| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
|
|
| 7 |
o pkg/ctrl/obcs/ecco: |
o pkg/obcs: |
| 8 |
|
- change OBCSfixTopo default from True to False (should not change the results); |
| 9 |
|
keep OBCSfixTopo=T in verification-exp. seaice_obcs. |
| 10 |
|
o pkg/thsice: |
| 11 |
|
- fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in |
| 12 |
|
2nd layer seaice sublimation (unlikely to happen) |
| 13 |
|
- use Interior mask for OBCS in thsice_advection.F (similar to what is |
| 14 |
|
done in gad_advection & seaice_advection). |
| 15 |
|
o adjoint: |
| 16 |
|
bug fix spotted by Gael Forget: |
| 17 |
|
seaice_advection and thsice_advection still had |
| 18 |
|
legacy CPP options to avoid CS corner updates for adjoint |
| 19 |
|
o pkg/seaice: |
| 20 |
|
=> Change some of the defaults (2011/05/29): |
| 21 |
|
- change SEAICEuseFluxForm default (from False to True) |
| 22 |
|
- change DIFF1 default (from 0.004 m/s to 0. m/s) |
| 23 |
|
And print warnings if DIFF1 is not set in data.seaice and centered |
| 24 |
|
avection scheme is used without any diffusion. |
| 25 |
|
also: |
| 26 |
|
- fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F; |
| 27 |
|
- set SEAICEdiffKh[] default in the same way as SEAICEadvSch[] |
| 28 |
|
- stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any |
| 29 |
|
other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with |
| 30 |
|
#undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE. |
| 31 |
|
update results of test exp.: |
| 32 |
|
lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20) |
| 33 |
|
output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200) |
| 34 |
|
output_adm.noseaicedyn (SEAICEuseFluxForm=T) |
| 35 |
|
offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T) |
| 36 |
|
seaice_obcs: output (SEAICEuseFluxForm=T) |
| 37 |
|
and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004) |
| 38 |
|
for standard fwd & AD lab_sea tests (to keep the same output). |
| 39 |
|
o pkg/seaice/seaice_growth.F: |
| 40 |
|
- use Ian Fenty's capping formulas for actual ice |
| 41 |
|
thickness thoughout EVOLUTION branch. |
| 42 |
|
- put treatment pathological case #2) in CPP brackets |
| 43 |
|
(ALLOW_AVOID_INFINITESIMAL_AREA, undef by default). |
| 44 |
|
- update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly. |
| 45 |
|
o pkg/seaice: |
| 46 |
|
- seaice_diffusion.F : remove the min(DX,DY) factor permanently; |
| 47 |
|
pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter; |
| 48 |
|
also pass fac as a param, which can be 1. (to update the tendency |
| 49 |
|
field) or the time step (to update the field itself). |
| 50 |
|
- seaice_advdiff.F: for multidim, call seaice_diffusion with |
| 51 |
|
e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call |
| 52 |
|
seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step. |
| 53 |
|
- SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F : |
| 54 |
|
hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc. |
| 55 |
|
o pkg/seaice: |
| 56 |
|
diffusion with centered advection scheme (diffus.F & advect.F): |
| 57 |
|
- simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside) |
| 58 |
|
to just compute the laplacian of input-field. |
| 59 |
|
- unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call. |
| 60 |
|
- fix flux-form version in diffus.F to conserve tracer. |
| 61 |
|
update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects |
| 62 |
|
machine truncation) and lab_sea.salt_plume (conservative flux-form modif) |
| 63 |
|
|
| 64 |
|
checkpoint62y (2011/05/26) |
| 65 |
|
o pkg/seaice: |
| 66 |
|
- seaice_growth.F : in EVOLUTION branch, always include |
| 67 |
|
a_QSWbyATM_cover in qnet (as it should be). |
| 68 |
|
- verification/global_ocean.cs32x15 : update results accordingly |
| 69 |
|
(output.seaice.txt output_adm.seaice.txt). |
| 70 |
|
o pkg/seaice + obcs: |
| 71 |
|
- use maskInW & maskInS in multi-dim advection and biharmonic diffusion: |
| 72 |
|
equivalent of assuming no tracer gradient outside the OB region. |
| 73 |
|
update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion) |
| 74 |
|
- remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed |
| 75 |
|
after changes above); |
| 76 |
|
- obcs+seaice cleaning: apply seaice-tracer OB values to tracer field |
| 77 |
|
only at OB location (instead of over a band of OLx width). |
| 78 |
|
o pkg/seaice: |
| 79 |
|
- fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F |
| 80 |
|
(dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid) |
| 81 |
|
o pkg/obcs: |
| 82 |
|
- split header file "OBCS.h" into 4 separated files: |
| 83 |
|
OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h |
| 84 |
|
Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h |
| 85 |
|
(contain no conditional statement which depends on OBCS options). |
| 86 |
|
- move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h) |
| 87 |
|
to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h). |
| 88 |
|
o ctrl, cost, grdchk & autodiff pkgs: |
| 89 |
|
- make options file more standard (like other {PKG}_OPTIONS.h file but |
| 90 |
|
with AD_CONFIG.h); clean-up some of the included header files. |
| 91 |
|
o pkg/obcs: |
| 92 |
|
- do not mask tracer when applying OB (tracer == 0 could generate problems) |
| 93 |
|
- apply tracer OB values to tracer field only at OB location (instead of |
| 94 |
|
over a band of OLx width) |
| 95 |
|
- clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R) |
| 96 |
|
- remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove |
| 97 |
|
obcs_apply_tloc.F & obcs_apply_sloc.F |
| 98 |
|
o obcs in model/src: |
| 99 |
|
- call OBCS_APPLY_W only if NonHydrostatic. |
| 100 |
|
- call OBCS_APPLY_ETA only if NonLinFreeSurf. |
| 101 |
|
- reset dEtaHdt and wVel to zero outside OB interior region ; |
| 102 |
|
- leave tracer unchanged outside OB interior region: This has no effect |
| 103 |
|
on the solution but just to prevent unrealistic tracer value outside OB. |
| 104 |
|
- zero out velocity outside OB interior region: This has no effect on |
| 105 |
|
the solution but just to prevent unrealistic velocity outside OB. |
| 106 |
|
o obcs and non-lin free-surf: |
| 107 |
|
move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F |
| 108 |
|
and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F |
| 109 |
|
+ add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR: |
| 110 |
|
this fixes missing EXCH + get consistent eta OB value (+ fix restart). |
| 111 |
|
update results of test-exp. exp4(nlfs). |
| 112 |
|
o exp4 (nlfs) test-exp: |
| 113 |
|
use OBC for Eta at Western & Eastern OB (to test prescribing Eta |
| 114 |
|
with NonLin-FreeSurf); update output.nlfs.txt |
| 115 |
|
o obcs and 2d/3d solver norm: |
| 116 |
|
use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB |
| 117 |
|
and outside OB interior region (will allow to place OB further inside the |
| 118 |
|
domain). Depending on the domain, can affects cg2d-Norm (previous |
| 119 |
|
cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl, |
| 120 |
|
and cg3d-Norm (previous Norm was computed before canceling OB terms), |
| 121 |
|
e.g. in tutorial_plume_on_slope. |
| 122 |
|
- update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope. |
| 123 |
|
o pkg rbcs: |
| 124 |
|
- split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h |
| 125 |
|
- add capability to apply relaxation to horizontal velocity uVel & vVel. |
| 126 |
|
o pkg/grdchk: add gradient check for control variable xx_shifwflx |
| 127 |
|
o pkg/shelfice/shelfice_init_fixed.F |
| 128 |
|
fix CPP-flag combinations |
| 129 |
|
o pkg/seaice: Merge iceage code of Pierre Rampal |
| 130 |
|
* update/change/correct ice age calculations |
| 131 |
|
* add age updates for pathological cases |
| 132 |
|
Probably needs more testing... |
| 133 |
|
|
| 134 |
|
checkpoint62x (2011/05/13) |
| 135 |
|
o pkg/mom_vecinv: |
| 136 |
|
high-order vorticity scheme: use interior masks (maskInW & S) |
| 137 |
|
to zero-out (outside OB) gradient of vorticity. |
| 138 |
|
o verification exp.: |
| 139 |
|
turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
| 140 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
| 141 |
|
o pkg/obcs: |
| 142 |
|
fix bug in OBeta for YZ sections in obcs_exf_load.F |
| 143 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
| 144 |
|
- add new control variable xx_shifwflx (fresh water flux underneath ice |
| 145 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
| 146 |
|
variables needs its own mask. |
| 147 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
| 148 |
|
from the first guess (zero) in analogy to other control variables |
| 149 |
|
o pkg/shelfice: |
| 150 |
|
- start basic adjoint |
| 151 |
|
o pkg/ctrl: |
| 152 |
|
- remove extra 2D field "for good measure" when initializing in |
| 153 |
|
ctrl_set_globfld_[xy/xz/yz].F |
| 154 |
|
- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
| 155 |
|
- improve error messages in ctrl_set_unpack_* |
| 156 |
|
o OBC implementation in momentum: |
| 157 |
|
use interior masks (maskInC,W & S) in momentum S/R: |
| 158 |
|
- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
| 159 |
|
- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
| 160 |
|
- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
| 161 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
| 162 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
| 163 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
| 164 |
|
Update output of experiment dome and exp4 (+nlfs). |
| 165 |
|
o exp4 test-exp: |
| 166 |
|
- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
| 167 |
|
and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
| 168 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 169 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
| 170 |
|
- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
| 171 |
|
and biharmonic-viscosity ; also use prescribed time varying OB. |
| 172 |
|
o pkg/obcs: |
| 173 |
|
fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
| 174 |
|
o model/src: |
| 175 |
|
- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
| 176 |
|
- initialise startTime & nIter0 with unlikely values: allows to set one |
| 177 |
|
from the other without ambiguity. |
| 178 |
|
o seaice_obcs test-exp.: |
| 179 |
|
add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
| 180 |
|
o pkg/obcs: |
| 181 |
|
- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
| 182 |
|
no longer needed with maskInC,W,S in pkg/generic_advdiff. |
| 183 |
|
o pkg/seaice: |
| 184 |
|
- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
| 185 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
| 186 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
| 187 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
| 188 |
|
o fizhi-cs test exp.: |
| 189 |
|
switch reference output convention for these 2 non-standard test-exp, |
| 190 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
| 191 |
|
to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
| 192 |
|
reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
| 193 |
|
o model/inc: |
| 194 |
|
- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
| 195 |
|
of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
| 196 |
|
o pkg/seaice: |
| 197 |
|
- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
| 198 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
| 199 |
|
- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
| 200 |
|
and initial HSALT |
| 201 |
|
|
| 202 |
|
checkpoint62w (2011/04/26) |
| 203 |
|
o pkg/mom_fluxform: |
| 204 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
| 205 |
|
- use parameter "sideDragFactor" in no-slip BC side-drag part. |
| 206 |
|
- update output of exp. global_ocean.90x40x15 |
| 207 |
|
o pkg/mom_vecinv: |
| 208 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
| 209 |
|
o update seaice exp.: |
| 210 |
|
use more consistent parameter values (remove "backward compatability only": |
| 211 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
| 212 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
| 213 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
| 214 |
|
o update test-exp global_ocean.90x40x15: |
| 215 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
| 216 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
| 217 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
| 218 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
| 219 |
|
and update output files: output.txt & output.dwnslp.txt |
| 220 |
|
o new AD-test experiment: obcs_ctrl |
| 221 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
| 222 |
|
o pkg/dic: |
| 223 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
| 224 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
| 225 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
| 226 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
| 227 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
| 228 |
|
at depth and bring the negative heat anomaly to the surface level |
| 229 |
|
o pkgs _fields_load: |
| 230 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
| 231 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
| 232 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
| 233 |
|
rbcs to get interpolation weights and time reccord number. |
| 234 |
|
- fix multi-threading in aim_fields_load.F |
| 235 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
| 236 |
|
o external_fields_load: |
| 237 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
| 238 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
| 239 |
|
time-step to convert to integer: |
| 240 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
| 241 |
|
(Thanks to Christopher L. Wolfe) |
| 242 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
| 243 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
| 244 |
|
store index of time-record which is currently loaded: |
| 245 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
| 246 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
| 247 |
|
(to be fixed soon) |
| 248 |
|
|
| 249 |
|
checkpoint62v (2011/04/02) |
| 250 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
| 251 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
| 252 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
| 253 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
| 254 |
|
o pkg/generic_advdiff with OBCS: |
| 255 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
| 256 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
| 257 |
|
This will affect the results if using obcs+biharmonic diffusion. |
| 258 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
| 259 |
|
o pkg/obcs: |
| 260 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
| 261 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
| 262 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
| 263 |
|
o pkg/ptracers (adjoint) |
| 264 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
| 265 |
|
tape file for each tracer |
| 266 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
| 267 |
|
of parts of the adjoint code at run time. For now, there are only |
| 268 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
| 269 |
|
parameters are set in data.pkg. |
| 270 |
|
This is the lazy coward's version of doing this, but still useful for |
| 271 |
|
debugging. In order to do it right, everything needs to be moved to |
| 272 |
|
pkg/autodiff. |
| 273 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
| 274 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
| 275 |
|
o pkg/ctrl: |
| 276 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
| 277 |
|
xx_${varname}period = 0., means time-independent control part |
| 278 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
| 279 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
| 280 |
|
clean up ctrl_init a little, remove unused variables |
| 281 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
| 282 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
| 283 |
|
|
| 284 |
|
checkpoint62u (2011/03/15) |
| 285 |
|
o model/src: |
| 286 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
| 287 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
| 288 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
| 289 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
| 290 |
|
o pkg/ctrl/obcs/ecco: |
| 291 |
- remove obsolete, unused, and partially broken code: |
- remove obsolete, unused, and partially broken code: |
| 292 |
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
| 293 |
ALLOW_CTRL_OBCS_BALANCE |
ALLOW_CTRL_OBCS_BALANCE |
| 294 |
- put a stop statement into ecco/cost_obcsvol.F, but also add |
- put a stop statement into ecco/cost_obcsvol.F, but also add |
| 295 |
cost_obcsvol to ecco_ad_diff.list |
cost_obcsvol to ecco_ad_diff.list |
| 296 |
o pkg/ecco: fix counting cost function contributions for obcs (code |
o pkg/ecco: fix counting cost function contributions for obcs (code |
| 297 |
by Matt M.) and diffkr for diagnostics |
by Matt M.) and diffkr for diagnostics |
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