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 undid all of cp51 pending some cleanups and discussion |
7 |
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8 |
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checkpoint51n_post |
9 |
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o modifications to make FREEZE flux visible to pkg/kpp |
10 |
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- moved surfaceTendencyTice from pkg/seaice to main code |
11 |
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- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
12 |
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- subroutine FREEZE now limits only surface temperature |
13 |
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(this means new output.txt for global_ocean.90x40x15, |
14 |
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global_ocean.cs32x15, and global_with_exf) |
15 |
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o added surface flux output variables to TIMEAVE_STATVARS |
16 |
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17 |
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checkpoint51n_pre |
18 |
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o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
19 |
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o added [#include "AD_CONFIG.h"] to all files that use the following |
20 |
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defines: |
21 |
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- ALLOW_ADJOINT_RUN |
22 |
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- ALLOW_TANGENTLINEAR_RUN |
23 |
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- ALLOW_ECCO_OPTIMIZATION |
24 |
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|
25 |
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checkpoint51m_post |
26 |
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o incorporating changes to get TAMC/TAF working in genmake2 |
27 |
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- added new TAMC/TAF targets to the Makefile |
28 |
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- various cleanups related to package handling |
29 |
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- these changes should have no impact on the forward model |
30 |
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|
31 |
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checkpoint51l_post |
32 |
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o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
33 |
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- faster algorithm for cal_addtime.F |
34 |
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- higher precision arithmetic, where needed |
35 |
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- pkg/exf *startdate variables changed from calendar date to |
36 |
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model integration time |
37 |
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|
38 |
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checkpoint51l_pre |
39 |
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o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
40 |
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o enable to apply restoring on S & T only in a latitude band. |
41 |
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o update output (external_forcing_surf modif. change truncation errors) |
42 |
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global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
43 |
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|
44 |
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checkpoint51k_post |
45 |
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o change default to: useNHMTerms=.FALSE. |
46 |
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- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
47 |
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adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
48 |
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- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
49 |
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exp1, ideal_2D_oce |
50 |
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- change data file of oceanic exp (leave the results unchanged for now) |
51 |
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exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
52 |
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o set gravitySign automatically according to the vertical coordinate used |
53 |
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(and change sign: back to "logical" value: +1 when R increases downward) |
54 |
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o added an include barrier to the default CPP_OPTIONS.h and |
55 |
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removed the #include "PACKAGES_CONFIG.h" from it |
56 |
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o fix a bug in mom_fluxform (from chk51j_post) |
57 |
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|
58 |
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checkpoint51j_post |
59 |
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o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
60 |
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o adjusted some flow directives (dynamics, thermodynamics) |
61 |
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o added cubed-sphere case to test cost function |
62 |
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o heckpoint_lev?_directives.h now include |
63 |
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pkg-specific directives, whenever those are enabled. |
64 |
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o Moving pkg-specific flow directives to corresponding pkg |
65 |
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Moving pkg-specific differentiation list to corresponding pkg |
66 |
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Moving pkg-specific checkpoint-lev storing to corresponding pkg |
67 |
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---> conventions are |
68 |
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- pkg_ad.flow |
69 |
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- pkg_ad_diff.list |
70 |
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- pkg_ad_check_lev?_dir.h |
71 |
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72 |
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checkpoint51i_post |
73 |
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o merge of the branch-genmake2 |
74 |
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- knowingly breaks the older genmake |
75 |
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- automatic generation of all ALLOW_${PKG_NAME} defines |
76 |
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- new testreport supersedes older testscript |
77 |
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o large number of package inclusion and header cleanups |
78 |
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checkpoint51i_pre |
79 |
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|
80 |
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o new output for adjoin of global ocean vector invariant |
81 |
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o fix for checkpoint of thermodynamic seaice and bulk_force |
82 |
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o Steph gchem various cleanups |
83 |
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|
84 |
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checkpoint 51h_pre |
85 |
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o fixed some single quotes |
86 |
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o modify gchem pkg to be more versatile |
87 |
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o modifications to clean up dic pkg |
88 |
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o add pkg/cfc |
89 |
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|
90 |
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checkpoint51g_post |
91 |
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o provide links for ARPACK and ADM*TLM |
92 |
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o start removing verification/vero/ |
93 |
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o update AD-related stuff |
94 |
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(in particular some IF-statements in model/src/ routines) |
95 |
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o adding to verification/global_ocean.90x40x15/ adjoint of |
96 |
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vector invariant setup |
97 |
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|
98 |
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checkpoint51f_post |
99 |
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o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
100 |
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o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
101 |
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of tracer Green's fucntions for ocean inversion project. |
102 |
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|
103 |
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checkpoint51f_pre |
104 |
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o Added on-the-fly spatial interpolation capability |
105 |
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"USE_EXF_INTERPOLATION" to pkg/exf. |
106 |
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- This is a temporary Cartesian-grid hack until |
107 |
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the super-duper ESMF coupler becomes available. |
108 |
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- See verification/global_with_exf/README for usage example. |
109 |
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- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
110 |
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flags and modified pkg/seaice accordingly. |
111 |
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o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
112 |
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and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
113 |
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non-local transport term. |
114 |
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|
115 |
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checkpoint51e_post |
116 |
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o pkg/mom_vecinv: |
117 |
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- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
118 |
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- add time-ave diagnostic of vorticity advection. |
119 |
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o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
120 |
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o atmospheric geopotential: - include water vapor effect; |
121 |
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- use p^kappa in p* scaling. |
122 |
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o land pkg: read initial state from files. |
123 |
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o AIM : add stratospheric drag in the upper level |
124 |
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|
125 |
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checkpoint51d_post |
126 |
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o change function ILNBLNK (=> last non-blank char.) to return zero |
127 |
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(instead of the string length) when the string. char is empty |
128 |
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o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
129 |
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o modif's to restore TAMC compatibility |
130 |
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- avoid "_d" constructs in PARAMETER declarations |
131 |
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- avoid interrupting lines by comment lines |
132 |
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o Use cluster local disks for purely local I/O |
133 |
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vs. globally visible disks needed for ctrl stuff |
134 |
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(merged from ecco-branch) |
135 |
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- new active_file_loc... and mdsio_..._loc routines |
136 |
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- affected packages: autodiff, ctrl, grdchk, mdsio |
137 |
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138 |
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checkpoint51c_post |
139 |
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o introducing integer flag debugLevel |
140 |
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- debLevZero: suppress all output |
141 |
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- debLevA: standard |
142 |
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- debLevB: equivalent to current debugMode=.TRUE. |
143 |
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o introducing pathname variable mdsioLocalDir for mdsio |
144 |
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that can be specified at runtime |
145 |
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(relevant for cluster I/O to local disk) |
146 |
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` |
147 |
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>>>checkpoint51b_post |
148 |
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adjoint of ptracers |
149 |
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o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
150 |
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o extended state in checkpoint_lev?, etc. |
151 |
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o alternative ctrl/cost with tr1 or ptracer |
152 |
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o new comlev1_bibj_ptracers |
153 |
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o new ptracers.flow |
154 |
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o made ptracers_forcing same as external_forcing_s |
155 |
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o added verification for adjoint with ptracers |
156 |
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- adm. grdchk fail so far |
157 |
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- tlm. grdchk OK |
158 |
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- checked tapelev/comlev recomputations: OK |
159 |
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<<<checkpoint51b_pre |
160 |
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161 |
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checkpoint51a_post |
162 |
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o added code for biogeochemistry package |
163 |
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- new pkgs: dic, gchem |
164 |
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- new subroutine in ptracers |
165 |
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o modify code for biogeo packages |
166 |
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- in model/src and pkg/ptracers |
167 |
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|
168 |
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checkpoint51 |
169 |
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o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
170 |
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- autodiff, ctrl, exf, grdchk, seaice |
171 |
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kept separate packages |
172 |
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- cost, ecco, obcs |
173 |
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o updating verification/internal_wave, verification/lab_sea |
174 |
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(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
175 |
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|
176 |
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checkpoint50i_post |
177 |
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o Preparing next differentiable checkpoint and sync |
178 |
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of MAIN vs. ecco-branch |
179 |
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- 1st step: this one is differentiable |
180 |
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- 2nd step: next(! not this) checkpoint will have updated packages |
181 |
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from ecco-branch) |
182 |
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183 |
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checkpoint50h_post |
184 |
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o new package "land": provide surface BC for AIM. |
185 |
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o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
186 |
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o AIM: use true log-P extrapolation for near surface temp (= as in |
187 |
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F.Molteni paper) ; update aim.5l_cs output. |
188 |
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o New variable in PARM03 for more flexible pickups |
189 |
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o somewhat cleaned package initialisation sequence for |
190 |
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ctrl/ cost/ ecco/ in packages_... routines |
191 |
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192 |
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checkpoint50g_post |
193 |
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o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
194 |
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- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
195 |
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- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
196 |
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made the default because of faster convergence than ADI |
197 |
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|
198 |
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checkpoint50f_post |
199 |
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o exf totally restructured |
200 |
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- replaced all exf_set_ routines by one generic exf_set_gen.F |
201 |
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and made sure it's still differentiable |
202 |
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- split exf_getffields.F into new exf_bulkformulae.F |
203 |
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- exf_inscal_/exf_outscal_ suffixes consistent with field names |
204 |
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- updated adjoint/makefile and relevant verif. accordingly |
205 |
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|
206 |
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checkpoint50f_pre |
207 |
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o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
208 |
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+ change Evap over land. (update aim.5l_cs output) |
209 |
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o added missing .cvsignores and made uniform across expts |
210 |
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o changed configuration of tidal_basin_2d expt |
211 |
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o added pkg/debug functions for tracing code in fatal crashes |
212 |
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o tidied pkg/monitor to use MONITOR_OPTIONS.h |
213 |
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o new fn in pkg/monitor to stop model if solution grows too big |
214 |
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o removed lots of single quotes from comments |
215 |
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|
216 |
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checkpoint50e_post |
217 |
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o make KPP work with PTRACERS |
218 |
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- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
219 |
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nearly a copy of kpp_transport_s |
220 |
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- there is no analogue to SurfaceTendencyS, so I have to use |
221 |
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gPtr(of the surface layer) instead |
222 |
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o add a new platform SunFire+mpi (SunFire 15000) to genmake |
223 |
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checkpoint50e_pre |
224 |
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|
225 |
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checkpoint50d_post |
226 |
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o change kpp output from multiple-record state files to single-record state |
227 |
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files analogous to write_state.F |
228 |
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o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
229 |
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analogous to the cg2d-related output. |
230 |
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o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
231 |
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so that writing to internal file fn (with length 512) fails. |
232 |
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checkpoint50d_pre |
233 |
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|
234 |
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checkpoint50c_post |
235 |
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o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
236 |
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o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
237 |
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o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
238 |
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o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
239 |
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o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
240 |
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|
241 |
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checkpoint50c_pre |
242 |
|
Merging from release1_p13: |
243 |
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o bug fix for pkg/seaice dynamic solver |
244 |
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o Added SEAICE_initialHEFF to pkg/seaice |
245 |
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|
246 |
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checkpoint50b_post |
247 |
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o store u*,v* in gU,V instead of in guNm1,gvNm1 |
248 |
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o in order to put the momForcing out of the Adams-Bashforth: |
249 |
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move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
250 |
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to timestep.F |
251 |
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o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
252 |
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o re-generate output for highly sensitive test-exp: |
253 |
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global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
254 |
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|
255 |
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checkpoint50b_pre |
256 |
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o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
257 |
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o corrected CPP option mismatch in exf_Bulk... functions for case |
258 |
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#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
259 |
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|
260 |
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checkpoint50a_post |
261 |
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o Bug fix for merging between c50 and KPP. |
262 |
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ikey was passed from thermodynamics to kpp_calc via |
263 |
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common block rather than being recomputed in kpp_calc, |
264 |
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in contradiction with new key itdkey. |
265 |
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New key ikppkey created, and tamc.h headers updated. |
266 |
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|
267 |
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checkpoint50 |
268 |
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- 2nd step of merge with ecco-branch: |
269 |
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merge changes in ecco-branch back into main trunk |
270 |
|
- bug fix in find_alpha |
271 |
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- more storing in gmredi_calc_tensor.F, kpp_routines.F |
272 |
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- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
273 |
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- merged some sliced AD support routines |
274 |
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|
275 |
|
checkpoint49 |
276 |
|
merged from ecco-branch: |
277 |
|
o exf: |
278 |
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- Enable initialisation of forcing fields to constant |
279 |
|
(runtime) values. |
280 |
|
- in exf_getffields.F |
281 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
282 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
283 |
|
with bulf formulae. |
284 |
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- exf_init.F modify #ifdef for exf_init_evap |
285 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
286 |
|
The following INT-usages are not safe: |
287 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
288 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
289 |
|
and were modified. |
290 |
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o autodiff: checkpoint_lev... |
291 |
|
- updated storing for bulk formulae (some arrays were missing) |
292 |
|
- added state for seaice package |
293 |
|
- synchronized with main branch |
294 |
|
o DIVA: |
295 |
|
Modif.s in |
296 |
|
- the_main_loop.F |
297 |
|
- the_model_main.F |
298 |
|
and added cost_final_restore.F cost_final_store.F |
299 |
|
o With these changes, it is possible to fully separate |
300 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
301 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
302 |
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into separate model executions. |
303 |
|
This enables better tuning of DIVA to given queue sizes. |
304 |
|
o Loss of cost function value in consecutive DIVA runs is |
305 |
|
fixed by storing to 'costfinal' file. |
306 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
307 |
|
beginning/end of adjoint integration is accounted for. |
308 |
|
The current changes apply to TAF-1.4.26. |
309 |
|
TAF has one remaining bug, requiring one manual change |
310 |
|
(see MITgcm manual). |
311 |
|
o cal: synchronized between MAIN and ecco-branch |
312 |
|
|
313 |
|
checkpoint48i_post |
314 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
315 |
|
(mostly adding new routines to make list and replacing |
316 |
|
pressure by totPhiHyd). |
317 |
|
o Updated and merged grdchk package |
318 |
|
- has both ADM and TLM checks |
319 |
|
- works for single- and multi-proc. |
320 |
|
- output cleaned |
321 |
|
- worked successfully for parallel DIVA |
322 |
|
o genmake: |
323 |
|
- Adding -platform=SP4 |
324 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
325 |
|
o Modif. for DIVA: |
326 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
327 |
|
(similar thing would apply for active files such as |
328 |
|
tbar, sbar, psbar, which should not be reinitialised; |
329 |
|
only relevant for ecco-branch) |
330 |
|
|
331 |
|
checkpoint48h_post |
332 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
333 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
334 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
335 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
336 |
|
|
337 |
|
checkpoint48g_post |
338 |
|
--- EOS: |
339 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
340 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
341 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
342 |
|
--- Pressure/geopotential gradient: |
343 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
344 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
345 |
|
( changes results of global_ocean_pressure ) |
346 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
347 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
348 |
|
( changes results of ideal_2D_oce ) |
349 |
|
o includes r* 2nd term in potential gradient. |
350 |
|
|
351 |
checkpoint48f_post |
checkpoint48f_post |
352 |
Merging from release1_p12: |
Merging from release1_p12: |
353 |
o Modifications for using pkg/exf with pkg/seaice |
o Modifications for using pkg/exf with pkg/seaice |