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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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checkpoint57e_post |
7 |
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o Adding eddy stress controls a la Ferreira et al. |
8 |
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checkpoint57e_pre |
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10 |
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o fizhi pkg: fix AtoC and CtoA when called with same input & output array |
11 |
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update output.txt of exp. fizhi-gridalt-hs |
12 |
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o add more "Z" dimensions and associated coordinate vars to MNC |
13 |
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o pkg/exf: added twoDigitYear capability for option useExfYearlyFields |
14 |
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o parameter calendarDumps: when set, approximate months (30-31 days) and years |
15 |
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(360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq, |
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KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar |
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months and years. Requires pkg/cal. |
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o diagnostics: add pickup functionality |
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- off by default for backwards compatibility |
20 |
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- current version only uses MDSIO -- MNC will be added |
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o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies. |
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o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2) |
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checkpoint57d_post |
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o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing |
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o modify verification/ideal_2D_oce so that it tests the creation of mnc |
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output from the diagnostics package |
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o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up |
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o make genmake2 more portable by using ".$FS" instead of ".f" for more |
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of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys) |
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o add coordinate variables to the MNC output from the diagnostics package |
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o change MNC-flags default value: true when useMNC=TRUE |
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o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F |
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the ability (off by default) to read the grid information using MNC |
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o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt |
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o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging |
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o do snap-shot diagnostics at the middle of the time-interval (instead of |
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at the end). |
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o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add |
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new test for AIM with thSIce + slab-ocean |
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o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
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o move state variable diagnostics to the beginning of the time step ; |
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(note: still needs some work specially for snap-shot diagnostics) |
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duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
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checkpoint57c_post |
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o Change testing option (-ieee) to get closer agreement between g77 & ifort |
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o generate new output.txt files on faulks with g77 & the new -ieee option |
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checkpoint57c_pre |
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|
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o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
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update output.txt of exp. global_ocean.90x40x15 |
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o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
54 |
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results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
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o add saltFlux(+File) forcing capability with periodicExternalForcing |
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o allow to use pkg diagnostics for GM-Redi & ThSIce output |
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o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
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o improvements for the MNC output from DIAGNOSTICS: |
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- correct handling of the unlimitied dimension |
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- all dims now have associated coordinate variables |
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- variables located at U, V, and Corner ("Z") points are now written |
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with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
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*all* data points are output |
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o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
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o added pkg/seaice/seaice_monitor.F |
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o mdsio_readfield.F can now read files visible only to master MPI process. |
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o pkg/seaice: some test code for ice-modified ocean stress |
68 |
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o exf_getffields interpolation defaults to bilinear for all scalar forcing |
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fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
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spurious negative numbers for precipitation and humidity. Will cause |
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
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o pkg/ctrl/ |
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* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
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May be enabled via doPackDiag |
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* introduce z-scaling of |
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+ gradient (doZscalePack) and |
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+ control (doZscaleUnpack) |
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o pkg/mdsio/ |
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* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
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* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
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|
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checkpoint57b_post |
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
84 |
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o fix MNC coordinate variables so that they now contain per-face index |
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values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
86 |
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general, EXCH2 grids are only aligned to a "local" coordinate system |
87 |
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o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
88 |
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o Implement instantaneous output within pkg diagnostics: |
89 |
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setting a negative frequency in data.diagnostics produces |
90 |
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"snap-shot" output (as opposed to time-average if freq > 0) |
91 |
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o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
92 |
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
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more than 9 tracers. Add also diagnostics of advect & diffus flux. |
94 |
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o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
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becomes the coordinate variable for the 'T' dimension |
96 |
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o add CF-style coordinate variables to MNC |
97 |
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- just a first cut: numbers are meaningless on the cubesphere and |
98 |
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missing along the T axis but otherwise it works! |
99 |
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o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
100 |
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o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
101 |
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o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
102 |
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this is based directly on what the model compute, so that the content of |
103 |
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each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
104 |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
105 |
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o clean up build options files for SunOS, in particular |
106 |
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- remove -traditional from xmakedepend |
107 |
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- change -xarch=v9 to -xarch=native for f77 |
108 |
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- restore use of make (not gmake) |
109 |
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- add CC=gcc if using g77 |
110 |
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o changes per discussion of AM, JMC, & EH3 today: |
111 |
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- move redundant "grid" variables out of "state" -- in preparation of |
112 |
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creating proper CF-style coordinate variables and in recognition |
113 |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
114 |
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the grid files into any of the other NetCDF files |
115 |
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- *always* output grid variables with MDSIO (this will eventually be |
116 |
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changed) |
117 |
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- output MNC grid file if useMNC is true |
118 |
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o every instance of _END_MASTER() has been found and replaced with |
119 |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
120 |
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preprocessors |
121 |
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o re-arrange diagnostics pkg initialisation: |
122 |
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- allow each package to extend the available diagnostics list |
123 |
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- add some checking and fix small problems (multi-threaded, ...) |
124 |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
125 |
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look through the short list of active diag. (instead of the long list) |
126 |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
127 |
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|
128 |
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checkpoint57a_post |
129 |
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o this set of changes restores TAMC compatibility |
130 |
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tested for global_ocean.90x40x15 adjoint on trough |
131 |
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(what a pain) |
132 |
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|
133 |
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checkpoint57a_pre |
134 |
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o some modifs in tools/build_options for sunos |
135 |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
136 |
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|
137 |
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checkpoint57 |
138 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
139 |
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- new parameter viscA4W (defaults to viscA4) |
140 |
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- affects only non-hydrostatic code |
141 |
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- to be done: no-slip lateral boundary conditions |
142 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
143 |
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o implement Implicit Vertical advection for pTracers |
144 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
145 |
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(implemented also for implicit vertical diffusion & advection) |
146 |
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o OBCS: extend application of tracer open boundary conditions |
147 |
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to a strip beyond the boundary of width Olx/Oly |
148 |
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o add call monitor to TAF set of required calls (flow directives) |
149 |
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and include in natl_box_adjoint |
150 |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
151 |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
152 |
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o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
153 |
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(theta2, salt2 in ecco_cost_weights) |
154 |
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155 |
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checkpoint56c_post |
156 |
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o OBCS as control variables |
157 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
158 |
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- remove balance of obcs controls from default |
159 |
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- fix index bug nobcs in ctrl_init |
160 |
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- fix dummy fields filen in ctrl_pack |
161 |
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- add dummy weights for obcs |
162 |
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o lsopt: comment out fort.94 output |
163 |
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o optim: |
164 |
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- remove unnecessary header files |
165 |
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- adjusted namelists |
166 |
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- add xerbla.F to Makefile |
167 |
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o exf: |
168 |
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- multiple modifications of exf_check_range |
169 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
170 |
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o mdsio: |
171 |
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- i/o-vector change debugLevel from debLevA to debLevB |
172 |
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|
173 |
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checkpoint56b_post |
174 |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
175 |
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is called from DO_THE_MODEL_IO |
176 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
177 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
178 |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
179 |
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o add another verification experiment that tests both the cfc-pkg and |
180 |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
181 |
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reactive tendencies treated inline with regular timestepping |
182 |
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o testreport previously did a lousy job of comparing small numbers, so |
183 |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
184 |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
185 |
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testreport. |
186 |
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o ptracers_monitor: bug fix for MPI |
187 |
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188 |
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checkpoint56a_post |
189 |
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o GCHEM: finish reorganizating the package |
190 |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
191 |
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(introduces another 3D-array for each passive tracer, but only if |
192 |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
193 |
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gchemTendency is not needed because the timestep is done separately) |
194 |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
195 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
196 |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
197 |
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so clear to me how that should be done in a general way. |
198 |
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o CFC: improve formatting of output in CFC_ATMOS |
199 |
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o PTRACERS: |
200 |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
201 |
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that ALL experiments with ptracers enable can be checked. This makes |
202 |
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GCHEM_MONITOR obsolete. |
203 |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
204 |
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monitorFreq |
205 |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
206 |
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o add PTRACERS (PTR0[1-5]) to testreport output |
207 |
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o exf_check_range: |
208 |
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* default changed to .TRUE. |
209 |
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* will check values for niter0 if debLevA, every timestep if debLevB |
210 |
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* STOP in exf_check_range if 'out of range' |
211 |
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* range chosen generous to allow for potential extema |
212 |
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TBD: a version with stricter range |
213 |
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permitted range would be runtime parameters |
214 |
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o GMredi: |
215 |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
216 |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
217 |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
218 |
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o GCHEM: |
219 |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
220 |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
221 |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
222 |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
223 |
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this flag is now only visible within GCHEM-pkg routines. |
224 |
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- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
225 |
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be replaced by a 3D array that is computed before thermodynamics; for |
226 |
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this, the tracer ID iTracer had to be included into the parameter list |
227 |
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of ptracers_forcing |
228 |
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- set up forward_step to call gchem_forcing, that will replace |
229 |
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gchem_forcing_int in ptracers_forcing |
230 |
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- cleaning up |
231 |
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o small cleaning of exch2: remove files that are also in eesupp/src |
232 |
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|
233 |
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checkpoint56 |
234 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
235 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
236 |
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o ECCO-GODAE |
237 |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
238 |
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* fully merged and updated from SIO code |
239 |
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windstress sign change affects |
240 |
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- exf_inscal_[u/v]stress |
241 |
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- sign of xx_tau[u/v] adjustments |
242 |
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- signs in cost_scat |
243 |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
244 |
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* natl_box_adjoint updated and compressed |
245 |
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* 2-level checkpoint switch added |
246 |
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(tested in EXP. 1 of natl_box_adjoint) |
247 |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
248 |
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o SVD |
249 |
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* first complete, non-hacked version for SVD calculations |
250 |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
251 |
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performed via direct access files admtlm_vector.it???? |
252 |
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(via ctrl_[un]pack) |
253 |
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* optimcycle is used for ARPACK iteration counter |
254 |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
255 |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
256 |
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and add linear transforms where necessary |
257 |
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* controls are initial/final SST, SSS (can be extended; need to check |
258 |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
259 |
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o mdsio: filename info to both stderr, stdout |
260 |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
261 |
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from sign change |
262 |
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|
263 |
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checkpoint55j_post |
264 |
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o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
265 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
266 |
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o add consistent build directories and .cvsignore files to verification |
267 |
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o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
268 |
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o make all subroutines 30 or less characters in length for certain older |
269 |
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compilers to work (a thorough search only turns up two routines in |
270 |
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pkg/ptracers) |
271 |
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o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
272 |
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affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
273 |
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|
274 |
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checkpoint55i_post |
275 |
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o change arrays for total vertical diffusivity (2.D if explicit, |
276 |
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3.D if implicit) ; each ptracer uses its own background value. |
277 |
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o added mnc/NetCDF output capability to ocn_compon_interf |
278 |
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- added bits to verification/cpl_aim+ocn so that it can run on |
279 |
|
ITRDA and other clusters without the mpirun "-wd" option |
280 |
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o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
281 |
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configuration |
282 |
|
o give MNC the ability to create additional files rather than |
283 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
284 |
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- the default is just less than 2GB which is a practical limit |
285 |
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on many systems |
286 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
287 |
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or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
288 |
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|
289 |
|
checkpoint55h_post |
290 |
|
o add verification test "vermix" |
291 |
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o remove all the *_ioinc flags and replace with the single global |
292 |
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outputTypesInclusive flag |
293 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
294 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
295 |
|
o useMNC moved from data.mnc to data.pkg |
296 |
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|
297 |
|
checkpoint55g_post |
298 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
299 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
300 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
301 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
302 |
|
Works well for global_ocean.90x40x15, |
303 |
|
but recomp. issue remains for carbon |
304 |
|
o Updating adjoint output for natl_box_adjoint after |
305 |
|
pkg/ecco has been modified (see taga c55d_post) |
306 |
|
|
307 |
checkpoint55f_post |
checkpoint55f_post |
308 |
o rename to timeave_init_fixed |
o rename to timeave_init_fixed |
309 |
|
|