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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o new code to compute profile cost |
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| 8 |
by Gael Forget |
o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux) |
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| 10 |
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checkpoint58p_post |
| 11 |
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o obcs: stop if obcs is used with useCDscheme = .true. |
| 12 |
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o shelfice: |
| 13 |
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- fix a sign error so that no slip at shelfice interface works |
| 14 |
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- remove stop for combination non-hydrostatic code and shelfice. That does |
| 15 |
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not mean, that the results are correct, but at least they are numerically |
| 16 |
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stable |
| 17 |
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o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted) |
| 18 |
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o added adjoint exch routined for all exch*3d* routines |
| 19 |
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and updated flow directives |
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| 21 |
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checkpoint58o_post |
| 22 |
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o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ; |
| 23 |
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remove old subroutines (_XY_ & _XYZ_); update the adjoint version. |
| 24 |
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o change controling S/R for writing pickup file (new S/R do_write_pickup) |
| 25 |
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and clean-up reading/writing of pickup files. |
| 26 |
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o fix local version of read/write pickup (NH part) in rotating_tank/code |
| 27 |
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o simplify EXCH interface: |
| 28 |
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- change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list) |
| 29 |
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- not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version |
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o added the regrid package |
| 31 |
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o shelfice: |
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- add a simple boundary layer scheme to reduce noise |
| 33 |
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- fix the indexing in shelfice_u/v_drag so that there will be actually drag |
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checkpoint58n_post |
| 36 |
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o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to |
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local variable (not in common block). |
| 38 |
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o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass. |
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- still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more); |
| 40 |
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- still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls |
| 41 |
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to work with SingleCpuIO. |
| 42 |
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o add "_d 0" to real constant of pkg/cfc subroutines ; |
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update exp. cfc_exemple & tutorial_cfc_offline output files. |
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o multi-threading and IO: |
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- all threads call READ_FLD S/R (needed if using SingleCpuIO): |
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(no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R. |
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- barrier before and after reading. |
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- stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE) |
| 49 |
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- avoid using MDS_WRITELOCAL for LAND pkg output. |
| 50 |
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- new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics |
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common-block variables ; Allows multi-threading with master-thread IO. |
| 52 |
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o change default MAX_NO_THREADS from 32 to 4 ; |
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and stop cleanly when MAX_NO_THREADS is too small. |
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o add S/R BAR_CHECK to check multi-threaded barrier synchronization |
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| 56 |
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checkpoint58m_post |
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o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc. |
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and side-drag) on CS-grid : global_ocean.cs32x15.viscA4 |
| 59 |
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o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp. |
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keep global_ocean.90x40x15 (for AD testing) with former secondary test |
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(".qshyd") as the main test (mv output.qshyd.txt to output.txt) |
| 62 |
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o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos; |
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add MITgcm_tutorials (= code + all the tutorials) |
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o ecco, option to compute cost for total ssh (mean+anom) |
| 65 |
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o consistent with addition of ptracer and ssh in pkg/profiles |
| 66 |
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o profiles: adding ptracer and ssh |
| 67 |
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o testreport: change multi-test output-file name |
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(from output.txt.{name} to output.{name}.txt) |
| 69 |
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o profiles: now ok for mutli-tiles case |
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o seaice: add 4 parameters for different advection schemes for area, |
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(effective) seaice thickness, enthalphy, and snow height. Their default |
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is the standard parameter SEAICEadvScheme |
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o calc_gw: |
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- add cosFacU in zonal viscous flux (harmonic.visc.). |
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- put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt. |
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of tutorial_plume_on_slope. |
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o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria). |
| 78 |
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o calc_gw: true flux-form, account for horizontal grid spacing. |
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update rotating_tank results, but not plume_on_slope (affected at |
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truncation level, 11 digits). |
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checkpoint58l_post |
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o calc_gw: |
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- take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V |
| 85 |
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- remove side-drag for now (need to fix it); update plume_on_slope results. |
| 86 |
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- fix for partial-cell & non-uniform dz; update plume_on_slope results. |
| 87 |
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o commit code to make SST/SSS weights spatially variable |
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(based on either variable in-situ or variable initial T/S weights) |
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o pkg/ecco: |
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* commit code to relax deviations of xx_theta, xx_salt to 5*sigma, |
| 91 |
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now based on horizontally varying weights wthetaLev, wsaltLev |
| 92 |
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* cost_averagesflags now returns year indices in addition to day, month |
| 93 |
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* sflux balance is performed on annual basis |
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(sflxumm, sfluxmm2, bal_sfluxmm) |
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* for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO, |
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including separate counting and multipliers |
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o pkg/rbcs |
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* add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing |
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checkpoint58k_post |
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o testreport: |
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- always build in dir. "build" (if not there, mkdir build instead of building |
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& running in input) |
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- run in dir run (if it exists), in build otherwise. |
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- call prepare_run (if input/prepare_run exists) |
| 106 |
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- run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists. |
| 107 |
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o pkg/exf modifications to interpolation and rotation routines for more |
| 108 |
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reasonable treatment of North Pole singularity: for tracers North Pole |
| 109 |
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value is set to northernmost zonal-mean value, for zonal velocity it is |
| 110 |
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set to zero, and for meridional velocity it is set to northernmost value. |
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o pkg/exf/exf_check_range.F |
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- add tile index to diagnostics and move stop statement to the very |
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end of the routine. |
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o pkg/diagnostics: (diagnostics_main_init.F) |
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define title of isomorphic variables according to the current config. |
| 116 |
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o pkg/thsice with pkg/seaice dynamics: |
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- fix domain of computation (interior only, required for exf) and do exchanges |
| 118 |
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- seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient |
| 119 |
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o towards a standard way of dealing with multi-threading in MONITOR |
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and ${PKG}_MONITOR (all except ptracers_monitor) subroutines. |
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o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith) |
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to W momentum equation in nonhydrostatic and quasihydrostatic runs. |
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o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor. |
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o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block) |
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o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL |
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(problems ? with gradient check in bottom_ctrl_5x5 adjoint test) |
| 127 |
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o tracer advection: |
| 128 |
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- clean-up and simplify calc_common_factors.F |
| 129 |
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- make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer |
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advection subroutine (but still not used within DST advection S/R) |
| 131 |
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o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim) |
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checkpoint58j_post |
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o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields |
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from file (collects calls previously in FORWARD_STEP) |
| 136 |
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o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS |
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o adjoint store dir. adjusted accordingly |
| 138 |
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o genmake2 |
| 139 |
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replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list. |
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| 141 |
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checkpoint58i_post |
| 142 |
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o pkg/seaice: add parameter that allows to scale/turn off effect of seaice |
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on wind stress (SEAICEstressFactor defaults to 1.) |
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o Total number of Timers is finite (<=40): comment out 2 non-essential one |
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in the_main_loop.F to avoid Pb (e.g., when running fizhi test) |
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o vector_invariant: fix highOrderVorticity(=4.th.Order) advection |
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on CS-grid: no longer loosing mass. |
| 148 |
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o exf & curvilinear-grid: no longer modify longitude xC & xG. |
| 149 |
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o pkg/ggl90: fix sloppy output and fix a bug |
| 150 |
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o pkg/seaice: added SEAICEuseEVPpickup parameter |
| 151 |
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- Set to false in order to start EVP solver with |
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non-EVP pickup files when using SEAICEuseEVP |
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- fix sign error in diffusion in seaice_calc_rhs |
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checkpoint58h_post |
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* Modifications for bottom topography control |
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o replace hFacC by _hFacC at various places |
| 158 |
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o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL |
| 159 |
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o add non-self-adjoint cg2d_nsa |
| 160 |
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o update autodiff support routines |
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o re-initialise hfac after ctrl_depth_ini |
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o works for 5x5 box, doesnt work for global_ocean.90x40x15 |
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* Adding verification for 5x5 box (4-layer) bottom topography control |
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checkpoint58g_post |
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o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g., |
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used for mean seasonal cycle, mean diurnal cycle); add an example |
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in verification/global_ocean.cs32x15/input.thsice/data.diagnostics |
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o pkg/ggl90: |
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- add parameter (minimum surface kinetic energy) |
| 171 |
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- fix bug (avoiding division by zero) |
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o couple pkg/thsice to pkg/seaice: |
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- modify advection in seaice to accomodate new scalar fields to be advected |
| 174 |
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- only muliDimAdection scheme work with seaice/thsice |
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- mapping of thsice-variables to seaice-variables, back and forth |
| 176 |
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- does not break the verification experiments, but does not give the |
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desired results either |
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o pkg/seaice |
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- make (default) second order advection a bit less confusing? |
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checkpoint58f_post |
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o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice |
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to pkg/seaice): |
| 184 |
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- new routines thsice_map_exf and thsice_get_exf provide the interface |
| 185 |
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- add an additional formal parameter to thsice_solve4temp |
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o pkg/exf: |
| 187 |
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- add new fields wspeed, snowprecip (to be able to couple to thsice) |
| 188 |
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- correct Stefan-Boltzmann constant |
| 189 |
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- new parameter for longwave surface emittance |
| 190 |
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- separate some stuff from exf_bulkformulae into new routines |
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exf_radiation, exf_wind |
| 192 |
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- add new parameters and constants: longwave emissivity for ocean, ice |
| 193 |
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and snow, evaporation parameters over ice |
| 194 |
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- decouple wind/stress computation from ALLOW_BULKFORMULA: always compute |
| 195 |
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either wind from stress or stress from wind |
| 196 |
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o pkg/thSIce: |
| 197 |
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- split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F |
| 198 |
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- put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND |
| 199 |
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and THSICE_CALC_THICKN |
| 200 |
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- for now, call to THSICE_GET_BULKF remains inside i,j loops. |
| 201 |
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- add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h |
| 202 |
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to make debugging easier. |
| 203 |
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- affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output |
| 204 |
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o pkg/bulk_force: |
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- clean-up comments and parameters ; |
| 206 |
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- add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ; |
| 207 |
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o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched; |
| 208 |
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generate new output for test-experiment: aim.5l_cs.thSI |
| 209 |
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o results_ad : rename "output.txt_adm" to "output_adm.txt" and change |
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testreport accordingly |
| 211 |
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| 212 |
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checkpoint58e_post |
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o SEAICE_CGRID adjoint done |
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o R_STAR adjoint implemented. |
| 215 |
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* Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ ) |
| 216 |
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* need to sort out init. of h0facc, etc. |
| 217 |
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o Make pkg/profile fully independent of ecco,cost, etc. stuff |
| 218 |
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to be able to use it in pure forward. |
| 219 |
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checkpoint58d_post |
| 221 |
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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. |
| 223 |
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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) |
| 225 |
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tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation) |
| 226 |
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tutorial_global_oce_biogeo <- copy of dic_example |
| 227 |
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tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection) |
| 228 |
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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 ?) |
| 231 |
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tutorial_global_oce_in_p <- copy of global_ocean_pressure |
| 232 |
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some tutorials (R1) were already checked-in under tutorial_examples in release1_branch |
| 233 |
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o correct a sign problem in cost_scat.F |
| 234 |
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o obcs and ptracers: fix boundary conditions for advections schemes |
| 235 |
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with larger stencil |
| 236 |
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o thsice adjoint: start |
| 237 |
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o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for |
| 238 |
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completeness |
| 239 |
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o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING |
| 240 |
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and COSINEMETH_III, add comments in default CPP_OPTIONS.h |
| 241 |
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o ptracers adjoint: |
| 242 |
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* avoid extensive recomputatations |
| 243 |
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* fix missing re-init. of gptr (missed by TAF) |
| 244 |
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o obcs: add a flag (OBCSprintDiags, defaults is true) that allows |
| 245 |
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me to turn off the excessive output to STDOUT that this package produces |
| 246 |
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o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common |
| 247 |
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and add those terms in Vector-Invariant formulation. |
| 248 |
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o in ctrl pkg, if ALLOW_CAL, use monthly mean controls |
| 249 |
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if the control period (xx_hfluxperiod etc) is 0 |
| 250 |
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o in profiles pkg, clean routines and fix details |
| 251 |
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o in ecco pkg, reading ssh data: |
| 252 |
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fix problem in case the model does not start at iter0=0 |
| 253 |
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o fix mnc-pickup/restart for ptracers |
| 254 |
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o new package prifiles: |
| 255 |
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code to compute profile-based cost by Gael Forget |
| 256 |
(modifs in ecco, ctrl, autodiff) |
(modifs in ecco, ctrl, autodiff) |
| 257 |
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o Benign bug fix in initialization (spotted by M. Mazloff) of |
| 258 |
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ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F |
| 259 |
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|
| 260 |
checkpoint58c_post |
checkpoint58c_post |
| 261 |
o adjoint: finish NLFS adjoint and provide reference output in |
o adjoint: finish NLFS adjoint and provide reference output in |
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