3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
4 |
============================== |
============================== |
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|
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o OBCS: extend application of tracer open boundary conditions |
7 |
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to a strip beyond the boundary of width Olx/Oly |
8 |
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|
9 |
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checkpoint56c_post |
10 |
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o OBCS as control variables |
11 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
12 |
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- remove balance of obcs controls from default |
13 |
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- fix index bug nobcs in ctrl_init |
14 |
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- fix dummy fields filen in ctrl_pack |
15 |
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- add dummy weights for obcs |
16 |
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o lsopt: comment out fort.94 output |
17 |
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o optim: |
18 |
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- remove unnecessary header files |
19 |
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- adjusted namelists |
20 |
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- add xerbla.F to Makefile |
21 |
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o exf: |
22 |
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- multiple modifications of exf_check_range |
23 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
24 |
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o mdsio: |
25 |
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- i/o-vector change debugLevel from debLevA to debLevB |
26 |
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|
27 |
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checkpoint56b_post |
28 |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
29 |
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is called from DO_THE_MODEL_IO |
30 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
31 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
32 |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
33 |
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o add another verification experiment that tests both the cfc-pkg and |
34 |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
35 |
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reactive tendencies treated inline with regular timestepping |
36 |
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o testreport previously did a lousy job of comparing small numbers, so |
37 |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
38 |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
39 |
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testreport. |
40 |
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o ptracers_monitor: bug fix for MPI |
41 |
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|
42 |
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checkpoint56a_post |
43 |
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o GCHEM: finish reorganizating the package |
44 |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
45 |
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(introduces another 3D-array for each passive tracer, but only if |
46 |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
47 |
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gchemTendency is not needed because the timestep is done separately) |
48 |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
49 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
50 |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
51 |
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so clear to me how that should be done in a general way. |
52 |
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o CFC: improve formatting of output in CFC_ATMOS |
53 |
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o PTRACERS: |
54 |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
55 |
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that ALL experiments with ptracers enable can be checked. This makes |
56 |
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GCHEM_MONITOR obsolete. |
57 |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
58 |
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monitorFreq |
59 |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
60 |
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o add PTRACERS (PTR0[1-5]) to testreport output |
61 |
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o exf_check_range: |
62 |
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* default changed to .TRUE. |
63 |
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* will check values for niter0 if debLevA, every timestep if debLevB |
64 |
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* STOP in exf_check_range if 'out of range' |
65 |
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* range chosen generous to allow for potential extema |
66 |
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TBD: a version with stricter range |
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permitted range would be runtime parameters |
68 |
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o GMredi: |
69 |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
70 |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
71 |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
72 |
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o GCHEM: |
73 |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
74 |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
75 |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
76 |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
77 |
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this flag is now only visible within GCHEM-pkg routines. |
78 |
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- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
79 |
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be replaced by a 3D array that is computed before thermodynamics; for |
80 |
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this, the tracer ID iTracer had to be included into the parameter list |
81 |
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of ptracers_forcing |
82 |
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- set up forward_step to call gchem_forcing, that will replace |
83 |
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gchem_forcing_int in ptracers_forcing |
84 |
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- cleaning up |
85 |
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o small cleaning of exch2: remove files that are also in eesupp/src |
86 |
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|
87 |
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checkpoint56 |
88 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
89 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
90 |
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o ECCO-GODAE |
91 |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
92 |
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* fully merged and updated from SIO code |
93 |
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windstress sign change affects |
94 |
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- exf_inscal_[u/v]stress |
95 |
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- sign of xx_tau[u/v] adjustments |
96 |
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- signs in cost_scat |
97 |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
98 |
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* natl_box_adjoint updated and compressed |
99 |
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* 2-level checkpoint switch added |
100 |
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(tested in EXP. 1 of natl_box_adjoint) |
101 |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
102 |
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o SVD |
103 |
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* first complete, non-hacked version for SVD calculations |
104 |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
105 |
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performed via direct access files admtlm_vector.it???? |
106 |
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(via ctrl_[un]pack) |
107 |
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* optimcycle is used for ARPACK iteration counter |
108 |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
109 |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
110 |
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and add linear transforms where necessary |
111 |
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* controls are initial/final SST, SSS (can be extended; need to check |
112 |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
113 |
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o mdsio: filename info to both stderr, stdout |
114 |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
115 |
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from sign change |
116 |
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|
117 |
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checkpoint55j_post |
118 |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
119 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
120 |
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o add consistent build directories and .cvsignore files to verification |
121 |
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o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
122 |
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o make all subroutines 30 or less characters in length for certain older |
123 |
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compilers to work (a thorough search only turns up two routines in |
124 |
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pkg/ptracers) |
125 |
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o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
126 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
127 |
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|
128 |
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checkpoint55i_post |
129 |
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o change arrays for total vertical diffusivity (2.D if explicit, |
130 |
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3.D if implicit) ; each ptracer uses its own background value. |
131 |
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o added mnc/NetCDF output capability to ocn_compon_interf |
132 |
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- added bits to verification/cpl_aim+ocn so that it can run on |
133 |
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ITRDA and other clusters without the mpirun "-wd" option |
134 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
135 |
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configuration |
136 |
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o give MNC the ability to create additional files rather than |
137 |
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exceeding a specified file size limit "MNC_MAX_FILESIZE" |
138 |
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- the default is just less than 2GB which is a practical limit |
139 |
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on many systems |
140 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
141 |
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or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
142 |
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|
143 |
|
checkpoint55h_post |
144 |
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o add verification test "vermix" |
145 |
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o remove all the *_ioinc flags and replace with the single global |
146 |
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outputTypesInclusive flag |
147 |
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o allow to set a vertical profile of vertical diffusivity for T & S |
148 |
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o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
149 |
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o useMNC moved from data.mnc to data.pkg |
150 |
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|
151 |
|
checkpoint55g_post |
152 |
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o Renaming carbon AD experiments to comply with testreport conventions |
153 |
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o Updating adjoint of Held-Suarez hs94.1x64x5 |
154 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
155 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
156 |
|
Works well for global_ocean.90x40x15, |
157 |
|
but recomp. issue remains for carbon |
158 |
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o Updating adjoint output for natl_box_adjoint after |
159 |
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pkg/ecco has been modified (see taga c55d_post) |
160 |
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|
161 |
|
checkpoint55f_post |
162 |
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o rename to timeave_init_fixed |
163 |
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|
164 |
|
checkpoint55e_post |
165 |
|
o some delicate re-shuffle of store directives to avoid one |
166 |
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extra call of do_oceanic_physics |
167 |
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affects ecco_the_main_loop.F, do_oceanic_physics.F |
168 |
|
checkpoint_lev1_directives.h |
169 |
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o NB: this may break global_ocean adjoint temporarily, |
170 |
|
but it is clear how to fix it. Will do later, need this now. |
171 |
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|
172 |
|
checkpoint55d_post |
173 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
174 |
|
o ecco_cost_weights is modified to 1x1 runs |
175 |
|
o modifs to allow observations to be read in as |
176 |
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single file or yearly files |
177 |
|
o enable to read exf forcing fields as either |
178 |
|
single file or yearly files (flag useExfYearlyFields) |
179 |
|
checkpoint55d_pre |
180 |
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|
181 |
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o switch between 2-level and 3-level checkpointing |
182 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
183 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
184 |
|
with the correct (that is, the complete multi-dimensional) set of |
185 |
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array indicies |
186 |
|
- used in mom_vecinv() to write the diagFreq output |
187 |
|
- tested (demonstrated) in verification/aim.5l_cs |
188 |
|
o further mnc-ification |
189 |
|
- add verification/lab_sea to the list with mnc setups |
190 |
|
- fix undefined mnc v-names in cd_code |
191 |
|
- add kpp to mnc output (both snapshot and timeave) |
192 |
|
o non-hydrostatic code |
193 |
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- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
194 |
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in calc_gw.F |
195 |
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- defaults to viscAh |
196 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
197 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
198 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
199 |
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o pkg/cost |
200 |
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extend simple cost functions to treat time mean quantities |
201 |
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(T,U,V) via cost_accumulate_state from cost_tile |
202 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
203 |
|
be 2 times larger than the minimum size the advection scheme requires. |
204 |
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now get a perfect conservation of salt in advect_cs test-exp (updated) |
205 |
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o GGL90 (Gaspar's TKE mixed layer) |
206 |
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- add horizontal diffusion of TKE, requires exchanges in |
207 |
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do_fields_blocking_exchanges, horizontal diffusivity is zero by |
208 |
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default. In OPA there is no horizontal diffusion of TKE but the |
209 |
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mixing coefficients are computed from a horizontal average of TKE of |
210 |
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6 points or so. I think that diffusion has a little more physical |
211 |
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justification. |
212 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
213 |
|
was in vain) |
214 |
|
- mask tke-variable in ggl90_init |
215 |
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o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
216 |
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o fix biharmonic diffusion on CS-grid. |
217 |
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o more obcs stuff |
218 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
219 |
|
for reading boundary values. This routine is called from |
220 |
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obcs_prescribe_read |
221 |
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- updated obcs_check |
222 |
|
- changed sponge layer relaxation parameter units for days to seconds |
223 |
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- turned off sponge layer by default |
224 |
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- changed argument list of OBCS_CALC to myTime+deltaTclock |
225 |
|
- fixed about 35 bugs in obcs_external_fields_load |
226 |
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|
227 |
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checkpoint55c_post |
228 |
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o obcs stuff |
229 |
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- new runtime flags useOBCSprescribe, useOBCSbalance |
230 |
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- re-arranged obcs_calc |
231 |
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- moved exf_getobcs to obcs_prescibe_read |
232 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
233 |
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and independent of it (executable can contain all). |
234 |
|
- updated obcs_check |
235 |
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- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
236 |
|
These may be necessary only if tangential velocities are |
237 |
|
prescribed at OB, not sure, needs testing. |
238 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
239 |
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which simplifies the calls and passes the ifc check-bounds test |
240 |
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|
241 |
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checkpoint55b_post |
242 |
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o add a 2D scalar, Z location, exchange_2 routine. |
243 |
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o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
244 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
245 |
|
affects advect_cs results (for the wrong reason): update output.txt |
246 |
|
o use a more standard discretization for biharmonic viscosity ; |
247 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
248 |
|
affects results of dome set-up: update output.txt |
249 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
250 |
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o fix bug in mom_vi_del2uv.F (CubedSphere part). |
251 |
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|
252 |
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checkpoint55a_post |
253 |
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o merged code to |
254 |
|
* prescribe/read time-dependent open boundaries |
255 |
|
(works in conjunction with exf, cal) |
256 |
|
* sponge layer code for open boundaries |
257 |
|
* each boundary N/S/E/W now has its own CPP option |
258 |
|
(healthy for the adjoint) |
259 |
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|
260 |
|
checkpoint55 |
261 |
|
o up-to-date adjoint of previous breaks |
262 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
263 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
264 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
265 |
|
- carbon: * remove tr1-related adjoint verification |
266 |
|
* add ptracer as control variable |
267 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
268 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
269 |
|
|
270 |
|
checkpoint54f_post |
271 |
|
o in verification/carbin/ remove experiment related to |
272 |
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ALLOW_PASSIVE_TRACER (array tr1 etc) |
273 |
|
code_ad/ input_ad/ results_ad |
274 |
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|
275 |
|
o add two new packages |
276 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
277 |
|
+ subject to optimization (memory) |
278 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
279 |
|
+ subject to reordering (many GOTOs in the original code) |
280 |
|
+ so far opps is called for every (i,j) point, and then operates in |
281 |
|
the vertical; one may want to reorder the scheme in order operate in |
282 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
283 |
|
fields) |
284 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
285 |
|
- all verification tests compile and run with linux_ia32_g77 |
286 |
|
- defaults are compatible with current input files--nothing |
287 |
|
should change if you were not previously using MNC |
288 |
|
- MNC output has been added in numerous places (eg. timeave) |
289 |
|
but there are still a few writes not yet do-able with MNC |
290 |
|
(this is in progress) |
291 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
292 |
|
documentation will soon follow |
293 |
|
- numerous small formatting cleanups for ProTeX |
294 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
295 |
|
|
296 |
|
checkpoint54e_post |
297 |
|
o add two new packages |
298 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
299 |
|
stratification dependent mixing |
300 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
301 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
302 |
|
course), however there is only one diffusivity that is used for both |
303 |
|
temperature and salinity (and passive tracers)ç |
304 |
|
o add offline package |
305 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
306 |
|
provided by Stephanie Dutkiewicz |
307 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
308 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
309 |
|
|
310 |
|
checkpoint54d_post |
311 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
312 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
313 |
|
leading to additional shift by 5 days each year of integration |
314 |
|
(i.e. leading to considerable offset over the years) |
315 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
316 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
317 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
318 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
319 |
|
(external loading & cpl import/export stay in forward_step.F) |
320 |
|
o update coupling interface to work with new staggerTimeStep |
321 |
|
o change MDSIO ptracers_pickup. |
322 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
323 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
324 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
325 |
|
|
326 |
|
checkpoint54c_post |
327 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
328 |
|
this affects (truncation error) output.txt of test-exp: |
329 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
330 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
331 |
|
o change Qnet to always be the net heat flux, (+upward). |
332 |
|
affects (truncation error) output of natl_box exp.: updated |
333 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
334 |
|
o start to test mnc routinely in exp0 |
335 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
336 |
|
|
337 |
|
checkpoint54b_post |
338 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
339 |
|
impressive on Altix and Opteron systems) |
340 |
|
o diagnostics can now write NetCDF files through the mnc package |
341 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
342 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
343 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
344 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
345 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
346 |
|
|
347 |
|
checkpoint54a_post |
348 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
349 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
350 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
351 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
352 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
353 |
|
checkpoint54a_pre |
354 |
|
|
355 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
356 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
357 |
|
|
358 |
|
checkpoint54 |
359 |
|
checkpoint53g_post |
360 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
361 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
362 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
363 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
364 |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
365 |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
366 |
|
o restore adjointability |
367 |
|
|
368 |
checkpoint53f_post |
checkpoint53f_post |
369 |
o modifications that affect AIM experiment results (update output.txt): |
o modifications that affect AIM experiment results (update output.txt): |