| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/obcs: |
| 8 |
|
- add additional compile-time options for sponge boundary layers |
| 9 |
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(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 10 |
|
o pkg/atm_phys: |
| 11 |
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- implement simple (obliquity only, assuming circular planet orbit) |
| 12 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 13 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 14 |
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o pkg/exf, pkg/ecco, pkg/ctrl: |
| 15 |
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- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 16 |
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- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 17 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 18 |
|
o pkg/ctrl, pkg/ecco : |
| 19 |
|
- fix and complement the generic controls implementation |
| 20 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 21 |
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pkg/shelfice/shelfice_thermodynamics.F, |
| 22 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 23 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 24 |
|
- add weight in CTRL_GET_GEN calls |
| 25 |
|
o pkg/ctrl : |
| 26 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 27 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 28 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 29 |
|
o pkg/ctrl : |
| 30 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 31 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 32 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 33 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 34 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 35 |
|
o pkg/ecco, pkg/ctrl : |
| 36 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 37 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 38 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 39 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 40 |
|
|
| 41 |
|
checkpoint65d (2014/09/15) |
| 42 |
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o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 43 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 44 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 45 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 46 |
|
- remove compilation failure |
| 47 |
|
- replace hard coded example |
| 48 |
|
- use ctrl_map_ini_gen2D, 3D |
| 49 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 50 |
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- on/off switch based upon xx_genarr2d_weight,3d |
| 51 |
|
o src/packages_init_variables.F : |
| 52 |
|
- regroup pkg/estimation calls |
| 53 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 54 |
|
(moved to ctrl_init_variables) |
| 55 |
|
o cost/cost_init_varia.F : |
| 56 |
|
- remove ecco_cost_init_varia |
| 57 |
|
(moved to ecco_init_varia) |
| 58 |
|
o ctrl/ctrl_init_variables.F : |
| 59 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 60 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 61 |
|
o ctrl/ctrl_map_ini.F : |
| 62 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 63 |
|
(moved to ctrl_init_variables) |
| 64 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 65 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 66 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 67 |
|
o ecco/ecco_ad_diff.list : |
| 68 |
|
- add ecco_init_varia.f |
| 69 |
|
o ecco/ecco_init_varia.F |
| 70 |
|
- new routine |
| 71 |
|
o pkg/streamice: |
| 72 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 73 |
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to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 74 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 75 |
|
o pkg/generic_advdiff: |
| 76 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 77 |
|
o pkg/exf: |
| 78 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 79 |
|
xxg_precip capability |
| 80 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 81 |
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o pkg/ctrl: |
| 82 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 83 |
|
o model/src/load_fields_driver.F : |
| 84 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 85 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 86 |
|
o OpenAD verification experiments: |
| 87 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 88 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 89 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 90 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 91 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 92 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 93 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 94 |
|
o OpenAD verification tests: |
| 95 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 96 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 97 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 98 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 99 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 100 |
|
o model/src & generic_advdiff: |
| 101 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 102 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 103 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 104 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 105 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 106 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 107 |
|
setting in temp/salt/ptracer_integrate.F |
| 108 |
|
o pkg/dic: |
| 109 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 110 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 111 |
|
in gchem_forcing_sep.F |
| 112 |
|
o pkg/autodiff & obcs: |
| 113 |
|
- add storage of current OB values for U & V (was already done for T & S). |
| 114 |
|
|
| 115 |
|
checkpoint65c (2014/08/30) |
| 116 |
|
o pkg/dic: |
| 117 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 118 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 119 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 120 |
|
o verification: |
| 121 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
| 122 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 123 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 124 |
|
conditions from t=1.yr while keeping the same forcing. |
| 125 |
|
o model/src: |
| 126 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 127 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 128 |
|
o pkg/diagnostics (Stats-Diags): |
| 129 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 130 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 131 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 132 |
|
c) extend regional stats over the region edges (for U or V pt location). |
| 133 |
|
o pkg/gchem: |
| 134 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 135 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 136 |
|
o verification (hs94): |
| 137 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 138 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 139 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 140 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 141 |
|
o pkg/ptracers: |
| 142 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 143 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 144 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 145 |
|
with AB-2 code (so that it get tested). |
| 146 |
|
o model/src: |
| 147 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 148 |
|
with AB-2 code (previously only available with AB-3 code). |
| 149 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 150 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 151 |
|
there, by calling CYCLE_AB_TRACER). |
| 152 |
|
o pkg/generic_advdiff: |
| 153 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 154 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 155 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 156 |
|
S/R temp/salt/ptracers_integrate.F |
| 157 |
|
o model/src & pkg/ptracers: |
| 158 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
| 159 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 160 |
|
- remove common block variable gPtr. |
| 161 |
|
o model/src & pkgs: |
| 162 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 163 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 164 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 165 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 166 |
|
+ change accordingly all calling S/R. |
| 167 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 168 |
|
in S/R temp/salt/ptracers_integrate.F |
| 169 |
|
o pkg/seaice: |
| 170 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 171 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 172 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 173 |
|
in seaice_lsr |
| 174 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 175 |
|
in s/r seaice_lsr_calc_coeffs |
| 176 |
|
o pkg/mdsio: |
| 177 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 178 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 179 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 180 |
|
|
| 181 |
|
checkpoint65b (2014/08/12) |
| 182 |
|
o pkg/matrix: |
| 183 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 184 |
|
o model/src: |
| 185 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 186 |
|
natl_box verification experiment. |
| 187 |
|
o model/src & pkg/down_slope: |
| 188 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 189 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 190 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 191 |
|
results at machine truncation level: update output of experiments |
| 192 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 193 |
|
o pkg/diagnostics (Stats-Diags): |
| 194 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 195 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 196 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 197 |
|
times (but Min,Max and StD are still wrong). |
| 198 |
|
o model/src: |
| 199 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 200 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 201 |
|
o model/src: |
| 202 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 203 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 204 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 205 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 206 |
|
o model/src: |
| 207 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 208 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 209 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 210 |
|
o pkg/seaice/seaice_lsr.F |
| 211 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 212 |
|
in the residual diagnostics |
| 213 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 214 |
|
default) for improved non-linear convergence of the first few steps |
| 215 |
|
- adjust a few comments and add new ones to explain some of the store |
| 216 |
|
directives |
| 217 |
|
o pkg/generic_advdiff (& ptracers): |
| 218 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 219 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 220 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 221 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 222 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 223 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 224 |
|
less exact gradients in my tests); but there are still |
| 225 |
|
recomputation warning (although gradients are sort of OK), when |
| 226 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 227 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 228 |
|
- update verification experiments lab_sea. |
| 229 |
|
- change some comments in S/R seaice_calc_viscosities |
| 230 |
|
o model/src: |
| 231 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 232 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 233 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 234 |
|
but affects AD results (at machine truncation level): update output of |
| 235 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 236 |
|
and isomip (oad: 12.d). |
| 237 |
|
o pkg/generic_advdiff: |
| 238 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 239 |
|
- refine warning related to stability of tracer time-stepping |
| 240 |
|
regarding internal wave dynamics. |
| 241 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 242 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 243 |
|
if potentially unstable). |
| 244 |
|
o pkg/kl10: |
| 245 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 246 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 247 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 248 |
|
verification/internal_wave/input.kl10/ |
| 249 |
|
o isomip experiment: |
| 250 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 251 |
|
(input.htd) and update the output. |
| 252 |
|
o cd_code experiments: |
| 253 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 254 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 255 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 256 |
|
update the corresponding output. |
| 257 |
|
o pkg/seaice: |
| 258 |
|
- reduce the number of include files and store directives in |
| 259 |
|
S/R seaice_lsr_tridiagu/v |
| 260 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 261 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 262 |
|
get rid off one store directive (a TAF bug?) |
| 263 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 264 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 265 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 266 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 267 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 268 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 269 |
|
|
| 270 |
|
checkpoint65a (2014/07/27) |
| 271 |
|
o model/src: |
| 272 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 273 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 274 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 275 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 276 |
|
o model/src: |
| 277 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 278 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 279 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 280 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 281 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 282 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 283 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 284 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 285 |
|
correction due to vertical advection). |
| 286 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 287 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 288 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 289 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 290 |
|
o pkg/ptracers & diagnostics: |
| 291 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 292 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 293 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 294 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 295 |
|
|
| 296 |
checkpoint65 (2014/07/18) |
checkpoint65 (2014/07/18) |
| 297 |
o pkg/fizhi: |
o pkg/fizhi: |
| 298 |
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
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