTfreesurf for free-surface time stepping |
| 159 |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 160 |
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o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 161 |
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o change phiMin in exp1 (to agree with documentation) |
| 162 |
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o add new flags: |
| 163 |
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- T,S forcing inside/outside Adams-Bashforth |
| 164 |
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- turn off temp,salt advection and/or forcing |
| 165 |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
| 166 |
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o monitor: change definition of KE to check conservation of Energy |
| 167 |
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| 168 |
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checkpoint45c_post |
| 169 |
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o Removed f90 comments ("!") |
| 170 |
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o Modified initialisations to enable exf package for MITgcm |
| 171 |
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(without invoking ECCO_PACKAGE). |
| 172 |
|
o modifications to gradient check package (Martin Losch) |
| 173 |
|
- enable centered differences |
| 174 |
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- modified format of standard output |
| 175 |
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| 176 |
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checkpoint45b_post |
| 177 |
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o cleaned exchange calls in cg2d |
| 178 |
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o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 179 |
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o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 180 |
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to configure barotropic setup (Martin Losch) |
| 181 |
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o moved some initialisations within bi,bj loop in dynamics |
| 182 |
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(TAF flow dependency) |
| 183 |
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o in initialise_varia, moved call packages_init_variables |
| 184 |
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before convective_adjustment_init |
| 185 |
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(corresponding adjustment of TAF tape initialisation). |
| 186 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 187 |
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| 188 |
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checkpoint45a_post |
| 189 |
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o compute Rho over the whole domain (extend iMin,jMin indices) |
| 190 |
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o specific exchange for X-slice domain (case Ny=1) |
| 191 |
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o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 192 |
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o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 193 |
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| 194 |
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checkpoint44h_post = checkpoint45 |
| 195 |
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o Fix to restore differentiability: |
| 196 |
|
place at which packages_init_variables is called in |
| 197 |
|
initialise_varia is crucial for reverse control flow. |
| 198 |
|
o modifications in GMRedi to enable stable adjoint |
| 199 |
|
(corresponding modif's in thermodynamics, dynamics) |
| 200 |
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o added missing hook for sponge layer code in external_forcing |
| 201 |
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o modified test cost functions |
| 202 |
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o storing in gad_advection (plus removal of write(0,*)! |
| 203 |
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o missing headers TR1.h added in convective_adjustment routines |
| 204 |
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o errorMessageUnit set non-equal zero in eeboot |
| 205 |
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(conflict on some platforms, e.g. IBM SP3) |
| 206 |
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o modified carbon verif. |
| 207 |
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| 208 |
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checkpoint44h_pre |
| 209 |
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o vertical grid option: allow to put the Interface at the middle between |
| 210 |
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2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 211 |
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o GM Advective form: Tracers are advected using the residual transport (= |
| 212 |
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Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 213 |
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| 214 |
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checkpoint44g_post |
| 215 |
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o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 216 |
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results) ; ifdef missing in thermodynamics.F |
| 217 |
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| 218 |
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checkpoint44f_pre,checkpoint44f_post |
| 219 |
|
o added PTRACERS package |
| 220 |
|
This allows an arbitrary number of passive tracers to be integrated |
| 221 |
|
forward simultaneously with the dynamicaly model. |
| 222 |
|
+ Implemented so far: |
| 223 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 224 |
|
- I/O and checkpointing |
| 225 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 226 |
|
+ Not implemented so far: |
| 227 |
|
- KPP |
| 228 |
|
- OBCS |
| 229 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 230 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 231 |
|
line in data.pkg. |
| 232 |
|
+ This package is disabled by default since it increases storage. |
| 233 |
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| 234 |
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| 235 |
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o testscript: added -cleanup option |
| 236 |
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o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 237 |
|
b) enable to filter 2D fields. |
| 238 |
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|
| 239 |
|
checkpoint44e_pre,post |
| 240 |
|
o re-wrote convective adjustment to use pre-calculated weights |
| 241 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 242 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 243 |
|
Original calls to convect() still in place. |
| 244 |
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|
| 245 |
|
chkpt44d_pre,post |
| 246 |
|
o added missing EXCLUDE_MONITOR flags |
| 247 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 248 |
|
(incompatible typ in MIN/MAX expressions caused problems |
| 249 |
|
on IBM SP3) |
| 250 |
|
o in genmake added variable MAKEDEPEND |
| 251 |
|
plus resetting for case SunOS |
| 252 |
|
o added timer_stats.c routine for IBM SP3 |
| 253 |
|
o removed variables in dynamics |
| 254 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
| 255 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
| 256 |
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| 257 |
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o real fresh water flux implemented with non-linear free-surface. |
| 258 |
|
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| 259 |
|
chkpt44c_pre,post |
| 260 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 261 |
|
USE_NATURAL_BCS in solve_for_P); |
| 262 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 263 |
|
|
| 264 |
|
checkpoint44b_pre/_post |
| 265 |
|
o merge of relevant stuff from the ecco-branch: |
| 266 |
- genmake: removed $S64 overwrite for case SunOS |
- genmake: removed $S64 overwrite for case SunOS |
| 267 |
- pkg/exf: update and corrections for field swapping and obcs |
- pkg/exf: update and corrections for field swapping and obcs |
| 268 |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 270 |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 271 |
updated checkpointing_lev... lists for obcs |
updated checkpointing_lev... lists for obcs |
| 272 |
- model/src: minor changes in forward_step, plot_field |
- model/src: minor changes in forward_step, plot_field |
| 273 |
|
added directive for divided adjoint in the_main_loop |
| 274 |
- pkg/mdsio: added mdsio_gl_slice |
- pkg/mdsio: added mdsio_gl_slice |
| 275 |
|
|
| 276 |
ecco-branch-mod3 |
o check parameters & config (chkpt44a_pre,post) |
| 277 |
o this is the first part of changes necessary to reconcile |
o OBC and NonLin_FrSurf. |
|
natl_box_adjoint verification (with and without grdchk). |
|
|
This set of changes is relevant for ECCO only. |
|
|
The next set/tag of changes (ecco-branch-mod4) |
|
|
should be merged into the main trunk. |
|
|
- update some options |
|
|
- parameter lists of ecco_the_model_main and ecco_the_main_loop |
|
|
differed from those of the MITgcm counterparts. |
|
|
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|
|
ecco-branch-mod2 |
|
|
o update ecco-branch-mod1 to checkpoint44 |
|
|
o exclude from updates: |
|
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- verification/ |
|
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- adjoint/ |
|
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- pkg/cost |
|
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- pkg/ctrl |
|
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- pkg/ecco |
|
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- pkg/obcs |
|
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- model/src/the_model_main.F |
|
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- model/src/the_main_loop.F |
|
| 278 |
|
|
| 279 |
checkpoint44 |
checkpoint44 |
|
o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping) |
|
| 280 |
o fix bug in mom_vi_del2uv |
o fix bug in mom_vi_del2uv |
| 281 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 282 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 283 |
|
o update AIM experiments (NCEP input files) |
| 284 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 285 |
o added some stuff for AD |
o added some stuff for AD |
| 286 |
|
|
|
ecco-branch-mod1 |
|
|
o based on c43 |
|
|
o replaced packages cost, ctrl, ecco, obcs |
|
|
o removed MITgcm verif.'s, added ECCO verif.'s |
|
|
o added lsopt, optim for line search optimization. |
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|
|
| 287 |
checkpoint43 |
checkpoint43 |
| 288 |
o added two new advection tests |
o added two new advection tests |
| 289 |
o added global 4x4 degree ocean test |
o added global 4x4 degree ocean test |
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