| 2 |
|
|
| 3 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 4 |
============================== |
============================== |
| 5 |
|
|
| 6 |
|
o pkg/seaice: some test code for ice-modified ocean stress |
| 7 |
|
o exf_getffields interpolation defaults to bilinear for all scalar forcing |
| 8 |
|
fields (remains bicubic for wind velocity and stress). This avoids, e.g., |
| 9 |
|
spurious negative numbers for precipitation and humidity. Will cause |
| 10 |
|
some small numerical differences for integrations using pkg/exf/exf_interp.F. |
| 11 |
|
|
| 12 |
|
checkpoint57b_post |
| 13 |
|
o simplify options in diagnostics_fill arguments (remove weird combinations) |
| 14 |
|
o fix MNC coordinate variables so that they now contain per-face index |
| 15 |
|
values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in |
| 16 |
|
general, EXCH2 grids are only aligned to a "local" coordinate system |
| 17 |
|
o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput) |
| 18 |
|
o Implement instantaneous output within pkg diagnostics: |
| 19 |
|
setting a negative frequency in data.diagnostics produces |
| 20 |
|
"snap-shot" output (as opposed to time-average if freq > 0) |
| 21 |
|
o move out off EQUIVALENCE all diagnostics that fizhi does not use ; |
| 22 |
|
NOTE: change ptracer diagnostics name: use 2 characters to work with |
| 23 |
|
more than 9 tracers. Add also diagnostics of advect & diffus flux. |
| 24 |
|
o more CF compliance: convert all MNC 'iter' variables to 'T' so that it |
| 25 |
|
becomes the coordinate variable for the 'T' dimension |
| 26 |
|
o add CF-style coordinate variables to MNC |
| 27 |
|
- just a first cut: numbers are meaningless on the cubesphere and |
| 28 |
|
missing along the T axis but otherwise it works! |
| 29 |
|
o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX |
| 30 |
|
o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC. |
| 31 |
|
o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon) |
| 32 |
|
this is based directly on what the model compute, so that the content of |
| 33 |
|
each diagnostics might be affected by switching options (e.g., implicitDiffusion) |
| 34 |
|
o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F) |
| 35 |
|
o clean up build options files for SunOS, in particular |
| 36 |
|
- remove -traditional from xmakedepend |
| 37 |
|
- change -xarch=v9 to -xarch=native for f77 |
| 38 |
|
- restore use of make (not gmake) |
| 39 |
|
- add CC=gcc if using g77 |
| 40 |
|
o changes per discussion of AM, JMC, & EH3 today: |
| 41 |
|
- move redundant "grid" variables out of "state" -- in preparation of |
| 42 |
|
creating proper CF-style coordinate variables and in recognition |
| 43 |
|
that any/all grid variables can be easily copied (eg. w/NCO) from |
| 44 |
|
the grid files into any of the other NetCDF files |
| 45 |
|
- *always* output grid variables with MDSIO (this will eventually be |
| 46 |
|
changed) |
| 47 |
|
- output MNC grid file if useMNC is true |
| 48 |
|
o every instance of _END_MASTER() has been found and replaced with |
| 49 |
|
_END_MASTER( myThid ) in order to satisfy certain picky Sun |
| 50 |
|
preprocessors |
| 51 |
|
o re-arrange diagnostics pkg initialisation: |
| 52 |
|
- allow each package to extend the available diagnostics list |
| 53 |
|
- add some checking and fix small problems (multi-threaded, ...) |
| 54 |
|
- new S/R diagnostics_fill (replace fill_diagnostics): |
| 55 |
|
look through the short list of active diag. (instead of the long list) |
| 56 |
|
create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active |
| 57 |
|
|
| 58 |
|
checkpoint57a_post |
| 59 |
|
o this set of changes restores TAMC compatibility |
| 60 |
|
tested for global_ocean.90x40x15 adjoint on trough |
| 61 |
|
(what a pain) |
| 62 |
|
|
| 63 |
|
checkpoint57a_pre |
| 64 |
|
o some modifs in tools/build_options for sunos |
| 65 |
|
o call ctrl_pack for ctrl at end for optimcycle=0 |
| 66 |
|
|
| 67 |
|
checkpoint57 |
| 68 |
|
o add horizontal bi-harmonic viscosity for vertical velocity |
| 69 |
|
- new parameter viscA4W (defaults to viscA4) |
| 70 |
|
- affects only non-hydrostatic code |
| 71 |
|
- to be done: no-slip lateral boundary conditions |
| 72 |
|
o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 73 |
|
o implement Implicit Vertical advection for pTracers |
| 74 |
|
o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 75 |
|
(implemented also for implicit vertical diffusion & advection) |
| 76 |
|
o OBCS: extend application of tracer open boundary conditions |
| 77 |
|
to a strip beyond the boundary of width Olx/Oly |
| 78 |
|
o add call monitor to TAF set of required calls (flow directives) |
| 79 |
|
and include in natl_box_adjoint |
| 80 |
|
o untangle a few ifdefs related to cost, ctrl, autodiff |
| 81 |
|
untangel a few ALLOW_ECCO_OPTIMIZATION |
| 82 |
|
o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr) |
| 83 |
|
(theta2, salt2 in ecco_cost_weights) |
| 84 |
|
|
| 85 |
|
checkpoint56c_post |
| 86 |
|
o OBCS as control variables |
| 87 |
|
- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 88 |
|
- remove balance of obcs controls from default |
| 89 |
|
- fix index bug nobcs in ctrl_init |
| 90 |
|
- fix dummy fields filen in ctrl_pack |
| 91 |
|
- add dummy weights for obcs |
| 92 |
|
o lsopt: comment out fort.94 output |
| 93 |
|
o optim: |
| 94 |
|
- remove unnecessary header files |
| 95 |
|
- adjusted namelists |
| 96 |
|
- add xerbla.F to Makefile |
| 97 |
|
o exf: |
| 98 |
|
- multiple modifications of exf_check_range |
| 99 |
|
- unit change in exf_init_runoff from [m/year] to [m/s] |
| 100 |
|
o mdsio: |
| 101 |
|
- i/o-vector change debugLevel from debLevA to debLevB |
| 102 |
|
|
| 103 |
|
checkpoint56b_post |
| 104 |
|
o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 105 |
|
is called from DO_THE_MODEL_IO |
| 106 |
|
- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 107 |
|
- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 108 |
|
- clean up PTRACERS_WRITE_TIMEAVE a little |
| 109 |
|
o add another verification experiment that tests both the cfc-pkg and |
| 110 |
|
the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 111 |
|
reactive tendencies treated inline with regular timestepping |
| 112 |
|
o testreport previously did a lousy job of comparing small numbers, so |
| 113 |
|
we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 114 |
|
implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 115 |
|
testreport. |
| 116 |
|
o ptracers_monitor: bug fix for MPI |
| 117 |
|
|
| 118 |
|
checkpoint56a_post |
| 119 |
|
o GCHEM: finish reorganizating the package |
| 120 |
|
- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 121 |
|
(introduces another 3D-array for each passive tracer, but only if |
| 122 |
|
GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 123 |
|
gchemTendency is not needed because the timestep is done separately) |
| 124 |
|
- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 125 |
|
- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 126 |
|
- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 127 |
|
so clear to me how that should be done in a general way. |
| 128 |
|
o CFC: improve formatting of output in CFC_ATMOS |
| 129 |
|
o PTRACERS: |
| 130 |
|
- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 131 |
|
that ALL experiments with ptracers enable can be checked. This makes |
| 132 |
|
GCHEM_MONITOR obsolete. |
| 133 |
|
- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 134 |
|
monitorFreq |
| 135 |
|
- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 136 |
|
o add PTRACERS (PTR0[1-5]) to testreport output |
| 137 |
|
o exf_check_range: |
| 138 |
|
* default changed to .TRUE. |
| 139 |
|
* will check values for niter0 if debLevA, every timestep if debLevB |
| 140 |
|
* STOP in exf_check_range if 'out of range' |
| 141 |
|
* range chosen generous to allow for potential extema |
| 142 |
|
TBD: a version with stricter range |
| 143 |
|
permitted range would be runtime parameters |
| 144 |
|
o GMredi: |
| 145 |
|
- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 146 |
|
- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 147 |
|
- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 148 |
|
o GCHEM: |
| 149 |
|
- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 150 |
|
the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 151 |
|
- introduced a useGCHEM runtime flag and applied it everywhere. |
| 152 |
|
- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 153 |
|
this flag is now only visible within GCHEM-pkg routines. |
| 154 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 155 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 156 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 157 |
|
of ptracers_forcing |
| 158 |
|
- set up forward_step to call gchem_forcing, that will replace |
| 159 |
|
gchem_forcing_int in ptracers_forcing |
| 160 |
|
- cleaning up |
| 161 |
|
o small cleaning of exch2: remove files that are also in eesupp/src |
| 162 |
|
|
| 163 |
|
checkpoint56 |
| 164 |
|
o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 165 |
|
o mnc: cleanup "full" files--fixes out-of-memory problem |
| 166 |
|
o ECCO-GODAE |
| 167 |
|
* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 168 |
|
* fully merged and updated from SIO code |
| 169 |
|
windstress sign change affects |
| 170 |
|
- exf_inscal_[u/v]stress |
| 171 |
|
- sign of xx_tau[u/v] adjustments |
| 172 |
|
- signs in cost_scat |
| 173 |
|
* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 174 |
|
* natl_box_adjoint updated and compressed |
| 175 |
|
* 2-level checkpoint switch added |
| 176 |
|
(tested in EXP. 1 of natl_box_adjoint) |
| 177 |
|
* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 178 |
|
o SVD |
| 179 |
|
* first complete, non-hacked version for SVD calculations |
| 180 |
|
* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 181 |
|
performed via direct access files admtlm_vector.it???? |
| 182 |
|
(via ctrl_[un]pack) |
| 183 |
|
* optimcycle is used for ARPACK iteration counter |
| 184 |
|
(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 185 |
|
* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 186 |
|
and add linear transforms where necessary |
| 187 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 188 |
|
ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 189 |
|
o mdsio: filename info to both stderr, stdout |
| 190 |
|
o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 191 |
|
from sign change |
| 192 |
|
|
| 193 |
|
checkpoint55j_post |
| 194 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 195 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 196 |
|
o add consistent build directories and .cvsignore files to verification |
| 197 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 198 |
|
o make all subroutines 30 or less characters in length for certain older |
| 199 |
|
compilers to work (a thorough search only turns up two routines in |
| 200 |
|
pkg/ptracers) |
| 201 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 202 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 203 |
|
|
| 204 |
|
checkpoint55i_post |
| 205 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 206 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 207 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 208 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 209 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 210 |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 211 |
configuration |
configuration |
| 212 |
o give MNC the ability to create additional files rather than |
o give MNC the ability to create additional files rather than |
Parent Directory
| 
Revision Log
| 
Revision Graph
| 
Patch