| 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 adjoint |
| 8 |
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* changed verification/global_ocean.cs32x15 ; adjoint now tests |
| 9 |
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Adams-Bashforth 3 + NLFS + RSTAR |
| 10 |
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* some more modifs required for ECCO-GODAE v4 |
| 11 |
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o pkg/seaice |
| 12 |
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add SEAICE_AGE_VOL option to use volume instead of area for |
| 13 |
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integrating SEAICE_AGE |
| 14 |
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o model/src: |
| 15 |
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first check-in of sigma & hybrid-sigma coordinate code ; also includes |
| 16 |
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non-linear free-surface parts ; but pressure-gradient not yet coded. |
| 17 |
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o pkg/ptracers: |
| 18 |
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option for ptracer to convert Salt Relax into additional EmP. |
| 19 |
|
tested in exp. global_ocean.90x40x15.dwnslp (update output) |
| 20 |
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|
| 21 |
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checkpoint62j (2010/08/25) |
| 22 |
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o pkg/ggl90: |
| 23 |
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other minor changes: remove 3-D temp array gTKE (+ add argument myIter) |
| 24 |
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o pkg/dic: car_flux.F, phos_flux.F |
| 25 |
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- reduce number of exp-calls in order to improve performance |
| 26 |
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- clean up a little (replace fields by their macros, etc., fix |
| 27 |
|
typo in CPP-flag) |
| 28 |
|
o pkg/ggl90: minor changes |
| 29 |
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- GGL90diffKrS was removed --> always use GGL90diffKr |
| 30 |
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- GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV |
| 31 |
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- hack of mxlMaxFlag=2 --> ensure mixing between first and second level |
| 32 |
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(commented out for now) |
| 33 |
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- change in max/min operations to ensure that smoothing is ok |
| 34 |
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- smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr) |
| 35 |
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- always use diffKrNrT as background profile (i.e. never use diffKr field) |
| 36 |
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o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj) |
| 37 |
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o pkg/dic: |
| 38 |
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- model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better |
| 39 |
|
vectorization |
| 40 |
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- small bug fix in insol for the unlikely case of a cartesian grid |
| 41 |
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- towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F |
| 42 |
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+ now vectorize, which also removes adjoint recomputations; |
| 43 |
|
+ replace integer maksp1 by _RL maskp1 |
| 44 |
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+ replace a**x by exp(x*log(a)) in phos_flux.F for speed |
| 45 |
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|
| 46 |
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checkpoint62i (2010/07/21) |
| 47 |
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o pkg/flt: |
| 48 |
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- with OBCS: stop floats which enter the OB region |
| 49 |
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o model/src: |
| 50 |
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- use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones) |
| 51 |
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for implicit vertical advection. |
| 52 |
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o pkg/seaice: |
| 53 |
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- account for melting in seaice age evolution. |
| 54 |
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- remove double counting of seaice ridging effect on seaice age. |
| 55 |
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|
| 56 |
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checkpoint62h (2010/06/18) |
| 57 |
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o pkg/exch2: |
| 58 |
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- remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1). |
| 59 |
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o tools/genmake2 |
| 60 |
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- remove "-pdefault" option: redundant with the use of "packages.conf"; |
| 61 |
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- remove file pkg/pkg_default : set the default as a pkg group |
| 62 |
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("default_pkg_list") defined in pkg/pkg_groups; |
| 63 |
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- fix for case pkg/pkg_depend is missing (was hanging before); |
| 64 |
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- add option "-pgroups" to specify a different pkg_groups than the default. |
| 65 |
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o verification/adjustment.cs-32x32x1: |
| 66 |
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add a "minimal" set-up test (code_min & input_min) which only compiles |
| 67 |
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eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc. |
| 68 |
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o tools/genmake2 |
| 69 |
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- extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg])) |
| 70 |
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- fix details of checking for mnc & profile pkg when NetCDF is unavailable. |
| 71 |
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o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these |
| 72 |
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files are nearly the same anyway. |
| 73 |
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Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04: |
| 74 |
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- redefinition of tau(i,i) (by a factor of ustar) |
| 75 |
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- 1./exf(Const/T) -> exf(-Const/T) (big change in the results) |
| 76 |
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- replace rhonil by rhoConstFresh in computation of evap (bug fix) |
| 77 |
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- replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results) |
| 78 |
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- replace |
| 79 |
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rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh ) |
| 80 |
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shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j) |
| 81 |
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by |
| 82 |
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shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh ) |
| 83 |
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(changes results) |
| 84 |
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-> exf_bulkformulae v1.22, |
| 85 |
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update verification experiments lab_sea, offline_exf_seaice, seaice_obcs |
| 86 |
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(lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13, |
| 87 |
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output.txt 1.63 |
| 88 |
|
offline_exf_seaice: output.seaicetd.txt 1.7 |
| 89 |
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seaice_obcs: output.txt 1.10) |
| 90 |
|
Step 2: do the actual merge and remove exf_bulk_largeyeager04.F |
| 91 |
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-> exf_bulkformulae v1.23, |
| 92 |
|
unfortunately requires updating lab_sea.salt_plume (6 matching digits), |
| 93 |
|
and global_ocean.cs32x15.icedyn (only 11 matching digits) |
| 94 |
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Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice. |
| 95 |
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o adjoint of exch-1: |
| 96 |
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- pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list) |
| 97 |
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(note: was already like this when using EXCH-2) and remove flow dir |
| 98 |
|
and hand-written AD version of high-level EXCH S/R (pkg/autodiff); |
| 99 |
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- provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow); |
| 100 |
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- update pkg/exch2 diff list. |
| 101 |
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|
| 102 |
|
checkpoint62g (2010/05/19) |
| 103 |
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o eesupp/src (exch-1): |
| 104 |
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- split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F) |
| 105 |
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and remove argument "simulationMode"; same thing for all exch_*rx_cube.F |
| 106 |
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(renamed to exch1_*rx_cube.F). |
| 107 |
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- change accordingly exch_*_rx.template and AD version in pkg/autodiff |
| 108 |
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to call new exch1 S/R ; update Makefile and .cvsignore. |
| 109 |
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- replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove |
| 110 |
|
exch2_xy_rx later) |
| 111 |
|
Note: after updating your code, need to run "make clean" in eesupp/src |
| 112 |
|
o test experiment bottom_ctrl_5x5: |
| 113 |
|
new output_adm.txt with fewer grdchk & less monitor output. |
| 114 |
|
o model/src: |
| 115 |
|
remove the call to ini_cori in initialise_varia.F (just keep the usual one |
| 116 |
|
in initialise_fixed.F). More consistent with coriolis & horizontal grid |
| 117 |
|
beeing treated in the same way (ini_grid is not called a 2nd time). |
| 118 |
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o pkg/exf: |
| 119 |
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- rewrite exf_bulk_largeyeager04.F for better vectorization, changes |
| 120 |
|
global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated |
| 121 |
|
- fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now) |
| 122 |
|
- cosmetic changes to exf_bulkformulae.F to make it look more like |
| 123 |
|
exf_bulk_largeyeager04.F |
| 124 |
|
o eesupp/src (exch-1): |
| 125 |
|
- Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1). |
| 126 |
|
- Separate buffer filling and MPI sending: allow EXCH-1 to work for local |
| 127 |
|
array (non-shared) when using MPI+MTH. Also reduces number of BARRIER |
| 128 |
|
(even without using MPI). |
| 129 |
|
- Message mode: move RecvAck setting (indicator of buffer being ready) |
| 130 |
|
from send_put to recv_get S/R (was useless before, but not sure if |
| 131 |
|
it's much more useful now); |
| 132 |
|
- Switch the order of sync: MPI-proc 1rst and then threads; |
| 133 |
|
- take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead. |
| 134 |
|
- fix AD code for communication mode ='get' (but not used). |
| 135 |
|
o model/src: |
| 136 |
|
initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does |
| 137 |
|
not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp). |
| 138 |
|
o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API |
| 139 |
|
o pkg/ctrl: require a specific set of control variables and exf-flags for |
| 140 |
|
adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied) |
| 141 |
|
o model/src: |
| 142 |
|
a) 1rst version of a new driver S/R to turn-off output freq and flags after the |
| 143 |
|
1rst forward sweep, to avoid over-writing output files during recomputations |
| 144 |
|
recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?) |
| 145 |
|
b) 2nd version: |
| 146 |
|
- add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO); |
| 147 |
|
- switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast, |
| 148 |
|
writePickupAtEnd) + seaice & ptracers output; |
| 149 |
|
- do not switch off MNC flags (otherwise, won't get admonitor netcdf file) |
| 150 |
|
o model/src: |
| 151 |
|
- new S/R rotate_uv2en_rl (..._rs) that rotates vector fields. |
| 152 |
|
o pkg/exch2: |
| 153 |
|
- remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ; |
| 154 |
|
- add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch). |
| 155 |
|
o pkg/autodiff & exch2: |
| 156 |
|
process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF |
| 157 |
|
(for now, only if ALLOW_EXCH2 is defined). |
| 158 |
|
o pkg/autodiff: |
| 159 |
|
- include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F |
| 160 |
|
(not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly. |
| 161 |
|
+ clean-up comments (_RS is not always real*4) |
| 162 |
|
- fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R) |
| 163 |
|
- add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2: |
| 164 |
|
was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs. |
| 165 |
|
o testreport (AD-tests): |
| 166 |
|
no longer link files from dir "../input" (1rst link files from |
| 167 |
|
"../input_ad.[xx]" if secondary test "xx" and then from "../input_ad") |
| 168 |
|
|
| 169 |
|
checkpoint62f (2010/04/29) |
| 170 |
|
o model/src/the_main_loop.F: |
| 171 |
|
adjust store directives for seaice evp and multicategory according to |
| 172 |
|
pkg/ecco/the_main_loop.F |
| 173 |
|
o adjoint: |
| 174 |
|
global_sum_ad was incomplete (noted many times by many people ;) |
| 175 |
|
nice description by Jean U. as follows: |
| 176 |
|
* allreduce(var) in global_sum.F can be interpreted as |
| 177 |
|
reduce(sum) followed by broadcast of sum. |
| 178 |
|
* The adjoint of that is |
| 179 |
|
sum(adjoint) followed by broadcast(summed adjoint value) |
| 180 |
|
or in other words, allreduce(sum, adjoint vars) |
| 181 |
|
We were missing the sum(adjoint)! |
| 182 |
|
Benign, except(!) for "global" scalars appearing in tile loops (bi,bj) |
| 183 |
|
(noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset). |
| 184 |
|
The fix should produce 16-digit accuracy between |
| 185 |
|
single-CPU multi-tile (e.g. nSx=2, nPx=1) and |
| 186 |
|
multi-CPU single-tile (e.g. nSx=1, nPx-2) |
| 187 |
|
We'll probably change this yet again shortly |
| 188 |
|
o eesupp/src: |
| 189 |
|
- fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?) |
| 190 |
|
o pkg/icefront |
| 191 |
|
- ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving |
| 192 |
|
specification of addmass array based on a 2D field, which is added |
| 193 |
|
at bottommost wet level at each horizontal location. |
| 194 |
|
o model/src: |
| 195 |
|
horizontal grid initialisation (other than curvilinear): add code for Exch2 IO |
| 196 |
|
layout; (not always compatible with delX,delY setting; commented out for now). |
| 197 |
|
o pkg/exch2: |
| 198 |
|
change tile to processor setting (case nSy*nPy > 1): allows default model mapping |
| 199 |
|
(myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config. |
| 200 |
|
|
| 201 |
|
checkpoint62e (2010/04/15) |
| 202 |
|
o pkg/obcs: |
| 203 |
|
- fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert). |
| 204 |
|
o pkg/dic: |
| 205 |
|
-fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up; |
| 206 |
|
(note: not presently tested in any forward verification exp.) |
| 207 |
|
update tutorial_global_oce_biogeo AD output file. |
| 208 |
|
o pkg/exf: |
| 209 |
|
- account for the variation of albedo as a function of zenith angle |
| 210 |
|
by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h |
| 211 |
|
o build_options: |
| 212 |
|
- rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas" |
| 213 |
|
o pkg/dic: |
| 214 |
|
change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart: |
| 215 |
|
- use binary pickup file for restart; |
| 216 |
|
- initialise atmos-CO2 box from dic_pCO2 parameter; |
| 217 |
|
- fix multi-threaded. |
| 218 |
|
o pkg/rbcs: |
| 219 |
|
- clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ; |
| 220 |
|
change (+ fix IO calls) type of array RBC_mask from _RL to _RS. |
| 221 |
|
- add RBCS to exp4 passive tracer 01 (rbcs was previously untested) |
| 222 |
|
and update output.txt |
| 223 |
|
o pkg/kpp: |
| 224 |
|
- add diagnostics for KPP non-local flux of Temp, Salinity and pTracers; |
| 225 |
|
- change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS |
| 226 |
|
(= ratio of KPP non-local (salt) flux relative to surface-flux) when |
| 227 |
|
using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat '); |
| 228 |
|
- change pkg/offline to read-in average KPPghat*KPPdiffKzS from file |
| 229 |
|
KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile). |
| 230 |
|
o pkg/offline: |
| 231 |
|
fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor |
| 232 |
|
(bug was added in version 1.10 on 2007-08-23). |
| 233 |
|
o pkg/offline: |
| 234 |
|
- no need to specify periodicExternalForcing, etc ... to use offline pack |
| 235 |
|
- offline input files no longer just single prec --> parameter offlineLoadPrec |
| 236 |
|
o verification/lab_sea: |
| 237 |
|
change AD test to multi-tile setup and update all 4 AD output. |
| 238 |
|
NOTE: while cost function values remain very similar, |
| 239 |
|
gradients are very different, although gradient checks are self-consistent |
| 240 |
|
Should try to get to the bottom of this (cost function summation order?) |
| 241 |
|
o pkg/dic: |
| 242 |
|
in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid |
| 243 |
|
a weakness of TAF that drops part of double precision in log10 derivative. |
| 244 |
|
<= changes removed since problem has been fixed in current TAF version 1.9.71 |
| 245 |
|
update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo. |
| 246 |
|
o pkg/ecco: |
| 247 |
|
add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F |
| 248 |
|
update all 4 lab_sea AD output. |
| 249 |
|
|
| 250 |
|
checkpoint62d (2010/03/22) |
| 251 |
|
o build_options: |
| 252 |
|
remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles. |
| 253 |
|
o remove unbalanced quote (single or double) in commented line of source code |
| 254 |
|
(may cause some warning with some preprocessor/makedepend versions). |
| 255 |
|
o pkg/seaice: |
| 256 |
|
fix seaice_model.F for adjoint (gael) and update AD results of experiments |
| 257 |
|
lab_sea (std + evp + noseaicedyn) and offline_exf_seaice. |
| 258 |
|
o testreport: |
| 259 |
|
add option '-runonly' (short: '-ro') to just do the run part (without make). |
| 260 |
|
o eesupp: remove JAM communication code (obsolete). |
| 261 |
|
o add option to genmake2 & testreport to switch "_RS" type to "real*4" |
| 262 |
|
(if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return |
| 263 |
|
to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1 |
| 264 |
|
(update also the output). |
| 265 |
|
|
| 266 |
|
checkpoint62c (2010/03/02) |
| 267 |
|
o tools/build_options : |
| 268 |
|
move (some) old optfiles from build_options/ to build_options/unsupported/ |
| 269 |
|
o model/src and pkg/exf |
| 270 |
|
surface relaxation -- separating data and data.exf options |
| 271 |
|
The point is to ensure that we specify the surface relaxation |
| 272 |
|
either in data or in data.exf (but not half and half) and to |
| 273 |
|
avoid an accidental relaxation to 0 (which happened if a time |
| 274 |
|
scale was specified but the file name was left empty) |
| 275 |
|
o model/src model/inc and pkg/mom_common |
| 276 |
|
ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity |
| 277 |
|
=> addition to the viscosity field as computed by others schemes |
| 278 |
|
o tools/build_options: |
| 279 |
|
- rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile) |
| 280 |
|
but keep the former optfile for few weeks for smooth transition |
| 281 |
|
o pkg/ecco |
| 282 |
|
- allow user defined cost function contributions |
| 283 |
|
CPP: ALLOW_USERCOST_CONTRIBUTION |
| 284 |
|
USAGE: compute contributions in cost_usercost_all.F |
| 285 |
|
- note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was. |
| 286 |
|
the two options are complementary. |
| 287 |
|
o pkg/smooth |
| 288 |
|
- migration from contrib to the main repository |
| 289 |
|
|
| 290 |
|
checkpoint62b (2010/01/26) |
| 291 |
|
o pkg/monitor: |
| 292 |
|
- change back mon_printstats_rl.F & mon_stats_rl.F and add a stop |
| 293 |
|
(in case someone forgot to update customized pieces of code) |
| 294 |
|
o nonHydrostatic: |
| 295 |
|
- add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested); |
| 296 |
|
- add a simple 2-D experiment (short_surf_wave) to test it. |
| 297 |
|
o pkg/icefront: |
| 298 |
|
adding the shell of, and the hooks to, a new package that |
| 299 |
|
will model melting and freezing of vertical glacier ice fronts |
| 300 |
|
o momentum: |
| 301 |
|
add diagnostics of momentum tendency from Hydrostatic pressure gradient |
| 302 |
|
(without surf.pressure term: would need a 2nd filling since implicit term). |
| 303 |
|
o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace |
| 304 |
|
two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR |
| 305 |
|
cannot deal with the former |
| 306 |
|
o cleaning: |
| 307 |
|
- remove all (except OpenAD) old TLM output from results_ad dirs. |
| 308 |
|
- remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R) |
| 309 |
|
- comment out maskH definition (replaced by maskInC) |
| 310 |
|
o pkg/monitor: |
| 311 |
|
- change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl |
| 312 |
|
& mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs. |
| 313 |
|
|
| 314 |
|
checkpoint62a (2010/01/15) |
| 315 |
|
o model/src: |
| 316 |
|
- bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4) |
| 317 |
|
o pkg/diagnostics: |
| 318 |
|
- add optional level number diagnostics (i.e., level number to be define |
| 319 |
|
explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X". |
| 320 |
|
- strictly check for valid parser-code(10) ; |
| 321 |
|
- check if adding diag to the list from the right place. |
| 322 |
|
o pkg/longstep: |
| 323 |
|
- change parameters and fix tracer conservation with rstar/nonlinear free surface |
| 324 |
|
o diagnostics: |
| 325 |
|
- in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer |
| 326 |
|
S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics. |
| 327 |
o pkg/diagnostics: |
o pkg/diagnostics: |
| 328 |
- Add option for writing vertical integral (sum of selected levels) of an output |
- Add option for writing vertical integral (sum of selected levels) of an output |
| 329 |
field instead of writing output field levels. Activate this option on a per |
field instead of writing output field levels. Activate this option on a per |
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