| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
|
|
| 7 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
| 8 |
|
the wrong key by inialising it before use -> fixes a recomputation |
| 9 |
|
problem but does not fix the gradient |
| 10 |
|
o pkg/layers: |
| 11 |
|
- move resetting of flux arrays to outside the iLa loop |
| 12 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
| 13 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
| 14 |
|
o pkg/layers: |
| 15 |
|
- remove from common block 3D layers fields (used to diagnose transport |
| 16 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
| 17 |
|
o pkg/seaice: |
| 18 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
| 19 |
|
in lab_sea forward experiment (changes results -> updated) |
| 20 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
| 21 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
| 22 |
|
computations; for SEAICE_VECTORIZE_LSR |
| 23 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
| 24 |
|
sweep to the outside, |
| 25 |
|
- remove store directives and add "CADJ loop sequential" directives |
| 26 |
|
in analogy to model/src/solve_tridiagonal.F |
| 27 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
| 28 |
|
boundaries to yield more readable code. This has also the charming side |
| 29 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
| 30 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
| 31 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
| 32 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
| 33 |
|
an additional option) |
| 34 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
| 35 |
|
but the adjoint gradients (which are affected by this change) still explode. |
| 36 |
|
o coupler (atm & ocn _compon_interf): |
| 37 |
|
- avoid using Exch2 IO mapping if not suitable. |
| 38 |
|
|
| 39 |
|
checkpoint65m (2015/06/15) |
| 40 |
|
o pkg/layers: |
| 41 |
|
- clean-up old parameters setting (from Sep 2012): |
| 42 |
|
+ remove old parameters setting from common block (declared locally); |
| 43 |
|
+ stop if any old parameter is mixed with new parameters; |
| 44 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
| 45 |
|
- check that layers_bounds for Pot.Density are in the right range; |
| 46 |
|
this is supposed to catch un-updated setting after recently shifting |
| 47 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
| 48 |
|
o pkg/layers: |
| 49 |
|
- Added missing call to layers_fill for keeping track of tottend in |
| 50 |
|
pkg/diagnostics/diagnostics_fill_state.F |
| 51 |
|
o pkg/layers: |
| 52 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 53 |
|
of diapycnal fluxes |
| 54 |
|
o pkg/layers: |
| 55 |
|
- reverted changes to interpolation to previous treatment; there |
| 56 |
|
was never actually a problem |
| 57 |
|
o pkg/layers: |
| 58 |
|
- fix interpolation of layers tracers in the presence of partial cells |
| 59 |
|
- add lots of new functionality to compute water mass transformation |
| 60 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 61 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
| 62 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 63 |
|
for layers_thermodynamics calculations |
| 64 |
|
o pkg/ptracers: |
| 65 |
|
- add capability of stepping a passive tracer forward without advection |
| 66 |
|
by setting PTRACERS_advScheme to 0. |
| 67 |
|
o pkg/diagnostics: |
| 68 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 69 |
|
o pkg/layers: |
| 70 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
| 71 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 72 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
| 73 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 74 |
|
o pkg/layers: |
| 75 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 76 |
|
- fix calculation of layer non-weighted velocity and layer probability |
| 77 |
|
- add diagnostics for pot.density used for layer averaging |
| 78 |
|
o pkg/seaice: |
| 79 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 80 |
|
positiveness, modify a few comments and improve variable names, |
| 81 |
|
- the changed computation of deltaC affects most seaice-related |
| 82 |
|
experiments at the truncation level. |
| 83 |
|
seaice_itd.thermo is affected by far the most, with |
| 84 |
|
only 7 digits of agreement remaining; update experiments. |
| 85 |
|
|
| 86 |
|
checkpoint65l (2015/05/04) |
| 87 |
|
o pkg/shelfice: |
| 88 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 89 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 90 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 91 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 92 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 93 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 94 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 95 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 96 |
|
o verification/testreport |
| 97 |
|
- add new option -small_f |
| 98 |
|
with this option testreport first makes the target small_f (*.f files) |
| 99 |
|
before running make (all). This is useful for explicit inlining when |
| 100 |
|
all sources need to be full available. |
| 101 |
|
o pkg/exf/exf_interp.F: |
| 102 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 103 |
|
|
| 104 |
|
checkpoint65k (2015/04/01) |
| 105 |
|
o pkg/ecco: |
| 106 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 107 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 108 |
|
instead of active read/write |
| 109 |
|
o pkg/ctrl: |
| 110 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 111 |
|
instead of active read/write. |
| 112 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 113 |
|
return if .NOT.useAUTODIFF |
| 114 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 115 |
|
o model/src: |
| 116 |
|
add useAUTODIFF run time switch. |
| 117 |
|
o pkg/exf/exf_interp.F: |
| 118 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 119 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 120 |
|
this feature. |
| 121 |
|
o verification/testreport: |
| 122 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 123 |
|
implementations of grep that cannot do contextual searches |
| 124 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 125 |
|
of "cat" have the option "-n" |
| 126 |
|
o model/src: |
| 127 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 128 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 129 |
|
convert from conservative to potential temperature. For now they are not |
| 130 |
|
called anywhere. |
| 131 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 132 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 133 |
|
are different for idemix into separate loops (changes verification |
| 134 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 135 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 136 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 137 |
|
s/r ggl90_idemix |
| 138 |
|
- fix and improve some comments |
| 139 |
|
|
| 140 |
|
checkpoint65j (2015/02/25) |
| 141 |
|
o pkg/openad |
| 142 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 143 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 144 |
|
o pkg/mnc: |
| 145 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 146 |
|
(since few features are missing in reading MNC pickup files). |
| 147 |
|
o model/src: |
| 148 |
|
- change default (background) vertical diffusivity for salt to be the |
| 149 |
|
temperature (background) vertical diffusivity. |
| 150 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 151 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 152 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 153 |
|
consistent with vertical mixing schemes. |
| 154 |
|
o verification/testreport: |
| 155 |
|
- fix typo in "-pcls" option ; |
| 156 |
|
- put temp files in /tmp (instead of in local dir) |
| 157 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 158 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 159 |
|
o pkg/ggl90 (idemix code): |
| 160 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 161 |
|
global_ocean.90x40x15.idemix |
| 162 |
|
o OpenAD |
| 163 |
|
- enable active file I/O and begin removal of work-around code |
| 164 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 165 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 166 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 167 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 168 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 169 |
|
o tools/genmake2: |
| 170 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 171 |
|
source files are sent to TAF (instead of all in one file). |
| 172 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 173 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 174 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 175 |
|
compile time; a runtime flag implementation is not yet complete |
| 176 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 177 |
|
o verification: |
| 178 |
|
- reduce length of the AD test run by half for experiments |
| 179 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 180 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 181 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 182 |
|
o verification/testreport: |
| 183 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 184 |
|
on Mac OS X |
| 185 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 186 |
|
o model/src/seawater.F: |
| 187 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 188 |
|
(following the matlab code), which would have avoided the bug caught |
| 189 |
|
by Matt (see below) in the first place |
| 190 |
|
o pkg/shelfice: |
| 191 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 192 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 193 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 194 |
|
ice-shelf case (i.e., within surface level). |
| 195 |
|
- add config summary in shelfice_check.F |
| 196 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 197 |
|
variable recip_latentHeat |
| 198 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 199 |
|
SHELFICEuseGammaFrict) |
| 200 |
|
- change verification experiment isomip.htd: |
| 201 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 202 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 203 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 204 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 205 |
|
o model/src: |
| 206 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 207 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 208 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 209 |
|
o pkg/shelfice: |
| 210 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 211 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 212 |
|
ice-shelf is. |
| 213 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 214 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 215 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 216 |
|
for thermodynamic calculations |
| 217 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 218 |
|
affects results of some verification experiments by up to 4 digits: |
| 219 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 220 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 221 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 222 |
|
-> updated |
| 223 |
|
|
| 224 |
|
checkpoint65i (2015/01/23) |
| 225 |
|
o model/src: |
| 226 |
|
- change units of frictionHeating field from W to W/m^2 |
| 227 |
|
- fix bug in frictional heating from stratospheric drag in |
| 228 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 229 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 230 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 231 |
|
- add diagnostics for frictional heating. |
| 232 |
|
o model/src & gmredi K3D: |
| 233 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 234 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 235 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 236 |
|
and name in pickup file). |
| 237 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 238 |
|
o model/src: |
| 239 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 240 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 241 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 242 |
|
o pkg/shelfice: |
| 243 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 244 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 245 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 246 |
|
o pkg/seaice: two new runtime parameters: |
| 247 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 248 |
|
long overdue |
| 249 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 250 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 251 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 252 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 253 |
|
o pkg/atm_phys: |
| 254 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 255 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 256 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 257 |
|
fixed-in-time pressure levels). |
| 258 |
|
o pkg/mom_common (bottomdrag): |
| 259 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 260 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 261 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 262 |
|
o pkg/shelfice (u/v_drag): |
| 263 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 264 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 265 |
|
(now similar to shelfice_u_drag.F) |
| 266 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 267 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 268 |
|
o pkg/mom_common (bottomdrag): |
| 269 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 270 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 271 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 272 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 273 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 274 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 275 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 276 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 277 |
|
off by default since this also reduces model stability (explicit bottom |
| 278 |
|
friction). Changes produce different machine truncation with linear-drag |
| 279 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 280 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 281 |
|
o model/src & mom pkgs: |
| 282 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 283 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 284 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 285 |
|
just copy level Nr value to level Nr+1. |
| 286 |
|
o doc: |
| 287 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 288 |
|
o pkg/streamice: |
| 289 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 290 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 291 |
|
from array shelficemassinit, which is set in init_fixed and |
| 292 |
|
has option to be set from file; introduce array |
| 293 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 294 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 295 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 296 |
|
pkg/streamice |
| 297 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 298 |
|
SHELFICEMassStepping = .true. |
| 299 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 300 |
|
|
| 301 |
|
checkpoint65h (2014/12/17) |
| 302 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 303 |
|
- update to generic controls. |
| 304 |
|
o pkg/ctrl: |
| 305 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 306 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 307 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 308 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 309 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 310 |
|
add time variable weights and cyclic controls (time mean, |
| 311 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 312 |
|
o pkg/ecco: |
| 313 |
|
- move reading of error, conversion to weights from |
| 314 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 315 |
|
o global_oce_llc90, cs32: |
| 316 |
|
- activte sbo. |
| 317 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 318 |
|
- activate the new genctrl capabilities. |
| 319 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 320 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 321 |
|
- add missing ctrl_init_rec.f |
| 322 |
|
o tools/OAD_support/keepOriginal: |
| 323 |
|
- add ctrl_init_rec.F |
| 324 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 325 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 326 |
|
o momentum diagnostics: |
| 327 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 328 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 329 |
|
o pkg/seaice/seaice_lsr.F: |
| 330 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 331 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 332 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 333 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 334 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 335 |
|
methods for LSR |
| 336 |
|
- update results/output.seaice.txt |
| 337 |
|
o verification/tutorial_global_oce_biogeo: |
| 338 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 339 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 340 |
|
update output_adm,_oadm,_tlm.txt |
| 341 |
|
o pkg/dic: |
| 342 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 343 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 344 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 345 |
|
o verification/tutorial_global_oce_biogeo: |
| 346 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 347 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 348 |
|
update output_adm,_oadm,_tlm.txt |
| 349 |
|
o eesupp/src: |
| 350 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 351 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 352 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 353 |
|
LSR (following Hutchings et al. 2004) |
| 354 |
|
- introduce zetaZ as a global variable (requires adjustments in |
| 355 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 356 |
|
in seaice_calc_viscosities.F |
| 357 |
|
- new flag SEAICEuseStrImpCpl (default off) |
| 358 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 359 |
|
momentum equations |
| 360 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
| 361 |
|
(where it does not have any positive effect) |
| 362 |
|
o pkg/seaice |
| 363 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
| 364 |
|
turn it off by default (because it only seems to work for non-cubed |
| 365 |
|
sphere/llc topologies) |
| 366 |
|
o pkg/autodiff |
| 367 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
| 368 |
|
o pkg/seaice: |
| 369 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 370 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 371 |
|
o pkg/obcs: |
| 372 |
|
- add option to specify domain-connected piece Id along OB though files |
| 373 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 374 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
| 375 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 376 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 377 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
| 378 |
|
o pkg/diagnostics: |
| 379 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 380 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 381 |
|
outside OB (i.e, where tracer OBCS are applied). |
| 382 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 383 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
| 384 |
|
|
| 385 |
|
checkpoint65g (2014/11/19) |
| 386 |
|
o pkg/diagnostcis: |
| 387 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 388 |
|
o pkg/my82,pp81,kl10: |
| 389 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 390 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 391 |
|
o pkg/seaice: |
| 392 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 393 |
|
Bouillon et al 2013) |
| 394 |
|
- add SEAICE_evpAlpha/Beta to namelist |
| 395 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 396 |
|
involve trivial re-ordering of divisions/multiplications that should not |
| 397 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
| 398 |
|
that only 2 digits of agreement remain, in line with the general |
| 399 |
|
instability/fragility of the evp-code. For now, I do not care and just |
| 400 |
|
update the verification experiment |
| 401 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 402 |
|
- remove xx_genarr2d_numsmooth etc |
| 403 |
|
- use xx_genarr2d_preproc etc instead |
| 404 |
|
- carry out smooth_correl2D at initialization stage rather than during |
| 405 |
|
time stepping. |
| 406 |
|
- get smoothOpNb from xx_gentim2d_preproc |
| 407 |
|
o global_oce_cs32 : |
| 408 |
|
- add test of generic ecco capabilities. |
| 409 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 410 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 411 |
|
o pkg/ctrl,ecco : |
| 412 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 413 |
|
is defined. |
| 414 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 415 |
|
o model/src: |
| 416 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 417 |
|
diffusivity (background) is specified but ignored. |
| 418 |
|
o verification: |
| 419 |
|
- in testreport, convert hostname to lower case for default output dir name |
| 420 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 421 |
|
o pkg/dic: add modifications from Hajoon: |
| 422 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 423 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 424 |
|
(read from file). |
| 425 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 426 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 427 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 428 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 429 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 430 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 431 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 432 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 433 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 434 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 435 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 436 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 437 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 438 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 439 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 440 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 441 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 442 |
|
o pkg/ctrl,ecco,exf : |
| 443 |
|
- remove variables associated with NON-generic costs, |
| 444 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 445 |
|
- remove NON-generic NON-obcs controls, |
| 446 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 447 |
|
o pkg/ctrl : added ctrl_local_params.h |
| 448 |
|
o pkg/ecco : added ecco_local_params.h |
| 449 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 450 |
|
experiments, which will progressively be removed once the |
| 451 |
|
experiments are revised to use only generic controls/costs. |
| 452 |
|
|
| 453 |
|
checkpoint65f (2014/10/13) |
| 454 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 455 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 456 |
|
cost function and control capabilities added since checkpoint65c. |
| 457 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 458 |
|
o pkg/ecco: increase modularity and improve logic |
| 459 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
| 460 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
| 461 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
| 462 |
|
- cost_gencal.F (new) : determine filnames and records. |
| 463 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
| 464 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
| 465 |
|
and exploit the above functions leading to more compact code. |
| 466 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
| 467 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
| 468 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
| 469 |
|
o pkg/ecco: extend generic cost capabilities |
| 470 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
| 471 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
| 472 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
| 473 |
|
gencost_outputlevel arguments to cost_generic |
| 474 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
| 475 |
|
and active_read, making room for gencost_preproc to take effect. |
| 476 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
| 477 |
|
- pkg/ecco/cost_generic.F : |
| 478 |
|
compute and store misfit maks*(model-data) in localdif that is |
| 479 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
| 480 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
| 481 |
|
rather gencost_barfile for deciding whether to write barfile |
| 482 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
| 483 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
| 484 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
| 485 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
| 486 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
| 487 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
| 488 |
|
o pkg/ecco: internal re-organization |
| 489 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
| 490 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
| 491 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
| 492 |
|
make sure gencost routines only include ecco.h) |
| 493 |
|
- throughout : add missing CCP switches, rm unused variables, |
| 494 |
|
and rm un-necessary CPP switches |
| 495 |
|
- throughout gencost routines : replace modelstartdate with |
| 496 |
|
gencost_startdate when needed |
| 497 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
| 498 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
| 499 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
| 500 |
|
- ecco_phys.F : compute etanFull |
| 501 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
| 502 |
|
bpv4-grace to gencost list, initialize added parameters |
| 503 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
| 504 |
|
|
| 505 |
|
checkpoint65e (2014/09/28) |
| 506 |
|
o pkg/obcs: |
| 507 |
|
- replaced the just-added CPP options with run-time variables |
| 508 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
| 509 |
|
o pkg/obcs: |
| 510 |
|
- add additional CPP options for sponge boundary layers |
| 511 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 512 |
|
o pkg/atm_phys: |
| 513 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
| 514 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 515 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 516 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
| 517 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 518 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 519 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 520 |
|
o pkg/ctrl, pkg/ecco : |
| 521 |
|
- fix and complement the generic controls implementation |
| 522 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 523 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
| 524 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 525 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 526 |
|
- add weight in CTRL_GET_GEN calls |
| 527 |
|
o pkg/ctrl : |
| 528 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 529 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 530 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 531 |
|
o pkg/ctrl : |
| 532 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 533 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 534 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 535 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 536 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 537 |
|
o pkg/ecco, pkg/ctrl : |
| 538 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 539 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 540 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 541 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 542 |
|
|
| 543 |
|
checkpoint65d (2014/09/15) |
| 544 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 545 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 546 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 547 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 548 |
|
- remove compilation failure |
| 549 |
|
- replace hard coded example |
| 550 |
|
- use ctrl_map_ini_gen2D, 3D |
| 551 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 552 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
| 553 |
|
o src/packages_init_variables.F : |
| 554 |
|
- regroup pkg/estimation calls |
| 555 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 556 |
|
(moved to ctrl_init_variables) |
| 557 |
|
o cost/cost_init_varia.F : |
| 558 |
|
- remove ecco_cost_init_varia |
| 559 |
|
(moved to ecco_init_varia) |
| 560 |
|
o ctrl/ctrl_init_variables.F : |
| 561 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 562 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 563 |
|
o ctrl/ctrl_map_ini.F : |
| 564 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 565 |
|
(moved to ctrl_init_variables) |
| 566 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 567 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 568 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 569 |
|
o ecco/ecco_ad_diff.list : |
| 570 |
|
- add ecco_init_varia.f |
| 571 |
|
o ecco/ecco_init_varia.F |
| 572 |
|
- new routine |
| 573 |
|
o pkg/streamice: |
| 574 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 575 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 576 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 577 |
|
o pkg/generic_advdiff: |
| 578 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 579 |
|
o pkg/exf: |
| 580 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 581 |
|
xxg_precip capability |
| 582 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 583 |
|
o pkg/ctrl: |
| 584 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 585 |
|
o model/src/load_fields_driver.F : |
| 586 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 587 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 588 |
|
o OpenAD verification experiments: |
| 589 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 590 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 591 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 592 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 593 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 594 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 595 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 596 |
|
o OpenAD verification tests: |
| 597 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 598 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 599 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 600 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 601 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 602 |
|
o model/src & generic_advdiff: |
| 603 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 604 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 605 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 606 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 607 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 608 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 609 |
|
setting in temp/salt/ptracer_integrate.F |
| 610 |
|
o pkg/dic: |
| 611 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 612 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 613 |
|
in gchem_forcing_sep.F |
| 614 |
|
o pkg/autodiff & obcs: |
| 615 |
|
- add storage of current OB values for U & V (was already done for T & S). |
| 616 |
|
|
| 617 |
|
checkpoint65c (2014/08/30) |
| 618 |
|
o pkg/dic: |
| 619 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 620 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 621 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 622 |
|
o verification: |
| 623 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
| 624 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 625 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 626 |
|
conditions from t=1.yr while keeping the same forcing. |
| 627 |
|
o model/src: |
| 628 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 629 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 630 |
|
o pkg/diagnostics (Stats-Diags): |
| 631 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 632 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 633 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 634 |
|
c) extend regional stats over the region edges (for U or V pt location). |
| 635 |
|
o pkg/gchem: |
| 636 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 637 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 638 |
|
o verification (hs94): |
| 639 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 640 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 641 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 642 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 643 |
|
o pkg/ptracers: |
| 644 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 645 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 646 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 647 |
|
with AB-2 code (so that it get tested). |
| 648 |
|
o model/src: |
| 649 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 650 |
|
with AB-2 code (previously only available with AB-3 code). |
| 651 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 652 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 653 |
|
there, by calling CYCLE_AB_TRACER). |
| 654 |
|
o pkg/generic_advdiff: |
| 655 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 656 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 657 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 658 |
|
S/R temp/salt/ptracers_integrate.F |
| 659 |
|
o model/src & pkg/ptracers: |
| 660 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
| 661 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 662 |
|
- remove common block variable gPtr. |
| 663 |
|
o model/src & pkgs: |
| 664 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 665 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 666 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 667 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 668 |
|
+ change accordingly all calling S/R. |
| 669 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 670 |
|
in S/R temp/salt/ptracers_integrate.F |
| 671 |
|
o pkg/seaice: |
| 672 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 673 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 674 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 675 |
|
in seaice_lsr |
| 676 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 677 |
|
in s/r seaice_lsr_calc_coeffs |
| 678 |
|
o pkg/mdsio: |
| 679 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 680 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 681 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 682 |
|
|
| 683 |
|
checkpoint65b (2014/08/12) |
| 684 |
|
o pkg/matrix: |
| 685 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 686 |
|
o model/src: |
| 687 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 688 |
|
natl_box verification experiment. |
| 689 |
|
o model/src & pkg/down_slope: |
| 690 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 691 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 692 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 693 |
|
results at machine truncation level: update output of experiments |
| 694 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 695 |
|
o pkg/diagnostics (Stats-Diags): |
| 696 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 697 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 698 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 699 |
|
times (but Min,Max and StD are still wrong). |
| 700 |
|
o model/src: |
| 701 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 702 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 703 |
|
o model/src: |
| 704 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 705 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 706 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 707 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 708 |
|
o model/src: |
| 709 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 710 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 711 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 712 |
|
o pkg/seaice/seaice_lsr.F |
| 713 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 714 |
|
in the residual diagnostics |
| 715 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 716 |
|
default) for improved non-linear convergence of the first few steps |
| 717 |
|
- adjust a few comments and add new ones to explain some of the store |
| 718 |
|
directives |
| 719 |
|
o pkg/generic_advdiff (& ptracers): |
| 720 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 721 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 722 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 723 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 724 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 725 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 726 |
|
less exact gradients in my tests); but there are still |
| 727 |
|
recomputation warning (although gradients are sort of OK), when |
| 728 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 729 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 730 |
|
- update verification experiments lab_sea. |
| 731 |
|
- change some comments in S/R seaice_calc_viscosities |
| 732 |
|
o model/src: |
| 733 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 734 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 735 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 736 |
|
but affects AD results (at machine truncation level): update output of |
| 737 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 738 |
|
and isomip (oad: 12.d). |
| 739 |
|
o pkg/generic_advdiff: |
| 740 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 741 |
|
- refine warning related to stability of tracer time-stepping |
| 742 |
|
regarding internal wave dynamics. |
| 743 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 744 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 745 |
|
if potentially unstable). |
| 746 |
|
o pkg/kl10: |
| 747 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 748 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 749 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 750 |
|
verification/internal_wave/input.kl10/ |
| 751 |
|
o isomip experiment: |
| 752 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 753 |
|
(input.htd) and update the output. |
| 754 |
|
o cd_code experiments: |
| 755 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 756 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 757 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 758 |
|
update the corresponding output. |
| 759 |
|
o pkg/seaice: |
| 760 |
|
- reduce the number of include files and store directives in |
| 761 |
|
S/R seaice_lsr_tridiagu/v |
| 762 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 763 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 764 |
|
get rid off one store directive (a TAF bug?) |
| 765 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 766 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 767 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 768 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 769 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 770 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 771 |
|
|
| 772 |
|
checkpoint65a (2014/07/27) |
| 773 |
|
o model/src: |
| 774 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 775 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 776 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 777 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 778 |
|
o model/src: |
| 779 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 780 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 781 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 782 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 783 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 784 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 785 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 786 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 787 |
|
correction due to vertical advection). |
| 788 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 789 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 790 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 791 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 792 |
|
o pkg/ptracers & diagnostics: |
| 793 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 794 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 795 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 796 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 797 |
|
|
| 798 |
|
checkpoint65 (2014/07/18) |
| 799 |
|
o pkg/fizhi: |
| 800 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 801 |
|
affects results at machine truncation level. Update output of experiments |
| 802 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 803 |
|
o pkg/seaice: more clean up |
| 804 |
|
- rename TAF common block tapes to be more consistent and remove |
| 805 |
|
unnecessary duplicates |
| 806 |
|
- add store directives to remove more recomputations, but use smaller |
| 807 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 808 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 809 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 810 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 811 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 812 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 813 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 814 |
|
this experiment): |
| 815 |
|
> size mitgcmuv_ad |
| 816 |
|
text data bss dec hex |
| 817 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 818 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 819 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 820 |
|
text data bss dec hex |
| 821 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 822 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 823 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 824 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 825 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 826 |
|
- in general, the AD gradients still are wrong |
| 827 |
|
o OpenAD |
| 828 |
|
- clean up code_oad/ directories somewhat by moving files |
| 829 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 830 |
|
o model/src: |
| 831 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 832 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 833 |
|
tendencies (previously done after). |
| 834 |
|
o pkg/diagnostics: |
| 835 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
| 836 |
|
o pkg/down_slope: |
| 837 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 838 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 839 |
|
o model/src: |
| 840 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 841 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 842 |
|
the current level tendency array to update (instead of a direct update |
| 843 |
|
of the common bloc array). Change the corresponding calls. |
| 844 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 845 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 846 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 847 |
|
- rearrange some code blocks, so that now all calculations for |
| 848 |
|
setting up the right-hand-sides done within one single block |
| 849 |
|
(I find that easier to read and understand) |
| 850 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 851 |
|
- adjust some indentations and comments |
| 852 |
|
|
| 853 |
|
checkpoint64z (2014/07/10) |
| 854 |
|
o model/src and several pkgs: |
| 855 |
|
- change argument list of all S/R called from external_forcing.F and |
| 856 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 857 |
|
to pass, as argument, the current level tendency array to update |
| 858 |
|
(instead of a direct update of the common bloc array). |
| 859 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 860 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 861 |
|
o pkg/seaice/seaice_lsr.F |
| 862 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 863 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 864 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 865 |
|
keep it in bi/bj loop; this seems to be essential |
| 866 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 867 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 868 |
|
o pkg/seaice |
| 869 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 870 |
|
generates unnecessary code in seaice_lsr_ad |
| 871 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 872 |
|
in seaice_lsr_ad |
| 873 |
|
- exclude some residual computations in seaice_lsr when |
| 874 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 875 |
|
in seaice_lsr_ad |
| 876 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 877 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 878 |
|
and klockey should be checked by a specialist) |
| 879 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 880 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 881 |
|
o pkg/autodiff: |
| 882 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 883 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 884 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 885 |
|
o pkg/ecco: |
| 886 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 887 |
|
temperature (for use in adjoint sensitivity studies). |
| 888 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 889 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 890 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 891 |
|
o pkg/seaice/seaice_summary.F: |
| 892 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 893 |
|
o pkg/seaice: |
| 894 |
|
- remove some store directives and add new ones in an effort to get |
| 895 |
|
finally rid off the recomputation warnings. This is successful |
| 896 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 897 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 898 |
|
are still too many recomputations on the solver iteration level |
| 899 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 900 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 901 |
|
SEAICE_SIZE.h |
| 902 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 903 |
|
o pkg/seaice (ITD code): |
| 904 |
|
- fix definition of Hlimit for multi-threaded case |
| 905 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 906 |
|
update output of experiment seaice_itd. |
| 907 |
|
o replace content of verification/seaice_itd |
| 908 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 909 |
|
to test the ice thickness distribution code with ridging |
| 910 |
|
- this is a first shot at this experiment |
| 911 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 912 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 913 |
|
and lot of new comments. |
| 914 |
|
|
| 915 |
|
checkpoint64y (2014/06/20) |
| 916 |
|
o pkg/seaice/seaice_reg_ridge.F: |
| 917 |
|
- modify the regularization of very small volumes of ice; only check |
| 918 |
|
total volume HEFF, and do not apply correction to individual ice |
| 919 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
| 920 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
| 921 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
| 922 |
|
o pkg/exf: |
| 923 |
|
- add code to process the case field period = -12. with UV interpolation. |
| 924 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
| 925 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
| 926 |
|
o verification/global_with_exf: |
| 927 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
| 928 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
| 929 |
|
o pkg/cal: |
| 930 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
| 931 |
|
o pkg/exf: |
| 932 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
| 933 |
|
to replace logical switch "exf_verbose" |
| 934 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
| 935 |
|
o pkg/sbo: |
| 936 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
| 937 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
| 938 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
| 939 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
| 940 |
|
- fix some multi-threading issues (in output part). |
| 941 |
|
o model/src & most packages: |
| 942 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
| 943 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
| 944 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
| 945 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
| 946 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
| 947 |
|
+ call LAND_READPARMS from packages_readparms.F |
| 948 |
|
o pkg/seaice: |
| 949 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
| 950 |
|
replace it by a warning in S/R seaice_check |
| 951 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
| 952 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
| 953 |
|
SEAICE_ITD is defined) |
| 954 |
|
|
| 955 |
|
checkpoint64x (2014/05/24) |
| 956 |
|
o verification/lab_sea: |
| 957 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
| 958 |
|
- un-do the update after putting back local recip_Cp in few places. |
| 959 |
|
o pkg/salt_plume: modifications by An Nguyen: |
| 960 |
|
- add capability to do brine rejection (salt-plume) as function of |
| 961 |
|
volume+tracers (instead of only salinity tracer). |
| 962 |
|
- conserve volume by exchanging volume from each kLev to above to |
| 963 |
|
accommodate in-coming brine volume |
| 964 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
| 965 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
| 966 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
| 967 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
| 968 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
| 969 |
|
in East/West Arctic. |
| 970 |
|
o pkg/sbo: |
| 971 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
| 972 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
| 973 |
|
output for future testreport verification (unfinished). |
| 974 |
|
o pkg/atm_phys: |
| 975 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
| 976 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
| 977 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
| 978 |
|
o pkg/seaice |
| 979 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
| 980 |
|
(affects truncation) |
| 981 |
|
seaice_do_ridging.F: clean up the insectarium |
| 982 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
| 983 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
| 984 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
| 985 |
|
- add some debugging information and error messages (warnings) |
| 986 |
|
o model/src: modifications relatd to atmosphere p*: |
| 987 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
| 988 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
| 989 |
|
of vertical profile tRef in geopotential background and anomaly. |
| 990 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
| 991 |
|
and pkg/atm_phys. |
| 992 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
| 993 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
| 994 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
| 995 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
| 996 |
|
not used right now, but can be used in BGC packages to fix conservation. |
| 997 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
| 998 |
|
other packages too. |
| 999 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
| 1000 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
| 1001 |
|
o model/src: |
| 1002 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
| 1003 |
|
as local variable (no longer in common block) to avoid any confusion. |
| 1004 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
| 1005 |
|
o pkg/exf: |
| 1006 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
| 1007 |
|
air density as function of air Temp, Humidity and atm pressure. |
| 1008 |
|
|
| 1009 |
|
checkpoint64w (2014/05/02) |
| 1010 |
|
o verification: |
| 1011 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
| 1012 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
| 1013 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
| 1014 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
| 1015 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
| 1016 |
|
o model/src: for atmosphere in p* coords: |
| 1017 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
| 1018 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
| 1019 |
|
but not yet activated. |
| 1020 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
| 1021 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
| 1022 |
|
- this changes the results (but not for any verification experiment, because |
| 1023 |
|
none tests this), but avoids having an extra field in the restart files |
| 1024 |
|
o pkg/seaice: remove global variable TICE (not needed) |
| 1025 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
| 1026 |
|
seaice_diagnostics_state) |
| 1027 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
| 1028 |
|
- use specific read/write routines for reading and writing individual leves |
| 1029 |
|
of a multilevel field |
| 1030 |
|
o pkg/ctrl & model/inc: |
| 1031 |
|
- move additional anomaly fields of control vars (related to options: |
| 1032 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
| 1033 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
| 1034 |
|
o pkg/seaice: some small modifications to the ridging code |
| 1035 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
| 1036 |
|
seaice_growth |
| 1037 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
| 1038 |
|
computed only in one place and compute it in the same way as in |
| 1039 |
|
seaice_growth |
| 1040 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
| 1041 |
|
point exceptions over land |
| 1042 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
| 1043 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
| 1044 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
| 1045 |
|
advection call the actual ridging routine; |
| 1046 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
| 1047 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
| 1048 |
|
- remove ridging code from seaice_advdiff |
| 1049 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
| 1050 |
|
more readable (this is probably subjective) |
| 1051 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
| 1052 |
|
conditions in the correct category |
| 1053 |
|
- finally: add new ridging routine for ITD code |
| 1054 |
|
|
| 1055 |
|
checkpoint64v (2014/04/11) |
| 1056 |
|
o pkg/ecco: |
| 1057 |
|
- add runtime parameters mdt[start,end]date[1,2] |
| 1058 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
| 1059 |
|
o pkg/seaice: |
| 1060 |
|
- make deltaC a global variable, so that it can be used in ridging code |
| 1061 |
|
- first step towards ridging: introduce new routines that compute |
| 1062 |
|
ice strength based on ridging parameters |
| 1063 |
|
- add diagnostic for HSNOWITD |
| 1064 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
| 1065 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
| 1066 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
| 1067 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
| 1068 |
|
o verification/hs94.1x64x5: |
| 1069 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
| 1070 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
| 1071 |
|
o autodiff: |
| 1072 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
| 1073 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
| 1074 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
| 1075 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
| 1076 |
|
which are specific to TAF/TAMC). |
| 1077 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
| 1078 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
| 1079 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
| 1080 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
| 1081 |
|
building mitgcmuv_ad (make adAll). |
| 1082 |
|
o pkg/ecco: |
| 1083 |
|
- cost_gencost_seaicev4.F: |
| 1084 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
| 1085 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
| 1086 |
|
- add stop statement if old names siv4-[sst,vol] are used |
| 1087 |
|
- add snapshots + cost reports for atmospheric longwave |
| 1088 |
|
- remove factor 0.1 in front of wtau[u,v] |
| 1089 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
| 1090 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
| 1091 |
|
o pkg/atm_phys: |
| 1092 |
|
- add some diagnostics for Short-wave and for convection S/R. |
| 1093 |
|
o pkg/seaice/seaice_growth: |
| 1094 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
| 1095 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
| 1096 |
|
- rearrange loop order for better vector code in the same code block |
| 1097 |
|
- rewrite the floeDiameter formula to have fewer divisions |
| 1098 |
|
- (miraculously) none of this changes the results of seaice_itd |
| 1099 |
|
o pkg/smooth: |
| 1100 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
| 1101 |
|
o pkg/salt_plume: |
| 1102 |
|
- salt_plume_frac.F: |
| 1103 |
|
clean up local param names |
| 1104 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
| 1105 |
|
o pkg/rw: |
| 1106 |
|
- add RS version of S/R READ_MFLDS_LEV. |
| 1107 |
|
o pkg/streamice: |
| 1108 |
|
- fix the restart test by writing/reading pickup_streamice files. |
| 1109 |
|
o pkg/seaice: |
| 1110 |
|
- refine checks for jfnk-related parameters |
| 1111 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
| 1112 |
|
is no IMEX code to avoid confusion and surprises |
| 1113 |
|
|
| 1114 |
|
checkpoint64u (2014/03/07) |
| 1115 |
|
o verification/MLAdjust: |
| 1116 |
|
- rename secondary test suffix: |
| 1117 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
| 1118 |
|
0.leithD -> AhFlxF + switch to flux-form |
| 1119 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
| 1120 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
| 1121 |
|
o pkg/mom_vecinv: |
| 1122 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
| 1123 |
|
to be before mom_calc_visc.F) |
| 1124 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
| 1125 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
| 1126 |
|
this is simpler for the adjoint and for diagnostics. |
| 1127 |
|
o model/src + pkg/momentum: |
| 1128 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
| 1129 |
|
(e.g., to add "thin-wall" where it is =1). |
| 1130 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
| 1131 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
| 1132 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
| 1133 |
|
coords; not working with CD-scheme neither. |
| 1134 |
|
o pkg/seaice: |
| 1135 |
|
- rename recently introduced parameters from (wrong name) AB to |
| 1136 |
|
BDF (backward difference time discretisation) |
| 1137 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
| 1138 |
|
o tools/adjoint_options: |
| 1139 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
| 1140 |
|
|
| 1141 |
|
checkpoint64t (2014/02/01) |
| 1142 |
|
o pkg/ecco |
| 1143 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
| 1144 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
| 1145 |
|
- replace hard-coded record number and period which only work for monthly |
| 1146 |
|
with read-in runtime param that works for other periods (month,day,year) |
| 1147 |
|
o pkg/thsice |
| 1148 |
|
- corrected store directive fixes thsice adjoint gradient checks |
| 1149 |
|
o genmake2 & testreport: |
| 1150 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
| 1151 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
| 1152 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
| 1153 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
| 1154 |
|
o pkg/shelfice: |
| 1155 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
| 1156 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
| 1157 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
| 1158 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
| 1159 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
| 1160 |
|
o model/src/temp_integrate.F and salt_integrate.F |
| 1161 |
|
- re-include store directives that were removed on Dec 27th. |
| 1162 |
|
o model/src/external_forcing_surf.F |
| 1163 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
| 1164 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
| 1165 |
|
turned off in the adjoint. The resolved issue dated back to July when |
| 1166 |
|
EXTERNAL_FORCING_SURF call was moved. |
| 1167 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
| 1168 |
|
o pkg/exf/exf_check.F |
| 1169 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
| 1170 |
|
- streamline error output |
| 1171 |
|
o pkg/streamice and aim_v23: |
| 1172 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
| 1173 |
|
Apple's /usr/bin/cpp knows what to do: |
| 1174 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
| 1175 |
|
Target: x86_64-apple-darwin13.0.0 |
| 1176 |
|
|
| 1177 |
|
checkpoint64s (2014/01/05) |
| 1178 |
|
o tools/adjoint_options: |
| 1179 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
| 1180 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
| 1181 |
|
o model/src: |
| 1182 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
| 1183 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
| 1184 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
| 1185 |
|
o model/src & pkg/ptracers: |
| 1186 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
| 1187 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
| 1188 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
| 1189 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
| 1190 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
| 1191 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
| 1192 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
| 1193 |
|
for now only implemented for in exf_interp_read.F |
| 1194 |
|
o verification/advect_xy: |
| 1195 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
| 1196 |
|
o momentum diagnostics: |
| 1197 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
| 1198 |
|
- fix typo in diagnostics for momentum tendency from AB. |
| 1199 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
| 1200 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
| 1201 |
|
|
| 1202 |
|
checkpoint64r (2013/12/08) |
| 1203 |
|
o verification/*/results: |
| 1204 |
|
- Update reference output of experiments that were passing with just 13 digits |
| 1205 |
|
(make it easier to detect future changes in results) |
| 1206 |
|
o model/src & pkg/ptracers: |
| 1207 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
| 1208 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
| 1209 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
| 1210 |
|
o coupling interface pkgs: |
| 1211 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
| 1212 |
|
- change the config check to test the agreement of Ocean Depth |
| 1213 |
|
with ATM land/sea mask (instead of ATM orography); |
| 1214 |
|
- send to coupler the number of coupler time-steps to do for this run: |
| 1215 |
|
this allows to check for consistency and don't need anymore to be |
| 1216 |
|
specified in parameter file "data"; |
| 1217 |
|
in coupler: |
| 1218 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 1219 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
| 1220 |
|
o pkg/compon_communic: |
| 1221 |
|
- add coupling send/receive for non-tiled integer vector; |
| 1222 |
|
- add S/R to check and stop if any proc has an error (similar to |
| 1223 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
| 1224 |
|
o pkg/exch2: |
| 1225 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 1226 |
|
through list of all tiles my proc owns. |
| 1227 |
|
o model/src: |
| 1228 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 1229 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 1230 |
|
calling S/R); this affects AD results at machine truncation level: |
| 1231 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 1232 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 1233 |
|
o tools/build_options: |
| 1234 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 1235 |
|
o coupling interface pkgs: |
| 1236 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 1237 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 1238 |
|
to each S/R that needs it; remove un-used variables. |
| 1239 |
|
- change component tile registration (cpl_register.F in both compon_interf |
| 1240 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
| 1241 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 1242 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 1243 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
| 1244 |
|
a) can now use different tiling between atm & ocn comp. |
| 1245 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
| 1246 |
|
even if using the same tiling between atm & ocn). |
| 1247 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 1248 |
|
full land tiles); not yet tested. |
| 1249 |
|
- check for valid mapping from comp. tile to coupler global array |
| 1250 |
|
- improve report of tile registration results to log file. |
| 1251 |
|
o pkg/exch2: |
| 1252 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 1253 |
|
tile-registration (CPL_REGISTER); |
| 1254 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 1255 |
|
store the local bi,bj indices of each tile; |
| 1256 |
|
- also print bi,bj in local report to log file; |
| 1257 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 1258 |
|
Jun 2009 modif of pkg/exch2). |
| 1259 |
|
o testing on baudelaire: |
| 1260 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 1261 |
|
get the full set of test done earlier |
| 1262 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 1263 |
|
o model/src/thermodynamics.F and routines called from it: |
| 1264 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 1265 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 1266 |
|
velocity (outp) by adding bolus velocity. |
| 1267 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 1268 |
|
mass transport from velocity + lateral grid cell area |
| 1269 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 1270 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
| 1271 |
|
in thermodynamics.F |
| 1272 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
| 1273 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
| 1274 |
|
loop). |
| 1275 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 1276 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 1277 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 1278 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 1279 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 1280 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 1281 |
|
tutorial_tracer_adjsens (+ TLM output). |
| 1282 |
|
o tools/OAD_support and (verification/*/) code_oad: |
| 1283 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 1284 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 1285 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 1286 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
| 1287 |
|
o model/src: |
| 1288 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 1289 |
|
retired list of parameters (routine FREEZE has been replace by surface |
| 1290 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 1291 |
|
o pkg/gmredi: |
| 1292 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 1293 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 1294 |
|
- update output of FWD experiments: front_relax.bvp, |
| 1295 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 1296 |
|
|
| 1297 |
|
checkpoint64q (2013/11/17) |
| 1298 |
|
o verification: |
| 1299 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 1300 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 1301 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
| 1302 |
|
updating the input pickup_seaice files (previously wrong). |
| 1303 |
|
o pkg/cost: |
| 1304 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 1305 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 1306 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 1307 |
|
cannot be applied to var in common block). |
| 1308 |
|
o allows to get results independent of tile-per-proc setting (if using |
| 1309 |
|
slower GLOBAL_SUM_SEND_RECV option). |
| 1310 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 1311 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 1312 |
|
forward gradients: update output). |
| 1313 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 1314 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 1315 |
|
o pkg/mom_common: |
| 1316 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 1317 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 1318 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 1319 |
|
ensure that all field value that are used are set. |
| 1320 |
|
o tutorial_deep_convection (smag3d): |
| 1321 |
|
- add missing scaling in mom_calc_smag_3d.F; |
| 1322 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
| 1323 |
|
o pkg/dic: |
| 1324 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
| 1325 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 1326 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 1327 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 1328 |
|
o eesupp/src & pkg/mdsio: |
| 1329 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 1330 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
| 1331 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 1332 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
| 1333 |
|
o verification/isomip: |
| 1334 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 1335 |
|
o tools/build_options: |
| 1336 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 1337 |
|
to get a working restart for all experiments, add "-fp-model source" |
| 1338 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 1339 |
|
|
| 1340 |
|
checkpoint64p (2013/10/20) |
| 1341 |
|
o pkg/autodiff: |
| 1342 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 1343 |
|
criteria, return to simple (default) tape IO format. |
| 1344 |
|
o pkg/mdsio (+ eesupp/src): |
| 1345 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 1346 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 1347 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
| 1348 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 1349 |
|
template) corresponding to simpler global mapping. |
| 1350 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 1351 |
|
to globalFile when parameter globalFiles is set to True. |
| 1352 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 1353 |
|
o pkg/autodiff: |
| 1354 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 1355 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 1356 |
|
missing, just add a STOP if array type do not match. |
| 1357 |
|
o pkg/exf: |
| 1358 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 1359 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 1360 |
|
and rename array obsSIce to exf_iceFraction. |
| 1361 |
|
o tutorial_deep_convection: |
| 1362 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 1363 |
|
for now all in this exp. code dir. |
| 1364 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 1365 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 1366 |
|
o eesupp/src: |
| 1367 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
| 1368 |
|
very large number of processors did not work with existing set-up |
| 1369 |
|
|
| 1370 |
|
checkpoint64o (2013/09/25) |
| 1371 |
|
o pkg/atm_phys & atm_compon_interf: |
| 1372 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 1373 |
|
o tools/build_options: |
| 1374 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 1375 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 1376 |
|
remove CPP setting (was identical to genmake2 default). |
| 1377 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 1378 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 1379 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
| 1380 |
|
external forcing via taueddy_external_forcing.F |
| 1381 |
|
- at the moment, it is very experimental and only works with the variable eddy |
| 1382 |
|
diffusivity calculated in gmredi_k3d.F |
| 1383 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 1384 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 1385 |
|
o testreport (& tools/do_tst_2+2): |
| 1386 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 1387 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 1388 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 1389 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 1390 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
| 1391 |
|
o pkg/atm_compon_interf: |
| 1392 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
| 1393 |
|
(which accumalate in time each coupling field) |
| 1394 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 1395 |
|
update accordingly + simplify aim_do_physics.F |
| 1396 |
|
|
| 1397 |
|
checkpoint64n (2013/08/26) |
| 1398 |
|
o pkg/bbl: |
| 1399 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
| 1400 |
|
- replaced horizontal and vertical transport parameters with velocities |
| 1401 |
|
- changes results for verification/global_with_exf.yearly |
| 1402 |
|
o verification/halfpipe_streamice: |
| 1403 |
|
- change to matrix construction; update both Fwd & AD output. |
| 1404 |
|
o verification/tutorial_tracer_adjsens: |
| 1405 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 1406 |
|
rStar causes problems with OpenAD; update output. |
| 1407 |
|
o tools: |
| 1408 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
| 1409 |
|
to local /tmp disk (but would be easy to move them back); |
| 1410 |
|
- xmakedepend: apply the same switch for temp-files. |
| 1411 |
|
o pkg/offline: |
| 1412 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
| 1413 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 1414 |
|
output files) and apply r* scaling at each time-step (function of the time |
| 1415 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 1416 |
|
o adjoint with OpenAD: |
| 1417 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 1418 |
|
package openad. This package has to be compiled for all runs with OpenAD |
| 1419 |
|
instead of specifying code_oad_all as a modification directory. |
| 1420 |
|
- link the fortran templates from tools/OAD_support to the build directory |
| 1421 |
|
for preprocessing to avoid conflicts between different setups compiled |
| 1422 |
|
simultaneously and simplify cleanup. |
| 1423 |
|
o pkg/exf: |
| 1424 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 1425 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 1426 |
|
o model/src: |
| 1427 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 1428 |
|
(similar to do_fields_blocking_exchanges.F). |
| 1429 |
|
o tools/genmake2: |
| 1430 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
| 1431 |
|
built, will stop if things go wrong with staf). |
| 1432 |
|
- fix target "adobj" (left from TAF version-2 transition) |
| 1433 |
|
o pkg/diagnostics: |
| 1434 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
| 1435 |
|
this replace/extend the use of logical param "settingDiags" (to check |
| 1436 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 1437 |
|
New S/R to print error message and stop when pkgStatus is not right. |
| 1438 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 1439 |
|
|
| 1440 |
|
checkpoint64m (2013/08/13) |
| 1441 |
|
o model/inc: |
| 1442 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 1443 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 1444 |
|
o pkg/kpp & aim_v23: |
| 1445 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 1446 |
|
o pkg/seaice: |
| 1447 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 1448 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 1449 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 1450 |
|
o eesupp/src: |
| 1451 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 1452 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 1453 |
|
o switch to TAF version-2: |
| 1454 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 1455 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 1456 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 1457 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 1458 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 1459 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 1460 |
|
out except for diva). |
| 1461 |
|
- the major change with TAF version-2 is that both the differentiated |
| 1462 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 1463 |
|
output source code. Update genmake2 accordingly. |
| 1464 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 1465 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 1466 |
|
output show minor changes (machine truncation level); update the few AD & |
| 1467 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 1468 |
|
|
| 1469 |
|
checkpoint64l (2013/08/05) |
| 1470 |
|
o model/src: |
| 1471 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 1472 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 1473 |
|
when using TAF but only if using OpenAD. |
| 1474 |
|
o pkg/mom_common+fluxform+vecinv: |
| 1475 |
|
- always set horiz. viscosity arrays to background value before calling |
| 1476 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 1477 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 1478 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 1479 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
| 1480 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 1481 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 1482 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 1483 |
|
useBiharmonicVisc & useVariableVisc. |
| 1484 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 1485 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 1486 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 1487 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 1488 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 1489 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 1490 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 1491 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 1492 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 1493 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 1494 |
|
default viscAh,viscA4 is zero). |
| 1495 |
|
o model/src: |
| 1496 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 1497 |
o Divided Adjoint (DIVA) with MPI: |
o Divided Adjoint (DIVA) with MPI: |
| 1498 |
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 1499 |
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
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