| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
o pkg/seaice/seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
o verification/global_ocean.cs32x15: |
| 8 |
a serious convergence problem when open boundaries are involved |
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
| 9 |
o pkg/ggl90: fix computation of control volumes for the case of |
thsice calling sequence and update "output.icedyn.txt" output file. |
| 10 |
|
o pkg/ptracers: |
| 11 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
| 12 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
| 13 |
|
o pkg/thsice: |
| 14 |
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- implement new sequence of calls for thsice+seaice: |
| 15 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
| 16 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
| 17 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
| 18 |
|
in CPP_OPTIONS.h) to recover old sequence; |
| 19 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
| 20 |
|
just before advection (instead of just after advection in old sequence); |
| 21 |
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- update output of experiment offline_exf_seaice (standard test); |
| 22 |
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- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
| 23 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
| 24 |
|
o pkg/aim_v23: |
| 25 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
| 26 |
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- use standard pkg/mdsio routines to read & write CO2 pickup file; |
| 27 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
| 28 |
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- Implement new sequence of calls for seaice advection (with thsice and |
| 29 |
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seaice diffusion): do ice advection after ice-Thermodynamic (previously |
| 30 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
| 31 |
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- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
| 32 |
|
o pkg/thsice: |
| 33 |
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- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
| 34 |
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where just seaice diffusion is used without seaice-dynamics. |
| 35 |
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|
| 36 |
|
checkpoint64c (2013/01/18) |
| 37 |
|
o pkg/seaice: |
| 38 |
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- add a parameter JFNKres_tFac that can replace JFNKres_t |
| 39 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
| 40 |
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- add a line search option to the JFNK solver |
| 41 |
|
- move update of u/vIce and computation of initial residual into a separate |
| 42 |
|
routine (same file); makes the code a little easier to read (?) |
| 43 |
|
- the line search requires computation of the residual and for some reason |
| 44 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
| 45 |
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without changing the results, so we move computation of the new residual |
| 46 |
|
also to the end of the Newton loop, even without the line search |
| 47 |
|
o pkg/mdsio: |
| 48 |
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- write missing value (corresponding to undefined array value) to meta files; |
| 49 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
| 50 |
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case of undefined missing value but it's current the default missing-value); |
| 51 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
| 52 |
|
o pkg/exf & thsice: |
| 53 |
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- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
| 54 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
| 55 |
|
o verification/cfc_example: |
| 56 |
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- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
| 57 |
|
illustrate how to use it). |
| 58 |
|
o verification/offline_exf_seaice: |
| 59 |
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in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
| 60 |
|
files to only one time-record. |
| 61 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
| 62 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
| 63 |
|
snapshot output; same mcPheePiston value as in thsice with |
| 64 |
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surf-current=0.2m/s. |
| 65 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
| 66 |
|
initial conditions). |
| 67 |
|
o verification/cfc_example: |
| 68 |
|
- update file "data" with more standard choice (default rotationPeriod, |
| 69 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
| 70 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
| 71 |
|
o pkg/layers: |
| 72 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
| 73 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
| 74 |
|
o verification/offline_exf_seaice: |
| 75 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
| 76 |
|
anywhere else). |
| 77 |
|
o verification/offline_exf_seaice: |
| 78 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
| 79 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
| 80 |
|
o model/src: |
| 81 |
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- implement Finite-Volume method for (hydrostatic) presure gradient |
| 82 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
| 83 |
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o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
| 84 |
|
- In order to be compatible with the default EVP code, this requires changing |
| 85 |
|
the EVP code around a little; and because any small change immediately |
| 86 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
| 87 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
| 88 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
| 89 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
| 90 |
|
The adjoint test lab_sea.evp also needed to be updated. |
| 91 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
| 92 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
| 93 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
| 94 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
| 95 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
| 96 |
|
kept obscure, because I need to test it a little more. |
| 97 |
|
o pkg/cheapaml: |
| 98 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
| 99 |
|
o pkg/seaice: |
| 100 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
| 101 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
| 102 |
|
o model/src: |
| 103 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
| 104 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
| 105 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
| 106 |
|
o pkg/cheapaml: |
| 107 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
| 108 |
|
update output of experiment cheapAML_box. |
| 109 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
| 110 |
|
and set them only in one place (cheapaml_readparms.F). |
| 111 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
| 112 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
| 113 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
| 114 |
|
o model/src/the_main_loop.F: |
| 115 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
| 116 |
|
o pkg/seaice: |
| 117 |
|
- remove legacy branch code. |
| 118 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
| 119 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
| 120 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
| 121 |
|
SEAICE_CAP_HEFF). |
| 122 |
|
o pkg/cheapaml: |
| 123 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
| 124 |
|
to load new forcing fields. |
| 125 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
| 126 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
| 127 |
|
cheapAML_box, keep same output (small trucation error differences). |
| 128 |
|
o verification/offline_exf_seaice: |
| 129 |
|
- add thermodynamics only test. |
| 130 |
|
o verification/cheapAML_box: |
| 131 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
| 132 |
|
keep same output (same 14 digits for cg2d). |
| 133 |
|
- switch on "-r8" compiler option (some numerical values are missing |
| 134 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
| 135 |
|
|
| 136 |
|
checkpoint64b (2012/12/24) |
| 137 |
|
o pkg/cheapaml: |
| 138 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
| 139 |
|
- store tendency of advected variables into cheapaml pickup file |
| 140 |
|
and fix the AB-2 restart. |
| 141 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
| 142 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
| 143 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
| 144 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
| 145 |
|
- update results after change of experiment seaice. |
| 146 |
|
o pkg/seaice: |
| 147 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
| 148 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
| 149 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
| 150 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
| 151 |
|
o model/src: |
| 152 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
| 153 |
|
(in case of a poor convergence). |
| 154 |
|
o pkg/seaice/seaice_lsr.F |
| 155 |
|
- move calculation of matrix coefficients into new |
| 156 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
| 157 |
|
file; the main purpose of this change is to be able to reuse the code |
| 158 |
|
in S/R SEAICE_PRECONDITIONER |
| 159 |
|
- modify the computation of the residual so that the mass of sea-ice |
| 160 |
|
is not used twice; this simplifies the calculations, but since |
| 161 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
| 162 |
|
not tested in testreport---this does not affect the testreport results. |
| 163 |
|
o verification/seaice_obcs: |
| 164 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
| 165 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
| 166 |
|
o model/src: |
| 167 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
| 168 |
|
o pkg/seaice: |
| 169 |
|
- improve description of parameters in seaice_fgmres.F and start |
| 170 |
|
cleaning up the code |
| 171 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
| 172 |
|
second argument |
| 173 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
| 174 |
|
results of offline_exf_seaice.dyn_jfnk |
| 175 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
| 176 |
|
o pkg/aim_v23: |
| 177 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
| 178 |
|
o model/src + pkg/seaice: |
| 179 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
| 180 |
|
along X and Y lines, respectively for U and V component. |
| 181 |
|
Note: 1) MPI and cube-exchange not yet coded. |
| 182 |
|
2) probably not accurate for poorly conditioned / large size problem. |
| 183 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
| 184 |
|
default: not compiled and not used. |
| 185 |
|
o pkg/seaice: |
| 186 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
| 187 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
| 188 |
|
mpi_allreduce in seaice_fgmres.F |
| 189 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
| 190 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
| 191 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
| 192 |
|
o verification: |
| 193 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
| 194 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
| 195 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
| 196 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
| 197 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
| 198 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
| 199 |
|
o pkg/exf: |
| 200 |
|
- disable "sstExtrapol" when Nr=1 |
| 201 |
|
o verification: |
| 202 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
| 203 |
|
to test pkg/cheapaml. |
| 204 |
|
o pkg/aim_v23 & pkg/shap_filt: |
| 205 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
| 206 |
|
o pkg/seaice: |
| 207 |
|
- remove unused field pressPre from jfnk solver |
| 208 |
|
- rename two subroutines in seaice_preconditioner.F |
| 209 |
|
o eesupp/src: |
| 210 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
| 211 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
| 212 |
|
- remove wrong parts of the rhs and the lhs (were in there |
| 213 |
|
because I did not understand the concept of this preconditioner) |
| 214 |
|
- add an exchange between u- and v-sweep. This increases communication |
| 215 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
| 216 |
|
one would like the u- and v-sweep to be independent. So far within |
| 217 |
|
undocumented ifdefs |
| 218 |
|
- reorganize the extra computations for printing the residuals |
| 219 |
|
o tools/genmake2: |
| 220 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
| 221 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
| 222 |
|
|
| 223 |
|
checkpoint64a (2012/11/16) |
| 224 |
|
o pkg/autodiff: |
| 225 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
| 226 |
|
autodiff_readparms.F no longer depends on calling order (within |
| 227 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
| 228 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
| 229 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
| 230 |
|
o pkg/obcs: |
| 231 |
|
- adding tidal velocity forcing capability to obcs |
| 232 |
|
for usage example, see verification/seaice_obcs/input.tides |
| 233 |
|
o pkg/seaice: |
| 234 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
| 235 |
|
SEAICE_LSRrelaxU/V |
| 236 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
| 237 |
|
o pkg/aim_v23: |
| 238 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
| 239 |
|
o pkg/shap_filt: |
| 240 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
| 241 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
| 242 |
|
o model/src: |
| 243 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
| 244 |
|
time-constant addMass field from file (addMassFile); |
| 245 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
| 246 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
| 247 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
| 248 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
| 249 |
|
o pkg/seaice: |
| 250 |
|
- complete merge of ITD code into seaice_growth.F |
| 251 |
|
from MITgcm_contrib/torge/itd/code/ |
| 252 |
|
no verification so far, but Torge Martin tested |
| 253 |
|
"1-D test case and Beaufort set up; |
| 254 |
|
deliver okay results after 1 model year." |
| 255 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
| 256 |
|
- move computation of eta at Z-points into calc_viscosities |
| 257 |
|
+ introduce global field etaZ |
| 258 |
|
+ add different methods for computing etaZ, for now the old |
| 259 |
|
method (simple averages of eta to Z-points) is hardwired |
| 260 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
| 261 |
|
seaice_preconditioner |
| 262 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
| 263 |
|
- seaice_preconditioner: |
| 264 |
|
+ replace one remaining press by pressLoc (mistake) |
| 265 |
|
+ adjust printing of residuals |
| 266 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
| 267 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
| 268 |
|
seaice_init_fixed.F) |
| 269 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
| 270 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
| 271 |
|
interval to STDOUT |
| 272 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
| 273 |
|
some operations |
| 274 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
| 275 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
| 276 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
| 277 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
| 278 |
|
a serious convergence problem when open boundaries are involved |
| 279 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
| 280 |
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
| 281 |
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
| 282 |
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
| 283 |
o pkg/autodiff |
o pkg/autodiff |
| 284 |
- Add inAdMode switch for SEAICEuseDYNAMICS: |
- Add inAdMode switch for SEAICEuseDYNAMICS: |
| 285 |
SEAICEuseDYNAMICSinAdMode |
SEAICEuseDYNAMICSinAdMode |
| 286 |
(extend logic in ADAUTODIFF_INADMODE_SET) |
(extend logic in ADAUTODIFF_INADMODE_SET) |
| 287 |
o pkg/seaice |
o pkg/seaice |
| 288 |
- Step 1 of merging ice-thickness distribution (ITD) code from |
- Step 1 of merging ice-thickness distribution (ITD) code from |
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