| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
|
|
| 7 |
|
o pkg/layers: |
| 8 |
|
- Added missing call to layers_fill for keeping track of tottend in |
| 9 |
|
pkg/diagnostics/diagnostics_fill_state.F |
| 10 |
|
o pkg/layers: |
| 11 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 12 |
|
of diapycnal fluxes |
| 13 |
|
o pkg/layers: |
| 14 |
|
- reverted changes to interpolation to previous treatment; there |
| 15 |
|
was never actually a problem |
| 16 |
|
o pkg/layers: |
| 17 |
|
- fix interpolation of layers tracers in the presence of partial cells |
| 18 |
|
- add lots of new functionality to compute water mass transformation |
| 19 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 20 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
| 21 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 22 |
|
for layers_thermodynamics calculations |
| 23 |
|
o pkg/ptracers: |
| 24 |
|
- add capability of stepping a passive tracer forward |
| 25 |
|
without advection by setting PTRACERS_advScheme to 0. |
| 26 |
|
o pkg/diagnostics: |
| 27 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 28 |
|
o pkg/layers: |
| 29 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
| 30 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 31 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
| 32 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 33 |
|
o pkg/layers: |
| 34 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 35 |
|
- fix calculation of layer non-weighted velocity and layer probability |
| 36 |
|
- add diagnostics for pot.density used for layer averaging |
| 37 |
|
o pkg/seaice: |
| 38 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 39 |
|
positiveness, modify a few comments and improve variable names, |
| 40 |
|
- the changed computation of deltaC affects most seaice-related |
| 41 |
|
experiments at the truncation level. |
| 42 |
|
seaice_itd.thermo is affected by far the most, with |
| 43 |
|
only 7 digits of agreement remaining; update experiments. |
| 44 |
|
|
| 45 |
|
checkpoint65l (2015/05/04) |
| 46 |
|
o pkg/shelfice: |
| 47 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 48 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 49 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 50 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 51 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 52 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 53 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 54 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 55 |
|
o verification/testreport |
| 56 |
|
- add new option -small_f |
| 57 |
|
with this option testreport first makes the target small_f (*.f files) |
| 58 |
|
before running make (all). This is useful for explicit inlining when |
| 59 |
|
all sources need to be full available. |
| 60 |
|
o pkg/exf/exf_interp.F: |
| 61 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 62 |
|
|
| 63 |
|
checkpoint65k (2015/04/01) |
| 64 |
|
o pkg/ecco: |
| 65 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 66 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 67 |
|
instead of active read/write |
| 68 |
|
o pkg/ctrl: |
| 69 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 70 |
|
instead of active read/write. |
| 71 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 72 |
|
return if .NOT.useAUTODIFF |
| 73 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 74 |
|
o model/src: |
| 75 |
|
add useAUTODIFF run time switch. |
| 76 |
|
o pkg/exf/exf_interp.F: |
| 77 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 78 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 79 |
|
this feature. |
| 80 |
|
o verification/testreport: |
| 81 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 82 |
|
implementations of grep that cannot do contextual searches |
| 83 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 84 |
|
of "cat" have the option "-n" |
| 85 |
|
o model/src: |
| 86 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 87 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 88 |
|
convert from conservative to potential temperature. For now they are not |
| 89 |
|
called anywhere. |
| 90 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 91 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 92 |
|
are different for idemix into separate loops (changes verification |
| 93 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 94 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 95 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 96 |
|
s/r ggl90_idemix |
| 97 |
|
- fix and improve some comments |
| 98 |
|
|
| 99 |
|
checkpoint65j (2015/02/25) |
| 100 |
|
o pkg/openad |
| 101 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 102 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 103 |
|
o pkg/mnc: |
| 104 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 105 |
|
(since few features are missing in reading MNC pickup files). |
| 106 |
|
o model/src: |
| 107 |
|
- change default (background) vertical diffusivity for salt to be the |
| 108 |
|
temperature (background) vertical diffusivity. |
| 109 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 110 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 111 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 112 |
|
consistent with vertical mixing schemes. |
| 113 |
|
o verification/testreport: |
| 114 |
|
- fix typo in "-pcls" option ; |
| 115 |
|
- put temp files in /tmp (instead of in local dir) |
| 116 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 117 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 118 |
|
o pkg/ggl90 (idemix code): |
| 119 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 120 |
|
global_ocean.90x40x15.idemix |
| 121 |
|
o OpenAD |
| 122 |
|
- enable active file I/O and begin removal of work-around code |
| 123 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 124 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 125 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 126 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 127 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 128 |
|
o tools/genmake2: |
| 129 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 130 |
|
source files are sent to TAF (instead of all in one file). |
| 131 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 132 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 133 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 134 |
|
compile time; a runtime flag implementation is not yet complete |
| 135 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 136 |
|
o verification: |
| 137 |
|
- reduce length of the AD test run by half for experiments |
| 138 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 139 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 140 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 141 |
|
o verification/testreport: |
| 142 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 143 |
|
on Mac OS X |
| 144 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 145 |
|
o model/src/seawater.F: |
| 146 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 147 |
|
(following the matlab code), which would have avoided the bug caught |
| 148 |
|
by Matt (see below) in the first place |
| 149 |
|
o pkg/shelfice: |
| 150 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 151 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 152 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 153 |
|
ice-shelf case (i.e., within surface level). |
| 154 |
|
- add config summary in shelfice_check.F |
| 155 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 156 |
|
variable recip_latentHeat |
| 157 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 158 |
|
SHELFICEuseGammaFrict) |
| 159 |
|
- change verification experiment isomip.htd: |
| 160 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 161 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 162 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 163 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 164 |
|
o model/src: |
| 165 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 166 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 167 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 168 |
|
o pkg/shelfice: |
| 169 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 170 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 171 |
|
ice-shelf is. |
| 172 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 173 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 174 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 175 |
|
for thermodynamic calculations |
| 176 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 177 |
|
affects results of some verification experiments by up to 4 digits: |
| 178 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 179 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 180 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 181 |
|
-> updated |
| 182 |
|
|
| 183 |
|
checkpoint65i (2015/01/23) |
| 184 |
|
o model/src: |
| 185 |
|
- change units of frictionHeating field from W to W/m^2 |
| 186 |
|
- fix bug in frictional heating from stratospheric drag in |
| 187 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 188 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 189 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 190 |
|
- add diagnostics for frictional heating. |
| 191 |
|
o model/src & gmredi K3D: |
| 192 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 193 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 194 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 195 |
|
and name in pickup file). |
| 196 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 197 |
|
o model/src: |
| 198 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 199 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 200 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 201 |
|
o pkg/shelfice: |
| 202 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 203 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 204 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 205 |
|
o pkg/seaice: two new runtime parameters: |
| 206 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 207 |
|
long overdue |
| 208 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 209 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 210 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 211 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 212 |
|
o pkg/atm_phys: |
| 213 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 214 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 215 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 216 |
|
fixed-in-time pressure levels). |
| 217 |
|
o pkg/mom_common (bottomdrag): |
| 218 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 219 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 220 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 221 |
|
o pkg/shelfice (u/v_drag): |
| 222 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 223 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 224 |
|
(now similar to shelfice_u_drag.F) |
| 225 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 226 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 227 |
|
o pkg/mom_common (bottomdrag): |
| 228 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 229 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 230 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 231 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 232 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 233 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 234 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 235 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 236 |
|
off by default since this also reduces model stability (explicit bottom |
| 237 |
|
friction). Changes produce different machine truncation with linear-drag |
| 238 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 239 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 240 |
|
o model/src & mom pkgs: |
| 241 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 242 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 243 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 244 |
|
just copy level Nr value to level Nr+1. |
| 245 |
|
o doc: |
| 246 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 247 |
|
o pkg/streamice: |
| 248 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 249 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 250 |
|
from array shelficemassinit, which is set in init_fixed and |
| 251 |
|
has option to be set from file; introduce array |
| 252 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 253 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 254 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 255 |
|
pkg/streamice |
| 256 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 257 |
|
SHELFICEMassStepping = .true. |
| 258 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 259 |
|
|
| 260 |
|
checkpoint65h (2014/12/17) |
| 261 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 262 |
|
- update to generic controls. |
| 263 |
|
o pkg/ctrl: |
| 264 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 265 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 266 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 267 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 268 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 269 |
|
add time variable weights and cyclic controls (time mean, |
| 270 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 271 |
|
o pkg/ecco: |
| 272 |
|
- move reading of error, conversion to weights from |
| 273 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 274 |
|
o global_oce_llc90, cs32: |
| 275 |
|
- activte sbo. |
| 276 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 277 |
|
- activate the new genctrl capabilities. |
| 278 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 279 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 280 |
|
- add missing ctrl_init_rec.f |
| 281 |
|
o tools/OAD_support/keepOriginal: |
| 282 |
|
- add ctrl_init_rec.F |
| 283 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 284 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 285 |
|
o momentum diagnostics: |
| 286 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 287 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 288 |
|
o pkg/seaice/seaice_lsr.F: |
| 289 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 290 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 291 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 292 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 293 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 294 |
|
methods for LSR |
| 295 |
|
- update results/output.seaice.txt |
| 296 |
|
o verification/tutorial_global_oce_biogeo: |
| 297 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 298 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 299 |
|
update output_adm,_oadm,_tlm.txt |
| 300 |
|
o pkg/dic: |
| 301 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 302 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 303 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 304 |
|
o verification/tutorial_global_oce_biogeo: |
| 305 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 306 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 307 |
|
update output_adm,_oadm,_tlm.txt |
| 308 |
|
o eesupp/src: |
| 309 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 310 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 311 |
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 312 |
LSR (following Hutchings et al. 2004) |
LSR (following Hutchings et al. 2004) |
| 313 |
- introduce zetaZ as a global variable (requires adjustments in |
- introduce zetaZ as a global variable (requires adjustments in |
| 314 |
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 315 |
in seaice_calc_viscosities.F |
in seaice_calc_viscosities.F |
| 316 |
- new flag SEAICEuseStrImpCpl (default off) |
- new flag SEAICEuseStrImpCpl (default off) |
| 317 |
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 318 |
momentum equations |
momentum equations |
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