| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/seaice/seaice_lsr.F: fix computation of BU/BV, make sure they are |
| 8 |
|
non-zero, only necessary for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 9 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 10 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 11 |
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- add test for strong implicit coupling and restricted addtive Schwarz |
| 12 |
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methods for LSR |
| 13 |
|
- update results/output.seaice.txt |
| 14 |
|
o verification/tutorial_global_oce_biogeo: |
| 15 |
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- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 16 |
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and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 17 |
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update output_adm,_oadm,_tlm.txt |
| 18 |
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o pkg/dic: |
| 19 |
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- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 20 |
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- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 21 |
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for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 22 |
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o verification/tutorial_global_oce_biogeo: |
| 23 |
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- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 24 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 25 |
|
update output_adm,_oadm,_tlm.txt |
| 26 |
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o eesupp/src: |
| 27 |
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- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 28 |
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and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 29 |
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o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 30 |
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LSR (following Hutchings et al. 2004) |
| 31 |
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- introduce zetaZ as a global variable (requires adjustments in |
| 32 |
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seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 33 |
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in seaice_calc_viscosities.F |
| 34 |
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- new flag SEAICEuseStrImpCpl (default off) |
| 35 |
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- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 36 |
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momentum equations |
| 37 |
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- JFNK-solver (preconditioner) adjusted to allow using this method |
| 38 |
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(where it does not have any positive effect) |
| 39 |
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o pkg/seaice |
| 40 |
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- add overlap for restrictive additive Schwartz method also to LSR, but |
| 41 |
|
turn it off by default (because it only seems to work for non-cubed |
| 42 |
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sphere/llc topologies) |
| 43 |
|
o pkg/autodiff |
| 44 |
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- add extra exchanges in addummy_in_steppging also for mnc output |
| 45 |
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o pkg/seaice: |
| 46 |
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- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 47 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 48 |
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o pkg/obcs: |
| 49 |
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- add option to specify domain-connected piece Id along OB though files |
| 50 |
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(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 51 |
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- modify obcs_diag_balance.F to process each connected-part separately; |
| 52 |
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exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 53 |
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Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 54 |
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- add example of OB-conect files in verification/so_box_biogeo/input. |
| 55 |
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o pkg/diagnostics: |
| 56 |
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- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 57 |
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a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 58 |
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outside OB (i.e, where tracer OBCS are applied). |
| 59 |
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b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 60 |
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velocity across OB, spread it uniformly along the OB in the RHS. |
| 61 |
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|
| 62 |
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checkpoint65g (2014/11/19) |
| 63 |
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o pkg/diagnostcis: |
| 64 |
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- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 65 |
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o pkg/my82,pp81,kl10: |
| 66 |
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- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 67 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 68 |
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o pkg/seaice: |
| 69 |
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- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 70 |
|
Bouillon et al 2013) |
| 71 |
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- add SEAICE_evpAlpha/Beta to namelist |
| 72 |
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- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 73 |
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involve trivial re-ordering of divisions/multiplications that should not |
| 74 |
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have any effects, but ... they do change the results of lab_sea.hb87 so |
| 75 |
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that only 2 digits of agreement remain, in line with the general |
| 76 |
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instability/fragility of the evp-code. For now, I do not care and just |
| 77 |
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update the verification experiment |
| 78 |
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o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 79 |
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- remove xx_genarr2d_numsmooth etc |
| 80 |
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- use xx_genarr2d_preproc etc instead |
| 81 |
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- carry out smooth_correl2D at initialization stage rather than during |
| 82 |
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time stepping. |
| 83 |
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- get smoothOpNb from xx_gentim2d_preproc |
| 84 |
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o global_oce_cs32 : |
| 85 |
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- add test of generic ecco capabilities. |
| 86 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 87 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 88 |
|
o pkg/ctrl,ecco : |
| 89 |
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- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 90 |
|
is defined. |
| 91 |
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o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 92 |
|
o model/src: |
| 93 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 94 |
|
diffusivity (background) is specified but ignored. |
| 95 |
|
o verification: |
| 96 |
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- in testreport, convert hostname to lower case for default output dir name |
| 97 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 98 |
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o pkg/dic: add modifications from Hajoon: |
| 99 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 100 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 101 |
|
(read from file). |
| 102 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 103 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 104 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 105 |
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AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 106 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 107 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 108 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 109 |
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o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 110 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 111 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 112 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 113 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 114 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 115 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 116 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 117 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 118 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 119 |
|
o pkg/ctrl,ecco,exf : |
| 120 |
|
- remove variables associated with NON-generic costs, |
| 121 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 122 |
|
- remove NON-generic NON-obcs controls, |
| 123 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 124 |
|
o pkg/ctrl : added ctrl_local_params.h |
| 125 |
|
o pkg/ecco : added ecco_local_params.h |
| 126 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 127 |
|
experiments, which will progressively be removed once the |
| 128 |
|
experiments are revised to use only generic controls/costs. |
| 129 |
|
|
| 130 |
|
checkpoint65f (2014/10/13) |
| 131 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 132 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 133 |
|
cost function and control capabilities added since checkpoint65c. |
| 134 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 135 |
|
o pkg/ecco: increase modularity and improve logic |
| 136 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
| 137 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
| 138 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
| 139 |
|
- cost_gencal.F (new) : determine filnames and records. |
| 140 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
| 141 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
| 142 |
|
and exploit the above functions leading to more compact code. |
| 143 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
| 144 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
| 145 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
| 146 |
|
o pkg/ecco: extend generic cost capabilities |
| 147 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
| 148 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
| 149 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
| 150 |
|
gencost_outputlevel arguments to cost_generic |
| 151 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
| 152 |
|
and active_read, making room for gencost_preproc to take effect. |
| 153 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
| 154 |
|
- pkg/ecco/cost_generic.F : |
| 155 |
|
compute and store misfit maks*(model-data) in localdif that is |
| 156 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
| 157 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
| 158 |
|
rather gencost_barfile for deciding whether to write barfile |
| 159 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
| 160 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
| 161 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
| 162 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
| 163 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
| 164 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
| 165 |
|
o pkg/ecco: internal re-organization |
| 166 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
| 167 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
| 168 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
| 169 |
|
make sure gencost routines only include ecco.h) |
| 170 |
|
- throughout : add missing CCP switches, rm unused variables, |
| 171 |
|
and rm un-necessary CPP switches |
| 172 |
|
- throughout gencost routines : replace modelstartdate with |
| 173 |
|
gencost_startdate when needed |
| 174 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
| 175 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
| 176 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
| 177 |
|
- ecco_phys.F : compute etanFull |
| 178 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
| 179 |
|
bpv4-grace to gencost list, initialize added parameters |
| 180 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
| 181 |
|
|
| 182 |
|
checkpoint65e (2014/09/28) |
| 183 |
|
o pkg/obcs: |
| 184 |
|
- replaced the just-added CPP options with run-time variables |
| 185 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
| 186 |
|
o pkg/obcs: |
| 187 |
|
- add additional CPP options for sponge boundary layers |
| 188 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 189 |
|
o pkg/atm_phys: |
| 190 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
| 191 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 192 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 193 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
| 194 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 195 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 196 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 197 |
|
o pkg/ctrl, pkg/ecco : |
| 198 |
|
- fix and complement the generic controls implementation |
| 199 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 200 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
| 201 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 202 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 203 |
|
- add weight in CTRL_GET_GEN calls |
| 204 |
|
o pkg/ctrl : |
| 205 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 206 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 207 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 208 |
|
o pkg/ctrl : |
| 209 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 210 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 211 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 212 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 213 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 214 |
|
o pkg/ecco, pkg/ctrl : |
| 215 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 216 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 217 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 218 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 219 |
|
|
| 220 |
|
checkpoint65d (2014/09/15) |
| 221 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 222 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 223 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 224 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 225 |
|
- remove compilation failure |
| 226 |
|
- replace hard coded example |
| 227 |
|
- use ctrl_map_ini_gen2D, 3D |
| 228 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 229 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
| 230 |
|
o src/packages_init_variables.F : |
| 231 |
|
- regroup pkg/estimation calls |
| 232 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 233 |
|
(moved to ctrl_init_variables) |
| 234 |
|
o cost/cost_init_varia.F : |
| 235 |
|
- remove ecco_cost_init_varia |
| 236 |
|
(moved to ecco_init_varia) |
| 237 |
|
o ctrl/ctrl_init_variables.F : |
| 238 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 239 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 240 |
|
o ctrl/ctrl_map_ini.F : |
| 241 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 242 |
|
(moved to ctrl_init_variables) |
| 243 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 244 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 245 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 246 |
|
o ecco/ecco_ad_diff.list : |
| 247 |
|
- add ecco_init_varia.f |
| 248 |
|
o ecco/ecco_init_varia.F |
| 249 |
|
- new routine |
| 250 |
|
o pkg/streamice: |
| 251 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 252 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 253 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 254 |
|
o pkg/generic_advdiff: |
| 255 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 256 |
|
o pkg/exf: |
| 257 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 258 |
|
xxg_precip capability |
| 259 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 260 |
|
o pkg/ctrl: |
| 261 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 262 |
|
o model/src/load_fields_driver.F : |
| 263 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 264 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 265 |
|
o OpenAD verification experiments: |
| 266 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 267 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 268 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 269 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 270 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 271 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 272 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 273 |
|
o OpenAD verification tests: |
| 274 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 275 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 276 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 277 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 278 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 279 |
|
o model/src & generic_advdiff: |
| 280 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 281 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 282 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 283 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 284 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 285 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 286 |
|
setting in temp/salt/ptracer_integrate.F |
| 287 |
|
o pkg/dic: |
| 288 |
|
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 289 |
|
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 290 |
|
in gchem_forcing_sep.F |
| 291 |
|
o pkg/autodiff & obcs: |
| 292 |
|
- add storage of current OB values for U & V (was already done for T & S). |
| 293 |
|
|
| 294 |
|
checkpoint65c (2014/08/30) |
| 295 |
|
o pkg/dic: |
| 296 |
|
- take out of dic_atmos.F the initialisation part (corresponding to istate=0) |
| 297 |
|
and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for |
| 298 |
|
AD compilers (but still a Pb with multi-threading and Ajoint dependencies). |
| 299 |
|
o verification: |
| 300 |
|
- new experiment testing OBCS and DIC pkgs, using params & output from |
| 301 |
|
tutorial_global_oce_biogeo but limited to a sub-domain around Drake |
| 302 |
|
passage: take OBCS from the last year of a 2 yrs simulation and initial |
| 303 |
|
conditions from t=1.yr while keeping the same forcing. |
| 304 |
|
o model/src: |
| 305 |
|
- when allowFreezing=T, only reset below freezing initial Temp to Tfreezing |
| 306 |
|
(at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T). |
| 307 |
|
o pkg/diagnostics (Stats-Diags): |
| 308 |
|
- re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to: |
| 309 |
|
a) refine region where stats are computed, excluding where arrhFac=0 ; |
| 310 |
|
b) fix missing interior mask (use with OBCS) in 3-D fields statistics; |
| 311 |
|
c) extend regional stats over the region edges (for U or V pt location). |
| 312 |
|
o pkg/gchem: |
| 313 |
|
- add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since |
| 314 |
|
pkg/dic is currently changing/updating ptracers values beyond the OB). |
| 315 |
|
o verification (hs94): |
| 316 |
|
- convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords |
| 317 |
|
bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments |
| 318 |
|
hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of |
| 319 |
|
apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged. |
| 320 |
|
o pkg/ptracers: |
| 321 |
|
- implement Adams-Bashforth on pTracers (instead of on tracer tendency), |
| 322 |
|
switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs) |
| 323 |
|
- change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer |
| 324 |
|
with AB-2 code (so that it get tested). |
| 325 |
|
o model/src: |
| 326 |
|
- allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS) |
| 327 |
|
with AB-2 code (previously only available with AB-3 code). |
| 328 |
|
Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F |
| 329 |
|
to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done |
| 330 |
|
there, by calling CYCLE_AB_TRACER). |
| 331 |
|
o pkg/generic_advdiff: |
| 332 |
|
- change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS, |
| 333 |
|
GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R |
| 334 |
|
+ also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in |
| 335 |
|
S/R temp/salt/ptracers_integrate.F |
| 336 |
|
o model/src & pkg/ptracers: |
| 337 |
|
- remove common block variables gT,gS (in DYNVARS.h), except when |
| 338 |
|
USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly. |
| 339 |
|
- remove common block variable gPtr. |
| 340 |
|
o model/src & pkgs: |
| 341 |
|
- change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R |
| 342 |
|
ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G, |
| 343 |
|
IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT, |
| 344 |
|
GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T |
| 345 |
|
+ change accordingly all calling S/R. |
| 346 |
|
- use local temperature/salinity/ptracer tendency array (without bi,bj) |
| 347 |
|
in S/R temp/salt/ptracers_integrate.F |
| 348 |
|
o pkg/seaice: |
| 349 |
|
- move computation of stress contributions to rhsU/V in s/r seaice_lsr |
| 350 |
|
to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code |
| 351 |
|
- make u/vIceC local variables if SEAICE_CGRID is defined only to be used |
| 352 |
|
in seaice_lsr |
| 353 |
|
- seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D |
| 354 |
|
in s/r seaice_lsr_calc_coeffs |
| 355 |
|
o pkg/mdsio: |
| 356 |
|
- in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long |
| 357 |
|
(e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is |
| 358 |
|
too long (e.g., > MAX_LEN_FNAM/2 ) |
| 359 |
|
|
| 360 |
|
checkpoint65b (2014/08/12) |
| 361 |
|
o pkg/matrix: |
| 362 |
|
- pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP |
| 363 |
|
o model/src: |
| 364 |
|
- fix initialisation of geothermalFile; compile geothermal-flux code in |
| 365 |
|
natl_box verification experiment. |
| 366 |
|
o model/src & pkg/down_slope: |
| 367 |
|
- push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop). |
| 368 |
|
- in dwnslp_apply.F, update tracer tendency instead of the future tracer |
| 369 |
|
field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects |
| 370 |
|
results at machine truncation level: update output of experiments |
| 371 |
|
global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD). |
| 372 |
|
o pkg/diagnostics (Stats-Diags): |
| 373 |
|
- do not cumulate the full volume when DIAGNOSTICS_FILL is |
| 374 |
|
called with bibjFlg < 0 (no increment of the counter for 2D/3D diag); |
| 375 |
|
This fix the mean statistics when DIAGNOSTICS_FILL is called multiple |
| 376 |
|
times (but Min,Max and StD are still wrong). |
| 377 |
|
o model/src: |
| 378 |
|
- add geothermal flux forcing: read in ini_forcing.F as time-constant |
| 379 |
|
field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F) |
| 380 |
|
o model/src: |
| 381 |
|
- move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer |
| 382 |
|
_integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac |
| 383 |
|
arrays are already updated while adjustments (filters, conv.adjustment) are |
| 384 |
|
still applied later, in S/R TRACERS_CORRECTION_STEP. |
| 385 |
|
o model/src: |
| 386 |
|
- store in common bloc array "rhoInSitu" the virtual potential temperature |
| 387 |
|
anomaly that is used to compute geopotential: this make the atmos code |
| 388 |
|
more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F |
| 389 |
|
o pkg/seaice/seaice_lsr.F |
| 390 |
|
- rename integer variable ilcall to ipass (that's what it is called |
| 391 |
|
in the residual diagnostics |
| 392 |
|
- change time stepping for NPSEUDOTIMESTEP > 2 (does not change the |
| 393 |
|
default) for improved non-linear convergence of the first few steps |
| 394 |
|
- adjust a few comments and add new ones to explain some of the store |
| 395 |
|
directives |
| 396 |
|
o pkg/generic_advdiff (& ptracers): |
| 397 |
|
- re-work the code to check for valid advection scheme and for minimum |
| 398 |
|
size of overlap (now stored in local common bloc in gad_advscheme.F) |
| 399 |
|
o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics |
| 400 |
|
- re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1 |
| 401 |
|
- add an auxilliary variable "bet" and fix store directives and keys in |
| 402 |
|
seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or |
| 403 |
|
less exact gradients in my tests); but there are still |
| 404 |
|
recomputation warning (although gradients are sort of OK), when |
| 405 |
|
SEAICE_LSR_VECTORIZE is not defined, so this flag and |
| 406 |
|
SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency. |
| 407 |
|
- update verification experiments lab_sea. |
| 408 |
|
- change some comments in S/R seaice_calc_viscosities |
| 409 |
|
o model/src: |
| 410 |
|
- if staggerTimeStep=T, always apply exchange to velocity field in |
| 411 |
|
do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F |
| 412 |
|
(independent of using multi-dim advection or not); no effect on FWD run |
| 413 |
|
but affects AD results (at machine truncation level): update output of |
| 414 |
|
experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d) |
| 415 |
|
and isomip (oad: 12.d). |
| 416 |
|
o pkg/generic_advdiff: |
| 417 |
|
- stop if doAB_onGtGs is set to FALSE but ignored |
| 418 |
|
- refine warning related to stability of tracer time-stepping |
| 419 |
|
regarding internal wave dynamics. |
| 420 |
|
- setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition |
| 421 |
|
on staggerTimeStep & implicitIntGravWave (will now get a warning |
| 422 |
|
if potentially unstable). |
| 423 |
|
o pkg/kl10: |
| 424 |
|
- add new pkg "kl10" for mixing due to internal wave breaking, from |
| 425 |
|
http://www.sciencedirect.com/science/article/pii/S1463500310000144 |
| 426 |
|
(contribution from Jody Klymak), tested in verification experiment |
| 427 |
|
verification/internal_wave/input.kl10/ |
| 428 |
|
o isomip experiment: |
| 429 |
|
- test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up |
| 430 |
|
(input.htd) and update the output. |
| 431 |
|
o cd_code experiments: |
| 432 |
|
- use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM & |
| 433 |
|
#undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd) |
| 434 |
|
global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and |
| 435 |
|
update the corresponding output. |
| 436 |
|
o pkg/seaice: |
| 437 |
|
- reduce the number of include files and store directives in |
| 438 |
|
S/R seaice_lsr_tridiagu/v |
| 439 |
|
- change the order of loops in one case in S/R seaice_lsr_tridiagv |
| 440 |
|
(only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to |
| 441 |
|
get rid off one store directive (a TAF bug?) |
| 442 |
|
- add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in |
| 443 |
|
S/R seaice_lsr_tridiagv to change the loop range for consistency |
| 444 |
|
- remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v |
| 445 |
|
- fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in |
| 446 |
|
S/R seaice_lsr_tridiagu/v (requires update of |
| 447 |
|
offline_exf_seaice/input.dyn_jfnk) |
| 448 |
|
|
| 449 |
|
checkpoint65a (2014/07/27) |
| 450 |
|
o model/src: |
| 451 |
|
- Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than |
| 452 |
|
surrounding hFacC=1 @ edge of a step with different kSurfC on either side |
| 453 |
|
(topo in p-coords, ice-shelf in z-coords); update output of experiments |
| 454 |
|
tutorial_global_oce_in_p and isomip (both AD and OpenAD output). |
| 455 |
|
o model/src: |
| 456 |
|
- collect momentum forcing tendency into local 2-D array (passed as argument |
| 457 |
|
to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE |
| 458 |
|
parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default); |
| 459 |
|
affects results at machine truncation level (e.g., if using OBCS_SPONGE). |
| 460 |
|
- collect T & S forcing tendency into local 2-D array (passed as argument to |
| 461 |
|
apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency. |
| 462 |
|
affects results at machine truncation level (e.g., ocean: if using |
| 463 |
|
SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist |
| 464 |
|
correction due to vertical advection). |
| 465 |
|
- update output of experiments: fizhi-cs-32x32x40 (13 digits), |
| 466 |
|
global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml: |
| 467 |
|
seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13), |
| 468 |
|
obcs_ctrl (ad & fwd grd @ 12 & 7). |
| 469 |
|
o pkg/ptracers & diagnostics: |
| 470 |
|
- use ptracers (short) name (instead of long one) to make ptracers diagnostics |
| 471 |
|
title (to avoid some unexpected truncation); sort out ptracers diags units. |
| 472 |
|
- collect ptracer forcing tendency into local 2-D array (passed as argument |
| 473 |
|
to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency. |
| 474 |
|
|
| 475 |
|
checkpoint65 (2014/07/18) |
| 476 |
|
o pkg/fizhi: |
| 477 |
|
- add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this |
| 478 |
|
affects results at machine truncation level. Update output of experiments |
| 479 |
|
fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits). |
| 480 |
|
o pkg/seaice: more clean up |
| 481 |
|
- rename TAF common block tapes to be more consistent and remove |
| 482 |
|
unnecessary duplicates |
| 483 |
|
- add store directives to remove more recomputations, but use smaller |
| 484 |
|
tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined. |
| 485 |
|
The idea behind this flag is to reduce the memory footprint when the |
| 486 |
|
adjoint of the LSR is not required. As of now, defining the flag |
| 487 |
|
SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by |
| 488 |
|
a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). |
| 489 |
|
For experiment offline_exf_seaice, this means on a linux box with gfortran |
| 490 |
|
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 491 |
|
this experiment): |
| 492 |
|
> size mitgcmuv_ad |
| 493 |
|
text data bss dec hex |
| 494 |
|
5100659 1216 220458952 225560827 d71c8fb |
| 495 |
|
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 496 |
|
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 497 |
|
text data bss dec hex |
| 498 |
|
6695027 1648 1014578664 1021275339 3cdf6ccb |
| 499 |
|
6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER) |
| 500 |
|
- note: there are still recomputations in global_ocean.cs32x15 and |
| 501 |
|
offline_exf_seaice and the gradient agreement changes (gets a |
| 502 |
|
little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt) |
| 503 |
|
- in general, the AD gradients still are wrong |
| 504 |
|
o OpenAD |
| 505 |
|
- clean up code_oad/ directories somewhat by moving files |
| 506 |
|
dontCompile, dontTransform, keepOriginal to OAD_support/ |
| 507 |
|
o model/src: |
| 508 |
|
- using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F |
| 509 |
|
(not currently tested): add dissipation terms before NLFS rescaling of |
| 510 |
|
tendencies (previously done after). |
| 511 |
|
o pkg/diagnostics: |
| 512 |
|
- write stats-diags in ascii file with more digits (same as in monitor). |
| 513 |
|
o pkg/down_slope: |
| 514 |
|
- drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with |
| 515 |
|
NLFS (not tested), use new recip_hFac value in order to conserve tracer. |
| 516 |
|
o model/src: |
| 517 |
|
- new file "apply_forcing.F" containing all the code previously in |
| 518 |
|
external_forcing.F, but with new argument list: pass, as new argument, |
| 519 |
|
the current level tendency array to update (instead of a direct update |
| 520 |
|
of the common bloc array). Change the corresponding calls. |
| 521 |
|
- add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use |
| 522 |
|
EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility). |
| 523 |
|
o pkg/seaice/seaice_lsr, a little bit of clean up |
| 524 |
|
- rearrange some code blocks, so that now all calculations for |
| 525 |
|
setting up the right-hand-sides done within one single block |
| 526 |
|
(I find that easier to read and understand) |
| 527 |
|
- rearrange freedrift-code to reduce the number of ifdefs |
| 528 |
|
- adjust some indentations and comments |
| 529 |
|
|
| 530 |
|
checkpoint64z (2014/07/10) |
| 531 |
|
o model/src and several pkgs: |
| 532 |
|
- change argument list of all S/R called from external_forcing.F and |
| 533 |
|
called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F) |
| 534 |
|
to pass, as argument, the current level tendency array to update |
| 535 |
|
(instead of a direct update of the common bloc array). |
| 536 |
|
- change also (in the same way) argument list of PTRACERS_APPLY_FORCING; |
| 537 |
|
- rename taueddy_external_forcing.f to taueddy_tendency_apply.F |
| 538 |
|
o pkg/seaice/seaice_lsr.F |
| 539 |
|
- always initialize local arrays in seaice_lsr_tridiagu/v |
| 540 |
|
- add more local tapes to seaice_lsr_tridiagu/v |
| 541 |
|
- move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but |
| 542 |
|
keep it in bi/bj loop; this seems to be essential |
| 543 |
|
- gradients are still wrong but only by 4-7 orders of magnitude |
| 544 |
|
instead of 15 orders of magnitude, lab_sea improves a little |
| 545 |
|
o pkg/seaice |
| 546 |
|
- (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that |
| 547 |
|
generates unnecessary code in seaice_lsr_ad |
| 548 |
|
- add more store directives in seaice_lsr to avoid unnecessary code |
| 549 |
|
in seaice_lsr_ad |
| 550 |
|
- exclude some residual computations in seaice_lsr when |
| 551 |
|
ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code |
| 552 |
|
in seaice_lsr_ad |
| 553 |
|
- add more storing, a new tape (model/src/the_main_loop.F) and |
| 554 |
|
another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey |
| 555 |
|
and klockey should be checked by a specialist) |
| 556 |
|
- modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER ) |
| 557 |
|
and update lab_sea after previous changes in pkg/seaice below |
| 558 |
|
o pkg/autodiff: |
| 559 |
|
- introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and |
| 560 |
|
viscFacInAd : run time parameters allowing for adjoint switches |
| 561 |
|
note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F |
| 562 |
|
o pkg/ecco: |
| 563 |
|
- introduce cost_gencost_boxmean.F that computes a box mean |
| 564 |
|
temperature (for use in adjoint sensitivity studies). |
| 565 |
|
o model/src/set_defaults.F : initialize viscFacAdj to 1. |
| 566 |
|
o pkg/mom_common/mom_calc_visc.F: |
| 567 |
|
- ifdef ALLOW_AUTODIFF then include viscFacAdj factor. |
| 568 |
|
o pkg/seaice/seaice_summary.F: |
| 569 |
|
- statement for SEAICEadjMODE now in autodiff_readparms.F |
| 570 |
|
o pkg/seaice: |
| 571 |
|
- remove some store directives and add new ones in an effort to get |
| 572 |
|
finally rid off the recomputation warnings. This is successful |
| 573 |
|
when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are |
| 574 |
|
defined (i.e. no extensive recomputation warnings left), but there |
| 575 |
|
are still too many recomputations on the solver iteration level |
| 576 |
|
- define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h |
| 577 |
|
- move definition of MPSEUDOTIMESTEPS into TAMC-block in |
| 578 |
|
SEAICE_SIZE.h |
| 579 |
|
- add a store directive in S/R seaice_calc_viscosities |
| 580 |
|
o pkg/seaice (ITD code): |
| 581 |
|
- fix definition of Hlimit for multi-threaded case |
| 582 |
|
- use double precision arithmetic to compute Hlimit: this affects results; |
| 583 |
|
update output of experiment seaice_itd. |
| 584 |
|
o replace content of verification/seaice_itd |
| 585 |
|
- instead of a 1D column use the configuration of offline_exf_seaice |
| 586 |
|
to test the ice thickness distribution code with ridging |
| 587 |
|
- this is a first shot at this experiment |
| 588 |
|
- change of some defaults of ridging parameters SEAICEhStar (from |
| 589 |
|
100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F |
| 590 |
|
and lot of new comments. |
| 591 |
|
|
| 592 |
checkpoint64y (2014/06/20) |
checkpoint64y (2014/06/20) |
| 593 |
o pkg/seaice/seaice_reg_ridge.F: |
o pkg/seaice/seaice_reg_ridge.F: |
| 594 |
- modify the regularization of very small volumes of ice; only check |
- modify the regularization of very small volumes of ice; only check |
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