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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o removed gravitySign from PARM04 |
| 7 |
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o switched to g77/ifc from pgf77 in aim experiments |
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| 9 |
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checkpoint46l_post |
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o made convective adjustment work with pressure coordinates: |
| 11 |
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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 |
| 14 |
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- adjusted the convection condition in convect.F (in analogy to |
| 15 |
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calc_ivdc.F) |
| 16 |
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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 |
| 18 |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
| 19 |
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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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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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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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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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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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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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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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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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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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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 |
| 102 |
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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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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. |
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checkpoint46d_pre |
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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. |
| 117 |
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| 118 |
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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). |
| 123 |
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X GM/Redi is not compatible (yet) |
| 124 |
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X bottom drag and no-slip need to be debugged. |
| 125 |
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checkpoint46c_pre |
| 126 |
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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 |
| 131 |
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- new routines ini_eos.F, store_pressure.F |
| 132 |
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o Added UNESCO EOS, but not recommended because it requires |
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in-situ temperature (see JMD95) |
| 134 |
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o Modified formatting for knudsen2.f in utils/knudsen2 and added |
| 135 |
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unesco.f to be used with POLY3 |
| 136 |
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checkpoint46b_pre |
| 137 |
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| 138 |
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checkpoint46a_post |
| 139 |
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o Added (atmospheric) pressure loading |
| 140 |
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- new field in FFIELDS.h, etc... |
| 141 |
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- new cpp flag ATMOSPHERIC_LOADING |
| 142 |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
| 143 |
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o Added SHORTWAVE_HEATING to some files for consistency |
| 144 |
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checkpoint46a_pre |
| 145 |
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|
| 146 |
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checkpoint46 |
| 147 |
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further merges from release1_p5 |
| 148 |
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o new ctrl package |
| 149 |
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- adopted from ECCO environment to enable optimization |
| 150 |
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- added Eliassen Palm fluxes to controls |
| 151 |
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o added Eliassen Palm flux controls to gradient check package |
| 152 |
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o cost package |
| 153 |
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- Compatible with new ctrl package |
| 154 |
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- added Eliassen Palm cost hooks |
| 155 |
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- modif's of existing cost functions |
| 156 |
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o Adjoint-related bug fixes in kpp: |
| 157 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
| 158 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
| 159 |
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o autodiff package |
| 160 |
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- flow directives: |
| 161 |
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+ new for S/R do_the_model_io |
| 162 |
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+ enhanced for S/R checkpoint |
| 163 |
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+ new gmredi.flow |
| 164 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
| 165 |
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disable adcommon.h/g_common.h by default. |
| 166 |
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- fixed problem for adjoint of global_max |
| 167 |
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o modified verification/carbon/ |
| 168 |
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o New setup for adjoint of global_ocean |
| 169 |
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o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
| 170 |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
| 171 |
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o incorporated hooks for sponge layer code (external_forcing.F) |
| 172 |
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| 173 |
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checkpoint45d_post |
| 174 |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
| 175 |
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o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
| 176 |
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(affects plume_on_slope "cg2d" output) |
| 177 |
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o add new parameter deltaTfreesurf for free-surface time stepping |
| 178 |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
| 179 |
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o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
| 180 |
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o change phiMin in exp1 (to agree with documentation) |
| 181 |
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o add new flags: |
| 182 |
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- T,S forcing inside/outside Adams-Bashforth |
| 183 |
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- turn off temp,salt advection and/or forcing |
| 184 |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
| 185 |
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o monitor: change definition of KE to check conservation of Energy |
| 186 |
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| 187 |
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checkpoint45c_post |
| 188 |
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o Removed f90 comments ("!") |
| 189 |
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o Modified initialisations to enable exf package for MITgcm |
| 190 |
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(without invoking ECCO_PACKAGE). |
| 191 |
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o modifications to gradient check package (Martin Losch) |
| 192 |
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- enable centered differences |
| 193 |
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- modified format of standard output |
| 194 |
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|
| 195 |
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checkpoint45b_post |
| 196 |
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o cleaned exchange calls in cg2d |
| 197 |
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o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
| 198 |
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o included CPP option SINGLE_LAYER_MODE in thermodynamics |
| 199 |
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to configure barotropic setup (Martin Losch) |
| 200 |
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o moved some initialisations within bi,bj loop in dynamics |
| 201 |
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(TAF flow dependency) |
| 202 |
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o in initialise_varia, moved call packages_init_variables |
| 203 |
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before convective_adjustment_init |
| 204 |
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(corresponding adjustment of TAF tape initialisation). |
| 205 |
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o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
| 206 |
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| 207 |
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checkpoint45a_post |
| 208 |
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o compute Rho over the whole domain (extend iMin,jMin indices) |
| 209 |
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o specific exchange for X-slice domain (case Ny=1) |
| 210 |
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o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
| 211 |
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o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
| 212 |
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| 213 |
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checkpoint44h_post = checkpoint45 |
| 214 |
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o Fix to restore differentiability: |
| 215 |
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place at which packages_init_variables is called in |
| 216 |
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initialise_varia is crucial for reverse control flow. |
| 217 |
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o modifications in GMRedi to enable stable adjoint |
| 218 |
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(corresponding modif's in thermodynamics, dynamics) |
| 219 |
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o added missing hook for sponge layer code in external_forcing |
| 220 |
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o modified test cost functions |
| 221 |
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o storing in gad_advection (plus removal of write(0,*)! |
| 222 |
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o missing headers TR1.h added in convective_adjustment routines |
| 223 |
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o errorMessageUnit set non-equal zero in eeboot |
| 224 |
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(conflict on some platforms, e.g. IBM SP3) |
| 225 |
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o modified carbon verif. |
| 226 |
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| 227 |
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checkpoint44h_pre |
| 228 |
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o vertical grid option: allow to put the Interface at the middle between |
| 229 |
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2 cell-centers ; replace delZ in pkg/kpp by drF. |
| 230 |
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o GM Advective form: Tracers are advected using the residual transport (= |
| 231 |
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Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
| 232 |
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| 233 |
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checkpoint44g_post |
| 234 |
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o fix surface correction term in multiDimAdvection (affects plume_on_slope |
| 235 |
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results) ; ifdef missing in thermodynamics.F |
| 236 |
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| 237 |
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checkpoint44f_pre,checkpoint44f_post |
| 238 |
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o added PTRACERS package |
| 239 |
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This allows an arbitrary number of passive tracers to be integrated |
| 240 |
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forward simultaneously with the dynamicaly model. |
| 241 |
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+ Implemented so far: |
| 242 |
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- basic forward algorithm (time-stepping, advection, diffusion, convection) |
| 243 |
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- I/O and checkpointing |
| 244 |
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- GM/Redi *but* using the GM/Redi coefficient of Salt |
| 245 |
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+ Not implemented so far: |
| 246 |
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- KPP |
| 247 |
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- OBCS |
| 248 |
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+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
| 249 |
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necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
| 250 |
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line in data.pkg. |
| 251 |
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+ This package is disabled by default since it increases storage. |
| 252 |
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|
| 253 |
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|
| 254 |
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o testscript: added -cleanup option |
| 255 |
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o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
| 256 |
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b) enable to filter 2D fields. |
| 257 |
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|
| 258 |
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checkpoint44e_pre,post |
| 259 |
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o re-wrote convective adjustment to use pre-calculated weights |
| 260 |
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Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
| 261 |
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Adds: model/src/convective_weights.F, convectively_mixtracer.F |
| 262 |
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Original calls to convect() still in place. |
| 263 |
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|
| 264 |
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chkpt44d_pre,post |
| 265 |
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o added missing EXCLUDE_MONITOR flags |
| 266 |
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o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
| 267 |
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(incompatible typ in MIN/MAX expressions caused problems |
| 268 |
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on IBM SP3) |
| 269 |
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o in genmake added variable MAKEDEPEND |
| 270 |
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plus resetting for case SunOS |
| 271 |
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o added timer_stats.c routine for IBM SP3 |
| 272 |
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o removed variables in dynamics |
| 273 |
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!!! I forgot to create tag chkpt44d_pre !!! |
| 274 |
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!!! But chkpt44d_pre = chkpt44c_post !!! |
| 275 |
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| 276 |
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o real fresh water flux implemented with non-linear free-surface. |
| 277 |
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|
| 278 |
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chkpt44c_pre,post |
| 279 |
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o few fix (mask in shap_s2, EmPmR in external_field_load, |
| 280 |
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USE_NATURAL_BCS in solve_for_P); |
| 281 |
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o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
| 282 |
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|
| 283 |
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checkpoint44b_pre/_post |
| 284 |
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o merge of relevant stuff from the ecco-branch: |
| 285 |
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- genmake: removed $S64 overwrite for case SunOS |
| 286 |
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- pkg/exf: update and corrections for field swapping and obcs |
| 287 |
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- pkg/ecco: parameter lists for the_model_main, the_main_loop |
| 288 |
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harmonized between ECCO and MITgcm |
| 289 |
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- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
| 290 |
|
updated checkpointing_lev... lists for obcs |
| 291 |
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- model/src: minor changes in forward_step, plot_field |
| 292 |
|
added directive for divided adjoint in the_main_loop |
| 293 |
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- pkg/mdsio: added mdsio_gl_slice |
| 294 |
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|
| 295 |
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o check parameters & config (chkpt44a_pre,post) |
| 296 |
|
o OBC and NonLin_FrSurf. |
| 297 |
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|
| 298 |
|
checkpoint44 |
| 299 |
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o fix bug in mom_vi_del2uv |
| 300 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
| 301 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
| 302 |
|
o update AIM experiments (NCEP input files) |
| 303 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
| 304 |
|
o added some stuff for AD |
| 305 |
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|
| 306 |
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checkpoint43 |
| 307 |
|
o added two new advection tests |
| 308 |
|
o added global 4x4 degree ocean test |
| 309 |
|
o added test of H&S94 with free surface on cube |
| 310 |
|
o some final mods for gradient check, adjoint,... |
| 311 |
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|
| 312 |
|
checkpoint42 |
| 313 |
|
Fixed AD-related problems: |
| 314 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
| 315 |
|
(mainly thermodynamics.F) |
| 316 |
|
o New store directives for multi-dim. advection schemes |
| 317 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
| 318 |
|
* new common block and key passkey |
| 319 |
|
(mainly gad_advection.F) |
| 320 |
|
o Modified store directives for split of dynamics/thermodynamics |
| 321 |
|
for the case ALLOW_KPP |
| 322 |
|
o Cleaned argument list for timestep_tracer.F |
| 323 |
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|
| 324 |
|
checkpoint41 |
| 325 |
|
o re-formatted/added comments in prologues of key subroutines |
| 326 |
|
to work with protex |
| 327 |
|
|
| 328 |
|
checkpoint40 |
| 329 |
|
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
| 330 |
|
o added FLT (floats) package from Arne along with demo. experiment |
| 331 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
| 332 |
|
implementation of forward-in-time forcing terms |
| 333 |
|
o more mods for non-linear free-surface including new variable |
| 334 |
|
o modified multi-dim method to work on cube |
| 335 |
|
o bug fix in KPP (from DM) |
| 336 |
|
|
| 337 |
|
checkpoint40pre9 |
| 338 |
|
o added DST advection schemes |
| 339 |
|
o fix MPI bug on SGI's |
| 340 |
|
o modifications for non-linear free-surface |
| 341 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
| 342 |
|
o added tension/strain form of stress tensor |
| 343 |
|
o changes to commenting of arguments for TAF/TAMC |
| 344 |
|
o added/updated many matlab scripts |
| 345 |
|
o added multi-dimensional advection method for tracers |
| 346 |
|
|
| 347 |
|
checkpoint40pre8 |
| 348 |
|
o new package rw/ |
| 349 |
|
Added method for dumping intermediate local arrays: |
| 350 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
| 351 |
|
bi,bj loop |
| 352 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
| 353 |
|
arrays |
| 354 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
| 355 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
| 356 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
| 357 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
| 358 |
|
control flux-form versus vector invariant code. |
| 359 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
| 360 |
|
or genmake -DISABLE ... |
| 361 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
| 362 |
|
(additional storing is now needed for case vecinv; |
| 363 |
|
currently nothing implemented to switch this storing off |
| 364 |
|
in case fluxform is used since no CPP flag available). |
| 365 |
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|
| 366 |
|
checkpoint40pre7 |
| 367 |
|
o bug fix in dynamics.F |
| 368 |
|
calc_viscosity called before k=1,Nr loop. |
| 369 |
|
o added some #ifdef's ALLOW_PASSIVE_TRACER |
| 370 |
|
o cleaned initialisations in ctrl_map_ini |
| 371 |
|
related to TAF |
| 372 |
|
|
| 373 |
|
checkpoint40pre6 |
| 374 |
|
o split dynamics into thermodynamics & dynamics |
| 375 |
|
o corresponding split of calc_diffusivity into |
| 376 |
|
calc_diffusivity, calc_viscosity |
| 377 |
|
(kpp_calc_diff, kpp_calc_visc). |
| 378 |
|
o Added diffkr, kapgm to control variables |
| 379 |
|
o bug fix in gmredi_slope_limit for ldd97 |
| 380 |
|
|
| 381 |
|
checkpoint40pre5 |
| 382 |
|
o proper initialization of Adams-Bashforth time stepping |
| 383 |
|
+ uses forward step for very first step of model (iter=0) |
| 384 |
|
o re-generated *all* output since almost all output is modified by this |
| 385 |
|
change (sorry but we've been putting this one off for about 2 years) |
| 386 |
|
+ natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were |
| 387 |
|
*not* regenerated since they are already out of date and I don't |
| 388 |
|
want to create the impression that they are suddenly working. |
| 389 |
|
o removed KAP stuff for DEC's |
| 390 |
|
o modified/added many .cvsignore files in */code and */input |
| 391 |
|
o added new expt "solid-body.cs-32x32x1" |
| 392 |
|
+ this uses an alternative form of ini_curvilinear_grid.F which |
| 393 |
|
is not necessarily any better than the current one... |
| 394 |
|
|
| 395 |
|
checkpoint40pre4 |
| 396 |
|
o added re-initialisations of utrans,vtrans,rtrans in |
| 397 |
|
calc_common_factors which are crucial for TAF. |
| 398 |
|
o extended iMin,jMin range for calc_common_factors, |
| 399 |
|
calc_diffusivity |
| 400 |
|
o added option ALLOW_PASSIVE_TRACER |
| 401 |
|
o a few minor updates and fixes |
| 402 |
|
|
| 403 |
|
checkpoint40pre3 |
| 404 |
|
o created calc_gtr1.F for gad package |
| 405 |
|
o split the_main_loop and re-introduced forward_step |
| 406 |
|
o some recomputations of nIter0 for TAMC |
| 407 |
|
|
| 408 |
|
checkpoint40pre2 |
| 409 |
|
o Updated to latest branch of AJA, JMC |
| 410 |
|
o Added gradient check package |
| 411 |
|
o Added routines for passive tracer handling |
| 412 |
|
o Added carbon sequestration sensitivity experiment |
| 413 |
|
|
| 414 |
checkpoint39 |
checkpoint39 |
| 415 |
o Modifications and fixes to support TAMC |
o Modifications and fixes to support TAMC |
| 416 |
(mainly missing or wrong directives) |
(mainly missing or wrong directives) |
| 423 |
exf: external forcing |
exf: external forcing |
| 424 |
ecco: essential routines to control use of cal, exf |
ecco: essential routines to control use of cal, exf |
| 425 |
(NB: this is not the full ECCO environment) |
(NB: this is not the full ECCO environment) |
| 426 |
|
o disabled some packages by default in genmake |
| 427 |
|
|
| 428 |
checkpoint38 |
checkpoint38 |
| 429 |
o see notes_c37_adj.txt |
o see notes_c37_adj.txt |
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