| 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 cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h) |
| 7 |
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o move state variable diagnostics to the beginning of the time step ; |
| 8 |
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(note: still needs some work specially for snap-shot diagnostics) |
| 9 |
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duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z |
| 10 |
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|
| 11 |
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checkpoint57c_post |
| 12 |
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o Change testing option (-ieee) to get closer agreement between g77 & ifort |
| 13 |
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o generate new output.txt files on faulks with g77 & the new -ieee option |
| 14 |
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checkpoint57c_pre |
| 15 |
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|
| 16 |
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o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF); |
| 17 |
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update output.txt of exp. global_ocean.90x40x15 |
| 18 |
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o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer |
| 19 |
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results; update global_ocean_pressure & global_ocean.cs32x15 output.txt |
| 20 |
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o add saltFlux(+File) forcing capability with periodicExternalForcing |
| 21 |
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o allow to use pkg diagnostics for GM-Redi & ThSIce output |
| 22 |
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o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc. |
| 23 |
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o improvements for the MNC output from DIAGNOSTICS: |
| 24 |
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- correct handling of the unlimitied dimension |
| 25 |
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- all dims now have associated coordinate variables |
| 26 |
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- variables located at U, V, and Corner ("Z") points are now written |
| 27 |
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with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that |
| 28 |
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*all* data points are output |
| 29 |
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o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice |
| 30 |
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o added pkg/seaice/seaice_monitor.F |
| 31 |
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o mdsio_readfield.F can now read files visible only to master MPI process. |
| 32 |
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o pkg/seaice: some test code for ice-modified ocean stress |
| 33 |
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o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 34 |
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fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 35 |
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spurious negative numbers for precipitation and humidity. Will cause |
| 36 |
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some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 37 |
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o pkg/ctrl/ |
| 38 |
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* Add ctrlvec diagnostics in pack/unpack for nondimensional I/O |
| 39 |
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May be enabled via doPackDiag |
| 40 |
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* introduce z-scaling of |
| 41 |
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+ gradient (doZscalePack) and |
| 42 |
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+ control (doZscaleUnpack) |
| 43 |
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o pkg/mdsio/ |
| 44 |
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* enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F |
| 45 |
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* N.B.: leave tiled I/O for tapelev (i.e. mds...vector) |
| 46 |
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|
| 47 |
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checkpoint57b_post |
| 48 |
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o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 49 |
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o fix MNC coordinate variables so that they now contain per-face index |
| 50 |
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values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 51 |
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general, EXCH2 grids are only aligned to a "local" coordinate system |
| 52 |
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o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 53 |
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o Implement instantaneous output within pkg diagnostics: |
| 54 |
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setting a negative frequency in data.diagnostics produces |
| 55 |
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"snap-shot" output (as opposed to time-average if freq > 0) |
| 56 |
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o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 57 |
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NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 58 |
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more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 59 |
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o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 60 |
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becomes the coordinate variable for the 'T' dimension |
| 61 |
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o add CF-style coordinate variables to MNC |
| 62 |
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- just a first cut: numbers are meaningless on the cubesphere and |
| 63 |
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missing along the T axis but otherwise it works! |
| 64 |
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o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 65 |
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o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 66 |
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o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 67 |
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this is based directly on what the model compute, so that the content of |
| 68 |
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each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 69 |
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o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 70 |
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o clean up build options files for SunOS, in particular |
| 71 |
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- remove -traditional from xmakedepend |
| 72 |
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- change -xarch=v9 to -xarch=native for f77 |
| 73 |
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- restore use of make (not gmake) |
| 74 |
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- add CC=gcc if using g77 |
| 75 |
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o changes per discussion of AM, JMC, & EH3 today: |
| 76 |
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- move redundant "grid" variables out of "state" -- in preparation of |
| 77 |
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creating proper CF-style coordinate variables and in recognition |
| 78 |
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that any/all grid variables can be easily copied (eg. w/NCO) from |
| 79 |
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the grid files into any of the other NetCDF files |
| 80 |
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- *always* output grid variables with MDSIO (this will eventually be |
| 81 |
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changed) |
| 82 |
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- output MNC grid file if useMNC is true |
| 83 |
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o every instance of _END_MASTER() has been found and replaced with |
| 84 |
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_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 85 |
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preprocessors |
| 86 |
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o re-arrange diagnostics pkg initialisation: |
| 87 |
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- allow each package to extend the available diagnostics list |
| 88 |
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- add some checking and fix small problems (multi-threaded, ...) |
| 89 |
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- new S/R diagnostics_fill (replace fill_diagnostics): |
| 90 |
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look through the short list of active diag. (instead of the long list) |
| 91 |
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create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 92 |
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|
| 93 |
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checkpoint57a_post |
| 94 |
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o this set of changes restores TAMC compatibility |
| 95 |
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tested for global_ocean.90x40x15 adjoint on trough |
| 96 |
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(what a pain) |
| 97 |
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|
| 98 |
|
checkpoint57a_pre |
| 99 |
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o some modifs in tools/build_options for sunos |
| 100 |
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o call ctrl_pack for ctrl at end for optimcycle=0 |
| 101 |
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|
| 102 |
|
checkpoint57 |
| 103 |
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o add horizontal bi-harmonic viscosity for vertical velocity |
| 104 |
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- new parameter viscA4W (defaults to viscA4) |
| 105 |
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- affects only non-hydrostatic code |
| 106 |
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- to be done: no-slip lateral boundary conditions |
| 107 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 108 |
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o implement Implicit Vertical advection for pTracers |
| 109 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 110 |
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(implemented also for implicit vertical diffusion & advection) |
| 111 |
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o OBCS: extend application of tracer open boundary conditions |
| 112 |
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to a strip beyond the boundary of width Olx/Oly |
| 113 |
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o add call monitor to TAF set of required calls (flow directives) |
| 114 |
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and include in natl_box_adjoint |
| 115 |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
| 116 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 117 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 118 |
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(theta2, salt2 in ecco_cost_weights) |
| 119 |
|
|
| 120 |
|
checkpoint56c_post |
| 121 |
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o OBCS as control variables |
| 122 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 123 |
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- remove balance of obcs controls from default |
| 124 |
|
- fix index bug nobcs in ctrl_init |
| 125 |
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- fix dummy fields filen in ctrl_pack |
| 126 |
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- add dummy weights for obcs |
| 127 |
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o lsopt: comment out fort.94 output |
| 128 |
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o optim: |
| 129 |
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- remove unnecessary header files |
| 130 |
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- adjusted namelists |
| 131 |
|
- add xerbla.F to Makefile |
| 132 |
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o exf: |
| 133 |
|
- multiple modifications of exf_check_range |
| 134 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
| 135 |
|
o mdsio: |
| 136 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 137 |
|
|
| 138 |
|
checkpoint56b_post |
| 139 |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 140 |
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is called from DO_THE_MODEL_IO |
| 141 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 142 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 143 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 144 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 145 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 146 |
|
reactive tendencies treated inline with regular timestepping |
| 147 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 148 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 149 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 150 |
|
testreport. |
| 151 |
|
o ptracers_monitor: bug fix for MPI |
| 152 |
|
|
| 153 |
|
checkpoint56a_post |
| 154 |
|
o GCHEM: finish reorganizating the package |
| 155 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 156 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 157 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 158 |
|
gchemTendency is not needed because the timestep is done separately) |
| 159 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 160 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 161 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 162 |
|
so clear to me how that should be done in a general way. |
| 163 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 164 |
|
o PTRACERS: |
| 165 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 166 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 167 |
|
GCHEM_MONITOR obsolete. |
| 168 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 169 |
|
monitorFreq |
| 170 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 171 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 172 |
|
o exf_check_range: |
| 173 |
|
* default changed to .TRUE. |
| 174 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 175 |
|
* STOP in exf_check_range if 'out of range' |
| 176 |
|
* range chosen generous to allow for potential extema |
| 177 |
|
TBD: a version with stricter range |
| 178 |
|
permitted range would be runtime parameters |
| 179 |
|
o GMredi: |
| 180 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 181 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 182 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 183 |
|
o GCHEM: |
| 184 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 185 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 186 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 187 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 188 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 189 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 190 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 191 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 192 |
|
of ptracers_forcing |
| 193 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 194 |
|
gchem_forcing_int in ptracers_forcing |
| 195 |
|
- cleaning up |
| 196 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 197 |
|
|
| 198 |
|
checkpoint56 |
| 199 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 200 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 201 |
|
o ECCO-GODAE |
| 202 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 203 |
|
* fully merged and updated from SIO code |
| 204 |
|
windstress sign change affects |
| 205 |
|
- exf_inscal_[u/v]stress |
| 206 |
|
- sign of xx_tau[u/v] adjustments |
| 207 |
|
- signs in cost_scat |
| 208 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 209 |
|
* natl_box_adjoint updated and compressed |
| 210 |
|
* 2-level checkpoint switch added |
| 211 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 212 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 213 |
|
o SVD |
| 214 |
|
* first complete, non-hacked version for SVD calculations |
| 215 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 216 |
|
performed via direct access files admtlm_vector.it???? |
| 217 |
|
(via ctrl_[un]pack) |
| 218 |
|
* optimcycle is used for ARPACK iteration counter |
| 219 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 220 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 221 |
|
and add linear transforms where necessary |
| 222 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 223 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 224 |
|
o mdsio: filename info to both stderr, stdout |
| 225 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 226 |
|
from sign change |
| 227 |
|
|
| 228 |
|
checkpoint55j_post |
| 229 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 230 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 231 |
|
o add consistent build directories and .cvsignore files to verification |
| 232 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 233 |
|
o make all subroutines 30 or less characters in length for certain older |
| 234 |
|
compilers to work (a thorough search only turns up two routines in |
| 235 |
|
pkg/ptracers) |
| 236 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 237 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 238 |
|
|
| 239 |
|
checkpoint55i_post |
| 240 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 241 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 242 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 243 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 244 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 245 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 246 |
|
configuration |
| 247 |
|
o give MNC the ability to create additional files rather than |
| 248 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 249 |
|
- the default is just less than 2GB which is a practical limit |
| 250 |
|
on many systems |
| 251 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 252 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 253 |
|
|
| 254 |
|
checkpoint55h_post |
| 255 |
|
o add verification test "vermix" |
| 256 |
|
o remove all the *_ioinc flags and replace with the single global |
| 257 |
|
outputTypesInclusive flag |
| 258 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 259 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 260 |
|
o useMNC moved from data.mnc to data.pkg |
| 261 |
|
|
| 262 |
|
checkpoint55g_post |
| 263 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 264 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 265 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 266 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 267 |
|
Works well for global_ocean.90x40x15, |
| 268 |
|
but recomp. issue remains for carbon |
| 269 |
|
o Updating adjoint output for natl_box_adjoint after |
| 270 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 271 |
|
|
| 272 |
|
checkpoint55f_post |
| 273 |
|
o rename to timeave_init_fixed |
| 274 |
|
|
| 275 |
|
checkpoint55e_post |
| 276 |
|
o some delicate re-shuffle of store directives to avoid one |
| 277 |
|
extra call of do_oceanic_physics |
| 278 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 279 |
|
checkpoint_lev1_directives.h |
| 280 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 281 |
|
but it is clear how to fix it. Will do later, need this now. |
| 282 |
|
|
| 283 |
|
checkpoint55d_post |
| 284 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 285 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 286 |
|
o modifs to allow observations to be read in as |
| 287 |
|
single file or yearly files |
| 288 |
|
o enable to read exf forcing fields as either |
| 289 |
|
single file or yearly files (flag useExfYearlyFields) |
| 290 |
|
checkpoint55d_pre |
| 291 |
|
|
| 292 |
|
o switch between 2-level and 3-level checkpointing |
| 293 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 294 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 295 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 296 |
|
array indicies |
| 297 |
|
- used in mom_vecinv() to write the diagFreq output |
| 298 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 299 |
|
o further mnc-ification |
| 300 |
|
- add verification/lab_sea to the list with mnc setups |
| 301 |
|
- fix undefined mnc v-names in cd_code |
| 302 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 303 |
|
o non-hydrostatic code |
| 304 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 305 |
|
in calc_gw.F |
| 306 |
|
- defaults to viscAh |
| 307 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 308 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 309 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 310 |
|
o pkg/cost |
| 311 |
|
extend simple cost functions to treat time mean quantities |
| 312 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 313 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 314 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 315 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 316 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 317 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 318 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 319 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 320 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 321 |
|
6 points or so. I think that diffusion has a little more physical |
| 322 |
|
justification. |
| 323 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 324 |
|
was in vain) |
| 325 |
|
- mask tke-variable in ggl90_init |
| 326 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 327 |
|
o fix biharmonic diffusion on CS-grid. |
| 328 |
|
o more obcs stuff |
| 329 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 330 |
|
for reading boundary values. This routine is called from |
| 331 |
|
obcs_prescribe_read |
| 332 |
|
- updated obcs_check |
| 333 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 334 |
|
- turned off sponge layer by default |
| 335 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 336 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 337 |
|
|
| 338 |
|
checkpoint55c_post |
| 339 |
|
o obcs stuff |
| 340 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 341 |
|
- re-arranged obcs_calc |
| 342 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 343 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 344 |
|
and independent of it (executable can contain all). |
| 345 |
|
- updated obcs_check |
| 346 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 347 |
|
These may be necessary only if tangential velocities are |
| 348 |
|
prescribed at OB, not sure, needs testing. |
| 349 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 350 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 351 |
|
|
| 352 |
|
checkpoint55b_post |
| 353 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 354 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 355 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 356 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 357 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 358 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 359 |
|
affects results of dome set-up: update output.txt |
| 360 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 361 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 362 |
|
|
| 363 |
|
checkpoint55a_post |
| 364 |
|
o merged code to |
| 365 |
|
* prescribe/read time-dependent open boundaries |
| 366 |
|
(works in conjunction with exf, cal) |
| 367 |
|
* sponge layer code for open boundaries |
| 368 |
|
* each boundary N/S/E/W now has its own CPP option |
| 369 |
|
(healthy for the adjoint) |
| 370 |
|
|
| 371 |
|
checkpoint55 |
| 372 |
|
o up-to-date adjoint of previous breaks |
| 373 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 374 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 375 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 376 |
|
- carbon: * remove tr1-related adjoint verification |
| 377 |
|
* add ptracer as control variable |
| 378 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 379 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 380 |
|
|
| 381 |
|
checkpoint54f_post |
| 382 |
|
o in verification/carbin/ remove experiment related to |
| 383 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 384 |
|
code_ad/ input_ad/ results_ad |
| 385 |
|
|
| 386 |
|
o add two new packages |
| 387 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 388 |
|
+ subject to optimization (memory) |
| 389 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 390 |
|
+ subject to reordering (many GOTOs in the original code) |
| 391 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 392 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 393 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 394 |
|
fields) |
| 395 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 396 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 397 |
|
- defaults are compatible with current input files--nothing |
| 398 |
|
should change if you were not previously using MNC |
| 399 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 400 |
|
but there are still a few writes not yet do-able with MNC |
| 401 |
|
(this is in progress) |
| 402 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 403 |
|
documentation will soon follow |
| 404 |
|
- numerous small formatting cleanups for ProTeX |
| 405 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 406 |
|
|
| 407 |
|
checkpoint54e_post |
| 408 |
|
o add two new packages |
| 409 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 410 |
|
stratification dependent mixing |
| 411 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 412 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 413 |
|
course), however there is only one diffusivity that is used for both |
| 414 |
|
temperature and salinity (and passive tracers)ç |
| 415 |
|
o add offline package |
| 416 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 417 |
|
provided by Stephanie Dutkiewicz |
| 418 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 419 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 420 |
|
|
| 421 |
|
checkpoint54d_post |
| 422 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 423 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 424 |
|
leading to additional shift by 5 days each year of integration |
| 425 |
|
(i.e. leading to considerable offset over the years) |
| 426 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 427 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 428 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 429 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 430 |
|
(external loading & cpl import/export stay in forward_step.F) |
| 431 |
|
o update coupling interface to work with new staggerTimeStep |
| 432 |
|
o change MDSIO ptracers_pickup. |
| 433 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 434 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 435 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 436 |
|
|
| 437 |
|
checkpoint54c_post |
| 438 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 439 |
|
this affects (truncation error) output.txt of test-exp: |
| 440 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 441 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 442 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 443 |
|
affects (truncation error) output of natl_box exp.: updated |
| 444 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 445 |
|
o start to test mnc routinely in exp0 |
| 446 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 447 |
|
|
| 448 |
|
checkpoint54b_post |
| 449 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 450 |
|
impressive on Altix and Opteron systems) |
| 451 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 452 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 453 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 454 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 455 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 456 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 457 |
|
|
| 458 |
|
checkpoint54a_post |
| 459 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 460 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 461 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 462 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 463 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 464 |
|
checkpoint54a_pre |
| 465 |
|
|
| 466 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 467 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 468 |
|
|
| 469 |
|
checkpoint54 |
| 470 |
|
checkpoint53g_post |
| 471 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 472 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 473 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 474 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 475 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 476 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 477 |
|
o restore adjointability |
| 478 |
|
|
| 479 |
|
checkpoint53f_post |
| 480 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 481 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 482 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 483 |
|
o AIM pkg: |
| 484 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 485 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 486 |
|
|
| 487 |
|
checkpoint53e_post |
| 488 |
|
o merged cylindrical coord configuration |
| 489 |
|
o added rotating_tank experiment |
| 490 |
|
checkpoint53e_pre |
| 491 |
|
|
| 492 |
|
checkpoint53d_post |
| 493 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 494 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 495 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 496 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 497 |
|
o added Sadourny discretization of Coriolis |
| 498 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 499 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 500 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 501 |
|
vector-invariant equations |
| 502 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 503 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 504 |
|
hopefully without new bugs |
| 505 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 506 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 507 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 508 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 509 |
|
of mom_common/ |
| 510 |
|
- simple re-arrangement of instructions within computing loop |
| 511 |
|
checkpoint53d_pre |
| 512 |
|
|
| 513 |
|
checkpoint53c_post |
| 514 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 515 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 516 |
|
- land: change Evaporation of snow |
| 517 |
|
- aim with thSIce: fix bug in snow-precip. |
| 518 |
|
o changes to calc_gw.F |
| 519 |
|
- bug fix for w^2 term near the bottom boundary |
| 520 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 521 |
|
partial/looped cells |
| 522 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 523 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 524 |
|
to the value of no_slip_sides |
| 525 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 526 |
|
o Adjoint of EBM package + verification |
| 527 |
|
* TLM OK |
| 528 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 529 |
|
|
| 530 |
|
checkpoint53b_post |
| 531 |
|
o Commiting new energy balance model to repository |
| 532 |
|
* package is pkg/ebm |
| 533 |
|
* verif. is verification/global_ocean_ebm |
| 534 |
|
* references are in ebm_driver.F |
| 535 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 536 |
|
C Global thermohaline circulation. Part I: |
| 537 |
|
C Sensitivity to atmospheric moisture transport. |
| 538 |
|
C J. Climate 12(1), 71-82 |
| 539 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 540 |
|
C Global thermohaline circulation. Part II: |
| 541 |
|
C Sensitivity with interactive transport. |
| 542 |
|
C J. Climate 12(1), 83-91 |
| 543 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 544 |
|
C Destabilization of the thermohaline circulation |
| 545 |
|
C by atmospheric eddy transports. |
| 546 |
|
C J. Climate 7(12), 1870-1882 |
| 547 |
|
o Will need long integration testing. |
| 548 |
|
checkpoint53b_pre |
| 549 |
|
|
| 550 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 551 |
|
o renamed and split ini_mnc_io |
| 552 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 553 |
|
o AIM using land: soil wetness availability account for snow |
| 554 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 555 |
|
|
| 556 |
|
checkpoint53a_post |
| 557 |
|
o restore TAMC compatiility for exf_constants.h |
| 558 |
|
(no usage of _d in .h) |
| 559 |
|
o Additional storing in KPP in an attempt to fix |
| 560 |
|
TAMC problem with adjoint of KPP code. |
| 561 |
|
(no success...) |
| 562 |
|
Identical code works fine with TAF. |
| 563 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 564 |
|
Initial conditions for Experiments 4 and 5 are now |
| 565 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 566 |
|
and hence gives results closer to that of Experiment 2. |
| 567 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 568 |
|
|
| 569 |
|
checkpoint53 |
| 570 |
|
o stable checkpoint with up to date adjoint |
| 571 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 572 |
|
this is a code problem or a problem with resetting code for g_ |
| 573 |
|
variables that is being autogenerated wrong. |
| 574 |
|
Otherwise: |
| 575 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 576 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 577 |
|
are both still in chaos following their security messes. |
| 578 |
|
|
| 579 |
|
checkpoint52n_post |
| 580 |
|
o various build (mostly genmake2) changes including: |
| 581 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 582 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 583 |
|
o pkg/seaice modifications |
| 584 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 585 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
| 586 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
| 587 |
|
- changed proxy for geostrophic velocity and updated |
| 588 |
|
verification/lab_sea/results/* accordingly |
| 589 |
|
- removed ADI dynamic solver from pkg/seaice |
| 590 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
| 591 |
|
they caused a segmentation fault under certain circumstances |
| 592 |
|
- removed unused field WATR |
| 593 |
|
o bug fix in exf-package: |
| 594 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
| 595 |
|
now reflect that. |
| 596 |
|
o small fixes in the cal-package: |
| 597 |
|
- set reference date to first of January for the 'model'-calendar |
| 598 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
| 599 |
|
warning |
| 600 |
|
o small modifications in exf-package to increase flexibility: |
| 601 |
|
- change climtempfreeze from a constant to a runtime parameter that |
| 602 |
|
is specified in data.exf_clim (default = -1.9) |
| 603 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
| 604 |
|
specified in data.exf |
| 605 |
|
o fix in pkg/thsice: |
| 606 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
| 607 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
| 608 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
| 609 |
|
|
| 610 |
|
checkpoint52m_post |
| 611 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
| 612 |
|
this does not change any of the results, because myIter=0 in swfrac always |
| 613 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
| 614 |
|
as a default |
| 615 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
| 616 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
| 617 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
| 618 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
| 619 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
| 620 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
| 621 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
| 622 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
| 623 |
|
o monitor package can write to NetCDF files and/or STDOUT |
| 624 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
| 625 |
|
o doc/api_reference added |
| 626 |
|
- a framework for building an API Reference Manual using all |
| 627 |
|
the "protex" comments embedded in the code |
| 628 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
| 629 |
|
o MNC: |
| 630 |
|
- make myThid the last argument for all subroutines |
| 631 |
|
- new default for the grid files: NO halos |
| 632 |
|
- add useMNC and other run-time flags |
| 633 |
|
- separate per-file-group handling of the unlimited dimension |
| 634 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
| 635 |
|
and lookup tables set in initialize_fixed |
| 636 |
|
- write all MNC output to a freshly-created directory |
| 637 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 638 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 639 |
|
o Added functionality to grdchk: |
| 640 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 641 |
|
|
| 642 |
|
checkpoint52l_post |
| 643 |
|
o new land formulation: |
| 644 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 645 |
|
energy conservation. |
| 646 |
|
b) account for water temperature and for latent heat of freezing |
| 647 |
|
in all processes (rain, run-off, ground storage) |
| 648 |
|
c) compute surface and ground temperature implicitly. |
| 649 |
|
o aim_v23 modification for new land model: |
| 650 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 651 |
|
to allow implicit computation of land & sea-ice surface temp. |
| 652 |
|
b) add snow precipitation. |
| 653 |
|
checkpoint52l_pre |
| 654 |
|
|
| 655 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
| 656 |
|
o fix bug in timeAve (u,vZetatave in common block) |
| 657 |
|
o no restoring terms under ice for pkg/seaice |
| 658 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 659 |
|
o bug fix for pkg/seaice pickups |
| 660 |
|
o change MNC call locations and add coordinate attributes |
| 661 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
| 662 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 663 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 664 |
|
o exf: Adding simple range check routine for exf fields after read |
| 665 |
|
|
| 666 |
|
checkpoint52k_post |
| 667 |
|
o removed top-level directory "diags" |
| 668 |
|
- we migrated these functions to pkg/timeave a long time ago |
| 669 |
|
o fixed bug introduced in pkg/monitor |
| 670 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 671 |
|
averaged fields (I/O via cost_averages) |
| 672 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
| 673 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
| 674 |
|
o added initial do_the_model_io to ecco |
| 675 |
|
o set all ...Freq to zero after cost_final |
| 676 |
|
taveFreq, dumpFreq, pChkptFreq |
| 677 |
|
o MAIN and ECCO differentiability restored |
| 678 |
|
|
| 679 |
|
checkpoint52j_post |
| 680 |
|
o fix nchklev in tamc.h for global_ocean... |
| 681 |
|
o Bringing flow and store directives up-to-date |
| 682 |
|
o Really weird thing! |
| 683 |
|
call do_the_model_io from the_main_loop with parameters |
| 684 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 685 |
|
TAF places a faulty re-call of initialise_varia |
| 686 |
|
after cost_final call which should not be there! |
| 687 |
|
checkpoint52j_pre |
| 688 |
|
|
| 689 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 690 |
|
error messages |
| 691 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 692 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 693 |
|
debug output |
| 694 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 695 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 696 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 697 |
|
o update AIM Equatorial Channel exp: |
| 698 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 699 |
|
o globalFile now works with exch2 |
| 700 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 701 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 702 |
|
o limit timeave output for hi-res integrations |
| 703 |
|
|
| 704 |
|
checkpoint52i_post |
| 705 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
| 706 |
|
o updated the tiling for global_ocean_pressure |
| 707 |
|
checkpoint52i_pre |
| 708 |
|
|
| 709 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 710 |
|
the old pkg/aim). |
| 711 |
|
|
| 712 |
|
checkpoint52h_pre |
| 713 |
|
o shortened offending lines in exch2_send_rx?.template |
| 714 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 715 |
o genmake2: add build & execute test for NetCDF code |
o genmake2: add build & execute test for NetCDF code |
| 716 |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
| 717 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
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