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$Header$ |
$Header$ |
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$Name$ |
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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 SEAICE_CGRID adjoint started |
| 8 |
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(all stores seem to be sorted out, but NANs in adjoint). |
| 9 |
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o R_STAR adjoint implemented. |
| 10 |
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* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 11 |
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* need to sort out init. of h0facc, etc. |
| 12 |
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|
| 13 |
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checkpoint58d_post |
| 14 |
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o upgrade simple test-experiment to tutorial example: |
| 15 |
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step.1: duplicate the experiment and (step.2) will remove the old copy. |
| 16 |
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tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box) |
| 17 |
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tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere) |
| 18 |
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tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 19 |
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tutorial_global_oce_biogeo <- copy of dic_example |
| 20 |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 21 |
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tutorial_plume_on_slope <- copy of plume_on_slope |
| 22 |
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tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity) |
| 23 |
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tutorial_global_oce_optim <- empty for now (David ?) |
| 24 |
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tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 25 |
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some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 26 |
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o correct a sign problem in cost_scat.F |
| 27 |
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o obcs and ptracers: fix boundary conditions for advections schemes |
| 28 |
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with larger stencil |
| 29 |
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o thsice adjoint: start |
| 30 |
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o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 31 |
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completeness |
| 32 |
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o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 33 |
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and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 34 |
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o ptracers adjoint: |
| 35 |
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* avoid extensive recomputatations |
| 36 |
|
* fix missing re-init. of gptr (missed by TAF) |
| 37 |
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o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 38 |
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me to turn off the excessive output to STDOUT that this package produces |
| 39 |
|
o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 40 |
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and add those terms in Vector-Invariant formulation. |
| 41 |
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o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 42 |
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if the control period (xx_hfluxperiod etc) is 0 |
| 43 |
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o in profiles pkg, clean routines and fix details |
| 44 |
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o in ecco pkg, reading ssh data: |
| 45 |
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fix problem in case the model does not start at iter0=0 |
| 46 |
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o fix mnc-pickup/restart for ptracers |
| 47 |
|
o new package prifiles: |
| 48 |
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code to compute profile-based cost by Gael Forget |
| 49 |
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(modifs in ecco, ctrl, autodiff) |
| 50 |
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o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 51 |
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ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 52 |
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|
| 53 |
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checkpoint58c_post |
| 54 |
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o adjoint: finish NLFS adjoint and provide reference output in |
| 55 |
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verification/global_ocean.90x40x15/results_ad_nlfs |
| 56 |
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o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the |
| 57 |
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documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in |
| 58 |
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SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only |
| 59 |
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with SEAICE_CGRID defined. |
| 60 |
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o move calendarDumps from "data" to "data.cal" and clean-up the code |
| 61 |
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with a simple call to pkg/cal S/R: CAL_TIME2WRITE |
| 62 |
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o add useEXF & useCAL flags (for now, set in hard-coded way) |
| 63 |
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o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum |
| 64 |
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(were missing in NH mode, and wrong in quasihydrostatic mode). |
| 65 |
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waiting for Chris updated version of calc_gw to add those CALLs. |
| 66 |
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o fix bug in quasihydrostatic S/R ; |
| 67 |
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add a test for this option: global_ocean.90x40x15.qshyd |
| 68 |
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o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs. |
| 69 |
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(called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS) |
| 70 |
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o add on/off flag useOffLine for package OFFLINE |
| 71 |
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o seaice: |
| 72 |
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- modify advection so that it works also on the C-grid |
| 73 |
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- extend loop ranges in seaice_lsr and seaice_dynsolver; fixes |
| 74 |
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problem in multi-tile runs with C-grid |
| 75 |
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- add flags for clipping ice velocities and/or masking solver forcing |
| 76 |
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- fix drag (ocean on ice) formulation and a bug that caused noise in the |
| 77 |
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C-grid solver |
| 78 |
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- added a few comments to seaice_diffusion.F |
| 79 |
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- separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V |
| 80 |
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are now exclusive) |
| 81 |
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- add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which |
| 82 |
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required re-ordering the code a little: |
| 83 |
|
+ make DAIRN global variable (defined in SEAICE) |
| 84 |
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+ move computation of the viscosities eta and zeta into a new separate |
| 85 |
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routine (because I need to recompute them in seaice_ocean_stress.F) |
| 86 |
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|
| 87 |
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checkpoint58b_post |
| 88 |
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o AIM+thSIce: fix sign of Short-Wave through the Ice ; |
| 89 |
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update output.txt of exp. aim.5l_cs.thSI |
| 90 |
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o various mnc cleanups and improvements: |
| 91 |
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+ shrink lookup tables by factor of ~4 |
| 92 |
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+ better error reporting when running out of lookup space |
| 93 |
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+ able to handle longer path/file names (up to 500 chars) |
| 94 |
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o adjoint: |
| 95 |
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- Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations. |
| 96 |
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- TBD: "hidden" mom_vecinv recomp. in dynamics |
| 97 |
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o change forcing_In_AB to affects both T,S forcing and Momentum forcing |
| 98 |
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(allow to differentiate between forcing components using new integer flags: |
| 99 |
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momForcingOutAB=1/0 & tracForcingOutAB=1/0) |
| 100 |
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and add new flag to put Dissipation tendency out of Adams-Bashforth. |
| 101 |
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o ecco |
| 102 |
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- enable trend removal from SSH anomaly obs. |
| 103 |
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o adjoint |
| 104 |
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- a fix for PmEpR when #undef EXACT_CONSERV |
| 105 |
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- fix of "hidden" recomp. in thermodynamics (no TAF warnings) |
| 106 |
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- try to fix "hidden" recomp. in forward_step for NLFS |
| 107 |
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(NLFS seems broken sometimes after I checked it in) |
| 108 |
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o seaice: |
| 109 |
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- add c-grid version of the dynamic solver: |
| 110 |
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+ three new routines that are the c-grid substitute lsr, dynsolver |
| 111 |
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and ostres |
| 112 |
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+ put a few fields that were local to dynsolver into global common |
| 113 |
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blocks, so that I can move the computation of stresses etc into |
| 114 |
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seaice_lsr (saves coding but may break the adjoint). |
| 115 |
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- replace more hardwired parameters by runtime parameters |
| 116 |
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- add ice masks that mask the rhs of the implicit solvers where there |
| 117 |
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is no ice (commented out in seaice_dynsolver, because i am not sure |
| 118 |
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if this works properly), eventually this should replace the clipping |
| 119 |
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of ice velocities in seaice_dynsolver to +/-40cm/s. |
| 120 |
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o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly |
| 121 |
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include it only where its needed |
| 122 |
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o move balancing of fluxes before the call of external_forcing_surf |
| 123 |
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o seaice: |
| 124 |
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- correct units of turning angles (now they are really in degrees) |
| 125 |
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- move computation of GWATX/Y out of main routine into dynsolver |
| 126 |
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- initialize GWATX/Y in seaice_init |
| 127 |
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o Apply mask on Fresh-Water flux (needed for SSH forcing). |
| 128 |
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update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual) |
| 129 |
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o seaice: add runtime flags for turning angles (default to zero) |
| 130 |
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o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean |
| 131 |
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and trend from exf forcing and ctrl control adjustments |
| 132 |
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o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF |
| 133 |
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(since checkpoint57x_post) |
| 134 |
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o change the default rotation period to 86164.s = the Earth rotation |
| 135 |
|
o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T) |
| 136 |
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and based on a reference stratification. Tested within hs94.cs-32x32x5. |
| 137 |
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o seaice advection: add code for choosing between the default (2nd order |
| 138 |
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central differences) and multiDim advection schemes provided by |
| 139 |
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pkg/generic_advdiff |
| 140 |
|
o seaice: |
| 141 |
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- removed all references to SEAICE_GRID.h fields from |
| 142 |
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dynsolver, advect, diffus, lsr, without changing the results of lab_sea |
| 143 |
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(cubed-sphere configuration will change a little) |
| 144 |
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- grid computations in seaice_init are obsolete now. |
| 145 |
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- cleaned up code a little so that is easier to read (hopefully). |
| 146 |
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- added new (better?) discretizations of default advection and diffusion |
| 147 |
|
(turn on with SEAICEuseFluxForm) |
| 148 |
|
- replace 1 in 3d global fields by kSurface in growth.F |
| 149 |
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|
| 150 |
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checkpoint58a_post |
| 151 |
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o seaice: |
| 152 |
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- bug fix in advect.F |
| 153 |
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o shelfice: |
| 154 |
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- separate shelfice load anomaly from pload (breaks with time |
| 155 |
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dependent forcing), => introduce constant field shelficeLoadAnomaly. |
| 156 |
|
Its default is 0., but it may be computed more cleverly from (unknown) |
| 157 |
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t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be |
| 158 |
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done offline. A good approximation of the pressure load anomaly is |
| 159 |
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necessary to avoid large initial adjustment processes underneath |
| 160 |
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deep-reaching shelfice. |
| 161 |
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- small fix in ISOMIP shelfice_thermodynamics |
| 162 |
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- add more sophisticated thermodynamics of Hellmer (1989), this is |
| 163 |
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now the default |
| 164 |
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- give a few constants more intuitive names |
| 165 |
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o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful |
| 166 |
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if bulk formulae are used in long integration (especially EmPmR). Turn |
| 167 |
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on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01 |
| 168 |
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if balancePrintMean, the imbalance that is substracted is printed to |
| 169 |
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STDOUT. |
| 170 |
|
o fix bug (typo) in obcs_apply_eta.F |
| 171 |
|
o add a new package shelfice which enables us to model the circulation |
| 172 |
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underneath shelf-ice with draughts of hundreds of meters. |
| 173 |
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- works |
| 174 |
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- to do: + include improved thermodynamics |
| 175 |
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+ check whether kSurfC (from model/inc/SURFACE.h) can be used |
| 176 |
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instead of new field kTopC |
| 177 |
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+ can we use topoFile, Ro_surf and existing code in ini_depth.F |
| 178 |
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instead of new field R_shelfIce and new code in ini_depth.F |
| 179 |
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and ini_mask_etc.F? |
| 180 |
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+ adjust vertical mixing schemes? |
| 181 |
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o seaice pkg: |
| 182 |
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- add a cpp-flag to include a simple formula for a salinity dependent |
| 183 |
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freezing point of sea water at the surface |
| 184 |
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- change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and |
| 185 |
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meridional stresses are now different (and hopefully correct) |
| 186 |
|
o AIM pkg: change threshold on large-scale condensation to conserve Heat. |
| 187 |
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update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics |
| 188 |
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and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG) |
| 189 |
|
o pkg/diagnostics: add options and parameters for regional-statistics |
| 190 |
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diagnostics ; define regions by reading a region-mask from a file |
| 191 |
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(might add other options later) |
| 192 |
|
o pkg/bulk_force: |
| 193 |
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- add option and parameters to use AIM surface-flux formulae. |
| 194 |
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- Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ; |
| 195 |
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others forcing fields (defined in PARM05, parameter file "data") are loaded |
| 196 |
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from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F). |
| 197 |
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- initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F |
| 198 |
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- use the right EXCH call for uwind,vwind (to work on CS-grid). |
| 199 |
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- re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h) |
| 200 |
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and parameters (note: calcWindStress replaces .NOT.readwindstress). |
| 201 |
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- cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP). |
| 202 |
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|
| 203 |
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checkpoint58 |
| 204 |
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o add "--embed-source" option to genmake2 which, when the supporting |
| 205 |
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tools can be compiled (as determined by genmake2) will turn on the |
| 206 |
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embed_files package which then embeds the entire MITgcm source code |
| 207 |
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(*.[fFhc] + Makefile) used for the build within the executable |
| 208 |
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- requested by CNH but off by default |
| 209 |
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- adds a paltry <9MB to the mitgcmuv executable in most cases |
| 210 |
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- only writes the output when useEMBEDSRC in eedata is true |
| 211 |
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o clean up 3-dim. relaxation codes: |
| 212 |
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* Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec |
| 213 |
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* Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs) |
| 214 |
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* Thanks to Tom Haine for testing! |
| 215 |
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|
| 216 |
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checkpoint57z_post |
| 217 |
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o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate): |
| 218 |
|
affects output (@ truncation level) of exp. plume_on_slope ; updated. |
| 219 |
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o fix the pickup behavior for obcs in combination with ptracers |
| 220 |
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o fix a bug in ptracers_external_fields_load |
| 221 |
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o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...) |
| 222 |
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affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!) |
| 223 |
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o transfered surface NH pressure to eta field (if exactConserv). |
| 224 |
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o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign) |
| 225 |
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and update lab_sea output.txt file. |
| 226 |
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o completing 3-dim. relaxation code: additional term |
| 227 |
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1/tau*( theta(i,j,k) - thetaStar(i,j,k) ) |
| 228 |
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in S/R EXTERNAL_FORCING_T (file external_forcing.F) |
| 229 |
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* At compile time, in "EXF_OPTIONS.h" set |
| 230 |
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#define ALLOW_CLIMTEMP_RELAXATION |
| 231 |
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#define ALLOW_CLIMSALT_RELAXATION |
| 232 |
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* At runtime in "data", under &PARM03 set (e.g., units in seconds) |
| 233 |
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tauThetaClimRelax3Dim = 15552000.0, |
| 234 |
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tauSaltClimRelax3Dim = 15552000.0, |
| 235 |
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* 3 cases: |
| 236 |
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1) Use a constant-in-time 3-dim. field |
| 237 |
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2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec. |
| 238 |
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3) Real-time relax. to time-evolving prescribed field |
| 239 |
|
o Adding Laplacian-type smoothness constraint on |
| 240 |
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initial and boundary (forcing) controls (ic, bc) |
| 241 |
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* enable at compile-time via |
| 242 |
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ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION |
| 243 |
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* enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1 |
| 244 |
|
* Absolute scale somewhat unclear so far |
| 245 |
|
* no area weighting was included since no other cost term does so far |
| 246 |
|
|
| 247 |
|
checkpoint57y_post |
| 248 |
|
First step for a NLFS adjoint |
| 249 |
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o initially suppress rStar (new flag DISABLE_RSTAR_CODE) |
| 250 |
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o new init. routines for calc_r_star, calc_surf_dr |
| 251 |
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o still need to deal with ini_masks_etc |
| 252 |
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o testreport seemed happy |
| 253 |
|
checkpoint57y_pre |
| 254 |
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|
| 255 |
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o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs. |
| 256 |
|
o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc) |
| 257 |
|
o add new offset feature to offline pkg (plus minor cleanup) |
| 258 |
|
o cfc fixes for final year of integration |
| 259 |
|
o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should |
| 260 |
|
be in GCHEM_OPTIONS). |
| 261 |
|
|
| 262 |
|
checkpoint57x_post |
| 263 |
|
o fix testreport Pb in multiple test experiment. |
| 264 |
|
o cleanup our namelist syntax in verification: |
| 265 |
|
- make it more F95 standards compliant (some work still needed) |
| 266 |
|
- allows the vast majority of our tests to work with gfortran |
| 267 |
|
o Non-Hydrostatic: |
| 268 |
|
- put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h |
| 269 |
|
- fix exchange calls for CS-grid using the new EXCH_S3D_RL. |
| 270 |
|
o Allow to apply AB on T,S rather than on AB(gT,gS): |
| 271 |
|
- implemented within #ifdef ALLOW_ADAMSBASHFORTH_3 |
| 272 |
|
- use the same arrays (gtNm,gsNm) to hold tracer field at previous |
| 273 |
|
time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)). |
| 274 |
|
- need a "clever" read_pickup to restart from the other AB formulation |
| 275 |
|
o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h |
| 276 |
|
o remove some unused variables (reduces number of compiler warnings) |
| 277 |
|
o adjoint |
| 278 |
|
* Disable useVariableViscosity for adjoint for time being |
| 279 |
|
(there are a number of extensive recomputations) |
| 280 |
|
* Initialize certain variables needed for adjoint |
| 281 |
|
|
| 282 |
|
checkpoint57w_post |
| 283 |
|
o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names |
| 284 |
|
fix the singleCpuIO RS version of MDSWRITEFIELD |
| 285 |
|
and add a WARNING if using globalFiles=T with multi-processors. |
| 286 |
|
o write grid-file(s) in only one format (MDS or MNC): default=MNC (if |
| 287 |
|
using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc |
| 288 |
|
o tracer advection scheme: |
| 289 |
|
add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get |
| 290 |
|
those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, |
| 291 |
|
was not very convenient). |
| 292 |
|
add implicit version for DST-3 & DST3_Flux_Limit vertical advection; |
| 293 |
|
(further tests needed for the implicit DST & Flux-Limiter schemes). |
| 294 |
|
o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef |
| 295 |
|
and sRef for convenience, handy, when you want to initialize |
| 296 |
|
ptracers in a large domain with a constant non-zero value. Also, |
| 297 |
|
untangle ptracers_init.F a little. |
| 298 |
|
|
| 299 |
|
checkpoint57v_post |
| 300 |
|
o change dome exp. to use variable viscosity in side-drag terms. |
| 301 |
|
o remove all the files from the cfc_offline test since they are now |
| 302 |
|
incorporated into tutorial_cfc_offline which has been producing |
| 303 |
|
identical results for a few days of testing |
| 304 |
|
o add new parameter: sideDragFactor to enable half-slip-side BC |
| 305 |
|
and change side-drag S/R to use viscosity from mom_calc_visc |
| 306 |
|
(can switch back by setting sideDragFactor=0.); affects results at |
| 307 |
|
truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), |
| 308 |
|
global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5). |
| 309 |
|
o vorticity & strain are now computed without masking, to account for |
| 310 |
|
no-slip-side BC in variable viscosity calculation ; mask is applied |
| 311 |
|
anyway later on, before computing advection/coriolis terms. |
| 312 |
|
o modify exp4 to test new obcs support for reading from external files |
| 313 |
|
and for passive tracers |
| 314 |
|
o fix behavior of ptracers_monitor when monitor output is written to a |
| 315 |
|
netcdf-file; still not independent of monitor.F (writes in the same |
| 316 |
|
file). |
| 317 |
|
o change default value of tRef (put a uniform, meaningful value for ocean |
| 318 |
|
& atmos) and initialize sRef (was missing, as Martin mentioned). |
| 319 |
|
o Redefine viscC?Leith*. Change the coefficients of Leith viscosity |
| 320 |
|
to be proportional to enstrophy dissipation length. Thus, |
| 321 |
|
viscC?leith?_new=pi*(viscC?leith?_old)^(1/3) |
| 322 |
|
This is now consistent with Smagorinsky and with the manual. |
| 323 |
|
|
| 324 |
|
checkpoint57u_post |
| 325 |
|
o OBCS and PTRACERS: add open boundary support for passive tracers |
| 326 |
|
- either use homogenous (pseudo) v.Neumann conditions or prescribe |
| 327 |
|
OB-values from file; this is not different from the way theta and salinity |
| 328 |
|
are treated |
| 329 |
|
- however, Orlanski-radiation conditions are not supported, and the model |
| 330 |
|
will stop if you use pTracers and Orlanski at the same time. |
| 331 |
|
- beefed up the rountine obcs_external_fields_load: now only those open |
| 332 |
|
boundary values are overwritten with values from files for which there |
| 333 |
|
are really files, otherwise the OB-fields remain untouched. This makes |
| 334 |
|
it possible to use different OBs at different ends of the domain (as |
| 335 |
|
with EXF) |
| 336 |
|
o reduce number of exch calls in shap_filt (s2). |
| 337 |
|
o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ |
| 338 |
|
truncation level) 4/5 MLAdjust test results (11&12 digits match). |
| 339 |
|
|
| 340 |
|
checkpoint57t_post |
| 341 |
|
o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4 |
| 342 |
|
o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get |
| 343 |
|
same truncation, independent of the face number: affects affects several |
| 344 |
|
test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5). |
| 345 |
|
o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times); |
| 346 |
|
note that biharmonic viscosity + no-slip was not tested in any experiment. |
| 347 |
|
o fix bug in non-linear free-surf side-drag ; generate new output for |
| 348 |
|
global_ocean.cs32x15(+.thsice) & global_ocean_pressure. |
| 349 |
|
o make mnc honor the writeBinaryPrec flag for most kinds of output |
| 350 |
|
o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum |
| 351 |
|
o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation |
| 352 |
|
error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5). |
| 353 |
|
o add brackets in multi-terms sum to get same truncation, independent of |
| 354 |
|
the face number (manage to get exactly same value of gU,gV at the cs-edge) |
| 355 |
|
affects several test. exp. Update global_ocean.cs32x15 (+.thsice). |
| 356 |
|
o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax |
| 357 |
|
and viscA4Remax, which allow one to limit the minimum viscosity by specifying |
| 358 |
|
a maximum grid-scale Reynolds number. Also, changes all length calculations |
| 359 |
|
in the case of grid anisotropy to geometric mean of dx**2 and dy**2. |
| 360 |
|
Suggested values of viscosity parameters found in mom_calc_visc. |
| 361 |
|
Many new viscosity diagnostics available. |
| 362 |
|
|
| 363 |
|
checkpoint57s_post |
| 364 |
|
o Add clearing-house for viscosity calculations, mom_calc_visc and |
| 365 |
|
correct numerous bugs in LeithD and Smagorinsky discretizations. |
| 366 |
|
mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be |
| 367 |
|
used simultaneously, and to be used in mom_vecinv and mom_fluxform. |
| 368 |
|
Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F) |
| 369 |
|
and with Strain-Tension viscous term calculation (mom_hdissip.F). |
| 370 |
|
The Strain-Tension form is now called with useStrainTensonVisc=.true. |
| 371 |
|
ViscAhStrain and viscAhTension are now retired. |
| 372 |
|
o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4". |
| 373 |
|
o In response to JMC's bug report, genmake2 now ignores any soft-links |
| 374 |
|
that it finds in the *current* directory when searching for files. |
| 375 |
|
Soft-links found in any other source directories will still work as |
| 376 |
|
they did before. |
| 377 |
|
o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls |
| 378 |
|
a C routine to unlimit the stack size |
| 379 |
|
o mnc-ify pkg/aim snapshot vars |
| 380 |
|
o mnc-ify pkg/land as requested by Daniel |
| 381 |
|
o various changes to mnc including: |
| 382 |
|
- all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format |
| 383 |
|
- output can now be grouped so that all files within a group |
| 384 |
|
change the ITER portion of their names in lock-step together |
| 385 |
|
- can now read ("global") PER-FACE (in addition to PER-TILE) files |
| 386 |
|
and works with both EXCH1 and EXCH2 (but needs more testing) |
| 387 |
|
- writing works for all verification test cases w/ g77 on Linux |
| 388 |
|
|
| 389 |
|
checkpoint57r_post |
| 390 |
|
o make MNC variable initialization happen earlier |
| 391 |
|
o add diagnostics for (almost) each term of the momentum Eq. |
| 392 |
|
o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics. |
| 393 |
|
o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups) |
| 394 |
|
o remove MINIMAL_TAVE_OUTPUT option ; |
| 395 |
|
add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT). |
| 396 |
|
o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src |
| 397 |
|
allows to compile without pkg/mdsio (& test successfully hs94.1x64x5) |
| 398 |
|
o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice) |
| 399 |
|
o add time-dependent SST, SSS control |
| 400 |
|
o cost terms in ecco/ modularized (new cost_generic.F) |
| 401 |
|
o cost_averages routines are modularized (new cost_averagesgeneric.F) |
| 402 |
|
o new infrastructure for seaice model vs. obs misfits in seaice/ |
| 403 |
|
* driver from the_main_loop.F is seaice_cost_driver.F |
| 404 |
|
* first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA) |
| 405 |
|
* gradient check in Exp. 6a of natl_box_adjoint/ |
| 406 |
|
o natl_box_adjoint input_seaice for Lab. Sea now available online via wget |
| 407 |
|
(see README file) |
| 408 |
|
|
| 409 |
|
checkpoint57q_post |
| 410 |
|
o fix initialisation Pb in calc_gw (get NANs in exp5 with g77) |
| 411 |
|
o fix annoying months-old bug in mnc/mdsio output for seaice pkg |
| 412 |
|
- bug was reported by Jean-Michel and Ian Fenty |
| 413 |
|
o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F) |
| 414 |
|
update exp. cpl_aim+ocn output. |
| 415 |
|
o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT |
| 416 |
|
Needed for high-res. runs with large global files |
| 417 |
|
to be able to limit tapelev size |
| 418 |
|
o Changed some tests for adjoint: |
| 419 |
|
* carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT |
| 420 |
|
* natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT |
| 421 |
|
* global_ocean.90x40x15/ back to default 3-level checkpointing |
| 422 |
|
o Modifications to enable scripted COMMON to MODULE conversion |
| 423 |
|
* verification/OpenAD/code/ has necessary scripts and description; |
| 424 |
|
* converts, compiles and runs successfully; |
| 425 |
|
|
| 426 |
|
checkpoint57p_post |
| 427 |
|
o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F |
| 428 |
|
o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED |
| 429 |
|
(already the case for some pkgs, including recent MNC_init, e.g. thsice) |
| 430 |
|
o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP) |
| 431 |
|
o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F |
| 432 |
|
(was already the case for dissipation with mom_vecinv, |
| 433 |
|
and also the case for grad.PhiHyd when staggered-timeStep) |
| 434 |
|
This will allow to put dissipation out-off the AB time-stepping. |
| 435 |
|
Unfortunately, affects truncation error. Update output of exp. that "fails" |
| 436 |
|
(cg2d matching number) and leave the others for later: front_relax(10), |
| 437 |
|
global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12), |
| 438 |
|
matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2). |
| 439 |
|
|
| 440 |
|
checkpoint57o_post |
| 441 |
|
o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and |
| 442 |
|
(2) its ready to be documented during the 20050801 DocFest |
| 443 |
|
o MNC-ify the gmredi package -- tested and works w/ and w/o mnc |
| 444 |
|
for ideal_2D_oce and lab_sea on linux_ia32_g77 |
| 445 |
|
o set to #undef CTRL_SET_OLD_MAXCVARS_30 |
| 446 |
|
in global1x1_tot/code_seaice_adj to access indices 32, 33 |
| 447 |
|
(worth another tag) |
| 448 |
|
|
| 449 |
|
checkpoint57n_post |
| 450 |
|
o adding precip control xx_precip 32 |
| 451 |
|
o adding swflux control xx_swflux 33 |
| 452 |
|
o Replacing 10 forcing penalty cost routines by 1 generic. |
| 453 |
|
o Implementing partitioning in time-mean and variable adjustment |
| 454 |
|
for atmos. state. |
| 455 |
|
o Time-mean constant error is now read in data.ecco (instead of hard-coded) |
| 456 |
|
o in natl_box_adjoint: |
| 457 |
|
* updated exp 1 to 10 |
| 458 |
|
(but does not have time-mean vs. variable split results yet) |
| 459 |
|
o updated global1x1/*_seaice_adj/ |
| 460 |
|
to incorporate latest changes |
| 461 |
|
o enable useSingleCpuIO for mdsio vector routines |
| 462 |
|
(applies in particular to tapelev I/O) |
| 463 |
|
o removed inefficient K-loop in all active_file*control*.F |
| 464 |
|
|
| 465 |
|
checkpoint57m_post |
| 466 |
|
o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into) |
| 467 |
|
and advect_cs (use EXCH-2 and standard cs-32 grid files). |
| 468 |
|
o pkg/exch2: filling of face-corner halo regions is optional |
| 469 |
|
(ifdef W2_FILL_NULL_REGIONS) and is turned off by default. |
| 470 |
|
|
| 471 |
|
checkpoint57l_post |
| 472 |
|
tag before updating tutorials (pre-release-2) |
| 473 |
|
o add cos & sin of grid-direction orientation angle (curvilinear grid only, |
| 474 |
|
for output and interpolation of input fields onto model grid) |
| 475 |
|
o fix radius in mom_v_metric_cylinder.F (wrong by dy/2). |
| 476 |
|
Affects results of exp. rotating_tank ; update output.txt. |
| 477 |
|
o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor |
| 478 |
|
and taking the square quantity and/or using a fraction-weight field. |
| 479 |
|
o fix aim_diagnostics_init.F mate numbers. |
| 480 |
|
o add mnc output capability to diagnostics/diagstat and update |
| 481 |
|
our cvsignore files for the ACSII output generated |
| 482 |
|
|
| 483 |
|
checkpoint57k_post |
| 484 |
|
o lab_sea now uses diagnostics package and provides a suite of |
| 485 |
|
new EXF diagnostics output. |
| 486 |
|
|
| 487 |
|
checkpoint57j_post |
| 488 |
|
o exf |
| 489 |
|
* bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton): |
| 490 |
|
Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982); |
| 491 |
|
terms -2*ATAN(x) + pi/2 were added to both stable and unstable case. |
| 492 |
|
* extended diagnostics output |
| 493 |
|
- now includes all EXF variables |
| 494 |
|
- hs, hl moved to common block |
| 495 |
|
- separate S/R for diagnostics, called after ctrl vector is added |
| 496 |
|
- name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet |
| 497 |
|
- EXFqnet contains true Qnet (i.e. includes qsw) |
| 498 |
|
* updated verif. lab_sea, global_with_exf |
| 499 |
|
* Rearranging hflux (exf_mapfields -> exf_getforcing) |
| 500 |
|
to ensure that diagnostics sees a true EXFqnet |
| 501 |
|
o add matlab scripts for CS-grid vectors (in utils/cs_grid) |
| 502 |
|
o diagnostics pkg: change pointers so that 1 diagnostic can be used |
| 503 |
|
several times with different frequencies. |
| 504 |
|
o mnc-ify the thsice package as requested by Daniel Enderton |
| 505 |
|
- the monitor--MNC output needs work |
| 506 |
|
- many attributes need to be added (most are currently blank) |
| 507 |
|
o mnc-ify theaim_v23 package as requested by Daniel Enderton |
| 508 |
|
- many attributes need to be added (most are currently blank) |
| 509 |
|
o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign) |
| 510 |
|
o add Sadourny like discretization to the 4th.O vorticity advection scheme |
| 511 |
|
o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. |
| 512 |
|
update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn, |
| 513 |
|
fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice). |
| 514 |
|
o fix few little things to avoid floating error with -ftrapuv (ifort v9) |
| 515 |
|
(ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F) |
| 516 |
|
|
| 517 |
|
checkpoint57i_post |
| 518 |
|
o Diagnostics package was changed: diagnostic allocation is now deactivated |
| 519 |
|
by setting an empty file name in the namelist (used to be by setting 0 frequency) |
| 520 |
|
o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ; |
| 521 |
|
add 1rst Order upwind vertical Shear. |
| 522 |
|
o add a quick fix for A/B checkpointing in OFFLINE mode |
| 523 |
|
o add IGNORE_TIME define and -ignore_time option to genmake2 as an |
| 524 |
|
end-run around the C/Fortran linking horror in eesup/src/timers.F |
| 525 |
|
o added pkg/runclock: allows user to terminate run based on wall clock |
| 526 |
|
o added non-hydrostatic scaling parameter: nh_am2 |
| 527 |
|
o pkg/my82: futile attempt to make results compiler-independent by adding |
| 528 |
|
some "_d 0", etc. no effect. |
| 529 |
|
o for mnc output, fill the 'T' coordinate var with myTime and create a |
| 530 |
|
separate 'iter' variable for iteration count |
| 531 |
|
o pkg/diagnostics: |
| 532 |
|
add new capability: output of Global/Regional & per-level statistics ; |
| 533 |
|
tested against monitor output (including land & thSIce) on various exp. |
| 534 |
|
o make seaice-pkg I/O type flags (MNC/MDS) more standard. |
| 535 |
|
|
| 536 |
|
checkpoint57h_done |
| 537 |
|
tag after changing user customized files (DIAGNOSTICS_SIZE.h, |
| 538 |
|
data.diagnostics, data.gchem, data.ptracers) is done. |
| 539 |
|
|
| 540 |
|
o pkg/diagnostics: prepare for Global/Regional statistics. |
| 541 |
|
add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h |
| 542 |
|
o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE |
| 543 |
|
and rename it: DIFFERENT_MULTIPLE |
| 544 |
|
|
| 545 |
|
checkpoint57h_post |
| 546 |
|
o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers |
| 547 |
|
o pkg/diagnostics: change output frequency, now in seconds (instead |
| 548 |
|
of Nb of iterations). This requires to change data.diagnostics. |
| 549 |
|
checkpoint57h_pre |
| 550 |
|
|
| 551 |
|
o in mnc, let the user create the output dir if both mnc_outdir_date |
| 552 |
|
and mnc_outdir_num are false |
| 553 |
|
o add fflags() to pkg/diagnostics which allows one to specify, on a |
| 554 |
|
per-file basis, the file precision [default behavior is unchanged] |
| 555 |
|
o added diagnostics to pkg/kpp, including computation of mixed layer |
| 556 |
|
depth based on a temperature/density criterion |
| 557 |
|
o updated verification/natl_box to test the new pkg/kpp diagnostics |
| 558 |
|
o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T) |
| 559 |
|
o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4) |
| 560 |
|
o fix mnc flags in pkg/seaice so that they are "owned" by seaice, |
| 561 |
|
not mnc -- this mistake was found by JMC and is now corrected |
| 562 |
|
|
| 563 |
|
checkpoint57g_post |
| 564 |
|
o add Adams-Bashforth 3rd Order time stepping: |
| 565 |
|
- default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3) |
| 566 |
|
- not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ... |
| 567 |
|
checkpoint57g_pre |
| 568 |
|
|
| 569 |
|
o make lambda[Theta,Salt]ClimRelax spatially varying |
| 570 |
|
(default remains spatially uniform constant based on tau) |
| 571 |
|
o added new control variables |
| 572 |
|
* init. uVel, vVel, etanN |
| 573 |
|
* lambda[Theta,Salt]ClimRelax |
| 574 |
|
o separate masks used for ctrl_pack/unpack 'from write_grid' output |
| 575 |
|
(suggested by G. Forget) |
| 576 |
|
|
| 577 |
|
checkpoint57f_post |
| 578 |
|
o add parameter "baseTime" = model base time = time at iteration zero |
| 579 |
|
new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to |
| 580 |
|
account for baseTime shift |
| 581 |
|
o move Coriolis arrays from PARAMS.h to GRID.h |
| 582 |
|
checkpoint57f_pre |
| 583 |
|
|
| 584 |
o mnc-ifying the seaice package |
o mnc-ifying the seaice package |
| 585 |
o introduced an alternative length scale calculation for use in the limiting |
o introduced an alternative length scale calculation for use in the limiting |
| 586 |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
maximum viscosity (off by default, see mom_vi_hdissip.F for details) |
| 595 |
o fix obscure MNC bug involving conversion between reals and integers |
o fix obscure MNC bug involving conversion between reals and integers |
| 596 |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
- it caused no problems with certain (eg. gcc, ifc) compilers but the |
| 597 |
new version is now more standards-compliant |
new version is now more standards-compliant |
| 598 |
|
o adjoint-related modifications |
| 599 |
|
* gad_dst3_adv_?: to be able to use advscheme=30 in adjoint |
| 600 |
|
* gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33 |
| 601 |
|
* mom_vi_hdissip: to be able to use Leith scheme in adjoint |
| 602 |
|
|
| 603 |
checkpoint57e_post |
checkpoint57e_post |
| 604 |
o Adding eddy stress controls a la Ferreira et al. |
o Adding eddy stress controls a la Ferreira et al. |
| 605 |
checkpoint57e_pre |
checkpoint57e_pre (actually was tagged: eckpoint57e_pre) |
| 606 |
|
|
| 607 |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
| 608 |
update output.txt of exp. fizhi-gridalt-hs |
update output.txt of exp. fizhi-gridalt-hs |
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