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revision 1.2250 by jmc, Sun May 8 19:15:17 2016 UTC revision 1.2325 by jmc, Wed Apr 12 18:50:25 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
9        to get same expression (regarding machine truncation) in different places
10        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
11        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
12        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
13    o pkg/shelfice:
14      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
15        to shelfice_init_fixed.F
16      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
17        ini_masks_etc.F for now) to update ocean upper boundary position according
18        to ice-shelf topography (instead of directly updating hFacC).
19    o model/src:
20      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
21        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
22    
23    checkpoint66f (2017/04/06)
24    o model/src:
25      - add specific run-time param to select level of printed plot-field-maps,
26        set by default to debugLevel. Remove internal param "printDomain".
27    o pkg/seaice:
28      - add flag to add snow mass to seaiceMassC/U/V, the default is
29        SEAICEaddSnowMass=.FALSE., not to change previous results
30    o pkg/bling
31      - Bug fix in bling_production regarding unit conversion for diagnostics
32        being put in the wrong place
33    o model/src:
34      - add back recomputation of rSurfW & S to ensure consistent column thickness
35        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
36        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
37        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
38    o pkg/autodiff:
39      - clean-up "checkpoint.flow"
40    o pkg/rw (Contribution from Jody Klymak):
41        option to set mds file suffix as function of time in simulation:
42        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
43           to select file suffix format; by default (=0), use iteration number;
44        *) add simple routine to return file suffix according to rwSuffixType;
45        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
46           use new S/R to get file suffix, except for debug output file (diagFreq)
47           and pkgs offline & rbcs input files.
48    o pkg/rw:
49      - uniform processing of "I10" suffix across writing fld routines; used to
50        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
51        (similar to cg3d.F, cg3d_ex0.F)
52    o pkg/mom_vecinv:
53      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
54        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
55    o pkg/bling:
56      - Many small changes intended to clean the code.
57        Unnecessary ADJOINT_SAFEs removed ;
58        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
59        diagnostics added.
60    
61    checkpoint66e (2017/03/14)
62    o pkg/exf:
63      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
64        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
65        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
66        avoid any dynamic allocation ;
67      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
68        read-in ; add warning when file is read-in but not used within pkg/exf ;
69        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
70      - update exf_summary.F (print {FLD}RepCycle).
71    o verification/global_with_exf:
72      - switch on exf interpolation in AD test (just like the forward test)
73    o pkg/mom_vecinv:
74      - add storage directives to avoid recomputations within mom_vecinv.F
75        which were generating seg. fault with gfortran -devel
76    o pkg/ctrl, pkg/smooth:
77      - initialize array halos which were generating seg. fault with
78        gfortran -devel in adjoint mode
79    o pkg/exf:
80      - for each input field, enable to specify a field specific repeat-cycle
81        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
82    o verification/lab_sea:
83      - update AD results of primary test and noseaicedyn test after switching
84        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
85        check stays about the same.
86    o pkg/exf:
87      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
88      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
89    o pkg/bling, USE_EXFCO2 code:
90      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
91      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
92    o pkg/exf:
93      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
94      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
95        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
96        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
97      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
98        EXF_INIT_FLD) and update calls in exf_init_varia.F
99      - For now, for backward compatibility, keep a simplified version of S/Rs
100        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
101      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
102        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
103    o tools/genmake2:
104      - replace "bc -l" (only used once) by "expr" (already used).
105    o verification/global_ocean.cs32x15:
106      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
107        Note: exf setting (data.exf) can be compared to other exf secondary exp
108        "seaice" (kept with useCAL=T) which has same time dependent forcing.
109    
110    checkpoint66d (2017/02/13)
111    o pkg/exf:
112      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
113        early on (in packages_boot.F) to stress this change in pkg setting.
114      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
115    o model/src:
116      - move call to ecco_phys to end of time step; this may induce minor
117        cost function changes by shifting time averages by one time step
118        for some variables; this revision resulted in changed adjoint results
119        in MITgcm_contrib/verification_other/global_oce_cs32
120    o pkg/exf:
121      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
122        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
123        e.g. precip, are not available.
124    o pkg/flt:
125      - flt_init_varia.F: use pickupSuff if specified
126      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
127        intermediate, step towards completing pkg/exch2 support within pkg/flt;
128        ifdef DEVEL_FLT_EXCH2 then:
129        - flt_init_fixed.F: comment out stop
130        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
131        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
132        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
133        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
134    o tools/genmake2 & pkg/pkg_depend:
135      - define new type of pkg dependency rule ("=pkg_x"), less strict than
136        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
137        (-pkg_x in packages.conf).
138      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
139      - add "+cal" to dependency list of pkg/ecco (needed to compile).
140      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
141    o utils/matlab:
142      - adding ocean_basin routines for defining basin masks.
143    o pkg/exf:
144      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
145        arguments, allowing to check (and stop) if parameter setting of
146         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
147        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
148        for backward compatibility.
149      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
150        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
151    o pkg/bling (USE_EXFCO2 code):
152      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
153        by adding a call to S/R EXF_GETFFIELD_START.
154    o pkg/exf:
155      - allows to compile without pkg/cal (but disabled by current dependency
156        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
157        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
158        of {FLD}startdate1 & date2 ; consistency check not yet coded.
159    o verification/global_ocean.cs32x15:
160      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
161        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
162    o pkg/exf:
163      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
164        calculations); change FWD experiment global_ocean.cs32x15
165        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
166    o pkg/exf:
167      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
168         {FIELD}startdate to {FIELD}StartTime
169        Note: new name also fit better the content, i.e, a start time in second.
170    o eesupp/src:
171      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
172    o pkg/exf:
173      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
174        to allow to read-in Sensible & Latent Heat flux ;
175      - simplify pkg/exf main options:
176        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
177           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
178           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
179        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
180           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
181        3) improve options documentation in EXF_OPTIONS.h.
182    o pkg/ecco:
183      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
184        ecco_summary.F: add passive tracer cost functions to gencost;
185        m_ptracer and m_boxmean_ptracer
186    o pkg/ctrl:
187      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
188        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
189        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
190        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
191    o model/src:
192      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
193        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
194    o pkg/exf:
195      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
196        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
197    
198    checkpoint66c (2017/01/19)
199    o verification:
200      - add new option "-src" to testreport to only produce source code (*.f),
201        including taf output src code (if using '-adm'/'-tlm' option).
202    o pkg/exf:
203      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
204    o pkg/diagnostics:
205      - add run-time variable diagMdsDir to specify a subdirectory for
206        diagnostic output when mds is being used and mdsioLocalDir is not.
207    o pkg/mnc:
208      - mnc_utils.F: edit stop message
209    o pkg/autodiff:
210      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
211        add HAVE_SYSTEM bracket around system call to mkdir
212    o pkg/profiles:
213      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
214        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
215      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
216        add HAVE_SYSTEM bracket around system call to mkdir
217    o pkg/smooth:
218      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
219      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
220      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
221    o pkg/exf:
222      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
223        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
224        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
225      - summary: skip detailed field report if not used (empty file-name).
226    o tools/xmakedepend:
227      - In case line editor "ed" is missing, switch to "sed" command to clean-up
228        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
229    o pkg/exf:
230      - change definition of "hflux" input file to always include Short-Wave;
231        this is now consistent with hflux computation (if using bulk-formulae)
232        and hflux diagnostic & documentation (in EXF_FIELDS.h).
233    
234    checkpoint66b (2016/12/01)
235    o model & momentum pkgs:
236      - implement fully implicit bottom friction combined with implicit surf.
237        pressure, for now, only in hydrostic formulation:
238        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
239          and run with selectImplicitDrag=2 ;
240        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
241      - partial implicit time-stepping (bot. friction + vert. visc first, then
242        surf. press) corresponding to selectImplicitDrag=1 should be applicable
243        to NH formulation but not available until we solve for surf. pressure
244        increment (instead of full etaN).
245      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
246        with implicit vertical viscosity.
247    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
248      - this is a first version that includes many regularisations that may
249        not all be necessary, to be sorted out,
250      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
251      - change one verification experiment in seaice_itd to use and test new code
252      - seaice_growth: catch a case where the argument of log can be zero
253        or smaller (important for code stability)
254    o model/src:
255      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
256        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
257        similar A.X'=Y' system (with same matrix A) in subsequent calls;
258        switch based on errCode (In/Out) argument value; in calling routines,
259        initialise errCode before first call.
260    
261    checkpoint66a (2016/10/18)
262    o pkg/bling:
263      - BLING package now loads in atmospheric pCO2 file using exf package routines
264        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
265    o model/src & pkg/ptracers:
266      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
267        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
268        implicitDiffusion (respectively) are used (even without momImplVertAdv
269        or temp,salt,PTRACERS_ImplVertAdv).
270    o model/src & generic_advdiff:
271      - add parenthesis in main diagonal calculation of implicit vertical
272        diffusion matrix (impldiff.F & gad_implicit_r.F).
273        This affects results at machine truncation level; update output of many
274        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
275    o pkg/mom_commom & generic_advdiff:
276      - add deep atmosphere and anelastic scaling factor in implicit vertical
277        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
278    o model/src:
279      - remove few unnecessary temp array copies in solve_tridiagonal.F
280        & solve_pentadiagonal.F
281    
282    checkpoint65z (2016/09/28)
283    o pkg/seaice: fix multithreading for seaice_fgmres.F
284      - remove unecessary variables from common blocks
285      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
286        basis, that are stored in commom blocks (including integer variable i1)
287      - clean up code a little by removing commented lines that refer to
288        original code
289      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
290    o MITgcm manual:
291      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
292        preliminary documentation for generic controls (8.3; ctrl.tex),
293        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
294        ecco_costfunction.tex
295    o pkg/ecco:
296      - update and cleanup list of CCP options
297      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
298        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
299      - add checks that retired run-time options are not used, and in relation
300        to gencost_mask and gencost_errfile
301      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
302        gencost_nrecperiod
303      - fix m_eta computation for virtual salt flux case
304      - add m_horflux_vol case (selected via gencost_barfile) that computes
305        transports via cost_gencost_boxmean (gencost_flag=-3)
306      - use gencost_flag more systematically (i.e., avoid using gencost_name)
307        for code switches (aside from physical variable selection)
308    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
309      attempt appears to be a bit of a hack and my need some repair down the road
310    o pkg/exf:
311      - interpolation near South Pole: fix criteria on input field latitude.
312    o pkg/icefront & pkg/exf:
313      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
314        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
315    o pkg/exf:
316      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
317        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
318        (add suffix "_out" instead of a prefix); keep same record number as in
319        input file but always write record 1 first (to avoid a STOP in I/O S/R).
320        Change output file content by writing interpolated field before applying
321        land-sea mask (helpful for debug).
322      - 2 compon. vector interpolation with rotation: apply scaling factor on
323        each compon. (Eastward and Northward) just before rotation.
324    o pkg/bling:
325      - Cleaned package. Removed not needed code and comments.
326      - adjoint example now works
327        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
328    o pkg/ptracers:
329      - add Bruno Deremble's code to complete the linear surface correction
330        for tracer conservation;
331      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
332    
333    checkpoint65y (2016/07/29)
334    o pkg/debug (stats):
335      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
336        proc/thread mapping);
337      - fix Min & Max for case where 1 thread has only empty tiles;
338      - use RL variable to count number of wet grid points (with big domain,
339        can be too large to fit into integer*4).
340    o pkg/monitor:
341      - use RL variable to count number of wet grid points (but used only for del2)
342      - add new routine to compute Advective CFL within tracer time-stepping with
343        writing delayed until next monitor output.
344    o pkg/obcs:
345      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
346    o pkg/cal:
347      - calandar-dump: treat case myTime < timePhase in the same way as in
348        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
349    o pkg/dic & seaice:
350      - fix compilation of ocean component for coupled atm+ocn model with
351        seaice dynamics & dic.
352    
353    checkpoint65x (2016/06/11)
354    o add a license text file in main MITgcm tree.
355    o added pkg/bling:
356      - intermediate complexity biogeochemical model
357      - see bling_description.txt for details
358      - verification experiment is global_oce_biogeo_bling (for now, in
359        Contrib/verification_other/); tested daily on baudelaire with gfortran.
360      - add entry point in pkg/gchem for new pkg "bling".
361    o pkg/seaice: fix tensile stength computation
362      - replace global field tensileStrength by tensileStrFac
363      - tensileStrFac can be computed once in S/R seaice_init_varia
364      - fortunately that does not affect any verification results
365    
366    checkpoint65w (2016/05/12)
367    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
368         with ECCO_CTRL_DEPRECATED defined
369  o verification/global_ocean.cs32x15:  o verification/global_ocean.cs32x15:
370    - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"    - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
371      with "selectNHfreeSurf=1".      with "selectNHfreeSurf=1".
# Line 759  o model/src & mom pkgs: Line 1121  o model/src & mom pkgs:
1121      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1122  o doc:  o doc:
1123    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1124  o pkg/streamice:  o pkg/shelfice:
1125    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1126      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1127      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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