| 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: |
| 8 |
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- prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0 |
| 9 |
|
- add the option to compute no-slip du/dy, dv/dx (i.e. |
| 10 |
|
the offdiagonal strain rate e12) by a second order approximation |
| 11 |
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on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because |
| 12 |
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it is too messy to implement for the implicit LSR matrix. |
| 13 |
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SEAICE_2ndOrderBC = .FALSE. by default |
| 14 |
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|
| 15 |
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checkpoint66h (2017/06/02) |
| 16 |
|
o pkg/seaice: |
| 17 |
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- add new routines to compute stress tensor components and stress tensor |
| 18 |
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divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs |
| 19 |
|
- change names of diagnostics SIsigI/II (commonly used for invariants) |
| 20 |
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to SIsig1/sig2 (more common for principal components) to avoid confusion |
| 21 |
|
o pkf/exf: |
| 22 |
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- add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant); |
| 23 |
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similarly, stop if rotateStressOnAgrid with constant wind-stress. |
| 24 |
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o pkg/seaice: |
| 25 |
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- remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of |
| 26 |
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EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent. |
| 27 |
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- add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice |
| 28 |
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fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy). |
| 29 |
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o pkg/diagnostics: |
| 30 |
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- small piece of code to rename (old) diagnostics, when namelist is processed. |
| 31 |
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o model/src: |
| 32 |
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- new run-time param (useMin4hFacEdges) to select method for setting hFacW,S: |
| 33 |
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originally, set as minimum of adjacent hFacC factor ; now (new default) |
| 34 |
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computed from rSurfW,S and rLowW,S by applying same rules as for hFacC. |
| 35 |
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Only matters when useShelfIce=T with particular ice-shelf cavity geometry. |
| 36 |
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o pkg/seaice: |
| 37 |
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- add momemtum advection, off by default, still in test phase |
| 38 |
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most of the momentum advection code is adapted and reused from mom_vecinv |
| 39 |
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o pkg/mom_vecinv: |
| 40 |
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- pass these runtime flags: |
| 41 |
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selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv |
| 42 |
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as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4, |
| 43 |
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so that these routines can also be used in pkg/seaice. |
| 44 |
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|
| 45 |
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checkpoint66g (2017/04/24) |
| 46 |
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o model/src: |
| 47 |
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- more robust ordering of column thickness integral (=Sum_k(drF*hFac) ) |
| 48 |
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to get same expression (regarding machine truncation) in different places |
| 49 |
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in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should). |
| 50 |
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Update forward output of experiments: global_ocean.cs32x15 (all 5 except |
| 51 |
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viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope. |
| 52 |
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o pkg/shelfice: |
| 53 |
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- ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F |
| 54 |
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to shelfice_init_fixed.F |
| 55 |
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- change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from |
| 56 |
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ini_masks_etc.F for now) to update ocean upper boundary position according |
| 57 |
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to ice-shelf topography (instead of directly updating hFacC). |
| 58 |
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o model/src: |
| 59 |
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- move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of |
| 60 |
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packages_init_fixed.F to allow other pkgs to set mask and weight fields. |
| 61 |
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|
| 62 |
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checkpoint66f (2017/04/06) |
| 63 |
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o model/src: |
| 64 |
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- add specific run-time param to select level of printed plot-field-maps, |
| 65 |
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set by default to debugLevel. Remove internal param "printDomain". |
| 66 |
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o pkg/seaice: |
| 67 |
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- add flag to add snow mass to seaiceMassC/U/V, the default is |
| 68 |
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SEAICEaddSnowMass=.FALSE., not to change previous results |
| 69 |
|
o pkg/bling |
| 70 |
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- Bug fix in bling_production regarding unit conversion for diagnostics |
| 71 |
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being put in the wrong place |
| 72 |
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o model/src: |
| 73 |
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- add back recomputation of rSurfW & S to ensure consistent column thickness |
| 74 |
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(needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only |
| 75 |
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when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F |
| 76 |
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revision 1.51) but was removed accidentally on 2014/02/08 (v1.53). |
| 77 |
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o pkg/autodiff: |
| 78 |
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- clean-up "checkpoint.flow" |
| 79 |
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o pkg/rw (Contribution from Jody Klymak): |
| 80 |
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option to set mds file suffix as function of time in simulation: |
| 81 |
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*) new input parameter "rwSuffixType" (read from PARM03 namelist) |
| 82 |
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to select file suffix format; by default (=0), use iteration number; |
| 83 |
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*) add simple routine to return file suffix according to rwSuffixType; |
| 84 |
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*) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice), |
| 85 |
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use new S/R to get file suffix, except for debug output file (diagFreq) |
| 86 |
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and pkgs offline & rbcs input files. |
| 87 |
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o pkg/rw: |
| 88 |
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- uniform processing of "I10" suffix across writing fld routines; used to |
| 89 |
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simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F |
| 90 |
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(similar to cg3d.F, cg3d_ex0.F) |
| 91 |
|
o pkg/mom_vecinv: |
| 92 |
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- highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted |
| 93 |
|
vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp). |
| 94 |
|
o pkg/bling: |
| 95 |
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- Many small changes intended to clean the code. |
| 96 |
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Unnecessary ADJOINT_SAFEs removed ; |
| 97 |
|
removed BLING_COST.h BLING_CTRL.h bling_cost.F ; |
| 98 |
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diagnostics added. |
| 99 |
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|
| 100 |
|
checkpoint66e (2017/03/14) |
| 101 |
|
o pkg/exf: |
| 102 |
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- interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size |
| 103 |
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definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h; |
| 104 |
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use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to |
| 105 |
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avoid any dynamic allocation ; |
| 106 |
|
- S/R EXF_CHECK: add new check & stop when file-name is defined but not |
| 107 |
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read-in ; add warning when file is read-in but not used within pkg/exf ; |
| 108 |
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+ check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC). |
| 109 |
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- update exf_summary.F (print {FLD}RepCycle). |
| 110 |
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o verification/global_with_exf: |
| 111 |
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- switch on exf interpolation in AD test (just like the forward test) |
| 112 |
|
o pkg/mom_vecinv: |
| 113 |
|
- add storage directives to avoid recomputations within mom_vecinv.F |
| 114 |
|
which were generating seg. fault with gfortran -devel |
| 115 |
|
o pkg/ctrl, pkg/smooth: |
| 116 |
|
- initialize array halos which were generating seg. fault with |
| 117 |
|
gfortran -devel in adjoint mode |
| 118 |
|
o pkg/exf: |
| 119 |
|
- for each input field, enable to specify a field specific repeat-cycle |
| 120 |
|
({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod". |
| 121 |
|
o verification/lab_sea: |
| 122 |
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- update AD results of primary test and noseaicedyn test after switching |
| 123 |
|
to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient |
| 124 |
|
check stays about the same. |
| 125 |
|
o pkg/exf: |
| 126 |
|
- fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T. |
| 127 |
|
- exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat |
| 128 |
|
o pkg/bling, USE_EXFCO2 code: |
| 129 |
|
- add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default); |
| 130 |
|
- update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD). |
| 131 |
|
o pkg/exf: |
| 132 |
|
- rename S/R EXF_INIT to EXF_INIT_VARIA ; |
| 133 |
|
- add arguments: fldName (for debug msg) and fldRepeatCycle (set to |
| 134 |
|
repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD) |
| 135 |
|
and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ; |
| 136 |
|
- add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed |
| 137 |
|
EXF_INIT_FLD) and update calls in exf_init_varia.F |
| 138 |
|
- For now, for backward compatibility, keep a simplified version of S/Rs |
| 139 |
|
EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F |
| 140 |
|
- add and pass new arguments: fldName (for debug msg) and fldRepeatCycle |
| 141 |
|
to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F |
| 142 |
|
o tools/genmake2: |
| 143 |
|
- replace "bc -l" (only used once) by "expr" (already used). |
| 144 |
|
o verification/global_ocean.cs32x15: |
| 145 |
|
- turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn". |
| 146 |
|
Note: exf setting (data.exf) can be compared to other exf secondary exp |
| 147 |
|
"seaice" (kept with useCAL=T) which has same time dependent forcing. |
| 148 |
|
|
| 149 |
|
checkpoint66d (2017/02/13) |
| 150 |
|
o pkg/exf: |
| 151 |
|
- remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning |
| 152 |
|
early on (in packages_boot.F) to stress this change in pkg setting. |
| 153 |
|
- In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg |
| 154 |
|
o model/src: |
| 155 |
|
- move call to ecco_phys to end of time step; this may induce minor |
| 156 |
|
cost function changes by shifting time averages by one time step |
| 157 |
|
for some variables; this revision resulted in changed adjoint results |
| 158 |
|
in MITgcm_contrib/verification_other/global_oce_cs32 |
| 159 |
|
o pkg/exf: |
| 160 |
|
- Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ; |
| 161 |
|
this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields, |
| 162 |
|
e.g. precip, are not available. |
| 163 |
|
o pkg/flt: |
| 164 |
|
- flt_init_varia.F: use pickupSuff if specified |
| 165 |
|
- add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first, |
| 166 |
|
intermediate, step towards completing pkg/exch2 support within pkg/flt; |
| 167 |
|
ifdef DEVEL_FLT_EXCH2 then: |
| 168 |
|
- flt_init_fixed.F: comment out stop |
| 169 |
|
- flt_exch2.F: conserve ipart, jpart (grid coordinates) |
| 170 |
|
- exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates) |
| 171 |
|
- flt_mapping.F: attempt to fix longitude diagnostic near date-line |
| 172 |
|
- flt_init_varia.F: hack initialization (for testing purposes w. LLC90) |
| 173 |
|
o tools/genmake2 & pkg/pkg_depend: |
| 174 |
|
- define new type of pkg dependency rule ("=pkg_x"), less strict than |
| 175 |
|
the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled |
| 176 |
|
(-pkg_x in packages.conf). |
| 177 |
|
- change pkg/exf dependency rule from "exf +cal" to "exf =cal"; |
| 178 |
|
- add "+cal" to dependency list of pkg/ecco (needed to compile). |
| 179 |
|
- simplify FWD experiment "offline_exf_seaice" by removing pkg/cal. |
| 180 |
|
o utils/matlab: |
| 181 |
|
- adding ocean_basin routines for defining basin masks. |
| 182 |
|
o pkg/exf: |
| 183 |
|
- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
| 184 |
|
arguments, allowing to check (and stop) if parameter setting of |
| 185 |
|
{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
| 186 |
|
useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
| 187 |
|
for backward compatibility. |
| 188 |
|
- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
| 189 |
|
exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
| 190 |
|
o pkg/bling (USE_EXFCO2 code): |
| 191 |
|
- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
| 192 |
|
by adding a call to S/R EXF_GETFFIELD_START. |
| 193 |
|
o pkg/exf: |
| 194 |
|
- allows to compile without pkg/cal (but disabled by current dependency |
| 195 |
|
rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
| 196 |
|
run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
| 197 |
|
of {FLD}startdate1 & date2 ; consistency check not yet coded. |
| 198 |
|
o verification/global_ocean.cs32x15: |
| 199 |
|
- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
| 200 |
|
corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
| 201 |
|
o pkg/exf: |
| 202 |
|
- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
| 203 |
|
calculations); change FWD experiment global_ocean.cs32x15 |
| 204 |
|
(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
| 205 |
|
o pkg/exf: |
| 206 |
|
- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
| 207 |
|
{FIELD}startdate to {FIELD}StartTime |
| 208 |
|
Note: new name also fit better the content, i.e, a start time in second. |
| 209 |
|
o eesupp/src: |
| 210 |
|
- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
| 211 |
|
o pkg/exf: |
| 212 |
|
- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
| 213 |
|
to allow to read-in Sensible & Latent Heat flux ; |
| 214 |
|
- simplify pkg/exf main options: |
| 215 |
|
1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
| 216 |
|
exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
| 217 |
|
compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
| 218 |
|
2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
| 219 |
|
ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
| 220 |
|
3) improve options documentation in EXF_OPTIONS.h. |
| 221 |
|
o pkg/ecco: |
| 222 |
|
- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
| 223 |
|
ecco_summary.F: add passive tracer cost functions to gencost; |
| 224 |
|
m_ptracer and m_boxmean_ptracer |
| 225 |
|
o pkg/ctrl: |
| 226 |
|
- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
| 227 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
| 228 |
|
of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
| 229 |
|
xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
| 230 |
|
o model/src: |
| 231 |
|
- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
| 232 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
| 233 |
|
o pkg/exf: |
| 234 |
|
- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
| 235 |
|
xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
| 236 |
|
|
| 237 |
|
checkpoint66c (2017/01/19) |
| 238 |
|
o verification: |
| 239 |
|
- add new option "-src" to testreport to only produce source code (*.f), |
| 240 |
|
including taf output src code (if using '-adm'/'-tlm' option). |
| 241 |
|
o pkg/exf: |
| 242 |
|
- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
| 243 |
|
o pkg/diagnostics: |
| 244 |
|
- add run-time variable diagMdsDir to specify a subdirectory for |
| 245 |
|
diagnostic output when mds is being used and mdsioLocalDir is not. |
| 246 |
|
o pkg/mnc: |
| 247 |
|
- mnc_utils.F: edit stop message |
| 248 |
|
o pkg/autodiff: |
| 249 |
|
- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 250 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 251 |
|
o pkg/profiles: |
| 252 |
|
- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
| 253 |
|
profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
| 254 |
|
- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 255 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 256 |
|
o pkg/smooth: |
| 257 |
|
- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
| 258 |
|
- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
| 259 |
|
- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
| 260 |
|
o pkg/exf: |
| 261 |
|
- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
| 262 |
|
issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
| 263 |
|
generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
| 264 |
|
- summary: skip detailed field report if not used (empty file-name). |
| 265 |
|
o tools/xmakedepend: |
| 266 |
|
- In case line editor "ed" is missing, switch to "sed" command to clean-up |
| 267 |
|
Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
| 268 |
|
o pkg/exf: |
| 269 |
|
- change definition of "hflux" input file to always include Short-Wave; |
| 270 |
|
this is now consistent with hflux computation (if using bulk-formulae) |
| 271 |
|
and hflux diagnostic & documentation (in EXF_FIELDS.h). |
| 272 |
|
|
| 273 |
|
checkpoint66b (2016/12/01) |
| 274 |
|
o model & momentum pkgs: |
| 275 |
|
- implement fully implicit bottom friction combined with implicit surf. |
| 276 |
|
pressure, for now, only in hydrostic formulation: |
| 277 |
|
+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
| 278 |
|
and run with selectImplicitDrag=2 ; |
| 279 |
|
+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
| 280 |
|
- partial implicit time-stepping (bot. friction + vert. visc first, then |
| 281 |
|
surf. press) corresponding to selectImplicitDrag=1 should be applicable |
| 282 |
|
to NH formulation but not available until we solve for surf. pressure |
| 283 |
|
increment (instead of full etaN). |
| 284 |
|
- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
| 285 |
|
with implicit vertical viscosity. |
| 286 |
|
o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
| 287 |
|
- this is a first version that includes many regularisations that may |
| 288 |
|
not all be necessary, to be sorted out, |
| 289 |
|
- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
| 290 |
|
- change one verification experiment in seaice_itd to use and test new code |
| 291 |
|
- seaice_growth: catch a case where the argument of log can be zero |
| 292 |
|
or smaller (important for code stability) |
| 293 |
|
o model/src: |
| 294 |
|
- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
| 295 |
|
& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
| 296 |
|
similar A.X'=Y' system (with same matrix A) in subsequent calls; |
| 297 |
|
switch based on errCode (In/Out) argument value; in calling routines, |
| 298 |
|
initialise errCode before first call. |
| 299 |
|
|
| 300 |
|
checkpoint66a (2016/10/18) |
| 301 |
|
o pkg/bling: |
| 302 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
| 303 |
|
Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
| 304 |
|
o model/src & pkg/ptracers: |
| 305 |
|
- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
| 306 |
|
GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
| 307 |
|
implicitDiffusion (respectively) are used (even without momImplVertAdv |
| 308 |
|
or temp,salt,PTRACERS_ImplVertAdv). |
| 309 |
|
o model/src & generic_advdiff: |
| 310 |
|
- add parenthesis in main diagonal calculation of implicit vertical |
| 311 |
|
diffusion matrix (impldiff.F & gad_implicit_r.F). |
| 312 |
|
This affects results at machine truncation level; update output of many |
| 313 |
|
verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
| 314 |
|
o pkg/mom_commom & generic_advdiff: |
| 315 |
|
- add deep atmosphere and anelastic scaling factor in implicit vertical |
| 316 |
|
advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
| 317 |
|
o model/src: |
| 318 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
| 319 |
|
& solve_pentadiagonal.F |
| 320 |
|
|
| 321 |
|
checkpoint65z (2016/09/28) |
| 322 |
|
o pkg/seaice: fix multithreading for seaice_fgmres.F |
| 323 |
|
- remove unecessary variables from common blocks |
| 324 |
|
- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
| 325 |
|
basis, that are stored in commom blocks (including integer variable i1) |
| 326 |
|
- clean up code a little by removing commented lines that refer to |
| 327 |
|
original code |
| 328 |
|
- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
| 329 |
|
o MITgcm manual: |
| 330 |
|
- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
| 331 |
|
preliminary documentation for generic controls (8.3; ctrl.tex), |
| 332 |
|
a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
| 333 |
|
ecco_costfunction.tex |
| 334 |
|
o pkg/ecco: |
| 335 |
|
- update and cleanup list of CCP options |
| 336 |
|
- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
| 337 |
|
is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
| 338 |
|
- add checks that retired run-time options are not used, and in relation |
| 339 |
|
to gencost_mask and gencost_errfile |
| 340 |
|
- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
| 341 |
|
gencost_nrecperiod |
| 342 |
|
- fix m_eta computation for virtual salt flux case |
| 343 |
|
- add m_horflux_vol case (selected via gencost_barfile) that computes |
| 344 |
|
transports via cost_gencost_boxmean (gencost_flag=-3) |
| 345 |
|
- use gencost_flag more systematically (i.e., avoid using gencost_name) |
| 346 |
|
for code switches (aside from physical variable selection) |
| 347 |
|
o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
| 348 |
|
attempt appears to be a bit of a hack and my need some repair down the road |
| 349 |
|
o pkg/exf: |
| 350 |
|
- interpolation near South Pole: fix criteria on input field latitude. |
| 351 |
|
o pkg/icefront & pkg/exf: |
| 352 |
|
- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
| 353 |
|
from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
| 354 |
|
o pkg/exf: |
| 355 |
|
- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
| 356 |
|
"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
| 357 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
| 358 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
| 359 |
|
Change output file content by writing interpolated field before applying |
| 360 |
|
land-sea mask (helpful for debug). |
| 361 |
|
- 2 compon. vector interpolation with rotation: apply scaling factor on |
| 362 |
|
each compon. (Eastward and Northward) just before rotation. |
| 363 |
|
o pkg/bling: |
| 364 |
|
- Cleaned package. Removed not needed code and comments. |
| 365 |
|
- adjoint example now works |
| 366 |
|
(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
| 367 |
|
o pkg/ptracers: |
| 368 |
|
- add Bruno Deremble's code to complete the linear surface correction |
| 369 |
|
for tracer conservation; |
| 370 |
|
- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 371 |
|
|
| 372 |
|
checkpoint65y (2016/07/29) |
| 373 |
|
o pkg/debug (stats): |
| 374 |
|
- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 375 |
|
proc/thread mapping); |
| 376 |
|
- fix Min & Max for case where 1 thread has only empty tiles; |
| 377 |
|
- use RL variable to count number of wet grid points (with big domain, |
| 378 |
|
can be too large to fit into integer*4). |
| 379 |
|
o pkg/monitor: |
| 380 |
|
- use RL variable to count number of wet grid points (but used only for del2) |
| 381 |
|
- add new routine to compute Advective CFL within tracer time-stepping with |
| 382 |
|
writing delayed until next monitor output. |
| 383 |
|
o pkg/obcs: |
| 384 |
|
- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 385 |
|
o pkg/cal: |
| 386 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
| 387 |
|
eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
| 388 |
|
o pkg/dic & seaice: |
| 389 |
|
- fix compilation of ocean component for coupled atm+ocn model with |
| 390 |
|
seaice dynamics & dic. |
| 391 |
|
|
| 392 |
|
checkpoint65x (2016/06/11) |
| 393 |
|
o add a license text file in main MITgcm tree. |
| 394 |
|
o added pkg/bling: |
| 395 |
|
- intermediate complexity biogeochemical model |
| 396 |
|
- see bling_description.txt for details |
| 397 |
|
- verification experiment is global_oce_biogeo_bling (for now, in |
| 398 |
|
Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 399 |
|
- add entry point in pkg/gchem for new pkg "bling". |
| 400 |
|
o pkg/seaice: fix tensile stength computation |
| 401 |
|
- replace global field tensileStrength by tensileStrFac |
| 402 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
| 403 |
|
- fortunately that does not affect any verification results |
| 404 |
|
|
| 405 |
|
checkpoint65w (2016/05/12) |
| 406 |
|
o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 407 |
|
with ECCO_CTRL_DEPRECATED defined |
| 408 |
|
o verification/global_ocean.cs32x15: |
| 409 |
|
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 410 |
|
with "selectNHfreeSurf=1". |
| 411 |
|
o model/src (non-hydrostatic free-surface): |
| 412 |
|
- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
| 413 |
|
was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
| 414 |
|
- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
| 415 |
|
for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
| 416 |
|
and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
| 417 |
|
This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
| 418 |
|
- Update output (changes at machine truncation level) of verification exp: |
| 419 |
|
exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
| 420 |
|
short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
| 421 |
|
o pkg/seaice: ITD code |
| 422 |
|
- fix picking up from a single category model by initialising |
| 423 |
|
heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
| 424 |
|
- split a long warning message in seaice_check_pickup.F into two lines, |
| 425 |
|
because NEC SX-ACE cannot deal with the long line. |
| 426 |
|
o model/src: |
| 427 |
|
- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
| 428 |
|
o pkg/seaice: |
| 429 |
|
- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
| 430 |
|
o pkg/seaice: |
| 431 |
|
- add basal stress as parameterisation for grounding ice |
| 432 |
|
following Lemieux et al. (2015) |
| 433 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
| 434 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
| 435 |
|
- The adjoint complains with extra recomputations so there is also a |
| 436 |
|
new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
| 437 |
|
order to postpone the problem |
| 438 |
|
- compile the new code in lab_sea |
| 439 |
|
o verification/halfpipe_streamice: |
| 440 |
|
- update both TAF and OpenAD adm output (machine truncation differences) |
| 441 |
|
|
| 442 |
|
checkpoint65v (2016/04/08) |
| 443 |
|
o verification/advect_xz: |
| 444 |
|
- increase overlap size from 3 to 4 and add new secondary test for PQM |
| 445 |
|
advection scheme (with mono & wino limiter). |
| 446 |
|
- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
| 447 |
|
o model/src: |
| 448 |
|
- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
| 449 |
|
added phi0Ref) to set vertical axis origin and phiRef origin; |
| 450 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
| 451 |
|
According to coordinate and fluid type: |
| 452 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
| 453 |
|
ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
| 454 |
|
OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
| 455 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
| 456 |
|
- remove Ro_SeaLevel from ATM experiment parameter files; |
| 457 |
|
- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
| 458 |
|
complement; update output.txt (changes at machine truncation level). |
| 459 |
|
o pkg/seaice/seaice_evp.F |
| 460 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
| 461 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
| 462 |
|
verification experiment lab_sea.hb87 -> updated |
| 463 |
|
|
| 464 |
|
checkpoint65u (2016/03/14) |
| 465 |
|
o pkg/generic_advdiff: |
| 466 |
|
- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
| 467 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
| 468 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
| 469 |
|
testing and not for actual use. |
| 470 |
|
o model/src: |
| 471 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
| 472 |
|
origin r = rF(1); |
| 473 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
| 474 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
| 475 |
|
more accurate pressure vertical profile; options not linked to EOS type |
| 476 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 477 |
|
- start to implement variable gravity (along vertical): for now, only with |
| 478 |
|
z-coords (not even z*). |
| 479 |
|
- add Ideal Gas equation of state for height coordinate. |
| 480 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
| 481 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
| 482 |
|
o pkg/exf: |
| 483 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
| 484 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
| 485 |
|
to velocity point) for each field that gets loaded from file. This option |
| 486 |
|
identically mimics the input file organization (e.g. record numbers in year |
| 487 |
|
by year input files) besides the change in horizontal grid. |
| 488 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 489 |
|
can be provided on the A-grid in zonal/meridional direction and |
| 490 |
|
rotated on the fly. This only applies to the case when the exf |
| 491 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
| 492 |
|
o model/src: |
| 493 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
| 494 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
| 495 |
|
inactive, src code yet to come) |
| 496 |
|
|
| 497 |
|
checkpoint65t (2016/02/10) |
| 498 |
|
o pkg/atm_phys: |
| 499 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
| 500 |
|
o model/src: |
| 501 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
| 502 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 503 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
| 504 |
|
o tools: |
| 505 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
| 506 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
| 507 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
| 508 |
|
o pkg/seaice: |
| 509 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
| 510 |
|
has an effect |
| 511 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
| 512 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
| 513 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
| 514 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
| 515 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
| 516 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
| 517 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
| 518 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
| 519 |
|
use with SEAICEuseKrylov |
| 520 |
|
o pkg/seaice/seaice_lsr.F |
| 521 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 522 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
| 523 |
|
an effect. |
| 524 |
|
o pkg/seaice: add two new parameters |
| 525 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
| 526 |
|
parameter is not in any namelist) |
| 527 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
| 528 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
| 529 |
|
solver |
| 530 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
| 531 |
|
affects some experiments at truncation level: |
| 532 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
| 533 |
|
- global_ocean.cs32x15.seaice (11 digits), |
| 534 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
| 535 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
| 536 |
|
o pkg/salt_plume & pkg/thsice: |
| 537 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
| 538 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
| 539 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
| 540 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
| 541 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
| 542 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 543 |
|
o pkg/dic: |
| 544 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
| 545 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 546 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 547 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
| 548 |
|
(previously done in ocn_apply_import.F). |
| 549 |
|
o tools/adjoint_options: |
| 550 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 551 |
|
has been changed on Jan 14, 2016. |
| 552 |
|
o pkg/ggl90: |
| 553 |
|
- add alternative discretisation of vertical shear (off by default), to |
| 554 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 555 |
|
vertical shear of mean flow (@ grid-cell center). |
| 556 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 557 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 558 |
|
o pkg/atm_compon_interf: |
| 559 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 560 |
|
pass last value, stored directly before export to CPL ; |
| 561 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 562 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
| 563 |
|
|
| 564 |
|
checkpoint65s (2016/01/13) |
| 565 |
|
o eesupp & genmake2: |
| 566 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
| 567 |
|
ETIME and consistent output; use the appropriate version in timers.F |
| 568 |
|
o model/src: |
| 569 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 570 |
|
integr_continuity; turned off by default. |
| 571 |
|
o pkg/dic: |
| 572 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
| 573 |
|
o tools/tst_2+2: |
| 574 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
| 575 |
|
to fail for no good reason. |
| 576 |
|
o eesupp & genmake2: |
| 577 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
| 578 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
| 579 |
|
o coupler pkgs: |
| 580 |
|
Finish implementation of optionally-exchanged variable switches (started on |
| 581 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
| 582 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
| 583 |
|
advection in OCN component; this requires sequential coupling. |
| 584 |
|
coupler (pkg/atm_ocn_coupler): |
| 585 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
| 586 |
|
routines (useful for debug). |
| 587 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
| 588 |
|
flux, DIC fields) if corresponding switch is ON. |
| 589 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
| 590 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
| 591 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 592 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
| 593 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
| 594 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
| 595 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
| 596 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
| 597 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
| 598 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
| 599 |
|
- hold in common block coupler optionally-exchanged variable switch |
| 600 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
| 601 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
| 602 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
| 603 |
|
to contain new additional exchanged fields). |
| 604 |
|
o pkg/dic: |
| 605 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
| 606 |
|
o pkg/thsice: |
| 607 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
| 608 |
|
and writing of thsice pickup files. |
| 609 |
|
o pkg/atm_compon_interf: |
| 610 |
|
- move all field individual export-call out of cpl_export_import_data.F |
| 611 |
|
into new S/R ATM_EXPORT_FIELDS |
| 612 |
|
o pkg/atm_compon_interf: |
| 613 |
|
- store state variables (for now, only thSIce fields) just before beeing |
| 614 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
| 615 |
|
atm_store_my_data.F like all exported fluxes. |
| 616 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
| 617 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
| 618 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
| 619 |
|
o pkg/dic: |
| 620 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
| 621 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
| 622 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
| 623 |
|
value can be from domain [0,1] to average between the two methods |
| 624 |
|
o pkg/atm_phys: |
| 625 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
| 626 |
|
hold fixed in time). |
| 627 |
|
|
| 628 |
|
checkpoint65r (2015/12/21) |
| 629 |
|
o pkg/seaice: |
| 630 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
| 631 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
| 632 |
|
o pkg/seaice: |
| 633 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
| 634 |
|
when SEAICEscaleSurfStress=.TRUE., |
| 635 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
| 636 |
|
o pkg/atm_phys: |
| 637 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 638 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 639 |
|
for individual contribution (convection, LSC cond, radiation) |
| 640 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 641 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 642 |
|
o pkg/ggl90: |
| 643 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
| 644 |
|
avoid instability problems in the explicit horizontal diffusion term for |
| 645 |
|
long time steps or high resolution |
| 646 |
|
o pkg/diagnostics: |
| 647 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
| 648 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
| 649 |
|
o testreport: |
| 650 |
|
- remove "-v" (verbose option) in default mpirun command. |
| 651 |
|
o pkg/seaice/seaice_growth: |
| 652 |
|
- catch potential division by zero in ITD code, does not change |
| 653 |
|
verification results |
| 654 |
|
o pkg/ecco: |
| 655 |
|
- retire old codes to the Attic. The calls to retired functions are |
| 656 |
|
left in a commented form in case they ever need to be re-activated. |
| 657 |
|
- ecco_check.F: issue warning if any old CPP option is |
| 658 |
|
defined that corresponds to retired codes -- then stop. |
| 659 |
|
o pkg/atm_compon_interf: |
| 660 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
| 661 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
| 662 |
|
time-step, similar to what is done for seaIceMass. |
| 663 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
| 664 |
|
o eesupp & genmake2: |
| 665 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
| 666 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
| 667 |
|
o pkg/seaice/seaice_evp: |
| 668 |
|
- refine residual computation |
| 669 |
|
|
| 670 |
|
checkpoint65q (2015/11/18) |
| 671 |
|
o pkg/seaice/seaice_evp: |
| 672 |
|
- fix residual computations so that they no longer affect the actual |
| 673 |
|
simulation code |
| 674 |
|
- fix seaice_readparams to be able to actually set new parameters |
| 675 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
| 676 |
|
o model/src: |
| 677 |
|
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
| 678 |
|
like: deltaT*FLOAT(myIter) when myIter is large: |
| 679 |
|
a) replaced by DFLOAT (if not seen by TAF); |
| 680 |
|
b) remove "FLOAT" and use implicit type conversion (if seen by TAF). |
| 681 |
|
o pkg/aim_v23: |
| 682 |
|
- write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading |
| 683 |
|
when pickupSuff is set ; do write rolling pickups + at the end of the run. |
| 684 |
|
o pkg/atm_ocn_coupler + ocn_compon_interf: |
| 685 |
|
- in prep for using pkg/seaice Dyn in coupled set-up, implement sequential |
| 686 |
|
coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ; |
| 687 |
|
add corresponding call in DO_OCEANIC_PHYS. |
| 688 |
|
o coupler pkgs: |
| 689 |
|
Start a new way to set-up optionally-exchanged variables (previously, only |
| 690 |
|
there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler |
| 691 |
|
data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ; |
| 692 |
|
send switch to ATM & OCN compon before reading their own "data.cpl" (so that |
| 693 |
|
compononent param default can be set accordingly). |
| 694 |
|
Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch |
| 695 |
|
but rather applies to a group a fields (going both ways like for DIC) |
| 696 |
|
and corresponds to an option of coupling config. |
| 697 |
|
coupler (pkg/atm_ocn_coupler): |
| 698 |
|
- change parameter file from "data" to "data.cpl" (in cpl_read_params.F), |
| 699 |
|
and read namelist directly (without eessup S/R calls) instead of |
| 700 |
|
in the very un-flexible old way, 1 param per line, in fixed order; |
| 701 |
|
- add error-counter to track errors (e.g., missing "data.cpl") and to stop |
| 702 |
|
cleanly in CPL_CHECK_CPLCONFIG |
| 703 |
|
- add new coupling-exchange selectors (some not yet active) including |
| 704 |
|
cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h |
| 705 |
|
and ocnCpl_exchange_DIC=T in OCNIDS.h); |
| 706 |
|
- add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each |
| 707 |
|
component ; called directly from coupler.F, after comp. registrations; |
| 708 |
|
- rename few variable-ID names (in ATMIDS.h & OCNIDS.h): |
| 709 |
|
atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name -> |
| 710 |
|
-> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName |
| 711 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 712 |
|
- add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding |
| 713 |
|
CPP header file in all pkg source files. |
| 714 |
|
- move checking of comp. configs out of cpl_exch_configs.F into new S/R |
| 715 |
|
ATM/OCN_CHECK_CPLCONFIG; |
| 716 |
|
- add error-counter to track errors (e.g., in "data.cpl") and to stop |
| 717 |
|
cleanly in ATM/OCN_CHECK_CPLCONFIG; |
| 718 |
|
- add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors |
| 719 |
|
from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and |
| 720 |
|
before PACKAGES_READPARMS; |
| 721 |
|
verification/cpl_aim+ocn/: |
| 722 |
|
- update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file |
| 723 |
|
"data.cpl" for coupler (in input_cpl). |
| 724 |
|
o eesupp/inc: |
| 725 |
|
- change the MPI-global-sum default (in CPP_EEOPTIONS.h) to: |
| 726 |
|
#define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F) |
| 727 |
|
to always cumulate tile local-sum in the same order (still uses |
| 728 |
|
MPI_Allreduce like standard code). |
| 729 |
|
- in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files |
| 730 |
|
that are now identical to standard version (in eesupp/inc). |
| 731 |
|
o pkg/shelfice: |
| 732 |
|
- add SHELFICETransCoeffTFile for initializing spatially varying |
| 733 |
|
heat and salt transfer coefficients |
| 734 |
|
o pkg/atm_compon_interf & ocn_compon_interf: |
| 735 |
|
- combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous |
| 736 |
|
S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA |
| 737 |
|
- move bi,bj loops inside S/R OCN_STORE_MY_DATA |
| 738 |
|
o pkg/atm_ocn_coupler: |
| 739 |
|
- initialise to zero ATMVARS.h & OCNVARS.h arrays. |
| 740 |
|
o pkg/rbcs: |
| 741 |
|
- select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows |
| 742 |
|
to compile with maskLEN=1 when all tracers use the same RBCS-mask. |
| 743 |
|
- add a short report (to STDOUT) about RBCS-mask settings. |
| 744 |
|
|
| 745 |
|
checkpoint65p (2015/10/23) |
| 746 |
|
o pkg/seaice/seaice_evp.F: fix store directives and key computations, since |
| 747 |
|
there is no adjoint test for EVP, we don't know what it does to the adjoint |
| 748 |
|
solution, but at least there are no more recomputation warnings left |
| 749 |
|
o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands |
| 750 |
|
a chance of giving the same results as a fully converged VP (JFNK) solver |
| 751 |
|
o tools/adjoint_options/adjoint_diva: |
| 752 |
|
- fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA |
| 753 |
|
o pkg/streamice: |
| 754 |
|
- spotted bug in streamice_driving_stress using dyG where should have been dxG |
| 755 |
|
o pkg/exf: |
| 756 |
|
- remove STOP statement that prevented to use wind or (wind-)stress |
| 757 |
|
interpolation for constant-in-time forcing fields (wind/stress period = 0). |
| 758 |
|
o pkg/seaice: |
| 759 |
|
- replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires |
| 760 |
|
5 additionals 2D fields and 6 new store directives |
| 761 |
|
- change logic in seaice_readparms.F: EVP code can now be turned on in |
| 762 |
|
various ways, setting SEAICE_deltaTev is no longer required, |
| 763 |
|
alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev, |
| 764 |
|
or SEAICEaEVPcoeff |
| 765 |
|
o pkg/shelfice/shelfice_thermodynamics.F |
| 766 |
|
- redefining uLoc/vLoc to u/v, instead of 2u/v |
| 767 |
|
o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz |
| 768 |
|
- this is an intermediate state of a truely converging EVP that has |
| 769 |
|
the potential of outperforming implicit VP methods, I do not recommend |
| 770 |
|
using it yet. |
| 771 |
|
- for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION |
| 772 |
|
and all parameters are hardwired |
| 773 |
|
- for convergence it still requires very smooth regularisations, that means, |
| 774 |
|
if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is |
| 775 |
|
different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also |
| 776 |
|
specific averaging appears to be required, still subject to tuning |
| 777 |
|
- still needs cleaning and I need to turn parameter into runtime parameters |
| 778 |
|
- add code to compute and print residuals of iteration, compile with |
| 779 |
|
defining ALLOW_SEAICE_EVP_RESIDUAL to enable it |
| 780 |
|
o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq) |
| 781 |
|
that entered with r1.54 on Sep04, 2015, -> update results |
| 782 |
|
|
| 783 |
|
checkpoint65o (2015/09/14) |
| 784 |
|
o pkg/mom_vecinv & mom_common: |
| 785 |
|
- add deep-atmosphere geometry factor in mom_calc_visc.F + in routines |
| 786 |
|
called from there. |
| 787 |
|
- add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this |
| 788 |
|
allows to use Vector-Invariant form in deep atmos and anelastic formulation |
| 789 |
|
o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015) |
| 790 |
|
and Koenig-Beatty+Holland (2012) |
| 791 |
|
- two new parameters SEAICE_tensilFac and SEAICE_tensilDepth |
| 792 |
|
- global 2D field tensileStrength, computed in seaice_calc_ice_strength |
| 793 |
|
- requires an extra input argument for S/R seaice_calc_viscosities |
| 794 |
|
- tensileStrength's depth dependence is different from Itkin et al. (2015) |
| 795 |
|
(to be changed and played with, for now exponential) |
| 796 |
|
o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.) |
| 797 |
|
- if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice |
| 798 |
|
by AREA according to Connelly et al. (2004), JPO. |
| 799 |
|
- For EVP and the LSR solver, the implicit part of the drag term is |
| 800 |
|
the only non-zero term in the denominator when there is no ice (which |
| 801 |
|
prevented running the model with zero ice-ocean drag). If |
| 802 |
|
SEAICEscaleSurfStress = .TRUE., this results in a division by zero |
| 803 |
|
(or zero main diagonals BU/BV) which need to be caught. A practical |
| 804 |
|
consequence is that for open water, the momentum equation reduce |
| 805 |
|
to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if |
| 806 |
|
they happen to be zero, often leading to a non-zero solution over |
| 807 |
|
open water. |
| 808 |
|
o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more |
| 809 |
|
efficient EVP method. |
| 810 |
|
- introduce area-weighted averages for e12 (analogously to |
| 811 |
|
seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits |
| 812 |
|
remain, but also changing the order of terms in the previous average |
| 813 |
|
changed the results as much) -> update experiment |
| 814 |
|
- add SEAICE_DELTA_SMOOTHREG code |
| 815 |
|
- disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for |
| 816 |
|
TEM-code |
| 817 |
|
- adjust loop bounds so that only required fields are computed |
| 818 |
|
- add new averaging code for zetaZ/deltaZ (again similar to |
| 819 |
|
seaice_calc_viscosities.F), inactive by default for now (will change |
| 820 |
|
results again), but will replace old code eventually |
| 821 |
|
o eesupp/src: |
| 822 |
|
- add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F) |
| 823 |
|
to always cumulate tile local-sum in the same order |
| 824 |
|
(option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h). |
| 825 |
|
Still uses MPI_Allreduce (like standard code) but on array of tiles |
| 826 |
|
and should be faster than GLOBAL_SUM_SEND_RECV code. |
| 827 |
|
- switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV |
| 828 |
|
(defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead. |
| 829 |
|
- add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.: |
| 830 |
|
aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40, |
| 831 |
|
fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example, |
| 832 |
|
natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre, |
| 833 |
|
tutorial_baroclinic_gyre and tutorial_held_suarez_cs. |
| 834 |
|
|
| 835 |
|
checkpoint65n (2015/07/29) |
| 836 |
|
o pkg/thsice: |
| 837 |
|
- add a warning when used with pkg/aim but without updating SST |
| 838 |
|
(stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ). |
| 839 |
|
o pkg/offline: |
| 840 |
|
- change where Offline-Fields are loaded, from load_fields_driver.F to |
| 841 |
|
directly within FORWARD_STEP, just after updating iter number and time; |
| 842 |
|
- move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new |
| 843 |
|
S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS; |
| 844 |
|
These changes allow: |
| 845 |
|
a) to recover exactly on-line results using deltaToffline=deltaTClock, |
| 846 |
|
tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2) |
| 847 |
|
both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous |
| 848 |
|
time-step, both with GM & KPP files and with recomputing these fields; |
| 849 |
|
b) no needs to switch on staggerTimeStep anymore; |
| 850 |
|
c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf. |
| 851 |
|
- update output of experiment tutorial_dic_adjoffline (only 3 digits left). |
| 852 |
|
o pkg/offline: |
| 853 |
|
- change (rarely used) offset-iteration parameter to an offset time (in s): |
| 854 |
|
can easily recover previous offset-iter effect by setting offset-time |
| 855 |
|
(offlineTimeOffset) to offset-iter x deltaToffline; |
| 856 |
|
- do not turn-off Temp & Salinity surface relaxation when using KPP (used |
| 857 |
|
in KPP as part of surface buoyancy forcing) in offline run. |
| 858 |
|
- fix ptracers KPP non-local term in the case where KPP is re-computed. |
| 859 |
|
o OpenAD |
| 860 |
|
- Adding preliminary ggl90 test to OpenAD verification. |
| 861 |
|
Config. with ggl90 currently diverges after 64 time steps |
| 862 |
|
so will need more work to become more stable |
| 863 |
|
- Adding preliminary kpp test to OpenAD verification. |
| 864 |
|
required small tweakes in kpp_routines.F |
| 865 |
|
- Merge and update from Krishna Narayanan's contrib area: |
| 866 |
|
* Add one variable for preliminary OpenAD DIVA |
| 867 |
|
* Add replacement time-stepping for OpenAD DIVA |
| 868 |
|
* genmake2 flag -diva (but only for OpenAD; preliminary) |
| 869 |
|
* required modifs for OAD_support |
| 870 |
|
successful preliminary test for tutorial_global_oce_biogeo/ |
| 871 |
|
o pkg/seaice: |
| 872 |
|
- initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr |
| 873 |
|
- add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising |
| 874 |
|
delta with a smooth function in s/r seaice_calc_viscosity |
| 875 |
|
(no effect on EVP) |
| 876 |
|
- rename local suffix "sqr" into "sq" for more consistent variable names |
| 877 |
|
o pkg/seaice: |
| 878 |
|
add new parameter SEAICE_deltaMin that is used ***only*** |
| 879 |
|
for regularizing Delta (and nothing else, like the parameter |
| 880 |
|
which is also used for all sorts of things SEAICE_EPS). |
| 881 |
|
Defaults to SEAICE_EPS for backward compatibility only. |
| 882 |
|
o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with |
| 883 |
|
the wrong key by inialising it before use -> fixes a recomputation |
| 884 |
|
problem but does not fix the gradient |
| 885 |
|
o pkg/layers: |
| 886 |
|
- move resetting of flux arrays to outside the iLa loop |
| 887 |
|
(this caused layers_diapycnal to not work with more than one layer coord.) |
| 888 |
|
- fix bug in calculation of layers_recip_delta in layers_init_fixed.F |
| 889 |
|
o pkg/layers: |
| 890 |
|
- remove from common block 3D layers fields (used to diagnose transport |
| 891 |
|
in tracer coords) and declare them as local arrays in layers_calc.F |
| 892 |
|
o pkg/seaice: |
| 893 |
|
- Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it |
| 894 |
|
in lab_sea forward experiment (changes results -> updated) |
| 895 |
|
- update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v |
| 896 |
|
o pkg/seaice: modify seaice_lsr.F in order to improve the gradient |
| 897 |
|
computations; for SEAICE_VECTORIZE_LSR |
| 898 |
|
- move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v) |
| 899 |
|
sweep to the outside, |
| 900 |
|
- remove store directives and add "CADJ loop sequential" directives |
| 901 |
|
in analogy to model/src/solve_tridiagonal.F |
| 902 |
|
- replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop |
| 903 |
|
boundaries to yield more readable code. This has also the charming side |
| 904 |
|
effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without |
| 905 |
|
SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in |
| 906 |
|
seaice_lsr_tridiagu/v now requires either of these flags, vectorization |
| 907 |
|
still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as |
| 908 |
|
an additional option) |
| 909 |
|
The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F |
| 910 |
|
but the adjoint gradients (which are affected by this change) still explode. |
| 911 |
|
o coupler (atm & ocn _compon_interf): |
| 912 |
|
- avoid using Exch2 IO mapping if not suitable. |
| 913 |
|
|
| 914 |
|
checkpoint65m (2015/06/15) |
| 915 |
|
o pkg/layers: |
| 916 |
|
- clean-up old parameters setting (from Sep 2012): |
| 917 |
|
+ remove old parameters setting from common block (declared locally); |
| 918 |
|
+ stop if any old parameter is mixed with new parameters; |
| 919 |
|
+ check for valid or consistent parameter setting (e.g., layers_name) |
| 920 |
|
- check that layers_bounds for Pot.Density are in the right range; |
| 921 |
|
this is supposed to catch un-updated setting after recently shifting |
| 922 |
|
potential density field "prho" by -1000 (now in "sigma" scale). |
| 923 |
|
o pkg/layers: |
| 924 |
|
- Added missing call to layers_fill for keeping track of tottend in |
| 925 |
|
pkg/diagnostics/diagnostics_fill_state.F |
| 926 |
|
o pkg/layers: |
| 927 |
|
- added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning |
| 928 |
|
of diapycnal fluxes |
| 929 |
|
o pkg/layers: |
| 930 |
|
- reverted changes to interpolation to previous treatment; there |
| 931 |
|
was never actually a problem |
| 932 |
|
o pkg/layers: |
| 933 |
|
- fix interpolation of layers tracers in the presence of partial cells |
| 934 |
|
- add lots of new functionality to compute water mass transformation |
| 935 |
|
(enabled by CPP flag LAYERS_THERMODYNAMICS) |
| 936 |
|
- add new calls from main code (diags_oceanic_surf_flux.F, |
| 937 |
|
thermodynamics.F, impldiff.F) and gad to save the necessary fields |
| 938 |
|
for layers_thermodynamics calculations |
| 939 |
|
o pkg/ptracers: |
| 940 |
|
- add capability of stepping a passive tracer forward without advection |
| 941 |
|
by setting PTRACERS_advScheme to 0. |
| 942 |
|
o pkg/diagnostics: |
| 943 |
|
- add few (threads) _BARRIER around any update of "diag_pkgStatus". |
| 944 |
|
o pkg/layers: |
| 945 |
|
- shift potential density field "prho" by -1000 for density layer averaging so |
| 946 |
|
that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000); |
| 947 |
|
Note that density bin boundaries (layers_bounds in data.layers) have |
| 948 |
|
to be set accordingly (i.e., shifted, in sigma scale). |
| 949 |
|
o pkg/layers: |
| 950 |
|
- fix snap-shot output of layer thickness @ V.pt and output of pot.density |
| 951 |
|
- fix calculation of layer non-weighted velocity and layer probability |
| 952 |
|
- add diagnostics for pot.density used for layer averaging |
| 953 |
|
o pkg/seaice: |
| 954 |
|
- seaice_calc_viscosity.F: change computation of deltaC**2 to ensure |
| 955 |
|
positiveness, modify a few comments and improve variable names, |
| 956 |
|
- the changed computation of deltaC affects most seaice-related |
| 957 |
|
experiments at the truncation level. |
| 958 |
|
seaice_itd.thermo is affected by far the most, with |
| 959 |
|
only 7 digits of agreement remaining; update experiments. |
| 960 |
|
|
| 961 |
|
checkpoint65l (2015/05/04) |
| 962 |
|
o pkg/shelfice: |
| 963 |
|
- in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set |
| 964 |
|
factor drKp1 to zero where it is negative (ie. do not use |
| 965 |
|
SHELFICEBoundaryLayer if hFacC>1) |
| 966 |
|
- the same for factor drLoc in shelfice_forcing.F |
| 967 |
|
o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem |
| 968 |
|
with modules in ptracers, when using testreport option "-small_f" |
| 969 |
|
o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD) |
| 970 |
|
- replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1)) |
| 971 |
|
o verification/testreport |
| 972 |
|
- add new option -small_f |
| 973 |
|
with this option testreport first makes the target small_f (*.f files) |
| 974 |
|
before running make (all). This is useful for explicit inlining when |
| 975 |
|
all sources need to be full available. |
| 976 |
|
o pkg/exf/exf_interp.F: |
| 977 |
|
remove previous changes related to reverse (decreasing) input grids latitude |
| 978 |
|
|
| 979 |
|
checkpoint65k (2015/04/01) |
| 980 |
|
o pkg/ecco: |
| 981 |
|
fix missing cosphi initialization; use eccoiter in place of optimcycle; |
| 982 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 983 |
|
instead of active read/write |
| 984 |
|
o pkg/ctrl: |
| 985 |
|
if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL |
| 986 |
|
instead of active read/write. |
| 987 |
|
o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F |
| 988 |
|
return if .NOT.useAUTODIFF |
| 989 |
|
o pkg/seaice: add CPP brackets (cost function related). |
| 990 |
|
o model/src: |
| 991 |
|
add useAUTODIFF run time switch. |
| 992 |
|
o pkg/exf/exf_interp.F: |
| 993 |
|
add code to allow input grids with latitude starting in the north (i.e. when |
| 994 |
|
j=1 corresponds to northern edge of field); modify global_with_exf to test |
| 995 |
|
this feature. |
| 996 |
|
o verification/testreport: |
| 997 |
|
- replace "grep -A3" with POSIX conformal sed command, because there are |
| 998 |
|
implementations of grep that cannot do contextual searches |
| 999 |
|
- replace "cat -n" by "nl" (two occurrences), because not all implementations |
| 1000 |
|
of "cat" have the option "-n" |
| 1001 |
|
o model/src: |
| 1002 |
|
add new file gsw_teos10.F that contains 3 functions, more or less a copy |
| 1003 |
|
of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to |
| 1004 |
|
convert from conservative to potential temperature. For now they are not |
| 1005 |
|
called anywhere. |
| 1006 |
|
o pkg/ggl90: make "useIDEMIX" useful |
| 1007 |
|
- re-organize code in s/r ggl90_calc a little to move computations that |
| 1008 |
|
are different for idemix into separate loops (changes verification |
| 1009 |
|
experiment idemix at truncation level, 12 digits remain -> updated) |
| 1010 |
|
- requires 2 new 2D fields KappaM, verticalShear |
| 1011 |
|
- make hFacI and recip_hFacI local 3D variables that are passed to |
| 1012 |
|
s/r ggl90_idemix |
| 1013 |
|
- fix and improve some comments |
| 1014 |
|
|
| 1015 |
|
checkpoint65j (2015/02/25) |
| 1016 |
|
o pkg/openad |
| 1017 |
|
- synchronize seawater.F with version in model/src: replace routine |
| 1018 |
|
body of sw_temp by calling sw_ptmp and fix/add a few comments. |
| 1019 |
|
o pkg/mnc: |
| 1020 |
|
- change default value of pickup_read/write_mnc params to FALSE |
| 1021 |
|
(since few features are missing in reading MNC pickup files). |
| 1022 |
|
o model/src: |
| 1023 |
|
- change default (background) vertical diffusivity for salt to be the |
| 1024 |
|
temperature (background) vertical diffusivity. |
| 1025 |
|
- change background vertical diffusivity in vertical mixing pkgs ggl90, |
| 1026 |
|
kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity. |
| 1027 |
|
This makes ptracers default diffusivity (that uses salt diffKr) more |
| 1028 |
|
consistent with vertical mixing schemes. |
| 1029 |
|
o verification/testreport: |
| 1030 |
|
- fix typo in "-pcls" option ; |
| 1031 |
|
- put temp files in /tmp (instead of in local dir) |
| 1032 |
|
- add option "-ncad" to use genmake2 new option "-nocat4ad" |
| 1033 |
|
- allow to use "-j" option (for multi-procs make) for AD, OAD and TLM. |
| 1034 |
|
o pkg/ggl90 (idemix code): |
| 1035 |
|
- apply few fixes ; add some missing "_d 0" ; update output of exp. |
| 1036 |
|
global_ocean.90x40x15.idemix |
| 1037 |
|
o OpenAD |
| 1038 |
|
- enable active file I/O and begin removal of work-around code |
| 1039 |
|
for OpenAD for handling control variables (memory vs. active files) |
| 1040 |
|
- new CPP options file OPENAD_OPTIONS.h |
| 1041 |
|
- revert to genarr2d gradient check for hs94.1x64x5 |
| 1042 |
|
- (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens) |
| 1043 |
|
- gentim2d works for halfpipe_streamice but not yet hs94.1x64x5 |
| 1044 |
|
o tools/genmake2: |
| 1045 |
|
- add option for an alternative Makefile (from Martin) where multiple |
| 1046 |
|
source files are sent to TAF (instead of all in one file). |
| 1047 |
|
o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013) |
| 1048 |
|
- code provided by Carsten Eden as an extension of ggl90 |
| 1049 |
|
- so far the code is turned on within ggl90 by setting a CPP-flag at |
| 1050 |
|
compile time; a runtime flag implementation is not yet complete |
| 1051 |
|
- tested in new verification experiment global_ocean.90x40x15.idemix |
| 1052 |
|
o verification: |
| 1053 |
|
- reduce length of the AD test run by half for experiments |
| 1054 |
|
global_ocean.cs32x15 (std + thsice) and isomip |
| 1055 |
|
- enable active file I/O for OpenAD, adjust verifications accordingly |
| 1056 |
|
- halfpipe_streamice: change gradient check from genarr2d to gentim2d |
| 1057 |
|
o verification/testreport: |
| 1058 |
|
- fix two non-POSIX sed statements so that there are no error messages |
| 1059 |
|
on Mac OS X |
| 1060 |
|
- replace hostname -s with hostname | sed 's/\..*$//' |
| 1061 |
|
o model/src/seawater.F: |
| 1062 |
|
- simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged |
| 1063 |
|
(following the matlab code), which would have avoided the bug caught |
| 1064 |
|
by Matt (see below) in the first place |
| 1065 |
|
o pkg/shelfice: |
| 1066 |
|
- implement alternative discretisation of quadratic drag (selectBotDragQuadr) |
| 1067 |
|
and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag. |
| 1068 |
|
- fix sign of friction tendency (no-slip BC) and fix u,v drag for thin |
| 1069 |
|
ice-shelf case (i.e., within surface level). |
| 1070 |
|
- add config summary in shelfice_check.F |
| 1071 |
|
- remove global variable recip_SHELFICElatentHeat and replace by a local |
| 1072 |
|
variable recip_latentHeat |
| 1073 |
|
- introduce diagnostics for friction velocity uStar (in case of |
| 1074 |
|
SHELFICEuseGammaFrict) |
| 1075 |
|
- change verification experiment isomip.htd: |
| 1076 |
|
+ start from pickup (as input_ad at nIter0=8640) |
| 1077 |
|
+ start from SHELFICEmassFile instead of SHELFICEloadAnomaly file |
| 1078 |
|
+ test SHELFICEuseGammaFrict = .TRUE. |
| 1079 |
|
+ test SHELFICEadvDiffHeatFlux = .TRUE. |
| 1080 |
|
o model/src: |
| 1081 |
|
- fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to |
| 1082 |
|
in-situ Temp) and in routine SW_TEMP (in pkg/openad); |
| 1083 |
|
update output of experiments global_with_exf.yearly and isomip (all 6). |
| 1084 |
|
o pkg/shelfice: |
| 1085 |
|
- change setting of kTopC to also be zero where there is no ice-shelf. |
| 1086 |
|
- zero out surface forcing arrays (for now, for T & S + EmPmR) where |
| 1087 |
|
ice-shelf is. |
| 1088 |
|
- first attempt to get RealFreshWaterFlux effects: for now, only without |
| 1089 |
|
SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping. |
| 1090 |
|
o pkg/seaice: add the option to prescribe a fixed thickness PDF |
| 1091 |
|
for thermodynamic calculations |
| 1092 |
|
- because of divisions of the type 7/7 not exactly equal to 1, this change |
| 1093 |
|
affects results of some verification experiments by up to 4 digits: |
| 1094 |
|
global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume, |
| 1095 |
|
seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides |
| 1096 |
|
adjoint: lab_sea, lab_sea.noseaicedyn |
| 1097 |
|
-> updated |
| 1098 |
|
|
| 1099 |
|
checkpoint65i (2015/01/23) |
| 1100 |
|
o model/src: |
| 1101 |
|
- change units of frictionHeating field from W to W/m^2 |
| 1102 |
|
- fix bug in frictional heating from stratospheric drag in |
| 1103 |
|
S/R ATM_PHYS_TENDENCY_APPLY_V |
| 1104 |
|
- with synchronous time-stepping: move resetting to zero of frictionHeating |
| 1105 |
|
field from load_fields_driver.F to thermodynamics.F ; |
| 1106 |
|
- add diagnostics for frictional heating. |
| 1107 |
|
o model/src & gmredi K3D: |
| 1108 |
|
- add frictionHeating field to pickup-files (for synchronous time-stepping) |
| 1109 |
|
- move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h |
| 1110 |
|
- rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name |
| 1111 |
|
and name in pickup file). |
| 1112 |
|
- fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F |
| 1113 |
|
o model/src: |
| 1114 |
|
- move (from ini_forcing.F) initialisation of all arrays in header file |
| 1115 |
|
FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart |
| 1116 |
|
(since Nov 2012) with option selectAddFluid=1. |
| 1117 |
|
o pkg/shelfice: |
| 1118 |
|
- change units (+ document) of newly added field "shelfIceMassDynTendency" |
| 1119 |
|
- upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays. |
| 1120 |
|
o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers |
| 1121 |
|
o pkg/seaice: two new runtime parameters: |
| 1122 |
|
- SEAICE_cStar replaces the hard wired "20" in the strength formulation, |
| 1123 |
|
long overdue |
| 1124 |
|
- SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012) |
| 1125 |
|
parameterization of tensil stress for fast ice (does not do anything yet) |
| 1126 |
|
o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method |
| 1127 |
|
for LSR: move checking overlaps out of JFNK-if-block |
| 1128 |
|
o pkg/atm_phys: |
| 1129 |
|
- move copy of grid and dynamical fields out of atm_phys_driver.F into |
| 1130 |
|
new S/R ATM_PHYS_DYN2PHYS. |
| 1131 |
|
- fix level height for Linear Free-Surf case (to be consistent with |
| 1132 |
|
fixed-in-time pressure levels). |
| 1133 |
|
o pkg/mom_common (bottomdrag): |
| 1134 |
|
- average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center |
| 1135 |
|
to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG; |
| 1136 |
|
update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag. |
| 1137 |
|
o pkg/shelfice (u/v_drag): |
| 1138 |
|
- add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG; |
| 1139 |
|
- use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F |
| 1140 |
|
(now similar to shelfice_u_drag.F) |
| 1141 |
|
- remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG |
| 1142 |
|
from mom_vecinv.F (similar to mom_fluxform calls). |
| 1143 |
|
o pkg/mom_common (bottomdrag): |
| 1144 |
|
- add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG; |
| 1145 |
|
- add options for alternative discretisation of velocity norm in quadratic |
| 1146 |
|
bottom drag: averaging of grid-cell-center KE to U.point and V.point |
| 1147 |
|
(selectBotDragQuadr=0, original code) can produce noisy patterns; this |
| 1148 |
|
improves when averaging only the other component (e.g. vVel for U bottom |
| 1149 |
|
drag) using wet-point method (selectBotDragQuadr=2) or not (=1). |
| 1150 |
|
- add options (bottomVisc_pCell) to account for partial-cell in bottom |
| 1151 |
|
friction (no-slip BC) thus getting the true distance from the bottom; |
| 1152 |
|
off by default since this also reduces model stability (explicit bottom |
| 1153 |
|
friction). Changes produce different machine truncation with linear-drag |
| 1154 |
|
+ no-slip BC: update output of experiments exp4.stevens (10 digits) and |
| 1155 |
|
front_relax (bvp & mxl, 10 & 11 digits). |
| 1156 |
|
o model/src & mom pkgs: |
| 1157 |
|
- add one more level to vertical viscosity local arrays (Nr+1, previously Nr) |
| 1158 |
|
since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k |
| 1159 |
|
- for now and until vertical mixing scheme are updated to fill up level Nr+1, |
| 1160 |
|
just copy level Nr value to level Nr+1. |
| 1161 |
|
o doc: |
| 1162 |
|
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 1163 |
|
o pkg/shelfice: |
| 1164 |
|
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 1165 |
|
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 1166 |
|
from array shelficemassinit, which is set in init_fixed and |
| 1167 |
|
has option to be set from file; introduce array |
| 1168 |
|
shelficeMassDynTend array, set thru file in init_fixed |
| 1169 |
|
- NEW FILE: shelfice_step_icemass.F: update shelficemass from either |
| 1170 |
|
shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in |
| 1171 |
|
pkg/streamice |
| 1172 |
|
- shelfice_thermodynamics.F: call shelfice_step_icemass if |
| 1173 |
|
SHELFICEMassStepping = .true. |
| 1174 |
|
- shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f |
| 1175 |
|
|
| 1176 |
|
checkpoint65h (2014/12/17) |
| 1177 |
|
o verification/global_ocean.90x40x15, global_ocean_ebm: |
| 1178 |
|
- update to generic controls. |
| 1179 |
|
o pkg/ctrl: |
| 1180 |
|
- ctrl_map_ini_genarr.F: test for igen>0 |
| 1181 |
|
- ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D. |
| 1182 |
|
- move gentim2d part of ctrl_map_ini_genarr.F to |
| 1183 |
|
new separate routine : ctrl_map_ini_gentim2d.F |
| 1184 |
|
- ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F: |
| 1185 |
|
add time variable weights and cyclic controls (time mean, |
| 1186 |
|
seasonal cycle, etc) capabilities to gentim2d |
| 1187 |
|
o pkg/ecco: |
| 1188 |
|
- move reading of error, conversion to weights from |
| 1189 |
|
ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei) |
| 1190 |
|
o global_oce_llc90, cs32: |
| 1191 |
|
- activte sbo. |
| 1192 |
|
- CTRL_SIZE.h : add maxCtrlProc. |
| 1193 |
|
- activate the new genctrl capabilities. |
| 1194 |
|
- update following reorganization of global_oce_input_fields.tar.gz |
| 1195 |
|
o pkg/ctrl/ctrl_ad_diff.list: |
| 1196 |
|
- add missing ctrl_init_rec.f |
| 1197 |
|
o tools/OAD_support/keepOriginal: |
| 1198 |
|
- add ctrl_init_rec.F |
| 1199 |
|
o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F: |
| 1200 |
|
- avoid recomputations of xx_gentim2d_dummy. |
| 1201 |
|
o momentum diagnostics: |
| 1202 |
|
- move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and |
| 1203 |
|
mom_vecinv.F to timestep.F (to include Smag-3D contribution). |
| 1204 |
|
o pkg/seaice/seaice_lsr.F: |
| 1205 |
|
- fix computation of BU/BV, make sure they are non-zero, only necessary |
| 1206 |
|
for cubed sphere exchanges and SEAICE_OLx/y>0. |
| 1207 |
|
This makes calling s/r fill_cs_corner_rl obsolete (removed). |
| 1208 |
|
o verification/global_ocean.cs32x15/input.seaice |
| 1209 |
|
- add test for strong implicit coupling and restricted addtive Schwarz |
| 1210 |
|
methods for LSR |
| 1211 |
|
- update results/output.seaice.txt |
| 1212 |
|
o verification/tutorial_global_oce_biogeo: |
| 1213 |
|
- AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up) |
| 1214 |
|
and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK); |
| 1215 |
|
update output_adm,_oadm,_tlm.txt |
| 1216 |
|
o pkg/dic: |
| 1217 |
|
- change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h |
| 1218 |
|
- add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn |
| 1219 |
|
for tracer 1 & 2 is set (to avoid double counting of dilution effect). |
| 1220 |
|
o verification/tutorial_global_oce_biogeo: |
| 1221 |
|
- AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since |
| 1222 |
|
dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ; |
| 1223 |
|
update output_adm,_oadm,_tlm.txt |
| 1224 |
|
o eesupp/src: |
| 1225 |
|
- add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F) |
| 1226 |
|
and call it in seaice_lsr when using nonzero SEAICE_OLx/y |
| 1227 |
|
o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing |
| 1228 |
|
LSR (following Hutchings et al. 2004) |
| 1229 |
|
- introduce zetaZ as a global variable (requires adjustments in |
| 1230 |
|
seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ |
| 1231 |
|
in seaice_calc_viscosities.F |
| 1232 |
|
- new flag SEAICEuseStrImpCpl (default off) |
| 1233 |
|
- add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the |
| 1234 |
|
momentum equations |
| 1235 |
|
- JFNK-solver (preconditioner) adjusted to allow using this method |
| 1236 |
|
(where it does not have any positive effect) |
| 1237 |
|
o pkg/seaice |
| 1238 |
|
- add overlap for restrictive additive Schwartz method also to LSR, but |
| 1239 |
|
turn it off by default (because it only seems to work for non-cubed |
| 1240 |
|
sphere/llc topologies) |
| 1241 |
|
o pkg/autodiff |
| 1242 |
|
- add extra exchanges in addummy_in_steppging also for mnc output |
| 1243 |
|
o pkg/seaice: |
| 1244 |
|
- add extra exchanges before dumping adjoint fields in seaice_ad_dump.F |
| 1245 |
|
to avoid stripes in the adjoint output (similar to addummy_in_stepping.F) |
| 1246 |
|
o pkg/obcs: |
| 1247 |
|
- add option to specify domain-connected piece Id along OB though files |
| 1248 |
|
(for now, only used to diagnose PhiVel; default =1 -> global correction) |
| 1249 |
|
- modify obcs_diag_balance.F to process each connected-part separately; |
| 1250 |
|
exclude OB where Id = 0 but keep the full divergence there (-> constant |
| 1251 |
|
Psi along this portion of OB and all inflow derived from grad(Phi)) |
| 1252 |
|
- add example of OB-conect files in verification/so_box_biogeo/input. |
| 1253 |
|
o pkg/diagnostics: |
| 1254 |
|
- improve treatment of Open-Boundaries in Velocity-Potential calculation: |
| 1255 |
|
a) use non zero matrix element across OB and solve for Phi 1 grid point |
| 1256 |
|
outside OB (i.e, where tracer OBCS are applied). |
| 1257 |
|
b) global imbalance of inFlow/outFlow across OB: instead of modifying |
| 1258 |
|
velocity across OB, spread it uniformly along the OB in the RHS. |
| 1259 |
|
|
| 1260 |
|
checkpoint65g (2014/11/19) |
| 1261 |
|
o pkg/diagnostcis: |
| 1262 |
|
- add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param |
| 1263 |
|
o pkg/my82,pp81,kl10: |
| 1264 |
|
- fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D |
| 1265 |
|
field diffKr as background diffusivity to set minimum diffusivity value. |
| 1266 |
|
o pkg/seaice: |
| 1267 |
|
- add new parameter SEAICEuseEVPrev (for revisited EVP by |
| 1268 |
|
Bouillon et al 2013) |
| 1269 |
|
- add SEAICE_evpAlpha/Beta to namelist |
| 1270 |
|
- modify seaice_evp code to able to use SEAICEuseEVPrev. These changes |
| 1271 |
|
involve trivial re-ordering of divisions/multiplications that should not |
| 1272 |
|
have any effects, but ... they do change the results of lab_sea.hb87 so |
| 1273 |
|
that only 2 digits of agreement remain, in line with the general |
| 1274 |
|
instability/fragility of the evp-code. For now, I do not care and just |
| 1275 |
|
update the verification experiment |
| 1276 |
|
o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc) |
| 1277 |
|
- remove xx_genarr2d_numsmooth etc |
| 1278 |
|
- use xx_genarr2d_preproc etc instead |
| 1279 |
|
- carry out smooth_correl2D at initialization stage rather than during |
| 1280 |
|
time stepping. |
| 1281 |
|
- get smoothOpNb from xx_gentim2d_preproc |
| 1282 |
|
o global_oce_cs32 : |
| 1283 |
|
- add test of generic ecco capabilities. |
| 1284 |
|
o pkg/exf/exf_getsurfacefluxes.F : |
| 1285 |
|
- add to tmpUE/tmpVN rather than re-initializing them (conventional behavior). |
| 1286 |
|
o pkg/ctrl,ecco : |
| 1287 |
|
- omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED |
| 1288 |
|
is defined. |
| 1289 |
|
o pkg/seaice: add diagnostics for Delta (deformation parameter) |
| 1290 |
|
o model/src: |
| 1291 |
|
- when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical |
| 1292 |
|
diffusivity (background) is specified but ignored. |
| 1293 |
|
o verification: |
| 1294 |
|
- in testreport, convert hostname to lower case for default output dir name |
| 1295 |
|
o model, pkg : add useCTRL, useECCO parameters (on/off run time switch). |
| 1296 |
|
o pkg/dic: add modifications from Hajoon: |
| 1297 |
|
- add iron sedimentation flux function of the flux of PO4 out of bottom layer |
| 1298 |
|
- light attenuation: add self-shading effect by climatological Chlorophyll |
| 1299 |
|
(read from file). |
| 1300 |
|
o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also |
| 1301 |
|
compiles when SEAICE_ALLOW_DYNAMICS is undefined |
| 1302 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate |
| 1303 |
|
AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than |
| 1304 |
|
ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted, |
| 1305 |
|
approach where CPP_OPTIONS.h includes an omnipotent |
| 1306 |
|
ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h'). |
| 1307 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where |
| 1308 |
|
ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong. |
| 1309 |
|
o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF |
| 1310 |
|
to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included |
| 1311 |
|
(it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...) |
| 1312 |
|
o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl : |
| 1313 |
|
add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed |
| 1314 |
|
- ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h |
| 1315 |
|
- AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h |
| 1316 |
|
- CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc |
| 1317 |
|
o pkg/ctrl,ecco,exf : |
| 1318 |
|
- remove variables associated with NON-generic costs, |
| 1319 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 1320 |
|
- remove NON-generic NON-obcs controls, |
| 1321 |
|
unless ECCO_CTRL_DEPRECATED is defined. |
| 1322 |
|
o pkg/ctrl : added ctrl_local_params.h |
| 1323 |
|
o pkg/ecco : added ecco_local_params.h |
| 1324 |
|
o verification : added ECCO_CTRL_DEPRECATED to most as and oad |
| 1325 |
|
experiments, which will progressively be removed once the |
| 1326 |
|
experiments are revised to use only generic controls/costs. |
| 1327 |
|
|
| 1328 |
|
checkpoint65f (2014/10/13) |
| 1329 |
|
o pkg/ctrl, ecco, seaice : minor changes in headers |
| 1330 |
|
o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic |
| 1331 |
|
cost function and control capabilities added since checkpoint65c. |
| 1332 |
|
o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h. |
| 1333 |
|
o pkg/ecco: increase modularity and improve logic |
| 1334 |
|
- ecco_toolbox.F (new) : basic operations that are often used, |
| 1335 |
|
including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk, |
| 1336 |
|
ecco_addcost, ecco_add, ecco_div, ecco_readbar. |
| 1337 |
|
- cost_gencal.F (new) : determine filnames and records. |
| 1338 |
|
- cost_genread.F, cost_generic.F : condense code using ecco_toolbox. |
| 1339 |
|
- cost_generic.F : use spzeroloc rather than hard-coded -9999, |
| 1340 |
|
and exploit the above functions leading to more compact code. |
| 1341 |
|
- cost_genread.F : rm un-necessary arguments, re-arrange args order. |
| 1342 |
|
- ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj, |
| 1343 |
|
using_ers, using_gfo, using_mdt is now only defined within gencost) |
| 1344 |
|
o pkg/ecco: extend generic cost capabilities |
| 1345 |
|
- pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost |
| 1346 |
|
capabilities via gencost_preproc (+ _c,_i,_r related params), |
| 1347 |
|
gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod, |
| 1348 |
|
gencost_outputlevel arguments to cost_generic |
| 1349 |
|
- pkg/ecco/cost_genread.F (new) : interface between cost_generic |
| 1350 |
|
and active_read, making room for gencost_preproc to take effect. |
| 1351 |
|
Added preproc code ('climmon') to replace GENERIC_BAR_MONTH. |
| 1352 |
|
- pkg/ecco/cost_generic.F : |
| 1353 |
|
compute and store misfit maks*(model-data) in localdif that is |
| 1354 |
|
then used in cost and for output, output misfit if outlev.GT.0 |
| 1355 |
|
- pkg/ecco/cost_averagesfields.F : depend on gencost_barskip |
| 1356 |
|
rather gencost_barfile for deciding whether to write barfile |
| 1357 |
|
- pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd |
| 1358 |
|
- pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from |
| 1359 |
|
ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip |
| 1360 |
|
- pkg/ecco/ecco_summary.F : report gencost variables |
| 1361 |
|
- pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs |
| 1362 |
|
o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA |
| 1363 |
|
o pkg/ecco: internal re-organization |
| 1364 |
|
- resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl |
| 1365 |
|
(rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter, |
| 1366 |
|
mv relevant variables definition from ecco_cost.h to ecco.h, |
| 1367 |
|
make sure gencost routines only include ecco.h) |
| 1368 |
|
- throughout : add missing CCP switches, rm unused variables, |
| 1369 |
|
and rm un-necessary CPP switches |
| 1370 |
|
- throughout gencost routines : replace modelstartdate with |
| 1371 |
|
gencost_startdate when needed |
| 1372 |
|
- cost_bp_read.F : use arguments, instead of common blocs |
| 1373 |
|
so that it can be used also by (new) cost_gencost_bpv4.F |
| 1374 |
|
- ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0 |
| 1375 |
|
- ecco_phys.F : compute etanFull |
| 1376 |
|
- ecco_readparms.F : rename using_topex as using_tpj, add |
| 1377 |
|
bpv4-grace to gencost list, initialize added parameters |
| 1378 |
|
- ecco_summary.F : include SIZE.h needed for augmented ecco.h |
| 1379 |
|
|
| 1380 |
|
checkpoint65e (2014/09/28) |
| 1381 |
|
o pkg/obcs: |
| 1382 |
|
- replaced the just-added CPP options with run-time variables |
| 1383 |
|
(see pkg/obcs/OBCS_PARAMS.h for details) |
| 1384 |
|
o pkg/obcs: |
| 1385 |
|
- add additional CPP options for sponge boundary layers |
| 1386 |
|
(see pkg/obcs/OBCS_OPTIONS.h for details) |
| 1387 |
|
o pkg/atm_phys: |
| 1388 |
|
- implement simple (obliquity only, assuming circular planet orbit) |
| 1389 |
|
seasonal cycle for incoming insolation ; used when run-time parameter |
| 1390 |
|
"select_incSW" is set to 1 ; by default (=0), uses old unchanged formula. |
| 1391 |
|
o pkg/exf, pkg/ecco, pkg/ctrl: |
| 1392 |
|
- add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets |
| 1393 |
|
- activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip |
| 1394 |
|
- implement gentim2d for xx_tauu, xx_tauv |
| 1395 |
|
o pkg/ctrl, pkg/ecco : |
| 1396 |
|
- fix and complement the generic controls implementation |
| 1397 |
|
o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F, |
| 1398 |
|
pkg/shelfice/shelfice_thermodynamics.F, |
| 1399 |
|
verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F, |
| 1400 |
|
verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F : |
| 1401 |
|
- add weight in CTRL_GET_GEN calls |
| 1402 |
|
o pkg/ctrl : |
| 1403 |
|
- ctrl_get_gen.F : add weight as input parameter, and apply |
| 1404 |
|
it directly rather than using smooth_correl2Dw (to be retired). |
| 1405 |
|
- ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call |
| 1406 |
|
o pkg/ctrl : |
| 1407 |
|
- introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F, |
| 1408 |
|
ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F) |
| 1409 |
|
- re-activate ctrl_summary (call in ctrl_init.F) |
| 1410 |
|
o pkg/ctrl/ctrl_cost_gen.F : |
| 1411 |
|
- fix CCP brackets, remove un-necessary myiter, mytime |
| 1412 |
|
o pkg/ecco, pkg/ctrl : |
| 1413 |
|
- remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F) |
| 1414 |
|
- remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F) |
| 1415 |
|
- add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F) |
| 1416 |
|
- add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F) |
| 1417 |
|
|
| 1418 |
|
checkpoint65d (2014/09/15) |
| 1419 |
|
o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F : |
| 1420 |
|
- add xx_genarr2d_bounds,xx_genarr3d_bounds, |
| 1421 |
|
xx_genarr2d_numsmooth, xx_genarr3d_numsmooth |
| 1422 |
|
o pkg/ctrl/ctrl_map_ini_genarr.F : |
| 1423 |
|
- remove compilation failure |
| 1424 |
|
- replace hard coded example |
| 1425 |
|
- use ctrl_map_ini_gen2D, 3D |
| 1426 |
|
o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F : |
| 1427 |
|
- on/off switch based upon xx_genarr2d_weight,3d |
| 1428 |
|
o src/packages_init_variables.F : |
| 1429 |
|
- regroup pkg/estimation calls |
| 1430 |
|
- remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 1431 |
|
(moved to ctrl_init_variables) |
| 1432 |
|
o cost/cost_init_varia.F : |
| 1433 |
|
- remove ecco_cost_init_varia |
| 1434 |
|
(moved to ecco_init_varia) |
| 1435 |
|
o ctrl/ctrl_init_variables.F : |
| 1436 |
|
- add CTRL_MAP_INI, CTRL_MAP_INI_ECCO |
| 1437 |
|
- add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI |
| 1438 |
|
o ctrl/ctrl_map_ini.F : |
| 1439 |
|
- remove ctrl_map_ini_genarr, seaice_ctrl_map_ini |
| 1440 |
|
(moved to ctrl_init_variables) |
| 1441 |
|
o ctrl/ctrl_map_ini_ecco.F : |
| 1442 |
|
- remove ECCO_PHYS (mv to ecco_init_varia) |
| 1443 |
|
- remove seaice_ctrl_map_ini (mv to ctrl_init_variables) |
| 1444 |
|
o ecco/ecco_ad_diff.list : |
| 1445 |
|
- add ecco_init_varia.f |
| 1446 |
|
o ecco/ecco_init_varia.F |
| 1447 |
|
- new routine |
| 1448 |
|
o pkg/streamice: |
| 1449 |
|
- move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F |
| 1450 |
|
to streamice_init_fixed.F ; fix setting of STREAMICEisOn. |
| 1451 |
|
- from model/src, only call pkg/streamice routines if useStreamIce is TRUE. |
| 1452 |
|
o pkg/generic_advdiff: |
| 1453 |
|
- fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014. |
| 1454 |
|
o pkg/exf: |
| 1455 |
|
- exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown, |
| 1456 |
|
xxg_precip capability |
| 1457 |
|
- exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch |
| 1458 |
|
o pkg/ctrl: |
| 1459 |
|
- ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d |
| 1460 |
|
o model/src/load_fields_driver.F : |
| 1461 |
|
- move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING |
| 1462 |
|
so xx_gentim2d can be applied to e.g. exf fields in a timely manner. |
| 1463 |
|
o OpenAD verification experiments: |
| 1464 |
|
- Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h |
| 1465 |
|
in src files (to enable to skip the ECCO_CPPOPTIONS.h); |
| 1466 |
|
for now, only in pkgs used in OpenAD verification experiments. |
| 1467 |
|
- Change all except one (halfpipe_streamice) OpenAD experiments to use pkg |
| 1468 |
|
specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h) |
| 1469 |
|
instead of using ECCO_CPPOPTIONS.h (with all relevant options in it). |
| 1470 |
|
This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests. |
| 1471 |
|
o OpenAD verification tests: |
| 1472 |
|
- finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD); |
| 1473 |
|
- finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for |
| 1474 |
|
tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp. |
| 1475 |
|
- leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/) |
| 1476 |
|
and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC). |
| 1477 |
|
o model/src & generic_advdiff: |
| 1478 |
|
- change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S |
| 1479 |
|
forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model |
| 1480 |
|
dynamics requires valid tracer forcing only over tile interior but, for |
| 1481 |
|
some diagnostics, may need to extend it over 1 point in tile halo region. |
| 1482 |
|
- in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid |
| 1483 |
|
tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max |
| 1484 |
|
setting in temp/salt/ptracer_integrate.F |
| 1485 |
o pkg/dic: |
o pkg/dic: |
| 1486 |
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
- multiply tracer tendencies by maskInC (if ussing OBCS) before updating |
| 1487 |
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER |
| 1688 |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
nearly a factor of 10 (but keep in mind there is mostly seaice code in |
| 1689 |
this experiment): |
this experiment): |
| 1690 |
> size mitgcmuv_ad |
> size mitgcmuv_ad |
| 1691 |
text data bss dec hex |
text data bss dec hex |
| 1692 |
5100659 1216 220458952 225560827 d71c8fb |
5100659 1216 220458952 225560827 d71c8fb |
| 1693 |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER) |
| 1694 |
but only a moderate increase of 36% for global_ocean.cs32x15: |
but only a moderate increase of 36% for global_ocean.cs32x15: |
| 1695 |
text data bss dec hex |
text data bss dec hex |
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