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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 change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
7 |
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o changes to permit hi-res, cubed-sphere, configuration |
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- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
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- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
10 |
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- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
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of surface winds for the cube |
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(A verification experiment, based on global_ocean.cs32x15, but with |
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pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
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Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
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complete with example surface forcing files and matlab scripts to look |
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at the output and compare it with that of global_ocean.cs32x15.) |
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o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
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but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
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to conform to the common rule. |
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o check-in the first version of the coupler + interfaces for multi-components |
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set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
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- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
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- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
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- ocean and atmos. share the same horizontal grid (no interpolation). |
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- exchanges between component and coupler is done in forward_step |
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o new verification experiment, cpl_aim+ocn: |
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coupled ocean - AIM atmosphere on cs32 grid. |
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checkpoint52d_pre |
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o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
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o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
32 |
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checkpoint52c_post |
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o Fixing OPTIONS files for use of exf: |
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- ALLOW_ECCO not needed |
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- ECCO_CPPOPTIONS.h should not be included from |
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EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
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as has been the case in the past |
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- All cal/exf related options are currently set in |
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single header file. Should remain so until we |
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agree on a consistent new policy. |
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o Removed all CPP options for cal package. |
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cal has no more CPP options. |
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o modified STOREs in GAD_ADVECTION |
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o corrected key comp. for passkey |
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checkpoint52b_post |
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o new version: "thsice" of thermodynamic sea-ice pkg: |
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- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
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- modify fluxes but do not change theta directly; |
51 |
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- light cleaning of bulk_force pkg (still needed with thsice). |
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- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
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+ output_thsice.txt to test thsice & bulk_force pkgs. |
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o put back grid & coriolis monitor output. |
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checkpoint52b_pre |
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o call "do_the_model_io" at the beginning (=> dump initial state) |
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o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
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o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
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(need info on NUMBER_OF_PTRACERS) |
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o missing PTRACERS headers in some routines |
62 |
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o default tamc.h in pkg/autodiff supposed to crash |
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to ensure proper customization |
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checkpoint52a_post |
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o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
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- moved surfaceTendencyTice from pkg/seaice to main code |
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- subroutine FREEZE_SURFACE now limits only surface temperature |
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and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
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=> new output.txt for global_ocean.cs32x15 & global_with_exf |
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- keep the old version of FREEZE for backward compatibility; |
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global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
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- corresponding modifs for TAF directives |
74 |
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o added surface flux output variables to TIMEAVE_STATVARS |
75 |
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o time-averaged output for pkg/ptracers |
76 |
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o fix problem with ECCO-related divided adjoint |
77 |
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snapshot file was missing some ad-variables, |
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but no warning issued by TAF |
79 |
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|
80 |
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checkpoint52a_pre |
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o some bug fixes for #undef REAL4_IS_SLOW |
82 |
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checkpoint52 = ecco_c52_e35 |
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o after testing adjoints of checkpoint51u_post |
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checkpoint51u_post |
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o this is the post-merge tag of the ecco-branch |
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(needs another clean checkout and re-testing) |
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o various natl_box_adjoint configs and results |
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but no input fields |
91 |
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o obcs adjoint not yet merged! |
92 |
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o adding ECCO global 1x1 and 2x2 degree configs |
93 |
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o updated/extended some store directives for seaice |
94 |
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o pkg/ecco now containes ecco-specific part of cost function |
95 |
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o top level routines the_main_loop, forward_step |
96 |
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supersede those in model/src/ |
97 |
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previous input data.cost now in data.ecco |
98 |
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(new namelist ecco_cost_nml) |
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o in ctrl/ cleaned some cross-dependencies and updated CPP options |
100 |
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101 |
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checkpoint51t_post |
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o this is the pre-merge tag of the ecco-branch |
103 |
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104 |
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checkpoint51s_post |
105 |
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o cleanup: removed various obsolete #define-s |
106 |
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o pkg/grdchk |
107 |
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- renamed 'ph-grd 3' to 'grad-res' |
108 |
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- merged from ecco-branch |
109 |
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(remaining bug fixes for obcs gradient checks) |
110 |
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- additional high-precision output for testreport |
111 |
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(grep for 'precision_grdchk_result') |
112 |
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|
113 |
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checkpoint51r_post |
114 |
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o cleaned up or removed CPP_OPTIONS.h files |
115 |
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o updated results for some of the tests to reflect the new |
116 |
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optfiles (-ieee: -O0 instead of -O3) |
117 |
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|
118 |
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checkpoint51q_post |
119 |
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o cd_code: |
120 |
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- moved cd_scheme.F -> cd_code_scheme.F |
121 |
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- separate read_checkpoint from cd_code_ini_vars.F |
122 |
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- separated cd_code part from write_checkpoint |
123 |
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- updated AD_SOURCE, generated .flow |
124 |
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- added CD_CODE_VARS.h to the_main_loop |
125 |
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- Moving cd_code specific store dir.s to pkg/cd_code |
126 |
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o ctrl package totally restructured |
127 |
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- pack/unpack now optional and decoupled from |
128 |
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xx_/adxx_ I/O |
129 |
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- ctrl_pack/unpack cleaned |
130 |
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(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
131 |
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- confined inclusion of AD_CONFIG.h to where necessary. |
132 |
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o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
133 |
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134 |
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checkpoint51p_post |
135 |
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o create initial cd_code package |
136 |
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- WARNING: the initialization of fields within packages |
137 |
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is broken because INI_FIELDS (where READ_CHECKPOINT is |
138 |
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called) is called *before* PACKAGES_INIT_VARIABLES. |
139 |
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This seems to be backwards since |
140 |
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1) its important to initially zero the entire field including |
141 |
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the "halo" region |
142 |
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2) zeroing needs to be done *before* reading pickup info |
143 |
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and the pickup call might or might not happen in any |
144 |
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particular run |
145 |
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- this needs an overhaul for R2 |
146 |
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o cleanup verification/*/code/GMREDI_OPTIONS.h |
147 |
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o cleanup testreport |
148 |
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|
149 |
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checkpoint51o_post |
150 |
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o bringing AD-related verif's up to date with genmake2 |
151 |
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- carbon/ |
152 |
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- global_ocean.90x40x15/ |
153 |
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- hs.94.1x64x5/ |
154 |
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- (front_relax/ ) |
155 |
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o (more) consistent directory structure for AD-related verif.'s |
156 |
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o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
157 |
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o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
158 |
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o bug fix in find_alpha.F for MDJWF: |
159 |
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- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
160 |
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change rho -> rho-rhoConst |
161 |
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- replace call find_rho to find_rhonum |
162 |
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o initialisation of rFlx extended to full array (required by TAF) |
163 |
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and shifted to thermodynamics |
164 |
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o removed PTRACERS.h in ptracers routine |
165 |
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o added surfacetendencyPtr to S/R parameter list pracers_forcing |
166 |
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o Correcting initialisations for fVerU, fVerV. |
167 |
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o helping TAF to recognize dependency on kUp for |
168 |
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fVerU, fVerV |
169 |
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o Replacing delZ by delR in pkg/ctrl/ |
170 |
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checkpoint51o_pre |
171 |
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|
172 |
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o undid all of cp51 pending some cleanups and discussion |
173 |
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o added the [#include "AD_CONFIG.h"] statement to all files that need |
174 |
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it for adjoint/tl #defines |
175 |
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o re-worked the build logic in genmake2 to support AD_CONFIG.h |
176 |
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o removed tools/genmake since it no longer works |
177 |
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|
178 |
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checkpoint51n_post |
179 |
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o modifications to make FREEZE flux visible to pkg/kpp |
180 |
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- moved surfaceTendencyTice from pkg/seaice to main code |
181 |
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- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
182 |
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- subroutine FREEZE now limits only surface temperature |
183 |
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(this means new output.txt for global_ocean.90x40x15, |
184 |
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global_ocean.cs32x15, and global_with_exf) |
185 |
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o added surface flux output variables to TIMEAVE_STATVARS |
186 |
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|
187 |
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checkpoint51n_pre |
188 |
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o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
189 |
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o added [#include "AD_CONFIG.h"] to all files that use the following |
190 |
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defines: |
191 |
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- ALLOW_ADJOINT_RUN |
192 |
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- ALLOW_TANGENTLINEAR_RUN |
193 |
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- ALLOW_ECCO_OPTIMIZATION |
194 |
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|
195 |
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checkpoint51m_post |
196 |
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o incorporating changes to get TAMC/TAF working in genmake2 |
197 |
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- added new TAMC/TAF targets to the Makefile |
198 |
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- various cleanups related to package handling |
199 |
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- these changes should have no impact on the forward model |
200 |
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|
201 |
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checkpoint51l_post |
202 |
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o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
203 |
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- faster algorithm for cal_addtime.F |
204 |
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- higher precision arithmetic, where needed |
205 |
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- pkg/exf *startdate variables changed from calendar date to |
206 |
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model integration time |
207 |
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|
208 |
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checkpoint51l_pre |
209 |
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o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
210 |
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o enable to apply restoring on S & T only in a latitude band. |
211 |
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o update output (external_forcing_surf modif. change truncation errors) |
212 |
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global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
213 |
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|
214 |
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checkpoint51k_post |
215 |
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o change default to: useNHMTerms=.FALSE. |
216 |
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- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
217 |
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adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
218 |
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- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
219 |
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exp1, ideal_2D_oce |
220 |
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- change data file of oceanic exp (leave the results unchanged for now) |
221 |
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exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
222 |
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o set gravitySign automatically according to the vertical coordinate used |
223 |
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(and change sign: back to "logical" value: +1 when R increases downward) |
224 |
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o added an include barrier to the default CPP_OPTIONS.h and |
225 |
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removed the #include "PACKAGES_CONFIG.h" from it |
226 |
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o fix a bug in mom_fluxform (from chk51j_post) |
227 |
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|
228 |
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checkpoint51j_post |
229 |
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o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
230 |
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o adjusted some flow directives (dynamics, thermodynamics) |
231 |
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o added cubed-sphere case to test cost function |
232 |
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o heckpoint_lev?_directives.h now include |
233 |
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pkg-specific directives, whenever those are enabled. |
234 |
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o Moving pkg-specific flow directives to corresponding pkg |
235 |
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Moving pkg-specific differentiation list to corresponding pkg |
236 |
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Moving pkg-specific checkpoint-lev storing to corresponding pkg |
237 |
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---> conventions are |
238 |
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- pkg_ad.flow |
239 |
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- pkg_ad_diff.list |
240 |
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- pkg_ad_check_lev?_dir.h |
241 |
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|
242 |
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checkpoint51i_post |
243 |
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o merge of the branch-genmake2 |
244 |
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- knowingly breaks the older genmake |
245 |
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- automatic generation of all ALLOW_${PKG_NAME} defines |
246 |
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- new testreport supersedes older testscript |
247 |
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o large number of package inclusion and header cleanups |
248 |
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checkpoint51i_pre |
249 |
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|
250 |
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o new output for adjoin of global ocean vector invariant |
251 |
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o fix for checkpoint of thermodynamic seaice and bulk_force |
252 |
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o Steph gchem various cleanups |
253 |
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|
254 |
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checkpoint 51h_pre |
255 |
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o fixed some single quotes |
256 |
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o modify gchem pkg to be more versatile |
257 |
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o modifications to clean up dic pkg |
258 |
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o add pkg/cfc |
259 |
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|
260 |
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checkpoint51g_post |
261 |
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o provide links for ARPACK and ADM*TLM |
262 |
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o start removing verification/vero/ |
263 |
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o update AD-related stuff |
264 |
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(in particular some IF-statements in model/src/ routines) |
265 |
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o adding to verification/global_ocean.90x40x15/ adjoint of |
266 |
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vector invariant setup |
267 |
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|
268 |
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checkpoint51f_post |
269 |
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o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
270 |
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o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
271 |
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of tracer Green's fucntions for ocean inversion project. |
272 |
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|
273 |
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checkpoint51f_pre |
274 |
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o Added on-the-fly spatial interpolation capability |
275 |
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"USE_EXF_INTERPOLATION" to pkg/exf. |
276 |
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- This is a temporary Cartesian-grid hack until |
277 |
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the super-duper ESMF coupler becomes available. |
278 |
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- See verification/global_with_exf/README for usage example. |
279 |
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- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
280 |
|
flags and modified pkg/seaice accordingly. |
281 |
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o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
282 |
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and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
283 |
|
non-local transport term. |
284 |
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|
285 |
|
checkpoint51e_post |
286 |
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o pkg/mom_vecinv: |
287 |
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- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
288 |
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- add time-ave diagnostic of vorticity advection. |
289 |
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o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
290 |
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o atmospheric geopotential: - include water vapor effect; |
291 |
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- use p^kappa in p* scaling. |
292 |
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o land pkg: read initial state from files. |
293 |
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o AIM : add stratospheric drag in the upper level |
294 |
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|
295 |
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checkpoint51d_post |
296 |
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o change function ILNBLNK (=> last non-blank char.) to return zero |
297 |
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(instead of the string length) when the string. char is empty |
298 |
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o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
299 |
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o modif's to restore TAMC compatibility |
300 |
|
- avoid "_d" constructs in PARAMETER declarations |
301 |
|
- avoid interrupting lines by comment lines |
302 |
|
o Use cluster local disks for purely local I/O |
303 |
|
vs. globally visible disks needed for ctrl stuff |
304 |
|
(merged from ecco-branch) |
305 |
|
- new active_file_loc... and mdsio_..._loc routines |
306 |
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- affected packages: autodiff, ctrl, grdchk, mdsio |
307 |
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|
308 |
|
checkpoint51c_post |
309 |
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o introducing integer flag debugLevel |
310 |
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- debLevZero: suppress all output |
311 |
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- debLevA: standard |
312 |
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- debLevB: equivalent to current debugMode=.TRUE. |
313 |
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o introducing pathname variable mdsioLocalDir for mdsio |
314 |
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that can be specified at runtime |
315 |
|
(relevant for cluster I/O to local disk) |
316 |
|
` |
317 |
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>>>checkpoint51b_post |
318 |
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adjoint of ptracers |
319 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
320 |
|
o extended state in checkpoint_lev?, etc. |
321 |
|
o alternative ctrl/cost with tr1 or ptracer |
322 |
|
o new comlev1_bibj_ptracers |
323 |
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o new ptracers.flow |
324 |
|
o made ptracers_forcing same as external_forcing_s |
325 |
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o added verification for adjoint with ptracers |
326 |
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- adm. grdchk fail so far |
327 |
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- tlm. grdchk OK |
328 |
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- checked tapelev/comlev recomputations: OK |
329 |
|
<<<checkpoint51b_pre |
330 |
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|
331 |
checkpoint51a_post |
checkpoint51a_post |
332 |
o added code for biogeochemistry package |
o added code for biogeochemistry package |
333 |
- new pkgs: dic, gchem |
- new pkgs: dic, gchem |