| 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/bling |
| 8 |
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- Bug fix in bling_production regarding unit conversion for diagnostics |
| 9 |
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being put in the wrong place |
| 10 |
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o model/src: |
| 11 |
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- add back recomputation of rSurfW & S to ensure consistent column thickness |
| 12 |
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(needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only |
| 13 |
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when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F |
| 14 |
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revision 1.51) but was removed accidentally on 2014/02/08 (v1.53). |
| 15 |
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o pkg/autodiff: |
| 16 |
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- clean-up "checkpoint.flow" |
| 17 |
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o pkg/rw (Contribution from Jody Klymak): |
| 18 |
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option to set mds file suffix as function of time in simulation: |
| 19 |
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*) new input parameter "rwSuffixType" (read from PARM03 namelist) |
| 20 |
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to select file suffix format; by default (=0), use iteration number; |
| 21 |
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*) add simple routine to return file suffix according to rwSuffixType; |
| 22 |
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*) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice), |
| 23 |
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use new S/R to get file suffix, except for debug output file (diagFreq) |
| 24 |
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and pkgs offline & rbcs input files. |
| 25 |
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o pkg/rw: |
| 26 |
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- uniform processing of "I10" suffix across writing fld routines; used to |
| 27 |
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simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F |
| 28 |
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(similar to cg3d.F, cg3d_ex0.F) |
| 29 |
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o pkg/mom_vecinv: |
| 30 |
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- highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted |
| 31 |
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vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp). |
| 32 |
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o pkg/bling: |
| 33 |
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- Many small changes intended to clean the code. |
| 34 |
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Unnecessary ADJOINT_SAFEs removed ; |
| 35 |
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removed BLING_COST.h BLING_CTRL.h bling_cost.F ; |
| 36 |
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diagnostics added. |
| 37 |
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|
| 38 |
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checkpoint66e (2017/03/14) |
| 39 |
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o pkg/exf: |
| 40 |
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- interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size |
| 41 |
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definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h; |
| 42 |
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use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to |
| 43 |
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avoid any dynamic allocation ; |
| 44 |
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- S/R EXF_CHECK: add new check & stop when file-name is defined but not |
| 45 |
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read-in ; add warning when file is read-in but not used within pkg/exf ; |
| 46 |
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+ check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC). |
| 47 |
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- update exf_summary.F (print {FLD}RepCycle). |
| 48 |
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o verification/global_with_exf: |
| 49 |
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- switch on exf interpolation in AD test (just like the forward test) |
| 50 |
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o pkg/mom_vecinv: |
| 51 |
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- add storage directives to avoid recomputations within mom_vecinv.F |
| 52 |
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which were generating seg. fault with gfortran -devel |
| 53 |
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o pkg/ctrl, pkg/smooth: |
| 54 |
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- initialize array halos which were generating seg. fault with |
| 55 |
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gfortran -devel in adjoint mode |
| 56 |
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o pkg/exf: |
| 57 |
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- for each input field, enable to specify a field specific repeat-cycle |
| 58 |
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({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod". |
| 59 |
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o verification/lab_sea: |
| 60 |
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- update AD results of primary test and noseaicedyn test after switching |
| 61 |
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to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient |
| 62 |
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check stays about the same. |
| 63 |
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o pkg/exf: |
| 64 |
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- fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T. |
| 65 |
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- exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat |
| 66 |
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o pkg/bling, USE_EXFCO2 code: |
| 67 |
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- add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default); |
| 68 |
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- update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD). |
| 69 |
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o pkg/exf: |
| 70 |
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- rename S/R EXF_INIT to EXF_INIT_VARIA ; |
| 71 |
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- add arguments: fldName (for debug msg) and fldRepeatCycle (set to |
| 72 |
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repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD) |
| 73 |
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and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ; |
| 74 |
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- add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed |
| 75 |
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EXF_INIT_FLD) and update calls in exf_init_varia.F |
| 76 |
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- For now, for backward compatibility, keep a simplified version of S/Rs |
| 77 |
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EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F |
| 78 |
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- add and pass new arguments: fldName (for debug msg) and fldRepeatCycle |
| 79 |
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to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F |
| 80 |
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o tools/genmake2: |
| 81 |
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- replace "bc -l" (only used once) by "expr" (already used). |
| 82 |
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o verification/global_ocean.cs32x15: |
| 83 |
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- turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn". |
| 84 |
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Note: exf setting (data.exf) can be compared to other exf secondary exp |
| 85 |
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"seaice" (kept with useCAL=T) which has same time dependent forcing. |
| 86 |
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|
| 87 |
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checkpoint66d (2017/02/13) |
| 88 |
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o pkg/exf: |
| 89 |
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- remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning |
| 90 |
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early on (in packages_boot.F) to stress this change in pkg setting. |
| 91 |
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- In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg |
| 92 |
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o model/src: |
| 93 |
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- move call to ecco_phys to end of time step; this may induce minor |
| 94 |
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cost function changes by shifting time averages by one time step |
| 95 |
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for some variables; this revision resulted in changed adjoint results |
| 96 |
|
in MITgcm_contrib/verification_other/global_oce_cs32 |
| 97 |
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o pkg/exf: |
| 98 |
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- Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ; |
| 99 |
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this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields, |
| 100 |
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e.g. precip, are not available. |
| 101 |
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o pkg/flt: |
| 102 |
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- flt_init_varia.F: use pickupSuff if specified |
| 103 |
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- add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first, |
| 104 |
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intermediate, step towards completing pkg/exch2 support within pkg/flt; |
| 105 |
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ifdef DEVEL_FLT_EXCH2 then: |
| 106 |
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- flt_init_fixed.F: comment out stop |
| 107 |
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- flt_exch2.F: conserve ipart, jpart (grid coordinates) |
| 108 |
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- exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates) |
| 109 |
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- flt_mapping.F: attempt to fix longitude diagnostic near date-line |
| 110 |
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- flt_init_varia.F: hack initialization (for testing purposes w. LLC90) |
| 111 |
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o tools/genmake2 & pkg/pkg_depend: |
| 112 |
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- define new type of pkg dependency rule ("=pkg_x"), less strict than |
| 113 |
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the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled |
| 114 |
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(-pkg_x in packages.conf). |
| 115 |
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- change pkg/exf dependency rule from "exf +cal" to "exf =cal"; |
| 116 |
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- add "+cal" to dependency list of pkg/ecco (needed to compile). |
| 117 |
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- simplify FWD experiment "offline_exf_seaice" by removing pkg/cal. |
| 118 |
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o utils/matlab: |
| 119 |
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- adding ocean_basin routines for defining basin masks. |
| 120 |
|
o pkg/exf: |
| 121 |
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- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
| 122 |
|
arguments, allowing to check (and stop) if parameter setting of |
| 123 |
|
{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
| 124 |
|
useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
| 125 |
|
for backward compatibility. |
| 126 |
|
- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
| 127 |
|
exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
| 128 |
|
o pkg/bling (USE_EXFCO2 code): |
| 129 |
|
- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
| 130 |
|
by adding a call to S/R EXF_GETFFIELD_START. |
| 131 |
|
o pkg/exf: |
| 132 |
|
- allows to compile without pkg/cal (but disabled by current dependency |
| 133 |
|
rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
| 134 |
|
run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
| 135 |
|
of {FLD}startdate1 & date2 ; consistency check not yet coded. |
| 136 |
|
o verification/global_ocean.cs32x15: |
| 137 |
|
- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
| 138 |
|
corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
| 139 |
|
o pkg/exf: |
| 140 |
|
- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
| 141 |
|
calculations); change FWD experiment global_ocean.cs32x15 |
| 142 |
|
(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
| 143 |
|
o pkg/exf: |
| 144 |
|
- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
| 145 |
|
{FIELD}startdate to {FIELD}StartTime |
| 146 |
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Note: new name also fit better the content, i.e, a start time in second. |
| 147 |
|
o eesupp/src: |
| 148 |
|
- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
| 149 |
|
o pkg/exf: |
| 150 |
|
- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
| 151 |
|
to allow to read-in Sensible & Latent Heat flux ; |
| 152 |
|
- simplify pkg/exf main options: |
| 153 |
|
1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
| 154 |
|
exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
| 155 |
|
compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
| 156 |
|
2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
| 157 |
|
ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
| 158 |
|
3) improve options documentation in EXF_OPTIONS.h. |
| 159 |
|
o pkg/ecco: |
| 160 |
|
- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
| 161 |
|
ecco_summary.F: add passive tracer cost functions to gencost; |
| 162 |
|
m_ptracer and m_boxmean_ptracer |
| 163 |
|
o pkg/ctrl: |
| 164 |
|
- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
| 165 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
| 166 |
|
of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
| 167 |
|
xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
| 168 |
|
o model/src: |
| 169 |
|
- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
| 170 |
|
parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
| 171 |
|
o pkg/exf: |
| 172 |
|
- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
| 173 |
|
xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
| 174 |
|
|
| 175 |
|
checkpoint66c (2017/01/19) |
| 176 |
|
o verification: |
| 177 |
|
- add new option "-src" to testreport to only produce source code (*.f), |
| 178 |
|
including taf output src code (if using '-adm'/'-tlm' option). |
| 179 |
|
o pkg/exf: |
| 180 |
|
- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
| 181 |
|
o pkg/diagnostics: |
| 182 |
|
- add run-time variable diagMdsDir to specify a subdirectory for |
| 183 |
|
diagnostic output when mds is being used and mdsioLocalDir is not. |
| 184 |
|
o pkg/mnc: |
| 185 |
|
- mnc_utils.F: edit stop message |
| 186 |
|
o pkg/autodiff: |
| 187 |
|
- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 188 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 189 |
|
o pkg/profiles: |
| 190 |
|
- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
| 191 |
|
profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
| 192 |
|
- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 193 |
|
add HAVE_SYSTEM bracket around system call to mkdir |
| 194 |
|
o pkg/smooth: |
| 195 |
|
- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
| 196 |
|
- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
| 197 |
|
- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
| 198 |
|
o pkg/exf: |
| 199 |
|
- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
| 200 |
|
issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
| 201 |
|
generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
| 202 |
|
- summary: skip detailed field report if not used (empty file-name). |
| 203 |
|
o tools/xmakedepend: |
| 204 |
|
- In case line editor "ed" is missing, switch to "sed" command to clean-up |
| 205 |
|
Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
| 206 |
|
o pkg/exf: |
| 207 |
|
- change definition of "hflux" input file to always include Short-Wave; |
| 208 |
|
this is now consistent with hflux computation (if using bulk-formulae) |
| 209 |
|
and hflux diagnostic & documentation (in EXF_FIELDS.h). |
| 210 |
|
|
| 211 |
|
checkpoint66b (2016/12/01) |
| 212 |
|
o model & momentum pkgs: |
| 213 |
|
- implement fully implicit bottom friction combined with implicit surf. |
| 214 |
|
pressure, for now, only in hydrostic formulation: |
| 215 |
|
+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
| 216 |
|
and run with selectImplicitDrag=2 ; |
| 217 |
|
+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
| 218 |
|
- partial implicit time-stepping (bot. friction + vert. visc first, then |
| 219 |
|
surf. press) corresponding to selectImplicitDrag=1 should be applicable |
| 220 |
|
to NH formulation but not available until we solve for surf. pressure |
| 221 |
|
increment (instead of full etaN). |
| 222 |
|
- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
| 223 |
|
with implicit vertical viscosity. |
| 224 |
|
o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
| 225 |
|
- this is a first version that includes many regularisations that may |
| 226 |
|
not all be necessary, to be sorted out, |
| 227 |
|
- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
| 228 |
|
- change one verification experiment in seaice_itd to use and test new code |
| 229 |
|
- seaice_growth: catch a case where the argument of log can be zero |
| 230 |
|
or smaller (important for code stability) |
| 231 |
|
o model/src: |
| 232 |
|
- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
| 233 |
|
& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
| 234 |
|
similar A.X'=Y' system (with same matrix A) in subsequent calls; |
| 235 |
|
switch based on errCode (In/Out) argument value; in calling routines, |
| 236 |
|
initialise errCode before first call. |
| 237 |
|
|
| 238 |
|
checkpoint66a (2016/10/18) |
| 239 |
|
o pkg/bling: |
| 240 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
| 241 |
|
Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
| 242 |
|
o model/src & pkg/ptracers: |
| 243 |
|
- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
| 244 |
|
GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
| 245 |
|
implicitDiffusion (respectively) are used (even without momImplVertAdv |
| 246 |
|
or temp,salt,PTRACERS_ImplVertAdv). |
| 247 |
|
o model/src & generic_advdiff: |
| 248 |
|
- add parenthesis in main diagonal calculation of implicit vertical |
| 249 |
|
diffusion matrix (impldiff.F & gad_implicit_r.F). |
| 250 |
|
This affects results at machine truncation level; update output of many |
| 251 |
|
verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
| 252 |
|
o pkg/mom_commom & generic_advdiff: |
| 253 |
|
- add deep atmosphere and anelastic scaling factor in implicit vertical |
| 254 |
|
advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
| 255 |
|
o model/src: |
| 256 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
| 257 |
|
& solve_pentadiagonal.F |
| 258 |
|
|
| 259 |
|
checkpoint65z (2016/09/28) |
| 260 |
|
o pkg/seaice: fix multithreading for seaice_fgmres.F |
| 261 |
|
- remove unecessary variables from common blocks |
| 262 |
|
- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
| 263 |
|
basis, that are stored in commom blocks (including integer variable i1) |
| 264 |
|
- clean up code a little by removing commented lines that refer to |
| 265 |
|
original code |
| 266 |
|
- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
| 267 |
|
o MITgcm manual: |
| 268 |
|
- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
| 269 |
|
preliminary documentation for generic controls (8.3; ctrl.tex), |
| 270 |
|
a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
| 271 |
|
ecco_costfunction.tex |
| 272 |
|
o pkg/ecco: |
| 273 |
|
- update and cleanup list of CCP options |
| 274 |
|
- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
| 275 |
|
is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
| 276 |
|
- add checks that retired run-time options are not used, and in relation |
| 277 |
|
to gencost_mask and gencost_errfile |
| 278 |
|
- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
| 279 |
|
gencost_nrecperiod |
| 280 |
|
- fix m_eta computation for virtual salt flux case |
| 281 |
|
- add m_horflux_vol case (selected via gencost_barfile) that computes |
| 282 |
|
transports via cost_gencost_boxmean (gencost_flag=-3) |
| 283 |
|
- use gencost_flag more systematically (i.e., avoid using gencost_name) |
| 284 |
|
for code switches (aside from physical variable selection) |
| 285 |
|
o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
| 286 |
|
attempt appears to be a bit of a hack and my need some repair down the road |
| 287 |
|
o pkg/exf: |
| 288 |
|
- interpolation near South Pole: fix criteria on input field latitude. |
| 289 |
|
o pkg/icefront & pkg/exf: |
| 290 |
|
- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
| 291 |
|
from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
| 292 |
|
o pkg/exf: |
| 293 |
|
- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
| 294 |
|
"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
| 295 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
| 296 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
| 297 |
|
Change output file content by writing interpolated field before applying |
| 298 |
|
land-sea mask (helpful for debug). |
| 299 |
|
- 2 compon. vector interpolation with rotation: apply scaling factor on |
| 300 |
|
each compon. (Eastward and Northward) just before rotation. |
| 301 |
|
o pkg/bling: |
| 302 |
|
- Cleaned package. Removed not needed code and comments. |
| 303 |
|
- adjoint example now works |
| 304 |
|
(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
| 305 |
|
o pkg/ptracers: |
| 306 |
|
- add Bruno Deremble's code to complete the linear surface correction |
| 307 |
|
for tracer conservation; |
| 308 |
|
- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 309 |
|
|
| 310 |
|
checkpoint65y (2016/07/29) |
| 311 |
|
o pkg/debug (stats): |
| 312 |
|
- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 313 |
|
proc/thread mapping); |
| 314 |
|
- fix Min & Max for case where 1 thread has only empty tiles; |
| 315 |
|
- use RL variable to count number of wet grid points (with big domain, |
| 316 |
|
can be too large to fit into integer*4). |
| 317 |
|
o pkg/monitor: |
| 318 |
|
- use RL variable to count number of wet grid points (but used only for del2) |
| 319 |
|
- add new routine to compute Advective CFL within tracer time-stepping with |
| 320 |
|
writing delayed until next monitor output. |
| 321 |
|
o pkg/obcs: |
| 322 |
|
- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 323 |
|
o pkg/cal: |
| 324 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
| 325 |
|
eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
| 326 |
|
o pkg/dic & seaice: |
| 327 |
|
- fix compilation of ocean component for coupled atm+ocn model with |
| 328 |
|
seaice dynamics & dic. |
| 329 |
|
|
| 330 |
|
checkpoint65x (2016/06/11) |
| 331 |
|
o add a license text file in main MITgcm tree. |
| 332 |
|
o added pkg/bling: |
| 333 |
|
- intermediate complexity biogeochemical model |
| 334 |
|
- see bling_description.txt for details |
| 335 |
|
- verification experiment is global_oce_biogeo_bling (for now, in |
| 336 |
|
Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 337 |
|
- add entry point in pkg/gchem for new pkg "bling". |
| 338 |
|
o pkg/seaice: fix tensile stength computation |
| 339 |
|
- replace global field tensileStrength by tensileStrFac |
| 340 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
| 341 |
|
- fortunately that does not affect any verification results |
| 342 |
|
|
| 343 |
|
checkpoint65w (2016/05/12) |
| 344 |
|
o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 345 |
|
with ECCO_CTRL_DEPRECATED defined |
| 346 |
|
o verification/global_ocean.cs32x15: |
| 347 |
|
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 348 |
|
with "selectNHfreeSurf=1". |
| 349 |
|
o model/src (non-hydrostatic free-surface): |
| 350 |
|
- More "natural" expression of NH free-surface term (case selectNHfreeSurf=1): |
| 351 |
|
was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf. |
| 352 |
|
- Calculate surface vertical velocity after 2-D solver adjustment (accounts |
| 353 |
|
for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv |
| 354 |
|
and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1. |
| 355 |
|
This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux. |
| 356 |
|
- Update output (changes at machine truncation level) of verification exp: |
| 357 |
|
exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d), |
| 358 |
|
short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d). |
| 359 |
|
o pkg/seaice: ITD code |
| 360 |
|
- fix picking up from a single category model by initialising |
| 361 |
|
heff/area/hsnowITD = 0. in seaice_itd_pickup.F |
| 362 |
|
- split a long warning message in seaice_check_pickup.F into two lines, |
| 363 |
|
because NEC SX-ACE cannot deal with the long line. |
| 364 |
|
o model/src: |
| 365 |
|
- fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3) |
| 366 |
|
o pkg/seaice: |
| 367 |
|
- add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG |
| 368 |
|
o pkg/seaice: |
| 369 |
|
- add basal stress as parameterisation for grounding ice |
| 370 |
|
following Lemieux et al. (2015) |
| 371 |
|
- turn on by setting new parameter SEAICEbasalDragK2 to a value |
| 372 |
|
larger than 0. Lemieux et al. (2015) recommend 15. |
| 373 |
|
- The adjoint complains with extra recomputations so there is also a |
| 374 |
|
new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in |
| 375 |
|
order to postpone the problem |
| 376 |
|
- compile the new code in lab_sea |
| 377 |
|
o verification/halfpipe_streamice: |
| 378 |
|
- update both TAF and OpenAD adm output (machine truncation differences) |
| 379 |
|
|
| 380 |
|
checkpoint65v (2016/04/08) |
| 381 |
|
o verification/advect_xz: |
| 382 |
|
- increase overlap size from 3 to 4 and add new secondary test for PQM |
| 383 |
|
advection scheme (with mono & wino limiter). |
| 384 |
|
- change main exp. to test PPM (with weno limiter) adv.scheme on Temp. |
| 385 |
|
o model/src: |
| 386 |
|
- new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently |
| 387 |
|
added phi0Ref) to set vertical axis origin and phiRef origin; |
| 388 |
|
keep Ro_SeaLevel for backward compatibility (with a warning). |
| 389 |
|
According to coordinate and fluid type: |
| 390 |
|
OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top) |
| 391 |
|
ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom) |
| 392 |
|
OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top) |
| 393 |
|
ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom) |
| 394 |
|
- remove Ro_SeaLevel from ATM experiment parameter files; |
| 395 |
|
- in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the |
| 396 |
|
complement; update output.txt (changes at machine truncation level). |
| 397 |
|
o pkg/seaice/seaice_evp.F |
| 398 |
|
- simplify computation of deltaZ and zetaZ to simple averaging following |
| 399 |
|
Bouillon et al. (2013). This removes a lot of code, but also changes |
| 400 |
|
verification experiment lab_sea.hb87 -> updated |
| 401 |
|
|
| 402 |
|
checkpoint65u (2016/03/14) |
| 403 |
|
o pkg/generic_advdiff: |
| 404 |
|
- from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52) |
| 405 |
|
with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP); |
| 406 |
|
Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for |
| 407 |
|
testing and not for actual use. |
| 408 |
|
o model/src: |
| 409 |
|
- add parameter "phi0Ref" to specify reference [pressure/geo] potential at |
| 410 |
|
origin r = rF(1); |
| 411 |
|
- add options (parameter selectP_inEOS_Zc) to select which pressure to use |
| 412 |
|
in EOS for height coordinate: enable to include NH Pressure or to use |
| 413 |
|
more accurate pressure vertical profile; options not linked to EOS type |
| 414 |
|
(as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type; |
| 415 |
|
- start to implement variable gravity (along vertical): for now, only with |
| 416 |
|
z-coords (not even z*). |
| 417 |
|
- add Ideal Gas equation of state for height coordinate. |
| 418 |
|
- update OpenAD output (affected at machine truncation level) of exp: |
| 419 |
|
global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo. |
| 420 |
|
o pkg/exf: |
| 421 |
|
- add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result |
| 422 |
|
of exf interpolation (before any rescaling, rotation or interpolation |
| 423 |
|
to velocity point) for each field that gets loaded from file. This option |
| 424 |
|
identically mimics the input file organization (e.g. record numbers in year |
| 425 |
|
by year input files) besides the change in horizontal grid. |
| 426 |
|
- add rotateStressOnAgrid run-time switch so that wind stress fields |
| 427 |
|
can be provided on the A-grid in zonal/meridional direction and |
| 428 |
|
rotated on the fly. This only applies to the case when the exf |
| 429 |
|
interpolation is off and rotateStressOnAgrid is false by default. |
| 430 |
|
o model/src: |
| 431 |
|
- rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since |
| 432 |
|
it's also used with pkg/atm_phys) and add few more parameters (but still |
| 433 |
|
inactive, src code yet to come) |
| 434 |
|
|
| 435 |
|
checkpoint65t (2016/02/10) |
| 436 |
|
o pkg/atm_phys: |
| 437 |
|
- from Ruth Geen: add optical depth dependence on CO2 concentration. |
| 438 |
|
o model/src: |
| 439 |
|
- fix vertical inter/extra-polation of density factor rhoFacF (for anelastic) |
| 440 |
|
for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F. |
| 441 |
|
Update output of exp. deep_anelastic (changes at truncation level). |
| 442 |
|
o tools: |
| 443 |
|
- add a hack in "remove_comments_sed" (used only with TAF) for recent |
| 444 |
|
version of OpenMPI (shipped with FC.23): comment out the new header |
| 445 |
|
file "mpif-sizeof.h" which causes problems to TAF. |
| 446 |
|
o pkg/seaice: |
| 447 |
|
- change the termination criterion so that maxits (SEAICElinearIterMax) |
| 448 |
|
has an effect |
| 449 |
|
- unify iteration parameters for implicit solvers (JFNK and Picard) |
| 450 |
|
SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS |
| 451 |
|
SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER |
| 452 |
|
SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner |
| 453 |
|
SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner |
| 454 |
|
SEAICEnonLinTol replaces JFNKgamma_nonlin |
| 455 |
|
- remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN |
| 456 |
|
- add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and |
| 457 |
|
use with SEAICEuseKrylov |
| 458 |
|
o pkg/seaice/seaice_lsr.F |
| 459 |
|
fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only |
| 460 |
|
relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have |
| 461 |
|
an effect. |
| 462 |
|
o pkg/seaice: add two new parameters |
| 463 |
|
- SEAICEuseLSR to simplify the logic in seaice_dynsolver (this |
| 464 |
|
parameter is not in any namelist) |
| 465 |
|
- SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as |
| 466 |
|
a preconditioner for the non-linear Newton iteration of the JFNK |
| 467 |
|
solver |
| 468 |
|
o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT, |
| 469 |
|
affects some experiments at truncation level: |
| 470 |
|
- global_ocean.cs32x15.icedyn (11 digits), |
| 471 |
|
- global_ocean.cs32x15.seaice (11 digits), |
| 472 |
|
- seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update |
| 473 |
|
- also update global_ocean.cs32x15 adjoint and tangent-linear results |
| 474 |
|
o pkg/salt_plume & pkg/thsice: |
| 475 |
|
- for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN, |
| 476 |
|
connect salt_plume flux to ATM-OCN coupling pkgs interface: |
| 477 |
|
a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for |
| 478 |
|
export to coupler interface) even without compiling pkg/salt_plume ; |
| 479 |
|
b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field |
| 480 |
|
(saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH. |
| 481 |
|
o pkg/dic: |
| 482 |
|
- use the updated seaice fraction (from seaice pkgs) for DIC forcing |
| 483 |
|
instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE |
| 484 |
|
called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD); |
| 485 |
|
- move also update with values from ATM-OCN Coupler in the same new S/R |
| 486 |
|
(previously done in ocn_apply_import.F). |
| 487 |
|
o tools/adjoint_options: |
| 488 |
|
- specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default) |
| 489 |
|
has been changed on Jan 14, 2016. |
| 490 |
|
o pkg/ggl90: |
| 491 |
|
- add alternative discretisation of vertical shear (off by default), to |
| 492 |
|
compute the mean (@ grid-cell center) of vertical shear compon instead of |
| 493 |
|
vertical shear of mean flow (@ grid-cell center). |
| 494 |
|
- add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated |
| 495 |
|
results on adjacent faces of cubed-sphere grids; this fix the restart. |
| 496 |
|
o pkg/atm_compon_interf: |
| 497 |
|
- skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just |
| 498 |
|
pass last value, stored directly before export to CPL ; |
| 499 |
|
Note: this affects results of Coupled set-up where OCN uses useImportSLP=T |
| 500 |
|
- remove atmSLPr from pickup files (no longer needed for restart) |
| 501 |
|
|
| 502 |
|
checkpoint65s (2016/01/13) |
| 503 |
|
o eesupp & genmake2: |
| 504 |
|
- first check for Function ETIME and, if it fails, then check for subroutine |
| 505 |
|
ETIME and consistent output; use the appropriate version in timers.F |
| 506 |
|
o model/src: |
| 507 |
|
- to check restart test, add option to apply EXCH to U,V earlier, just before |
| 508 |
|
integr_continuity; turned off by default. |
| 509 |
|
o pkg/dic: |
| 510 |
|
- remove CPP option USE_ATMOSCO2 (not needed) |
| 511 |
|
o tools/tst_2+2: |
| 512 |
|
- try to ignore difference between +0 and -0 in binary file, causing test |
| 513 |
|
to fail for no good reason. |
| 514 |
|
o eesupp & genmake2: |
| 515 |
|
- put back modif from Jinxuan Zhu - change etime fct call to S/R call - |
| 516 |
|
but also check (in genmake2) that test runs and returns meaningful results. |
| 517 |
|
o coupler pkgs: |
| 518 |
|
Finish implementation of optionally-exchanged variable switches (started on |
| 519 |
|
Nov 12) with addition of few more exchanged fields, including 2-way exchange |
| 520 |
|
of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice |
| 521 |
|
advection in OCN component; this requires sequential coupling. |
| 522 |
|
coupler (pkg/atm_ocn_coupler): |
| 523 |
|
- add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS |
| 524 |
|
routines (useful for debug). |
| 525 |
|
- only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume |
| 526 |
|
flux, DIC fields) if corresponding switch is ON. |
| 527 |
|
- add option to export RunOff to OCN (to use for DIC river input) |
| 528 |
|
- add 2-way thSIce vars exchange; check for consistent cpl_sequential setting. |
| 529 |
|
components (pkg/atm_ & ocn_compon_interf): |
| 530 |
|
- to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around |
| 531 |
|
optionally exchanged fields; add a check & stop in cpl_readparms.F. |
| 532 |
|
ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2; |
| 533 |
|
OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice. |
| 534 |
|
- rename: fracIce -> sIceFrac_cpl (<- match coupler var name) |
| 535 |
|
+ in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime. |
| 536 |
|
- add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN. |
| 537 |
|
- hold in common block coupler optionally-exchanged variable switch |
| 538 |
|
and set default "useImportXXX" accordingly; + check & stop if inconsistent. |
| 539 |
|
- add diagnostics for all imported fields from coupler (in both OCN & ATM); |
| 540 |
|
this is intended to replace the OCN cplFldtave.* output files (not updated |
| 541 |
|
to contain new additional exchanged fields). |
| 542 |
|
o pkg/dic: |
| 543 |
|
- fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code. |
| 544 |
|
o pkg/thsice: |
| 545 |
|
- when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading |
| 546 |
|
and writing of thsice pickup files. |
| 547 |
|
o pkg/atm_compon_interf: |
| 548 |
|
- move all field individual export-call out of cpl_export_import_data.F |
| 549 |
|
into new S/R ATM_EXPORT_FIELDS |
| 550 |
|
o pkg/atm_compon_interf: |
| 551 |
|
- store state variables (for now, only thSIce fields) just before beeing |
| 552 |
|
exported (in cpl_export_import_data.F, like on ocean side) instead of from |
| 553 |
|
atm_store_my_data.F like all exported fluxes. |
| 554 |
|
- new version of pickup_cpl: write field names into meta file and read meta |
| 555 |
|
file to find field postion in pickup. Also only write/read fields meeded for |
| 556 |
|
restart (same logic as main pickup file ; also using pickupStrictlyMatch) |
| 557 |
|
o pkg/dic: |
| 558 |
|
- fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3. |
| 559 |
|
o pkg/seaice: add new parameter SEAICEpressReplFac to choose between |
| 560 |
|
pressure replacement method (=1., default) or original Hibler (1979) (=0.) |
| 561 |
|
value can be from domain [0,1] to average between the two methods |
| 562 |
|
o pkg/atm_phys: |
| 563 |
|
- allow to provide 2-d map of albedo and mixed-layer depth from files (but |
| 564 |
|
hold fixed in time). |
| 565 |
|
|
| 566 |
checkpoint65r (2015/12/21) |
checkpoint65r (2015/12/21) |
| 567 |
o pkg/seaice: |
o pkg/seaice: |
| 568 |
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
| 575 |
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
| 576 |
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
| 577 |
for individual contribution (convection, LSC cond, radiation) |
for individual contribution (convection, LSC cond, radiation) |
| 578 |
- add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp. |
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
| 579 |
information); activated with: solar_exponent=0. and wv_exponent=-1. |
information); activated with: solar_exponent=0. and wv_exponent=-1. |
| 580 |
o pkg/ggl90: |
o pkg/ggl90: |
| 581 |
- within IDEMIX add upper limit for horizontal group velocity to |
- within IDEMIX add upper limit for horizontal group velocity to |
| 1098 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
| 1099 |
o doc: |
o doc: |
| 1100 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 1101 |
o pkg/streamice: |
o pkg/shelfice: |
| 1102 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 1103 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 1104 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |
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