| 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/exf: |
| 8 |
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- fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T. |
| 9 |
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o pkg/bling, USE_EXFCO2 code: |
| 10 |
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- add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default); |
| 11 |
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- update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD). |
| 12 |
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o pkg/exf: |
| 13 |
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- rename S/R EXF_INIT to EXF_INIT_VARIA ; |
| 14 |
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- add arguments: fldName (for debug msg) and fldRepeatCycle (set to |
| 15 |
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repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD) |
| 16 |
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and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ; |
| 17 |
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- add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed |
| 18 |
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EXF_INIT_FLD) and update calls in exf_init_varia.F |
| 19 |
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- For now, for backward compatibility, keep a simplified version of S/Rs |
| 20 |
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EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F |
| 21 |
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- add and pass new arguments: fldName (for debug msg) and fldRepeatCycle |
| 22 |
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to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F |
| 23 |
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o tools/genmake2: |
| 24 |
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- replace "bc -l" (only used once) by "expr" (already used). |
| 25 |
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o verification/global_ocean.cs32x15: |
| 26 |
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- turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn". |
| 27 |
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Note: exf setting (data.exf) can be compared to other exf secondary exp |
| 28 |
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"seaice" (kept with useCAL=T) which has same time dependent forcing. |
| 29 |
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|
| 30 |
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checkpoint66d (2017/02/13) |
| 31 |
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o pkg/exf: |
| 32 |
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- remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning |
| 33 |
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early on (in packages_boot.F) to stress this change in pkg setting. |
| 34 |
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- In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg |
| 35 |
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o model/src: |
| 36 |
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- move call to ecco_phys to end of time step; this may induce minor |
| 37 |
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cost function changes by shifting time averages by one time step |
| 38 |
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for some variables; this revision resulted in changed adjoint results |
| 39 |
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in MITgcm_contrib/verification_other/global_oce_cs32 |
| 40 |
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o pkg/exf: |
| 41 |
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- Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ; |
| 42 |
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this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields, |
| 43 |
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e.g. precip, are not available. |
| 44 |
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o pkg/flt: |
| 45 |
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- flt_init_varia.F: use pickupSuff if specified |
| 46 |
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- add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first, |
| 47 |
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intermediate, step towards completing pkg/exch2 support within pkg/flt; |
| 48 |
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ifdef DEVEL_FLT_EXCH2 then: |
| 49 |
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- flt_init_fixed.F: comment out stop |
| 50 |
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- flt_exch2.F: conserve ipart, jpart (grid coordinates) |
| 51 |
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- exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates) |
| 52 |
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- flt_mapping.F: attempt to fix longitude diagnostic near date-line |
| 53 |
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- flt_init_varia.F: hack initialization (for testing purposes w. LLC90) |
| 54 |
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o tools/genmake2 & pkg/pkg_depend: |
| 55 |
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- define new type of pkg dependency rule ("=pkg_x"), less strict than |
| 56 |
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the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled |
| 57 |
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(-pkg_x in packages.conf). |
| 58 |
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- change pkg/exf dependency rule from "exf +cal" to "exf =cal"; |
| 59 |
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- add "+cal" to dependency list of pkg/ecco (needed to compile). |
| 60 |
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- simplify FWD experiment "offline_exf_seaice" by removing pkg/cal. |
| 61 |
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o utils/matlab: |
| 62 |
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- adding ocean_basin routines for defining basin masks. |
| 63 |
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o pkg/exf: |
| 64 |
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- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
| 65 |
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arguments, allowing to check (and stop) if parameter setting of |
| 66 |
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{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
| 67 |
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useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
| 68 |
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for backward compatibility. |
| 69 |
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- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
| 70 |
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exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
| 71 |
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o pkg/bling (USE_EXFCO2 code): |
| 72 |
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- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
| 73 |
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by adding a call to S/R EXF_GETFFIELD_START. |
| 74 |
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o pkg/exf: |
| 75 |
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- allows to compile without pkg/cal (but disabled by current dependency |
| 76 |
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rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
| 77 |
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run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
| 78 |
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of {FLD}startdate1 & date2 ; consistency check not yet coded. |
| 79 |
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o verification/global_ocean.cs32x15: |
| 80 |
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- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
| 81 |
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corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
| 82 |
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o pkg/exf: |
| 83 |
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- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
| 84 |
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calculations); change FWD experiment global_ocean.cs32x15 |
| 85 |
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(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
| 86 |
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o pkg/exf: |
| 87 |
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- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
| 88 |
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{FIELD}startdate to {FIELD}StartTime |
| 89 |
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Note: new name also fit better the content, i.e, a start time in second. |
| 90 |
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o eesupp/src: |
| 91 |
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- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
| 92 |
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o pkg/exf: |
| 93 |
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- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
| 94 |
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to allow to read-in Sensible & Latent Heat flux ; |
| 95 |
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- simplify pkg/exf main options: |
| 96 |
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1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
| 97 |
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exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
| 98 |
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compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
| 99 |
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2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
| 100 |
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ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
| 101 |
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3) improve options documentation in EXF_OPTIONS.h. |
| 102 |
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o pkg/ecco: |
| 103 |
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- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
| 104 |
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ecco_summary.F: add passive tracer cost functions to gencost; |
| 105 |
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m_ptracer and m_boxmean_ptracer |
| 106 |
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o pkg/ctrl: |
| 107 |
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- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
| 108 |
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parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
| 109 |
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of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
| 110 |
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xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
| 111 |
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o model/src: |
| 112 |
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- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
| 113 |
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parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
| 114 |
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o pkg/exf: |
| 115 |
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- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
| 116 |
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xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
| 117 |
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|
| 118 |
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checkpoint66c (2017/01/19) |
| 119 |
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o verification: |
| 120 |
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- add new option "-src" to testreport to only produce source code (*.f), |
| 121 |
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including taf output src code (if using '-adm'/'-tlm' option). |
| 122 |
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o pkg/exf: |
| 123 |
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- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
| 124 |
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o pkg/diagnostics: |
| 125 |
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- add run-time variable diagMdsDir to specify a subdirectory for |
| 126 |
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diagnostic output when mds is being used and mdsioLocalDir is not. |
| 127 |
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o pkg/mnc: |
| 128 |
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- mnc_utils.F: edit stop message |
| 129 |
|
o pkg/autodiff: |
| 130 |
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- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 131 |
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add HAVE_SYSTEM bracket around system call to mkdir |
| 132 |
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o pkg/profiles: |
| 133 |
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- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
| 134 |
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profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
| 135 |
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- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
| 136 |
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add HAVE_SYSTEM bracket around system call to mkdir |
| 137 |
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o pkg/smooth: |
| 138 |
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- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
| 139 |
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- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
| 140 |
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- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
| 141 |
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o pkg/exf: |
| 142 |
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- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
| 143 |
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issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
| 144 |
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generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
| 145 |
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- summary: skip detailed field report if not used (empty file-name). |
| 146 |
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o tools/xmakedepend: |
| 147 |
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- In case line editor "ed" is missing, switch to "sed" command to clean-up |
| 148 |
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Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
| 149 |
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o pkg/exf: |
| 150 |
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- change definition of "hflux" input file to always include Short-Wave; |
| 151 |
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this is now consistent with hflux computation (if using bulk-formulae) |
| 152 |
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and hflux diagnostic & documentation (in EXF_FIELDS.h). |
| 153 |
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|
| 154 |
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checkpoint66b (2016/12/01) |
| 155 |
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o model & momentum pkgs: |
| 156 |
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- implement fully implicit bottom friction combined with implicit surf. |
| 157 |
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pressure, for now, only in hydrostic formulation: |
| 158 |
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+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
| 159 |
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and run with selectImplicitDrag=2 ; |
| 160 |
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+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
| 161 |
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- partial implicit time-stepping (bot. friction + vert. visc first, then |
| 162 |
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surf. press) corresponding to selectImplicitDrag=1 should be applicable |
| 163 |
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to NH formulation but not available until we solve for surf. pressure |
| 164 |
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increment (instead of full etaN). |
| 165 |
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- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
| 166 |
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with implicit vertical viscosity. |
| 167 |
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o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
| 168 |
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- this is a first version that includes many regularisations that may |
| 169 |
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not all be necessary, to be sorted out, |
| 170 |
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- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
| 171 |
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- change one verification experiment in seaice_itd to use and test new code |
| 172 |
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- seaice_growth: catch a case where the argument of log can be zero |
| 173 |
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or smaller (important for code stability) |
| 174 |
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o model/src: |
| 175 |
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- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
| 176 |
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& solve_pentadiagonal.F to enable to re-used inverse matrix for solving |
| 177 |
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similar A.X'=Y' system (with same matrix A) in subsequent calls; |
| 178 |
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switch based on errCode (In/Out) argument value; in calling routines, |
| 179 |
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initialise errCode before first call. |
| 180 |
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|
| 181 |
|
checkpoint66a (2016/10/18) |
| 182 |
|
o pkg/bling: |
| 183 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
| 184 |
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Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
| 185 |
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o model/src & pkg/ptracers: |
| 186 |
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- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
| 187 |
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GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
| 188 |
|
implicitDiffusion (respectively) are used (even without momImplVertAdv |
| 189 |
|
or temp,salt,PTRACERS_ImplVertAdv). |
| 190 |
|
o model/src & generic_advdiff: |
| 191 |
|
- add parenthesis in main diagonal calculation of implicit vertical |
| 192 |
|
diffusion matrix (impldiff.F & gad_implicit_r.F). |
| 193 |
|
This affects results at machine truncation level; update output of many |
| 194 |
|
verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
| 195 |
|
o pkg/mom_commom & generic_advdiff: |
| 196 |
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- add deep atmosphere and anelastic scaling factor in implicit vertical |
| 197 |
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advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
| 198 |
|
o model/src: |
| 199 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
| 200 |
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& solve_pentadiagonal.F |
| 201 |
|
|
| 202 |
|
checkpoint65z (2016/09/28) |
| 203 |
|
o pkg/seaice: fix multithreading for seaice_fgmres.F |
| 204 |
|
- remove unecessary variables from common blocks |
| 205 |
|
- use extra dimension MAX_NO_THREADS for all variables of the Krylov space |
| 206 |
|
basis, that are stored in commom blocks (including integer variable i1) |
| 207 |
|
- clean up code a little by removing commented lines that refer to |
| 208 |
|
original code |
| 209 |
|
- turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk. |
| 210 |
|
o MITgcm manual: |
| 211 |
|
- add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex), |
| 212 |
|
preliminary documentation for generic controls (8.3; ctrl.tex), |
| 213 |
|
a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated |
| 214 |
|
ecco_costfunction.tex |
| 215 |
|
o pkg/ecco: |
| 216 |
|
- update and cleanup list of CCP options |
| 217 |
|
- re-assign gencost_mask to specify masks rather than gencost_errfile; 'c' |
| 218 |
|
is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM |
| 219 |
|
- add checks that retired run-time options are not used, and in relation |
| 220 |
|
to gencost_mask and gencost_errfile |
| 221 |
|
- finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and |
| 222 |
|
gencost_nrecperiod |
| 223 |
|
- fix m_eta computation for virtual salt flux case |
| 224 |
|
- add m_horflux_vol case (selected via gencost_barfile) that computes |
| 225 |
|
transports via cost_gencost_boxmean (gencost_flag=-3) |
| 226 |
|
- use gencost_flag more systematically (i.e., avoid using gencost_name) |
| 227 |
|
for code switches (aside from physical variable selection) |
| 228 |
|
o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first |
| 229 |
|
attempt appears to be a bit of a hack and my need some repair down the road |
| 230 |
|
o pkg/exf: |
| 231 |
|
- interpolation near South Pole: fix criteria on input field latitude. |
| 232 |
|
o pkg/icefront & pkg/exf: |
| 233 |
|
- move setting of icefront Sub-Glacial RunOff forcing (currently unused) |
| 234 |
|
from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront) |
| 235 |
|
o pkg/exf: |
| 236 |
|
- replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter |
| 237 |
|
"exf_output_interp" (in namelist: EXF_NML_04); change output file name |
| 238 |
|
(add suffix "_out" instead of a prefix); keep same record number as in |
| 239 |
|
input file but always write record 1 first (to avoid a STOP in I/O S/R). |
| 240 |
|
Change output file content by writing interpolated field before applying |
| 241 |
|
land-sea mask (helpful for debug). |
| 242 |
|
- 2 compon. vector interpolation with rotation: apply scaling factor on |
| 243 |
|
each compon. (Eastward and Northward) just before rotation. |
| 244 |
|
o pkg/bling: |
| 245 |
|
- Cleaned package. Removed not needed code and comments. |
| 246 |
|
- adjoint example now works |
| 247 |
|
(MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad) |
| 248 |
|
o pkg/ptracers: |
| 249 |
|
- add Bruno Deremble's code to complete the linear surface correction |
| 250 |
|
for tracer conservation; |
| 251 |
|
- enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE. |
| 252 |
|
|
| 253 |
|
checkpoint65y (2016/07/29) |
| 254 |
|
o pkg/debug (stats): |
| 255 |
|
- change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to |
| 256 |
|
proc/thread mapping); |
| 257 |
|
- fix Min & Max for case where 1 thread has only empty tiles; |
| 258 |
|
- use RL variable to count number of wet grid points (with big domain, |
| 259 |
|
can be too large to fit into integer*4). |
| 260 |
|
o pkg/monitor: |
| 261 |
|
- use RL variable to count number of wet grid points (but used only for del2) |
| 262 |
|
- add new routine to compute Advective CFL within tracer time-stepping with |
| 263 |
|
writing delayed until next monitor output. |
| 264 |
|
o pkg/obcs: |
| 265 |
|
- fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW) |
| 266 |
|
o pkg/cal: |
| 267 |
|
- calandar-dump: treat case myTime < timePhase in the same way as in |
| 268 |
|
eesupp/src/diff_phase_multiple.F (when not using calandar-dump). |
| 269 |
|
o pkg/dic & seaice: |
| 270 |
|
- fix compilation of ocean component for coupled atm+ocn model with |
| 271 |
|
seaice dynamics & dic. |
| 272 |
|
|
| 273 |
|
checkpoint65x (2016/06/11) |
| 274 |
|
o add a license text file in main MITgcm tree. |
| 275 |
|
o added pkg/bling: |
| 276 |
|
- intermediate complexity biogeochemical model |
| 277 |
|
- see bling_description.txt for details |
| 278 |
|
- verification experiment is global_oce_biogeo_bling (for now, in |
| 279 |
|
Contrib/verification_other/); tested daily on baudelaire with gfortran. |
| 280 |
|
- add entry point in pkg/gchem for new pkg "bling". |
| 281 |
|
o pkg/seaice: fix tensile stength computation |
| 282 |
|
- replace global field tensileStrength by tensileStrFac |
| 283 |
|
- tensileStrFac can be computed once in S/R seaice_init_varia |
| 284 |
|
- fortunately that does not affect any verification results |
| 285 |
|
|
| 286 |
|
checkpoint65w (2016/05/12) |
| 287 |
|
o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles |
| 288 |
|
with ECCO_CTRL_DEPRECATED defined |
| 289 |
o verification/global_ocean.cs32x15: |
o verification/global_ocean.cs32x15: |
| 290 |
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
- change secondary test "viscA4" to also test "selectP_inEOS_Zc=3" |
| 291 |
with "selectNHfreeSurf=1". |
with "selectNHfreeSurf=1". |
| 1041 |
just copy level Nr value to level Nr+1. |
just copy level Nr value to level Nr+1. |
| 1042 |
o doc: |
o doc: |
| 1043 |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
- add notes form Abhisek Chakraborty on how to close Heat & Salt budgets. |
| 1044 |
o pkg/streamice: |
o pkg/shelfice: |
| 1045 |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
- shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F, |
| 1046 |
SHELFICE.h: move array shelficemass to init_varia, initialise |
SHELFICE.h: move array shelficemass to init_varia, initialise |
| 1047 |
from array shelficemassinit, which is set in init_fixed and |
from array shelficemassinit, which is set in init_fixed and |
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