| 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/grdchk: add gradient check for control variable xx_shifwflx |
| 8 |
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o pkg/shelfice/shelfice_init_fixed.F |
| 9 |
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fix CPP-flag combinations |
| 10 |
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|
| 11 |
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checkpoint62x (2011/05/13) |
| 12 |
|
o pkg/mom_vecinv: |
| 13 |
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high-order vorticity scheme: use interior masks (maskInW & S) |
| 14 |
|
to zero-out (outside OB) gradient of vorticity. |
| 15 |
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o verification exp.: |
| 16 |
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turn on "useEnergyConservingCoriolis" (better discretisation) in exp. |
| 17 |
|
hs94.128x64x5 and seaice_obcs ; update results. |
| 18 |
|
o pkg/obcs: |
| 19 |
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fix bug in OBeta for YZ sections in obcs_exf_load.F |
| 20 |
|
o pkg/ctrl, pkg/shelfice, and optim: |
| 21 |
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- add new control variable xx_shifwflx (fresh water flux underneath ice |
| 22 |
|
shelves). This is almost as tedious as obcs-ctrl, because the |
| 23 |
|
variables needs its own mask. |
| 24 |
|
- add a cost function term that penalizes the deviation of xx_shifwflx |
| 25 |
|
from the first guess (zero) in analogy to other control variables |
| 26 |
|
o pkg/shelfice: |
| 27 |
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- start basic adjoint |
| 28 |
|
o pkg/ctrl: |
| 29 |
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- remove extra 2D field "for good measure" when initializing in |
| 30 |
|
ctrl_set_globfld_[xy/xz/yz].F |
| 31 |
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- replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec |
| 32 |
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- improve error messages in ctrl_set_unpack_* |
| 33 |
|
o OBC implementation in momentum: |
| 34 |
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use interior masks (maskInC,W & S) in momentum S/R: |
| 35 |
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- multiply divergence, tension and some del^i.u or del^j.v by maskInC |
| 36 |
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- multiply del2u,del2v by maskInW/S (biharmonic viscosity) |
| 37 |
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- multiply horiz. grad of vorticity by maskInW/S (in Leith scheme) |
| 38 |
|
- multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd) |
| 39 |
|
Motivation: fix/clean implementation of OBC with biharmonic-viscosity |
| 40 |
|
(and also with Leith/Smagorinsky harmonic-viscosity). |
| 41 |
|
Update output of experiment dome and exp4 (+nlfs). |
| 42 |
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o exp4 test-exp: |
| 43 |
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- turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F) |
| 44 |
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and prescribe time-varying OB (without pkg/exf) for zonal-velocity |
| 45 |
|
at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe |
| 46 |
|
time-varying OB at Western-side for wVel (NonHyd); update output. |
| 47 |
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- add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv |
| 48 |
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and biharmonic-viscosity ; also use prescribed time varying OB. |
| 49 |
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o pkg/obcs: |
| 50 |
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fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F |
| 51 |
|
o model/src: |
| 52 |
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- fix startTime setting when baseTime<>0 & nIter0=0 are specified ; |
| 53 |
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- initialise startTime & nIter0 with unlikely values: allows to set one |
| 54 |
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from the other without ambiguity. |
| 55 |
|
o seaice_obcs test-exp.: |
| 56 |
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add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output. |
| 57 |
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o pkg/obcs: |
| 58 |
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- remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer: |
| 59 |
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no longer needed with maskInC,W,S in pkg/generic_advdiff. |
| 60 |
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o pkg/seaice: |
| 61 |
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- retired SEAICE_SALINITY and SEAICE_salinity in favor of |
| 62 |
|
SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively. |
| 63 |
|
- fixed bug in the initialization of sea ice salinity variable HSALT |
| 64 |
|
in seaice_init_varia.F (removed dependence on ICE2WATR) |
| 65 |
|
o fizhi-cs test exp.: |
| 66 |
|
switch reference output convention for these 2 non-standard test-exp, |
| 67 |
|
from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5) |
| 68 |
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to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11) |
| 69 |
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reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran |
| 70 |
|
o model/inc: |
| 71 |
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- change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4") |
| 72 |
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of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS) |
| 73 |
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o pkg/seaice: |
| 74 |
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- fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY |
| 75 |
|
o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15 |
| 76 |
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- updated output*.txt files due to bug fixes in salt, saltPlumeFlux, |
| 77 |
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and initial HSALT |
| 78 |
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|
| 79 |
|
checkpoint62w (2011/04/26) |
| 80 |
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o pkg/mom_fluxform: |
| 81 |
|
- fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf. |
| 82 |
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- use parameter "sideDragFactor" in no-slip BC side-drag part. |
| 83 |
|
- update output of exp. global_ocean.90x40x15 |
| 84 |
|
o pkg/mom_vecinv: |
| 85 |
|
mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform) |
| 86 |
|
o update seaice exp.: |
| 87 |
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use more consistent parameter values (remove "backward compatability only": |
| 88 |
|
ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh) |
| 89 |
|
related to thermodynamics seaice. Update output (fwd+AD) of exp.: |
| 90 |
|
1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs |
| 91 |
|
o update test-exp global_ocean.90x40x15: |
| 92 |
|
o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis). |
| 93 |
|
o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.) |
| 94 |
|
o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params) |
| 95 |
|
o turn on zStar & viscA4 in standard set-up (dir input/) |
| 96 |
|
and update output files: output.txt & output.dwnslp.txt |
| 97 |
|
o new AD-test experiment: obcs_ctrl |
| 98 |
|
(From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector. |
| 99 |
|
o pkg/dic: |
| 100 |
|
fix two bugs in handling water vapour pressure in carbonate chemistry |
| 101 |
|
and air-sea fluxes. Found by Val Bennington and Galen McKinley |
| 102 |
|
(add DIC Option = WATERVAP_BUG to recover old results) |
| 103 |
|
update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline |
| 104 |
|
o adding allowInteriorFreezing option to check for water below freezing point |
| 105 |
|
at depth and bring the negative heat anomaly to the surface level |
| 106 |
|
o pkgs _fields_load: |
| 107 |
|
- extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs) |
| 108 |
|
- use new S/R GET_PERIODIC_INTERVAL in pkgs: |
| 109 |
|
bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and |
| 110 |
|
rbcs to get interpolation weights and time reccord number. |
| 111 |
|
- fix multi-threading in aim_fields_load.F |
| 112 |
|
- apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F |
| 113 |
|
o external_fields_load: |
| 114 |
|
new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear |
| 115 |
|
interpolation weights) to use in a periodic time-series ; do not divide by |
| 116 |
|
time-step to convert to integer: |
| 117 |
|
- this fixes case where externForcingPeriod is not multiple of time-step |
| 118 |
|
(Thanks to Christopher L. Wolfe) |
| 119 |
|
- this fixes case where externForcingPeriod is an odd multiple of time-step |
| 120 |
|
(was wrong by half of time-step); update results of tutorial_global_oce_in_p. |
| 121 |
|
store index of time-record which is currently loaded: |
| 122 |
|
- works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ; |
| 123 |
|
- needed for the adjoint but not yet used because of extensive recomputations; |
| 124 |
|
(to be fixed soon) |
| 125 |
|
|
| 126 |
|
checkpoint62v (2011/04/02) |
| 127 |
|
o verification/1D_ocean_ice_column added to test Ian Fenty's |
| 128 |
|
pkg/seaice_growth.F modifications for improving sea ice code differentiability |
| 129 |
|
o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope |
| 130 |
|
(new velocity statistics after changing maskInW & maskInS definition) |
| 131 |
|
o pkg/generic_advdiff with OBCS: |
| 132 |
|
use maksInW & maskInS in advective flux and in biharmonic diffusion calculation: |
| 133 |
|
equivalent to assumption of no tracer gradient outside the OB region. |
| 134 |
|
This will affect the results if using obcs+biharmonic diffusion. |
| 135 |
|
update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc) |
| 136 |
|
o pkg/obcs: |
| 137 |
|
change definition of maskInW & maskInS: leave OB edges inside (maskIn=1) |
| 138 |
|
(e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still |
| 139 |
|
in Interior region. No impact on solution but affects Velocity monitor stats. |
| 140 |
|
o pkg/ptracers (adjoint) |
| 141 |
|
New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate |
| 142 |
|
tape file for each tracer |
| 143 |
|
o model/inc/src and pkg/autodiff: add parameters that allow to turn |
| 144 |
|
of parts of the adjoint code at run time. For now, there are only |
| 145 |
|
useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These |
| 146 |
|
parameters are set in data.pkg. |
| 147 |
|
This is the lazy coward's version of doing this, but still useful for |
| 148 |
|
debugging. In order to do it right, everything needs to be moved to |
| 149 |
|
pkg/autodiff. |
| 150 |
|
o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at |
| 151 |
|
the end; this fixes the adjoint balancing code for open boundaries. |
| 152 |
|
o pkg/ctrl: |
| 153 |
|
- change behavior of xx_${varname}period to be analogous to exf-conventions: |
| 154 |
|
xx_${varname}period = 0., means time-independent control part |
| 155 |
|
xx_${varname}period = -12., means one-year-periodic monthly control part |
| 156 |
|
- introduce helper routine ctrl_init_rec (part of ctrl_init.F) to |
| 157 |
|
clean up ctrl_init a little, remove unused variables |
| 158 |
|
- ctrl_init: fixed the handling of the start/endrec for obcs-variables |
| 159 |
|
- move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec |
| 160 |
|
|
| 161 |
|
checkpoint62u (2011/03/15) |
| 162 |
|
o model/src: |
| 163 |
|
- for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in |
| 164 |
|
h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ; |
| 165 |
|
- in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to |
| 166 |
|
INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF. |
| 167 |
|
o pkg/ctrl/obcs/ecco: |
| 168 |
|
- remove obsolete, unused, and partially broken code: |
| 169 |
|
ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within |
| 170 |
|
ALLOW_CTRL_OBCS_BALANCE |
| 171 |
|
- put a stop statement into ecco/cost_obcsvol.F, but also add |
| 172 |
|
cost_obcsvol to ecco_ad_diff.list |
| 173 |
|
o pkg/ecco: fix counting cost function contributions for obcs (code |
| 174 |
|
by Matt M.) and diffkr for diagnostics |
| 175 |
|
o pkg/ecco, pkg/ctrl, pkg/grdchk: |
| 176 |
|
add cost penalty terms for initial uvel, vvel, eta controls |
| 177 |
|
and I/O for prior error files |
| 178 |
|
o pkg/mdsio: |
| 179 |
|
move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option |
| 180 |
|
(new argument) to check for tiled file in mdsioLocalDir : this fix the |
| 181 |
|
restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir. |
| 182 |
|
o pkg/ctrl: |
| 183 |
|
- ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by |
| 184 |
|
ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove |
| 185 |
|
unused and superfluous variables |
| 186 |
|
- ctrl_get_gen_rec.F: catch the case of xx_genperiod=0. |
| 187 |
|
o pkg/ecco |
| 188 |
|
- enable adjoint of Stevens OB |
| 189 |
|
o pkg/ctrl/ecco/grdchk: |
| 190 |
|
- remove global declaration of tmpfldx/yz and tmpfldx/yz2. |
| 191 |
|
Fortunately, we do not have any tests for the numerous cpp-flagged |
| 192 |
|
option of "obcs as control parameters" so we will never know |
| 193 |
|
if this is an improvement (but at least now things compile). |
| 194 |
|
- remove an obsolete initialization from ecco_cost_init_barfiles.F |
| 195 |
|
- fix some problems within never used ifdefs to make the code compile |
| 196 |
|
o pkg/obcs: |
| 197 |
|
- Refine Interior mask definition to work with more complex OB (e.g. |
| 198 |
|
if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to |
| 199 |
|
read in Interior mask from file. Check if Interior mask is consistent |
| 200 |
|
with OB list of indices. |
| 201 |
|
o pkg/seaice |
| 202 |
|
- beginning code for a seaice tracer package, |
| 203 |
|
but currently only used for seaice age: SEAICE_AGE |
| 204 |
|
SEAICE_num = 4 |
| 205 |
|
iTracer = 1: area-weighted ice age |
| 206 |
|
= 2: volume-weighted ice age |
| 207 |
|
= 3, 4: template for one-year vs. multi-year ice |
| 208 |
|
data.seaice has new namelist SEAICE_PARM03 for arrays related to |
| 209 |
|
SEAICE_num |
| 210 |
|
|
| 211 |
|
checkpoint62t (2011/03/05) |
| 212 |
|
o pkg/obcs: |
| 213 |
|
- obcs_apply_uv.F: change to a 2 steps method, first tangential component; |
| 214 |
|
then normal component. This ensures that the normal component is set |
| 215 |
|
correctly even when it conficts with tangential setting from an other OB. |
| 216 |
|
Affects results of test-experiment seaice_obcs: update the output.txt |
| 217 |
|
o pkg/obcs: |
| 218 |
|
- add code to monitor statistics of dynamical fields at OB. |
| 219 |
|
- take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW : |
| 220 |
|
- fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection). |
| 221 |
|
- change default: balance the Net inflow through all OB (instead of balancing |
| 222 |
|
each OB separately); keep the old method if setting OBC_balanceFacX < 0. |
| 223 |
|
- switch on useOBCSbalance in dome experiment: only correct Western OB outflow |
| 224 |
|
to match Nortern OB inflow (OBCS_balanceFacN=0). |
| 225 |
|
o pkg/seaice: |
| 226 |
|
- redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL |
| 227 |
|
o pkg/seaice (seaice_growth v 1.113): |
| 228 |
|
- reverting seaice_growth to v 1.111 in order to have code with exact bit |
| 229 |
|
compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge |
| 230 |
|
CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced |
| 231 |
|
runtime flag SEAICEareaFormula is kept but is inactive |
| 232 |
|
o model/src: |
| 233 |
|
- add new param to scale curvilinear grid distance and area when using |
| 234 |
|
a different sphere radius from the grid-files. |
| 235 |
|
- test/check multi-threads EXCH applied to local variable (cg2d_x) |
| 236 |
|
o adjoint: |
| 237 |
|
- enable adjoint of Stevens OB |
| 238 |
|
- add dummy_in_dynamics to enable extraction of ADJrhoinsitu |
| 239 |
|
(a bit delicate because of potentially modified adj. common block structure; |
| 240 |
|
current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later) |
| 241 |
|
|
| 242 |
|
checkpoint62s (2011/02/15) |
| 243 |
|
o pkg/seaice (seaice_growth v 1.112): |
| 244 |
|
- introduce SEAICEareaFormula run time parameter, which selects the recipe for |
| 245 |
|
computing the ice cover tendency from effective thickness tendencies. Include |
| 246 |
|
Ian Fenty's formula. |
| 247 |
|
- remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using |
| 248 |
|
SEAICEareaFormula. |
| 249 |
|
- simplify notations for the various d_HEFF/d_AREA terms. |
| 250 |
|
o pkg/gmredi: |
| 251 |
|
- add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code |
| 252 |
|
from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative; |
| 253 |
|
add a verification test-run (front_relax.bvp) to test GM_useBVP. |
| 254 |
|
o pkg/seaice (seaice_growth v 1.111): |
| 255 |
|
- for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's. |
| 256 |
|
- the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to |
| 257 |
|
also melt ice. |
| 258 |
|
o pkg/seaice: |
| 259 |
|
- McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty). |
| 260 |
|
- can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h |
| 261 |
|
o pkg/cheapaml: |
| 262 |
|
- from Nico Wienders: New version of this package. |
| 263 |
|
o pkg/flt: |
| 264 |
|
- add CPP options to prevent floats to re-enter the opposite side of |
| 265 |
|
a periodic domain (default: keep periodicity) |
| 266 |
|
o pkg/gmredi: |
| 267 |
|
- apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners |
| 268 |
|
(needed for multi-dim advection). |
| 269 |
|
- switch on GM Advective form in global_ocean.cs32x15 and update output.txt |
| 270 |
|
o model/src: |
| 271 |
|
- fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run. |
| 272 |
|
o tutorial_tracer_adjsens |
| 273 |
|
- extend to NLFS and replace maskC by hFacC |
| 274 |
|
(change reference output accordingly) |
| 275 |
|
|
| 276 |
|
checkpoint62r (2011/01/24) |
| 277 |
|
o testreport: |
| 278 |
|
- add option -deloutp (-do) to remove output file after successful run |
| 279 |
|
- add option -mfile (-mf) for MPI machile-file and for each test-exp, |
| 280 |
|
extract exact list of procs from this file ; adjust COMMAND by |
| 281 |
|
replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs. |
| 282 |
|
o pkg/ecco: replace old ineffective way of penalizing deviations from |
| 283 |
|
first guess (of obcs) with code by Matt Mazloff |
| 284 |
|
o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without |
| 285 |
|
exf/cal |
| 286 |
|
- ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl |
| 287 |
|
and handle case of obcs?period == 0 |
| 288 |
|
Not affected by these changes: There is still an inconsistency in |
| 289 |
|
the computation of start/endrec for the obcs variables for ALLOW_CAL |
| 290 |
|
defined (see comment by Menemenlis, 7-Mar-2003) |
| 291 |
|
- make S/R ctrl_get_gen_rec return something meaningful even if |
| 292 |
|
ALLOW_CAL is not defined |
| 293 |
|
- ctrl_getobcs?: simplify code so that it does not need to use |
| 294 |
|
S/R exf_swapfields |
| 295 |
|
o testreport: |
| 296 |
|
allow to test MPI with different number of processors for each experiment: |
| 297 |
|
create file "SIZE.h.mpi" in each build dir. |
| 298 |
|
Note: update of "-command" argument not yet implemented. |
| 299 |
|
o model/src, pkg/autodiff, pkg/ecco, pkg/seaice: |
| 300 |
|
alleviate the need for additional 3D tapes when using |
| 301 |
|
the non-inear free surface in the adjoint. This is done |
| 302 |
|
by adding an 'update' of hfacc etc. to their current |
| 303 |
|
value at the beginning of forward_step.F. |
| 304 |
|
o pkg/seaice |
| 305 |
|
seaice_lsr: move stress-divergence computations out of outer pseudo- |
| 306 |
|
timestepping loop |
| 307 |
|
o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD' |
| 308 |
|
up, so that the calls of the ctrl_* subroutines are really at the end |
| 309 |
|
of the routine. |
| 310 |
|
o pkg/gmredi: |
| 311 |
|
allow to specify a 2-D horizontal map and a 1-D vertical profil |
| 312 |
|
as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity. |
| 313 |
|
o pkg/seaice: |
| 314 |
|
move lsr iterations from seaice_dynsolver to seaice_lsr. |
| 315 |
|
o pkg/seaice: |
| 316 |
|
reduce memory footprint of seaice mutldim advection tapes, |
| 317 |
|
by using a 2D tape independent of the generic_advdiff ones, |
| 318 |
|
and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc. |
| 319 |
|
|
| 320 |
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checkpoint62q (2010/12/29) |
| 321 |
o model/src: |
o model/src: |
| 322 |
- check horizontal grid-spacing for unset or zero/negative values. |
- check horizontal grid-spacing for unset or zero/negative values. |
| 323 |
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
- change AD test hs94.1x64x5 to be truly a 2-D set-up. |
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