| 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 add horizontal bi-harmonic viscosity for vertical velocity |
| 7 |
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- new parameter viscA4W (defaults to viscA4) |
| 8 |
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- affects only non-hydrostatic code |
| 9 |
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- to be done: no-slip lateral boundary conditions |
| 10 |
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o switch back to "sflux = sflux - runoff" in exf_getforcing.F |
| 11 |
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o implement Implicit Vertical advection for pTracers |
| 12 |
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o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k) |
| 13 |
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(implemented also for implicit vertical diffusion & advection) |
| 14 |
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o OBCS: extend application of tracer open boundary conditions |
| 15 |
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to a strip beyond the boundary of width Olx/Oly |
| 16 |
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o add call monitor to TAF set of required calls (flow directives) |
| 17 |
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and include in natl_box_adjoint |
| 18 |
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o untangle a few ifdefs related to cost, ctrl, autodiff |
| 19 |
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untangel a few ALLOW_ECCO_OPTIMIZATION |
| 20 |
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|
| 21 |
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checkpoint56c_post |
| 22 |
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o OBCS as control variables |
| 23 |
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- update ctrl_ad_diff.list, obcs_ad_diff.list |
| 24 |
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- remove balance of obcs controls from default |
| 25 |
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- fix index bug nobcs in ctrl_init |
| 26 |
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- fix dummy fields filen in ctrl_pack |
| 27 |
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- add dummy weights for obcs |
| 28 |
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o lsopt: comment out fort.94 output |
| 29 |
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o optim: |
| 30 |
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- remove unnecessary header files |
| 31 |
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- adjusted namelists |
| 32 |
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- add xerbla.F to Makefile |
| 33 |
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o exf: |
| 34 |
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- multiple modifications of exf_check_range |
| 35 |
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- unit change in exf_init_runoff from [m/year] to [m/s] |
| 36 |
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o mdsio: |
| 37 |
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- i/o-vector change debugLevel from debLevA to debLevB |
| 38 |
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|
| 39 |
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checkpoint56b_post |
| 40 |
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o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that |
| 41 |
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is called from DO_THE_MODEL_IO |
| 42 |
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- rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE |
| 43 |
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- introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq) |
| 44 |
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- clean up PTRACERS_WRITE_TIMEAVE a little |
| 45 |
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o add another verification experiment that tests both the cfc-pkg and |
| 46 |
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the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with |
| 47 |
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reactive tendencies treated inline with regular timestepping |
| 48 |
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o testreport previously did a lousy job of comparing small numbers, so |
| 49 |
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we (Ed and Martin) changed the way the cut-off of 1.e-12 is |
| 50 |
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implemented in the little c-progam tmp_cmpnum.c which is embedded in |
| 51 |
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testreport. |
| 52 |
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o ptracers_monitor: bug fix for MPI |
| 53 |
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|
| 54 |
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checkpoint56a_post |
| 55 |
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o GCHEM: finish reorganizating the package |
| 56 |
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- forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency |
| 57 |
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(introduces another 3D-array for each passive tracer, but only if |
| 58 |
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GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING |
| 59 |
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gchemTendency is not needed because the timestep is done separately) |
| 60 |
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- gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY |
| 61 |
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- GCHEM is now---more or less cleanly---separate from PTRACERS |
| 62 |
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- to bo done: handling of surfaceForcingPtr that is needed for KPP not |
| 63 |
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so clear to me how that should be done in a general way. |
| 64 |
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o CFC: improve formatting of output in CFC_ATMOS |
| 65 |
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o PTRACERS: |
| 66 |
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- rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so |
| 67 |
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that ALL experiments with ptracers enable can be checked. This makes |
| 68 |
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GCHEM_MONITOR obsolete. |
| 69 |
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- include a runtime parameter PTRACERS_monitorFreq that defaults to |
| 70 |
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monitorFreq |
| 71 |
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- set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true |
| 72 |
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o add PTRACERS (PTR0[1-5]) to testreport output |
| 73 |
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o exf_check_range: |
| 74 |
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* default changed to .TRUE. |
| 75 |
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* will check values for niter0 if debLevA, every timestep if debLevB |
| 76 |
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* STOP in exf_check_range if 'out of range' |
| 77 |
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* range chosen generous to allow for potential extema |
| 78 |
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TBD: a version with stricter range |
| 79 |
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permitted range would be runtime parameters |
| 80 |
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o GMredi: |
| 81 |
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- fix ldd97 slope limit ; extend valid domain of Psi-Bolus ; |
| 82 |
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- change S/R GRAD_SIGMA to be valid in the overlap on CS-grid. |
| 83 |
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- change the default GMREDI_OPTIONS.h: compile everything except Visbeck |
| 84 |
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o GCHEM: |
| 85 |
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- move call to GCHEM_FORCING_SEP, so that it is now called before |
| 86 |
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the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP |
| 87 |
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- introduced a useGCHEM runtime flag and applied it everywhere. |
| 88 |
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- renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING; |
| 89 |
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this flag is now only visible within GCHEM-pkg routines. |
| 90 |
|
- moved gchem_forcing_int temporarily into ptracers_forcing, this will |
| 91 |
|
be replaced by a 3D array that is computed before thermodynamics; for |
| 92 |
|
this, the tracer ID iTracer had to be included into the parameter list |
| 93 |
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of ptracers_forcing |
| 94 |
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- set up forward_step to call gchem_forcing, that will replace |
| 95 |
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gchem_forcing_int in ptracers_forcing |
| 96 |
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- cleaning up |
| 97 |
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o small cleaning of exch2: remove files that are also in eesupp/src |
| 98 |
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|
| 99 |
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checkpoint56 |
| 100 |
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o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0 |
| 101 |
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o mnc: cleanup "full" files--fixes out-of-memory problem |
| 102 |
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o ECCO-GODAE |
| 103 |
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* model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup |
| 104 |
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* fully merged and updated from SIO code |
| 105 |
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windstress sign change affects |
| 106 |
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- exf_inscal_[u/v]stress |
| 107 |
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- sign of xx_tau[u/v] adjustments |
| 108 |
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- signs in cost_scat |
| 109 |
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* ctrl_get_gen: avoid update of tau[u/v] for first few days |
| 110 |
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* natl_box_adjoint updated and compressed |
| 111 |
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* 2-level checkpoint switch added |
| 112 |
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(tested in EXP. 1 of natl_box_adjoint) |
| 113 |
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* new switch doInitXX to avoid init. of xx_... in optimcycle=0 |
| 114 |
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o SVD |
| 115 |
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* first complete, non-hacked version for SVD calculations |
| 116 |
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* all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_... |
| 117 |
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performed via direct access files admtlm_vector.it???? |
| 118 |
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(via ctrl_[un]pack) |
| 119 |
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* optimcycle is used for ARPACK iteration counter |
| 120 |
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(note: adxx_... is iterated, rather than xx_...; latter is constant!) |
| 121 |
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* EV problem ok w.r.t. L2-norm in tangent space; need to check other norms |
| 122 |
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and add linear transforms where necessary |
| 123 |
|
* controls are initial/final SST, SSS (can be extended; need to check |
| 124 |
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ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F |
| 125 |
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o mdsio: filename info to both stderr, stdout |
| 126 |
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o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec] |
| 127 |
|
from sign change |
| 128 |
|
|
| 129 |
|
checkpoint55j_post |
| 130 |
|
o isolate dissipation tendency (allow to keep it out off AB) in V.I form. |
| 131 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 132 |
|
o add consistent build directories and .cvsignore files to verification |
| 133 |
|
o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity |
| 134 |
|
o make all subroutines 30 or less characters in length for certain older |
| 135 |
|
compilers to work (a thorough search only turns up two routines in |
| 136 |
|
pkg/ptracers) |
| 137 |
|
o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; |
| 138 |
|
affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice) |
| 139 |
|
|
| 140 |
|
checkpoint55i_post |
| 141 |
|
o change arrays for total vertical diffusivity (2.D if explicit, |
| 142 |
|
3.D if implicit) ; each ptracer uses its own background value. |
| 143 |
|
o added mnc/NetCDF output capability to ocn_compon_interf |
| 144 |
|
- added bits to verification/cpl_aim+ocn so that it can run on |
| 145 |
|
ITRDA and other clusters without the mpirun "-wd" option |
| 146 |
|
o fixed wayward endif in mom_fluxform.F that messed up cyclindrical |
| 147 |
|
configuration |
| 148 |
|
o give MNC the ability to create additional files rather than |
| 149 |
|
exceeding a specified file size limit "MNC_MAX_FILESIZE" |
| 150 |
|
- the default is just less than 2GB which is a practical limit |
| 151 |
|
on many systems |
| 152 |
|
o Compute the non-local term using either KPP vertical diffusivity (=default) |
| 153 |
|
or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T) |
| 154 |
|
|
| 155 |
|
checkpoint55h_post |
| 156 |
|
o add verification test "vermix" |
| 157 |
|
o remove all the *_ioinc flags and replace with the single global |
| 158 |
|
outputTypesInclusive flag |
| 159 |
|
o allow to set a vertical profile of vertical diffusivity for T & S |
| 160 |
|
o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS |
| 161 |
|
o useMNC moved from data.mnc to data.pkg |
| 162 |
|
|
| 163 |
|
checkpoint55g_post |
| 164 |
|
o Renaming carbon AD experiments to comply with testreport conventions |
| 165 |
|
o Updating adjoint of Held-Suarez hs94.1x64x5 |
| 166 |
|
o Fixing directives for non-ECCO forward_step, after ECCO directives |
| 167 |
|
have been fixed to avoid recomp. of do_oceanic_phys |
| 168 |
|
Works well for global_ocean.90x40x15, |
| 169 |
|
but recomp. issue remains for carbon |
| 170 |
|
o Updating adjoint output for natl_box_adjoint after |
| 171 |
|
pkg/ecco has been modified (see taga c55d_post) |
| 172 |
|
|
| 173 |
|
checkpoint55f_post |
| 174 |
|
o rename to timeave_init_fixed |
| 175 |
|
|
| 176 |
|
checkpoint55e_post |
| 177 |
|
o some delicate re-shuffle of store directives to avoid one |
| 178 |
|
extra call of do_oceanic_physics |
| 179 |
|
affects ecco_the_main_loop.F, do_oceanic_physics.F |
| 180 |
|
checkpoint_lev1_directives.h |
| 181 |
|
o NB: this may break global_ocean adjoint temporarily, |
| 182 |
|
but it is clear how to fix it. Will do later, need this now. |
| 183 |
|
|
| 184 |
|
checkpoint55d_post |
| 185 |
|
o ECCO specific cost function terms (up-to-date with 1x1 runs) |
| 186 |
|
o ecco_cost_weights is modified to 1x1 runs |
| 187 |
|
o modifs to allow observations to be read in as |
| 188 |
|
single file or yearly files |
| 189 |
|
o enable to read exf forcing fields as either |
| 190 |
|
single file or yearly files (flag useExfYearlyFields) |
| 191 |
|
checkpoint55d_pre |
| 192 |
|
|
| 193 |
|
o switch between 2-level and 3-level checkpointing |
| 194 |
|
o add ability of MNC to write local and "partial" (eg. 2D slices where |
| 195 |
|
the full 3D field is never actually stored) arrays to NetCDF files |
| 196 |
|
with the correct (that is, the complete multi-dimensional) set of |
| 197 |
|
array indicies |
| 198 |
|
- used in mom_vecinv() to write the diagFreq output |
| 199 |
|
- tested (demonstrated) in verification/aim.5l_cs |
| 200 |
|
o further mnc-ification |
| 201 |
|
- add verification/lab_sea to the list with mnc setups |
| 202 |
|
- fix undefined mnc v-names in cd_code |
| 203 |
|
- add kpp to mnc output (both snapshot and timeave) |
| 204 |
|
o non-hydrostatic code |
| 205 |
|
- added horizontal viscosity parameter viscAhW for w, that replaces viscAh |
| 206 |
|
in calc_gw.F |
| 207 |
|
- defaults to viscAh |
| 208 |
|
- this is useful, when I want to use viscAh=0 (e.g., only biharmonic |
| 209 |
|
friction or Leith) in non-hydrostatic mode, as long as there is |
| 210 |
|
no biharmonic friction and/or Leigth or equivalent for vertical velocity. |
| 211 |
|
o pkg/cost |
| 212 |
|
extend simple cost functions to treat time mean quantities |
| 213 |
|
(T,U,V) via cost_accumulate_state from cost_tile |
| 214 |
|
o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to |
| 215 |
|
be 2 times larger than the minimum size the advection scheme requires. |
| 216 |
|
now get a perfect conservation of salt in advect_cs test-exp (updated) |
| 217 |
|
o GGL90 (Gaspar's TKE mixed layer) |
| 218 |
|
- add horizontal diffusion of TKE, requires exchanges in |
| 219 |
|
do_fields_blocking_exchanges, horizontal diffusivity is zero by |
| 220 |
|
default. In OPA there is no horizontal diffusion of TKE but the |
| 221 |
|
mixing coefficients are computed from a horizontal average of TKE of |
| 222 |
|
6 points or so. I think that diffusion has a little more physical |
| 223 |
|
justification. |
| 224 |
|
- clean up ggl90_calc in the hope of reducing memory usage (this hope |
| 225 |
|
was in vain) |
| 226 |
|
- mask tke-variable in ggl90_init |
| 227 |
|
o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass) |
| 228 |
|
o fix biharmonic diffusion on CS-grid. |
| 229 |
|
o more obcs stuff |
| 230 |
|
- added obcs_external_fields_load as an alternative to the EXF-pkg option |
| 231 |
|
for reading boundary values. This routine is called from |
| 232 |
|
obcs_prescribe_read |
| 233 |
|
- updated obcs_check |
| 234 |
|
- changed sponge layer relaxation parameter units for days to seconds |
| 235 |
|
- turned off sponge layer by default |
| 236 |
|
- changed argument list of OBCS_CALC to myTime+deltaTclock |
| 237 |
|
- fixed about 35 bugs in obcs_external_fields_load |
| 238 |
|
|
| 239 |
|
checkpoint55c_post |
| 240 |
|
o obcs stuff |
| 241 |
|
- new runtime flags useOBCSprescribe, useOBCSbalance |
| 242 |
|
- re-arranged obcs_calc |
| 243 |
|
- moved exf_getobcs to obcs_prescibe_read |
| 244 |
|
obcs_prescibe_read is called after ORLANSKI stuff |
| 245 |
|
and independent of it (executable can contain all). |
| 246 |
|
- updated obcs_check |
| 247 |
|
- added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE. |
| 248 |
|
These may be necessary only if tangential velocities are |
| 249 |
|
prescribed at OB, not sure, needs testing. |
| 250 |
|
o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments |
| 251 |
|
which simplifies the calls and passes the ifc check-bounds test |
| 252 |
|
|
| 253 |
|
checkpoint55b_post |
| 254 |
|
o add a 2D scalar, Z location, exchange_2 routine. |
| 255 |
|
o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows |
| 256 |
|
to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)] |
| 257 |
|
affects advect_cs results (for the wrong reason): update output.txt |
| 258 |
|
o use a more standard discretization for biharmonic viscosity ; |
| 259 |
|
(original version still available with #define MOM_VI_ORIGINAL_VISCA4 ) |
| 260 |
|
affects results of dome set-up: update output.txt |
| 261 |
|
o fix gad_advection.F (CubedSphere part), back to version 1.23 |
| 262 |
|
o fix bug in mom_vi_del2uv.F (CubedSphere part). |
| 263 |
|
|
| 264 |
|
checkpoint55a_post |
| 265 |
|
o merged code to |
| 266 |
|
* prescribe/read time-dependent open boundaries |
| 267 |
|
(works in conjunction with exf, cal) |
| 268 |
|
* sponge layer code for open boundaries |
| 269 |
|
* each boundary N/S/E/W now has its own CPP option |
| 270 |
|
(healthy for the adjoint) |
| 271 |
|
|
| 272 |
|
checkpoint55 |
| 273 |
|
o up-to-date adjoint of previous breaks |
| 274 |
|
- natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix |
| 275 |
|
- global_ocean_ebm: adjoint still needs fix (TLM ok) |
| 276 |
|
- global_ocean.90x40x15: extended GMREDI_OPTIONS.h |
| 277 |
|
- carbon: * remove tr1-related adjoint verification |
| 278 |
|
* add ptracer as control variable |
| 279 |
|
o remove all tr1-related code (ALLOW_PASSIVE_TRACER) |
| 280 |
|
(adjoint stuff still has some tr1 'names', but all use ptracer arrays) |
| 281 |
|
|
| 282 |
|
checkpoint54f_post |
| 283 |
|
o in verification/carbin/ remove experiment related to |
| 284 |
|
ALLOW_PASSIVE_TRACER (array tr1 etc) |
| 285 |
|
code_ad/ input_ad/ results_ad |
| 286 |
|
|
| 287 |
|
o add two new packages |
| 288 |
|
- ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993) |
| 289 |
|
+ subject to optimization (memory) |
| 290 |
|
- opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997) |
| 291 |
|
+ subject to reordering (many GOTOs in the original code) |
| 292 |
|
+ so far opps is called for every (i,j) point, and then operates in |
| 293 |
|
the vertical; one may want to reorder the scheme in order operate in |
| 294 |
|
horizontal slabs at the cost of (a lot of) memory, at least ten new 3D |
| 295 |
|
fields) |
| 296 |
|
o overhaul of IO so that we now have flags for MDSIO and/or MNC |
| 297 |
|
- all verification tests compile and run with linux_ia32_g77 |
| 298 |
|
- defaults are compatible with current input files--nothing |
| 299 |
|
should change if you were not previously using MNC |
| 300 |
|
- MNC output has been added in numerous places (eg. timeave) |
| 301 |
|
but there are still a few writes not yet do-able with MNC |
| 302 |
|
(this is in progress) |
| 303 |
|
- flags now allow for either/or/both use of MDSIO and MNC and |
| 304 |
|
documentation will soon follow |
| 305 |
|
- numerous small formatting cleanups for ProTeX |
| 306 |
|
o add version info (via BUILD_INFO.h) to MNC and stdout |
| 307 |
|
|
| 308 |
|
checkpoint54e_post |
| 309 |
|
o add two new packages |
| 310 |
|
- pp81 (Packanowski and Philander, 1981), Richardson number and |
| 311 |
|
stratification dependent mixing |
| 312 |
|
- my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme |
| 313 |
|
- these scheme operate in a similar manner as KPP (without ghat, of |
| 314 |
|
course), however there is only one diffusivity that is used for both |
| 315 |
|
temperature and salinity (and passive tracers)ç |
| 316 |
|
o add offline package |
| 317 |
|
o add "verification/dic_example" which contains a dic-gchem-ptracer setup |
| 318 |
|
provided by Stephanie Dutkiewicz |
| 319 |
|
o genmake2: add ability to search for C compilers and cleanup test output |
| 320 |
|
- fixes recent SX-6 problems and should help with others (eg. HP-UX) |
| 321 |
|
|
| 322 |
|
checkpoint54d_post |
| 323 |
|
o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed |
| 324 |
|
o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, |
| 325 |
|
leading to additional shift by 5 days each year of integration |
| 326 |
|
(i.e. leading to considerable offset over the years) |
| 327 |
|
o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep |
| 328 |
|
o start with no AB and no initial filtering (staggerTimeStep): |
| 329 |
|
change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5 |
| 330 |
|
o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F |
| 331 |
|
(external loading & cpl import/export stay in forward_step.F) |
| 332 |
|
o update coupling interface to work with new staggerTimeStep |
| 333 |
|
o change MDSIO ptracers_pickup. |
| 334 |
|
o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F); |
| 335 |
|
o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*") |
| 336 |
|
o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell) |
| 337 |
|
|
| 338 |
|
checkpoint54c_post |
| 339 |
|
o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr |
| 340 |
|
this affects (truncation error) output.txt of test-exp: |
| 341 |
|
global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box |
| 342 |
|
o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array) |
| 343 |
|
o change Qnet to always be the net heat flux, (+upward). |
| 344 |
|
affects (truncation error) output of natl_box exp.: updated |
| 345 |
|
o define the max number of passive tracers in PTRACERS_SIZE.h |
| 346 |
|
o start to test mnc routinely in exp0 |
| 347 |
|
o add sea-ice loading (sIceLoad) as a new forcing field. |
| 348 |
|
|
| 349 |
|
checkpoint54b_post |
| 350 |
|
o add testreport "-j JOBS" option for parallel builds (tested and pretty |
| 351 |
|
impressive on Altix and Opteron systems) |
| 352 |
|
o diagnostics can now write NetCDF files through the mnc package |
| 353 |
|
o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output |
| 354 |
|
o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added |
| 355 |
|
o staggerTimeStep & NLFS: rescale T & S surface tendencies. |
| 356 |
|
affects (truncation error) output of lab_sea & natl_box exp.: updated |
| 357 |
|
o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.) |
| 358 |
|
|
| 359 |
|
checkpoint54a_post |
| 360 |
|
o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order). |
| 361 |
|
o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.) |
| 362 |
|
o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished) |
| 363 |
|
o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D) |
| 364 |
|
+ internal_wave (shift in writing cg2d_ini_res) |
| 365 |
|
checkpoint54a_pre |
| 366 |
|
|
| 367 |
|
o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice |
| 368 |
|
- modified verification/lab_sea and natl_box_adjoint accordingly |
| 369 |
|
|
| 370 |
|
checkpoint54 |
| 371 |
|
checkpoint53g_post |
| 372 |
|
o prepare splitting of thermodynamics: store convect.counter in common block |
| 373 |
|
o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error) |
| 374 |
|
output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave |
| 375 |
|
o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection |
| 376 |
|
o new parameter "nShapS": allow to treat differently S from T (nShapT) |
| 377 |
|
o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S) |
| 378 |
|
o restore adjointability |
| 379 |
|
|
| 380 |
|
checkpoint53f_post |
| 381 |
|
o modifications that affect AIM experiment results (update output.txt): |
| 382 |
|
- no advection of S at top interface Nr (pkg/generic_advdiff) |
| 383 |
|
- air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F) |
| 384 |
|
o AIM pkg: |
| 385 |
|
- include stability function into surf.Flux derivative relative to Tsurf |
| 386 |
|
- calculate clear-sky radiation & surface temp. change (for diagnostics) |
| 387 |
|
|
| 388 |
|
checkpoint53e_post |
| 389 |
|
o merged cylindrical coord configuration |
| 390 |
|
o added rotating_tank experiment |
| 391 |
|
checkpoint53e_pre |
| 392 |
|
|
| 393 |
|
checkpoint53d_post |
| 394 |
|
o faulks upgraded: re-generate output.txt that have changed: |
| 395 |
|
global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box |
| 396 |
|
o Added Bryan and Lewis, 1979, vertical diffusivity profile |
| 397 |
|
o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. |
| 398 |
|
o added Sadourny discretization of Coriolis |
| 399 |
|
- moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h |
| 400 |
|
- re-enabled use of omega3 (useAbsVorticity) |
| 401 |
|
o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for |
| 402 |
|
vector-invariant equations |
| 403 |
|
- note: does *NOT* yet use same variable visc. for no-slip BC's. |
| 404 |
|
o recoded the lateral boundary conditions for non-hydrostatic w, this time |
| 405 |
|
hopefully without new bugs |
| 406 |
|
- still to do: biharmonic friction for non-hydrostatic w |
| 407 |
|
o bug fix for mom_*_sidedrag: rA -> rAs,rAw |
| 408 |
|
o regenerated output for global_ocean_ebm (using -ieee) |
| 409 |
|
o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation |
| 410 |
|
of mom_common/ |
| 411 |
|
- simple re-arrangement of instructions within computing loop |
| 412 |
|
checkpoint53d_pre |
| 413 |
|
|
| 414 |
|
checkpoint53c_post |
| 415 |
|
o new version of coupler for AIM+thSIce and Ocean models |
| 416 |
|
- new fields (SSS,h_MixLayer ...) are exchanged through the coupler |
| 417 |
|
- land: change Evaporation of snow |
| 418 |
|
- aim with thSIce: fix bug in snow-precip. |
| 419 |
|
o changes to calc_gw.F |
| 420 |
|
- bug fix for w^2 term near the bottom boundary |
| 421 |
|
- (hopefully) improve the lateral slip boundary condtions for use with |
| 422 |
|
partial/looped cells |
| 423 |
|
- because the bug fix changes two verification experiments anyway (exp5 |
| 424 |
|
and plume on slope), change the lateral boundary condition from half slip |
| 425 |
|
to the value of no_slip_sides |
| 426 |
|
o ebm package wasnt quite up to the parallel task. Fixed that. |
| 427 |
|
o Adjoint of EBM package + verification |
| 428 |
|
* TLM OK |
| 429 |
|
* ADM not sufficient accuracy yet (needs further testing) |
| 430 |
|
|
| 431 |
|
checkpoint53b_post |
| 432 |
|
o Commiting new energy balance model to repository |
| 433 |
|
* package is pkg/ebm |
| 434 |
|
* verif. is verification/global_ocean_ebm |
| 435 |
|
* references are in ebm_driver.F |
| 436 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 437 |
|
C Global thermohaline circulation. Part I: |
| 438 |
|
C Sensitivity to atmospheric moisture transport. |
| 439 |
|
C J. Climate 12(1), 71-82 |
| 440 |
|
C * X. Wang, P. Stone and J. Marotzke, 1999: |
| 441 |
|
C Global thermohaline circulation. Part II: |
| 442 |
|
C Sensitivity with interactive transport. |
| 443 |
|
C J. Climate 12(1), 83-91 |
| 444 |
|
C * M. Nakamura, P. Stone and J. Marotzke, 1994: |
| 445 |
|
C Destabilization of the thermohaline circulation |
| 446 |
|
C by atmospheric eddy transports. |
| 447 |
|
C J. Climate 7(12), 1870-1882 |
| 448 |
|
o Will need long integration testing. |
| 449 |
|
checkpoint53b_pre |
| 450 |
|
|
| 451 |
|
o created pkg/mom_common in preparation for variable viscosity code |
| 452 |
|
o renamed and split ini_mnc_io |
| 453 |
|
o pkg/land: only liquid water can diffuse or run-off |
| 454 |
|
o AIM using land: soil wetness availability account for snow |
| 455 |
|
o added printMapIncludesZeros to EEPARMS namelist |
| 456 |
|
|
| 457 |
|
checkpoint53a_post |
| 458 |
|
o restore TAMC compatiility for exf_constants.h |
| 459 |
|
(no usage of _d in .h) |
| 460 |
|
o Additional storing in KPP in an attempt to fix |
| 461 |
|
TAMC problem with adjoint of KPP code. |
| 462 |
|
(no success...) |
| 463 |
|
Identical code works fine with TAF. |
| 464 |
|
o Fixed verification/natl_box_adjoint experiments. |
| 465 |
|
Initial conditions for Experiments 4 and 5 are now |
| 466 |
|
set to "SEAICE_initialHEFF=0", which is more reasonable, |
| 467 |
|
and hence gives results closer to that of Experiment 2. |
| 468 |
|
Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again. |
| 469 |
|
|
| 470 |
|
checkpoint53 |
| 471 |
|
o stable checkpoint with up to date adjoint |
| 472 |
|
TLM tests only run for 1st grdchk at the moment. Its unclear if |
| 473 |
|
this is a code problem or a problem with resetting code for g_ |
| 474 |
|
variables that is being autogenerated wrong. |
| 475 |
|
Otherwise: |
| 476 |
|
o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix. |
| 477 |
|
o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ) |
| 478 |
|
are both still in chaos following their security messes. |
| 479 |
|
|
| 480 |
|
checkpoint52n_post |
| 481 |
|
o various build (mostly genmake2) changes including: |
| 482 |
|
- ability to build/run more easily within Cygwin and MacOS X |
| 483 |
|
- more complicated Makefiles with a stronger dependence on Gnu Make |
| 484 |
|
o pkg/seaice modifications |
| 485 |
|
- added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost |
| 486 |
|
of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer |
| 487 |
|
and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm |
| 488 |
|
- changed proxy for geostrophic velocity and updated |
| 489 |
|
verification/lab_sea/results/* accordingly |
| 490 |
|
- removed ADI dynamic solver from pkg/seaice |
| 491 |
|
- replaced all occurrences of 1/CSTICE or 1/CSUICE |
| 492 |
|
they caused a segmentation fault under certain circumstances |
| 493 |
|
- removed unused field WATR |
| 494 |
|
o bug fix in exf-package: |
| 495 |
|
- u/vwind are defined at tracer/pressure points. The values of u/vwindmask |
| 496 |
|
now reflect that. |
| 497 |
|
o small fixes in the cal-package: |
| 498 |
|
- set reference date to first of January for the 'model'-calendar |
| 499 |
|
- failing of cal_CheckDate in cal_FullDate now actually results in a |
| 500 |
|
warning |
| 501 |
|
o small modifications in exf-package to increase flexibility: |
| 502 |
|
- change climtempfreeze from a constant to a runtime parameter that |
| 503 |
|
is specified in data.exf_clim (default = -1.9) |
| 504 |
|
- introduce runtime parameter windstressmax (default = 2.0) that is |
| 505 |
|
specified in data.exf |
| 506 |
|
o fix in pkg/thsice: |
| 507 |
|
- update Evap (Tsf changes) to be consistent with Latent heat flux |
| 508 |
|
- maintain snow precipitation unchanged (even if Tsf >=0). |
| 509 |
|
both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice |
| 510 |
|
|
| 511 |
|
checkpoint52m_post |
| 512 |
|
o commented out call to cal_GetMonthsRec in swfrac.F and added some comments; |
| 513 |
|
this does not change any of the results, because myIter=0 in swfrac always |
| 514 |
|
lead to jwtype=2 (the default anyway), but the call makes little sense |
| 515 |
|
as a default |
| 516 |
|
o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated |
| 517 |
|
o re-work pkg/thsice interface with ocean & bulk_force pkg to allow |
| 518 |
|
atmospheric model (AIM) to use it ; add a "slab ocean" component. |
| 519 |
|
o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice) |
| 520 |
|
o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice |
| 521 |
|
o extending useSingleCpuIO option to work with new exch2 I/O format |
| 522 |
|
- old-style, missing-tile I/O is still accessible by defining CPP |
| 523 |
|
option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h |
| 524 |
|
o monitor package can write to NetCDF files and/or STDOUT |
| 525 |
|
o fix re-definition bug in MNC_GRID_INIT_ALL() |
| 526 |
|
o doc/api_reference added |
| 527 |
|
- a framework for building an API Reference Manual using all |
| 528 |
|
the "protex" comments embedded in the code |
| 529 |
|
- see pkg/generic_advdiff, pkg/mnc for examples |
| 530 |
|
o MNC: |
| 531 |
|
- make myThid the last argument for all subroutines |
| 532 |
|
- new default for the grid files: NO halos |
| 533 |
|
- add useMNC and other run-time flags |
| 534 |
|
- separate per-file-group handling of the unlimited dimension |
| 535 |
|
- early initialization of MNC w/ flags read at the eeboot stage |
| 536 |
|
and lookup tables set in initialize_fixed |
| 537 |
|
- write all MNC output to a freshly-created directory |
| 538 |
|
o thermodynamics sea-ice (thsice) is now tested with testreport. |
| 539 |
|
o test exp. advect_cs: use the standard cs32 grid ; update output. |
| 540 |
|
o Added functionality to grdchk: |
| 541 |
|
pick global i,j,k position (or nearest wet) where to perform check. |
| 542 |
|
|
| 543 |
|
checkpoint52l_post |
| 544 |
|
o new land formulation: |
| 545 |
|
a) use ground enthalpy as prognostic variable to ensure exact |
| 546 |
|
energy conservation. |
| 547 |
|
b) account for water temperature and for latent heat of freezing |
| 548 |
|
in all processes (rain, run-off, ground storage) |
| 549 |
|
c) compute surface and ground temperature implicitly. |
| 550 |
|
o aim_v23 modification for new land model: |
| 551 |
|
a) Treat separately land / ocean / sea-ice surface fluxes |
| 552 |
|
to allow implicit computation of land & sea-ice surface temp. |
| 553 |
|
b) add snow precipitation. |
| 554 |
|
checkpoint52l_pre |
| 555 |
|
|
| 556 |
|
o fix problem (when 1 tile is empty) in min/max monitor. |
| 557 |
|
o fix bug in timeAve (u,vZetatave in common block) |
| 558 |
|
o no restoring terms under ice for pkg/seaice |
| 559 |
|
o moved SEAICE_DO_DIAGS to S/R do_the_model_io |
| 560 |
|
o bug fix for pkg/seaice pickups |
| 561 |
|
o change MNC call locations and add coordinate attributes |
| 562 |
|
o mask vorticity at the corner ; affects global_ocean.cs output |
| 563 |
|
o fix ini_curvilinear_grid ; test CS experiments with mpi |
| 564 |
|
o aim.5l_cs: modify sea-ice fraction input file ; update output |
| 565 |
|
o exf: Adding simple range check routine for exf fields after read |
| 566 |
|
|
| 567 |
|
checkpoint52k_post |
| 568 |
|
o removed top-level directory "diags" |
| 569 |
|
- we migrated these functions to pkg/timeave a long time ago |
| 570 |
|
o fixed bug introduced in pkg/monitor |
| 571 |
|
o accuracy ctrlprec = 32 insuffient for gradient checks using |
| 572 |
|
averaged fields (I/O via cost_averages) |
| 573 |
|
-> use ctrl.h in active_file*.F to control I/O precision. |
| 574 |
|
o paramter list of CALL ADTHE_MAIN_LOOP |
| 575 |
|
o added initial do_the_model_io to ecco |
| 576 |
|
o set all ...Freq to zero after cost_final |
| 577 |
|
taveFreq, dumpFreq, pChkptFreq |
| 578 |
|
o MAIN and ECCO differentiability restored |
| 579 |
|
|
| 580 |
|
checkpoint52j_post |
| 581 |
|
o fix nchklev in tamc.h for global_ocean... |
| 582 |
|
o Bringing flow and store directives up-to-date |
| 583 |
|
o Really weird thing! |
| 584 |
|
call do_the_model_io from the_main_loop with parameters |
| 585 |
|
starttime, niter0, instead of mytime, myiter, screws up the adjoint: |
| 586 |
|
TAF places a faulty re-call of initialise_varia |
| 587 |
|
after cost_final call which should not be there! |
| 588 |
|
checkpoint52j_pre |
| 589 |
|
|
| 590 |
|
o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and |
| 591 |
|
error messages |
| 592 |
|
o fix errorMessageUnit problem. remove old version of mdsio from eesup/src |
| 593 |
|
o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating |
| 594 |
|
debug output |
| 595 |
|
o modfied mdsio_writefield.F to handle non-global files under exch2 |
| 596 |
|
o update AIM Cubed-Sphere exp (aim.5l_cs): |
| 597 |
|
use land, p*, and Franco.M forcing fields with fractional land-sea mask. |
| 598 |
|
o update AIM Equatorial Channel exp: |
| 599 |
|
use standard aim_v23 pkg and change the SST fields to be more realistic. |
| 600 |
|
o globalFile now works with exch2 |
| 601 |
|
o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and |
| 602 |
|
mon_vort3.F to make exch2 friendly with >1 tile per cube face |
| 603 |
|
o limit timeave output for hi-res integrations |
| 604 |
|
|
| 605 |
|
checkpoint52i_post |
| 606 |
|
o removed CPP_EEOPTIONS.h from verification/*/code |
| 607 |
|
o updated the tiling for global_ocean_pressure |
| 608 |
|
checkpoint52i_pre |
| 609 |
|
|
| 610 |
|
o update aim.5l_LatLon using the standard aim_v23 pkg (instead of |
| 611 |
|
the old pkg/aim). |
| 612 |
|
|
| 613 |
|
checkpoint52h_pre |
| 614 |
|
o shortened offending lines in exch2_send_rx?.template |
| 615 |
|
o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator |
| 616 |
|
o genmake2: add build & execute test for NetCDF code |
| 617 |
|
o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed |
| 618 |
|
old grid files, moved CPP_EEMACROS.h to pkg/exch2 |
| 619 |
|
o added useSingleCPUIO flag to monitor.F and mon_out.F |
| 620 |
|
o added temporary hack for sea-ice dynamics on the cube: |
| 621 |
|
metric terms are ignored and it is assumed that |
| 622 |
|
there is no sea-ice on cube faces 1, 2, 4, and 5. |
| 623 |
|
|
| 624 |
|
checkpoint52f_post |
| 625 |
|
o added exch2 cube routines to pkg/exch2 |
| 626 |
|
o modified hs94.cs-32x32x5 to use it |
| 627 |
|
o added new grid files to hs94.cs-32x32x5 |
| 628 |
|
checkpoint52f_pre |
| 629 |
|
|
| 630 |
|
checkpoint52e_post |
| 631 |
|
o first attempt to solve vertical advection (momemtum & T,S) Implicitly |
| 632 |
|
for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom) |
| 633 |
|
o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F) |
| 634 |
|
to work with implicit vertical advection and AB ; |
| 635 |
|
o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme. |
| 636 |
|
o update output (gad_calc_rhs.F changes affect truncation error) of exp: |
| 637 |
|
front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box |
| 638 |
|
checkpoint52e_pre |
| 639 |
|
|
| 640 |
|
o fix bug in impldiff when Nr=1 or Nr=2. |
| 641 |
|
o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt |
| 642 |
|
o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test. |
| 643 |
|
o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2 |
| 644 |
|
ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure |
| 645 |
|
o added exf_offset_atemp for Celsius to Kelvin conversion of atemp |
| 646 |
|
o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024 |
| 647 |
|
o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations |
| 648 |
|
|
| 649 |
|
checkpoint52d_post |
| 650 |
|
o re-tiled many expts to allow comparison in multi-processor mode |
| 651 |
|
- updated output accordingly |
| 652 |
|
- changed hs94.128x64x5 to use intial T from file rather than use the |
| 653 |
|
random number generator |
| 654 |
|
o add infrastructure in model routines for fizhi and gridalt packages |
| 655 |
|
o change global_ocean.cs32x15 because of Pb with GM on CS-grid. |
| 656 |
|
o changes to permit hi-res, cubed-sphere, configuration |
| 657 |
|
- added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F |
| 658 |
|
- added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F |
| 659 |
|
- added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation |
| 660 |
|
of surface winds for the cube |
| 661 |
|
(A verification experiment, based on global_ocean.cs32x15, but with |
| 662 |
|
pkg/seaice turned on and with on-the-fly interpolation from the NCEP |
| 663 |
|
Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice, |
| 664 |
|
complete with example surface forcing files and matlab scripts to look |
| 665 |
|
at the output and compare it with that of global_ocean.cs32x15.) |
| 666 |
|
o packages pickup: $PKG_write_pickup called from packages_write_pickup ; |
| 667 |
|
but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code |
| 668 |
|
to conform to the common rule. |
| 669 |
|
o check-in the first version of the coupler + interfaces for multi-components |
| 670 |
|
set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI. |
| 671 |
|
- imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD). |
| 672 |
|
- atmosphere: use pkg aim_v23 ; no sea-ice for now. |
| 673 |
|
- ocean and atmos. share the same horizontal grid (no interpolation). |
| 674 |
|
- exchanges between component and coupler is done in forward_step |
| 675 |
|
o new verification experiment, cpl_aim+ocn: |
| 676 |
|
coupled ocean - AIM atmosphere on cs32 grid. |
| 677 |
|
|
| 678 |
|
checkpoint52d_pre |
| 679 |
|
o surface flux time-av diagnostic modified for NLFS & RealFreshWater |
| 680 |
|
o add call to AIM pendant S/R in external_forcing & external_fields_load.F |
| 681 |
|
|
| 682 |
|
checkpoint52c_post |
| 683 |
|
o Fixing OPTIONS files for use of exf: |
| 684 |
|
- ALLOW_ECCO not needed |
| 685 |
|
- ECCO_CPPOPTIONS.h should not be included from |
| 686 |
|
EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h |
| 687 |
|
as has been the case in the past |
| 688 |
|
- All cal/exf related options are currently set in |
| 689 |
|
single header file. Should remain so until we |
| 690 |
|
agree on a consistent new policy. |
| 691 |
|
o Removed all CPP options for cal package. |
| 692 |
|
cal has no more CPP options. |
| 693 |
|
o modified STOREs in GAD_ADVECTION |
| 694 |
|
o corrected key comp. for passkey |
| 695 |
|
|
| 696 |
|
checkpoint52b_post |
| 697 |
|
o new version: "thsice" of thermodynamic sea-ice pkg: |
| 698 |
|
- only 1 call from "forward_step"; conserve energy, fresh-water & salt. |
| 699 |
|
- modify fluxes but do not change theta directly; |
| 700 |
|
- light cleaning of bulk_force pkg (still needed with thsice). |
| 701 |
|
- add forcing fields + data files in global_ocean.cs32x15/inp_thsice |
| 702 |
|
+ output_thsice.txt to test thsice & bulk_force pkgs. |
| 703 |
|
o put back grid & coriolis monitor output. |
| 704 |
|
checkpoint52b_pre |
| 705 |
|
|
| 706 |
|
o call "do_the_model_io" at the beginning (=> dump initial state) |
| 707 |
|
o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P) |
| 708 |
|
o sort out interplay between tamc.h and PTRACERS_OPTIONS.h |
| 709 |
|
(need info on NUMBER_OF_PTRACERS) |
| 710 |
|
o missing PTRACERS headers in some routines |
| 711 |
|
o default tamc.h in pkg/autodiff supposed to crash |
| 712 |
|
to ensure proper customization |
| 713 |
|
|
| 714 |
|
checkpoint52a_post |
| 715 |
|
o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp |
| 716 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 717 |
|
- subroutine FREEZE_SURFACE now limits only surface temperature |
| 718 |
|
and is called in FORWARD_STEP (if allowFreezing=.TRUE.) |
| 719 |
|
=> new output.txt for global_ocean.cs32x15 & global_with_exf |
| 720 |
|
- keep the old version of FREEZE for backward compatibility; |
| 721 |
|
global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE. |
| 722 |
|
- corresponding modifs for TAF directives |
| 723 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 724 |
|
o time-averaged output for pkg/ptracers |
| 725 |
|
o fix problem with ECCO-related divided adjoint |
| 726 |
|
snapshot file was missing some ad-variables, |
| 727 |
|
but no warning issued by TAF |
| 728 |
|
|
| 729 |
|
checkpoint52a_pre |
| 730 |
|
o some bug fixes for #undef REAL4_IS_SLOW |
| 731 |
|
|
| 732 |
|
checkpoint52 = ecco_c52_e35 |
| 733 |
|
o after testing adjoints of checkpoint51u_post |
| 734 |
|
|
| 735 |
|
checkpoint51u_post |
| 736 |
|
o this is the post-merge tag of the ecco-branch |
| 737 |
|
(needs another clean checkout and re-testing) |
| 738 |
|
o various natl_box_adjoint configs and results |
| 739 |
|
but no input fields |
| 740 |
|
o obcs adjoint not yet merged! |
| 741 |
|
o adding ECCO global 1x1 and 2x2 degree configs |
| 742 |
|
o updated/extended some store directives for seaice |
| 743 |
|
o pkg/ecco now containes ecco-specific part of cost function |
| 744 |
|
o top level routines the_main_loop, forward_step |
| 745 |
|
supersede those in model/src/ |
| 746 |
|
previous input data.cost now in data.ecco |
| 747 |
|
(new namelist ecco_cost_nml) |
| 748 |
|
o in ctrl/ cleaned some cross-dependencies and updated CPP options |
| 749 |
|
|
| 750 |
|
checkpoint51t_post |
| 751 |
|
o this is the pre-merge tag of the ecco-branch |
| 752 |
|
|
| 753 |
|
checkpoint51s_post |
| 754 |
|
o cleanup: removed various obsolete #define-s |
| 755 |
|
o pkg/grdchk |
| 756 |
|
- renamed 'ph-grd 3' to 'grad-res' |
| 757 |
|
- merged from ecco-branch |
| 758 |
|
(remaining bug fixes for obcs gradient checks) |
| 759 |
|
- additional high-precision output for testreport |
| 760 |
|
(grep for 'precision_grdchk_result') |
| 761 |
|
|
| 762 |
|
checkpoint51r_post |
| 763 |
|
o cleaned up or removed CPP_OPTIONS.h files |
| 764 |
|
o updated results for some of the tests to reflect the new |
| 765 |
|
optfiles (-ieee: -O0 instead of -O3) |
| 766 |
|
|
| 767 |
|
checkpoint51q_post |
| 768 |
|
o cd_code: |
| 769 |
|
- moved cd_scheme.F -> cd_code_scheme.F |
| 770 |
|
- separate read_checkpoint from cd_code_ini_vars.F |
| 771 |
|
- separated cd_code part from write_checkpoint |
| 772 |
|
- updated AD_SOURCE, generated .flow |
| 773 |
|
- added CD_CODE_VARS.h to the_main_loop |
| 774 |
|
- Moving cd_code specific store dir.s to pkg/cd_code |
| 775 |
|
o ctrl package totally restructured |
| 776 |
|
- pack/unpack now optional and decoupled from |
| 777 |
|
xx_/adxx_ I/O |
| 778 |
|
- ctrl_pack/unpack cleaned |
| 779 |
|
(new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F) |
| 780 |
|
- confined inclusion of AD_CONFIG.h to where necessary. |
| 781 |
|
o genmake2: changed AD dependencies from SRCFILES to AD_FILES |
| 782 |
|
|
| 783 |
|
checkpoint51p_post |
| 784 |
|
o create initial cd_code package |
| 785 |
|
- WARNING: the initialization of fields within packages |
| 786 |
|
is broken because INI_FIELDS (where READ_CHECKPOINT is |
| 787 |
|
called) is called *before* PACKAGES_INIT_VARIABLES. |
| 788 |
|
This seems to be backwards since |
| 789 |
|
1) its important to initially zero the entire field including |
| 790 |
|
the "halo" region |
| 791 |
|
2) zeroing needs to be done *before* reading pickup info |
| 792 |
|
and the pickup call might or might not happen in any |
| 793 |
|
particular run |
| 794 |
|
- this needs an overhaul for R2 |
| 795 |
|
o cleanup verification/*/code/GMREDI_OPTIONS.h |
| 796 |
|
o cleanup testreport |
| 797 |
|
|
| 798 |
|
checkpoint51o_post |
| 799 |
|
o bringing AD-related verif's up to date with genmake2 |
| 800 |
|
- carbon/ |
| 801 |
|
- global_ocean.90x40x15/ |
| 802 |
|
- hs.94.1x64x5/ |
| 803 |
|
- (front_relax/ ) |
| 804 |
|
o (more) consistent directory structure for AD-related verif.'s |
| 805 |
|
o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK |
| 806 |
|
o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF |
| 807 |
|
o bug fix in find_alpha.F for MDJWF: |
| 808 |
|
- modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for |
| 809 |
|
change rho -> rho-rhoConst |
| 810 |
|
- replace call find_rho to find_rhonum |
| 811 |
|
o initialisation of rFlx extended to full array (required by TAF) |
| 812 |
|
and shifted to thermodynamics |
| 813 |
|
o removed PTRACERS.h in ptracers routine |
| 814 |
|
o added surfacetendencyPtr to S/R parameter list pracers_forcing |
| 815 |
|
o Correcting initialisations for fVerU, fVerV. |
| 816 |
|
o helping TAF to recognize dependency on kUp for |
| 817 |
|
fVerU, fVerV |
| 818 |
|
o Replacing delZ by delR in pkg/ctrl/ |
| 819 |
|
checkpoint51o_pre |
| 820 |
|
|
| 821 |
|
o undid all of cp51 pending some cleanups and discussion |
| 822 |
|
o added the [#include "AD_CONFIG.h"] statement to all files that need |
| 823 |
|
it for adjoint/tl #defines |
| 824 |
|
o re-worked the build logic in genmake2 to support AD_CONFIG.h |
| 825 |
|
o removed tools/genmake since it no longer works |
| 826 |
|
|
| 827 |
|
checkpoint51n_post |
| 828 |
|
o modifications to make FREEZE flux visible to pkg/kpp |
| 829 |
|
- moved surfaceTendencyTice from pkg/seaice to main code |
| 830 |
|
- FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP |
| 831 |
|
- subroutine FREEZE now limits only surface temperature |
| 832 |
|
(this means new output.txt for global_ocean.90x40x15, |
| 833 |
|
global_ocean.cs32x15, and global_with_exf) |
| 834 |
|
o added surface flux output variables to TIMEAVE_STATVARS |
| 835 |
|
|
| 836 |
|
checkpoint51n_pre |
| 837 |
|
o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F |
| 838 |
|
o added [#include "AD_CONFIG.h"] to all files that use the following |
| 839 |
|
defines: |
| 840 |
|
- ALLOW_ADJOINT_RUN |
| 841 |
|
- ALLOW_TANGENTLINEAR_RUN |
| 842 |
|
- ALLOW_ECCO_OPTIMIZATION |
| 843 |
|
|
| 844 |
|
checkpoint51m_post |
| 845 |
|
o incorporating changes to get TAMC/TAF working in genmake2 |
| 846 |
|
- added new TAMC/TAF targets to the Makefile |
| 847 |
|
- various cleanups related to package handling |
| 848 |
|
- these changes should have no impact on the forward model |
| 849 |
|
|
| 850 |
|
checkpoint51l_post |
| 851 |
|
o changes to pkg/cal and pkg/exf that allow and speed-up long integrations |
| 852 |
|
- faster algorithm for cal_addtime.F |
| 853 |
|
- higher precision arithmetic, where needed |
| 854 |
|
- pkg/exf *startdate variables changed from calendar date to |
| 855 |
|
model integration time |
| 856 |
|
|
| 857 |
|
checkpoint51l_pre |
| 858 |
|
o add salt flux to forcing fields (used when salty sea-ice forms or melts) |
| 859 |
|
o enable to apply restoring on S & T only in a latitude band. |
| 860 |
|
o update output (external_forcing_surf modif. change truncation errors) |
| 861 |
|
global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box |
| 862 |
|
|
| 863 |
|
checkpoint51k_post |
| 864 |
|
o change default to: useNHMTerms=.FALSE. |
| 865 |
|
- new output.txt for atmos. exp (NHMTerms were wrong but now turned off): |
| 866 |
|
adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5 |
| 867 |
|
- new output.txt for idealized oceanic exp (NHMTerms are now turned off): |
| 868 |
|
exp1, ideal_2D_oce |
| 869 |
|
- change data file of oceanic exp (leave the results unchanged for now) |
| 870 |
|
exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box |
| 871 |
|
o set gravitySign automatically according to the vertical coordinate used |
| 872 |
|
(and change sign: back to "logical" value: +1 when R increases downward) |
| 873 |
|
o added an include barrier to the default CPP_OPTIONS.h and |
| 874 |
|
removed the #include "PACKAGES_CONFIG.h" from it |
| 875 |
|
o fix a bug in mom_fluxform (from chk51j_post) |
| 876 |
|
|
| 877 |
|
checkpoint51j_post |
| 878 |
|
o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/ |
| 879 |
|
o adjusted some flow directives (dynamics, thermodynamics) |
| 880 |
|
o added cubed-sphere case to test cost function |
| 881 |
|
o heckpoint_lev?_directives.h now include |
| 882 |
|
pkg-specific directives, whenever those are enabled. |
| 883 |
|
o Moving pkg-specific flow directives to corresponding pkg |
| 884 |
|
Moving pkg-specific differentiation list to corresponding pkg |
| 885 |
|
Moving pkg-specific checkpoint-lev storing to corresponding pkg |
| 886 |
|
---> conventions are |
| 887 |
|
- pkg_ad.flow |
| 888 |
|
- pkg_ad_diff.list |
| 889 |
|
- pkg_ad_check_lev?_dir.h |
| 890 |
|
|
| 891 |
|
checkpoint51i_post |
| 892 |
|
o merge of the branch-genmake2 |
| 893 |
|
- knowingly breaks the older genmake |
| 894 |
|
- automatic generation of all ALLOW_${PKG_NAME} defines |
| 895 |
|
- new testreport supersedes older testscript |
| 896 |
|
o large number of package inclusion and header cleanups |
| 897 |
|
checkpoint51i_pre |
| 898 |
|
|
| 899 |
|
o new output for adjoin of global ocean vector invariant |
| 900 |
|
o fix for checkpoint of thermodynamic seaice and bulk_force |
| 901 |
|
o Steph gchem various cleanups |
| 902 |
|
|
| 903 |
|
checkpoint 51h_pre |
| 904 |
|
o fixed some single quotes |
| 905 |
|
o modify gchem pkg to be more versatile |
| 906 |
|
o modifications to clean up dic pkg |
| 907 |
|
o add pkg/cfc |
| 908 |
|
|
| 909 |
|
checkpoint51g_post |
| 910 |
|
o provide links for ARPACK and ADM*TLM |
| 911 |
|
o start removing verification/vero/ |
| 912 |
|
o update AD-related stuff |
| 913 |
|
(in particular some IF-statements in model/src/ routines) |
| 914 |
|
o adding to verification/global_ocean.90x40x15/ adjoint of |
| 915 |
|
vector invariant setup |
| 916 |
|
|
| 917 |
|
checkpoint51f_post |
| 918 |
|
o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif) |
| 919 |
|
o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation |
| 920 |
|
of tracer Green's fucntions for ocean inversion project. |
| 921 |
|
|
| 922 |
|
checkpoint51f_pre |
| 923 |
|
o Added on-the-fly spatial interpolation capability |
| 924 |
|
"USE_EXF_INTERPOLATION" to pkg/exf. |
| 925 |
|
- This is a temporary Cartesian-grid hack until |
| 926 |
|
the super-duper ESMF coupler becomes available. |
| 927 |
|
- See verification/global_with_exf/README for usage example. |
| 928 |
|
- Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid |
| 929 |
|
flags and modified pkg/seaice accordingly. |
| 930 |
|
o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F, |
| 931 |
|
and pkg/kpp/kpp_transport_ptr.F for dealing with tracer |
| 932 |
|
non-local transport term. |
| 933 |
|
|
| 934 |
|
checkpoint51e_post |
| 935 |
|
o pkg/mom_vecinv: |
| 936 |
|
- changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec) |
| 937 |
|
- add time-ave diagnostic of vorticity advection. |
| 938 |
|
o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV. |
| 939 |
|
o atmospheric geopotential: - include water vapor effect; |
| 940 |
|
- use p^kappa in p* scaling. |
| 941 |
|
o land pkg: read initial state from files. |
| 942 |
|
o AIM : add stratospheric drag in the upper level |
| 943 |
|
|
| 944 |
|
checkpoint51d_post |
| 945 |
|
o change function ILNBLNK (=> last non-blank char.) to return zero |
| 946 |
|
(instead of the string length) when the string. char is empty |
| 947 |
|
o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid) |
| 948 |
|
o modif's to restore TAMC compatibility |
| 949 |
|
- avoid "_d" constructs in PARAMETER declarations |
| 950 |
|
- avoid interrupting lines by comment lines |
| 951 |
|
o Use cluster local disks for purely local I/O |
| 952 |
|
vs. globally visible disks needed for ctrl stuff |
| 953 |
|
(merged from ecco-branch) |
| 954 |
|
- new active_file_loc... and mdsio_..._loc routines |
| 955 |
|
- affected packages: autodiff, ctrl, grdchk, mdsio |
| 956 |
|
|
| 957 |
|
checkpoint51c_post |
| 958 |
|
o introducing integer flag debugLevel |
| 959 |
|
- debLevZero: suppress all output |
| 960 |
|
- debLevA: standard |
| 961 |
|
- debLevB: equivalent to current debugMode=.TRUE. |
| 962 |
|
o introducing pathname variable mdsioLocalDir for mdsio |
| 963 |
|
that can be specified at runtime |
| 964 |
|
(relevant for cluster I/O to local disk) |
| 965 |
|
` |
| 966 |
|
>>>checkpoint51b_post |
| 967 |
|
adjoint of ptracers |
| 968 |
|
o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM |
| 969 |
|
o extended state in checkpoint_lev?, etc. |
| 970 |
|
o alternative ctrl/cost with tr1 or ptracer |
| 971 |
|
o new comlev1_bibj_ptracers |
| 972 |
|
o new ptracers.flow |
| 973 |
|
o made ptracers_forcing same as external_forcing_s |
| 974 |
|
o added verification for adjoint with ptracers |
| 975 |
|
- adm. grdchk fail so far |
| 976 |
|
- tlm. grdchk OK |
| 977 |
|
- checked tapelev/comlev recomputations: OK |
| 978 |
|
<<<checkpoint51b_pre |
| 979 |
|
|
| 980 |
|
checkpoint51a_post |
| 981 |
|
o added code for biogeochemistry package |
| 982 |
|
- new pkgs: dic, gchem |
| 983 |
|
- new subroutine in ptracers |
| 984 |
|
o modify code for biogeo packages |
| 985 |
|
- in model/src and pkg/ptracers |
| 986 |
|
|
| 987 |
|
checkpoint51 |
| 988 |
|
o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN |
| 989 |
|
- autodiff, ctrl, exf, grdchk, seaice |
| 990 |
|
kept separate packages |
| 991 |
|
- cost, ecco, obcs |
| 992 |
|
o updating verification/internal_wave, verification/lab_sea |
| 993 |
|
(all verif's pass on faulks.lcs.mit.edu RH7.3, g77) |
| 994 |
|
|
| 995 |
|
checkpoint50i_post |
| 996 |
|
o Preparing next differentiable checkpoint and sync |
| 997 |
|
of MAIN vs. ecco-branch |
| 998 |
|
- 1st step: this one is differentiable |
| 999 |
|
- 2nd step: next(! not this) checkpoint will have updated packages |
| 1000 |
|
from ecco-branch) |
| 1001 |
|
|
| 1002 |
|
checkpoint50h_post |
| 1003 |
|
o new package "land": provide surface BC for AIM. |
| 1004 |
|
o pkg/ptracers: apply exchange to all tracers after reading a pickup. |
| 1005 |
|
o AIM: use true log-P extrapolation for near surface temp (= as in |
| 1006 |
|
F.Molteni paper) ; update aim.5l_cs output. |
| 1007 |
|
o New variable in PARM03 for more flexible pickups |
| 1008 |
|
o somewhat cleaned package initialisation sequence for |
| 1009 |
|
ctrl/ cost/ ecco/ in packages_... routines |
| 1010 |
|
|
| 1011 |
|
checkpoint50g_post |
| 1012 |
|
o merged with release1_p17 (pkg/seaice and verification/lab_sea) |
| 1013 |
|
- added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics |
| 1014 |
|
- LSR sea-ice dynamic solver moved to SouthWest B-grid location and |
| 1015 |
|
made the default because of faster convergence than ADI |
| 1016 |
|
|
| 1017 |
|
checkpoint50f_post |
| 1018 |
|
o exf totally restructured |
| 1019 |
|
- replaced all exf_set_ routines by one generic exf_set_gen.F |
| 1020 |
|
and made sure it's still differentiable |
| 1021 |
|
- split exf_getffields.F into new exf_bulkformulae.F |
| 1022 |
|
- exf_inscal_/exf_outscal_ suffixes consistent with field names |
| 1023 |
|
- updated adjoint/makefile and relevant verif. accordingly |
| 1024 |
|
|
| 1025 |
|
checkpoint50f_pre |
| 1026 |
|
o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ; |
| 1027 |
|
+ change Evap over land. (update aim.5l_cs output) |
| 1028 |
|
o added missing .cvsignores and made uniform across expts |
| 1029 |
|
o changed configuration of tidal_basin_2d expt |
| 1030 |
|
o added pkg/debug functions for tracing code in fatal crashes |
| 1031 |
|
o tidied pkg/monitor to use MONITOR_OPTIONS.h |
| 1032 |
|
o new fn in pkg/monitor to stop model if solution grows too big |
| 1033 |
|
o removed lots of single quotes from comments |
| 1034 |
|
|
| 1035 |
|
checkpoint50e_post |
| 1036 |
|
o make KPP work with PTRACERS |
| 1037 |
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 1038 |
|
nearly a copy of kpp_transport_s |
| 1039 |
|
- there is no analogue to SurfaceTendencyS, so I have to use |
| 1040 |
|
gPtr(of the surface layer) instead |
| 1041 |
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 1042 |
|
checkpoint50e_pre |
| 1043 |
|
|
| 1044 |
|
checkpoint50d_post |
| 1045 |
|
o change kpp output from multiple-record state files to single-record state |
| 1046 |
|
files analogous to write_state.F |
| 1047 |
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 1048 |
|
analogous to the cg2d-related output. |
| 1049 |
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 1050 |
|
so that writing to internal file fn (with length 512) fails. |
| 1051 |
|
checkpoint50d_pre |
| 1052 |
|
|
| 1053 |
|
checkpoint50c_post |
| 1054 |
|
o fix problem in ini_procs.F when using MPI (was there since checkpoint48f) |
| 1055 |
|
o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy. |
| 1056 |
|
o add time-average diagnostic of U*V and vertical diffusive flux for theta. |
| 1057 |
|
o bug fixed in convective adjustment diagnostic (multi-tile set-up). |
| 1058 |
|
o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries. |
| 1059 |
|
|
| 1060 |
|
checkpoint50c_pre |
| 1061 |
|
Merging from release1_p13: |
| 1062 |
|
o bug fix for pkg/seaice dynamic solver |
| 1063 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 1064 |
|
|
| 1065 |
|
checkpoint50b_post |
| 1066 |
|
o store u*,v* in gU,V instead of in guNm1,gvNm1 |
| 1067 |
|
o in order to put the momForcing out of the Adams-Bashforth: |
| 1068 |
|
move forcing & CD-scheme calls from mom_fluxform & mom_vecinv |
| 1069 |
|
to timestep.F |
| 1070 |
|
o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays |
| 1071 |
|
o re-generate output for highly sensitive test-exp: |
| 1072 |
|
global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box |
| 1073 |
|
|
| 1074 |
|
checkpoint50b_pre |
| 1075 |
|
o restore the use of momAdvection & useCoriolis flags (mom_vecinv) |
| 1076 |
|
o corrected CPP option mismatch in exf_Bulk... functions for case |
| 1077 |
|
#define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP |
| 1078 |
|
|
| 1079 |
|
checkpoint50a_post |
| 1080 |
|
o Bug fix for merging between c50 and KPP. |
| 1081 |
|
ikey was passed from thermodynamics to kpp_calc via |
| 1082 |
|
common block rather than being recomputed in kpp_calc, |
| 1083 |
|
in contradiction with new key itdkey. |
| 1084 |
|
New key ikppkey created, and tamc.h headers updated. |
| 1085 |
|
|
| 1086 |
|
checkpoint50 |
| 1087 |
|
- 2nd step of merge with ecco-branch: |
| 1088 |
|
merge changes in ecco-branch back into main trunk |
| 1089 |
|
- bug fix in find_alpha |
| 1090 |
|
- more storing in gmredi_calc_tensor.F, kpp_routines.F |
| 1091 |
|
- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC |
| 1092 |
|
- merged some sliced AD support routines |
| 1093 |
|
|
| 1094 |
|
checkpoint49 |
| 1095 |
|
merged from ecco-branch: |
| 1096 |
|
o exf: |
| 1097 |
|
- Enable initialisation of forcing fields to constant |
| 1098 |
|
(runtime) values. |
| 1099 |
|
- in exf_getffields.F |
| 1100 |
|
Reduce i-/j-loop to interior domain, discarding overlaps. |
| 1101 |
|
That also fixes wrong TAF-key computations for key_1, key_2 |
| 1102 |
|
with bulf formulae. |
| 1103 |
|
- exf_init.F modify #ifdef for exf_init_evap |
| 1104 |
|
- exf_getffieldrec.F, ctrl_getrec.F |
| 1105 |
|
The following INT-usages are not safe: |
| 1106 |
|
fldsecs = int(fldsecs/fldperiod)*fldperiod |
| 1107 |
|
fldcount = int(fldsecs/fldperiod) + 1 |
| 1108 |
|
and were modified. |
| 1109 |
|
o autodiff: checkpoint_lev... |
| 1110 |
|
- updated storing for bulk formulae (some arrays were missing) |
| 1111 |
|
- added state for seaice package |
| 1112 |
|
- synchronized with main branch |
| 1113 |
|
o DIVA: |
| 1114 |
|
Modif.s in |
| 1115 |
|
- the_main_loop.F |
| 1116 |
|
- the_model_main.F |
| 1117 |
|
and added cost_final_restore.F cost_final_store.F |
| 1118 |
|
o With these changes, it is possible to fully separate |
| 1119 |
|
the first forward run to compute the cost function (mdthe_main_loop) |
| 1120 |
|
and adjoint runs over individual DIVA intervals (adthe_main_loop) |
| 1121 |
|
into separate model executions. |
| 1122 |
|
This enables better tuning of DIVA to given queue sizes. |
| 1123 |
|
o Loss of cost function value in consecutive DIVA runs is |
| 1124 |
|
fixed by storing to 'costfinal' file. |
| 1125 |
|
o Appropriate call of ctrl_unpack/_pack,grdchk_main at |
| 1126 |
|
beginning/end of adjoint integration is accounted for. |
| 1127 |
|
The current changes apply to TAF-1.4.26. |
| 1128 |
|
TAF has one remaining bug, requiring one manual change |
| 1129 |
|
(see MITgcm manual). |
| 1130 |
|
o cal: synchronized between MAIN and ecco-branch |
| 1131 |
|
|
| 1132 |
|
checkpoint48i_post |
| 1133 |
|
o Changes to restore differentiability of code w.r.t. previous tag |
| 1134 |
|
(mostly adding new routines to make list and replacing |
| 1135 |
|
pressure by totPhiHyd). |
| 1136 |
|
o Updated and merged grdchk package |
| 1137 |
|
- has both ADM and TLM checks |
| 1138 |
|
- works for single- and multi-proc. |
| 1139 |
|
- output cleaned |
| 1140 |
|
- worked successfully for parallel DIVA |
| 1141 |
|
o genmake: |
| 1142 |
|
- Adding -platform=SP4 |
| 1143 |
|
- Modif. for DEC Alpha (many don't have makedepend; use mkdep instead). |
| 1144 |
|
o Modif. for DIVA: |
| 1145 |
|
ctrl_unpack should not be called in intermediate DIVA interval. |
| 1146 |
|
(similar thing would apply for active files such as |
| 1147 |
|
tbar, sbar, psbar, which should not be reinitialised; |
| 1148 |
|
only relevant for ecco-branch) |
| 1149 |
|
|
| 1150 |
|
checkpoint48h_post |
| 1151 |
|
o improve "ini_p_ground" when using finite difference form for calc_phi_hyd |
| 1152 |
|
o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F |
| 1153 |
|
o Added SEAICE_initialHEFF to pkg/seaice |
| 1154 |
|
o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT |
| 1155 |
|
|
| 1156 |
|
checkpoint48g_post |
| 1157 |
|
--- EOS: |
| 1158 |
|
o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF |
| 1159 |
|
store total Potential in totPhyHyd for diagnostics & EOS. |
| 1160 |
|
o fix restart and overlap Pb when using Z-coord and EOS funct. of P |
| 1161 |
|
--- Pressure/geopotential gradient: |
| 1162 |
|
o use Ro_surf & R_low instead of hFac in cal_phi_hyd: |
| 1163 |
|
o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind |
| 1164 |
|
( changes results of global_ocean_pressure ) |
| 1165 |
|
o NLFS + z-coord.: add eta*Rho' contribution. |
| 1166 |
|
o accurate phiHyd when using interface-W at the middle between 2 centers |
| 1167 |
|
( changes results of ideal_2D_oce ) |
| 1168 |
|
o includes r* 2nd term in potential gradient. |
| 1169 |
|
|
| 1170 |
|
checkpoint48f_post |
| 1171 |
|
Merging from release1_p12: |
| 1172 |
|
o Modifications for using pkg/exf with pkg/seaice |
| 1173 |
|
- improved description of the various forcing configurations |
| 1174 |
|
- added basic radiation bulk formulae to pkg/exf |
| 1175 |
|
- units/sign fix for evap computation in exf_getffields.F |
| 1176 |
|
- updated verification/global_with_exf/results/output.txt |
| 1177 |
|
o Added pkg/sbo for computing IERS Special Bureau for the Oceans |
| 1178 |
|
(SBO) core products, including oceanic mass, center-of-mass, |
| 1179 |
|
angular, and bottom pressure (see pkg/sbo/README.sbo). |
| 1180 |
|
o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F |
| 1181 |
|
to avoid negative values in shallow regions. |
| 1182 |
|
- updated verification/natl_box/results/output.txt |
| 1183 |
|
- updated verification/lab_sea/results/output.txt |
| 1184 |
|
o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F |
| 1185 |
|
o Added useSingleCpuIO option (see PARAMS.h). |
| 1186 |
|
o Updated useSingleCpuIO option in mdsio_writefield.F to |
| 1187 |
|
work with multi-field files, e.g., for single-file pickup. |
| 1188 |
|
o pkg/seaice: |
| 1189 |
|
- bug fix in growth.F: QNET for no shortwave case |
| 1190 |
|
- added HeffFile for specifying initial sea-ice thickness |
| 1191 |
|
- changed SEAICE_EXTERNAL_FLUXES wind stress implementation |
| 1192 |
|
o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, |
| 1193 |
|
kpp_transport_t.F, forward_step.F, and the_main_loop.F |
| 1194 |
|
o pkg/seaice: |
| 1195 |
|
- adjoint-friendly modifications |
| 1196 |
|
- added a SEAICE_WRITE_PICKUP at end of the_model_main.F |
| 1197 |
|
|
| 1198 |
|
checkpoint48e_post |
| 1199 |
|
o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post) |
| 1200 |
|
o dynamics: change definition of computational domain & adapt mom_fluxform |
| 1201 |
|
accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. |
| 1202 |
|
o following exp works with Olx=Oly=2 (and pass through checkbounds option): |
| 1203 |
|
adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1 |
| 1204 |
|
exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5 |
| 1205 |
|
global_ocean.90x40x15 global_with_exf global_ocean_pressure |
| 1206 |
|
inverted_barometer solid-body.cs-32x32x1 |
| 1207 |
|
(high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure) |
| 1208 |
|
|
| 1209 |
|
checkpoint48d_post |
| 1210 |
|
o in preparation for r*: |
| 1211 |
|
a) use pre-computed gradient of hydrostatic potential: |
| 1212 |
|
changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce |
| 1213 |
|
b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd: |
| 1214 |
|
=> affects results of glob_oce_pressure (different truncation error) |
| 1215 |
|
update output.txt of ideal_2D_oce & global_ocean_pressure |
| 1216 |
|
|
| 1217 |
|
checkpoint48d_pre |
| 1218 |
|
o in preparation for r*: |
| 1219 |
|
new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient. |
| 1220 |
|
pass the 2 comp. of the grad. as arguments to momentum S/R. |
| 1221 |
|
but for the moment, only used if it does not change the results. |
| 1222 |
|
o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP |
| 1223 |
|
|
| 1224 |
|
checkpoint48c_post |
| 1225 |
|
Modifications in treatment of initial flux forcing controls |
| 1226 |
|
to avoid extra storing of flux fields. |
| 1227 |
|
|
| 1228 |
|
checkpoint48c_pre |
| 1229 |
|
o Added tidal_basin_2d experiment (currently 1D!) |
| 1230 |
|
o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) |
| 1231 |
|
|
| 1232 |
|
checkpoint48b_post |
| 1233 |
|
o r* coordinate added in #ifdef NONLIN_FRSURF block. |
| 1234 |
|
(modification to pressure gradient not yet implemented) |
| 1235 |
|
o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports |
| 1236 |
|
(for U & V) that are used for vertical advection of momentum. |
| 1237 |
|
|
| 1238 |
|
checkpoint48a_post |
| 1239 |
|
o In preparation for r*, use temp. array to compute vertical transport |
| 1240 |
|
in flux-form momentum pkg. => change results of few test-exp. |
| 1241 |
|
Update output of: exp4, exp5, front_relax, global_ocean_pressure, |
| 1242 |
|
lab_sea, natl_box & plume_on_slope |
| 1243 |
|
|
| 1244 |
|
checkpoint48 |
| 1245 |
|
o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D') |
| 1246 |
|
|
| 1247 |
|
checkpoint47j_post |
| 1248 |
|
o add new exp. (ideal_2D_oce) to test "exotic" parameters and options. |
| 1249 |
|
o moved adexch from forward_step to addummy_in_stepping |
| 1250 |
|
o added exch in ctrl_map_... |
| 1251 |
|
o aveFreq.=0. at end of cost_final to avoid overwrite in |
| 1252 |
|
reverse checkpointing loop |
| 1253 |
|
o Yet more changes in gmredi: |
| 1254 |
|
* adgmredi_calc_tensor |
| 1255 |
|
avoiding all recomputation of gmredi_slope_limit |
| 1256 |
|
* adgmredi_x/y/rtransport |
| 1257 |
|
added flag for excessive storing to avoid recomp. of |
| 1258 |
|
u/v/rtans, dTdx/y/z |
| 1259 |
|
-> this is not really necessary and very memory-consuming |
| 1260 |
|
* adgmredi_slope_psi: |
| 1261 |
|
consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff |
| 1262 |
|
* gmredi_slope_limit |
| 1263 |
|
re-activated full calculation of taperfct for case 'ac02' |
| 1264 |
|
o updating verification/ adjoints of carbon, global_ocean.90x40x15 |
| 1265 |
|
|
| 1266 |
|
checkpoint47i_post |
| 1267 |
|
o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled. |
| 1268 |
|
o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi) |
| 1269 |
|
default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post) |
| 1270 |
|
o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) |
| 1271 |
|
o gmredi: fix few bugs. |
| 1272 |
|
|
| 1273 |
|
checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48) |
| 1274 |
|
This will be a good checkpoint to plug into the ecco-branch. |
| 1275 |
|
o few modif.'s to get latest version adjointed |
| 1276 |
|
(mainly kick out code in ini_linear_phisurf) |
| 1277 |
|
o modif's to run adjoint with exactConserv |
| 1278 |
|
o case GM_BOLUS_ADVEC should be cleaned |
| 1279 |
|
S/R gmredi_slope_psi should be cleaned |
| 1280 |
|
o verification/carbon now has exactConserv=.TRUE. |
| 1281 |
|
|
| 1282 |
|
checkpoint47g_post |
| 1283 |
|
o time-average AIM output: becomes independent from statvars time-average |
| 1284 |
|
(can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH) |
| 1285 |
|
o After TAF bug fix: |
| 1286 |
|
Tested adjoint of gmredi package. |
| 1287 |
|
Tests were done with checkpoint47 rather than with latest |
| 1288 |
|
checkpoint47f_post since the latter is broken for the adjoint |
| 1289 |
|
verification/carbon/ contains both ADM and TLM gradient checks. |
| 1290 |
|
Here they are, before they get changed/lost/stolen. |
| 1291 |
|
Mostly modif.'s to fix numerical sensitivities. |
| 1292 |
|
Gradient checks OK for |
| 1293 |
|
- GM_taper_scheme: |
| 1294 |
|
* clipping |
| 1295 |
|
* ac02 |
| 1296 |
|
* linear |
| 1297 |
|
* glw91 |
| 1298 |
|
* dm95 |
| 1299 |
|
* ldd97 |
| 1300 |
|
- GMREDI_OPTIONS: |
| 1301 |
|
* GM_VISBECK_VARIABLE_K |
| 1302 |
|
* GM_NON_UNITY_DIAGONAL |
| 1303 |
|
* GM_EXTRA_DIAGONAL |
| 1304 |
|
* GM_BOLUS_ADVEC |
| 1305 |
|
in conjunction with data.gmredi parameters to be checked in |
| 1306 |
|
in a few minutes under verification/carbon/code/ |
| 1307 |
|
|
| 1308 |
|
checkpoint47f_post |
| 1309 |
|
Merging from release1_p10: |
| 1310 |
|
o modifications for using pkg/exf with pkg/seaice |
| 1311 |
|
- pkg/seaice CPP options SEAICE_EXTERNAL_FORCING |
| 1312 |
|
and SEAICE_EXTERNAL_FLUXES |
| 1313 |
|
- pkg/exf CPP options EXF_READ_EVAP and |
| 1314 |
|
EXF_NO_BULK_COMPUTATIONS |
| 1315 |
|
- usage examples are Experiments 8 and 9 in |
| 1316 |
|
verification/lab_sea/README |
| 1317 |
|
- verification/lab_sea default experiment now uses |
| 1318 |
|
pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf |
| 1319 |
|
|
| 1320 |
|
checkpoint47e_post |
| 1321 |
|
o created a tag prior to creating a branch |
| 1322 |
|
|
| 1323 |
|
checkpoint47d_post |
| 1324 |
|
o fixed bug in the oceanic pressure coordinates code: vertical viscosity |
| 1325 |
|
at the bottom boundary had an erroneous half slip boundary condition |
| 1326 |
|
o added bottom drag and no slip boundary condition capabilities to |
| 1327 |
|
oceanic pressure coordinates code |
| 1328 |
|
o added new verification experiment global_ocean_pressure, this experiment is |
| 1329 |
|
also described in the tutorial section of the manual |
| 1330 |
|
checkpoint47d_pre |
| 1331 |
|
|
| 1332 |
|
checkpoint47c_post |
| 1333 |
|
o Added a verification experiment for a global cubed-sphere ocean run |
| 1334 |
|
- verification/global_ocean.cubed32x32x30 |
| 1335 |
|
- uses pkg/therm_seaice and pkg/bulk_forcing |
| 1336 |
|
|
| 1337 |
|
o allow to run AIM physics with SPEEDY input files (from Franco Molteni) |
| 1338 |
|
o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1) |
| 1339 |
|
when using P-coordinate; only implemented for atmospheric config. |
| 1340 |
|
o OCEANICP & realFreshWater: include P-E direct effect on wVel ; |
| 1341 |
|
NOTES: requires option NONLIN_FRSURF to be "#define". |
| 1342 |
|
o update advect_xz/results/output.txt (left from checkpoint44g_post) |
| 1343 |
|
|
| 1344 |
|
checkpoint47b_post |
| 1345 |
|
Merging from release1_p9: |
| 1346 |
|
o pkg/seaice |
| 1347 |
|
- removed GOTO's and added taf directives |
| 1348 |
|
- double precision constants to reduce the g77 (Linux) |
| 1349 |
|
to F77 (SGI) differences reported in release1_p8 |
| 1350 |
|
o tools/genmake |
| 1351 |
|
- added SGI options |
| 1352 |
|
o verification/testscript |
| 1353 |
|
- updated to that of checkpoint47a_post |
| 1354 |
|
o verification/global_ocean.90x40x15/input/eedata |
| 1355 |
|
- modified for SGI f77 compatibility |
| 1356 |
|
o verification/lab_sea |
| 1357 |
|
- added description of sea-ice model |
| 1358 |
|
- added missing matlab routines |
| 1359 |
|
- added test of thermodynamics parallelization |
| 1360 |
|
|
| 1361 |
|
checkpoint47a_post |
| 1362 |
|
o new pkg: aim_v23 |
| 1363 |
|
= F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. |
| 1364 |
|
for now, keep the same surface forcing as before. |
| 1365 |
|
- Part-Cell implemented into AIM; check that Heat & Water are conserved |
| 1366 |
|
- aim.5l_cs: use new aim pkg (run 10yr & get better results than before) |
| 1367 |
|
- aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg |
| 1368 |
|
o add diagnostic of surface correction term in monitor output |
| 1369 |
|
|
| 1370 |
|
o bulk_force and therm_seaice |
| 1371 |
|
- Two packages: bulk_force (Bulk forcing) |
| 1372 |
|
and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2 |
| 1373 |
|
- Earlier integration from Stephaine Dutkiewicz |
| 1374 |
|
and Patrick Heimbach. |
| 1375 |
|
- Two ifdef statements for compile time, |
| 1376 |
|
ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE |
| 1377 |
|
|
| 1378 |
|
checkpoint47 |
| 1379 |
|
differentiable version of checkpoint46n_post |
| 1380 |
|
o bug fix in quasihydrostaticterms |
| 1381 |
|
o * "clean" adjoint code (in terms of extensive recomputations) |
| 1382 |
|
can now be obtained for all GMREDI options (i.e. for |
| 1383 |
|
- GM_VISBECK_VARIABLE_K |
| 1384 |
|
- GM_NON_UNITY_DIAGONAL |
| 1385 |
|
- GM_EXTRA_DIAGONAL |
| 1386 |
|
- GM_BOLUS_ADVEC ) |
| 1387 |
|
* However, wrong gradient check problem remains unsolved. |
| 1388 |
|
* New CPP options have been introduced for different |
| 1389 |
|
tapering schemes |
| 1390 |
|
o external_fields_load now part of differentiation list |
| 1391 |
|
o pressure needs multiple storing; |
| 1392 |
|
would be nice to have store_pressure at beginning or |
| 1393 |
|
end of forward_step, e.g. by having phiHyd global (5-dim.) |
| 1394 |
|
(NB: pressure is needed for certain cases in find_rho, |
| 1395 |
|
which is also invoked through convective_adjustment). |
| 1396 |
|
o recomputations in find_rho for cases |
| 1397 |
|
'JMD95'/'UNESCO' or 'MDJWF' are OK. |
| 1398 |
|
o #define ATMOSPHERIC_LOADING should be differentiable |
| 1399 |
|
o ini_forcing shifted to begining of initialise_varia |
| 1400 |
|
o Incorporating QNVS line search routines into MITgcm |
| 1401 |
|
(this is separate code, and therefore not under pkg) |
| 1402 |
|
lsopt/, optim/ |
| 1403 |
|
o Updated verification/carbon/ |
| 1404 |
|
- #define GM_VISBECK_VARIABLE_K |
| 1405 |
|
- GM_taper_scheme = 'ldd97' |
| 1406 |
|
|
| 1407 |
|
checkpoint46n_post |
| 1408 |
|
Merging from release1_p8: |
| 1409 |
|
o verification/natl_box: |
| 1410 |
|
updating new external_fields_load routine |
| 1411 |
|
o New package: pkg/seaice |
| 1412 |
|
Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). |
| 1413 |
|
The sea-ice code is based on Hibler (1979-1980). |
| 1414 |
|
Two sea-ice dynamic solvers, ADI and LSR, are included. |
| 1415 |
|
In addition to computing prognostic sea-ice variables and diagnosing |
| 1416 |
|
the forcing/external data fields that drive the ocean model, |
| 1417 |
|
SEAICE_MODEL also sets theta to the freezing point under sea-ice. |
| 1418 |
|
The implied surface heat flux is then stored in variable |
| 1419 |
|
surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and |
| 1420 |
|
kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the |
| 1421 |
|
non-local transport term. Because this call precedes model |
| 1422 |
|
thermodynamics, temperature under sea-ice may not be "exactly" at |
| 1423 |
|
the freezing point by the time theta is dumped or time-averaged. |
| 1424 |
|
N.B.: fairly large differences in accuracy occur across |
| 1425 |
|
different platforms/compilers; comparison between |
| 1426 |
|
g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) |
| 1427 |
|
generated output gives: |
| 1428 |
|
T S U V |
| 1429 |
|
C D M c m s m s m s m s |
| 1430 |
|
n p a R g m m e . m m e . m m e . m m e . |
| 1431 |
|
f n k u 2 i a a d i a a d i a a d i a a d |
| 1432 |
|
g d e n d n x n . n x n . n x n . n x n . |
| 1433 |
|
|
| 1434 |
|
Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea |
| 1435 |
|
o GAD: |
| 1436 |
|
- generated new common blocks to account for call of |
| 1437 |
|
same gad routines with differing traceridentities |
| 1438 |
|
(needed to modify tracerIdentity indices in GAD.h) |
| 1439 |
|
- generated separate common blocks for case useCubedSphereExchange |
| 1440 |
|
(Department of Futurology) |
| 1441 |
|
- parameter lists to gmredi_?transport: added tracerIdentity |
| 1442 |
|
- added new key indices to tamc.h |
| 1443 |
|
o external_fields_load: |
| 1444 |
|
- added this routine to TAF list |
| 1445 |
|
- needed to make some common blocks global and additional storing |
| 1446 |
|
along the same lines as exf package (checkpoint_lev?_directives.h) |
| 1447 |
|
o exf: |
| 1448 |
|
updated external forcing package |
| 1449 |
|
- bug fixes carried over from ecco-branch |
| 1450 |
|
(missing OBCS_OPTIONS.h in two routines) |
| 1451 |
|
- enable easy to use "no forcing". |
| 1452 |
|
- added exf I/O for atmospheric loading |
| 1453 |
|
- added exf I/O for runoff data |
| 1454 |
|
- transfered scaling between exf <-> MITgcm to exf namelist |
| 1455 |
|
o Adding new verification experiment global_with_exf. |
| 1456 |
|
This verification experiment is almost identical to the |
| 1457 |
|
global_ocean.90x40x15 experiment, except that it uses |
| 1458 |
|
the exf (and cal) package instead of the |
| 1459 |
|
external_fields_load routine (cf README file). |
| 1460 |
|
|
| 1461 |
|
checkpoint46m_post |
| 1462 |
|
o modified testscript to return -- when there are no lines of "%MON" output |
| 1463 |
|
o added new flag "quasiHydrostatic" for QH mode |
| 1464 |
|
and new routine quasihydrostaticterms() |
| 1465 |
|
o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term) |
| 1466 |
|
New routine: mom_u_coriolis_nh() |
| 1467 |
|
o fixed sign of non-hydrostatic metric terms in u and v equations. |
| 1468 |
|
Depend on correct sign of gravitySign. |
| 1469 |
|
o added work.pc* to .cvsignore in aim directories using ifc |
| 1470 |
|
o introduced flag for controllin non-hydrostatic metric terms |
| 1471 |
|
o removed gravitySign from PARM04 |
| 1472 |
o switched to g77/ifc from pgf77 in aim experiments |
o switched to g77/ifc from pgf77 in aim experiments |
| 1473 |
|
|
| 1474 |
checkpoint46l_post |
checkpoint46l_post |
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