4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
5 |
============================== |
============================== |
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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 |
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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 |
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o pkg/exf: |
121 |
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- new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more |
122 |
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arguments, allowing to check (and stop) if parameter setting of |
123 |
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{FLD}startdate1 & date2 and of {FLD}StartTime are consistent with |
124 |
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useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START |
125 |
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for backward compatibility. |
126 |
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- change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in |
127 |
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exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field). |
128 |
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o pkg/bling (USE_EXFCO2 code): |
129 |
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- fix missing setting of apco2StartTime according to apco2startdate1 & date2 |
130 |
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by adding a call to S/R EXF_GETFFIELD_START. |
131 |
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o pkg/exf: |
132 |
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- allows to compile without pkg/cal (but disabled by current dependency |
133 |
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rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to |
134 |
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run with useCAL=F ; this involves setting directly {FLD}StartTime instead |
135 |
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of {FLD}startdate1 & date2 ; consistency check not yet coded. |
136 |
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o verification/global_ocean.cs32x15: |
137 |
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- fix all data.exf for a shift of 1 day in all field startdate1 so that it now |
138 |
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corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm). |
139 |
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o pkg/exf: |
140 |
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- allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some |
141 |
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calculations); change FWD experiment global_ocean.cs32x15 |
142 |
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(#define ALLOW_ZENITHANGLE) to test/check that this code compiles. |
143 |
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o pkg/exf: |
144 |
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- In preparation for addition to NAMELIST, rename internal (_RL) parameter |
145 |
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{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 |
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o eesupp/src: |
148 |
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- add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF |
149 |
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o pkg/exf: |
150 |
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- add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters) |
151 |
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to allow to read-in Sensible & Latent Heat flux ; |
152 |
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- simplify pkg/exf main options: |
153 |
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1) move small piece of code (case ALLOW_ATM_TEMP undef) out of |
154 |
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exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is |
155 |
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compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined; |
156 |
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2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option |
157 |
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ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ; |
158 |
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3) improve options documentation in EXF_OPTIONS.h. |
159 |
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o pkg/ecco: |
160 |
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- cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and |
161 |
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ecco_summary.F: add passive tracer cost functions to gencost; |
162 |
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m_ptracer and m_boxmean_ptracer |
163 |
|
o pkg/ctrl: |
164 |
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- ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input |
165 |
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parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list |
166 |
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of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw, |
167 |
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xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn |
168 |
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o model/src: |
169 |
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- forward_step.F: pass myIter and myTime to ctrl_map_forcing as input |
170 |
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parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing |
171 |
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o pkg/exf: |
172 |
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- exf_getffields.F: add to list of implemented gentim2d contol parameters: |
173 |
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xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask |
174 |
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|
175 |
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checkpoint66c (2017/01/19) |
176 |
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o verification: |
177 |
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- add new option "-src" to testreport to only produce source code (*.f), |
178 |
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including taf output src code (if using '-adm'/'-tlm' option). |
179 |
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o pkg/exf: |
180 |
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- add saltflx :: Net upward salt flux in psu.kg/m^2/s |
181 |
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o pkg/diagnostics: |
182 |
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- add run-time variable diagMdsDir to specify a subdirectory for |
183 |
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diagnostic output when mds is being used and mdsioLocalDir is not. |
184 |
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o pkg/mnc: |
185 |
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- mnc_utils.F: edit stop message |
186 |
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o pkg/autodiff: |
187 |
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- autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
188 |
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add HAVE_SYSTEM bracket around system call to mkdir |
189 |
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o pkg/profiles: |
190 |
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- profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F, |
191 |
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profiles_readparms.F: call ALL_PROC_DIE before 'stop' |
192 |
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- profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER, |
193 |
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add HAVE_SYSTEM bracket around system call to mkdir |
194 |
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o pkg/smooth: |
195 |
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- smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop' |
196 |
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- smooth_init2d.F, smooth_init3d.F: move print statements to readparms |
197 |
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- smooth_readparms.F: add cleaner print statements from smooth_init?d.F |
198 |
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o pkg/exf: |
199 |
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- check: count errors and stop cleanly at the end (call to ALL_PROC_DIE); |
200 |
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issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500 |
201 |
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generalize tests on interpMethod, nlat, and lon_inc to all exf variables. |
202 |
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- summary: skip detailed field report if not used (empty file-name). |
203 |
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o tools/xmakedepend: |
204 |
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- In case line editor "ed" is missing, switch to "sed" command to clean-up |
205 |
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Makefile from previous dependencies (anything after "# DO NOT DELETE" line). |
206 |
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o pkg/exf: |
207 |
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- change definition of "hflux" input file to always include Short-Wave; |
208 |
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this is now consistent with hflux computation (if using bulk-formulae) |
209 |
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and hflux diagnostic & documentation (in EXF_FIELDS.h). |
210 |
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|
211 |
|
checkpoint66b (2016/12/01) |
212 |
|
o model & momentum pkgs: |
213 |
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- implement fully implicit bottom friction combined with implicit surf. |
214 |
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pressure, for now, only in hydrostic formulation: |
215 |
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+ to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h |
216 |
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and run with selectImplicitDrag=2 ; |
217 |
|
+ currently missing diagnostics of bottom drag and vert. viscosity tendency; |
218 |
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- partial implicit time-stepping (bot. friction + vert. visc first, then |
219 |
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surf. press) corresponding to selectImplicitDrag=1 should be applicable |
220 |
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to NH formulation but not available until we solve for surf. pressure |
221 |
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increment (instead of full etaN). |
222 |
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- change exp. global_ocean.cs32x15.thsice to test implicit bottom drag |
223 |
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with implicit vertical viscosity. |
224 |
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o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model |
225 |
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- this is a first version that includes many regularisations that may |
226 |
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not all be necessary, to be sorted out, |
227 |
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- turned on by runtime parameter SEAICEuseLinRemapITD (true by default) |
228 |
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- change one verification experiment in seaice_itd to use and test new code |
229 |
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- seaice_growth: catch a case where the argument of log can be zero |
230 |
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or smaller (important for code stability) |
231 |
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o model/src: |
232 |
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- modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F |
233 |
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& 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 |
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switch based on errCode (In/Out) argument value; in calling routines, |
236 |
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initialise errCode before first call. |
237 |
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|
238 |
|
checkpoint66a (2016/10/18) |
239 |
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o pkg/bling: |
240 |
|
- BLING package now loads in atmospheric pCO2 file using exf package routines |
241 |
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Enable with #define USE_EXFCO2 in BLING_OPTIONS.h |
242 |
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o model/src & pkg/ptracers: |
243 |
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- with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R & |
244 |
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GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and |
245 |
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implicitDiffusion (respectively) are used (even without momImplVertAdv |
246 |
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or temp,salt,PTRACERS_ImplVertAdv). |
247 |
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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 |
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verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad). |
252 |
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o pkg/mom_commom & generic_advdiff: |
253 |
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- add deep atmosphere and anelastic scaling factor in implicit vertical |
254 |
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advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F). |
255 |
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o model/src: |
256 |
|
- remove few unnecessary temp array copies in solve_tridiagonal.F |
257 |
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& 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) |
567 |
|
o pkg/seaice: |
568 |
|
fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK |
569 |
|
solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated |
570 |
|
o pkg/seaice: |
571 |
|
- fix a bug in computing areaS in (J-J -> J-1) that affects runs |
572 |
|
when SEAICEscaleSurfStress=.TRUE., |
573 |
|
- apply areaW and areaS in S/R seaice_calc_lhs |
574 |
|
o pkg/atm_phys: |
575 |
|
- add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes |
576 |
|
(shortwave & longwave, net & downward) and diagnostics of temp. tendency |
577 |
|
for individual contribution (convection, LSC cond, radiation) |
578 |
|
- add Ruth Geen etal, GRL 2016, radiation options (see paper supp. |
579 |
|
information); activated with: solar_exponent=0. and wv_exponent=-1. |
580 |
|
o pkg/ggl90: |
581 |
|
- within IDEMIX add upper limit for horizontal group velocity to |
582 |
|
avoid instability problems in the explicit horizontal diffusion term for |
583 |
|
long time steps or high resolution |
584 |
|
o pkg/diagnostics: |
585 |
|
- simplify setting of local-array size in diagstats_output.F: uses "numLevels" |
586 |
|
(from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels. |
587 |
|
o testreport: |
588 |
|
- remove "-v" (verbose option) in default mpirun command. |
589 |
|
o pkg/seaice/seaice_growth: |
590 |
|
- catch potential division by zero in ITD code, does not change |
591 |
|
verification results |
592 |
|
o pkg/ecco: |
593 |
|
- retire old codes to the Attic. The calls to retired functions are |
594 |
|
left in a commented form in case they ever need to be re-activated. |
595 |
|
- ecco_check.F: issue warning if any old CPP option is |
596 |
|
defined that corresponds to retired codes -- then stop. |
597 |
|
o pkg/atm_compon_interf: |
598 |
|
- change seaice fraction (use for OCN dic surf.flux) stored and sent to |
599 |
|
coupler: use last time-step value instead of average over cplSendFrq_iter |
600 |
|
time-step, similar to what is done for seaIceMass. |
601 |
|
This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up. |
602 |
|
o eesupp & genmake2: |
603 |
|
- from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME); |
604 |
|
<= remove until a fix is found for some ifort version on ia32 machine. |
605 |
|
o pkg/seaice/seaice_evp: |
606 |
|
- refine residual computation |
607 |
|
|
608 |
|
checkpoint65q (2015/11/18) |
609 |
|
o pkg/seaice/seaice_evp: |
610 |
|
- fix residual computations so that they no longer affect the actual |
611 |
|
simulation code |
612 |
|
- fix seaice_readparams to be able to actually set new parameters |
613 |
|
SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little |
614 |
o model/src: |
o model/src: |
615 |
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
- fix wrong truncation (single prec) from "FLOAT" function in expressions |
616 |
like: deltaT*FLOAT(myIter) when myIter is large: |
like: deltaT*FLOAT(myIter) when myIter is large: |
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 |