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revision 1.2200 by mlosch, Tue Nov 17 14:37:12 2015 UTC revision 1.2354 by jmc, Wed Sep 20 18:46:57 2017 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint66k (2017/09/20)
8    o model/src:
9      - add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F
10        and the_model_main.F)
11    o ctrl:
12      - use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F)
13      - call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated
14        mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F,
15        ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F )
16    o eesupp:
17      - add CPP option to activate some pieces of code for coupling to GEOS AGCM;
18      - shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM.
19    o pkg/bling:
20      - bling_production: Fix typo in calcium carbonate uptake. Also rearranging
21        and cleaning
22    o model/src:
23      - move k loop inside correction_step.F (+ update calling S/R)
24      - collect implicit pressure gradient tendencies in local 2-D array;
25        affect results (at machine truncation level) when using 3-D solver; update
26        output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
27                        rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
28                        & tutorial_plume_on_slope.
29    
30    checkpoint66j (2017/08/15)
31    o pkg/ptracers:
32      - fix surface forcing under ice-shelf (useShelfIce=T).
33    o pkg/atm_phys:
34      - use hFac weighted average when applying A-grid atm-phys momentum tendency
35        to C-grid dynamics; this ensures wind-stress match mom tendency.
36    o eesupp/src:
37      - change default for opening scratch files to avoid STATUS='SCRATCH'
38      - close scratch files with STATUS='DELETE'
39      - changes affect eeset_parms.F and open_copy_data_file.F and many routines
40        that read namelists (because they close the scratch files)
41      - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
42        in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
43    o pkg/atm_phys:
44      - fix unset arguments in (unused) S/R surface_flux_0d.
45    o eesupp/src:
46      - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
47        (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
48        called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
49    o pkg/streamice:
50      - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
51        preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
52        streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
53    o pkg/diagnostics:
54      - new option to allow to cumulate thickness-factor (hFac) weighted field
55        (if field permitted); implemented by changing sign of "jdiag" pointer
56        (> 0: cumlulate field, < 0: cumulate hFac weighted field).
57        a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
58           center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
59        b) for now, activated by setting fileFlags 3rd character to 'h'.
60    
61    checkpoint66i (2017/07/18)
62    o pkg/cheapaml:
63      - add parameter "useRelativeWind", default set to False; this change the
64        previous setting which was always using relative wind.
65    o add hooks for the Parallel Data Assimilation Framework PDAF
66        (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
67        to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
68    o pkg/exf:
69      - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
70        of South-Pole mean value.  
71      - interpolation near the poles, case where second additional row is at the
72        pole (or beyond the pole and moved to the pole): change first addition row
73        value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
74        row (instead of just a copy of it).
75    o pkg/seaice:
76      - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
77      - add the option to compute no-slip du/dy, dv/dx (i.e.
78        the offdiagonal strain rate e12) by a second order approximation
79        on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
80        it is too messy to implement for the implicit LSR matrix.
81        SEAICE_2ndOrderBC = .FALSE. by default
82    
83    checkpoint66h (2017/06/02)
84    o pkg/seaice:
85      - add new routines to compute stress tensor components and stress tensor
86        divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
87      - change names of diagnostics SIsigI/II (commonly used for invariants)
88        to SIsig1/sig2 (more common for principal components) to avoid confusion
89    o pkf/exf:
90      - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
91        similarly, stop if rotateStressOnAgrid with constant wind-stress.
92    o pkg/seaice:
93      - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
94        EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
95      - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
96        fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
97    o pkg/diagnostics:
98      - small piece of code to rename (old) diagnostics, when namelist is processed.
99    o model/src:
100      - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
101        originally, set as minimum of adjacent hFacC factor ; now (new default)
102        computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
103        Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
104    o pkg/seaice:
105      - add momemtum advection, off by default, still in test phase
106        most of the momentum advection code is adapted and reused from mom_vecinv
107    o pkg/mom_vecinv:
108      - pass these runtime flags:
109        selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
110        as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
111        so that these routines can also be used in pkg/seaice.
112    
113    checkpoint66g (2017/04/24)
114    o model/src:
115      - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
116        to get same expression (regarding machine truncation) in different places
117        in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
118        Update forward output of experiments: global_ocean.cs32x15 (all 5 except
119        viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
120    o pkg/shelfice:
121      - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
122        to shelfice_init_fixed.F
123      - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
124        ini_masks_etc.F for now) to update ocean upper boundary position according
125        to ice-shelf topography (instead of directly updating hFacC).
126    o model/src:
127      - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
128        packages_init_fixed.F to allow other pkgs to set mask and weight fields.
129    
130    checkpoint66f (2017/04/06)
131    o model/src:
132      - add specific run-time param to select level of printed plot-field-maps,
133        set by default to debugLevel. Remove internal param "printDomain".
134    o pkg/seaice:
135      - add flag to add snow mass to seaiceMassC/U/V, the default is
136        SEAICEaddSnowMass=.FALSE., not to change previous results
137    o pkg/bling
138      - Bug fix in bling_production regarding unit conversion for diagnostics
139        being put in the wrong place
140    o model/src:
141      - add back recomputation of rSurfW & S to ensure consistent column thickness
142        (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
143        when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
144        revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
145    o pkg/autodiff:
146      - clean-up "checkpoint.flow"
147    o pkg/rw (Contribution from Jody Klymak):
148        option to set mds file suffix as function of time in simulation:
149        *) new input parameter "rwSuffixType" (read from PARM03 namelist)
150           to select file suffix format; by default (=0), use iteration number;
151        *) add simple routine to return file suffix according to rwSuffixType;
152        *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
153           use new S/R to get file suffix, except for debug output file (diagFreq)
154           and pkgs offline & rbcs input files.
155    o pkg/rw:
156      - uniform processing of "I10" suffix across writing fld routines; used to
157        simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
158        (similar to cg3d.F, cg3d_ex0.F)
159    o pkg/mom_vecinv:
160      - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
161        vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
162    o pkg/bling:
163      - Many small changes intended to clean the code.
164        Unnecessary ADJOINT_SAFEs removed ;
165        removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
166        diagnostics added.
167    
168    checkpoint66e (2017/03/14)
169    o pkg/exf:
170      - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
171        definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
172        use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
173        avoid any dynamic allocation ;
174      - S/R EXF_CHECK: add new check & stop when file-name is defined but not
175        read-in ; add warning when file is read-in but not used within pkg/exf ;
176        + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
177      - update exf_summary.F (print {FLD}RepCycle).
178    o verification/global_with_exf:
179      - switch on exf interpolation in AD test (just like the forward test)
180    o pkg/mom_vecinv:
181      - add storage directives to avoid recomputations within mom_vecinv.F
182        which were generating seg. fault with gfortran -devel
183    o pkg/ctrl, pkg/smooth:
184      - initialize array halos which were generating seg. fault with
185        gfortran -devel in adjoint mode
186    o pkg/exf:
187      - for each input field, enable to specify a field specific repeat-cycle
188        ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
189    o verification/lab_sea:
190      - update AD results of primary test and noseaicedyn test after switching
191        to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
192        check stays about the same.
193    o pkg/exf:
194      - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
195      - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
196    o pkg/bling, USE_EXFCO2 code:
197      - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
198      - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
199    o pkg/exf:
200      - rename S/R EXF_INIT to EXF_INIT_VARIA ;
201      - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
202        repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
203        and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
204      - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
205        EXF_INIT_FLD) and update calls in exf_init_varia.F
206      - For now, for backward compatibility, keep a simplified version of S/Rs
207        EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
208      - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
209        to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
210    o tools/genmake2:
211      - replace "bc -l" (only used once) by "expr" (already used).
212    o verification/global_ocean.cs32x15:
213      - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
214        Note: exf setting (data.exf) can be compared to other exf secondary exp
215        "seaice" (kept with useCAL=T) which has same time dependent forcing.
216    
217    checkpoint66d (2017/02/13)
218    o pkg/exf:
219      - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
220        early on (in packages_boot.F) to stress this change in pkg setting.
221      - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
222    o model/src:
223      - move call to ecco_phys to end of time step; this may induce minor
224        cost function changes by shifting time averages by one time step
225        for some variables; this revision resulted in changed adjoint results
226        in MITgcm_contrib/verification_other/global_oce_cs32
227    o pkg/exf:
228      - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
229        this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
230        e.g. precip, are not available.
231    o pkg/flt:
232      - flt_init_varia.F: use pickupSuff if specified
233      - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
234        intermediate, step towards completing pkg/exch2 support within pkg/flt;
235        ifdef DEVEL_FLT_EXCH2 then:
236        - flt_init_fixed.F: comment out stop
237        - flt_exch2.F: conserve ipart, jpart (grid coordinates)
238        - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
239        - flt_mapping.F: attempt to fix longitude diagnostic near date-line
240        - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
241    o tools/genmake2 & pkg/pkg_depend:
242      - define new type of pkg dependency rule ("=pkg_x"), less strict than
243        the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
244        (-pkg_x in packages.conf).
245      - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
246      - add "+cal" to dependency list of pkg/ecco (needed to compile).
247      - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
248    o utils/matlab:
249      - adding ocean_basin routines for defining basin masks.
250    o pkg/exf:
251      - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
252        arguments, allowing to check (and stop) if parameter setting of
253         {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
254        useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
255        for backward compatibility.
256      - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
257        exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
258    o pkg/bling (USE_EXFCO2 code):
259      - fix missing setting of apco2StartTime according to apco2startdate1 & date2
260        by adding a call to S/R EXF_GETFFIELD_START.
261    o pkg/exf:
262      - allows to compile without pkg/cal (but disabled by current dependency
263        rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
264        run with useCAL=F ; this involves setting directly {FLD}StartTime instead
265        of {FLD}startdate1 & date2 ; consistency check not yet coded.
266    o verification/global_ocean.cs32x15:
267      - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
268        corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
269    o pkg/exf:
270      - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
271        calculations); change FWD experiment global_ocean.cs32x15
272        (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
273    o pkg/exf:
274      - In preparation for addition to NAMELIST, rename internal (_RL) parameter
275         {FIELD}startdate to {FIELD}StartTime
276        Note: new name also fit better the content, i.e, a start time in second.
277    o eesupp/src:
278      - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
279    o pkg/exf:
280      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
281        to allow to read-in Sensible & Latent Heat flux ;
282      - simplify pkg/exf main options:
283        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
284           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
285           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
286        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
287           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
288        3) improve options documentation in EXF_OPTIONS.h.
289    o pkg/ecco:
290      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
291        ecco_summary.F: add passive tracer cost functions to gencost;
292        m_ptracer and m_boxmean_ptracer
293    o pkg/ctrl:
294      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
295        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
296        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
297        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
298    o model/src:
299      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
300        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
301    o pkg/exf:
302      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
303        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
304    
305    checkpoint66c (2017/01/19)
306    o verification:
307      - add new option "-src" to testreport to only produce source code (*.f),
308        including taf output src code (if using '-adm'/'-tlm' option).
309    o pkg/exf:
310      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
311    o pkg/diagnostics:
312      - add run-time variable diagMdsDir to specify a subdirectory for
313        diagnostic output when mds is being used and mdsioLocalDir is not.
314    o pkg/mnc:
315      - mnc_utils.F: edit stop message
316    o pkg/autodiff:
317      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
318        add HAVE_SYSTEM bracket around system call to mkdir
319    o pkg/profiles:
320      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
321        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
322      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
323        add HAVE_SYSTEM bracket around system call to mkdir
324    o pkg/smooth:
325      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
326      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
327      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
328    o pkg/exf:
329      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
330        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
331        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
332      - summary: skip detailed field report if not used (empty file-name).
333    o tools/xmakedepend:
334      - In case line editor "ed" is missing, switch to "sed" command to clean-up
335        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
336    o pkg/exf:
337      - change definition of "hflux" input file to always include Short-Wave;
338        this is now consistent with hflux computation (if using bulk-formulae)
339        and hflux diagnostic & documentation (in EXF_FIELDS.h).
340    
341    checkpoint66b (2016/12/01)
342    o model & momentum pkgs:
343      - implement fully implicit bottom friction combined with implicit surf.
344        pressure, for now, only in hydrostic formulation:
345        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
346          and run with selectImplicitDrag=2 ;
347        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
348      - partial implicit time-stepping (bot. friction + vert. visc first, then
349        surf. press) corresponding to selectImplicitDrag=1 should be applicable
350        to NH formulation but not available until we solve for surf. pressure
351        increment (instead of full etaN).
352      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
353        with implicit vertical viscosity.
354    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
355      - this is a first version that includes many regularisations that may
356        not all be necessary, to be sorted out,
357      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
358      - change one verification experiment in seaice_itd to use and test new code
359      - seaice_growth: catch a case where the argument of log can be zero
360        or smaller (important for code stability)
361    o model/src:
362      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
363        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
364        similar A.X'=Y' system (with same matrix A) in subsequent calls;
365        switch based on errCode (In/Out) argument value; in calling routines,
366        initialise errCode before first call.
367    
368    checkpoint66a (2016/10/18)
369    o pkg/bling:
370      - BLING package now loads in atmospheric pCO2 file using exf package routines
371        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
372    o model/src & pkg/ptracers:
373      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
374        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
375        implicitDiffusion (respectively) are used (even without momImplVertAdv
376        or temp,salt,PTRACERS_ImplVertAdv).
377    o model/src & generic_advdiff:
378      - add parenthesis in main diagonal calculation of implicit vertical
379        diffusion matrix (impldiff.F & gad_implicit_r.F).
380        This affects results at machine truncation level; update output of many
381        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
382    o pkg/mom_commom & generic_advdiff:
383      - add deep atmosphere and anelastic scaling factor in implicit vertical
384        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
385    o model/src:
386      - remove few unnecessary temp array copies in solve_tridiagonal.F
387        & solve_pentadiagonal.F
388    
389    checkpoint65z (2016/09/28)
390    o pkg/seaice: fix multithreading for seaice_fgmres.F
391      - remove unecessary variables from common blocks
392      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
393        basis, that are stored in commom blocks (including integer variable i1)
394      - clean up code a little by removing commented lines that refer to
395        original code
396      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
397    o MITgcm manual:
398      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
399        preliminary documentation for generic controls (8.3; ctrl.tex),
400        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
401        ecco_costfunction.tex
402    o pkg/ecco:
403      - update and cleanup list of CCP options
404      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
405        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
406      - add checks that retired run-time options are not used, and in relation
407        to gencost_mask and gencost_errfile
408      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
409        gencost_nrecperiod
410      - fix m_eta computation for virtual salt flux case
411      - add m_horflux_vol case (selected via gencost_barfile) that computes
412        transports via cost_gencost_boxmean (gencost_flag=-3)
413      - use gencost_flag more systematically (i.e., avoid using gencost_name)
414        for code switches (aside from physical variable selection)
415    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
416      attempt appears to be a bit of a hack and my need some repair down the road
417    o pkg/exf:
418      - interpolation near South Pole: fix criteria on input field latitude.
419    o pkg/icefront & pkg/exf:
420      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
421        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
422    o pkg/exf:
423      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
424        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
425        (add suffix "_out" instead of a prefix); keep same record number as in
426        input file but always write record 1 first (to avoid a STOP in I/O S/R).
427        Change output file content by writing interpolated field before applying
428        land-sea mask (helpful for debug).
429      - 2 compon. vector interpolation with rotation: apply scaling factor on
430        each compon. (Eastward and Northward) just before rotation.
431    o pkg/bling:
432      - Cleaned package. Removed not needed code and comments.
433      - adjoint example now works
434        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
435    o pkg/ptracers:
436      - add Bruno Deremble's code to complete the linear surface correction
437        for tracer conservation;
438      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
439    
440    checkpoint65y (2016/07/29)
441    o pkg/debug (stats):
442      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
443        proc/thread mapping);
444      - fix Min & Max for case where 1 thread has only empty tiles;
445      - use RL variable to count number of wet grid points (with big domain,
446        can be too large to fit into integer*4).
447    o pkg/monitor:
448      - use RL variable to count number of wet grid points (but used only for del2)
449      - add new routine to compute Advective CFL within tracer time-stepping with
450        writing delayed until next monitor output.
451    o pkg/obcs:
452      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
453    o pkg/cal:
454      - calandar-dump: treat case myTime < timePhase in the same way as in
455        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
456    o pkg/dic & seaice:
457      - fix compilation of ocean component for coupled atm+ocn model with
458        seaice dynamics & dic.
459    
460    checkpoint65x (2016/06/11)
461    o add a license text file in main MITgcm tree.
462    o added pkg/bling:
463      - intermediate complexity biogeochemical model
464      - see bling_description.txt for details
465      - verification experiment is global_oce_biogeo_bling (for now, in
466        Contrib/verification_other/); tested daily on baudelaire with gfortran.
467      - add entry point in pkg/gchem for new pkg "bling".
468    o pkg/seaice: fix tensile stength computation
469      - replace global field tensileStrength by tensileStrFac
470      - tensileStrFac can be computed once in S/R seaice_init_varia
471      - fortunately that does not affect any verification results
472    
473    checkpoint65w (2016/05/12)
474    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
475         with ECCO_CTRL_DEPRECATED defined
476    o verification/global_ocean.cs32x15:
477      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
478        with "selectNHfreeSurf=1".
479    o model/src (non-hydrostatic free-surface):
480      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
481        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
482      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
483        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
484        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
485        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
486      - Update output (changes at machine truncation level) of verification exp:
487        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
488        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
489    o pkg/seaice: ITD code
490      - fix picking up from a single category model by initialising
491        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
492      - split a long warning message in seaice_check_pickup.F into two lines,
493        because NEC SX-ACE cannot deal with the long line.
494    o model/src:
495      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
496    o pkg/seaice:
497      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
498    o pkg/seaice:
499      - add basal stress as parameterisation for grounding ice
500        following Lemieux et al. (2015)
501      - turn on by setting new parameter SEAICEbasalDragK2 to a value
502        larger than 0. Lemieux et al. (2015) recommend 15.
503      - The adjoint complains with extra recomputations so there is also a
504        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
505        order to postpone the problem
506      - compile the new code in lab_sea
507    o verification/halfpipe_streamice:
508      - update both TAF and OpenAD adm output (machine truncation differences)
509    
510    checkpoint65v (2016/04/08)
511    o verification/advect_xz:
512      - increase overlap size from 3 to 4 and add new secondary test for PQM
513        advection scheme (with mono & wino limiter).
514      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
515    o model/src:
516      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
517        added phi0Ref) to set vertical axis origin and phiRef origin;
518        keep Ro_SeaLevel for backward compatibility (with a warning).
519       According to coordinate and fluid type:
520        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
521        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
522        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
523        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
524      - remove Ro_SeaLevel from ATM experiment parameter files;
525      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
526        complement; update output.txt (changes at machine truncation level).
527  o pkg/seaice/seaice_evp.F  o pkg/seaice/seaice_evp.F
528      - simplify computation of deltaZ and zetaZ to simple averaging following
529        Bouillon et al. (2013). This removes a lot of code, but also changes
530        verification experiment lab_sea.hb87 -> updated
531    
532    checkpoint65u (2016/03/14)
533    o pkg/generic_advdiff:
534      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
535        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
536        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
537        testing and not for actual use.
538    o model/src:
539      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
540        origin r = rF(1);
541      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
542        in EOS for height coordinate: enable to include NH Pressure or to use
543        more accurate pressure vertical profile; options not linked to EOS type
544        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
545      - start to implement variable gravity (along vertical): for now, only with
546        z-coords (not even z*).
547      - add Ideal Gas equation of state for height coordinate.
548      - update OpenAD output (affected at machine truncation level) of exp:
549        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
550    o pkg/exf:
551      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
552        of exf interpolation (before any rescaling, rotation or interpolation
553        to velocity point) for each field that gets loaded from file. This option
554        identically mimics the input file organization (e.g. record numbers in year
555        by year input files) besides the change in horizontal grid.
556      - add rotateStressOnAgrid run-time switch so that wind stress fields
557        can be provided on the A-grid in zonal/meridional direction and
558        rotated on the fly. This only applies to the case when the exf
559        interpolation is off and rotateStressOnAgrid is false by default.
560    o model/src:
561      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
562        it's also used with pkg/atm_phys) and add few more parameters (but still
563        inactive, src code yet to come)
564    
565    checkpoint65t (2016/02/10)
566    o pkg/atm_phys:
567      - from Ruth Geen: add optical depth dependence on CO2 concentration.
568    o model/src:
569      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
570        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
571        Update output of exp. deep_anelastic (changes at truncation level).
572    o tools:
573      - add a hack in "remove_comments_sed" (used only with TAF) for recent
574        version of OpenMPI (shipped with FC.23): comment out the new header
575        file "mpif-sizeof.h" which causes problems to TAF.
576    o pkg/seaice:
577      - change the termination criterion so that maxits (SEAICElinearIterMax)
578        has an effect
579      - unify iteration parameters for implicit solvers (JFNK and Picard)
580        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
581        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
582        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
583        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
584        SEAICEnonLinTol     replaces JFNKgamma_nonlin
585      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
586      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
587        use with SEAICEuseKrylov
588    o pkg/seaice/seaice_lsr.F
589        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
590        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
591        an effect.
592    o pkg/seaice: add two new parameters
593      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
594        parameter is not in any namelist)
595      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
596        a preconditioner for the non-linear Newton iteration of the JFNK
597        solver
598    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
599      affects some experiments at truncation level:
600      - global_ocean.cs32x15.icedyn (11 digits),
601      - global_ocean.cs32x15.seaice (11 digits),
602      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
603      - also update global_ocean.cs32x15 adjoint and tangent-linear results
604    o pkg/salt_plume & pkg/thsice:
605      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
606        connect salt_plume flux to ATM-OCN coupling pkgs interface:
607       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
608         export to coupler interface) even without compiling pkg/salt_plume ;
609       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
610         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
611    o pkg/dic:
612      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
613        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
614        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
615      - move also update with values from ATM-OCN Coupler in the same new S/R
616        (previously done in ocn_apply_import.F).
617    o tools/adjoint_options:
618      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
619        has been changed on Jan 14, 2016.
620    o pkg/ggl90:
621      - add alternative discretisation of vertical shear (off by default), to
622        compute the mean (@ grid-cell center) of vertical shear compon instead of
623        vertical shear of mean flow (@ grid-cell center).
624      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
625        results on adjacent faces of cubed-sphere grids; this fix the restart.
626    o pkg/atm_compon_interf:
627      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
628        pass last value, stored directly before export to CPL ;
629        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
630      - remove atmSLPr from pickup files (no longer needed for restart)
631    
632    checkpoint65s (2016/01/13)
633    o eesupp & genmake2:
634       - first check for Function ETIME and, if it fails, then check for subroutine
635         ETIME and consistent output; use the appropriate version in timers.F
636    o model/src:
637      - to check restart test, add option to apply EXCH to U,V earlier, just before
638        integr_continuity; turned off by default.
639    o pkg/dic:
640      - remove CPP option USE_ATMOSCO2 (not needed)
641    o tools/tst_2+2:
642      - try to ignore difference between +0 and -0 in binary file, causing test
643        to fail for no good reason.
644    o eesupp & genmake2:
645      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
646        but also check (in genmake2) that test runs and returns meaningful results.
647    o coupler pkgs:
648      Finish implementation of optionally-exchanged variable switches (started on
649       Nov 12) with addition of few more exchanged fields, including 2-way exchange
650       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
651       advection in OCN component; this requires sequential coupling.
652      coupler (pkg/atm_ocn_coupler):
653      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
654        routines (useful for debug).
655      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
656         flux, DIC fields) if corresponding switch is ON.
657      - add option to export RunOff to OCN (to use for DIC river input)
658      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
659      components (pkg/atm_ & ocn_compon_interf):
660      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
661        optionally exchanged fields; add a check & stop in cpl_readparms.F.
662        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
663        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
664      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
665        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
666      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
667      - hold in common block coupler optionally-exchanged variable switch
668        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
669      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
670        this is intended to replace the OCN cplFldtave.* output files (not updated
671        to contain new additional exchanged fields).
672    o pkg/dic:
673      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
674    o pkg/thsice:
675      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
676        and writing of thsice pickup files.
677    o pkg/atm_compon_interf:
678      - move all field individual export-call out of cpl_export_import_data.F
679        into new S/R ATM_EXPORT_FIELDS
680    o pkg/atm_compon_interf:
681      - store state variables (for now, only thSIce fields) just before beeing
682        exported (in cpl_export_import_data.F, like on ocean side) instead of from
683        atm_store_my_data.F like all exported fluxes.
684      - new version of pickup_cpl: write field names into meta file and read meta
685        file to find field postion in pickup. Also only write/read fields meeded for
686        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
687    o pkg/dic:
688      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
689    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
690        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
691        value can be from domain [0,1] to average between the two methods
692    o pkg/atm_phys:
693      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
694        hold fixed in time).
695    
696    checkpoint65r (2015/12/21)
697    o pkg/seaice:
698        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
699        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
700    o pkg/seaice:
701      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
702        when SEAICEscaleSurfStress=.TRUE.,
703      - apply areaW and areaS in S/R seaice_calc_lhs
704    o pkg/atm_phys:
705      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
706        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
707        for individual contribution (convection, LSC cond, radiation)
708      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
709        information); activated with: solar_exponent=0. and wv_exponent=-1.
710    o pkg/ggl90:
711      - within IDEMIX add upper limit for horizontal group velocity to
712        avoid instability problems in the explicit horizontal diffusion term for
713        long time steps or high resolution
714    o pkg/diagnostics:
715      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
716        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
717    o testreport:
718      - remove "-v" (verbose option) in default mpirun command.
719    o pkg/seaice/seaice_growth:
720      - catch potential division by zero in ITD code, does not change
721        verification results
722    o pkg/ecco:
723      - retire old codes to the Attic. The calls to retired functions are
724        left in a commented form in case they ever need to be re-activated.
725      - ecco_check.F: issue warning if any old CPP option is
726        defined that corresponds to retired codes -- then stop.
727    o pkg/atm_compon_interf:
728      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
729        coupler: use last time-step value instead of average over cplSendFrq_iter
730        time-step, similar to what is done for seaIceMass.
731        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
732    o eesupp & genmake2:
733      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
734        <= remove until a fix is found for some ifort version on ia32 machine.
735    o pkg/seaice/seaice_evp:
736      - refine residual computation
737    
738    checkpoint65q (2015/11/18)
739    o pkg/seaice/seaice_evp:
740    - fix residual computations so that they no longer affect the actual    - fix residual computations so that they no longer affect the actual
741      simulation code      simulation code
742      - fix seaice_readparams to be able to actually set new parameters
743        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
744  o model/src:  o model/src:
745    - fix wrong truncation (single prec) from "FLOAT" function in expressions    - fix wrong truncation (single prec) from "FLOAT" function in expressions
746      like: deltaT*FLOAT(myIter) when myIter is large:      like: deltaT*FLOAT(myIter) when myIter is large:
# Line 494  o model/src & mom pkgs: Line 1228  o model/src & mom pkgs:
1228      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
1229  o doc:  o doc:
1230    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1231  o pkg/streamice:  o pkg/shelfice:
1232    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1233      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
1234      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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