| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
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|
| 6 |
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o doc/api_reference added |
| 7 |
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- a framework for building an API Reference Manual using all |
| 8 |
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the "protex" comments embedded in the code |
| 9 |
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- see pkg/generic_advdiff, pkg/mnc for examples |
| 10 |
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o MNC: |
| 11 |
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- make myThid the last argument for all subroutines |
| 12 |
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- new default for the grid files: NO halos |
| 13 |
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- add useMNC and other run-time flags |
| 14 |
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- separate per-file-group handling of the unlimited dimension |
| 15 |
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- early initialization of MNC w/ flags read at the eeboot stage |
| 16 |
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and lookup tables set in initialize_fixed |
| 17 |
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- write all MNC output to a freshly-created directory |
| 18 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 19 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 20 |
|
o Added functionality to grdchk: |
| 21 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 22 |
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|
| 23 |
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checkpoint52l_post |
| 24 |
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o new land formulation: |
| 25 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 26 |
|
energy conservation. |
| 27 |
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b) account for water temperature and for latent heat of freezing |
| 28 |
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in all processes (rain, run-off, ground storage) |
| 29 |
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c) compute surface and ground temperature implicitly. |
| 30 |
|
o aim_v23 modification for new land model: |
| 31 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 32 |
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to allow implicit computation of land & sea-ice surface temp. |
| 33 |
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b) add snow precipitation. |
| 34 |
|
checkpoint52l_pre |
| 35 |
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|
| 36 |
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o fix problem (when 1 tile is empty) in min/max monitor. |
| 37 |
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o fix bug in timeAve (u,vZetatave in common block) |
| 38 |
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o no restoring terms under ice for pkg/seaice |
| 39 |
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o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 40 |
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o bug fix for pkg/seaice pickups |
| 41 |
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o change MNC call locations and add coordinate attributes |
| 42 |
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o mask vorticity at the corner ; affects global_ocean.cs output |
| 43 |
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o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 44 |
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o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 45 |
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o exf: Adding simple range check routine for exf fields after read |
| 46 |
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|
| 47 |
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checkpoint52k_post |
| 48 |
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o removed top-level directory "diags" |
| 49 |
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- we migrated these functions to pkg/timeave a long time ago |
| 50 |
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o fixed bug introduced in pkg/monitor |
| 51 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 52 |
|
averaged fields (I/O via cost_averages) |
| 53 |
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-> use ctrl.h in active_file*.F to control I/O precision. |
| 54 |
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o paramter list of CALL ADTHE_MAIN_LOOP |
| 55 |
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o added initial do_the_model_io to ecco |
| 56 |
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o set all ...Freq to zero after cost_final |
| 57 |
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taveFreq, dumpFreq, pChkptFreq |
| 58 |
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o MAIN and ECCO differentiability restored |
| 59 |
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|
| 60 |
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checkpoint52j_post |
| 61 |
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o fix nchklev in tamc.h for global_ocean... |
| 62 |
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o Bringing flow and store directives up-to-date |
| 63 |
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o Really weird thing! |
| 64 |
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call do_the_model_io from the_main_loop with parameters |
| 65 |
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starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 66 |
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TAF places a faulty re-call of initialise_varia |
| 67 |
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after cost_final call which should not be there! |
| 68 |
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checkpoint52j_pre |
| 69 |
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|
| 70 |
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o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 71 |
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error messages |
| 72 |
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o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 73 |
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o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 74 |
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debug output |
| 75 |
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o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 76 |
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o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 77 |
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use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 78 |
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o update AIM Equatorial Channel exp: |
| 79 |
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use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 80 |
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o globalFile now works with exch2 |
| 81 |
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o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 82 |
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mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 83 |
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o limit timeave output for hi-res integrations |
| 84 |
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|
| 85 |
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checkpoint52i_post |
| 86 |
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o removed CPP_EEOPTIONS.h from verification/*/code |
| 87 |
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o updated the tiling for global_ocean_pressure |
| 88 |
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checkpoint52i_pre |
| 89 |
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|
| 90 |
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o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 91 |
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the old pkg/aim). |
| 92 |
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|
| 93 |
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checkpoint52h_pre |
| 94 |
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o shortened offending lines in exch2_send_rx?.template |
| 95 |
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o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 96 |
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o genmake2: add build & execute test for NetCDF code |
| 97 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
| 98 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
| 99 |
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o added useSingleCPUIO flag to monitor.F and mon_out.F |
| 100 |
|
o added temporary hack for sea-ice dynamics on the cube: |
| 101 |
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metric terms are ignored and it is assumed that |
| 102 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
| 103 |
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|
| 104 |
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checkpoint52f_post |
| 105 |
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o added exch2 cube routines to pkg/exch2 |
| 106 |
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o modified hs94.cs-32x32x5 to use it |
| 107 |
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o added new grid files to hs94.cs-32x32x5 |
| 108 |
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checkpoint52f_pre |
| 109 |
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|
| 110 |
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checkpoint52e_post |
| 111 |
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o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
| 112 |
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for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
| 113 |
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o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
| 114 |
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to work with implicit vertical advection and AB ; |
| 115 |
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o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
| 116 |
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o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
| 117 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
| 118 |
|
checkpoint52e_pre |
| 119 |
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|
| 120 |
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o fix bug in impldiff when Nr=1 or Nr=2. |
| 121 |
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o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
| 122 |
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o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
| 123 |
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o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
| 124 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
| 125 |
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o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
| 126 |
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o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
| 127 |
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o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
| 128 |
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|
| 129 |
|
checkpoint52d_post |
| 130 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
| 131 |
|
- updated output accordingly |
| 132 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
| 133 |
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random number generator |
| 134 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
| 135 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
| 136 |
|
o changes to permit hi-res, cubed-sphere, configuration |
| 137 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
| 138 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
| 139 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
| 140 |
|
of surface winds for the cube |
| 141 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
| 142 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
| 143 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
| 144 |
|
complete with example surface forcing files and matlab scripts to look |
| 145 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
| 146 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
| 147 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
| 148 |
|
to conform to the common rule. |
| 149 |
|
o check-in the first version of the coupler + interfaces for multi-components |
| 150 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
| 151 |
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- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
| 152 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
| 153 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
| 154 |
|
- exchanges between component and coupler is done in forward_step |
| 155 |
|
o new verification experiment, cpl_aim+ocn: |
| 156 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
| 157 |
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|
| 158 |
|
checkpoint52d_pre |
| 159 |
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o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
| 160 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
| 161 |
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|
| 162 |
|
checkpoint52c_post |
| 163 |
|
o Fixing OPTIONS files for use of exf: |
| 164 |
|
- ALLOW_ECCO not needed |
| 165 |
|
- ECCO_CPPOPTIONS.h should not be included from |
| 166 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
| 167 |
|
as has been the case in the past |
| 168 |
|
- All cal/exf related options are currently set in |
| 169 |
|
single header file. Should remain so until we |
| 170 |
|
agree on a consistent new policy. |
| 171 |
|
o Removed all CPP options for cal package. |
| 172 |
|
cal has no more CPP options. |
| 173 |
|
o modified STOREs in GAD_ADVECTION |
| 174 |
|
o corrected key comp. for passkey |
| 175 |
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|
| 176 |
|
checkpoint52b_post |
| 177 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
| 178 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
| 179 |
|
- modify fluxes but do not change theta directly; |
| 180 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
| 181 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
| 182 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
| 183 |
|
o put back grid & coriolis monitor output. |
| 184 |
|
checkpoint52b_pre |
| 185 |
|
|
| 186 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
| 187 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
| 188 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
| 189 |
|
(need info on NUMBER_OF_PTRACERS) |
| 190 |
|
o missing PTRACERS headers in some routines |
| 191 |
|
o default tamc.h in pkg/autodiff supposed to crash |
| 192 |
|
to ensure proper customization |
| 193 |
|
|
| 194 |
|
checkpoint52a_post |
| 195 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
| 196 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 197 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
| 198 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
| 199 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
| 200 |
|
- keep the old version of FREEZE for backward compatibility; |
| 201 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
| 202 |
|
- corresponding modifs for TAF directives |
| 203 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 204 |
|
o time-averaged output for pkg/ptracers |
| 205 |
|
o fix problem with ECCO-related divided adjoint |
| 206 |
|
snapshot file was missing some ad-variables, |
| 207 |
|
but no warning issued by TAF |
| 208 |
|
|
| 209 |
|
checkpoint52a_pre |
| 210 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
| 211 |
|
|
| 212 |
|
checkpoint52 = ecco_c52_e35 |
| 213 |
|
o after testing adjoints of checkpoint51u_post |
| 214 |
|
|
| 215 |
|
checkpoint51u_post |
| 216 |
|
o this is the post-merge tag of the ecco-branch |
| 217 |
|
(needs another clean checkout and re-testing) |
| 218 |
|
o various natl_box_adjoint configs and results |
| 219 |
|
but no input fields |
| 220 |
|
o obcs adjoint not yet merged! |
| 221 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
| 222 |
|
o updated/extended some store directives for seaice |
| 223 |
|
o pkg/ecco now containes ecco-specific part of cost function |
| 224 |
|
o top level routines the_main_loop, forward_step |
| 225 |
|
supersede those in model/src/ |
| 226 |
|
previous input data.cost now in data.ecco |
| 227 |
|
(new namelist ecco_cost_nml) |
| 228 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
| 229 |
|
|
| 230 |
|
checkpoint51t_post |
| 231 |
|
o this is the pre-merge tag of the ecco-branch |
| 232 |
|
|
| 233 |
|
checkpoint51s_post |
| 234 |
|
o cleanup: removed various obsolete #define-s |
| 235 |
|
o pkg/grdchk |
| 236 |
|
- renamed 'ph-grd 3' to 'grad-res' |
| 237 |
|
- merged from ecco-branch |
| 238 |
|
(remaining bug fixes for obcs gradient checks) |
| 239 |
|
- additional high-precision output for testreport |
| 240 |
|
(grep for 'precision_grdchk_result') |
| 241 |
|
|
| 242 |
|
checkpoint51r_post |
| 243 |
|
o cleaned up or removed CPP_OPTIONS.h files |
| 244 |
|
o updated results for some of the tests to reflect the new |
| 245 |
|
optfiles (-ieee: -O0 instead of -O3) |
| 246 |
|
|
| 247 |
|
checkpoint51q_post |
| 248 |
|
o cd_code: |
| 249 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
| 250 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
| 251 |
|
- separated cd_code part from write_checkpoint |
| 252 |
|
- updated AD_SOURCE, generated .flow |
| 253 |
|
- added CD_CODE_VARS.h to the_main_loop |
| 254 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
| 255 |
|
o ctrl package totally restructured |
| 256 |
|
- pack/unpack now optional and decoupled from |
| 257 |
|
xx_/adxx_ I/O |
| 258 |
|
- ctrl_pack/unpack cleaned |
| 259 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
| 260 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
| 261 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
| 262 |
|
|
| 263 |
|
checkpoint51p_post |
| 264 |
|
o create initial cd_code package |
| 265 |
|
- WARNING: the initialization of fields within packages |
| 266 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
| 267 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
| 268 |
|
This seems to be backwards since |
| 269 |
|
1) its important to initially zero the entire field including |
| 270 |
|
the "halo" region |
| 271 |
|
2) zeroing needs to be done *before* reading pickup info |
| 272 |
|
and the pickup call might or might not happen in any |
| 273 |
|
particular run |
| 274 |
|
- this needs an overhaul for R2 |
| 275 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
| 276 |
|
o cleanup testreport |
| 277 |
|
|
| 278 |
|
checkpoint51o_post |
| 279 |
|
o bringing AD-related verif's up to date with genmake2 |
| 280 |
|
- carbon/ |
| 281 |
|
- global_ocean.90x40x15/ |
| 282 |
|
- hs.94.1x64x5/ |
| 283 |
|
- (front_relax/ ) |
| 284 |
|
o (more) consistent directory structure for AD-related verif.'s |
| 285 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
| 286 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
| 287 |
|
o bug fix in find_alpha.F for MDJWF: |
| 288 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
| 289 |
|
change rho -> rho-rhoConst |
| 290 |
|
- replace call find_rho to find_rhonum |
| 291 |
|
o initialisation of rFlx extended to full array (required by TAF) |
| 292 |
|
and shifted to thermodynamics |
| 293 |
|
o removed PTRACERS.h in ptracers routine |
| 294 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
| 295 |
|
o Correcting initialisations for fVerU, fVerV. |
| 296 |
|
o helping TAF to recognize dependency on kUp for |
| 297 |
|
fVerU, fVerV |
| 298 |
|
o Replacing delZ by delR in pkg/ctrl/ |
| 299 |
|
checkpoint51o_pre |
| 300 |
|
|
| 301 |
|
o undid all of cp51 pending some cleanups and discussion |
| 302 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
| 303 |
|
it for adjoint/tl #defines |
| 304 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
| 305 |
|
o removed tools/genmake since it no longer works |
| 306 |
|
|
| 307 |
|
checkpoint51n_post |
| 308 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
| 309 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 310 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
| 311 |
|
- subroutine FREEZE now limits only surface temperature |
| 312 |
|
(this means new output.txt for global_ocean.90x40x15, |
| 313 |
|
global_ocean.cs32x15, and global_with_exf) |
| 314 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 315 |
|
|
| 316 |
|
checkpoint51n_pre |
| 317 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
| 318 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
| 319 |
|
defines: |
| 320 |
|
- ALLOW_ADJOINT_RUN |
| 321 |
|
- ALLOW_TANGENTLINEAR_RUN |
| 322 |
|
- ALLOW_ECCO_OPTIMIZATION |
| 323 |
|
|
| 324 |
|
checkpoint51m_post |
| 325 |
o incorporating changes to get TAMC/TAF working in genmake2 |
o incorporating changes to get TAMC/TAF working in genmake2 |
| 326 |
- added new TAMC/TAF targets to the Makefile |
- added new TAMC/TAF targets to the Makefile |
| 327 |
- various cleanups related to package handling |
- various cleanups related to package handling |
| 328 |
|
- these changes should have no impact on the forward model |
| 329 |
|
|
| 330 |
checkpoint51l_post |
checkpoint51l_post |
| 331 |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
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