| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o OpenAD |
| 8 |
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- Adding preliminary ggl90 test to OpenAD verification. |
| 9 |
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Config. with ggl90 currently diverges after 64 time steps |
| 10 |
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so will need more work to become more stable |
| 11 |
|
o pkg/seaice: |
| 12 |
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- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
| 13 |
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- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
| 14 |
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delta with a smooth function in s/r seaice_calc_viscosity |
| 15 |
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(no effect on EVP) |
| 16 |
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- rename local suffix "sqr" into "sq" for more consistent variable names |
| 17 |
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o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only*** |
| 18 |
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for regularizing Delta (and nothing else, like the parameter |
| 19 |
|
which is also used for all sorts of things SEAICE_EPS). Defaults to |
| 20 |
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SEAICE_EPS for backward compatibility only. |
| 21 |
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o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
| 22 |
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the wrong key by inialising it before use -> fixes a recomputation |
| 23 |
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problem but does not fix the gradient |
| 24 |
|
o pkg/layers: |
| 25 |
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- move resetting of flux arrays to outside the iLa loop |
| 26 |
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(this caused layers_diapycnal to not work with more than one layer coord.) |
| 27 |
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- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
| 28 |
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o pkg/layers: |
| 29 |
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- remove from common block 3D layers fields (used to diagnose transport |
| 30 |
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in tracer coords) and declare them as local arrays in layers_calc.F |
| 31 |
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o pkg/seaice: |
| 32 |
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- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
| 33 |
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in lab_sea forward experiment (changes results -> updated) |
| 34 |
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- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
| 35 |
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o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
| 36 |
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computations; for SEAICE_VECTORIZE_LSR |
| 37 |
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- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
| 38 |
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sweep to the outside, |
| 39 |
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- remove store directives and add "CADJ loop sequential" directives |
| 40 |
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in analogy to model/src/solve_tridiagonal.F |
| 41 |
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- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
| 42 |
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boundaries to yield more readable code. This has also the charming side |
| 43 |
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effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
| 44 |
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SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
| 45 |
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seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
| 46 |
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still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
| 47 |
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an additional option) |
| 48 |
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The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
| 49 |
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but the adjoint gradients (which are affected by this change) still explode. |
| 50 |
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o coupler (atm & ocn _compon_interf): |
| 51 |
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- avoid using Exch2 IO mapping if not suitable. |
| 52 |
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|
| 53 |
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checkpoint65m (2015/06/15) |
| 54 |
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o pkg/layers: |
| 55 |
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- clean-up old parameters setting (from Sep 2012): |
| 56 |
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+ remove old parameters setting from common block (declared locally); |
| 57 |
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+ stop if any old parameter is mixed with new parameters; |
| 58 |
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+ check for valid or consistent parameter setting (e.g., layers_name) |
| 59 |
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- check that layers_bounds for Pot.Density are in the right range; |
| 60 |
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this is supposed to catch un-updated setting after recently shifting |
| 61 |
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potential density field "prho" by -1000 (now in "sigma" scale). |
| 62 |
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o pkg/layers: |
| 63 |
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- Added missing call to layers_fill for keeping track of tottend in |
| 64 |
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pkg/diagnostics/diagnostics_fill_state.F |
| 65 |
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o pkg/layers: |
| 66 |
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- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 67 |
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of diapycnal fluxes |
| 68 |
|
o pkg/layers: |
| 69 |
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- reverted changes to interpolation to previous treatment; there |
| 70 |
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was never actually a problem |
| 71 |
|
o pkg/layers: |
| 72 |
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- fix interpolation of layers tracers in the presence of partial cells |
| 73 |
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- add lots of new functionality to compute water mass transformation |
| 74 |
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(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 75 |
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- add new calls from main code (diags_oceanic_surf_flux.F, |
| 76 |
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thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 77 |
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for layers_thermodynamics calculations |
| 78 |
|
o pkg/ptracers: |
| 79 |
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- add capability of stepping a passive tracer forward without advection |
| 80 |
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by setting PTRACERS_advScheme to 0. |
| 81 |
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o pkg/diagnostics: |
| 82 |
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- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 83 |
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o pkg/layers: |
| 84 |
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- shift potential density field "prho" by -1000 for density layer averaging so |
| 85 |
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that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 86 |
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Note that density bin boundaries (layers_bounds in data.layers) have |
| 87 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 88 |
|
o pkg/layers: |
| 89 |
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- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 90 |
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- fix calculation of layer non-weighted velocity and layer probability |
| 91 |
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- add diagnostics for pot.density used for layer averaging |
| 92 |
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o pkg/seaice: |
| 93 |
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- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 94 |
|
positiveness, modify a few comments and improve variable names, |
| 95 |
|
- the changed computation of deltaC affects most seaice-related |
| 96 |
|
experiments at the truncation level. |
| 97 |
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seaice_itd.thermo is affected by far the most, with |
| 98 |
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only 7 digits of agreement remaining; update experiments. |
| 99 |
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|
| 100 |
|
checkpoint65l (2015/05/04) |
| 101 |
|
o pkg/shelfice: |
| 102 |
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- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 103 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 104 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 105 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 106 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 107 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 108 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 109 |
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- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 110 |
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o verification/testreport |
| 111 |
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- add new option -small_f |
| 112 |
|
with this option testreport first makes the target small_f (*.f files) |
| 113 |
|
before running make (all). This is useful for explicit inlining when |
| 114 |
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all sources need to be full available. |
| 115 |
|
o pkg/exf/exf_interp.F: |
| 116 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 117 |
|
|
| 118 |
|
checkpoint65k (2015/04/01) |
| 119 |
|
o pkg/ecco: |
| 120 |
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fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 121 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 122 |
|
instead of active read/write |
| 123 |
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o pkg/ctrl: |
| 124 |
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if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 125 |
|
instead of active read/write. |
| 126 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 127 |
|
return if .NOT.useAUTODIFF |
| 128 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 129 |
|
o model/src: |
| 130 |
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add useAUTODIFF run time switch. |
| 131 |
|
o pkg/exf/exf_interp.F: |
| 132 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 133 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 134 |
|
this feature. |
| 135 |
|
o verification/testreport: |
| 136 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 137 |
|
implementations of grep that cannot do contextual searches |
| 138 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 139 |
|
of "cat" have the option "-n" |
| 140 |
|
o model/src: |
| 141 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 142 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 143 |
|
convert from conservative to potential temperature. For now they are not |
| 144 |
|
called anywhere. |
| 145 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 146 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 147 |
|
are different for idemix into separate loops (changes verification |
| 148 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 149 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 150 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 151 |
|
s/r ggl90_idemix |
| 152 |
|
- fix and improve some comments |
| 153 |
|
|
| 154 |
|
checkpoint65j (2015/02/25) |
| 155 |
|
o pkg/openad |
| 156 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 157 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 158 |
|
o pkg/mnc: |
| 159 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 160 |
|
(since few features are missing in reading MNC pickup files). |
| 161 |
|
o model/src: |
| 162 |
|
- change default (background) vertical diffusivity for salt to be the |
| 163 |
|
temperature (background) vertical diffusivity. |
| 164 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 165 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 166 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 167 |
|
consistent with vertical mixing schemes. |
| 168 |
|
o verification/testreport: |
| 169 |
|
- fix typo in "-pcls" option ; |
| 170 |
|
- put temp files in /tmp (instead of in local dir) |
| 171 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 172 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 173 |
|
o pkg/ggl90 (idemix code): |
| 174 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 175 |
|
global_ocean.90x40x15.idemix |
| 176 |
|
o OpenAD |
| 177 |
|
- enable active file I/O and begin removal of work-around code |
| 178 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 179 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 180 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 181 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 182 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 183 |
|
o tools/genmake2: |
| 184 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 185 |
|
source files are sent to TAF (instead of all in one file). |
| 186 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 187 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 188 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 189 |
|
compile time; a runtime flag implementation is not yet complete |
| 190 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 191 |
|
o verification: |
| 192 |
|
- reduce length of the AD test run by half for experiments |
| 193 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 194 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 195 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 196 |
|
o verification/testreport: |
| 197 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 198 |
|
on Mac OS X |
| 199 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 200 |
|
o model/src/seawater.F: |
| 201 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 202 |
|
(following the matlab code), which would have avoided the bug caught |
| 203 |
|
by Matt (see below) in the first place |
| 204 |
|
o pkg/shelfice: |
| 205 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 206 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 207 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 208 |
|
ice-shelf case (i.e., within surface level). |
| 209 |
|
- add config summary in shelfice_check.F |
| 210 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 211 |
|
variable recip_latentHeat |
| 212 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 213 |
|
SHELFICEuseGammaFrict) |
| 214 |
|
- change verification experiment isomip.htd: |
| 215 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 216 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 217 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 218 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 219 |
|
o model/src: |
| 220 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 221 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 222 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 223 |
|
o pkg/shelfice: |
| 224 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 225 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 226 |
|
ice-shelf is. |
| 227 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 228 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 229 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 230 |
|
for thermodynamic calculations |
| 231 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 232 |
|
affects results of some verification experiments by up to 4 digits: |
| 233 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 234 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 235 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 236 |
|
-> updated |
| 237 |
|
|
| 238 |
|
checkpoint65i (2015/01/23) |
| 239 |
|
o model/src: |
| 240 |
|
- change units of frictionHeating field from W to W/m^2 |
| 241 |
|
- fix bug in frictional heating from stratospheric drag in |
| 242 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 243 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 244 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 245 |
|
- add diagnostics for frictional heating. |
| 246 |
|
o model/src & gmredi K3D: |
| 247 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 248 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 249 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 250 |
|
and name in pickup file). |
| 251 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 252 |
|
o model/src: |
| 253 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 254 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 255 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 256 |
|
o pkg/shelfice: |
| 257 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 258 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 259 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 260 |
|
o pkg/seaice: two new runtime parameters: |
| 261 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 262 |
|
long overdue |
| 263 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 264 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 265 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 266 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 267 |
|
o pkg/atm_phys: |
| 268 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 269 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 270 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 271 |
|
fixed-in-time pressure levels). |
| 272 |
|
o pkg/mom_common (bottomdrag): |
| 273 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 274 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 275 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 276 |
|
o pkg/shelfice (u/v_drag): |
| 277 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 278 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 279 |
|
(now similar to shelfice_u_drag.F) |
| 280 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 281 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 282 |
|
o pkg/mom_common (bottomdrag): |
| 283 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 284 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 285 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 286 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 287 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 288 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 289 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 290 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 291 |
|
off by default since this also reduces model stability (explicit bottom |
| 292 |
|
friction). Changes produce different machine truncation with linear-drag |
| 293 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 294 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 295 |
|
o model/src & mom pkgs: |
| 296 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 297 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 298 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 299 |
|
just copy level Nr value to level Nr+1. |
| 300 |
|
o doc: |
| 301 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 302 |
|
o pkg/streamice: |
| 303 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 304 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 305 |
|
from array shelficemassinit, which is set in init_fixed and |
| 306 |
|
has option to be set from file; introduce array |
| 307 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 308 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 309 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 310 |
|
pkg/streamice |
| 311 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 312 |
|
SHELFICEMassStepping = .true. |
| 313 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 314 |
|
|
| 315 |
|
checkpoint65h (2014/12/17) |
| 316 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 317 |
|
- update to generic controls. |
| 318 |
|
o pkg/ctrl: |
| 319 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 320 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 321 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 322 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 323 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 324 |
|
add time variable weights and cyclic controls (time mean, |
| 325 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 326 |
|
o pkg/ecco: |
| 327 |
|
- move reading of error, conversion to weights from |
| 328 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 329 |
|
o global_oce_llc90, cs32: |
| 330 |
|
- activte sbo. |
| 331 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 332 |
|
- activate the new genctrl capabilities. |
| 333 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 334 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 335 |
|
- add missing ctrl_init_rec.f |
| 336 |
|
o tools/OAD_support/keepOriginal: |
| 337 |
|
- add ctrl_init_rec.F |
| 338 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 339 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 340 |
|
o momentum diagnostics: |
| 341 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 342 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 343 |
|
o pkg/seaice/seaice_lsr.F: |
| 344 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 345 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 346 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 347 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 348 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 349 |
|
methods for LSR |
| 350 |
|
- update results/output.seaice.txt |
| 351 |
|
o verification/tutorial_global_oce_biogeo: |
| 352 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 353 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 354 |
|
update output_adm,_oadm,_tlm.txt |
| 355 |
|
o pkg/dic: |
| 356 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 357 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 358 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 359 |
|
o verification/tutorial_global_oce_biogeo: |
| 360 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 361 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 362 |
|
update output_adm,_oadm,_tlm.txt |
| 363 |
|
o eesupp/src: |
| 364 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 365 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 366 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 367 |
|
LSR (following Hutchings et al. 2004) |
| 368 |
|
- introduce zetaZ as a global variable (requires adjustments in |
| 369 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 370 |
|
in seaice_calc_viscosities.F |
| 371 |
|
- new flag SEAICEuseStrImpCpl (default off) |
| 372 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 373 |
|
momentum equations |
| 374 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
| 375 |
|
(where it does not have any positive effect) |
| 376 |
|
o pkg/seaice |
| 377 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
| 378 |
|
turn it off by default (because it only seems to work for non-cubed |
| 379 |
|
sphere/llc topologies) |
| 380 |
|
o pkg/autodiff |
| 381 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
| 382 |
|
o pkg/seaice: |
| 383 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 384 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 385 |
|
o pkg/obcs: |
| 386 |
|
- add option to specify domain-connected piece Id along OB though files |
| 387 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 388 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
| 389 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 390 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 391 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
| 392 |
|
o pkg/diagnostics: |
| 393 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 394 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 395 |
|
outside OB (i.e, where tracer OBCS are applied). |
| 396 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 397 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
| 398 |
|
|
| 399 |
|
checkpoint65g (2014/11/19) |
| 400 |
|
o pkg/diagnostcis: |
| 401 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 402 |
|
o pkg/my82,pp81,kl10: |
| 403 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 404 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 405 |
|
o pkg/seaice: |
| 406 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 407 |
|
Bouillon et al 2013) |
| 408 |
|
- add SEAICE_evpAlpha/Beta to namelist |
| 409 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 410 |
|
involve trivial re-ordering of divisions/multiplications that should not |
| 411 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
| 412 |
|
that only 2 digits of agreement remain, in line with the general |
| 413 |
|
instability/fragility of the evp-code. For now, I do not care and just |
| 414 |
|
update the verification experiment |
| 415 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 416 |
|
- remove xx_genarr2d_numsmooth etc |
| 417 |
|
- use xx_genarr2d_preproc etc instead |
| 418 |
|
- carry out smooth_correl2D at initialization stage rather than during |
| 419 |
|
time stepping. |
| 420 |
|
- get smoothOpNb from xx_gentim2d_preproc |
| 421 |
|
o global_oce_cs32 : |
| 422 |
|
- add test of generic ecco capabilities. |
| 423 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 424 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 425 |
|
o pkg/ctrl,ecco : |
| 426 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 427 |
|
is defined. |
| 428 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 429 |
|
o model/src: |
| 430 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 431 |
|
diffusivity (background) is specified but ignored. |
| 432 |
|
o verification: |
| 433 |
|
- in testreport, convert hostname to lower case for default output dir name |
| 434 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 435 |
|
o pkg/dic: add modifications from Hajoon: |
| 436 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 437 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 438 |
|
(read from file). |
| 439 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 440 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 441 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 442 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 443 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 444 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 445 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 446 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 447 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 448 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 449 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 450 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 451 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 452 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 453 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 454 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 455 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 456 |
|
o pkg/ctrl,ecco,exf : |
| 457 |
|
- remove variables associated with NON-generic costs, |
| 458 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 459 |
|
- remove NON-generic NON-obcs controls, |
| 460 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 461 |
|
o pkg/ctrl : added ctrl_local_params.h |
| 462 |
|
o pkg/ecco : added ecco_local_params.h |
| 463 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 464 |
|
experiments, which will progressively be removed once the |
| 465 |
|
experiments are revised to use only generic controls/costs. |
| 466 |
|
|
| 467 |
|
checkpoint65f (2014/10/13) |
| 468 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 469 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 470 |
|
cost function and control capabilities added since checkpoint65c. |
| 471 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 472 |
|
o pkg/ecco: increase modularity and improve logic |
| 473 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
| 474 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
| 475 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
| 476 |
|
- cost_gencal.F (new) : determine filnames and records. |
| 477 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
| 478 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
| 479 |
|
and exploit the above functions leading to more compact code. |
| 480 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
| 481 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
| 482 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
| 483 |
|
o pkg/ecco: extend generic cost capabilities |
| 484 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
| 485 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
| 486 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
| 487 |
|
gencost_outputlevel arguments to cost_generic |
| 488 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
| 489 |
|
and active_read, making room for gencost_preproc to take effect. |
| 490 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
| 491 |
|
- pkg/ecco/cost_generic.F : |
| 492 |
|
compute and store misfit maks*(model-data) in localdif that is |
| 493 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
| 494 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
| 495 |
|
rather gencost_barfile for deciding whether to write barfile |
| 496 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
| 497 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
| 498 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
| 499 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
| 500 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
| 501 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
| 502 |
|
o pkg/ecco: internal re-organization |
| 503 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
| 504 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
| 505 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
| 506 |
|
make sure gencost routines only include ecco.h) |
| 507 |
|
- throughout : add missing CCP switches, rm unused variables, |
| 508 |
|
and rm un-necessary CPP switches |
| 509 |
|
- throughout gencost routines : replace modelstartdate with |
| 510 |
|
gencost_startdate when needed |
| 511 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
| 512 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
| 513 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
| 514 |
|
- ecco_phys.F : compute etanFull |
| 515 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
| 516 |
|
bpv4-grace to gencost list, initialize added parameters |
| 517 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
| 518 |
|
|
| 519 |
|
checkpoint65e (2014/09/28) |
| 520 |
|
o pkg/obcs: |
| 521 |
|
- replaced the just-added CPP options with run-time variables |
| 522 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
| 523 |
|
o pkg/obcs: |
| 524 |
|
- add additional CPP options for sponge boundary layers |
| 525 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 526 |
|
o pkg/atm_phys: |
| 527 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
| 528 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 529 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 530 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
| 531 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 532 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 533 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 534 |
|
o pkg/ctrl, pkg/ecco : |
| 535 |
|
- fix and complement the generic controls implementation |
| 536 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 537 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
| 538 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 539 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 540 |
|
- add weight in CTRL_GET_GEN calls |
| 541 |
|
o pkg/ctrl : |
| 542 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 543 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 544 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 545 |
|
o pkg/ctrl : |
| 546 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 547 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 548 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 549 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 550 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 551 |
|
o pkg/ecco, pkg/ctrl : |
| 552 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 553 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 554 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 555 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 556 |
|
|
| 557 |
|
checkpoint65d (2014/09/15) |
| 558 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 559 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 560 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 561 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 562 |
|
- remove compilation failure |
| 563 |
|
- replace hard coded example |
| 564 |
|
- use ctrl_map_ini_gen2D, 3D |
| 565 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 566 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
| 567 |
|
o src/packages_init_variables.F : |
| 568 |
|
- regroup pkg/estimation calls |
| 569 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 570 |
|
(moved to ctrl_init_variables) |
| 571 |
|
o cost/cost_init_varia.F : |
| 572 |
|
- remove ecco_cost_init_varia |
| 573 |
|
(moved to ecco_init_varia) |
| 574 |
|
o ctrl/ctrl_init_variables.F : |
| 575 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 576 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 577 |
|
o ctrl/ctrl_map_ini.F : |
| 578 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 579 |
|
(moved to ctrl_init_variables) |
| 580 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 581 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 582 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 583 |
|
o ecco/ecco_ad_diff.list : |
| 584 |
|
- add ecco_init_varia.f |
| 585 |
|
o ecco/ecco_init_varia.F |
| 586 |
|
- new routine |
| 587 |
|
o pkg/streamice: |
| 588 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 589 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 590 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 591 |
|
o pkg/generic_advdiff: |
| 592 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 593 |
|
o pkg/exf: |
| 594 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 595 |
|
xxg_precip capability |
| 596 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 597 |
|
o pkg/ctrl: |
| 598 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 599 |
|
o model/src/load_fields_driver.F : |
| 600 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 601 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 602 |
|
o OpenAD verification experiments: |
| 603 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 604 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 605 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 606 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 607 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 608 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 609 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 610 |
|
o OpenAD verification tests: |
| 611 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 612 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 613 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 614 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 615 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 616 |
|
o model/src & generic_advdiff: |
| 617 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 618 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 619 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 620 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 621 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 622 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 623 |
|
setting in temp/salt/ptracer_integrate.F |
| 624 |
|
o pkg/dic: |
| 625 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 626 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 627 |
|
in gchem_forcing_sep.F |
| 628 |
|
o pkg/autodiff & obcs: |
| 629 |
|
- add storage of current OB values for U & V (was already done for T & S). |
| 630 |
|
|
| 631 |
|
checkpoint65c (2014/08/30) |
| 632 |
|
o pkg/dic: |
| 633 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 634 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 635 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 636 |
|
o verification: |
| 637 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
| 638 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 639 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 640 |
|
conditions from t=1.yr while keeping the same forcing. |
| 641 |
|
o model/src: |
| 642 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 643 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 644 |
|
o pkg/diagnostics (Stats-Diags): |
| 645 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 646 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 647 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 648 |
|
c) extend regional stats over the region edges (for U or V pt location). |
| 649 |
|
o pkg/gchem: |
| 650 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 651 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 652 |
|
o verification (hs94): |
| 653 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 654 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 655 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 656 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 657 |
|
o pkg/ptracers: |
| 658 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 659 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 660 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 661 |
|
with AB-2 code (so that it get tested). |
| 662 |
|
o model/src: |
| 663 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 664 |
|
with AB-2 code (previously only available with AB-3 code). |
| 665 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 666 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 667 |
|
there, by calling CYCLE_AB_TRACER). |
| 668 |
|
o pkg/generic_advdiff: |
| 669 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 670 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 671 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 672 |
|
S/R temp/salt/ptracers_integrate.F |
| 673 |
|
o model/src & pkg/ptracers: |
| 674 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
| 675 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 676 |
|
- remove common block variable gPtr. |
| 677 |
|
o model/src & pkgs: |
| 678 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 679 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 680 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 681 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 682 |
|
+ change accordingly all calling S/R. |
| 683 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 684 |
|
in S/R temp/salt/ptracers_integrate.F |
| 685 |
|
o pkg/seaice: |
| 686 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 687 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 688 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 689 |
|
in seaice_lsr |
| 690 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 691 |
|
in s/r seaice_lsr_calc_coeffs |
| 692 |
|
o pkg/mdsio: |
| 693 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 694 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 695 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 696 |
|
|
| 697 |
|
checkpoint65b (2014/08/12) |
| 698 |
|
o pkg/matrix: |
| 699 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 700 |
|
o model/src: |
| 701 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 702 |
|
natl_box verification experiment. |
| 703 |
|
o model/src & pkg/down_slope: |
| 704 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 705 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 706 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 707 |
|
results at machine truncation level: update output of experiments |
| 708 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 709 |
|
o pkg/diagnostics (Stats-Diags): |
| 710 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 711 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 712 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 713 |
|
times (but Min,Max and StD are still wrong). |
| 714 |
|
o model/src: |
| 715 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 716 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 717 |
|
o model/src: |
| 718 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 719 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 720 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 721 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 722 |
|
o model/src: |
| 723 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 724 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 725 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 726 |
|
o pkg/seaice/seaice_lsr.F |
| 727 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 728 |
|
in the residual diagnostics |
| 729 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 730 |
|
default) for improved non-linear convergence of the first few steps |
| 731 |
|
- adjust a few comments and add new ones to explain some of the store |
| 732 |
|
directives |
| 733 |
|
o pkg/generic_advdiff (& ptracers): |
| 734 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 735 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 736 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 737 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 738 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 739 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 740 |
|
less exact gradients in my tests); but there are still |
| 741 |
|
recomputation warning (although gradients are sort of OK), when |
| 742 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 743 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 744 |
|
- update verification experiments lab_sea. |
| 745 |
|
- change some comments in S/R seaice_calc_viscosities |
| 746 |
|
o model/src: |
| 747 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 748 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 749 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 750 |
|
but affects AD results (at machine truncation level): update output of |
| 751 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 752 |
|
and isomip (oad: 12.d). |
| 753 |
|
o pkg/generic_advdiff: |
| 754 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 755 |
|
- refine warning related to stability of tracer time-stepping |
| 756 |
|
regarding internal wave dynamics. |
| 757 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 758 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 759 |
|
if potentially unstable). |
| 760 |
|
o pkg/kl10: |
| 761 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 762 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 763 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 764 |
|
verification/internal_wave/input.kl10/ |
| 765 |
|
o isomip experiment: |
| 766 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 767 |
|
(input.htd) and update the output. |
| 768 |
|
o cd_code experiments: |
| 769 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 770 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 771 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 772 |
|
update the corresponding output. |
| 773 |
|
o pkg/seaice: |
| 774 |
|
- reduce the number of include files and store directives in |
| 775 |
|
S/R seaice_lsr_tridiagu/v |
| 776 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 777 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 778 |
|
get rid off one store directive (a TAF bug?) |
| 779 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 780 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 781 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 782 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 783 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 784 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 785 |
|
|
| 786 |
|
checkpoint65a (2014/07/27) |
| 787 |
|
o model/src: |
| 788 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 789 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 790 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 791 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 792 |
|
o model/src: |
| 793 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 794 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 795 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 796 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 797 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 798 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 799 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 800 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 801 |
|
correction due to vertical advection). |
| 802 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 803 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 804 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 805 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 806 |
|
o pkg/ptracers & diagnostics: |
| 807 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 808 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 809 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 810 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 811 |
|
|
| 812 |
|
checkpoint65 (2014/07/18) |
| 813 |
|
o pkg/fizhi: |
| 814 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 815 |
|
affects results at machine truncation level. Update output of experiments |
| 816 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 817 |
|
o pkg/seaice: more clean up |
| 818 |
|
- rename TAF common block tapes to be more consistent and remove |
| 819 |
|
unnecessary duplicates |
| 820 |
|
- add store directives to remove more recomputations, but use smaller |
| 821 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 822 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 823 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 824 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 825 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 826 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 827 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 828 |
|
this experiment): |
| 829 |
|
> size mitgcmuv_ad |
| 830 |
|
text data bss dec hex |
| 831 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 832 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 833 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 834 |
|
text data bss dec hex |
| 835 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 836 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 837 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 838 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 839 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 840 |
|
- in general, the AD gradients still are wrong |
| 841 |
|
o OpenAD |
| 842 |
|
- clean up code_oad/ directories somewhat by moving files |
| 843 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 844 |
|
o model/src: |
| 845 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 846 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 847 |
|
tendencies (previously done after). |
| 848 |
|
o pkg/diagnostics: |
| 849 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
| 850 |
|
o pkg/down_slope: |
| 851 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 852 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 853 |
|
o model/src: |
| 854 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 855 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 856 |
|
the current level tendency array to update (instead of a direct update |
| 857 |
|
of the common bloc array). Change the corresponding calls. |
| 858 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 859 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 860 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 861 |
|
- rearrange some code blocks, so that now all calculations for |
| 862 |
|
setting up the right-hand-sides done within one single block |
| 863 |
|
(I find that easier to read and understand) |
| 864 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 865 |
|
- adjust some indentations and comments |
| 866 |
|
|
| 867 |
|
checkpoint64z (2014/07/10) |
| 868 |
|
o model/src and several pkgs: |
| 869 |
|
- change argument list of all S/R called from external_forcing.F and |
| 870 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 871 |
|
to pass, as argument, the current level tendency array to update |
| 872 |
|
(instead of a direct update of the common bloc array). |
| 873 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 874 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 875 |
|
o pkg/seaice/seaice_lsr.F |
| 876 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 877 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 878 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 879 |
|
keep it in bi/bj loop; this seems to be essential |
| 880 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 881 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 882 |
|
o pkg/seaice |
| 883 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 884 |
|
generates unnecessary code in seaice_lsr_ad |
| 885 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 886 |
|
in seaice_lsr_ad |
| 887 |
|
- exclude some residual computations in seaice_lsr when |
| 888 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 889 |
|
in seaice_lsr_ad |
| 890 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 891 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 892 |
|
and klockey should be checked by a specialist) |
| 893 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 894 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 895 |
|
o pkg/autodiff: |
| 896 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 897 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 898 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 899 |
|
o pkg/ecco: |
| 900 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 901 |
|
temperature (for use in adjoint sensitivity studies). |
| 902 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 903 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 904 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 905 |
|
o pkg/seaice/seaice_summary.F: |
| 906 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 907 |
|
o pkg/seaice: |
| 908 |
|
- remove some store directives and add new ones in an effort to get |
| 909 |
|
finally rid off the recomputation warnings. This is successful |
| 910 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 911 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 912 |
|
are still too many recomputations on the solver iteration level |
| 913 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 914 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 915 |
|
SEAICE_SIZE.h |
| 916 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 917 |
|
o pkg/seaice (ITD code): |
| 918 |
|
- fix definition of Hlimit for multi-threaded case |
| 919 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 920 |
|
update output of experiment seaice_itd. |
| 921 |
|
o replace content of verification/seaice_itd |
| 922 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 923 |
|
to test the ice thickness distribution code with ridging |
| 924 |
|
- this is a first shot at this experiment |
| 925 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 926 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 927 |
|
and lot of new comments. |
| 928 |
|
|
| 929 |
|
checkpoint64y (2014/06/20) |
| 930 |
|
o pkg/seaice/seaice_reg_ridge.F: |
| 931 |
|
- modify the regularization of very small volumes of ice; only check |
| 932 |
|
total volume HEFF, and do not apply correction to individual ice |
| 933 |
|
classes because that leads to funny patterns in the heat and fw-fluxes |
| 934 |
|
into the ocean. Adjust seaice_itd/results/output.txt |
| 935 |
|
- replace nITD by SEAICE_multDim in loop-ranges |
| 936 |
|
o pkg/exf: |
| 937 |
|
- add code to process the case field period = -12. with UV interpolation. |
| 938 |
|
- move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec |
| 939 |
|
into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F) |
| 940 |
|
o verification/global_with_exf: |
| 941 |
|
- switch all fields period to -12. (was previously untested) in input/data.exf |
| 942 |
|
(but keep secondary test ".yearly" unchanged); update the reference output. |
| 943 |
|
o pkg/cal: |
| 944 |
|
- new calendar type "noLeapYear" for 365 days calendar without any leap year. |
| 945 |
|
o pkg/exf: |
| 946 |
|
- new integer parameter "exf_debugLev" (default set to main model debugLevel) |
| 947 |
|
to replace logical switch "exf_verbose" |
| 948 |
|
- report in STDOUT when loading a new record (if exf_debugLev >= 3) |
| 949 |
|
o pkg/sbo: |
| 950 |
|
- update from Katherine Quinn: evaluate mass directly from density and SSH |
| 951 |
|
(budget using Finite Volume method) instead of from bottom pressure. |
| 952 |
|
- allow testreport to collect few selected SBO output ; tested in exp. |
| 953 |
|
global_ocean.90x40x15 (after updating the results, to include SBO output). |
| 954 |
|
- fix some multi-threading issues (in output part). |
| 955 |
|
o model/src & most packages: |
| 956 |
|
- always call {PKG}_READPARMS even if corresponding use{PKG}=F; |
| 957 |
|
- in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R |
| 958 |
|
PACKAGES_UNUSED_MSG to print a weak warning when parameter file |
| 959 |
|
"data.{pkg}" exist ; and leave the S/R (return) just after. |
| 960 |
|
- more standard LAND pkg interface (land_init_fixed.F, land_check.F). |
| 961 |
|
+ call LAND_READPARMS from packages_readparms.F |
| 962 |
|
o pkg/seaice: |
| 963 |
|
- remove code that resets useThSice in S/R seaice_readparms and |
| 964 |
|
replace it by a warning in S/R seaice_check |
| 965 |
|
- remove parameter MULTDIM, replace with nITD and runtime |
| 966 |
|
parameter SEAICE_multDim (still hard-wired to nITD if |
| 967 |
|
SEAICE_ITD is defined) |
| 968 |
|
|
| 969 |
|
checkpoint64x (2014/05/24) |
| 970 |
|
o verification/lab_sea: |
| 971 |
|
- update adjoint and TLM output following changes to pkg/salt_plume |
| 972 |
|
- un-do the update after putting back local recip_Cp in few places. |
| 973 |
|
o pkg/salt_plume: modifications by An Nguyen: |
| 974 |
|
- add capability to do brine rejection (salt-plume) as function of |
| 975 |
|
volume+tracers (instead of only salinity tracer). |
| 976 |
|
- conserve volume by exchanging volume from each kLev to above to |
| 977 |
|
accommodate in-coming brine volume |
| 978 |
|
- store surface and klev exchanged fraction + volume in 4 new 3-d arrays |
| 979 |
|
- switch KPP surf buoyancy due to brine forcing to 3-d |
| 980 |
|
(3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume) |
| 981 |
|
- add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t |
| 982 |
|
- unrelatedly, also add ad-hoc capability to vary salt_plume scheme |
| 983 |
|
in East/West Arctic. |
| 984 |
|
o pkg/sbo: |
| 985 |
|
- incorporate modifications from Katherine Quinn to enable the use of sbo |
| 986 |
|
pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like |
| 987 |
|
output for future testreport verification (unfinished). |
| 988 |
|
o pkg/atm_phys: |
| 989 |
|
- change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R: |
| 990 |
|
skip the reseting of t_ref & q_ref to initial t & q ; this preserve the |
| 991 |
|
output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics. |
| 992 |
|
o pkg/seaice |
| 993 |
|
seaice_calc_ice_strength.F: modify expression to avoid divisions |
| 994 |
|
(affects truncation) |
| 995 |
|
seaice_do_ridging.F: clean up the insectarium |
| 996 |
|
- fix a bug that was compensated by areaScaling (-> remove areaScaling code) |
| 997 |
|
- added SEAICEsnowFracRidge to redistributed snow (2nd bug) |
| 998 |
|
- set closing/openingRate to zero where no extra iteration is need (3rd bug) |
| 999 |
|
- add some debugging information and error messages (warnings) |
| 1000 |
|
o model/src: modifications relatd to atmosphere p*: |
| 1001 |
|
- Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F) |
| 1002 |
|
- With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead |
| 1003 |
|
of vertical profile tRef in geopotential background and anomaly. |
| 1004 |
|
- Acount for true p* correction in theta <-> T conversion in pkg/aim_v23 |
| 1005 |
|
and pkg/atm_phys. |
| 1006 |
|
- Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40, |
| 1007 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn. |
| 1008 |
|
o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt |
| 1009 |
|
o pkg/ptracers: compute ptracer source/sink due to linear free surface. |
| 1010 |
|
not used right now, but can be used in BGC packages to fix conservation. |
| 1011 |
|
o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by |
| 1012 |
|
other packages too. |
| 1013 |
|
o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by |
| 1014 |
|
SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix) |
| 1015 |
|
o model/src: |
| 1016 |
|
- since we have several heat capacity (even in model/src), define "recip_Cp" |
| 1017 |
|
as local variable (no longer in common block) to avoid any confusion. |
| 1018 |
|
- add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords). |
| 1019 |
|
o pkg/exf: |
| 1020 |
|
- from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local |
| 1021 |
|
air density as function of air Temp, Humidity and atm pressure. |
| 1022 |
|
|
| 1023 |
|
checkpoint64w (2014/05/02) |
| 1024 |
|
o verification: |
| 1025 |
|
- update output_adm.txt files for experiment global_ocean.cs32x15 (seaice & |
| 1026 |
|
seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing |
| 1027 |
|
code from seaice_growth.F & seaice_advdiff.F to new ridging routines |
| 1028 |
|
seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient |
| 1029 |
|
(down to 8-7 matching digits for global_ocean and 5-6 for lab_sea). |
| 1030 |
|
o model/src: for atmosphere in p* coords: |
| 1031 |
|
- store factor rStarFacC**atm_kappa (= pStarFacK) in common block |
| 1032 |
|
- implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F), |
| 1033 |
|
but not yet activated. |
| 1034 |
|
o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation: |
| 1035 |
|
- move computation of opnWtrFrac = 1-AREA to before computing ice strength |
| 1036 |
|
- this changes the results (but not for any verification experiment, because |
| 1037 |
|
none tests this), but avoids having an extra field in the restart files |
| 1038 |
|
o pkg/seaice: remove global variable TICE (not needed) |
| 1039 |
|
- replace by TICES or local variable where necessary (cost_seaice_test, |
| 1040 |
|
seaice_diagnostics_state) |
| 1041 |
|
- move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup |
| 1042 |
|
- use specific read/write routines for reading and writing individual leves |
| 1043 |
|
of a multilevel field |
| 1044 |
|
o pkg/ctrl & model/inc: |
| 1045 |
|
- move additional anomaly fields of control vars (related to options: |
| 1046 |
|
ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL) |
| 1047 |
|
from DYNVARS.h into new header file: CTRL_FIELDS.h |
| 1048 |
|
o pkg/seaice: some small modifications to the ridging code |
| 1049 |
|
- make fw2ObyRidge a global variable and add the freshwater flux to |
| 1050 |
|
seaice_growth |
| 1051 |
|
- pass actual thickness from seaice_prepare_ridging, so that it is |
| 1052 |
|
computed only in one place and compute it in the same way as in |
| 1053 |
|
seaice_growth |
| 1054 |
|
- initialise more fields in seaice_do_ridging that where cause floating |
| 1055 |
|
point exceptions over land |
| 1056 |
|
o pkg/seaice: preparations for ridging code and first real ridging code |
| 1057 |
|
- move most of "PART 1" of S/R seaice_growth into a new and separate |
| 1058 |
|
S/R seaice_reg_ridge that will both regularize the state variable after |
| 1059 |
|
advection call the actual ridging routine; |
| 1060 |
|
- requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG, |
| 1061 |
|
d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust; |
| 1062 |
|
- remove ridging code from seaice_advdiff |
| 1063 |
|
- clean up remaining part 1 of seaice_growth in an attempt to make it |
| 1064 |
|
more readable (this is probably subjective) |
| 1065 |
|
- call seaice_itd_redist once in the initialisation phase to have the initial |
| 1066 |
|
conditions in the correct category |
| 1067 |
|
- finally: add new ridging routine for ITD code |
| 1068 |
|
|
| 1069 |
|
checkpoint64v (2014/04/11) |
| 1070 |
|
o pkg/ecco: |
| 1071 |
|
- add runtime parameters mdt[start,end]date[1,2] |
| 1072 |
|
- rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile" |
| 1073 |
|
o pkg/seaice: |
| 1074 |
|
- make deltaC a global variable, so that it can be used in ridging code |
| 1075 |
|
- first step towards ridging: introduce new routines that compute |
| 1076 |
|
ice strength based on ridging parameters |
| 1077 |
|
- add diagnostic for HSNOWITD |
| 1078 |
|
- add opnWtrFrac as a global variable (required for ridging scheme) |
| 1079 |
|
o pkg/salt_plume + pkg/seaice/seaice_growth.F |
| 1080 |
|
- add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice |
| 1081 |
|
AREA exceeds a threshold (code contributed by I.Fenty in 2011) |
| 1082 |
|
o verification/hs94.1x64x5: |
| 1083 |
|
- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
| 1084 |
|
- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
| 1085 |
|
o autodiff: |
| 1086 |
|
- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
| 1087 |
|
and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
| 1088 |
|
For now, only in pkgs used in verification/hs94.1x64x5. |
| 1089 |
|
- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
| 1090 |
|
which are specific to TAF/TAMC). |
| 1091 |
|
- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
| 1092 |
|
since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
| 1093 |
|
is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
| 1094 |
|
- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
| 1095 |
|
building mitgcmuv_ad (make adAll). |
| 1096 |
|
o pkg/ecco: |
| 1097 |
|
- cost_gencost_seaicev4.F: |
| 1098 |
|
reformulate proxy cost as function of sst and local param SEAICE_freeze |
| 1099 |
|
change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
| 1100 |
|
- add stop statement if old names siv4-[sst,vol] are used |
| 1101 |
|
- add snapshots + cost reports for atmospheric longwave |
| 1102 |
|
- remove factor 0.1 in front of wtau[u,v] |
| 1103 |
|
- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
| 1104 |
|
ALLOW_TMI_SST_COST_CONTRIBUTION |
| 1105 |
|
o pkg/atm_phys: |
| 1106 |
|
- add some diagnostics for Short-wave and for convection S/R. |
| 1107 |
|
o pkg/seaice/seaice_growth: |
| 1108 |
|
- fix a bug in the lateral melt parameterization for SEAICE_ITD |
| 1109 |
|
in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
| 1110 |
|
- rearrange loop order for better vector code in the same code block |
| 1111 |
|
- rewrite the floeDiameter formula to have fewer divisions |
| 1112 |
|
- (miraculously) none of this changes the results of seaice_itd |
| 1113 |
|
o pkg/smooth: |
| 1114 |
|
- move param smooth2Ddiffnbt to pkg/ecco |
| 1115 |
|
o pkg/salt_plume: |
| 1116 |
|
- salt_plume_frac.F: |
| 1117 |
|
clean up local param names |
| 1118 |
|
reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
| 1119 |
|
o pkg/rw: |
| 1120 |
|
- add RS version of S/R READ_MFLDS_LEV. |
| 1121 |
|
o pkg/streamice: |
| 1122 |
|
- fix the restart test by writing/reading pickup_streamice files. |
| 1123 |
|
o pkg/seaice: |
| 1124 |
|
- refine checks for jfnk-related parameters |
| 1125 |
|
- comment out if statement with SEAICEuseIMEX parameter as long as there |
| 1126 |
|
is no IMEX code to avoid confusion and surprises |
| 1127 |
|
|
| 1128 |
|
checkpoint64u (2014/03/07) |
| 1129 |
|
o verification/MLAdjust: |
| 1130 |
|
- rename secondary test suffix: |
| 1131 |
|
1.leith -> A4FlxF + switch to flux-form & add side-drag |
| 1132 |
|
0.leithD -> AhFlxF + switch to flux-form |
| 1133 |
|
0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
| 1134 |
|
0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
| 1135 |
|
o pkg/mom_vecinv: |
| 1136 |
|
- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
| 1137 |
|
to be before mom_calc_visc.F) |
| 1138 |
|
- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
| 1139 |
|
- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
| 1140 |
|
this is simpler for the adjoint and for diagnostics. |
| 1141 |
|
o model/src + pkg/momentum: |
| 1142 |
|
- add input files for 2-D additional Western and Southern cell-edge wall |
| 1143 |
|
(e.g., to add "thin-wall" where it is =1). |
| 1144 |
|
- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
| 1145 |
|
using 2nd hFacZ that is computed from initial (fix domain) hFac |
| 1146 |
|
- known limitations of thin wall implementation: not yet coded for sigma |
| 1147 |
|
coords; not working with CD-scheme neither. |
| 1148 |
|
o pkg/seaice: |
| 1149 |
|
- rename recently introduced parameters from (wrong name) AB to |
| 1150 |
|
BDF (backward difference time discretisation) |
| 1151 |
|
- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
| 1152 |
|
o tools/adjoint_options: |
| 1153 |
|
- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
| 1154 |
|
|
| 1155 |
|
checkpoint64t (2014/02/01) |
| 1156 |
|
o pkg/ecco |
| 1157 |
|
- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
| 1158 |
|
runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
| 1159 |
|
- replace hard-coded record number and period which only work for monthly |
| 1160 |
|
with read-in runtime param that works for other periods (month,day,year) |
| 1161 |
|
o pkg/thsice |
| 1162 |
|
- corrected store directive fixes thsice adjoint gradient checks |
| 1163 |
|
o genmake2 & testreport: |
| 1164 |
|
- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
| 1165 |
|
in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
| 1166 |
|
Update testreport accordingly. No need to set "export OPENAD=true" |
| 1167 |
|
in adjoint_options/adjoint_oad anymore (will be removed later). |
| 1168 |
|
o pkg/shelfice: |
| 1169 |
|
- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
| 1170 |
|
only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
| 1171 |
|
so that surface forcing applies to k=kSurf if using pkg/shelfice. |
| 1172 |
|
o pkg/ctrl, pkg/grdchk, pkg/ecco: |
| 1173 |
|
- Changes to make GENARR more modular (i.e. invisible if not used) |
| 1174 |
|
o model/src/temp_integrate.F and salt_integrate.F |
| 1175 |
|
- re-include store directives that were removed on Dec 27th. |
| 1176 |
|
o model/src/external_forcing_surf.F |
| 1177 |
|
- add storage directives for EmPmR and PmEpR to avoid recomputation of |
| 1178 |
|
seaice_model in the adjoint that is problematic when seaice_model is |
| 1179 |
|
turned off in the adjoint. The resolved issue dated back to July when |
| 1180 |
|
EXTERNAL_FORCING_SURF call was moved. |
| 1181 |
|
Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
| 1182 |
|
o pkg/exf/exf_check.F |
| 1183 |
|
- fix a small bug again (originally found by Wentao Liu, now found again) |
| 1184 |
|
- streamline error output |
| 1185 |
|
o pkg/streamice and aim_v23: |
| 1186 |
|
- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
| 1187 |
|
Apple's /usr/bin/cpp knows what to do: |
| 1188 |
|
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
| 1189 |
|
Target: x86_64-apple-darwin13.0.0 |
| 1190 |
|
|
| 1191 |
|
checkpoint64s (2014/01/05) |
| 1192 |
|
o tools/adjoint_options: |
| 1193 |
|
- switch to fastopt.net TAF server (instead of default fastopt.de) for |
| 1194 |
|
AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
| 1195 |
|
o model/src: |
| 1196 |
|
- remove some unnecessary TAF storage directives in forward_step.F and |
| 1197 |
|
in dynamics.F (note: not always removed by TAF, e.g., double storage |
| 1198 |
|
of kappaRU,kappaRV in former version of dynamics.F). |
| 1199 |
|
o model/src & pkg/ptracers: |
| 1200 |
|
- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
| 1201 |
|
salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
| 1202 |
|
and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
| 1203 |
|
- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
| 1204 |
|
- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
| 1205 |
|
- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
| 1206 |
|
o useSingleCpuInput separates single-CPU input from single-CPU output; |
| 1207 |
|
for now only implemented for in exf_interp_read.F |
| 1208 |
|
o verification/advect_xy: |
| 1209 |
|
- fix missing EXCH call in local version of ini_salt.F and update output. |
| 1210 |
|
o momentum diagnostics: |
| 1211 |
|
- fix which deltaT is used in Total-Tendency diagnostics. |
| 1212 |
|
- fix typo in diagnostics for momentum tendency from AB. |
| 1213 |
|
o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
| 1214 |
|
SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
| 1215 |
|
|
| 1216 |
|
checkpoint64r (2013/12/08) |
| 1217 |
|
o verification/*/results: |
| 1218 |
|
- Update reference output of experiments that were passing with just 13 digits |
| 1219 |
|
(make it easier to detect future changes in results) |
| 1220 |
|
o model/src & pkg/ptracers: |
| 1221 |
|
- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
| 1222 |
|
inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
| 1223 |
|
to inside ptracers_integrate.F ; remove ptracers_advection.F |
| 1224 |
|
o coupling interface pkgs: |
| 1225 |
|
[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
| 1226 |
|
- change the config check to test the agreement of Ocean Depth |
| 1227 |
|
with ATM land/sea mask (instead of ATM orography); |
| 1228 |
|
- send to coupler the number of coupler time-steps to do for this run: |
| 1229 |
|
this allows to check for consistency and don't need anymore to be |
| 1230 |
|
specified in parameter file "data"; |
| 1231 |
|
in coupler: |
| 1232 |
|
- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 1233 |
|
- improve report to log-file of config setting (pass log-file unit to few S/R) |
| 1234 |
|
o pkg/compon_communic: |
| 1235 |
|
- add coupling send/receive for non-tiled integer vector; |
| 1236 |
|
- add S/R to check and stop if any proc has an error (similar to |
| 1237 |
|
eesupp/src/stop_if_error.F but single thread and across Comm_World). |
| 1238 |
|
o pkg/exch2: |
| 1239 |
|
- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 1240 |
|
through list of all tiles my proc owns. |
| 1241 |
|
o model/src: |
| 1242 |
|
- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 1243 |
|
from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 1244 |
|
calling S/R); this affects AD results at machine truncation level: |
| 1245 |
|
update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 1246 |
|
bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 1247 |
|
o tools/build_options: |
| 1248 |
|
- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 1249 |
|
o coupling interface pkgs: |
| 1250 |
|
[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 1251 |
|
- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 1252 |
|
to each S/R that needs it; remove un-used variables. |
| 1253 |
|
- change component tile registration (cpl_register.F in both compon_interf |
| 1254 |
|
and mitcomponent_tile_register.F) to pass the full list of tiles |
| 1255 |
|
information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 1256 |
|
- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 1257 |
|
towards coupler global array (unless W2_useE2ioLayOut=F): |
| 1258 |
|
a) can now use different tiling between atm & ocn comp. |
| 1259 |
|
b) no needs to modify the run-Off map when changing tiling (was needed |
| 1260 |
|
even if using the same tiling between atm & ocn). |
| 1261 |
|
c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 1262 |
|
full land tiles); not yet tested. |
| 1263 |
|
- check for valid mapping from comp. tile to coupler global array |
| 1264 |
|
- improve report of tile registration results to log file. |
| 1265 |
|
o pkg/exch2: |
| 1266 |
|
- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 1267 |
|
tile-registration (CPL_REGISTER); |
| 1268 |
|
- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 1269 |
|
store the local bi,bj indices of each tile; |
| 1270 |
|
- also print bi,bj in local report to log file; |
| 1271 |
|
- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 1272 |
|
Jun 2009 modif of pkg/exch2). |
| 1273 |
|
o testing on baudelaire: |
| 1274 |
|
- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 1275 |
|
get the full set of test done earlier |
| 1276 |
|
- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 1277 |
|
o model/src/thermodynamics.F and routines called from it: |
| 1278 |
|
- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 1279 |
|
gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 1280 |
|
velocity (outp) by adding bolus velocity. |
| 1281 |
|
- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 1282 |
|
mass transport from velocity + lateral grid cell area |
| 1283 |
|
- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 1284 |
|
- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
| 1285 |
|
in thermodynamics.F |
| 1286 |
|
- remove k from thermodynamics.F and move it to temp_integrate.F |
| 1287 |
|
salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
| 1288 |
|
loop). |
| 1289 |
|
- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 1290 |
|
advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 1291 |
|
PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 1292 |
|
GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 1293 |
|
- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 1294 |
|
global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 1295 |
|
tutorial_tracer_adjsens (+ TLM output). |
| 1296 |
|
o tools/OAD_support and (verification/*/) code_oad: |
| 1297 |
|
- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 1298 |
|
module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 1299 |
|
- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 1300 |
|
version (closer to model/inc/CPP_OPTIONS.h). |
| 1301 |
|
o model/src: |
| 1302 |
|
- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 1303 |
|
retired list of parameters (routine FREEZE has been replace by surface |
| 1304 |
|
freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 1305 |
|
o pkg/gmredi: |
| 1306 |
|
- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 1307 |
|
velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 1308 |
|
- update output of FWD experiments: front_relax.bvp, |
| 1309 |
|
global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 1310 |
|
|
| 1311 |
|
checkpoint64q (2013/11/17) |
| 1312 |
|
o verification: |
| 1313 |
|
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 1314 |
|
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 1315 |
|
- generate new output (growth & melt) for seaice_itd experiment after |
| 1316 |
|
updating the input pickup_seaice files (previously wrong). |
| 1317 |
|
o pkg/cost: |
| 1318 |
|
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 1319 |
|
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 1320 |
|
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 1321 |
|
cannot be applied to var in common block). |
| 1322 |
|
o allows to get results independent of tile-per-proc setting (if using |
| 1323 |
|
slower GLOBAL_SUM_SEND_RECV option). |
| 1324 |
|
- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 1325 |
|
thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 1326 |
|
forward gradients: update output). |
| 1327 |
|
- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 1328 |
|
S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 1329 |
|
o pkg/mom_common: |
| 1330 |
|
- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 1331 |
|
code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 1332 |
|
viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 1333 |
|
ensure that all field value that are used are set. |
| 1334 |
|
o tutorial_deep_convection (smag3d): |
| 1335 |
|
- add missing scaling in mom_calc_smag_3d.F; |
| 1336 |
|
- set smag3D_coeff in input.smag3d such that results do not change. |
| 1337 |
|
o pkg/dic: |
| 1338 |
|
- change dic_cost.F to compute cost on each tile first and then apply |
| 1339 |
|
GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 1340 |
|
tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 1341 |
|
- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 1342 |
|
o eesupp/src & pkg/mdsio: |
| 1343 |
|
- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 1344 |
|
(from pkg/mdsio) since they are no longer used for tape IO. |
| 1345 |
|
- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 1346 |
|
(+ keep a copy in pkg/atm_ocn_coupler). |
| 1347 |
|
o verification/isomip: |
| 1348 |
|
- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 1349 |
|
o tools/build_options: |
| 1350 |
|
- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 1351 |
|
to get a working restart for all experiments, add "-fp-model source" |
| 1352 |
|
to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 1353 |
|
|
| 1354 |
|
checkpoint64p (2013/10/20) |
| 1355 |
|
o pkg/autodiff: |
| 1356 |
|
- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 1357 |
|
criteria, return to simple (default) tape IO format. |
| 1358 |
|
o pkg/mdsio (+ eesupp/src): |
| 1359 |
|
- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 1360 |
|
previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 1361 |
|
- fix globalFile and singleCpuIO options using simpler global mapping. |
| 1362 |
|
- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 1363 |
|
template) corresponding to simpler global mapping. |
| 1364 |
|
- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 1365 |
|
to globalFile when parameter globalFiles is set to True. |
| 1366 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 1367 |
|
o pkg/autodiff: |
| 1368 |
|
- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 1369 |
|
with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 1370 |
|
missing, just add a STOP if array type do not match. |
| 1371 |
|
o pkg/exf: |
| 1372 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 1373 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 1374 |
|
and rename array obsSIce to exf_iceFraction. |
| 1375 |
|
o tutorial_deep_convection: |
| 1376 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 1377 |
|
for now all in this exp. code dir. |
| 1378 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 1379 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 1380 |
|
o eesupp/src: |
| 1381 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
| 1382 |
|
very large number of processors did not work with existing set-up |
| 1383 |
|
|
| 1384 |
|
checkpoint64o (2013/09/25) |
| 1385 |
|
o pkg/atm_phys & atm_compon_interf: |
| 1386 |
|
- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 1387 |
|
o tools/build_options: |
| 1388 |
|
- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 1389 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 1390 |
|
remove CPP setting (was identical to genmake2 default). |
| 1391 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 1392 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 1393 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
| 1394 |
|
external forcing via taueddy_external_forcing.F |
| 1395 |
|
- at the moment, it is very experimental and only works with the variable eddy |
| 1396 |
|
diffusivity calculated in gmredi_k3d.F |
| 1397 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 1398 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 1399 |
|
o testreport (& tools/do_tst_2+2): |
| 1400 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 1401 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 1402 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 1403 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 1404 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
| 1405 |
|
o pkg/atm_compon_interf: |
| 1406 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
| 1407 |
|
(which accumalate in time each coupling field) |
| 1408 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 1409 |
|
update accordingly + simplify aim_do_physics.F |
| 1410 |
|
|
| 1411 |
|
checkpoint64n (2013/08/26) |
| 1412 |
|
o pkg/bbl: |
| 1413 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
| 1414 |
|
- replaced horizontal and vertical transport parameters with velocities |
| 1415 |
|
- changes results for verification/global_with_exf.yearly |
| 1416 |
|
o verification/halfpipe_streamice: |
| 1417 |
|
- change to matrix construction; update both Fwd & AD output. |
| 1418 |
|
o verification/tutorial_tracer_adjsens: |
| 1419 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 1420 |
|
rStar causes problems with OpenAD; update output. |
| 1421 |
|
o tools: |
| 1422 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
| 1423 |
|
to local /tmp disk (but would be easy to move them back); |
| 1424 |
|
- xmakedepend: apply the same switch for temp-files. |
| 1425 |
|
o pkg/offline: |
| 1426 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
| 1427 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 1428 |
|
output files) and apply r* scaling at each time-step (function of the time |
| 1429 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 1430 |
|
o adjoint with OpenAD: |
| 1431 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 1432 |
|
package openad. This package has to be compiled for all runs with OpenAD |
| 1433 |
|
instead of specifying code_oad_all as a modification directory. |
| 1434 |
|
- link the fortran templates from tools/OAD_support to the build directory |
| 1435 |
|
for preprocessing to avoid conflicts between different setups compiled |
| 1436 |
|
simultaneously and simplify cleanup. |
| 1437 |
|
o pkg/exf: |
| 1438 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 1439 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 1440 |
|
o model/src: |
| 1441 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 1442 |
|
(similar to do_fields_blocking_exchanges.F). |
| 1443 |
|
o tools/genmake2: |
| 1444 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
| 1445 |
|
built, will stop if things go wrong with staf). |
| 1446 |
|
- fix target "adobj" (left from TAF version-2 transition) |
| 1447 |
|
o pkg/diagnostics: |
| 1448 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
| 1449 |
|
this replace/extend the use of logical param "settingDiags" (to check |
| 1450 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 1451 |
|
New S/R to print error message and stop when pkgStatus is not right. |
| 1452 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 1453 |
|
|
| 1454 |
|
checkpoint64m (2013/08/13) |
| 1455 |
|
o model/inc: |
| 1456 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 1457 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 1458 |
|
o pkg/kpp & aim_v23: |
| 1459 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 1460 |
|
o pkg/seaice: |
| 1461 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 1462 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 1463 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 1464 |
|
o eesupp/src: |
| 1465 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 1466 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 1467 |
|
o switch to TAF version-2: |
| 1468 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 1469 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 1470 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 1471 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 1472 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 1473 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 1474 |
|
out except for diva). |
| 1475 |
|
- the major change with TAF version-2 is that both the differentiated |
| 1476 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 1477 |
|
output source code. Update genmake2 accordingly. |
| 1478 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 1479 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 1480 |
|
output show minor changes (machine truncation level); update the few AD & |
| 1481 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 1482 |
|
|
| 1483 |
|
checkpoint64l (2013/08/05) |
| 1484 |
|
o model/src: |
| 1485 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 1486 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 1487 |
|
when using TAF but only if using OpenAD. |
| 1488 |
|
o pkg/mom_common+fluxform+vecinv: |
| 1489 |
|
- always set horiz. viscosity arrays to background value before calling |
| 1490 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 1491 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 1492 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 1493 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
| 1494 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 1495 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 1496 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 1497 |
|
useBiharmonicVisc & useVariableVisc. |
| 1498 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 1499 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 1500 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 1501 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 1502 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 1503 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 1504 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 1505 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 1506 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 1507 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 1508 |
|
default viscAh,viscA4 is zero). |
| 1509 |
|
o model/src: |
| 1510 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 1511 |
|
o Divided Adjoint (DIVA) with MPI: |
| 1512 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 1513 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
| 1514 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
| 1515 |
|
|
| 1516 |
|
checkpoint64k (2013/07/23) |
| 1517 |
|
o tools/OAD_support: |
| 1518 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
| 1519 |
|
and remove it from genmake2. |
| 1520 |
|
o tools/build_options: |
| 1521 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
| 1522 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
| 1523 |
|
o verification/halfpipe_streamice: |
| 1524 |
|
- change to driving stress formulation; update both Fwd & AD output. |
| 1525 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
| 1526 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 1527 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 1528 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 1529 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 1530 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
| 1531 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
| 1532 |
|
o testreport: |
| 1533 |
|
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 1534 |
|
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
| 1535 |
|
from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h"). |
| 1536 |
|
o verification/lab_sea (AD test): |
| 1537 |
|
- change to test Divided Adjoint Run in this set-up (both standard AD test |
| 1538 |
|
and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test. |
| 1539 |
|
o pkg atm_ & ocn_compon_interf: |
| 1540 |
|
- remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old |
| 1541 |
|
staggerTimeStep implementation) and disable (retired) corresponding |
| 1542 |
|
parameter. |
| 1543 |
|
o pkg/offline: |
| 1544 |
|
- comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01]; |
| 1545 |
|
- add S/R OFFLINE_CHECK to print offline parameter summary |
| 1546 |
|
and stop if loading a file that is not used; |
| 1547 |
|
- enable to calculate GMRedi tensor, KPP mixing and convective index |
| 1548 |
|
when the corresponding file(s) is/are not specified (but pkg is used). |
| 1549 |
|
- comment out resetting of monitorFreq (to endTime) since it still useful |
| 1550 |
|
for monitoring CFL numbers and checking offline fields. |
| 1551 |
|
o OpenAD: |
| 1552 |
|
- do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get |
| 1553 |
|
smaller standard output) and generate new (smaller) output (on baudelaire |
| 1554 |
|
using gfortran with -ieee) for exp. tutorial_tracer_adjsens |
| 1555 |
|
o model/src: |
| 1556 |
|
- call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F), |
| 1557 |
|
(where external_forcing_adjust was called) and change list of arguments; |
| 1558 |
|
- merge external_forcing_adjust.F into external_forcing_surf.F |
| 1559 |
|
- put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F) |
| 1560 |
|
which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX, |
| 1561 |
|
previously in file "balance_relax.F", now removed); remove corresponding |
| 1562 |
|
arrays in FFIELDS.h. |
| 1563 |
|
- EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement |
| 1564 |
|
a hack for getting back surfaceForcingS (loaded from file) when using |
| 1565 |
|
ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up. |
| 1566 |
|
- update output of AD test experiment global_ocean.cs32x15.seaice_dynmix |
| 1567 |
|
(was getting only 11 digits for AD-grad, due to different truncation |
| 1568 |
|
error in AD code). |
| 1569 |
|
|
| 1570 |
|
checkpoint64j (2013/07/04) |
| 1571 |
|
o pkg/offline: |
| 1572 |
|
- to enable the use of other features with pkg offline (e.g., obcs), |
| 1573 |
|
also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come. |
| 1574 |
|
- comment out "allowFreezing" (now active) in 2 offline testing exp. |
| 1575 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 1576 |
|
- fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL |
| 1577 |
|
- ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice |
| 1578 |
|
- changes verification/global_ocean.cs32x15/results/output.seaice.txt |
| 1579 |
|
o pkg/atm_phys: |
| 1580 |
|
- allows to add some damping on uVel,vVel (strength only function of k). |
| 1581 |
|
o verification, ad-tests: |
| 1582 |
|
- reduce length of the simulation for AD test: global_ocean.cs32x15.seaice, |
| 1583 |
|
global_ocean_ebm and offline_exf_seaice.thsice. |
| 1584 |
|
o verification/halfpipe_streamice: |
| 1585 |
|
- found a bug in s/r pkg/streamice/streamice_advect_thickness which caused |
| 1586 |
|
flux input boundary conditions to be ignored; a fix for this bug changed |
| 1587 |
|
verification results for forward test. |
| 1588 |
|
- add adjoint test. |
| 1589 |
|
o pkg/ptracers: |
| 1590 |
|
- allow to restart without SOM pickup (resetting SOM to zero). |
| 1591 |
|
o pkg/gmredi: |
| 1592 |
|
- New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added. |
| 1593 |
|
- It uses mixing length theory and suppression by steering level effects to |
| 1594 |
|
calculate a diffusivity used in the Redi tensor (see Bates et al., submitted |
| 1595 |
|
to JPO, for more details). |
| 1596 |
|
- It also uses the diffusivity to calculate an eddy induced streamfunction |
| 1597 |
|
based on a PV closure (rather than a buoyancy closure as in GM). |
| 1598 |
|
- New files added to pkg/gmredi: |
| 1599 |
|
gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy |
| 1600 |
|
induced overturning streamfunction (called from gmredi_calc_tensor) |
| 1601 |
|
gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required |
| 1602 |
|
for use in gmredi_k3d |
| 1603 |
|
gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate |
| 1604 |
|
the eddy diffusivity |
| 1605 |
|
|
| 1606 |
|
checkpoint64i (2013/06/18) |
| 1607 |
|
o pkg/cheapaml: |
| 1608 |
|
- take src files from MITgcm_contrib/verification_other/offline_cheapaml/code |
| 1609 |
|
that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics) |
| 1610 |
|
with pkg/cheapaml. |
| 1611 |
|
o utils/python: add subpackage for cubed sphere function, first example is |
| 1612 |
|
simple cs.pcol to plot 2D fields on a map |
| 1613 |
|
o pkg/streamice: |
| 1614 |
|
- This is a new package in MITgcm, which solves dynamic equations for ice |
| 1615 |
|
sheets and ice streams |
| 1616 |
|
- At the moment it is independent of atmosphere/ocean dynamics, or any |
| 1617 |
|
other physical packages in MITgcm, even ShelfIce (although it is anticipat- |
| 1618 |
|
ed that this will change) |
| 1619 |
|
- There is a new verification exercise that tests it, halfpipe_streamice, |
| 1620 |
|
evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a |
| 1621 |
|
rectangular embayment |
| 1622 |
|
- halfpipe_streamice is forward-only for now, will have TAF test soon |
| 1623 |
|
- for questions, email dgoldber@mit.edu |
| 1624 |
|
o pkg/thsice: |
| 1625 |
|
- fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing |
| 1626 |
|
of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40); |
| 1627 |
|
- remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new |
| 1628 |
|
call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect ); |
| 1629 |
|
- allow precip from pkg/cheapaml to make snow over seaice. |
| 1630 |
|
o pkg/cfc: |
| 1631 |
|
- move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC |
| 1632 |
|
- remove atmos CFC 2-D arrays from common bloc (now local variables) |
| 1633 |
|
- change some hard-coded constant to run time parameter for reading and |
| 1634 |
|
and interpolating atmospheric CFC ; keep same default as previously. |
| 1635 |
|
- more flexible reading of Atmos CFC (number of records no longer hard-coded) |
| 1636 |
|
- put arguments in standard order: myTime, myIter, myThid |
| 1637 |
|
- use standard S/R GET_PERIODIC_INTERVAL for time interpolation of |
| 1638 |
|
atmospheric CFC ; fix for the case myIter < PTRACERS_iter0. |
| 1639 |
|
- fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf |
| 1640 |
|
- new routine to print summary of CFC params and check for consistency. |
| 1641 |
|
o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff, |
| 1642 |
|
similar to thsice_advdiff. |
| 1643 |
|
Note that for the B-grid case the routine parameters uc/vc are overwritten. |
| 1644 |
|
o pkg/cfc: |
| 1645 |
|
- change time interpolation for atmospheric CFC-11 (now same as for CFC-12); |
| 1646 |
|
update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline. |
| 1647 |
|
- fix interpolation of atmphspheric CFC between Sorthern and Northern |
| 1648 |
|
hemisphere value. |
| 1649 |
|
o pkg/seaice: |
| 1650 |
|
- allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml) |
| 1651 |
|
o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics; |
| 1652 |
|
so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE. |
| 1653 |
|
- requires an additional time level that is stored in the pickup |
| 1654 |
|
- you can start with AB2 from a pickup without this time level with |
| 1655 |
|
pickupStrictlyMatch = .false. |
| 1656 |
|
|
| 1657 |
|
checkpoint64h (2013/05/26) |
| 1658 |
|
o pkg/cheapaml: |
| 1659 |
|
- replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux); |
| 1660 |
|
affect machine truncation (but exp cheapAML_box still pass with 13 digits). |
| 1661 |
|
- consistent treatment of uWind,vWind location: assume everywhere in |
| 1662 |
|
pkg/cheapaml that they are on C-grid (@ uVel,vVel location) |
| 1663 |
|
(Note: was already the case for Tair,Qair advection); |
| 1664 |
|
add option (INCONSISTENT_WIND_LOCATION) to recover old results. |
| 1665 |
|
- compute diabatic forcing only in the interior (excluding overlap regions) |
| 1666 |
|
- fill in array "Qsw" (for short-wave heating); |
| 1667 |
|
- add diagnostic for precip ; fill-in diagnostics for cheapAML state vars |
| 1668 |
|
before any update (consistent with MITgcm state var diagnostics); |
| 1669 |
|
- cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if |
| 1670 |
|
non periodic ; + adjusted for uWind,vWind (C-grid). |
| 1671 |
|
o pkg/seaice: |
| 1672 |
|
- remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and |
| 1673 |
|
add explicitly pkg/exf in experiments that currently use pkg/seaice. |
| 1674 |
|
- allows to compile pkg/seaice without pkg/exf. |
| 1675 |
|
o tools/OAD_support: |
| 1676 |
|
- use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds |
| 1677 |
|
of array "ourStepOf" in function rvNextAction (revolve.F90). |
| 1678 |
|
o pkg/aim_compon_interf renamed to pkg/atm_compon_interf |
| 1679 |
|
- change pkg name (to be used with other atmospheric physics pkg) |
| 1680 |
|
but by-pass CVS when making the new pkg so that we keep the CVS history. |
| 1681 |
|
o pkg/offline: |
| 1682 |
|
- call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F |
| 1683 |
|
(previously called from pkg/dic_surfforcing_init.F) |
| 1684 |
|
o model/src: |
| 1685 |
|
- re-order sequence of calls within packages_init_variables.F, using |
| 1686 |
|
standard order, except for: |
| 1687 |
|
DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top), |
| 1688 |
|
CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom) |
| 1689 |
|
o new pkg: atm_phys |
| 1690 |
|
- add entry point and source code (previously in contrib |
| 1691 |
|
verification_other/atm_gray/code_gray/) for new pkg "atm_phys" |
| 1692 |
|
(atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008). |
| 1693 |
|
- re-order sequence of calls within packages_readparms.F, |
| 1694 |
|
packages_init_fixed.F and packages_write_pickup.F |
| 1695 |
|
(but skip packages_init_variables.F because of TAF issues). |
| 1696 |
|
- update contrib/*/atm_gray/ experiment. |
| 1697 |
|
o pkg/seaice (ITD code): |
| 1698 |
|
- simplify and fix the writing of pickup-files for ITD case |
| 1699 |
|
o pkg/seaice (ITD code): |
| 1700 |
|
- introduce floe size dependent lateral melt for ITD case; |
| 1701 |
|
- cleaning (avoid division by zero, change to f77 syntax, remove tabs) |
| 1702 |
|
- update seaice_itd experiment main output. |
| 1703 |
|
o pkg/thsice: |
| 1704 |
|
- remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and |
| 1705 |
|
declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F; |
| 1706 |
|
changed accordingly pkg/atm2d. |
| 1707 |
|
|
| 1708 |
|
checkpoint64g (2013/05/01) |
| 1709 |
|
o pkg/exf ALLOW_RUNOFTEMP |
| 1710 |
|
- if defined, river and glacier runoff temperature can be read-in from |
| 1711 |
|
runoftempfile; runoftempfile needs to have same format as runofffile |
| 1712 |
|
o pkg/thsice (& pkg/bulk_force): |
| 1713 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 1714 |
|
for energy content of Precip + RunOff & Evap (like with pkg/exf). |
| 1715 |
|
- change computation domain to always be the interior (without overlap). |
| 1716 |
|
- fix bug (wrong overlap) when using EXF and stressReduction > 0. |
| 1717 |
|
o verification/tutorial_global_oce_biogeo: |
| 1718 |
|
- add preliminary OpenAD setup (still has problems) |
| 1719 |
|
o pkg/seaice: |
| 1720 |
|
- turn some parameters for choosing the convergence criterion of |
| 1721 |
|
the inexact Newton method (JFNK) into runtime parameters for convenience |
| 1722 |
|
- clean up seaice_calc_viscosities.F: remove/retire two options for |
| 1723 |
|
SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes |
| 1724 |
|
the results of lab_sea/input because a division has been replaced by |
| 1725 |
|
a multiplication with the reciprocal (sumNorm) |
| 1726 |
|
- modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve |
| 1727 |
|
convergence of solver (changes results, of course), and to test some |
| 1728 |
|
new features |
| 1729 |
|
o model/src: |
| 1730 |
|
- remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call. |
| 1731 |
|
- remove unused forcing field "dQdT" and associated parameter "dQdTFile". |
| 1732 |
|
- move forcing adjustment (balancing surface forcing) in specific S/R |
| 1733 |
|
where might also be applied exchanges (if needed) to forcing arrays. |
| 1734 |
|
o pkg/shelfice: |
| 1735 |
|
- allow to specify the Ice-Shelf mass per unit area (instead of |
| 1736 |
|
shelficeLoadAnomaly) and do the conversion from one to the other |
| 1737 |
|
- move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA |
| 1738 |
|
to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and |
| 1739 |
|
(b) will be loaded in time (before calling INI_PRESSURE) in case it is |
| 1740 |
|
needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc |
| 1741 |
|
- update isomip experiment forward output (get machine truncation error |
| 1742 |
|
from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly) |
| 1743 |
|
o verification/offline_exf_seaice: |
| 1744 |
|
revise data.seaice in input.thermo and input_ad and update results accordingly |
| 1745 |
|
HO = 0.2, SEAICE_areaLossFormula = 2, |
| 1746 |
|
SEAICE_growMeltByConv = .TRUE., |
| 1747 |
|
SEAICE_doOpenWaterMelt = .TRUE., |
| 1748 |
|
Improve consistency with input.thsice and fix the spurious 500m ice corners |
| 1749 |
|
o verification/global_ocean.cs32x15: |
| 1750 |
|
- set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0., |
| 1751 |
|
in icedyn (thsice+seaice-dyn) test and update output. |
| 1752 |
|
o verification/offline_exf_seaice: |
| 1753 |
|
- adjust list of tested variables (with testreport) and update |
| 1754 |
|
standard test output with better slection of monitored fields. |
| 1755 |
|
o pkg/cd_code: |
| 1756 |
|
- swtich off Adams-Bashforth on the 1rst iteration. Update output of |
| 1757 |
|
experiment lab_sea.hb87 |
| 1758 |
|
o tools/genmake2: |
| 1759 |
|
- change default makedepend from the system default to tools/xmakedepend: |
| 1760 |
|
When no makedepend is specified, select tools/xmakedepend it the test pass, |
| 1761 |
|
otherwise select the system default (if exist and pass the test) or |
| 1762 |
|
try to build cyrus-makedepend ; stop if none of the 3 works. |
| 1763 |
|
o pkg/exf & pkg/thsice: |
| 1764 |
|
- In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account |
| 1765 |
|
for energy content of Precip + RunOff & Evap. Assumes: |
| 1766 |
|
1) Rain has same temp as Air. |
| 1767 |
|
2) Snow has no heat capacity (consistent with seaice & thsice pkgs) |
| 1768 |
|
3) Run-Off comes at the temp of surface water (with same Cp) |
| 1769 |
|
4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be |
| 1770 |
|
put directly into Latent Heat flux & should use water-vapor heat capacity. |
| 1771 |
|
5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent |
| 1772 |
|
with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL). |
| 1773 |
|
o pkg/seaice: simplify the use of CPP flags in JFNK-related files |
| 1774 |
|
(compile when SEAICE_ALLOW_JFNK is defined) |
| 1775 |
|
o pkg/thsice: |
| 1776 |
|
- fix oceanic flux diagnostics & timeave (left from new sequence of calls |
| 1777 |
|
implementation): move THSICE_AVE call after the advection (called directly |
| 1778 |
|
from thsice_do_advect.F). |
| 1779 |
|
o verification/global_ocean.90x40x15 and OpenAD: |
| 1780 |
|
New experiment for OpenAD is identical to the one in input_ad except that |
| 1781 |
|
multiDimAdvection=.FALSE., |
| 1782 |
|
There is still an issue with this. |
| 1783 |
|
o pkg/thsice: |
| 1784 |
|
- account for ice velocity (ocean relative velocity) in turbulent heat flux |
| 1785 |
|
at the base of the ice; update output of global_ocean.cs32x15 (icedyn) |
| 1786 |
|
and offline_exf_seaice (main test). |
| 1787 |
|
|
| 1788 |
|
checkpoint64f (2013/03/31) |
| 1789 |
|
o verification/OpenAD: |
| 1790 |
|
- new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran. |
| 1791 |
|
o verification/isomip, pkg/shelfice and OpenAD: |
| 1792 |
|
- add OpenAD setup to this exp and make shelfice package work with OpenAD |
| 1793 |
|
o verification/tutorial_global_oce_biogeo: |
| 1794 |
|
- update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h) |
| 1795 |
|
o verification/offline_exf_seaice: |
| 1796 |
|
- replace adjoint experiment (now similar to fwd input.thermo/ setup). |
| 1797 |
|
o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD: |
| 1798 |
|
- add OpenAD setup to this exp and make ptracers package work with OpenAD |
| 1799 |
|
o pkg/seaice/seaice_evp.F: |
| 1800 |
|
mask the asymmetric contribution of the ice-ocean stress (when |
| 1801 |
|
the turningAngle is non-zero) over open water to avoid stripes |
| 1802 |
|
in the EVP-solutions after many EVP-substeps. This does not change |
| 1803 |
|
the verification experiment (because turningAngle=0 in that experiment), |
| 1804 |
|
but will affect other EVP solutions with turningAngle.ne.0 |
| 1805 |
|
o verification, AD & TLM output: |
| 1806 |
|
- new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple |
| 1807 |
|
additions and multiplications which affect results at machine truncation |
| 1808 |
|
level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5, |
| 1809 |
|
lab_sea.noseaicedyn & offline_exf_seaice) and TLM output |
| 1810 |
|
(1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12 |
| 1811 |
|
digits of matching. |
| 1812 |
|
o pkg/seaice: |
| 1813 |
|
modify lsr-algorithm so that it vectorizes AND converges by using a |
| 1814 |
|
"zebra" method: split vector loop into two with step size 2; this |
| 1815 |
|
solves a general convergence problem for the JFNK solver on a vector |
| 1816 |
|
computer. It has the potential to even improve convergence for |
| 1817 |
|
non-vector machines, but it does change the results so it is turned |
| 1818 |
|
off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and |
| 1819 |
|
SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h |
| 1820 |
|
|
| 1821 |
|
checkpoint64e (2013/03/05) |
| 1822 |
|
o pkg/ecco and several verification experiments: |
| 1823 |
|
Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F |
| 1824 |
|
from ecco package, and revert to unified routine in model/src/ |
| 1825 |
|
Adjust verification experiments accordingly, especially gloal_oce_llc90 |
| 1826 |
|
Should conclude long-standing work by Gael to reconsile the_main_loop with |
| 1827 |
|
ECCO and will enable OpenAD's revolve loop in ECCO setup. |
| 1828 |
|
o pkg/generic_advdiff: |
| 1829 |
|
- implement compressible flow method for multi-dim advection (similar to |
| 1830 |
|
gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since |
| 1831 |
|
TAF generates many recomputations) to use it; no yet coded with implicit |
| 1832 |
|
vertical advection. |
| 1833 |
|
- change experiment advect_cs (new output) and advect_xy (same output) |
| 1834 |
|
to test compressible flow multi-dim advection. |
| 1835 |
|
o pkg/generic_advdiff: |
| 1836 |
|
- fix SOM advection for unusual cases (linear Free-Surf in r*, other |
| 1837 |
|
cases where linear Free-Surf is not @ k=1, e.g., useShelfIce) |
| 1838 |
|
o pkg/seaice: |
| 1839 |
|
- fix bug in the no-slip implementation in seaice_calc_strainrates.F, this |
| 1840 |
|
bug affects two verification experiments (lab_sea and lab_sea.hb87), |
| 1841 |
|
recover old (wrong) results by setting noSlipFac = 2. in |
| 1842 |
|
seaice_calc_strainrates.F; |
| 1843 |
|
- add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0 |
| 1844 |
|
- add runtime parameter SEAICE_JFNKepsilon for that finite difference |
| 1845 |
|
gradient in the Jacobian times vector operation (s/r seaice_jacvec) |
| 1846 |
|
- fix line search in seaice_jfnk.F (s/r seaice_jfnk_update) |
| 1847 |
|
o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code: |
| 1848 |
|
- new subroutines seaice_lsr_tridiagu/v |
| 1849 |
|
- introduce loop bounds i/jmin/max to be able to use a restricted |
| 1850 |
|
additive Schwarz method, but not used for now. |
| 1851 |
|
- rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS |
| 1852 |
|
- use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner |
| 1853 |
|
o OpenAD support |
| 1854 |
|
Reorganize S/R call for overall time-stepping loop to facilitate |
| 1855 |
|
OpenAD revolve loop replacement |
| 1856 |
|
(new S/R main_do_loop.F) |
| 1857 |
|
o model/src: |
| 1858 |
|
- add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3; |
| 1859 |
|
- pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R |
| 1860 |
|
ADAMS_BASHFORTH2. |
| 1861 |
|
o pkg/cheapaml: |
| 1862 |
|
- add new parameter (default=F, same as before) to disable full domain |
| 1863 |
|
(including land) periodicity in X & Y dir. |
| 1864 |
|
- new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of |
| 1865 |
|
prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer |
| 1866 |
|
into single S/R CHEAPAML_TIMESTEP. |
| 1867 |
|
|
| 1868 |
|
checkpoint64d (2013/02/17) |
| 1869 |
|
o pkg/monitor (angular momentum): |
| 1870 |
|
- do not add Eta contribution to the total AM if using rigid-lid; |
| 1871 |
|
- correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta). |
| 1872 |
|
- horizontal discretisation: compute Zonal wind contribution separately for |
| 1873 |
|
each component (instead of from cell centered averaged) and use the 4 |
| 1874 |
|
grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part. |
| 1875 |
|
- Check that AM is conserved with linear dynamics (momAdvection=F and linear |
| 1876 |
|
FreeSurf) if using vectorInvariant momentum. |
| 1877 |
|
o model/src (horizontal grid): |
| 1878 |
|
- move initialisation of all horizontal grid arrays to null value |
| 1879 |
|
from specific horizontal grid S/R to main S/R INI_GRID; |
| 1880 |
|
- add 2 new arrays to project model C-grid velocity on to zonal direction |
| 1881 |
|
(similar to AngleCosC & -AngleSinC but at U and V point location) and |
| 1882 |
|
compute them in S/R CALC_GRID_ANGLES. |
| 1883 |
|
o pkg/seaice: replace a hard coded parameter by a runtime parameter |
| 1884 |
|
SEAICE_JFNK_tolIter |
| 1885 |
|
o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in |
| 1886 |
|
preconditioner for JFNK (run LSR into the overlaps as far as possible, |
| 1887 |
|
i.e OLx/y-2, but overwrite the solution in the overlaps) |
| 1888 |
|
- extend loop range in seaice_calc_viscosity |
| 1889 |
|
- add new parameters SEAICE_OLx/y (default = OLx/y-2) |
| 1890 |
|
- add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs |
| 1891 |
|
- slightly modify loops in tridiagonal solver lsr-preconditioner |
| 1892 |
|
- by default remove the extra exchange in seaice_preconditioner with a |
| 1893 |
|
replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE |
| 1894 |
|
- modify offline_exf_seaice so that old results without RAS are reproduced |
| 1895 |
|
for output.dyn_jfnk.txt |
| 1896 |
|
in seaice_fgmres.F (unrelated to RAS) |
| 1897 |
|
- add a cpp-flag option for a re-ordered mapping (potentially more |
| 1898 |
|
efficient), but because this changes the results, turn it off by |
| 1899 |
|
default |
| 1900 |
|
- replace the save statement by local common blocks |
| 1901 |
|
o utils/matlab: |
| 1902 |
|
- fix tile-offset in rdmnc.m when output was produced using EXCH2. |
| 1903 |
|
- update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab) |
| 1904 |
|
instead of local script "load_cs.m". |
| 1905 |
|
o pkg/seaice: |
| 1906 |
|
- fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected |
| 1907 |
|
to the scalarProductMetric and the unrolling. By chance this does not |
| 1908 |
|
change the verification experiment, because of the particular domain |
| 1909 |
|
decomposition |
| 1910 |
|
o pkg/diagnostics: |
| 1911 |
|
- change default missing_value from UNSET_RL to -999. |
| 1912 |
|
o pkg/layers: improve vectorization of layers_fluxcalc.F |
| 1913 |
|
- step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu |
| 1914 |
|
time spent in this routine by more than a factor of 3 on an NEC-SX8 |
| 1915 |
|
- step 2: replace search algorithm by a bisection algorithm found in |
| 1916 |
|
Press et al. Numerical Recipes in Fortran. This algorithm can be |
| 1917 |
|
vectorized and finds the correct bin in approx. log2(Nlayers) steps. |
| 1918 |
|
For now, use this algorithm only for TARGET_NEC_SX defined. |
| 1919 |
|
- moved the search algorithm into a separate subroutine, that is kept |
| 1920 |
|
within the same file for automatic inlining. |
| 1921 |
|
- modified catching potential errors |
| 1922 |
|
o pkg/ecco: |
| 1923 |
|
- add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY. |
| 1924 |
|
o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : |
| 1925 |
|
- modifications for ALLOW_GENTIM2D_CONTROL |
| 1926 |
|
-- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes. |
| 1927 |
|
-- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid ) |
| 1928 |
|
-- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc |
| 1929 |
|
-- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F |
| 1930 |
|
o model/src: |
| 1931 |
|
- account for moist thermodynamics in (dry) potential temperature equation; |
| 1932 |
|
update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev) |
| 1933 |
|
and cpl_aim+ocn. |
| 1934 |
|
- also switch to standard compiler (gfortran, was using ifort previously) |
| 1935 |
|
for fizhi-cs experiments reference output. |
| 1936 |
|
o pkg/ctrl: |
| 1937 |
|
- 1st step toward generic time-varying control variable (2D) via CPP option |
| 1938 |
|
ALLOW_GENTIM2D_CONTROL |
| 1939 |
|
- note new namelist ctrl_nml_genarr in data.ctrl |
| 1940 |
|
o verification/global_ocean.cs32x15: |
| 1941 |
|
- switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new |
| 1942 |
|
thsice calling sequence and update "output.icedyn.txt" output file. |
| 1943 |
|
o pkg/ptracers: |
| 1944 |
|
- from Ryan A.: code to allow to restart a tracer at regular time interval |
| 1945 |
|
specifying a reset frequency and a reset-phase (for each tracers). |
| 1946 |
|
o pkg/thsice: |
| 1947 |
|
- implement new sequence of calls for thsice+seaice: |
| 1948 |
|
previously: ice-Dyn,ice-Advect,ice-Thermo(thsice) |
| 1949 |
|
new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect |
| 1950 |
|
- allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE" |
| 1951 |
|
in CPP_OPTIONS.h) to recover old sequence; |
| 1952 |
|
- update diagnostics for Intermediate State thsice diagnostics: now filled |
| 1953 |
|
just before advection (instead of just after advection in old sequence); |
| 1954 |
|
- update output of experiment offline_exf_seaice (standard test); |
| 1955 |
|
- in global_ocean.cs32x15 exp., postpone output.icedyn.txt update |
| 1956 |
|
by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h |
| 1957 |
|
o pkg/aim_v23: |
| 1958 |
|
- use tiled array for aim_CO2 and surface wind speed for export to coupler; |
| 1959 |
|
- use standard pkg/mdsio routines to read & write CO2 pickup file; |
| 1960 |
|
- in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F; |
| 1961 |
|
- Implement new sequence of calls for seaice advection (with thsice and |
| 1962 |
|
seaice diffusion): do ice advection after ice-Thermodynamic (previously |
| 1963 |
|
was done before); change aim_do_physics.F (split the bi,bj loops block); |
| 1964 |
|
- use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence; |
| 1965 |
|
o pkg/thsice: |
| 1966 |
|
- add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case |
| 1967 |
|
where just seaice diffusion is used without seaice-dynamics. |
| 1968 |
|
|
| 1969 |
|
checkpoint64c (2013/01/18) |
| 1970 |
|
o pkg/seaice: |
| 1971 |
|
- add a parameter JFNKres_tFac that can replace JFNKres_t |
| 1972 |
|
(= JFNKres_tFac*JFNKresidual before JFNK solver) |
| 1973 |
|
- add a line search option to the JFNK solver |
| 1974 |
|
- move update of u/vIce and computation of initial residual into a separate |
| 1975 |
|
routine (same file); makes the code a little easier to read (?) |
| 1976 |
|
- the line search requires computation of the residual and for some reason |
| 1977 |
|
I cannot do the update of u/vIce at the beginning of the Newton loop |
| 1978 |
|
without changing the results, so we move computation of the new residual |
| 1979 |
|
also to the end of the Newton loop, even without the line search |
| 1980 |
|
o pkg/mdsio: |
| 1981 |
|
- write missing value (corresponding to undefined array value) to meta files; |
| 1982 |
|
skip this if missing value is one (UNSET_RL would be a better value for the |
| 1983 |
|
case of undefined missing value but it's current the default missing-value); |
| 1984 |
|
Also update mdsio_read_meta.F (reading timeInterval & missing-value). |
| 1985 |
|
o pkg/exf & thsice: |
| 1986 |
|
- for diagnostics purpose, fill-up and update Qsw array (+ fill the |
| 1987 |
|
diagnostics) even when SHORTWAVE_HEATING is #undef; |
| 1988 |
|
o verification/cfc_example: |
| 1989 |
|
- turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to |
| 1990 |
|
illustrate how to use it). |
| 1991 |
|
o verification/offline_exf_seaice: |
| 1992 |
|
in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing |
| 1993 |
|
files to only one time-record. |
| 1994 |
|
in input.thermo: narrow the 2 bands of low initial ice-concentration near |
| 1995 |
|
N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for |
| 1996 |
|
snapshot output; same mcPheePiston value as in thsice with |
| 1997 |
|
surf-current=0.2m/s. |
| 1998 |
|
in input.thsice: similar set-up as in input.thermo (channel with same seaice |
| 1999 |
|
initial conditions). |
| 2000 |
|
o verification/cfc_example: |
| 2001 |
|
- update file "data" with more standard choice (default rotationPeriod, |
| 2002 |
|
exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F, |
| 2003 |
|
set deltaTFreeSurf to deltaTtracer) and update the output. |
| 2004 |
|
o pkg/layers: |
| 2005 |
|
- fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC; |
| 2006 |
|
- ensure that "layers_bolus" is switched to False when useGMRedi=False. |
| 2007 |
|
o verification/offline_exf_seaice: |
| 2008 |
|
- set all {field}period to zero for constant-in-time forcing (not tested |
| 2009 |
|
anywhere else). |
| 2010 |
|
o verification/offline_exf_seaice: |
| 2011 |
|
- dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice; |
| 2012 |
|
- dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice. |
| 2013 |
|
o model/src: |
| 2014 |
|
- implement Finite-Volume method for (hydrostatic) presure gradient |
| 2015 |
|
from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate. |
| 2016 |
|
o pkg/seaice: implement EVP* by Lemieux et al. (2012). |
| 2017 |
|
- In order to be compatible with the default EVP code, this requires changing |
| 2018 |
|
the EVP code around a little; and because any small change immediately |
| 2019 |
|
breaks the lab_sea.hb87 verification experiment, the reference output is |
| 2020 |
|
updated two times (each time the remaining aggrement was only 2 digits): |
| 2021 |
|
- after replacing 1/dt by 1*recip_dt with a precomputed recip_dt |
| 2022 |
|
- after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt |
| 2023 |
|
The adjoint test lab_sea.evp also needed to be updated. |
| 2024 |
|
- Turn on EVP* by setting SEAICE_deltaTevp as before, and setting |
| 2025 |
|
SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be |
| 2026 |
|
a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps |
| 2027 |
|
explicitly with SEAICEnEVPstarSteps (thereby overriding the default of |
| 2028 |
|
INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately |
| 2029 |
|
kept obscure, because I need to test it a little more. |
| 2030 |
|
o pkg/cheapaml: |
| 2031 |
|
- fix few incorrect type (_RL/_RS) in subroutine calls. |
| 2032 |
|
o pkg/seaice: |
| 2033 |
|
- new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays |
| 2034 |
|
to _RL vector; this fixes JFNK code when compiling with "-use_r4" option. |
| 2035 |
|
o model/src: |
| 2036 |
|
- add a warning if using select_rStar=2 with nonlinFreeSurf <> 4; |
| 2037 |
|
change (in input_ad*/data) select_rStar from 2 to 1 for AD verification |
| 2038 |
|
experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output) |
| 2039 |
|
o pkg/cheapaml: |
| 2040 |
|
- replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and |
| 2041 |
|
update output of experiment cheapAML_box. |
| 2042 |
|
- store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity, |
| 2043 |
|
and set them only in one place (cheapaml_readparms.F). |
| 2044 |
|
- replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI" |
| 2045 |
|
- remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms) |
| 2046 |
|
and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia). |
| 2047 |
|
o model/src/the_main_loop.F: |
| 2048 |
|
- fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION. |
| 2049 |
|
o pkg/seaice: |
| 2050 |
|
- remove legacy branch code. |
| 2051 |
|
- retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly. |
| 2052 |
|
o verification/*/code*/SEAICE_OPTIONS.h: |
| 2053 |
|
- remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY, |
| 2054 |
|
SEAICE_CAP_HEFF). |
| 2055 |
|
o pkg/cheapaml: |
| 2056 |
|
- use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time |
| 2057 |
|
to load new forcing fields. |
| 2058 |
|
- add missing "_d 0" where it's needed; + some editing (improve indentation). |
| 2059 |
|
- remove switch to "-r8" compiler option (no longer needed) in verification |
| 2060 |
|
cheapAML_box, keep same output (small trucation error differences). |
| 2061 |
|
o verification/offline_exf_seaice: |
| 2062 |
|
- add thermodynamics only test. |
| 2063 |
|
o verification/cheapAML_box: |
| 2064 |
|
- split the domain in 8 (2x4) tiles; add MPI and multi-threaded test; |
| 2065 |
|
keep same output (same 14 digits for cg2d). |
| 2066 |
|
- switch on "-r8" compiler option (some numerical values are missing |
| 2067 |
|
the "_d 0") and update output (only 6 digits for cg2d were preserved). |
| 2068 |
|
|
| 2069 |
|
checkpoint64b (2012/12/24) |
| 2070 |
|
o pkg/cheapaml: |
| 2071 |
|
- remove un-used variables (Qnet,EmPmR) from pickup files. |
| 2072 |
|
- store tendency of advected variables into cheapaml pickup file |
| 2073 |
|
and fix the AB-2 restart. |
| 2074 |
|
o verification/offline_exf_seaice and lab_sea adjoint: |
| 2075 |
|
- switch to new code (#undef SEAICE_GROWTH_LEGACY). |
| 2076 |
|
- switch to 4 time steps in offline, consistent with lab_sea. |
| 2077 |
|
- match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice. |
| 2078 |
|
- update results after change of experiment seaice. |
| 2079 |
|
o pkg/seaice: |
| 2080 |
|
- remove option SEAICE_MULTICATEGORY; has been replaced with run-time |
| 2081 |
|
parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is |
| 2082 |
|
still defined since SEAICE_multDim needs to be set to MULTDIM value (from |
| 2083 |
|
SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default. |
| 2084 |
|
o model/src: |
| 2085 |
|
- add run-time parameter to select CG2D solver minimum-residual solution |
| 2086 |
|
(in case of a poor convergence). |
| 2087 |
|
o pkg/seaice/seaice_lsr.F |
| 2088 |
|
- move calculation of matrix coefficients into new |
| 2089 |
|
S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same |
| 2090 |
|
file; the main purpose of this change is to be able to reuse the code |
| 2091 |
|
in S/R SEAICE_PRECONDITIONER |
| 2092 |
|
- modify the computation of the residual so that the mass of sea-ice |
| 2093 |
|
is not used twice; this simplifies the calculations, but since |
| 2094 |
|
the residual is never used except when LSR_mixIniGuess.ge.4---and this is |
| 2095 |
|
not tested in testreport---this does not affect the testreport results. |
| 2096 |
|
o verification/seaice_obcs: |
| 2097 |
|
- disable SEAICE_GROWTH_LEGACY; reset input files to match those of |
| 2098 |
|
verification/lab_sea/input.salt_plume; changes results/output.txt* |
| 2099 |
|
o model/src: |
| 2100 |
|
- adapt quasi-hydrostatic formulation to work with p or p* coordinate. |
| 2101 |
|
o pkg/seaice: |
| 2102 |
|
- improve description of parameters in seaice_fgmres.F and start |
| 2103 |
|
cleaning up the code |
| 2104 |
|
- change name of SCALPROD to SEAICE_SCALPROD and modify meaning of |
| 2105 |
|
second argument |
| 2106 |
|
- add a metric based on grid cell area to SEAICE_SCALPROD; update |
| 2107 |
|
results of offline_exf_seaice.dyn_jfnk |
| 2108 |
|
- compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD |
| 2109 |
|
o pkg/aim_v23: |
| 2110 |
|
- fix an other bug in dissipation heating (grid-cell area was missing). |
| 2111 |
|
o model/src + pkg/seaice: |
| 2112 |
|
- add global (multi-tile) linear solver for pair of tri-diagonal system |
| 2113 |
|
along X and Y lines, respectively for U and V component. |
| 2114 |
|
Note: 1) MPI and cube-exchange not yet coded. |
| 2115 |
|
2) probably not accurate for poorly conditioned / large size problem. |
| 2116 |
|
- add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver; |
| 2117 |
|
default: not compiled and not used. |
| 2118 |
|
o pkg/seaice: |
| 2119 |
|
- first attempt at a multi-threaded fgmres solver for the JFNK solver: |
| 2120 |
|
introduce bi/bj loops and use global_sum_tile_rl instead of |
| 2121 |
|
mpi_allreduce in seaice_fgmres.F |
| 2122 |
|
- improve diagnostics output for fgmres solver (seaice_fgmres.F) |
| 2123 |
|
- replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F) |
| 2124 |
|
- add a verification experiment for JFNK in offline_exf_seaice |
| 2125 |
|
o verification: |
| 2126 |
|
- change (for now, only fwd test) offline_exf_seaice experiment: |
| 2127 |
|
use a re-entrant channel with idealized coastline (trapezoidal shape) |
| 2128 |
|
at southern boundary to explore seaice dynamics and thermodynamics |
| 2129 |
|
with simple forcing. Main set-up has dynamics+thermo and SST relaxation; |
| 2130 |
|
secondary test (input.thsice) use thermodynamics only with SST relaxation. |
| 2131 |
|
- add seaice-dynamics only secondary test using LSR and pkg/thsice advection. |
| 2132 |
|
o pkg/exf: |
| 2133 |
|
- disable "sstExtrapol" when Nr=1 |
| 2134 |
|
o verification: |
| 2135 |
|
- add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble) |
| 2136 |
|
to test pkg/cheapaml. |
| 2137 |
|
o pkg/aim_v23 & pkg/shap_filt: |
| 2138 |
|
- fix dissipation heating (erroneous gravity multiplication factor). |
| 2139 |
|
o pkg/seaice: |
| 2140 |
|
- remove unused field pressPre from jfnk solver |
| 2141 |
|
- rename two subroutines in seaice_preconditioner.F |
| 2142 |
|
o eesupp/src: |
| 2143 |
|
- S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...) |
| 2144 |
|
o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again |
| 2145 |
|
- remove wrong parts of the rhs and the lhs (were in there |
| 2146 |
|
because I did not understand the concept of this preconditioner) |
| 2147 |
|
- add an exchange between u- and v-sweep. This increases communication |
| 2148 |
|
by a factor of two but improves the convergence of jfnk. Ideally, |
| 2149 |
|
one would like the u- and v-sweep to be independent. So far within |
| 2150 |
|
undocumented ifdefs |
| 2151 |
|
- reorganize the extra computations for printing the residuals |
| 2152 |
|
o tools/genmake2: |
| 2153 |
|
- comment out the "mpif.h" include in NetCDF test programm (for MPI built) |
| 2154 |
|
since it's not necessary (and was preventing to use MNC in some cases). |
| 2155 |
|
|
| 2156 |
|
checkpoint64a (2012/11/16) |
| 2157 |
|
o pkg/autodiff: |
| 2158 |
|
- improve pkg-internal logical parameter switch (inAd/inFwd mode) so that |
| 2159 |
|
autodiff_readparms.F no longer depends on calling order (within |
| 2160 |
|
packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h): |
| 2161 |
|
rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd |
| 2162 |
|
and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd. |
| 2163 |
|
o pkg/obcs: |
| 2164 |
|
- adding tidal velocity forcing capability to obcs |
| 2165 |
|
for usage example, see verification/seaice_obcs/input.tides |
| 2166 |
|
o pkg/seaice: |
| 2167 |
|
- turn the LSR-relaxation parameters WFAU/V into runtime parameters |
| 2168 |
|
SEAICE_LSRrelaxU/V |
| 2169 |
|
- introduce runtime parameter SEAICEetaZmethod (=0 by default) |
| 2170 |
|
o pkg/aim_v23: |
| 2171 |
|
- implement heating from friction (bottom friction and stratospheric drag). |
| 2172 |
|
o pkg/shap_filt: |
| 2173 |
|
- fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from |
| 2174 |
|
dissipation but only for Shap_funct=2, active when addFrictionHeating=T. |
| 2175 |
|
o model/src: |
| 2176 |
|
- move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in |
| 2177 |
|
time-constant addMass field from file (addMassFile); |
| 2178 |
|
- support for heating due to friction (and Kinetic Energy dissipation): |
| 2179 |
|
add option, run-time switch and 3-D field array + support code ; each pkg |
| 2180 |
|
or S/R can add heating contribution (if there is a sink of KE); the sum is |
| 2181 |
|
accounted for as a Temperature tendency term (EXTERNAL_FORCING_T). |
| 2182 |
|
o pkg/seaice: |
| 2183 |
|
- complete merge of ITD code into seaice_growth.F |
| 2184 |
|
from MITgcm_contrib/torge/itd/code/ |
| 2185 |
|
no verification so far, but Torge Martin tested |
| 2186 |
|
"1-D test case and Beaufort set up; |
| 2187 |
|
deliver okay results after 1 model year." |
| 2188 |
|
- complete merge of SEAICE_SIZE.h into all relevant routines |
| 2189 |
|
- move computation of eta at Z-points into calc_viscosities |
| 2190 |
|
+ introduce global field etaZ |
| 2191 |
|
+ add different methods for computing etaZ, for now the old |
| 2192 |
|
method (simple averages of eta to Z-points) is hardwired |
| 2193 |
|
+ replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, |
| 2194 |
|
seaice_preconditioner |
| 2195 |
|
- simplify computations for SEAICE_ZETA_SMOOTHREG |
| 2196 |
|
- seaice_preconditioner: |
| 2197 |
|
+ replace one remaining press by pressLoc (mistake) |
| 2198 |
|
+ adjust printing of residuals |
| 2199 |
|
- improve I/O of diagnostics of JFNK in seaice_jfnk.F: |
| 2200 |
|
+ add (SEAICE.h) and rename some counters (initiliased in |
| 2201 |
|
seaice_init_fixed.F) |
| 2202 |
|
+ add _BEGIN/END_MASTER (myThid) around print statements |
| 2203 |
|
+ print total number of iterations and failures over SEAICE_monFreq |
| 2204 |
|
interval to STDOUT |
| 2205 |
|
- move control over output-messages by fgmres to seaice_jfnk to save |
| 2206 |
|
some operations |
| 2207 |
|
- move resetting initial guess for fgmres outside of seaice_fgmres_driver |
| 2208 |
|
in order to make restarts with sol .ne. zero (fgmres with restarts) |
| 2209 |
|
(seaice_jfnk.F, seaice_fgmres.F) |
| 2210 |
|
- seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes |
| 2211 |
|
a serious convergence problem when open boundaries are involved |
| 2212 |
|
o pkg/ggl90: fix computation of control volumes for the case of |
| 2213 |
|
ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes |
| 2214 |
|
up half a grid cell from C-centered to W-centered (pointed out by C. Eden) |
| 2215 |
|
o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC |
| 2216 |
|
o pkg/autodiff |
| 2217 |
|
- Add inAdMode switch for SEAICEuseDYNAMICS: |
| 2218 |
|
SEAICEuseDYNAMICSinAdMode |
| 2219 |
|
(extend logic in ADAUTODIFF_INADMODE_SET) |
| 2220 |
|
o pkg/seaice |
| 2221 |
|
- Step 1 of merging ice-thickness distribution (ITD) code from |
| 2222 |
|
MITgcm_contrib/torge/itd/ (author: Torge Martin) |
| 2223 |
|
The code implements concept laid out in Thorndike et al. (1975); |
| 2224 |
|
code is enabled via CPP flag SEAICE_ITD |
| 2225 |
|
nITD (in SEAICE_SIZE.h) defines number of ice thickness categories; |
| 2226 |
|
code is not complete yet!! |
| 2227 |
|
- SEAICE_SIZE.h now included in almost all seaice routines |
| 2228 |
|
o verification (using seaice): |
| 2229 |
|
- switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp. |
| 2230 |
|
global_ocean.cs32x15.seaice ; update results. |
| 2231 |
|
- compile B-grid dynamics in FW test exp 1D_ocean_ice_column ; |
| 2232 |
|
- compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp |
| 2233 |
|
offline_exf_seaice (previously compiling B-grid). |
| 2234 |
|
o pkg/exf: |
| 2235 |
|
- fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow |
| 2236 |
|
to specify neither just 1 comp of wind or wind-stress, nor no surface momentum |
| 2237 |
|
forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind. |
| 2238 |
|
o pkg/layers (adjust changes from Sept 19): |
| 2239 |
|
- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
| 2240 |
|
this allows to remove "layers_maxNum" dimension from all layers arrays. |
| 2241 |
|
o pkg/layers (adjust changes from Sept 19): |
| 2242 |
|
- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
| 2243 |
|
- snap-shot extended to all type of layers (not just the 1rst type); |
| 2244 |
|
- remove layers variables when corresponding CPP option is undef. |
| 2245 |
|
o pkg/layers: |
| 2246 |
|
- rename pkg/layers variable and add new output (layer exist & un-weighted |
| 2247 |
|
velocity in layer) |
| 2248 |
|
o pkg/seaice: |
| 2249 |
|
- simplify (?) ocean-drag coefficent computations by using |
| 2250 |
|
the same routine in all three solvers (saves some code lines) |
| 2251 |
|
- remove global fields DRAGA and DRAGS from C-grid code and |
| 2252 |
|
declare them locally in lsr.F (the only place where they are |
| 2253 |
|
still used) |
| 2254 |
|
- update AD output of lab_sea.evp (very sensitive anyway). |
| 2255 |
|
o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
| 2256 |
|
(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
| 2257 |
|
and SEAICEuseJFNK=.true. A few things to note: |
| 2258 |
|
- involves a FGMRES, that is parallel but very inefficient, |
| 2259 |
|
because of many scalar products (global sums) in the Gram-Schmidt |
| 2260 |
|
orthogonalization method. Needs to be replaced. Original code |
| 2261 |
|
from J.-F. Lemieux |
| 2262 |
|
- preconditioner for FGMRES is a stripped down version of LSOR |
| 2263 |
|
- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
| 2264 |
|
preconditioner. For the preconditioner, the default is set to 10. |
| 2265 |
|
- Jacobian times vector is computed with finite differences |
| 2266 |
|
- marginally related to JFNK-solver: add a smooth regularization for |
| 2267 |
|
zeta with tanh that will improve convergence (Lemieux and Tremblay, |
| 2268 |
|
2009) for any implicit solver (not implemented for EVP because EVP |
| 2269 |
|
does not need this regularization in the first place). Define |
| 2270 |
|
SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
| 2271 |
|
o eesupp/src: |
| 2272 |
|
- check in genmake2 that intrinsic S/R flush is available. |
| 2273 |
|
- add S/R to flush IO unit (if intrinsic S/R flush is available) |
| 2274 |
|
- flush standard & error msg unit before MPI termination |
| 2275 |
|
- if debugMode, flush IO unit after printing msg |
| 2276 |
|
o pkg/ctrl: |
| 2277 |
|
- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
| 2278 |
|
to ctrl_set_unpack_xyz. |
| 2279 |
|
|
| 2280 |
|
checkpoint64 (2012/10/09) |
| 2281 |
|
o pkg/shelfice |
| 2282 |
|
- in mom_fluxform.F, mom_vecinv.F: |
| 2283 |
|
CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
| 2284 |
|
Bug fix KappaRU -> KappaRV |
| 2285 |
|
does not change verification/isomip but may change other setups |
| 2286 |
|
(presumably constant KappaRU=KappaRV) |
| 2287 |
|
- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
| 2288 |
|
o pkg/obcs: |
| 2289 |
|
- fixed some indexing bugs in obcs_seaice_sponge.F |
| 2290 |
|
- added obcs relaxation subroutines for HSALT and HSNOW |
| 2291 |
|
- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
| 2292 |
|
o pkg/seaice: |
| 2293 |
|
- add "multicategory" parameterization for snow in analogy to ice, |
| 2294 |
|
default is off for now. |
| 2295 |
|
o pkg/obcs: |
| 2296 |
|
- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
| 2297 |
|
see verification/seaice_obcs/input.seaiceSponge for example application. |
| 2298 |
|
- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
| 2299 |
|
index setting by master-thread. This fix multi-threads Pb in previous modifs. |
| 2300 |
|
o pkg/layers : |
| 2301 |
|
- add diagnostics to pkg/layers |
| 2302 |
|
- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
| 2303 |
|
(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
| 2304 |
|
o pkg/generic_advdiff/gad_implicit_r.F : |
| 2305 |
|
- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
| 2306 |
|
o pkg/seaice/seaice_growth.F: |
| 2307 |
|
- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
| 2308 |
|
o pkg/obcs: |
| 2309 |
|
- change default setting of OBCS_UVICE_OLD from defined to undef; |
| 2310 |
|
- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
| 2311 |
|
in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
| 2312 |
|
- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
| 2313 |
|
- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
| 2314 |
|
with Southern & Western OB at a tile edge (at least in a simple set-up). |
| 2315 |
|
o pkg/obcs: |
| 2316 |
|
- change settings of OB index in case OB coincides with tile edge (shared by |
| 2317 |
|
2 tiles), so that common OB location is registered by both tiles (instead of |
| 2318 |
|
only 1). However, for Southern and Western OB, index value = 0 is not |
| 2319 |
|
recognized as valid OB index (=default null value) and needs to be fixed. |
| 2320 |
|
- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
| 2321 |
|
- new parameter "OB_indexNone" for null index value (for now, still zero) |
| 2322 |
|
to replace hard-coded null index value of zero. |
| 2323 |
|
o pkg/exch2: |
| 2324 |
|
- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
| 2325 |
|
always check buffer-size (but outside the loop); move checking for valid |
| 2326 |
|
index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
| 2327 |
|
print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
| 2328 |
|
o pkg/ctrl (pack & unpack): |
| 2329 |
|
- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
| 2330 |
|
(locally defined) for different variables (+ remove the variable-specific |
| 2331 |
|
file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
| 2332 |
|
(to be extended to other local file names in ctrl.h). |
| 2333 |
|
o pkg/flt: |
| 2334 |
|
- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
| 2335 |
|
o pkg/mdsio: |
| 2336 |
|
- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
| 2337 |
|
o tools/genmake2: |
| 2338 |
|
- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
| 2339 |
|
(added by Alistair in version 1.51 for building without make depend); |
| 2340 |
|
- remove Header files list (H_SRC_FILES) from the dependence of targets |
| 2341 |
|
ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
| 2342 |
|
place in version 1.23): this save going through staf when unrelated header |
| 2343 |
|
file has been modified. |
| 2344 |
|
Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
| 2345 |
|
"make depend" step, still need to do "make links" before "make adtaf". |
| 2346 |
|
o eesupp/src (+ few pkg src files) & genmake2: |
| 2347 |
|
- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
| 2348 |
|
- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
| 2349 |
|
- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
| 2350 |
|
upper/lower case ; account for space between "#" and undef/define) |
| 2351 |
|
o pkg/flt (with exch2): |
| 2352 |
|
- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
| 2353 |
|
- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
| 2354 |
|
|
| 2355 |
|
checkpoint63s (2012/09/05) |
| 2356 |
|
o pkg/ecco: |
| 2357 |
|
- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
| 2358 |
|
- add more relevant #ifdef ALLOW_SMOOTH ones. |
| 2359 |
|
- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
| 2360 |
|
o pkg/ctrl: |
| 2361 |
|
- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
| 2362 |
|
ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
| 2363 |
|
- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
| 2364 |
|
doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
| 2365 |
|
ctrlSmoothCorrel3D (new). |
| 2366 |
|
The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
| 2367 |
|
- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
| 2368 |
|
- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
| 2369 |
|
controls when useAtmWind, and vice versa. |
| 2370 |
|
- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
| 2371 |
|
- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
| 2372 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
| 2373 |
|
- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
| 2374 |
|
#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
| 2375 |
|
- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
| 2376 |
|
replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
| 2377 |
|
o pkg/smooth: |
| 2378 |
|
- remove un-necessary includes. |
| 2379 |
|
- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
| 2380 |
|
Those CPP options were never defined, and not necessary. |
| 2381 |
|
o model/src: |
| 2382 |
|
- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
| 2383 |
|
- standard treatment of useSMOOTH. |
| 2384 |
|
o pkg/autodiff: |
| 2385 |
|
- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
| 2386 |
|
useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
| 2387 |
|
o pkg/exch2: |
| 2388 |
|
- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
| 2389 |
|
+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
| 2390 |
|
- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
| 2391 |
|
and tiles to process mapping. |
| 2392 |
|
- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
| 2393 |
|
moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
| 2394 |
|
rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
| 2395 |
|
from w2_eeboot.F to w2_readparms.F. |
| 2396 |
|
o eesupp/src: |
| 2397 |
|
- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
| 2398 |
|
ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
| 2399 |
|
also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
| 2400 |
|
- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
| 2401 |
|
is defined (remove condition on usingMPI) to match cases where MPI_INIT |
| 2402 |
|
has been called. |
| 2403 |
|
- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
| 2404 |
|
- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
| 2405 |
|
(so that on 1 proc, get same myPid independently of usingMPI) |
| 2406 |
|
- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
| 2407 |
|
useCubedSphereExchange with EXCH-1 (safer). |
| 2408 |
|
- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
| 2409 |
|
o pkg/ggl90: |
| 2410 |
|
- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
| 2411 |
|
used in ALLOW_GGL90_SMOOTH code. |
| 2412 |
|
o pkg/flt: |
| 2413 |
|
- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
| 2414 |
|
floats at the Southern end of the domain). |
| 2415 |
|
o eesupp/inc: |
| 2416 |
|
- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
| 2417 |
|
but not used (and not to be used) anywhere, just for documentation. |
| 2418 |
|
o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
| 2419 |
|
- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
| 2420 |
|
a) can damage previously written records in any other multi-record files. |
| 2421 |
|
b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
| 2422 |
|
o tools/genmake2: |
| 2423 |
|
- define variable MAKE within Makefile and use it in place of 'make'; |
| 2424 |
|
- update AD_CONFIG.h (if needed) before building any of the executable |
| 2425 |
|
(forward, adjoint or tangent-lin); this involves a 2nd invocation of make; |
| 2426 |
|
and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h; |
| 2427 |
|
- always print usual warning comment 'this file is automatically generated' |
| 2428 |
|
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
| 2429 |
|
o pkg/cheapaml: |
| 2430 |
|
- updated to correspond to the code used in accepted paper (Nico Wienders). |
| 2431 |
|
o pkg/exf: |
| 2432 |
|
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
| 2433 |
|
ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F) |
| 2434 |
|
and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h). |
| 2435 |
|
o pkg/exf, autodiff, ctrl, ecco and seaice: |
| 2436 |
|
remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones. |
| 2437 |
|
o pkg/ctrl, ecco: |
| 2438 |
|
allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL. |
| 2439 |
|
Depending on useAtmWind, one is inactive, and the other is active (see |
| 2440 |
|
exf_getffields.F/exf_getsurfacefluxes.F). |
| 2441 |
|
o tools/genmake2: |
| 2442 |
|
- improve error msg when failing in 2nd test of check_for_broken_Ff |
| 2443 |
|
- fix option '-makefile' short-name (-mf according to genmake2 -help) |
| 2444 |
|
- source local config file "genmake_local" just after processing the genmake2 |
| 2445 |
|
command arguments (previously done before processing arg). |
| 2446 |
|
o pkg/grdchk: |
| 2447 |
|
- add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call |
| 2448 |
|
to this routine from cost_final has been dropped in g_cost_final) |
| 2449 |
|
- improve printed information (more explicit msg, no longer using "print *," |
| 2450 |
|
fix fcpertminus printed value). |
| 2451 |
|
o model/src: |
| 2452 |
|
- move call to COST_INIT_VARIA out of packages_init_variables.F directly |
| 2453 |
|
into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES): |
| 2454 |
|
this prevents getting cost-funct reset in adinitialise_varia recomputations. |
| 2455 |
|
o pkg/dic: |
| 2456 |
|
- move initialisation of "freefe" array from from dic_biotic_forcing.F to |
| 2457 |
|
fe_chem.F: this prevents TAF from dropping this initialisation in TLM code. |
| 2458 |
|
o pkg/grdchk: |
| 2459 |
|
- grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid ) |
| 2460 |
|
- grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0 |
| 2461 |
|
o pkg/autodiff/ctrl/grdchk : |
| 2462 |
|
- attempt to sort out what works and what does not, |
| 2463 |
|
with regard to I/O, and to warn/stop accordingly. |
| 2464 |
|
o pkg/grdchk: |
| 2465 |
|
- attempt to fix grdchk in the case of useSingleCpuIO. |
| 2466 |
|
- "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )" |
| 2467 |
|
statements were moved from grdchk_main.F and into |
| 2468 |
|
grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F. |
| 2469 |
|
- a global sum is applied to record numbers icvrec/layer |
| 2470 |
|
out of grdchk_loc so that they be passed to I/O routines. |
| 2471 |
|
o pkg/smooth: |
| 2472 |
|
- fix recomputation that appeared with nlfs : use smooth_recip_hFacC, |
| 2473 |
|
smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case. |
| 2474 |
|
o verification/testreport: |
| 2475 |
|
- add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive); |
| 2476 |
|
- can also use compressed (gzip) reference output file; |
| 2477 |
|
- change format (in pkg/grdchk) of TLM output (+ add forward gradient) |
| 2478 |
|
to be easier to collect by testreport. |
| 2479 |
|
- update existing TLM output (half out-of-date by more than 3 yrs). |
| 2480 |
|
- report NETCDF & LAPACK settings (from genmake2) in output dir. |
| 2481 |
|
- report run-time in each individual summary (previously only for AD test); |
| 2482 |
|
for TLM test, add also TAF version. |
| 2483 |
|
- add daily TLM test on (old) aces cluster + weekly test on baudelaire. |
| 2484 |
|
|
| 2485 |
|
checkpoint63r (2012/08/15) |
| 2486 |
|
o tools/genmake2: |
| 2487 |
|
- fix Makefile for target ftlall (+ update files to clean after make ftlall) |
| 2488 |
|
o pkg/ecco/ecco_cost_final.F : |
| 2489 |
|
- fix fc print statements (to stdout and costfunction0000) so |
| 2490 |
|
that the printed value is always after the global sum. |
| 2491 |
|
o pkg/seaice/seaice_dynsolver.F : |
| 2492 |
|
- fix ice strength assymptote at SEAICE_area_max<1 |
| 2493 |
|
(no change for the standard case of SEAICE_area_max=1) |
| 2494 |
|
o some cleaning: |
| 2495 |
|
- pkg source files: ensure that all *.F files from each pkg included the |
| 2496 |
|
corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which |
| 2497 |
|
only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment |
| 2498 |
|
code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding |
| 2499 |
|
includes; |
| 2500 |
|
- model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used. |
| 2501 |
|
- ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR |
| 2502 |
|
is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when |
| 2503 |
|
ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop. |
| 2504 |
|
- update option-file CPP_OPTIONS.h of all AD experiments: |
| 2505 |
|
* no longer include PACKAGES_CONFIG.h ; |
| 2506 |
|
* includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ; |
| 2507 |
|
* def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before |
| 2508 |
|
including ECCO_CPPOPTIONS.h). |
| 2509 |
|
o pkg/cost, pkg/ctrl, pkg/ecco option-file: |
| 2510 |
|
- clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into |
| 2511 |
|
separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h, |
| 2512 |
|
not necessary accurate). |
| 2513 |
|
- add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in |
| 2514 |
|
pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to |
| 2515 |
|
deliberately break compilation (a remainder that it needs to be customized) |
| 2516 |
|
- in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h |
| 2517 |
|
- rename COST_CPPOPTIONS.h to COST_OPTIONS.h |
| 2518 |
|
- rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h |
| 2519 |
|
o tools/genamke2: |
| 2520 |
|
- check for lapack. |
| 2521 |
|
o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies. |
| 2522 |
|
- pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions |
| 2523 |
|
jointly. The exclusive ifdefs were removed, to add costs terms (when defined) |
| 2524 |
|
from both packages. |
| 2525 |
|
- the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly. |
| 2526 |
|
- for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs. |
| 2527 |
|
- pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes |
| 2528 |
|
of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly. |
| 2529 |
|
o pkg/cost : add comments to explain special and/or untested setups. |
| 2530 |
|
o pkg/exf: |
| 2531 |
|
- use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h |
| 2532 |
|
(previously, ALLOW_AUTODIFF_TAMC was controling this switch). |
| 2533 |
|
o verification/*/code_ad: |
| 2534 |
|
mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file: |
| 2535 |
|
- reccord when this file is included (define ECCO_CPPOPTIONS_H) |
| 2536 |
|
- remove the most obvious obsolete features (e.g., #define ALLOW_COST not |
| 2537 |
|
allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h) |
| 2538 |
|
o pkg/seaice : |
| 2539 |
|
- added possibility to change ice strength/PRESS0 relationship to |
| 2540 |
|
HEFF, according to the following run time parameters |
| 2541 |
|
SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0) |
| 2542 |
|
SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0) |
| 2543 |
|
SEAICEpresH0 :: HEFF threshold for ice strength (m) |
| 2544 |
|
o pkg/ggl90 : |
| 2545 |
|
- added run time flag mxlSurfFlag to include the code that ensure |
| 2546 |
|
mixing between first and second level (previously included as a comment) |
| 2547 |
|
o verification/1D_ocean_ice_column/input_ad/data.autodiff : |
| 2548 |
|
- add test of newly added dumpAdByRec=T option where |
| 2549 |
|
we write all records to one file per variable. |
| 2550 |
|
o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h : |
| 2551 |
|
- switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES |
| 2552 |
|
to check that this code is ok with taf and compiles in adjoint. |
| 2553 |
|
o pkg/autodiff : |
| 2554 |
|
- added run time param dumpAdByRec : ad dump format switch. |
| 2555 |
|
If true then write all records to one file per variable. |
| 2556 |
|
Else write one file per record (remains the default). |
| 2557 |
|
- revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly. |
| 2558 |
|
o pkg/seaice: |
| 2559 |
|
- Added SEAICEuseTILT run time switch : if set to |
| 2560 |
|
false then omit the tilt term in seaice dynamics. |
| 2561 |
|
- Fix free drift calculation. |
| 2562 |
|
o pkg/shelfice: |
| 2563 |
|
When initializing SHELFICEDragQuadratic, set default to be |
| 2564 |
|
consistent with shiCdrag in case SHELFICEuseGammaFrict is used, |
| 2565 |
|
but retain option to set it independently |
| 2566 |
|
(inconsistenty spotted by Veronique Dansereau) |
| 2567 |
|
o eesupp/inc: |
| 2568 |
|
- in EEPARAMS.h, add real-type constant for some frequently used simple number |
| 2569 |
|
(0,1,2,1/2), with name explicitly referring to RS/RL type. |
| 2570 |
|
o model/src: |
| 2571 |
|
- move balancing of relaxation terms to new S/R balance_relax.F. |
| 2572 |
|
o pkg/autodiff: |
| 2573 |
|
re-write active I/O high-level (control) S/R: |
| 2574 |
|
- rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL |
| 2575 |
|
- add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R. |
| 2576 |
|
- use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and |
| 2577 |
|
MDS_READ/WRITE_FIELD); change loops to multi-threads. |
| 2578 |
|
- update and merge active_file_control_slice.flow into active_file_control.flow |
| 2579 |
|
- update the calls in lower level S/R (active_file.F, active_file_g.F and |
| 2580 |
|
active_file_ad.F) keeping the argument list and function unchanged. |
| 2581 |
|
- also update lower-level "_LOC" version (call same S/R with "useCurrentDir |
| 2582 |
|
=.TRUE.") and remove high-level (control) _loc version (not called anymore). |
| 2583 |
|
- new low-level active I/O routines, one for each type (RL/RS), for active var |
| 2584 |
|
of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr); |
| 2585 |
|
fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the |
| 2586 |
|
right type. |
| 2587 |
|
o autodiff and RS=real*4: |
| 2588 |
|
- call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf |
| 2589 |
|
ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ; |
| 2590 |
|
- change argument type of 3-D mask argument to _RS to match type in the call |
| 2591 |
|
(in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued. |
| 2592 |
|
o pkg/thsice: |
| 2593 |
|
- re-anable balanceEmPmR when useSEAICE=T with useThSIce=T. |
| 2594 |
|
- option to correct ocean fresh-water flux for imbalance of Atmos+Land |
| 2595 |
|
fresh-water flux: uniform correction or proportional to local precip. |
| 2596 |
|
o pkg/ctrl: |
| 2597 |
|
- new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D |
| 2598 |
|
- redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to |
| 2599 |
|
ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC |
| 2600 |
|
- verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL |
| 2601 |
|
|
| 2602 |
|
checkpoint63q (2012/07/30) |
| 2603 |
|
o pkg/autodiff: |
| 2604 |
|
note about monitor and snap-shot of ad-variables: |
| 2605 |
|
a) need to apply ADEXCH before monitor or output of ad-vars to include |
| 2606 |
|
overlap contributions (was done for adjDump but missing for monitor). |
| 2607 |
|
b) since ADEXCH implies adding overlap values to interior array, machine |
| 2608 |
|
truncation error is expected when adding an ADEXCH call in the middle of |
| 2609 |
|
the time-stepping (although mathematically identical). |
| 2610 |
|
modifs: |
| 2611 |
|
- fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars |
| 2612 |
|
declaration (adEddyPsiX,adEddyPsiY in adcommon.h). |
| 2613 |
|
- add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to |
| 2614 |
|
apply ADEXCH before monitor or snap-shot of ad-variables: |
| 2615 |
|
=0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy. |
| 2616 |
|
- implement new method (copy+adexch) for snap-shot and monitor of main model |
| 2617 |
|
ad-vars (initially not used by default -> output unchanged). |
| 2618 |
|
- change default (set to 2) to use new method and update few output_adm.txt |
| 2619 |
|
with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo |
| 2620 |
|
and both tutorial_tracer_adjsens tests). |
| 2621 |
|
- switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice) |
| 2622 |
|
and turn off momDissip_In_AB in the 2 other (needed for stable AB-3). |
| 2623 |
|
o pkg/ctrl: |
| 2624 |
|
enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of |
| 2625 |
|
generic control variables via |
| 2626 |
|
#define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL |
| 2627 |
|
Only required customization should be S/R ctrl_map_ini_genarr.F |
| 2628 |
|
(routine in repository contains example) |
| 2629 |
|
o pkg/exf: |
| 2630 |
|
- fix and refine checking of surface-relaxation setting when using EXF |
| 2631 |
|
o verification (adjoint exp): |
| 2632 |
|
- reduce length of simulation by half for experiment global_ocean.cs32x15 |
| 2633 |
|
(std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output. |
| 2634 |
|
o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag) |
| 2635 |
|
- replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers |
| 2636 |
|
of KE that can occur with aggressive optimization |
| 2637 |
|
+ put quadratic bottom drag calculation in separated loops (only done if |
| 2638 |
|
using bottomDragQuadratic) |
| 2639 |
|
o model/src: CG2D_NSA |
| 2640 |
|
- clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF |
| 2641 |
|
and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE. |
| 2642 |
|
- in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens), |
| 2643 |
|
change cg2d residual target to be expressed in Wunits (=> do not normalise |
| 2644 |
|
RHS ; this fix global_max Pb with TAF); update output. |
| 2645 |
|
o verification/tutorial_tracer_adjsens: |
| 2646 |
|
improve parameter consistency (and get rid of warnings): |
| 2647 |
|
- use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf); |
| 2648 |
|
- switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical) |
| 2649 |
|
- use staggerTimeStep (for stability) in som81; use default rotation period. |
| 2650 |
|
o pkg/exch2: |
| 2651 |
|
- with empty facet: fix compact-format (W2_mapIO=1) definition (was previously |
| 2652 |
|
reset to 0 = 1 long line in X) |
| 2653 |
|
o pkg/mdsio: |
| 2654 |
|
- fix reading of dimensions from meta file for large-size domain |
| 2655 |
|
o model/src: |
| 2656 |
|
- fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long); |
| 2657 |
|
- to refine CS-grid check, add logical flag "hasWetCSCorners": true if using |
| 2658 |
|
Cubed-Sphere Exch with CS-corners inside the domain; |
| 2659 |
|
make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate |
| 2660 |
|
globalArea and to set hasWetCSCorners. |
| 2661 |
|
- add warning if usingCurvilinearGrid and momAdvection in flux-form (missing |
| 2662 |
|
metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form. |
| 2663 |
|
- re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if |
| 2664 |
|
useCDscheme and useCubedSphereExchange). |
| 2665 |
|
o pkg/seaice/seaice_growth.F : |
| 2666 |
|
- compute the SEAICE_DISABLE_HEATCONSFIX term accordingly |
| 2667 |
|
for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0) |
| 2668 |
|
when the previous code was not correct. |
| 2669 |
|
- in all cases diagnoze the boundary condition mismatch to SIaaflux |
| 2670 |
|
- in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add |
| 2671 |
|
that term to QNET (essentially to set the melt/freeze water to 0degC). |
| 2672 |
|
when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed. |
| 2673 |
|
o verification/global_ocean.cs32x15/input.seaice : |
| 2674 |
|
- add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget. |
| 2675 |
|
- add diagnostics (commented out) for budget test using my matlab codes (gcmfaces). |
| 2676 |
|
- update results (output.seaice.txt) accordingly. |
| 2677 |
|
o verification/lab_sea/input/data.seaice : |
| 2678 |
|
- remove SEAICEheatConsFix, which is now be tested |
| 2679 |
|
in global_ocean.cs32x15. The presently coded fix |
| 2680 |
|
is only consistent with real fresh water + nlfs. |
| 2681 |
|
- update results (output.txt) accordingly. |
| 2682 |
|
o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd). |
| 2683 |
|
o AD_CONFIG.h file: |
| 2684 |
|
- in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h; |
| 2685 |
|
- remove #include "AD_CONFIG.h" from all included OPTIONS files and |
| 2686 |
|
add it explicitly in each fortran src file where it is needed. |
| 2687 |
|
motivation: header file AD_CONFIG.h is generated/modified after "make depend" |
| 2688 |
|
thus introducing potentially wrong dependency; therefore, better to include |
| 2689 |
|
it only where it's really needed, and after any other included OPTIONS file |
| 2690 |
|
(less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN |
| 2691 |
|
or ALLOW_TANGENTLINEAR_RUN). |
| 2692 |
|
|
| 2693 |
|
checkpoint63p (2012/07/06) |
| 2694 |
|
o pkg/autodiff: |
| 2695 |
|
- rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ; |
| 2696 |
|
- create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters |
| 2697 |
|
which are now read from new parameter file "data.autodiff" (inAdExact |
| 2698 |
|
previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg) |
| 2699 |
|
- add file "data.autodiff" in all verification/*/input_ad/ directories. |
| 2700 |
|
- add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward |
| 2701 |
|
mode (used in global_ocean.cs32x15.seaice_dynmix test exp.) |
| 2702 |
|
o verification/tutorial_tracer_adjsens/ |
| 2703 |
|
- add extra sub-verification which uses "SOM" advection scheme |
| 2704 |
|
(2nd Order-Moment Advection Scheme, Prather Limiter) with |
| 2705 |
|
#define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h |
| 2706 |
|
and in data: |
| 2707 |
|
multiDimAdvection=.TRUE., |
| 2708 |
|
tempAdvScheme=81, |
| 2709 |
|
saltAdvScheme=81, |
| 2710 |
|
o model/src: |
| 2711 |
|
- introduce ALLOW_BALANCE_RELAX which allow the removal |
| 2712 |
|
of the global mean of relaxation terms by setting |
| 2713 |
|
balanceThetaClimRelax and balanceSaltClimRelax |
| 2714 |
|
- disable balanceEmPmR and balanceQnet in the case when useSeaice. |
| 2715 |
|
This case is now treated appropriately in seaice_growth.F |
| 2716 |
|
o pkg/seaice: |
| 2717 |
|
- do balanceEmPmR and balanceQnet based on the net fluxes |
| 2718 |
|
(SItflux) that enter the ocean+ice system rather than QNET |
| 2719 |
|
and EMPMR. Works best in real fresh water. |
| 2720 |
|
- SIatmFW, SIatmQnet, and SItflux computations had to be moved |
| 2721 |
|
out of the diagnotics bloc, and stored in global arrays. |
| 2722 |
|
|
| 2723 |
|
checkpoint63o (2012/06/29) |
| 2724 |
|
o vertical mixing schemes: |
| 2725 |
|
- remove unused S/R CALC_BUOYANCY (left from branch-atmos merging) |
| 2726 |
|
- replace computation of density (in Function STATE1, opps_calc.F) by a call |
| 2727 |
|
to S/R FIND_RHO_SCALAR |
| 2728 |
|
- pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC |
| 2729 |
|
and use it for N^2 calculation in ggl90_calc.F (save 2 density computations); |
| 2730 |
|
affects output (vermix.ggl90) at truncation level. |
| 2731 |
|
o testreport: |
| 2732 |
|
- change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles |
| 2733 |
|
(nSx,nSy) for the number of threads (from eedata.mth) |
| 2734 |
|
o model/src: |
| 2735 |
|
- remove 2nd set of calls at the top of initialise_varia.F (Adjoint part) |
| 2736 |
|
related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary). |
| 2737 |
o verification/tutorial_tracer_adjsens/ |
o verification/tutorial_tracer_adjsens/ |
| 2738 |
- compile with ALLOW_CG2D_NSA |
- compile with ALLOW_CG2D_NSA |
| 2739 |
- run with nonlinFreeSurf=3 |
- run with nonlinFreeSurf=3 |
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