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revision 1.2250 by jmc, Sun May 8 19:15:17 2016 UTC revision 1.2322 by jmc, Thu Apr 6 16:29:09 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint66f (2017/04/06)
8    o model/src:
9      - add specific run-time param to select level of printed plot-field-maps,
10        set by default to debugLevel. Remove internal param "printDomain".
11    o pkg/seaice:
12      - add flag to add snow mass to seaiceMassC/U/V, the default is
13        SEAICEaddSnowMass=.FALSE., not to change previous results
14    o pkg/bling
15      - Bug fix in bling_production regarding unit conversion for diagnostics
16        being put in the wrong place
17    o model/src:
18      - add back recomputation of rSurfW & S to ensure consistent column thickness
19        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
20        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
21        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
22    o pkg/autodiff:
23      - clean-up "checkpoint.flow"
24    o pkg/rw (Contribution from Jody Klymak):
25        option to set mds file suffix as function of time in simulation:
26        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
27           to select file suffix format; by default (=0), use iteration number;
28        *) add simple routine to return file suffix according to rwSuffixType;
29        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
30           use new S/R to get file suffix, except for debug output file (diagFreq)
31           and pkgs offline & rbcs input files.
32    o pkg/rw:
33      - uniform processing of "I10" suffix across writing fld routines; used to
34        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
35        (similar to cg3d.F, cg3d_ex0.F)
36    o pkg/mom_vecinv:
37      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
38        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
39    o pkg/bling:
40      - Many small changes intended to clean the code.
41        Unnecessary ADJOINT_SAFEs removed ;
42        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
43        diagnostics added.
44    
45    checkpoint66e (2017/03/14)
46    o pkg/exf:
47      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
48        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
49        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
50        avoid any dynamic allocation ;
51      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
52        read-in ; add warning when file is read-in but not used within pkg/exf ;
53        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
54      - update exf_summary.F (print {FLD}RepCycle).
55    o verification/global_with_exf:
56      - switch on exf interpolation in AD test (just like the forward test)
57    o pkg/mom_vecinv:
58      - add storage directives to avoid recomputations within mom_vecinv.F
59        which were generating seg. fault with gfortran -devel
60    o pkg/ctrl, pkg/smooth:
61      - initialize array halos which were generating seg. fault with
62        gfortran -devel in adjoint mode
63    o pkg/exf:
64      - for each input field, enable to specify a field specific repeat-cycle
65        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
66    o verification/lab_sea:
67      - update AD results of primary test and noseaicedyn test after switching
68        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
69        check stays about the same.
70    o pkg/exf:
71      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
72      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
73    o pkg/bling, USE_EXFCO2 code:
74      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
75      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
76    o pkg/exf:
77      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
78      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
79        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
80        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
81      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
82        EXF_INIT_FLD) and update calls in exf_init_varia.F
83      - For now, for backward compatibility, keep a simplified version of S/Rs
84        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
85      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
86        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
87    o tools/genmake2:
88      - replace "bc -l" (only used once) by "expr" (already used).
89    o verification/global_ocean.cs32x15:
90      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
91        Note: exf setting (data.exf) can be compared to other exf secondary exp
92        "seaice" (kept with useCAL=T) which has same time dependent forcing.
93    
94    checkpoint66d (2017/02/13)
95    o pkg/exf:
96      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
97        early on (in packages_boot.F) to stress this change in pkg setting.
98      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
99    o model/src:
100      - move call to ecco_phys to end of time step; this may induce minor
101        cost function changes by shifting time averages by one time step
102        for some variables; this revision resulted in changed adjoint results
103        in MITgcm_contrib/verification_other/global_oce_cs32
104    o pkg/exf:
105      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
106        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
107        e.g. precip, are not available.
108    o pkg/flt:
109      - flt_init_varia.F: use pickupSuff if specified
110      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
111        intermediate, step towards completing pkg/exch2 support within pkg/flt;
112        ifdef DEVEL_FLT_EXCH2 then:
113        - flt_init_fixed.F: comment out stop
114        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
115        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
116        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
117        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
118    o tools/genmake2 & pkg/pkg_depend:
119      - define new type of pkg dependency rule ("=pkg_x"), less strict than
120        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
121        (-pkg_x in packages.conf).
122      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
123      - add "+cal" to dependency list of pkg/ecco (needed to compile).
124      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
125    o utils/matlab:
126      - adding ocean_basin routines for defining basin masks.
127    o pkg/exf:
128      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
129        arguments, allowing to check (and stop) if parameter setting of
130         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
131        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
132        for backward compatibility.
133      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
134        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
135    o pkg/bling (USE_EXFCO2 code):
136      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
137        by adding a call to S/R EXF_GETFFIELD_START.
138    o pkg/exf:
139      - allows to compile without pkg/cal (but disabled by current dependency
140        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
141        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
142        of {FLD}startdate1 & date2 ; consistency check not yet coded.
143    o verification/global_ocean.cs32x15:
144      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
145        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
146    o pkg/exf:
147      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
148        calculations); change FWD experiment global_ocean.cs32x15
149        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
150    o pkg/exf:
151      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
152         {FIELD}startdate to {FIELD}StartTime
153        Note: new name also fit better the content, i.e, a start time in second.
154    o eesupp/src:
155      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
156    o pkg/exf:
157      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
158        to allow to read-in Sensible & Latent Heat flux ;
159      - simplify pkg/exf main options:
160        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
161           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
162           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
163        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
164           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
165        3) improve options documentation in EXF_OPTIONS.h.
166    o pkg/ecco:
167      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
168        ecco_summary.F: add passive tracer cost functions to gencost;
169        m_ptracer and m_boxmean_ptracer
170    o pkg/ctrl:
171      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
172        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
173        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
174        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
175    o model/src:
176      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
177        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
178    o pkg/exf:
179      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
180        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
181    
182    checkpoint66c (2017/01/19)
183    o verification:
184      - add new option "-src" to testreport to only produce source code (*.f),
185        including taf output src code (if using '-adm'/'-tlm' option).
186    o pkg/exf:
187      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
188    o pkg/diagnostics:
189      - add run-time variable diagMdsDir to specify a subdirectory for
190        diagnostic output when mds is being used and mdsioLocalDir is not.
191    o pkg/mnc:
192      - mnc_utils.F: edit stop message
193    o pkg/autodiff:
194      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
195        add HAVE_SYSTEM bracket around system call to mkdir
196    o pkg/profiles:
197      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
198        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
199      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
200        add HAVE_SYSTEM bracket around system call to mkdir
201    o pkg/smooth:
202      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
203      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
204      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
205    o pkg/exf:
206      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
207        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
208        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
209      - summary: skip detailed field report if not used (empty file-name).
210    o tools/xmakedepend:
211      - In case line editor "ed" is missing, switch to "sed" command to clean-up
212        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
213    o pkg/exf:
214      - change definition of "hflux" input file to always include Short-Wave;
215        this is now consistent with hflux computation (if using bulk-formulae)
216        and hflux diagnostic & documentation (in EXF_FIELDS.h).
217    
218    checkpoint66b (2016/12/01)
219    o model & momentum pkgs:
220      - implement fully implicit bottom friction combined with implicit surf.
221        pressure, for now, only in hydrostic formulation:
222        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
223          and run with selectImplicitDrag=2 ;
224        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
225      - partial implicit time-stepping (bot. friction + vert. visc first, then
226        surf. press) corresponding to selectImplicitDrag=1 should be applicable
227        to NH formulation but not available until we solve for surf. pressure
228        increment (instead of full etaN).
229      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
230        with implicit vertical viscosity.
231    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
232      - this is a first version that includes many regularisations that may
233        not all be necessary, to be sorted out,
234      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
235      - change one verification experiment in seaice_itd to use and test new code
236      - seaice_growth: catch a case where the argument of log can be zero
237        or smaller (important for code stability)
238    o model/src:
239      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
240        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
241        similar A.X'=Y' system (with same matrix A) in subsequent calls;
242        switch based on errCode (In/Out) argument value; in calling routines,
243        initialise errCode before first call.
244    
245    checkpoint66a (2016/10/18)
246    o pkg/bling:
247      - BLING package now loads in atmospheric pCO2 file using exf package routines
248        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
249    o model/src & pkg/ptracers:
250      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
251        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
252        implicitDiffusion (respectively) are used (even without momImplVertAdv
253        or temp,salt,PTRACERS_ImplVertAdv).
254    o model/src & generic_advdiff:
255      - add parenthesis in main diagonal calculation of implicit vertical
256        diffusion matrix (impldiff.F & gad_implicit_r.F).
257        This affects results at machine truncation level; update output of many
258        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
259    o pkg/mom_commom & generic_advdiff:
260      - add deep atmosphere and anelastic scaling factor in implicit vertical
261        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
262    o model/src:
263      - remove few unnecessary temp array copies in solve_tridiagonal.F
264        & solve_pentadiagonal.F
265    
266    checkpoint65z (2016/09/28)
267    o pkg/seaice: fix multithreading for seaice_fgmres.F
268      - remove unecessary variables from common blocks
269      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
270        basis, that are stored in commom blocks (including integer variable i1)
271      - clean up code a little by removing commented lines that refer to
272        original code
273      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
274    o MITgcm manual:
275      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
276        preliminary documentation for generic controls (8.3; ctrl.tex),
277        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
278        ecco_costfunction.tex
279    o pkg/ecco:
280      - update and cleanup list of CCP options
281      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
282        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
283      - add checks that retired run-time options are not used, and in relation
284        to gencost_mask and gencost_errfile
285      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
286        gencost_nrecperiod
287      - fix m_eta computation for virtual salt flux case
288      - add m_horflux_vol case (selected via gencost_barfile) that computes
289        transports via cost_gencost_boxmean (gencost_flag=-3)
290      - use gencost_flag more systematically (i.e., avoid using gencost_name)
291        for code switches (aside from physical variable selection)
292    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
293      attempt appears to be a bit of a hack and my need some repair down the road
294    o pkg/exf:
295      - interpolation near South Pole: fix criteria on input field latitude.
296    o pkg/icefront & pkg/exf:
297      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
298        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
299    o pkg/exf:
300      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
301        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
302        (add suffix "_out" instead of a prefix); keep same record number as in
303        input file but always write record 1 first (to avoid a STOP in I/O S/R).
304        Change output file content by writing interpolated field before applying
305        land-sea mask (helpful for debug).
306      - 2 compon. vector interpolation with rotation: apply scaling factor on
307        each compon. (Eastward and Northward) just before rotation.
308    o pkg/bling:
309      - Cleaned package. Removed not needed code and comments.
310      - adjoint example now works
311        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
312    o pkg/ptracers:
313      - add Bruno Deremble's code to complete the linear surface correction
314        for tracer conservation;
315      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
316    
317    checkpoint65y (2016/07/29)
318    o pkg/debug (stats):
319      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
320        proc/thread mapping);
321      - fix Min & Max for case where 1 thread has only empty tiles;
322      - use RL variable to count number of wet grid points (with big domain,
323        can be too large to fit into integer*4).
324    o pkg/monitor:
325      - use RL variable to count number of wet grid points (but used only for del2)
326      - add new routine to compute Advective CFL within tracer time-stepping with
327        writing delayed until next monitor output.
328    o pkg/obcs:
329      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
330    o pkg/cal:
331      - calandar-dump: treat case myTime < timePhase in the same way as in
332        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
333    o pkg/dic & seaice:
334      - fix compilation of ocean component for coupled atm+ocn model with
335        seaice dynamics & dic.
336    
337    checkpoint65x (2016/06/11)
338    o add a license text file in main MITgcm tree.
339    o added pkg/bling:
340      - intermediate complexity biogeochemical model
341      - see bling_description.txt for details
342      - verification experiment is global_oce_biogeo_bling (for now, in
343        Contrib/verification_other/); tested daily on baudelaire with gfortran.
344      - add entry point in pkg/gchem for new pkg "bling".
345    o pkg/seaice: fix tensile stength computation
346      - replace global field tensileStrength by tensileStrFac
347      - tensileStrFac can be computed once in S/R seaice_init_varia
348      - fortunately that does not affect any verification results
349    
350    checkpoint65w (2016/05/12)
351    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
352         with ECCO_CTRL_DEPRECATED defined
353  o verification/global_ocean.cs32x15:  o verification/global_ocean.cs32x15:
354    - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"    - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
355      with "selectNHfreeSurf=1".      with "selectNHfreeSurf=1".
# Line 759  o model/src & mom pkgs: Line 1105  o model/src & mom pkgs:
1105      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1106  o doc:  o doc:
1107    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1108  o pkg/streamice:  o pkg/shelfice:
1109    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1110      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1111      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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