3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o new pkg: aim_v23 |
7 |
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= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
8 |
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for now, keep the same surface forcing as before. |
9 |
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- Part-Cell implemented into AIM; check that Heat & Water are conserved |
10 |
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- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
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- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
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o add diagnostic of surface correction term in monitor output |
13 |
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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 |
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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 |
26 |
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o external_fields_load now part of differentiation list |
27 |
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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.) |
30 |
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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 |
36 |
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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. |
51 |
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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, |
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SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
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The implied surface heat flux is then stored in variable |
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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 |
85 |
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- bug fixes carried over from ecco-branch |
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(missing OBCS_OPTIONS.h in two routines) |
87 |
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- enable easy to use "no forcing". |
88 |
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- added exf I/O for atmospheric loading |
89 |
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- added exf I/O for runoff data |
90 |
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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() |
101 |
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o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
102 |
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New routine: mom_u_coriolis_nh() |
103 |
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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 |
106 |
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o introduced flag for controllin non-hydrostatic metric terms |
107 |
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o removed gravitySign from PARM04 |
108 |
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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: |
112 |
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- changed the direction of k-loop in convective_adjustment.F for the |
113 |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
114 |
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- adjusted the reference pressure k-index in convective_adjustment.F |
115 |
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- adjusted the convection condition in convect.F (in analogy to |
116 |
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calc_ivdc.F) |
117 |
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- convective_adjustment no longer computes anything on the halos |
118 |
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- removed the warnings about negative salinity from find_rho.F and |
119 |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
120 |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
121 |
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check of the entire slice, if CPP-option |
122 |
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CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
123 |
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checkpoint46l_pre |
124 |
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|
125 |
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checkpoint46k_post |
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o fixed the verification/global_ocean.90x40x15 experiment: |
127 |
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- new bathymetry (the world according to A., JMC, and M.) |
128 |
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- new initial fields and forcing fields (*.bin files) |
129 |
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- new POLY3.COEFFS (for the next release one should switch to a full |
130 |
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equation of state: JMD95P or MDJWF) |
131 |
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- fixed several errors and redundancies in the data file |
132 |
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- experiment uses looped cells |
133 |
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- added matlab directory with diagnostic scripts for plotting of output |
134 |
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|
135 |
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
136 |
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- read AIM physics parameters from a file (data.aimphys) |
137 |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
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|
139 |
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checkpoint46j_post |
140 |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
141 |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
142 |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
143 |
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o update timeave pkg for wVel diagnostic. |
144 |
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checkpoint46j_pre |
145 |
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|
146 |
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checkpoint46i_post |
147 |
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o Clean up AIM package (and keep the results unchanged): |
148 |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
149 |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
150 |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
151 |
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|
152 |
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checkpoint46h_post |
153 |
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o cleaned up the use of rhoNil and rhoConst. |
154 |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
155 |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
156 |
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and the dynamical equations are all divided by rhoConst |
157 |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
158 |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
159 |
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value is 999.8 kg/m^3 |
160 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
161 |
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- can now be used by both OCEANIC and OCEANICP |
162 |
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checkpoint46h_pre |
163 |
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|
164 |
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Added code to convert surface volume flux (fresh water) into |
165 |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
166 |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
167 |
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|
168 |
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checkpoint46g_post |
169 |
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o Include a new diagnostic variable phiHydLow for the ocean model |
170 |
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- in z-coordinates, it is the bottom pressure anomaly |
171 |
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- in p-coordinates, it is the sea surface elevation |
172 |
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- in both cases, these variable have global drift, reflecting the mass |
173 |
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drift in z-coordinates and the volume drift in p-coordinates |
174 |
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- included time averaging for phiHydLow, be aware of the drift! |
175 |
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o depth-dependent computation of Bo_surf for pressure coordinates |
176 |
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in the ocean (buoyancyRelation='OCEANICP') |
177 |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
178 |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
179 |
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presently contained in find_rho.F. This routine does not give the |
180 |
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correct density for 'POLY3', which would be a z-dependent reference |
181 |
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density. |
182 |
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o cleaned up find_rho |
183 |
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- removed obsolete 'eqn' from the parameter list. |
184 |
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o added two new verification experiments: gop and goz |
185 |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
186 |
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checkpoint46g_pre |
187 |
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|
188 |
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checkpoint46f_post |
189 |
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o Enable tangent linear (forward mode) gradient checks: |
190 |
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- extended active file handling to g_... files |
191 |
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- added TANGENT_SIMULATION to theSimulationMode |
192 |
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- extended grdchk package accordingly |
193 |
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o added tangent linear setup in verification/carbon/code_ftl |
194 |
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o added adjoint setup in verification/front_relax/code_ad |
195 |
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|
196 |
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checkpoint46e_post |
197 |
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o Added new equation of state -> MDJWF |
198 |
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- EOS of McDougall et al., 2002, JAOT, submitted |
199 |
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- caveat: the equation of state is only valid for a smaller (more |
200 |
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realistic?) range of values than JMD95P/Z and UNESCO |
201 |
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- added masks to the calculation of pressure in store_pressure |
202 |
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- added more check values for density in check_eos (ini_eos.F), some of |
203 |
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the old check values are out of the range of the MDJWF-eos, so don't |
204 |
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expect perfect matches for those |
205 |
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checkpoint46e_pre |
206 |
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|
207 |
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checkpoint46d_post |
208 |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
209 |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
210 |
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case of pressure coordinates. eosType='JMD95Z' in |
211 |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
212 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
213 |
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in find_alpha/beta. |
214 |
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checkpoint46d_pre |
215 |
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|
216 |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
217 |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
218 |
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|
219 |
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checkpoint46c_post |
220 |
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o Changes necessary for ocean in p-coordinates |
221 |
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- Added new buoyancy relation = 'OCEANICP' |
222 |
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- Added new parameters = gravitySign (this used to be contained inside |
223 |
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the factor dRdZ which I added when we first switched to R coordinates). |
224 |
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X GM/Redi is not compatible (yet) |
225 |
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X bottom drag and no-slip need to be debugged. |
226 |
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checkpoint46c_pre |
227 |
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|
228 |
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checkpoint46b_post |
229 |
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o Added new equation of state -> JMD95Z and JMD95P |
230 |
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- EOS of Jackett and McDougall, 1995, JAOT |
231 |
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- moved all EOS parameters into EOS.h |
232 |
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- new routines ini_eos.F, store_pressure.F |
233 |
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o Added UNESCO EOS, but not recommended because it requires |
234 |
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in-situ temperature (see JMD95) |
235 |
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o Modified formatting for knudsen2.f in utils/knudsen2 and added |
236 |
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unesco.f to be used with POLY3 |
237 |
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checkpoint46b_pre |
238 |
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|
239 |
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checkpoint46a_post |
240 |
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o Added (atmospheric) pressure loading |
241 |
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- new field in FFIELDS.h, etc... |
242 |
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- new cpp flag ATMOSPHERIC_LOADING |
243 |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
244 |
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o Added SHORTWAVE_HEATING to some files for consistency |
245 |
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checkpoint46a_pre |
246 |
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|
247 |
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checkpoint46 |
248 |
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further merges from release1_p5 |
249 |
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o new ctrl package |
250 |
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- adopted from ECCO environment to enable optimization |
251 |
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- added Eliassen Palm fluxes to controls |
252 |
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o added Eliassen Palm flux controls to gradient check package |
253 |
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o cost package |
254 |
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- Compatible with new ctrl package |
255 |
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- added Eliassen Palm cost hooks |
256 |
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- modif's of existing cost functions |
257 |
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o Adjoint-related bug fixes in kpp: |
258 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
259 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
260 |
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o autodiff package |
261 |
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- flow directives: |
262 |
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+ new for S/R do_the_model_io |
263 |
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+ enhanced for S/R checkpoint |
264 |
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+ new gmredi.flow |
265 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
266 |
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disable adcommon.h/g_common.h by default. |
267 |
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- fixed problem for adjoint of global_max |
268 |
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o modified verification/carbon/ |
269 |
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o New setup for adjoint of global_ocean |
270 |
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o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
271 |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
272 |
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o incorporated hooks for sponge layer code (external_forcing.F) |
273 |
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|
274 |
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checkpoint45d_post |
275 |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
276 |
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o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
277 |
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(affects plume_on_slope "cg2d" output) |
278 |
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o add new parameter deltaTfreesurf for free-surface time stepping |
279 |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
280 |
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o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
281 |
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o change phiMin in exp1 (to agree with documentation) |
282 |
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o add new flags: |
283 |
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- T,S forcing inside/outside Adams-Bashforth |
284 |
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- turn off temp,salt advection and/or forcing |
285 |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
286 |
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o monitor: change definition of KE to check conservation of Energy |
287 |
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|
288 |
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checkpoint45c_post |
289 |
|
o Removed f90 comments ("!") |
290 |
|
o Modified initialisations to enable exf package for MITgcm |
291 |
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(without invoking ECCO_PACKAGE). |
292 |
|
o modifications to gradient check package (Martin Losch) |
293 |
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- enable centered differences |
294 |
|
- modified format of standard output |
295 |
|
|
296 |
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checkpoint45b_post |
297 |
|
o cleaned exchange calls in cg2d |
298 |
|
o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
299 |
|
o included CPP option SINGLE_LAYER_MODE in thermodynamics |
300 |
|
to configure barotropic setup (Martin Losch) |
301 |
|
o moved some initialisations within bi,bj loop in dynamics |
302 |
|
(TAF flow dependency) |
303 |
|
o in initialise_varia, moved call packages_init_variables |
304 |
|
before convective_adjustment_init |
305 |
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(corresponding adjustment of TAF tape initialisation). |
306 |
|
o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
307 |
|
|
308 |
|
checkpoint45a_post |
309 |
|
o compute Rho over the whole domain (extend iMin,jMin indices) |
310 |
|
o specific exchange for X-slice domain (case Ny=1) |
311 |
|
o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
312 |
|
o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
313 |
|
|
314 |
|
checkpoint44h_post = checkpoint45 |
315 |
|
o Fix to restore differentiability: |
316 |
|
place at which packages_init_variables is called in |
317 |
|
initialise_varia is crucial for reverse control flow. |
318 |
|
o modifications in GMRedi to enable stable adjoint |
319 |
|
(corresponding modif's in thermodynamics, dynamics) |
320 |
|
o added missing hook for sponge layer code in external_forcing |
321 |
|
o modified test cost functions |
322 |
|
o storing in gad_advection (plus removal of write(0,*)! |
323 |
|
o missing headers TR1.h added in convective_adjustment routines |
324 |
|
o errorMessageUnit set non-equal zero in eeboot |
325 |
|
(conflict on some platforms, e.g. IBM SP3) |
326 |
|
o modified carbon verif. |
327 |
|
|
328 |
|
checkpoint44h_pre |
329 |
|
o vertical grid option: allow to put the Interface at the middle between |
330 |
|
2 cell-centers ; replace delZ in pkg/kpp by drF. |
331 |
|
o GM Advective form: Tracers are advected using the residual transport (= |
332 |
|
Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
333 |
|
|
334 |
|
checkpoint44g_post |
335 |
|
o fix surface correction term in multiDimAdvection (affects plume_on_slope |
336 |
|
results) ; ifdef missing in thermodynamics.F |
337 |
|
|
338 |
|
checkpoint44f_pre,checkpoint44f_post |
339 |
|
o added PTRACERS package |
340 |
|
This allows an arbitrary number of passive tracers to be integrated |
341 |
|
forward simultaneously with the dynamicaly model. |
342 |
|
+ Implemented so far: |
343 |
|
- basic forward algorithm (time-stepping, advection, diffusion, convection) |
344 |
|
- I/O and checkpointing |
345 |
|
- GM/Redi *but* using the GM/Redi coefficient of Salt |
346 |
|
+ Not implemented so far: |
347 |
|
- KPP |
348 |
|
- OBCS |
349 |
|
+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
350 |
|
necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
351 |
|
line in data.pkg. |
352 |
|
+ This package is disabled by default since it increases storage. |
353 |
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|
354 |
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|
355 |
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o testscript: added -cleanup option |
356 |
|
o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
357 |
|
b) enable to filter 2D fields. |
358 |
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|
359 |
|
checkpoint44e_pre,post |
360 |
|
o re-wrote convective adjustment to use pre-calculated weights |
361 |
|
Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
362 |
|
Adds: model/src/convective_weights.F, convectively_mixtracer.F |
363 |
|
Original calls to convect() still in place. |
364 |
|
|
365 |
|
chkpt44d_pre,post |
366 |
|
o added missing EXCLUDE_MONITOR flags |
367 |
|
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
368 |
|
(incompatible typ in MIN/MAX expressions caused problems |
369 |
|
on IBM SP3) |
370 |
|
o in genmake added variable MAKEDEPEND |
371 |
|
plus resetting for case SunOS |
372 |
|
o added timer_stats.c routine for IBM SP3 |
373 |
|
o removed variables in dynamics |
374 |
|
!!! I forgot to create tag chkpt44d_pre !!! |
375 |
|
!!! But chkpt44d_pre = chkpt44c_post !!! |
376 |
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|
377 |
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o real fresh water flux implemented with non-linear free-surface. |
378 |
|
|
379 |
|
chkpt44c_pre,post |
380 |
|
o few fix (mask in shap_s2, EmPmR in external_field_load, |
381 |
|
USE_NATURAL_BCS in solve_for_P); |
382 |
|
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
383 |
|
|
384 |
|
checkpoint44b_pre/_post |
385 |
|
o merge of relevant stuff from the ecco-branch: |
386 |
|
- genmake: removed $S64 overwrite for case SunOS |
387 |
|
- pkg/exf: update and corrections for field swapping and obcs |
388 |
|
- pkg/ecco: parameter lists for the_model_main, the_main_loop |
389 |
|
harmonized between ECCO and MITgcm |
390 |
|
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
391 |
|
updated checkpointing_lev... lists for obcs |
392 |
|
- model/src: minor changes in forward_step, plot_field |
393 |
|
added directive for divided adjoint in the_main_loop |
394 |
|
- pkg/mdsio: added mdsio_gl_slice |
395 |
|
|
396 |
|
o check parameters & config (chkpt44a_pre,post) |
397 |
|
o OBC and NonLin_FrSurf. |
398 |
|
|
399 |
|
checkpoint44 |
400 |
|
o fix bug in mom_vi_del2uv |
401 |
|
o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
402 |
|
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
403 |
|
o update AIM experiments (NCEP input files) |
404 |
|
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
405 |
|
o added some stuff for AD |
406 |
|
|
407 |
|
checkpoint43 |
408 |
|
o added two new advection tests |
409 |
|
o added global 4x4 degree ocean test |
410 |
|
o added test of H&S94 with free surface on cube |
411 |
|
o some final mods for gradient check, adjoint,... |
412 |
|
|
413 |
|
checkpoint42 |
414 |
|
Fixed AD-related problems: |
415 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
416 |
|
(mainly thermodynamics.F) |
417 |
|
o New store directives for multi-dim. advection schemes |
418 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
419 |
|
* new common block and key passkey |
420 |
|
(mainly gad_advection.F) |
421 |
|
o Modified store directives for split of dynamics/thermodynamics |
422 |
|
for the case ALLOW_KPP |
423 |
|
o Cleaned argument list for timestep_tracer.F |
424 |
|
|
425 |
|
checkpoint41 |
426 |
|
o re-formatted/added comments in prologues of key subroutines |
427 |
|
to work with protex |
428 |
|
|
429 |
checkpoint40 |
checkpoint40 |
430 |
o all changes of checkpoint40pre? |
o moved calc_gs, calc_gt and calc_tr1 back to model/src |
431 |
|
o added FLT (floats) package from Arne along with demo. experiment |
432 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
433 |
|
implementation of forward-in-time forcing terms |
434 |
|
o more mods for non-linear free-surface including new variable |
435 |
|
o modified multi-dim method to work on cube |
436 |
|
o bug fix in KPP (from DM) |
437 |
|
|
438 |
|
checkpoint40pre9 |
439 |
|
o added DST advection schemes |
440 |
|
o fix MPI bug on SGI's |
441 |
|
o modifications for non-linear free-surface |
442 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
443 |
|
o added tension/strain form of stress tensor |
444 |
|
o changes to commenting of arguments for TAF/TAMC |
445 |
|
o added/updated many matlab scripts |
446 |
|
o added multi-dimensional advection method for tracers |
447 |
|
|
448 |
|
checkpoint40pre8 |
449 |
o new package rw/ |
o new package rw/ |
450 |
Added method for dumping intermediate local arrays: |
Added method for dumping intermediate local arrays: |
451 |
mdsio_writetile - same as mdsio_writefield except works from inside |
mdsio_writetile - same as mdsio_writefield except works from inside |