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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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| 7 |
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o upgrade simple test-experiment to tutorial example: |
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step.1: duplicate the experiment and (step.2) will remove the old copy. |
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tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
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tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
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tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
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tutorial_global_oce_biogeo <- copy of dic_example |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
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tutorial_plume_on_slope <- copy of plume_on_slope |
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tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
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tutorial_global_oce_optim <- empty for now (David ?) |
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tutorial_global_oce_in_p <- copy of global_ocean_pressure |
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some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 19 |
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|
| 20 |
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o correct a sign problem in cost_scat.F |
| 21 |
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o obcs and ptracers: fix boundary conditions for advections schemes |
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with larger stencil |
| 23 |
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o thsice adjoint: start |
| 24 |
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o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
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completeness |
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o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
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and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
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o ptracers adjoint: |
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* avoid extensive recomputatations |
| 30 |
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* fix missing re-init. of gptr (missed by TAF) |
| 31 |
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o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
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me to turn off the excessive output to STDOUT that this package produces |
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o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
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and add those terms in Vector-Invariant formulation. |
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o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
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if the control period (xx_hfluxperiod etc) is 0 |
| 37 |
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o in profiles pkg, clean routines and fix details |
| 38 |
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o in ecco pkg, reading ssh data: |
| 39 |
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fix problem in case the model does not start at iter0=0 |
| 40 |
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o fix mnc-pickup/restart for ptracers |
| 41 |
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o new package prifiles: |
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code to compute profile-based cost by Gael Forget |
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(modifs in ecco, ctrl, autodiff) |
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o Benign bug fix in initialization (spotted by M. Mazloff) of |
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ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
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|
| 47 |
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checkpoint58c_post |
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o adjoint: finish NLFS adjoint and provide reference output in |
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verification/global_ocean.90x40x15/results_ad_nlfs |
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o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
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documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
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SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
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with SEAICE_CGRID defined. |
| 54 |
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o move calendarDumps from "data" to "data.cal" and clean-up the code |
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with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
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o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 57 |
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o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
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(were missing in NH mode, and wrong in quasihydrostatic mode). |
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waiting for Chris updated version of calc_gw to add those CALLs. |
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o fix bug in quasihydrostatic S/R ; |
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add a test for this option: global_ocean.90x40x15.qshyd |
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o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
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(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
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o add on/off flag useOffLine for package OFFLINE |
| 65 |
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o seaice: |
| 66 |
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- modify advection so that it works also on the C-grid |
| 67 |
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- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
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problem in multi-tile runs with C-grid |
| 69 |
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- add flags for clipping ice velocities and/or masking solver forcing |
| 70 |
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- fix drag (ocean on ice) formulation and a bug that caused noise in the |
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C-grid solver |
| 72 |
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- added a few comments to seaice_diffusion.F |
| 73 |
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- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
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are now exclusive) |
| 75 |
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- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 76 |
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required re-ordering the code a little: |
| 77 |
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+ make DAIRN global variable (defined in SEAICE) |
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+ move computation of the viscosities eta and zeta into a new separate |
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routine (because I need to recompute them in seaice_ocean_stress.F) |
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|
| 81 |
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checkpoint58b_post |
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o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 83 |
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update output.txt of exp. aim.5l_cs.thSI |
| 84 |
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o various mnc cleanups and improvements: |
| 85 |
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+ shrink lookup tables by factor of ~4 |
| 86 |
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+ better error reporting when running out of lookup space |
| 87 |
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+ able to handle longer path/file names (up to 500 chars) |
| 88 |
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o adjoint: |
| 89 |
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- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 90 |
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- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 91 |
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o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 92 |
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(allow to differentiate between forcing components using new integer flags: |
| 93 |
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momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 94 |
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and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 95 |
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o ecco |
| 96 |
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- enable trend removal from SSH anomaly obs. |
| 97 |
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o adjoint |
| 98 |
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- a fix for PmEpR when #undef EXACT_CONSERV |
| 99 |
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- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 100 |
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- try to fix "hidden" recomp. in forward_step for NLFS |
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(NLFS seems broken sometimes after I checked it in) |
| 102 |
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o seaice: |
| 103 |
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- add c-grid version of the dynamic solver: |
| 104 |
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+ three new routines that are the c-grid substitute lsr, dynsolver |
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and ostres |
| 106 |
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+ put a few fields that were local to dynsolver into global common |
| 107 |
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blocks, so that I can move the computation of stresses etc into |
| 108 |
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seaice_lsr (saves coding but may break the adjoint). |
| 109 |
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- replace more hardwired parameters by runtime parameters |
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- add ice masks that mask the rhs of the implicit solvers where there |
| 111 |
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is no ice (commented out in seaice_dynsolver, because i am not sure |
| 112 |
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if this works properly), eventually this should replace the clipping |
| 113 |
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of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 114 |
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o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
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include it only where its needed |
| 116 |
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o move balancing of fluxes before the call of external_forcing_surf |
| 117 |
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o seaice: |
| 118 |
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- correct units of turning angles (now they are really in degrees) |
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- move computation of GWATX/Y out of main routine into dynsolver |
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- initialize GWATX/Y in seaice_init |
| 121 |
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o Apply mask on Fresh-Water flux (needed for SSH forcing). |
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update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 123 |
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o seaice: add runtime flags for turning angles (default to zero) |
| 124 |
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o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
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and trend from exf forcing and ctrl control adjustments |
| 126 |
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o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
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(since checkpoint57x_post) |
| 128 |
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o change the default rotation period to 86164.s = the Earth rotation |
| 129 |
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o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
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and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 131 |
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o seaice advection: add code for choosing between the default (2nd order |
| 132 |
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central differences) and multiDim advection schemes provided by |
| 133 |
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pkg/generic_advdiff |
| 134 |
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o seaice: |
| 135 |
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- removed all references to SEAICE_GRID.h fields from |
| 136 |
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dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 137 |
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(cubed-sphere configuration will change a little) |
| 138 |
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- grid computations in seaice_init are obsolete now. |
| 139 |
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- cleaned up code a little so that is easier to read (hopefully). |
| 140 |
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- added new (better?) discretizations of default advection and diffusion |
| 141 |
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(turn on with SEAICEuseFluxForm) |
| 142 |
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- replace 1 in 3d global fields by kSurface in growth.F |
| 143 |
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|
| 144 |
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checkpoint58a_post |
| 145 |
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o seaice: |
| 146 |
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- bug fix in advect.F |
| 147 |
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o shelfice: |
| 148 |
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- separate shelfice load anomaly from pload (breaks with time |
| 149 |
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dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 150 |
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Its default is 0., but it may be computed more cleverly from (unknown) |
| 151 |
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t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 152 |
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done offline. A good approximation of the pressure load anomaly is |
| 153 |
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necessary to avoid large initial adjustment processes underneath |
| 154 |
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deep-reaching shelfice. |
| 155 |
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- small fix in ISOMIP shelfice_thermodynamics |
| 156 |
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- add more sophisticated thermodynamics of Hellmer (1989), this is |
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now the default |
| 158 |
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- give a few constants more intuitive names |
| 159 |
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o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 160 |
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if bulk formulae are used in long integration (especially EmPmR). Turn |
| 161 |
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on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 162 |
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if balancePrintMean, the imbalance that is substracted is printed to |
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STDOUT. |
| 164 |
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o fix bug (typo) in obcs_apply_eta.F |
| 165 |
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o add a new package shelfice which enables us to model the circulation |
| 166 |
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underneath shelf-ice with draughts of hundreds of meters. |
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- works |
| 168 |
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- to do: + include improved thermodynamics |
| 169 |
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+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 170 |
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instead of new field kTopC |
| 171 |
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+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 172 |
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instead of new field R_shelfIce and new code in ini_depth.F |
| 173 |
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and ini_mask_etc.F? |
| 174 |
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+ adjust vertical mixing schemes? |
| 175 |
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o seaice pkg: |
| 176 |
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- add a cpp-flag to include a simple formula for a salinity dependent |
| 177 |
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freezing point of sea water at the surface |
| 178 |
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- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 179 |
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meridional stresses are now different (and hopefully correct) |
| 180 |
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o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 181 |
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update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 182 |
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and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 183 |
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o pkg/diagnostics: add options and parameters for regional-statistics |
| 184 |
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diagnostics ; define regions by reading a region-mask from a file |
| 185 |
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(might add other options later) |
| 186 |
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o pkg/bulk_force: |
| 187 |
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- add option and parameters to use AIM surface-flux formulae. |
| 188 |
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- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 189 |
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others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 190 |
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from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 191 |
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- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 192 |
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- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 193 |
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- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 194 |
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and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 195 |
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- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 196 |
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|
| 197 |
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checkpoint58 |
| 198 |
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o add "--embed-source" option to genmake2 which, when the supporting |
| 199 |
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tools can be compiled (as determined by genmake2) will turn on the |
| 200 |
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embed_files package which then embeds the entire MITgcm source code |
| 201 |
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(*.[fFhc] + Makefile) used for the build within the executable |
| 202 |
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- requested by CNH but off by default |
| 203 |
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- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 204 |
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- only writes the output when useEMBEDSRC in eedata is true |
| 205 |
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o clean up 3-dim. relaxation codes: |
| 206 |
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* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 207 |
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* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 208 |
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* Thanks to Tom Haine for testing! |
| 209 |
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|
| 210 |
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checkpoint57z_post |
| 211 |
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o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 212 |
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affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 213 |
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o fix the pickup behavior for obcs in combination with ptracers |
| 214 |
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o fix a bug in ptracers_external_fields_load |
| 215 |
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o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 216 |
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affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 217 |
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o transfered surface NH pressure to eta field (if exactConserv). |
| 218 |
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o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 219 |
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and update lab_sea output.txt file. |
| 220 |
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o completing 3-dim. relaxation code: additional term |
| 221 |
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1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 222 |
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in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 223 |
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* At compile time, in "EXF_OPTIONS.h" set |
| 224 |
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#define ALLOW_CLIMTEMP_RELAXATION |
| 225 |
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#define ALLOW_CLIMSALT_RELAXATION |
| 226 |
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* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 227 |
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tauThetaClimRelax3Dim = 15552000.0, |
| 228 |
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tauSaltClimRelax3Dim = 15552000.0, |
| 229 |
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* 3 cases: |
| 230 |
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1) Use a constant-in-time 3-dim. field |
| 231 |
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2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 232 |
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3) Real-time relax. to time-evolving prescribed field |
| 233 |
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o Adding Laplacian-type smoothness constraint on |
| 234 |
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initial and boundary (forcing) controls (ic, bc) |
| 235 |
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* enable at compile-time via |
| 236 |
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ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 237 |
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* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 238 |
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* Absolute scale somewhat unclear so far |
| 239 |
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* no area weighting was included since no other cost term does so far |
| 240 |
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|
| 241 |
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checkpoint57y_post |
| 242 |
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First step for a NLFS adjoint |
| 243 |
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o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 244 |
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o new init. routines for calc_r_star, calc_surf_dr |
| 245 |
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o still need to deal with ini_masks_etc |
| 246 |
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o testreport seemed happy |
| 247 |
checkpoint57y_pre |
checkpoint57y_pre |
| 248 |
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|
| 249 |
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
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