| 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/seaice (SItracer pickup) |
| 8 |
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* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
| 9 |
|
To be done: |
| 10 |
|
- thorough testing of missing fields in S/R seaice_read_pickup |
| 11 |
|
- thorough matching between generic tracers and specific fields used |
| 12 |
|
(e.g. volume-weighted age, area-weighted age, salinity, ...) |
| 13 |
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o pkg/grdchk: |
| 14 |
|
- all procs calculate and print finite-difference gradient (for testreport) |
| 15 |
|
- change description output used by testreport; |
| 16 |
|
- AD testing: also compare and report Finite-difference gradient; |
| 17 |
|
=> update all output_adm*.txt |
| 18 |
|
o test exp. global_ocean_ebm: |
| 19 |
|
- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
| 20 |
|
and turn on exactConserve; update (fwd) output. |
| 21 |
|
o pkg/seaice (LSR): |
| 22 |
|
- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
| 23 |
|
- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
| 24 |
|
* identical results with non-CS topology (but save up to half of EXCH calls) |
| 25 |
|
* no much changes in cs-32 verification tests since no ice at face edges |
| 26 |
|
(differences due to convergence criteria, since nb of iterations changed) |
| 27 |
|
* expect some differences on lat-lon-cap grid. |
| 28 |
|
update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
| 29 |
|
o pkg/exch2: |
| 30 |
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- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
| 31 |
|
many tiles); until alternative coding is added, just add a stop. |
| 32 |
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o pkg/kpp: |
| 33 |
|
- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
| 34 |
|
to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
| 35 |
|
o optfiles: |
| 36 |
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- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
| 37 |
|
into corresponding standard one, which now support different build: |
| 38 |
|
(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
| 39 |
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- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
| 40 |
|
o pkg/obcs (seaice): |
| 41 |
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- add missing EXCH for uIce,vIce after applying OBCS; |
| 42 |
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- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
| 43 |
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argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
| 44 |
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EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
| 45 |
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- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
| 46 |
|
- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
| 47 |
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and eedata.mth for MPI and mutlti-threaded testing. |
| 48 |
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o pkg/flt: |
| 49 |
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- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
| 50 |
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- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
| 51 |
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- fix pickup and trajectories + profiles output with multi-threads; |
| 52 |
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- add parameter to select group of fields to write along trajectory and |
| 53 |
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profile (default unchanged); |
| 54 |
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- only call PORT_RAND* function when flt_noise <> 0; |
| 55 |
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- add multi-threaded test for verification exp. flt_example. |
| 56 |
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o eesupp/src: |
| 57 |
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- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
| 58 |
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- USE_OMP_THREADING: check that number of threads (from eedata) matches |
| 59 |
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actual number (from env.var. setting). |
| 60 |
|
o pkg/ebm: |
| 61 |
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- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
| 62 |
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- add multi-threaded test for verification exp. global_ocean_ebm |
| 63 |
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|
| 64 |
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checkpoint63b (2011/08/29) |
| 65 |
|
o pkg/ebm: |
| 66 |
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- fix sign of runoff; |
| 67 |
|
- update directly forcing fields (Qnet,EmPmR) to use standard |
| 68 |
|
external_forcing_surf.F (remove ebm_forcing_surf.F); |
| 69 |
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- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
| 70 |
|
- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
| 71 |
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and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
| 72 |
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- update global_ocean_ebm parameters file data and update output (fwd+ad). |
| 73 |
|
o verification/matrix_example: |
| 74 |
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- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
| 75 |
|
MPI and mutlti-threaded testing. |
| 76 |
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o pkg/matrix: |
| 77 |
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- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
| 78 |
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- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
| 79 |
|
- fix for multi-threaded (remove DATA statement); |
| 80 |
|
- use standard DIFFERENT_MULTIPLE function; |
| 81 |
|
- add MATRIX_OPTIONS.h |
| 82 |
|
o verification/matrix_example: |
| 83 |
|
To allow to split the domain in several tiles, change the domain size |
| 84 |
|
from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
| 85 |
|
Western side) of land points. |
| 86 |
|
o (*_)write_pickup: |
| 87 |
|
- fix few bugs in mypackage_read/write_pickup.F |
| 88 |
|
- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
| 89 |
|
array of length 1 (was caught by compiler syntax-check). |
| 90 |
|
o pkg/diagnostics (velocity potential solver): |
| 91 |
|
- fix initialisation of main diagonal matrix (for overlap values) |
| 92 |
|
o tools/build_options: |
| 93 |
|
- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
| 94 |
|
into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
| 95 |
|
- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
| 96 |
|
* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
| 97 |
|
* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
| 98 |
|
and use "-devel" testreport option for standard testing on baudelaire. |
| 99 |
|
o pkg/grdchk: |
| 100 |
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- Assume that all gradient-check position are within the same tile |
| 101 |
|
corresponding to global indices (iGloTile,jGloTile) and that |
| 102 |
|
positions (i,j indices or nbeg) are local to this tile; |
| 103 |
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- set tile local-indices and proc. number according to tile global-indices; |
| 104 |
|
- remove grdchkwhichproc from namelist (retired param); |
| 105 |
|
- send adjoint gradient to all procs so that all procs print it to STDOUT; |
| 106 |
|
- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
| 107 |
|
o adding package bbl (Bottom Boundary Layer) |
| 108 |
|
description in MITgcm/pkg/bbl/bbl_description.tex |
| 109 |
|
example/test experiment in MITgcm_contrib/bbl |
| 110 |
|
o adjoint verifications |
| 111 |
|
- changed 5 experiments to multi-tiles |
| 112 |
|
* global_ocean.90x40x15 |
| 113 |
|
* obcs_ctrl |
| 114 |
|
* offline_exf_seaice |
| 115 |
|
* tutorial_dic_adjoffline |
| 116 |
|
* tutorial_tracer_adjsens |
| 117 |
|
changed reference output for those that crossed tile boundaries |
| 118 |
|
(changed choices of gradient check positions) |
| 119 |
|
- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
| 120 |
|
- temporary bug fix in grdchk_loc.F for obcs |
| 121 |
|
o genmake2 & testreport |
| 122 |
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- add target "obj" (just for OBJFILES files) to Makefile; |
| 123 |
|
- add option to specify FEXTRAFLAGS on command line. |
| 124 |
|
o pkg/mypackage: |
| 125 |
|
- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
| 126 |
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|
| 127 |
|
checkpoint63a (2011/08/02) |
| 128 |
|
o pkg/diagnostics (velocity potential): |
| 129 |
|
- fix velocity-potential calculation when using OBCS: balance net inflow |
| 130 |
|
at each level (new S/R OBCS_DIAG_BALANCE). |
| 131 |
|
- fix some of the problems with OBCS in stream-function calculation. |
| 132 |
|
o pkg/exf/exf_readparms.F |
| 133 |
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- make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF, |
| 134 |
|
EXF_NML_OBCS) more consistent, so that you need not have these lists |
| 135 |
|
in data.exf when they are not used. |
| 136 |
|
o optim/optim_readdata.F: |
| 137 |
|
- add some output about obcs variables that might help debugging |
| 138 |
|
- add a check about nvarlength |
| 139 |
|
o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec |
| 140 |
|
o pkg/diagnostics (velocity potential): |
| 141 |
|
- fix mask for OBCS (still problems in stream-function with OBCS); |
| 142 |
|
- add specific parameter (default = main code CG2D params) for solver; |
| 143 |
|
- in case of poor convergence, use solution corresponding to lowest residual. |
| 144 |
|
o pkg/seaice/seaice_growth.F: small changes that permit vectorizable |
| 145 |
|
adjoint code. In general statements like tmpscal=fld(i,j) are problematic |
| 146 |
|
and should be avoided where possible. |
| 147 |
|
o model/src (rStar): |
| 148 |
|
- include r* effect on reference-state (PhiRef) in totPhiHyd |
| 149 |
|
(so that it's really the potential anomaly at the cell center); |
| 150 |
|
affect solution only if z* with full pressure in EOS. |
| 151 |
|
- test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and |
| 152 |
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update output (because of z* in totPhiHyd and viscA4 changes); |
| 153 |
|
- keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly |
| 154 |
|
@ constant r) until interpolation at constant r is implemented. |
| 155 |
|
o pkg/diagnostics |
| 156 |
|
- fix RCENTER diagnostics in case cell center is not at interface middle |
| 157 |
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o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use |
| 158 |
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this eos with eosType = 'TEOS10', in data (PARM01). This eos implies |
| 159 |
|
that THETA and SALT are "conservative temperature" and "absolute |
| 160 |
|
salinity" |
| 161 |
|
o pkg/ctrl |
| 162 |
|
- fix computation of endrec in s/r ctrl_init_rec |
| 163 |
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- ctrl_pack/unpack_*: remove unused variables and some obsolete code |
| 164 |
|
o pkg/seaice/seaice_growth.F |
| 165 |
|
- fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code, |
| 166 |
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remove then obsolete STORE directives |
| 167 |
|
- fix STORE directives for tice and tices, so that only the |
| 168 |
|
appropriate part of the fields are stored (and not the entire |
| 169 |
|
field); update global_ocean.cs32x15.seaice AD output. |
| 170 |
|
- cosmetic changes: adjust CPP flags and indentation for better |
| 171 |
|
legibilty |
| 172 |
|
o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by |
| 173 |
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Chris Wilson) |
| 174 |
|
o pkg/gmredi: |
| 175 |
|
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
| 176 |
|
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
| 177 |
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|
| 178 |
|
checkpoint63 (2011/07/11) |
| 179 |
|
o pkg/exch2: |
| 180 |
|
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
| 181 |
|
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
| 182 |
|
(2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y |
| 183 |
|
increments, calculates Cumul-Sum @ tile origin and sends results to each tile. |
| 184 |
|
o pkg/diagnostics: |
| 185 |
|
- deal with pairs of post-processed diags which are computed together; in |
| 186 |
|
particular, re-order list of diags within 1 file to save 2nd computation. |
| 187 |
|
- add S/R to compute velocity stream-function (called after velocity-potential |
| 188 |
|
calculation) from divergence free transport -> new diagnostics "PsiVEL". |
| 189 |
|
- add parameter to select grid-point location where PsiVEL == 0. |
| 190 |
|
o eesupp/src: |
| 191 |
|
new S/R to calculate cumulated sum on tiled array, corner grid-cell location |
| 192 |
|
(specific S/R needed with exch2 topology - for now, just print an error msg) |
| 193 |
|
o pkg/shelfice |
| 194 |
|
- Implement friction velocity-dependent transfer coefficients following |
| 195 |
|
Holland and Jenkins, JPO, 1999 |
| 196 |
|
Original code by M. Losch with small modifs. |
| 197 |
|
Enable with CPP option SHI_ALLOW_GAMMAFRICT |
| 198 |
|
and runtime flag SHELFICEuseGammaFrict |
| 199 |
|
o verification lab_sea & global_ocean.cs32x15: |
| 200 |
|
- use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local): |
| 201 |
|
does not miss some dependencies (but is slower) and also works with many files |
| 202 |
|
(default makedepend limitation for AD built). |
| 203 |
|
- use cyrus_makedepend in adjustment.128x64x1 (so that it still tested). |
| 204 |
|
o pkg/diagnostics: |
| 205 |
|
- add run-time parameter "useMissingValue" (def=False) to fill land-point |
| 206 |
|
(i.e., where mask=0) with MissingValue ; used only in MNC output file. |
| 207 |
|
This replaces CPP-option DIAGNOSTICS_MISSING_VALUE. |
| 208 |
|
- Extend the use of "missing_value" setting from data.diagnostics for the case |
| 209 |
|
of counter-diagnostics (where fraction-weight is zero). This applies both to |
| 210 |
|
MNC and MDS output files. |
| 211 |
|
o pkg/seaice/seaice_growth.F: |
| 212 |
|
- add 'a priori' cap of latent heat flux based on actual mass considerations |
| 213 |
|
when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the |
| 214 |
|
non-legacy seaice_solve4temp. |
| 215 |
|
- add diagnostic of the residual sublimation freshwater flux (the freshwater |
| 216 |
|
flux taken from the ocean if the total actual latent heat fluxes exceed |
| 217 |
|
the maximum) |
| 218 |
|
- remove the CPP switch around the *_FWbySublim unit change and move diagnostic |
| 219 |
|
fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F. |
| 220 |
|
- add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef |
| 221 |
|
SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim). |
| 222 |
|
- bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET. |
| 223 |
|
- bug fix : missing part to Martin's r_FWbySublim pathological case fix. |
| 224 |
|
o verification 1D_ocean_ice_column: |
| 225 |
|
made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet |
| 226 |
|
update results |
| 227 |
|
o pkg/diagnostics: |
| 228 |
|
- Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P') |
| 229 |
|
which are not filled-up but computed from other diags ; In this case, the mate |
| 230 |
|
diag points to the primary (filled-up) diag to used for post processing. |
| 231 |
|
- Update Velocity-potential computation using post-processed diag framework. |
| 232 |
|
==> Change the ordering of fields and time-periods in MDS output file |
| 233 |
|
when using periodic averaging: now writes one time record with the full set |
| 234 |
|
of fields for this time period, then the next time reccord (it used to be |
| 235 |
|
one field with the full set of time records then the next field). |
| 236 |
|
Note: this is now similar to NetCDF (MNC) output file. <== |
| 237 |
|
|
| 238 |
|
checkpoint62z (2011/06/21) |
| 239 |
|
o adjoint monitor: |
| 240 |
|
- Add adjoint monitor output for packages exf, seaice |
| 241 |
|
and update relevant testreport output |
| 242 |
|
o pkg/seaice: |
| 243 |
|
- re-order diags inits so that they appear in order in available_diagnostics.log |
| 244 |
|
- added diags: hsnow thermo. rates of change, area preceeding ridiging process, |
| 245 |
|
area/heff/hsnow preceeding thermodynamic growth/melt. |
| 246 |
|
- modified diag: SIdA; output actual effect, as the description states. |
| 247 |
|
- modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW. |
| 248 |
|
- retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh. |
| 249 |
|
(SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO; |
| 250 |
|
and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO) |
| 251 |
|
- modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates. |
| 252 |
|
- added diagnostics for seaice generic tracers (SItr*). |
| 253 |
|
- added SItrUnit and SItrNameLong run time param (for SItr* diags). |
| 254 |
|
- in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'. |
| 255 |
|
I. Fenty: 18-Jun-2011: |
| 256 |
|
Minor changes to seaice package: |
| 257 |
|
1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and |
| 258 |
|
added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor) |
| 259 |
|
- Differentiated "regularization variables" from "floor variables" |
| 260 |
|
* areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor |
| 261 |
|
* hiceMin became SEAICE_hice_reg (old hiceMin) |
| 262 |
|
(with _reg meaning regularization variable) |
| 263 |
|
- SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion |
| 264 |
|
so as to ensure energy conservation when going between phases |
| 265 |
|
- A22 was not used anywhere |
| 266 |
|
2) Changed regularization procedure for heffActual and hsnowActual to ensure |
| 267 |
|
well-boundedness and smooth adjoint in seaice_growth.F |
| 268 |
|
3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells |
| 269 |
|
because the old regularization always set heffActual >= 0.05 cm |
| 270 |
|
4) Changed the model so that the default behavior is to put a small (10^-5) "floor" |
| 271 |
|
on AREA when HEFF > 0. |
| 272 |
|
- went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to |
| 273 |
|
requiring that DISABLE_AREA_FLOOR *not* be defined |
| 274 |
|
Affected verifications: |
| 275 |
|
- 1D_ocean_ice_column (output.txt output_adm.txt) |
| 276 |
|
- global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt) |
| 277 |
o pkg/diagnostics: |
o pkg/diagnostics: |
| 278 |
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
- move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R). |
| 279 |
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
- rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument |
| 280 |
(was _RL, now integer) with option = 0 to retrieve all levels. |
(was _RL, now integer) with option = 0 to retrieve all levels. |
| 281 |
|
- add pieces of code to compute velocity potential at each level (new diagnostics |
| 282 |
|
PhiVEL, works only when UVELMASS & VVELMASS are also turned on); |
| 283 |
|
for now, using same params as CG2D (target-resisual, max Nb of iter ...). |
| 284 |
|
- fix few issues with counter diagnostics in diagnostics_setdiag.F & |
| 285 |
|
diagstats_setdiag.F (if diagnostic counter is itself a counter diag) |
| 286 |
|
and in diagnostics_fract_fill.F (do not need a valid pointer for the |
| 287 |
|
diagnostics counter-mate); check that definition of counter-diagnostic |
| 288 |
|
includes a valid counter-mate (in diagnostics_set_levels.F). |
| 289 |
o model/src (rStar): |
o model/src (rStar): |
| 290 |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
- add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F); |
| 291 |
affect solution only if z* with full pressure in EOS; |
affect solution only if z* with full pressure in EOS; |
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