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 change MNC-flags default value: true when useMNC=TRUE |
7 |
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o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
8 |
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the ability (off by default) to read the grid information using MNC |
9 |
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o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
10 |
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o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
11 |
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o do snap-shot diagnostics at the middle of the time-interval (instead of |
12 |
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at the end). |
13 |
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o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
14 |
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new test for AIM with thSIce + slab-ocean |
15 |
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o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
16 |
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o move state variable diagnostics to the beginning of the time step ; |
17 |
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(note: still needs some work specially for snap-shot diagnostics) |
18 |
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duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
19 |
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|
20 |
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checkpoint57c_post |
21 |
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o Change testing option (-ieee) to get closer agreement between g77 & ifort |
22 |
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o generate new output.txt files on faulks with g77 & the new -ieee option |
23 |
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checkpoint57c_pre |
24 |
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|
25 |
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o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
26 |
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update output.txt of exp. global_ocean.90x40x15 |
27 |
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o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
28 |
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results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
29 |
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o add saltFlux(+File) forcing capability with periodicExternalForcing |
30 |
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o allow to use pkg diagnostics for GM-Redi & ThSIce output |
31 |
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o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
32 |
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o improvements for the MNC output from DIAGNOSTICS: |
33 |
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- correct handling of the unlimitied dimension |
34 |
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- all dims now have associated coordinate variables |
35 |
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- variables located at U, V, and Corner ("Z") points are now written |
36 |
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with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
37 |
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*all* data points are output |
38 |
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o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
39 |
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o added pkg/seaice/seaice_monitor.F |
40 |
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o mdsio_readfield.F can now read files visible only to master MPI process. |
41 |
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o pkg/seaice: some test code for ice-modified ocean stress |
42 |
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o exf_getffields interpolation defaults to bilinear for all scalar forcing |
43 |
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fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
44 |
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spurious negative numbers for precipitation and humidity. Will cause |
45 |
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
46 |
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o pkg/ctrl/ |
47 |
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* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
48 |
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May be enabled via doPackDiag |
49 |
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* introduce z-scaling of |
50 |
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+ gradient (doZscalePack) and |
51 |
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+ control (doZscaleUnpack) |
52 |
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o pkg/mdsio/ |
53 |
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* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
54 |
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* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
55 |
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|
56 |
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checkpoint57b_post |
57 |
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
58 |
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o fix MNC coordinate variables so that they now contain per-face index |
59 |
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values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
60 |
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general, EXCH2 grids are only aligned to a "local" coordinate system |
61 |
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o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
62 |
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o Implement instantaneous output within pkg diagnostics: |
63 |
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setting a negative frequency in data.diagnostics produces |
64 |
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"snap-shot" output (as opposed to time-average if freq > 0) |
65 |
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o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
66 |
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
67 |
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more than 9 tracers. Add also diagnostics of advect & diffus flux. |
68 |
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o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
69 |
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becomes the coordinate variable for the 'T' dimension |
70 |
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o add CF-style coordinate variables to MNC |
71 |
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- just a first cut: numbers are meaningless on the cubesphere and |
72 |
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missing along the T axis but otherwise it works! |
73 |
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o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
74 |
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o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
75 |
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o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
76 |
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this is based directly on what the model compute, so that the content of |
77 |
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each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
78 |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
79 |
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o clean up build options files for SunOS, in particular |
80 |
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- remove -traditional from xmakedepend |
81 |
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- change -xarch=v9 to -xarch=native for f77 |
82 |
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- restore use of make (not gmake) |
83 |
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- add CC=gcc if using g77 |
84 |
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o changes per discussion of AM, JMC, & EH3 today: |
85 |
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- move redundant "grid" variables out of "state" -- in preparation of |
86 |
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creating proper CF-style coordinate variables and in recognition |
87 |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
88 |
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the grid files into any of the other NetCDF files |
89 |
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- *always* output grid variables with MDSIO (this will eventually be |
90 |
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changed) |
91 |
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- output MNC grid file if useMNC is true |
92 |
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o every instance of _END_MASTER() has been found and replaced with |
93 |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
94 |
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preprocessors |
95 |
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o re-arrange diagnostics pkg initialisation: |
96 |
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- allow each package to extend the available diagnostics list |
97 |
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- add some checking and fix small problems (multi-threaded, ...) |
98 |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
99 |
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look through the short list of active diag. (instead of the long list) |
100 |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
101 |
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|
102 |
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checkpoint57a_post |
103 |
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o this set of changes restores TAMC compatibility |
104 |
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tested for global_ocean.90x40x15 adjoint on trough |
105 |
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(what a pain) |
106 |
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|
107 |
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checkpoint57a_pre |
108 |
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o some modifs in tools/build_options for sunos |
109 |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
110 |
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|
111 |
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checkpoint57 |
112 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
113 |
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- new parameter viscA4W (defaults to viscA4) |
114 |
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- affects only non-hydrostatic code |
115 |
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- to be done: no-slip lateral boundary conditions |
116 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
117 |
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o implement Implicit Vertical advection for pTracers |
118 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
119 |
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(implemented also for implicit vertical diffusion & advection) |
120 |
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o OBCS: extend application of tracer open boundary conditions |
121 |
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to a strip beyond the boundary of width Olx/Oly |
122 |
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o add call monitor to TAF set of required calls (flow directives) |
123 |
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and include in natl_box_adjoint |
124 |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
125 |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
126 |
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o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
127 |
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(theta2, salt2 in ecco_cost_weights) |
128 |
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|
129 |
|
checkpoint56c_post |
130 |
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o OBCS as control variables |
131 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
132 |
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- remove balance of obcs controls from default |
133 |
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- fix index bug nobcs in ctrl_init |
134 |
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- fix dummy fields filen in ctrl_pack |
135 |
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- add dummy weights for obcs |
136 |
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o lsopt: comment out fort.94 output |
137 |
|
o optim: |
138 |
|
- remove unnecessary header files |
139 |
|
- adjusted namelists |
140 |
|
- add xerbla.F to Makefile |
141 |
|
o exf: |
142 |
|
- multiple modifications of exf_check_range |
143 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
144 |
|
o mdsio: |
145 |
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- i/o-vector change debugLevel from debLevA to debLevB |
146 |
|
|
147 |
|
checkpoint56b_post |
148 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
149 |
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is called from DO_THE_MODEL_IO |
150 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
151 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
152 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
153 |
|
o add another verification experiment that tests both the cfc-pkg and |
154 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
155 |
|
reactive tendencies treated inline with regular timestepping |
156 |
|
o testreport previously did a lousy job of comparing small numbers, so |
157 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
158 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
159 |
|
testreport. |
160 |
|
o ptracers_monitor: bug fix for MPI |
161 |
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|
162 |
|
checkpoint56a_post |
163 |
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o GCHEM: finish reorganizating the package |
164 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
165 |
|
(introduces another 3D-array for each passive tracer, but only if |
166 |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
167 |
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gchemTendency is not needed because the timestep is done separately) |
168 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
169 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
170 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
171 |
|
so clear to me how that should be done in a general way. |
172 |
|
o CFC: improve formatting of output in CFC_ATMOS |
173 |
|
o PTRACERS: |
174 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
175 |
|
that ALL experiments with ptracers enable can be checked. This makes |
176 |
|
GCHEM_MONITOR obsolete. |
177 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
178 |
|
monitorFreq |
179 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
180 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
181 |
|
o exf_check_range: |
182 |
|
* default changed to .TRUE. |
183 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
184 |
|
* STOP in exf_check_range if 'out of range' |
185 |
|
* range chosen generous to allow for potential extema |
186 |
|
TBD: a version with stricter range |
187 |
|
permitted range would be runtime parameters |
188 |
|
o GMredi: |
189 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
190 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
191 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
192 |
|
o GCHEM: |
193 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
194 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
195 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
196 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
197 |
|
this flag is now only visible within GCHEM-pkg routines. |
198 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
199 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
200 |
|
this, the tracer ID iTracer had to be included into the parameter list |
201 |
|
of ptracers_forcing |
202 |
|
- set up forward_step to call gchem_forcing, that will replace |
203 |
|
gchem_forcing_int in ptracers_forcing |
204 |
|
- cleaning up |
205 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
206 |
|
|
207 |
|
checkpoint56 |
208 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
209 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
210 |
|
o ECCO-GODAE |
211 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
212 |
|
* fully merged and updated from SIO code |
213 |
|
windstress sign change affects |
214 |
|
- exf_inscal_[u/v]stress |
215 |
|
- sign of xx_tau[u/v] adjustments |
216 |
|
- signs in cost_scat |
217 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
218 |
|
* natl_box_adjoint updated and compressed |
219 |
|
* 2-level checkpoint switch added |
220 |
|
(tested in EXP. 1 of natl_box_adjoint) |
221 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
222 |
|
o SVD |
223 |
|
* first complete, non-hacked version for SVD calculations |
224 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
225 |
|
performed via direct access files admtlm_vector.it???? |
226 |
|
(via ctrl_[un]pack) |
227 |
|
* optimcycle is used for ARPACK iteration counter |
228 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
229 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
230 |
|
and add linear transforms where necessary |
231 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
232 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
233 |
|
o mdsio: filename info to both stderr, stdout |
234 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
235 |
|
from sign change |
236 |
|
|
237 |
|
checkpoint55j_post |
238 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
239 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
240 |
|
o add consistent build directories and .cvsignore files to verification |
241 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
242 |
|
o make all subroutines 30 or less characters in length for certain older |
243 |
|
compilers to work (a thorough search only turns up two routines in |
244 |
|
pkg/ptracers) |
245 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
246 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
247 |
|
|
248 |
|
checkpoint55i_post |
249 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
250 |
|
3.D if implicit) ; each ptracer uses its own background value. |
251 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
252 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
253 |
|
ITRDA and other clusters without the mpirun "-wd" option |
254 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
255 |
|
configuration |
256 |
|
o give MNC the ability to create additional files rather than |
257 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
258 |
|
- the default is just less than 2GB which is a practical limit |
259 |
|
on many systems |
260 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
261 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
262 |
|
|
263 |
|
checkpoint55h_post |
264 |
|
o add verification test "vermix" |
265 |
|
o remove all the *_ioinc flags and replace with the single global |
266 |
|
outputTypesInclusive flag |
267 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
268 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
269 |
|
o useMNC moved from data.mnc to data.pkg |
270 |
|
|
271 |
|
checkpoint55g_post |
272 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
273 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
274 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
275 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
276 |
|
Works well for global_ocean.90x40x15, |
277 |
|
but recomp. issue remains for carbon |
278 |
|
o Updating adjoint output for natl_box_adjoint after |
279 |
|
pkg/ecco has been modified (see taga c55d_post) |
280 |
|
|
281 |
|
checkpoint55f_post |
282 |
|
o rename to timeave_init_fixed |
283 |
|
|
284 |
|
checkpoint55e_post |
285 |
|
o some delicate re-shuffle of store directives to avoid one |
286 |
|
extra call of do_oceanic_physics |
287 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
288 |
|
checkpoint_lev1_directives.h |
289 |
|
o NB: this may break global_ocean adjoint temporarily, |
290 |
|
but it is clear how to fix it. Will do later, need this now. |
291 |
|
|
292 |
|
checkpoint55d_post |
293 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
294 |
|
o ecco_cost_weights is modified to 1x1 runs |
295 |
|
o modifs to allow observations to be read in as |
296 |
|
single file or yearly files |
297 |
|
o enable to read exf forcing fields as either |
298 |
|
single file or yearly files (flag useExfYearlyFields) |
299 |
|
checkpoint55d_pre |
300 |
|
|
301 |
|
o switch between 2-level and 3-level checkpointing |
302 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
303 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
304 |
|
with the correct (that is, the complete multi-dimensional) set of |
305 |
|
array indicies |
306 |
|
- used in mom_vecinv() to write the diagFreq output |
307 |
|
- tested (demonstrated) in verification/aim.5l_cs |
308 |
|
o further mnc-ification |
309 |
|
- add verification/lab_sea to the list with mnc setups |
310 |
|
- fix undefined mnc v-names in cd_code |
311 |
|
- add kpp to mnc output (both snapshot and timeave) |
312 |
|
o non-hydrostatic code |
313 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
314 |
|
in calc_gw.F |
315 |
|
- defaults to viscAh |
316 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
317 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
318 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
319 |
|
o pkg/cost |
320 |
|
extend simple cost functions to treat time mean quantities |
321 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
322 |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
323 |
be 2 times larger than the minimum size the advection scheme requires. |
be 2 times larger than the minimum size the advection scheme requires. |
324 |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
now get a perfect conservation of salt in advect_cs test-exp (updated) |
341 |
- updated obcs_check |
- updated obcs_check |
342 |
- changed sponge layer relaxation parameter units for days to seconds |
- changed sponge layer relaxation parameter units for days to seconds |
343 |
- turned off sponge layer by default |
- turned off sponge layer by default |
344 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
345 |
|
- fixed about 35 bugs in obcs_external_fields_load |
346 |
|
|
347 |
checkpoint55c_post |
checkpoint55c_post |
348 |
o obcs stuff |
o obcs stuff |